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Add single point calculations #31

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merged 21 commits into from
Feb 16, 2024
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@ElliottKasoar ElliottKasoar commented Feb 15, 2024

Resolves #30

Initial code to configure calculators and perform single point calculations for energies, forces and stress.

Largely based on code already in lavello, but refactors, fixes various issues to get tests etc. to pass, and adds more general tests.

Now also adds the ability to return forces and stress.

To do:

  • Fix pylint
    • I had previously fixed with with try...except clauses, but it makes it quite verbose. Disabling pylint's complaint is an alternative, since the error message is pretty understandable.
  • Add support for trajectory energies
    • The obvious solution is change read to read a specified slice/all structures, and attach the calculator to each image.
    • Are there better ways of doing this? As far as I can tell, calculators can only be attached to Atoms objects.
  • Update docstrings in various places
  • Add single point forces, stresses etc.
    • How (probably a dictionary)/when do we want to return these?
  • Replace UiO66 with smaller structure that we are still able to calculate stress for e.g. NaCl from @alinelena

Note: CI is currently not working due to issues with pulling ASE from GitLab, but all tests pass locally.

@ElliottKasoar ElliottKasoar added enhancement New/improved feature or request janus labels Feb 15, 2024
@ElliottKasoar ElliottKasoar self-assigned this Feb 15, 2024
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Current temporary solution to ASE installation is to update the commit once tests start failing, but this may be a problem for publishing etc. if it passes here, but fails when rerun.

@ElliottKasoar ElliottKasoar marked this pull request as ready for review February 16, 2024 13:38
@ElliottKasoar ElliottKasoar changed the title Add single point calculations and geometry optimisation Add single point calculations Feb 16, 2024
@alinelena alinelena self-requested a review February 16, 2024 16:14
alinelena
alinelena previously approved these changes Feb 16, 2024
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@alinelena alinelena merged commit 53072d0 into stfc:main Feb 16, 2024
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@ElliottKasoar ElliottKasoar deleted the add-single-point branch February 19, 2024 13:00
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Not sure if these will come through.

janus_core/mlip_calculators.py Show resolved Hide resolved
janus_core/mlip_calculators.py Show resolved Hide resolved
janus_core/mlip_calculators.py Show resolved Hide resolved
janus_core/single_point.py Show resolved Hide resolved
janus_core/single_point.py Show resolved Hide resolved
janus_core/single_point.py Show resolved Hide resolved
janus_core/single_point.py Show resolved Hide resolved
tests/test_mlip_calculators.py Show resolved Hide resolved
tests/test_single_point.py Show resolved Hide resolved
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create single point calculation driver
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