deploy: bcae55c

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 798fcda09776c00173518fd6e6e6aaa7
+config: b5d0ff58eedd87b93894b95d734e1b60
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_downloads/819e10305ddd6839cd7da05935b17060/mass-inference.txt

@@ -1,17 +1,17 @@
-2024-05-13 23:24:55 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
+2024-05-14 21:21:35 (INFO): Project root: /home/runner/work/fairchem/fairchem/src/fairchem
 /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/cuda/amp/grad_scaler.py:126: UserWarning: torch.cuda.amp.GradScaler is enabled, but CUDA is not available.  Disabling.
   warnings.warn(
-2024-05-13 23:24:57 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
-2024-05-13 23:24:57 (INFO): amp: true
+2024-05-14 21:21:36 (WARNING): Detected old config, converting to new format. Consider updating to avoid potential incompatibilities.
+2024-05-14 21:21:36 (INFO): amp: true
 cmd:
-  checkpoint_dir: ./checkpoints/2024-05-13-23-25-52
-  commit: 967b18e
+  checkpoint_dir: ./checkpoints/2024-05-14-21-22-08
+  commit: bcae55c
   identifier: ''
-  logs_dir: ./logs/tensorboard/2024-05-13-23-25-52
+  logs_dir: ./logs/tensorboard/2024-05-14-21-22-08
   print_every: 10
-  results_dir: ./results/2024-05-13-23-25-52
+  results_dir: ./results/2024-05-14-21-22-08
   seed: 0
-  timestamp_id: 2024-05-13-23-25-52
+  timestamp_id: 2024-05-14-21-22-08
 dataset:
   a2g_args:
     r_energy: false
@@ -122,25 +122,25 @@ test_dataset:
 trainer: ocp
 val_dataset: null
 
-2024-05-13 23:24:57 (INFO): Loading dataset: ase_db
-2024-05-13 23:24:57 (INFO): rank: 0: Sampler created...
-2024-05-13 23:24:57 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-13 23:24:57 (INFO): rank: 0: Sampler created...
-2024-05-13 23:24:57 (INFO): Batch balancing is disabled for single GPU training.
-2024-05-13 23:24:57 (INFO): Loading model: gemnet_t
-2024-05-13 23:24:59 (INFO): Loaded GemNetT with 31671825 parameters.
-2024-05-13 23:24:59 (WARNING): Model gradient logging to tensorboard not yet supported.
-2024-05-13 23:24:59 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
-2024-05-13 23:24:59 (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. 
-2024-05-13 23:24:59 (WARNING): Scale factor comment not found in model
-2024-05-13 23:24:59 (INFO): Predicting on test.
+2024-05-14 21:21:36 (INFO): Loading dataset: ase_db
+2024-05-14 21:21:36 (INFO): rank: 0: Sampler created...
+2024-05-14 21:21:36 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-14 21:21:36 (INFO): rank: 0: Sampler created...
+2024-05-14 21:21:36 (INFO): Batch balancing is disabled for single GPU training.
+2024-05-14 21:21:36 (INFO): Loading model: gemnet_t
+2024-05-14 21:21:38 (INFO): Loaded GemNetT with 31671825 parameters.
+2024-05-14 21:21:38 (WARNING): Model gradient logging to tensorboard not yet supported.
+2024-05-14 21:21:38 (INFO): Loading checkpoint from: /tmp/ocp_checkpoints/gndt_oc22_all_s2ef.pt
+2024-05-14 21:21:38 (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. 
+2024-05-14 21:21:38 (WARNING): Scale factor comment not found in model
+2024-05-14 21:21:38 (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)
 /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/torch/amp/autocast_mode.py:250: UserWarning: User provided device_type of 'cuda', but CUDA is not available. Disabling
   warnings.warn(
-device 0:  33%|███████████▋                       | 1/3 [00:05<00:11,  5.79s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:07<00:03,  3.58s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:10<00:00,  3.12s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:10<00:00,  3.47s/it]
-2024-05-13 23:25:09 (INFO): Writing results to ./results/2024-05-13-23-25-52/ocp_predictions.npz
-2024-05-13 23:25:09 (INFO): Total time taken: 10.557064294815063
-Elapsed time = 16.9 seconds
+device 0:  33%|███████████▋                       | 1/3 [00:03<00:06,  3.11s/it]device 0:  67%|███████████████████████▎           | 2/3 [00:04<00:02,  2.38s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.39s/it]device 0: 100%|███████████████████████████████████| 3/3 [00:07<00:00,  2.47s/it]
+2024-05-14 21:21:46 (INFO): Writing results to ./results/2024-05-14-21-22-08/ocp_predictions.npz
+2024-05-14 21:21:46 (INFO): Total time taken: 7.559128284454346
+Elapsed time = 14.1 seconds

_sources/autoapi/ocpneb/core/autoframe/index.rst → _sources/autoapi/cattsunami/core/autoframe/index.rst

@@ -1,7 +1,7 @@
-:py:mod:`ocpneb.core.autoframe`
-===============================
+:py:mod:`cattsunami.core.autoframe`
+===================================
 
-.. py:module:: ocpneb.core.autoframe
+.. py:module:: cattsunami.core.autoframe
 
 .. autoapi-nested-parse::
 
@@ -18,10 +18,10 @@ Classes
 
 .. autoapisummary::
 
-   ocpneb.core.autoframe.AutoFrame
-   ocpneb.core.autoframe.AutoFrameDissociation
-   ocpneb.core.autoframe.AutoFrameTransfer
-   ocpneb.core.autoframe.AutoFrameDesorption
+   cattsunami.core.autoframe.AutoFrame
+   cattsunami.core.autoframe.AutoFrameDissociation
+   cattsunami.core.autoframe.AutoFrameTransfer
+   cattsunami.core.autoframe.AutoFrameDesorption
 
 
 
@@ -30,18 +30,18 @@ Functions
 
 .. autoapisummary::
 
-   ocpneb.core.autoframe.interpolate_and_correct_frames
-   ocpneb.core.autoframe.get_shortest_path
-   ocpneb.core.autoframe.traverse_adsorbate_transfer
-   ocpneb.core.autoframe.traverse_adsorbate_dissociation
-   ocpneb.core.autoframe.traverse_adsorbate_desorption
-   ocpneb.core.autoframe.get_product2_idx
-   ocpneb.core.autoframe.traverse_adsorbate_general
-   ocpneb.core.autoframe.unwrap_atoms
-   ocpneb.core.autoframe.interpolate
-   ocpneb.core.autoframe.is_edge_list_respected
-   ocpneb.core.autoframe.reorder_edge_list
-   ocpneb.core.autoframe.is_adsorbate_adsorbed
+   cattsunami.core.autoframe.interpolate_and_correct_frames
+   cattsunami.core.autoframe.get_shortest_path
+   cattsunami.core.autoframe.traverse_adsorbate_transfer
+   cattsunami.core.autoframe.traverse_adsorbate_dissociation
+   cattsunami.core.autoframe.traverse_adsorbate_desorption
+   cattsunami.core.autoframe.get_product2_idx
+   cattsunami.core.autoframe.traverse_adsorbate_general
+   cattsunami.core.autoframe.unwrap_atoms
+   cattsunami.core.autoframe.interpolate
+   cattsunami.core.autoframe.is_edge_list_respected
+   cattsunami.core.autoframe.reorder_edge_list
+   cattsunami.core.autoframe.is_adsorbate_adsorbed
 
 
 
@@ -115,7 +115,7 @@ Functions
 
 
 
-.. py:class:: AutoFrameDissociation(reaction: ocpneb.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, r_product2_max: float = None, r_product2_min: float = None)
 
 
    Bases: :py:obj:`AutoFrame`
@@ -213,7 +213,7 @@ Functions
 
 
 
-.. py:class:: AutoFrameTransfer(reaction: ocpneb.core.Reaction, reactant1_systems: list, reactant2_systems: list, reactant1_energies: list, reactant2_energies: list, product1_systems: list, product1_energies: list, product2_systems: list, product2_energies: list, r_traverse_max: float, r_react_max: float, r_react_min: float)
+.. py:class:: AutoFrameTransfer(reaction: fairchem.applications.cattsunami.core.Reaction, reactant1_systems: list, reactant2_systems: list, reactant1_energies: list, reactant2_energies: list, product1_systems: list, product1_energies: list, product2_systems: list, product2_energies: list, r_traverse_max: float, r_react_max: float, r_react_min: float)
 
 
    Bases: :py:obj:`AutoFrame`
@@ -270,7 +270,7 @@ Functions
 
 
 
-.. py:class:: AutoFrameDesorption(reaction: ocpneb.core.Reaction, reactant_systems: list, reactant_energies: list, z_desorption: float)
+.. py:class:: AutoFrameDesorption(reaction: fairchem.applications.cattsunami.core.Reaction, reactant_systems: list, reactant_energies: list, z_desorption: float)
 
 
    Bases: :py:obj:`AutoFrame`
@@ -303,7 +303,7 @@ Functions
 
 
 
-.. py:function:: interpolate_and_correct_frames(initial: ase.Atoms, final: ase.Atoms, n_frames: int, reaction: ocpneb.core.Reaction, map_idx: int)
+.. py:function:: interpolate_and_correct_frames(initial: ase.Atoms, final: ase.Atoms, n_frames: int, reaction: fairchem.applications.cattsunami.core.Reaction, map_idx: int)
 
    Given the initial and final frames, perform the following:
    (1) Unwrap the final frame if it is wrapped around the cell
@@ -316,7 +316,7 @@ Functions
    :param n_frames: The desired number of frames for the NEB (not including initial and final)
    :type n_frames: int
    :param reaction: the reaction object which provides pertinent info
-   :type reaction: ocpneb.core.Reaction
+   :type reaction: Reaction
    :param map_idx: the index of the mapping to use for the final frame
    :type map_idx: int
 
@@ -338,15 +338,15 @@ Functions
    :rtype: (ase.Atoms)
 
 
-.. py:function:: traverse_adsorbate_transfer(reaction: ocpneb.core.Reaction, initial: ase.Atoms, final: ase.Atoms, initial_tiled: ase.Atoms, final_tiled: ase.Atoms, edge_list_final: list)
+.. py:function:: traverse_adsorbate_transfer(reaction: fairchem.applications.cattsunami.core.Reaction, initial: ase.Atoms, final: ase.Atoms, initial_tiled: ase.Atoms, final_tiled: ase.Atoms, edge_list_final: list)
 
    Traverse reactant 1, reactant 2, product 1 and product 2 in a depth first search of
    the bond graph. Unwrap the atoms to minimize the distance over the bonds. This ensures
    that when we perform the linear interpolation, the adsorbate moves as a single moity
    and avoids accidental bond breaking events over pbc.
 
    :param reaction: the reaction object which provides pertinent info
-   :type reaction: ocpneb.core.Reaction
+   :type reaction: Reaction
    :param initial: the initial frame of the NEB
    :type initial: ase.Atoms
    :param final: the proposed final frame of the NEB to be corrected
@@ -364,15 +364,15 @@ Functions
    :rtype: (ase.Atoms)
 
 
-.. py:function:: traverse_adsorbate_dissociation(reaction: ocpneb.core.Reaction, initial: ase.Atoms, final: ase.Atoms, initial_tiled: ase.Atoms, final_tiled: ase.Atoms, edge_list_final: int)
+.. py:function:: traverse_adsorbate_dissociation(reaction: fairchem.applications.cattsunami.core.Reaction, initial: ase.Atoms, final: ase.Atoms, initial_tiled: ase.Atoms, final_tiled: ase.Atoms, edge_list_final: int)
 
    Traverse reactant 1, product 1 and product 2 in a depth first search of
    the bond graph. Unwrap the atoms to minimize the distance over the bonds. This ensures
    that when we perform the linear interpolation, the adsorbate moves as a single moity
    and avoids accidental bond breaking events over pbc.
 
    :param reaction: the reaction object which provides pertinent info
-   :type reaction: ocpneb.core.Reaction
+   :type reaction: Reaction
    :param initial: the initial frame of the NEB
    :type initial: ase.Atoms
    :param final: the proposed final frame of the NEB to be corrected
@@ -390,15 +390,15 @@ Functions
    :rtype: (ase.Atoms)
 
 
-.. py:function:: traverse_adsorbate_desorption(reaction: ocpneb.core.Reaction, initial: ase.Atoms, final: ase.Atoms, initial_tiled: ase.Atoms, final_tiled: ase.Atoms)
+.. py:function:: traverse_adsorbate_desorption(reaction: fairchem.applications.cattsunami.core.Reaction, initial: ase.Atoms, final: ase.Atoms, initial_tiled: ase.Atoms, final_tiled: ase.Atoms)
 
    Traverse reactant 1 and  product 1 in a depth first search of
    the bond graph. Unwrap the atoms to minimize the distance over the bonds. This ensures
    that when we perform the linear interpolation, the adsorbate moves as a single moity
    and avoids accidental bond breaking events over pbc.
 
    :param reaction: the reaction object which provides pertinent info
-   :type reaction: ocpneb.core.Reaction
+   :type reaction: Reaction
    :param initial: the initial frame of the NEB
    :type initial: ase.Atoms
    :param final: the proposed final frame of the NEB to be corrected
@@ -416,14 +416,14 @@ Functions
    :rtype: (ase.Atoms)
 
 
-.. py:function:: get_product2_idx(reaction: ocpneb.core.Reaction, edge_list_final: list, traversal_rxt1_final: list)
+.. py:function:: get_product2_idx(reaction: fairchem.applications.cattsunami.core.Reaction, edge_list_final: list, traversal_rxt1_final: list)
 
    For dissociation only. Use the information about the initial edge list and final edge
    list to determine which atom in product 2 lost a bond in the reaction and use this
    as the binding index for traversal in `traverse_adsorbate_dissociation`.
 
    :param reaction: the reaction object which provides pertinent info
-   :type reaction: ocpneb.core.Reaction
+   :type reaction: Reaction
    :param edge_list_final: the edge list of the final frame corrected with mapping
                            idx changes
    :type edge_list_final: list
@@ -459,7 +459,7 @@ Functions
    :rtype: (ase.Atoms)
 
 
-.. py:function:: unwrap_atoms(initial: ase.Atoms, final: ase.Atoms, reaction: ocpneb.core.Reaction, map_idx: int)
+.. py:function:: unwrap_atoms(initial: ase.Atoms, final: ase.Atoms, reaction: fairchem.applications.cattsunami.core.Reaction, map_idx: int)
 
    Make corrections to the final frame so it is no longer wrapped around the cell,
    if it has jumpped over the pbc. Ensure that for each adsorbate moity, absolute bond distances
@@ -473,7 +473,7 @@ Functions
    :param final: the final atoms object to be corrected
    :type final: ase.Atoms
    :param reaction: the reaction object which provides pertinent info
-   :type reaction: ocpneb.core.Reaction
+   :type reaction: Reaction
    :param map_idx: the index of the mapping to use for the final frame
    :type map_idx: int
 

_sources/autoapi/ocpneb/core/index.rst → _sources/autoapi/cattsunami/core/index.rst

@@ -1,7 +1,7 @@
-:py:mod:`ocpneb.core`
-=====================
+:py:mod:`cattsunami.core`
+=========================
 
-.. py:module:: ocpneb.core
+.. py:module:: cattsunami.core
 
 
 Submodules
@@ -23,8 +23,8 @@ Classes
 
 .. autoapisummary::
 
-   ocpneb.core.Reaction
-   ocpneb.core.OCPNEB
+   cattsunami.core.Reaction
+   cattsunami.core.OCPNEB
 
 
 

_sources/autoapi/ocpneb/core/ocpneb/index.rst → _sources/autoapi/cattsunami/core/ocpneb/index.rst

@@ -1,7 +1,7 @@
-:py:mod:`ocpneb.core.ocpneb`
-============================
+:py:mod:`cattsunami.core.ocpneb`
+================================
 
-.. py:module:: ocpneb.core.ocpneb
+.. py:module:: cattsunami.core.ocpneb
 
 
 Module Contents
@@ -12,7 +12,7 @@ Classes
 
 .. autoapisummary::
 
-   ocpneb.core.ocpneb.OCPNEB
+   cattsunami.core.ocpneb.OCPNEB
 
 
 

_sources/autoapi/ocpneb/core/reaction/index.rst → _sources/autoapi/cattsunami/core/reaction/index.rst

@@ -1,7 +1,7 @@
-:py:mod:`ocpneb.core.reaction`
-==============================
+:py:mod:`cattsunami.core.reaction`
+==================================
 
-.. py:module:: ocpneb.core.reaction
+.. py:module:: cattsunami.core.reaction
 
 
 Module Contents
@@ -12,7 +12,7 @@ Classes
 
 .. autoapisummary::
 
-   ocpneb.core.reaction.Reaction
+   cattsunami.core.reaction.Reaction
 
 
 

_sources/autoapi/ocpneb/databases/index.rst → _sources/autoapi/cattsunami/databases/index.rst

@@ -1,7 +1,7 @@
-:py:mod:`ocpneb.databases`
-==========================
+:py:mod:`cattsunami.databases`
+==============================
 
-.. py:module:: ocpneb.databases
+.. py:module:: cattsunami.databases
 
 
 Package Contents

_sources/autoapi/cattsunami/index.rst

@@ -0,0 +1,16 @@
+:py:mod:`cattsunami`
+====================
+
+.. py:module:: cattsunami
+
+
+Subpackages
+-----------
+.. toctree::
+   :titlesonly:
+   :maxdepth: 3
+
+   core/index.rst
+   databases/index.rst
+
+

_sources/autoapi/ocpneb/run_validation/run_validation/index.rst → _sources/autoapi/cattsunami/run_validation/run_validation/index.rst

@@ -1,7 +1,7 @@
-:py:mod:`ocpneb.run_validation.run_validation`
-==============================================
+:py:mod:`cattsunami.run_validation.run_validation`
+==================================================
 
-.. py:module:: ocpneb.run_validation.run_validation
+.. py:module:: cattsunami.run_validation.run_validation
 
 .. autoapi-nested-parse::
 
@@ -19,15 +19,15 @@ Functions
 
 .. autoapisummary::
 
-   ocpneb.run_validation.run_validation.get_results_sp
-   ocpneb.run_validation.run_validation.get_results_ml
-   ocpneb.run_validation.run_validation.all_converged
-   ocpneb.run_validation.run_validation.both_barrierless
-   ocpneb.run_validation.run_validation.both_barriered
-   ocpneb.run_validation.run_validation.barrierless_converged
-   ocpneb.run_validation.run_validation.is_failed_sp
-   ocpneb.run_validation.run_validation.parse_neb_info
-   ocpneb.run_validation.run_validation.get_single_point
+   cattsunami.run_validation.run_validation.get_results_sp
+   cattsunami.run_validation.run_validation.get_results_ml
+   cattsunami.run_validation.run_validation.all_converged
+   cattsunami.run_validation.run_validation.both_barrierless
+   cattsunami.run_validation.run_validation.both_barriered
+   cattsunami.run_validation.run_validation.barrierless_converged
+   cattsunami.run_validation.run_validation.is_failed_sp
+   cattsunami.run_validation.run_validation.parse_neb_info
+   cattsunami.run_validation.run_validation.get_single_point
 
 
 
@@ -36,7 +36,7 @@ Attributes
 
 .. autoapisummary::
 
-   ocpneb.run_validation.run_validation.parser
+   cattsunami.run_validation.run_validation.parser
 
 
 .. py:function:: get_results_sp(df2: pandas.DataFrame)