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Graphs_integration#161

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EnricoTrizio wants to merge 245 commits intomainluigibonati/mlcolvar:mainfrom graphs_integrationluigibonati/mlcolvar:graphs_integrationCopy head branch name to clipboard

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Commits

Commits on May 9, 2024

• Added placeholders.

  jintuzhang

  committed
  8a582a1

• Changed importing styles.

  jintuzhang

  committed
  e3d3e78

• Added the neighbor list module.

  jintuzhang

  committed
  7d2b499

• Added more placeholders.

  jintuzhang

  committed
  a6fc30d

• Added doc.

  jintuzhang

  committed
  12a944b

• Fixed some styles.

  jintuzhang

  committed
  f07d4b5

• Added more placeholders.

  jintuzhang

  committed
  17ad4ae

• Added the graph data module.

  jintuzhang

  committed
  11d55bd

• Added doc and more tests.

  jintuzhang

  committed
  417bb85

• Minor fix.

  jintuzhang

  committed
  727561c

• Switched to new pyg grammar.

  jintuzhang

  committed
  8c6c3b2

• Modified file layouts.

  jintuzhang

  committed
  0c095c4

• Added more helper functions.

  jintuzhang

  committed
  6591511

• Added datamodule.

  jintuzhang

  committed
  96edcd0

• Added more functions.

  jintuzhang

  committed
  7f4b830

• Fixed some styles.

  jintuzhang

  committed
  8cb7218

• Added an alias to the dataset object.

  jintuzhang

  committed
  6c5e85c

• Resolved the circular dependency problem.

  jintuzhang

  committed
  3930be3

• Added missing type hints.

  jintuzhang

  committed
  0dc2e1d

• Modified file layouts.

  jintuzhang

  committed
  8ff7203

• Changed filenames.

  jintuzhang

  committed
  bb2edec

• Introduced the dataset class.

  jintuzhang

  committed
  a662346

• Added the IO function.

  jintuzhang

  committed
  9eaf323

• Added selection checks and changed tests.

  jintuzhang

  committed
  2beb7f3

• Updated __repr__.

  jintuzhang

  committed
  2c876d1

• Isolated nodes are not that bad.

  jintuzhang

  committed
  31975aa

• Added radial functions.

  jintuzhang

  committed
  b3b5420

• Modified file layouts.

  jintuzhang

  committed
  cab127d

• Added a dataset field to distinguish receivers.

  jintuzhang

  committed
  39846f3

• Added edge encoding function.

  jintuzhang

  committed
  4d85d66

• Modified file layouts.

  jintuzhang

  committed
  f8bfab6

• Fixed typos.

  jintuzhang

  committed
  27a79bc

• Fixed typos.

  jintuzhang

  committed
  c163ba2

• Added scatter functions.

  jintuzhang

  committed
  6b9deb5

• Minor fix.

  jintuzhang

  committed
  3cc1e36

• Updated torch tools.

  jintuzhang

  committed
  12f37dd

• Modified shapes of some dataset fields.

  jintuzhang

  committed
  167e608

• Added models.

  jintuzhang

  committed
  9a8867a

• Modified import schemes.

  jintuzhang

  committed
  debec0e

• Renamed a directory.

  jintuzhang

  committed
  6ed1c87

• Modified import schemes.

  jintuzhang

  committed
  0998a66

• Added a doc string.

  jintuzhang

  committed
  016c1e4

• Changed test function outputs.

  jintuzhang

  committed
  ca194f2

• Modified shapes of some dataset fields.

  jintuzhang

  committed
  31e0064

• Minor fix.

  jintuzhang

  committed
  4b04f18

• Added DeepTDA.

  jintuzhang

  committed
  00b3734

• Fixed lightning training.

  jintuzhang

  committed
  5b4550c

• Changed the default batch size.

  jintuzhang

  committed
  ef44fc6

• Removed nonlinearity in the readout function.

  jintuzhang

  committed
  07db17d

• Updated default parameters.

  jintuzhang

  committed
  9a5ad39

• Made everything compilable.

  Show description for 18c4c27
  jintuzhang

  committed
  18c4c27

• Change units to Angstrom.

  jintuzhang

  committed
  99afa6a

• Fixed cell size.

  jintuzhang

  committed
  98ac5b1

• Added more model attributes.

  jintuzhang

  committed
  927c55d

• Fixed for plumed interface.

  jintuzhang

  committed
  cda2b31

• Added tests

  jintuzhang

  committed
  6e50651

• Fixed dtype.

  jintuzhang

  committed
  c2b821a

• Modified default parameters.

  jintuzhang

  committed
  c81dd46

• Removed unused code.

  jintuzhang

  committed
  eeec208

• Added a dataset option.

  jintuzhang

  committed
  58845a8

• Added a progress bar.

  jintuzhang

  committed
  c1bf864

• Be quiet during testing.

  jintuzhang

  committed
  b5d986c

• Fixed spaces.

  jintuzhang

  committed
  3d27e1a

• Added a very basic readme.

  jintuzhang

  committed
  39afb95

• Fixed normal DeepTDA training.

  jintuzhang

  committed
  ec0b715

• Added utils.py back.

  jintuzhang

  committed
  c531e4e

Commits on May 13, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  76b82f6

Commits on May 17, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  80d647e

Commits on May 23, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  db06dd5

Commits on Jun 4, 2024

• Updated the dataset code.

  jintuzhang

  committed
  144674e

• Added comments.

  jintuzhang

  committed
  9e37a3b

• Added the metaphysics module.

  jintuzhang

  committed
  587b62c

• Allowed to index dataset with a range.

  jintuzhang

  committed
  f06c5f6

• Added components to the metaphysics module.

  jintuzhang

  committed
  a0653be

Commits on Jun 5, 2024

• Added more tests.

  jintuzhang

  committed
  a292a9f

• Changed import order.

  jintuzhang

  committed
  156e7d1

• Used batchs in analysis.

  jintuzhang

  committed
  db6aea7

• Removed extra keywords.

  jintuzhang

  committed
  6b5d273

Commits on Jun 6, 2024

• Sync directory layout from upstream.

  jintuzhang

  committed
  3ff8326

• Cleaned code.

  jintuzhang

  committed
  fd26ea9

• Fixed node indices in output.

  jintuzhang

  committed
  a330cc8

Commits on Jun 10, 2024

• Read n_out from model options.

  jintuzhang

  committed
  b5d4a2e

• Added dataset support for DeepTICA.

  jintuzhang

  committed
  4052466

Commits on Jun 11, 2024

• Make more parameter tests.

  jintuzhang

  committed
  dc6e132

• Added GraphDeepTICA.

  jintuzhang

  committed
  0b6ee02

• Changed data type.

  jintuzhang

  committed
  77c52b7

• Made GraphDeepTICA compilable.

  jintuzhang

  committed
  e6c9aa4

• Fixed for PLUMED.

  jintuzhang

  committed
  94937ad

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  d8d96fa

Commits on Jun 13, 2024

• Set default dtype.

  jintuzhang

  committed
  c501e8e

• Added tests.

  jintuzhang

  committed
  aea9d5a

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  01a9a5c

• Added a logo.

  jintuzhang

  committed
  bb5507f

• Centered logo.

  jintuzhang

  committed
  b1c6b29

• Centered logo.

  jintuzhang

  committed
  8b28254

• Centered logo.

  jintuzhang

  committed
  882d732

Commits on Jun 14, 2024

• Added a normalizing option.

  jintuzhang

  committed
  c84dd46

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  8470491

• Changed default parameter.

  jintuzhang

  committed
  e7a3d10

Commits on Jun 15, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  fa8ce5e

• Changed image width.

  jintuzhang

  committed
  764c3c4

Commits on Jun 16, 2024

• Also mask node features.

  jintuzhang

  committed
  62e0e23

Commits on Jul 1, 2024

• Added extra loss function options.

  jintuzhang

  committed
  6bfb902

Commits on Jul 5, 2024

• Fixed multiple CV sensitivity.

  jintuzhang

  committed
  e923576

Commits on Jul 7, 2024

• Modified default analysis method.

  jintuzhang

  committed
  fc5d692

Commits on Jul 8, 2024

• Fixed import

  jintuzhang

  committed
  1bfb626

Commits on Aug 5, 2024

• Added the Gaussian basis function.

  jintuzhang

  committed
  f602acb

• Fixed dim.

  jintuzhang

  committed
  2b207f1

• Changed some variable names to be compatible with old models.

  jintuzhang

  committed
  1cbc7f0

Commits on Aug 7, 2024

• Allowed to switch basis function types.

  jintuzhang

  committed
  a535a5f

Commits on Aug 12, 2024

• Added SchNet.

  jintuzhang

  committed
  0373b6c

• Fixed attributes.

  jintuzhang

  committed
  5158a10

Commits on Aug 13, 2024

• Fixed import.

  jintuzhang

  committed
  c2f6c92

• Updated one link.

  jintuzhang

  committed
  50b04a3

Commits on Aug 21, 2024

• Moved example inputs to the base class.

  jintuzhang

  committed
  5ae9707

• Removed unused imports.

  jintuzhang

  committed
  401523d

Commits on Aug 23, 2024

• Changed the behavior of building graphs.

  jintuzhang

  committed
  97d6097

Commits on Aug 24, 2024

• Fixed typo.

  jintuzhang

  committed
  93e9ca4

• Added a method to dump dataset.

  jintuzhang

  committed
  f79bdeb

Commits on Aug 26, 2024

• Made the dataset function more robust.

  jintuzhang

  committed
  58853c3

Commits on Aug 28, 2024

• Added buffer region support.

  jintuzhang

  committed
  1bb36d8

Commits on Sep 2, 2024

• Changed the default aggr operation.

  jintuzhang

  committed
  3e9b42c

Commits on Sep 3, 2024

• Only use system node features as CV values.

  jintuzhang

  committed
  205f5fe

• Fixed tests.

  jintuzhang

  committed
  c6aa16c

Commits on Sep 4, 2024

• Merge pull request #1 from jintuzhang/neighbor

  Show description for 8f745b8
  jintuzhang

  authored
  8f745b8

Commits on Sep 12, 2024

• Do not compile torch_scatter.

  jintuzhang

  committed
  21d807a

Commits on Sep 16, 2024

• Changed the behavior of create_label.

  jintuzhang

  committed
  c1b9418

• Added a mass function.

  jintuzhang

  committed
  b527107

Commits on Sep 24, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  da4bb0d

Commits on Sep 30, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  4293b6a

Commits on Oct 2, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  59e9fc2

Commits on Oct 9, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  d64f3d9

Commits on Nov 7, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  259d8fd

Commits on Nov 13, 2024

• Create graph module in nn

  EnricoTrizio

  committed
  a2c4a7a

• Added tda graph and tda merged as working examples

  EnricoTrizio

  committed
  c84f59d

• Moved graph.data into data.graph

  EnricoTrizio

  committed
  2e36371

• modified DictDataset to include metadata and handle graph data

  EnricoTrizio

  committed
  9d720f0

• First test to unify data hadling on ff and gnn

  EnricoTrizio

  committed
  674be27

• Moved graph.utils.io into main.utils.io

  EnricoTrizio

  committed
  c37eebf

• Moved progress bar utils to main.utils.plot

  EnricoTrizio

  committed
  064d3df

• added notebook and data for testing

  EnricoTrizio

  committed
  f467b24

Commits on Nov 14, 2024

• Fixed requirements and test env

  EnricoTrizio

  committed
  fb25800

• update example notebook

  EnricoTrizio

  committed
  e6bf404

• Moved matscipy to pip

  EnricoTrizio

  committed
  d50c12b

• Fixed metadata initialization

  EnricoTrizio

  committed
  af5d238

• added data type key to dict dataset and metadata

  EnricoTrizio

  committed
  911e213

• fixed typo

  EnricoTrizio

  committed
  c27f2aa

Commits on Nov 15, 2024

• Added utils to save and load datasets

  EnricoTrizio

  committed
  21a2103

• Grouped utils functions for graph datasets

  EnricoTrizio

  committed
  2f7995e

• Fixed typo

  EnricoTrizio

  committed
  d1e859d

• Fixed imports and first test

  EnricoTrizio

  committed
  85b5672

• Added test files for graphs

  EnricoTrizio

  committed
  48eb8bc

• Added first test

  EnricoTrizio

  committed
  8d41415

• Added test for io utils

  EnricoTrizio

  committed
  34d1703

• Merged datamodule for descritpors and graphs

  EnricoTrizio

  committed
  353b069

Commits on Nov 19, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  6883531

Commits on Nov 20, 2024

• first test scripting

  EnricoTrizio

  committed
  84bce7d

• Removed useless file

  EnricoTrizio

  committed
  a8f689d

• Fixed imports

  EnricoTrizio

  committed
  ddcded4

• Cleaned and fixed useless imports

  EnricoTrizio

  committed
  f0dfeb0

• Test changing layers to model

  EnricoTrizio

  committed
  5925c86

Commits on Nov 21, 2024

• Fixed typings

  EnricoTrizio

  committed
  4b39bc3

• First attmpt of committor.

  jintuzhang

  committed
  6c8d539

• Changed loss function expressions.

  jintuzhang

  committed
  9e2a1a1

• Added two model options.

  jintuzhang

  committed
  4b45a9d

• Fixed Kolmogorov bias.

  jintuzhang

  committed
  1382fc3

• Fixed output dim.

  jintuzhang

  committed
  dc4e1d4

• Fixed training.

  jintuzhang

  committed
  b3bcd6c

• Fixed deltaF bug.

  jintuzhang

  committed
  f11d1c4

• Added a loss term.

  jintuzhang

  committed
  4b4ebac

• Smooth GVP.

  jintuzhang

  committed
  0341bcf

• Added utils to create graph example input for tests

  EnricoTrizio

  committed
  cba40eb

Commits on Nov 22, 2024

• Intermediate test CV models

  EnricoTrizio

  committed
  67b96ee

Commits on Nov 25, 2024

• Fixed test

  EnricoTrizio

  committed
  5565118

Commits on Nov 26, 2024

• Merge branch 'luigibonati:main' into gnn

  jintuzhang

  authored
  6c0b72e

Commits on Nov 27, 2024

• Merge branch 'main' of https://github.com/luigibonati/mlcolvar into graphs_integration

  EnricoTrizio

  committed
  4940a98

Commits on Nov 28, 2024

• added out_features property

  EnricoTrizio

  committed
  1700a6b

Commits on Dec 3, 2024

• removed if_tracing and in_features, added setup and model_blocks

  EnricoTrizio

  committed
  1343836

• Improved test data utils with number of atoms

  EnricoTrizio

  committed
  52d3886

• Updated DeepTDA

  EnricoTrizio

  committed
  d3e7b89

• Updated DeepLDA

  EnricoTrizio

  committed
  a4f76c1

• Updated test notebook

  EnricoTrizio

  committed
  c47d7e3

• Added backward method

  EnricoTrizio

  committed
  b072ec6

• removed out_features keyword

  EnricoTrizio

  committed
  0debbcc

• simplified training_step

  EnricoTrizio

  committed
  fe63894

• Added random weights keyword

  EnricoTrizio

  committed
  5338da9

• Updated regression CV

  EnricoTrizio

  committed
  41eba20

• Update autoencoder-based CVs

  EnricoTrizio

  committed
  dfee8ea

• Added more general slicing of datasets

  EnricoTrizio

  committed
  1c657e8

• Fixe dataset representation

  EnricoTrizio

  committed
  3ad1692

• First timelagged utils for graphs

  EnricoTrizio

  committed
  781015a

Commits on Dec 4, 2024

• Fixed __getitem__

  EnricoTrizio

  committed
  919aa9b

• Added optional key

  EnricoTrizio

  committed
  94c40ef

Commits on Dec 5, 2024

• Make timelagged utils work with graphs

  EnricoTrizio

  committed
  0dd0d05

• updated deepTICA

  EnricoTrizio

  committed
  3a1c0f1

• Fixed formats

  EnricoTrizio

  committed
  fd2a0f9

• Fixed typo

  EnricoTrizio

  committed
  a766446

• Renabled original test with new signature of BaseCV

  EnricoTrizio

  committed
  53a52ef

• Added not implemented error for GNN-based

  EnricoTrizio

  committed
  adadd41

• Merge branch 'gnn' of https://github.com/jintuzhang/mlcolvar into graphs_integration

  EnricoTrizio

  committed
  dc650a3

• Added two model options, see also commit 4b45a9d

  EnricoTrizio

  committed
  4f89aa8

• Added two model options

  EnricoTrizio

  committed
  d27fa01

• Fixed model check

  EnricoTrizio

  committed
  8797481

Commits on Dec 6, 2024

• First tests committor

  EnricoTrizio

  committed
  031aa7f

Commits on Dec 9, 2024

• Updated layers key to model in notebooks

  EnricoTrizio

  committed
  409da50

• Udate layers key to model in tests

  EnricoTrizio

  committed
  bb94a9a

• Fixed checkpointing AE based CVs

  EnricoTrizio

  committed
  1fe47a3

• Update notebook tda

  EnricoTrizio

  committed
  f263791

Commits on Dec 10, 2024

• Fixed json notebook

  EnricoTrizio

  committed
  56ad2a9

• Added np.ndarray to typings

  EnricoTrizio

  committed
  cfdc531

• Fixed index of mask for separate datasets

  EnricoTrizio

  committed
  73745d2

• Temporary fix with new signature of BaseCV

  EnricoTrizio

  committed
  72e1804

Commits on Dec 11, 2024

• modified scratch notebooks

  EnricoTrizio

  committed
  d8a1ddd

• Fixed batch elements

  EnricoTrizio

  committed
  87484a0

• Added GVP model

  EnricoTrizio

  committed
  2f95b3e

• Added GVP model

  EnricoTrizio

  committed
  29b1481

• Added basic tests for gnn models

  EnricoTrizio

  committed
  9396c9a

• Fixed imports

  EnricoTrizio

  committed
  0fa5296

• Removed already ported code

  EnricoTrizio

  committed
  74045e8

• Condensed variational mask defintion

  EnricoTrizio

  committed
  d902665

• added in_features and removed model type

  EnricoTrizio

  committed
  d5671ea

• Simplified model parsing

  EnricoTrizio

  committed
  8b21a15

Commits on Dec 12, 2024

• Restore default dtype after test

  EnricoTrizio

  committed
  b105989

• Improved streamline and tests

  EnricoTrizio

  committed
  468a746

• Added tests

  EnricoTrizio

  committed
  de43be1

• fixed save dataset

  EnricoTrizio

  committed
  7c2ea79

• Update testing notebook

  EnricoTrizio

  committed
  d28d9b8

• Removed already ported files

  EnricoTrizio

  committed
  73c100e

• Fixed test

  EnricoTrizio

  committed
  285db63

Commits on Dec 13, 2024

• Fixed test

  EnricoTrizio

  committed
  a834b9e

• Added load_args

  EnricoTrizio

  committed
  ec91fbb

• Updated committor weights

  EnricoTrizio

  committed
  2a6bd06

• Removed ported files

  EnricoTrizio

  committed
  16392d8

• Added log var

  EnricoTrizio

  committed
  1971070

• Improved test coverage

  EnricoTrizio

  committed
  2bd81f6

Commits on Dec 16, 2024

• Improved tests

  EnricoTrizio

  committed
  3311f3f

• Removed already ported files

  EnricoTrizio

  committed
  e9dca7d

• Imporved tests

  EnricoTrizio

  committed
  290034f

• Fixed typo

  EnricoTrizio

  committed
  a08d9a7

Commits on Dec 20, 2024

• Added atom names and indexing to dataset

  EnricoTrizio

  committed
  06167b1

• Added graph node sensitivity

  EnricoTrizio

  committed
  f4569a6

• Fixed typo

  EnricoTrizio

  committed
  1306f61

• Added z and z_reg to commmittor loss

  EnricoTrizio

  committed
  55d07b5

Commits on Dec 23, 2024

• FIxed default atom names with env

  EnricoTrizio

  committed
  e59d038

• Fixed committor forward

  EnricoTrizio

  committed
  e6d90f8