16. Working with Geometries


Pleas see pysistrj --help for a list of possible invocations.

usage: Utility to transform .xyz and .trj files. [-h]
                                                 (--between BETWEEN | --align | --split | --reverse | --cleantrj | --spline | --first FIRST | --every EVERY | --center | --centerm | --translate TRANSLATE TRANSLATE TRANSLATE | --append | --join | --match | --std | --shake | --internals | --get GET | --origin | --fragsort)
                                                 [--scale SCALE] [--seed SEED]
                                                 [--idpp | --lst | --redund]
                                                 [--noipalign] [--bohr]
                                                 [--atoms ATOMS [ATOMS ...]]
                                                 [--add_prims ADD_PRIMS]
                                                 fns [fns ...]

positional arguments:
  fns                   Filenames of .xyz and/or .trj files (xyz and trj can
                        be mixed).

optional arguments:
  -h, --help            show this help message and exit
  --between BETWEEN     Interpolate additional images.
  --align               Align geometries onto the first geometry.
  --split               Split a supplied geometries in multiple .xyz files.
  --reverse             Reverse a .trj file.
  --cleantrj            Keep only the first four columns of xyz/trj files.
  --spline              Evenly redistribute geometries along a splined path.
  --first FIRST         Copy the first N geometries to a new .trj file.
  --every EVERY         Create new .trj with every N-th geometry. Always
                        includes the first and last point.
  --center              Move the molecules centroid into the origin.
  --centerm             Move the molecules center of mass into the origin.
                        Translate the molecule by the given vector given in
  --append              Combine the given .xyz files into one .xyz file.
  --join                Combine the given .xyz/.trj files into one .trj file.
  --match               Resort the second .xyz file so the atom order matches
                        the first .xyz file. Uses the hungarian method.
  --std                 Move supplied geometry to its standard orientation.
  --shake               Shake (randomly displace) coordiantes.
  --internals           Print automatically generated internals.
  --get GET             Get n-th geometry. Expects 0-based index input.
  --origin              Translate geometry, so that min(X/Y/Z) == 0.
  --fragsort            Resort atoms by fragments.
  --idpp                Interpolate using Image Dependent Pair Potential.
  --lst                 Interpolate by linear synchronous transit.
  --redund              Interpolate in internal coordinates.
  --noipalign           Don't align geometries when interpolating.
  --bohr                Input geometries are in Bohr instead of Angstrom.
  --noxyz               Disable dumping of single .xyz files.
  --atoms ATOMS [ATOMS ...]
                        Used with --internals. Only print primitives including
                        the given atoms.
  --add_prims ADD_PRIMS
                        Used with --internals. Define additional primitives.
                        Expects a string representation of a nested list that
                        can be parsed as YAML e.g.

  --scale SCALE         Scales the displacement in --shake.
  --seed SEED           Initialize the RNG for reproducible results.