Bump sevenn from 0.9.3.post1 to 0.10.0

[dependabot]

Bumps sevenn from 0.9.3.post1 to 0.10.0.

Release notes

Sourced from sevenn's releases.

v0.10.0

[0.10.0]

SevenNet now has CI workflows and its python coverage is 78%! Substantial changes in command-line apps and their outputs. Previous functionalities are still accessible with correct flags (sevenn -m train_v1 ... , sevennet_graph_build --legacy ...)

Added

• sevenn_preset for below changes
• [train_v2]: train_v2, with lots of refactoring, support load_testset_path.
• [train_v2]: SevenNetGraphDataset replaces old AtomGrpahDataset, which extends InMemoryDataset of PyG.
• [train_v2]: sevenn_graph_build for SevenNetGraphDataset.
• [train_v2]: Any additional datasets will be evaluated and recorded if it is given as 'load_{NAME}set_path' key.
• Univ keyword for chemical_species
• More options: energy_key, force_key, stress_key for sevenn_graph_build, than ase.calculator @​thangckt
• OpenMPI distributed training @​thangckt

Changed

• Some cumbersome things(type_map, requires_grad ), that hurt readability, are now hidden inside AtomGraphSequential.
• 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.
• [train_v2]: Train valid split by ratio is temporarily removed
• Previous presets are renamed with _v1 suffix

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.

New Contributors

• @​thangckt made their first contribution in MDIL-SNU/SevenNet#89
• @​gasplant64 made their first contribution in MDIL-SNU/SevenNet#81
• @​pre-commit-ci made their first contribution in MDIL-SNU/SevenNet#101

Changelog

Sourced from sevenn's changelog.

[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)

... (truncated)

Commits

• 326a78d Merge pull request #106 from MDIL-SNU/dev
• 685b39d add: save num graphs to meta yaml in dataset
• f55bd44 fix: zero graph raise err
• 99c5631 fix: filter and transform for graph dataset
• d2ca235 Merge pull request #105 from MDIL-SNU/chem_list_input
• e0dde0c fix: list chem inputs
• b64d195 Merge pull request #101 from MDIL-SNU/pre-commit-ci-update-config
• 9b07335 Merge pull request #98 from MDIL-SNU/refactor
• 747153a [pre-commit.ci] auto fixes from pre-commit.com hooks
• 88534a4 Merge pull request #73 from Andrew-S-Rosen/patch-2
• Additional commits viewable in compare view

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