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Use mctc library for geometry input / output #591

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merged 5 commits into from
Feb 27, 2022
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@awvwgk awvwgk commented Feb 26, 2022

Another step to an uniform geometry handling library for our computational chemistry projects. This patch removes the geometry readers from xtb and replaces them with the implementations available in mctc-lib.

This gives xtb automatic support for

  • QCSchema JSON files
  • SDF files with V3000 formatted connection tables
  • FHI-aims geometry.in files
  • Q-Chem molecule files
  • future implemented formats in mctc-lib

Todo:

  • synchronize the vasp_info, turbo_info and struc_info types (xtb) with the structure_info type (mctc-lib)
  • catch structures not supported by xtb:
    • 1D/2D periodic structure (tmol, aims)
    • helical objective boundary conditions (gen)
    • 2D flat molecules (ctfile)
    • hydrogen atom queries (ctfile)
    • protein missing hydrogen (pdb)
  • replace writer routines with mctc-lib provided ones
  • check geometry conversion factors in mctc-lib against xtb (different CODATA versions)
    Include CODATA2018 constants mctc-lib#37

@awvwgk awvwgk force-pushed the mctc-lib branch 5 times, most recently from 7cb7b36 to 85444a5 Compare February 27, 2022 08:12
@awvwgk awvwgk merged commit b9dbd81 into grimme-lab:main Feb 27, 2022
@awvwgk awvwgk deleted the mctc-lib branch February 27, 2022 14:01
@awvwgk awvwgk added this to the v6.5.0 milestone Apr 13, 2022
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