Command line scripts¶
convgeom¶
Command line script for converting geometries between formats.
Usage¶
To convert from one format to another:
convgeom input_file output_file [options]
By default, the input format is determined from the file structure and the output format is set by the file extension.
Options¶
-i, --in-format- The input format (xyz, col, gdat, …)
-o, --out-format- The output format (xyz, col, gdat, …)
-iu, --in-units- The input distance units (ang, bohr, …)
-ou, --out-units- The output distance units (ang, bohr, …)
-c, --has-comment- Boolean argument, whether or not comment is read
-v, --has-vector- Boolean argument, whether or not vector is read
measure¶
Command line script for measuring internal coordinates from a geometry file.
Usage¶
To measure a coordinate for one or multiple geometries in an input file:
measure input_file coord_type {inds} [options]
The number of indices must match the coordinate type (e.g. 2 for stre, 3 for bend, …).
Options¶
-f, --format- The input file format (xyz, col, gdat, …)
-u, --units- The output units (auto, ang, rad, …)
-a, --absolute- Boolean argument, if present returns absolute values
-o, --output- The output filename. Defaults to writing to stdout
-v, --val-format- The format of an output value, given as a format string
subst¶
Command line script for adding substituents to a geometry file.
Usage¶
To add a substituent to all geometries in an input file:
subst input_file sublbl {inds} [options]
The inds mark which position is substituted. If multiple indices are given, the first will be the position of the substituent.
Options¶
-i, --in-place- Boolean argument, whether or not the geometry file is overwritten.
-b, --bond-ind- The index of the atom bound to the substituent. If not specified, the nearest atom is used.
-p, --plane-ind- The index of the atom used to specify the xz-plane of the substituent. The substituent index, bonding index and plane index make up the plane.
-f, --format- The input/output format (xyz, col, gdat, …)
-c, --has-comment- Boolean argument, whether or not comment is read.
-v, --has-vector- Boolean argument, whether or not vector is read.
nudge¶
Command line script for translating/rotating/reflecting a geometry file.
Usage¶
To displace a molecule about/along a given axis:
nudge input_file amp axis_string [options]
The axis (and origin, if given) is parsed based on
displace.VectorParser, which interprets integers as indices of
the cartesian coordinates and includes scalar and vector operations.
Options¶
-i, --in-place- Boolean argument, whether or not the geometry file is overwritten.
-t, --translate- Boolean argument, whether or not translate is used instead of rotate.
-n, --indices- Indices to displace, given as a string of integers separated by spaces.
-u, --units- Units for displacement amplitude.
-r, --reflect- Boolean argument, whether rotation is proper or improper.
-o, --origin- String defining the origin of rotation.
-f, --format- The input/output format (xyz, col, gdat, …)
-c, --has_comment- Boolean argument, whether or not comment is read.
-v, --has-vector- Boolean argument, whether or not vector is read.