diff --git a/_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt b/_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt index 4123fb3d41..f562f0aac4 100644 --- a/_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt +++ b/_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt @@ -1,17 +1,17 @@ -2024-08-03 02:07:49 (INFO): Running in non-distributed local mode -2024-08-03 02:07:49 (INFO): Setting env PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True -2024-08-03 02:07:49 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem -2024-08-03 02:07:50 (INFO): amp: true +2024-08-14 00:48:23 (INFO): Running in non-distributed local mode +2024-08-14 00:48:23 (INFO): Setting env PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True +2024-08-14 00:48:23 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem +2024-08-14 00:48:24 (INFO): amp: true cmd: - checkpoint_dir: fine-tuning/checkpoints/2024-08-03-02-08-00-ft-oxides - commit: 08b8c1e + checkpoint_dir: fine-tuning/checkpoints/2024-08-14-00-49-04-ft-oxides + commit: 8fb16d6 identifier: ft-oxides - logs_dir: fine-tuning/logs/tensorboard/2024-08-03-02-08-00-ft-oxides + logs_dir: fine-tuning/logs/tensorboard/2024-08-14-00-49-04-ft-oxides print_every: 10 - results_dir: fine-tuning/results/2024-08-03-02-08-00-ft-oxides + results_dir: fine-tuning/results/2024-08-14-00-49-04-ft-oxides seed: 0 - timestamp_id: 2024-08-03-02-08-00-ft-oxides - version: 0.1.dev1+g08b8c1e + timestamp_id: 2024-08-14-00-49-04-ft-oxides + version: 1.1.0 dataset: a2g_args: r_energy: true @@ -42,8 +42,7 @@ loss_functions: - forces: coefficient: 1 fn: l2mae -model: gemnet_oc -model_attributes: +model: activation: silu atom_edge_interaction: true atom_interaction: true @@ -75,6 +74,7 @@ model_attributes: max_neighbors_aeaint: 20 max_neighbors_aint: 1000 max_neighbors_qint: 8 + name: gemnet_oc num_after_skip: 2 num_atom: 3 num_atom_emb_layers: 2 @@ -142,92 +142,93 @@ val_dataset: format: ase_db src: val.db -2024-08-03 02:07:50 (INFO): Loading dataset: ase_db -2024-08-03 02:07:50 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('train.db')]' -2024-08-03 02:07:50 (WARNING): Disabled BalancedBatchSampler because num_replicas=1. -2024-08-03 02:07:50 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms. -2024-08-03 02:07:50 (INFO): rank: 0: Sampler created... -2024-08-03 02:07:50 (INFO): Created BalancedBatchSampler with sampler=, batch_size=4, drop_last=False -2024-08-03 02:07:50 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('val.db')]' -2024-08-03 02:07:50 (WARNING): Disabled BalancedBatchSampler because num_replicas=1. -2024-08-03 02:07:50 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms. -2024-08-03 02:07:50 (INFO): rank: 0: Sampler created... -2024-08-03 02:07:50 (INFO): Created BalancedBatchSampler with sampler=, batch_size=16, drop_last=False -2024-08-03 02:07:50 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('test.db')]' -2024-08-03 02:07:50 (WARNING): Disabled BalancedBatchSampler because num_replicas=1. -2024-08-03 02:07:50 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms. -2024-08-03 02:07:50 (INFO): rank: 0: Sampler created... -2024-08-03 02:07:50 (INFO): Created BalancedBatchSampler with sampler=, batch_size=16, drop_last=False -2024-08-03 02:07:50 (INFO): Loading model: gemnet_oc -2024-08-03 02:07:50 (WARNING): Unrecognized arguments: ['symmetric_edge_symmetrization'] -2024-08-03 02:07:52 (INFO): Loaded GemNetOC with 38864438 parameters. -2024-08-03 02:07:52 (WARNING): log_summary for Tensorboard not supported -2024-08-03 02:07:52 (WARNING): Using `weight_decay` from `optim` instead of `optim.optimizer_params`.Please update your config to use `optim.optimizer_params.weight_decay`.`optim.weight_decay` will soon be deprecated. -2024-08-03 02:07:53 (INFO): Loading checkpoint from: /tmp/fairchem_checkpoints/gnoc_oc22_oc20_all_s2ef.pt -2024-08-03 02:07:53 (INFO): Overwriting scaling factors with those loaded from checkpoint. If you're generating predictions with a pretrained checkpoint, this is the correct behavior. To disable this, delete `scale_dict` from the checkpoint. +2024-08-14 00:48:24 (INFO): Loading dataset: ase_db +2024-08-14 00:48:24 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('train.db')]' +2024-08-14 00:48:24 (WARNING): Disabled BalancedBatchSampler because num_replicas=1. +2024-08-14 00:48:24 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms. +2024-08-14 00:48:24 (INFO): rank: 0: Sampler created... +2024-08-14 00:48:24 (INFO): Created BalancedBatchSampler with sampler=, batch_size=4, drop_last=False +2024-08-14 00:48:24 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('val.db')]' +2024-08-14 00:48:24 (WARNING): Disabled BalancedBatchSampler because num_replicas=1. +2024-08-14 00:48:24 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms. +2024-08-14 00:48:24 (INFO): rank: 0: Sampler created... +2024-08-14 00:48:24 (INFO): Created BalancedBatchSampler with sampler=, batch_size=16, drop_last=False +2024-08-14 00:48:24 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('test.db')]' +2024-08-14 00:48:24 (WARNING): Disabled BalancedBatchSampler because num_replicas=1. +2024-08-14 00:48:24 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms. +2024-08-14 00:48:24 (INFO): rank: 0: Sampler created... +2024-08-14 00:48:24 (INFO): Created BalancedBatchSampler with sampler=, batch_size=16, drop_last=False +2024-08-14 00:48:24 (INFO): Loading model: gemnet_oc +2024-08-14 00:48:24 (WARNING): Unrecognized arguments: ['symmetric_edge_symmetrization'] +2024-08-14 00:48:27 (INFO): Loaded GemNetOC with 38864438 parameters. +2024-08-14 00:48:27 (WARNING): log_summary for Tensorboard not supported +2024-08-14 00:48:27 (WARNING): Using `weight_decay` from `optim` instead of `optim.optimizer_params`.Please update your config to use `optim.optimizer_params.weight_decay`.`optim.weight_decay` will soon be deprecated. +2024-08-14 00:48:27 (INFO): Attemping to load user specified checkpoint at /tmp/fairchem_checkpoints/gnoc_oc22_oc20_all_s2ef.pt +2024-08-14 00:48:27 (INFO): Loading checkpoint from: /tmp/fairchem_checkpoints/gnoc_oc22_oc20_all_s2ef.pt +2024-08-14 00:48:27 (INFO): Overwriting scaling factors with those loaded from checkpoint. If you're generating predictions with a pretrained checkpoint, this is the correct behavior. To disable this, delete `scale_dict` from the checkpoint. /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly. To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage() storage = elem.storage()._new_shared(numel) /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly. To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage() storage = elem.storage()._new_shared(numel) -2024-08-03 02:08:15 (INFO): energy_mae: 9.52e+00, forcesx_mae: 7.22e-02, forcesy_mae: 3.94e-02, forcesz_mae: 5.74e-02, forces_mae: 5.63e-02, forces_cosine_similarity: 1.39e-01, forces_magnitude_error: 1.11e-01, energy_forces_within_threshold: 0.00e+00, loss: 9.65e+00, lr: 5.00e-04, epoch: 1.69e-01, step: 1.00e+01 -2024-08-03 02:08:16 (INFO): Evaluating on val. +2024-08-14 00:48:51 (INFO): energy_mae: 9.52e+00, forcesx_mae: 7.22e-02, forcesy_mae: 3.94e-02, forcesz_mae: 5.74e-02, forces_mae: 5.63e-02, forces_cosine_similarity: 1.39e-01, forces_magnitude_error: 1.11e-01, energy_forces_within_threshold: 0.00e+00, loss: 9.65e+00, lr: 5.00e-04, epoch: 1.69e-01, step: 1.00e+01 +2024-08-14 00:48:51 (INFO): Evaluating on val. device 0: 0%| | 0/2 [00:00, batch_size=16, drop_last=False -2024-08-03 02:13:06 (INFO): Loading model: gemnet_t -2024-08-03 02:13:08 (INFO): Loaded GemNetT with 31671825 parameters. -2024-08-03 02:13:08 (WARNING): log_summary for Tensorboard not supported -2024-08-03 02:13:08 (INFO): Loading checkpoint from: /tmp/fairchem_checkpoints/gndt_oc22_all_s2ef.pt -2024-08-03 02:13:08 (INFO): Overwriting scaling factors with those loaded from checkpoint. If you're generating predictions with a pretrained checkpoint, this is the correct behavior. To disable this, delete `scale_dict` from the checkpoint. -2024-08-03 02:13:08 (WARNING): Scale factor comment not found in model -2024-08-03 02:13:08 (INFO): Predicting on test. +2024-08-14 00:54:10 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data.db')]' +2024-08-14 00:54:10 (WARNING): Disabled BalancedBatchSampler because num_replicas=1. +2024-08-14 00:54:10 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms. +2024-08-14 00:54:10 (INFO): rank: 0: Sampler created... +2024-08-14 00:54:10 (INFO): Created BalancedBatchSampler with sampler=, batch_size=16, drop_last=False +2024-08-14 00:54:10 (INFO): Loading model: gemnet_t +2024-08-14 00:54:12 (INFO): Loaded GemNetT with 31671825 parameters. +2024-08-14 00:54:12 (WARNING): log_summary for Tensorboard not supported +2024-08-14 00:54:12 (INFO): Attemping to load user specified checkpoint at /tmp/fairchem_checkpoints/gndt_oc22_all_s2ef.pt +2024-08-14 00:54:12 (INFO): Loading checkpoint from: /tmp/fairchem_checkpoints/gndt_oc22_all_s2ef.pt +2024-08-14 00:54:12 (INFO): Overwriting scaling factors with those loaded from checkpoint. If you're generating predictions with a pretrained checkpoint, this is the correct behavior. To disable this, delete `scale_dict` from the checkpoint. +2024-08-14 00:54:12 (WARNING): Scale factor comment not found in model +2024-08-14 00:54:12 (INFO): Predicting on test. device 0: 0%| | 0/3 [00:00 None +.. py:function:: broadcast_object_list(object_list: list[Any], src: int, group=dist.group.WORLD, device: str | None = None) -> None + .. py:function:: all_reduce(data, group=dist.group.WORLD, average: bool = False, device=None) -> torch.Tensor .. py:function:: all_gather(data, group=dist.group.WORLD, device=None) -> list[torch.Tensor] diff --git a/_sources/autoapi/core/common/index.rst b/_sources/autoapi/core/common/index.rst index 77058574c3..9017d93f67 100644 --- a/_sources/autoapi/core/common/index.rst +++ b/_sources/autoapi/core/common/index.rst @@ -35,6 +35,7 @@ Submodules /autoapi/core/common/logger/index /autoapi/core/common/profiler_utils/index /autoapi/core/common/registry/index + /autoapi/core/common/slurm/index /autoapi/core/common/test_utils/index /autoapi/core/common/transforms/index /autoapi/core/common/tutorial_utils/index diff --git a/_sources/autoapi/core/common/slurm/index.rst b/_sources/autoapi/core/common/slurm/index.rst new file mode 100644 index 0000000000..8dac343fa8 --- /dev/null +++ b/_sources/autoapi/core/common/slurm/index.rst @@ -0,0 +1,19 @@ +core.common.slurm +================= + +.. py:module:: core.common.slurm + + +Functions +--------- + +.. autoapisummary:: + + core.common.slurm.add_timestamp_id_to_submission_pickle + + +Module Contents +--------------- + +.. py:function:: add_timestamp_id_to_submission_pickle(slurm_folder: str, slurm_job_id: str, timestamp_id: str) + diff --git a/_sources/autoapi/core/common/utils/index.rst b/_sources/autoapi/core/common/utils/index.rst index 975cde5fae..1cc3c2c65e 100644 --- a/_sources/autoapi/core/common/utils/index.rst +++ b/_sources/autoapi/core/common/utils/index.rst @@ -66,6 +66,7 @@ Functions core.common.utils.new_trainer_context core.common.utils._resolve_scale_factor_submodule core.common.utils._report_incompat_keys + core.common.utils.match_state_dict core.common.utils.load_state_dict core.common.utils.scatter_det core.common.utils.get_commit_hash @@ -255,6 +256,8 @@ Module Contents .. py:function:: _report_incompat_keys(model: torch.nn.Module, keys: torch.nn.modules.module._IncompatibleKeys, strict: bool = False) -> tuple[list[str], list[str]] +.. py:function:: match_state_dict(model_state_dict: collections.abc.Mapping[str, torch.Tensor], checkpoint_state_dict: collections.abc.Mapping[str, torch.Tensor]) -> dict + .. py:function:: load_state_dict(module: torch.nn.Module, state_dict: collections.abc.Mapping[str, torch.Tensor], strict: bool = True) -> tuple[list[str], list[str]] .. py:function:: scatter_det(*args, **kwargs) diff --git a/_sources/autoapi/core/models/base/index.rst b/_sources/autoapi/core/models/base/index.rst index c4257651e4..2ac238368c 100644 --- a/_sources/autoapi/core/models/base/index.rst +++ b/_sources/autoapi/core/models/base/index.rst @@ -21,6 +21,7 @@ Classes core.models.base.GraphModelMixin core.models.base.HeadInterface core.models.base.BackboneInterface + core.models.base.HydraInterface core.models.base.HydraModel @@ -75,7 +76,7 @@ Module Contents Mixin Model class implementing some general convenience properties and methods. - .. py:method:: generate_graph(data, cutoff=None, max_neighbors=None, use_pbc=None, otf_graph=None, enforce_max_neighbors_strictly=None) + .. py:method:: generate_graph(data, cutoff=None, max_neighbors=None, use_pbc=None, otf_graph=None, enforce_max_neighbors_strictly=None, use_pbc_single=False) .. py:property:: num_params @@ -123,9 +124,28 @@ Module Contents +.. py:class:: HydraInterface + + Bases: :py:obj:`abc.ABC` + + + Helper class that provides a standard way to create an ABC using + inheritance. + + + .. py:method:: get_backbone() -> BackboneInterface + :abstractmethod: + + + + .. py:method:: get_heads() -> dict[str, HeadInterface] + :abstractmethod: + + + .. py:class:: HydraModel(backbone: dict, heads: dict, otf_graph: bool = True) - Bases: :py:obj:`torch.nn.Module`, :py:obj:`GraphModelMixin` + Bases: :py:obj:`torch.nn.Module`, :py:obj:`GraphModelMixin`, :py:obj:`HydraInterface` Base class for all neural network modules. @@ -163,11 +183,13 @@ Module Contents .. py:attribute:: otf_graph - .. py:attribute:: backbone_model_name + .. py:attribute:: backbone - .. py:attribute:: backbone - :type: BackboneInterface + .. py:attribute:: heads + + + .. py:attribute:: backbone_model_name .. py:attribute:: output_heads @@ -180,3 +202,9 @@ Module Contents .. py:method:: forward(data: torch_geometric.data.Batch) + .. py:method:: get_backbone() -> BackboneInterface + + + .. py:method:: get_heads() -> dict[str, HeadInterface] + + diff --git a/_sources/autoapi/core/models/dimenet_plus_plus/index.rst b/_sources/autoapi/core/models/dimenet_plus_plus/index.rst index 09634fbd7e..562febb15a 100644 --- a/_sources/autoapi/core/models/dimenet_plus_plus/index.rst +++ b/_sources/autoapi/core/models/dimenet_plus_plus/index.rst @@ -336,7 +336,7 @@ Module Contents -.. py:class:: DimeNetPlusPlusWrap(use_pbc: bool = True, regress_forces: bool = True, hidden_channels: int = 128, num_blocks: int = 4, int_emb_size: int = 64, basis_emb_size: int = 8, out_emb_channels: int = 256, num_spherical: int = 7, num_radial: int = 6, otf_graph: bool = False, cutoff: float = 10.0, envelope_exponent: int = 5, num_before_skip: int = 1, num_after_skip: int = 2, num_output_layers: int = 3) +.. py:class:: DimeNetPlusPlusWrap(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, hidden_channels: int = 128, num_blocks: int = 4, int_emb_size: int = 64, basis_emb_size: int = 8, out_emb_channels: int = 256, num_spherical: int = 7, num_radial: int = 6, otf_graph: bool = False, cutoff: float = 10.0, envelope_exponent: int = 5, num_before_skip: int = 1, num_after_skip: int = 2, num_output_layers: int = 3) Bases: :py:obj:`DimeNetPlusPlus`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -380,6 +380,9 @@ Module Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: cutoff @@ -402,7 +405,7 @@ Module Contents -.. py:class:: DimeNetPlusPlusWrapBackbone(use_pbc: bool = True, regress_forces: bool = True, hidden_channels: int = 128, num_blocks: int = 4, int_emb_size: int = 64, basis_emb_size: int = 8, out_emb_channels: int = 256, num_spherical: int = 7, num_radial: int = 6, otf_graph: bool = False, cutoff: float = 10.0, envelope_exponent: int = 5, num_before_skip: int = 1, num_after_skip: int = 2, num_output_layers: int = 3) +.. py:class:: DimeNetPlusPlusWrapBackbone(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, hidden_channels: int = 128, num_blocks: int = 4, int_emb_size: int = 64, basis_emb_size: int = 8, out_emb_channels: int = 256, num_spherical: int = 7, num_radial: int = 6, otf_graph: bool = False, cutoff: float = 10.0, envelope_exponent: int = 5, num_before_skip: int = 1, num_after_skip: int = 2, num_output_layers: int = 3) Bases: :py:obj:`DimeNetPlusPlusWrap`, :py:obj:`fairchem.core.models.base.BackboneInterface` diff --git a/_sources/autoapi/core/models/equiformer_v2/equiformer_v2/index.rst b/_sources/autoapi/core/models/equiformer_v2/equiformer_v2/index.rst index 418930d59b..1752be4ca9 100644 --- a/_sources/autoapi/core/models/equiformer_v2/equiformer_v2/index.rst +++ b/_sources/autoapi/core/models/equiformer_v2/equiformer_v2/index.rst @@ -35,7 +35,7 @@ Module Contents :value: 23.395238876342773 -.. py:class:: EquiformerV2(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = True, max_neighbors: int = 500, max_radius: float = 5.0, max_num_elements: int = 90, num_layers: int = 12, sphere_channels: int = 128, attn_hidden_channels: int = 128, num_heads: int = 8, attn_alpha_channels: int = 32, attn_value_channels: int = 16, ffn_hidden_channels: int = 512, norm_type: str = 'rms_norm_sh', lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, grid_resolution: int | None = None, num_sphere_samples: int = 128, edge_channels: int = 128, use_atom_edge_embedding: bool = True, share_atom_edge_embedding: bool = False, use_m_share_rad: bool = False, distance_function: str = 'gaussian', num_distance_basis: int = 512, attn_activation: str = 'scaled_silu', use_s2_act_attn: bool = False, use_attn_renorm: bool = True, ffn_activation: str = 'scaled_silu', use_gate_act: bool = False, use_grid_mlp: bool = False, use_sep_s2_act: bool = True, alpha_drop: float = 0.1, drop_path_rate: float = 0.05, proj_drop: float = 0.0, weight_init: str = 'normal', enforce_max_neighbors_strictly: bool = True, avg_num_nodes: float | None = None, avg_degree: float | None = None, use_energy_lin_ref: bool | None = False, load_energy_lin_ref: bool | None = False) +.. py:class:: EquiformerV2(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, otf_graph: bool = True, max_neighbors: int = 500, max_radius: float = 5.0, max_num_elements: int = 90, num_layers: int = 12, sphere_channels: int = 128, attn_hidden_channels: int = 128, num_heads: int = 8, attn_alpha_channels: int = 32, attn_value_channels: int = 16, ffn_hidden_channels: int = 512, norm_type: str = 'rms_norm_sh', lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, grid_resolution: int | None = None, num_sphere_samples: int = 128, edge_channels: int = 128, use_atom_edge_embedding: bool = True, share_atom_edge_embedding: bool = False, use_m_share_rad: bool = False, distance_function: str = 'gaussian', num_distance_basis: int = 512, attn_activation: str = 'scaled_silu', use_s2_act_attn: bool = False, use_attn_renorm: bool = True, ffn_activation: str = 'scaled_silu', use_gate_act: bool = False, use_grid_mlp: bool = False, use_sep_s2_act: bool = True, alpha_drop: float = 0.1, drop_path_rate: float = 0.05, proj_drop: float = 0.0, weight_init: str = 'normal', enforce_max_neighbors_strictly: bool = True, avg_num_nodes: float | None = None, avg_degree: float | None = None, use_energy_lin_ref: bool | None = False, load_energy_lin_ref: bool | None = False) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -44,6 +44,8 @@ Module Contents :param use_pbc: Use periodic boundary conditions :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time + :type use_pbc_single: bool :param regress_forces: Compute forces :type regress_forces: bool :param otf_graph: Compute graph On The Fly (OTF) @@ -129,6 +131,9 @@ Module Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: regress_forces @@ -326,7 +331,7 @@ Module Contents -.. py:class:: EquiformerV2Backbone(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = True, max_neighbors: int = 500, max_radius: float = 5.0, max_num_elements: int = 90, num_layers: int = 12, sphere_channels: int = 128, attn_hidden_channels: int = 128, num_heads: int = 8, attn_alpha_channels: int = 32, attn_value_channels: int = 16, ffn_hidden_channels: int = 512, norm_type: str = 'rms_norm_sh', lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, grid_resolution: int | None = None, num_sphere_samples: int = 128, edge_channels: int = 128, use_atom_edge_embedding: bool = True, share_atom_edge_embedding: bool = False, use_m_share_rad: bool = False, distance_function: str = 'gaussian', num_distance_basis: int = 512, attn_activation: str = 'scaled_silu', use_s2_act_attn: bool = False, use_attn_renorm: bool = True, ffn_activation: str = 'scaled_silu', use_gate_act: bool = False, use_grid_mlp: bool = False, use_sep_s2_act: bool = True, alpha_drop: float = 0.1, drop_path_rate: float = 0.05, proj_drop: float = 0.0, weight_init: str = 'normal', enforce_max_neighbors_strictly: bool = True, avg_num_nodes: float | None = None, avg_degree: float | None = None, use_energy_lin_ref: bool | None = False, load_energy_lin_ref: bool | None = False) +.. py:class:: EquiformerV2Backbone(*args, **kwargs) Bases: :py:obj:`EquiformerV2`, :py:obj:`fairchem.core.models.base.BackboneInterface` @@ -335,6 +340,8 @@ Module Contents :param use_pbc: Use periodic boundary conditions :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time + :type use_pbc_single: bool :param regress_forces: Compute forces :type regress_forces: bool :param otf_graph: Compute graph On The Fly (OTF) @@ -417,6 +424,16 @@ Module Contents :type load_energy_lin_ref: bool + .. py:attribute:: energy_block + :value: None + + + + .. py:attribute:: force_block + :value: None + + + .. py:method:: forward(data: torch_geometric.data.batch.Batch) -> dict[str, torch.Tensor] Backbone forward. diff --git a/_sources/autoapi/core/models/equiformer_v2/index.rst b/_sources/autoapi/core/models/equiformer_v2/index.rst index 6e37fd57de..452b29a995 100644 --- a/_sources/autoapi/core/models/equiformer_v2/index.rst +++ b/_sources/autoapi/core/models/equiformer_v2/index.rst @@ -45,7 +45,7 @@ Classes Package Contents ---------------- -.. py:class:: EquiformerV2(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = True, max_neighbors: int = 500, max_radius: float = 5.0, max_num_elements: int = 90, num_layers: int = 12, sphere_channels: int = 128, attn_hidden_channels: int = 128, num_heads: int = 8, attn_alpha_channels: int = 32, attn_value_channels: int = 16, ffn_hidden_channels: int = 512, norm_type: str = 'rms_norm_sh', lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, grid_resolution: int | None = None, num_sphere_samples: int = 128, edge_channels: int = 128, use_atom_edge_embedding: bool = True, share_atom_edge_embedding: bool = False, use_m_share_rad: bool = False, distance_function: str = 'gaussian', num_distance_basis: int = 512, attn_activation: str = 'scaled_silu', use_s2_act_attn: bool = False, use_attn_renorm: bool = True, ffn_activation: str = 'scaled_silu', use_gate_act: bool = False, use_grid_mlp: bool = False, use_sep_s2_act: bool = True, alpha_drop: float = 0.1, drop_path_rate: float = 0.05, proj_drop: float = 0.0, weight_init: str = 'normal', enforce_max_neighbors_strictly: bool = True, avg_num_nodes: float | None = None, avg_degree: float | None = None, use_energy_lin_ref: bool | None = False, load_energy_lin_ref: bool | None = False) +.. py:class:: EquiformerV2(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, otf_graph: bool = True, max_neighbors: int = 500, max_radius: float = 5.0, max_num_elements: int = 90, num_layers: int = 12, sphere_channels: int = 128, attn_hidden_channels: int = 128, num_heads: int = 8, attn_alpha_channels: int = 32, attn_value_channels: int = 16, ffn_hidden_channels: int = 512, norm_type: str = 'rms_norm_sh', lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, grid_resolution: int | None = None, num_sphere_samples: int = 128, edge_channels: int = 128, use_atom_edge_embedding: bool = True, share_atom_edge_embedding: bool = False, use_m_share_rad: bool = False, distance_function: str = 'gaussian', num_distance_basis: int = 512, attn_activation: str = 'scaled_silu', use_s2_act_attn: bool = False, use_attn_renorm: bool = True, ffn_activation: str = 'scaled_silu', use_gate_act: bool = False, use_grid_mlp: bool = False, use_sep_s2_act: bool = True, alpha_drop: float = 0.1, drop_path_rate: float = 0.05, proj_drop: float = 0.0, weight_init: str = 'normal', enforce_max_neighbors_strictly: bool = True, avg_num_nodes: float | None = None, avg_degree: float | None = None, use_energy_lin_ref: bool | None = False, load_energy_lin_ref: bool | None = False) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -54,6 +54,8 @@ Package Contents :param use_pbc: Use periodic boundary conditions :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time + :type use_pbc_single: bool :param regress_forces: Compute forces :type regress_forces: bool :param otf_graph: Compute graph On The Fly (OTF) @@ -139,6 +141,9 @@ Package Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: regress_forces diff --git a/_sources/autoapi/core/models/escn/escn/index.rst b/_sources/autoapi/core/models/escn/escn/index.rst index 136fcbc303..3977626f37 100644 --- a/_sources/autoapi/core/models/escn/escn/index.rst +++ b/_sources/autoapi/core/models/escn/escn/index.rst @@ -33,7 +33,7 @@ Classes Module Contents --------------- -.. py:class:: eSCN(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_neighbors: int = 40, cutoff: float = 8.0, max_num_elements: int = 90, num_layers: int = 8, lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, sphere_channels: int = 128, hidden_channels: int = 256, edge_channels: int = 128, num_sphere_samples: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False) +.. py:class:: eSCN(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, otf_graph: bool = False, max_neighbors: int = 40, cutoff: float = 8.0, max_num_elements: int = 90, num_layers: int = 8, lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, sphere_channels: int = 128, hidden_channels: int = 256, edge_channels: int = 128, num_sphere_samples: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -44,6 +44,8 @@ Module Contents :param use_pbc: Use periodic boundary conditions :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time + :type use_pbc_single: bool :param regress_forces: Compute forces :type regress_forces: bool :param otf_graph: Compute graph On The Fly (OTF) @@ -84,6 +86,9 @@ Module Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: cutoff @@ -190,7 +195,7 @@ Module Contents -.. py:class:: eSCNBackbone(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_neighbors: int = 40, cutoff: float = 8.0, max_num_elements: int = 90, num_layers: int = 8, lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, sphere_channels: int = 128, hidden_channels: int = 256, edge_channels: int = 128, num_sphere_samples: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False) +.. py:class:: eSCNBackbone(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, otf_graph: bool = False, max_neighbors: int = 40, cutoff: float = 8.0, max_num_elements: int = 90, num_layers: int = 8, lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, sphere_channels: int = 128, hidden_channels: int = 256, edge_channels: int = 128, num_sphere_samples: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False) Bases: :py:obj:`eSCN`, :py:obj:`fairchem.core.models.base.BackboneInterface` @@ -201,6 +206,8 @@ Module Contents :param use_pbc: Use periodic boundary conditions :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time + :type use_pbc_single: bool :param regress_forces: Compute forces :type regress_forces: bool :param otf_graph: Compute graph On The Fly (OTF) @@ -285,6 +292,8 @@ Module Contents .. py:attribute:: energy_block + :value: None + .. py:method:: forward(data: torch_geometric.data.batch.Batch, emb: dict[str, torch.Tensor]) -> dict[str, torch.Tensor] @@ -339,6 +348,8 @@ Module Contents .. py:attribute:: force_block + :value: None + .. py:method:: forward(data: torch_geometric.data.batch.Batch, emb: dict[str, torch.Tensor]) -> dict[str, torch.Tensor] diff --git a/_sources/autoapi/core/models/escn/index.rst b/_sources/autoapi/core/models/escn/index.rst index 875e7791f3..79744c19c4 100644 --- a/_sources/autoapi/core/models/escn/index.rst +++ b/_sources/autoapi/core/models/escn/index.rst @@ -25,7 +25,7 @@ Classes Package Contents ---------------- -.. py:class:: eSCN(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_neighbors: int = 40, cutoff: float = 8.0, max_num_elements: int = 90, num_layers: int = 8, lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, sphere_channels: int = 128, hidden_channels: int = 256, edge_channels: int = 128, num_sphere_samples: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False) +.. py:class:: eSCN(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, otf_graph: bool = False, max_neighbors: int = 40, cutoff: float = 8.0, max_num_elements: int = 90, num_layers: int = 8, lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, sphere_channels: int = 128, hidden_channels: int = 256, edge_channels: int = 128, num_sphere_samples: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -36,6 +36,8 @@ Package Contents :param use_pbc: Use periodic boundary conditions :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time + :type use_pbc_single: bool :param regress_forces: Compute forces :type regress_forces: bool :param otf_graph: Compute graph On The Fly (OTF) @@ -76,6 +78,9 @@ Package Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: cutoff diff --git a/_sources/autoapi/core/models/finetune_hydra/index.rst b/_sources/autoapi/core/models/finetune_hydra/index.rst new file mode 100644 index 0000000000..8703af0ec1 --- /dev/null +++ b/_sources/autoapi/core/models/finetune_hydra/index.rst @@ -0,0 +1,203 @@ +core.models.finetune_hydra +========================== + +.. py:module:: core.models.finetune_hydra + + +Attributes +---------- + +.. autoapisummary:: + + core.models.finetune_hydra.FTHYDRA_NAME + + +Classes +------- + +.. autoapisummary:: + + core.models.finetune_hydra.FineTuneMode + core.models.finetune_hydra.FTConfig + core.models.finetune_hydra.FineTuneHydra + + +Functions +--------- + +.. autoapisummary:: + + core.models.finetune_hydra.get_model_config_from_checkpoint + core.models.finetune_hydra.load_hydra_model + + +Module Contents +--------------- + +.. py:data:: FTHYDRA_NAME + :value: 'finetune_hydra' + + +.. py:class:: FineTuneMode(*args, **kwds) + + Bases: :py:obj:`enum.Enum` + + + Create a collection of name/value pairs. + + Example enumeration: + + >>> class Color(Enum): + ... RED = 1 + ... BLUE = 2 + ... GREEN = 3 + + Access them by: + + - attribute access:: + + >>> Color.RED + + + - value lookup: + + >>> Color(1) + + + - name lookup: + + >>> Color['RED'] + + + Enumerations can be iterated over, and know how many members they have: + + >>> len(Color) + 3 + + >>> list(Color) + [, , ] + + Methods can be added to enumerations, and members can have their own + attributes -- see the documentation for details. + + + .. py:attribute:: DATA_ONLY + :value: 1 + + + + .. py:attribute:: RETAIN_BACKBONE_ONLY + :value: 2 + + + +.. py:function:: get_model_config_from_checkpoint(checkpoint_path: str) -> dict + +.. py:function:: load_hydra_model(checkpoint_path: str) -> fairchem.core.models.base.HydraInterface + +.. py:class:: FTConfig(config: dict) + + .. py:attribute:: FT_CONFIG_NAME + :value: 'finetune_config' + + + + .. py:attribute:: STARTING_CHECKPOINT + :value: 'starting_checkpoint' + + + + .. py:attribute:: STARTING_MODEL + :value: 'starting_model' + + + + .. py:attribute:: MODE + :value: 'mode' + + + + .. py:attribute:: HEADS + :value: 'heads' + + + + .. py:attribute:: config + + + .. py:attribute:: _mode + + + .. py:method:: load_model() -> torch.nn.Module + + + .. py:method:: get_standalone_config() -> dict + + + .. py:property:: mode + :type: FineTuneMode + + + + .. py:property:: head_config + :type: dict + + + +.. py:class:: FineTuneHydra(finetune_config: dict) + + Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.HydraInterface` + + + Base class for all neural network modules. + + Your models should also subclass this class. + + Modules can also contain other Modules, allowing to nest them in + a tree structure. You can assign the submodules as regular attributes:: + + import torch.nn as nn + import torch.nn.functional as F + + class Model(nn.Module): + def __init__(self): + super().__init__() + self.conv1 = nn.Conv2d(1, 20, 5) + self.conv2 = nn.Conv2d(20, 20, 5) + + def forward(self, x): + x = F.relu(self.conv1(x)) + return F.relu(self.conv2(x)) + + Submodules assigned in this way will be registered, and will have their + parameters converted too when you call :meth:`to`, etc. + + .. note:: + As per the example above, an ``__init__()`` call to the parent class + must be made before assignment on the child. + + :ivar training: Boolean represents whether this module is in training or + evaluation mode. + :vartype training: bool + + + .. py:attribute:: ft_config + + + .. py:attribute:: hydra_model + :type: fairchem.core.models.base.HydraInterface + + + .. py:attribute:: backbone + :type: fairchem.core.models.base.BackboneInterface + + + .. py:method:: forward(data: torch_geometric.data.Batch) + + + .. py:method:: get_backbone() -> fairchem.core.models.base.BackboneInterface + + + .. py:method:: get_heads() -> dict[str, fairchem.core.models.base.HeadInterface] + + diff --git a/_sources/autoapi/core/models/gemnet/gemnet/index.rst b/_sources/autoapi/core/models/gemnet/gemnet/index.rst index f09b49d192..cdab48634a 100644 --- a/_sources/autoapi/core/models/gemnet/gemnet/index.rst +++ b/_sources/autoapi/core/models/gemnet/gemnet/index.rst @@ -26,7 +26,7 @@ Classes Module Contents --------------- -.. py:class:: GemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None) +.. py:class:: GemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -103,6 +103,9 @@ Module Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: direct_forces @@ -189,7 +192,7 @@ Module Contents .. py:property:: num_params -.. py:class:: GemNetTBackbone(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None) +.. py:class:: GemNetTBackbone(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None) Bases: :py:obj:`GemNetT`, :py:obj:`fairchem.core.models.base.BackboneInterface` diff --git a/_sources/autoapi/core/models/gemnet/index.rst b/_sources/autoapi/core/models/gemnet/index.rst index 70cbf598b7..0054b377af 100644 --- a/_sources/autoapi/core/models/gemnet/index.rst +++ b/_sources/autoapi/core/models/gemnet/index.rst @@ -35,7 +35,7 @@ Classes Package Contents ---------------- -.. py:class:: GemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None) +.. py:class:: GemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -112,6 +112,9 @@ Package Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: direct_forces diff --git a/_sources/autoapi/core/models/gemnet_gp/gemnet/index.rst b/_sources/autoapi/core/models/gemnet_gp/gemnet/index.rst index bfe2f7cca2..03a10dbd9d 100644 --- a/_sources/autoapi/core/models/gemnet_gp/gemnet/index.rst +++ b/_sources/autoapi/core/models/gemnet_gp/gemnet/index.rst @@ -23,7 +23,7 @@ Classes Module Contents --------------- -.. py:class:: GraphParallelGemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, output_init: str = 'HeOrthogonal', activation: str = 'swish', scale_num_blocks: bool = False, scatter_atoms: bool = True, scale_file: str | None = None) +.. py:class:: GraphParallelGemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'swish', scale_num_blocks: bool = False, scatter_atoms: bool = True, scale_file: str | None = None) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -106,6 +106,9 @@ Module Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: direct_forces diff --git a/_sources/autoapi/core/models/gemnet_gp/index.rst b/_sources/autoapi/core/models/gemnet_gp/index.rst index e5378365f8..5c816a7e88 100644 --- a/_sources/autoapi/core/models/gemnet_gp/index.rst +++ b/_sources/autoapi/core/models/gemnet_gp/index.rst @@ -35,7 +35,7 @@ Classes Package Contents ---------------- -.. py:class:: GraphParallelGemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, output_init: str = 'HeOrthogonal', activation: str = 'swish', scale_num_blocks: bool = False, scatter_atoms: bool = True, scale_file: str | None = None) +.. py:class:: GraphParallelGemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'swish', scale_num_blocks: bool = False, scatter_atoms: bool = True, scale_file: str | None = None) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -118,6 +118,9 @@ Package Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: direct_forces diff --git a/_sources/autoapi/core/models/gemnet_oc/gemnet_oc/index.rst b/_sources/autoapi/core/models/gemnet_oc/gemnet_oc/index.rst index a3fedc041c..8cd7f902f2 100644 --- a/_sources/autoapi/core/models/gemnet_oc/gemnet_oc/index.rst +++ b/_sources/autoapi/core/models/gemnet_oc/gemnet_oc/index.rst @@ -25,7 +25,7 @@ Classes Module Contents --------------- -.. py:class:: GemNetOC(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs) +.. py:class:: GemNetOC(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -84,6 +84,7 @@ Module Contents :type direct_forces: bool :param use_pbc: Whether to use periodic boundary conditions. :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time :param scale_backprop_forces: Whether to scale up the energy and then scales down the forces to prevent NaNs and infs in backpropagated forces. :type scale_backprop_forces: bool @@ -183,6 +184,9 @@ Module Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: direct_forces @@ -321,7 +325,7 @@ Module Contents -.. py:class:: GemNetOCBackbone(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs) +.. py:class:: GemNetOCBackbone(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs) Bases: :py:obj:`GemNetOC`, :py:obj:`fairchem.core.models.base.BackboneInterface` @@ -380,6 +384,7 @@ Module Contents :type direct_forces: bool :param use_pbc: Whether to use periodic boundary conditions. :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time :param scale_backprop_forces: Whether to scale up the energy and then scales down the forces to prevent NaNs and infs in backpropagated forces. :type scale_backprop_forces: bool @@ -508,9 +513,13 @@ Module Contents .. py:attribute:: out_mlp_E + :value: None + .. py:attribute:: out_energy + :value: None + .. py:attribute:: out_initializer diff --git a/_sources/autoapi/core/models/gemnet_oc/index.rst b/_sources/autoapi/core/models/gemnet_oc/index.rst index 5091731b03..f3cdaeea82 100644 --- a/_sources/autoapi/core/models/gemnet_oc/index.rst +++ b/_sources/autoapi/core/models/gemnet_oc/index.rst @@ -36,7 +36,7 @@ Classes Package Contents ---------------- -.. py:class:: GemNetOC(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs) +.. py:class:: GemNetOC(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -95,6 +95,7 @@ Package Contents :type direct_forces: bool :param use_pbc: Whether to use periodic boundary conditions. :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time :param scale_backprop_forces: Whether to scale up the energy and then scales down the forces to prevent NaNs and infs in backpropagated forces. :type scale_backprop_forces: bool @@ -194,6 +195,9 @@ Package Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: direct_forces diff --git a/_sources/autoapi/core/models/index.rst b/_sources/autoapi/core/models/index.rst index 70d41039c5..ba40934668 100644 --- a/_sources/autoapi/core/models/index.rst +++ b/_sources/autoapi/core/models/index.rst @@ -28,6 +28,7 @@ Submodules /autoapi/core/models/base/index /autoapi/core/models/dimenet_plus_plus/index + /autoapi/core/models/finetune_hydra/index /autoapi/core/models/model_registry/index /autoapi/core/models/schnet/index diff --git a/_sources/autoapi/core/models/painn/index.rst b/_sources/autoapi/core/models/painn/index.rst index 2c1f3791e2..0f7494b1f6 100644 --- a/_sources/autoapi/core/models/painn/index.rst +++ b/_sources/autoapi/core/models/painn/index.rst @@ -25,7 +25,7 @@ Classes Package Contents ---------------- -.. py:class:: PaiNN(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None) +.. py:class:: PaiNN(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, use_pbc_single: bool = False, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -62,6 +62,9 @@ Package Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: symmetric_edge_symmetrization :value: False diff --git a/_sources/autoapi/core/models/painn/painn/index.rst b/_sources/autoapi/core/models/painn/painn/index.rst index 9d5c550699..97247a9caf 100644 --- a/_sources/autoapi/core/models/painn/painn/index.rst +++ b/_sources/autoapi/core/models/painn/painn/index.rst @@ -54,7 +54,7 @@ Classes Module Contents --------------- -.. py:class:: PaiNN(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None) +.. py:class:: PaiNN(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, use_pbc_single: bool = False, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -91,6 +91,9 @@ Module Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: symmetric_edge_symmetrization :value: False @@ -151,7 +154,7 @@ Module Contents -.. py:class:: PaiNNBackbone(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None) +.. py:class:: PaiNNBackbone(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, use_pbc_single: bool = False, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None) Bases: :py:obj:`PaiNN`, :py:obj:`fairchem.core.models.base.BackboneInterface` @@ -483,6 +486,8 @@ Module Contents .. py:attribute:: out_energy + :value: None + .. py:method:: forward(data: torch_geometric.data.batch.Batch, emb: dict[str, torch.Tensor]) -> dict[str, torch.Tensor] diff --git a/_sources/autoapi/core/models/schnet/index.rst b/_sources/autoapi/core/models/schnet/index.rst index b25ccdc7e0..9b3ada6c3f 100644 --- a/_sources/autoapi/core/models/schnet/index.rst +++ b/_sources/autoapi/core/models/schnet/index.rst @@ -23,7 +23,7 @@ Classes Module Contents --------------- -.. py:class:: SchNetWrap(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = False, hidden_channels: int = 128, num_filters: int = 128, num_interactions: int = 6, num_gaussians: int = 50, cutoff: float = 10.0, readout: str = 'add') +.. py:class:: SchNetWrap(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, otf_graph: bool = False, hidden_channels: int = 128, num_filters: int = 128, num_interactions: int = 6, num_gaussians: int = 50, cutoff: float = 10.0, readout: str = 'add') Bases: :py:obj:`torch_geometric.nn.SchNet`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -40,6 +40,8 @@ Module Contents :param use_pbc: If set to :obj:`True`, account for periodic boundary conditions. (default: :obj:`True`) :type use_pbc: bool, optional + :param use_pbc_single: Process batch PBC graphs one at a time + :type use_pbc_single: bool,optional :param regress_forces: If set to :obj:`True`, predict forces by differentiating energy with respect to positions. (default: :obj:`True`) @@ -78,6 +80,9 @@ Module Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: cutoff diff --git a/_sources/autoapi/core/models/scn/index.rst b/_sources/autoapi/core/models/scn/index.rst index 31ca3f6cf4..4fa6a9baab 100644 --- a/_sources/autoapi/core/models/scn/index.rst +++ b/_sources/autoapi/core/models/scn/index.rst @@ -27,7 +27,7 @@ Classes Package Contents ---------------- -.. py:class:: SphericalChannelNetwork(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_num_neighbors: int = 20, cutoff: float = 8.0, max_num_elements: int = 90, num_interactions: int = 8, lmax: int = 6, mmax: int = 1, num_resolutions: int = 2, sphere_channels: int = 128, sphere_channels_reduce: int = 128, hidden_channels: int = 256, num_taps: int = -1, use_grid: bool = True, num_bands: int = 1, num_sphere_samples: int = 128, num_basis_functions: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False, direct_forces: bool = True) +.. py:class:: SphericalChannelNetwork(use_pbc: bool = True, use_pbc_single: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_num_neighbors: int = 20, cutoff: float = 8.0, max_num_elements: int = 90, num_interactions: int = 8, lmax: int = 6, mmax: int = 1, num_resolutions: int = 2, sphere_channels: int = 128, sphere_channels_reduce: int = 128, hidden_channels: int = 256, num_taps: int = -1, use_grid: bool = True, num_bands: int = 1, num_sphere_samples: int = 128, num_basis_functions: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False, direct_forces: bool = True) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -37,6 +37,8 @@ Package Contents :param use_pbc: Use periodic boundary conditions :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time + :type use_pbc_single: bool :param regress_forces: Compute forces :type regress_forces: bool :param otf_graph: Compute graph On The Fly (OTF) @@ -111,6 +113,9 @@ Package Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: cutoff diff --git a/_sources/autoapi/core/models/scn/scn/index.rst b/_sources/autoapi/core/models/scn/scn/index.rst index fc45235087..1dfc5333aa 100644 --- a/_sources/autoapi/core/models/scn/scn/index.rst +++ b/_sources/autoapi/core/models/scn/scn/index.rst @@ -26,7 +26,7 @@ Classes Module Contents --------------- -.. py:class:: SphericalChannelNetwork(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_num_neighbors: int = 20, cutoff: float = 8.0, max_num_elements: int = 90, num_interactions: int = 8, lmax: int = 6, mmax: int = 1, num_resolutions: int = 2, sphere_channels: int = 128, sphere_channels_reduce: int = 128, hidden_channels: int = 256, num_taps: int = -1, use_grid: bool = True, num_bands: int = 1, num_sphere_samples: int = 128, num_basis_functions: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False, direct_forces: bool = True) +.. py:class:: SphericalChannelNetwork(use_pbc: bool = True, use_pbc_single: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_num_neighbors: int = 20, cutoff: float = 8.0, max_num_elements: int = 90, num_interactions: int = 8, lmax: int = 6, mmax: int = 1, num_resolutions: int = 2, sphere_channels: int = 128, sphere_channels_reduce: int = 128, hidden_channels: int = 256, num_taps: int = -1, use_grid: bool = True, num_bands: int = 1, num_sphere_samples: int = 128, num_basis_functions: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False, direct_forces: bool = True) Bases: :py:obj:`torch.nn.Module`, :py:obj:`fairchem.core.models.base.GraphModelMixin` @@ -36,6 +36,8 @@ Module Contents :param use_pbc: Use periodic boundary conditions :type use_pbc: bool + :param use_pbc_single: Process batch PBC graphs one at a time + :type use_pbc_single: bool :param regress_forces: Compute forces :type regress_forces: bool :param otf_graph: Compute graph On The Fly (OTF) @@ -110,6 +112,9 @@ Module Contents .. py:attribute:: use_pbc + .. py:attribute:: use_pbc_single + + .. py:attribute:: cutoff diff --git a/_sources/autoapi/core/modules/index.rst b/_sources/autoapi/core/modules/index.rst index ebced4f1c1..0a2b0c0394 100644 --- a/_sources/autoapi/core/modules/index.rst +++ b/_sources/autoapi/core/modules/index.rst @@ -18,6 +18,7 @@ Subpackages .. toctree:: :maxdepth: 1 + /autoapi/core/modules/normalization/index /autoapi/core/modules/scaling/index @@ -30,7 +31,6 @@ Submodules /autoapi/core/modules/evaluator/index /autoapi/core/modules/exponential_moving_average/index /autoapi/core/modules/loss/index - /autoapi/core/modules/normalizer/index /autoapi/core/modules/scheduler/index /autoapi/core/modules/transforms/index diff --git a/_sources/autoapi/core/modules/normalization/_load_utils/index.rst b/_sources/autoapi/core/modules/normalization/_load_utils/index.rst new file mode 100644 index 0000000000..9a80e62334 --- /dev/null +++ b/_sources/autoapi/core/modules/normalization/_load_utils/index.rst @@ -0,0 +1,52 @@ +core.modules.normalization._load_utils +====================================== + +.. py:module:: core.modules.normalization._load_utils + +.. autoapi-nested-parse:: + + Copyright (c) Meta, Inc. and its affiliates. + + This source code is licensed under the MIT license found in the + LICENSE file in the root directory of this source tree. + + + +Functions +--------- + +.. autoapisummary:: + + core.modules.normalization._load_utils._load_check_duplicates + core.modules.normalization._load_utils._load_from_config + + +Module Contents +--------------- + +.. py:function:: _load_check_duplicates(config: dict, name: str) -> dict[str, torch.nn.Module] + + Attempt to load a single file with normalizers/element references and check config for duplicate targets. + + :param config: configuration dictionary + :param name: Name of module to use for logging + + :returns: dictionary of normalizer or element reference modules + + +.. py:function:: _load_from_config(config: dict, name: str, fit_fun: Callable[[list[str], torch.utils.data.Dataset, Any, Ellipsis], dict[str, torch.nn.Module]], create_fun: Callable[[str | pathlib.Path], torch.nn.Module], dataset: torch.utils.data.Dataset, checkpoint_dir: str | pathlib.Path | None = None, **fit_kwargs) -> dict[str, torch.nn.Module] + + Load or fit normalizers or element references from config + + If a fit is done, a fitted key with value true is added to the config to avoid re-fitting + once a checkpoint has been saved. + + :param config: configuration dictionary + :param name: Name of module to use for logging + :param fit_fun: Function to fit modules + :param create_fun: Function to create a module from file + :param checkpoint_dir: directory to save modules. If not given, modules won't be saved. + + :returns: dictionary of normalizer or element reference modules + + diff --git a/_sources/autoapi/core/modules/normalization/element_references/index.rst b/_sources/autoapi/core/modules/normalization/element_references/index.rst new file mode 100644 index 0000000000..44620f5de9 --- /dev/null +++ b/_sources/autoapi/core/modules/normalization/element_references/index.rst @@ -0,0 +1,117 @@ +core.modules.normalization.element_references +============================================= + +.. py:module:: core.modules.normalization.element_references + +.. autoapi-nested-parse:: + + Copyright (c) Meta, Inc. and its affiliates. + + This source code is licensed under the MIT license found in the + LICENSE file in the root directory of this source tree. + + + +Classes +------- + +.. autoapisummary:: + + core.modules.normalization.element_references.LinearReferences + + +Functions +--------- + +.. autoapisummary:: + + core.modules.normalization.element_references.create_element_references + core.modules.normalization.element_references.fit_linear_references + core.modules.normalization.element_references.load_references_from_config + + +Module Contents +--------------- + +.. py:class:: LinearReferences(element_references: torch.Tensor | None = None, max_num_elements: int = 118) + + Bases: :py:obj:`torch.nn.Module` + + + Represents an elemental linear references model for a target property. + + In an elemental reference associates a value with each chemical element present in the dataset. + Elemental references define a chemical composition model, i.e. a rough approximation of a target + property (energy) using elemental references is done by summing the elemental references multiplied + by the number of times the corresponding element is present. + + Elemental references energies can be taken as: + - the energy of a chemical species in its elemental state + (i.e. lowest energy polymorph of single element crystal structures for solids) + - fitting a linear model to a dataset, where the features are the counts of each element in each data point. + see the function fit_linear references below for details + + Training GNNs to predict the difference between DFT and the predictions of a chemical composition + model represent a useful normalization scheme that can improve model accuracy. See for example the + "Alternative reference scheme" section of the OC22 manuscript: https://arxiv.org/pdf/2206.08917 + + + .. py:method:: _apply_refs(target: torch.Tensor, batch: torch_geometric.data.Batch, sign: int, reshaped: bool = True) -> torch.Tensor + + Apply references batch-wise + + + + .. py:method:: dereference(target: torch.Tensor, batch: torch_geometric.data.Batch, reshaped: bool = True) -> torch.Tensor + + Remove linear references + + + + .. py:method:: forward(target: torch.Tensor, batch: torch_geometric.data.Batch, reshaped: bool = True) -> torch.Tensor + + Add linear references + + + +.. py:function:: create_element_references(file: str | pathlib.Path | None = None, state_dict: dict | None = None) -> LinearReferences + + Create an element reference module. + + :param type: type of reference (only linear implemented) + :type type: str + :param file: path to pt or npz file + :type file: str or Path + :param state_dict: a state dict of a element reference module + :type state_dict: dict + + :returns: LinearReference + + +.. py:function:: fit_linear_references(targets: list[str], dataset: torch.utils.data.Dataset, batch_size: int, num_batches: int | None = None, num_workers: int = 0, max_num_elements: int = 118, log_metrics: bool = True, use_numpy: bool = True, driver: str | None = None, shuffle: bool = True, seed: int = 0) -> dict[str, LinearReferences] + + Fit a set linear references for a list of targets using a given number of batches. + + :param targets: list of target names + :param dataset: data set to fit linear references with + :param batch_size: size of batch + :param num_batches: number of batches to use in fit. If not given will use all batches + :param num_workers: number of workers to use in data loader. + Note setting num_workers > 1 leads to finicky multiprocessing issues when using this function + in distributed mode. The issue has to do with pickling the functions in load_references_from_config + see function below... + :param max_num_elements: max number of elements in dataset. If not given will use an ambitious value of 118 + :param log_metrics: if true will compute MAE, RMSE and R2 score of fit and log. + :param use_numpy: use numpy.linalg.lstsq instead of torch. This tends to give better solutions. + :param driver: backend used to solve linear system. See torch.linalg.lstsq docs. Ignored if use_numpy=True + :param shuffle: whether to shuffle when loading the dataset + :param seed: random seed used to shuffle the sampler if shuffle=True + + :returns: dict of fitted LinearReferences objects + + +.. py:function:: load_references_from_config(config: dict[str, Any], dataset: torch.utils.data.Dataset, seed: int = 0, checkpoint_dir: str | pathlib.Path | None = None) -> dict[str, LinearReferences] + + Create a dictionary with element references from a config. + + diff --git a/_sources/autoapi/core/modules/normalization/index.rst b/_sources/autoapi/core/modules/normalization/index.rst new file mode 100644 index 0000000000..b4665eb3ef --- /dev/null +++ b/_sources/autoapi/core/modules/normalization/index.rst @@ -0,0 +1,17 @@ +core.modules.normalization +========================== + +.. py:module:: core.modules.normalization + + +Submodules +---------- + +.. toctree:: + :maxdepth: 1 + + /autoapi/core/modules/normalization/_load_utils/index + /autoapi/core/modules/normalization/element_references/index + /autoapi/core/modules/normalization/normalizer/index + + diff --git a/_sources/autoapi/core/modules/normalization/normalizer/index.rst b/_sources/autoapi/core/modules/normalization/normalizer/index.rst new file mode 100644 index 0000000000..27e53d3421 --- /dev/null +++ b/_sources/autoapi/core/modules/normalization/normalizer/index.rst @@ -0,0 +1,142 @@ +core.modules.normalization.normalizer +===================================== + +.. py:module:: core.modules.normalization.normalizer + +.. autoapi-nested-parse:: + + Copyright (c) Meta, Inc. and its affiliates. + + This source code is licensed under the MIT license found in the + LICENSE file in the root directory of this source tree. + + + +Classes +------- + +.. autoapisummary:: + + core.modules.normalization.normalizer.Normalizer + + +Functions +--------- + +.. autoapisummary:: + + core.modules.normalization.normalizer.create_normalizer + core.modules.normalization.normalizer.fit_normalizers + core.modules.normalization.normalizer.load_normalizers_from_config + + +Module Contents +--------------- + +.. py:class:: Normalizer(mean: float | torch.Tensor = 0.0, rmsd: float | torch.Tensor = 1.0) + + Bases: :py:obj:`torch.nn.Module` + + + Normalize/denormalize a tensor and optionally add a atom reference offset. + + + .. py:method:: norm(tensor: torch.Tensor) -> torch.Tensor + + + .. py:method:: denorm(normed_tensor: torch.Tensor) -> torch.Tensor + + + .. py:method:: forward(normed_tensor: torch.Tensor) -> torch.Tensor + + + .. py:method:: load_state_dict(state_dict: collections.abc.Mapping[str, Any], strict: bool = True, assign: bool = False) + + Copy parameters and buffers from :attr:`state_dict` into this module and its descendants. + + If :attr:`strict` is ``True``, then + the keys of :attr:`state_dict` must exactly match the keys returned + by this module's :meth:`~torch.nn.Module.state_dict` function. + + .. warning:: + If :attr:`assign` is ``True`` the optimizer must be created after + the call to :attr:`load_state_dict`. + + :param state_dict: a dict containing parameters and + persistent buffers. + :type state_dict: dict + :param strict: whether to strictly enforce that the keys + in :attr:`state_dict` match the keys returned by this module's + :meth:`~torch.nn.Module.state_dict` function. Default: ``True`` + :type strict: bool, optional + :param assign: whether to assign items in the state + dictionary to their corresponding keys in the module instead + of copying them inplace into the module's current parameters and buffers. + When ``False``, the properties of the tensors in the current + module are preserved while when ``True``, the properties of the + Tensors in the state dict are preserved. + Default: ``False`` + :type assign: bool, optional + + :returns: * **missing_keys** is a list of str containing the missing keys + * **unexpected_keys** is a list of str containing the unexpected keys + :rtype: ``NamedTuple`` with ``missing_keys`` and ``unexpected_keys`` fields + + .. note:: + + If a parameter or buffer is registered as ``None`` and its corresponding key + exists in :attr:`state_dict`, :meth:`load_state_dict` will raise a + ``RuntimeError``. + + + +.. py:function:: create_normalizer(file: str | pathlib.Path | None = None, state_dict: dict | None = None, tensor: torch.Tensor | None = None, mean: float | torch.Tensor | None = None, rmsd: float | torch.Tensor | None = None, stdev: float | torch.Tensor | None = None) -> Normalizer + + Build a target data normalizers with optional atom ref + + Only one of file, state_dict, tensor, or (mean and rmsd) will be used to create a normalizer. + If more than one set of inputs are given priority will be given following the order in which they are listed above. + + :param file: path to pt or npz file. + :type file: str or Path + :param state_dict: a state dict for Normalizer module + :type state_dict: dict + :param tensor: a tensor with target values used to compute mean and std + :type tensor: Tensor + :param mean: mean of target data + :type mean: float | Tensor + :param rmsd: rmsd of target data, rmsd from mean = stdev, rmsd from 0 = rms + :type rmsd: float | Tensor + :param stdev: standard deviation (deprecated, use rmsd instead) + + :returns: Normalizer + + +.. py:function:: fit_normalizers(targets: list[str], dataset: torch.utils.data.Dataset, batch_size: int, override_values: dict[str, dict[str, float]] | None = None, rmsd_correction: int | None = None, element_references: dict | None = None, num_batches: int | None = None, num_workers: int = 0, shuffle: bool = True, seed: int = 0) -> dict[str, Normalizer] + + Estimate mean and rmsd from data to create normalizers + + :param targets: list of target names + :param dataset: data set to fit linear references with + :param batch_size: size of batch + :param override_values: dictionary with target names and values to override. i.e. {"forces": {"mean": 0.0}} will set + the forces mean to zero. + :param rmsd_correction: correction to use when computing mean in std/rmsd. See docs for torch.std. + If not given, will always use 0 when mean == 0, and 1 otherwise. + :param element_references: + :param num_batches: number of batches to use in fit. If not given will use all batches + :param num_workers: number of workers to use in data loader + Note setting num_workers > 1 leads to finicky multiprocessing issues when using this function + in distributed mode. The issue has to do with pickling the functions in load_normalizers_from_config + see function below... + :param shuffle: whether to shuffle when loading the dataset + :param seed: random seed used to shuffle the sampler if shuffle=True + + :returns: dict of normalizer objects + + +.. py:function:: load_normalizers_from_config(config: dict[str, Any], dataset: torch.utils.data.Dataset, seed: int = 0, checkpoint_dir: str | pathlib.Path | None = None, element_references: dict[str, fairchem.core.modules.normalization.element_references.LinearReferences] | None = None) -> dict[str, Normalizer] + + Create a dictionary with element references from a config. + + diff --git a/_sources/autoapi/core/modules/normalizer/index.rst b/_sources/autoapi/core/modules/normalizer/index.rst deleted file mode 100644 index 5dae6fb437..0000000000 --- a/_sources/autoapi/core/modules/normalizer/index.rst +++ /dev/null @@ -1,53 +0,0 @@ -core.modules.normalizer -======================= - -.. py:module:: core.modules.normalizer - -.. autoapi-nested-parse:: - - Copyright (c) Meta, Inc. and its affiliates. - - This source code is licensed under the MIT license found in the - LICENSE file in the root directory of this source tree. - - - -Classes -------- - -.. autoapisummary:: - - core.modules.normalizer.Normalizer - - -Module Contents ---------------- - -.. py:class:: Normalizer(tensor: torch.Tensor | None = None, mean=None, std=None, device=None) - - Normalize a Tensor and restore it later. - - - .. py:attribute:: mean - :type: torch.Tensor - - - .. py:attribute:: std - :type: torch.Tensor - - - .. py:method:: to(device) -> None - - - .. py:method:: norm(tensor: torch.Tensor) -> torch.Tensor - - - .. py:method:: denorm(normed_tensor: torch.Tensor) -> torch.Tensor - - - .. py:method:: state_dict() - - - .. py:method:: load_state_dict(state_dict) -> None - - diff --git a/_sources/autoapi/core/scripts/fit_normalizers/index.rst b/_sources/autoapi/core/scripts/fit_normalizers/index.rst new file mode 100644 index 0000000000..375919e1f3 --- /dev/null +++ b/_sources/autoapi/core/scripts/fit_normalizers/index.rst @@ -0,0 +1,45 @@ +core.scripts.fit_normalizers +============================ + +.. py:module:: core.scripts.fit_normalizers + +.. autoapi-nested-parse:: + + Copyright (c) Meta, Inc. and its affiliates. + + This source code is licensed under the MIT license found in the + LICENSE file in the root directory of this source tree. + + + +Attributes +---------- + +.. autoapisummary:: + + core.scripts.fit_normalizers.parser + + +Functions +--------- + +.. autoapisummary:: + + core.scripts.fit_normalizers.fit_norms + + +Module Contents +--------------- + +.. py:function:: fit_norms(config: dict, output_path: str | pathlib.Path, linref_file: str | pathlib.Path | None = None, linref_target: str = 'energy') -> None + + Fit dataset mean and std using the standard config + + :param config: config + :param output_path: output path + :param linref_file: path to fitted linear references. IF these are used in training they must be used to compute mean/std + :param linref_target: target using linear references, basically always energy. + + +.. py:data:: parser + diff --git a/_sources/autoapi/core/scripts/fit_references/index.rst b/_sources/autoapi/core/scripts/fit_references/index.rst new file mode 100644 index 0000000000..06696cd7a3 --- /dev/null +++ b/_sources/autoapi/core/scripts/fit_references/index.rst @@ -0,0 +1,43 @@ +core.scripts.fit_references +=========================== + +.. py:module:: core.scripts.fit_references + +.. autoapi-nested-parse:: + + Copyright (c) Meta, Inc. and its affiliates. + + This source code is licensed under the MIT license found in the + LICENSE file in the root directory of this source tree. + + + +Attributes +---------- + +.. autoapisummary:: + + core.scripts.fit_references.parser + + +Functions +--------- + +.. autoapisummary:: + + core.scripts.fit_references.fit_linref + + +Module Contents +--------------- + +.. py:function:: fit_linref(config: dict, output_path: str | pathlib.Path) -> None + + Fit linear references using the standard config + + :param config: config + :param output_path: output path + + +.. py:data:: parser + diff --git a/_sources/autoapi/core/scripts/index.rst b/_sources/autoapi/core/scripts/index.rst index f74f19c0d9..bd9c6ee940 100644 --- a/_sources/autoapi/core/scripts/index.rst +++ b/_sources/autoapi/core/scripts/index.rst @@ -29,6 +29,8 @@ Submodules /autoapi/core/scripts/download_data/index /autoapi/core/scripts/download_large_files/index + /autoapi/core/scripts/fit_normalizers/index + /autoapi/core/scripts/fit_references/index /autoapi/core/scripts/gif_maker_parallelized/index /autoapi/core/scripts/make_challenge_submission_file/index /autoapi/core/scripts/make_lmdb_sizes/index diff --git a/_sources/autoapi/core/trainers/base_trainer/index.rst b/_sources/autoapi/core/trainers/base_trainer/index.rst index f0b299f53a..1c31f43805 100644 --- a/_sources/autoapi/core/trainers/base_trainer/index.rst +++ b/_sources/autoapi/core/trainers/base_trainer/index.rst @@ -67,6 +67,27 @@ Module Contents .. py:attribute:: scaler + .. py:attribute:: elementrefs + + + .. py:attribute:: normalizers + + + .. py:attribute:: train_dataset + :value: None + + + + .. py:attribute:: val_dataset + :value: None + + + + .. py:attribute:: test_dataset + :value: None + + + .. py:method:: train(disable_eval_tqdm: bool = False) -> None :abstractmethod: @@ -101,6 +122,12 @@ Module Contents .. py:method:: load_datasets() -> None + .. py:method:: load_references_and_normalizers() + + Load or create element references and normalizers from config + + + .. py:method:: load_task() diff --git a/_sources/autoapi/core/trainers/index.rst b/_sources/autoapi/core/trainers/index.rst index 95c8989727..7bbddd4d7f 100644 --- a/_sources/autoapi/core/trainers/index.rst +++ b/_sources/autoapi/core/trainers/index.rst @@ -70,6 +70,27 @@ Package Contents .. py:attribute:: scaler + .. py:attribute:: elementrefs + + + .. py:attribute:: normalizers + + + .. py:attribute:: train_dataset + :value: None + + + + .. py:attribute:: val_dataset + :value: None + + + + .. py:attribute:: test_dataset + :value: None + + + .. py:method:: train(disable_eval_tqdm: bool = False) -> None :abstractmethod: @@ -104,6 +125,12 @@ Package Contents .. py:method:: load_datasets() -> None + .. py:method:: load_references_and_normalizers() + + Load or create element references and normalizers from config + + + .. py:method:: load_task() @@ -204,6 +231,12 @@ Package Contents + .. py:method:: _denorm_preds(target_key: str, prediction: torch.Tensor, batch: torch_geometric.data.Batch) + + Convert model output from a batch into raw prediction by denormalizing and adding references + + + .. py:method:: _forward(batch) diff --git a/_sources/autoapi/core/trainers/ocp_trainer/index.rst b/_sources/autoapi/core/trainers/ocp_trainer/index.rst index 405db7d6c4..0dffbab7d0 100644 --- a/_sources/autoapi/core/trainers/ocp_trainer/index.rst +++ b/_sources/autoapi/core/trainers/ocp_trainer/index.rst @@ -87,6 +87,12 @@ Module Contents + .. py:method:: _denorm_preds(target_key: str, prediction: torch.Tensor, batch: torch_geometric.data.Batch) + + Convert model output from a batch into raw prediction by denormalizing and adding references + + + .. py:method:: _forward(batch) diff --git a/_sources/autoapi/data/oc/core/index.rst b/_sources/autoapi/data/oc/core/index.rst index 353a09352a..b63dc393c3 100644 --- a/_sources/autoapi/data/oc/core/index.rst +++ b/_sources/autoapi/data/oc/core/index.rst @@ -13,8 +13,11 @@ Submodules /autoapi/data/oc/core/adsorbate/index /autoapi/data/oc/core/adsorbate_slab_config/index /autoapi/data/oc/core/bulk/index + /autoapi/data/oc/core/interface_config/index + /autoapi/data/oc/core/ion/index /autoapi/data/oc/core/multi_adsorbate_slab_config/index /autoapi/data/oc/core/slab/index + /autoapi/data/oc/core/solvent/index Classes @@ -25,8 +28,11 @@ Classes data.oc.core.Adsorbate data.oc.core.AdsorbateSlabConfig data.oc.core.Bulk + data.oc.core.InterfaceConfig + data.oc.core.Ion data.oc.core.MultipleAdsorbateSlabConfig data.oc.core.Slab + data.oc.core.Solvent Package Contents @@ -310,6 +316,171 @@ Package Contents +.. py:class:: InterfaceConfig(slab: fairchem.data.oc.core.slab.Slab, adsorbates: list[fairchem.data.oc.core.adsorbate.Adsorbate], solvent: fairchem.data.oc.core.solvent.Solvent, ions: list[fairchem.data.oc.core.ion.Ion] | None = None, num_sites: int = 100, num_configurations: int = 1, interstitial_gap: float = 0.1, vacuum_size: int = 15, solvent_interstitial_gap: float = 2, solvent_depth: float = 8, pbc_shift: float = 0.0, packmol_tolerance: float = 2, mode: str = 'random_site_heuristic_placement') + + Bases: :py:obj:`fairchem.data.oc.core.multi_adsorbate_slab_config.MultipleAdsorbateSlabConfig` + + + Class to represent a solvent, adsorbate, slab, ion config. This class only + returns a fixed combination of adsorbates placed on the surface. Solvent + placement is performed by packmol + (https://m3g.github.io/packmol/userguide.shtml), with the number of solvent + molecules controlled by its corresponding density. Ion placement is random + within the desired volume. + + :param slab: Slab object. + :type slab: Slab + :param adsorbates: List of adsorbate objects to place on the slab. + :type adsorbates: List[Adsorbate] + :param solvent: Solvent object + :type solvent: Solvent + :param ions: List of ion objects to place + :type ions: List[Ion] = [] + :param num_sites: Number of sites to sample. + :type num_sites: int + :param num_configurations: Number of configurations to generate per slab+adsorbate(s) combination. + This corresponds to selecting different site combinations to place + the adsorbates on. + :type num_configurations: int + :param interstitial_gap: Minimum distance, in Angstroms, between adsorbate and slab atoms as + well as the inter-adsorbate distance. + :type interstitial_gap: float + :param vacuum_size: Size of vacuum layer to add to both ends of the resulting atoms object. + :type vacuum_size: int + :param solvent_interstitial_gap: Minimum distance, in Angstroms, between the solvent environment and the + adsorbate-slab environment. + :type solvent_interstitial_gap: float + :param solvent_depth: Volume depth to be used to pack solvents inside. + :type solvent_depth: float + :param pbc_shift: Cushion to add to the packmol volume to avoid overlapping atoms over pbc. + :type pbc_shift: float + :param packmol_tolerance: Packmol minimum distance to impose between molecules. + :type packmol_tolerance: float + :param mode: "random", "heuristic", or "random_site_heuristic_placement". + This affects surface site sampling and adsorbate placement on each site. + + In "random", we do a Delaunay triangulation of the surface atoms, then + sample sites uniformly at random within each triangle. When placing the + adsorbate, we randomly rotate it along xyz, and place it such that the + center of mass is at the site. + + In "heuristic", we use Pymatgen's AdsorbateSiteFinder to find the most + energetically favorable sites, i.e., ontop, bridge, or hollow sites. + When placing the adsorbate, we randomly rotate it along z with only + slight rotation along x and y, and place it such that the binding atom + is at the site. + + In "random_site_heuristic_placement", we do a Delaunay triangulation of + the surface atoms, then sample sites uniformly at random within each + triangle. When placing the adsorbate, we randomly rotate it along z with + only slight rotation along x and y, and place it such that the binding + atom is at the site. + + In all cases, the adsorbate is placed at the closest position of no + overlap with the slab plus `interstitial_gap` along the surface normal. + :type mode: str + + + .. py:attribute:: solvent + + + .. py:attribute:: ions + + + .. py:attribute:: vacuum_size + + + .. py:attribute:: solvent_depth + + + .. py:attribute:: solvent_interstitial_gap + + + .. py:attribute:: pbc_shift + + + .. py:attribute:: packmol_tolerance + + + .. py:attribute:: n_mol_per_volume + + + .. py:method:: create_interface_on_sites(atoms_list: list[ase.Atoms], metadata_list: list[dict]) + + Given adsorbate+slab configurations generated from + (Multi)AdsorbateSlabConfig and its corresponding metadata, create the + solvent/ion interface on top of the provided atoms objects. + + + + .. py:method:: create_packmol_atoms(geometry: fairchem.data.oc.utils.geometry.Geometry, n_solvent_mols: int) + + Pack solvent molecules in a provided unit cell volume. Packmol is used + to randomly pack solvent molecules in the desired volume. + + :param geometry: Geometry object corresponding to the desired cell. + :type geometry: Geometry + :param n_solvent_mols: Number of solvent molecules to pack in the volume. + :type n_solvent_mols: int + + + + .. py:method:: run_packmol(packmol_input: str) + + Run packmol. + + + + .. py:method:: randomize_coords(atoms: ase.Atoms) + + Randomly place the atoms in its unit cell. + + + +.. py:class:: Ion(ion_atoms: ase.Atoms = None, ion_id_from_db: int | None = None, ion_db_path: str = ION_PKL_PATH) + + Initializes an ion object in one of 2 ways: + - Directly pass in an ase.Atoms object. + - Pass in index of ion to select from ion database. + + :param ion_atoms: ion structure. + :type ion_atoms: ase.Atoms + :param ion_id_from_db: Index of ion to select. + :type ion_id_from_db: int + :param ion_db_path: Path to ion database. + :type ion_db_path: str + + + .. py:attribute:: ion_id_from_db + + + .. py:attribute:: ion_db_path + + + .. py:method:: __len__() + + + .. py:method:: __str__() + + Return str(self). + + + + .. py:method:: _load_ion(ion: dict) -> None + + Saves the fields from an ion stored in a database. Fields added + after the first revision are conditionally added for backwards + compatibility with older database files. + + + + .. py:method:: get_ion_concentration(volume) + + Compute the ion concentration units of M, given a volume in units of + Angstrom^3. + + + .. py:class:: MultipleAdsorbateSlabConfig(slab: fairchem.data.oc.core.slab.Slab, adsorbates: list[fairchem.data.oc.core.adsorbate.Adsorbate], num_sites: int = 100, num_configurations: int = 1, interstitial_gap: float = 0.1, mode: str = 'random_site_heuristic_placement') Bases: :py:obj:`fairchem.data.oc.core.adsorbate_slab_config.AdsorbateSlabConfig` @@ -488,3 +659,54 @@ Package Contents +.. py:class:: Solvent(solvent_atoms: ase.Atoms = None, solvent_id_from_db: int | None = None, solvent_db_path: str | None = SOLVENT_PKL_PATH, solvent_density: float | None = None) + + Initializes a solvent object in one of 2 ways: + - Directly pass in an ase.Atoms object. + - Pass in index of solvent to select from solvent database. + + :param solvent_atoms: Solvent molecule + :type solvent_atoms: ase.Atoms + :param solvent_id_from_db: Index of solvent to select. + :type solvent_id_from_db: int + :param solvent_db_path: Path to solvent database. + :type solvent_db_path: str + :param solvent_density: Desired solvent density to use. If not specified, the default is used + from the solvent databases. + :type solvent_density: float + + + .. py:attribute:: solvent_id_from_db + + + .. py:attribute:: solvent_db_path + + + .. py:attribute:: solvent_density + + + .. py:attribute:: molar_mass + + + .. py:method:: __len__() + + + .. py:method:: __str__() + + Return str(self). + + + + .. py:method:: _load_solvent(solvent: dict) -> None + + Saves the fields from an adsorbate stored in a database. Fields added + after the first revision are conditionally added for backwards + compatibility with older database files. + + + + .. py:property:: molecules_per_volume + Convert the solvent density in g/cm3 to the number of molecules per + angstrom cubed of volume. + + diff --git a/_sources/autoapi/data/oc/core/interface_config/index.rst b/_sources/autoapi/data/oc/core/interface_config/index.rst new file mode 100644 index 0000000000..4eaf5eefe6 --- /dev/null +++ b/_sources/autoapi/data/oc/core/interface_config/index.rst @@ -0,0 +1,138 @@ +data.oc.core.interface_config +============================= + +.. py:module:: data.oc.core.interface_config + + +Classes +------- + +.. autoapisummary:: + + data.oc.core.interface_config.InterfaceConfig + + +Module Contents +--------------- + +.. py:class:: InterfaceConfig(slab: fairchem.data.oc.core.slab.Slab, adsorbates: list[fairchem.data.oc.core.adsorbate.Adsorbate], solvent: fairchem.data.oc.core.solvent.Solvent, ions: list[fairchem.data.oc.core.ion.Ion] | None = None, num_sites: int = 100, num_configurations: int = 1, interstitial_gap: float = 0.1, vacuum_size: int = 15, solvent_interstitial_gap: float = 2, solvent_depth: float = 8, pbc_shift: float = 0.0, packmol_tolerance: float = 2, mode: str = 'random_site_heuristic_placement') + + Bases: :py:obj:`fairchem.data.oc.core.multi_adsorbate_slab_config.MultipleAdsorbateSlabConfig` + + + Class to represent a solvent, adsorbate, slab, ion config. This class only + returns a fixed combination of adsorbates placed on the surface. Solvent + placement is performed by packmol + (https://m3g.github.io/packmol/userguide.shtml), with the number of solvent + molecules controlled by its corresponding density. Ion placement is random + within the desired volume. + + :param slab: Slab object. + :type slab: Slab + :param adsorbates: List of adsorbate objects to place on the slab. + :type adsorbates: List[Adsorbate] + :param solvent: Solvent object + :type solvent: Solvent + :param ions: List of ion objects to place + :type ions: List[Ion] = [] + :param num_sites: Number of sites to sample. + :type num_sites: int + :param num_configurations: Number of configurations to generate per slab+adsorbate(s) combination. + This corresponds to selecting different site combinations to place + the adsorbates on. + :type num_configurations: int + :param interstitial_gap: Minimum distance, in Angstroms, between adsorbate and slab atoms as + well as the inter-adsorbate distance. + :type interstitial_gap: float + :param vacuum_size: Size of vacuum layer to add to both ends of the resulting atoms object. + :type vacuum_size: int + :param solvent_interstitial_gap: Minimum distance, in Angstroms, between the solvent environment and the + adsorbate-slab environment. + :type solvent_interstitial_gap: float + :param solvent_depth: Volume depth to be used to pack solvents inside. + :type solvent_depth: float + :param pbc_shift: Cushion to add to the packmol volume to avoid overlapping atoms over pbc. + :type pbc_shift: float + :param packmol_tolerance: Packmol minimum distance to impose between molecules. + :type packmol_tolerance: float + :param mode: "random", "heuristic", or "random_site_heuristic_placement". + This affects surface site sampling and adsorbate placement on each site. + + In "random", we do a Delaunay triangulation of the surface atoms, then + sample sites uniformly at random within each triangle. When placing the + adsorbate, we randomly rotate it along xyz, and place it such that the + center of mass is at the site. + + In "heuristic", we use Pymatgen's AdsorbateSiteFinder to find the most + energetically favorable sites, i.e., ontop, bridge, or hollow sites. + When placing the adsorbate, we randomly rotate it along z with only + slight rotation along x and y, and place it such that the binding atom + is at the site. + + In "random_site_heuristic_placement", we do a Delaunay triangulation of + the surface atoms, then sample sites uniformly at random within each + triangle. When placing the adsorbate, we randomly rotate it along z with + only slight rotation along x and y, and place it such that the binding + atom is at the site. + + In all cases, the adsorbate is placed at the closest position of no + overlap with the slab plus `interstitial_gap` along the surface normal. + :type mode: str + + + .. py:attribute:: solvent + + + .. py:attribute:: ions + + + .. py:attribute:: vacuum_size + + + .. py:attribute:: solvent_depth + + + .. py:attribute:: solvent_interstitial_gap + + + .. py:attribute:: pbc_shift + + + .. py:attribute:: packmol_tolerance + + + .. py:attribute:: n_mol_per_volume + + + .. py:method:: create_interface_on_sites(atoms_list: list[ase.Atoms], metadata_list: list[dict]) + + Given adsorbate+slab configurations generated from + (Multi)AdsorbateSlabConfig and its corresponding metadata, create the + solvent/ion interface on top of the provided atoms objects. + + + + .. py:method:: create_packmol_atoms(geometry: fairchem.data.oc.utils.geometry.Geometry, n_solvent_mols: int) + + Pack solvent molecules in a provided unit cell volume. Packmol is used + to randomly pack solvent molecules in the desired volume. + + :param geometry: Geometry object corresponding to the desired cell. + :type geometry: Geometry + :param n_solvent_mols: Number of solvent molecules to pack in the volume. + :type n_solvent_mols: int + + + + .. py:method:: run_packmol(packmol_input: str) + + Run packmol. + + + + .. py:method:: randomize_coords(atoms: ase.Atoms) + + Randomly place the atoms in its unit cell. + + + diff --git a/_sources/autoapi/data/oc/core/ion/index.rst b/_sources/autoapi/data/oc/core/ion/index.rst new file mode 100644 index 0000000000..261584bfab --- /dev/null +++ b/_sources/autoapi/data/oc/core/ion/index.rst @@ -0,0 +1,61 @@ +data.oc.core.ion +================ + +.. py:module:: data.oc.core.ion + + +Classes +------- + +.. autoapisummary:: + + data.oc.core.ion.Ion + + +Module Contents +--------------- + +.. py:class:: Ion(ion_atoms: ase.Atoms = None, ion_id_from_db: int | None = None, ion_db_path: str = ION_PKL_PATH) + + Initializes an ion object in one of 2 ways: + - Directly pass in an ase.Atoms object. + - Pass in index of ion to select from ion database. + + :param ion_atoms: ion structure. + :type ion_atoms: ase.Atoms + :param ion_id_from_db: Index of ion to select. + :type ion_id_from_db: int + :param ion_db_path: Path to ion database. + :type ion_db_path: str + + + .. py:attribute:: ion_id_from_db + + + .. py:attribute:: ion_db_path + + + .. py:method:: __len__() + + + .. py:method:: __str__() + + Return str(self). + + + + .. py:method:: _load_ion(ion: dict) -> None + + Saves the fields from an ion stored in a database. Fields added + after the first revision are conditionally added for backwards + compatibility with older database files. + + + + .. py:method:: get_ion_concentration(volume) + + Compute the ion concentration units of M, given a volume in units of + Angstrom^3. + + + diff --git a/_sources/autoapi/data/oc/core/solvent/index.rst b/_sources/autoapi/data/oc/core/solvent/index.rst new file mode 100644 index 0000000000..71dcb0c200 --- /dev/null +++ b/_sources/autoapi/data/oc/core/solvent/index.rst @@ -0,0 +1,68 @@ +data.oc.core.solvent +==================== + +.. py:module:: data.oc.core.solvent + + +Classes +------- + +.. autoapisummary:: + + data.oc.core.solvent.Solvent + + +Module Contents +--------------- + +.. py:class:: Solvent(solvent_atoms: ase.Atoms = None, solvent_id_from_db: int | None = None, solvent_db_path: str | None = SOLVENT_PKL_PATH, solvent_density: float | None = None) + + Initializes a solvent object in one of 2 ways: + - Directly pass in an ase.Atoms object. + - Pass in index of solvent to select from solvent database. + + :param solvent_atoms: Solvent molecule + :type solvent_atoms: ase.Atoms + :param solvent_id_from_db: Index of solvent to select. + :type solvent_id_from_db: int + :param solvent_db_path: Path to solvent database. + :type solvent_db_path: str + :param solvent_density: Desired solvent density to use. If not specified, the default is used + from the solvent databases. + :type solvent_density: float + + + .. py:attribute:: solvent_id_from_db + + + .. py:attribute:: solvent_db_path + + + .. py:attribute:: solvent_density + + + .. py:attribute:: molar_mass + + + .. py:method:: __len__() + + + .. py:method:: __str__() + + Return str(self). + + + + .. py:method:: _load_solvent(solvent: dict) -> None + + Saves the fields from an adsorbate stored in a database. Fields added + after the first revision are conditionally added for backwards + compatibility with older database files. + + + + .. py:property:: molecules_per_volume + Convert the solvent density in g/cm3 to the number of molecules per + angstrom cubed of volume. + + diff --git a/_sources/autoapi/data/oc/databases/pkls/index.rst b/_sources/autoapi/data/oc/databases/pkls/index.rst index a212daacf8..6083ee787d 100644 --- a/_sources/autoapi/data/oc/databases/pkls/index.rst +++ b/_sources/autoapi/data/oc/databases/pkls/index.rst @@ -11,6 +11,8 @@ Attributes data.oc.databases.pkls.BULK_PKL_PATH data.oc.databases.pkls.ADSORBATE_PKL_PATH + data.oc.databases.pkls.SOLVENT_PKL_PATH + data.oc.databases.pkls.ION_PKL_PATH Package Contents @@ -20,3 +22,7 @@ Package Contents .. py:data:: ADSORBATE_PKL_PATH +.. py:data:: SOLVENT_PKL_PATH + +.. py:data:: ION_PKL_PATH + diff --git a/_sources/autoapi/data/oc/index.rst b/_sources/autoapi/data/oc/index.rst index 4497af8161..138690ea35 100644 --- a/_sources/autoapi/data/oc/index.rst +++ b/_sources/autoapi/data/oc/index.rst @@ -20,7 +20,6 @@ Subpackages /autoapi/data/oc/core/index /autoapi/data/oc/databases/index - /autoapi/data/oc/tests/index /autoapi/data/oc/utils/index diff --git a/_sources/autoapi/data/oc/tests/index.rst b/_sources/autoapi/data/oc/tests/index.rst deleted file mode 100644 index b3d9ebb9c2..0000000000 --- a/_sources/autoapi/data/oc/tests/index.rst +++ /dev/null @@ -1,6 +0,0 @@ -data.oc.tests -============= - -.. py:module:: data.oc.tests - - diff --git a/_sources/autoapi/data/oc/utils/geometry/index.rst b/_sources/autoapi/data/oc/utils/geometry/index.rst new file mode 100644 index 0000000000..98868334b4 --- /dev/null +++ b/_sources/autoapi/data/oc/utils/geometry/index.rst @@ -0,0 +1,179 @@ +data.oc.utils.geometry +====================== + +.. py:module:: data.oc.utils.geometry + + +Classes +------- + +.. autoapisummary:: + + data.oc.utils.geometry.Geometry + data.oc.utils.geometry.PlaneBoundTriclinicGeometry + data.oc.utils.geometry.BoxGeometry + + +Module Contents +--------------- + +.. py:class:: Geometry + + Bases: :py:obj:`abc.ABC` + + + Base class for geometries + + + .. py:method:: distance_point_plane(vec: numpy.array, point_plane: numpy.array, point_ext: numpy.array) + :staticmethod: + + + Returns the (shortest) distance between a plane with normal vector + 'vec' through point 'point_plane' and a point 'point_ext'. + + :param vec: normal vector of plane + :type vec: np.array + :param point_plane: point on line + :type point_plane: np.array + :param point_ext: external point(s) + :type point_ext: np.array + + :returns: (np.array) Distance between plane and external point(s) + + + + .. py:method:: vec_and_point_to_plane(vec: numpy.array, point: numpy.array) + :staticmethod: + + + Returns the (unique) plane, given a normal vector 'vec' and a + point 'point' in the plane. ax + by + cz - d = 0 + + :param vec: normal vector of plane + :type vec: np.array + :param point: point in plane + :type point: np.array + + :returns: (np.array) Paramterization of plane + + + + .. py:method:: cell2planes(cell: ase.cell.Cell, pbc: float) + :staticmethod: + + + Get the parameterization of the sizes of a ase.Atom cell + + cell: ase.cell.Cell + pbc (float): shift of boundaries to be used with periodic boundary condition + + Return + (List[np.array]) Parameterization of cell plane sides + + 3 planes intersect the origin by ase design. + + + + .. py:method:: extract_box_properties(center: numpy.array, length: numpy.array, lo_corner: numpy.array, hi_corner: numpy.array) + :staticmethod: + + + Given two of the properties 'center', 'length', 'lo_corner', + 'hi_corner', return all the properties. The properties that + are not given are expected to be 'None'. + + + + .. py:method:: packmol_structure(filename: str, number: int, side: str) + :abstractmethod: + + + How to write packmol input file. To be defined by inherited class. + + + +.. py:class:: PlaneBoundTriclinicGeometry(cell: ase.cell.Cell, pbc: float = 0.0) + + Bases: :py:obj:`Geometry` + + + Triclinic crystal geometry based on ase.Atom cell + + + .. py:attribute:: planes + + + .. py:attribute:: cell + + + .. py:attribute:: ll_corner + :value: [0, 0, 0] + + + + .. py:attribute:: a + + + .. py:attribute:: b + + + .. py:attribute:: c + + + .. py:attribute:: ur_corner + + + .. py:method:: packmol_structure(filename: str, number: int, side: str) + + Make file structure to be used in packmol input script + + :param filename: output filename to save structure + :type filename: str + :param number: number of solvent molecules + :type number: int + :param side: pack solvent inside/outside of geometry + :type side: str + + :returns: String with information about the structure + + + +.. py:class:: BoxGeometry(center=None, length=None, lo_corner=None, hi_corner=None, **kwargs) + + Bases: :py:obj:`Geometry` + + + Box geometry for orthorhombic cells. + + + .. py:attribute:: props + + + .. py:attribute:: params + + + .. py:attribute:: length + + + .. py:method:: __repr__() + + Return repr(self). + + + + .. py:method:: packmol_structure(filename: str, number: int, side: str) + + Make file structure to be used in packmol input script + + :param filename: output filename to save structure + :type filename: str + :param number: number of solvent molecules + :type number: int + :param side: pack solvent inside/outside of geometry + :type side: str + + :returns: String with information about the structure + + + diff --git a/_sources/autoapi/data/oc/utils/index.rst b/_sources/autoapi/data/oc/utils/index.rst index ab6cafa544..c0f625df3c 100644 --- a/_sources/autoapi/data/oc/utils/index.rst +++ b/_sources/autoapi/data/oc/utils/index.rst @@ -11,7 +11,9 @@ Submodules :maxdepth: 1 /autoapi/data/oc/utils/flag_anomaly/index + /autoapi/data/oc/utils/geometry/index /autoapi/data/oc/utils/vasp/index + /autoapi/data/oc/utils/vasp_flags/index Classes diff --git a/_sources/autoapi/data/oc/utils/vasp/index.rst b/_sources/autoapi/data/oc/utils/vasp/index.rst index d226172df9..8af6e8ab97 100644 --- a/_sources/autoapi/data/oc/utils/vasp/index.rst +++ b/_sources/autoapi/data/oc/utils/vasp/index.rst @@ -19,8 +19,6 @@ Attributes data.oc.utils.vasp.__author__ data.oc.utils.vasp.__email__ - data.oc.utils.vasp.VASP_FLAGS - data.oc.utils.vasp.BULK_VASP_FLAGS Functions @@ -44,10 +42,6 @@ Module Contents :value: 'ktran@andrew.cmu.edu' -.. py:data:: VASP_FLAGS - -.. py:data:: BULK_VASP_FLAGS - .. py:function:: _clean_up_inputs(atoms, vasp_flags) Parses the inputs and makes sure some things are straightened out. diff --git a/_sources/autoapi/data/oc/utils/vasp_flags/index.rst b/_sources/autoapi/data/oc/utils/vasp_flags/index.rst new file mode 100644 index 0000000000..e8115e8a1e --- /dev/null +++ b/_sources/autoapi/data/oc/utils/vasp_flags/index.rst @@ -0,0 +1,37 @@ +data.oc.utils.vasp_flags +======================== + +.. py:module:: data.oc.utils.vasp_flags + + +Attributes +---------- + +.. autoapisummary:: + + data.oc.utils.vasp_flags.VASP_FLAGS + data.oc.utils.vasp_flags.BULK_VASP_FLAGS + data.oc.utils.vasp_flags.SOLVENT_BASE_FLAGS + data.oc.utils.vasp_flags.SOLVENT_BULK_VASP_FLAGS + data.oc.utils.vasp_flags.RELAX_FLAGS + data.oc.utils.vasp_flags.MD_FLAGS + data.oc.utils.vasp_flags.ML_FLAGS + + +Module Contents +--------------- + +.. py:data:: VASP_FLAGS + +.. py:data:: BULK_VASP_FLAGS + +.. py:data:: SOLVENT_BASE_FLAGS + +.. py:data:: SOLVENT_BULK_VASP_FLAGS + +.. py:data:: RELAX_FLAGS + +.. py:data:: MD_FLAGS + +.. py:data:: ML_FLAGS + diff --git a/_sources/core/inference.md b/_sources/core/inference.md index d10dc6fed2..63ce484653 100644 --- a/_sources/core/inference.md +++ b/_sources/core/inference.md @@ -23,7 +23,8 @@ Boes, J. R., Groenenboom, M. C., Keith, J. A., & Kitchin, J. R. (2016). Neural n You can retrieve the dataset below. In this notebook we learn how to do "mass inference" without an ASE calculator. You do this by creating a config.yml file, and running the `main.py` command line utility. ```{code-cell} ipython3 -! wget https://figshare.com/ndownloader/files/11948267 -O data.db +from fairchem.core.scripts.download_large_files import download_file_group +download_file_group('docs') ``` diff --git a/autoapi/adsorbml/2023_neurips_challenge/challenge_eval/index.html b/autoapi/adsorbml/2023_neurips_challenge/challenge_eval/index.html index 7551c88879..02a876122e 100644 --- a/autoapi/adsorbml/2023_neurips_challenge/challenge_eval/index.html +++ b/autoapi/adsorbml/2023_neurips_challenge/challenge_eval/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/adsorbml/scripts/dense_eval/index.html b/autoapi/adsorbml/scripts/dense_eval/index.html index 39b1442ae3..464a2f805b 100644 --- a/autoapi/adsorbml/scripts/dense_eval/index.html +++ b/autoapi/adsorbml/scripts/dense_eval/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/adsorbml/scripts/process_mlrs/index.html b/autoapi/adsorbml/scripts/process_mlrs/index.html index d6f99484b9..41689c90a7 100644 --- a/autoapi/adsorbml/scripts/process_mlrs/index.html +++ b/autoapi/adsorbml/scripts/process_mlrs/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/adsorbml/scripts/utils/index.html b/autoapi/adsorbml/scripts/utils/index.html index 0fe68f046b..98a5adaf74 100644 --- a/autoapi/adsorbml/scripts/utils/index.html +++ b/autoapi/adsorbml/scripts/utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/adsorbml/scripts/write_top_k_vasp/index.html b/autoapi/adsorbml/scripts/write_top_k_vasp/index.html index 4c45b6eb74..9a416750da 100644 --- a/autoapi/adsorbml/scripts/write_top_k_vasp/index.html +++ b/autoapi/adsorbml/scripts/write_top_k_vasp/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/cattsunami/core/autoframe/index.html b/autoapi/cattsunami/core/autoframe/index.html index 5700166b92..ebfbefef93 100644 --- a/autoapi/cattsunami/core/autoframe/index.html +++ b/autoapi/cattsunami/core/autoframe/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/cattsunami/core/index.html b/autoapi/cattsunami/core/index.html index fd5f21776f..d7ffce33da 100644 --- a/autoapi/cattsunami/core/index.html +++ b/autoapi/cattsunami/core/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/cattsunami/core/ocpneb/index.html b/autoapi/cattsunami/core/ocpneb/index.html index dbc9a9cea4..c20fc37d44 100644 --- a/autoapi/cattsunami/core/ocpneb/index.html +++ b/autoapi/cattsunami/core/ocpneb/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/cattsunami/core/reaction/index.html b/autoapi/cattsunami/core/reaction/index.html index 6dcd50e154..b71a6a4870 100644 --- a/autoapi/cattsunami/core/reaction/index.html +++ b/autoapi/cattsunami/core/reaction/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/cattsunami/databases/index.html b/autoapi/cattsunami/databases/index.html index 67907b4c4e..4753c72371 100644 --- a/autoapi/cattsunami/databases/index.html +++ b/autoapi/cattsunami/databases/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/cattsunami/index.html b/autoapi/cattsunami/index.html index ca22d01d0a..9112443659 100644 --- a/autoapi/cattsunami/index.html +++ b/autoapi/cattsunami/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/cattsunami/run_validation/run_validation/index.html b/autoapi/cattsunami/run_validation/run_validation/index.html index 0572e2633a..0c1fa6381a 100644 --- a/autoapi/cattsunami/run_validation/run_validation/index.html +++ b/autoapi/cattsunami/run_validation/run_validation/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/_cli/index.html b/autoapi/core/_cli/index.html index 5bd5d704d2..f25266ee3a 100644 --- a/autoapi/core/_cli/index.html +++ b/autoapi/core/_cli/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/data_parallel/index.html b/autoapi/core/common/data_parallel/index.html index 725a8f1df8..f54d66faa2 100644 --- a/autoapi/core/common/data_parallel/index.html +++ b/autoapi/core/common/data_parallel/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/distutils/index.html b/autoapi/core/common/distutils/index.html index 02076b9103..89a85081e1 100644 --- a/autoapi/core/common/distutils/index.html +++ b/autoapi/core/common/distutils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -635,6 +638,7 @@

    Contents

  • is_master()
  • synchronize()
  • broadcast()
    • +
  • broadcast_object_list()
  • all_reduce()
  • all_gather()
  • gather_objects()
    • @@ -698,13 +702,16 @@

    Functions

    broadcast(→ None)

    -

    all_reduce(→ torch.Tensor)

    +

    broadcast_object_list(→ None)

    -

    all_gather(→ list[torch.Tensor])

    +

    all_reduce(→ torch.Tensor)

    -

    gather_objects(→ list[T])

    +

    all_gather(→ list[torch.Tensor])

    +

    + +

    gather_objects(→ list[T])

    Gather a list of pickleable objects into rank 0

    @@ -763,6 +770,11 @@

    Module Contentscore.common.distutils.broadcast(tensor: torch.Tensor, src, group=dist.group.WORLD, async_op: bool = False) → None#
    +
    +
    +core.common.distutils.broadcast_object_list(object_list: list[Any], src: int, group=dist.group.WORLD, device: str | None = None) → None#
    +
    +
    core.common.distutils.all_reduce(data, group=dist.group.WORLD, average: bool = False, device=None) → torch.Tensor#
    @@ -859,6 +871,7 @@

    Module Contentsis_master()

  • synchronize()
  • broadcast()
    • +
  • broadcast_object_list()
  • all_reduce()
  • all_gather()
  • gather_objects()
    • diff --git a/autoapi/core/common/flags/index.html b/autoapi/core/common/flags/index.html index 93e5b013a0..c65f6283e1 100644 --- a/autoapi/core/common/flags/index.html +++ b/autoapi/core/common/flags/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/gp_utils/index.html b/autoapi/core/common/gp_utils/index.html index 9c53223ee8..7e0ea2708a 100644 --- a/autoapi/core/common/gp_utils/index.html +++ b/autoapi/core/common/gp_utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/hpo_utils/index.html b/autoapi/core/common/hpo_utils/index.html index 82e77c5119..4ddd4e3ac4 100644 --- a/autoapi/core/common/hpo_utils/index.html +++ b/autoapi/core/common/hpo_utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/index.html b/autoapi/core/common/index.html index 8eccc85efb..96b234dcd4 100644 --- a/autoapi/core/common/index.html +++ b/autoapi/core/common/index.html @@ -307,6 +307,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -336,16 +337,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
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    • @@ -383,7 +387,6 @@
  • data.oc
    @@ -662,6 +665,7 @@

    Submodulescore.common.logger

  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • diff --git a/autoapi/core/common/logger/index.html b/autoapi/core/common/logger/index.html index 25c05c452c..e16fc7fc01 100644 --- a/autoapi/core/common/logger/index.html +++ b/autoapi/core/common/logger/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
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    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
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  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/profiler_utils/index.html b/autoapi/core/common/profiler_utils/index.html index 80f77b28ad..63305c70eb 100644 --- a/autoapi/core/common/profiler_utils/index.html +++ b/autoapi/core/common/profiler_utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
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    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/registry/index.html b/autoapi/core/common/registry/index.html index e8b8b48953..e7c7f7b009 100644 --- a/autoapi/core/common/registry/index.html +++ b/autoapi/core/common/registry/index.html @@ -61,7 +61,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
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    • +
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  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -982,11 +985,11 @@

    Module Contents

    next

    -

    core.common.test_utils

    +

    core.common.slurm

     diff --git a/autoapi/core/common/relaxation/ase_utils/index.html b/autoapi/core/common/relaxation/ase_utils/index.html index 7d10354cc3..a5fe780389 100644 --- a/autoapi/core/common/relaxation/ase_utils/index.html +++ b/autoapi/core/common/relaxation/ase_utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
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    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/relaxation/index.html b/autoapi/core/common/relaxation/index.html index 7eaf89e816..f75e02d68e 100644 --- a/autoapi/core/common/relaxation/index.html +++ b/autoapi/core/common/relaxation/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/relaxation/ml_relaxation/index.html b/autoapi/core/common/relaxation/ml_relaxation/index.html index 6231c0416a..761ad89e37 100644 --- a/autoapi/core/common/relaxation/ml_relaxation/index.html +++ b/autoapi/core/common/relaxation/ml_relaxation/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/relaxation/optimizers/index.html b/autoapi/core/common/relaxation/optimizers/index.html index 1af85fe75c..8b5528e544 100644 --- a/autoapi/core/common/relaxation/optimizers/index.html +++ b/autoapi/core/common/relaxation/optimizers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
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    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
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  • core.scripts.hpo
  • core.scripts.download_data
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    • +
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  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/relaxation/optimizers/lbfgs_torch/index.html b/autoapi/core/common/relaxation/optimizers/lbfgs_torch/index.html index b3b65e9f0d..83e3caf19d 100644 --- a/autoapi/core/common/relaxation/optimizers/lbfgs_torch/index.html +++ b/autoapi/core/common/relaxation/optimizers/lbfgs_torch/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/slurm/index.html b/autoapi/core/common/slurm/index.html new file mode 100644 index 0000000000..518ef62b7d --- /dev/null +++ b/autoapi/core/common/slurm/index.html @@ -0,0 +1,790 @@ + + + + + + + + + + + core.common.slurm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    core.common.slurm

    + +
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    + + + + +
    + +
    +

    core.common.slurm#

    +
    +

    Functions#

    +
    + + + + + +

    add_timestamp_id_to_submission_pickle(slurm_folder, ...)

    +
    +
    +
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    Module Contents#

    +
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    +core.common.slurm.add_timestamp_id_to_submission_pickle(slurm_folder: str, slurm_job_id: str, timestamp_id: str)#
    +
    + +
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    + Contents +
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    +By FAIR Chemistry & Collaborators +

    + +
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    + + © Copyright 2024. +
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  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -802,12 +805,12 @@

    Module Contents

    previous

    -

    core.common.registry

    +

    core.common.slurm

     core.common.logger

  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -336,16 +337,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    diff --git a/autoapi/core/common/tutorial_utils/index.html b/autoapi/core/common/tutorial_utils/index.html index 3a09d6b706..b7f04232b3 100644 --- a/autoapi/core/common/tutorial_utils/index.html +++ b/autoapi/core/common/tutorial_utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/typing/index.html b/autoapi/core/common/typing/index.html index e1a167b0c6..cb13364b92 100644 --- a/autoapi/core/common/typing/index.html +++ b/autoapi/core/common/typing/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/common/utils/index.html b/autoapi/core/common/utils/index.html index 240c49d55d..ceb91d84df 100644 --- a/autoapi/core/common/utils/index.html +++ b/autoapi/core/common/utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -672,6 +675,7 @@

    Contents

  • new_trainer_context()
  • _resolve_scale_factor_submodule()
  • _report_incompat_keys()
    • +
  • match_state_dict()
  • load_state_dict()
  • scatter_det()
  • get_commit_hash()
    • @@ -822,25 +826,28 @@

    Functions

    _report_incompat_keys(→ tuple[list[str], list[str]])

    -

    load_state_dict(→ tuple[list[str], list[str]])

    +

    match_state_dict(→ dict)

    -

    scatter_det(*args, **kwargs)

    +

    load_state_dict(→ tuple[list[str], list[str]])

    -

    get_commit_hash()

    +

    scatter_det(*args, **kwargs)

    -

    cg_change_mat(→ torch.tensor)

    +

    get_commit_hash()

    -

    irreps_sum(→ int)

    +

    cg_change_mat(→ torch.tensor)

    +

    + +

    irreps_sum(→ int)

    Returns the sum of the dimensions of the irreps up to the specified angular momentum.

    -

    update_config(base_config)

    +

    update_config(base_config)

    Configs created prior to FAIRChem/OCP 2.0 are organized a little different than they

    -

    get_loss_module(loss_name)

    +

    get_loss_module(loss_name)

    @@ -1120,6 +1127,11 @@

    Module Contentscore.common.utils._report_incompat_keys(model: torch.nn.Module, keys: torch.nn.modules.module._IncompatibleKeys, strict: bool = False) → tuple[list[str], list[str]]#
    +
    +
    +core.common.utils.match_state_dict(model_state_dict: collections.abc.Mapping[str, torch.Tensor], checkpoint_state_dict: collections.abc.Mapping[str, torch.Tensor]) → dict#
    +
    +
    core.common.utils.load_state_dict(module: torch.nn.Module, state_dict: collections.abc.Mapping[str, torch.Tensor], strict: bool = True) → tuple[list[str], list[str]]#
    @@ -1280,6 +1292,7 @@

    Module Contentsnew_trainer_context()

  • _resolve_scale_factor_submodule()
  • _report_incompat_keys()
    • +
  • match_state_dict()
  • load_state_dict()
  • scatter_det()
  • get_commit_hash()
    • diff --git a/autoapi/core/datasets/_utils/index.html b/autoapi/core/datasets/_utils/index.html index 3376928265..8b5f353acc 100644 --- a/autoapi/core/datasets/_utils/index.html +++ b/autoapi/core/datasets/_utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/ase_datasets/index.html b/autoapi/core/datasets/ase_datasets/index.html index 7bfd809bae..c176dbdf50 100644 --- a/autoapi/core/datasets/ase_datasets/index.html +++ b/autoapi/core/datasets/ase_datasets/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/base_dataset/index.html b/autoapi/core/datasets/base_dataset/index.html index 512b49d6b1..f1b8279a46 100644 --- a/autoapi/core/datasets/base_dataset/index.html +++ b/autoapi/core/datasets/base_dataset/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/embeddings/atomic_radii/index.html b/autoapi/core/datasets/embeddings/atomic_radii/index.html index 1b4b08d0a7..3504e0598f 100644 --- a/autoapi/core/datasets/embeddings/atomic_radii/index.html +++ b/autoapi/core/datasets/embeddings/atomic_radii/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/embeddings/continuous_embeddings/index.html b/autoapi/core/datasets/embeddings/continuous_embeddings/index.html index 09d99ba3ad..8acf015b01 100644 --- a/autoapi/core/datasets/embeddings/continuous_embeddings/index.html +++ b/autoapi/core/datasets/embeddings/continuous_embeddings/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/embeddings/index.html b/autoapi/core/datasets/embeddings/index.html index 5756cead15..47d481042f 100644 --- a/autoapi/core/datasets/embeddings/index.html +++ b/autoapi/core/datasets/embeddings/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/embeddings/khot_embeddings/index.html b/autoapi/core/datasets/embeddings/khot_embeddings/index.html index b4cc67e1db..c49468b88f 100644 --- a/autoapi/core/datasets/embeddings/khot_embeddings/index.html +++ b/autoapi/core/datasets/embeddings/khot_embeddings/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/embeddings/qmof_khot_embeddings/index.html b/autoapi/core/datasets/embeddings/qmof_khot_embeddings/index.html index 89921107e1..e85a65affd 100644 --- a/autoapi/core/datasets/embeddings/qmof_khot_embeddings/index.html +++ b/autoapi/core/datasets/embeddings/qmof_khot_embeddings/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/index.html b/autoapi/core/datasets/index.html index 9735b32c9f..1c6942acf0 100644 --- a/autoapi/core/datasets/index.html +++ b/autoapi/core/datasets/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/lmdb_database/index.html b/autoapi/core/datasets/lmdb_database/index.html index 71266a7631..42064b9495 100644 --- a/autoapi/core/datasets/lmdb_database/index.html +++ b/autoapi/core/datasets/lmdb_database/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/lmdb_dataset/index.html b/autoapi/core/datasets/lmdb_dataset/index.html index 0d42ebe5c9..774d2aa0b7 100644 --- a/autoapi/core/datasets/lmdb_dataset/index.html +++ b/autoapi/core/datasets/lmdb_dataset/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/oc22_lmdb_dataset/index.html b/autoapi/core/datasets/oc22_lmdb_dataset/index.html index 3d2eff0d26..c45f9b274c 100644 --- a/autoapi/core/datasets/oc22_lmdb_dataset/index.html +++ b/autoapi/core/datasets/oc22_lmdb_dataset/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/datasets/target_metadata_guesser/index.html b/autoapi/core/datasets/target_metadata_guesser/index.html index ebbcd2457c..9745473960 100644 --- a/autoapi/core/datasets/target_metadata_guesser/index.html +++ b/autoapi/core/datasets/target_metadata_guesser/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/index.html b/autoapi/core/index.html index 4ef4b7bdf7..0f3d247d50 100644 --- a/autoapi/core/index.html +++ b/autoapi/core/index.html @@ -307,6 +307,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -336,16 +337,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    diff --git a/autoapi/core/models/base/index.html b/autoapi/core/models/base/index.html index 1e970ee0df..3da66c8b12 100644 --- a/autoapi/core/models/base/index.html +++ b/autoapi/core/models/base/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -650,13 +653,21 @@

    Contents

  • BackboneInterface.forward()
    • +
  • HydraInterface +
  • HydraModel
    • @@ -693,7 +704,10 @@

    Classes#<

    BackboneInterface

    -

    HydraModel

    +

    HydraInterface

    +

    Helper class that provides a standard way to create an ABC using

    + +

    HydraModel

    Base class for all neural network modules.

    @@ -759,7 +773,7 @@

    Module Contents
    -generate_graph(data, cutoff=None, max_neighbors=None, use_pbc=None, otf_graph=None, enforce_max_neighbors_strictly=None)#
    +generate_graph(data, cutoff=None, max_neighbors=None, use_pbc=None, otf_graph=None, enforce_max_neighbors_strictly=None, use_pbc_single=False)#
    @@ -822,10 +836,28 @@

    Module Contents +
    +class core.models.base.HydraInterface#
    +

    Bases: abc.ABC

    +

    Helper class that provides a standard way to create an ABC using +inheritance.

    +
    +
    +abstract get_backbone() → BackboneInterface#
    +
    + +
    +
    +abstract get_heads() → dict[str, HeadInterface]#
    +
    + +

    +
    class core.models.base.HydraModel(backbone: dict, heads: dict, otf_graph: bool = True)#
    -

    Bases: torch.nn.Module, GraphModelMixin

    +

    Bases: torch.nn.Module, GraphModelMixin, HydraInterface

    Base class for all neural network modules.

    Your models should also subclass this class.

    Modules can also contain other Modules, allowing to nest them in @@ -863,13 +895,18 @@

    Module Contents -
    -backbone_model_name#
    +
    +backbone#

    -
    -backbone: BackboneInterface#
    +
    +heads#
    +
    + +
    +
    +backbone_model_name#
    @@ -887,6 +924,16 @@

    Module Contentsforward(data: torch_geometric.data.Batch)#

    +
    +
    +get_backbone() → BackboneInterface#
    +
    + +
    +
    +get_heads() → dict[str, HeadInterface]#
    +
    + @@ -984,13 +1031,21 @@

    Module ContentsBackboneInterface.forward()

    • +
  • HydraInterface +
  • HydraModel
    • diff --git a/autoapi/core/models/dimenet_plus_plus/index.html b/autoapi/core/models/dimenet_plus_plus/index.html index 29061ba28f..b441c78a6e 100644 --- a/autoapi/core/models/dimenet_plus_plus/index.html +++ b/autoapi/core/models/dimenet_plus_plus/index.html @@ -61,7 +61,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -676,6 +679,7 @@

    Contents

  • DimeNetPlusPlusWrap
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/drop/index.html b/autoapi/core/models/equiformer_v2/drop/index.html index 6341c36e91..e86d6c394e 100644 --- a/autoapi/core/models/equiformer_v2/drop/index.html +++ b/autoapi/core/models/equiformer_v2/drop/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/edge_rot_mat/index.html b/autoapi/core/models/equiformer_v2/edge_rot_mat/index.html index e3cc5957bc..16b704b25b 100644 --- a/autoapi/core/models/equiformer_v2/edge_rot_mat/index.html +++ b/autoapi/core/models/equiformer_v2/edge_rot_mat/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/equiformer_v2/index.html b/autoapi/core/models/equiformer_v2/equiformer_v2/index.html index e22e8b6ca2..4c1cd7b31c 100644 --- a/autoapi/core/models/equiformer_v2/equiformer_v2/index.html +++ b/autoapi/core/models/equiformer_v2/equiformer_v2/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -629,6 +632,7 @@

    Contents

  • _AVG_DEGREE
  • EquiformerV2
  • EquiformerV2Backbone
    • @@ -770,13 +776,14 @@

    Module Contents
    -class core.models.equiformer_v2.equiformer_v2.EquiformerV2(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = True, max_neighbors: int = 500, max_radius: float = 5.0, max_num_elements: int = 90, num_layers: int = 12, sphere_channels: int = 128, attn_hidden_channels: int = 128, num_heads: int = 8, attn_alpha_channels: int = 32, attn_value_channels: int = 16, ffn_hidden_channels: int = 512, norm_type: str = 'rms_norm_sh', lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, grid_resolution: int | None = None, num_sphere_samples: int = 128, edge_channels: int = 128, use_atom_edge_embedding: bool = True, share_atom_edge_embedding: bool = False, use_m_share_rad: bool = False, distance_function: str = 'gaussian', num_distance_basis: int = 512, attn_activation: str = 'scaled_silu', use_s2_act_attn: bool = False, use_attn_renorm: bool = True, ffn_activation: str = 'scaled_silu', use_gate_act: bool = False, use_grid_mlp: bool = False, use_sep_s2_act: bool = True, alpha_drop: float = 0.1, drop_path_rate: float = 0.05, proj_drop: float = 0.0, weight_init: str = 'normal', enforce_max_neighbors_strictly: bool = True, avg_num_nodes: float | None = None, avg_degree: float | None = None, use_energy_lin_ref: bool | None = False, load_energy_lin_ref: bool | None = False)#
    +class core.models.equiformer_v2.equiformer_v2.EquiformerV2(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, otf_graph: bool = True, max_neighbors: int = 500, max_radius: float = 5.0, max_num_elements: int = 90, num_layers: int = 12, sphere_channels: int = 128, attn_hidden_channels: int = 128, num_heads: int = 8, attn_alpha_channels: int = 32, attn_value_channels: int = 16, ffn_hidden_channels: int = 512, norm_type: str = 'rms_norm_sh', lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, grid_resolution: int | None = None, num_sphere_samples: int = 128, edge_channels: int = 128, use_atom_edge_embedding: bool = True, share_atom_edge_embedding: bool = False, use_m_share_rad: bool = False, distance_function: str = 'gaussian', num_distance_basis: int = 512, attn_activation: str = 'scaled_silu', use_s2_act_attn: bool = False, use_attn_renorm: bool = True, ffn_activation: str = 'scaled_silu', use_gate_act: bool = False, use_grid_mlp: bool = False, use_sep_s2_act: bool = True, alpha_drop: float = 0.1, drop_path_rate: float = 0.05, proj_drop: float = 0.0, weight_init: str = 'normal', enforce_max_neighbors_strictly: bool = True, avg_num_nodes: float | None = None, avg_degree: float | None = None, use_energy_lin_ref: bool | None = False, load_energy_lin_ref: bool | None = False)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    Equiformer with graph attention built upon SO(2) convolution and feedforward network built upon S2 activation

    Parameters:

    • use_pbc (bool) – Use periodic boundary conditions

      • +

    • use_pbc_single (bool) – Process batch PBC graphs one at a time

    • regress_forces (bool) – Compute forces

    • otf_graph (bool) – Compute graph On The Fly (OTF)

    • max_neighbors (int) – Maximum number of neighbors per atom

      • @@ -827,6 +834,11 @@

      Module Contentsuse_pbc#

    +
    +
    +use_pbc_single#
    +
    +
    regress_forces#
    @@ -1140,13 +1152,14 @@

    Module Contents
    -class core.models.equiformer_v2.equiformer_v2.EquiformerV2Backbone(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = True, max_neighbors: int = 500, max_radius: float = 5.0, max_num_elements: int = 90, num_layers: int = 12, sphere_channels: int = 128, attn_hidden_channels: int = 128, num_heads: int = 8, attn_alpha_channels: int = 32, attn_value_channels: int = 16, ffn_hidden_channels: int = 512, norm_type: str = 'rms_norm_sh', lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, grid_resolution: int | None = None, num_sphere_samples: int = 128, edge_channels: int = 128, use_atom_edge_embedding: bool = True, share_atom_edge_embedding: bool = False, use_m_share_rad: bool = False, distance_function: str = 'gaussian', num_distance_basis: int = 512, attn_activation: str = 'scaled_silu', use_s2_act_attn: bool = False, use_attn_renorm: bool = True, ffn_activation: str = 'scaled_silu', use_gate_act: bool = False, use_grid_mlp: bool = False, use_sep_s2_act: bool = True, alpha_drop: float = 0.1, drop_path_rate: float = 0.05, proj_drop: float = 0.0, weight_init: str = 'normal', enforce_max_neighbors_strictly: bool = True, avg_num_nodes: float | None = None, avg_degree: float | None = None, use_energy_lin_ref: bool | None = False, load_energy_lin_ref: bool | None = False)#
    +class core.models.equiformer_v2.equiformer_v2.EquiformerV2Backbone(*args, **kwargs)#

    Bases: EquiformerV2, fairchem.core.models.base.BackboneInterface

    Equiformer with graph attention built upon SO(2) convolution and feedforward network built upon S2 activation

    Parameters:

    • use_pbc (bool) – Use periodic boundary conditions

      • +

    • use_pbc_single (bool) – Process batch PBC graphs one at a time

    • regress_forces (bool) – Compute forces

    • otf_graph (bool) – Compute graph On The Fly (OTF)

    • max_neighbors (int) – Maximum number of neighbors per atom

      • @@ -1192,6 +1205,16 @@

      Module Contents +
      +energy_block = None#
      +

    + +
    +
    +force_block = None#
    +
    +
    forward(data: torch_geometric.data.batch.Batch) → dict[str, torch.Tensor]#
    @@ -1414,6 +1437,7 @@

    Module Contents_AVG_DEGREE

  • EquiformerV2
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/index.html b/autoapi/core/models/equiformer_v2/index.html index 76a0a0bd73..c33ea1c5b5 100644 --- a/autoapi/core/models/equiformer_v2/index.html +++ b/autoapi/core/models/equiformer_v2/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -628,6 +631,7 @@

    Contents

  • Package Contents
    • EquiformerV2
      • EquiformerV2.use_pbc
        • +
      • EquiformerV2.use_pbc_single
      • EquiformerV2.regress_forces
      • EquiformerV2.otf_graph
      • EquiformerV2.max_neighbors
        • @@ -749,13 +753,14 @@

        Classes#<

        Package Contents#

        -class core.models.equiformer_v2.EquiformerV2(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = True, max_neighbors: int = 500, max_radius: float = 5.0, max_num_elements: int = 90, num_layers: int = 12, sphere_channels: int = 128, attn_hidden_channels: int = 128, num_heads: int = 8, attn_alpha_channels: int = 32, attn_value_channels: int = 16, ffn_hidden_channels: int = 512, norm_type: str = 'rms_norm_sh', lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, grid_resolution: int | None = None, num_sphere_samples: int = 128, edge_channels: int = 128, use_atom_edge_embedding: bool = True, share_atom_edge_embedding: bool = False, use_m_share_rad: bool = False, distance_function: str = 'gaussian', num_distance_basis: int = 512, attn_activation: str = 'scaled_silu', use_s2_act_attn: bool = False, use_attn_renorm: bool = True, ffn_activation: str = 'scaled_silu', use_gate_act: bool = False, use_grid_mlp: bool = False, use_sep_s2_act: bool = True, alpha_drop: float = 0.1, drop_path_rate: float = 0.05, proj_drop: float = 0.0, weight_init: str = 'normal', enforce_max_neighbors_strictly: bool = True, avg_num_nodes: float | None = None, avg_degree: float | None = None, use_energy_lin_ref: bool | None = False, load_energy_lin_ref: bool | None = False)#
        +class core.models.equiformer_v2.EquiformerV2(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, otf_graph: bool = True, max_neighbors: int = 500, max_radius: float = 5.0, max_num_elements: int = 90, num_layers: int = 12, sphere_channels: int = 128, attn_hidden_channels: int = 128, num_heads: int = 8, attn_alpha_channels: int = 32, attn_value_channels: int = 16, ffn_hidden_channels: int = 512, norm_type: str = 'rms_norm_sh', lmax_list: list[int] | None = None, mmax_list: list[int] | None = None, grid_resolution: int | None = None, num_sphere_samples: int = 128, edge_channels: int = 128, use_atom_edge_embedding: bool = True, share_atom_edge_embedding: bool = False, use_m_share_rad: bool = False, distance_function: str = 'gaussian', num_distance_basis: int = 512, attn_activation: str = 'scaled_silu', use_s2_act_attn: bool = False, use_attn_renorm: bool = True, ffn_activation: str = 'scaled_silu', use_gate_act: bool = False, use_grid_mlp: bool = False, use_sep_s2_act: bool = True, alpha_drop: float = 0.1, drop_path_rate: float = 0.05, proj_drop: float = 0.0, weight_init: str = 'normal', enforce_max_neighbors_strictly: bool = True, avg_num_nodes: float | None = None, avg_degree: float | None = None, use_energy_lin_ref: bool | None = False, load_energy_lin_ref: bool | None = False)#

        Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

        Equiformer with graph attention built upon SO(2) convolution and feedforward network built upon S2 activation

        Parameters:

        • use_pbc (bool) – Use periodic boundary conditions

          • +

        • use_pbc_single (bool) – Process batch PBC graphs one at a time

        • regress_forces (bool) – Compute forces

        • otf_graph (bool) – Compute graph On The Fly (OTF)

        • max_neighbors (int) – Maximum number of neighbors per atom

          • @@ -806,6 +811,11 @@

          Package Contentsuse_pbc#

        +
        +
        +use_pbc_single#
        +
        +
        regress_forces#
        @@ -1190,6 +1200,7 @@

        Package ContentsPackage Contents

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/layer_norm/index.html b/autoapi/core/models/equiformer_v2/layer_norm/index.html index 2720be7fa3..a74d250cf0 100644 --- a/autoapi/core/models/equiformer_v2/layer_norm/index.html +++ b/autoapi/core/models/equiformer_v2/layer_norm/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/module_list/index.html b/autoapi/core/models/equiformer_v2/module_list/index.html index 57e2b19203..6116fcce21 100644 --- a/autoapi/core/models/equiformer_v2/module_list/index.html +++ b/autoapi/core/models/equiformer_v2/module_list/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/radial_function/index.html b/autoapi/core/models/equiformer_v2/radial_function/index.html index 9818c7bc5e..807f9f80d7 100644 --- a/autoapi/core/models/equiformer_v2/radial_function/index.html +++ b/autoapi/core/models/equiformer_v2/radial_function/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
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    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/so2_ops/index.html b/autoapi/core/models/equiformer_v2/so2_ops/index.html index 8458595f5e..dbb9801c20 100644 --- a/autoapi/core/models/equiformer_v2/so2_ops/index.html +++ b/autoapi/core/models/equiformer_v2/so2_ops/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/so3/index.html b/autoapi/core/models/equiformer_v2/so3/index.html index 302b73b40b..c0f5d9b2b6 100644 --- a/autoapi/core/models/equiformer_v2/so3/index.html +++ b/autoapi/core/models/equiformer_v2/so3/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
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    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/trainers/energy_trainer/index.html b/autoapi/core/models/equiformer_v2/trainers/energy_trainer/index.html index 2345d6aeb8..ab6910eca3 100644 --- a/autoapi/core/models/equiformer_v2/trainers/energy_trainer/index.html +++ b/autoapi/core/models/equiformer_v2/trainers/energy_trainer/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
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  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/trainers/forces_trainer/index.html b/autoapi/core/models/equiformer_v2/trainers/forces_trainer/index.html index b9a9b8ef4c..b60ad72fad 100644 --- a/autoapi/core/models/equiformer_v2/trainers/forces_trainer/index.html +++ b/autoapi/core/models/equiformer_v2/trainers/forces_trainer/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
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  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
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  • core.scripts.download_data
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    • +
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  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/trainers/index.html b/autoapi/core/models/equiformer_v2/trainers/index.html index cb3951a528..eaf4cef4ef 100644 --- a/autoapi/core/models/equiformer_v2/trainers/index.html +++ b/autoapi/core/models/equiformer_v2/trainers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
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    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/trainers/lr_scheduler/index.html b/autoapi/core/models/equiformer_v2/trainers/lr_scheduler/index.html index 331bc7dfc4..cfc6116797 100644 --- a/autoapi/core/models/equiformer_v2/trainers/lr_scheduler/index.html +++ b/autoapi/core/models/equiformer_v2/trainers/lr_scheduler/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/transformer_block/index.html b/autoapi/core/models/equiformer_v2/transformer_block/index.html index 620d9a5c9d..0c03314379 100644 --- a/autoapi/core/models/equiformer_v2/transformer_block/index.html +++ b/autoapi/core/models/equiformer_v2/transformer_block/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/equiformer_v2/wigner/index.html b/autoapi/core/models/equiformer_v2/wigner/index.html index fb5c977364..f10818b2db 100644 --- a/autoapi/core/models/equiformer_v2/wigner/index.html +++ b/autoapi/core/models/equiformer_v2/wigner/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/escn/escn/index.html b/autoapi/core/models/escn/escn/index.html index b44f3f5345..0e531258aa 100644 --- a/autoapi/core/models/escn/escn/index.html +++ b/autoapi/core/models/escn/escn/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -627,6 +630,7 @@

    Contents

  • eSCN
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -628,6 +631,7 @@

    Contents

  • eSCN
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/finetune_hydra/index.html b/autoapi/core/models/finetune_hydra/index.html new file mode 100644 index 0000000000..624a5c6616 --- /dev/null +++ b/autoapi/core/models/finetune_hydra/index.html @@ -0,0 +1,1079 @@ + + + + + + + + + + + core.models.finetune_hydra + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    + +
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    + + + +
    +

    core.models.finetune_hydra

    + +
    + +
    +
    + + + + +
    + +
    +

    core.models.finetune_hydra#

    +
    +

    Attributes#

    +
    + + + + + +

    FTHYDRA_NAME

    +
    +
    +
    +

    Classes#

    +
    + + + + + + + + + + + +

    FineTuneMode

    Create a collection of name/value pairs.

    FTConfig

    FineTuneHydra

    Base class for all neural network modules.

    +
    +
    +
    +

    Functions#

    +
    + + + + + + + + +

    get_model_config_from_checkpoint(→ dict)

    load_hydra_model(...)

    +
    +
    +
    +

    Module Contents#

    +
    +
    +core.models.finetune_hydra.FTHYDRA_NAME = 'finetune_hydra'#
    +
    + +
    +
    +class core.models.finetune_hydra.FineTuneMode(*args, **kwds)#
    +

    Bases: enum.Enum

    +

    Create a collection of name/value pairs.

    +

    Example enumeration:

    +
    >>> class Color(Enum):
+...     RED = 1
+...     BLUE = 2
+...     GREEN = 3
+
    +
    +

    Access them by:

    +
      +

    • attribute access:

      • +
    +
    >>> Color.RED
+<Color.RED: 1>
+
    +
    +
      +

    • value lookup:

      • +
    +
    >>> Color(1)
+<Color.RED: 1>
+
    +
    +
      +

    • name lookup:

      • +
    +
    >>> Color['RED']
+<Color.RED: 1>
+
    +
    +

    Enumerations can be iterated over, and know how many members they have:

    +
    >>> len(Color)
+3
+
    +
    +
    >>> list(Color)
+[<Color.RED: 1>, <Color.BLUE: 2>, <Color.GREEN: 3>]
+
    +
    +

    Methods can be added to enumerations, and members can have their own +attributes – see the documentation for details.

    +
    +
    +DATA_ONLY = 1#
    +
    + +
    +
    +RETAIN_BACKBONE_ONLY = 2#
    +
    + +
    + +
    +
    +core.models.finetune_hydra.get_model_config_from_checkpoint(checkpoint_path: str) → dict#
    +
    + +
    +
    +core.models.finetune_hydra.load_hydra_model(checkpoint_path: str) → fairchem.core.models.base.HydraInterface#
    +
    + +
    +
    +class core.models.finetune_hydra.FTConfig(config: dict)#
    +
    +
    +FT_CONFIG_NAME = 'finetune_config'#
    +
    + +
    +
    +STARTING_CHECKPOINT = 'starting_checkpoint'#
    +
    + +
    +
    +STARTING_MODEL = 'starting_model'#
    +
    + +
    +
    +MODE = 'mode'#
    +
    + +
    +
    +HEADS = 'heads'#
    +
    + +
    +
    +config#
    +
    + +
    +
    +_mode#
    +
    + +
    +
    +load_model() → torch.nn.Module#
    +
    + +
    +
    +get_standalone_config() → dict#
    +
    + +
    +
    +property mode: FineTuneMode#
    +
    + +
    +
    +property head_config: dict#
    +
    + +
    + +
    +
    +class core.models.finetune_hydra.FineTuneHydra(finetune_config: dict)#
    +

    Bases: torch.nn.Module, fairchem.core.models.base.HydraInterface

    +

    Base class for all neural network modules.

    +

    Your models should also subclass this class.

    +

    Modules can also contain other Modules, allowing to nest them in +a tree structure. You can assign the submodules as regular attributes:

    +
    import torch.nn as nn
+import torch.nn.functional as F
+
+class Model(nn.Module):
+    def __init__(self):
+        super().__init__()
+        self.conv1 = nn.Conv2d(1, 20, 5)
+        self.conv2 = nn.Conv2d(20, 20, 5)
+
+    def forward(self, x):
+        x = F.relu(self.conv1(x))
+        return F.relu(self.conv2(x))
+
    +
    +

    Submodules assigned in this way will be registered, and will have their +parameters converted too when you call to(), etc.

    +
    +

    Note

    +

    As per the example above, an __init__() call to the parent class +must be made before assignment on the child.

    +
    +
    +
    Variables:
    +

    training (bool) – Boolean represents whether this module is in training or +evaluation mode.

    +
    +
    +
    +
    +ft_config#
    +
    + +
    +
    +hydra_model: fairchem.core.models.base.HydraInterface#
    +
    + +
    +
    +backbone: fairchem.core.models.base.BackboneInterface#
    +
    + +
    +
    +forward(data: torch_geometric.data.Batch)#
    +
    + +
    +
    +get_backbone() → fairchem.core.models.base.BackboneInterface#
    +
    + +
    +
    +get_heads() → dict[str, fairchem.core.models.base.HeadInterface]#
    +
    + +
    + +
    +
    + + + + +
    + + + + + + + + +
    + + + +
    + + +
    +
    + Contents +
    +
    + +
    + + +
    +
    + +
    + +
    + +

    +By FAIR Chemistry & Collaborators +

    + +
    + +
    + + +

    + + © Copyright 2024. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
    +
    + + +
    +
    +
    + + + + + +
    +
    + + \ No newline at end of file diff --git a/autoapi/core/models/gemnet/gemnet/index.html b/autoapi/core/models/gemnet/gemnet/index.html index 16caacbef1..5a946061ed 100644 --- a/autoapi/core/models/gemnet/gemnet/index.html +++ b/autoapi/core/models/gemnet/gemnet/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -632,6 +635,7 @@

    Contents

  • GemNetT.regress_forces
  • GemNetT.otf_graph
  • GemNetT.use_pbc
    • +
  • GemNetT.use_pbc_single
  • GemNetT.direct_forces
  • GemNetT.radial_basis
  • GemNetT.radial_basis_cbf3
    • @@ -713,7 +717,7 @@

    Classes#<

    Module Contents#

    -class core.models.gemnet.gemnet.GemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None)#
    +class core.models.gemnet.gemnet.GemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    GemNet-T, triplets-only variant of GemNet

    @@ -781,6 +785,11 @@

    Module Contentsuse_pbc#

    +
    +
    +use_pbc_single#
    +
    +
    direct_forces#
    @@ -910,7 +919,7 @@

    Module Contents
    -class core.models.gemnet.gemnet.GemNetTBackbone(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None)#
    +class core.models.gemnet.gemnet.GemNetTBackbone(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None)#

    Bases: GemNetT, fairchem.core.models.base.BackboneInterface

    GemNet-T, triplets-only variant of GemNet

    @@ -1173,6 +1182,7 @@

    Module ContentsGemNetT.regress_forces

  • GemNetT.otf_graph
  • GemNetT.use_pbc
    • +
  • GemNetT.use_pbc_single
  • GemNetT.direct_forces
  • GemNetT.radial_basis
  • GemNetT.radial_basis_cbf3
    • diff --git a/autoapi/core/models/gemnet/index.html b/autoapi/core/models/gemnet/index.html index d764cec939..c0dfe14143 100644 --- a/autoapi/core/models/gemnet/index.html +++ b/autoapi/core/models/gemnet/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -634,6 +637,7 @@

    Contents

  • GemNetT.regress_forces
  • GemNetT.otf_graph
  • GemNetT.use_pbc
    • +
  • GemNetT.use_pbc_single
  • GemNetT.direct_forces
  • GemNetT.radial_basis
  • GemNetT.radial_basis_cbf3
    • @@ -705,7 +709,7 @@

    Classes#<

    Package Contents#

    -class core.models.gemnet.GemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None)#
    +class core.models.gemnet.GemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'swish', num_elements: int = 83, scale_file: str | None = None)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    GemNet-T, triplets-only variant of GemNet

    @@ -773,6 +777,11 @@

    Package Contentsuse_pbc#

    +
    +
    +use_pbc_single#
    +
    +
    direct_forces#
    @@ -979,6 +988,7 @@

    Package ContentsGemNetT.regress_forces

  • GemNetT.otf_graph
  • GemNetT.use_pbc
    • +
  • GemNetT.use_pbc_single
  • GemNetT.direct_forces
  • GemNetT.radial_basis
  • GemNetT.radial_basis_cbf3
    • diff --git a/autoapi/core/models/gemnet/initializers/index.html b/autoapi/core/models/gemnet/initializers/index.html index e7dbb7f38a..948fc82736 100644 --- a/autoapi/core/models/gemnet/initializers/index.html +++ b/autoapi/core/models/gemnet/initializers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet/layers/atom_update_block/index.html b/autoapi/core/models/gemnet/layers/atom_update_block/index.html index df206fbadf..da2253ec59 100644 --- a/autoapi/core/models/gemnet/layers/atom_update_block/index.html +++ b/autoapi/core/models/gemnet/layers/atom_update_block/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
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    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
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  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet/layers/base_layers/index.html b/autoapi/core/models/gemnet/layers/base_layers/index.html index 6b1cf08170..3cb4cd336a 100644 --- a/autoapi/core/models/gemnet/layers/base_layers/index.html +++ b/autoapi/core/models/gemnet/layers/base_layers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
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  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
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    • +
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  • core.models.model_registry
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  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
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    • +
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  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet/layers/basis_utils/index.html b/autoapi/core/models/gemnet/layers/basis_utils/index.html index 8ba8fa10a5..e776154876 100644 --- a/autoapi/core/models/gemnet/layers/basis_utils/index.html +++ b/autoapi/core/models/gemnet/layers/basis_utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
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    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet/layers/efficient/index.html b/autoapi/core/models/gemnet/layers/efficient/index.html index f54ebb88c3..223a309e6d 100644 --- a/autoapi/core/models/gemnet/layers/efficient/index.html +++ b/autoapi/core/models/gemnet/layers/efficient/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
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  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
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    • +
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  • core.models.model_registry
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  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
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    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet/layers/embedding_block/index.html b/autoapi/core/models/gemnet/layers/embedding_block/index.html index 6267b0574e..ba19d79c23 100644 --- a/autoapi/core/models/gemnet/layers/embedding_block/index.html +++ b/autoapi/core/models/gemnet/layers/embedding_block/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet/layers/index.html b/autoapi/core/models/gemnet/layers/index.html index 43fb61a4df..ffa0d3281f 100644 --- a/autoapi/core/models/gemnet/layers/index.html +++ b/autoapi/core/models/gemnet/layers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
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    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet/layers/interaction_block/index.html b/autoapi/core/models/gemnet/layers/interaction_block/index.html index 7d91a77e13..42ef3fb5fa 100644 --- a/autoapi/core/models/gemnet/layers/interaction_block/index.html +++ b/autoapi/core/models/gemnet/layers/interaction_block/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet/layers/radial_basis/index.html b/autoapi/core/models/gemnet/layers/radial_basis/index.html index 783afd4bef..9d0c651426 100644 --- a/autoapi/core/models/gemnet/layers/radial_basis/index.html +++ b/autoapi/core/models/gemnet/layers/radial_basis/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
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    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet/layers/spherical_basis/index.html b/autoapi/core/models/gemnet/layers/spherical_basis/index.html index 1d5b6f0017..158b8b7839 100644 --- a/autoapi/core/models/gemnet/layers/spherical_basis/index.html +++ b/autoapi/core/models/gemnet/layers/spherical_basis/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet/utils/index.html b/autoapi/core/models/gemnet/utils/index.html index 4af4b2ab31..a6ac79a427 100644 --- a/autoapi/core/models/gemnet/utils/index.html +++ b/autoapi/core/models/gemnet/utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
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    • +
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  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/gemnet/index.html b/autoapi/core/models/gemnet_gp/gemnet/index.html index fee826494d..8ce960c53a 100644 --- a/autoapi/core/models/gemnet_gp/gemnet/index.html +++ b/autoapi/core/models/gemnet_gp/gemnet/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
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    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
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    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -634,6 +637,7 @@

    Contents

  • GraphParallelGemNetT.regress_forces
  • GraphParallelGemNetT.otf_graph
  • GraphParallelGemNetT.use_pbc
    • +
  • GraphParallelGemNetT.use_pbc_single
  • GraphParallelGemNetT.direct_forces
  • GraphParallelGemNetT.radial_basis
  • GraphParallelGemNetT.radial_basis_cbf3
    • @@ -689,7 +693,7 @@

    Classes#<

    Module Contents#

    -class core.models.gemnet_gp.gemnet.GraphParallelGemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, output_init: str = 'HeOrthogonal', activation: str = 'swish', scale_num_blocks: bool = False, scatter_atoms: bool = True, scale_file: str | None = None)#
    +class core.models.gemnet_gp.gemnet.GraphParallelGemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'swish', scale_num_blocks: bool = False, scatter_atoms: bool = True, scale_file: str | None = None)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    GemNet-T, triplets-only variant of GemNet

    @@ -767,6 +771,11 @@

    Module Contentsuse_pbc#

    +
    +
    +use_pbc_single#
    +
    +
    direct_forces#
    @@ -968,6 +977,7 @@

    Module ContentsGraphParallelGemNetT.regress_forces

  • GraphParallelGemNetT.otf_graph
  • GraphParallelGemNetT.use_pbc
    • +
  • GraphParallelGemNetT.use_pbc_single
  • GraphParallelGemNetT.direct_forces
  • GraphParallelGemNetT.radial_basis
  • GraphParallelGemNetT.radial_basis_cbf3
    • diff --git a/autoapi/core/models/gemnet_gp/index.html b/autoapi/core/models/gemnet_gp/index.html index c044f89aeb..9a79ca6e44 100644 --- a/autoapi/core/models/gemnet_gp/index.html +++ b/autoapi/core/models/gemnet_gp/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -636,6 +639,7 @@

    Contents

  • GraphParallelGemNetT.regress_forces
  • GraphParallelGemNetT.otf_graph
  • GraphParallelGemNetT.use_pbc
    • +
  • GraphParallelGemNetT.use_pbc_single
  • GraphParallelGemNetT.direct_forces
  • GraphParallelGemNetT.radial_basis
  • GraphParallelGemNetT.radial_basis_cbf3
    • @@ -706,7 +710,7 @@

    Classes#<

    Package Contents#

    -class core.models.gemnet_gp.GraphParallelGemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, output_init: str = 'HeOrthogonal', activation: str = 'swish', scale_num_blocks: bool = False, scatter_atoms: bool = True, scale_file: str | None = None)#
    +class core.models.gemnet_gp.GraphParallelGemNetT(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_bil_trip: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, regress_forces: bool = True, direct_forces: bool = False, cutoff: float = 6.0, max_neighbors: int = 50, rbf: dict | None = None, envelope: dict | None = None, cbf: dict | None = None, extensive: bool = True, otf_graph: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'swish', scale_num_blocks: bool = False, scatter_atoms: bool = True, scale_file: str | None = None)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    GemNet-T, triplets-only variant of GemNet

    @@ -784,6 +788,11 @@

    Package Contentsuse_pbc#

    +
    +
    +use_pbc_single#
    +
    +
    direct_forces#
    @@ -987,6 +996,7 @@

    Package ContentsGraphParallelGemNetT.regress_forces

  • GraphParallelGemNetT.otf_graph
  • GraphParallelGemNetT.use_pbc
    • +
  • GraphParallelGemNetT.use_pbc_single
  • GraphParallelGemNetT.direct_forces
  • GraphParallelGemNetT.radial_basis
  • GraphParallelGemNetT.radial_basis_cbf3
    • diff --git a/autoapi/core/models/gemnet_gp/initializers/index.html b/autoapi/core/models/gemnet_gp/initializers/index.html index 02e6591441..a071c90a79 100644 --- a/autoapi/core/models/gemnet_gp/initializers/index.html +++ b/autoapi/core/models/gemnet_gp/initializers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/layers/atom_update_block/index.html b/autoapi/core/models/gemnet_gp/layers/atom_update_block/index.html index b640362d28..9180f8729a 100644 --- a/autoapi/core/models/gemnet_gp/layers/atom_update_block/index.html +++ b/autoapi/core/models/gemnet_gp/layers/atom_update_block/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/layers/base_layers/index.html b/autoapi/core/models/gemnet_gp/layers/base_layers/index.html index 78230956ca..803ce65da4 100644 --- a/autoapi/core/models/gemnet_gp/layers/base_layers/index.html +++ b/autoapi/core/models/gemnet_gp/layers/base_layers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/layers/basis_utils/index.html b/autoapi/core/models/gemnet_gp/layers/basis_utils/index.html index a8b713ca4e..99b8dcc31e 100644 --- a/autoapi/core/models/gemnet_gp/layers/basis_utils/index.html +++ b/autoapi/core/models/gemnet_gp/layers/basis_utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/layers/efficient/index.html b/autoapi/core/models/gemnet_gp/layers/efficient/index.html index cc4e002bc9..160029bd29 100644 --- a/autoapi/core/models/gemnet_gp/layers/efficient/index.html +++ b/autoapi/core/models/gemnet_gp/layers/efficient/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/layers/embedding_block/index.html b/autoapi/core/models/gemnet_gp/layers/embedding_block/index.html index cdaccca65a..3efc25c941 100644 --- a/autoapi/core/models/gemnet_gp/layers/embedding_block/index.html +++ b/autoapi/core/models/gemnet_gp/layers/embedding_block/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/layers/index.html b/autoapi/core/models/gemnet_gp/layers/index.html index 0b452e0361..4f925edad2 100644 --- a/autoapi/core/models/gemnet_gp/layers/index.html +++ b/autoapi/core/models/gemnet_gp/layers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/layers/interaction_block/index.html b/autoapi/core/models/gemnet_gp/layers/interaction_block/index.html index 4f7a04c1f8..25e1f133bd 100644 --- a/autoapi/core/models/gemnet_gp/layers/interaction_block/index.html +++ b/autoapi/core/models/gemnet_gp/layers/interaction_block/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/layers/radial_basis/index.html b/autoapi/core/models/gemnet_gp/layers/radial_basis/index.html index 2c2f19de41..cd2d3a12f5 100644 --- a/autoapi/core/models/gemnet_gp/layers/radial_basis/index.html +++ b/autoapi/core/models/gemnet_gp/layers/radial_basis/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/layers/spherical_basis/index.html b/autoapi/core/models/gemnet_gp/layers/spherical_basis/index.html index cf7aad9398..92b3560206 100644 --- a/autoapi/core/models/gemnet_gp/layers/spherical_basis/index.html +++ b/autoapi/core/models/gemnet_gp/layers/spherical_basis/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_gp/utils/index.html b/autoapi/core/models/gemnet_gp/utils/index.html index e71b9cfe68..18f7b429b6 100644 --- a/autoapi/core/models/gemnet_gp/utils/index.html +++ b/autoapi/core/models/gemnet_gp/utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/gemnet_oc/index.html b/autoapi/core/models/gemnet_oc/gemnet_oc/index.html index 23a7ae18af..b6a3eb29ba 100644 --- a/autoapi/core/models/gemnet_oc/gemnet_oc/index.html +++ b/autoapi/core/models/gemnet_oc/gemnet_oc/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -636,6 +639,7 @@

    Contents

  • GemNetOC.otf_graph
  • GemNetOC.enforce_max_neighbors_strictly
  • GemNetOC.use_pbc
    • +
  • GemNetOC.use_pbc_single
  • GemNetOC.direct_forces
  • GemNetOC.forces_coupled
  • GemNetOC.regress_forces
    • @@ -727,7 +731,7 @@

    Classes#<

    Module Contents#

    -class core.models.gemnet_oc.gemnet_oc.GemNetOC(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs)#
    +class core.models.gemnet_oc.gemnet_oc.GemNetOC(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    Parameters:
    @@ -762,6 +766,7 @@

    Module Contentsuse_pbc#

    +
    +
    +use_pbc_single#
    +
    +
    direct_forces#
    @@ -1037,7 +1047,7 @@

    Module Contents
    -class core.models.gemnet_oc.gemnet_oc.GemNetOCBackbone(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs)#
    +class core.models.gemnet_oc.gemnet_oc.GemNetOCBackbone(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs)#

    Bases: GemNetOC, fairchem.core.models.base.BackboneInterface

    Parameters:
    @@ -1072,6 +1082,7 @@

    Module Contents
    -out_mlp_E#
    +out_mlp_E = None#

    -out_energy#
    +out_energy = None#
    @@ -1377,6 +1388,7 @@

    Module ContentsGemNetOC.otf_graph

  • GemNetOC.enforce_max_neighbors_strictly
  • GemNetOC.use_pbc
    • +
  • GemNetOC.use_pbc_single
  • GemNetOC.direct_forces
  • GemNetOC.forces_coupled
  • GemNetOC.regress_forces
    • diff --git a/autoapi/core/models/gemnet_oc/index.html b/autoapi/core/models/gemnet_oc/index.html index 2ffb4e8999..b231085d91 100644 --- a/autoapi/core/models/gemnet_oc/index.html +++ b/autoapi/core/models/gemnet_oc/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -638,6 +641,7 @@

    Contents

  • GemNetOC.otf_graph
  • GemNetOC.enforce_max_neighbors_strictly
  • GemNetOC.use_pbc
    • +
  • GemNetOC.use_pbc_single
  • GemNetOC.direct_forces
  • GemNetOC.forces_coupled
  • GemNetOC.regress_forces
    • @@ -714,7 +718,7 @@

    Classes#<

    Package Contents#

    -class core.models.gemnet_oc.GemNetOC(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs)#
    +class core.models.gemnet_oc.GemNetOC(num_spherical: int, num_radial: int, num_blocks: int, emb_size_atom: int, emb_size_edge: int, emb_size_trip_in: int, emb_size_trip_out: int, emb_size_quad_in: int, emb_size_quad_out: int, emb_size_aint_in: int, emb_size_aint_out: int, emb_size_rbf: int, emb_size_cbf: int, emb_size_sbf: int, num_before_skip: int, num_after_skip: int, num_concat: int, num_atom: int, num_output_afteratom: int, num_atom_emb_layers: int = 0, num_global_out_layers: int = 2, regress_forces: bool = True, direct_forces: bool = False, use_pbc: bool = True, use_pbc_single: bool = False, scale_backprop_forces: bool = False, cutoff: float = 6.0, cutoff_qint: float | None = None, cutoff_aeaint: float | None = None, cutoff_aint: float | None = None, max_neighbors: int = 50, max_neighbors_qint: int | None = None, max_neighbors_aeaint: int | None = None, max_neighbors_aint: int | None = None, enforce_max_neighbors_strictly: bool = True, rbf: dict[str, str] | None = None, rbf_spherical: dict | None = None, envelope: dict[str, str | int] | None = None, cbf: dict[str, str] | None = None, sbf: dict[str, str] | None = None, extensive: bool = True, forces_coupled: bool = False, output_init: str = 'HeOrthogonal', activation: str = 'silu', quad_interaction: bool = False, atom_edge_interaction: bool = False, edge_atom_interaction: bool = False, atom_interaction: bool = False, scale_basis: bool = False, qint_tags: list | None = None, num_elements: int = 83, otf_graph: bool = False, scale_file: str | None = None, **kwargs)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    Parameters:
    @@ -749,6 +753,7 @@

    Package Contentsuse_pbc#

    +
    +
    +use_pbc_single#
    +
    +
    direct_forces#
    @@ -1105,6 +1115,7 @@

    Package ContentsGemNetOC.otf_graph

  • GemNetOC.enforce_max_neighbors_strictly
  • GemNetOC.use_pbc
    • +
  • GemNetOC.use_pbc_single
  • GemNetOC.direct_forces
  • GemNetOC.forces_coupled
  • GemNetOC.regress_forces
    • diff --git a/autoapi/core/models/gemnet_oc/initializers/index.html b/autoapi/core/models/gemnet_oc/initializers/index.html index 6ea26d2d1b..0607796af3 100644 --- a/autoapi/core/models/gemnet_oc/initializers/index.html +++ b/autoapi/core/models/gemnet_oc/initializers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/interaction_indices/index.html b/autoapi/core/models/gemnet_oc/interaction_indices/index.html index 6666eb04b0..21b2ac3fa3 100644 --- a/autoapi/core/models/gemnet_oc/interaction_indices/index.html +++ b/autoapi/core/models/gemnet_oc/interaction_indices/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/layers/atom_update_block/index.html b/autoapi/core/models/gemnet_oc/layers/atom_update_block/index.html index 6314342253..36c8ac9684 100644 --- a/autoapi/core/models/gemnet_oc/layers/atom_update_block/index.html +++ b/autoapi/core/models/gemnet_oc/layers/atom_update_block/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/layers/base_layers/index.html b/autoapi/core/models/gemnet_oc/layers/base_layers/index.html index fe1ffa03b4..f6d6e2ff2e 100644 --- a/autoapi/core/models/gemnet_oc/layers/base_layers/index.html +++ b/autoapi/core/models/gemnet_oc/layers/base_layers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/layers/basis_utils/index.html b/autoapi/core/models/gemnet_oc/layers/basis_utils/index.html index 0f75751eeb..92f5947b0d 100644 --- a/autoapi/core/models/gemnet_oc/layers/basis_utils/index.html +++ b/autoapi/core/models/gemnet_oc/layers/basis_utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/layers/efficient/index.html b/autoapi/core/models/gemnet_oc/layers/efficient/index.html index 3a3f677482..088942ed8b 100644 --- a/autoapi/core/models/gemnet_oc/layers/efficient/index.html +++ b/autoapi/core/models/gemnet_oc/layers/efficient/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/layers/embedding_block/index.html b/autoapi/core/models/gemnet_oc/layers/embedding_block/index.html index fae69fe3ec..a831719331 100644 --- a/autoapi/core/models/gemnet_oc/layers/embedding_block/index.html +++ b/autoapi/core/models/gemnet_oc/layers/embedding_block/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/layers/force_scaler/index.html b/autoapi/core/models/gemnet_oc/layers/force_scaler/index.html index 1ad24b345e..f37d976b0d 100644 --- a/autoapi/core/models/gemnet_oc/layers/force_scaler/index.html +++ b/autoapi/core/models/gemnet_oc/layers/force_scaler/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/layers/index.html b/autoapi/core/models/gemnet_oc/layers/index.html index 7cad99acae..f919f3f120 100644 --- a/autoapi/core/models/gemnet_oc/layers/index.html +++ b/autoapi/core/models/gemnet_oc/layers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/layers/interaction_block/index.html b/autoapi/core/models/gemnet_oc/layers/interaction_block/index.html index 0f6b7e9cdb..8f80632cdc 100644 --- a/autoapi/core/models/gemnet_oc/layers/interaction_block/index.html +++ b/autoapi/core/models/gemnet_oc/layers/interaction_block/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/layers/radial_basis/index.html b/autoapi/core/models/gemnet_oc/layers/radial_basis/index.html index af6b394c5c..3353a6a510 100644 --- a/autoapi/core/models/gemnet_oc/layers/radial_basis/index.html +++ b/autoapi/core/models/gemnet_oc/layers/radial_basis/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/layers/spherical_basis/index.html b/autoapi/core/models/gemnet_oc/layers/spherical_basis/index.html index fc0946724b..9ab606736c 100644 --- a/autoapi/core/models/gemnet_oc/layers/spherical_basis/index.html +++ b/autoapi/core/models/gemnet_oc/layers/spherical_basis/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/gemnet_oc/utils/index.html b/autoapi/core/models/gemnet_oc/utils/index.html index 429fc2b469..808ad40d34 100644 --- a/autoapi/core/models/gemnet_oc/utils/index.html +++ b/autoapi/core/models/gemnet_oc/utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/index.html b/autoapi/core/models/index.html index ec03f0c141..c3c2e1ca88 100644 --- a/autoapi/core/models/index.html +++ b/autoapi/core/models/index.html @@ -307,6 +307,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -336,16 +337,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    @@ -667,6 +670,7 @@

    Submodulescore.models.base

  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
    • diff --git a/autoapi/core/models/model_registry/index.html b/autoapi/core/models/model_registry/index.html index a9c62e3c81..ba3613f394 100644 --- a/autoapi/core/models/model_registry/index.html +++ b/autoapi/core/models/model_registry/index.html @@ -62,7 +62,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -737,12 +740,12 @@

    Module Contents

    previous

    -

    core.models.dimenet_plus_plus

    +

    core.models.finetune_hydra

     core.common.logger

  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -336,16 +337,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    @@ -637,6 +640,7 @@

    Contents

  • PaiNN.direct_forces
  • PaiNN.otf_graph
  • PaiNN.use_pbc
    • +
  • PaiNN.use_pbc_single
  • PaiNN.symmetric_edge_symmetrization
  • PaiNN.atom_emb
  • PaiNN.radial_basis
    • @@ -692,7 +696,7 @@

    Classes#<

    Package Contents#

    -class core.models.painn.PaiNN(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None)#
    +class core.models.painn.PaiNN(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, use_pbc_single: bool = False, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    PaiNN model based on the description in Schütt et al. (2021): Equivariant message passing for the prediction of tensorial properties @@ -742,6 +746,11 @@

    Package Contentsuse_pbc#

    +
    +
    +use_pbc_single#
    +
    +
    symmetric_edge_symmetrization = False#
    @@ -903,6 +912,7 @@

    Package ContentsPaiNN.direct_forces

  • PaiNN.otf_graph
  • PaiNN.use_pbc
    • +
  • PaiNN.use_pbc_single
  • PaiNN.symmetric_edge_symmetrization
  • PaiNN.atom_emb
  • PaiNN.radial_basis
    • diff --git a/autoapi/core/models/painn/painn/index.html b/autoapi/core/models/painn/painn/index.html index 5e56951b26..f325654eb9 100644 --- a/autoapi/core/models/painn/painn/index.html +++ b/autoapi/core/models/painn/painn/index.html @@ -307,6 +307,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -336,16 +337,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    @@ -636,6 +639,7 @@

    Contents

  • PaiNN.direct_forces
  • PaiNN.otf_graph
  • PaiNN.use_pbc
    • +
  • PaiNN.use_pbc_single
  • PaiNN.symmetric_edge_symmetrization
  • PaiNN.atom_emb
  • PaiNN.radial_basis
    • @@ -779,7 +783,7 @@

    Classes#<

    Module Contents#

    -class core.models.painn.painn.PaiNN(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None)#
    +class core.models.painn.painn.PaiNN(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, use_pbc_single: bool = False, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    PaiNN model based on the description in Schütt et al. (2021): Equivariant message passing for the prediction of tensorial properties @@ -829,6 +833,11 @@

    Module Contentsuse_pbc#

    +
    +
    +use_pbc_single#
    +
    +
    symmetric_edge_symmetrization = False#
    @@ -912,7 +921,7 @@

    Module Contents
    -class core.models.painn.painn.PaiNNBackbone(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None)#
    +class core.models.painn.painn.PaiNNBackbone(hidden_channels: int = 512, num_layers: int = 6, num_rbf: int = 128, cutoff: float = 12.0, max_neighbors: int = 50, rbf: dict[str, str] | None = None, envelope: dict[str, str | int] | None = None, regress_forces: bool = True, direct_forces: bool = True, use_pbc: bool = True, use_pbc_single: bool = False, otf_graph: bool = True, num_elements: int = 83, scale_file: str | None = None)#

    Bases: PaiNN, fairchem.core.models.base.BackboneInterface

    PaiNN model based on the description in Schütt et al. (2021): Equivariant message passing for the prediction of tensorial properties @@ -1285,7 +1294,7 @@

    Module Contents
    -out_energy#
    +out_energy = None#

    @@ -1451,6 +1460,7 @@

    Module ContentsPaiNN.direct_forces

  • PaiNN.otf_graph
  • PaiNN.use_pbc
    • +
  • PaiNN.use_pbc_single
  • PaiNN.symmetric_edge_symmetrization
  • PaiNN.atom_emb
  • PaiNN.radial_basis
    • diff --git a/autoapi/core/models/painn/utils/index.html b/autoapi/core/models/painn/utils/index.html index f0ec4eaac8..d94ce6216f 100644 --- a/autoapi/core/models/painn/utils/index.html +++ b/autoapi/core/models/painn/utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/schnet/index.html b/autoapi/core/models/schnet/index.html index 496f3fe379..d3df0990be 100644 --- a/autoapi/core/models/schnet/index.html +++ b/autoapi/core/models/schnet/index.html @@ -307,6 +307,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -336,16 +337,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    @@ -630,6 +633,7 @@

    Contents

  • SchNetWrap.num_targets
  • SchNetWrap.regress_forces
  • SchNetWrap.use_pbc
    • +
  • SchNetWrap.use_pbc_single
  • SchNetWrap.cutoff
  • SchNetWrap.otf_graph
  • SchNetWrap.max_neighbors
    • @@ -672,7 +676,7 @@

    Classes#<

    Module Contents#

    -class core.models.schnet.SchNetWrap(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = False, hidden_channels: int = 128, num_filters: int = 128, num_interactions: int = 6, num_gaussians: int = 50, cutoff: float = 10.0, readout: str = 'add')#
    +class core.models.schnet.SchNetWrap(use_pbc: bool = True, use_pbc_single: bool = False, regress_forces: bool = True, otf_graph: bool = False, hidden_channels: int = 128, num_filters: int = 128, num_interactions: int = 6, num_gaussians: int = 50, cutoff: float = 10.0, readout: str = 'add')#

    Bases: torch_geometric.nn.SchNet, fairchem.core.models.base.GraphModelMixin

    Wrapper around the continuous-filter convolutional neural network SchNet from the “SchNet: A Continuous-filter Convolutional Neural Network for Modeling @@ -686,6 +690,7 @@

    Module Contents

    +
    +
    +use_pbc_single#
    +
    +
    cutoff#
    @@ -844,6 +854,7 @@

    Module ContentsSchNetWrap.num_targets

  • SchNetWrap.regress_forces
  • SchNetWrap.use_pbc
    • +
  • SchNetWrap.use_pbc_single
  • SchNetWrap.cutoff
  • SchNetWrap.otf_graph
  • SchNetWrap.max_neighbors
    • diff --git a/autoapi/core/models/scn/index.html b/autoapi/core/models/scn/index.html index c839f49511..3bb9967b29 100644 --- a/autoapi/core/models/scn/index.html +++ b/autoapi/core/models/scn/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -634,6 +637,7 @@

    Contents

  • SphericalChannelNetwork.force_fc3
  • SphericalChannelNetwork.regress_forces
  • SphericalChannelNetwork.use_pbc
    • +
  • SphericalChannelNetwork.use_pbc_single
  • SphericalChannelNetwork.cutoff
  • SphericalChannelNetwork.otf_graph
  • SphericalChannelNetwork.show_timing_info
    • @@ -707,7 +711,7 @@

    Classes#<

    Package Contents#

    -class core.models.scn.SphericalChannelNetwork(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_num_neighbors: int = 20, cutoff: float = 8.0, max_num_elements: int = 90, num_interactions: int = 8, lmax: int = 6, mmax: int = 1, num_resolutions: int = 2, sphere_channels: int = 128, sphere_channels_reduce: int = 128, hidden_channels: int = 256, num_taps: int = -1, use_grid: bool = True, num_bands: int = 1, num_sphere_samples: int = 128, num_basis_functions: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False, direct_forces: bool = True)#
    +class core.models.scn.SphericalChannelNetwork(use_pbc: bool = True, use_pbc_single: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_num_neighbors: int = 20, cutoff: float = 8.0, max_num_elements: int = 90, num_interactions: int = 8, lmax: int = 6, mmax: int = 1, num_resolutions: int = 2, sphere_channels: int = 128, sphere_channels_reduce: int = 128, hidden_channels: int = 256, num_taps: int = -1, use_grid: bool = True, num_bands: int = 1, num_sphere_samples: int = 128, num_basis_functions: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False, direct_forces: bool = True)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    Spherical Channel Network Paper: Spherical Channels for Modeling Atomic Interactions

    @@ -715,6 +719,7 @@

    Package ContentsParameters:

    +
    +
    +use_pbc_single#
    +
    +
    cutoff#
    @@ -1010,6 +1020,7 @@

    Package ContentsSphericalChannelNetwork.force_fc3

  • SphericalChannelNetwork.regress_forces
  • SphericalChannelNetwork.use_pbc
    • +
  • SphericalChannelNetwork.use_pbc_single
  • SphericalChannelNetwork.cutoff
  • SphericalChannelNetwork.otf_graph
  • SphericalChannelNetwork.show_timing_info
    • diff --git a/autoapi/core/models/scn/sampling/index.html b/autoapi/core/models/scn/sampling/index.html index be8556600f..ee0eae193a 100644 --- a/autoapi/core/models/scn/sampling/index.html +++ b/autoapi/core/models/scn/sampling/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/scn/scn/index.html b/autoapi/core/models/scn/scn/index.html index c7d0205ee8..1cea40a441 100644 --- a/autoapi/core/models/scn/scn/index.html +++ b/autoapi/core/models/scn/scn/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -633,6 +636,7 @@

    Contents

  • SphericalChannelNetwork.force_fc3
  • SphericalChannelNetwork.regress_forces
  • SphericalChannelNetwork.use_pbc
    • +
  • SphericalChannelNetwork.use_pbc_single
  • SphericalChannelNetwork.cutoff
  • SphericalChannelNetwork.otf_graph
  • SphericalChannelNetwork.show_timing_info
    • @@ -751,7 +755,7 @@

    Classes#<

    Module Contents#

    -class core.models.scn.scn.SphericalChannelNetwork(use_pbc: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_num_neighbors: int = 20, cutoff: float = 8.0, max_num_elements: int = 90, num_interactions: int = 8, lmax: int = 6, mmax: int = 1, num_resolutions: int = 2, sphere_channels: int = 128, sphere_channels_reduce: int = 128, hidden_channels: int = 256, num_taps: int = -1, use_grid: bool = True, num_bands: int = 1, num_sphere_samples: int = 128, num_basis_functions: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False, direct_forces: bool = True)#
    +class core.models.scn.scn.SphericalChannelNetwork(use_pbc: bool = True, use_pbc_single: bool = True, regress_forces: bool = True, otf_graph: bool = False, max_num_neighbors: int = 20, cutoff: float = 8.0, max_num_elements: int = 90, num_interactions: int = 8, lmax: int = 6, mmax: int = 1, num_resolutions: int = 2, sphere_channels: int = 128, sphere_channels_reduce: int = 128, hidden_channels: int = 256, num_taps: int = -1, use_grid: bool = True, num_bands: int = 1, num_sphere_samples: int = 128, num_basis_functions: int = 128, distance_function: str = 'gaussian', basis_width_scalar: float = 1.0, distance_resolution: float = 0.02, show_timing_info: bool = False, direct_forces: bool = True)#

    Bases: torch.nn.Module, fairchem.core.models.base.GraphModelMixin

    Spherical Channel Network Paper: Spherical Channels for Modeling Atomic Interactions

    @@ -759,6 +763,7 @@

    Module ContentsParameters:

    +
    +
    +use_pbc_single#
    +
    +
    cutoff#
    @@ -1339,6 +1349,7 @@

    Module ContentsSphericalChannelNetwork.force_fc3

  • SphericalChannelNetwork.regress_forces
  • SphericalChannelNetwork.use_pbc
    • +
  • SphericalChannelNetwork.use_pbc_single
  • SphericalChannelNetwork.cutoff
  • SphericalChannelNetwork.otf_graph
  • SphericalChannelNetwork.show_timing_info
    • diff --git a/autoapi/core/models/scn/smearing/index.html b/autoapi/core/models/scn/smearing/index.html index b69a02e60f..69b506a233 100644 --- a/autoapi/core/models/scn/smearing/index.html +++ b/autoapi/core/models/scn/smearing/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/scn/spherical_harmonics/index.html b/autoapi/core/models/scn/spherical_harmonics/index.html index e730a2d33f..7c890ac3ba 100644 --- a/autoapi/core/models/scn/spherical_harmonics/index.html +++ b/autoapi/core/models/scn/spherical_harmonics/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/utils/activations/index.html b/autoapi/core/models/utils/activations/index.html index c042015af6..59a5a580bb 100644 --- a/autoapi/core/models/utils/activations/index.html +++ b/autoapi/core/models/utils/activations/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/utils/basis/index.html b/autoapi/core/models/utils/basis/index.html index cdc3c47a04..495f9a2a35 100644 --- a/autoapi/core/models/utils/basis/index.html +++ b/autoapi/core/models/utils/basis/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/models/utils/index.html b/autoapi/core/models/utils/index.html index d4db6504f8..5ae899829b 100644 --- a/autoapi/core/models/utils/index.html +++ b/autoapi/core/models/utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/modules/evaluator/index.html b/autoapi/core/modules/evaluator/index.html index 029ccf401a..6185fa65ff 100644 --- a/autoapi/core/modules/evaluator/index.html +++ b/autoapi/core/modules/evaluator/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/modules/exponential_moving_average/index.html b/autoapi/core/modules/exponential_moving_average/index.html index 866ebf7467..f5b4a0f29f 100644 --- a/autoapi/core/modules/exponential_moving_average/index.html +++ b/autoapi/core/modules/exponential_moving_average/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/modules/index.html b/autoapi/core/modules/index.html index 4a5fcb8573..d50c2adc2a 100644 --- a/autoapi/core/modules/index.html +++ b/autoapi/core/modules/index.html @@ -61,7 +61,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -644,6 +647,7 @@

    Contents

    Subpackages#

    @@ -655,7 +659,6 @@

    Submodulescore.modules.evaluator

  • core.modules.exponential_moving_average
  • core.modules.loss
    • -
  • core.modules.normalizer
  • core.modules.scheduler
  • core.modules.transforms
    • @@ -703,11 +706,11 @@

    Submodules

    next

    -

    core.modules.scaling

    +

    core.modules.normalization

     diff --git a/autoapi/core/modules/loss/index.html b/autoapi/core/modules/loss/index.html index 587d96f60b..70248a899a 100644 --- a/autoapi/core/modules/loss/index.html +++ b/autoapi/core/modules/loss/index.html @@ -61,7 +61,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -869,11 +872,11 @@

    Module Contents

    next

    -

    core.modules.normalizer

    +

    core.modules.scheduler

     diff --git a/autoapi/core/modules/normalization/_load_utils/index.html b/autoapi/core/modules/normalization/_load_utils/index.html new file mode 100644 index 0000000000..384dd7a1e9 --- /dev/null +++ b/autoapi/core/modules/normalization/_load_utils/index.html @@ -0,0 +1,832 @@ + + + + + + + + + + + core.modules.normalization._load_utils + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    core.modules.normalization._load_utils

    + +
    + +
    +
    + + + + +
    + +
    +

    core.modules.normalization._load_utils#

    +

    Copyright (c) Meta, Inc. and its affiliates.

    +

    This source code is licensed under the MIT license found in the +LICENSE file in the root directory of this source tree.

    +
    +

    Functions#

    +
    + + + + + + + + +

    _load_check_duplicates(→ dict[str, torch.nn.Module])

    Attempt to load a single file with normalizers/element references and check config for duplicate targets.

    _load_from_config(→ dict[str, torch.nn.Module])

    Load or fit normalizers or element references from config

    +
    +
    +
    +

    Module Contents#

    +
    +
    +core.modules.normalization._load_utils._load_check_duplicates(config: dict, name: str) → dict[str, torch.nn.Module]#
    +

    Attempt to load a single file with normalizers/element references and check config for duplicate targets.

    +
    +
    Parameters:
    +
      +

    • config – configuration dictionary

      • +

    • name – Name of module to use for logging

      • +
    +
    +
    Returns:
    +

    dictionary of normalizer or element reference modules

    +
    +
    +
    + +
    +
    +core.modules.normalization._load_utils._load_from_config(config: dict, name: str, fit_fun: Callable[[list[str], torch.utils.data.Dataset, Any, Ellipsis], dict[str, torch.nn.Module]], create_fun: Callable[[str | pathlib.Path], torch.nn.Module], dataset: torch.utils.data.Dataset, checkpoint_dir: str | pathlib.Path | None = None, **fit_kwargs) → dict[str, torch.nn.Module]#
    +

    Load or fit normalizers or element references from config

    +

    If a fit is done, a fitted key with value true is added to the config to avoid re-fitting +once a checkpoint has been saved.

    +
    +
    Parameters:
    +
      +

    • config – configuration dictionary

      • +

    • name – Name of module to use for logging

      • +

    • fit_fun – Function to fit modules

      • +

    • create_fun – Function to create a module from file

      • +

    • checkpoint_dir – directory to save modules. If not given, modules won’t be saved.

      • +
    +
    +
    Returns:
    +

    dictionary of normalizer or element reference modules

    +
    +
    +
    + +
    +
    + + + + +
    + + + + + + + + +
    + + + +
    + + +
    +
    + Contents +
    +
    + +
    + + +
    +
    + +
    + +
    + +

    +By FAIR Chemistry & Collaborators +

    + +
    + +
    + + +

    + + © Copyright 2024. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
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    + + +
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    + + + + + +
    +
    + + \ No newline at end of file diff --git a/autoapi/core/modules/normalization/element_references/index.html b/autoapi/core/modules/normalization/element_references/index.html new file mode 100644 index 0000000000..0137d00e9d --- /dev/null +++ b/autoapi/core/modules/normalization/element_references/index.html @@ -0,0 +1,917 @@ + + + + + + + + + + + core.modules.normalization.element_references + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    + + + +
    +

    core.modules.normalization.element_references

    + +
    + +
    +
    + + + + +
    + +
    +

    core.modules.normalization.element_references#

    +

    Copyright (c) Meta, Inc. and its affiliates.

    +

    This source code is licensed under the MIT license found in the +LICENSE file in the root directory of this source tree.

    +
    +

    Classes#

    +
    + + + + + +

    LinearReferences

    Represents an elemental linear references model for a target property.

    +
    +
    +
    +

    Functions#

    +
    + + + + + + + + + + + +

    create_element_references(→ LinearReferences)

    Create an element reference module.

    fit_linear_references(→ dict[str, LinearReferences])

    Fit a set linear references for a list of targets using a given number of batches.

    load_references_from_config(→ dict[str, LinearReferences])

    Create a dictionary with element references from a config.

    +
    +
    +
    +

    Module Contents#

    +
    +
    +class core.modules.normalization.element_references.LinearReferences(element_references: torch.Tensor | None = None, max_num_elements: int = 118)#
    +

    Bases: torch.nn.Module

    +

    Represents an elemental linear references model for a target property.

    +

    In an elemental reference associates a value with each chemical element present in the dataset. +Elemental references define a chemical composition model, i.e. a rough approximation of a target +property (energy) using elemental references is done by summing the elemental references multiplied +by the number of times the corresponding element is present.

    +
    +
    Elemental references energies can be taken as:
      +

    • the energy of a chemical species in its elemental state +(i.e. lowest energy polymorph of single element crystal structures for solids)

      • +

    • fitting a linear model to a dataset, where the features are the counts of each element in each data point. +see the function fit_linear references below for details

      • +
    +
    +
    +

    Training GNNs to predict the difference between DFT and the predictions of a chemical composition +model represent a useful normalization scheme that can improve model accuracy. See for example the +“Alternative reference scheme” section of the OC22 manuscript: https://arxiv.org/pdf/2206.08917

    +
    +
    +_apply_refs(target: torch.Tensor, batch: torch_geometric.data.Batch, sign: int, reshaped: bool = True) → torch.Tensor#
    +

    Apply references batch-wise

    +
    + +
    +
    +dereference(target: torch.Tensor, batch: torch_geometric.data.Batch, reshaped: bool = True) → torch.Tensor#
    +

    Remove linear references

    +
    + +
    +
    +forward(target: torch.Tensor, batch: torch_geometric.data.Batch, reshaped: bool = True) → torch.Tensor#
    +

    Add linear references

    +
    + +
    + +
    +
    +core.modules.normalization.element_references.create_element_references(file: str | pathlib.Path | None = None, state_dict: dict | None = None) → LinearReferences#
    +

    Create an element reference module.

    +
    +
    Parameters:
    +
      +

    • type (str) – type of reference (only linear implemented)

      • +

    • file (str or Path) – path to pt or npz file

      • +

    • state_dict (dict) – a state dict of a element reference module

      • +
    +
    +
    Returns:
    +

    LinearReference

    +
    +
    +
    + +
    +
    +core.modules.normalization.element_references.fit_linear_references(targets: list[str], dataset: torch.utils.data.Dataset, batch_size: int, num_batches: int | None = None, num_workers: int = 0, max_num_elements: int = 118, log_metrics: bool = True, use_numpy: bool = True, driver: str | None = None, shuffle: bool = True, seed: int = 0) → dict[str, LinearReferences]#
    +

    Fit a set linear references for a list of targets using a given number of batches.

    +
    +
    Parameters:
    +
      +

    • targets – list of target names

      • +

    • dataset – data set to fit linear references with

      • +

    • batch_size – size of batch

      • +

    • num_batches – number of batches to use in fit. If not given will use all batches

      • +

    • num_workers – number of workers to use in data loader. +Note setting num_workers > 1 leads to finicky multiprocessing issues when using this function +in distributed mode. The issue has to do with pickling the functions in load_references_from_config +see function below…

      • +

    • max_num_elements – max number of elements in dataset. If not given will use an ambitious value of 118

      • +

    • log_metrics – if true will compute MAE, RMSE and R2 score of fit and log.

      • +

    • use_numpy – use numpy.linalg.lstsq instead of torch. This tends to give better solutions.

      • +

    • driver – backend used to solve linear system. See torch.linalg.lstsq docs. Ignored if use_numpy=True

      • +

    • shuffle – whether to shuffle when loading the dataset

      • +

    • seed – random seed used to shuffle the sampler if shuffle=True

      • +
    +
    +
    Returns:
    +

    dict of fitted LinearReferences objects

    +
    +
    +
    + +
    +
    +core.modules.normalization.element_references.load_references_from_config(config: dict[str, Any], dataset: torch.utils.data.Dataset, seed: int = 0, checkpoint_dir: str | pathlib.Path | None = None) → dict[str, LinearReferences]#
    +

    Create a dictionary with element references from a config.

    +
    + +
    +
    + + + + +
    + + + + + + + + +
    + + + +
    + + +
    +
    + Contents +
    +
    + +
    + + +
    +
    + +
    + +
    + +

    +By FAIR Chemistry & Collaborators +

    + +
    + +
    + + +

    + + © Copyright 2024. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
    +
    + + +
    +
    +
    + + + + + +
    +
    + + \ No newline at end of file diff --git a/autoapi/data/oc/tests/index.html b/autoapi/core/modules/normalization/index.html similarity index 76% rename from autoapi/data/oc/tests/index.html rename to autoapi/core/modules/normalization/index.html index 416d8540bd..1c2d20ecbe 100644 --- a/autoapi/data/oc/tests/index.html +++ b/autoapi/core/modules/normalization/index.html @@ -8,7 +8,7 @@ - data.oc.tests + core.modules.normalization @@ -58,11 +58,11 @@ - + - - + + @@ -294,103 +294,106 @@

    fairchem documentation

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/scripts/make_lmdb_sizes/index.html b/autoapi/core/scripts/make_lmdb_sizes/index.html index 14ea1c50f8..a3708d040a 100644 --- a/autoapi/core/scripts/make_lmdb_sizes/index.html +++ b/autoapi/core/scripts/make_lmdb_sizes/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/scripts/make_submission_file/index.html b/autoapi/core/scripts/make_submission_file/index.html index 6a59964a60..16aa4cf7b2 100644 --- a/autoapi/core/scripts/make_submission_file/index.html +++ b/autoapi/core/scripts/make_submission_file/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/scripts/preprocess_ef/index.html b/autoapi/core/scripts/preprocess_ef/index.html index 9afeaf5f3f..a5abb5814b 100644 --- a/autoapi/core/scripts/preprocess_ef/index.html +++ b/autoapi/core/scripts/preprocess_ef/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/scripts/preprocess_relaxed/index.html b/autoapi/core/scripts/preprocess_relaxed/index.html index dc67f7eb2e..ff8f991a76 100644 --- a/autoapi/core/scripts/preprocess_relaxed/index.html +++ b/autoapi/core/scripts/preprocess_relaxed/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/scripts/uncompress/index.html b/autoapi/core/scripts/uncompress/index.html index 0f76da5229..6270c78808 100644 --- a/autoapi/core/scripts/uncompress/index.html +++ b/autoapi/core/scripts/uncompress/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/tasks/index.html b/autoapi/core/tasks/index.html index f79584041b..3c4c223f30 100644 --- a/autoapi/core/tasks/index.html +++ b/autoapi/core/tasks/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/tasks/task/index.html b/autoapi/core/tasks/task/index.html index 4fae89d95b..9fb18c4dc5 100644 --- a/autoapi/core/tasks/task/index.html +++ b/autoapi/core/tasks/task/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/core/trainers/base_trainer/index.html b/autoapi/core/trainers/base_trainer/index.html index a016f15a88..14bc09ba88 100644 --- a/autoapi/core/trainers/base_trainer/index.html +++ b/autoapi/core/trainers/base_trainer/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -635,6 +638,11 @@

    Contents

  • BaseTrainer.logger_name
  • BaseTrainer.config
  • BaseTrainer.scaler
    • +
  • BaseTrainer.elementrefs
    • +
  • BaseTrainer.normalizers
    • +
  • BaseTrainer.train_dataset
    • +
  • BaseTrainer.val_dataset
    • +
  • BaseTrainer.test_dataset
  • BaseTrainer.train()
  • BaseTrainer._get_timestamp()
  • BaseTrainer.load()
    • @@ -644,6 +652,7 @@

    Contents

  • BaseTrainer.get_sampler()
  • BaseTrainer.get_dataloader()
  • BaseTrainer.load_datasets()
    • +
  • BaseTrainer.load_references_and_normalizers()
  • BaseTrainer.load_task()
  • BaseTrainer.load_model()
  • BaseTrainer._unwrapped_model
    • @@ -745,6 +754,31 @@

    Module Contentsscaler#
    +
    +
    +elementrefs#
    +
    + +
    +
    +normalizers#
    +
    + +
    +
    +train_dataset = None#
    +
    + +
    +
    +val_dataset = None#
    +
    + +
    +
    +test_dataset = None#
    +
    +
    abstract train(disable_eval_tqdm: bool = False) → None#
    @@ -791,6 +825,12 @@

    Module Contentsload_datasets() → None#

    +
    +
    +load_references_and_normalizers()#
    +

    Load or create element references and normalizers from config

    +
    +
    load_task()#
    @@ -933,6 +973,11 @@

    Module ContentsBaseTrainer.logger_name

  • BaseTrainer.config
  • BaseTrainer.scaler
    • +
  • BaseTrainer.elementrefs
    • +
  • BaseTrainer.normalizers
    • +
  • BaseTrainer.train_dataset
    • +
  • BaseTrainer.val_dataset
    • +
  • BaseTrainer.test_dataset
  • BaseTrainer.train()
  • BaseTrainer._get_timestamp()
  • BaseTrainer.load()
    • @@ -942,6 +987,7 @@

    Module ContentsBaseTrainer.get_sampler()

  • BaseTrainer.get_dataloader()
  • BaseTrainer.load_datasets()
    • +
  • BaseTrainer.load_references_and_normalizers()
  • BaseTrainer.load_task()
  • BaseTrainer.load_model()
  • BaseTrainer._unwrapped_model
    • diff --git a/autoapi/core/trainers/index.html b/autoapi/core/trainers/index.html index 28979a6756..217c39ee25 100644 --- a/autoapi/core/trainers/index.html +++ b/autoapi/core/trainers/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -636,6 +639,11 @@

    Contents

  • BaseTrainer.logger_name
  • BaseTrainer.config
  • BaseTrainer.scaler
    • +
  • BaseTrainer.elementrefs
    • +
  • BaseTrainer.normalizers
    • +
  • BaseTrainer.train_dataset
    • +
  • BaseTrainer.val_dataset
    • +
  • BaseTrainer.test_dataset
  • BaseTrainer.train()
  • BaseTrainer._get_timestamp()
  • BaseTrainer.load()
    • @@ -645,6 +653,7 @@

    Contents

  • BaseTrainer.get_sampler()
  • BaseTrainer.get_dataloader()
  • BaseTrainer.load_datasets()
    • +
  • BaseTrainer.load_references_and_normalizers()
  • BaseTrainer.load_task()
  • BaseTrainer.load_model()
  • BaseTrainer._unwrapped_model
    • @@ -661,6 +670,7 @@

    Contents

  • OCPTrainer
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -626,6 +629,7 @@

    Contents

  • Module Contents
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/oc/core/adsorbate/index.html b/autoapi/data/oc/core/adsorbate/index.html index c1047beec8..76e3538673 100644 --- a/autoapi/data/oc/core/adsorbate/index.html +++ b/autoapi/data/oc/core/adsorbate/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/oc/core/adsorbate_slab_config/index.html b/autoapi/data/oc/core/adsorbate_slab_config/index.html index 4efee9b303..45d0346c5f 100644 --- a/autoapi/data/oc/core/adsorbate_slab_config/index.html +++ b/autoapi/data/oc/core/adsorbate_slab_config/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/oc/core/bulk/index.html b/autoapi/data/oc/core/bulk/index.html index 18af79551e..d1d6ff2c41 100644 --- a/autoapi/data/oc/core/bulk/index.html +++ b/autoapi/data/oc/core/bulk/index.html @@ -61,7 +61,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -783,11 +786,11 @@

    Module Contents

    next

    -

    data.oc.core.multi_adsorbate_slab_config

    +

    data.oc.core.interface_config

     diff --git a/autoapi/data/oc/core/index.html b/autoapi/data/oc/core/index.html index ce01a4935c..aea126ef21 100644 --- a/autoapi/data/oc/core/index.html +++ b/autoapi/data/oc/core/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -665,6 +668,30 @@

    Contents

  • Bulk.__eq__()
    • +
  • InterfaceConfig +
    • +
  • Ion +
  • MultipleAdsorbateSlabConfig
    • +
  • Solvent +
    • @@ -718,8 +756,11 @@

    Submodulesdata.oc.core.adsorbate

  • data.oc.core.adsorbate_slab_config
  • data.oc.core.bulk
    • +
  • data.oc.core.interface_config
    • +
  • data.oc.core.ion
  • data.oc.core.multi_adsorbate_slab_config
  • data.oc.core.slab
    • +
  • data.oc.core.solvent
    • @@ -736,12 +777,21 @@

    Classes#<

    Bulk

    Initializes a bulk object in one of 4 ways:

    +

    InterfaceConfig

    +

    Class to represent a solvent, adsorbate, slab, ion config. This class only

    + +

    Ion

    +

    Initializes an ion object in one of 2 ways:

    +

    MultipleAdsorbateSlabConfig

    Class to represent a slab with multiple adsorbates on it. This class only

    Slab

    Initializes a slab object, i.e. a particular slab tiled along xyz, in

    +

    Solvent

    +

    Initializes a solvent object in one of 2 ways:

    + @@ -1092,6 +1142,187 @@

    Package Contents +
    +class data.oc.core.InterfaceConfig(slab: fairchem.data.oc.core.slab.Slab, adsorbates: list[fairchem.data.oc.core.adsorbate.Adsorbate], solvent: fairchem.data.oc.core.solvent.Solvent, ions: list[fairchem.data.oc.core.ion.Ion] | None = None, num_sites: int = 100, num_configurations: int = 1, interstitial_gap: float = 0.1, vacuum_size: int = 15, solvent_interstitial_gap: float = 2, solvent_depth: float = 8, pbc_shift: float = 0.0, packmol_tolerance: float = 2, mode: str = 'random_site_heuristic_placement')#
    +

    Bases: fairchem.data.oc.core.multi_adsorbate_slab_config.MultipleAdsorbateSlabConfig

    +

    Class to represent a solvent, adsorbate, slab, ion config. This class only +returns a fixed combination of adsorbates placed on the surface. Solvent +placement is performed by packmol +(https://m3g.github.io/packmol/userguide.shtml), with the number of solvent +molecules controlled by its corresponding density. Ion placement is random +within the desired volume.

    +
    +
    Parameters:
    +
      +

    • slab (Slab) – Slab object.

      • +

    • adsorbates (List[Adsorbate]) – List of adsorbate objects to place on the slab.

      • +

    • solvent (Solvent) – Solvent object

      • +

    • ions (List[Ion] = []) – List of ion objects to place

      • +

    • num_sites (int) – Number of sites to sample.

      • +

    • num_configurations (int) – Number of configurations to generate per slab+adsorbate(s) combination. +This corresponds to selecting different site combinations to place +the adsorbates on.

      • +

    • interstitial_gap (float) – Minimum distance, in Angstroms, between adsorbate and slab atoms as +well as the inter-adsorbate distance.

      • +

    • vacuum_size (int) – Size of vacuum layer to add to both ends of the resulting atoms object.

      • +

    • solvent_interstitial_gap (float) – Minimum distance, in Angstroms, between the solvent environment and the +adsorbate-slab environment.

      • +

    • solvent_depth (float) – Volume depth to be used to pack solvents inside.

      • +

    • pbc_shift (float) – Cushion to add to the packmol volume to avoid overlapping atoms over pbc.

      • +

    • packmol_tolerance (float) – Packmol minimum distance to impose between molecules.

      • +

    • mode (str) –

      “random”, “heuristic”, or “random_site_heuristic_placement”. +This affects surface site sampling and adsorbate placement on each site.

      +

      In “random”, we do a Delaunay triangulation of the surface atoms, then +sample sites uniformly at random within each triangle. When placing the +adsorbate, we randomly rotate it along xyz, and place it such that the +center of mass is at the site.

      +

      In “heuristic”, we use Pymatgen’s AdsorbateSiteFinder to find the most +energetically favorable sites, i.e., ontop, bridge, or hollow sites. +When placing the adsorbate, we randomly rotate it along z with only +slight rotation along x and y, and place it such that the binding atom +is at the site.

      +

      In “random_site_heuristic_placement”, we do a Delaunay triangulation of +the surface atoms, then sample sites uniformly at random within each +triangle. When placing the adsorbate, we randomly rotate it along z with +only slight rotation along x and y, and place it such that the binding +atom is at the site.

      +

      In all cases, the adsorbate is placed at the closest position of no +overlap with the slab plus interstitial_gap along the surface normal.

      +

      • +
    +
    +
    +
    +
    +solvent#
    +
    + +
    +
    +ions#
    +
    + +
    +
    +vacuum_size#
    +
    + +
    +
    +solvent_depth#
    +
    + +
    +
    +solvent_interstitial_gap#
    +
    + +
    +
    +pbc_shift#
    +
    + +
    +
    +packmol_tolerance#
    +
    + +
    +
    +n_mol_per_volume#
    +
    + +
    +
    +create_interface_on_sites(atoms_list: list[ase.Atoms], metadata_list: list[dict])#
    +

    Given adsorbate+slab configurations generated from +(Multi)AdsorbateSlabConfig and its corresponding metadata, create the +solvent/ion interface on top of the provided atoms objects.

    +
    + +
    +
    +create_packmol_atoms(geometry: fairchem.data.oc.utils.geometry.Geometry, n_solvent_mols: int)#
    +

    Pack solvent molecules in a provided unit cell volume. Packmol is used +to randomly pack solvent molecules in the desired volume.

    +
    +
    Parameters:
    +
      +

    • geometry (Geometry) – Geometry object corresponding to the desired cell.

      • +

    • n_solvent_mols (int) – Number of solvent molecules to pack in the volume.

      • +
    +
    +
    +
    + +
    +
    +run_packmol(packmol_input: str)#
    +

    Run packmol.

    +
    + +
    +
    +randomize_coords(atoms: ase.Atoms)#
    +

    Randomly place the atoms in its unit cell.

    +
    + +
    + +
    +
    +class data.oc.core.Ion(ion_atoms: ase.Atoms = None, ion_id_from_db: int | None = None, ion_db_path: str = ION_PKL_PATH)#
    +

    Initializes an ion object in one of 2 ways: +- Directly pass in an ase.Atoms object. +- Pass in index of ion to select from ion database.

    +
    +
    Parameters:
    +
      +

    • ion_atoms (ase.Atoms) – ion structure.

      • +

    • ion_id_from_db (int) – Index of ion to select.

      • +

    • ion_db_path (str) – Path to ion database.

      • +
    +
    +
    +
    +
    +ion_id_from_db#
    +
    + +
    +
    +ion_db_path#
    +
    + +
    +
    +__len__()#
    +
    + +
    +
    +__str__()#
    +

    Return str(self).

    +
    + +
    +
    +_load_ion(ion: dict) → None#
    +

    Saves the fields from an ion stored in a database. Fields added +after the first revision are conditionally added for backwards +compatibility with older database files.

    +
    + +
    +
    +get_ion_concentration(volume)#
    +

    Compute the ion concentration units of M, given a volume in units of +Angstrom^3.

    +
    + +
    +
    class data.oc.core.MultipleAdsorbateSlabConfig(slab: fairchem.data.oc.core.slab.Slab, adsorbates: list[fairchem.data.oc.core.adsorbate.Adsorbate], num_sites: int = 100, num_configurations: int = 1, interstitial_gap: float = 0.1, mode: str = 'random_site_heuristic_placement')#
    @@ -1294,6 +1525,73 @@

    Package Contents +
    +class data.oc.core.Solvent(solvent_atoms: ase.Atoms = None, solvent_id_from_db: int | None = None, solvent_db_path: str | None = SOLVENT_PKL_PATH, solvent_density: float | None = None)#
    +

    Initializes a solvent object in one of 2 ways: +- Directly pass in an ase.Atoms object. +- Pass in index of solvent to select from solvent database.

    +
    +
    Parameters:
    +
      +

    • solvent_atoms (ase.Atoms) – Solvent molecule

      • +

    • solvent_id_from_db (int) – Index of solvent to select.

      • +

    • solvent_db_path (str) – Path to solvent database.

      • +

    • solvent_density (float) – Desired solvent density to use. If not specified, the default is used +from the solvent databases.

      • +
    +
    +
    +
    +
    +solvent_id_from_db#
    +
    + +
    +
    +solvent_db_path#
    +
    + +
    +
    +solvent_density#
    +
    + +
    +
    +molar_mass#
    +
    + +
    +
    +__len__()#
    +
    + +
    +
    +__str__()#
    +

    Return str(self).

    +
    + +
    +
    +_load_solvent(solvent: dict) → None#
    +

    Saves the fields from an adsorbate stored in a database. Fields added +after the first revision are conditionally added for backwards +compatibility with older database files.

    +
    + +
    +
    +property molecules_per_volume#
    +
    +Convert the solvent density in g/cm3 to the number of molecules per
    +
    +angstrom cubed of volume.
    +
    + +

    + @@ -1404,6 +1702,30 @@

    Package ContentsBulk.__eq__()

    • +
  • InterfaceConfig +
    • +
  • Ion +
  • MultipleAdsorbateSlabConfig
    • +
  • Solvent +
    • diff --git a/autoapi/data/oc/core/interface_config/index.html b/autoapi/data/oc/core/interface_config/index.html new file mode 100644 index 0000000000..593de58c43 --- /dev/null +++ b/autoapi/data/oc/core/interface_config/index.html @@ -0,0 +1,941 @@ + + + + + + + + + + + data.oc.core.interface_config + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + +
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    data.oc.core.interface_config

    + +
    + +
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    + + + + +
    + +
    +

    data.oc.core.interface_config#

    +
    +

    Classes#

    +
    + + + + + +

    InterfaceConfig

    Class to represent a solvent, adsorbate, slab, ion config. This class only

    +
    +
    +
    +

    Module Contents#

    +
    +
    +class data.oc.core.interface_config.InterfaceConfig(slab: fairchem.data.oc.core.slab.Slab, adsorbates: list[fairchem.data.oc.core.adsorbate.Adsorbate], solvent: fairchem.data.oc.core.solvent.Solvent, ions: list[fairchem.data.oc.core.ion.Ion] | None = None, num_sites: int = 100, num_configurations: int = 1, interstitial_gap: float = 0.1, vacuum_size: int = 15, solvent_interstitial_gap: float = 2, solvent_depth: float = 8, pbc_shift: float = 0.0, packmol_tolerance: float = 2, mode: str = 'random_site_heuristic_placement')#
    +

    Bases: fairchem.data.oc.core.multi_adsorbate_slab_config.MultipleAdsorbateSlabConfig

    +

    Class to represent a solvent, adsorbate, slab, ion config. This class only +returns a fixed combination of adsorbates placed on the surface. Solvent +placement is performed by packmol +(https://m3g.github.io/packmol/userguide.shtml), with the number of solvent +molecules controlled by its corresponding density. Ion placement is random +within the desired volume.

    +
    +
    Parameters:
    +
      +

    • slab (Slab) – Slab object.

      • +

    • adsorbates (List[Adsorbate]) – List of adsorbate objects to place on the slab.

      • +

    • solvent (Solvent) – Solvent object

      • +

    • ions (List[Ion] = []) – List of ion objects to place

      • +

    • num_sites (int) – Number of sites to sample.

      • +

    • num_configurations (int) – Number of configurations to generate per slab+adsorbate(s) combination. +This corresponds to selecting different site combinations to place +the adsorbates on.

      • +

    • interstitial_gap (float) – Minimum distance, in Angstroms, between adsorbate and slab atoms as +well as the inter-adsorbate distance.

      • +

    • vacuum_size (int) – Size of vacuum layer to add to both ends of the resulting atoms object.

      • +

    • solvent_interstitial_gap (float) – Minimum distance, in Angstroms, between the solvent environment and the +adsorbate-slab environment.

      • +

    • solvent_depth (float) – Volume depth to be used to pack solvents inside.

      • +

    • pbc_shift (float) – Cushion to add to the packmol volume to avoid overlapping atoms over pbc.

      • +

    • packmol_tolerance (float) – Packmol minimum distance to impose between molecules.

      • +

    • mode (str) –

      “random”, “heuristic”, or “random_site_heuristic_placement”. +This affects surface site sampling and adsorbate placement on each site.

      +

      In “random”, we do a Delaunay triangulation of the surface atoms, then +sample sites uniformly at random within each triangle. When placing the +adsorbate, we randomly rotate it along xyz, and place it such that the +center of mass is at the site.

      +

      In “heuristic”, we use Pymatgen’s AdsorbateSiteFinder to find the most +energetically favorable sites, i.e., ontop, bridge, or hollow sites. +When placing the adsorbate, we randomly rotate it along z with only +slight rotation along x and y, and place it such that the binding atom +is at the site.

      +

      In “random_site_heuristic_placement”, we do a Delaunay triangulation of +the surface atoms, then sample sites uniformly at random within each +triangle. When placing the adsorbate, we randomly rotate it along z with +only slight rotation along x and y, and place it such that the binding +atom is at the site.

      +

      In all cases, the adsorbate is placed at the closest position of no +overlap with the slab plus interstitial_gap along the surface normal.

      +

      • +
    +
    +
    +
    +
    +solvent#
    +
    + +
    +
    +ions#
    +
    + +
    +
    +vacuum_size#
    +
    + +
    +
    +solvent_depth#
    +
    + +
    +
    +solvent_interstitial_gap#
    +
    + +
    +
    +pbc_shift#
    +
    + +
    +
    +packmol_tolerance#
    +
    + +
    +
    +n_mol_per_volume#
    +
    + +
    +
    +create_interface_on_sites(atoms_list: list[ase.Atoms], metadata_list: list[dict])#
    +

    Given adsorbate+slab configurations generated from +(Multi)AdsorbateSlabConfig and its corresponding metadata, create the +solvent/ion interface on top of the provided atoms objects.

    +
    + +
    +
    +create_packmol_atoms(geometry: fairchem.data.oc.utils.geometry.Geometry, n_solvent_mols: int)#
    +

    Pack solvent molecules in a provided unit cell volume. Packmol is used +to randomly pack solvent molecules in the desired volume.

    +
    +
    Parameters:
    +
      +

    • geometry (Geometry) – Geometry object corresponding to the desired cell.

      • +

    • n_solvent_mols (int) – Number of solvent molecules to pack in the volume.

      • +
    +
    +
    +
    + +
    +
    +run_packmol(packmol_input: str)#
    +

    Run packmol.

    +
    + +
    +
    +randomize_coords(atoms: ase.Atoms)#
    +

    Randomly place the atoms in its unit cell.

    +
    + +
    + +
    +
    + + + + +
    + + + + + + + + +
    + + + +
    + + +
    +
    + Contents +
    +
    + +
    + + +
    +
    + +
    + +
    + +

    +By FAIR Chemistry & Collaborators +

    + +
    + +
    + + +

    + + © Copyright 2024. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
    +
    + + +
    +
    +
    + + + + + +
    +
    + + \ No newline at end of file diff --git a/autoapi/data/oc/core/ion/index.html b/autoapi/data/oc/core/ion/index.html new file mode 100644 index 0000000000..5dccb6556f --- /dev/null +++ b/autoapi/data/oc/core/ion/index.html @@ -0,0 +1,854 @@ + + + + + + + + + + + data.oc.core.ion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + +
    +
    +
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    + + + Ctrl+K +
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    + +
    + +
    +
    + + + +
    +

    data.oc.core.ion

    + +
    + +
    +
    + + + + +
    + +
    +

    data.oc.core.ion#

    +
    +

    Classes#

    +
    + + + + + +

    Ion

    Initializes an ion object in one of 2 ways:

    +
    +
    +
    +

    Module Contents#

    +
    +
    +class data.oc.core.ion.Ion(ion_atoms: ase.Atoms = None, ion_id_from_db: int | None = None, ion_db_path: str = ION_PKL_PATH)#
    +

    Initializes an ion object in one of 2 ways: +- Directly pass in an ase.Atoms object. +- Pass in index of ion to select from ion database.

    +
    +
    Parameters:
    +
      +

    • ion_atoms (ase.Atoms) – ion structure.

      • +

    • ion_id_from_db (int) – Index of ion to select.

      • +

    • ion_db_path (str) – Path to ion database.

      • +
    +
    +
    +
    +
    +ion_id_from_db#
    +
    + +
    +
    +ion_db_path#
    +
    + +
    +
    +__len__()#
    +
    + +
    +
    +__str__()#
    +

    Return str(self).

    +
    + +
    +
    +_load_ion(ion: dict) → None#
    +

    Saves the fields from an ion stored in a database. Fields added +after the first revision are conditionally added for backwards +compatibility with older database files.

    +
    + +
    +
    +get_ion_concentration(volume)#
    +

    Compute the ion concentration units of M, given a volume in units of +Angstrom^3.

    +
    + +
    + +
    +
    + + + + +
    + + + + + + + + +
    + + + +
    + + +
    +
    + Contents +
    +
    + +
    + + +
    +
    + +
    + +
    + +

    +By FAIR Chemistry & Collaborators +

    + +
    + +
    + + +

    + + © Copyright 2024. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
    +
    + + +
    +
    +
    + + + + + +
    +
    + + \ No newline at end of file diff --git a/autoapi/data/oc/core/multi_adsorbate_slab_config/index.html b/autoapi/data/oc/core/multi_adsorbate_slab_config/index.html index 935d84f776..fb8d0516e1 100644 --- a/autoapi/data/oc/core/multi_adsorbate_slab_config/index.html +++ b/autoapi/data/oc/core/multi_adsorbate_slab_config/index.html @@ -62,7 +62,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -811,12 +814,12 @@

    Module Contents

    previous

    -

    data.oc.core.bulk

    +

    data.oc.core.ion

     DOCUMENTATION_OPTIONS.pagename = 'autoapi/data/oc/core/slab/index'; - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -1152,11 +1155,11 @@

    Module Contents

    next

    -

    data.oc.databases

    +

    data.oc.core.solvent

     diff --git a/autoapi/data/oc/core/solvent/index.html b/autoapi/data/oc/core/solvent/index.html new file mode 100644 index 0000000000..cd2b9680b4 --- /dev/null +++ b/autoapi/data/oc/core/solvent/index.html @@ -0,0 +1,872 @@ + + + + + + + + + + + data.oc.core.solvent + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + +
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    + + + Ctrl+K +
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    + + + + + + +
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    + + + + + + + + + + + + + +
    + +
    + +
    +
    + + + +
    +

    data.oc.core.solvent

    + +
    + +
    +
    + + + + +
    + +
    +

    data.oc.core.solvent#

    +
    +

    Classes#

    +
    + + + + + +

    Solvent

    Initializes a solvent object in one of 2 ways:

    +
    +
    +
    +

    Module Contents#

    +
    +
    +class data.oc.core.solvent.Solvent(solvent_atoms: ase.Atoms = None, solvent_id_from_db: int | None = None, solvent_db_path: str | None = SOLVENT_PKL_PATH, solvent_density: float | None = None)#
    +

    Initializes a solvent object in one of 2 ways: +- Directly pass in an ase.Atoms object. +- Pass in index of solvent to select from solvent database.

    +
    +
    Parameters:
    +
      +

    • solvent_atoms (ase.Atoms) – Solvent molecule

      • +

    • solvent_id_from_db (int) – Index of solvent to select.

      • +

    • solvent_db_path (str) – Path to solvent database.

      • +

    • solvent_density (float) – Desired solvent density to use. If not specified, the default is used +from the solvent databases.

      • +
    +
    +
    +
    +
    +solvent_id_from_db#
    +
    + +
    +
    +solvent_db_path#
    +
    + +
    +
    +solvent_density#
    +
    + +
    +
    +molar_mass#
    +
    + +
    +
    +__len__()#
    +
    + +
    +
    +__str__()#
    +

    Return str(self).

    +
    + +
    +
    +_load_solvent(solvent: dict) → None#
    +

    Saves the fields from an adsorbate stored in a database. Fields added +after the first revision are conditionally added for backwards +compatibility with older database files.

    +
    + +
    +
    +property molecules_per_volume#
    +
    +Convert the solvent density in g/cm3 to the number of molecules per
    +
    +angstrom cubed of volume.
    +
    + +
    + +
    +
    + + + + +
    + + + + + + + + +
    + + + +
    + + +
    +
    + Contents +
    +
    + +
    + + +
    +
    + +
    + +
    + +

    +By FAIR Chemistry & Collaborators +

    + +
    + +
    + + +

    + + © Copyright 2024. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
    +
    + + +
    +
    +
    + + + + + +
    +
    + + \ No newline at end of file diff --git a/autoapi/data/oc/databases/index.html b/autoapi/data/oc/databases/index.html index 5dec28457d..3add3cb44c 100644 --- a/autoapi/data/oc/databases/index.html +++ b/autoapi/data/oc/databases/index.html @@ -62,7 +62,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -686,12 +689,12 @@

    Submodules

    previous

    -

    data.oc.core.slab

    +

    data.oc.core.solvent

     core.common.logger

  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -626,6 +629,8 @@

    Contents

  • Package Contents
    • @@ -651,6 +656,12 @@

    Attributes

    ADSORBATE_PKL_PATH

    +

    SOLVENT_PKL_PATH

    +

    + +

    ION_PKL_PATH

    +

    + @@ -667,6 +678,16 @@

    Package Contentsdata.oc.databases.pkls.ADSORBATE_PKL_PATH#
    +
    +
    +data.oc.databases.pkls.SOLVENT_PKL_PATH#
    +
    + +
    +
    +data.oc.databases.pkls.ION_PKL_PATH#
    +
    + @@ -738,6 +759,8 @@

    Package ContentsPackage Contents

    • diff --git a/autoapi/data/oc/databases/update/index.html b/autoapi/data/oc/databases/update/index.html index d9fa035087..8f1d388f8f 100644 --- a/autoapi/data/oc/databases/update/index.html +++ b/autoapi/data/oc/databases/update/index.html @@ -61,7 +61,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -730,11 +733,11 @@

    Module Contents

    next

    -

    data.oc.tests

    +

    data.oc.utils

     diff --git a/autoapi/data/oc/experimental/get_energies/index.html b/autoapi/data/oc/experimental/get_energies/index.html index 130cd32ebb..586300e259 100644 --- a/autoapi/data/oc/experimental/get_energies/index.html +++ b/autoapi/data/oc/experimental/get_energies/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/oc/experimental/merge_traj/index.html b/autoapi/data/oc/experimental/merge_traj/index.html index f0837b9b22..c5bd21577a 100644 --- a/autoapi/data/oc/experimental/merge_traj/index.html +++ b/autoapi/data/oc/experimental/merge_traj/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/oc/experimental/perturb_systems/index.html b/autoapi/data/oc/experimental/perturb_systems/index.html index 4274648d29..b3fe85be2e 100644 --- a/autoapi/data/oc/experimental/perturb_systems/index.html +++ b/autoapi/data/oc/experimental/perturb_systems/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/oc/experimental/rattle_test/index.html b/autoapi/data/oc/experimental/rattle_test/index.html index bcf122c019..7c005ba897 100644 --- a/autoapi/data/oc/experimental/rattle_test/index.html +++ b/autoapi/data/oc/experimental/rattle_test/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/oc/experimental/utils/index.html b/autoapi/data/oc/experimental/utils/index.html index 16a82de8a8..0618ab1b75 100644 --- a/autoapi/data/oc/experimental/utils/index.html +++ b/autoapi/data/oc/experimental/utils/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/oc/index.html b/autoapi/data/oc/index.html index 23557b63de..6362483969 100644 --- a/autoapi/data/oc/index.html +++ b/autoapi/data/oc/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -651,7 +654,6 @@

    Subpackagesdata.oc.core

  • data.oc.databases
    • -
  • data.oc.tests
  • data.oc.utils
    • diff --git a/autoapi/data/oc/scripts/precompute_sample_structures/index.html b/autoapi/data/oc/scripts/precompute_sample_structures/index.html index b9e87a0ed2..f35e31a735 100644 --- a/autoapi/data/oc/scripts/precompute_sample_structures/index.html +++ b/autoapi/data/oc/scripts/precompute_sample_structures/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/oc/structure_generator/index.html b/autoapi/data/oc/structure_generator/index.html index e4f6241c1c..7657969835 100644 --- a/autoapi/data/oc/structure_generator/index.html +++ b/autoapi/data/oc/structure_generator/index.html @@ -62,7 +62,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -847,12 +850,12 @@

    Module Contents

    previous

    -

    data.oc.utils.vasp

    +

    data.oc.utils.vasp_flags

     DOCUMENTATION_OPTIONS.pagename = 'autoapi/data/oc/utils/flag_anomaly/index'; - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -824,11 +827,11 @@

    Module Contents

    next

    -

    data.oc.utils.vasp

    +

    data.oc.utils.geometry

     diff --git a/autoapi/data/oc/utils/geometry/index.html b/autoapi/data/oc/utils/geometry/index.html new file mode 100644 index 0000000000..de9bc89dce --- /dev/null +++ b/autoapi/data/oc/utils/geometry/index.html @@ -0,0 +1,1020 @@ + + + + + + + + + + + data.oc.utils.geometry + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + +
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    + + + +
    +

    data.oc.utils.geometry

    + +
    + +
    +
    + + + + +
    + +
    +

    data.oc.utils.geometry#

    +
    +

    Classes#

    +
    + + + + + + + + + + + +

    Geometry

    Base class for geometries

    PlaneBoundTriclinicGeometry

    Triclinic crystal geometry based on ase.Atom cell

    BoxGeometry

    Box geometry for orthorhombic cells.

    +
    +
    +
    +

    Module Contents#

    +
    +
    +class data.oc.utils.geometry.Geometry#
    +

    Bases: abc.ABC

    +

    Base class for geometries

    +
    +
    +static distance_point_plane(vec: numpy.array, point_plane: numpy.array, point_ext: numpy.array)#
    +

    Returns the (shortest) distance between a plane with normal vector +‘vec’ through point ‘point_plane’ and a point ‘point_ext’.

    +
    +
    Parameters:
    +
      +

    • vec (np.array) – normal vector of plane

      • +

    • point_plane (np.array) – point on line

      • +

    • point_ext (np.array) – external point(s)

      • +
    +
    +
    Returns:
    +

    (np.array) Distance between plane and external point(s)

    +
    +
    +
    + +
    +
    +static vec_and_point_to_plane(vec: numpy.array, point: numpy.array)#
    +

    Returns the (unique) plane, given a normal vector ‘vec’ and a +point ‘point’ in the plane. ax + by + cz - d = 0

    +
    +
    Parameters:
    +
      +

    • vec (np.array) – normal vector of plane

      • +

    • point (np.array) – point in plane

      • +
    +
    +
    Returns:
    +

    (np.array) Paramterization of plane

    +
    +
    +
    + +
    +
    +static cell2planes(cell: ase.cell.Cell, pbc: float)#
    +

    Get the parameterization of the sizes of a ase.Atom cell

    +

    cell: ase.cell.Cell +pbc (float): shift of boundaries to be used with periodic boundary condition

    +
    +
    Return

    (List[np.array]) Parameterization of cell plane sides

    +
    +
    +

    3 planes intersect the origin by ase design.

    +
    + +
    +
    +static extract_box_properties(center: numpy.array, length: numpy.array, lo_corner: numpy.array, hi_corner: numpy.array)#
    +

    Given two of the properties ‘center’, ‘length’, ‘lo_corner’, +‘hi_corner’, return all the properties. The properties that +are not given are expected to be ‘None’.

    +
    + +
    +
    +abstract packmol_structure(filename: str, number: int, side: str)#
    +

    How to write packmol input file. To be defined by inherited class.

    +
    + +
    + +
    +
    +class data.oc.utils.geometry.PlaneBoundTriclinicGeometry(cell: ase.cell.Cell, pbc: float = 0.0)#
    +

    Bases: Geometry

    +

    Triclinic crystal geometry based on ase.Atom cell

    +
    +
    +planes#
    +
    + +
    +
    +cell#
    +
    + +
    +
    +ll_corner = [0, 0, 0]#
    +
    + +
    +
    +a#
    +
    + +
    +
    +b#
    +
    + +
    +
    +c#
    +
    + +
    +
    +ur_corner#
    +
    + +
    +
    +packmol_structure(filename: str, number: int, side: str)#
    +

    Make file structure to be used in packmol input script

    +
    +
    Parameters:
    +
      +

    • filename (str) – output filename to save structure

      • +

    • number (int) – number of solvent molecules

      • +

    • side (str) – pack solvent inside/outside of geometry

      • +
    +
    +
    Returns:
    +

    String with information about the structure

    +
    +
    +
    + +
    + +
    +
    +class data.oc.utils.geometry.BoxGeometry(center=None, length=None, lo_corner=None, hi_corner=None, **kwargs)#
    +

    Bases: Geometry

    +

    Box geometry for orthorhombic cells.

    +
    +
    +props#
    +
    + +
    +
    +params#
    +
    + +
    +
    +length#
    +
    + +
    +
    +__repr__()#
    +

    Return repr(self).

    +
    + +
    +
    +packmol_structure(filename: str, number: int, side: str)#
    +

    Make file structure to be used in packmol input script

    +
    +
    Parameters:
    +
      +

    • filename (str) – output filename to save structure

      • +

    • number (int) – number of solvent molecules

      • +

    • side (str) – pack solvent inside/outside of geometry

      • +
    +
    +
    Returns:
    +

    String with information about the structure

    +
    +
    +
    + +
    + +
    +
    + + + + +
    + + + + + + + + +
    + + + +
    + + +
    +
    + Contents +
    +
    + +
    + + +
    +
    + +
    + +
    + +

    +By FAIR Chemistry & Collaborators +

    + +
    + +
    + + +

    + + © Copyright 2024. +
    + +

    + +
    + +
    + +
    + +
    + +
    + +
    +
    + + +
    +
    +
    + + + + + +
    +
    + + \ No newline at end of file diff --git a/autoapi/data/oc/utils/index.html b/autoapi/data/oc/utils/index.html index 5589eb8075..3e27d04c83 100644 --- a/autoapi/data/oc/utils/index.html +++ b/autoapi/data/oc/utils/index.html @@ -62,7 +62,7 @@ - + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -659,7 +662,9 @@

    Submodules @@ -825,12 +830,12 @@

    Package Contents

    previous

    -

    data.oc.tests

    +

    data.oc.databases.update

     DOCUMENTATION_OPTIONS.pagename = 'autoapi/data/oc/utils/vasp/index'; - - + + @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -627,8 +630,6 @@

    Contents

  • Module Contents
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/odac/index.html b/autoapi/data/odac/index.html index 024a55653f..9747474626 100644 --- a/autoapi/data/odac/index.html +++ b/autoapi/data/odac/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/odac/promising_mof/promising_mof_energies/energy/index.html b/autoapi/data/odac/promising_mof/promising_mof_energies/energy/index.html index f8972ce45d..be5f7e4c4a 100644 --- a/autoapi/data/odac/promising_mof/promising_mof_energies/energy/index.html +++ b/autoapi/data/odac/promising_mof/promising_mof_energies/energy/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/odac/setup_vasp/index.html b/autoapi/data/odac/setup_vasp/index.html index 71c5f2028d..c8882f21a4 100644 --- a/autoapi/data/odac/setup_vasp/index.html +++ b/autoapi/data/odac/setup_vasp/index.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
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  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
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    • +
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    • +
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  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/om/biomolecules/geom/sample_geom_drugs/index.html b/autoapi/data/om/biomolecules/geom/sample_geom_drugs/index.html index d7f66197fc..e721157efe 100644 --- a/autoapi/data/om/biomolecules/geom/sample_geom_drugs/index.html +++ b/autoapi/data/om/biomolecules/geom/sample_geom_drugs/index.html @@ -305,6 +305,7 @@
  • core.common.logger
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  • core.common.registry
    • +
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  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
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  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/om/biomolecules/geom/write_geom_drugs_structures/index.html b/autoapi/data/om/biomolecules/geom/write_geom_drugs_structures/index.html index 8e03f2c8b1..a0735fb100 100644 --- a/autoapi/data/om/biomolecules/geom/write_geom_drugs_structures/index.html +++ b/autoapi/data/om/biomolecules/geom/write_geom_drugs_structures/index.html @@ -305,6 +305,7 @@
  • core.common.logger
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  • core.common.registry
    • +
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  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
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  • core.models.dimenet_plus_plus
    • +
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  • core.models.model_registry
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  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/om/index.html b/autoapi/data/om/index.html index 31b3b0856b..f376975882 100644 --- a/autoapi/data/om/index.html +++ b/autoapi/data/om/index.html @@ -305,6 +305,7 @@
  • core.common.logger
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    • +
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    • @@ -334,16 +335,17 @@
  • core.models.utils
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    • +
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  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
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    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/om/omdata/orca/calc/index.html b/autoapi/data/om/omdata/orca/calc/index.html index e4193ac71e..94a82f8fc7 100644 --- a/autoapi/data/om/omdata/orca/calc/index.html +++ b/autoapi/data/om/omdata/orca/calc/index.html @@ -303,6 +303,7 @@
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    • +
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  • core.common.tutorial_utils
    • @@ -332,16 +333,17 @@
  • core.models.utils
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    • +
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  • core.models.schnet
  • core.modules
    @@ -354,6 +356,8 @@
  • core.scripts.hpo
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    • +
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    • +
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  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -379,7 +383,6 @@
  • data.oc
    diff --git a/autoapi/data/om/omdata/orca/index.html b/autoapi/data/om/omdata/orca/index.html index 330aa90b14..5fd92e1a91 100644 --- a/autoapi/data/om/omdata/orca/index.html +++ b/autoapi/data/om/omdata/orca/index.html @@ -305,6 +305,7 @@
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    • +
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    • @@ -334,16 +335,17 @@
  • core.models.utils
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    • +
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  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
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    • +
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    • +
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  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/data/om/omdata/orca/recipes/index.html b/autoapi/data/om/omdata/orca/recipes/index.html index 183346bdae..de9585b77d 100644 --- a/autoapi/data/om/omdata/orca/recipes/index.html +++ b/autoapi/data/om/omdata/orca/recipes/index.html @@ -303,6 +303,7 @@
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    • +
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    • @@ -332,16 +333,17 @@
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    • +
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  • core.modules
    @@ -354,6 +356,8 @@
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    • +
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    • +
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  • core.scripts.make_lmdb_sizes
    • @@ -379,7 +383,6 @@
  • data.oc
    diff --git a/autoapi/index.html b/autoapi/index.html index 968e8e54e9..02975744ad 100644 --- a/autoapi/index.html +++ b/autoapi/index.html @@ -307,6 +307,7 @@
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    • +
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    • @@ -336,16 +337,17 @@
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    @@ -358,6 +360,8 @@
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    • @@ -383,7 +387,6 @@
  • data.oc
    @@ -650,6 +653,7 @@

    API Referencecore.common.logger

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  • core.common.registry
    • +
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    • @@ -774,11 +778,18 @@

    API Referencecore.models.base

  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
  • data.oc.databases
    • -
  • data.oc.tests
  • data.oc.utils
  • data.oc.structure_generator
    • diff --git a/autoapi/ocpapi/client/client/index.html b/autoapi/ocpapi/client/client/index.html index 708b3f2637..e9ac8a56f2 100644 --- a/autoapi/ocpapi/client/client/index.html +++ b/autoapi/ocpapi/client/client/index.html @@ -305,6 +305,7 @@
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    • +
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  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
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  • core.models.dimenet_plus_plus
    • +
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  • core.modules
    @@ -356,6 +358,8 @@
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  • core.scripts.download_large_files
    • +
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    • +
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  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/client/index.html b/autoapi/ocpapi/client/index.html index 8c87b80214..157ca1aa65 100644 --- a/autoapi/ocpapi/client/index.html +++ b/autoapi/ocpapi/client/index.html @@ -305,6 +305,7 @@
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    • +
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  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
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  • core.models.dimenet_plus_plus
    • +
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  • core.modules
    @@ -356,6 +358,8 @@
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    • +
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    • +
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  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/client/models/index.html b/autoapi/ocpapi/client/models/index.html index 069ef9737f..231c878abe 100644 --- a/autoapi/ocpapi/client/models/index.html +++ b/autoapi/ocpapi/client/models/index.html @@ -305,6 +305,7 @@
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    • +
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    • @@ -334,16 +335,17 @@
  • core.models.utils
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    • +
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  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
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    • +
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    • +
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  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/client/ui/index.html b/autoapi/ocpapi/client/ui/index.html index 75173b2ee7..9ea6785f6e 100644 --- a/autoapi/ocpapi/client/ui/index.html +++ b/autoapi/ocpapi/client/ui/index.html @@ -305,6 +305,7 @@
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    • +
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    • @@ -334,16 +335,17 @@
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  • core.models.dimenet_plus_plus
    • +
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  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
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    • +
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    • +
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  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/index.html b/autoapi/ocpapi/index.html index 943e8d05ae..8f221c635f 100644 --- a/autoapi/ocpapi/index.html +++ b/autoapi/ocpapi/index.html @@ -305,6 +305,7 @@
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    • +
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  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
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  • core.models.dimenet_plus_plus
    • +
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  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
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  • core.scripts.download_large_files
    • +
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    • +
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  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/version/index.html b/autoapi/ocpapi/version/index.html index 68afa7b202..b0cb17b183 100644 --- a/autoapi/ocpapi/version/index.html +++ b/autoapi/ocpapi/version/index.html @@ -305,6 +305,7 @@
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    • +
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    • @@ -334,16 +335,17 @@
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  • core.models.dimenet_plus_plus
    • +
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  • core.models.model_registry
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  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
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  • core.scripts.download_large_files
    • +
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    • +
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  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/workflows/adsorbates/index.html b/autoapi/ocpapi/workflows/adsorbates/index.html index 9df8f02d78..24d63c9f0d 100644 --- a/autoapi/ocpapi/workflows/adsorbates/index.html +++ b/autoapi/ocpapi/workflows/adsorbates/index.html @@ -305,6 +305,7 @@
  • core.common.logger
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    • +
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  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
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  • core.models.dimenet_plus_plus
    • +
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  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
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    • +
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    • +
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  • core.scripts.make_challenge_submission_file
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    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/workflows/context/index.html b/autoapi/ocpapi/workflows/context/index.html index 338adaefdb..a42a2a5064 100644 --- a/autoapi/ocpapi/workflows/context/index.html +++ b/autoapi/ocpapi/workflows/context/index.html @@ -305,6 +305,7 @@
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    • +
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    • @@ -334,16 +335,17 @@
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    • +
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    @@ -356,6 +358,8 @@
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    • +
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    • +
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    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/workflows/filter/index.html b/autoapi/ocpapi/workflows/filter/index.html index d6c5e8f033..e0db9ff6a1 100644 --- a/autoapi/ocpapi/workflows/filter/index.html +++ b/autoapi/ocpapi/workflows/filter/index.html @@ -305,6 +305,7 @@
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    • +
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    • @@ -334,16 +335,17 @@
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    • +
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    @@ -356,6 +358,8 @@
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    • +
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    • +
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    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/workflows/index.html b/autoapi/ocpapi/workflows/index.html index f421be4613..4fda283e4c 100644 --- a/autoapi/ocpapi/workflows/index.html +++ b/autoapi/ocpapi/workflows/index.html @@ -305,6 +305,7 @@
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    • +
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  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
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    • +
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    @@ -356,6 +358,8 @@
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    • +
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    • +
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    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/workflows/log/index.html b/autoapi/ocpapi/workflows/log/index.html index 4b4e7173e4..a659fd67db 100644 --- a/autoapi/ocpapi/workflows/log/index.html +++ b/autoapi/ocpapi/workflows/log/index.html @@ -305,6 +305,7 @@
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    • +
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    • @@ -334,16 +335,17 @@
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    • +
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    @@ -356,6 +358,8 @@
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    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/autoapi/ocpapi/workflows/retry/index.html b/autoapi/ocpapi/workflows/retry/index.html index 67ca33d3e5..efcfd66278 100644 --- a/autoapi/ocpapi/workflows/retry/index.html +++ b/autoapi/ocpapi/workflows/retry/index.html @@ -305,6 +305,7 @@
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    • @@ -381,7 +385,6 @@
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    diff --git a/core/ase_dataset_creation.html b/core/ase_dataset_creation.html index 96bea84a00..20ec9c378a 100644 --- a/core/ase_dataset_creation.html +++ b/core/ase_dataset_creation.html @@ -305,6 +305,7 @@
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    @@ -356,6 +358,8 @@
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    • @@ -381,7 +385,6 @@
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    diff --git a/core/datasets/oc20.html b/core/datasets/oc20.html index b0c35736a1..a032eecaf4 100644 --- a/core/datasets/oc20.html +++ b/core/datasets/oc20.html @@ -305,6 +305,7 @@
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    • @@ -334,16 +335,17 @@
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    @@ -356,6 +358,8 @@
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    • @@ -381,7 +385,6 @@
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    diff --git a/core/datasets/oc20dense.html b/core/datasets/oc20dense.html index aee9c2362b..254324f596 100644 --- a/core/datasets/oc20dense.html +++ b/core/datasets/oc20dense.html @@ -305,6 +305,7 @@
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    @@ -356,6 +358,8 @@
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    diff --git a/core/datasets/oc20neb.html b/core/datasets/oc20neb.html index 20aefe617f..3bc66d1b55 100644 --- a/core/datasets/oc20neb.html +++ b/core/datasets/oc20neb.html @@ -305,6 +305,7 @@
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    @@ -356,6 +358,8 @@
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  • data.oc
    diff --git a/core/datasets/oc22.html b/core/datasets/oc22.html index 4fb0b48619..7e057386aa 100644 --- a/core/datasets/oc22.html +++ b/core/datasets/oc22.html @@ -305,6 +305,7 @@
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    • @@ -334,16 +335,17 @@
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    @@ -356,6 +358,8 @@
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    diff --git a/core/datasets/odac.html b/core/datasets/odac.html index 1c6a670222..36c041e186 100644 --- a/core/datasets/odac.html +++ b/core/datasets/odac.html @@ -305,6 +305,7 @@
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    • @@ -334,16 +335,17 @@
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    @@ -356,6 +358,8 @@
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    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/core/fine-tuning/fine-tuning-oxides.html b/core/fine-tuning/fine-tuning-oxides.html index 6ed4010fb5..6508c0c7b9 100644 --- a/core/fine-tuning/fine-tuning-oxides.html +++ b/core/fine-tuning/fine-tuning-oxides.html @@ -305,6 +305,7 @@
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    • @@ -334,16 +335,17 @@
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    @@ -356,6 +358,8 @@
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    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -831,10 +834,10 @@

    Fine tuning a model -
    Elapsed time 68.3 seconds.
+
    Elapsed time 85.7 seconds.
 
    
 
    
-../../_images/e09235df67f6a4f604e2dc396140b3979de3a415db6696093790df3189ca2edf.png
+../../_images/341531b0218eea408d04046d981d55fe218d43494f1ecf51297aeefb6668761e.png
    @@ -865,7 +868,7 @@

    Fine tuning a model -../../_images/ac62bef9bb42a8dd7dd1f92200161f8670209306f784fd9ebc25a09415ef715b.png +../../_images/06bfbae8ad0fd185eb61fd56188dac1591ce89e9e71d245404f81779a21d57fd.png

    We can improve this by fine-tuning the model.

    @@ -910,7 +913,7 @@

    Fine tuning the checkpoint -
    /tmp/ipykernel_2319/1448814737.py:12: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2304/1448814737.py:12: DeprecationWarning: Please use atoms.calc = calc
   atoms.set_calculator(calc)
 
    
 
    
@@ -1203,7 +1206,7 @@ 
    Running the training jobHide code cell output
 
 
    
-
    Elapsed time = 202.0 seconds
+
    Elapsed time = 209.6 seconds
 
    
 
    
 
    
@@ -1219,7 +1222,7 @@ 
    Running the training job
-
    'fine-tuning/checkpoints/2024-08-03-02-08-00-ft-oxides'
+
    'fine-tuning/checkpoints/2024-08-14-00-49-04-ft-oxides'
 
    
 
    
 
    
@@ -1278,7 +1281,7 @@ 
    Running the training job
-../../_images/e7ce684c03eda3f18545b9385f2ed3f95fe9fdaea9a1fa0ad15e5a88f24474eb.png
+../../_images/3816f188adda51da6bba2f3ddd2f58b75389bf4fe2c38c5be2797959e6141007.png
 
    
 
    
 
    
@@ -1289,7 +1292,7 @@ 
    Running the training job
-
    New MAE = 0.986 eV/atom
+
    New MAE = 0.449 eV/atom
 
    
 
    
 
    
@@ -1308,7 +1311,7 @@ 
    Running the training job
-../../_images/ad1d711bb77a15852a06b27c3f353d97e613c695ca9499873d11a81c9a482bde.png
+../../_images/93fd374619c9385d5f826655d6448bf6324a1c298de48748d5ca06bd521a1ada.png
 
    
 
    
 
    It is possible to continue refining the fit. The simple things to do are to use more epochs of training. Eventually the MAE will stabilize, and then it may be necessary to adjust other optimization parameters like the learning rate (usually you decrease it).
    
diff --git a/core/gotchas.html b/core/gotchas.html
index d3ba497869..5f525b0e8b 100644
--- a/core/gotchas.html
+++ b/core/gotchas.html
@@ -305,6 +305,7 @@
 
  • core.common.logger
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+
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+
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    @@ -356,6 +358,8 @@
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    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -748,23 +751,23 @@

    I want the energy of a gas phase atom 114 with ctx_factory(): --> 115 return func(*args, **kwargs) -File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:430, in OCPTrainer.predict(self, data_loader, per_image, results_file, disable_tqdm) - 422 for _i, batch in tqdm( - 423 enumerate(data_loader), - 424 total=len(data_loader), +File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:443, in OCPTrainer.predict(self, data_loader, per_image, results_file, disable_tqdm) + 435 for _, batch in tqdm( + 436 enumerate(data_loader), + 437 total=len(data_loader), (...) - 427 disable=disable_tqdm, - 428 ): - 429 with torch.cuda.amp.autocast(enabled=self.scaler is not None): ---> 430 out = self._forward(batch) - 432 for target_key in self.config["outputs"]: - 433 pred = out[target_key] - -File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:231, in OCPTrainer._forward(self, batch) - 230 def _forward(self, batch): ---> 231 out = self.model(batch.to(self.device)) - 233 ### TODO: Move into BaseModel in OCP 2.0 - 234 outputs = {} + 440 disable=disable_tqdm, + 441 ): + 442 with torch.cuda.amp.autocast(enabled=self.scaler is not None): +--> 443 out = self._forward(batch) + 445 for target_key in self.config["outputs"]: + 446 pred = self._denorm_preds(target_key, out[target_key], batch) + +File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:246, in OCPTrainer._forward(self, batch) + 245 def _forward(self, batch): +--> 246 out = self.model(batch.to(self.device)) + 248 outputs = {} + 249 batch_size = batch.natoms.numel() File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs) 1509 return self._compiled_call_impl(*args, **kwargs) # type: ignore[misc] @@ -781,58 +784,58 @@

    I want the energy of a gas phase atom 1522 try: 1523 result = None -File ~/work/fairchem/fairchem/src/fairchem/core/common/utils.py:162, in conditional_grad.<locals>.decorator.<locals>.cls_method(self, *args, **kwargs) - 160 if self.regress_forces and not getattr(self, "direct_forces", 0): - 161 f = dec(func) ---> 162 return f(self, *args, **kwargs) +File ~/work/fairchem/fairchem/src/fairchem/core/common/utils.py:163, in conditional_grad.<locals>.decorator.<locals>.cls_method(self, *args, **kwargs) + 161 if self.regress_forces and not getattr(self, "direct_forces", 0): + 162 f = dec(func) +--> 163 return f(self, *args, **kwargs) -File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1214, in GemNetOC.forward(self, data) - 1192 ( - 1193 main_graph, - 1194 a2a_graph, +File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1218, in GemNetOC.forward(self, data) + 1196 ( + 1197 main_graph, + 1198 a2a_graph, (...) - 1201 quad_idx, - 1202 ) = self.get_graphs_and_indices(data) - 1203 _, idx_t = main_graph["edge_index"] - 1205 ( - 1206 basis_rad_raw, - 1207 basis_atom_update, - 1208 basis_output, - 1209 bases_qint, - 1210 bases_e2e, - 1211 bases_a2e, - 1212 bases_e2a, - 1213 basis_a2a_rad, --> 1214 ) = self.get_bases( - 1215 main_graph=main_graph, - 1216 a2a_graph=a2a_graph, - 1217 a2ee2a_graph=a2ee2a_graph, - 1218 qint_graph=qint_graph, - 1219 trip_idx_e2e=trip_idx_e2e, - 1220 trip_idx_a2e=trip_idx_a2e, - 1221 trip_idx_e2a=trip_idx_e2a, - 1222 quad_idx=quad_idx, - 1223 num_atoms=num_atoms, - 1224 ) - 1226 # Embedding block - 1227 h = self.atom_emb(atomic_numbers) - -File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1087, in GemNetOC.get_bases(self, main_graph, a2a_graph, a2ee2a_graph, qint_graph, trip_idx_e2e, trip_idx_a2e, trip_idx_e2a, quad_idx, num_atoms) - 1078 cosφ_cab_q, cosφ_abd, angle_cabd = self.calculate_quad_angles( - 1079 main_graph["vector"], - 1080 qint_graph["vector"], - 1081 quad_idx, - 1082 ) - 1084 basis_rad_cir_qint_raw, basis_cir_qint_raw = self.cbf_basis_qint( - 1085 qint_graph["distance"], cosφ_abd + 1205 quad_idx, + 1206 ) = self.get_graphs_and_indices(data) + 1207 _, idx_t = main_graph["edge_index"] + 1209 ( + 1210 basis_rad_raw, + 1211 basis_atom_update, + 1212 basis_output, + 1213 bases_qint, + 1214 bases_e2e, + 1215 bases_a2e, + 1216 bases_e2a, + 1217 basis_a2a_rad, +-> 1218 ) = self.get_bases( + 1219 main_graph=main_graph, + 1220 a2a_graph=a2a_graph, + 1221 a2ee2a_graph=a2ee2a_graph, + 1222 qint_graph=qint_graph, + 1223 trip_idx_e2e=trip_idx_e2e, + 1224 trip_idx_a2e=trip_idx_a2e, + 1225 trip_idx_e2a=trip_idx_e2a, + 1226 quad_idx=quad_idx, + 1227 num_atoms=num_atoms, + 1228 ) + 1230 # Embedding block + 1231 h = self.atom_emb(atomic_numbers) + +File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1091, in GemNetOC.get_bases(self, main_graph, a2a_graph, a2ee2a_graph, qint_graph, trip_idx_e2e, trip_idx_a2e, trip_idx_e2a, quad_idx, num_atoms) + 1082 cosφ_cab_q, cosφ_abd, angle_cabd = self.calculate_quad_angles( + 1083 main_graph["vector"], + 1084 qint_graph["vector"], + 1085 quad_idx, 1086 ) --> 1087 basis_rad_sph_qint_raw, basis_sph_qint_raw = self.sbf_basis_qint( - 1088 main_graph["distance"], - 1089 cosφ_cab_q[quad_idx["trip_out_to_quad"]], - 1090 angle_cabd, - 1091 ) - 1092 if self.atom_edge_interaction: - 1093 basis_rad_a2ee2a_raw = self.radial_basis_aeaint(a2ee2a_graph["distance"]) + 1088 basis_rad_cir_qint_raw, basis_cir_qint_raw = self.cbf_basis_qint( + 1089 qint_graph["distance"], cosφ_abd + 1090 ) +-> 1091 basis_rad_sph_qint_raw, basis_sph_qint_raw = self.sbf_basis_qint( + 1092 main_graph["distance"], + 1093 cosφ_cab_q[quad_idx["trip_out_to_quad"]], + 1094 angle_cabd, + 1095 ) + 1096 if self.atom_edge_interaction: + 1097 basis_rad_a2ee2a_raw = self.radial_basis_aeaint(a2ee2a_graph["distance"]) File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs) 1509 return self._compiled_call_impl(*args, **kwargs) # type: ignore[misc] @@ -923,14 +926,16 @@

    I get wildly different energies from the different models
    WARNING:root:Using `weight_decay` from `optim` instead of `optim.optimizer_params`.Please update your config to use `optim.optimizer_params.weight_decay`.`optim.weight_decay` will soon be deprecated.
    -
    WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+
    /home/runner/work/fairchem/fairchem/src/fairchem/core/modules/normalization/normalizer.py:69: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
+  "mean": torch.tensor(state_dict["mean"]),
+WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 
    
 
    
-
    /tmp/ipykernel_2654/2356712572.py:11: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2626/2356712572.py:11: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 
    
 
    
-
    1.2779738903045654
+
    1.2851653099060059
 
    
 
    
 
    
@@ -963,11 +968,11 @@ 
    I get wildly different energies from the different models
    WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 
    
 
    
-
    /tmp/ipykernel_2654/2054440827.py:9: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2626/2054440827.py:9: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 
    
 
    
-
    -110.3986587524414
+
    -110.40040588378906
 
    
 
    
 
    
@@ -989,14 +994,16 @@ 
    I get wildly different energies from the different models
    WARNING:root:Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
 
    
 
    
-
    WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+
    /home/runner/work/fairchem/fairchem/src/fairchem/core/modules/normalization/normalizer.py:69: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
+  "mean": torch.tensor(state_dict["mean"]),
+WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 
    
 
    
-
    /tmp/ipykernel_2654/1817216860.py:7: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2626/1817216860.py:7: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 
    
 
    
-
    1.677858829498291
+
    1.6737589836120605
 
    
 
    
 
    
@@ -1116,23 +1123,23 @@ 
    You need at least four atoms for molecules with some models    114     with ctx_factory():
 --> 115         return func(*args, **kwargs)
 
-File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:430, in OCPTrainer.predict(self, data_loader, per_image, results_file, disable_tqdm)
-    422 for _i, batch in tqdm(
-    423     enumerate(data_loader),
-    424     total=len(data_loader),
+File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:443, in OCPTrainer.predict(self, data_loader, per_image, results_file, disable_tqdm)
+    435 for _, batch in tqdm(
+    436     enumerate(data_loader),
+    437     total=len(data_loader),
    (...)
-    427     disable=disable_tqdm,
-    428 ):
-    429     with torch.cuda.amp.autocast(enabled=self.scaler is not None):
---> 430         out = self._forward(batch)
-    432     for target_key in self.config["outputs"]:
-    433         pred = out[target_key]
-
-File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:231, in OCPTrainer._forward(self, batch)
-    230 def _forward(self, batch):
---> 231     out = self.model(batch.to(self.device))
-    233     ### TODO: Move into BaseModel in OCP 2.0
-    234     outputs = {}
+    440     disable=disable_tqdm,
+    441 ):
+    442     with torch.cuda.amp.autocast(enabled=self.scaler is not None):
+--> 443         out = self._forward(batch)
+    445     for target_key in self.config["outputs"]:
+    446         pred = self._denorm_preds(target_key, out[target_key], batch)
+
+File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:246, in OCPTrainer._forward(self, batch)
+    245 def _forward(self, batch):
+--> 246     out = self.model(batch.to(self.device))
+    248     outputs = {}
+    249     batch_size = batch.natoms.numel()
 
 File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs)
    1509     return self._compiled_call_impl(*args, **kwargs)  # type: ignore[misc]
@@ -1149,58 +1156,58 @@ 
    You need at least four atoms for molecules with some models   1522 try:
    1523     result = None
 
-File ~/work/fairchem/fairchem/src/fairchem/core/common/utils.py:162, in conditional_grad.<locals>.decorator.<locals>.cls_method(self, *args, **kwargs)
-    160 if self.regress_forces and not getattr(self, "direct_forces", 0):
-    161     f = dec(func)
---> 162 return f(self, *args, **kwargs)
+File ~/work/fairchem/fairchem/src/fairchem/core/common/utils.py:163, in conditional_grad.<locals>.decorator.<locals>.cls_method(self, *args, **kwargs)
+    161 if self.regress_forces and not getattr(self, "direct_forces", 0):
+    162     f = dec(func)
+--> 163 return f(self, *args, **kwargs)
 
-File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1214, in GemNetOC.forward(self, data)
-   1192 (
-   1193     main_graph,
-   1194     a2a_graph,
+File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1218, in GemNetOC.forward(self, data)
+   1196 (
+   1197     main_graph,
+   1198     a2a_graph,
    (...)
-   1201     quad_idx,
-   1202 ) = self.get_graphs_and_indices(data)
-   1203 _, idx_t = main_graph["edge_index"]
-   1205 (
-   1206     basis_rad_raw,
-   1207     basis_atom_update,
-   1208     basis_output,
-   1209     bases_qint,
-   1210     bases_e2e,
-   1211     bases_a2e,
-   1212     bases_e2a,
-   1213     basis_a2a_rad,
--> 1214 ) = self.get_bases(
-   1215     main_graph=main_graph,
-   1216     a2a_graph=a2a_graph,
-   1217     a2ee2a_graph=a2ee2a_graph,
-   1218     qint_graph=qint_graph,
-   1219     trip_idx_e2e=trip_idx_e2e,
-   1220     trip_idx_a2e=trip_idx_a2e,
-   1221     trip_idx_e2a=trip_idx_e2a,
-   1222     quad_idx=quad_idx,
-   1223     num_atoms=num_atoms,
-   1224 )
-   1226 # Embedding block
-   1227 h = self.atom_emb(atomic_numbers)
-
-File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1087, in GemNetOC.get_bases(self, main_graph, a2a_graph, a2ee2a_graph, qint_graph, trip_idx_e2e, trip_idx_a2e, trip_idx_e2a, quad_idx, num_atoms)
-   1078     cosφ_cab_q, cosφ_abd, angle_cabd = self.calculate_quad_angles(
-   1079         main_graph["vector"],
-   1080         qint_graph["vector"],
-   1081         quad_idx,
-   1082     )
-   1084     basis_rad_cir_qint_raw, basis_cir_qint_raw = self.cbf_basis_qint(
-   1085         qint_graph["distance"], cosφ_abd
+   1205     quad_idx,
+   1206 ) = self.get_graphs_and_indices(data)
+   1207 _, idx_t = main_graph["edge_index"]
+   1209 (
+   1210     basis_rad_raw,
+   1211     basis_atom_update,
+   1212     basis_output,
+   1213     bases_qint,
+   1214     bases_e2e,
+   1215     bases_a2e,
+   1216     bases_e2a,
+   1217     basis_a2a_rad,
+-> 1218 ) = self.get_bases(
+   1219     main_graph=main_graph,
+   1220     a2a_graph=a2a_graph,
+   1221     a2ee2a_graph=a2ee2a_graph,
+   1222     qint_graph=qint_graph,
+   1223     trip_idx_e2e=trip_idx_e2e,
+   1224     trip_idx_a2e=trip_idx_a2e,
+   1225     trip_idx_e2a=trip_idx_e2a,
+   1226     quad_idx=quad_idx,
+   1227     num_atoms=num_atoms,
+   1228 )
+   1230 # Embedding block
+   1231 h = self.atom_emb(atomic_numbers)
+
+File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1091, in GemNetOC.get_bases(self, main_graph, a2a_graph, a2ee2a_graph, qint_graph, trip_idx_e2e, trip_idx_a2e, trip_idx_e2a, quad_idx, num_atoms)
+   1082     cosφ_cab_q, cosφ_abd, angle_cabd = self.calculate_quad_angles(
+   1083         main_graph["vector"],
+   1084         qint_graph["vector"],
+   1085         quad_idx,
    1086     )
--> 1087     basis_rad_sph_qint_raw, basis_sph_qint_raw = self.sbf_basis_qint(
-   1088         main_graph["distance"],
-   1089         cosφ_cab_q[quad_idx["trip_out_to_quad"]],
-   1090         angle_cabd,
-   1091     )
-   1092 if self.atom_edge_interaction:
-   1093     basis_rad_a2ee2a_raw = self.radial_basis_aeaint(a2ee2a_graph["distance"])
+   1088     basis_rad_cir_qint_raw, basis_cir_qint_raw = self.cbf_basis_qint(
+   1089         qint_graph["distance"], cosφ_abd
+   1090     )
+-> 1091     basis_rad_sph_qint_raw, basis_sph_qint_raw = self.sbf_basis_qint(
+   1092         main_graph["distance"],
+   1093         cosφ_cab_q[quad_idx["trip_out_to_quad"]],
+   1094         angle_cabd,
+   1095     )
+   1096 if self.atom_edge_interaction:
+   1097     basis_rad_a2ee2a_raw = self.radial_basis_aeaint(a2ee2a_graph["distance"])
 
 File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs)
    1509     return self._compiled_call_impl(*args, **kwargs)  # type: ignore[misc]
@@ -1326,23 +1333,23 @@ 
    To tag or not?    114     with ctx_factory():
 --> 115         return func(*args, **kwargs)
 
-File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:430, in OCPTrainer.predict(self, data_loader, per_image, results_file, disable_tqdm)
-    422 for _i, batch in tqdm(
-    423     enumerate(data_loader),
-    424     total=len(data_loader),
+File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:443, in OCPTrainer.predict(self, data_loader, per_image, results_file, disable_tqdm)
+    435 for _, batch in tqdm(
+    436     enumerate(data_loader),
+    437     total=len(data_loader),
    (...)
-    427     disable=disable_tqdm,
-    428 ):
-    429     with torch.cuda.amp.autocast(enabled=self.scaler is not None):
---> 430         out = self._forward(batch)
-    432     for target_key in self.config["outputs"]:
-    433         pred = out[target_key]
-
-File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:231, in OCPTrainer._forward(self, batch)
-    230 def _forward(self, batch):
---> 231     out = self.model(batch.to(self.device))
-    233     ### TODO: Move into BaseModel in OCP 2.0
-    234     outputs = {}
+    440     disable=disable_tqdm,
+    441 ):
+    442     with torch.cuda.amp.autocast(enabled=self.scaler is not None):
+--> 443         out = self._forward(batch)
+    445     for target_key in self.config["outputs"]:
+    446         pred = self._denorm_preds(target_key, out[target_key], batch)
+
+File ~/work/fairchem/fairchem/src/fairchem/core/trainers/ocp_trainer.py:246, in OCPTrainer._forward(self, batch)
+    245 def _forward(self, batch):
+--> 246     out = self.model(batch.to(self.device))
+    248     outputs = {}
+    249     batch_size = batch.natoms.numel()
 
 File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs)
    1509     return self._compiled_call_impl(*args, **kwargs)  # type: ignore[misc]
@@ -1359,58 +1366,58 @@ 
    To tag or not?   1522 try:
    1523     result = None
 
-File ~/work/fairchem/fairchem/src/fairchem/core/common/utils.py:162, in conditional_grad.<locals>.decorator.<locals>.cls_method(self, *args, **kwargs)
-    160 if self.regress_forces and not getattr(self, "direct_forces", 0):
-    161     f = dec(func)
---> 162 return f(self, *args, **kwargs)
+File ~/work/fairchem/fairchem/src/fairchem/core/common/utils.py:163, in conditional_grad.<locals>.decorator.<locals>.cls_method(self, *args, **kwargs)
+    161 if self.regress_forces and not getattr(self, "direct_forces", 0):
+    162     f = dec(func)
+--> 163 return f(self, *args, **kwargs)
 
-File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1214, in GemNetOC.forward(self, data)
-   1192 (
-   1193     main_graph,
-   1194     a2a_graph,
+File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1218, in GemNetOC.forward(self, data)
+   1196 (
+   1197     main_graph,
+   1198     a2a_graph,
    (...)
-   1201     quad_idx,
-   1202 ) = self.get_graphs_and_indices(data)
-   1203 _, idx_t = main_graph["edge_index"]
-   1205 (
-   1206     basis_rad_raw,
-   1207     basis_atom_update,
-   1208     basis_output,
-   1209     bases_qint,
-   1210     bases_e2e,
-   1211     bases_a2e,
-   1212     bases_e2a,
-   1213     basis_a2a_rad,
--> 1214 ) = self.get_bases(
-   1215     main_graph=main_graph,
-   1216     a2a_graph=a2a_graph,
-   1217     a2ee2a_graph=a2ee2a_graph,
-   1218     qint_graph=qint_graph,
-   1219     trip_idx_e2e=trip_idx_e2e,
-   1220     trip_idx_a2e=trip_idx_a2e,
-   1221     trip_idx_e2a=trip_idx_e2a,
-   1222     quad_idx=quad_idx,
-   1223     num_atoms=num_atoms,
-   1224 )
-   1226 # Embedding block
-   1227 h = self.atom_emb(atomic_numbers)
-
-File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1087, in GemNetOC.get_bases(self, main_graph, a2a_graph, a2ee2a_graph, qint_graph, trip_idx_e2e, trip_idx_a2e, trip_idx_e2a, quad_idx, num_atoms)
-   1078     cosφ_cab_q, cosφ_abd, angle_cabd = self.calculate_quad_angles(
-   1079         main_graph["vector"],
-   1080         qint_graph["vector"],
-   1081         quad_idx,
-   1082     )
-   1084     basis_rad_cir_qint_raw, basis_cir_qint_raw = self.cbf_basis_qint(
-   1085         qint_graph["distance"], cosφ_abd
+   1205     quad_idx,
+   1206 ) = self.get_graphs_and_indices(data)
+   1207 _, idx_t = main_graph["edge_index"]
+   1209 (
+   1210     basis_rad_raw,
+   1211     basis_atom_update,
+   1212     basis_output,
+   1213     bases_qint,
+   1214     bases_e2e,
+   1215     bases_a2e,
+   1216     bases_e2a,
+   1217     basis_a2a_rad,
+-> 1218 ) = self.get_bases(
+   1219     main_graph=main_graph,
+   1220     a2a_graph=a2a_graph,
+   1221     a2ee2a_graph=a2ee2a_graph,
+   1222     qint_graph=qint_graph,
+   1223     trip_idx_e2e=trip_idx_e2e,
+   1224     trip_idx_a2e=trip_idx_a2e,
+   1225     trip_idx_e2a=trip_idx_e2a,
+   1226     quad_idx=quad_idx,
+   1227     num_atoms=num_atoms,
+   1228 )
+   1230 # Embedding block
+   1231 h = self.atom_emb(atomic_numbers)
+
+File ~/work/fairchem/fairchem/src/fairchem/core/models/gemnet_oc/gemnet_oc.py:1091, in GemNetOC.get_bases(self, main_graph, a2a_graph, a2ee2a_graph, qint_graph, trip_idx_e2e, trip_idx_a2e, trip_idx_e2a, quad_idx, num_atoms)
+   1082     cosφ_cab_q, cosφ_abd, angle_cabd = self.calculate_quad_angles(
+   1083         main_graph["vector"],
+   1084         qint_graph["vector"],
+   1085         quad_idx,
    1086     )
--> 1087     basis_rad_sph_qint_raw, basis_sph_qint_raw = self.sbf_basis_qint(
-   1088         main_graph["distance"],
-   1089         cosφ_cab_q[quad_idx["trip_out_to_quad"]],
-   1090         angle_cabd,
-   1091     )
-   1092 if self.atom_edge_interaction:
-   1093     basis_rad_a2ee2a_raw = self.radial_basis_aeaint(a2ee2a_graph["distance"])
+   1088     basis_rad_cir_qint_raw, basis_cir_qint_raw = self.cbf_basis_qint(
+   1089         qint_graph["distance"], cosφ_abd
+   1090     )
+-> 1091     basis_rad_sph_qint_raw, basis_sph_qint_raw = self.sbf_basis_qint(
+   1092         main_graph["distance"],
+   1093         cosφ_cab_q[quad_idx["trip_out_to_quad"]],
+   1094         angle_cabd,
+   1095     )
+   1096 if self.atom_edge_interaction:
+   1097     basis_rad_a2ee2a_raw = self.radial_basis_aeaint(a2ee2a_graph["distance"])
 
 File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/nn/modules/module.py:1511, in Module._wrapped_call_impl(self, *args, **kwargs)
    1509     return self._compiled_call_impl(*args, **kwargs)  # type: ignore[misc]
@@ -1461,7 +1468,7 @@ 
    To tag or not?
-
    /tmp/ipykernel_2654/3906293788.py:3: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2626/3906293788.py:3: DeprecationWarning: Please use atoms.calc = calc
   atoms.set_calculator(calc)
 
    
 
    
@@ -1490,7 +1497,9 @@ 
    To tag or not?
    WARNING:root:Skipping scheduler setup. No training set found.
 
    
 
    
-
    WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+
    /home/runner/work/fairchem/fairchem/src/fairchem/core/modules/normalization/normalizer.py:69: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
+  "mean": torch.tensor(state_dict["mean"]),
+WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 
    
 
    
 
    
@@ -1505,11 +1514,11 @@ 
    To tag or not?
-
    /tmp/ipykernel_2654/4094489779.py:3: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2626/4094489779.py:3: DeprecationWarning: Please use atoms.calc = calc
   atoms.set_calculator(calc)
 
    
 
    
-
    -0.4297371804714203
+
    -0.429736852645874
 
    
 
    
 
    
@@ -1553,24 +1562,26 @@ 
    Stochastic simulation results
    WARNING:root:Skipping scheduler setup. No training set found.
 
    
 
    
-
    WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+
    /home/runner/work/fairchem/fairchem/src/fairchem/core/modules/normalization/normalizer.py:69: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
+  "mean": torch.tensor(state_dict["mean"]),
+WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 
    
 
    
-
    /tmp/ipykernel_2654/3396863997.py:11: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2626/3396863997.py:11: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 
    
 
    
-
    1.2139858722686767 1.8706364866192848e-06
-1.2139887809753418
-1.213982343673706
-1.2139866352081299
-1.213987112045288
-1.2139854431152344
-1.2139878273010254
-1.213986873626709
-1.2139854431152344
-1.213984727859497
-1.2139835357666016
+
    1.2127598762512206 1.9492085872621248e-06
+1.2127623558044434
+1.212761640548706
+1.2127630710601807
+1.2127599716186523
+1.2127587795257568
+1.2127602100372314
+1.2127585411071777
+1.212756872177124
+1.2127573490142822
+1.2127599716186523
 
    
 
    
 
    
@@ -1605,14 +1616,16 @@ 
    The forces don’t sum to zero
    WARNING:root:Skipping scheduler setup. No training set found.
 
    
 
    
-
    WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+
    /home/runner/work/fairchem/fairchem/src/fairchem/core/modules/normalization/normalizer.py:69: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
+  "mean": torch.tensor(state_dict["mean"]),
+WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 
    
 
    
-
    /tmp/ipykernel_2654/4037009387.py:11: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2626/4037009387.py:11: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 
    
 
    
-
    array([ 0.0084795 ,  0.01409519, -0.05882609], dtype=float32)
+
    array([ 0.01599075,  0.00170346, -0.07197964], dtype=float32)
 
    
 
    
 
    
@@ -1625,7 +1638,7 @@ 
    The forces don’t sum to zero
-
    array([-4.9127266e-08,  1.9790605e-08,  2.3841858e-07], dtype=float32)
+
    array([-9.1735274e-08, -3.5390258e-08,  3.5762787e-07], dtype=float32)
 
    
 
    
 
    
diff --git a/core/inference.html b/core/inference.html
index 60f5c23188..301d6dedb9 100644
--- a/core/inference.html
+++ b/core/inference.html
@@ -305,6 +305,7 @@
 
  • core.common.logger
    • 
 
  • core.common.profiler_utils
    • 
 
  • core.common.registry
    • 
+
  • core.common.slurm
    • 
 
  • core.common.test_utils
    • 
 
  • core.common.transforms
    • 
 
  • core.common.tutorial_utils
    • 
@@ -334,16 +335,17 @@
 
  • core.models.utils
    • 
 
  • core.models.base
    • 
 
  • core.models.dimenet_plus_plus
    • 
+
  • core.models.finetune_hydra
    • 
 
  • core.models.model_registry
    • 
 
  • core.models.schnet
    •

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -645,71 +648,15 @@

    Fast batched inferenceYou can retrieve the dataset below. In this notebook we learn how to do “mass inference” without an ASE calculator. You do this by creating a config.yml file, and running the main.py command line utility.

    -
    ! wget https://figshare.com/ndownloader/files/11948267 -O data.db
+
    from fairchem.core.scripts.download_large_files import download_file_group
+download_file_group('docs')
    -
    --2024-08-03 02:12:54--  https://figshare.com/ndownloader/files/11948267
-Resolving figshare.com (figshare.com)... 
-
    -
    -
    34.251.200.7, 18.203.35.208, 2a05:d018:1f4:d000:1396:2ead:ffc3:8b6c, ...
-Connecting to figshare.com (figshare.com)|34.251.200.7|:443... 
-
    -
    -
    connected.
-
    -
    -
    HTTP request sent, awaiting response... 
-
    -
    -
    302 Found
-Location: https://s3-eu-west-1.amazonaws.com/pstorage-cmu-348901238291901/11948267/data.db?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAI266R7V6O36O5JUA/20240803/eu-west-1/s3/aws4_request&X-Amz-Date=20240803T021254Z&X-Amz-Expires=10&X-Amz-SignedHeaders=host&X-Amz-Signature=8392082962903229ece4324b2f08f868d64c84b6272715a532977d64271d0c81 [following]
---2024-08-03 02:12:54--  https://s3-eu-west-1.amazonaws.com/pstorage-cmu-348901238291901/11948267/data.db?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAI266R7V6O36O5JUA/20240803/eu-west-1/s3/aws4_request&X-Amz-Date=20240803T021254Z&X-Amz-Expires=10&X-Amz-SignedHeaders=host&X-Amz-Signature=8392082962903229ece4324b2f08f868d64c84b6272715a532977d64271d0c81
-Resolving s3-eu-west-1.amazonaws.com (s3-eu-west-1.amazonaws.com)... 52.218.29.11, 52.218.61.163
-
    -
    -
    , 52.92.4.40, ...
-Connecting to s3-eu-west-1.amazonaws.com (s3-eu-west-1.amazonaws.com)|52.218.29.11|:443... 
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    connected.
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    HTTP request sent, awaiting response... 
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-Length: 43125760 (41M) [binary/octet-stream]
-Saving to: ‘data.db’
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-2024-08-03 02:12:56 (27.4 MB/s) - ‘data.db’ saved [43125760/43125760]
+
    docs/tutorials/NRR/NRR_example_bulks.pkl already exists
+docs/core/fine-tuning/supporting-information.json already exists
+Downloading docs/core/data.db...
    @@ -751,29 +698,29 @@

    Fast batched inference

    -
    id|age|user  |formula|calculator|  energy|natoms| fmax|pbc|  volume|charge|     mass
- 1| 0s|runner|Au26   |unknown   | -82.906|    26|0.973|TTT| 483.391| 0.000| 5121.131
- 2| 0s|runner|Au44   |unknown   |-114.109|    44|0.262|TTT|6257.369| 0.000| 8666.529
- 3| 0s|runner|Au115  |vasp      |-351.890|   115|0.266|TTT|9178.098| 0.000|22651.155
- 4| 0s|runner|Au7    |unknown   | -14.220|     7|0.103|TTT|3511.808| 0.000| 1378.766
- 5| 0s|runner|Au16   |unknown   | -38.155|    16|0.271|TTT|3746.637| 0.000| 3151.465
- 6| 0s|runner|Au40   |unknown   |-102.387|    40|0.404|TTT|5868.580| 0.000| 7878.663
- 7| 0s|runner|Au4    |unknown   | -11.336|     4|1.022|TTT| 156.940| 0.000|  787.866
- 8| 0s|runner|Au41   |unknown   |-106.119|    41|0.203|TTT|6012.425| 0.000| 8075.629
- 9| 0s|runner|Au10   |unknown   | -21.719|    10|0.310|TTT|2868.259| 0.000| 1969.666
-10| 0s|runner|Au2    |unknown   |  -5.155|     2|0.000|TTT|  51.653| 0.000|  393.933
-11| 0s|runner|Au55   |unknown   |-134.315|    55|0.231|TTT|7703.754| 0.000|10833.161
-12| 0s|runner|Au45   |unknown   |-117.580|    45|0.186|TTT|6185.400| 0.000| 8863.496
-13| 0s|runner|Au     |unknown   |  -0.374|     1|0.000|TTT| 101.172| 0.000|  196.967
-14| 0s|runner|Au51   |unknown   |-117.953|    51|3.109|TTT|6691.718| 0.000|10045.295
-15| 0s|runner|Au20   |unknown   | -48.167|    20|0.072|TTT|4413.396| 0.000| 3939.331
-16| 0s|runner|Au51   |unknown   |-132.357|    51|0.404|TTT|6691.718| 0.000|10045.295
-17| 0s|runner|Au40   |unknown   |-104.532|    40|0.272|TTT|5868.580| 0.000| 7878.663
-18| 0s|runner|Au21   |unknown   | -49.936|    21|0.271|TTT|4395.170| 0.000| 4136.298
-19| 0s|runner|Au4    |unknown   | -12.106|     4|0.517|TTT| 143.096| 0.000|  787.866
-20| 0s|runner|Au12   |unknown   | -25.401|    12|0.066|TTT|5639.752| 0.000| 2363.599
+
    id|age|user  |formula|calculator|  energy|natoms| fmax|pbc|  volume|charge|    mass
+ 1| 0s|runner|Au35   |unknown   | -90.008|    35|0.297|TTT|5504.869| 0.000|6893.830
+ 2| 0s|runner|Au4    |unknown   | -11.571|     4|0.037|TTT| 156.940| 0.000| 787.866
+ 3| 0s|runner|Au36   |unknown   | -93.656|    36|0.103|TTT|5663.627| 0.000|7090.796
+ 4| 0s|runner|Au33   |unknown   | -84.963|    33|0.122|TTT|5480.808| 0.000|6499.897
+ 5| 0s|runner|Au8    |unknown   | -16.956|     8|0.095|TTT|2863.348| 0.000|1575.733
+ 6| 0s|runner|Au10   |unknown   | -21.428|    10|0.820|TTT|4112.512| 0.000|1969.666
+ 7| 0s|runner|Au22   |unknown   | -53.824|    22|0.223|TTT|4335.494| 0.000|4333.265
+ 8| 0s|runner|Au34   |unknown   | -87.528|    34|0.384|TTT|5583.053| 0.000|6696.863
+ 9| 0s|runner|Au31   |unknown   | -78.954|    31|0.349|TTT|5304.824| 0.000|6105.964
+10| 0s|runner|Au41   |unknown   |-103.985|    41|0.518|TTT|6012.425| 0.000|8075.629
+11| 0s|runner|Au6    |unknown   | -12.130|     6|1.703|TTT|3148.232| 0.000|1181.799
+12| 0s|runner|Au25   |unknown   | -61.465|    25|0.174|TTT|4771.343| 0.000|4924.164
+13| 0s|runner|Au25   |unknown   | -60.787|    25|0.272|TTT|4771.343| 0.000|4924.164
+14| 0s|runner|Au41   |unknown   |-105.780|    41|0.186|TTT|6012.425| 0.000|8075.629
+15| 0s|runner|Au48   |unknown   |-123.644|    48|0.296|TTT|6440.631| 0.000|9454.395
+16| 0s|runner|Au35   |unknown   | -90.285|    35|0.179|TTT|5504.869| 0.000|6893.830
+17| 0s|runner|Au2    |unknown   |  -0.675|     2|0.000|TTT| 175.694| 0.000| 393.933
+18| 0s|runner|Au35   |unknown   | -89.839|    35|0.125|TTT|5504.869| 0.000|6893.830
+19| 0s|runner|Au4    |unknown   | -11.728|     4|0.798|TTT| 156.940| 0.000| 787.866
+20| 0s|runner|Au24   |unknown   | -59.252|    24|0.204|TTT|4672.311| 0.000|4727.198
 Rows: 50 (showing first 20)
-Keys: NEB, bulk, calc_time, cluster, concentration, config, diffusion, ediff, ediffg, encut, factor, fermi, gga, group, identity, image, kpt1, kpt2, kpt3, lattice, miller, neural_energy, reax_energy, strain, structure, surf, tag, train_set, traj, type, vacuum, volume, xc
+Keys: NEB, bulk, calc_time, cluster, config, diffusion, ediff, ediffg, encut, factor, fermi, fit, gga, group, image, kpt1, kpt2, kpt3, miller, neural_energy, reax_energy, strain, structure, surf, train_set, traj, vacuum, volume, xc
    @@ -874,7 +821,7 @@

    Fast batched inference

    -
    2024-08-03 02:13:15 (INFO): Total time taken: 7.171952247619629
+
    2024-08-14 00:54:19 (INFO): Total time taken: 6.979607820510864
    @@ -914,7 +861,7 @@

    Fast batched inference 
    array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16,
        17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
-       34, 35, 36])
+       34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])

    @@ -943,7 +890,7 @@

    Fast batched inference

    -../_images/42d04c02da635cd2935230cb4d8801936d732bdb07786af8bfdbe1653be90c35.png +../_images/be6d6479182addd7af258bf1a50fa2168faf1753ead198212fe7552454caf9ea.png
    @@ -992,98 +939,143 @@

    The ASE calculator way
    0it [00:00, ?it/s]

    -
    /tmp/ipykernel_2695/402181013.py:7: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2670/402181013.py:7: DeprecationWarning: Please use atoms.calc = calc
   atoms.set_calculator(calc)
 
    
 
    
-
    1it [00:00,  3.64it/s]
+
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-
    Elapsed time 7e+00 seconds
+
    Elapsed time 1e+01 seconds
 
    
 
    
 
    
@@ -1101,7 +1093,7 @@ 
    The ASE calculator way
 
    
 
    
-../_images/840fd9b56d89510820efe17927a6a44338394f247338c8dab39ebf2f6a876883.png
+../_images/cbf6f972547cd82a6c7de3707996ed6e1b89d813d7267fd3e16032a553c20447.png
 
    
 
    
 
@@ -1117,7 +1109,7 @@ 
    Comparing ASE calculator and main.py
-
    50.25553682409472
+
    43.381978050514505
 
    
 
    
 
    
@@ -1129,7 +1121,7 @@ 
    Comparing ASE calculator and main.py
-
    (-148.4094009399414, 148.4094009399414)
+
    (-141.65926933288574, 141.65926933288574)
 
    
 
    
 
    
@@ -1141,7 +1133,7 @@ 
    Comparing ASE calculator and main.py
-../_images/b1252f464df0e847d99658867f29ece2c8d6c5a669e58c282aedda2412ba8974.png
+../_images/919f9c13992e9b8260b9d339e886d5401a2db470a695bfdbb11033673d722a02.png
 
    
 
    
 
    Here we see many of the differences are very small. 0.0078125 = 1 / 128, and these errors strongly suggest some kind of mixed precision is responsible for these differences. It is an open issue to remove them and identify where the cause is.
    
@@ -1152,19 +1144,19 @@ 
    Comparing ASE calculator and main.py
-
    array([[ 0.00000000e+00, -1.06605972e+02, -8.06813393e+01, ...,
-        -5.81016159e+01, -3.86192932e+01, -5.80107803e+01],
-       [ 1.06605972e+02,  0.00000000e+00,  2.59246330e+01, ...,
-         4.85043564e+01,  6.79866791e+01,  4.85951920e+01],
-       [ 8.06813393e+01, -2.59246330e+01,  0.00000000e+00, ...,
-         2.25797234e+01,  4.20620461e+01,  2.26705589e+01],
+
    array([[ 0.00000000e+00,  4.40606689e+00, -4.58051300e+00, ...,
+        -5.23437805e+01, -4.47119522e+01, -7.43546219e+01],
+       [-4.40606689e+00,  0.00000000e+00, -8.98657990e+00, ...,
+        -5.67498474e+01, -4.91180191e+01, -7.87606888e+01],
+       [ 4.58051300e+00,  8.98657990e+00,  0.00000000e+00, ...,
+        -4.77632675e+01, -4.01314392e+01, -6.97741089e+01],
        ...,
-       [ 5.81016159e+01, -4.85043564e+01, -2.25797234e+01, ...,
-         0.00000000e+00,  1.94823227e+01,  9.08355713e-02],
-       [ 3.86192932e+01, -6.79866791e+01, -4.20620461e+01, ...,
-        -1.94823227e+01,  0.00000000e+00, -1.93914871e+01],
-       [ 5.80107803e+01, -4.85951920e+01, -2.26705589e+01, ...,
-        -9.08355713e-02,  1.93914871e+01,  0.00000000e+00]])
+       [ 5.23437805e+01,  5.67498474e+01,  4.77632675e+01, ...,
+         0.00000000e+00,  7.63182831e+00, -2.20108414e+01],
+       [ 4.47119522e+01,  4.91180191e+01,  4.01314392e+01, ...,
+        -7.63182831e+00,  0.00000000e+00, -2.96426697e+01],
+       [ 7.43546257e+01,  7.87606926e+01,  6.97741127e+01, ...,
+         2.20108452e+01,  2.96426735e+01,  3.81469727e-06]])
 
    
 
    
 
    
diff --git a/core/install.html b/core/install.html
index d3c2ccd157..fe6a5f3296 100644
--- a/core/install.html
+++ b/core/install.html
@@ -305,6 +305,7 @@
 
  • core.common.logger
    • 
 
  • core.common.profiler_utils
    • 
 
  • core.common.registry
    • 
+
  • core.common.slurm
    • 
 
  • core.common.test_utils
    • 
 
  • core.common.transforms
    • 
 
  • core.common.tutorial_utils
    • 
@@ -334,16 +335,17 @@
 
  • core.models.utils
    • 
 
  • core.models.base
    • 
 
  • core.models.dimenet_plus_plus
    • 
+
  • core.models.finetune_hydra
    • 
 
  • core.models.model_registry
    • 
 
  • core.models.schnet
    •

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/core/intro_series.html b/core/intro_series.html index f147068e97..2a10ace884 100644 --- a/core/intro_series.html +++ b/core/intro_series.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/core/license.html b/core/license.html index df12b0bad3..39f49522e2 100644 --- a/core/license.html +++ b/core/license.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/core/lmdb_dataset_creation.html b/core/lmdb_dataset_creation.html index 8630fd3a8b..6f6c8b84f7 100644 --- a/core/lmdb_dataset_creation.html +++ b/core/lmdb_dataset_creation.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -691,7 +694,7 @@

    Generate toy dataset: Relaxation of CO on Cu -
    /tmp/ipykernel_2780/901556023.py:8: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2758/901556023.py:8: DeprecationWarning: Please use atoms.calc = calc
   adslab.set_calculator(EMT())
 
    
 
    
@@ -833,7 +836,7 @@ 
    Write data to LMDB
-
    Data(pos=[14, 3], cell=[1, 3, 3], atomic_numbers=[14], natoms=14, tags=[14], edge_index=[2, 636], cell_offsets=[636, 3], energy=3.9893144106683787, forces=[14, 3], fixed=[14], pos_relaxed=[14, 3], sid=0)
+
    Data(pos=[14, 3], cell=[1, 3, 3], atomic_numbers=[14], natoms=14, tags=[14], edge_index=[2, 635], cell_offsets=[635, 3], energy=3.9893144106683787, forces=[14, 3], fixed=[14], pos_relaxed=[14, 3], sid=0)
 
    
 
    
 
    
@@ -906,43 +909,49 @@ 
    Structure to Energy and Forces (S2EF) LMDBs
      0%|          | 0/1001 [00:00<?, ?it/s]
 
    
 
    
-
      6%|▌         | 59/1001 [00:00<00:01, 586.66it/s]
+
      5%|▌         | 53/1001 [00:00<00:01, 527.72it/s]
 
    
 
    
-
     14%|█▍        | 141/1001 [00:00<00:01, 718.15it/s]
+
     12%|█▏        | 122/1001 [00:00<00:01, 618.81it/s]
 
    
 
    
-
     22%|██▏       | 221/1001 [00:00<00:01, 753.81it/s]
+
     19%|█▉        | 192/1001 [00:00<00:01, 654.74it/s]
 
    
 
    
-
     30%|███       | 301/1001 [00:00<00:00, 770.05it/s]
+
     26%|██▌       | 258/1001 [00:00<00:01, 615.47it/s]
 
    
 
    
-
     38%|███▊      | 378/1001 [00:00<00:00, 734.75it/s]
+
     33%|███▎      | 331/1001 [00:00<00:01, 653.66it/s]
 
    
 
    
-
     46%|████▌     | 459/1001 [00:00<00:00, 757.16it/s]
+
     40%|████      | 401/1001 [00:00<00:00, 668.80it/s]
 
    
 
    
-
     54%|█████▍    | 539/1001 [00:00<00:00, 767.96it/s]
+
     47%|████▋     | 472/1001 [00:00<00:00, 681.72it/s]
 
    
 
    
-
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+
     54%|█████▍    | 541/1001 [00:00<00:00, 682.08it/s]
 
    
 
    
-
     70%|███████   | 701/1001 [00:00<00:00, 787.61it/s]
+
     61%|██████    | 611/1001 [00:00<00:00, 684.88it/s]
 
    
 
    
-
     78%|███████▊  | 780/1001 [00:01<00:00, 775.59it/s]
+
     68%|██████▊   | 680/1001 [00:01<00:00, 661.68it/s]
 
    
 
    
-
     86%|████████▌ | 861/1001 [00:01<00:00, 782.60it/s]
+
     75%|███████▌  | 752/1001 [00:01<00:00, 676.70it/s]
 
    
 
    
-
     94%|█████████▍| 940/1001 [00:01<00:00, 779.82it/s]
+
     83%|████████▎ | 828/1001 [00:01<00:00, 699.50it/s]
 
    
 
    
-
    100%|██████████| 1001/1001 [00:01<00:00, 756.24it/s]
+
     91%|█████████ | 907/1001 [00:01<00:00, 725.51it/s]
+
    
+
    
+
     98%|█████████▊| 985/1001 [00:01<00:00, 741.54it/s]
+
    
+
    
+
    100%|██████████| 1001/1001 [00:01<00:00, 686.67it/s]
 
    
 
    
 
    
@@ -970,7 +979,7 @@ 
    Structure to Energy and Forces (S2EF) LMDBs
-
    Data(pos=[14, 3], cell=[1, 3, 3], atomic_numbers=[14], natoms=14, tags=[14], edge_index=[2, 636], cell_offsets=[636, 3], energy=3.9893144106683787, forces=[14, 3], fixed=[14], sid=[1], fid=[1], id='0_0')
+
    Data(pos=[14, 3], cell=[1, 3, 3], atomic_numbers=[14], natoms=14, tags=[14], edge_index=[2, 635], cell_offsets=[635, 3], energy=3.9893144106683787, forces=[14, 3], fixed=[14], sid=[1], fid=[1], id='0_0')
 
    
 
    
 
    
@@ -998,7 +1007,7 @@ 
    Interacting with the LMDBs
-
    Data(pos=[14, 3], cell=[1, 3, 3], atomic_numbers=[14], natoms=14, tags=[14], edge_index=[2, 636], cell_offsets=[636, 3], energy=3.9893144106683787, forces=[14, 3], fixed=[14], sid=[1], fid=[1], id='0_0')
+
    Data(pos=[14, 3], cell=[1, 3, 3], atomic_numbers=[14], natoms=14, tags=[14], edge_index=[2, 635], cell_offsets=[635, 3], energy=3.9893144106683787, forces=[14, 3], fixed=[14], sid=[1], fid=[1], id='0_0')
 
    
 
    
 
    
@@ -1026,7 +1035,7 @@ 
    Interacting with the LMDBs
-../_images/b8284e835b356d7f68fe10199f75ad35ff59c61539962b4f9738817de79022ed.png
+../_images/70ff966b9de81dc742342614c724a59eb856b0be98cff6b7329d09daf084fa31.png
 
    
 
    
 
diff --git a/core/model_checkpoints.html b/core/model_checkpoints.html
index 31bc6b7fcb..286da8927c 100644
--- a/core/model_checkpoints.html
+++ b/core/model_checkpoints.html
@@ -307,6 +307,7 @@
 
  • core.common.logger
    • 
 
  • core.common.profiler_utils
    • 
 
  • core.common.registry
    • 
+
  • core.common.slurm
    • 
 
  • core.common.test_utils
    • 
 
  • core.common.transforms
    • 
 
  • core.common.tutorial_utils
    • 
@@ -336,16 +337,17 @@
 
  • core.models.utils
    • 
 
  • core.models.base
    • 
 
  • core.models.dimenet_plus_plus
    • 
+
  • core.models.finetune_hydra
    • 
 
  • core.models.model_registry
    • 
 
  • core.models.schnet
    •

  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    diff --git a/core/model_faq.html b/core/model_faq.html index b7973a578e..6c905e0865 100644 --- a/core/model_faq.html +++ b/core/model_faq.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/core/model_training.html b/core/model_training.html index a69143cc19..8cf7749c65 100644 --- a/core/model_training.html +++ b/core/model_training.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/core/ocpapi.html b/core/ocpapi.html index 74e23e062f..33d16a5040 100644 --- a/core/ocpapi.html +++ b/core/ocpapi.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -668,10 +671,10 @@

    Installation
    ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
    -
    pymatgen 2024.7.18 requires requests>=2.32, but you have requests 2.31.0 which is incompatible.
+
    pymatgen 2024.8.9 requires requests>=2.32, but you have requests 2.31.0 which is incompatible.
 
    
 
    
-
    fairchem-demo-ocpapi 0.1.dev1+g08b8c1e requires requests==2.32.0, but you have requests 2.31.0 which is incompatible.
+
    fairchem-demo-ocpapi 0.1.dev1+g8fb16d6 requires requests==2.32.0, but you have requests 2.31.0 which is incompatible.
 
    
 
    
 
    
diff --git a/core/papers_using_models.html b/core/papers_using_models.html
index 6bf1d22586..0fdf0b6d74 100644
--- a/core/papers_using_models.html
+++ b/core/papers_using_models.html
@@ -305,6 +305,7 @@
 
  • core.common.logger
    • 
 
  • core.common.profiler_utils
    • 
 
  • core.common.registry
    • 
+
  • core.common.slurm
    • 
 
  • core.common.test_utils
    • 
 
  • core.common.transforms
    • 
 
  • core.common.tutorial_utils
    • 
@@ -334,16 +335,17 @@
 
  • core.models.utils
    • 
 
  • core.models.base
    • 
 
  • core.models.dimenet_plus_plus
    • 
+
  • core.models.finetune_hydra
    • 
 
  • core.models.model_registry
    • 
 
  • core.models.schnet
    •

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/core/quickstart.html b/core/quickstart.html index 669de3f1b8..b506fd92bc 100644 --- a/core/quickstart.html +++ b/core/quickstart.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -705,63 +708,63 @@

    Using pre-trained models in ASE
    WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
    -
    /tmp/ipykernel_2837/3462928393.py:13: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2817/3462928393.py:13: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 
    
 
    
 
          Step     Time          Energy          fmax
-BFGS:    0 02:13:49     -110.398659        1.630680
+BFGS:    0 00:54:56     -110.400406        1.627233
 
    
 
    
-
    BFGS:    1 02:13:49     -110.545036        0.925020
+
    BFGS:    1 00:54:57     -110.542839        0.924819
 
    
 
    
-
    BFGS:    2 02:13:49     -110.622719        0.562895
+
    BFGS:    2 00:54:57     -110.626541        0.568005
 
    
 
    
-
    BFGS:    3 02:13:50     -110.613007        0.583018
+
    BFGS:    3 00:54:58     -110.605003        0.585444
 
    
 
    
-
    BFGS:    4 02:13:50     -110.641937        0.461219
+
    BFGS:    4 00:54:58     -110.652641        0.443063
 
    
 
    
-
    BFGS:    5 02:13:51     -110.691620        0.362131
+
    BFGS:    5 00:54:59     -110.698265        0.369424
 
    
 
    
-
    BFGS:    6 02:13:51     -110.723862        0.592763
+
    BFGS:    6 00:54:59     -110.729652        0.604163
 
    
 
    
-
    BFGS:    7 02:13:51     -110.764206        0.712022
+
    BFGS:    7 00:55:00     -110.766403        0.711393
 
    
 
    
-
    BFGS:    8 02:13:52     -110.869545        0.522792
+
    BFGS:    8 00:55:00     -110.869637        0.512456
 
    
 
    
-
    BFGS:    9 02:13:52     -110.938713        0.170553
+
    BFGS:    9 00:55:01     -110.945900        0.158336
 
    
 
    
-
    BFGS:   10 02:13:52     -110.977699        0.083886
+
    BFGS:   10 00:55:01     -110.976570        0.086625
 
    
 
    
-
    BFGS:   11 02:13:53     -110.992668        0.071652
+
    BFGS:   11 00:55:02     -110.992783        0.074964
 
    
 
    
-
    BFGS:   12 02:13:53     -110.999657        0.061177
+
    BFGS:   12 00:55:02     -111.000832        0.063625
 
    
 
    
-
    BFGS:   13 02:13:54     -110.995178        0.059450
+
    BFGS:   13 00:55:02     -111.000153        0.061604
 
    
 
    
-
    BFGS:   14 02:13:54     -111.005981        0.060318
+
    BFGS:   14 00:55:03     -111.009369        0.058362
 
    
 
    
-
    BFGS:   15 02:13:54     -111.007721        0.062097
+
    BFGS:   15 00:55:03     -111.015068        0.054439
 
    
 
    
-
    BFGS:   16 02:13:55     -111.010895        0.035077
+
    BFGS:   16 00:55:04     -111.019554        0.033223
 
    
 
    
-../_images/ea7ac8e20e191a15de6e417770d86a627492010be04a5f6c56083ee6b1ac9289.png
+../_images/c7a08733db67560974d22b6e0bd9aa7142c8604fa4d168284f4df59a924ad306.png
 
    
 
    
 
    To learn more about what this simulation means and how it fits into catalysis, see the catalysis tutorial!
    
diff --git a/execution_time.html b/execution_time.html
index 86059f1d23..aae84b3f73 100644
--- a/execution_time.html
+++ b/execution_time.html
@@ -304,6 +304,7 @@
 
  • core.common.logger
    • 
 
  • core.common.profiler_utils
    • 
 
  • core.common.registry
    • 
+
  • core.common.slurm
    • 
 
  • core.common.test_utils
    • 
 
  • core.common.transforms
    • 
 
  • core.common.tutorial_utils
    • 
@@ -333,16 +334,17 @@
 
  • core.models.utils
    • 
 
  • core.models.base
    • 
 
  • core.models.dimenet_plus_plus
    • 
+
  • core.models.finetune_hydra
    • 
 
  • core.models.model_registry
    • 
 
  • core.models.schnet
    •

  • core.modules
    @@ -355,6 +357,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -380,7 +384,6 @@
  • data.oc
    @@ -638,105 +641,105 @@

    Notebook execution times

    core/fine-tuning/fine-tuning-oxides

    -

    2024-08-03 02:12

    +

    2024-08-14 00:53

    auto

    -

    356.18

    +

    400.95

    ✅

    core/gotchas

    -

    2024-08-03 02:12

    +

    2024-08-14 00:53

    auto

    -

    32.06

    +

    33.93

    ✅

    core/inference

    -

    2024-08-03 02:13

    +

    2024-08-14 00:54

    auto

    -

    34.35

    +

    38.66

    ✅

    core/lmdb_dataset_creation

    -

    2024-08-03 02:13

    +

    2024-08-14 00:54

    auto

    -

    11.32

    +

    11.73

    ✅

    core/ocpapi

    -

    2024-08-03 02:13

    +

    2024-08-14 00:54

    auto

    -

    2.92

    +

    3.08

    ✅

    core/quickstart

    -

    2024-08-03 02:13

    +

    2024-08-14 00:55

    auto

    -

    14.71

    +

    16.37

    ✅

    legacy_tutorials/OCP_Tutorial

    -

    2024-08-03 02:27

    +

    2024-08-14 01:09

    auto

    -

    826.81

    +

    843.31

    ✅

    legacy_tutorials/data_preprocessing

    -

    2024-08-03 02:27

    +

    2024-08-14 01:09

    auto

    -

    10.86

    +

    12.02

    ✅

    legacy_tutorials/data_visualization

    -

    2024-08-03 02:28

    +

    2024-08-14 01:10

    auto

    -

    43.06

    +

    43.85

    ✅

    tutorials/NRR/NRR_example

    -

    2024-08-03 02:40

    +

    2024-08-14 01:22

    auto

    -

    715.27

    +

    721.27

    ✅

    tutorials/OCP-introduction

    -

    2024-08-03 02:44

    +

    2024-08-14 01:26

    auto

    -

    235.43

    +

    247.87

    ✅

    tutorials/adsorbml_walkthrough

    -

    2024-08-03 02:51

    +

    2024-08-14 01:37

    auto

    -

    448.14

    +

    644.6

    ✅

    tutorials/advanced/embeddings

    -

    2024-08-03 02:53

    +

    2024-08-14 01:38

    auto

    -

    85.34

    +

    107.05

    ✅

    tutorials/advanced/fine-tuning-in-python

    -

    2024-08-03 02:56

    +

    2024-08-14 01:42

    auto

    -

    214.6

    +

    211.71

    ✅

    tutorials/cattsunami_tutorial

    -

    2024-08-03 02:56

    +

    2024-08-14 01:42

    auto

    -

    0.9

    +

    0.93

    ✅

    tutorials/fairchem_models_for_nebs

    -

    2024-08-03 02:56

    +

    2024-08-14 01:42

    auto

    0.7

    ✅

    tutorials/intro

    -

    2024-08-03 02:57

    +

    2024-08-14 01:42

    auto

    -

    3.88

    +

    4.16

    ✅

    diff --git a/genindex.html b/genindex.html index 2913c33ee2..8e0e875346 100644 --- a/genindex.html +++ b/genindex.html @@ -304,6 +304,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -333,16 +334,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -355,6 +357,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -380,7 +384,6 @@
  • data.oc
    @@ -718,10 +721,18 @@

    _

  • (data.oc.core.Bulk method)
  • (data.oc.core.bulk.Bulk method) +
    • +
  • (data.oc.core.Ion method) +
    • +
  • (data.oc.core.ion.Ion method)
  • (data.oc.core.Slab method)
  • (data.oc.core.slab.Slab method) +
    • +
  • (data.oc.core.Solvent method) +
    • +
  • (data.oc.core.solvent.Solvent method)
  • __repr__() (core.common.transforms.RandomRotate method) @@ -760,6 +771,8 @@

    _

  • (data.oc.core.Slab method)
  • (data.oc.core.slab.Slab method) +
    • +
  • (data.oc.utils.geometry.BoxGeometry method)
  • __str__() (data.oc.core.Adsorbate method) @@ -770,10 +783,18 @@

    _

  • (data.oc.core.Bulk method)
  • (data.oc.core.bulk.Bulk method) +
    • +
  • (data.oc.core.Ion method) +
    • +
  • (data.oc.core.ion.Ion method)
  • (data.oc.core.Slab method)
  • (data.oc.core.slab.Slab method) +
    • +
  • (data.oc.core.Solvent method) +
    • +
  • (data.oc.core.solvent.Solvent method)
  • (ocpapi.client.models.Status method)
    • @@ -803,6 +824,8 @@

    _

  • _API_TO_UI_HOSTS (in module ocpapi.client.ui) +
    • +
  • _apply_refs() (core.modules.normalization.element_references.LinearReferences method)
  • _AVG_DEGREE (in module core.models.equiformer_v2.equiformer_v2)
    • @@ -854,6 +877,12 @@

    _

  • _delete_system() (in module ocpapi.workflows.adsorbates)
    • +
  • _denorm_preds() (core.trainers.ocp_trainer.OCPTrainer method) + +
  • _dist_enabled() (core.common.data_parallel.BalancedBatchSampler static method)
  • _enforce_consistency() (core.modules.scaling.scale_factor.ScaleFactor method) @@ -906,14 +935,14 @@

    _

  • _gather() (in module core.common.gp_utils)
    • + + -
    • +
  • _load_check_duplicates() (in module core.modules.normalization._load_utils) +
  • _load_dataset_get_ids() (core.datasets.ase_datasets.AseAtomsDataset method)
    • +
  • _load_from_config() (in module core.modules.normalization._load_utils) +
  • _load_ids() (core.datasets.lmdb_database.LMDBDatabase method)
    • +
  • _load_ion() (data.oc.core.Ion method) + +
  • _load_scale_dict() (in module core.modules.scaling.compat)
    • +
  • _load_solvent() (data.oc.core.Solvent method) + +
  • _m_primary() (core.models.equiformer_v2.so3.SO3_Embedding method)
    • +
  • _mode (core.models.finetune_hydra.FTConfig attribute) +
  • _nextid (core.datasets.lmdb_database.LMDBDatabase property)
  • a2g (cattsunami.core.OCPNEB attribute) @@ -1347,6 +1396,8 @@

    A

  • add_core_args() (core.common.flags.Flags method)
  • add_edge_distance_to_graph() (in module core.common.utils) +
    • +
  • add_timestamp_id_to_submission_pickle() (in module core.common.slurm)
  • Adsorbate (class in data.oc.core) @@ -1516,6 +1567,8 @@

    A

  • module
    • + +
    • adsorbml.scripts.process_mlrs @@ -1523,8 +1576,6 @@

      A

    • module
    • - -
  • backbone (core.models.base.HydraModel attribute) + +
  • backbone_model_name (core.models.base.HydraModel attribute)
  • BackboneInterface (class in core.models.base) @@ -1922,8 +1979,12 @@

    B

  • both_barrierless() (in module cattsunami.run_validation.run_validation)
  • bound (core.models.equiformer_v2.so3.SO3_LinearV2 attribute) +
    • +
  • BoxGeometry (class in data.oc.utils.geometry)
  • broadcast() (in module core.common.distutils) +
    • +
  • broadcast_object_list() (in module core.common.distutils)
  • build_config() (in module core.common.utils)
    • @@ -1983,7 +2044,7 @@

    B

  • (ocpapi.SlabMetadata attribute)
    • -
  • BULK_VASP_FLAGS (in module data.oc.utils.vasp) +
  • BULK_VASP_FLAGS (in module data.oc.utils.vasp_flags)
  • Bulks (class in ocpapi) @@ -2013,6 +2074,8 @@

    C

  • (core.models.gemnet_gp.layers.radial_basis.PolynomialEnvelope attribute)
  • (core.models.gemnet_oc.layers.radial_basis.PolynomialEnvelope attribute) +
    • +
  • (data.oc.utils.geometry.PlaneBoundTriclinicGeometry attribute)
  • cached (cattsunami.core.OCPNEB attribute) @@ -2126,9 +2189,11 @@

    C

  • (core.models.gemnet_oc.layers.spherical_basis.CircularBasisLayer attribute)
    • -
  • cell (ocpapi.AdsorbateSlabRelaxationResult attribute) +
  • cell (data.oc.utils.geometry.PlaneBoundTriclinicGeometry attribute)
    • +
  • cell2planes() (data.oc.utils.geometry.Geometry static method) +
  • cell_offsets (core.models.base.GraphData attribute)
  • centering (core.models.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute) @@ -2296,6 +2363,8 @@

    C

  • (core.datasets.base_dataset.Subset attribute)
  • (core.models.equiformer_v2.trainers.lr_scheduler.LRScheduler attribute) +
    • +
  • (core.models.finetune_hydra.FTConfig attribute)
  • (core.modules.scheduler.LRScheduler attribute)
    • @@ -2488,6 +2557,13 @@

    C

    • +
  • + core.common.slurm + +
  • @@ -2686,8 +2762,6 @@

    C

  • module
    • - -
    • core.models.equiformer_v2.layer_norm @@ -2709,6 +2783,8 @@

      C

    • module
    • + +
    • core.models.equiformer_v2.so2_ops @@ -2784,6 +2860,13 @@

      C

      • +
    • + core.models.finetune_hydra + +
    • @@ -3193,10 +3276,31 @@

      C

  • - core.modules.normalizer + core.modules.normalization
    • +
  • + core.modules.normalization._load_utils + +
    • +
  • + core.modules.normalization.element_references + +
    • +
  • + core.modules.normalization.normalizer + +
  • @@ -3281,6 +3385,20 @@

    C

    • +
  • + core.scripts.fit_normalizers + +
    • +
  • + core.scripts.fit_references + +
  • @@ -3427,9 +3545,25 @@

    C

  • create_dict_from_args() (in module core.common.utils) +
    • +
  • create_element_references() (in module core.modules.normalization.element_references)
  • create_grid() (in module core.common.utils)
    • +
  • create_interface_on_sites() (data.oc.core.interface_config.InterfaceConfig method) + +
    • +
  • create_normalizer() (in module core.modules.normalization.normalizer) +
    • +
  • create_packmol_atoms() (data.oc.core.interface_config.InterfaceConfig method) + +
  • current_entry (in module data.odac.promising_mof.promising_mof_energies.energy), [1], [2], [3], [4], [5], [6], [7]
  • custom_tile_atoms() (in module data.oc.core.adsorbate_slab_config) @@ -3518,6 +3652,20 @@

    D

    • +
  • + data.oc.core.interface_config + +
    • +
  • + data.oc.core.ion + +
  • @@ -3532,6 +3680,13 @@

    D

    • +
  • + data.oc.core.solvent + +
  • @@ -3605,24 +3760,24 @@

    D

  • - data.oc.tests + data.oc.utils
  • - data.oc.utils + data.oc.utils.flag_anomaly
  • - data.oc.utils.flag_anomaly + data.oc.utils.geometry
  • @@ -3630,6 +3785,13 @@

    D

    • +
  • + data.oc.utils.vasp_flags + +
  • @@ -3710,6 +3872,8 @@

    D

  • (in module core.datasets.lmdb_dataset)
    • +
  • DATA_ONLY (core.models.finetune_hydra.FineTuneMode attribute) +
  • DatasetMetadata (class in core.datasets.base_dataset)
  • DataTransforms (class in core.modules.transforms) @@ -3758,7 +3922,7 @@

    D

  • (core.datasets.LMDBDatabase attribute)
    • -
  • denorm() (core.modules.normalizer.Normalizer method) +
  • denorm() (core.modules.normalization.normalizer.Normalizer method)
  • Dense (class in core.models.gemnet.layers.base_layers) @@ -3776,6 +3940,8 @@

    D

  • (core.models.gemnet_oc.layers.embedding_block.EdgeEmbedding attribute)
    • + + -
    • +
  • distance_point_plane() (data.oc.utils.geometry.Geometry static method) +
  • distance_resolution (core.models.escn.eSCN attribute)
    • +
  • extract_box_properties() (data.oc.utils.geometry.Geometry static method) +
  • extract_file() (in module data.oc.experimental.get_energies)
    • +
  • fit_linear_references() (in module core.modules.normalization.element_references) +
    • +
  • fit_linref() (in module core.scripts.fit_references) +
    • +
  • fit_normalizers() (in module core.modules.normalization.normalizer) +
    • +
  • fit_norms() (in module core.scripts.fit_normalizers) +
  • fitted (core.modules.scaling.scale_factor.ScaleFactor property)
      @@ -4608,9 +4798,11 @@

      F

  • FlipGrid() (core.models.scn.spherical_harmonics.SphericalHarmonicsHelper method)
    • -
  • force_block (core.models.equiformer_v2.equiformer_v2.EquiformerV2ForceHead attribute) +
  • force_block (core.models.equiformer_v2.equiformer_v2.EquiformerV2Backbone attribute)
    • @@ -4804,6 +4996,8 @@

    F

  • (core.models.escn.escn.SO2Block method)
  • (core.models.escn.escn.SO2Conv method) +
    • +
  • (core.models.finetune_hydra.FineTuneHydra method)
  • (core.models.gemnet.gemnet.GemNetT method)
    • @@ -5002,6 +5196,10 @@

    F

  • (core.modules.loss.DDPLoss method)
  • (core.modules.loss.L2MAELoss method) +
    • +
  • (core.modules.normalization.element_references.LinearReferences method) +
    • +
  • (core.modules.normalization.normalizer.Normalizer method)
  • (core.modules.scaling.scale_factor.ScaleFactor method)
    • @@ -5069,6 +5267,14 @@

    F

  • FromGrid() (core.models.scn.spherical_harmonics.SphericalHarmonicsHelper method) +
    • +
  • ft_config (core.models.finetune_hydra.FineTuneHydra attribute) +
    • +
  • FT_CONFIG_NAME (core.models.finetune_hydra.FTConfig attribute) +
    • +
  • FTConfig (class in core.models.finetune_hydra) +
    • +
  • FTHYDRA_NAME (in module core.models.finetune_hydra)
    • @@ -5151,6 +5357,8 @@

    G

  • generate_yml_config() (in module core.common.tutorial_utils) +
    • +
  • Geometry (class in data.oc.utils.geometry)
  • get() (core.common.registry.Registry class method)
    • @@ -5210,6 +5418,14 @@

    G

  • (core.datasets.AseReadDataset method)
  • (core.datasets.AseReadMultiStructureDataset method) +
    • +
    • +
  • get_backbone() (core.models.base.HydraInterface method) + +
  • get_bases() (core.models.gemnet_oc.gemnet_oc.GemNetOC method) @@ -5322,14 +5538,28 @@

    G

  • (core.models.gemnet_oc.GemNetOC method)
    • -
  • get_initializer() (in module core.models.gemnet_oc.initializers) +
  • get_heads() (core.models.base.HydraInterface method) + +
  • get_model_class() (core.common.registry.Registry class method) +
    • +
  • get_model_config_from_checkpoint() (in module core.models.finetune_hydra)
  • get_models() (ocpapi.Client method) @@ -5489,6 +5721,8 @@

    G

  • get_sph_harm_basis() (in module core.models.gemnet_oc.layers.basis_utils) +
    • +
  • get_standalone_config() (core.models.finetune_hydra.FTConfig method)
  • get_system_pairs_final() (cattsunami.core.autoframe.AutoFrameTransfer method)
    • @@ -5590,9 +5824,15 @@

    H

  • (in module core.models.gemnet_oc.initializers)
    • +
  • head_config (core.models.finetune_hydra.FTConfig property) +
  • head_names_sorted (core.models.base.HydraModel attribute)
  • HeadInterface (class in core.models.base) +
    • +
  • heads (core.models.base.HydraModel attribute) +
    • +
  • HEADS (core.models.finetune_hydra.FTConfig attribute)
  • hidden_channels (core.models.equiformer_v2.transformer_block.FeedForwardNetwork attribute) @@ -5638,6 +5878,10 @@

    H

  • (ocpapi.client.client.Client property)
    • +
  • hydra_model (core.models.finetune_hydra.FineTuneHydra attribute) +
    • +
  • HydraInterface (class in core.models.base) +
  • HydraModel (class in core.models.base)
    • @@ -5790,8 +6034,6 @@

    I

  • (core.models.gemnet_gp.GraphParallelGemNetT attribute)
    • - -
  • InteractionPPBlock (class in core.models.dimenet_plus_plus)
    • + +
    • +
  • load_hydra_model() (in module core.models.finetune_hydra) +
  • load_logger() (core.trainers.base_trainer.BaseTrainer method)
    • -
  • load_model() (core.trainers.base_trainer.BaseTrainer method) +
  • load_model() (core.models.finetune_hydra.FTConfig method)
    • +
  • load_normalizers_from_config() (in module core.modules.normalization.normalizer) +
  • load_optimizer() (core.trainers.base_trainer.BaseTrainer method)
    • +
  • load_references_and_normalizers() (core.trainers.base_trainer.BaseTrainer method) + +
    • +
  • load_references_from_config() (in module core.modules.normalization.element_references) +
  • load_scales_compat() (in module core.modules.scaling.compat)
  • load_seed_from_config() (core.trainers.base_trainer.BaseTrainer method) @@ -6281,7 +6577,7 @@

    L

  • load_state_dict() (core.modules.exponential_moving_average.ExponentialMovingAverage method)
  • masked_select_sparsetensor_flat() (in module core.models.gemnet_oc.utils) +
    • +
  • match_state_dict() (in module core.common.utils)
  • max_epochs (core.models.equiformer_v2.trainers.lr_scheduler.CosineLRLambda attribute)
    • @@ -6599,13 +6897,11 @@

    M

  • maxstep (core.common.relaxation.optimizers.lbfgs_torch.LBFGS attribute) +
    • +
  • MD_FLAGS (in module data.oc.utils.vasp_flags)
  • mean (core.models.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) - -
  • mean_init_max (core.models.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute)
  • mean_init_min (core.models.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) @@ -6673,6 +6969,8 @@

    M

  • missing_DDEC_defective (in module data.odac.promising_mof.promising_mof_energies.energy)
  • missing_DDEC_pristine (in module data.odac.promising_mof.promising_mof_energies.energy) +
    • +
  • ML_FLAGS (in module data.oc.utils.vasp_flags)
  • ml_relax() (in module core.common.relaxation.ml_relaxation)
    • @@ -6790,9 +7088,13 @@

    M

  • (core.models.escn.so3.CoefficientMapping attribute)
    • -
  • mode (data.oc.core.adsorbate_slab_config.AdsorbateSlabConfig attribute) +
  • MODE (core.models.finetune_hydra.FTConfig attribute) +
    • +
  • mode (core.models.finetune_hydra.FTConfig property)
    • -
  • norm() (core.modules.normalizer.Normalizer method) +
  • norm() (core.modules.normalization.normalizer.Normalizer method)
  • norm_1 (core.models.equiformer_v2.transformer_block.TransBlockV2 attribute)
    • @@ -7397,8 +7739,14 @@

    N

  • (core.models.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2 attribute)
    • -
  • Normalizer (class in core.modules.normalizer) +
  • Normalizer (class in core.modules.normalization.normalizer) +
    • +
  • normalizers (core.trainers.base_trainer.BaseTrainer attribute) + +
  • NOT_AVAILABLE (ocpapi.client.models.Status attribute)
      @@ -7507,14 +7855,14 @@

      N

  • num_components (core.models.equiformer_v2.activation.GateActivation attribute)
    • + + -
    • +
  • packmol_structure() (data.oc.utils.geometry.BoxGeometry method) + +
    • +
  • packmol_tolerance (data.oc.core.interface_config.InterfaceConfig attribute) + +
  • pad_tensor() (in module core.common.gp_utils) @@ -8088,6 +8450,8 @@

    P

  • parallelize_generation() (in module core.scripts.gif_maker_parallelized)
  • parameters (core.modules.exponential_moving_average.ExponentialMovingAverage attribute) +
    • +
  • params (data.oc.utils.geometry.BoxGeometry attribute)
  • parse_args() (in module adsorbml.2023_neurips_challenge.challenge_eval) @@ -8117,6 +8481,10 @@

    P

  • (in module cattsunami.run_validation.run_validation)
  • (in module core.scripts.download_data) +
    • +
  • (in module core.scripts.fit_normalizers) +
    • +
  • (in module core.scripts.fit_references)
  • (in module core.scripts.gif_maker_parallelized)
    • @@ -8158,11 +8526,17 @@

    P

  • pbc_patch() (in module data.oc.databases.update) -
    • -
  • PGConfig (class in core.common.test_utils)
    • +
  • PlaneBoundTriclinicGeometry (class in data.oc.utils.geometry) +
    • +
  • planes (data.oc.utils.geometry.PlaneBoundTriclinicGeometry attribute) +
  • plot_histogram() (in module core.common.utils)
  • plot_traj() (in module data.oc.experimental.utils) @@ -8279,6 +8657,8 @@

    P

  • (class in ocpapi.workflows.filter)
    • +
  • props (data.oc.utils.geometry.BoxGeometry attribute) +
  • pyg2_data_transform() (in module core.common.utils)
    • @@ -8435,6 +8815,12 @@

    R

  • (in module core.models.gemnet_gp.utils)
  • (in module core.models.gemnet_oc.utils) +
    • +
    • +
  • randomize_coords() (data.oc.core.interface_config.InterfaceConfig method) + +
  • randomly_rotate_adsorbate() (in module data.oc.core.adsorbate) @@ -8601,6 +8987,8 @@

    R

    • - - +
    • +
  • Solvent (class in data.oc.core) + +
    • +
  • solvent (data.oc.core.interface_config.InterfaceConfig attribute) + +
    • +
  • SOLVENT_BASE_FLAGS (in module data.oc.utils.vasp_flags) +
    • +
  • SOLVENT_BULK_VASP_FLAGS (in module data.oc.utils.vasp_flags) +
    • +
  • solvent_db_path (data.oc.core.Solvent attribute) + +
    • +
  • solvent_density (data.oc.core.Solvent attribute) + +
    • +
  • solvent_depth (data.oc.core.interface_config.InterfaceConfig attribute) + +
    • +
  • solvent_id_from_db (data.oc.core.Solvent attribute) + +
    • +
  • solvent_interstitial_gap (data.oc.core.interface_config.InterfaceConfig attribute) + +
    • +
  • SOLVENT_PKL_PATH (in module data.oc.databases.pkls) +
  • source_embedding (core.models.escn.escn.EdgeBlock attribute)
  • std (core.models.equiformer_v2.gaussian_rbf.GaussianRadialBasisLayer attribute) - -
  • std_balance_degrees (core.models.equiformer_v2.layer_norm.EquivariantLayerNormArraySphericalHarmonics attribute)
    • -
  • to() (core.modules.normalizer.Normalizer method) -
  • to_ase_atoms() (ocpapi.AdsorbateSlabRelaxationResult method)
    • +
  • train_dataset (core.trainers.base_trainer.BaseTrainer attribute) + +
  • train_on_oc20_total_energies (core.datasets.oc22_lmdb_dataset.OC22LmdbDataset attribute) @@ -9982,6 +10432,8 @@

    U

  • update_net (core.models.painn.painn.GatedEquivariantBlock attribute)
  • update_pkls() (in module data.oc.databases.update) +
    • +
  • ur_corner (data.oc.utils.geometry.PlaneBoundTriclinicGeometry attribute)
  • url (core.models.dimenet_plus_plus.DimeNetPlusPlus attribute)
    • @@ -9995,8 +10447,6 @@

    U

  • (core.models.equiformer_v2.transformer_block.SO2EquivariantGraphAttention attribute)
    • - - +
  • core.modules
    @@ -359,6 +361,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -384,7 +388,6 @@
  • data.oc
    diff --git a/legacy_tutorials/OCP_Tutorial.html b/legacy_tutorials/OCP_Tutorial.html index 5f1eb700f8..fc8ca08959 100644 --- a/legacy_tutorials/OCP_Tutorial.html +++ b/legacy_tutorials/OCP_Tutorial.html @@ -307,6 +307,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -336,16 +337,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    @@ -1045,311 +1048,311 @@

    Structural relaxations 
           Step     Time          Energy          fmax
-LBFGS:    0 02:14:00       15.804700        6.776430
+LBFGS:    0 00:55:09       15.804700        6.776430
    -
    LBFGS:    1 02:14:00       12.190607        4.323222
+
    LBFGS:    1 00:55:09       12.190607        4.323222
 
    
 
    
-
    LBFGS:    2 02:14:00       10.240169        2.265527
+
    LBFGS:    2 00:55:09       10.240169        2.265527
 
    
 
    
-
    LBFGS:    3 02:14:00        9.779223        0.937247
+
    LBFGS:    3 00:55:09        9.779223        0.937247
 
    
 
    
-
    LBFGS:    4 02:14:00        9.671525        0.770173
+
    LBFGS:    4 00:55:09        9.671525        0.770173
 
    
 
    
-
    LBFGS:    5 02:14:00        9.574461        0.663540
+
    LBFGS:    5 00:55:09        9.574461        0.663540
 
    
 
    
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    LBFGS:    6 02:14:00        9.537502        0.571800
+
    LBFGS:    6 00:55:09        9.537502        0.571800
 
    
 
    
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    LBFGS:    7 02:14:00        9.516673        0.446620
+
    LBFGS:    7 00:55:09        9.516673        0.446620
 
    
 
    
-
    LBFGS:    8 02:14:00        9.481330        0.461143
+
    LBFGS:    8 00:55:09        9.481330        0.461143
 
    
 
    
-
    LBFGS:    9 02:14:00        9.462255        0.293081
+
    LBFGS:    9 00:55:09        9.462255        0.293081
 
    
 
    
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    LBFGS:   10 02:14:00        9.448937        0.249010
+
    LBFGS:   10 00:55:09        9.448937        0.249010
 
    
 
    
-
    LBFGS:   11 02:14:00        9.433813        0.237051
+
    LBFGS:   11 00:55:09        9.433813        0.237051
 
    
 
    
-
    LBFGS:   12 02:14:00        9.418884        0.260245
+
    LBFGS:   12 00:55:09        9.418884        0.260245
 
    
 
    
-
    LBFGS:   13 02:14:00        9.409649        0.253162
+
    LBFGS:   13 00:55:09        9.409649        0.253162
 
    
 
    
-
    LBFGS:   14 02:14:00        9.404838        0.162398
+
    LBFGS:   14 00:55:09        9.404838        0.162398
 
    
 
    
-
    LBFGS:   15 02:14:00        9.401753        0.182298
+
    LBFGS:   15 00:55:09        9.401753        0.182298
 
    
 
    
-
    LBFGS:   16 02:14:00        9.397314        0.259163
+
    LBFGS:   16 00:55:09        9.397314        0.259163
 
    
 
    
-
    LBFGS:   17 02:14:00        9.387947        0.345022
+
    LBFGS:   17 00:55:09        9.387947        0.345022
 
    
 
    
-
    /tmp/ipykernel_2867/747130225.py:23: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2852/747130225.py:23: DeprecationWarning: Please use atoms.calc = calc
   adslab.set_calculator(EMT())
 
    
 
    
-
    LBFGS:   18 02:14:00        9.370825        0.407041
+
    LBFGS:   18 00:55:09        9.370825        0.407041
 
    
 
    
-
    LBFGS:   19 02:14:01        9.342222        0.433340
+
    LBFGS:   19 00:55:09        9.342222        0.433340
 
    
 
    
-
    LBFGS:   20 02:14:01        9.286822        0.500200
+
    LBFGS:   20 00:55:09        9.286822        0.500200
 
    
 
    
-
    LBFGS:   21 02:14:01        9.249910        0.524052
+
    LBFGS:   21 00:55:09        9.249910        0.524052
 
    
 
    
-
    LBFGS:   22 02:14:01        9.187179        0.511994
+
    LBFGS:   22 00:55:09        9.187179        0.511994
 
    
 
    
-
    LBFGS:   23 02:14:01        9.124811        0.571796
+
    LBFGS:   23 00:55:09        9.124811        0.571796
 
    
 
    
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    LBFGS:   24 02:14:01        9.066185        0.540934
+
    LBFGS:   24 00:55:09        9.066185        0.540934
 
    
 
    
-
    LBFGS:   25 02:14:01        9.000116        1.079833
+
    LBFGS:   25 00:55:09        9.000116        1.079833
 
    
 
    
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    LBFGS:   26 02:14:01        8.893632        0.752759
+
    LBFGS:   26 00:55:09        8.893632        0.752759
 
    
 
    
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    LBFGS:   27 02:14:01        8.845939        0.332051
+
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    LBFGS:   28 02:14:01        8.815173        0.251242
+
    LBFGS:   28 00:55:09        8.815173        0.251242
 
    
 
    
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    LBFGS:   29 02:14:01        8.808721        0.214337
+
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    LBFGS:   30 02:14:01        8.794643        0.154611
+
    LBFGS:   30 00:55:10        8.794643        0.154611
 
    
 
    
-
    LBFGS:   31 02:14:01        8.789162        0.201404
+
    LBFGS:   31 00:55:10        8.789162        0.201404
 
    
 
    
-
    LBFGS:   32 02:14:01        8.782320        0.175517
+
    LBFGS:   32 00:55:10        8.782320        0.175517
 
    
 
    
-
    LBFGS:   33 02:14:01        8.780394        0.103718
+
    LBFGS:   33 00:55:10        8.780394        0.103718
 
    
 
    
-
    LBFGS:   34 02:14:01        8.778410        0.107611
+
    LBFGS:   34 00:55:10        8.778410        0.107611
 
    
 
    
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    LBFGS:   35 02:14:01        8.775079        0.179747
+
    LBFGS:   35 00:55:10        8.775079        0.179747
 
    
 
    
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    LBFGS:   36 02:14:01        8.766987        0.333401
+
    LBFGS:   36 00:55:10        8.766987        0.333401
 
    
 
    
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    LBFGS:   37 02:14:01        8.750249        0.530715
+
    LBFGS:   37 00:55:10        8.750249        0.530715
 
    
 
    
-
    LBFGS:   38 02:14:01        8.725928        0.685116
+
    LBFGS:   38 00:55:10        8.725928        0.685116
 
    
 
    
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    LBFGS:   39 02:14:01        8.702312        0.582260
+
    LBFGS:   39 00:55:10        8.702312        0.582260
 
    
 
    
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    LBFGS:   40 02:14:01        8.661515        0.399625
+
    LBFGS:   40 00:55:10        8.661515        0.399625
 
    
 
    
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    LBFGS:   41 02:14:01        8.643432        0.558474
+
    LBFGS:   41 00:55:10        8.643432        0.558474
 
    
 
    
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    LBFGS:   42 02:14:01        8.621201        0.367288
+
    LBFGS:   42 00:55:10        8.621201        0.367288
 
    
 
    
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    LBFGS:   43 02:14:01        8.614414        0.139424
+
    LBFGS:   43 00:55:10        8.614414        0.139424
 
    
 
    
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    LBFGS:   44 02:14:01        8.610785        0.137160
+
    LBFGS:   44 00:55:10        8.610785        0.137160
 
    
 
    
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    LBFGS:   45 02:14:01        8.608134        0.146375
+
    LBFGS:   45 00:55:10        8.608134        0.146375
 
    
 
    
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    LBFGS:   46 02:14:01        8.604928        0.119648
+
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    LBFGS:   47 02:14:01        8.599151        0.135424
+
    LBFGS:   47 00:55:10        8.599151        0.135424
 
    
 
    
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    LBFGS:   48 02:14:01        8.594063        0.147913
+
    LBFGS:   48 00:55:10        8.594063        0.147913
 
    
 
    
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    LBFGS:   49 02:14:01        8.589493        0.153840
+
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    LBFGS:   50 02:14:01        8.587274        0.088460
+
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    LBFGS:   51 02:14:01        8.584633        0.093750
+
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    LBFGS:   52 02:14:01        8.580239        0.140870
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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    LBFGS:   63 02:14:01        8.515424        0.101902
+
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    LBFGS:   64 02:14:01        8.511240        0.212223
+
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    LBFGS:   65 02:14:01        8.507967        0.266593
+
    LBFGS:   65 00:55:10        8.507967        0.266593
 
    
 
    
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+
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    LBFGS:   67 02:14:01        8.497575        0.162253
+
    LBFGS:   67 00:55:10        8.497575        0.162253
 
    
 
    
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    LBFGS:   68 02:14:01        8.485434        0.202203
+
    LBFGS:   68 00:55:10        8.485434        0.202203
 
    
 
    
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    LBFGS:   69 02:14:01        8.466738        0.215895
+
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    LBFGS:   70 02:14:01        8.467607        0.334764
+
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+
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    LBFGS:   72 02:14:01        8.448980        0.119721
+
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+
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+
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    LBFGS:   75 02:14:01        8.443403        0.038831
+
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    LBFGS:   76 02:14:01        8.442646        0.054772
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
    LBFGS:  100 00:55:10        8.358921        0.013159
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/ase/io/extxyz.py:311: UserWarning: Skipping unhashable information adsorbate_info
@@ -1401,7 +1404,7 @@ 
    Viewing a trajectory
    <Axes: title={'center': 'final'}>
 
    
 
    
-../_images/6e93e34104c6236abbd25466bec810cc5a44f1fce8c2eef3ccb492932b39d7ac.png
+../_images/57fc29d6b458f6d6888e1ee0b717ee77535081c6ef989960bdcb2fb141022503.png
 
    
 
    
 
@@ -1518,7 +1521,7 @@ 
    Periodic boundary conditions (PBC)
    <Axes: title={'center': 'final'}>
 
    
 
    
-../_images/602efc1bfe102d11b640d4fa22736f0192d4cb2ec5cca76c32812c02f35ec424.png
+../_images/9f84ba124ebf741b5afc847f63508397b1de4a4506c555154294231e66b6d757.png
 
    
 
    
 
@@ -1617,7 +1620,7 @@ 
    Adsorption energy
    /tmp/ipykernel_2867/2478225434.py:7: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_2852/2478225434.py:7: DeprecationWarning: Please use atoms.calc = calc
   raw_slab.set_calculator(EMT())
 
    
 
    
@@ -1642,7 +1645,7 @@ 
    Plot energy profile of toy trajectory
    Text(0, 0.5, 'Energy, eV')
 
    
 
    
-../_images/c345947e7668b33a314d59121094f353e2623573ea3dd213d23a6b486bfbee9e.png
+../_images/441a9966a5b92807bb6c44051b68e2d8f68c6ea2df63b5fa0cdd822583379c1e.png
 
    
 
    
 
@@ -1829,7 +1832,7 @@ 
    Interacting with the OC20 datasets
-../_images/2f5258505cbaf133d92a049e74a43d8084112179d0ac78623e14191fa46c4bff.png
+../_images/788344ba64740a0f0cf4c2a7898aac5955c808a7740ac978f586fd458b12aac0.png
 
    
 
    
 
@@ -1907,7 +1910,7 @@ 
    Imports#<
 
    
 
    
 
    
-
    2024-08-03 02:14:07 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+
    2024-08-14 00:55:16 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
 
    
 
    
 
    
@@ -1960,13 +1963,13 @@ 
    Define the Config
-
    --2024-08-03 02:14:08--  https://github.com/FAIR-Chem/fairchem/raw/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc-large.pt
+
    --2024-08-14 00:55:17--  https://github.com/FAIR-Chem/fairchem/raw/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc-large.pt
 
    
 
    
-
    Resolving github.com (github.com)... 140.82.112.3
+
    Resolving github.com (github.com)... 140.82.114.3
 
    
 
    
-
    Connecting to github.com (github.com)|140.82.112.3|:443... connected.
+
    Connecting to github.com (github.com)|140.82.114.3|:443... connected.
 
    
 
    
 
    HTTP request sent, awaiting response... 302 Found
@@ -1975,13 +1978,13 @@ 
    Define the Config
    Location: https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc-large.pt [following]
 
    
 
    
-
    --2024-08-03 02:14:08--  https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc-large.pt
+
    --2024-08-14 00:55:17--  https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc-large.pt
 
    
 
    
-
    Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.108.133, ...
+
    Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.111.133, 185.199.110.133, ...
 
    
 
    
-
    Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
+
    Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
 
    
 
    
 
    HTTP request sent, awaiting response... 200 OK
@@ -1996,25 +1999,25 @@ 
    Define the Config
    
 
    
 
    
-
         0K .......... .......... ......                          100% 32.6M=0.001s
+
         0K .......... .......... ......                          100% 83.3M=0s
 
    
 
    
 
    
 
    
 
    
-
    2024-08-03 02:14:08 (32.6 MB/s) - ‘gemnet-oc-large.pt’ saved [27199/27199]
+
    2024-08-14 00:55:17 (83.3 MB/s) - ‘gemnet-oc-large.pt’ saved [27199/27199]
 
    
 
    
 
    
 
    
 
    
-
    --2024-08-03 02:14:08--  https://github.com/FAIR-Chem/fairchem/raw/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc.pt
+
    --2024-08-14 00:55:17--  https://github.com/FAIR-Chem/fairchem/raw/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc.pt
 
    
 
    
-
    Resolving github.com (github.com)... 140.82.112.3
+
    Resolving github.com (github.com)... 140.82.114.3
 
    
 
    
-
    Connecting to github.com (github.com)|140.82.112.3|:443... connected.
+
    Connecting to github.com (github.com)|140.82.114.3|:443... connected.
 
    
 
    
 
    HTTP request sent, awaiting response... 302 Found
@@ -2023,10 +2026,10 @@ 
    Define the Config
    Location: https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc.pt [following]
 
    
 
    
-
    --2024-08-03 02:14:08--  https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc.pt
+
    --2024-08-14 00:55:17--  https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-oc.pt
 
    
 
    
-
    Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.109.133, 185.199.111.133, ...
+
    Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.109.133, ...
 
    
 
    
 
    Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
@@ -2044,25 +2047,25 @@ 
    Define the Config
    
 
    
 
    
-
         0K .......... ......                                     100% 22.8M=0.001s
+
         0K .......... ......                                     100% 75.7M=0s
 
    
 
    
 
    
 
    
 
    
-
    2024-08-03 02:14:08 (22.8 MB/s) - ‘gemnet-oc.pt’ saved [16963/16963]
+
    2024-08-14 00:55:17 (75.7 MB/s) - ‘gemnet-oc.pt’ saved [16963/16963]
 
    
 
    
 
    
 
    
 
    
-
    --2024-08-03 02:14:08--  https://github.com/FAIR-Chem/fairchem/raw/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-dT.json
+
    --2024-08-14 00:55:17--  https://github.com/FAIR-Chem/fairchem/raw/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-dT.json
 
    
 
    
-
    Resolving github.com (github.com)... 140.82.112.3
+
    Resolving github.com (github.com)... 140.82.114.3
 
    
 
    
-
    Connecting to github.com (github.com)|140.82.112.3|:443... connected.
+
    Connecting to github.com (github.com)|140.82.114.3|:443... connected.
 
    
 
    
 
    HTTP request sent, awaiting response... 302 Found
@@ -2071,13 +2074,13 @@ 
    Define the Config
    Location: https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-dT.json [following]
 
    
 
    
-
    --2024-08-03 02:14:08--  https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-dT.json
+
    --2024-08-14 00:55:18--  https://raw.githubusercontent.com/FAIR-Chem/fairchem/main/configs/s2ef/all/gemnet/scaling_factors/gemnet-dT.json
 
    
 
    
-
    Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.108.133, 185.199.109.133, ...
+
    Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.111.133, 185.199.109.133, ...
 
    
 
    
-
    Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
+
    Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
 
    
 
    
 
    HTTP request sent, awaiting response... 200 OK
@@ -2092,13 +2095,13 @@ 
    Define the Config
    
 
    
 
    
-
         0K                                                       100% 52.8M=0s
+
         0K                                                       100% 55.5M=0s
 
    
 
    
 
    
 
    
 
    
-
    2024-08-03 02:14:08 (52.8 MB/s) - ‘gemnet-dT.json’ saved [816/816]
+
    2024-08-14 00:55:18 (55.5 MB/s) - ‘gemnet-dT.json’ saved [816/816]
 
    
 
    
 
    
@@ -2240,20 +2243,20 @@ 
    Create the trainer
-
    2024-08-03 02:14:08 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+
    2024-08-14 00:55:18 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
 
    
 
    
-
    2024-08-03 02:14:08 (INFO): amp: true
+
    2024-08-14 00:55:18 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-08-03-02-14-24-S2EF-example
-  commit: 08b8c1e
+  checkpoint_dir: ./checkpoints/2024-08-14-00-55-28-S2EF-example
+  commit: 8fb16d6
   identifier: S2EF-example
-  logs_dir: ./logs/tensorboard/2024-08-03-02-14-24-S2EF-example
+  logs_dir: ./logs/tensorboard/2024-08-14-00-55-28-S2EF-example
   print_every: 5
-  results_dir: ./results/2024-08-03-02-14-24-S2EF-example
+  results_dir: ./results/2024-08-14-00-55-28-S2EF-example
   seed: 0
-  timestamp_id: 2024-08-03-02-14-24-S2EF-example
-  version: 0.1.dev1+g08b8c1e
+  timestamp_id: 2024-08-14-00-55-28-S2EF-example
+  version: 1.1.0
 dataset:
   format: lmdb
   grad_target_mean: 0.0
@@ -2327,8 +2330,7 @@ 
    Create the trainer
    2024-08-03 02:14:08 (INFO): Loading dataset: lmdb
+
    2024-08-14 00:55:18 (INFO): Loading dataset: lmdb
 
    
 
    
-
    2024-08-03 02:14:08 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/train_100')]'
+
    2024-08-14 00:55:18 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/train_100')]'
 
    
 
    
-
    2024-08-03 02:14:08 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 00:55:18 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:14:08 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 00:55:18 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:14:08 (INFO): rank: 0: Sampler created...
+
    2024-08-14 00:55:18 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:14:08 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff8eb5a7b50>, batch_size=1, drop_last=False
+
    2024-08-14 00:55:18 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd84c48d610>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:14:08 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
+
    2024-08-14 00:55:18 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
 
    
 
    
-
    2024-08-03 02:14:08 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 00:55:18 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:14:08 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 00:55:18 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:14:08 (INFO): rank: 0: Sampler created...
+
    2024-08-14 00:55:18 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:14:08 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff8eb1e1e50>, batch_size=1, drop_last=False
+
    2024-08-14 00:55:18 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd84e4eb390>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:14:08 (INFO): Loading model: gemnet_oc
+
    2024-08-14 00:55:18 (INFO): normalizers checkpoint for targets ['energy'] have been saved to: ./checkpoints/2024-08-14-00-55-28-S2EF-example/normalizers.pt
 
    
 
    
-
    2024-08-03 02:14:10 (INFO): Loaded GemNetOC with 2596214 parameters.
+
    2024-08-14 00:55:18 (INFO): normalizers checkpoint for targets ['energy', 'forces'] have been saved to: ./checkpoints/2024-08-14-00-55-28-S2EF-example/normalizers.pt
 
    
 
    
-
    2024-08-03 02:14:10 (WARNING): log_summary for Tensorboard not supported
+
    2024-08-14 00:55:18 (INFO): Normalization values for output energy: mean=0.45158625849998374, rmsd=1.5156444102461508.
+
    
+
    
+
    2024-08-14 00:55:18 (INFO): Normalization values for output forces: mean=0.0, rmsd=1.5156444102461508.
+
    
+
    
+
    2024-08-14 00:55:18 (INFO): Loading model: gemnet_oc
+
    
+
    
+
    2024-08-14 00:55:19 (INFO): Loaded GemNetOC with 2596214 parameters.
+
    
+
    
+
    2024-08-14 00:55:19 (WARNING): log_summary for Tensorboard not supported
 
    
 
    
 
    
@@ -2487,67 +2502,67 @@ 
    Train the model
    2024-08-03 02:14:15 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.09e+01, forcesx_mae: 3.30e-01, forcesy_mae: 3.57e-01, forcesz_mae: 4.72e-01, forces_mae: 3.87e-01, forces_cosine_similarity: 1.86e-02, forces_magnitude_error: 6.38e-01, loss: 7.25e+01, lr: 5.00e-04, epoch: 5.00e-02, step: 5.00e+00
+
    2024-08-14 00:55:24 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.09e+01, forcesx_mae: 3.30e-01, forcesy_mae: 3.57e-01, forcesz_mae: 4.72e-01, forces_mae: 3.87e-01, forces_cosine_similarity: 1.86e-02, forces_magnitude_error: 6.38e-01, loss: 7.25e+01, lr: 5.00e-04, epoch: 5.00e-02, step: 5.00e+00
 
    
 
    
-
    2024-08-03 02:14:20 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 8.43e+00, forcesx_mae: 1.68e-01, forcesy_mae: 1.81e-01, forcesz_mae: 2.19e-01, forces_mae: 1.89e-01, forces_cosine_similarity: 4.28e-02, forces_magnitude_error: 2.69e-01, loss: 3.04e+01, lr: 5.00e-04, epoch: 1.00e-01, step: 1.00e+01
+
    2024-08-14 00:55:29 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 8.43e+00, forcesx_mae: 1.68e-01, forcesy_mae: 1.81e-01, forcesz_mae: 2.19e-01, forces_mae: 1.89e-01, forces_cosine_similarity: 4.28e-02, forces_magnitude_error: 2.69e-01, loss: 3.04e+01, lr: 5.00e-04, epoch: 1.00e-01, step: 1.00e+01
 
    
 
    
-
    2024-08-03 02:14:25 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 4.58e+00, forcesx_mae: 1.44e-01, forcesy_mae: 2.21e-01, forcesz_mae: 2.22e-01, forces_mae: 1.95e-01, forces_cosine_similarity: 8.30e-02, forces_magnitude_error: 2.61e-01, loss: 2.73e+01, lr: 5.00e-04, epoch: 1.50e-01, step: 1.50e+01
+
    2024-08-14 00:55:35 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 4.58e+00, forcesx_mae: 1.44e-01, forcesy_mae: 2.21e-01, forcesz_mae: 2.22e-01, forces_mae: 1.95e-01, forces_cosine_similarity: 8.30e-02, forces_magnitude_error: 2.61e-01, loss: 2.73e+01, lr: 5.00e-04, epoch: 1.50e-01, step: 1.50e+01
 
    
 
    
-
    2024-08-03 02:14:31 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.41e+01, forcesx_mae: 3.02e-01, forcesy_mae: 1.15e+00, forcesz_mae: 5.77e-01, forces_mae: 6.76e-01, forces_cosine_similarity: -1.29e-01, forces_magnitude_error: 1.09e+00, loss: 1.00e+02, lr: 5.00e-04, epoch: 2.00e-01, step: 2.00e+01
+
    2024-08-14 00:55:40 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.41e+01, forcesx_mae: 3.02e-01, forcesy_mae: 1.15e+00, forcesz_mae: 5.77e-01, forces_mae: 6.76e-01, forces_cosine_similarity: -1.29e-01, forces_magnitude_error: 1.09e+00, loss: 1.00e+02, lr: 5.00e-04, epoch: 2.00e-01, step: 2.00e+01
 
    
 
    
-
    2024-08-03 02:14:36 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 9.50e+00, forcesx_mae: 2.23e-01, forcesy_mae: 4.82e-01, forcesz_mae: 3.30e-01, forces_mae: 3.45e-01, forces_cosine_similarity: 1.79e-01, forces_magnitude_error: 4.21e-01, loss: 4.95e+01, lr: 5.00e-04, epoch: 2.50e-01, step: 2.50e+01
+
    2024-08-14 00:55:45 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 9.50e+00, forcesx_mae: 2.23e-01, forcesy_mae: 4.82e-01, forcesz_mae: 3.30e-01, forces_mae: 3.45e-01, forces_cosine_similarity: 1.79e-01, forces_magnitude_error: 4.21e-01, loss: 4.95e+01, lr: 5.00e-04, epoch: 2.50e-01, step: 2.50e+01
 
    
 
    
-
    2024-08-03 02:14:41 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.92e+00, forcesx_mae: 9.23e-02, forcesy_mae: 1.45e-01, forcesz_mae: 1.41e-01, forces_mae: 1.26e-01, forces_cosine_similarity: 1.35e-01, forces_magnitude_error: 1.37e-01, loss: 1.81e+01, lr: 5.00e-04, epoch: 3.00e-01, step: 3.00e+01
+
    2024-08-14 00:55:50 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.92e+00, forcesx_mae: 9.23e-02, forcesy_mae: 1.45e-01, forcesz_mae: 1.41e-01, forces_mae: 1.26e-01, forces_cosine_similarity: 1.35e-01, forces_magnitude_error: 1.37e-01, loss: 1.81e+01, lr: 5.00e-04, epoch: 3.00e-01, step: 3.00e+01
 
    
 
    
-
    2024-08-03 02:14:46 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.27e+00, forcesx_mae: 9.02e-02, forcesy_mae: 1.01e-01, forcesz_mae: 1.37e-01, forces_mae: 1.09e-01, forces_cosine_similarity: 1.75e-01, forces_magnitude_error: 1.57e-01, loss: 1.53e+01, lr: 5.00e-04, epoch: 3.50e-01, step: 3.50e+01
+
    2024-08-14 00:55:55 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.27e+00, forcesx_mae: 9.02e-02, forcesy_mae: 1.01e-01, forcesz_mae: 1.37e-01, forces_mae: 1.09e-01, forces_cosine_similarity: 1.75e-01, forces_magnitude_error: 1.57e-01, loss: 1.53e+01, lr: 5.00e-04, epoch: 3.50e-01, step: 3.50e+01
 
    
 
    
-
    2024-08-03 02:14:51 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.54e+00, forcesx_mae: 1.15e-01, forcesy_mae: 2.91e-01, forcesz_mae: 1.59e-01, forces_mae: 1.88e-01, forces_cosine_similarity: 1.06e-01, forces_magnitude_error: 2.78e-01, loss: 2.80e+01, lr: 5.00e-04, epoch: 4.00e-01, step: 4.00e+01
+
    2024-08-14 00:56:01 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.54e+00, forcesx_mae: 1.15e-01, forcesy_mae: 2.91e-01, forcesz_mae: 1.59e-01, forces_mae: 1.88e-01, forces_cosine_similarity: 1.06e-01, forces_magnitude_error: 2.78e-01, loss: 2.80e+01, lr: 5.00e-04, epoch: 4.00e-01, step: 4.00e+01
 
    
 
    
-
    2024-08-03 02:14:57 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 5.46e+00, forcesx_mae: 2.24e-01, forcesy_mae: 4.34e-01, forcesz_mae: 2.30e-01, forces_mae: 2.96e-01, forces_cosine_similarity: 6.79e-02, forces_magnitude_error: 5.51e-01, loss: 3.59e+01, lr: 5.00e-04, epoch: 4.50e-01, step: 4.50e+01
+
    2024-08-14 00:56:06 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 5.46e+00, forcesx_mae: 2.24e-01, forcesy_mae: 4.34e-01, forcesz_mae: 2.30e-01, forces_mae: 2.96e-01, forces_cosine_similarity: 6.79e-02, forces_magnitude_error: 5.51e-01, loss: 3.59e+01, lr: 5.00e-04, epoch: 4.50e-01, step: 4.50e+01
 
    
 
    
-
    2024-08-03 02:15:02 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.35e+00, forcesx_mae: 9.93e-02, forcesy_mae: 1.12e-01, forcesz_mae: 1.72e-01, forces_mae: 1.28e-01, forces_cosine_similarity: 2.90e-01, forces_magnitude_error: 2.32e-01, loss: 1.78e+01, lr: 5.00e-04, epoch: 5.00e-01, step: 5.00e+01
+
    2024-08-14 00:56:11 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.35e+00, forcesx_mae: 9.93e-02, forcesy_mae: 1.12e-01, forcesz_mae: 1.72e-01, forces_mae: 1.28e-01, forces_cosine_similarity: 2.90e-01, forces_magnitude_error: 2.32e-01, loss: 1.78e+01, lr: 5.00e-04, epoch: 5.00e-01, step: 5.00e+01
 
    
 
    
-
    2024-08-03 02:15:07 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.67e+00, forcesx_mae: 1.29e-01, forcesy_mae: 2.21e-01, forcesz_mae: 1.52e-01, forces_mae: 1.67e-01, forces_cosine_similarity: 8.87e-02, forces_magnitude_error: 1.98e-01, loss: 2.35e+01, lr: 5.00e-04, epoch: 5.50e-01, step: 5.50e+01
+
    2024-08-14 00:56:16 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.67e+00, forcesx_mae: 1.29e-01, forcesy_mae: 2.21e-01, forcesz_mae: 1.52e-01, forces_mae: 1.67e-01, forces_cosine_similarity: 8.87e-02, forces_magnitude_error: 1.98e-01, loss: 2.35e+01, lr: 5.00e-04, epoch: 5.50e-01, step: 5.50e+01
 
    
 
    
-
    2024-08-03 02:15:12 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.80e+00, forcesx_mae: 1.35e-01, forcesy_mae: 1.67e-01, forcesz_mae: 1.72e-01, forces_mae: 1.58e-01, forces_cosine_similarity: 1.41e-01, forces_magnitude_error: 2.35e-01, loss: 1.84e+01, lr: 5.00e-04, epoch: 6.00e-01, step: 6.00e+01
+
    2024-08-14 00:56:21 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.80e+00, forcesx_mae: 1.35e-01, forcesy_mae: 1.67e-01, forcesz_mae: 1.72e-01, forces_mae: 1.58e-01, forces_cosine_similarity: 1.41e-01, forces_magnitude_error: 2.35e-01, loss: 1.84e+01, lr: 5.00e-04, epoch: 6.00e-01, step: 6.00e+01
 
    
 
    
-
    2024-08-03 02:15:18 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.54e+00, forcesx_mae: 1.12e-01, forcesy_mae: 1.63e-01, forcesz_mae: 1.58e-01, forces_mae: 1.44e-01, forces_cosine_similarity: 2.15e-01, forces_magnitude_error: 1.86e-01, loss: 1.87e+01, lr: 5.00e-04, epoch: 6.50e-01, step: 6.50e+01
+
    2024-08-14 00:56:27 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.54e+00, forcesx_mae: 1.12e-01, forcesy_mae: 1.63e-01, forcesz_mae: 1.58e-01, forces_mae: 1.44e-01, forces_cosine_similarity: 2.15e-01, forces_magnitude_error: 1.86e-01, loss: 1.87e+01, lr: 5.00e-04, epoch: 6.50e-01, step: 6.50e+01
 
    
 
    
-
    2024-08-03 02:15:23 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 5.65e+00, forcesx_mae: 8.02e-02, forcesy_mae: 7.68e-02, forcesz_mae: 1.02e-01, forces_mae: 8.65e-02, forces_cosine_similarity: 2.34e-01, forces_magnitude_error: 1.13e-01, loss: 1.31e+01, lr: 5.00e-04, epoch: 7.00e-01, step: 7.00e+01
+
    2024-08-14 00:56:32 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 5.65e+00, forcesx_mae: 8.02e-02, forcesy_mae: 7.68e-02, forcesz_mae: 1.02e-01, forces_mae: 8.65e-02, forces_cosine_similarity: 2.34e-01, forces_magnitude_error: 1.13e-01, loss: 1.31e+01, lr: 5.00e-04, epoch: 7.00e-01, step: 7.00e+01
 
    
 
    
-
    2024-08-03 02:15:28 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.50e+00, forcesx_mae: 1.66e-01, forcesy_mae: 1.86e-01, forcesz_mae: 2.47e-01, forces_mae: 2.00e-01, forces_cosine_similarity: 1.88e-01, forces_magnitude_error: 3.13e-01, loss: 2.87e+01, lr: 5.00e-04, epoch: 7.50e-01, step: 7.50e+01
+
    2024-08-14 00:56:37 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.50e+00, forcesx_mae: 1.66e-01, forcesy_mae: 1.86e-01, forcesz_mae: 2.47e-01, forces_mae: 2.00e-01, forces_cosine_similarity: 1.88e-01, forces_magnitude_error: 3.13e-01, loss: 2.87e+01, lr: 5.00e-04, epoch: 7.50e-01, step: 7.50e+01
 
    
 
    
-
    2024-08-03 02:15:33 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.48e+00, forcesx_mae: 9.29e-02, forcesy_mae: 1.61e-01, forcesz_mae: 1.26e-01, forces_mae: 1.27e-01, forces_cosine_similarity: 1.74e-01, forces_magnitude_error: 1.60e-01, loss: 1.78e+01, lr: 5.00e-04, epoch: 8.00e-01, step: 8.00e+01
+
    2024-08-14 00:56:42 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.48e+00, forcesx_mae: 9.29e-02, forcesy_mae: 1.61e-01, forcesz_mae: 1.26e-01, forces_mae: 1.27e-01, forces_cosine_similarity: 1.74e-01, forces_magnitude_error: 1.60e-01, loss: 1.78e+01, lr: 5.00e-04, epoch: 8.00e-01, step: 8.00e+01
 
    
 
    
-
    2024-08-03 02:15:39 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 4.68e+00, forcesx_mae: 1.63e-01, forcesy_mae: 2.52e-01, forcesz_mae: 2.53e-01, forces_mae: 2.23e-01, forces_cosine_similarity: 1.71e-01, forces_magnitude_error: 3.72e-01, loss: 3.41e+01, lr: 5.00e-04, epoch: 8.50e-01, step: 8.50e+01
+
    2024-08-14 00:56:48 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 4.68e+00, forcesx_mae: 1.63e-01, forcesy_mae: 2.52e-01, forcesz_mae: 2.53e-01, forces_mae: 2.23e-01, forces_cosine_similarity: 1.71e-01, forces_magnitude_error: 3.72e-01, loss: 3.41e+01, lr: 5.00e-04, epoch: 8.50e-01, step: 8.50e+01
 
    
 
    
-
    2024-08-03 02:15:44 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.49e+00, forcesx_mae: 4.96e-02, forcesy_mae: 7.33e-02, forcesz_mae: 5.31e-02, forces_mae: 5.86e-02, forces_cosine_similarity: 1.68e-01, forces_magnitude_error: 7.36e-02, loss: 7.56e+00, lr: 5.00e-04, epoch: 9.00e-01, step: 9.00e+01
+
    2024-08-14 00:56:53 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.49e+00, forcesx_mae: 4.96e-02, forcesy_mae: 7.33e-02, forcesz_mae: 5.31e-02, forces_mae: 5.86e-02, forces_cosine_similarity: 1.68e-01, forces_magnitude_error: 7.36e-02, loss: 7.56e+00, lr: 5.00e-04, epoch: 9.00e-01, step: 9.00e+01
 
    
 
    
-
    2024-08-03 02:15:49 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.72e+00, forcesx_mae: 2.11e-01, forcesy_mae: 2.87e-01, forcesz_mae: 3.33e-01, forces_mae: 2.77e-01, forces_cosine_similarity: 2.29e-01, forces_magnitude_error: 5.15e-01, loss: 3.04e+01, lr: 5.00e-04, epoch: 9.50e-01, step: 9.50e+01
+
    2024-08-14 00:56:58 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.72e+00, forcesx_mae: 2.11e-01, forcesy_mae: 2.87e-01, forcesz_mae: 3.33e-01, forces_mae: 2.77e-01, forces_cosine_similarity: 2.29e-01, forces_magnitude_error: 5.15e-01, loss: 3.04e+01, lr: 5.00e-04, epoch: 9.50e-01, step: 9.50e+01
 
    
 
    
-
    2024-08-03 02:15:54 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 7.20e-01, forcesx_mae: 3.24e-02, forcesy_mae: 3.54e-02, forcesz_mae: 5.30e-02, forces_mae: 4.03e-02, forces_cosine_similarity: 2.61e-01, forces_magnitude_error: 5.69e-02, loss: 5.80e+00, lr: 5.00e-04, epoch: 1.00e+00, step: 1.00e+02
+
    2024-08-14 00:57:03 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 7.19e-01, forcesx_mae: 3.24e-02, forcesy_mae: 3.54e-02, forcesz_mae: 5.30e-02, forces_mae: 4.03e-02, forces_cosine_similarity: 2.61e-01, forces_magnitude_error: 5.69e-02, loss: 5.80e+00, lr: 5.00e-04, epoch: 1.00e+00, step: 1.00e+02
 
    
 
    
-
    2024-08-03 02:15:54 (INFO): Evaluating on val.
+
    2024-08-14 00:57:03 (INFO): Evaluating on val.
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
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    2024-08-03 02:15:59 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 9.1440, forcesx_mae: 0.3023, forcesy_mae: 0.2598, forcesz_mae: 0.4722, forces_mae: 0.3448, forces_cosine_similarity: 0.0188, forces_magnitude_error: 0.4904, loss: 53.1097, epoch: 1.0000
+
    2024-08-14 00:57:08 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 9.1440, forcesx_mae: 0.3023, forcesy_mae: 0.2598, forcesz_mae: 0.4722, forces_mae: 0.3448, forces_cosine_similarity: 0.0188, forces_magnitude_error: 0.4904, loss: 53.1097, epoch: 1.0000
 
    
 
    
 
    
@@ -2651,7 +2666,7 @@ 
    Load the best checkpoint
-
    './checkpoints/2024-08-03-02-14-24-S2EF-example/best_checkpoint.pt'
+
    './checkpoints/2024-08-14-00-55-28-S2EF-example/best_checkpoint.pt'
 
    
 
    
 
    
@@ -2707,20 +2722,20 @@ 
    Load the best checkpoint
-
    2024-08-03 02:15:59 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+
    2024-08-14 00:57:08 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
 
    
 
    
-
    2024-08-03 02:15:59 (INFO): amp: true
+
    2024-08-14 00:57:08 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-08-03-02-16-32-S2EF-val-example
-  commit: 08b8c1e
+  checkpoint_dir: ./checkpoints/2024-08-14-00-57-36-S2EF-val-example
+  commit: 8fb16d6
   identifier: S2EF-val-example
-  logs_dir: ./logs/tensorboard/2024-08-03-02-16-32-S2EF-val-example
+  logs_dir: ./logs/tensorboard/2024-08-14-00-57-36-S2EF-val-example
   print_every: 5
-  results_dir: ./results/2024-08-03-02-16-32-S2EF-val-example
+  results_dir: ./results/2024-08-14-00-57-36-S2EF-val-example
   seed: 0
-  timestamp_id: 2024-08-03-02-16-32-S2EF-val-example
-  version: 0.1.dev1+g08b8c1e
+  timestamp_id: 2024-08-14-00-57-36-S2EF-val-example
+  version: 1.1.0
 dataset:
   format: lmdb
   grad_target_mean: 0.0
@@ -2794,8 +2809,7 @@ 
    Load the best checkpoint
    2024-08-03 02:15:59 (INFO): Loading dataset: lmdb
+
    2024-08-14 00:57:08 (INFO): Loading dataset: lmdb
+
    
+
    
+
    2024-08-14 00:57:08 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/train_100')]'
+
    
+
    
+
    2024-08-14 00:57:08 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    
+
    
+
    2024-08-14 00:57:08 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    
+
    
+
    2024-08-14 00:57:08 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:15:59 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/train_100')]'
+
    2024-08-14 00:57:08 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd8853f2410>, batch_size=1, drop_last=False
 
    
 
    
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    2024-08-03 02:15:59 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 00:57:08 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
 
    
 
    
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    2024-08-03 02:15:59 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
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    2024-08-14 00:57:08 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
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    2024-08-03 02:15:59 (INFO): rank: 0: Sampler created...
+
    2024-08-14 00:57:08 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:15:59 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff8e8177510>, batch_size=1, drop_last=False
+
    2024-08-14 00:57:08 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:15:59 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
+
    2024-08-14 00:57:08 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd885285a10>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:15:59 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 00:57:08 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
 
    
 
    
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    2024-08-03 02:15:59 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 00:57:08 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:15:59 (INFO): rank: 0: Sampler created...
+
    2024-08-14 00:57:08 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:15:59 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff924a6eb90>, batch_size=1, drop_last=False
+
    2024-08-14 00:57:08 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:15:59 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
+
    2024-08-14 00:57:08 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd885285310>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:15:59 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 00:57:08 (INFO): normalizers checkpoint for targets ['energy'] have been saved to: ./checkpoints/2024-08-14-00-57-36-S2EF-val-example/normalizers.pt
 
    
 
    
-
    2024-08-03 02:15:59 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 00:57:08 (INFO): normalizers checkpoint for targets ['energy', 'forces'] have been saved to: ./checkpoints/2024-08-14-00-57-36-S2EF-val-example/normalizers.pt
 
    
 
    
-
    2024-08-03 02:15:59 (INFO): rank: 0: Sampler created...
+
    2024-08-14 00:57:08 (INFO): Normalization values for output energy: mean=0.45158625849998374, rmsd=1.5156444102461508.
 
    
 
    
-
    2024-08-03 02:15:59 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff9249fb690>, batch_size=1, drop_last=False
+
    2024-08-14 00:57:08 (INFO): Normalization values for output forces: mean=0.0, rmsd=1.5156444102461508.
 
    
 
    
-
    2024-08-03 02:15:59 (INFO): Loading model: gemnet_oc
+
    2024-08-14 00:57:08 (INFO): Loading model: gemnet_oc
 
    
 
    
-
    2024-08-03 02:16:00 (INFO): Loaded GemNetOC with 2596214 parameters.
+
    2024-08-14 00:57:09 (INFO): Loaded GemNetOC with 2596214 parameters.
 
    
 
    
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    2024-08-03 02:16:00 (WARNING): log_summary for Tensorboard not supported
+
    2024-08-14 00:57:09 (WARNING): log_summary for Tensorboard not supported
 
    
 
    
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    2024-08-14 00:57:09 (INFO): Loading checkpoint from: ./checkpoints/2024-08-14-00-55-28-S2EF-example/best_checkpoint.pt
 
    
 
    
 
    
@@ -2966,7 +2993,7 @@ 
    Run on the test set
-
    2024-08-03 02:16:00 (INFO): Predicting on test.
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    2024-08-14 00:57:09 (INFO): Predicting on test.
 
    
 
    
 
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+
    device 0:  90%|█████████ | 18/20 [00:04<00:00,  4.97it/s]
 
    
 
    
-
    device 0:  95%|█████████▌| 19/20 [00:04<00:00,  4.92it/s]
+
    device 0:  95%|█████████▌| 19/20 [00:04<00:00,  4.74it/s]
 
    
 
    
-
    device 0: 100%|██████████| 20/20 [00:04<00:00,  4.86it/s]
+
    device 0: 100%|██████████| 20/20 [00:04<00:00,  4.75it/s]
 
    
 
    
-
    device 0: 100%|██████████| 20/20 [00:04<00:00,  4.38it/s]
+
    device 0: 100%|██████████| 20/20 [00:04<00:00,  4.41it/s]
 
    
 
    
-
    2024-08-03 02:16:04 (INFO): Writing results to ./results/2024-08-03-02-16-32-S2EF-val-example/s2ef_s2ef_results.npz
+
    2024-08-14 00:57:13 (INFO): Writing results to ./results/2024-08-14-00-57-36-S2EF-val-example/s2ef_s2ef_results.npz
 
    
 
    
 
    
@@ -3233,20 +3260,20 @@ 
    Define the Config
-
    2024-08-03 02:16:05 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+
    2024-08-14 00:57:14 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
 
    
 
    
-
    2024-08-03 02:16:05 (INFO): amp: true
+
    2024-08-14 00:57:14 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-08-03-02-16-32-IS2RE-example
-  commit: 08b8c1e
+  checkpoint_dir: ./checkpoints/2024-08-14-00-57-36-IS2RE-example
+  commit: 8fb16d6
   identifier: IS2RE-example
-  logs_dir: ./logs/tensorboard/2024-08-03-02-16-32-IS2RE-example
+  logs_dir: ./logs/tensorboard/2024-08-14-00-57-36-IS2RE-example
   print_every: 5
-  results_dir: ./results/2024-08-03-02-16-32-IS2RE-example
+  results_dir: ./results/2024-08-14-00-57-36-IS2RE-example
   seed: 0
-  timestamp_id: 2024-08-03-02-16-32-IS2RE-example
-  version: 0.1.dev1+g08b8c1e
+  timestamp_id: 2024-08-14-00-57-36-IS2RE-example
+  version: 1.1.0
 dataset:
   format: single_point_lmdb
   key_mapping:
@@ -3301,8 +3328,7 @@ 
    Define the Config
    2024-08-03 02:16:05 (INFO): Loading dataset: single_point_lmdb
+
    2024-08-14 00:57:14 (INFO): Loading dataset: single_point_lmdb
 
    
 
    
-
    2024-08-03 02:16:05 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/train_100/data.lmdb')]'
+
    2024-08-14 00:57:14 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/train_100/data.lmdb')]'
 
    
 
    
-
    2024-08-03 02:16:05 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 00:57:14 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:16:05 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 00:57:14 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:16:05 (INFO): rank: 0: Sampler created...
+
    2024-08-14 00:57:14 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:16:05 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff8e2bdb090>, batch_size=1, drop_last=False
+
    2024-08-14 00:57:14 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd8854f9d10>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:16:05 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/val_20/data.lmdb')]'
+
    2024-08-14 00:57:14 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/val_20/data.lmdb')]'
 
    
 
    
-
    2024-08-03 02:16:05 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 00:57:14 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:16:05 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 00:57:14 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:16:05 (INFO): rank: 0: Sampler created...
+
    2024-08-14 00:57:14 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:16:05 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff8e2aaa510>, batch_size=1, drop_last=False
+
    2024-08-14 00:57:14 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd87adc1790>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:16:05 (INFO): Loading model: gemnet_t
+
    2024-08-14 00:57:14 (INFO): normalizers checkpoint for targets ['energy'] have been saved to: ./checkpoints/2024-08-14-00-57-36-IS2RE-example/normalizers.pt
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor OutBlock_0_had not found in model
+
    2024-08-14 00:57:14 (INFO): normalizers checkpoint for targets ['energy', 'forces'] have been saved to: ./checkpoints/2024-08-14-00-57-36-IS2RE-example/normalizers.pt
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor OutBlock_1_had not found in model
+
    2024-08-14 00:57:14 (INFO): Normalization values for output energy: mean=-1.4570415561499996, rmsd=1.8371084209427546.
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor OutBlock_2_had not found in model
+
    2024-08-14 00:57:14 (INFO): Normalization values for output forces: mean=0, rmsd=1.
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor OutBlock_3_had not found in model
+
    2024-08-14 00:57:14 (INFO): Loading model: gemnet_t
 
    
 
    
-
    2024-08-03 02:16:06 (INFO): Loaded GemNetT with 22774037 parameters.
+
    2024-08-14 00:57:15 (WARNING): Scale factor OutBlock_0_had not found in model
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): log_summary for Tensorboard not supported
+
    2024-08-14 00:57:15 (WARNING): Scale factor OutBlock_1_had not found in model
+
    
+
    
+
    2024-08-14 00:57:15 (WARNING): Scale factor OutBlock_2_had not found in model
+
    
+
    
+
    2024-08-14 00:57:15 (WARNING): Scale factor OutBlock_3_had not found in model
+
    
+
    
+
    2024-08-14 00:57:15 (INFO): Loaded GemNetT with 22774037 parameters.
+
    
+
    
+
    2024-08-14 00:57:15 (WARNING): log_summary for Tensorboard not supported
 
    
 
    
 
    
@@ -3433,28 +3472,28 @@ 
    Train the Model
-
    2024-08-03 02:16:06 (WARNING): Scale factor OutBlock_4_sum (out_blocks.4.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 00:57:15 (WARNING): Scale factor OutBlock_4_sum (out_blocks.4.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor OutBlock_5_sum (out_blocks.5.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 00:57:15 (WARNING): Scale factor OutBlock_5_sum (out_blocks.5.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor TripInteraction_4_had_rbf (int_blocks.3.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 00:57:15 (WARNING): Scale factor TripInteraction_4_had_rbf (int_blocks.3.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor TripInteraction_4_sum_cbf (int_blocks.3.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 00:57:15 (WARNING): Scale factor TripInteraction_4_sum_cbf (int_blocks.3.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor AtomUpdate_4_sum (int_blocks.3.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 00:57:15 (WARNING): Scale factor AtomUpdate_4_sum (int_blocks.3.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor TripInteraction_5_had_rbf (int_blocks.4.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 00:57:15 (WARNING): Scale factor TripInteraction_5_had_rbf (int_blocks.4.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor TripInteraction_5_sum_cbf (int_blocks.4.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 00:57:15 (WARNING): Scale factor TripInteraction_5_sum_cbf (int_blocks.4.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:16:06 (WARNING): Scale factor AtomUpdate_5_sum (int_blocks.4.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 00:57:15 (WARNING): Scale factor AtomUpdate_5_sum (int_blocks.4.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
@@ -3465,126 +3504,126 @@ 
    Train the Model
    2024-08-03 02:16:16 (INFO): energy_mae: 3.27e+03, energy_mse: 2.48e+07, energy_within_threshold: 0.00e+00, loss: 1.78e+03, lr: 1.00e-04, epoch: 5.00e-02, step: 5.00e+00
+
    2024-08-14 00:57:26 (INFO): energy_mae: 3.27e+03, energy_mse: 2.48e+07, energy_within_threshold: 0.00e+00, loss: 1.78e+03, lr: 1.00e-04, epoch: 5.00e-02, step: 5.00e+00
 
    
 
    
-
    2024-08-03 02:16:29 (INFO): energy_mae: 3.39e+04, energy_mse: 4.47e+09, energy_within_threshold: 0.00e+00, loss: 1.85e+04, lr: 1.00e-04, epoch: 1.00e-01, step: 1.00e+01
+
    2024-08-14 00:57:38 (INFO): energy_mae: 3.39e+04, energy_mse: 4.47e+09, energy_within_threshold: 0.00e+00, loss: 1.85e+04, lr: 1.00e-04, epoch: 1.00e-01, step: 1.00e+01
 
    
 
    
-
    2024-08-03 02:16:42 (INFO): energy_mae: 5.03e+03, energy_mse: 5.01e+07, energy_within_threshold: 0.00e+00, loss: 2.74e+03, lr: 1.00e-04, epoch: 1.50e-01, step: 1.50e+01
+
    2024-08-14 00:57:51 (INFO): energy_mae: 5.04e+03, energy_mse: 5.03e+07, energy_within_threshold: 0.00e+00, loss: 2.75e+03, lr: 1.00e-04, epoch: 1.50e-01, step: 1.50e+01
 
    
 
    
-
    2024-08-03 02:16:54 (INFO): energy_mae: 1.87e+03, energy_mse: 9.16e+06, energy_within_threshold: 0.00e+00, loss: 1.02e+03, lr: 1.00e-04, epoch: 2.00e-01, step: 2.00e+01
+
    2024-08-14 00:58:03 (INFO): energy_mae: 1.84e+03, energy_mse: 8.68e+06, energy_within_threshold: 0.00e+00, loss: 1.00e+03, lr: 1.00e-04, epoch: 2.00e-01, step: 2.00e+01
 
    
 
    
-
    2024-08-03 02:17:07 (INFO): energy_mae: 3.58e+03, energy_mse: 2.63e+07, energy_within_threshold: 0.00e+00, loss: 1.95e+03, lr: 1.00e-04, epoch: 2.50e-01, step: 2.50e+01
+
    2024-08-14 00:58:16 (INFO): energy_mae: 3.65e+03, energy_mse: 2.68e+07, energy_within_threshold: 0.00e+00, loss: 1.98e+03, lr: 1.00e-04, epoch: 2.50e-01, step: 2.50e+01
 
    
 
    
-
    2024-08-03 02:17:17 (INFO): energy_mae: 2.30e+03, energy_mse: 2.25e+07, energy_within_threshold: 0.00e+00, loss: 1.25e+03, lr: 1.00e-04, epoch: 3.00e-01, step: 3.00e+01
+
    2024-08-14 00:58:26 (INFO): energy_mae: 2.09e+03, energy_mse: 1.83e+07, energy_within_threshold: 0.00e+00, loss: 1.14e+03, lr: 1.00e-04, epoch: 3.00e-01, step: 3.00e+01
 
    
 
    
-
    2024-08-03 02:17:32 (INFO): energy_mae: 1.65e+03, energy_mse: 4.06e+06, energy_within_threshold: 0.00e+00, loss: 9.00e+02, lr: 1.00e-04, epoch: 3.50e-01, step: 3.50e+01
+
    2024-08-14 00:58:41 (INFO): energy_mae: 1.36e+03, energy_mse: 2.91e+06, energy_within_threshold: 0.00e+00, loss: 7.42e+02, lr: 1.00e-04, epoch: 3.50e-01, step: 3.50e+01
 
    
 
    
-
    2024-08-03 02:17:41 (INFO): energy_mae: 5.63e+02, energy_mse: 1.13e+06, energy_within_threshold: 0.00e+00, loss: 3.06e+02, lr: 1.00e-04, epoch: 4.00e-01, step: 4.00e+01
+
    2024-08-14 00:58:50 (INFO): energy_mae: 5.61e+02, energy_mse: 1.15e+06, energy_within_threshold: 0.00e+00, loss: 3.06e+02, lr: 1.00e-04, epoch: 4.00e-01, step: 4.00e+01
 
    
 
    
-
    2024-08-03 02:17:53 (INFO): energy_mae: 5.13e+02, energy_mse: 8.35e+05, energy_within_threshold: 0.00e+00, loss: 2.79e+02, lr: 1.00e-04, epoch: 4.50e-01, step: 4.50e+01
+
    2024-08-14 00:59:02 (INFO): energy_mae: 5.48e+02, energy_mse: 9.61e+05, energy_within_threshold: 0.00e+00, loss: 2.98e+02, lr: 1.00e-04, epoch: 4.50e-01, step: 4.50e+01
 
    
 
    
-
    2024-08-03 02:18:11 (INFO): energy_mae: 6.99e+02, energy_mse: 8.35e+05, energy_within_threshold: 0.00e+00, loss: 3.80e+02, lr: 1.00e-04, epoch: 5.00e-01, step: 5.00e+01
+
    2024-08-14 00:59:20 (INFO): energy_mae: 7.98e+02, energy_mse: 1.23e+06, energy_within_threshold: 0.00e+00, loss: 4.34e+02, lr: 1.00e-04, epoch: 5.00e-01, step: 5.00e+01
 
    
 
    
-
    2024-08-03 02:18:21 (INFO): energy_mae: 2.25e+02, energy_mse: 1.27e+05, energy_within_threshold: 0.00e+00, loss: 1.22e+02, lr: 1.00e-04, epoch: 5.50e-01, step: 5.50e+01
+
    2024-08-14 00:59:30 (INFO): energy_mae: 3.57e+02, energy_mse: 3.62e+05, energy_within_threshold: 0.00e+00, loss: 1.95e+02, lr: 1.00e-04, epoch: 5.50e-01, step: 5.50e+01
 
    
 
    
-
    2024-08-03 02:18:32 (INFO): energy_mae: 1.86e+02, energy_mse: 7.67e+04, energy_within_threshold: 0.00e+00, loss: 1.01e+02, lr: 1.00e-04, epoch: 6.00e-01, step: 6.00e+01
+
    2024-08-14 00:59:41 (INFO): energy_mae: 1.98e+02, energy_mse: 9.53e+04, energy_within_threshold: 0.00e+00, loss: 1.08e+02, lr: 1.00e-04, epoch: 6.00e-01, step: 6.00e+01
 
    
 
    
-
    2024-08-03 02:18:44 (INFO): energy_mae: 3.63e+02, energy_mse: 1.96e+05, energy_within_threshold: 0.00e+00, loss: 1.98e+02, lr: 1.00e-04, epoch: 6.50e-01, step: 6.50e+01
+
    2024-08-14 00:59:53 (INFO): energy_mae: 4.07e+02, energy_mse: 2.19e+05, energy_within_threshold: 0.00e+00, loss: 2.22e+02, lr: 1.00e-04, epoch: 6.50e-01, step: 6.50e+01
 
    
 
    
-
    2024-08-03 02:18:54 (INFO): energy_mae: 1.45e+02, energy_mse: 3.17e+04, energy_within_threshold: 0.00e+00, loss: 7.89e+01, lr: 1.00e-04, epoch: 7.00e-01, step: 7.00e+01
+
    2024-08-14 01:00:03 (INFO): energy_mae: 1.22e+02, energy_mse: 2.44e+04, energy_within_threshold: 0.00e+00, loss: 6.66e+01, lr: 1.00e-04, epoch: 7.00e-01, step: 7.00e+01
 
    
 
    
-
    2024-08-03 02:19:05 (INFO): energy_mae: 1.83e+02, energy_mse: 5.15e+04, energy_within_threshold: 0.00e+00, loss: 9.94e+01, lr: 1.00e-04, epoch: 7.50e-01, step: 7.50e+01
+
    2024-08-14 01:00:15 (INFO): energy_mae: 2.51e+02, energy_mse: 9.04e+04, energy_within_threshold: 0.00e+00, loss: 1.37e+02, lr: 1.00e-04, epoch: 7.50e-01, step: 7.50e+01
 
    
 
    
-
    2024-08-03 02:19:15 (INFO): energy_mae: 1.40e+02, energy_mse: 2.91e+04, energy_within_threshold: 0.00e+00, loss: 7.62e+01, lr: 1.00e-04, epoch: 8.00e-01, step: 8.00e+01
+
    2024-08-14 01:00:24 (INFO): energy_mae: 1.49e+02, energy_mse: 3.07e+04, energy_within_threshold: 0.00e+00, loss: 8.14e+01, lr: 1.00e-04, epoch: 8.00e-01, step: 8.00e+01
 
    
 
    
-
    2024-08-03 02:19:30 (INFO): energy_mae: 1.98e+02, energy_mse: 6.42e+04, energy_within_threshold: 0.00e+00, loss: 1.08e+02, lr: 1.00e-04, epoch: 8.50e-01, step: 8.50e+01
+
    2024-08-14 01:00:39 (INFO): energy_mae: 1.48e+02, energy_mse: 3.81e+04, energy_within_threshold: 0.00e+00, loss: 8.05e+01, lr: 1.00e-04, epoch: 8.50e-01, step: 8.50e+01
 
    
 
    
-
    2024-08-03 02:19:39 (INFO): energy_mae: 2.51e+02, energy_mse: 1.27e+05, energy_within_threshold: 0.00e+00, loss: 1.36e+02, lr: 1.00e-04, epoch: 9.00e-01, step: 9.00e+01
+
    2024-08-14 01:00:48 (INFO): energy_mae: 2.88e+02, energy_mse: 1.64e+05, energy_within_threshold: 0.00e+00, loss: 1.57e+02, lr: 1.00e-04, epoch: 9.00e-01, step: 9.00e+01
 
    
 
    
-
    2024-08-03 02:19:52 (INFO): energy_mae: 2.20e+02, energy_mse: 1.03e+05, energy_within_threshold: 0.00e+00, loss: 1.20e+02, lr: 1.00e-04, epoch: 9.50e-01, step: 9.50e+01
+
    2024-08-14 01:01:01 (INFO): energy_mae: 2.65e+02, energy_mse: 1.58e+05, energy_within_threshold: 0.00e+00, loss: 1.44e+02, lr: 1.00e-04, epoch: 9.50e-01, step: 9.50e+01
 
    
 
    
-
    2024-08-03 02:20:01 (INFO): energy_mae: 1.32e+02, energy_mse: 3.31e+04, energy_within_threshold: 0.00e+00, loss: 7.18e+01, lr: 1.00e-04, epoch: 1.00e+00, step: 1.00e+02
+
    2024-08-14 01:01:10 (INFO): energy_mae: 4.13e+01, energy_mse: 3.10e+03, energy_within_threshold: 0.00e+00, loss: 2.25e+01, lr: 1.00e-04, epoch: 1.00e+00, step: 1.00e+02
 
    
 
    
-
    2024-08-03 02:20:02 (WARNING): Scale factor OutBlock_4_sum (out_blocks.4.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:11 (WARNING): Scale factor OutBlock_4_sum (out_blocks.4.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:02 (WARNING): Scale factor OutBlock_5_sum (out_blocks.5.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:11 (WARNING): Scale factor OutBlock_5_sum (out_blocks.5.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:02 (WARNING): Scale factor TripInteraction_4_had_rbf (int_blocks.3.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:11 (WARNING): Scale factor TripInteraction_4_had_rbf (int_blocks.3.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:02 (WARNING): Scale factor TripInteraction_4_sum_cbf (int_blocks.3.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:11 (WARNING): Scale factor TripInteraction_4_sum_cbf (int_blocks.3.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:02 (WARNING): Scale factor AtomUpdate_4_sum (int_blocks.3.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:11 (WARNING): Scale factor AtomUpdate_4_sum (int_blocks.3.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:02 (WARNING): Scale factor TripInteraction_5_had_rbf (int_blocks.4.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:11 (WARNING): Scale factor TripInteraction_5_had_rbf (int_blocks.4.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:02 (WARNING): Scale factor TripInteraction_5_sum_cbf (int_blocks.4.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:11 (WARNING): Scale factor TripInteraction_5_sum_cbf (int_blocks.4.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:02 (WARNING): Scale factor AtomUpdate_5_sum (int_blocks.4.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:11 (WARNING): Scale factor AtomUpdate_5_sum (int_blocks.4.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:02 (INFO): Evaluating on val.
-
    
-
    
-
    device 0:   0%|          | 0/20 [00:00<?, ?it/s]
+
    2024-08-14 01:01:11 (INFO): Evaluating on val.
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 
    
 
    
+
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+
    
+
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 
    
 
    
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+
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+
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+
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+
    device 0:  40%|████      | 8/20 [00:08<00:11,  1.01it/s]
 
    
 
    
 
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@@ -3596,37 +3635,37 @@ 
    Train the Model
    device 0:  55%|█████▌    | 11/20 [00:13<00:12,  1.41s/it]
 
    
 
    
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    device 0:  60%|██████    | 12/20 [00:14<00:09,  1.25s/it]
+
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+
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+
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+
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+
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+
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+
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+
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+
    device 0: 100%|██████████| 20/20 [00:19<00:00,  1.01it/s]
 
    
 
    
-
    2024-08-03 02:20:21 (INFO): energy_mae: 1363.8962, energy_mse: 9843100.0997, energy_within_threshold: 0.0000, loss: 742.4147, epoch: 1.0000
+
    2024-08-14 01:01:31 (INFO): energy_mae: 1276.4371, energy_mse: 9179704.0717, energy_within_threshold: 0.0000, loss: 694.8078, epoch: 1.0000
 
    
 
    
 
    
@@ -3648,7 +3687,7 @@ 
    Load the best checkpoint
-
    './checkpoints/2024-08-03-02-16-32-IS2RE-example/best_checkpoint.pt'
+
    './checkpoints/2024-08-14-00-57-36-IS2RE-example/best_checkpoint.pt'
 
    
 
    
 
    
@@ -3702,20 +3741,20 @@ 
    Load the best checkpoint
-
    2024-08-03 02:20:22 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+
    2024-08-14 01:01:31 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
 
    
 
    
-
    2024-08-03 02:20:22 (INFO): amp: true
+
    2024-08-14 01:01:31 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-08-03-02-20-48-IS2RE-val-example
-  commit: 08b8c1e
+  checkpoint_dir: ./checkpoints/2024-08-14-01-01-52-IS2RE-val-example
+  commit: 8fb16d6
   identifier: IS2RE-val-example
-  logs_dir: ./logs/tensorboard/2024-08-03-02-20-48-IS2RE-val-example
+  logs_dir: ./logs/tensorboard/2024-08-14-01-01-52-IS2RE-val-example
   print_every: 5
-  results_dir: ./results/2024-08-03-02-20-48-IS2RE-val-example
+  results_dir: ./results/2024-08-14-01-01-52-IS2RE-val-example
   seed: 0
-  timestamp_id: 2024-08-03-02-20-48-IS2RE-val-example
-  version: 0.1.dev1+g08b8c1e
+  timestamp_id: 2024-08-14-01-01-52-IS2RE-val-example
+  version: 1.1.0
 dataset:
   format: single_point_lmdb
   key_mapping:
@@ -3770,8 +3809,7 @@ 
    Load the best checkpoint
    2024-08-03 02:20:22 (INFO): Loading dataset: single_point_lmdb
+
    2024-08-14 01:01:31 (INFO): Loading dataset: single_point_lmdb
 
    
 
    
-
    2024-08-03 02:20:22 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/train_100/data.lmdb')]'
+
    2024-08-14 01:01:31 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/train_100/data.lmdb')]'
 
    
 
    
-
    2024-08-03 02:20:22 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 01:01:31 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:20:22 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 01:01:31 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:20:22 (INFO): rank: 0: Sampler created...
+
    2024-08-14 01:01:31 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:20:22 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff923ccea50>, batch_size=1, drop_last=False
+
    2024-08-14 01:01:31 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd87ad6f110>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:20:22 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/val_20/data.lmdb')]'
+
    2024-08-14 01:01:31 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/val_20/data.lmdb')]'
 
    
 
    
-
    2024-08-03 02:20:22 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 01:01:31 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:20:22 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 01:01:31 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:20:22 (INFO): rank: 0: Sampler created...
+
    2024-08-14 01:01:31 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:20:22 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff8e29baf50>, batch_size=1, drop_last=False
+
    2024-08-14 01:01:31 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd843b13b90>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:20:22 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/val_20/data.lmdb')]'
+
    2024-08-14 01:01:31 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/val_20/data.lmdb')]'
 
    
 
    
-
    2024-08-03 02:20:22 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 01:01:31 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:20:22 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 01:01:31 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:20:22 (INFO): rank: 0: Sampler created...
+
    2024-08-14 01:01:31 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:20:22 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff918dab690>, batch_size=1, drop_last=False
+
    2024-08-14 01:01:31 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd879ee0a90>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:20:22 (INFO): Loading model: gemnet_t
+
    2024-08-14 01:01:31 (INFO): normalizers checkpoint for targets ['energy'] have been saved to: ./checkpoints/2024-08-14-01-01-52-IS2RE-val-example/normalizers.pt
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor OutBlock_0_had not found in model
+
    2024-08-14 01:01:31 (INFO): normalizers checkpoint for targets ['energy', 'forces'] have been saved to: ./checkpoints/2024-08-14-01-01-52-IS2RE-val-example/normalizers.pt
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor OutBlock_1_had not found in model
+
    2024-08-14 01:01:31 (INFO): Normalization values for output energy: mean=-1.4570415561499996, rmsd=1.8371084209427546.
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor OutBlock_2_had not found in model
+
    2024-08-14 01:01:31 (INFO): Normalization values for output forces: mean=0, rmsd=1.
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor OutBlock_3_had not found in model
+
    2024-08-14 01:01:31 (INFO): Loading model: gemnet_t
 
    
 
    
-
    2024-08-03 02:20:23 (INFO): Loaded GemNetT with 22774037 parameters.
+
    2024-08-14 01:01:32 (WARNING): Scale factor OutBlock_0_had not found in model
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): log_summary for Tensorboard not supported
+
    2024-08-14 01:01:32 (WARNING): Scale factor OutBlock_1_had not found in model
 
    
 
    
-
    2024-08-03 02:20:23 (INFO): Loading checkpoint from: ./checkpoints/2024-08-03-02-16-32-IS2RE-example/best_checkpoint.pt
+
    2024-08-14 01:01:32 (WARNING): Scale factor OutBlock_2_had not found in model
+
    
+
    
+
    2024-08-14 01:01:32 (WARNING): Scale factor OutBlock_3_had not found in model
+
    
+
    
+
    2024-08-14 01:01:32 (INFO): Loaded GemNetT with 22774037 parameters.
+
    
+
    
+
    2024-08-14 01:01:32 (WARNING): log_summary for Tensorboard not supported
+
    
+
    
+
    2024-08-14 01:01:32 (INFO): Loading checkpoint from: ./checkpoints/2024-08-14-00-57-36-IS2RE-example/best_checkpoint.pt
 
    
 
    
 
    
@@ -3922,31 +3973,31 @@ 
    Test the model
-
    2024-08-03 02:20:23 (WARNING): Scale factor OutBlock_4_sum (out_blocks.4.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:32 (WARNING): Scale factor OutBlock_4_sum (out_blocks.4.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor OutBlock_5_sum (out_blocks.5.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:32 (WARNING): Scale factor OutBlock_5_sum (out_blocks.5.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor TripInteraction_4_had_rbf (int_blocks.3.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:32 (WARNING): Scale factor TripInteraction_4_had_rbf (int_blocks.3.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor TripInteraction_4_sum_cbf (int_blocks.3.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:32 (WARNING): Scale factor TripInteraction_4_sum_cbf (int_blocks.3.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor AtomUpdate_4_sum (int_blocks.3.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:32 (WARNING): Scale factor AtomUpdate_4_sum (int_blocks.3.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor TripInteraction_5_had_rbf (int_blocks.4.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:32 (WARNING): Scale factor TripInteraction_5_had_rbf (int_blocks.4.trip_interaction.scale_rbf) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor TripInteraction_5_sum_cbf (int_blocks.4.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:32 (WARNING): Scale factor TripInteraction_5_sum_cbf (int_blocks.4.trip_interaction.scale_cbf_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:23 (WARNING): Scale factor AtomUpdate_5_sum (int_blocks.4.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
+
    2024-08-14 01:01:32 (WARNING): Scale factor AtomUpdate_5_sum (int_blocks.4.atom_update.scale_sum) is not fitted. Please make sure that you either (1) load a checkpoint with fitted scale factors, (2) explicitly load scale factors using the `model.scale_file` attribute, or (3) fit the scale factors using the `fit.py` script.
 
    
 
    
-
    2024-08-03 02:20:23 (INFO): Predicting on test.
+
    2024-08-14 01:01:32 (INFO): Predicting on test.
 
    
 
    
 
    device 0:   0%|          | 0/20 [00:00<?, ?it/s]
@@ -3960,70 +4011,70 @@ 
    Test the model
    device 0:   5%|▌         | 1/20 [00:00<00:07,  2.61it/s]
+
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+
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+
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+
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+
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+
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-
    2024-08-03 02:20:28 (INFO): Writing results to ./results/2024-08-03-02-20-48-IS2RE-val-example/is2re_is2re_results.npz
+
    2024-08-14 01:01:37 (INFO): Writing results to ./results/2024-08-14-01-01-52-IS2RE-val-example/is2re_is2re_results.npz
 
    
 
    
 
    
@@ -4104,7 +4155,7 @@ 
    Download pretrained checkpoint
-
    2024-08-03 02:20:28 (INFO): Checking local cache: /tmp/fairchem_checkpoints/ for model GemNet-dT-S2EF-OC20-All
+
    2024-08-14 01:01:37 (INFO): Checking local cache: /tmp/fairchem_checkpoints/ for model GemNet-dT-S2EF-OC20-All
 
    
 
    
 
    
@@ -4238,20 +4289,20 @@ 
    Create the trainer
-
    2024-08-03 02:20:28 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+
    2024-08-14 01:01:38 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
 
    
 
    
-
    2024-08-03 02:20:28 (INFO): amp: true
+
    2024-08-14 01:01:38 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-08-03-02-20-48-is2rs-example
-  commit: 08b8c1e
+  checkpoint_dir: ./checkpoints/2024-08-14-01-01-52-is2rs-example
+  commit: 8fb16d6
   identifier: is2rs-example
-  logs_dir: ./logs/tensorboard/2024-08-03-02-20-48-is2rs-example
+  logs_dir: ./logs/tensorboard/2024-08-14-01-01-52-is2rs-example
   print_every: 5
-  results_dir: ./results/2024-08-03-02-20-48-is2rs-example
+  results_dir: ./results/2024-08-14-01-01-52-is2rs-example
   seed: 0
-  timestamp_id: 2024-08-03-02-20-48-is2rs-example
-  version: 0.1.dev1+g08b8c1e
+  timestamp_id: 2024-08-14-01-01-52-is2rs-example
+  version: 1.1.0
 dataset:
   format: lmdb
   key_mapping:
@@ -4282,8 +4333,7 @@ 
    Create the trainer
    2024-08-03 02:20:28 (INFO): Loading dataset: lmdb
+
    2024-08-14 01:01:38 (INFO): Loading dataset: lmdb
 
    
 
    
-
    2024-08-03 02:20:28 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/train_100')]'
+
    2024-08-14 01:01:38 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/train_100')]'
 
    
 
    
-
    2024-08-03 02:20:28 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 01:01:38 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:20:28 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 01:01:38 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:20:28 (INFO): rank: 0: Sampler created...
+
    2024-08-14 01:01:38 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:20:28 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff918dece10>, batch_size=1, drop_last=False
+
    2024-08-14 01:01:38 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd8482cb1d0>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:20:28 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
+
    2024-08-14 01:01:38 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
 
    
 
    
-
    2024-08-03 02:20:28 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 01:01:38 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:20:28 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 01:01:38 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:20:28 (INFO): rank: 0: Sampler created...
+
    2024-08-14 01:01:38 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:20:28 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff903ed7a50>, batch_size=1, drop_last=False
+
    2024-08-14 01:01:38 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd8716f8b10>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:20:28 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 01:01:38 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:20:28 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/val_20/data.lmdb')]'
+
    2024-08-14 01:01:38 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/is2re/val_20/data.lmdb')]'
 
    
 
    
-
    2024-08-03 02:20:28 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 01:01:38 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:20:28 (INFO): rank: 0: Sampler created...
+
    2024-08-14 01:01:38 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:20:28 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff924a11050>, batch_size=1, drop_last=False
+
    2024-08-14 01:01:38 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd8716db410>, batch_size=1, drop_last=False
 
    
 
    
-
    2024-08-03 02:20:28 (INFO): Loading model: gemnet_t
+
    2024-08-14 01:01:38 (INFO): Loading model: gemnet_t
 
    
 
    
-
    2024-08-03 02:20:30 (INFO): Loaded GemNetT with 31671825 parameters.
+
    2024-08-14 01:01:39 (INFO): Loaded GemNetT with 31671825 parameters.
 
    
 
    
-
    2024-08-03 02:20:30 (WARNING): log_summary for Tensorboard not supported
+
    2024-08-14 01:01:39 (WARNING): log_summary for Tensorboard not supported
 
    
 
    
 
    
@@ -4434,7 +4485,7 @@ 
    Load the best checkpoint
-
    2024-08-03 02:20:30 (INFO): Loading checkpoint from: /tmp/fairchem_checkpoints/gemnet_t_direct_h512_all.pt
+
    2024-08-14 01:01:39 (INFO): Loading checkpoint from: /tmp/fairchem_checkpoints/gemnet_t_direct_h512_all.pt
 
    
 
    
 
    
@@ -4450,7 +4501,7 @@ 
    Run relaxations
-
    2024-08-03 02:20:30 (INFO): Running ML-relaxations
+
    2024-08-14 01:01:39 (INFO): Running ML-relaxations
 
    
 
    
 
      0%|          | 0/20 [00:00<?, ?it/s]
@@ -4464,469 +4515,469 @@ 
    Run relaxations
    2024-08-03 02:20:30 (INFO): Step   Fmax(eV/A)
+
    2024-08-14 01:01:40 (INFO): Step   Fmax(eV/A)
 
    
 
    
-
    2024-08-03 02:20:31 (INFO): 0 2.630
+
    2024-08-14 01:01:41 (INFO): 0 2.630
 
    
 
    
-
    2024-08-03 02:20:32 (INFO): 1 2.094
+
    2024-08-14 01:01:42 (INFO): 1 2.094
 
    
 
    
-
    2024-08-03 02:20:33 (INFO): 2 1.509
+
    2024-08-14 01:01:43 (INFO): 2 1.509
 
    
 
    
-
    2024-08-03 02:20:35 (INFO): 3 1.128
+
    2024-08-14 01:01:44 (INFO): 3 1.128
 
    
 
    
-
    2024-08-03 02:20:36 (INFO): 4 1.405
+
    2024-08-14 01:01:45 (INFO): 4 1.405
 
    
 
    
-
    2024-08-03 02:20:37 (INFO): 5 1.649
+
    2024-08-14 01:01:46 (INFO): 5 1.649
 
    
 
    
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    2024-08-03 02:20:38 (INFO): 6 1.798
+
    2024-08-14 01:01:47 (INFO): 6 1.798
 
    
 
    
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    2024-08-03 02:20:39 (INFO): 7 1.882
+
    2024-08-14 01:01:48 (INFO): 7 1.882
 
    
 
    
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    2024-08-03 02:20:40 (INFO): 8 1.930
+
    2024-08-14 01:01:49 (INFO): 8 1.930
 
    
 
    
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    2024-08-03 02:20:41 (INFO): 9 1.935
+
    2024-08-14 01:01:50 (INFO): 9 1.935
 
    
 
    
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    2024-08-03 02:20:42 (INFO): 10 1.884
+
    2024-08-14 01:01:51 (INFO): 10 1.884
 
    
 
    
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    2024-08-03 02:20:43 (INFO): 11 1.773
+
    2024-08-14 01:01:52 (INFO): 11 1.773
 
    
 
    
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    2024-08-03 02:20:44 (INFO): 12 1.602
+
    2024-08-14 01:01:53 (INFO): 12 1.602
 
    
 
    
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    2024-08-03 02:20:45 (INFO): 13 1.378
+
    2024-08-14 01:01:54 (INFO): 13 1.378
 
    
 
    
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    2024-08-03 02:20:46 (INFO): 14 1.120
+
    2024-08-14 01:01:55 (INFO): 14 1.120
 
    
 
    
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    2024-08-03 02:20:47 (INFO): 15 0.928
+
    2024-08-14 01:01:56 (INFO): 15 0.928
 
    
 
    
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    2024-08-03 02:20:48 (INFO): 16 0.874
+
    2024-08-14 01:01:57 (INFO): 16 0.874
 
    
 
    
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    2024-08-03 02:20:49 (INFO): 17 0.880
+
    2024-08-14 01:01:58 (INFO): 17 0.880
 
    
 
    
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    2024-08-03 02:20:50 (INFO): 18 0.846
+
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    2024-08-03 02:20:51 (INFO): 19 0.758
+
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    2024-08-03 02:20:52 (INFO): 20 0.751
+
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    2024-08-03 02:20:53 (INFO): 21 0.862
+
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    2024-08-03 02:20:54 (INFO): 22 0.893
+
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    2024-08-03 02:20:55 (INFO): 23 0.920
+
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    2024-08-03 02:20:56 (INFO): 24 0.930
+
    2024-08-14 01:02:06 (INFO): 24 0.930
 
    
 
    
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    2024-08-03 02:20:57 (INFO): 25 0.718
+
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    2024-08-03 02:20:58 (INFO): 26 0.369
+
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    2024-08-03 02:20:59 (INFO): 27 0.341
+
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    2024-08-03 02:21:00 (INFO): 28 0.418
+
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    2024-08-03 02:21:01 (INFO): 29 0.447
+
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    2024-08-03 02:21:02 (INFO): 30 0.509
+
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    2024-08-03 02:21:03 (INFO): 31 0.516
+
    2024-08-14 01:02:13 (INFO): 31 0.516
 
    
 
    
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    2024-08-03 02:21:04 (INFO): 32 0.480
+
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    2024-08-03 02:21:05 (INFO): 33 0.417
+
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    2024-08-03 02:21:06 (INFO): 34 0.387
+
    2024-08-14 01:02:16 (INFO): 34 0.387
 
    
 
    
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    2024-08-03 02:21:07 (INFO): 35 0.370
+
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    2024-08-03 02:21:08 (INFO): 36 0.340
+
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    2024-08-03 02:21:09 (INFO): 37 0.300
+
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    2024-08-03 02:21:10 (INFO): 38 0.310
+
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    2024-08-03 02:21:11 (INFO): 39 0.313
+
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    2024-08-03 02:21:12 (INFO): 40 0.306
+
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    2024-08-03 02:21:13 (INFO): 41 0.343
+
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    2024-08-03 02:21:14 (INFO): 42 0.390
+
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    2024-08-03 02:21:15 (INFO): 43 0.431
+
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    2024-08-03 02:21:16 (INFO): 44 0.464
+
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    2024-08-03 02:21:17 (INFO): 45 0.486
+
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+
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+
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    2024-08-03 02:21:20 (INFO): 48 0.480
+
    2024-08-14 01:02:30 (INFO): 48 0.480
 
    
 
    
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    2024-08-03 02:21:21 (INFO): 49 0.440
+
    2024-08-14 01:02:31 (INFO): 49 0.440
 
    
 
    
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    2024-08-03 02:21:22 (INFO): 50 0.363
+
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    2024-08-03 02:21:23 (INFO): 51 0.239
+
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    2024-08-03 02:21:24 (INFO): 52 0.255
+
    2024-08-14 01:02:34 (INFO): 52 0.255
 
    
 
    
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    2024-08-03 02:21:25 (INFO): 53 0.257
+
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+
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+
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+
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+
    2024-08-14 01:02:39 (INFO): 57 0.308
 
    
 
    
-
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+
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-
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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-
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+
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+
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-
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+
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-
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+
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+
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+
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-
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+
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-
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+
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-
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+
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-
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+
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-
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+
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-
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+
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-
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+
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-
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+
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-
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+
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-
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+
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-
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+
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+
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+
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+
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+
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+
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-
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
    2024-08-14 01:03:36 (INFO): 113 0.095
 
    
 
    
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+
    2024-08-14 01:03:37 (INFO): 114 0.082
 
    
 
    
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+
    2024-08-14 01:03:38 (INFO): 115 0.052
 
    
 
    
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+
    2024-08-14 01:03:39 (INFO): 116 0.034
 
    
 
    
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+
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+
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+
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+
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+
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+
    2024-08-14 01:03:45 (INFO): 122 0.029
 
    
 
    
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+
    2024-08-14 01:03:46 (INFO): 123 0.043
 
    
 
    
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+
    2024-08-14 01:03:47 (INFO): 124 0.045
 
    
 
    
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+
    2024-08-14 01:03:48 (INFO): 125 0.047
 
    
 
    
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+
    2024-08-14 01:03:49 (INFO): 126 0.041
 
    
 
    
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+
    2024-08-14 01:03:50 (INFO): 127 0.043
 
    
 
    
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+
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+
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+
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+
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+
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+
    2024-08-14 01:03:56 (INFO): 133 0.034
 
    
 
    
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+
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+
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+
    2024-08-14 01:03:59 (INFO): 136 0.024
 
    
 
    
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+
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+
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+
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+
    2024-08-14 01:04:03 (INFO): 140 0.024
 
    
 
    
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+
    2024-08-14 01:04:04 (INFO): 141 0.021
 
    
 
    
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+
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+
    2024-08-14 01:04:06 (INFO): 143 0.022
 
    
 
    
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+
    2024-08-14 01:04:07 (INFO): 144 0.025
 
    
 
    
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+
    2024-08-14 01:04:08 (INFO): 145 0.034
 
    
 
    
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    2024-08-03 02:22:59 (INFO): 146 0.038
+
    2024-08-14 01:04:09 (INFO): 146 0.038
 
    
 
    
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+
    2024-08-14 01:04:10 (INFO): 147 0.030
 
    
 
    
-
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+
    2024-08-14 01:04:11 (INFO): 148 0.016
 
    
 
    
-
      5%|▌         | 1/20 [02:32<48:08, 152.00s/it]
+
      5%|▌         | 1/20 [02:32<48:21, 152.73s/it]
 
    
 
    
-
      5%|▌         | 1/20 [02:32<48:08, 152.03s/it]
+
      5%|▌         | 1/20 [02:32<48:22, 152.76s/it]
 
    
 
    
-
    2024-08-03 02:23:02 (INFO): Writing results to ./results/2024-08-03-02-20-48-is2rs-example/relaxed_positions.npz
+
    2024-08-14 01:04:12 (INFO): Writing results to ./results/2024-08-14-01-01-52-is2rs-example/relaxed_positions.npz
 
    
 
    
-
    2024-08-03 02:23:02 (INFO): {'positions_average_distance_within_threshold': {'total': 247, 'numel': 490, 'metric': 0.5040816326530613}, 'positions_mae': {'total': 23.29319953918457, 'numel': 60, 'metric': 0.38821999231974286}, 'positions_mse': {'total': 133.68051147460938, 'numel': 60, 'metric': 2.228008524576823}}
+
    2024-08-14 01:04:12 (INFO): {'positions_average_distance_within_threshold': {'total': 247, 'numel': 490, 'metric': 0.5040816326530613}, 'positions_mae': {'total': 23.29319953918457, 'numel': 60, 'metric': 0.38821999231974286}, 'positions_mse': {'total': 133.68051147460938, 'numel': 60, 'metric': 2.228008524576823}}
 
    
 
    
-
    2024-08-03 02:23:02 (INFO): {'energy_mae': {'total': 0.0, 'numel': 1, 'metric': 0.0}, 'energy_mse': {'total': 0.0, 'numel': 1, 'metric': 0.0}, 'energy_within_threshold': {'total': 1, 'numel': 1, 'metric': 1.0}}
+
    2024-08-14 01:04:12 (INFO): {'energy_mae': {'total': 0.0, 'numel': 1, 'metric': 0.0}, 'energy_mse': {'total': 0.0, 'numel': 1, 'metric': 0.0}, 'energy_within_threshold': {'total': 1, 'numel': 1, 'metric': 1.0}}
 
    
 
    
 
    
@@ -4983,7 +5034,7 @@ 
    Visualize ML-driven relaxations
    'ml-relaxations/is2rs-test/1700380.traj'
 
    
 
    
-../_images/41af445d4daca68a749345776ce0892ee5bce34b89af1d4aef5a7470ec70845e.png
+../_images/e0c00879fa25cd255545d9cbe5240b9ebd4602954c1b9b069e15ac4d92ded1d6.png
 
    
 
    
 
    Qualitatively, the ML relaxation is behaving as expected - decreasing energies over the course of the relaxation.
    
@@ -5020,7 +5071,7 @@ 
    Visualize ML-driven relaxations
    <Axes: title={'center': 'ml-final'}>
 
    
 
    
-../_images/be0f87d705459fb656d44d6c1e42a8735e9356d6c7fbee9c46215d7a2682e1cb.png
+../_images/1bed36523f1a2551e087028ab1cbc7e0237390cc630e7e7c366a651ca0c21e99.png
 
    
 
    
 
    Qualitatively, the generated structures seem reasonable with no obvious issues we had previously mentioned to look out for.
    
@@ -5285,20 +5336,20 @@ 
    Training the model
-
    2024-08-03 02:23:04 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+
    2024-08-14 01:04:14 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
 
    
 
    
-
    2024-08-03 02:23:04 (INFO): amp: true
+
    2024-08-14 01:04:14 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-08-03-02-22-56-S2EF-simple
-  commit: 08b8c1e
+  checkpoint_dir: ./checkpoints/2024-08-14-01-04-00-S2EF-simple
+  commit: 8fb16d6
   identifier: S2EF-simple
-  logs_dir: ./logs/tensorboard/2024-08-03-02-22-56-S2EF-simple
+  logs_dir: ./logs/tensorboard/2024-08-14-01-04-00-S2EF-simple
   print_every: 5
-  results_dir: ./results/2024-08-03-02-22-56-S2EF-simple
+  results_dir: ./results/2024-08-14-01-04-00-S2EF-simple
   seed: 0
-  timestamp_id: 2024-08-03-02-22-56-S2EF-simple
-  version: 0.1.dev1+g08b8c1e
+  timestamp_id: 2024-08-14-01-04-00-S2EF-simple
+  version: 1.1.0
 dataset:
   format: trajectory_lmdb
   grad_target_mean: 0.0
@@ -5341,11 +5392,11 @@ 
    Training the model
    2024-08-03 02:23:04 (INFO): Loading dataset: trajectory_lmdb
+
    2024-08-14 01:04:14 (INFO): Loading dataset: trajectory_lmdb
 
    
 
    
-
    2024-08-03 02:23:04 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/train_100')]'
+
    2024-08-14 01:04:14 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/train_100')]'
 
    
 
    
-
    2024-08-03 02:23:04 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 01:04:14 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:23:04 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 01:04:14 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:23:04 (INFO): rank: 0: Sampler created...
+
    2024-08-14 01:04:14 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:23:04 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff8e85aea50>, batch_size=16, drop_last=False
+
    2024-08-14 01:04:14 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd870ae6a10>, batch_size=16, drop_last=False
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/utils/data/dataloader.py:558: UserWarning: This DataLoader will create 8 worker processes in total. Our suggested max number of worker in current system is 4, which is smaller than what this DataLoader is going to create. Please be aware that excessive worker creation might get DataLoader running slow or even freeze, lower the worker number to avoid potential slowness/freeze if necessary.
   warnings.warn(_create_warning_msg(
-2024-08-03 02:23:04 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
+2024-08-14 01:04:14 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
 
    
 
    
-
    2024-08-03 02:23:04 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 01:04:14 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:23:04 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 01:04:14 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:23:04 (INFO): rank: 0: Sampler created...
+
    2024-08-14 01:04:14 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:23:04 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff8f54ce350>, batch_size=8, drop_last=False
+
    2024-08-14 01:04:14 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd856571c10>, batch_size=8, drop_last=False
 
    
 
    
-
    2024-08-03 02:23:04 (INFO): Loading model: simple
+
    2024-08-14 01:04:14 (INFO): normalizers checkpoint for targets ['energy'] have been saved to: ./checkpoints/2024-08-14-01-04-00-S2EF-simple/normalizers.pt
 
    
 
    
-
    2024-08-03 02:23:04 (INFO): Loaded SimpleAtomEdgeModel with 185602 parameters.
+
    2024-08-14 01:04:14 (INFO): normalizers checkpoint for targets ['energy', 'forces'] have been saved to: ./checkpoints/2024-08-14-01-04-00-S2EF-simple/normalizers.pt
 
    
 
    
-
    2024-08-03 02:23:04 (WARNING): log_summary for Tensorboard not supported
+
    2024-08-14 01:04:14 (INFO): Normalization values for output energy: mean=-0.7554450631141663, rmsd=2.887317180633545.
 
    
 
    
-
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
-  storage = elem.storage()._new_shared(numel)
+
    2024-08-14 01:04:14 (INFO): Normalization values for output forces: mean=0.0, rmsd=2.887317180633545.
+
    
+
    
+
    2024-08-14 01:04:14 (INFO): Loading model: simple
+
    
+
    
+
    2024-08-14 01:04:14 (INFO): Loaded SimpleAtomEdgeModel with 185602 parameters.
+
    
+
    
+
    2024-08-14 01:04:14 (WARNING): log_summary for Tensorboard not supported
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
@@ -5456,13 +5515,14 @@ 
    Training the model
    2024-08-03 02:23:07 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 4.11e+02, forcesx_mae: 3.24e-01, forcesy_mae: 4.73e-01, forcesz_mae: 1.61e+00, forces_mae: 8.01e-01, forces_cosine_similarity: 1.95e-02, forces_magnitude_error: 1.59e+00, loss: 2.07e+02, lr: 1.00e-04, epoch: 7.14e-01, step: 5.00e+00
+
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
+  storage = elem.storage()._new_shared(numel)
 
    
 
    
-
    2024-08-03 02:23:08 (INFO): Evaluating on val.
+
    2024-08-14 01:04:18 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 4.11e+02, forcesx_mae: 3.24e-01, forcesy_mae: 4.73e-01, forcesz_mae: 1.61e+00, forces_mae: 8.01e-01, forces_cosine_similarity: 1.95e-02, forces_magnitude_error: 1.59e+00, loss: 2.07e+02, lr: 1.00e-04, epoch: 7.14e-01, step: 5.00e+00
 
    
 
    
-
    device 0:   0%|          | 0/3 [00:00<?, ?it/s]
+
    2024-08-14 01:04:19 (INFO): Evaluating on val.
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
@@ -5473,17 +5533,20 @@ 
    Training the model
    device 0:   0%|          | 0/3 [00:00<?, ?it/s]
+
    
+
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 
    
 
    
-
    device 0:  67%|██████▋   | 2/3 [00:00<00:00, 14.36it/s]
+
    device 0:  33%|███▎      | 1/3 [00:00<00:00,  9.25it/s]
 
    
 
    
-
    device 0: 100%|██████████| 3/3 [00:00<00:00,  7.49it/s]
+
    device 0: 100%|██████████| 3/3 [00:00<00:00,  7.55it/s]
 
    
 
    
-
    2024-08-03 02:23:09 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 197.5696, forcesx_mae: 0.2953, forcesy_mae: 0.2344, forcesz_mae: 0.8644, forces_mae: 0.4647, forces_cosine_similarity: -0.0500, forces_magnitude_error: 0.7782, loss: 103.0341, epoch: 1.0000
+
    2024-08-14 01:04:20 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 197.5696, forcesx_mae: 0.2953, forcesy_mae: 0.2344, forcesz_mae: 0.8644, forces_mae: 0.4647, forces_cosine_similarity: -0.0500, forces_magnitude_error: 0.7782, loss: 103.0341, epoch: 1.0000
 
    
 
    
 
    
@@ -5517,19 +5580,19 @@ 
    Training the model
    2024-08-03 02:23:12 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.80e+02, forcesx_mae: 2.55e-01, forcesy_mae: 3.87e-01, forcesz_mae: 1.02e+00, forces_mae: 5.54e-01, forces_cosine_similarity: -1.38e-02, forces_magnitude_error: 9.78e-01, loss: 1.26e+02, lr: 1.00e-04, epoch: 1.43e+00, step: 1.00e+01
-
    
-
    
-
    2024-08-03 02:23:13 (INFO): Evaluating on val.
+
    2024-08-14 01:04:22 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.80e+02, forcesx_mae: 2.55e-01, forcesy_mae: 3.87e-01, forcesz_mae: 1.02e+00, forces_mae: 5.54e-01, forces_cosine_similarity: -1.38e-02, forces_magnitude_error: 9.78e-01, loss: 1.26e+02, lr: 1.00e-04, epoch: 1.43e+00, step: 1.00e+01
 
    
 
    
-
    device 0:   0%|          | 0/3 [00:00<?, ?it/s]
+
    2024-08-14 01:04:24 (INFO): Evaluating on val.
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 
    
 
    
+
    device 0:   0%|          | 0/3 [00:00<?, ?it/s]
+
    
+
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 
    
@@ -5538,13 +5601,13 @@ 
    Training the model
    device 0:  67%|██████▋   | 2/3 [00:00<00:00, 13.35it/s]
+
    device 0:  33%|███▎      | 1/3 [00:00<00:00,  8.53it/s]
 
    
 
    
-
    device 0: 100%|██████████| 3/3 [00:00<00:00,  6.38it/s]
+
    device 0: 100%|██████████| 3/3 [00:00<00:00,  7.60it/s]
 
    
 
    
-
    2024-08-03 02:23:14 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 191.2872, forcesx_mae: 0.3271, forcesy_mae: 0.2744, forcesz_mae: 0.9364, forces_mae: 0.5126, forces_cosine_similarity: -0.0479, forces_magnitude_error: 0.8843, loss: 104.5027, epoch: 2.0000
+
    2024-08-14 01:04:25 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 191.2872, forcesx_mae: 0.3271, forcesy_mae: 0.2744, forcesz_mae: 0.9364, forces_mae: 0.5126, forces_cosine_similarity: -0.0479, forces_magnitude_error: 0.8843, loss: 104.5027, epoch: 2.0000
 
    
 
    
 
    
@@ -5578,16 +5641,13 @@ 
    Training the model
    2024-08-03 02:23:16 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.28e+02, forcesx_mae: 2.67e-01, forcesy_mae: 3.55e-01, forcesz_mae: 1.05e+00, forces_mae: 5.58e-01, forces_cosine_similarity: -1.39e-02, forces_magnitude_error: 1.01e+00, loss: 1.26e+02, lr: 1.00e-04, epoch: 2.14e+00, step: 1.50e+01
+
    2024-08-14 01:04:27 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.28e+02, forcesx_mae: 2.67e-01, forcesy_mae: 3.55e-01, forcesz_mae: 1.05e+00, forces_mae: 5.58e-01, forces_cosine_similarity: -1.39e-02, forces_magnitude_error: 1.01e+00, loss: 1.26e+02, lr: 1.00e-04, epoch: 2.14e+00, step: 1.50e+01
 
    
 
    
-
    2024-08-03 02:23:18 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.47e+02, forcesx_mae: 2.23e-01, forcesy_mae: 3.52e-01, forcesz_mae: 8.08e-01, forces_mae: 4.61e-01, forces_cosine_similarity: 7.62e-02, forces_magnitude_error: 7.88e-01, loss: 1.21e+02, lr: 1.00e-04, epoch: 2.86e+00, step: 2.00e+01
+
    2024-08-14 01:04:29 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.47e+02, forcesx_mae: 2.23e-01, forcesy_mae: 3.52e-01, forcesz_mae: 8.08e-01, forces_mae: 4.61e-01, forces_cosine_similarity: 7.62e-02, forces_magnitude_error: 7.88e-01, loss: 1.21e+02, lr: 1.00e-04, epoch: 2.86e+00, step: 2.00e+01
 
    
 
    
-
    2024-08-03 02:23:19 (INFO): Evaluating on val.
-
    
-
    
-
    device 0:   0%|          | 0/3 [00:00<?, ?it/s]
+
    2024-08-14 01:04:29 (INFO): Evaluating on val.
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
@@ -5598,17 +5658,20 @@ 
    Training the model
    device 0:   0%|          | 0/3 [00:00<?, ?it/s]
+
    
+
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 
    
 
    
-
    device 0:  33%|███▎      | 1/3 [00:00<00:00,  8.22it/s]
+
    device 0:  67%|██████▋   | 2/3 [00:00<00:00, 16.02it/s]
 
    
 
    
-
    device 0: 100%|██████████| 3/3 [00:00<00:00,  6.89it/s]
+
    device 0: 100%|██████████| 3/3 [00:00<00:00,  6.92it/s]
 
    
 
    
-
    2024-08-03 02:23:20 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 198.2147, forcesx_mae: 0.3246, forcesy_mae: 0.2725, forcesz_mae: 0.9452, forces_mae: 0.5141, forces_cosine_similarity: -0.0507, forces_magnitude_error: 0.8909, loss: 107.1592, epoch: 3.0000
+
    2024-08-14 01:04:30 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 198.2147, forcesx_mae: 0.3246, forcesy_mae: 0.2725, forcesz_mae: 0.9452, forces_mae: 0.5141, forces_cosine_similarity: -0.0507, forces_magnitude_error: 0.8909, loss: 107.1592, epoch: 3.0000
 
    
 
    
 
    
@@ -5642,10 +5705,10 @@ 
    Training the model
    2024-08-03 02:23:23 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.27e+02, forcesx_mae: 1.63e-01, forcesy_mae: 2.30e-01, forcesz_mae: 4.96e-01, forces_mae: 2.97e-01, forces_cosine_similarity: -3.68e-02, forces_magnitude_error: 4.65e-01, loss: 6.43e+01, lr: 1.00e-04, epoch: 3.57e+00, step: 2.50e+01
+
    2024-08-14 01:04:34 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.27e+02, forcesx_mae: 1.63e-01, forcesy_mae: 2.30e-01, forcesz_mae: 4.96e-01, forces_mae: 2.97e-01, forces_cosine_similarity: -3.68e-02, forces_magnitude_error: 4.65e-01, loss: 6.43e+01, lr: 1.00e-04, epoch: 3.57e+00, step: 2.50e+01
 
    
 
    
-
    2024-08-03 02:23:24 (INFO): Evaluating on val.
+
    2024-08-14 01:04:35 (INFO): Evaluating on val.
 
    
 
    
 
    device 0:   0%|          | 0/3 [00:00<?, ?it/s]
@@ -5663,13 +5726,13 @@ 
    Training the model
    device 0:  67%|██████▋   | 2/3 [00:00<00:00, 14.51it/s]
+
    device 0:  33%|███▎      | 1/3 [00:00<00:00,  9.32it/s]
 
    
 
    
-
    device 0: 100%|██████████| 3/3 [00:00<00:00,  7.63it/s]
+
    device 0: 100%|██████████| 3/3 [00:00<00:00,  7.28it/s]
 
    
 
    
-
    2024-08-03 02:23:25 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 193.6992, forcesx_mae: 0.3220, forcesy_mae: 0.2708, forcesz_mae: 0.9639, forces_mae: 0.5189, forces_cosine_similarity: -0.0511, forces_magnitude_error: 0.9075, loss: 106.1556, epoch: 4.0000
+
    2024-08-14 01:04:36 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 193.6992, forcesx_mae: 0.3220, forcesy_mae: 0.2708, forcesz_mae: 0.9639, forces_mae: 0.5189, forces_cosine_similarity: -0.0511, forces_magnitude_error: 0.9075, loss: 106.1556, epoch: 4.0000
 
    
 
    
 
    
@@ -5703,16 +5766,13 @@ 
    Training the model
    2024-08-03 02:23:27 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.43e+02, forcesx_mae: 1.99e-01, forcesy_mae: 3.15e-01, forcesz_mae: 5.12e-01, forces_mae: 3.42e-01, forces_cosine_similarity: -1.52e-03, forces_magnitude_error: 5.13e-01, loss: 7.14e+01, lr: 1.00e-04, epoch: 4.29e+00, step: 3.00e+01
-
    
-
    
-
    2024-08-03 02:23:29 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.44e+02, forcesx_mae: 1.45e-01, forcesy_mae: 2.35e-01, forcesz_mae: 3.94e-01, forces_mae: 2.58e-01, forces_cosine_similarity: 3.66e-02, forces_magnitude_error: 4.01e-01, loss: 9.90e+01, lr: 1.00e-04, epoch: 5.00e+00, step: 3.50e+01
+
    2024-08-14 01:04:38 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.43e+02, forcesx_mae: 1.99e-01, forcesy_mae: 3.15e-01, forcesz_mae: 5.12e-01, forces_mae: 3.42e-01, forces_cosine_similarity: -1.52e-03, forces_magnitude_error: 5.13e-01, loss: 7.14e+01, lr: 1.00e-04, epoch: 4.29e+00, step: 3.00e+01
 
    
 
    
-
    2024-08-03 02:23:29 (INFO): Evaluating on val.
+
    2024-08-14 01:04:40 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.44e+02, forcesx_mae: 1.45e-01, forcesy_mae: 2.35e-01, forcesz_mae: 3.94e-01, forces_mae: 2.58e-01, forces_cosine_similarity: 3.66e-02, forces_magnitude_error: 4.01e-01, loss: 9.90e+01, lr: 1.00e-04, epoch: 5.00e+00, step: 3.50e+01
 
    
 
    
-
    device 0:   0%|          | 0/3 [00:00<?, ?it/s]
+
    2024-08-14 01:04:40 (INFO): Evaluating on val.
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
@@ -5723,17 +5783,20 @@ 
    Training the model
    device 0:   0%|          | 0/3 [00:00<?, ?it/s]
+
    
+
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 
    
 
    
-
    device 0:  67%|██████▋   | 2/3 [00:00<00:00, 15.36it/s]
+
    device 0:  67%|██████▋   | 2/3 [00:00<00:00, 14.69it/s]
 
    
 
    
-
    device 0: 100%|██████████| 3/3 [00:00<00:00,  7.67it/s]
+
    device 0: 100%|██████████| 3/3 [00:00<00:00,  6.87it/s]
 
    
 
    
-
    2024-08-03 02:23:30 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 201.6972, forcesx_mae: 0.3385, forcesy_mae: 0.2883, forcesz_mae: 1.0024, forces_mae: 0.5431, forces_cosine_similarity: -0.0537, forces_magnitude_error: 0.9617, loss: 110.8121, epoch: 5.0000
+
    2024-08-14 01:04:41 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 201.6972, forcesx_mae: 0.3385, forcesy_mae: 0.2883, forcesz_mae: 1.0024, forces_mae: 0.5431, forces_cosine_similarity: -0.0537, forces_magnitude_error: 0.9617, loss: 110.8121, epoch: 5.0000
 
    
 
    
 
    
@@ -5806,20 +5869,20 @@ 
    Incorporating triplets and training GemNet-T
-
    2024-08-03 02:23:30 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+
    2024-08-14 01:04:41 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
 
    
 
    
-
    2024-08-03 02:23:30 (INFO): amp: true
+
    2024-08-14 01:04:41 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-08-03-02-22-56-S2EF-gemnet-t
-  commit: 08b8c1e
+  checkpoint_dir: ./checkpoints/2024-08-14-01-04-00-S2EF-gemnet-t
+  commit: 8fb16d6
   identifier: S2EF-gemnet-t
-  logs_dir: ./logs/tensorboard/2024-08-03-02-22-56-S2EF-gemnet-t
+  logs_dir: ./logs/tensorboard/2024-08-14-01-04-00-S2EF-gemnet-t
   print_every: 5
-  results_dir: ./results/2024-08-03-02-22-56-S2EF-gemnet-t
+  results_dir: ./results/2024-08-14-01-04-00-S2EF-gemnet-t
   seed: 0
-  timestamp_id: 2024-08-03-02-22-56-S2EF-gemnet-t
-  version: 0.1.dev1+g08b8c1e
+  timestamp_id: 2024-08-14-01-04-00-S2EF-gemnet-t
+  version: 1.1.0
 dataset:
   format: trajectory_lmdb
   grad_target_mean: 0.0
@@ -5862,8 +5925,7 @@ 
    Incorporating triplets and training GemNet-T
    2024-08-03 02:23:30 (INFO): Loading dataset: trajectory_lmdb
+
    2024-08-14 01:04:41 (INFO): Loading dataset: trajectory_lmdb
 
    
 
    
-
    2024-08-03 02:23:30 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/train_100')]'
+
    2024-08-14 01:04:41 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/train_100')]'
 
    
 
    
-
    2024-08-03 02:23:30 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 01:04:41 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
 
    
 
    
-
    2024-08-03 02:23:30 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 01:04:41 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
 
    
 
    
-
    2024-08-03 02:23:30 (INFO): rank: 0: Sampler created...
+
    2024-08-14 01:04:41 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:23:30 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff8ec41a8d0>, batch_size=16, drop_last=False
+
    2024-08-14 01:04:41 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd848509290>, batch_size=16, drop_last=False
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/utils/data/dataloader.py:558: UserWarning: This DataLoader will create 8 worker processes in total. Our suggested max number of worker in current system is 4, which is smaller than what this DataLoader is going to create. Please be aware that excessive worker creation might get DataLoader running slow or even freeze, lower the worker number to avoid potential slowness/freeze if necessary.
   warnings.warn(_create_warning_msg(
-2024-08-03 02:23:30 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
+2024-08-14 01:04:41 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data/s2ef/val_20')]'
+
    
+
    
+
    2024-08-14 01:04:41 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    
+
    
+
    2024-08-14 01:04:41 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    
+
    
+
    2024-08-14 01:04:41 (INFO): rank: 0: Sampler created...
 
    
 
    
-
    2024-08-03 02:23:30 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    2024-08-14 01:04:41 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7fd87adb0850>, batch_size=8, drop_last=False
 
    
 
    
-
    2024-08-03 02:23:30 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+
    2024-08-14 01:04:41 (INFO): normalizers checkpoint for targets ['energy'] have been saved to: ./checkpoints/2024-08-14-01-04-00-S2EF-gemnet-t/normalizers.pt
 
    
 
    
-
    2024-08-03 02:23:30 (INFO): rank: 0: Sampler created...
+
    2024-08-14 01:04:41 (INFO): normalizers checkpoint for targets ['energy', 'forces'] have been saved to: ./checkpoints/2024-08-14-01-04-00-S2EF-gemnet-t/normalizers.pt
 
    
 
    
-
    2024-08-03 02:23:30 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7ff918d71750>, batch_size=8, drop_last=False
+
    2024-08-14 01:04:41 (INFO): Normalization values for output energy: mean=-0.7554450631141663, rmsd=2.887317180633545.
 
    
 
    
-
    2024-08-03 02:23:30 (INFO): Loading model: gemnet_t
+
    2024-08-14 01:04:41 (INFO): Normalization values for output forces: mean=0.0, rmsd=2.887317180633545.
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): Scale factor TripInteraction_2_had_rbf not found in model
+
    2024-08-14 01:04:41 (INFO): Loading model: gemnet_t
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): Scale factor TripInteraction_2_sum_cbf not found in model
+
    2024-08-14 01:04:42 (WARNING): Scale factor TripInteraction_2_had_rbf not found in model
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): Scale factor AtomUpdate_2_sum not found in model
+
    2024-08-14 01:04:42 (WARNING): Scale factor TripInteraction_2_sum_cbf not found in model
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): Scale factor TripInteraction_3_had_rbf not found in model
+
    2024-08-14 01:04:42 (WARNING): Scale factor AtomUpdate_2_sum not found in model
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): Scale factor TripInteraction_3_sum_cbf not found in model
+
    2024-08-14 01:04:42 (WARNING): Scale factor TripInteraction_3_had_rbf not found in model
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): Scale factor AtomUpdate_3_sum not found in model
+
    2024-08-14 01:04:42 (WARNING): Scale factor TripInteraction_3_sum_cbf not found in model
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): Scale factor OutBlock_2_sum not found in model
+
    2024-08-14 01:04:42 (WARNING): Scale factor AtomUpdate_3_sum not found in model
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): Scale factor OutBlock_2_had not found in model
+
    2024-08-14 01:04:42 (WARNING): Scale factor OutBlock_2_sum not found in model
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): Scale factor OutBlock_3_sum not found in model
+
    2024-08-14 01:04:42 (WARNING): Scale factor OutBlock_2_had not found in model
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): Scale factor OutBlock_3_had not found in model
+
    2024-08-14 01:04:42 (WARNING): Scale factor OutBlock_3_sum not found in model
 
    
 
    
-
    2024-08-03 02:23:31 (INFO): Loaded GemNetT with 3360519 parameters.
+
    2024-08-14 01:04:42 (WARNING): Scale factor OutBlock_3_had not found in model
 
    
 
    
-
    2024-08-03 02:23:31 (WARNING): log_summary for Tensorboard not supported
+
    2024-08-14 01:04:42 (INFO): Loaded GemNetT with 3360519 parameters.
+
    
+
    
+
    2024-08-14 01:04:42 (WARNING): log_summary for Tensorboard not supported
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
@@ -6032,17 +6107,17 @@ 
    Incorporating triplets and training GemNet-T
    2024-08-03 02:24:09 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.05e+02, forcesx_mae: 3.30e+00, forcesy_mae: 4.12e+00, forcesz_mae: 3.19e+00, forces_mae: 3.54e+00, forces_cosine_similarity: -1.29e-02, forces_magnitude_error: 6.83e+00, loss: 2.84e+02, lr: 1.00e-04, epoch: 7.14e-01, step: 5.00e+00
+
    2024-08-14 01:05:21 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.05e+02, forcesx_mae: 3.30e+00, forcesy_mae: 4.12e+00, forcesz_mae: 3.19e+00, forces_mae: 3.54e+00, forces_cosine_similarity: -1.29e-02, forces_magnitude_error: 6.83e+00, loss: 2.84e+02, lr: 1.00e-04, epoch: 7.14e-01, step: 5.00e+00
 
    
 
    
-
    2024-08-03 02:24:17 (INFO): Evaluating on val.
+
    2024-08-14 01:05:30 (INFO): Evaluating on val.
 
    
 
    
-
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
-  storage = elem.storage()._new_shared(numel)
+
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    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
+  storage = elem.storage()._new_shared(numel)
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
@@ -6053,19 +6128,19 @@ 
    Incorporating triplets and training GemNet-T
    device 0:  33%|███▎      | 1/3 [00:00<00:01,  1.91it/s]
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-
    2024-08-03 02:24:19 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 2.1859, forcesx_mae: 2.3018, forcesy_mae: 1.8443, forcesz_mae: 1.9866, forces_mae: 2.0442, forces_cosine_similarity: -0.1886, forces_magnitude_error: 3.8822, loss: 146.1000, epoch: 1.0000
+
    2024-08-14 01:05:32 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 2.1859, forcesx_mae: 2.3018, forcesy_mae: 1.8443, forcesz_mae: 1.9866, forces_mae: 2.0442, forces_cosine_similarity: -0.1886, forces_magnitude_error: 3.8822, loss: 146.1000, epoch: 1.0000
 
    
 
    
 
    
@@ -6099,10 +6174,10 @@ 
    Incorporating triplets and training GemNet-T
    2024-08-03 02:24:42 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.40e+01, forcesx_mae: 1.67e+00, forcesy_mae: 2.28e+00, forcesz_mae: 1.70e+00, forces_mae: 1.88e+00, forces_cosine_similarity: -6.95e-03, forces_magnitude_error: 3.54e+00, loss: 1.38e+02, lr: 1.00e-04, epoch: 1.43e+00, step: 1.00e+01
+
    2024-08-14 01:05:56 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 3.40e+01, forcesx_mae: 1.67e+00, forcesy_mae: 2.28e+00, forcesz_mae: 1.70e+00, forces_mae: 1.88e+00, forces_cosine_similarity: -6.95e-03, forces_magnitude_error: 3.54e+00, loss: 1.38e+02, lr: 1.00e-04, epoch: 1.43e+00, step: 1.00e+01
 
    
 
    
-
    2024-08-03 02:25:04 (INFO): Evaluating on val.
+
    2024-08-14 01:06:17 (INFO): Evaluating on val.
 
    
 
    
 
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@@ -6120,19 +6195,19 @@ 
    Incorporating triplets and training GemNet-T
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-
    2024-08-03 02:25:06 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 2.8872, forcesx_mae: 2.2966, forcesy_mae: 1.8156, forcesz_mae: 1.9075, forces_mae: 2.0066, forces_cosine_similarity: -0.1919, forces_magnitude_error: 3.7918, loss: 143.2075, epoch: 2.0000
+
    2024-08-14 01:06:19 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 2.8872, forcesx_mae: 2.2966, forcesy_mae: 1.8156, forcesz_mae: 1.9075, forces_mae: 2.0066, forces_cosine_similarity: -0.1919, forces_magnitude_error: 3.7918, loss: 143.2075, epoch: 2.0000
 
    
 
    
 
    
@@ -6166,13 +6241,13 @@ 
    Incorporating triplets and training GemNet-T
    2024-08-03 02:25:16 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 4.95e+01, forcesx_mae: 1.18e+00, forcesy_mae: 1.38e+00, forcesz_mae: 1.18e+00, forces_mae: 1.25e+00, forces_cosine_similarity: 1.80e-02, forces_magnitude_error: 2.22e+00, loss: 9.82e+01, lr: 1.00e-04, epoch: 2.14e+00, step: 1.50e+01
+
    2024-08-14 01:06:30 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 4.95e+01, forcesx_mae: 1.18e+00, forcesy_mae: 1.38e+00, forcesz_mae: 1.18e+00, forces_mae: 1.25e+00, forces_cosine_similarity: 1.80e-02, forces_magnitude_error: 2.22e+00, loss: 9.82e+01, lr: 1.00e-04, epoch: 2.14e+00, step: 1.50e+01
 
    
 
    
-
    2024-08-03 02:25:48 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 5.73e+01, forcesx_mae: 8.89e-01, forcesy_mae: 1.20e+00, forcesz_mae: 9.26e-01, forces_mae: 1.01e+00, forces_cosine_similarity: -2.94e-02, forces_magnitude_error: 1.74e+00, loss: 9.04e+01, lr: 1.00e-04, epoch: 2.86e+00, step: 2.00e+01
+
    2024-08-14 01:07:06 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 5.73e+01, forcesx_mae: 8.89e-01, forcesy_mae: 1.20e+00, forcesz_mae: 9.26e-01, forces_mae: 1.01e+00, forces_cosine_similarity: -2.94e-02, forces_magnitude_error: 1.74e+00, loss: 9.04e+01, lr: 1.00e-04, epoch: 2.86e+00, step: 2.00e+01
 
    
 
    
-
    2024-08-03 02:25:50 (INFO): Evaluating on val.
+
    2024-08-14 01:07:11 (INFO): Evaluating on val.
 
    
 
    
 
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@@ -6190,19 +6265,19 @@ 
    Incorporating triplets and training GemNet-T
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    2024-08-03 02:25:52 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 1.6403, forcesx_mae: 2.2450, forcesy_mae: 1.7636, forcesz_mae: 1.8652, forces_mae: 1.9579, forces_cosine_similarity: -0.1887, forces_magnitude_error: 3.6963, loss: 139.6124, epoch: 3.0000
+
    2024-08-14 01:07:13 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 1.6403, forcesx_mae: 2.2450, forcesy_mae: 1.7636, forcesz_mae: 1.8652, forces_mae: 1.9579, forces_cosine_similarity: -0.1887, forces_magnitude_error: 3.6963, loss: 139.6124, epoch: 3.0000
 
    
 
    
 
    
@@ -6236,13 +6311,10 @@ 
    Incorporating triplets and training GemNet-T
    2024-08-03 02:26:22 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.06e+01, forcesx_mae: 6.35e-01, forcesy_mae: 7.63e-01, forcesz_mae: 6.23e-01, forces_mae: 6.74e-01, forces_cosine_similarity: 4.42e-02, forces_magnitude_error: 1.12e+00, loss: 5.37e+01, lr: 1.00e-04, epoch: 3.57e+00, step: 2.50e+01
-
    
-
    
-
    2024-08-03 02:26:36 (INFO): Evaluating on val.
+
    2024-08-14 01:07:44 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 2.06e+01, forcesx_mae: 6.35e-01, forcesy_mae: 7.63e-01, forcesz_mae: 6.23e-01, forces_mae: 6.74e-01, forces_cosine_similarity: 4.42e-02, forces_magnitude_error: 1.12e+00, loss: 5.37e+01, lr: 1.00e-04, epoch: 3.57e+00, step: 2.50e+01
 
    
 
    
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+
    2024-08-14 01:07:59 (INFO): Evaluating on val.
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
@@ -6253,23 +6325,26 @@ 
    Incorporating triplets and training GemNet-T
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+
    
+
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
   storage = elem.storage()._new_shared(numel)
 
    
 
    
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    2024-08-03 02:26:38 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 2.1157, forcesx_mae: 2.2045, forcesy_mae: 1.7296, forcesz_mae: 1.8392, forces_mae: 1.9244, forces_cosine_similarity: -0.1851, forces_magnitude_error: 3.6256, loss: 137.3321, epoch: 4.0000
+
    2024-08-14 01:08:01 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 2.1157, forcesx_mae: 2.2045, forcesy_mae: 1.7296, forcesz_mae: 1.8392, forces_mae: 1.9244, forces_cosine_similarity: -0.1851, forces_magnitude_error: 3.6256, loss: 137.3321, epoch: 4.0000
 
    
 
    
 
    
@@ -6303,13 +6378,13 @@ 
    Incorporating triplets and training GemNet-T
    2024-08-03 02:26:55 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.13e+01, forcesx_mae: 5.82e-01, forcesy_mae: 8.45e-01, forcesz_mae: 6.18e-01, forces_mae: 6.82e-01, forces_cosine_similarity: 5.76e-02, forces_magnitude_error: 1.08e+00, loss: 5.14e+01, lr: 1.00e-04, epoch: 4.29e+00, step: 3.00e+01
+
    2024-08-14 01:08:18 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.13e+01, forcesx_mae: 5.82e-01, forcesy_mae: 8.45e-01, forcesz_mae: 6.18e-01, forces_mae: 6.82e-01, forces_cosine_similarity: 5.76e-02, forces_magnitude_error: 1.08e+00, loss: 5.14e+01, lr: 1.00e-04, epoch: 4.29e+00, step: 3.00e+01
 
    
 
    
-
    2024-08-03 02:27:23 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.02e+01, forcesx_mae: 4.69e-01, forcesy_mae: 6.54e-01, forcesz_mae: 5.04e-01, forces_mae: 5.42e-01, forces_cosine_similarity: 3.08e-02, forces_magnitude_error: 8.93e-01, loss: 4.17e+01, lr: 1.00e-04, epoch: 5.00e+00, step: 3.50e+01
+
    2024-08-14 01:08:46 (INFO): energy_forces_within_threshold: 0.00e+00, energy_mae: 1.02e+01, forcesx_mae: 4.69e-01, forcesy_mae: 6.54e-01, forcesz_mae: 5.04e-01, forces_mae: 5.42e-01, forces_cosine_similarity: 3.08e-02, forces_magnitude_error: 8.93e-01, loss: 4.17e+01, lr: 1.00e-04, epoch: 5.00e+00, step: 3.50e+01
 
    
 
    
-
    2024-08-03 02:27:23 (INFO): Evaluating on val.
+
    2024-08-14 01:08:46 (INFO): Evaluating on val.
 
    
 
    
 
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    Incorporating triplets and training GemNet-T
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    2024-08-03 02:27:25 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 1.9943, forcesx_mae: 2.1967, forcesy_mae: 1.7273, forcesz_mae: 1.8153, forces_mae: 1.9131, forces_cosine_similarity: -0.1857, forces_magnitude_error: 3.6056, loss: 136.5640, epoch: 5.0000
+
    2024-08-14 01:08:48 (INFO): energy_forces_within_threshold: 0.0000, energy_mae: 1.9943, forcesx_mae: 2.1967, forcesy_mae: 1.7273, forcesz_mae: 1.8153, forces_mae: 1.9131, forces_cosine_similarity: -0.1857, forces_magnitude_error: 3.6056, loss: 136.5640, epoch: 5.0000
 
    
 
    
 
    
@@ -6367,7 +6442,7 @@ 
    Download pretrained checkpoint
-
    2024-08-03 02:27:25 (INFO): Checking local cache: /tmp/fairchem_checkpoints/ for model GemNet-dT-S2EF-OC20-All
+
    2024-08-14 01:08:48 (INFO): Checking local cache: /tmp/fairchem_checkpoints/ for model GemNet-dT-S2EF-OC20-All
 
    
 
    
 
    
@@ -6411,20 +6486,20 @@ 
    Using the OCP Calculator
-
    2024-08-03 02:27:25 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+
    2024-08-14 01:08:48 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
 
    
 
    
-
    2024-08-03 02:27:25 (INFO): amp: false
+
    2024-08-14 01:08:49 (INFO): amp: false
 cmd:
-  checkpoint_dir: /home/runner/work/fairchem/fairchem/docs/legacy_tutorials/checkpoints/2024-08-03-02-27-12
-  commit: 08b8c1e
+  checkpoint_dir: /home/runner/work/fairchem/fairchem/docs/legacy_tutorials/checkpoints/2024-08-14-01-08-16
+  commit: 8fb16d6
   identifier: ''
-  logs_dir: /home/runner/work/fairchem/fairchem/docs/legacy_tutorials/logs/wandb/2024-08-03-02-27-12
+  logs_dir: /home/runner/work/fairchem/fairchem/docs/legacy_tutorials/logs/wandb/2024-08-14-01-08-16
   print_every: 100
-  results_dir: /home/runner/work/fairchem/fairchem/docs/legacy_tutorials/results/2024-08-03-02-27-12
+  results_dir: /home/runner/work/fairchem/fairchem/docs/legacy_tutorials/results/2024-08-14-01-08-16
   seed: null
-  timestamp_id: 2024-08-03-02-27-12
-  version: 0.1.dev1+g08b8c1e
+  timestamp_id: 2024-08-14-01-08-16
+  version: 1.1.0
 dataset:
   format: trajectory_lmdb
   grad_target_mean: 0.0
@@ -6466,8 +6541,7 @@ 
    Using the OCP Calculator
    2024-08-03 02:27:25 (INFO): Loading model: gemnet_t
+
    2024-08-14 01:08:49 (INFO): Normalization values for output energy: mean=-0.7554450631141663, rmsd=2.887317180633545.
+
    
+
    
+
    2024-08-14 01:08:49 (INFO): Normalization values for output forces: mean=0.0, rmsd=2.887317180633545.
+
    
+
    
+
    2024-08-14 01:08:49 (INFO): Loading model: gemnet_t
 
    
 
    
-
    2024-08-03 02:27:27 (INFO): Loaded GemNetT with 31671825 parameters.
+
    2024-08-14 01:08:50 (INFO): Loaded GemNetT with 31671825 parameters.
 
    
 
    
-
    2024-08-03 02:27:27 (WARNING): No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+
    /home/runner/work/fairchem/fairchem/src/fairchem/core/modules/normalization/normalizer.py:69: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
+  "mean": torch.tensor(state_dict["mean"]),
+2024-08-14 01:08:50 (WARNING): No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 
    
 
    
 
          Step     Time          Energy          fmax
-BFGS:    0 02:27:27       -4.099784        1.567516
+BFGS:    0 01:08:51       -4.099784        1.567516
 
    
 
    
-
    BFGS:    1 02:27:28       -4.244461        1.136988
+
    BFGS:    1 01:08:51       -4.244472        1.136985
 
    
 
    
-
    BFGS:    2 02:27:28       -4.403120        0.763538
+
    BFGS:    2 01:08:52       -4.403122        0.763561
 
    
 
    
-
    BFGS:    3 02:27:29       -4.503652        0.836403
+
    BFGS:    3 01:08:52       -4.503644        0.836383
 
    
 
    
-
    BFGS:    4 02:27:30       -4.558208        0.733873
+
    BFGS:    4 01:08:53       -4.558209        0.733877
 
    
 
    
-
    BFGS:    5 02:27:30       -4.592069        0.409536
+
    BFGS:    5 01:08:53       -4.592066        0.409535
 
    
 
    
-
    BFGS:    6 02:27:31       -4.619347        0.731239
+
    BFGS:    6 01:08:54       -4.619359        0.731256
 
    
 
    
-
    BFGS:    7 02:27:31       -4.671473        0.971220
+
    BFGS:    7 01:08:55       -4.671464        0.971141
 
    
 
    
-
    BFGS:    8 02:27:32       -4.796453        0.921123
+
    BFGS:    8 01:08:55       -4.796473        0.921026
 
    
 
    
-
    BFGS:    9 02:27:33       -4.957974        0.976140
+
    BFGS:    9 01:08:56       -4.957972        0.976196
 
    
 
    
-
    BFGS:   10 02:27:33       -5.109447        1.038363
+
    BFGS:   10 01:08:56       -5.109419        1.038484
 
    
 
    
-
    BFGS:   11 02:27:34       -5.295602        1.224861
+
    BFGS:   11 01:08:57       -5.295610        1.224973
 
    
 
    
-
    BFGS:   12 02:27:34       -5.498971        1.127107
+
    BFGS:   12 01:08:57       -5.498995        1.127049
 
    
 
    
-
    BFGS:   13 02:27:35       -5.618084        1.066881
+
    BFGS:   13 01:08:58       -5.618104        1.066863
 
    
 
    
-
    BFGS:   14 02:27:35       -5.737121        0.950872
+
    BFGS:   14 01:08:59       -5.737133        0.950848
 
    
 
    
-
    BFGS:   15 02:27:36       -5.901947        0.926001
+
    BFGS:   15 01:08:59       -5.901944        0.926049
 
    
 
    
-
    BFGS:   16 02:27:37       -6.076138        1.273703
+
    BFGS:   16 01:09:00       -6.076124        1.273782
 
    
 
    
-
    BFGS:   17 02:27:37       -6.198372        1.202876
+
    BFGS:   17 01:09:00       -6.198373        1.202949
 
    
 
    
-
    BFGS:   18 02:27:38       -6.250344        0.685223
+
    BFGS:   18 01:09:01       -6.250327        0.685198
 
    
 
    
-
    BFGS:   19 02:27:38       -6.254098        0.200815
+
    BFGS:   19 01:09:01       -6.254099        0.200784
 
    
 
    
-
    BFGS:   20 02:27:39       -6.293970        0.177886
+
    BFGS:   20 01:09:02       -6.293955        0.177882
 
    
 
    
-
    BFGS:   21 02:27:39       -6.326332        0.229425
+
    BFGS:   21 01:09:03       -6.326336        0.229420
 
    
 
    
-
    BFGS:   22 02:27:40       -6.324463        0.170005
+
    BFGS:   22 01:09:03       -6.324459        0.170037
 
    
 
    
-
    BFGS:   23 02:27:40       -6.321269        0.101603
+
    BFGS:   23 01:09:04       -6.321297        0.101550
 
    
 
    
-
    BFGS:   24 02:27:41       -6.328320        0.084661
+
    BFGS:   24 01:09:04       -6.328354        0.084693
 
    
 
    
-
    BFGS:   25 02:27:41       -6.331771        0.058621
+
    BFGS:   25 01:09:05       -6.331687        0.058673
 
    
 
    
-
    BFGS:   26 02:27:42       -6.331944        0.044489
+
    BFGS:   26 01:09:05       -6.331860        0.044462
 
    
 
    
 
    True
@@ -6858,10 +6941,10 @@ 
    Structure to Energy and Forces (S2EF) LMDBs
      0%|          | 0/101 [00:00<?, ?it/s]
 
    
 
    
-
     58%|█████▊    | 59/101 [00:00<00:00, 584.65it/s]
+
     57%|█████▋    | 58/101 [00:00<00:00, 574.71it/s]
 
    
 
    
-
    100%|██████████| 101/101 [00:00<00:00, 612.60it/s]
+
    100%|██████████| 101/101 [00:00<00:00, 580.13it/s]
 
    
 
    
 
    
diff --git a/legacy_tutorials/data_preprocessing.html b/legacy_tutorials/data_preprocessing.html
index 89ac98fdb4..f758d36341 100644
--- a/legacy_tutorials/data_preprocessing.html
+++ b/legacy_tutorials/data_preprocessing.html
@@ -305,6 +305,7 @@
 
  • core.common.logger
    • 
 
  • core.common.profiler_utils
    • 
 
  • core.common.registry
    • 
+
  • core.common.slurm
    • 
 
  • core.common.test_utils
    • 
 
  • core.common.transforms
    • 
 
  • core.common.tutorial_utils
    • 
@@ -334,16 +335,17 @@
 
  • core.models.utils
    • 
 
  • core.models.base
    • 
 
  • core.models.dimenet_plus_plus
    • 
+
  • core.models.finetune_hydra
    • 
 
  • core.models.model_registry
    • 
 
  • core.models.schnet
    •

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -673,7 +676,7 @@

    Generate toy dataset: Relaxation of CO on Cu -
    /tmp/ipykernel_4368/901556023.py:8: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_4404/901556023.py:8: DeprecationWarning: Please use atoms.calc = calc
   adslab.set_calculator(EMT())
 
    
 
    
@@ -738,7 +741,7 @@ 
    Convert Atoms object to Data object
-
    Data(pos=[14, 3], cell=[1, 3, 3], atomic_numbers=[14], natoms=14, tags=[14], edge_index=[2, 636], cell_offsets=[636, 3], energy=3.9893144106683787, forces=[14, 3], fixed=[14])
+
    Data(pos=[14, 3], cell=[1, 3, 3], atomic_numbers=[14], natoms=14, tags=[14], edge_index=[2, 635], cell_offsets=[635, 3], energy=3.9893144106683787, forces=[14, 3], fixed=[14])
 
    
 
    
 
    
@@ -776,7 +779,7 @@ 
    Convert Atoms object to Data object
-
    tensor([[ 1,  2,  2,  ...,  4,  6,  3],
+
    tensor([[ 1,  2,  2,  ...,  5,  6,  3],
         [ 0,  0,  0,  ..., 13, 13, 13]])
 
    
 
    
@@ -793,7 +796,7 @@ 
    Convert Atoms object to Data object
-
    tensor([45., 45., 45., 46., 49., 49., 49., 49., 50., 49., 49., 50., 26., 35.])
+
    tensor([45., 45., 45., 46., 49., 49., 49., 49., 50., 49., 49., 49., 26., 35.])
 
    
 
    
 
    
@@ -903,7 +906,7 @@ 
    Adding additional info to your Data objects
-
    Data(pos=[14, 3], cell=[1, 3, 3], atomic_numbers=[14], natoms=14, tags=[14], edge_index=[2, 635], cell_offsets=[635, 3], energy=3.9683558933958047, forces=[14, 3], fixed=[14], fid=100, sid=0)
+
    Data(pos=[14, 3], cell=[1, 3, 3], atomic_numbers=[14], natoms=14, tags=[14], edge_index=[2, 638], cell_offsets=[638, 3], energy=3.9683558933958047, forces=[14, 3], fixed=[14], fid=100, sid=0)
 
    
 
    
 
    
diff --git a/legacy_tutorials/data_visualization.html b/legacy_tutorials/data_visualization.html
index ae42ff73eb..db54582c90 100644
--- a/legacy_tutorials/data_visualization.html
+++ b/legacy_tutorials/data_visualization.html
@@ -307,6 +307,7 @@
 
  • core.common.logger
    • 
 
  • core.common.profiler_utils
    • 
 
  • core.common.registry
    • 
+
  • core.common.slurm
    • 
 
  • core.common.test_utils
    • 
 
  • core.common.transforms
    • 
 
  • core.common.tutorial_utils
    • 
@@ -336,16 +337,17 @@
 
  • core.models.utils
    • 
 
  • core.models.base
    • 
 
  • core.models.dimenet_plus_plus
    • 
+
  • core.models.finetune_hydra
    • 
 
  • core.models.model_registry
    • 
 
  • core.models.schnet
    •

  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    @@ -761,311 +764,311 @@

    Generating sample data 
           Step     Time          Energy          fmax
-LBFGS:    0 02:27:57       15.804700        6.776430
+LBFGS:    0 01:09:23       15.804700        6.776430
    -
    LBFGS:    1 02:27:57       12.190607        4.323222
+
    LBFGS:    1 01:09:23       12.190607        4.323222
 
    
 
    
-
    LBFGS:    2 02:27:57       10.240169        2.265527
+
    LBFGS:    2 01:09:23       10.240169        2.265527
 
    
 
    
-
    LBFGS:    3 02:27:57        9.779223        0.937247
+
    LBFGS:    3 01:09:23        9.779223        0.937247
 
    
 
    
-
    LBFGS:    4 02:27:57        9.671525        0.770173
+
    LBFGS:    4 01:09:23        9.671525        0.770173
 
    
 
    
-
    LBFGS:    5 02:27:57        9.574461        0.663540
+
    LBFGS:    5 01:09:24        9.574461        0.663540
 
    
 
    
-
    LBFGS:    6 02:27:57        9.537502        0.571800
+
    LBFGS:    6 01:09:24        9.537502        0.571800
 
    
 
    
-
    LBFGS:    7 02:27:57        9.516673        0.446620
+
    LBFGS:    7 01:09:24        9.516673        0.446620
 
    
 
    
-
    LBFGS:    8 02:27:57        9.481330        0.461143
+
    LBFGS:    8 01:09:24        9.481330        0.461143
 
    
 
    
-
    LBFGS:    9 02:27:57        9.462255        0.293081
+
    LBFGS:    9 01:09:24        9.462255        0.293081
 
    
 
    
-
    LBFGS:   10 02:27:57        9.448937        0.249010
+
    LBFGS:   10 01:09:24        9.448937        0.249010
 
    
 
    
-
    LBFGS:   11 02:27:57        9.433813        0.237051
+
    LBFGS:   11 01:09:24        9.433813        0.237051
 
    
 
    
-
    LBFGS:   12 02:27:57        9.418884        0.260245
+
    LBFGS:   12 01:09:24        9.418884        0.260245
 
    
 
    
-
    LBFGS:   13 02:27:57        9.409649        0.253162
+
    LBFGS:   13 01:09:24        9.409649        0.253162
 
    
 
    
-
    LBFGS:   14 02:27:57        9.404838        0.162398
+
    LBFGS:   14 01:09:24        9.404838        0.162398
 
    
 
    
-
    LBFGS:   15 02:27:57        9.401753        0.182298
+
    LBFGS:   15 01:09:24        9.401753        0.182298
 
    
 
    
-
    /tmp/ipykernel_4394/2542206394.py:19: DeprecationWarning: Please use atoms.calc = calc
-  adslab.set_calculator(EMT())
+
    LBFGS:   16 01:09:24        9.397314        0.259163
 
    
 
    
-
    LBFGS:   16 02:27:57        9.397314        0.259163
+
    LBFGS:   17 01:09:24        9.387947        0.345022
 
    
 
    
-
    LBFGS:   17 02:27:57        9.387947        0.345022
+
    /tmp/ipykernel_4429/2542206394.py:19: DeprecationWarning: Please use atoms.calc = calc
+  adslab.set_calculator(EMT())
 
    
 
    
-
    LBFGS:   18 02:27:57        9.370825        0.407041
+
    LBFGS:   18 01:09:24        9.370825        0.407041
 
    
 
    
-
    LBFGS:   19 02:27:57        9.342222        0.433340
+
    LBFGS:   19 01:09:24        9.342222        0.433340
 
    
 
    
-
    LBFGS:   20 02:27:57        9.286822        0.500200
+
    LBFGS:   20 01:09:24        9.286822        0.500200
 
    
 
    
-
    LBFGS:   21 02:27:57        9.249910        0.524052
+
    LBFGS:   21 01:09:24        9.249910        0.524052
 
    
 
    
-
    LBFGS:   22 02:27:57        9.187179        0.511994
+
    LBFGS:   22 01:09:24        9.187179        0.511994
 
    
 
    
-
    LBFGS:   23 02:27:57        9.124811        0.571796
+
    LBFGS:   23 01:09:24        9.124811        0.571796
 
    
 
    
-
    LBFGS:   24 02:27:57        9.066185        0.540934
+
    LBFGS:   24 01:09:24        9.066185        0.540934
 
    
 
    
-
    LBFGS:   25 02:27:57        9.000116        1.079833
+
    LBFGS:   25 01:09:24        9.000116        1.079833
 
    
 
    
-
    LBFGS:   26 02:27:57        8.893632        0.752759
+
    LBFGS:   26 01:09:24        8.893632        0.752759
 
    
 
    
-
    LBFGS:   27 02:27:57        8.845939        0.332051
+
    LBFGS:   27 01:09:24        8.845939        0.332051
 
    
 
    
-
    LBFGS:   28 02:27:57        8.815173        0.251242
+
    LBFGS:   28 01:09:24        8.815173        0.251242
 
    
 
    
-
    LBFGS:   29 02:27:57        8.808721        0.214337
+
    LBFGS:   29 01:09:24        8.808721        0.214337
 
    
 
    
-
    LBFGS:   30 02:27:57        8.794643        0.154611
+
    LBFGS:   30 01:09:24        8.794643        0.154611
 
    
 
    
-
    LBFGS:   31 02:27:57        8.789162        0.201404
+
    LBFGS:   31 01:09:24        8.789162        0.201404
 
    
 
    
-
    LBFGS:   32 02:27:57        8.782320        0.175517
+
    LBFGS:   32 01:09:24        8.782320        0.175517
 
    
 
    
-
    LBFGS:   33 02:27:57        8.780394        0.103718
+
    LBFGS:   33 01:09:24        8.780394        0.103718
 
    
 
    
-
    LBFGS:   34 02:27:57        8.778410        0.107611
+
    LBFGS:   34 01:09:24        8.778410        0.107611
 
    
 
    
-
    LBFGS:   35 02:27:57        8.775079        0.179747
+
    LBFGS:   35 01:09:24        8.775079        0.179747
 
    
 
    
-
    LBFGS:   36 02:27:57        8.766987        0.333401
+
    LBFGS:   36 01:09:24        8.766987        0.333401
 
    
 
    
-
    LBFGS:   37 02:27:57        8.750249        0.530715
+
    LBFGS:   37 01:09:24        8.750249        0.530715
 
    
 
    
-
    LBFGS:   38 02:27:57        8.725928        0.685116
+
    LBFGS:   38 01:09:24        8.725928        0.685116
 
    
 
    
-
    LBFGS:   39 02:27:57        8.702312        0.582260
+
    LBFGS:   39 01:09:24        8.702312        0.582260
 
    
 
    
-
    LBFGS:   40 02:27:57        8.661515        0.399625
+
    LBFGS:   40 01:09:24        8.661515        0.399625
 
    
 
    
-
    LBFGS:   41 02:27:57        8.643432        0.558474
+
    LBFGS:   41 01:09:24        8.643432        0.558474
 
    
 
    
-
    LBFGS:   42 02:27:57        8.621201        0.367288
+
    LBFGS:   42 01:09:24        8.621201        0.367288
 
    
 
    
-
    LBFGS:   43 02:27:57        8.614414        0.139424
+
    LBFGS:   43 01:09:24        8.614414        0.139424
 
    
 
    
-
    LBFGS:   44 02:27:57        8.610785        0.137160
+
    LBFGS:   44 01:09:24        8.610785        0.137160
 
    
 
    
-
    LBFGS:   45 02:27:57        8.608134        0.146375
+
    LBFGS:   45 01:09:24        8.608134        0.146375
 
    
 
    
-
    LBFGS:   46 02:27:57        8.604928        0.119648
+
    LBFGS:   46 01:09:24        8.604928        0.119648
 
    
 
    
-
    LBFGS:   47 02:27:57        8.599151        0.135424
+
    LBFGS:   47 01:09:24        8.599151        0.135424
 
    
 
    
-
    LBFGS:   48 02:27:57        8.594063        0.147913
+
    LBFGS:   48 01:09:24        8.594063        0.147913
 
    
 
    
-
    LBFGS:   49 02:27:57        8.589493        0.153840
+
    LBFGS:   49 01:09:24        8.589493        0.153840
 
    
 
    
-
    LBFGS:   50 02:27:57        8.587274        0.088460
+
    LBFGS:   50 01:09:24        8.587274        0.088460
 
    
 
    
-
    LBFGS:   51 02:27:57        8.584633        0.093750
+
    LBFGS:   51 01:09:24        8.584633        0.093750
 
    
 
    
-
    LBFGS:   52 02:27:57        8.580239        0.140870
+
    LBFGS:   52 01:09:24        8.580239        0.140870
 
    
 
    
-
    LBFGS:   53 02:27:57        8.572938        0.254272
+
    LBFGS:   53 01:09:24        8.572938        0.254272
 
    
 
    
-
    LBFGS:   54 02:27:57        8.563343        0.291885
+
    LBFGS:   54 01:09:24        8.563343        0.291885
 
    
 
    
-
    LBFGS:   55 02:27:57        8.554117        0.196557
+
    LBFGS:   55 01:09:24        8.554117        0.196557
 
    
 
    
-
    LBFGS:   56 02:27:57        8.547597        0.129064
+
    LBFGS:   56 01:09:24        8.547597        0.129064
 
    
 
    
-
    LBFGS:   57 02:27:57        8.542086        0.128020
+
    LBFGS:   57 01:09:24        8.542086        0.128020
 
    
 
    
-
    LBFGS:   58 02:27:57        8.535432        0.098202
+
    LBFGS:   58 01:09:24        8.535432        0.098202
 
    
 
    
-
    LBFGS:   59 02:27:57        8.533622        0.127672
+
    LBFGS:   59 01:09:24        8.533622        0.127672
 
    
 
    
-
    LBFGS:   60 02:27:57        8.527487        0.116729
+
    LBFGS:   60 01:09:24        8.527487        0.116729
 
    
 
    
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    LBFGS:   61 02:27:57        8.523863        0.121762
+
    LBFGS:   61 01:09:24        8.523863        0.121762
 
    
 
    
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    LBFGS:   62 01:09:24        8.519229        0.130541
 
    
 
    
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+
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+
    LBFGS:   64 01:09:24        8.511240        0.212223
 
    
 
    
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+
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    LBFGS:   66 02:27:57        8.503903        0.237734
+
    LBFGS:   66 01:09:24        8.503903        0.237734
 
    
 
    
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    LBFGS:   67 02:27:57        8.497575        0.162253
+
    LBFGS:   67 01:09:24        8.497575        0.162253
 
    
 
    
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    LBFGS:   68 02:27:57        8.485434        0.202203
+
    LBFGS:   68 01:09:24        8.485434        0.202203
 
    
 
    
-
    LBFGS:   69 02:27:57        8.466738        0.215895
+
    LBFGS:   69 01:09:24        8.466738        0.215895
 
    
 
    
-
    LBFGS:   70 02:27:57        8.467607        0.334764
+
    LBFGS:   70 01:09:24        8.467607        0.334764
 
    
 
    
-
    LBFGS:   71 02:27:57        8.454037        0.106310
+
    LBFGS:   71 01:09:24        8.454037        0.106310
 
    
 
    
-
    LBFGS:   72 02:27:57        8.448980        0.119721
+
    LBFGS:   72 01:09:24        8.448980        0.119721
 
    
 
    
-
    LBFGS:   73 02:27:57        8.446550        0.099221
+
    LBFGS:   73 01:09:24        8.446550        0.099221
 
    
 
    
-
    LBFGS:   74 02:27:57        8.444705        0.056244
+
    LBFGS:   74 01:09:24        8.444705        0.056244
 
    
 
    
-
    LBFGS:   75 02:27:57        8.443403        0.038831
+
    LBFGS:   75 01:09:24        8.443403        0.038831
 
    
 
    
-
    LBFGS:   76 02:27:57        8.442646        0.054772
+
    LBFGS:   76 01:09:24        8.442646        0.054772
 
    
 
    
-
    LBFGS:   77 02:27:57        8.442114        0.061370
+
    LBFGS:   77 01:09:24        8.442114        0.061370
 
    
 
    
-
    LBFGS:   78 02:27:58        8.440960        0.058800
+
    LBFGS:   78 01:09:24        8.440960        0.058800
 
    
 
    
-
    LBFGS:   79 02:27:58        8.439820        0.048198
+
    LBFGS:   79 01:09:24        8.439820        0.048198
 
    
 
    
-
    LBFGS:   80 02:27:58        8.438600        0.051251
+
    LBFGS:   80 01:09:24        8.438600        0.051251
 
    
 
    
-
    LBFGS:   81 02:27:58        8.437429        0.054130
+
    LBFGS:   81 01:09:24        8.437429        0.054130
 
    
 
    
-
    LBFGS:   82 02:27:58        8.435695        0.067234
+
    LBFGS:   82 01:09:24        8.435695        0.067234
 
    
 
    
-
    LBFGS:   83 02:27:58        8.431957        0.085678
+
    LBFGS:   83 01:09:24        8.431957        0.085678
 
    
 
    
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    LBFGS:   84 02:27:58        8.423485        0.133240
+
    LBFGS:   84 01:09:24        8.423485        0.133240
 
    
 
    
-
    LBFGS:   85 02:27:58        8.413846        0.207812
+
    LBFGS:   85 01:09:24        8.413846        0.207812
 
    
 
    
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    LBFGS:   86 02:27:58        8.404849        0.178747
+
    LBFGS:   86 01:09:24        8.404849        0.178747
 
    
 
    
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    LBFGS:   87 02:27:58        8.385339        0.169017
+
    LBFGS:   87 01:09:24        8.385339        0.169017
 
    
 
    
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    LBFGS:   88 02:27:58        8.386849        0.187645
+
    LBFGS:   88 01:09:24        8.386849        0.187645
 
    
 
    
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    LBFGS:   89 02:27:58        8.371078        0.118124
+
    LBFGS:   89 01:09:24        8.371078        0.118124
 
    
 
    
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    LBFGS:   90 02:27:58        8.368801        0.094222
+
    LBFGS:   90 01:09:24        8.368801        0.094222
 
    
 
    
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    LBFGS:   91 02:27:58        8.366226        0.066960
+
    LBFGS:   91 01:09:25        8.366226        0.066960
 
    
 
    
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    LBFGS:   92 02:27:58        8.361680        0.054964
+
    LBFGS:   92 01:09:25        8.361680        0.054964
 
    
 
    
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    LBFGS:   93 02:27:58        8.360631        0.047342
+
    LBFGS:   93 01:09:25        8.360631        0.047342
 
    
 
    
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    LBFGS:   94 02:27:58        8.359692        0.024179
+
    LBFGS:   94 01:09:25        8.359692        0.024179
 
    
 
    
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    LBFGS:   95 02:27:58        8.359361        0.015549
+
    LBFGS:   95 01:09:25        8.359361        0.015549
 
    
 
    
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    LBFGS:   96 02:27:58        8.359163        0.014284
+
    LBFGS:   96 01:09:25        8.359163        0.014284
 
    
 
    
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    LBFGS:   97 02:27:58        8.359102        0.015615
+
    LBFGS:   97 01:09:25        8.359102        0.015615
 
    
 
    
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    LBFGS:   98 02:27:58        8.359048        0.015492
+
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+
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    LBFGS:  100 02:27:58        8.358921        0.013159
+
    LBFGS:  100 01:09:25        8.358921        0.013159
 
    
 
    
 
    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/ase/io/extxyz.py:311: UserWarning: Skipping unhashable information adsorbate_info
@@ -1108,7 +1111,7 @@ 
    Viewing a trajectory
    <Axes: title={'center': 'final'}>
 
    
 
    
-../_images/6e93e34104c6236abbd25466bec810cc5a44f1fce8c2eef3ccb492932b39d7ac.png
+../_images/57fc29d6b458f6d6888e1ee0b717ee77535081c6ef989960bdcb2fb141022503.png
 
    
 
    
 
@@ -1314,7 +1317,7 @@ 
    Energy#
    
 
    
-
    /tmp/ipykernel_4394/1528962.py:7: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_4429/1528962.py:7: DeprecationWarning: Please use atoms.calc = calc
   raw_slab.set_calculator(EMT())
 
    
 
    
@@ -1336,7 +1339,7 @@ 
    Energy#
    Text(0, 0.5, 'Energy, eV')
 
    
 
    
-../_images/c345947e7668b33a314d59121094f353e2623573ea3dd213d23a6b486bfbee9e.png
+../_images/441a9966a5b92807bb6c44051b68e2d8f68c6ea2df63b5fa0cdd822583379c1e.png
 
    
 
    
 
diff --git a/legacy_tutorials/legacy_tutorials.html b/legacy_tutorials/legacy_tutorials.html
index 9e16c492bf..ed5db72661 100644
--- a/legacy_tutorials/legacy_tutorials.html
+++ b/legacy_tutorials/legacy_tutorials.html
@@ -307,6 +307,7 @@
 
  • core.common.logger
    • 
 
  • core.common.profiler_utils
    • 
 
  • core.common.registry
    • 
+
  • core.common.slurm
    • 
 
  • core.common.test_utils
    • 
 
  • core.common.transforms
    • 
 
  • core.common.tutorial_utils
    • 
@@ -336,16 +337,17 @@
 
  • core.models.utils
    • 
 
  • core.models.base
    • 
 
  • core.models.dimenet_plus_plus
    • 
+
  • core.models.finetune_hydra
    • 
 
  • core.models.model_registry
    • 
 
  • core.models.schnet
    •

  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    diff --git a/objects.inv b/objects.inv index b8c4825af2..3f51c71ae5 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/py-modindex.html b/py-modindex.html index 470272d03d..5e4b903b5a 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -307,6 +307,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -336,16 +337,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -358,6 +360,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -383,7 +387,6 @@
  • data.oc
    @@ -743,6 +746,11 @@

    Python Module Index

        core.common.relaxation.optimizers.lbfgs_torch + + +     + core.common.slurm +     @@ -953,6 +961,11 @@

    Python Module Index

        core.models.escn.so3 + + +     + core.models.finetune_hydra +     @@ -1246,7 +1259,22 @@

    Python Module Index

        - core.modules.normalizer + core.modules.normalization + + + +     + core.modules.normalization._load_utils + + + +     + core.modules.normalization.element_references + + + +     + core.modules.normalization.normalizer @@ -1308,6 +1336,16 @@

    Python Module Index

        core.scripts.download_large_files + + +     + core.scripts.fit_normalizers + + + +     + core.scripts.fit_references +     @@ -1417,6 +1455,16 @@

    Python Module Index

        data.oc.core.bulk + + +     + data.oc.core.interface_config + + + +     + data.oc.core.ion +     @@ -1427,6 +1475,11 @@

    Python Module Index

        data.oc.core.slab + + +     + data.oc.core.solvent +     @@ -1480,23 +1533,28 @@

    Python Module Index

        - data.oc.tests + data.oc.utils     - data.oc.utils + data.oc.utils.flag_anomaly     - data.oc.utils.flag_anomaly + data.oc.utils.geometry     data.oc.utils.vasp + + +     + data.oc.utils.vasp_flags +     diff --git a/search.html b/search.html index 79ac64e19c..48c0908b8d 100644 --- a/search.html +++ b/search.html @@ -306,6 +306,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -335,16 +336,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -357,6 +359,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -382,7 +386,6 @@
  • data.oc
    diff --git a/searchindex.js b/searchindex.js index 575d41a988..b5ac8251f5 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"": [[205, "id1"], [205, "id2"]], "(Optional) Creating your own LMDBs for use in the OCP repository": [[222, "optional-creating-your-own-lmdbs-for-use-in-the-ocp-repository"]], "(Optional) Deduplicate structures": [[229, "optional-deduplicate-structures"]], "(Optional) OCP Calculator ": [[222, "optional-ocp-calculator"]], "A clustering example": [[231, "a-clustering-example"]], "A diagnostic example": [[231, "a-diagnostic-example"]], "A simple vector search example": [[231, "a-simple-vector-search-example"]], "API Reference": [[188, null]], "About the compute environment": [[235, "about-the-compute-environment"]], "Abstract": [[235, "abstract"]], "Accelerating computational catalysis": [[218, "accelerating-computational-catalysis"]], "Acknowledgements": [[221, "acknowledgements"]], "Adding additional info to your Data 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"core.models.gemnet_oc.utils.get_angle", false]], "get_atoms() (core.datasets.ase_datasets.aseatomsdataset method)": [[33, "core.datasets.ase_datasets.AseAtomsDataset.get_atoms", false]], "get_atoms() (core.datasets.ase_datasets.asedbdataset method)": [[33, "core.datasets.ase_datasets.AseDBDataset.get_atoms", false]], "get_atoms() (core.datasets.ase_datasets.asereaddataset method)": [[33, "core.datasets.ase_datasets.AseReadDataset.get_atoms", false]], "get_atoms() (core.datasets.ase_datasets.asereadmultistructuredataset method)": [[33, "core.datasets.ase_datasets.AseReadMultiStructureDataset.get_atoms", false]], "get_atoms() (core.datasets.asedbdataset method)": [[40, "core.datasets.AseDBDataset.get_atoms", false]], "get_atoms() (core.datasets.asereaddataset method)": [[40, "core.datasets.AseReadDataset.get_atoms", false]], "get_atoms() (core.datasets.asereadmultistructuredataset method)": [[40, "core.datasets.AseReadMultiStructureDataset.get_atoms", false]], "get_bases() 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false]], "get_bulks() (ocpapi.client.client method)": [[190, "ocpapi.client.Client.get_bulks", false]], "get_bulks() (ocpapi.client.client.client method)": [[189, "ocpapi.client.client.Client.get_bulks", false]], "get_class() (core.common.registry.registry class method)": [[21, "core.common.registry.Registry.get_class", false]], "get_commit_hash() (in module core.common.utils)": [[31, "core.common.utils.get_commit_hash", false]], "get_data() (in module core.scripts.download_data)": [[138, "core.scripts.download_data.get_data", false]], "get_data() (in module core.scripts.make_lmdb_sizes)": [[146, "core.scripts.make_lmdb_sizes.get_data", false]], "get_data() (in module data.odac.force_field.ff_analysis)": [[178, "data.odac.force_field.FF_analysis.get_data", false]], "get_dataloader() (core.trainers.base_trainer.basetrainer method)": [[153, "core.trainers.base_trainer.BaseTrainer.get_dataloader", false]], "get_dataloader() (core.trainers.basetrainer method)": [[154, 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"cattsunami.core.autoframe.AutoFrameTransfer.get_neb_frames", false]], "get_neighbor_order() (in module core.models.gemnet_oc.utils)": [[109, "core.models.gemnet_oc.utils.get_neighbor_order", false]], "get_normalization_layer() (in module core.models.equiformer_v2.layer_norm)": [[55, "core.models.equiformer_v2.layer_norm.get_normalization_layer", false]], "get_parser() (core.common.flags.flags method)": [[15, "core.common.flags.Flags.get_parser", false]], "get_parser() (in module core.scripts.gif_maker_parallelized)": [[140, "core.scripts.gif_maker_parallelized.get_parser", false]], "get_parser() (in module core.scripts.preprocess_ef)": [[148, "core.scripts.preprocess_ef.get_parser", false]], "get_parser() (in module core.scripts.uncompress)": [[150, "core.scripts.uncompress.get_parser", false]], "get_pbc_distances() (in module core.common.utils)": [[31, "core.common.utils.get_pbc_distances", false]], "get_precon_forces() (cattsunami.core.ocpneb method)": [[6, 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"expand_edge() (core.models.escn.so3.so3_embedding method)": [[69, "core.models.escn.so3.SO3_Embedding.expand_edge", false]], "expand_index (core.models.equiformer_v2.activation.gateactivation attribute)": [[49, "core.models.equiformer_v2.activation.GateActivation.expand_index", false]], "expand_index (core.models.equiformer_v2.layer_norm.equivariantdegreelayerscale attribute)": [[56, "core.models.equiformer_v2.layer_norm.EquivariantDegreeLayerScale.expand_index", false]], "expand_index (core.models.equiformer_v2.layer_norm.equivariantrmsnormarraysphericalharmonicsv2 attribute)": [[56, "core.models.equiformer_v2.layer_norm.EquivariantRMSNormArraySphericalHarmonicsV2.expand_index", false]], "expand_index (core.models.equiformer_v2.so3.so3_linearv2 attribute)": [[60, "core.models.equiformer_v2.so3.SO3_LinearV2.expand_index", false]], "exponentialenvelope (class in core.models.gemnet.layers.radial_basis)": [[81, "core.models.gemnet.layers.radial_basis.ExponentialEnvelope", false]], 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"core.models.gemnet_gp.gemnet.GraphParallelGemNetT.extensive", false]], "extensive (core.models.gemnet_gp.graphparallelgemnett attribute)": [[85, "core.models.gemnet_gp.GraphParallelGemNetT.extensive", false]], "extensive (core.models.gemnet_oc.gemnet_oc.gemnetoc attribute)": [[97, "core.models.gemnet_oc.gemnet_oc.GemNetOC.extensive", false]], "extensive (core.models.gemnet_oc.gemnet_oc.gemnetocenergyandgradforcehead attribute)": [[97, "core.models.gemnet_oc.gemnet_oc.GemNetOCEnergyAndGradForceHead.extensive", false]], "extensive (core.models.gemnet_oc.gemnetoc attribute)": [[98, "core.models.gemnet_oc.GemNetOC.extensive", false]], "extra_m0_output_channels (core.models.equiformer_v2.so2_ops.so2_convolution attribute)": [[59, "core.models.equiformer_v2.so2_ops.SO2_Convolution.extra_m0_output_channels", false]], "extra_m0_output_channels (core.models.equiformer_v2.transformer_block.so2equivariantgraphattention attribute)": [[65, 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"visual": [233, 235, 244, 245], "wai": [220, 233], "walkthrough": 246, "want": 219, "warn": 219, "web": 228, "what": 226, "why": 222, "wigner": 66, "wildli": 219, "window": 221, "work": [237, 242], "workflow": [206, 207, 208, 209, 210, 211], "write": [224, 240], "write_geom_drugs_structur": 194, "write_top_k_vasp": 4, "yaml": [218, 227], "you": [219, 245], "your": [219, 233, 234, 245], "zero": 219, "\u03b8_cabd": 226}}) \ No newline at end of file diff --git a/tutorials/NRR/NRR_example.html b/tutorials/NRR/NRR_example.html index c9389664d4..3b950ee2c2 100644 --- a/tutorials/NRR/NRR_example.html +++ b/tutorials/NRR/NRR_example.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -785,7 +788,7 @@

    Work out a single example -../../_images/aee96fc3ceee5280ecb2704288b1ef4902bbe3b113f789e61756f34ec2983c3e.png +../../_images/124b91af2b0ba6e1506ab4090a72f25071c1ca7dde279d9c04e27ca09e12cb35.png
    @@ -809,7 +812,9 @@

    Run an ML relaxation
    WARNING:root:Skipping scheduler setup. No training set found.
    -
    WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+
    /home/runner/work/fairchem/fairchem/src/fairchem/core/modules/normalization/normalizer.py:69: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
+  "mean": torch.tensor(state_dict["mean"]),
+WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
    @@ -830,49 +835,49 @@

    Run an ML relaxation 
          Step     Time          Energy          fmax
-BFGS:    0 02:28:53        0.195044        0.716552
+BFGS:    0 01:10:21        0.193124        0.716220
    -
    BFGS:    1 02:28:55        0.175054        0.672982
+
    BFGS:    1 01:10:23        0.175033        0.673152
 
    
 
    
-
    BFGS:    2 02:28:56        0.059278        0.372825
+
    BFGS:    2 01:10:24        0.059609        0.388686
 
    
 
    
-
    BFGS:    3 02:28:58        0.056324        0.226600
+
    BFGS:    3 01:10:25        0.056407        0.223205
 
    
 
    
-
    BFGS:    4 02:28:59        0.052357        0.162363
+
    BFGS:    4 01:10:27        0.052641        0.171620
 
    
 
    
-
    BFGS:    5 02:29:00        0.044132        0.144192
+
    BFGS:    5 01:10:28        0.043569        0.134679
 
    
 
    
-
    BFGS:    6 02:29:02        0.041685        0.127932
+
    BFGS:    6 01:10:30        0.041664        0.118764
 
    
 
    
-
    BFGS:    7 02:29:03        0.041343        0.083160
+
    BFGS:    7 01:10:31        0.041300        0.080831
 
    
 
    
-
    BFGS:    8 02:29:04        0.040578        0.071778
+
    BFGS:    8 01:10:32        0.040333        0.065349
 
    
 
    
-
    BFGS:    9 02:29:06        0.032566        0.081608
+
    BFGS:    9 01:10:34        0.034361        0.081541
 
    
 
    
-
    BFGS:   10 02:29:07        0.031598        0.075652
+
    BFGS:   10 01:10:35        0.031855        0.078439
 
    
 
    
-
    BFGS:   11 02:29:09        0.030103        0.068318
+
    BFGS:   11 01:10:36        0.029978        0.070751
 
    
 
    
-
    BFGS:   12 02:29:10        0.028286        0.058980
+
    BFGS:   12 01:10:38        0.027738        0.059904
 
    
 
    
-
    BFGS:   13 02:29:11        0.023511        0.029246
+
    BFGS:   13 01:10:39        0.024114        0.037796
 
    
 
    
-
    Elapsed time 19.3 seconds
+
    Elapsed time 19.0 seconds
 
    
 
    
 
    
@@ -1008,42 +1013,42 @@ 
    Run all the systems
      Elapsed time: 28.8 seconds for data/oqmd-349719_H/0
+
      Elapsed time: 26.5 seconds for data/oqmd-349719_H/0
 Running data/oqmd-349719_H/1
 
    
 
    
-
      Elapsed time: 38.9 seconds for data/oqmd-349719_H/1
+
      Elapsed time: 39.4 seconds for data/oqmd-349719_H/1
 Running data/oqmd-349719_H/2
 
    
 
    
-
      Elapsed time: 17.9 seconds for data/oqmd-349719_H/2
+
      Elapsed time: 18.4 seconds for data/oqmd-349719_H/2
 Running data/oqmd-349719_H/3
 
    
 
    
-
      Elapsed time: 53.9 seconds for data/oqmd-349719_H/3
+
      Elapsed time: 55.1 seconds for data/oqmd-349719_H/3
 Running data/oqmd-349719_NNH/0
 
    
 
    
-
      Elapsed time: 133.1 seconds for data/oqmd-349719_NNH/0
+
      Elapsed time: 135.6 seconds for data/oqmd-349719_NNH/0
 Running data/oqmd-349719_NNH/1
 
    
 
    
-
      Elapsed time: 134.7 seconds for data/oqmd-349719_NNH/1
+
      Elapsed time: 135.6 seconds for data/oqmd-349719_NNH/1
 Running data/oqmd-349719_NNH/2
 
    
 
    
-
      Elapsed time: 133.1 seconds for data/oqmd-349719_NNH/2
+
      Elapsed time: 135.2 seconds for data/oqmd-349719_NNH/2
 Running data/oqmd-349719_NNH/3
 
    
 
    
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+
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+
    100%|██████████| 1/1 [11:22<00:00, 682.73s/it]
 
    
 
    
-
      Elapsed time: 135.4 seconds for data/oqmd-349719_NNH/3
-Elapsed time: 677.0 seconds
+
      Elapsed time: 135.8 seconds for data/oqmd-349719_NNH/3
+Elapsed time: 682.7 seconds
 
    
 
    
 
    
@@ -1234,7 +1239,7 @@ 
    Make parity plots for values obtained by ML v. reported in the paper
    
 
    
-../../_images/8a574cdd3c97cf99f5398bf0656d0e8970b961d4ebf7fc48ef4f9c5d9cf84cd3.png
+../../_images/9c0441622f4caa09c1f1383885c831ce1a37a7b31a6ffd5114bd46338d1e93ce.png

    @@ -1288,7 +1293,7 @@

    Make figure 6b and compare to literature results -../../_images/7d7623cdd0d173b6b3433cefb4aee239df66b0e0bf970b5a312cde3fd4fa5fdf.png +../../_images/49b63d472f6e407371466dfc822b337a6bf9417900b90da5894dd488e25a7fdd.png diff --git a/tutorials/NRR/NRR_toc.html b/tutorials/NRR/NRR_toc.html index 8958703a89..55c99dafa5 100644 --- a/tutorials/NRR/NRR_toc.html +++ b/tutorials/NRR/NRR_toc.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/tutorials/OCP-introduction.html b/tutorials/OCP-introduction.html index 3493d13f63..0012f73210 100644 --- a/tutorials/OCP-introduction.html +++ b/tutorials/OCP-introduction.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -716,7 +719,9 @@

    Calculating adsorption energies
    WARNING:root:Skipping scheduler setup. No training set found.
    -
    WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+
    /home/runner/work/fairchem/fairchem/src/fairchem/core/modules/normalization/normalizer.py:69: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
+  "mean": torch.tensor(state_dict["mean"]),
+WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
    @@ -746,60 +751,60 @@

    Calculating adsorption energies -
    /tmp/ipykernel_4599/3494085424.py:6: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_4569/3494085424.py:6: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 
    
 
    
 
          Step     Time          Energy          fmax
-BFGS:    0 02:40:40        1.213985        1.630879
+BFGS:    0 01:22:13        1.212762        1.631530
 
    
 
    
-
    BFGS:    1 02:40:40        1.072816        0.906401
+
    BFGS:    1 01:22:14        1.071970        0.906285
 
    
 
    
-
    BFGS:    2 02:40:41        0.981515        0.639873
+
    BFGS:    2 01:22:15        0.981419        0.637568
 
    
 
    
-
    BFGS:    3 02:40:42        0.960242        0.689923
+
    BFGS:    3 01:22:15        0.960159        0.689581
 
    
 
    
-
    BFGS:    4 02:40:42        0.880960        0.556052
+
    BFGS:    4 01:22:16        0.881590        0.561221
 
    
 
    
-
    BFGS:    5 02:40:43        0.835475        0.376717
+
    BFGS:    5 01:22:17        0.835984        0.376775
 
    
 
    
-
    BFGS:    6 02:40:43        0.823639        0.422308
+
    BFGS:    6 01:22:17        0.824549        0.420578
 
    
 
    
-
    BFGS:    7 02:40:44        0.812699        0.515625
+
    BFGS:    7 01:22:18        0.814233        0.512942
 
    
 
    
-
    BFGS:    8 02:40:44        0.826009        0.889862
+
    BFGS:    8 01:22:19        0.827345        0.902118
 
    
 
    
-
    BFGS:    9 02:40:45        0.780840        0.355196
+
    BFGS:    9 01:22:19        0.779739        0.358875
 
    
 
    
-
    BFGS:   10 02:40:46        0.770576        0.201155
+
    BFGS:   10 01:22:20        0.770977        0.205396
 
    
 
    
-
    BFGS:   11 02:40:46        0.757533        0.122655
+
    BFGS:   11 01:22:21        0.757477        0.122986
 
    
 
    
-
    BFGS:   12 02:40:47        0.755184        0.112419
+
    BFGS:   12 01:22:21        0.755319        0.112767
 
    
 
    
-
    BFGS:   13 02:40:47        0.754078        0.104468
+
    BFGS:   13 01:22:22        0.754126        0.105066
 
    
 
    
-
    BFGS:   14 02:40:48        0.755144        0.086691
+
    BFGS:   14 01:22:23        0.755008        0.087155
 
    
 
    
-
    BFGS:   15 02:40:49        0.758543        0.049224
+
    BFGS:   15 01:22:23        0.758033        0.048096
 
    
 
    
-
    -2.2714570450782774
+
    -2.271967499256134
 
    
 
    
 
    
@@ -819,7 +824,7 @@ 
    Calculating adsorption energies
-../_images/dfb88b463e26635b4902ab9b3ecefc883be8031dcfdc33109236e95bff60b69f.png
+../_images/1a9fb3219e8052dc1bac3858ba1d4635c45cbb8a7a4650172d1d692c0c2b4b68.png
 
    
 
    
 
    How did we do? We need a reference point. In the paper below, there is an atomic adsorption energy for O on Pt(111) of about -4.264 eV. This is for the reaction O + * -> O*. To convert this to the dissociative adsorption energy, we have to add the reaction:
    
@@ -924,27 +929,27 @@ 
    Trends in adsorption energies across metals.
-
    /tmp/ipykernel_4599/2476004300.py:10: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_4569/2476004300.py:10: DeprecationWarning: Please use atoms.calc = calc
   atoms.set_calculator(calc)
 
    
 
    
 
          Step     Time          Energy          fmax
-BFGS:    0 02:40:50        0.720972        0.217973
+BFGS:    0 01:22:25        0.720971        0.217973
 
    
 
    
-
    BFGS:    1 02:40:50        0.717582        0.182150
+
    BFGS:    1 01:22:25        0.717581        0.182150
 
    
 
    
-
    BFGS:    2 02:40:51        0.707522        0.067374
+
    BFGS:    2 01:22:26        0.707523        0.067379
 
    
 
    
-
    BFGS:    3 02:40:51        0.705302        0.062102
+
    BFGS:    3 01:22:26        0.705305        0.062094
 
    
 
    
-
    BFGS:    4 02:40:52        0.701208        0.049769
+
    BFGS:    4 01:22:27        0.701212        0.049768
 
    
 
    
-
    -4.908791706562042
+
    -4.908788487911224
 
    
 
    
 
    
@@ -1007,14 +1012,14 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    /tmp/ipykernel_4599/1169188772.py:27: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_4569/1169188772.py:27: DeprecationWarning: Please use atoms.calc = calc
   atoms.set_calculator(calc)
 
    
 
    
-
    100%|██████████| 1/1 [00:02<00:00,  2.85s/it]
+
    100%|██████████| 1/1 [00:03<00:00,  3.41s/it]
 
    
 
    
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    100%|██████████| 1/1 [00:02<00:00,  2.85s/it]
+
    100%|██████████| 1/1 [00:03<00:00,  3.41s/it]
 
    
 
    
 
    
@@ -1023,10 +1028,10 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:03<00:00,  3.36s/it]
+
    100%|██████████| 1/1 [00:04<00:00,  4.06s/it]
 
    
 
    
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    100%|██████████| 1/1 [00:03<00:00,  3.36s/it]
+
    100%|██████████| 1/1 [00:04<00:00,  4.06s/it]
 
    
 
    
 
    
@@ -1038,10 +1043,10 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:01<00:00,  1.92s/it]
+
    100%|██████████| 1/1 [00:02<00:00,  2.23s/it]
 
    
 
    
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    100%|██████████| 1/1 [00:01<00:00,  1.92s/it]
+
    100%|██████████| 1/1 [00:02<00:00,  2.23s/it]
 
    
 
    
 
    
@@ -1050,10 +1055,10 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:03<00:00,  3.36s/it]
+
    100%|██████████| 1/1 [00:03<00:00,  3.81s/it]
 
    
 
    
-
    100%|██████████| 1/1 [00:03<00:00,  3.36s/it]
+
    100%|██████████| 1/1 [00:03<00:00,  3.81s/it]
 
    
 
    
 
    
@@ -1065,10 +1070,10 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:02<00:00,  2.85s/it]
+
    100%|██████████| 1/1 [00:03<00:00,  3.32s/it]
 
    
 
    
-
    100%|██████████| 1/1 [00:02<00:00,  2.85s/it]
+
    100%|██████████| 1/1 [00:03<00:00,  3.32s/it]
 
    
 
    
 
    
@@ -1077,10 +1082,10 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:03<00:00,  3.30s/it]
+
    100%|██████████| 1/1 [00:03<00:00,  3.82s/it]
 
    
 
    
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    100%|██████████| 1/1 [00:03<00:00,  3.30s/it]
+
    100%|██████████| 1/1 [00:03<00:00,  3.82s/it]
 
    
 
    
 
    
@@ -1092,10 +1097,10 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:02<00:00,  2.38s/it]
+
    100%|██████████| 1/1 [00:02<00:00,  2.70s/it]
 
    
 
    
-
    100%|██████████| 1/1 [00:02<00:00,  2.38s/it]
+
    100%|██████████| 1/1 [00:02<00:00,  2.71s/it]
 
    
 
    
 
    
@@ -1104,10 +1109,10 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:01<00:00,  1.42s/it]
+
    100%|██████████| 1/1 [00:01<00:00,  1.58s/it]
 
    
 
    
-
    100%|██████████| 1/1 [00:01<00:00,  1.42s/it]
+
    100%|██████████| 1/1 [00:01<00:00,  1.58s/it]
 
    
 
    
 
    
@@ -1119,10 +1124,10 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:00<00:00,  2.12it/s]
+
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    100%|██████████| 1/1 [00:00<00:00,  2.11it/s]
+
    100%|██████████| 1/1 [00:00<00:00,  1.82it/s]
 
    
 
    
 
    
@@ -1131,10 +1136,10 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:00<00:00,  2.15it/s]
+
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    100%|██████████| 1/1 [00:00<00:00,  2.15it/s]
+
    100%|██████████| 1/1 [00:00<00:00,  1.75it/s]
 
    
 
    
 
    
@@ -1146,10 +1151,10 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:01<00:00,  1.41s/it]
+
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+
    100%|██████████| 1/1 [00:01<00:00,  1.60s/it]
 
    
 
    
 
    
@@ -1158,16 +1163,16 @@ 
    Site correlations
      0%|          | 0/1 [00:00<?, ?it/s]
 
    
 
    
-
    100%|██████████| 1/1 [00:00<00:00,  1.06it/s]
+
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-
    100%|██████████| 1/1 [00:00<00:00,  1.06it/s]
+
    100%|██████████| 1/1 [00:01<00:00,  1.09s/it]
 
    
 
    
 
    
 
    
 
    
-
    'Elapsed time = 24.73701500892639 seconds'
+
    'Elapsed time = 28.764322996139526 seconds'
 
    
 
    
 
    
@@ -1184,7 +1189,7 @@ 
    Site correlations
-../_images/0da8ae9263053ad6dea8831c1b426aa505675d316d1ade29791c024dcc3bfd3e.png
+../_images/de2a492d5ce82347c660d361bdccc9b38715519741c2457444cb3e02ff820b7e.png
 
    
 
    
 
    Next we compare the correlation between the hcp and fcc sites. Here we see the same trends. The data falls below the parity line because the hcp sites tend to be a little weaker binding than the fcc sites.
    
@@ -1200,7 +1205,7 @@ 
    Site correlations
-../_images/849bc2a9ccc55b56b8a57b26df643b6141ad5db11591e03e0e91e693b2b18c4e.png
+../_images/cef7761a57d7e051d50034d2b417cff65416b5c779ebb4ca1958e08ded2883bc.png
 
    
 
    
 
    
@@ -1238,7 +1243,7 @@ 
    Effects of number of layers
-
    /tmp/ipykernel_4599/4214609233.py:5: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_4569/4214609233.py:5: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 
    
 
    
@@ -1286,26 +1291,26 @@ 
    Effects of relaxation
 
    
 
    
-
    /tmp/ipykernel_4599/2738246227.py:9: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_4569/2738246227.py:9: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 
    
 
    
 
    nlayers = 3: -2.22 eV
 
    
 
    
-
    nlayers = 4: -2.08 eV
+
    nlayers = 4: -2.07 eV
 
    
 
    
 
    nlayers = 5: -2.09 eV
 
    
 
    
-
    nlayers = 6: -2.09 eV
+
    nlayers = 6: -2.08 eV
 
    
 
    
 
    nlayers = 7: -2.09 eV
 
    
 
    
-
    nlayers = 8: -2.05 eV
+
    nlayers = 8: -2.10 eV
 
    
 
    
 
    
@@ -1331,7 +1336,7 @@ 
    Unit cell size
-
    /tmp/ipykernel_4599/1073633840.py:7: DeprecationWarning: Please use atoms.calc = calc
+
    /tmp/ipykernel_4569/1073633840.py:7: DeprecationWarning: Please use atoms.calc = calc
   slab.set_calculator(calc)
 
    
 
    
@@ -1341,13 +1346,13 @@ 
    Unit cell size
    (2x2): -2.09 eV
 
    
 
    
-
    (3x3): -1.43 eV
+
    (3x3): -1.44 eV
 
    
 
    
 
    (4x4): -1.48 eV
 
    
 
    
-
    (5x5): -1.39 eV
+
    (5x5): -1.37 eV
 
    
 
    
 
    
diff --git a/tutorials/adsorbml_walkthrough.html b/tutorials/adsorbml_walkthrough.html
index 10a9e1f2e1..fa187a3701 100644
--- a/tutorials/adsorbml_walkthrough.html
+++ b/tutorials/adsorbml_walkthrough.html
@@ -305,6 +305,7 @@
 
  • core.common.logger
    • 
 
  • core.common.profiler_utils
    • 
 
  • core.common.registry
    • 
+
  • core.common.slurm
    • 
 
  • core.common.test_utils
    • 
 
  • core.common.transforms
    • 
 
  • core.common.tutorial_utils
    • 
@@ -334,16 +335,17 @@
 
  • core.models.utils
    • 
 
  • core.models.base
    • 
 
  • core.models.dimenet_plus_plus
    • 
+
  • core.models.finetune_hydra
    • 
 
  • core.models.model_registry
    • 
 
  • core.models.schnet
    •

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -740,528 +743,761 @@

    Run ML relaxations:
    WARNING:root:Skipping scheduler setup. No training set found.
    -
    WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+
    /home/runner/work/fairchem/fairchem/src/fairchem/core/modules/normalization/normalizer.py:69: UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
+  "mean": torch.tensor(state_dict["mean"]),
+WARNING:root:No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
 
    
 
    
 
          Step     Time          Energy          fmax
-BFGS:    0 02:44:40       -0.446366        1.874194
+BFGS:    0 01:26:26       -0.360350        1.327491
 
    
 
    
-
    BFGS:    1 02:44:43       -0.444925        2.293103
+
    BFGS:    1 01:26:29       -0.367729        1.660890
 
    
 
    
-
    BFGS:    2 02:44:45       -0.475816        0.712347
+
    BFGS:    2 01:26:31       -0.398991        1.067621
 
    
 
    
-
    BFGS:    3 02:44:48       -0.494549        0.655961
+
    BFGS:    3 01:26:34       -0.506128        0.854963
 
    
 
    
-
    BFGS:    4 02:44:50       -0.530943        1.155536
+
    BFGS:    4 01:26:37       -0.508746        0.261653
 
    
 
    
-
    BFGS:    5 02:44:53       -0.553124        0.608653
+
    BFGS:    5 01:26:39       -0.508902        0.218186
 
    
 
    
-
    BFGS:    6 02:44:55       -0.556189        0.177773
+
    BFGS:    6 01:26:42       -0.510034        0.415451
 
    
 
    
-
    BFGS:    7 02:44:58       -0.556510        0.136846
+
    BFGS:    7 01:26:44       -0.510827        0.436334
 
    
 
    
-
    BFGS:    8 02:45:00       -0.556509        0.230004
+
    BFGS:    8 01:26:47       -0.515024        0.260579
 
    
 
    
-
    BFGS:    9 02:45:03       -0.558626        0.236779
+
    BFGS:    9 01:26:49       -0.517022        0.089716
 
    
 
    
-
    BFGS:   10 02:45:06       -0.562539        0.154330
+
    BFGS:   10 01:26:52       -0.518503        0.185789
 
    
 
    
-
    BFGS:   11 02:45:08       -0.563364        0.062644
+
    BFGS:   11 01:26:55       -0.519619        0.337784
 
    
 
    
-
    BFGS:   12 02:45:11       -0.563565        0.067319
+
    BFGS:   12 01:26:57       -0.520616        0.361943
 
    
 
    
-
    BFGS:   13 02:45:13       -0.563607        0.189096
+
    BFGS:   13 01:27:00       -0.521755        0.205455
 
    
 
    
-
    BFGS:   14 02:45:16       -0.564045        0.209567
+
    BFGS:   14 01:27:02       -0.522659        0.063617
 
    
 
    
-
    BFGS:   15 02:45:18       -0.565976        0.127807
+
    BFGS:   15 01:27:05       -0.523237        0.065409
 
    
 
    
-
    BFGS:   16 02:45:21       -0.566823        0.050107
+
    BFGS:   16 01:27:08       -0.523285        0.096172
 
    
 
    
-
    BFGS:   17 02:45:24       -0.567389        0.019879
+
    BFGS:   17 01:27:10       -0.524091        0.099694
 
    
 
    
-
          Step     Time          Energy          fmax
-BFGS:    0 02:45:27       -0.331135        1.356109
+
    BFGS:   18 01:27:13       -0.523439        0.067539
 
    
 
    
-
    BFGS:    1 02:45:29       -0.341314        1.645448
+
    BFGS:   19 01:27:15       -0.523130        0.026789
 
    
 
    
-
    BFGS:    2 02:45:32       -0.375205        1.104580
+
          Step     Time          Energy          fmax
+BFGS:    0 01:27:18       -0.447710        1.851359
 
    
 
    
-
    BFGS:    3 02:45:34       -0.499090        0.293108
+
    BFGS:    1 01:27:20       -0.447247        2.270751
 
    
 
    
-
    BFGS:    4 02:45:37       -0.500080        0.192380
+
    BFGS:    2 01:27:23       -0.477489        0.701559
 
    
 
    
-
    BFGS:    5 02:45:39       -0.501938        0.212583
+
    BFGS:    3 01:27:25       -0.495535        0.650975
 
    
 
    
-
    BFGS:    6 02:45:42       -0.507168        0.344516
+
    BFGS:    4 01:27:28       -0.530454        1.188816
 
    
 
    
-
    BFGS:    7 02:45:44       -0.512177        0.274864
+
    BFGS:    5 01:27:30       -0.552972        0.682416
 
    
 
    
-
    BFGS:    8 02:45:47       -0.516015        0.123270
+
    BFGS:    6 01:27:33       -0.557125        0.189261
 
    
 
    
-
    BFGS:    9 02:45:49       -0.518156        0.091079
+
    BFGS:    7 01:27:35       -0.558170        0.106825
 
    
 
    
-
    BFGS:   10 02:45:52       -0.519781        0.167892
+
    BFGS:    8 01:27:38       -0.557899        0.194074
 
    
 
    
-
    BFGS:   11 02:45:55       -0.521580        0.178083
+
    BFGS:    9 01:27:41       -0.559832        0.210646
 
    
 
    
-
    BFGS:   12 02:45:57       -0.522948        0.132521
+
    BFGS:   10 01:27:43       -0.563132        0.144399
 
    
 
    
-
    BFGS:   13 02:46:00       -0.524319        0.095828
+
    BFGS:   11 01:27:46       -0.564518        0.058970
 
    
 
    
-
    BFGS:   14 02:46:02       -0.525389        0.032620
+
    BFGS:   12 01:27:48       -0.564694        0.045731
 
    
 
    
 
          Step     Time          Energy          fmax
-BFGS:    0 02:46:05       -0.389762        1.878736
+BFGS:    0 01:27:51       -0.215406        1.043336
 
    
 
    
-
    BFGS:    1 02:46:07       -0.389577        2.288156
+
    BFGS:    1 01:27:53       -0.246962        1.504874
 
    
 
    
-
    BFGS:    2 02:46:10       -0.424647        0.813583
+
    BFGS:    2 01:27:56       -0.339080        1.760877
 
    
 
    
-
    BFGS:    3 02:46:12       -0.450944        0.803427
+
    BFGS:    3 01:27:58       -0.427483        1.513991
 
    
 
    
-
    BFGS:    4 02:46:15       -0.503894        1.260830
+
    BFGS:    4 01:28:01       -0.461510        0.754286
 
    
 
    
-
    BFGS:    5 02:46:17       -0.542157        0.304042
+
    BFGS:    5 01:28:04       -0.482332        0.353887
 
    
 
    
-
    BFGS:    6 02:46:20       -0.543190        0.196933
+
    BFGS:    6 01:28:06       -0.490697        0.260090
 
    
 
    
-
    BFGS:    7 02:46:22       -0.544736        0.345210
+
    BFGS:    7 01:28:09       -0.493133        0.244777
 
    
 
    
-
    BFGS:    8 02:46:25       -0.547420        0.376138
+
    BFGS:    8 01:28:11       -0.511005        0.454325
 
    
 
    
-
    BFGS:    9 02:46:28       -0.554735        0.297208
+
    BFGS:    9 01:28:14       -0.513632        0.193024
 
    
 
    
-
    BFGS:   10 02:46:30       -0.558071        0.147488
+
    BFGS:   10 01:28:17       -0.516160        0.114549
 
    
 
    
-
    BFGS:   11 02:46:33       -0.559800        0.113200
+
    BFGS:   11 01:28:19       -0.517613        0.180939
 
    
 
    
-
    BFGS:   12 02:46:35       -0.560892        0.160902
+
    BFGS:   12 01:28:22       -0.520020        0.261265
 
    
 
    
-
    BFGS:   13 02:46:38       -0.561571        0.226513
+
    BFGS:   13 01:28:24       -0.522651        0.291253
 
    
 
    
-
    BFGS:   14 02:46:40       -0.561605        0.185256
+
    BFGS:   14 01:28:27       -0.526016        0.278622
 
    
 
    
-
    BFGS:   15 02:46:43       -0.561798        0.194812
+
    BFGS:   15 01:28:30       -0.528241        0.191540
 
    
 
    
-
    BFGS:   16 02:46:45       -0.563569        0.080170
+
    BFGS:   16 01:28:32       -0.528900        0.079070
 
    
 
    
-
    BFGS:   17 02:46:48       -0.563278        0.055310
+
    BFGS:   17 01:28:35       -0.528943        0.092503
 
    
 
    
-
    BFGS:   18 02:46:50       -0.563777        0.060194
+
    BFGS:   18 01:28:37       -0.529594        0.108658
 
    
 
    
-
    BFGS:   19 02:46:53       -0.564592        0.063203
+
    BFGS:   19 01:28:40       -0.530787        0.080229
 
    
 
    
-
    BFGS:   20 02:46:55       -0.565111        0.045783
+
    BFGS:   20 01:28:42       -0.532668        0.029314
 
    
 
    
 
          Step     Time          Energy          fmax
-BFGS:    0 02:46:58       -0.232162        1.091916
+BFGS:    0 01:28:45       -0.428282        1.881472
+
    
+
    
+
    BFGS:    1 01:28:48       -0.428980        2.297700
 
    
 
    
-
    BFGS:    1 02:47:00       -0.262601        1.499953
+
    BFGS:    2 01:28:50       -0.460811        0.747121
 
    
 
    
-
    BFGS:    2 02:47:03       -0.358648        1.812539
+
    BFGS:    3 01:28:53       -0.481119        0.703617
 
    
 
    
-
    BFGS:    3 02:47:05       -0.438322        1.474399
+
    BFGS:    4 01:28:55       -0.522681        1.180539
 
    
 
    
-
    BFGS:    4 02:47:08       -0.473926        0.667289
+
    BFGS:    5 01:28:58       -0.550218        0.523051
 
    
 
    
-
    BFGS:    5 02:47:11       -0.492034        0.308619
+
    BFGS:    6 01:29:00       -0.552374        0.182801
 
    
 
    
-
    BFGS:    6 02:47:13       -0.498132        0.190516
+
    BFGS:    7 01:29:03       -0.552480        0.204510
 
    
 
    
-
    BFGS:    7 02:47:16       -0.499698        0.178951
+
    BFGS:    8 01:29:05       -0.553343        0.299151
 
    
 
    
-
    BFGS:    8 02:47:18       -0.514732        0.275423
+
    BFGS:    9 01:29:08       -0.556213        0.293822
 
    
 
    
-
    BFGS:    9 02:47:21       -0.518187        0.203405
+
    BFGS:   10 01:29:10       -0.559627        0.184240
 
    
 
    
-
    BFGS:   10 02:47:24       -0.520099        0.104805
+
    BFGS:   11 01:29:13       -0.560895        0.072652
 
    
 
    
-
    BFGS:   11 02:47:26       -0.521465        0.195024
+
    BFGS:   12 01:29:16       -0.561568        0.131073
 
    
 
    
-
    BFGS:   12 02:47:29       -0.524561        0.304310
+
    BFGS:   13 01:29:18       -0.562124        0.213469
 
    
 
    
-
    BFGS:   13 02:47:31       -0.526659        0.284775
+
    BFGS:   14 01:29:21       -0.563103        0.210109
 
    
 
    
-
    BFGS:   14 02:47:34       -0.528441        0.243533
+
    BFGS:   15 01:29:23       -0.564499        0.140083
 
    
 
    
-
    BFGS:   15 02:47:36       -0.528411        0.122601
+
    BFGS:   16 01:29:26       -0.565588        0.095877
 
    
 
    
-
    BFGS:   16 02:47:39       -0.528298        0.057545
+
    BFGS:   17 01:29:28       -0.566627        0.035124
 
    
 
    
-
    BFGS:   17 02:47:41       -0.530894        0.152663
+
          Step     Time          Energy          fmax
+BFGS:    0 01:29:31       -0.208872        0.853364
 
    
 
    
-
    BFGS:   18 02:47:44       -0.532649        0.140441
+
    BFGS:    1 01:29:33       -0.232693        0.824829
 
    
 
    
-
    BFGS:   19 02:47:47       -0.535030        0.053276
+
    BFGS:    2 01:29:36       -0.410101        1.057809
 
    
 
    
-
    BFGS:   20 02:47:49       -0.536182        0.012109
+
    BFGS:    3 01:29:38       -0.413617        1.359400
 
    
 
    
-
          Step     Time          Energy          fmax
-BFGS:    0 02:47:52       -0.219158        1.081786
+
    BFGS:    4 01:29:41       -0.431860        0.487647
+
    
+
    
+
    BFGS:    5 01:29:44       -0.442998        0.557402
+
    
+
    
+
    BFGS:    6 01:29:46       -0.446843        0.328255
+
    
+
    
+
    BFGS:    7 01:29:49       -0.452121        0.336969
+
    
+
    
+
    BFGS:    8 01:29:51       -0.466988        0.630952
+
    
+
    
+
    BFGS:    9 01:29:54       -0.474231        0.524258
+
    
+
    
+
    BFGS:   10 01:29:57       -0.481070        0.192678
+
    
+
    
+
    BFGS:   11 01:29:59       -0.482908        0.088008
+
    
+
    
+
    BFGS:   12 01:30:02       -0.483704        0.103063
+
    
+
    
+
    BFGS:   13 01:30:04       -0.484523        0.124385
 
    
 
    
-
    BFGS:    1 02:47:55       -0.251396        1.205418
+
    BFGS:   14 01:30:07       -0.486130        0.162473
 
    
 
    
-
    BFGS:    2 02:47:57       -0.395909        1.992370
+
    BFGS:   15 01:30:09       -0.488095        0.075563
 
    
 
    
-
    BFGS:    3 02:48:00       -0.322061        2.531046
+
    BFGS:   16 01:30:12       -0.487531        0.075804
 
    
 
    
-
    BFGS:    4 02:48:03       -0.455093        0.689381
+
    BFGS:   17 01:30:14       -0.488007        0.062157
 
    
 
    
-
    BFGS:    5 02:48:05       -0.469977        0.347335
+
    BFGS:   18 01:30:17       -0.490876        0.135212
 
    
 
    
-
    BFGS:    6 02:48:08       -0.478581        0.189910
+
    BFGS:   19 01:30:19       -0.491628        0.205059
 
    
 
    
-
    BFGS:    7 02:48:10       -0.479201        0.159769
+
    BFGS:   20 01:30:22       -0.492220        0.198452
 
    
 
    
-
    BFGS:    8 02:48:13       -0.488391        0.129512
+
    BFGS:   21 01:30:24       -0.495433        0.085621
 
    
 
    
-
    BFGS:    9 02:48:15       -0.494780        0.120259
+
    BFGS:   22 01:30:27       -0.496256        0.064734
 
    
 
    
-
    BFGS:   10 02:48:18       -0.497985        0.130117
+
    BFGS:   23 01:30:29       -0.497454        0.147525
 
    
 
    
-
    BFGS:   11 02:48:21       -0.499035        0.102928
+
    BFGS:   24 01:30:32       -0.498507        0.232464
 
    
 
    
-
    BFGS:   12 02:48:23       -0.505778        0.151722
+
    BFGS:   25 01:30:35       -0.499545        0.282274
 
    
 
    
-
    BFGS:   13 02:48:26       -0.507807        0.175169
+
    BFGS:   26 01:30:37       -0.501753        0.195035
 
    
 
    
-
    BFGS:   14 02:48:28       -0.509557        0.161297
+
    BFGS:   27 01:30:40       -0.502927        0.079464
 
    
 
    
-
    BFGS:   15 02:48:31       -0.509419        0.113880
+
    BFGS:   28 01:30:43       -0.504056        0.121113
 
    
 
    
-
    BFGS:   16 02:48:33       -0.509620        0.111930
+
    BFGS:   29 01:30:45       -0.505909        0.134812
 
    
 
    
-
    BFGS:   17 02:48:36       -0.511545        0.180261
+
    BFGS:   30 01:30:48       -0.507626        0.154392
 
    
 
    
-
    BFGS:   18 02:48:38       -0.514115        0.161220
+
    BFGS:   31 01:30:50       -0.509817        0.123380
 
    
 
    
-
    BFGS:   19 02:48:41       -0.517262        0.069136
+
    BFGS:   32 01:30:53       -0.507971        0.104700
 
    
 
    
-
    BFGS:   20 02:48:44       -0.518067        0.031238
+
    BFGS:   33 01:30:55       -0.508551        0.090869
+
    
+
    
+
    BFGS:   34 01:30:58       -0.511628        0.121140
+
    
+
    
+
    BFGS:   35 01:31:00       -0.513616        0.177891
+
    
+
    
+
    BFGS:   36 01:31:03       -0.518110        0.351538
+
    
+
    
+
    BFGS:   37 01:31:05       -0.522790        0.164242
+
    
+
    
+
    BFGS:   38 01:31:08       -0.524998        0.222148
+
    
+
    
+
    BFGS:   39 01:31:10       -0.527051        0.254513
+
    
+
    
+
    BFGS:   40 01:31:13       -0.527174        0.537219
+
    
+
    
+
    BFGS:   41 01:31:15       -0.530616        0.073473
+
    
+
    
+
    BFGS:   42 01:31:18       -0.531560        0.074909
+
    
+
    
+
    BFGS:   43 01:31:21       -0.533907        0.137751
+
    
+
    
+
    BFGS:   44 01:31:23       -0.536962        0.054816
+
    
+
    
+
    BFGS:   45 01:31:26       -0.538084        0.016353
 
    
 
    
 
          Step     Time          Energy          fmax
-BFGS:    0 02:48:46       -0.156862        0.928527
+BFGS:    0 01:31:28       -0.188161        0.915917
+
    
+
    
+
    BFGS:    1 01:31:31       -0.202910        0.978045
+
    
+
    
+
    BFGS:    2 01:31:33       -0.280274        1.821665
+
    
+
    
+
    BFGS:    3 01:31:36       -0.255189        4.110635
+
    
+
    
+
    BFGS:    4 01:31:39       -0.370512        0.917597
+
    
+
    
+
    BFGS:    5 01:31:41       -0.390939        0.621762
+
    
+
    
+
    BFGS:    6 01:31:44       -0.411730        0.533000
+
    
+
    
+
    BFGS:    7 01:31:46       -0.420999        0.516921
+
    
+
    
+
    BFGS:    8 01:31:49       -0.453249        0.211395
+
    
+
    
+
    BFGS:    9 01:31:51       -0.457622        0.226419
+
    
+
    
+
    BFGS:   10 01:31:54       -0.459558        0.232435
+
    
+
    
+
    BFGS:   11 01:31:56       -0.463843        0.298176
 
    
 
    
-
    BFGS:    1 02:48:48       -0.169100        0.933797
+
    BFGS:   12 01:31:59       -0.469359        0.331082
 
    
 
    
-
    BFGS:    2 02:48:51       -0.238858        1.843278
+
    BFGS:   13 01:32:01       -0.472859        0.498008
 
    
 
    
-
    BFGS:    3 02:48:54       -0.130877        5.543751
+
    BFGS:   14 01:32:04       -0.476869        0.237944
 
    
 
    
-
    BFGS:    4 02:48:56       -0.319004        1.099189
+
    BFGS:   15 01:32:06       -0.481530        0.218443
 
    
 
    
-
    BFGS:    5 02:48:59       -0.346072        0.847354
+
    BFGS:   16 01:32:09       -0.484231        0.270163
 
    
 
    
-
    BFGS:    6 02:49:01       -0.379388        0.775981
+
    BFGS:   17 01:32:11       -0.484321        0.414016
 
    
 
    
-
    BFGS:    7 02:49:04       -0.392091        0.542679
+
    BFGS:   18 01:32:14       -0.486466        0.566237
 
    
 
    
-
    BFGS:    8 02:49:06       -0.423686        0.664021
+
    BFGS:   19 01:32:17       -0.491129        0.423233
 
    
 
    
-
    BFGS:    9 02:49:09       -0.450572        0.206118
+
    BFGS:   20 01:32:19       -0.498331        0.270735
 
    
 
    
-
    BFGS:   10 02:49:11       -0.453608        0.180083
+
    BFGS:   21 01:32:22       -0.500228        0.207756
 
    
 
    
-
    BFGS:   11 02:49:14       -0.464408        0.248852
+
    BFGS:   22 01:32:24       -0.500514        0.300980
 
    
 
    
-
    BFGS:   12 02:49:16       -0.471751        0.263879
+
    BFGS:   23 01:32:27       -0.502198        0.537967
 
    
 
    
-
    BFGS:   13 02:49:19       -0.476171        0.226894
+
    BFGS:   24 01:32:29       -0.508071        0.506379
 
    
 
    
-
    BFGS:   14 02:49:22       -0.475922        0.235396
+
    BFGS:   25 01:32:32       -0.514635        0.176626
 
    
 
    
-
    BFGS:   15 02:49:24       -0.478387        0.106779
+
    BFGS:   26 01:32:34       -0.516071        0.096304
 
    
 
    
-
    BFGS:   16 02:49:27       -0.479742        0.064571
+
    BFGS:   27 01:32:37       -0.518239        0.120440
 
    
 
    
-
    BFGS:   17 02:49:29       -0.481231        0.111858
+
    BFGS:   28 01:32:39       -0.520637        0.121325
 
    
 
    
-
    BFGS:   18 02:49:32       -0.482219        0.068799
+
    BFGS:   29 01:32:42       -0.522814        0.094179
 
    
 
    
-
    BFGS:   19 02:49:34       -0.481917        0.063296
+
    BFGS:   30 01:32:44       -0.523523        0.073084
 
    
 
    
-
    BFGS:   20 02:49:37       -0.481595        0.064242
+
    BFGS:   31 01:32:47       -0.525618        0.067335
 
    
 
    
-
    BFGS:   21 02:49:39       -0.481425        0.051976
+
    BFGS:   32 01:32:49       -0.525872        0.056396
 
    
 
    
-
    BFGS:   22 02:49:42       -0.481379        0.039550
+
    BFGS:   33 01:32:52       -0.525409        0.115540
+
    
+
    
+
    BFGS:   34 01:32:55       -0.524813        0.143824
+
    
+
    
+
    BFGS:   35 01:32:57       -0.526907        0.210660
+
    
+
    
+
    BFGS:   36 01:33:00       -0.527453        0.184262
+
    
+
    
+
    BFGS:   37 01:33:02       -0.529463        0.115718
+
    
+
    
+
    BFGS:   38 01:33:05       -0.533276        0.143690
+
    
+
    
+
    BFGS:   39 01:33:07       -0.533776        0.183871
+
    
+
    
+
    BFGS:   40 01:33:10       -0.536702        0.226010
+
    
+
    
+
    BFGS:   41 01:33:12       -0.539870        0.177208
+
    
+
    
+
    BFGS:   42 01:33:15       -0.542716        0.101785
+
    
+
    
+
    BFGS:   43 01:33:17       -0.545167        0.167106
+
    
+
    
+
    BFGS:   44 01:33:20       -0.546812        0.092302
+
    
+
    
+
    BFGS:   45 01:33:22       -0.548846        0.090917
+
    
+
    
+
    BFGS:   46 01:33:25       -0.552786        0.169869
+
    
+
    
+
    BFGS:   47 01:33:28       -0.554395        0.217941
+
    
+
    
+
    BFGS:   48 01:33:30       -0.557450        0.134796
+
    
+
    
+
    BFGS:   49 01:33:33       -0.557912        0.066186
+
    
+
    
+
    BFGS:   50 01:33:35       -0.558465        0.079840
+
    
+
    
+
    BFGS:   51 01:33:38       -0.560035        0.139564
+
    
+
    
+
    BFGS:   52 01:33:40       -0.560575        0.207204
+
    
+
    
+
    BFGS:   53 01:33:43       -0.561303        0.185187
+
    
+
    
+
    BFGS:   54 01:33:45       -0.561921        0.100577
+
    
+
    
+
    BFGS:   55 01:33:48       -0.562289        0.046883
 
    
 
    
 
          Step     Time          Energy          fmax
-BFGS:    0 02:49:44       -0.200719        0.993535
+BFGS:    0 01:33:50       -0.341079        1.380608
+
    
+
    
+
    BFGS:    1 01:33:53       -0.348889        1.725997
+
    
+
    
+
    BFGS:    2 01:33:55       -0.380796        1.097569
+
    
+
    
+
    BFGS:    3 01:33:58       -0.496403        1.211265
+
    
+
    
+
    BFGS:    4 01:34:01       -0.503858        0.429164
+
    
+
    
+
    BFGS:    5 01:34:03       -0.504276        0.240553
+
    
+
    
+
    BFGS:    6 01:34:06       -0.506930        0.459862
+
    
+
    
+
    BFGS:    7 01:34:08       -0.513199        0.600702
+
    
+
    
+
    BFGS:    8 01:34:11       -0.521231        0.450177
+
    
+
    
+
    BFGS:    9 01:34:13       -0.526704        0.174989
+
    
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    BFGS:   10 01:34:16       -0.529482        0.232346
+
    
+
    
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    BFGS:   11 01:34:18       -0.531925        0.478213
+
    
+
    
+
    BFGS:   12 01:34:21       -0.535589        0.613177
+
    
+
    
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    BFGS:   13 01:34:23       -0.538051        0.399628
+
    
+
    
+
    BFGS:   14 01:34:26       -0.538251        0.145509
 
    
 
    
-
    BFGS:    1 02:49:47       -0.231153        1.215792
+
    BFGS:   15 01:34:29       -0.538801        0.116430
 
    
 
    
-
    BFGS:    2 02:49:49       -0.391111        1.975266
+
    BFGS:   16 01:34:31       -0.540214        0.203905
 
    
 
    
-
    BFGS:    3 02:49:52       -0.244688        3.307821
+
    BFGS:   17 01:34:34       -0.539993        0.259718
 
    
 
    
-
    BFGS:    4 02:49:54       -0.448762        0.859265
+
    BFGS:   18 01:34:36       -0.540843        0.193437
 
    
 
    
-
    BFGS:    5 02:49:57       -0.465171        0.466434
+
    BFGS:   19 01:34:39       -0.542130        0.084501
 
    
 
    
-
    BFGS:    6 02:49:59       -0.477021        0.376650
+
    BFGS:   20 01:34:41       -0.542706        0.075015
 
    
 
    
-
    BFGS:    7 02:50:02       -0.479151        0.282509
+
    BFGS:   21 01:34:44       -0.541724        0.191178
 
    
 
    
-
    BFGS:    8 02:50:04       -0.491227        0.185544
+
    BFGS:   22 01:34:46       -0.541870        0.299087
 
    
 
    
-
    BFGS:    9 02:50:07       -0.496768        0.170835
+
    BFGS:   23 01:34:49       -0.543727        0.402931
 
    
 
    
-
    BFGS:   10 02:50:09       -0.499412        0.213575
+
    BFGS:   24 01:34:51       -0.546533        0.397072
 
    
 
    
-
    BFGS:   11 02:50:12       -0.500814        0.123357
+
    BFGS:   25 01:34:54       -0.549238        0.132997
 
    
 
    
-
    BFGS:   12 02:50:14       -0.502900        0.149147
+
    BFGS:   26 01:34:56       -0.550362        0.128348
 
    
 
    
-
    BFGS:   13 02:50:17       -0.505106        0.243934
+
    BFGS:   27 01:34:59       -0.550618        0.249142
 
    
 
    
-
    BFGS:   14 02:50:20       -0.508576        0.288505
+
    BFGS:   28 01:35:01       -0.553287        0.314978
 
    
 
    
-
    BFGS:   15 02:50:22       -0.511997        0.281353
+
    BFGS:   29 01:35:04       -0.557522        0.255890
 
    
 
    
-
    BFGS:   16 02:50:25       -0.514187        0.189832
+
    BFGS:   30 01:35:07       -0.562020        0.062410
 
    
 
    
-
    BFGS:   17 02:50:27       -0.514217        0.068394
+
    BFGS:   31 01:35:09       -0.562887        0.062906
 
    
 
    
-
    BFGS:   18 02:50:30       -0.515205        0.167969
+
    BFGS:   32 01:35:12       -0.563551        0.103897
 
    
 
    
-
    BFGS:   19 02:50:32       -0.516432        0.213740
+
    BFGS:   33 01:35:14       -0.564825        0.146358
 
    
 
    
-
    BFGS:   20 02:50:35       -0.519153        0.172959
+
    BFGS:   34 01:35:17       -0.565948        0.138301
 
    
 
    
-
    BFGS:   21 02:50:37       -0.520934        0.052707
+
    BFGS:   35 01:35:19       -0.567552        0.079658
 
    
 
    
-
    BFGS:   22 02:50:40       -0.521562        0.037769
+
    BFGS:   36 01:35:22       -0.566492        0.038046
 
    
 
    
 
          Step     Time          Energy          fmax
-BFGS:    0 02:50:42       -0.254624        1.351575
+BFGS:    0 01:35:24       -0.319215        1.386092
+
    
+
    
+
    BFGS:    1 01:35:27       -0.329107        1.713861
+
    
+
    
+
    BFGS:    2 01:35:30       -0.362902        1.102481
+
    
+
    
+
    BFGS:    3 01:35:32       -0.492719        0.782695
 
    
 
    
-
    BFGS:    1 02:50:45       -0.260809        1.633570
+
    BFGS:    4 01:35:35       -0.498690        0.241213
 
    
 
    
-
    BFGS:    2 02:50:47       -0.290564        1.130489
+
    BFGS:    5 01:35:37       -0.499377        0.243577
 
    
 
    
-
    BFGS:    3 02:50:50       -0.446851        0.636818
+
    BFGS:    6 01:35:40       -0.502258        0.598422
 
    
 
    
-
    BFGS:    4 02:50:52       -0.451590        0.439125
+
    BFGS:    7 01:35:42       -0.507038        0.585736
 
    
 
    
-
    BFGS:    5 02:50:55       -0.463683        0.265089
+
    BFGS:    8 01:35:45       -0.514617        0.323634
 
    
 
    
-
    BFGS:    6 02:50:58       -0.490400        0.454778
+
    BFGS:    9 01:35:47       -0.518302        0.145188
 
    
 
    
-
    BFGS:    7 02:51:00       -0.496138        0.344395
+
    BFGS:   10 01:35:50       -0.521389        0.311403
 
    
 
    
-
    BFGS:    8 02:51:03       -0.503928        0.304566
+
    BFGS:   11 01:35:52       -0.523066        0.429920
 
    
 
    
-
    BFGS:    9 02:51:05       -0.508306        0.443929
+
    BFGS:   12 01:35:55       -0.524592        0.330427
 
    
 
    
-
    BFGS:   10 02:51:08       -0.516868        0.582383
+
    BFGS:   13 01:35:57       -0.525021        0.301874
 
    
 
    
-
    BFGS:   11 02:51:10       -0.527751        0.605925
+
    BFGS:   14 01:36:00       -0.526415        0.129004
 
    
 
    
-
    BFGS:   12 02:51:13       -0.536219        0.321690
+
    BFGS:   15 01:36:02       -0.527990        0.118857
 
    
 
    
-
    BFGS:   13 02:51:15       -0.539605        0.142617
+
    BFGS:   16 01:36:05       -0.528291        0.247388
 
    
 
    
-
    BFGS:   14 02:51:18       -0.541820        0.227342
+
    BFGS:   17 01:36:07       -0.529813        0.301299
 
    
 
    
-
    BFGS:   15 02:51:20       -0.546661        0.383315
+
    BFGS:   18 01:36:10       -0.532610        0.254078
 
    
 
    
-
    BFGS:   16 02:51:23       -0.554483        0.319720
+
    BFGS:   19 01:36:12       -0.534719        0.130149
 
    
 
    
-
    BFGS:   17 02:51:25       -0.556925        0.129211
+
    BFGS:   20 01:36:15       -0.535350        0.110446
 
    
 
    
-
    BFGS:   18 02:51:28       -0.555839        0.088538
+
    BFGS:   21 01:36:18       -0.535770        0.304221
 
    
 
    
-
    BFGS:   19 02:51:30       -0.554508        0.132156
+
    BFGS:   22 01:36:20       -0.537545        0.420296
 
    
 
    
-
    BFGS:   20 02:51:33       -0.554556        0.160423
+
    BFGS:   23 01:36:23       -0.539549        0.520655
 
    
 
    
-
    BFGS:   21 02:51:36       -0.554357        0.153788
+
    BFGS:   24 01:36:25       -0.545751        0.441860
 
    
 
    
-
    BFGS:   22 02:51:38       -0.557701        0.102895
+
    BFGS:   25 01:36:28       -0.547464        0.101493
 
    
 
    
-
    BFGS:   23 02:51:41       -0.559299        0.057429
+
    BFGS:   26 01:36:30       -0.548075        0.172627
 
    
 
    
-
    BFGS:   24 02:51:43       -0.559725        0.052322
+
    BFGS:   27 01:36:33       -0.548373        0.245001
 
    
 
    
-
    BFGS:   25 02:51:46       -0.560699        0.067044
+
    BFGS:   28 01:36:35       -0.552560        0.279658
 
    
 
    
-
    BFGS:   26 02:51:48       -0.561689        0.073885
+
    BFGS:   29 01:36:38       -0.557619        0.158653
 
    
 
    
-
    BFGS:   27 02:51:51       -0.563146        0.059753
+
    BFGS:   30 01:36:40       -0.560037        0.065841
 
    
 
    
-
    BFGS:   28 02:51:53       -0.564859        0.035346
+
    BFGS:   31 01:36:43       -0.560901        0.080508
+
    
+
    
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    BFGS:   32 01:36:46       -0.562027        0.142981
+
    
+
    
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    BFGS:   33 01:36:48       -0.562564        0.180084
+
    
+
    
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    BFGS:   34 01:36:51       -0.565080        0.139280
+
    
+
    
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    BFGS:   35 01:36:53       -0.567337        0.068610
+
    
+
    
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    BFGS:   36 01:36:56       -0.568155        0.024572
 
    
 
    
 
    
@@ -1338,58 +1574,58 @@ 
    Parse the trajectories and post-process
-
    The lowest 5 energies are: [-0.567 -0.536 -0.525 -0.481]
+
    The lowest 5 energies are: [-0.568 -0.538 -0.523]

  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/tutorials/advanced/embeddings.html b/tutorials/advanced/embeddings.html index dff05574bd..144cdab758 100644 --- a/tutorials/advanced/embeddings.html +++ b/tutorials/advanced/embeddings.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -730,7 +733,7 @@

    Bulk Cu equation of state example +../../_images/d95f1e9e1a2053f463c216a6c931977c945f1e8bd8c2b6bf59be64da41ae3a66.png

    Something is a little off in this equation of state, there is an unphysical bump in it. We now rerun this and get the embeddings. You simply call the calc.embed method. We need a reference configuration to compare too. We choose a lattice constant of 3.63 angstroms and compute three different embeddings.

    @@ -803,7 +806,7 @@

    Bulk Cu equation of state example -../../_images/c3cad5fabd7d194f682c7781df8cb29fb801535cb4cbcb2c830584b6c6ffc72d.png +../../_images/b618a440ac6e28c1074cbc44d70c947600061410b1bf9e4328b62a023dee925a.png

    We can see that near the minimum the different embeddings are all quite similar. But, near the unphysical peak, the x_E embedding shows a significant deviation. The atomic energy is linear in this embedding, which is why we see the peak. This means the embedding is not sufficiently trained in this region, and fine-tuning should be considered with data in that region.

    @@ -888,7 +891,7 @@

    A clustering example
    -../../_images/756ffd7fe413dd24a1c8d3824960c35167f5a303e78d4971c1eaf1382c82fe73.png +../../_images/9b352c76d25a9ed9f842185220fcb7d663b56fe2cc68da33f0cfa626f2d799d7.png
    @@ -936,7 +939,7 @@

    Clustering individual atoms +../../_images/57f11d76813d1e21dd04af0b0b64c72549156f7c76bdfb81616387ecb9619555.png

    You can see from this there are roughly three kinds of atoms. One is bulk like, with the lowest energy (the dark red points), the second is also lower in energy (the reddish-orange points), and the others are surface atoms, with higher energies (the bluish points).

    @@ -1056,7 +1059,7 @@

    A simple vector search example
    <Axes: >
    -../../_images/4e62701901a436db91accf959034131fa3f13737244e437740ddae980ebd1e28.png +../../_images/8f4b96a1fa7c2b561281842fe2ac549124fff2cce7a0746b6d3a762b322e60a1.png

    diff --git a/tutorials/advanced/fine-tuning-in-python.html b/tutorials/advanced/fine-tuning-in-python.html index 664c9c1e87..13e52aad54 100644 --- a/tutorials/advanced/fine-tuning-in-python.html +++ b/tutorials/advanced/fine-tuning-in-python.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -683,26 +686,26 @@

    Fine-tuning with Python 
    id|age|user  |formula|calculator| energy|natoms| fmax|pbc| volume|charge|   mass
- 1|46m|runner|Sn2O4  |unknown   |-41.359|     6|0.045|TTT| 64.258| 0.000|301.416
- 2|46m|runner|Sn2O4  |unknown   |-41.853|     6|0.025|TTT| 66.526| 0.000|301.416
- 3|46m|runner|Sn2O4  |unknown   |-42.199|     6|0.010|TTT| 68.794| 0.000|301.416
- 4|46m|runner|Sn2O4  |unknown   |-42.419|     6|0.006|TTT| 71.062| 0.000|301.416
- 5|46m|runner|Sn2O4  |unknown   |-42.534|     6|0.011|TTT| 73.330| 0.000|301.416
- 6|46m|runner|Sn2O4  |unknown   |-42.562|     6|0.029|TTT| 75.598| 0.000|301.416
- 7|46m|runner|Sn2O4  |unknown   |-42.518|     6|0.033|TTT| 77.866| 0.000|301.416
- 8|46m|runner|Sn2O4  |unknown   |-42.415|     6|0.010|TTT| 80.134| 0.000|301.416
- 9|46m|runner|Sn2O4  |unknown   |-42.266|     6|0.006|TTT| 82.402| 0.000|301.416
-10|46m|runner|Sn2O4  |unknown   |-42.083|     6|0.017|TTT| 84.670| 0.000|301.416
-11|46m|runner|Sn4O8  |unknown   |-81.424|    12|0.012|TTT|117.473| 0.000|602.832
-12|46m|runner|Sn4O8  |unknown   |-82.437|    12|0.005|TTT|121.620| 0.000|602.832
-13|46m|runner|Sn4O8  |unknown   |-83.147|    12|0.015|TTT|125.766| 0.000|602.832
-14|46m|runner|Sn4O8  |unknown   |-83.599|    12|0.047|TTT|129.912| 0.000|602.832
-15|46m|runner|Sn4O8  |unknown   |-83.831|    12|0.081|TTT|134.058| 0.000|602.832
-16|46m|runner|Sn4O8  |unknown   |-83.898|    12|0.001|TTT|138.204| 0.000|602.832
-17|46m|runner|Sn4O8  |unknown   |-83.805|    12|0.001|TTT|142.350| 0.000|602.832
-18|46m|runner|Sn4O8  |unknown   |-83.586|    12|0.002|TTT|146.496| 0.000|602.832
-19|46m|runner|Sn4O8  |unknown   |-83.262|    12|0.002|TTT|150.642| 0.000|602.832
-20|46m|runner|Sn4O8  |unknown   |-82.851|    12|0.013|TTT|154.788| 0.000|602.832
+ 1|51m|runner|Sn2O4  |unknown   |-41.359|     6|0.045|TTT| 64.258| 0.000|301.416
+ 2|51m|runner|Sn2O4  |unknown   |-41.853|     6|0.025|TTT| 66.526| 0.000|301.416
+ 3|51m|runner|Sn2O4  |unknown   |-42.199|     6|0.010|TTT| 68.794| 0.000|301.416
+ 4|51m|runner|Sn2O4  |unknown   |-42.419|     6|0.006|TTT| 71.062| 0.000|301.416
+ 5|51m|runner|Sn2O4  |unknown   |-42.534|     6|0.011|TTT| 73.330| 0.000|301.416
+ 6|51m|runner|Sn2O4  |unknown   |-42.562|     6|0.029|TTT| 75.598| 0.000|301.416
+ 7|51m|runner|Sn2O4  |unknown   |-42.518|     6|0.033|TTT| 77.866| 0.000|301.416
+ 8|51m|runner|Sn2O4  |unknown   |-42.415|     6|0.010|TTT| 80.134| 0.000|301.416
+ 9|51m|runner|Sn2O4  |unknown   |-42.266|     6|0.006|TTT| 82.402| 0.000|301.416
+10|51m|runner|Sn2O4  |unknown   |-42.083|     6|0.017|TTT| 84.670| 0.000|301.416
+11|51m|runner|Sn4O8  |unknown   |-81.424|    12|0.012|TTT|117.473| 0.000|602.832
+12|51m|runner|Sn4O8  |unknown   |-82.437|    12|0.005|TTT|121.620| 0.000|602.832
+13|51m|runner|Sn4O8  |unknown   |-83.147|    12|0.015|TTT|125.766| 0.000|602.832
+14|51m|runner|Sn4O8  |unknown   |-83.599|    12|0.047|TTT|129.912| 0.000|602.832
+15|51m|runner|Sn4O8  |unknown   |-83.831|    12|0.081|TTT|134.058| 0.000|602.832
+16|51m|runner|Sn4O8  |unknown   |-83.898|    12|0.001|TTT|138.204| 0.000|602.832
+17|51m|runner|Sn4O8  |unknown   |-83.805|    12|0.001|TTT|142.350| 0.000|602.832
+18|51m|runner|Sn4O8  |unknown   |-83.586|    12|0.002|TTT|146.496| 0.000|602.832
+19|51m|runner|Sn4O8  |unknown   |-83.262|    12|0.002|TTT|150.642| 0.000|602.832
+20|51m|runner|Sn4O8  |unknown   |-82.851|    12|0.013|TTT|154.788| 0.000|602.832
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    @@ -982,13 +985,13 @@

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    /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch_geometric/data/collate.py:145: UserWarning: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be the only storage class. This should only matter to you if you are using storages directly.  To access UntypedStorage directly, use tensor.untyped_storage() instead of tensor.storage()
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@@ -1188,28 +1168,28 @@ 
    Run the training task
 
    
 
    
-
    2024-08-03 02:53:27 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
-2024-08-03 02:53:27 (WARNING): Unrecognized arguments: ['symmetric_edge_symmetrization']
-2024-08-03 02:53:29 (WARNING): Using `weight_decay` from `optim` instead of `optim.optimizer_params`.Please update your config to use `optim.optimizer_params.weight_decay`.`optim.weight_decay` will soon be deprecated.
-2024-08-03 02:53:30 (WARNING): No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
-2024-08-03 02:53:31 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
-2024-08-03 02:53:31 (WARNING): Unrecognized arguments: ['symmetric_edge_symmetrization']
-2024-08-03 02:53:33 (WARNING): Using `weight_decay` from `optim` instead of `optim.optimizer_params`.Please update your config to use `optim.optimizer_params.weight_decay`.`optim.weight_decay` will soon be deprecated.
-2024-08-03 02:53:33 (WARNING): No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
-2024-08-03 02:53:33 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('train.db')]'
-2024-08-03 02:53:33 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
-
    
-
    
-
    2024-08-03 02:55:26 (INFO): Writing results to ./results/2024-08-03-02-52-48/ocp_predictions.npz
-2024-08-03 02:55:49 (INFO): energy_mae: 4.77e+00, forcesx_mae: 1.70e-02, forcesy_mae: 1.43e-02, forcesz_mae: 2.00e-02, forces_mae: 1.71e-02, forces_cosine_similarity: -4.15e-02, forces_magnitude_error: 1.90e-02, energy_forces_within_threshold: 0.00e+00, loss: 4.81e+00, lr: 5.00e-04, epoch: 6.78e-01, step: 4.00e+01
-2024-08-03 02:55:51 (INFO): Evaluating on val.
-2024-08-03 02:55:59 (INFO): energy_mae: 5.0575, forcesx_mae: 0.0426, forcesy_mae: 0.0285, forcesz_mae: 0.0175, forces_mae: 0.0295, forces_cosine_similarity: -0.0088, forces_magnitude_error: 0.0482, energy_forces_within_threshold: 0.0000, loss: 5.1766, epoch: 0.6780
-2024-08-03 02:56:19 (INFO): energy_mae: 4.83e+00, forcesx_mae: 2.47e-02, forcesy_mae: 2.33e-02, forcesz_mae: 2.95e-02, forces_mae: 2.58e-02, forces_cosine_similarity: -1.17e-01, forces_magnitude_error: 3.22e-02, energy_forces_within_threshold: 0.00e+00, loss: 4.88e+00, lr: 5.00e-04, epoch: 8.47e-01, step: 5.00e+01
-2024-08-03 02:56:21 (INFO): Evaluating on val.
-2024-08-03 02:56:28 (INFO): energy_mae: 2.8122, forcesx_mae: 0.0181, forcesy_mae: 0.0226, forcesz_mae: 0.0186, forces_mae: 0.0197, forces_cosine_similarity: -0.0252, forces_magnitude_error: 0.0201, energy_forces_within_threshold: 0.0000, loss: 2.8746, epoch: 0.8475
-2024-08-03 02:56:29 (INFO): Predicting on test.
-2024-08-03 02:56:35 (INFO): Writing results to ./results/2024-08-03-02-52-48/ocp_predictions.npz
-2024-08-03 02:56:55 (INFO): Total time taken: 200.10807967185974
+
    2024-08-14 01:38:51 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+2024-08-14 01:38:51 (WARNING): Unrecognized arguments: ['symmetric_edge_symmetrization']
+2024-08-14 01:38:54 (WARNING): Using `weight_decay` from `optim` instead of `optim.optimizer_params`.Please update your config to use `optim.optimizer_params.weight_decay`.`optim.weight_decay` will soon be deprecated.
+2024-08-14 01:38:54 (WARNING): No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+2024-08-14 01:38:55 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+2024-08-14 01:38:55 (WARNING): Unrecognized arguments: ['symmetric_edge_symmetrization']
+2024-08-14 01:38:57 (WARNING): Using `weight_decay` from `optim` instead of `optim.optimizer_params`.Please update your config to use `optim.optimizer_params.weight_decay`.`optim.weight_decay` will soon be deprecated.
+2024-08-14 01:38:57 (WARNING): No seed has been set in modelcheckpoint or OCPCalculator! Results may not be reproducible on re-run
+2024-08-14 01:38:57 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('train.db')]'
+2024-08-14 01:38:57 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+
    
+
    
+
    2024-08-14 01:38:57 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+2024-08-14 01:38:57 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('val.db')]'
+2024-08-14 01:38:57 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+2024-08-14 01:38:57 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+2024-08-14 01:38:57 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('test.db')]'
+2024-08-14 01:38:57 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+2024-08-14 01:38:57 (WARNING): Failed to get data sizes, falling back to uniform partitioning. BalancedBatchSampler requires a dataset that has a metadata attributed with number of atoms.
+2024-08-14 01:38:57 (WARNING): Unrecognized arguments: ['symmetric_edge_symmetrization']
+2024-08-14 01:38:59 (WARNING): log_summary for Tensorboard not supported
+2024-08-14 01:38:59 (WARNING): Using `weight_decay` from `optim` instead of `optim.optimizer_params`.Please update your config to use `optim.optimizer_params.weight_decay`.`optim.weight_decay` will soon be deprecated.
 
    
 
    
 
    
diff --git a/tutorials/cattsunami_tutorial.html b/tutorials/cattsunami_tutorial.html
index ed985301d1..1f8fd889e0 100644
--- a/tutorials/cattsunami_tutorial.html
+++ b/tutorials/cattsunami_tutorial.html
@@ -305,6 +305,7 @@
 
  • core.common.logger
    • 
 
  • core.common.profiler_utils
    • 
 
  • core.common.registry
    • 
+
  • core.common.slurm
    • 
 
  • core.common.test_utils
    • 
 
  • core.common.transforms
    • 
 
  • core.common.tutorial_utils
    • 
@@ -334,16 +335,17 @@
 
  • core.models.utils
    • 
 
  • core.models.base
    • 
 
  • core.models.dimenet_plus_plus
    • 
+
  • core.models.finetune_hydra
    • 
 
  • core.models.model_registry
    • 
 
  • core.models.schnet
    •

  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/tutorials/fairchem_models_for_nebs.html b/tutorials/fairchem_models_for_nebs.html index 480c7ce90a..ee4374fd2a 100644 --- a/tutorials/fairchem_models_for_nebs.html +++ b/tutorials/fairchem_models_for_nebs.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    diff --git a/tutorials/intro.html b/tutorials/intro.html index c8f223f422..6a1cb3cb30 100644 --- a/tutorials/intro.html +++ b/tutorials/intro.html @@ -305,6 +305,7 @@
  • core.common.logger
  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc
    @@ -726,12 +729,12 @@

    About the compute environment 
    /opt/hostedtoolcache/Python/3.11.9/x64/bin/python 3.11.9 (main, Jul 15 2024, 21:50:21) [GCC 11.4.0]
 fairchem is installed at /home/runner/work/fairchem/fairchem/src/fairchem
-fairchem repo is at git commit: 08b8c1e
+fairchem repo is at git commit: 8fb16d6
 numba: 0.60.0
 numpy: 1.26.4
 ase: 3.23.0
 e3nn: 0.5.1
-pymatgen: 2024.7.18
+pymatgen: 2024.8.9
 torch: 2.2.0+cu121
 torch.version.cuda: 12.1
 torch.cuda: is_available: False
@@ -739,9 +742,9 @@ 
    About the compute environmentcore.common.logger

  • core.common.profiler_utils
  • core.common.registry
    • +
  • core.common.slurm
  • core.common.test_utils
  • core.common.transforms
  • core.common.tutorial_utils
    • @@ -334,16 +335,17 @@
  • core.models.utils
  • core.models.base
  • core.models.dimenet_plus_plus
    • +
  • core.models.finetune_hydra
  • core.models.model_registry
  • core.models.schnet
  • core.modules
    @@ -356,6 +358,8 @@
  • core.scripts.hpo
  • core.scripts.download_data
  • core.scripts.download_large_files
    • +
  • core.scripts.fit_normalizers
    • +
  • core.scripts.fit_references
  • core.scripts.gif_maker_parallelized
  • core.scripts.make_challenge_submission_file
  • core.scripts.make_lmdb_sizes
    • @@ -381,7 +385,6 @@
  • data.oc