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  1. 13 Jul, 2020 2 commits
    • Adam J. Jackson's avatar
      Abins: Additional tests for DMOL3 import · 40d618eb
      Adam J. Jackson authored
      New test cases have been added for molecular calculations with no
      periodic boundary conditions. Compared to the already-tested periodic
      systems, these calculations yield lattice vectors of zero and
      have 3N-6 vibrational modes. This tests some different paths in the
      parsing logic.
      40d618eb
    • Adam J. Jackson's avatar
      Add support for non-periodic systems to DMOL3 Abins parser · 11e75181
      Adam J. Jackson authored
      Based on a user report and sample files. Two main differences were
      identified which caused the parser to trip up on a calculation without
      periodic boundary conditions:
      
      - No lattice vectors are printed in the output file, but the parser
        requires this data to exist, as does Abins' data format.
      
        - Here we apply the same convention as the Gaussian parser, setting
          lattice vectors to a 3x3 zero matrix
      
      - The lowest 6 vibrational modes, which theoretically correspond to
        translation and rotation, are discarded from the output data. This
        breaks an assumption that there are 3N vibrational modes (where N is
        number of atoms). Abins in general does _not_ make this assumption,
        so it can be fixed in the parser.
      
        - Now the number of atoms is obtained from the coordinates data, and
          a check is made that the number of modes is either 3N or 3N-6. There
          _might_ be an issue with dimers (which have 3 translational modes,
          two rotational modes and a non-zero stretching mode); need to get
          access to Materials Studio and test this.
      
      Some error messages were also cleaned up to remove a confusing "bytes"
      type signature.
      11e75181
  2. 10 Jul, 2020 1 commit
  3. 09 Jul, 2020 5 commits
  4. 08 Jul, 2020 7 commits
  5. 07 Jul, 2020 2 commits
  6. 06 Jul, 2020 2 commits
  7. 03 Jul, 2020 5 commits
  8. 02 Jul, 2020 10 commits
  9. 01 Jul, 2020 6 commits