[WIP] Better input set generator and sets for io.lammps #4368

vir-k01 · 2025-04-19T21:06:52Z

Summary

This PR is part of an effort to include workflows for running LAMMPS via atomate2. A concurrent PR will be opened in atomate2 that has the flows, while this PR aims to update the input set generators to match the inputs required there.
These changes are based on initial work here: https://github.com/Matgenix/atomate2-lammps done by @ml-evs and @gbrunin. Also tagging in @esoteric-ephemera who helped structure the code in this PR, and @davidwaroquiers.
Major changes:

Updated templates for running NVT/NPT/Minimization jobs with the upcoming flows in atomate2.
Added in a data class to validate commonly utilized settings (based on the updated templates)
The new input set generator is written (to the best of my ability) to provide input settings consistent with classical MD run through other codes on solids (matched defaults to ASE MD)

Marked this as a WIP as there might be further updates here dependent on the updates made in the concurrent atomate2 PR.

TODO:

Add tests
I've made most of the design decisions here assuming these sets will be used with solids through the Structure object, but one could also argue including support for Molecules. I'm looking for suggestions on how that can be incorporated without varying too much of the logic (ex : for the default inputs, atom styles, force field parameters)
I'm also looking for suggestions on how to best check/validate user specified force field parameters, which is difficult to do considering the numerous force field formats that exist out there. The existing ForceField object in io.lammps.data is not very intuitive to set-up for a user and does not support lammps integrated MLIPs yet.

…LammpsInputFile objects as input for the template to make use of all the other io.lammps functions in pmg

update - 12/3

…rd lammps) files with the input set that are prepared independent of the input file

Merge updates - 1/6/2025

Added a new (and probs better?) implementation for generating lammps input sets, with a more expressive MD template. Everything is now based on the template to ensure the atomate2 workflows being written work without the user having to specify too much. Inputs and states have to be enumed.

…LammpsInputFile objects as input for the template to make use of all the other io.lammps functions in pmg

…rd lammps) files with the input set that are prepared independent of the input file

Added a new (and probs better?) implementation for generating lammps input sets, with a more expressive MD template. Everything is now based on the template to ensure the atomate2 workflows being written work without the user having to specify too much. Inputs and states have to be enumed.

…_sets

…o lammps_sets" This reverts commit c1f2ed6, reversing changes made to 410d4b4.

…class for storing and validating user defined settings

Changes to be committed: Reworked the way the input set generator generates the input file to be less cumbersome and use fewer if-else clauses, this new approach goes back to the original generator in order to be a lot more flexible (esp for custom lammps jobs). A LammpsSettings object is now present in order to validate the inputs specified by the user prior to actually passing them to lammps. This approach works out for the makers implemented currently (NVT/NPT/NVE/Minimization).

…ated

Redid how input sets are validated, in particular how "general" settings can also be stored as attrs of LammpsSettings, and only validate keys from _BASE_LAMMPS_SETTINGS. This way, allows for very flexible inputs from user to also be present in the final taskdoc.inputs. Also used PathLike instead of Path objects.

DanielYang59 · 2025-04-20T10:03:03Z

src/pymatgen/core/periodic_table.py

@@ -776,6 +777,19 @@ def is_rare_earth(self) -> bool:
        """
        return self.is_lanthanoid or self.is_actinoid or self.symbol in {"Sc", "Y"}

+    @property
+    @deprecated(


I guess reverting changes to core.periodic_table and io.exciting is not intended?

If so you could revert those changes with (warning, this would drop all changes to that file, make sure this is what you need) git checkout upstream/master -- file_to_revert

Just behind the master branch, synced up now

…ated

vir-k01 and others added 20 commits October 30, 2024 17:17

fixed atom_style issue when converting from structure

fecef55

BaseLammpsGenerator can def benefit from taking both raw strings and …

159be72

…LammpsInputFile objects as input for the template to make use of all the other io.lammps functions in pmg

Merge pull request #1 from materialsproject/master

b6edc3d

update - 12/3

Need this to have a general way to write out FF (and other non-standa…

cfac0bf

…rd lammps) files with the input set that are prepared independent of the input file

Merge pull request #2 from materialsproject/master

fd0cc72

Merge updates - 1/6/2025

fixed atom_style issue when converting from structure

37c387f

BaseLammpsGenerator can def benefit from taking both raw strings and …

f736361

…LammpsInputFile objects as input for the template to make use of all the other io.lammps functions in pmg

Need this to have a general way to write out FF (and other non-standa…

fc0bb82

…rd lammps) files with the input set that are prepared independent of the input file

Add LammpsSettings to check convenience input

74a2ce5

Merge branch 'lammps_sets' of github.com:vir-k01/pymatgen into lammps…

c1f2ed6

…_sets

Revert "Merge branch 'lammps_sets' of github.com:vir-k01/pymatgen int…

608e889

…o lammps_sets" This reverts commit c1f2ed6, reversing changes made to 410d4b4.

Fixed commit merge issues

363fee6

Removed LammpsInputSettings class, moved to convience LammpsSettings …

3f2d0b1

…class for storing and validating user defined settings

Updated docstring for LammpsInput

f88cc2d

Merge remote-tracking branch 'upstream/master' into lammps_sets_templ…

0ab2389

…ated

removed debugging print statements

be77b06

vir-k01 requested review from shyuep and mkhorton as code owners April 19, 2025 21:06

vir-k01 changed the title ~~[WIPBetter input set generator and sets for io.lammps~~ [WIP] Better input set generator and sets for io.lammps Apr 19, 2025

pre-commit auto-fixes

aa32a30

DanielYang59 reviewed Apr 20, 2025

View reviewed changes

esoteric-ephemera and others added 4 commits April 21, 2025 08:50

Merge remote-tracking branch 'upstream/master' into lammps_sets_templ…

75b0637

…ated

precommit / sync head

f8f33b4

Account for species specified through the FF dict

3e2a5a0

bug fix in latest commit

192dcb0

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[WIP] Better input set generator and sets for io.lammps #4368

[WIP] Better input set generator and sets for io.lammps #4368

vir-k01 commented Apr 19, 2025 •

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DanielYang59 Apr 20, 2025 •

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esoteric-ephemera Apr 21, 2025

[WIP] Better input set generator and sets for io.lammps #4368

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[WIP] Better input set generator and sets for io.lammps #4368

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vir-k01 commented Apr 19, 2025 • edited Loading

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