diff --git a/.coderabbit b/.coderabbit new file mode 100644 index 00000000..59ad8ee9 --- /dev/null +++ b/.coderabbit @@ -0,0 +1,5 @@ +reviews: + high_level_summary: false + auto_review: + enabled: false + drafts: false diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 03afc521..7aeabd47 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -58,7 +58,7 @@ jobs: path: ./docs_build deploy: - if: github.repository_owner == 'Radical-AI' && github.ref == 'refs/heads/main' + if: github.repository_owner == 'TorchSim' && github.ref == 'refs/heads/main' environment: name: github-pages url: ${{ steps.deployment.outputs.page_url }} diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a133410..12046fe2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,89 +6,89 @@ ### ๐Ÿ’ฅ Breaking Changes -* Remove higher level model imports by @CompRhys in https://github.com/Radical-AI/torch-sim/pull/179 +* Remove higher level model imports by @CompRhys in https://github.com/TorchSim/torch-sim/pull/179 ### ๐Ÿ›  Enhancements -* Add per atom energies and stresses for batched LJ by @abhijeetgangan in https://github.com/Radical-AI/torch-sim/pull/144 -* throw error if autobatcher type is wrong by @orionarcher in https://github.com/Radical-AI/torch-sim/pull/167 +* Add per atom energies and stresses for batched LJ by @abhijeetgangan in https://github.com/TorchSim/torch-sim/pull/144 +* throw error if autobatcher type is wrong by @orionarcher in https://github.com/TorchSim/torch-sim/pull/167 ### ๐Ÿ› Bug Fixes -* Fix column->row cell vector mismatch in integrators by @CompRhys in https://github.com/Radical-AI/torch-sim/pull/175 -* Mattersim fix tensors on wrong device (CPU->GPU) by @orionarcher in https://github.com/Radical-AI/torch-sim/pull/154 -* fix `npt_langevin` by @jla-gardner in https://github.com/Radical-AI/torch-sim/pull/153 -* Make sure to move data to CPU before calling vesin by @Luthaf in https://github.com/Radical-AI/torch-sim/pull/156 -* Fix virial calculations in `optimizers` and `integrators` by @janosh in https://github.com/Radical-AI/torch-sim/pull/163 -* Pad memory estimation by @orionarcher in https://github.com/Radical-AI/torch-sim/pull/160 -* Refactor sevennet model by @YutackPark in https://github.com/Radical-AI/torch-sim/pull/172 -* `io` optional dependencies in `pyproject.toml` by @curtischong in https://github.com/Radical-AI/torch-sim/pull/185 +* Fix column->row cell vector mismatch in integrators by @CompRhys in https://github.com/TorchSim/torch-sim/pull/175 +* Mattersim fix tensors on wrong device (CPU->GPU) by @orionarcher in https://github.com/TorchSim/torch-sim/pull/154 +* fix `npt_langevin` by @jla-gardner in https://github.com/TorchSim/torch-sim/pull/153 +* Make sure to move data to CPU before calling vesin by @Luthaf in https://github.com/TorchSim/torch-sim/pull/156 +* Fix virial calculations in `optimizers` and `integrators` by @janosh in https://github.com/TorchSim/torch-sim/pull/163 +* Pad memory estimation by @orionarcher in https://github.com/TorchSim/torch-sim/pull/160 +* Refactor sevennet model by @YutackPark in https://github.com/TorchSim/torch-sim/pull/172 +* `io` optional dependencies in `pyproject.toml` by @curtischong in https://github.com/TorchSim/torch-sim/pull/185 ### ๐Ÿ“– Documentation -* (tiny) add graph-pes to README by @jla-gardner in https://github.com/Radical-AI/torch-sim/pull/149 -* Better module fig by @janosh in https://github.com/Radical-AI/torch-sim/pull/168 +* (tiny) add graph-pes to README by @jla-gardner in https://github.com/TorchSim/torch-sim/pull/149 +* Better module fig by @janosh in https://github.com/TorchSim/torch-sim/pull/168 ### ๐Ÿš€ Performance -* More efficient Orb `state_to_atoms_graph` calculation by @AdeeshKolluru in https://github.com/Radical-AI/torch-sim/pull/165 +* More efficient Orb `state_to_atoms_graph` calculation by @AdeeshKolluru in https://github.com/TorchSim/torch-sim/pull/165 ### ๐Ÿšง CI -* Refactor `test_math.py` and `test_transforms.py` by @janosh in https://github.com/Radical-AI/torch-sim/pull/151 +* Refactor `test_math.py` and `test_transforms.py` by @janosh in https://github.com/TorchSim/torch-sim/pull/151 ### ๐Ÿฅ Package Health -* Try out hatchling for build vs setuptools by @CompRhys in https://github.com/Radical-AI/torch-sim/pull/177 +* Try out hatchling for build vs setuptools by @CompRhys in https://github.com/TorchSim/torch-sim/pull/177 ### ๐Ÿท๏ธ Type Hints -* Add `torch_sim/typing.py` by @janosh in https://github.com/Radical-AI/torch-sim/pull/157 +* Add `torch_sim/typing.py` by @janosh in https://github.com/TorchSim/torch-sim/pull/157 ### ๐Ÿ“ฆ Dependencies -* Bump `mace-torch` to v0.3.12 by @janosh in https://github.com/Radical-AI/torch-sim/pull/170 -* Update metatrain dependency by @Luthaf in https://github.com/Radical-AI/torch-sim/pull/186 +* Bump `mace-torch` to v0.3.12 by @janosh in https://github.com/TorchSim/torch-sim/pull/170 +* Update metatrain dependency by @Luthaf in https://github.com/TorchSim/torch-sim/pull/186 ## New Contributors -* @Luthaf made their first contribution in https://github.com/Radical-AI/torch-sim/pull/156 -* @YutackPark made their first contribution in https://github.com/Radical-AI/torch-sim/pull/172 -* @curtischong made their first contribution in https://github.com/Radical-AI/torch-sim/pull/185 +* @Luthaf made their first contribution in https://github.com/TorchSim/torch-sim/pull/156 +* @YutackPark made their first contribution in https://github.com/TorchSim/torch-sim/pull/172 +* @curtischong made their first contribution in https://github.com/TorchSim/torch-sim/pull/185 -**Full Changelog**: https://github.com/Radical-AI/torch-sim/compare/v0.2.0...v0.2.1 +**Full Changelog**: https://github.com/TorchSim/torch-sim/compare/v0.2.0...v0.2.1 ## v0.2.0 ### Bug Fixes ๐Ÿ› -* Fix integrate reporting kwarg to arg error, https://github.com/Radical-AI/torch-sim/issues/113 (raised by @hn-yu) -* Allow runners to take large initial batches, https://github.com/Radical-AI/torch-sim/issues/128 (raised by @YutackPark) -* Add Fairchem model support for PBC, https://github.com/Radical-AI/torch-sim/issues/111 (raised by @ryanliu30) +* Fix integrate reporting kwarg to arg error, https://github.com/TorchSim/torch-sim/issues/113 (raised by @hn-yu) +* Allow runners to take large initial batches, https://github.com/TorchSim/torch-sim/issues/128 (raised by @YutackPark) +* Add Fairchem model support for PBC, https://github.com/TorchSim/torch-sim/issues/111 (raised by @ryanliu30) ### Enhancements ๐Ÿ›  -* **breaking** Rename `HotSwappingAutobatcher` to `InFlightAutobatcher` and `ChunkingAutoBatcher` to `BinningAutoBatcher`, https://github.com/Radical-AI/torch-sim/pull/143 @orionarcher -* Support for Orbv3, https://github.com/Radical-AI/torch-sim/pull/140, @AdeeshKolluru -* Support metatensor models, https://github.com/Radical-AI/torch-sim/pull/141, @frostedoyter @Luthaf -* Support for graph-pes models, https://github.com/Radical-AI/torch-sim/pull/118 @jla-gardner -* Support MatterSim and fix ASE cell convention issues, https://github.com/Radical-AI/torch-sim/pull/112 @CompRhys -* Implement positions only FIRE optimization, https://github.com/Radical-AI/torch-sim/pull/139 @abhijeetgangan -* Allow different temperatures in batches, https://github.com/Radical-AI/torch-sim/pull/123 @orionarcher -* FairChem model updates: PBC handling, test on OMat24 e-trained model, https://github.com/Radical-AI/torch-sim/pull/126 @AdeeshKolluru -* FairChem model from_data_list support, https://github.com/Radical-AI/torch-sim/pull/138 @ryanliu30 -* New correlation function module, https://github.com/Radical-AI/torch-sim/pull/115 @stefanbringuier +* **breaking** Rename `HotSwappingAutobatcher` to `InFlightAutobatcher` and `ChunkingAutoBatcher` to `BinningAutoBatcher`, https://github.com/TorchSim/torch-sim/pull/143 @orionarcher +* Support for Orbv3, https://github.com/TorchSim/torch-sim/pull/140, @AdeeshKolluru +* Support metatensor models, https://github.com/TorchSim/torch-sim/pull/141, @frostedoyter @Luthaf +* Support for graph-pes models, https://github.com/TorchSim/torch-sim/pull/118 @jla-gardner +* Support MatterSim and fix ASE cell convention issues, https://github.com/TorchSim/torch-sim/pull/112 @CompRhys +* Implement positions only FIRE optimization, https://github.com/TorchSim/torch-sim/pull/139 @abhijeetgangan +* Allow different temperatures in batches, https://github.com/TorchSim/torch-sim/pull/123 @orionarcher +* FairChem model updates: PBC handling, test on OMat24 e-trained model, https://github.com/TorchSim/torch-sim/pull/126 @AdeeshKolluru +* FairChem model from_data_list support, https://github.com/TorchSim/torch-sim/pull/138 @ryanliu30 +* New correlation function module, https://github.com/TorchSim/torch-sim/pull/115 @stefanbringuier ### Documentation ๐Ÿ“– -* Improved model documentation, https://github.com/Radical-AI/torch-sim/pull/121 @orionarcher -* Plot of TorchSim module graph in docs, https://github.com/Radical-AI/torch-sim/pull/132 @janosh +* Improved model documentation, https://github.com/TorchSim/torch-sim/pull/121 @orionarcher +* Plot of TorchSim module graph in docs, https://github.com/TorchSim/torch-sim/pull/132 @janosh ### House-Keeping ๐Ÿงน -* Only install HF for fairchem tests, https://github.com/Radical-AI/torch-sim/pull/134 @CompRhys -* Don't download MBD in CI, https://github.com/Radical-AI/torch-sim/pull/135 @orionarcher -* Tighten graph-pes test bounds, https://github.com/Radical-AI/torch-sim/pull/143 @orionarcher +* Only install HF for fairchem tests, https://github.com/TorchSim/torch-sim/pull/134 @CompRhys +* Don't download MBD in CI, https://github.com/TorchSim/torch-sim/pull/135 @orionarcher +* Tighten graph-pes test bounds, https://github.com/TorchSim/torch-sim/pull/143 @orionarcher ## v0.1.0 diff --git a/README.md b/README.md index c48c8058..b41511a4 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # TorchSim -[![CI](https://github.com/radical-ai/torch-sim/actions/workflows/test.yml/badge.svg)](https://github.com/radical-ai/torch-sim/actions/workflows/test.yml) +[![CI](https://github.com/TorchSim/torch-sim/actions/workflows/test.yml/badge.svg)](https://github.com/TorchSim/torch-sim/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/radical-ai/torch-sim/branch/main/graph/badge.svg)](https://codecov.io/gh/radical-ai/torch-sim) [![This project supports Python 3.11+](https://img.shields.io/badge/Python-3.11+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads) [![PyPI](https://img.shields.io/pypi/v/torch_sim_atomistic?logo=pypi&logoColor=white)](https://pypi.org/project/torch_sim_atomistic) @@ -113,7 +113,7 @@ pip install torch-sim-atomistic ### Installing from source ```sh -git clone https://github.com/radical-ai/torch-sim +git clone https://github.com/TorchSim/torch-sim cd torch-sim pip install . ``` diff --git a/citation.cff b/citation.cff index 79eb7956..16faa6b7 100644 --- a/citation.cff +++ b/citation.cff @@ -15,8 +15,8 @@ authors: - family-names: Falletta given-names: Stefano license: MIT -license-url: https://github.com/Radical-AI/torch-sim/blob/main/LICENSE -repository-code: https://github.com/Radical-AI/torch-sim -url: https://github.com/Radical-AI/torch-sim +license-url: https://github.com/TorchSim/torch-sim/blob/main/LICENSE +repository-code: https://github.com/TorchSim/torch-sim +url: https://github.com/TorchSim/torch-sim type: software date-released: 2025-04-02 diff --git a/docs/conf.py b/docs/conf.py index 34e59dd5..d127c771 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -156,7 +156,7 @@ "footer_icons": [ { "name": "GitHub", - "url": "https://github.com/Radical-AI/torch-sim", + "url": "https://github.com/TorchSim/torch-sim", "html": """ @@ -165,7 +165,7 @@ "class": "", }, ], - "source_repository": "https://github.com/Radical-AI/torch-sim/", + "source_repository": "https://github.com/TorchSim/torch-sim/", "source_branch": "main", "source_directory": "docs/", } diff --git a/docs/dev/add_model.md b/docs/dev/add_model.md index 6967f979..3b5c9052 100644 --- a/docs/dev/add_model.md +++ b/docs/dev/add_model.md @@ -5,7 +5,7 @@ We welcome the addition of new models to `torch_sim`. We want easy batched simulations to be available to the whole community of MLIP developers and users. -See https://github.com/Radical-AI/torch-sim/discussions/120 for +See https://github.com/TorchSim/torch-sim/discussions/120 for our current posture on adding models to TorchSim. 1. Open a PR or an issue to get feedback. We are happy to take a look, diff --git a/docs/dev/dev_install.md b/docs/dev/dev_install.md index 363c920f..273bbb61 100644 --- a/docs/dev/dev_install.md +++ b/docs/dev/dev_install.md @@ -12,10 +12,10 @@ pip install torch-sim-atomistic ## Install from source -To install torch-sim from source, clone the repository from [github](https://github.com/Radical-AI/torch-sim) +To install torch-sim from source, clone the repository from [github](https://github.com/TorchSim/torch-sim) ```bash -git clone https://github.com/Radical-AI/torch-sim +git clone https://github.com/TorchSim/torch-sim cd torch-sim pip install . -e ``` diff --git a/docs/index.md b/docs/index.md index eede93c5..a7dc91d9 100644 --- a/docs/index.md +++ b/docs/index.md @@ -4,7 +4,6 @@ :hidden: user/introduction user/overview -user/models tutorials/index ``` @@ -19,7 +18,6 @@ reference/index :hidden: dev/dev_install dev/add_model -dev/batching ``` ```{toctree} @@ -35,8 +33,8 @@ about/license **Date**: {sub-ref}`today` **Useful links**: -[Source Repository](https://github.com/Radical-AI/torch-sim) | -[Issues & Ideas](https://github.com/Radical-AI/torch-sim/issues) +[Source Repository](https://github.com/TorchSim/torch-sim) | +[Issues & Ideas](https://github.com/TorchSim/torch-sim/issues) TorchSim is a next-generation open-source atomistic simulation engine for the MLIP era. diff --git a/docs/tutorials/index.rst b/docs/tutorials/index.rst index 8dad9bc2..fd3ca21c 100644 --- a/docs/tutorials/index.rst +++ b/docs/tutorials/index.rst @@ -5,7 +5,7 @@ Tutorials For a high-level overview of the tutorials see :doc:`../user/overview`. Runnable versions of the tutorials can also be found in the `torch-sim /examples/tutorials -`_ directory. +`_ directory. .. currentmodule:: torch_sim diff --git a/examples/readme.md b/examples/readme.md index e22f3ad1..f799f48f 100644 --- a/examples/readme.md +++ b/examples/readme.md @@ -3,7 +3,7 @@ Examples are provided in two foms: * Tutorials are intended to provide pedagogical walkthroughs of TorchSim's core functionality -* Scripts are a holdover from early torch-sim development, they are not currently recommended as a learning resource. See issue [issue 109](https://github.com/Radical-AI/torch-sim/issues/109). +* Scripts are a holdover from early torch-sim development, they are not currently recommended as a learning resource. See issue [issue 109](https://github.com/TorchSim/torch-sim/issues/109). ## Tutorial Formatting diff --git a/pyproject.toml b/pyproject.toml index 77867d4e..8667285d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,8 +32,7 @@ dependencies = [ "tables>=3.10.2", "torch>=2", "tqdm>=4.67", - "vesin-torch>=0.3.7", - "vesin>=0.3.7", + "vesin[torch]>=0.3.7", ] [project.optional-dependencies] @@ -61,14 +60,14 @@ docs = [ "jupytext==1.16.7", "myst_parser==4.0.0", "nbsphinx>=0.9.7", - "numpydoc==1.8.0", + "numpydoc==1.6.0", "sphinx-copybutton==0.5.2", - "sphinx==8.1.3", + "sphinx==7.2.6", "sphinx_design==0.6.1", ] [project.urls] -Repo = "https://github.com/radical-ai/torch-sim" +Repo = "https://github.com/TorchSim/torch-sim" [build-system] requires = ["uv_build>=0.7.12"] diff --git a/tests/test_autobatching.py b/tests/test_autobatching.py index 4bce4165..81d90472 100644 --- a/tests/test_autobatching.py +++ b/tests/test_autobatching.py @@ -453,7 +453,7 @@ def test_in_flight_auto_batcher_restore_order( [ 5, # At 5 steps, not every state will converge before the next batch. # This tests the merging of partially converged states with new states - # which has been a bug in the past. See https://github.com/Radical-AI/torch-sim/pull/219 + # which has been a bug in the past. See https://github.com/TorchSim/torch-sim/pull/219 10, # At 10 steps, all states will converge before the next batch ], ) diff --git a/tests/test_integrators.py b/tests/test_integrators.py index d5b210d1..67621a5b 100644 --- a/tests/test_integrators.py +++ b/tests/test_integrators.py @@ -335,7 +335,7 @@ def test_compare_single_vs_batched_integrators( ) -> None: """Test NVE single vs batched for a tilted cell to verify PBC wrapping. - NOTE: added triclinic cell after https://github.com/Radical-AI/torch-sim/issues/171. + NOTE: added triclinic cell after https://github.com/TorchSim/torch-sim/issues/171. Although the addition doesn't fail if we do not add the changes suggested in issue. """ sim_state = request.getfixturevalue(sim_state_fixture_name) @@ -383,7 +383,7 @@ def test_compare_single_vs_batched_integrators( def test_compute_cell_force_atoms_per_system(): """Test that compute_cell_force correctly scales by number of atoms per system. - Covers fix in https://github.com/Radical-AI/torch-sim/pull/153.""" + Covers fix in https://github.com/TorchSim/torch-sim/pull/153.""" from torch_sim.integrators.npt import _compute_cell_force # Setup minimal state with two systems having 8:1 atom ratio diff --git a/torch_sim/autobatching.py b/torch_sim/autobatching.py index a691de36..83c341bf 100644 --- a/torch_sim/autobatching.py +++ b/torch_sim/autobatching.py @@ -591,18 +591,20 @@ def next_batch( where indices are the original positions of the states, or None if no more batches. - Example:: + Examples: + Get batches one by one: - # Get batches one by one - all_converged_state, convergence = [], None - while (result := batcher.next_batch(state, convergence))[0] is not None: - state, converged_states = result - all_converged_states.extend(converged_states) + .. code-block:: python - evolve_batch(state) - convergence = convergence_criterion(state) - else: - all_converged_states.extend(result[1]) + all_converged_state, convergence = [], None + while (result := batcher.next_batch(state, convergence))[0] is not None: + state, converged_states = result + all_converged_states.extend(converged_states) + + evolve_batch(state) + convergence = convergence_criterion(state) + else: + all_converged_states.extend(result[1]) """ # TODO: need to think about how this intersects with reporting too @@ -989,17 +991,20 @@ def next_batch( # noqa: C901 AssertionError: If convergence_tensor doesn't match the expected shape or if other validation checks fail. - Example:: + Examples: + Process states with convergence checking: - # Initial call - batch, completed = batcher.next_batch(None, None) + .. code-block:: python - # Process batch and check for convergence - batch = process_batch(batch) - convergence = check_convergence(batch) + # Initial call + batch, completed = batcher.next_batch(None, None) + + # Process batch and check for convergence + batch = process_batch(batch) + convergence = check_convergence(batch) - # Get next batch with converged states removed and new states added - batch, completed = batcher.next_batch(batch, convergence) + # Get next batch with converged states removed and new states added + batch, completed = batcher.next_batch(batch, convergence) Notes: When max_iterations is set, states that exceed this limit will be diff --git a/torch_sim/elastic.py b/torch_sim/elastic.py index a067e03d..6c8a740d 100644 --- a/torch_sim/elastic.py +++ b/torch_sim/elastic.py @@ -15,8 +15,8 @@ Physical Review B, 90(22), 224104 Online Resources: -- Materials Project Documentation - https://docs.materialsproject.org/methodology/elasticity/ + +- Materials Project Documentation: https://docs.materialsproject.org/methodology/elasticity/ """ from collections.abc import Callable @@ -551,13 +551,13 @@ def triclinic_symmetry(strains: torch.Tensor) -> torch.Tensor: Returns: torch.Tensor: Matrix of shape (6, 21) where columns correspond to - all possible elastic constants in order: - [C11, C12, C13, C14, C15, C16, - C22, C23, C24, C25, C26, - C33, C34, C35, C36, - C44, C45, C46, - C55, C56, - C66] + all possible elastic constants in order: + [C11, C12, C13, C14, C15, C16, + C22, C23, C24, C25, C26, + C33, C34, C35, C36, + C44, C45, C46, + C55, C56, + C66] """ if not isinstance(strains, torch.Tensor): strains = torch.tensor(strains) diff --git a/torch_sim/integrators/npt.py b/torch_sim/integrators/npt.py index f5f23c5c..e7d42844 100644 --- a/torch_sim/integrators/npt.py +++ b/torch_sim/integrators/npt.py @@ -85,7 +85,7 @@ def momenta(self) -> torch.Tensor: return self.velocities * self.masses.unsqueeze(-1) -# Extracted out from npt_langevin body to test fix in https://github.com/Radical-AI/torch-sim/pull/153 +# Extracted out from npt_langevin body to test fix in https://github.com/TorchSim/torch-sim/pull/153 def _compute_cell_force( state: NPTLangevinState, external_pressure: torch.Tensor, diff --git a/torch_sim/math.py b/torch_sim/math.py index ab1e9fa0..7b4596f7 100644 --- a/torch_sim/math.py +++ b/torch_sim/math.py @@ -79,9 +79,10 @@ def expm_frechet_with_matrix_exp( # noqa: C901 infinities or NaNs. Defaults to True. Returns: - expm_A: torch.Tensor. Matrix exponential of A. - expm_frechet_AE: torch.Tensor. Frechet derivative of the matrix exponential of A - in the direction E. + tuple[torch.Tensor, torch.Tensor]: A tuple containing: + - expm_A: Matrix exponential of A + - expm_frechet_AE: Frechet derivative of the matrix exponential of A + in the direction E """ # Convert inputs to torch tensors if they aren't already if not isinstance(A, torch.Tensor): @@ -125,9 +126,10 @@ def expm_frechet_block_enlarge( E: Direction matrix Returns: - expm_A: Matrix exponential of A - expm_frechet_AE: Frechet derivative of the matrix exponential of A - in the direction E. + tuple[torch.Tensor, torch.Tensor]: A tuple containing: + - expm_A: Matrix exponential of A + - expm_frechet_AE: Frechet derivative of the matrix exponential of A + in the direction E. """ n = A.shape[0] # Create block matrix M = [[A, E], [0, A]] diff --git a/torch_sim/models/orb.py b/torch_sim/models/orb.py index fd65b23f..acc6f4a1 100644 --- a/torch_sim/models/orb.py +++ b/torch_sim/models/orb.py @@ -387,7 +387,7 @@ def forward(self, state: ts.SimState | StateDict) -> dict[str, torch.Tensor]: state = state.to(self._device) half_supercell = ( - torch.max(torch.det(state.cell)) > 1000 + torch.min(torch.det(state.cell)) > 1000 if self._half_supercell is None else self._half_supercell ) diff --git a/torch_sim/models/soft_sphere.py b/torch_sim/models/soft_sphere.py index 75598aaf..e97c9046 100644 --- a/torch_sim/models/soft_sphere.py +++ b/torch_sim/models/soft_sphere.py @@ -713,7 +713,7 @@ def unbatched_forward( # noqa: PLR0915 cell=cell, pbc=self.pbc, cutoff=self.cutoff, - sorti=False, + sort_id=False, ) # Get displacements between neighbor pairs dr_vec, distances = transforms.get_pair_displacements( diff --git a/torch_sim/optimizers.py b/torch_sim/optimizers.py index 2a746ef7..d715c5c5 100644 --- a/torch_sim/optimizers.py +++ b/torch_sim/optimizers.py @@ -579,7 +579,7 @@ def fire( Notes: - md_flavor="vv_fire" follows the original paper closely, including integration with Velocity Verlet steps. See https://doi.org/10.1103/PhysRevLett.97.170201 - and https://github.com/Radical-AI/torch-sim/issues/90#issuecomment-2826179997 + and https://github.com/TorchSim/torch-sim/issues/90#issuecomment-2826179997 for details. - md_flavor="ase_fire" mimics the implementation in ASE, which differs slightly in the update steps and does not explicitly use atomic masses in the @@ -803,7 +803,7 @@ def unit_cell_fire( Notes: - md_flavor="vv_fire" follows the original paper closely, including integration with Velocity Verlet steps. See https://doi.org/10.1103/PhysRevLett.97.170201 - and https://github.com/Radical-AI/torch-sim/issues/90#issuecomment-2826179997 + and https://github.com/TorchSim/torch-sim/issues/90#issuecomment-2826179997 for details. - md_flavor="ase_fire" mimics the implementation in ASE, which differs slightly in the update steps and does not explicitly use atomic masses in the @@ -1095,7 +1095,7 @@ def frechet_cell_fire( Notes: - md_flavor="vv_fire" follows the original paper closely, including integration with Velocity Verlet steps. See https://doi.org/10.1103/PhysRevLett.97.170201 - and https://github.com/Radical-AI/torch-sim/issues/90#issuecomment-2826179997 + and https://github.com/TorchSim/torch-sim/issues/90#issuecomment-2826179997 for details. - md_flavor="ase_fire" mimics the implementation in ASE, which differs slightly in the update steps and does not explicitly use atomic masses in the diff --git a/torch_sim/state.py b/torch_sim/state.py index fa898e1c..a36312a9 100644 --- a/torch_sim/state.py +++ b/torch_sim/state.py @@ -415,7 +415,7 @@ def __getitem__(self, system_indices: int | list[int] | slice | torch.Tensor) -> def __init_subclass__(cls, **kwargs) -> None: """Enforce that all derived states cannot have tensor attributes that can also be None. This is because torch.concatenate cannot concat between a tensor and a None. - See https://github.com/Radical-AI/torch-sim/pull/219 for more details. + See https://github.com/TorchSim/torch-sim/pull/219 for more details. Also enforce all of child classes's attributes are specified in _atom_attributes, _system_attributes, or _global_attributes.