deploy: aacb883

FAIR-Chem · Jul 13, 2024 · 546bac2 · 546bac2
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diff --git a/_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt b/_downloads/5fdddbed2260616231dbf7b0d94bb665/train.txt
diff --git a/_downloads/819e10305ddd6839cd7da05935b17060/mass-inference.txt b/_downloads/819e10305ddd6839cd7da05935b17060/mass-inference.txt
@@ -1,17 +1,17 @@
-2024-07-10 16:34:01 (INFO): Running in non-distributed local mode
-2024-07-10 16:34:01 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
-2024-07-10 16:34:02 (INFO): amp: true
+2024-07-13 04:31:12 (INFO): Running in non-distributed local mode
+2024-07-13 04:31:12 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-07-13 04:31:13 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-07-10-16-34-08
-  commit: 36a17ad
+  checkpoint_dir: ./checkpoints/2024-07-13-04-30-56
+  commit: aacb883
   identifier: ''
-  logs_dir: ./logs/tensorboard/2024-07-10-16-34-08
+  logs_dir: ./logs/tensorboard/2024-07-13-04-30-56
   print_every: 10
-  results_dir: ./results/2024-07-10-16-34-08
+  results_dir: ./results/2024-07-13-04-30-56
   seed: 0
-  timestamp_id: 2024-07-10-16-34-08
-  version: 0.1.dev1+g36a17ad
-dataset: null
+  timestamp_id: 2024-07-13-04-30-56
+  version: 0.1.dev1+gaacb883
+dataset: {}
 evaluation_metrics:
   metrics:
     energy:
@@ -98,6 +98,7 @@ outputs:
     eval_on_free_atoms: true
     level: atom
     train_on_free_atoms: true
+relax_dataset: {}
 slurm: {}
 task:
   prediction_dtype: float32
@@ -110,22 +111,22 @@ test_dataset:
     selection: natoms>5,xc=PBE
   src: data.db
 trainer: ocp
-val_dataset: null
+val_dataset: {}
 
-2024-07-10 16:34:02 (INFO): rank: 0: Sampler created...
-2024-07-10 16:34:02 (INFO): Batch balancing is disabled for single GPU training.
-2024-07-10 16:34:02 (INFO): Loading model: gemnet_t
-2024-07-10 16:34:04 (INFO): Loaded GemNetT with 31671825 parameters.
-2024-07-10 16:34:04 (WARNING): log_summary for Tensorboard not supported
-2024-07-10 16:34:04 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
-2024-07-10 16:34:04 (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. 
-2024-07-10 16:34:04 (WARNING): Scale factor comment not found in model
-2024-07-10 16:34:04 (INFO): Predicting on test.
+2024-07-13 04:31:13 (INFO): rank: 0: Sampler created...
+2024-07-13 04:31:13 (INFO): Batch balancing is disabled for single GPU training.
+2024-07-13 04:31:13 (INFO): Loading model: gemnet_t
+2024-07-13 04:31:15 (INFO): Loaded GemNetT with 31671825 parameters.
+2024-07-13 04:31:15 (WARNING): log_summary for Tensorboard not supported
+2024-07-13 04:31:16 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
+2024-07-13 04:31:16 (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. 
+2024-07-13 04:31:16 (WARNING): Scale factor comment not found in model
+2024-07-13 04:31:16 (INFO): Predicting on test.
 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)
 /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 [00:03<00:07,  3.82s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:07<00:03,  3.47s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:08<00:00,  2.43s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:08<00:00,  2.76s/it]
-2024-07-10 16:34:13 (INFO): Writing results to ./results/2024-07-10-16-34-08/ocp_predictions.npz
-2024-07-10 16:34:13 (INFO): Total time taken: 8.430647373199463
-Elapsed time = 14.9 seconds
+device 0:  33%|███████████▋                       | 1/3 [00:05<00:11,  5.70s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:08<00:03,  3.96s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:11<00:00,  3.49s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:11<00:00,  3.80s/it]
+2024-07-13 04:31:27 (INFO): Writing results to ./results/2024-07-13-04-30-56/ocp_predictions.npz
+2024-07-13 04:31:27 (INFO): Total time taken: 11.534403562545776
+Elapsed time = 17.8 seconds

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diff --git a/_sources/autoapi/cattsunami/core/autoframe/index.rst b/_sources/autoapi/cattsunami/core/autoframe/index.rst
@@ -116,7 +116,7 @@ Module Contents
 
 
 
-.. py:class:: AutoFrameDissociation(reaction: fairchem.applications.cattsunami.core.Reaction, reactant_system: ase.Atoms, product1_systems: list, product1_energies: list, product2_systems: list, product2_energies: list, r_product1_max: float = None, r_product2_max: float = None, r_product2_min: float = None)
+.. py:class:: AutoFrameDissociation(reaction: fairchem.applications.cattsunami.core.Reaction, reactant_system: ase.Atoms, product1_systems: list, product1_energies: list, product2_systems: list, product2_energies: list, r_product1_max: float | None = None, r_product2_max: float | None = None, r_product2_min: float | None = None)
 
    Bases: :py:obj:`AutoFrame`
 

diff --git a/_sources/autoapi/cattsunami/core/index.rst b/_sources/autoapi/cattsunami/core/index.rst
@@ -20,24 +20,13 @@ Classes
 
 .. autoapisummary::
 
-   cattsunami.core.Reaction
    cattsunami.core.OCPNEB
+   cattsunami.core.Reaction
 
 
 Package Contents
 ----------------
 
-.. py:class:: Reaction(reaction_db_path: str, adsorbate_db_path: str, reaction_id_from_db: int = None, reaction_str_from_db: str = None, reaction_type: str = None)
-
-   Initialize Reaction object
-
-
-   .. py:method:: get_desorption_mapping(reactant)
-
-      Get mapping for desorption reaction
-
-
-
 .. py:class:: OCPNEB(images, checkpoint_path, k=0.1, fmax=0.05, climb=False, parallel=False, remove_rotation_and_translation=False, world=None, dynamic_relaxation=True, scale_fmax=0.0, method='aseneb', allow_shared_calculator=False, precon=None, cpu=False, batch_size=4)
 
    Bases: :py:obj:`ase.neb.DyNEB`
@@ -64,3 +53,14 @@ Package Contents
    .. py:method:: get_precon_forces(forces, energies, images)
 
 
+.. py:class:: Reaction(reaction_db_path: str, adsorbate_db_path: str, reaction_id_from_db: int | None = None, reaction_str_from_db: str | None = None, reaction_type: str | None = None)
+
+   Initialize Reaction object
+
+
+   .. py:method:: get_desorption_mapping(reactant)
+
+      Get mapping for desorption reaction
+
+
+
diff --git a/_sources/autoapi/cattsunami/core/reaction/index.rst b/_sources/autoapi/cattsunami/core/reaction/index.rst
@@ -15,7 +15,7 @@ Classes
 Module Contents
 ---------------
 
-.. py:class:: Reaction(reaction_db_path: str, adsorbate_db_path: str, reaction_id_from_db: int = None, reaction_str_from_db: str = None, reaction_type: str = None)
+.. py:class:: Reaction(reaction_db_path: str, adsorbate_db_path: str, reaction_id_from_db: int | None = None, reaction_str_from_db: str | None = None, reaction_type: str | None = None)
 
    Initialize Reaction object
 

diff --git a/_sources/autoapi/core/common/index.rst b/_sources/autoapi/core/common/index.rst
@@ -33,6 +33,7 @@ Submodules
    /autoapi/core/common/gp_utils/index
    /autoapi/core/common/hpo_utils/index
    /autoapi/core/common/logger/index
+   /autoapi/core/common/profiler_utils/index
    /autoapi/core/common/registry/index
    /autoapi/core/common/test_utils/index
    /autoapi/core/common/transforms/index

diff --git a/_sources/autoapi/core/common/logger/index.rst b/_sources/autoapi/core/common/logger/index.rst
@@ -63,6 +63,11 @@ Module Contents
 
 
 
+   .. py:method:: log_artifact(name: str, type: str, file_location: str) -> None
+      :abstractmethod:
+
+
+
 .. py:class:: WandBLogger(config)
 
    Bases: :py:obj:`Logger`
@@ -93,6 +98,9 @@ Module Contents
    .. py:method:: mark_preempting() -> None
 
 
+   .. py:method:: log_artifact(name: str, type: str, file_location: str) -> None
+
+
 .. py:class:: TensorboardLogger(config)
 
    Bases: :py:obj:`Logger`
@@ -123,3 +131,6 @@ Module Contents
    .. py:method:: log_summary(summary_dict: dict[str, Any]) -> None
 
 
+   .. py:method:: log_artifact(name: str, type: str, file_location: str) -> None
+
+
diff --git a/_sources/autoapi/core/common/profiler_utils/index.rst b/_sources/autoapi/core/common/profiler_utils/index.rst
@@ -0,0 +1,46 @@
+core.common.profiler_utils
+==========================
+
+.. py:module:: core.common.profiler_utils
+
+
+Functions
+---------
+
+.. autoapisummary::
+
+   core.common.profiler_utils.get_default_profiler_handler
+   core.common.profiler_utils.get_profile_schedule
+
+
+Module Contents
+---------------
+
+.. py:function:: get_default_profiler_handler(run_id: str, output_dir: str, logger: fairchem.core.common.logger.Logger)
+
+   Get a standard callback handle for the pytorch profiler
+
+
+.. py:function:: get_profile_schedule(wait: int = 5, warmup: int = 5, active: int = 2)
+
+   Get a profile schedule and total number of steps to run
+   check pytorch docs on the meaning of these paramters:
+   https://pytorch.org/docs/stable/profiler.html#torch.profiler.schedule
+   Example usage:
+   ```
+   trace_handler = get_default_profiler_handler(run_id = self.config["cmd"]["timestamp_id"],
+                                                   output_dir = self.config["cmd"]["results_dir"],
+                                                   logger = self.logger)
+   profile_schedule, total_profile_steps = get_profile_schedule()
+
+   with profile(
+       activities=[ProfilerActivity.CPU, ProfilerActivity.CUDA],
+       schedule=profile_schedule,
+       on_trace_ready=trace_handler
+   ) as p:
+       for i in steps:
+           <code block to profile>
+           if i < total_profile_steps:
+               p.step()
+
+
diff --git a/_sources/autoapi/data/oc/core/adsorbate/index.rst b/_sources/autoapi/data/oc/core/adsorbate/index.rst
@@ -23,7 +23,7 @@ Functions
 Module Contents
 ---------------
 
-.. py:class:: Adsorbate(adsorbate_atoms: ase.Atoms = None, adsorbate_id_from_db: int = None, adsorbate_smiles_from_db: str = None, adsorbate_db_path: str = ADSORBATE_PKL_PATH, adsorbate_db: Dict[int, Tuple[Any, Ellipsis]] = None, adsorbate_binding_indices: list = None)
+.. py:class:: Adsorbate(adsorbate_atoms: ase.Atoms = None, adsorbate_id_from_db: int | None = None, adsorbate_smiles_from_db: str | None = None, adsorbate_db_path: str = ADSORBATE_PKL_PATH, adsorbate_db: dict[int, tuple[Any, Ellipsis]] | None = None, adsorbate_binding_indices: list | None = None)
 
    Initializes an adsorbate object in one of 4 ways:
    - Directly pass in an ase.Atoms object.
@@ -62,13 +62,13 @@ Module Contents
    .. py:method:: _get_adsorbate_from_random(adsorbate_db)
 
 
-   .. py:method:: _load_adsorbate(adsorbate: Tuple[Any, Ellipsis]) -> None
+   .. py:method:: _load_adsorbate(adsorbate: tuple[Any, Ellipsis]) -> 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:function:: randomly_rotate_adsorbate(adsorbate_atoms: ase.Atoms, mode: str = 'random', binding_idx: int = None)
+.. py:function:: randomly_rotate_adsorbate(adsorbate_atoms: ase.Atoms, mode: str = 'random', binding_idx: int | None = None)
 
diff --git a/_sources/autoapi/data/oc/core/adsorbate_slab_config/index.rst b/_sources/autoapi/data/oc/core/adsorbate_slab_config/index.rst
@@ -26,7 +26,7 @@ Functions
 Module Contents
 ---------------
 
-.. py:class:: AdsorbateSlabConfig(slab: fairchem.data.oc.core.Slab, adsorbate: fairchem.data.oc.core.Adsorbate, num_sites: int = 100, num_augmentations_per_site: int = 1, interstitial_gap: float = 0.1, mode: str = 'random')
+.. py:class:: AdsorbateSlabConfig(slab: fairchem.data.oc.core.slab.Slab, adsorbate: fairchem.data.oc.core.slab.Adsorbate, num_sites: int = 100, num_augmentations_per_site: int = 1, interstitial_gap: float = 0.1, mode: str = 'random')
 
    Initializes a list of adsorbate-catalyst systems for a given Adsorbate and Slab.
 
@@ -72,7 +72,7 @@ Module Contents
 
 
 
-   .. py:method:: place_adsorbate_on_site(adsorbate: fairchem.data.oc.core.Adsorbate, site: numpy.ndarray, interstitial_gap: float = 0.1)
+   .. py:method:: place_adsorbate_on_site(adsorbate: fairchem.data.oc.core.slab.Adsorbate, site: numpy.ndarray, interstitial_gap: float = 0.1)
 
       Place the adsorbate at the given binding site.
 

diff --git a/_sources/autoapi/data/oc/core/bulk/index.rst b/_sources/autoapi/data/oc/core/bulk/index.rst
@@ -15,7 +15,7 @@ Classes
 Module Contents
 ---------------
 
-.. py:class:: Bulk(bulk_atoms: ase.Atoms = None, bulk_id_from_db: int = None, bulk_src_id_from_db: str = None, bulk_db_path: str = BULK_PKL_PATH, bulk_db: List[Dict[str, Any]] = None)
+.. py:class:: Bulk(bulk_atoms: ase.Atoms = None, bulk_id_from_db: int | None = None, bulk_src_id_from_db: str | None = None, bulk_db_path: str = BULK_PKL_PATH, bulk_db: list[dict[str, Any]] | None = None)
 
    Initializes a bulk object in one of 4 ways:
    - Directly pass in an ase.Atoms object.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -116,7 +116,7 @@ Module Contents



		.. py:class:: AutoFrameDissociation(reaction: fairchem.applications.cattsunami.core.Reaction, reactant_system: ase.Atoms, product1_systems: list, product1_energies: list, product2_systems: list, product2_energies: list, r_product1_max: float = None, r_product2_max: float = None, r_product2_min: float = None)
		.. py:class:: AutoFrameDissociation(reaction: fairchem.applications.cattsunami.core.Reaction, reactant_system: ase.Atoms, product1_systems: list, product1_energies: list, product2_systems: list, product2_energies: list, r_product1_max: float \| None = None, r_product2_max: float \| None = None, r_product2_min: float \| None = None)

		Bases: :py:obj:`AutoFrame`

Expand Down