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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

[0.10.2]

Added

  • Accelerated graph build routine if matscipy is installed @hexagonerose

Changed

  • matscipy is included as dependency

[0.10.1]

Added

  • experimental SevenNetAtomsDataset which is memory efficient, can be enabled with dataset_type='atoms'
  • Save meta data & statistics when the SevenNetGraphDataset saves its data.

Changed

  • Save checkpoint_0.pth (model before any training)
  • SevenNetGraphDataset._file_to_graph_list -> SevenNetGraphDataset.file_to_graph_list
  • Refactoring SevenNetGraphDataset, skips computing statistics if it is loaded, more detailed logging
  • Prefer use .get when accessing config dict

Fixed

  • Fix error when loading SevenNetGraphDataset with other types of data (ex: extxyz) in one dataset

[0.10.0]

SevenNet now have CI workflows using pytest and its coverage is 78%! Substantial changes in cli apps and some outputs.

Added

  • [train_v2]: train_v2, with lots of refactoring + support load_testset_path. Original routine is accessible: sevenn -m train_v1.
  • [train_v2]: SevenNetGraphDataset replaces old AtomGrpahDataset, which extends InMemoryDataset of PyG.
  • [train_v2]: sevenn_graph_build for SevenNetGraphDataset. Previous .sevenn_data is accessible with --legacy option
  • [train_v2]: Any number of additional datasets will be evaluated and recorded if it is given as 'load_{NAME}set_path' key (input.yaml).
  • 'Univ' keyword for 'chemical_species'
  • energy_key, force_key, stress_key options for sevenn_graph_build, @thangckt
  • OpenMPI distributed training @thangckt

Changed

  • Read EFS of atoms from y_* keys of .info or .arrays dict, instead of caclculator results
  • Now type_map and requires_grad is hidden inside AtomGraphSequential, and don't need to care about it.
  • log.sevenn and lc.csv automatically find a safe filename (log0.sevenn, log1.sevenn, ...) to avoid overwriting.
  • [train_v2]: train_v2 loads its training set via load_trainset_path, rather than previous load_dataset_path.
  • [train_v2]: log.csv -> lc.csv, and columns have no units, (easier to postprocess with it) but still on log.sevenn.

Fixed

  • [e3gnn_serial]: can continue simulation even when atom tag becomes not consecutive (removing atom dynamically), @gasplant64
  • [e3gnn_parallel]: undefined behavior when there is no atoms to send/recv (for non pbc system)
  • [e3gnn_parallel]: incorrect force/stress in some edge cases (too small simulation cell & 2 process)
  • [e3gnn_parallel]: revert commit 14851ef, now e3gnn_parallel is sane.
  • [e3gnn_*]: += instead of = when saving virial stress and forces @gasplant64
  • Now Logger correctly closes a file.
  • ... and lots of small bugs I found during writing pytest.

[0.9.5]

Note

This version is not stable, but I tag it as v0.9.5 before making further changes. LAMMPS pair_e3gnn_parallel.* should be re-compiled for the below changes regarding LAMMPS parallel. This is the first changelog and may not reflect all the changes.

Added

  • Stress compute for LAMMPS sevennet parallel
  • sevenn_inference now takes .extxyz input
  • sevenn_inference gives MAE error
  • Experimental sevenn_inference on the fly graph build option

Changed

  • [Breaking] Parallel LAMMPS model changed, old deployed parallel models will not work
  • [Breaking] Parallel LAMMPS takes the directory of potentials as input. Accordingly, sevenn_get_model -p creates a folder with potentials.
  • [Breaking] Except for serial LAMMPS models, force and stress are computed from gradients of edge vectors, not positions.
  • Separate interaction block from model build
  • Add typing for most of functions
  • Remove clang pre-commit hook as it breaks lammps pair files
  • torch.load with weights_only=False
  • Line length limit 80 -> 85
  • Refactor

Fixed

  • Correct batch size for SevenNet-0(11July2024)

[0.9.4] - 2024-08-26

Added

  • D3 correction (contributed from dambi3613) for LAMMPS serial