update changelog for v0.2.0 #147
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orionarcher
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Apr 14, 2025
* update changelog for v0.2.0 * minor modification for PR template * formatting fixes * formatting and typos * remove contributors bc they aren't linked
abhijeetgangan
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Apr 15, 2025
* Add per atom energies and stresses for batched LJ * update changelog for v0.2.0 (#147) * update changelog for v0.2.0 * minor modification for PR template * formatting fixes * formatting and typos * remove contributors bc they aren't linked * Add tests * simplify results --------- Signed-off-by: Abhijeet Gangan <[email protected]> Co-authored-by: Orion Cohen <[email protected]>
CompRhys
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May 2, 2025
* update changelog for v0.2.0 * minor modification for PR template * formatting fixes * formatting and typos * remove contributors bc they aren't linked
janosh
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May 14, 2025
* adds comparative test for fire optimizer with ase * rm a few comments * updates CI for the test * update changelog for v0.2.0 (#147) * update changelog for v0.2.0 * minor modification for PR template * formatting fixes * formatting and typos * remove contributors bc they aren't linked * update test with a harder system * fix torch.device not iterable error in test_torchsim_vs_ase_fire_mace.py * fix: should compare the row_vector cell, clean: fix changelog typo * clean: delete .coverage and newline for pytest command * Introduce ASE-style `FIRE` optimizer (departing from velocity Verlet in orig FIRE paper) and improve coverage in `test_optimizers.py` (#174) * feat(fire-optimizer-changes) Update fire_step in optimizers.py based feature/neb-workflow * reset optimizers.py to main version prior to adding updated changes * (feat:fire-optimizer-changes) - Added ase_fire_step and renamed fire_step to vv_fire_step. Allowed for selection of md_flavor * (feat:fire-optimizer-changes) - lint check on optimizers.py with ruff * (feat:fire-optimizer-changes) - added test cases and example script in examples/scripts/7_Others/7.6_Compare_ASE_to_VV_FIRE.py * (feat:fire-optimizer-changes) - updated FireState, UnitCellFireState, and FrechetCellFireState to have md_flavor to select vv or ase. ASE currently coverges in 1/3 as long. test cases for all three FIRE schemes added to test_optimizers.py with both md_flavors * ruff auto format * minor refactor of 7.6_Compare_ASE_to_VV_FIRE.py * refactor optimizers.py: define MdFlavor type alias for SSoT on MD flavors * new optimizer tests: FIRE and UnitCellFIRE initialization with dictionary states, md_flavor validation, non-positive volume warnings brings optimizers.py test coverage up to 96% * cleanup test_optimizers.py: parameterize tests for FIRE and UnitCellFIRE initialization and batch consistency checks maintains same 96% coverage * refactor optimizers.py: consolidate vv_fire_step logic into a single _vv_fire_step function modified by functools.partial for different unit cell optimizations (unit/frechet/bare fire=no cell relax) - more concise and maintainable code * same as prev commit but for _ase_fire_step instead of _vv_fire_step * (feat:fire-optimizer-changes) - added references to ASE implementation of FIRE and a link to the original FIRE paper. * (feat:fire-optimizer-changes) switched md_flavor type from str to MdFlavor and set default to ase_fire_step * pytest.mark.xfail frechet_cell_fire with ase_fire flavor, reason: shows asymmetry in batched mode, batch 0 stalls * rename maxstep to max_step for consistent snake_case fix RuntimeError: a leaf Variable that requires grad is being used in an in-place operation: 7. Position / cell update state.positions += dr_atom * unskip frechet_cell_fire in test_optimizer_batch_consistency, can no longer repro error locally * code cleanup * bumpy set-up action to v6, more descriptive CI test names * pin to fairchem_core-1.10.0 in CI * explain differences between vv_fire and ase_fire and link references in fire|unit_cell_fire|frechet_cell_fire doc strings * merge test_torchsim_frechet_cell_fire_vs_ase_mace.py with comparative ASE vs torch-sim test for Frechet Cell FIRE optimizer into test_optimizers.py - move `ase_mace_mpa` and `torchsim_mace_mpa` fixtures into `conftest.py` for wider reuse * redirect MACE_CHECKPOINT_URL to mace_agnesi_small for faster tests * on 2nd thought, keep test_torchsim_frechet_cell_fire_vs_ase_mace in a separate file (thanks @CompRhys) * define MaceUrls StrEnum to avoid breaking tests when "small" checkpoints get redirected in mace-torch --------- Co-authored-by: Orion Cohen <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]> Co-authored-by: Rhys Goodall <[email protected]> Co-authored-by: Myles Stapelberg <[email protected]>
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Summary
Update changelog for new release.
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