Fix virial sign in NPT ensemble, wrap coordinates to unit cell, and support charge/spin configuration #1546
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It seems that the CI test stopped due to a temporary environment error (EADDRINUSE in PyTorch distributed initialization), rather than an issue with this PR’s code. |
Thanks for making this PR and contributing!, the CI tests all look good, we'll review it soon and looks mostly good! |
| # virials need to be in this order: xx, yy, zz, xy, xz, yz. https://docs.lammps.org/Library_utility.html#_CPPv437lammps_fix_external_set_virial_globalPvPKcPd | ||
| virial_arr = [v[0], v[4], v[8], v[1], v[2], v[5]] | ||
| lmp.fix_external_set_virial_global(FIX_EXT_ID, virial_arr) | ||
| def wrap_to_unit_cell( |
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Can we use ASE's wrap positions instead since we already use this function in our code?
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Agreed, we can use ASE wrap_positions inside this function. Relatedly, it would be useful to add some simple lammps box to ASE unit cell and back tests to ensure consistency between lammps and ASE representation.
| # stress is defined as virial/volume in lammps | ||
| assert "stress" in results, "stress must be in results to compute virial" | ||
| volume = torch.det(cell).abs().item() | ||
| v = (-results["stress"].detach().cpu() * volume)[0].tolist() |
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Thanks for catching this! The ASE v lammps test looks good. Can you update the comment as well: virial = - stress * volume? (in the lammps doc they didn't add the negative)
| ase_kinetic, ase_pot = run_ase_npt() | ||
| lammps_kinetic, lammps_pot = run_lammps("tests/lammps/lammps_npt.file") | ||
| assert np.isclose(ase_kinetic, lammps_kinetic, atol=1.0) | ||
| assert np.isclose(ase_pot, lammps_pot, atol=1.0) |
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should we add a check for pressure as well since this is a NPT sim?
| fix 1 all npt temp 300.0 300.0 0.1 iso 0.0 0.0 1.0 | ||
| thermo_style custom step temp pe ke etotal press vol | ||
| thermo 1 | ||
| run 300 |
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can we run this for 100 steps instead to reduce the test time?
Looks great, mostly just cosmetic comments, thanks for the adding the NPT example test case, very useful! |
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Summary
This PR includes three main updates to improve stability and correctness in LAMMPS-based simulations.
Fix overestimated pressure in NPT ensemble
The virial term was incorrectly signed, leading to systematically higher pressure evaluations in NPT simulations.
This PR corrects the sign convention and adds a dedicated NPT test to verify the fix.
Wrap atomic positions to the unit cell
Although this normally has no effect on computed energies or forces, large atomic displacements occasionally caused PyTorch warnings due to numerical instability.
Wrapping positions mitigates such issues and improves numerical robustness.
Add charge and spin configuration support
Extended input options to allow specifying total charge and spin states, which is useful for systems that require explicit electronic parameters.
Implementation Details
Testing
Motivation
This patch improves both physical correctness (pressure evaluation) and numerical stability (coordinate wrapping).