Code

Ase dataset updates#622

Code

Merged

mshuaibii merged 71 commits intomainFAIR-Chem/fairchem:mainfrom ase_data_updatesFAIR-Chem/fairchem:ase_data_updatesCopy head branch name to clipboardApr 1, 2024

+604-644

Commits

Commits on Jan 17, 2024

• minor cleanup of lmbddatabase

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  committed
  826598f

Commits on Jan 18, 2024

• ase dataset compat for unified trainer and cleanup

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  324a645

• typo in docstring

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  6bb3b81

Commits on Jan 19, 2024

• key_mapping docstring

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  b4614c4

• add stress to atoms_to_graphs.py and test

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  d736b00

• allow adding target properties in atoms.info

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  0a17008

Commits on Jan 23, 2024

• test using generic tensor property in ase_datasets

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  3a7f810

• minor docstring/comments

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  f47a0b8

• handle stress in voigt notation in metadata guesser

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  c2a789e

Commits on Jan 24, 2024

• handle scalar generic values in a2g

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  47f4578

• clean up ase dataset unit tests

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  48dc7d0

Commits on Jan 25, 2024

• allow .aselmdb extensions

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  8549411

• fix minor bugs in lmdb database and update tests

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  3371cae

• make connect_db staticmethod

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  a0a2b2e

• remove redundant methods and make some private

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  237f000

Commits on Jan 26, 2024

• allow a list of paths in AseDBdataset

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  cae0765

• remove sprinkled print statement

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  dd0b5fc

Commits on Jan 29, 2024

• remove deprecated transform kwarg

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  303120a

• fix doctring typo

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  56df36d

• rename keys function

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  597e421

• fix missing comma in tests

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  11bd455

• set default r_edges in a2g in AseDatasets to false

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  07f2172

• simple unit-test for good measure

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  d99d383

Commits on Jan 31, 2024

• call _get_row directly

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  18fd2f1

Commits on Feb 1, 2024

• [wip] allow string sids

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  fd30b43

Commits on Feb 2, 2024

• raise a helpful error if AseAtomsAdaptor not available

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  77a40dd

Commits on Feb 9, 2024

• remove db extension in filepaths

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  c441734

Commits on Feb 16, 2024

• set logger to info level when trying to read non db files, remove print

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  5b13296

Commits on Feb 17, 2024

• set logging.debug to avoid saturating logs

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  242b54f

Commits on Feb 26, 2024

• Update documentation for dataset config changes

  Show description for 6c678f1
  emsunshine

  authored
  6c678f1

• Update atoms_to_graphs.py

  emsunshine

  authored
  fd4d3e8

• Update test_ase_datasets.py

  emsunshine

  authored
  61ffef3

• Update test_ase_datasets.py

  emsunshine

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  e3ea559

• Update test_atoms_to_graphs.py

  emsunshine

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  21ccf6a

• Update test_atoms_to_graphs.py

  emsunshine

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  b8a4c2f

• Merge branch 'main' into ase_data_updates

  lbluque

  authored
  d0cf20b

Commits on Feb 27, 2024

• case for explicit a2g_args None values

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  ec17ce8

• Merge remote-tracking branch 'origin/ase_data_updates' into ase_data_updates

  lbluque

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  8b3cfac

• Update update_config()

  emsunshine

  authored
  01863dd

• Update utils.py

  emsunshine

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  1c5ca26

• Update utils.py

  emsunshine

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  90a6f6e

• Update ocp_trainer.py

  Show description for 885deba
  emsunshine

  authored
  885deba

• Update ocp_trainer.py

  emsunshine

  authored
  0903f03

• Update ocp_trainer.py

  emsunshine

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  17ca6a9

• Update TRAIN.md

  emsunshine

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  c4ca1b0

• Merge branch 'main' into dataset-config-changes-documentation

  emsunshine

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  1fdc538

• fix concatenating predictions

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  ce52b2f

• check if keys exist in atoms.info

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  5741907

Commits on Feb 28, 2024

• Merge branch 'ase_data_updates' into dataset-config-changes-documentation

  emsunshine

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  7f7c0b4

• Update test_ase_datasets.py

  emsunshine

  authored
  068b053

Commits on Mar 5, 2024

• use list() to cast all batch.sid/fid

  lbluque

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  987ba9f

• Merge pull request #630 from Open-Catalyst-Project/dataset-config-changes-documentation

  Show description for 3b4ad43
  lbluque

  authored
  3b4ad43

Commits on Mar 6, 2024

• correctly stack predictions

  lbluque

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  7995b5e

Commits on Mar 12, 2024

• Merge branch 'main' into ase_data_updates

  lbluque

  authored
  3b6e2f9

Commits on Mar 19, 2024

• raise error on empty datasets

  lbluque

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  f0982bb

• raise ValueError instead of exception

  lbluque

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  56531d7

• code cleanup

  lbluque

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  b9e758d

• rename get_atoms object -> get_atoms for brevity

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  f6bb5d5

Commits on Mar 22, 2024

• merge upstream

  lbluque

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  cdc509a

• revert to raise keyerror when data_keys are missing

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  2f6ac22

• cast tensors to list using tolist and vstack relaxation pos

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  b426842

• remove r_energy, r_forces, r_stress and r_data_keys from test_dataset w use_train_settings

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  0709e46

Commits on Mar 23, 2024

• fix test_dataset key

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  310468d

• fix test_dataset key!

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  2422bb9

Commits on Mar 26, 2024

• revert to not setting a2g_args dataset keys

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  3f2f4bb

• fix debug predict logic

  mshuaibii

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  ac3c1c3

Commits on Mar 28, 2024

• support numpy 1.26

  mshuaibii

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  a4087a7

• fix numpy version

  mshuaibii

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  07ea92f

• revert write_pos

  mshuaibii

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  47f47e2

• no list casting on batch lists

  lbluque

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  ca9dbaf

Commits on Mar 29, 2024

• pretty logging

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  bdbba48