metatensor models have been renamed to metatomic models #205
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CompRhys
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May 30, 2025
janosh
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* clean: move pair fn logic into batched model code * clean: begin to remove unbatched scripts * clean: update the dynamics scripts, remove old code, refactor the integrators into folder * fix: all unit tests run * fix: remove circular import * wip: address more issues with removing unbatched code * wip: another attempt to fix examples * fix: mace needs the shifts? we should add a unit test that needs them as the MaceModel unit tests didn't fail removing them. * metatensor models have been renamed to metatomic models (#205) * Fix discrepancies between `FIRE` optimisations in `ASE` and `torch-sim` (#203) * fea: use batched vdot --------- Co-authored-by: Janosh Riebesell <[email protected]> * clean: remove ai slop * clean: further attempts to clean but still not matching PR * fix: dr is vdt rather than fdt * typing: fix typing issue * wip: still not sure where the difference is now * update forces per comment * Fix ASE pos only implementation * Initialize velocities to None in the pos-only case, see previous changes to the optimizers. (ensures that the correct `dt` is used) * Change the order of the increase of `n_pos`. Again, this ensures the usage of the correct `dt` compared to ASE * Fix torch-sim ASE-FIRE (Frechet Cell) * Remove rescaling of positions when updating cell, it's not relevant * Correctly rescale the positions with respect to the deformation gradient * Consider the `cell_forces` in the convergence when doing cell optimizations * linting * test: still differ significantly after step 1 for distorted structures * Fix test comparing ASE and torch-sim optimization * Include the `cell_forces` in the convergence check * Fix the number of iterations that are performed. `steps_between_swaps` is set to 1, so the number of iterations is equal to the number of swaps. In the previous version, less iterations would have been performed when reaching the maximum number of swaps. For example, when trying to run 32 steps with `steps_between_swaps=5`, the optimization would have stopped after 30 iterations, i.e., 6 swaps. * Fix `autobatching.py`. The if statement would have been triggered for `max_attempts=0`, which was the case when running one iteration and `steps_between_swaps=5` * Fix `optimizers` when using `UnitCellFilter` * Fix the `None` initialization * Fix the cell update when using `UnitCellFilter` * fix test_optimize_fire * allow FireState.velocities = None since it's being set to None in multiple places * safer `batched_vdot`: check dimensionality of input tensors `y` and `batch_indices` - fix stale docstring mentioning is_sum_sq kwarg * generate_force_convergence_fn raise informative error on needed but missing cell_forces * pascal case VALID_FIRE_CELL_STATES->AnyFireCellState and fix non-f-string error messages * fix FireState TypeError: non-default argument 'dt' follows default argument * allow None but don't set default for state.velocities * fix bad merge conflict resolution * tweaks --------- Co-authored-by: Rhys Goodall <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]> * bump pre-commit hooks and fix new errors * fix MACE examples not using ts.io state conversion utilities * fix unused shifts_list not torch.cat()-ed in mace.py * fix examples/scripts/3_Dynamics/3.9_MACE_NVT_staggered_stress.py using nvt_langevin in place of nvt_nose_hoover_invariant remove debug print in torch_sim/runners.py * just calc total energy manually in nvt_langevin_invariant in torch_sim/integrators/nvt.py also fix broadcasting bug in Ornstein-Uhlenbeck (ou_step) * fix calculate_momenta() in npt_nose_hoover_init also fix 3.8_MACE_NPT_Nose_Hoover.py broken imports from torch_sim.integrators.npt * fix unpack of n_particles, dim = state.positions.shape * fix missing external_pressure in npt_nose_hoover call in 3.8_MACE_NPT_Nose_Hoover.py * update cell_position in npt_nose_hoover before downstream usage * refactor (no bug fixes) * fix npt_nose_hoover transposing cell that's already in column-vector convention * feat: Add batching support to NPT Nose-Hoover integrator - Update NPTNoseHooverState cell properties to support batch dimensions - reference_cell: [n_batches, 3, 3] instead of [3, 3] - cell_position, cell_momentum, cell_mass: [n_batches] instead of scalar - Fix tensor broadcasting in exp_iL1, exp_iL2 with proper atom-to-batch mapping - Update compute_cell_force for per-batch kinetic energy and stress calculations - Fix npt_nose_hoover_init to properly initialize batched cell variables - Update npt_nose_hoover_invariant for per-batch energy conservation - Replace pbc_wrap_general with pbc_wrap_batched for proper PBC handling - Fix example script 3.8_MACE_NPT_Nose_Hoover.py output formatting Enables multiple independent NPT systems in a single simulation while maintaining backward compatibility for single-batch systems. * fix: Remove cell dimension squeezing in NVT Nose-Hoover integrator - Remove problematic cell.squeeze(0) that breaks batching support - Fix calculate_momenta function call to use correct signature with batch parameter - Resolves RuntimeError when using MACE with NVT Nose-Hoover thermostat Fixes example script 3.5_MACE_NVT_Nose_Hoover.py which was failing due to neighbor list function receiving wrong tensor shapes when cell batch dimension was incorrectly removed. * fix: Handle scalar kT and batched stress tensors in NPT Nose-Hoover - Convert scalar kT to tensor before accessing .ndim attribute in npt_nose_hoover_init and update_cell_mass - Fix stress tensor trace computation in compute_cell_force to handle 3D batched tensors - Use torch.diagonal().sum() for batched stress tensors instead of torch.trace() Fixes Lennard-Jones NPT Nose-Hoover script that was failing with: - AttributeError: 'float' object has no attribute 'ndim' - RuntimeError: trace: expected a matrix, but got tensor with dim 3 * fix: Handle batched cell tensors in get_fractional_coordinates - Replace deprecated .T with .mT for matrix transpose on 3D tensors - Add support for batched cell tensors with shape [n_batches, 3, 3] - Extract first batch cell matrix when cell.ndim == 3 - Maintains backward compatibility with 2D cell matrices Fixes batched silicon workflow script that was failing with: - UserWarning about deprecated .T usage on >2D tensors - RuntimeError: linalg.solve: A must be batches of square matrices The get_fractional_coordinates function now properly handles both single [3,3] and batched [n_batches,3,3] cell tensors, enabling a2c_silicon_batched.py workflow to run * replace .transpose(-2, -1) with .mT everywhere * fix nvt + npt integrators: ensure consistent batch dimensions in kinetic energy calculations - Add missing `batch=state.batch` parameter to `calc_kinetic_energy` calls in NPT integrator - Enhance NVT/NPT invariant functions with explicit broadcasting for chain variables - Replace inefficient manual loops with batch-aware kinetic energy calculation in NPT invariant - Fix undefined variable reference in NPT invariant function (n_batches → state.n_batches) Resolves broadcasting issues where scalar kinetic energy was incorrectly combined with batched energy and temperature tensors, ensuring all energy terms have consistent batch dimensions before addition. * fix transforms.py: prevent silent data corruption in get_fractional_coordinates Replace problematic batched cell handling that only processed the first batch (cell[0]) with explicit NotImplementedError. This prevents silent data corruption where multi-batch systems would incorrectly use only the first batch's cell parameters for all coordinate transformations. - Raise NotImplementedError for 3D batched cell tensors instead of silently ignoring batches 1, 2, ... N - Preserve existing functionality for 2D cell matrices - Add clear error message indicating limitation and suggesting workarounds Breaking change: Code that previously silently failed will now explicitly error, but this prevents incorrect results in multi-batch scenarios. * fix nvt_langevin: handle None gamma parameter correctly * fix npt: missing PBC check in Nose-Hoover position update - Check state.pbc before applying ts.transforms.pbc_wrap_batched - Return unwrapped positions when state.pbc is False - Ensure consistent behavior with NPT Langevin implementation * Initialize cur_deform_grad to prevent UnboundLocalError * fix nvt: compute degrees of freedom per batch in Nose-Hoover init Replace count_dof() with proper batch-aware DOF calculation using torch.bincount(state.batch) to ensure consistency with invariant function. Previously ignored batch structure, causing incorrect DOF for batched systems. * fix /5.1_a2c_silicon_batched.py: restore single-batch cell tensors support in transforms.py's get_fractional_coordinates - Handle batched cell tensors with shape [1, 3, 3] by auto-squeezing to [3, 3] - Improve error messages for multi-batch cases to be more informative - Add comprehensive tests for batched cell tensor scenarios - Fixes NotImplementedError in examples/scripts/5_Workflow/5.1_a2c_silicon_batched.py:159 - Maintains full backward compatibility with existing 2D cell matrix usage --------- Signed-off-by: Janosh Riebesell <[email protected]> Co-authored-by: Janosh Riebesell <[email protected]>
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Summary
We split the atomistic models part of metatensor into its own package, called
metatomic. This PR updates the interface to use the new package.Checklist
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