deploy: 08b8c1e

FAIR-Chem · Aug 3, 2024 · c23cea7 · c23cea7
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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
@@ -1,16 +1,17 @@
-2024-07-19 20:42:08 (INFO): Running in non-distributed local mode
-2024-07-19 20:42:08 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
-2024-07-19 20:42:10 (INFO): amp: true
+2024-08-03 02:13:05 (INFO): Running in non-distributed local mode
+2024-08-03 02:13:05 (INFO): Setting env PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True
+2024-08-03 02:13:05 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-08-03 02:13:06 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-07-19-20-41-36
-  commit: f9ecf73
+  checkpoint_dir: ./checkpoints/2024-08-03-02-12-16
+  commit: 08b8c1e
   identifier: ''
-  logs_dir: ./logs/tensorboard/2024-07-19-20-41-36
+  logs_dir: ./logs/tensorboard/2024-08-03-02-12-16
   print_every: 10
-  results_dir: ./results/2024-07-19-20-41-36
+  results_dir: ./results/2024-08-03-02-12-16
   seed: 0
-  timestamp_id: 2024-07-19-20-41-36
-  version: 0.1.dev1+gf9ecf73
+  timestamp_id: 2024-08-03-02-12-16
+  version: 0.1.dev1+g08b8c1e
 dataset: {}
 evaluation_metrics:
   metrics:
@@ -113,20 +114,23 @@ test_dataset:
 trainer: ocp
 val_dataset: {}
 
-2024-07-19 20:42:10 (INFO): rank: 0: Sampler created...
-2024-07-19 20:42:10 (INFO): Batch balancing is disabled for single GPU training.
-2024-07-19 20:42:10 (INFO): Loading model: gemnet_t
-2024-07-19 20:42:11 (INFO): Loaded GemNetT with 31671825 parameters.
-2024-07-19 20:42:11 (WARNING): log_summary for Tensorboard not supported
-2024-07-19 20:42:12 (INFO): Loading checkpoint from: /tmp/fairchem_checkpoints/gndt_oc22_all_s2ef.pt
-2024-07-19 20:42:12 (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. 
-2024-07-19 20:42:12 (WARNING): Scale factor comment not found in model
-2024-07-19 20:42:12 (INFO): Predicting on test.
+2024-08-03 02:13:06 (WARNING): Could not find dataset metadata.npz files in '[PosixPath('data.db')]'
+2024-08-03 02:13:06 (WARNING): Disabled BalancedBatchSampler because num_replicas=1.
+2024-08-03 02:13:06 (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 02:13:06 (INFO): rank: 0: Sampler created...
+2024-08-03 02:13:06 (INFO): Created BalancedBatchSampler with sampler=<fairchem.core.common.data_parallel.StatefulDistributedSampler object at 0x7f2bf30d1310>, 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.
 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,  3.55s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:03,  3.23s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.27s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:09<00:00,  3.30s/it]
-2024-07-19 20:42:22 (INFO): Writing results to ./results/2024-07-19-20-41-36/ocp_predictions.npz
-2024-07-19 20:42:22 (INFO): Total time taken: 10.0305335521698
-Elapsed time = 16.3 seconds
+device 0:  33%|███████████▋                       | 1/3 [00:02<00:05,  2.56s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:06<00:03,  3.21s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.10s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.35s/it]
+2024-08-03 02:13:15 (INFO): Writing results to ./results/2024-08-03-02-12-16/ocp_predictions.npz
+2024-08-03 02:13:15 (INFO): Total time taken: 7.171952247619629
+Elapsed time = 13.2 seconds

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diff --git a/_images/f508405455676bf2a7ab2b64f3133d6a31c7e2bed12b4e68b1bae30fb759e03b.png b/_images/f508405455676bf2a7ab2b64f3133d6a31c7e2bed12b4e68b1bae30fb759e03b.png
diff --git a/_sources/autoapi/cattsunami/core/autoframe/index.rst b/_sources/autoapi/cattsunami/core/autoframe/index.rst
@@ -124,6 +124,12 @@ Module Contents
    Base class to hold functions that are shared across the reaction types.
 
 
+   .. py:attribute:: reaction
+
+
+   .. py:attribute:: reactant1_systems
+
+
    .. py:method:: get_neb_frames(calculator, n_frames: int = 5, n_pdt1_sites: int = 5, n_pdt2_sites: int = 5, fmax: float = 0.05, steps: int = 200)
 
       Propose final frames for NEB calculations. Perform a relaxation on the final
@@ -226,6 +232,18 @@ Module Contents
    Base class to hold functions that are shared across the reaction types.
 
 
+   .. py:attribute:: reaction
+
+
+   .. py:attribute:: r_traverse_max
+
+
+   .. py:attribute:: r_react_max
+
+
+   .. py:attribute:: r_react_min
+
+
    .. py:method:: get_neb_frames(calculator, n_frames: int = 10, n_initial_frames: int = 5, n_final_frames_per_initial: int = 5, fmax: float = 0.05, steps: int = 200)
 
       Propose final frames for NEB calculations. Perform a relaxation on the final
@@ -286,6 +304,12 @@ Module Contents
    Base class to hold functions that are shared across the reaction types.
 
 
+   .. py:attribute:: z_desorption
+
+
+   .. py:attribute:: reaction
+
+
    .. py:method:: get_neb_frames(calculator, n_frames: int = 5, n_systems: int = 5, fmax: float = 0.05, steps: int = 200)
 
       Propose final frames for NEB calculations. Perform a relaxation on the final

diff --git a/_sources/autoapi/cattsunami/core/index.rst b/_sources/autoapi/cattsunami/core/index.rst
@@ -32,6 +32,33 @@ Package Contents
    Bases: :py:obj:`ase.neb.DyNEB`
 
 
+   .. py:attribute:: batch_size
+
+
+   .. py:attribute:: config
+
+
+   .. py:attribute:: trainer
+
+
+   .. py:attribute:: a2g
+
+
+   .. py:attribute:: intermediate_energies
+      :value: []
+
+
+
+   .. py:attribute:: intermediate_forces
+      :value: []
+
+
+
+   .. py:attribute:: cached
+      :value: False
+
+
+
    .. py:method:: load_checkpoint(checkpoint_path: str) -> None
 
       Load existing trained model
@@ -58,6 +85,18 @@ Package Contents
    Initialize Reaction object
 
 
+   .. py:attribute:: reaction_db_path
+
+
+   .. py:attribute:: reaction_db
+
+
+   .. py:attribute:: adsorbate_db
+
+
+   .. py:attribute:: entry
+
+
    .. py:method:: get_desorption_mapping(reactant)
 
       Get mapping for desorption reaction

diff --git a/_sources/autoapi/cattsunami/core/ocpneb/index.rst b/_sources/autoapi/cattsunami/core/ocpneb/index.rst
@@ -20,6 +20,33 @@ Module Contents
    Bases: :py:obj:`ase.neb.DyNEB`
 
 
+   .. py:attribute:: batch_size
+
+
+   .. py:attribute:: config
+
+
+   .. py:attribute:: trainer
+
+
+   .. py:attribute:: a2g
+
+
+   .. py:attribute:: intermediate_energies
+      :value: []
+
+
+
+   .. py:attribute:: intermediate_forces
+      :value: []
+
+
+
+   .. py:attribute:: cached
+      :value: False
+
+
+
    .. py:method:: load_checkpoint(checkpoint_path: str) -> None
 
       Load existing trained model

diff --git a/_sources/autoapi/cattsunami/core/reaction/index.rst b/_sources/autoapi/cattsunami/core/reaction/index.rst
@@ -20,6 +20,18 @@ Module Contents
    Initialize Reaction object
 
 
+   .. py:attribute:: reaction_db_path
+
+
+   .. py:attribute:: reaction_db
+
+
+   .. py:attribute:: adsorbate_db
+
+
+   .. py:attribute:: entry
+
+
    .. py:method:: get_desorption_mapping(reactant)
 
       Get mapping for desorption reaction

diff --git a/_sources/autoapi/core/_cli/index.rst b/_sources/autoapi/core/_cli/index.rst
@@ -50,6 +50,14 @@ Module Contents
       the state so that not to pickle it) and change/remove the initial parameters.
 
 
+   .. py:attribute:: config
+      :value: None
+
+
+
+   .. py:attribute:: distributed
+
+
    .. py:method:: __call__(config: dict) -> None