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  1. 14 Jul, 2020 6 commits
  2. 13 Jul, 2020 5 commits
    • Neil Vaytet's avatar
      Add warning message. · e042c0de
      Neil Vaytet authored
    • Neil Vaytet's avatar
      Use unix epoch as reference · a37cf2ce
      Neil Vaytet authored
      According to the Nexus standard, if the offset is not present, it implies
      the offset is and absolute timestamp, which is relative to the start of
      Unix epoch (
      So instead fo throwing an error, we use unix epoch.
    • Adam J. Jackson's avatar
    • 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.
    • 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.
  3. 12 Jul, 2020 2 commits
  4. 10 Jul, 2020 2 commits
  5. 09 Jul, 2020 5 commits
  6. 08 Jul, 2020 7 commits
  7. 07 Jul, 2020 2 commits
  8. 06 Jul, 2020 4 commits
  9. 03 Jul, 2020 6 commits
  10. 02 Jul, 2020 1 commit