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.