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Add ReadWriteGaussian interface and tests #24

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@lauramurgatroyd lauramurgatroyd commented Mar 16, 2021

This is a draft pull request because it relies on ASE code which has not yet been released.

My changes to the Gaussian interface have been merged into the ASE Gitlab repo, but not yet released: https://gitlab.com/ase/ase/-/commit/85da80312f8232bf21860f9769b2968fa4882f50

Details of the changes in ASE are documented here: https://gitlab.com/ase/ase/-/merge_requests/2278

At the time of writing, the current ASE release (without the Gaussian changes) is: 3.21.1

The ReadWriteGaussian interface in pymuonsuite allows:

  • Reading of gaussian output files, including reading the fermi contact term in MHz for all of the atoms.
  • Writing gaussian input files with the muon's properties added [mass and nuclear magnetic moment] - this assumes the muon is the final atom in the structure, as is the case when we run muairss and this assumption is also made with the other ReadWrite interfaces.
  • Reading a gaussian input file, and the settings read (such as keywords, options, basis set) can be written out in another input file plus muon.

Also tests are included for:

  • Reading a gaussian output file
  • Writing gaussian input files:
    • when giving an input files' settings to use
    • when providing no input file - this checks default values are set
    • when providing a calculator - checks the calculator's properties are written to the file.

specified in the input parameters to the object, instead of from
the structure file
Because it is not supported in ASE.
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lauramurgatroyd commented Mar 16, 2021

Further changes that I will be working on this week:

  • Allowing gaussian to be used in muairss.
  • Adding a test for gaussian in muairss.
  • Setting default values for the gaussian input files generated, in the case that a user has not provided a gaussian input file. This will also have to ensure that PBCs are set.
  • Add a test that the correct default values are applied in this case.

@lauramurgatroyd lauramurgatroyd self-assigned this Mar 17, 2021
@lauramurgatroyd lauramurgatroyd added the enhancement New feature or request label Mar 17, 2021
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I believe this is now ready for merging, after the next ASE release.

@lauramurgatroyd lauramurgatroyd requested a review from stur86 March 19, 2021 16:06
@elichad elichad removed the request for review from stur86 May 27, 2022 14:13
@elichad elichad marked this pull request as ready for review May 27, 2022 14:13
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elichad commented May 27, 2022

@lauramurgatroyd thanks for this work! I didn't realise it was ready to go and just waiting on an ASE release (which obviously was done long ago).

I'll be picking this up at some point so any comments are for me, not you :)

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