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! |
src/fairchem/lammps/lammps_fc.py
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| # 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.
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Resolved in 5466c17.
Thanks for the feedback! I agree about adding consistency tests, but I’m not completely sure how to implement them. Could you please advise on the best approach?
tests/lammps/test_ase_vs_lammps.py
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| 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?
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Pressure can fluctuate significantly in NPT simulations, so comparing only the last frame after this short run is not really feasible.
If we want to implement a pressure check, it would be better to run a longer simulation and take an average over several tens of frames. However, this would take a bit more time.
Looks great, mostly just cosmetic comments, thanks for the adding the NPT example test case, very useful! |
Thank you for your review! I have addressed most of your comments and would be grateful if you could kindly review it again. |
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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).