Internal Coordinates

MATILDA provides a variety of tools for analysing internal coordinates.

Basic analysis

Analyse internal coordinates of a molecule. This also works for a file containing multiple geometries of one molecule (e.g. coming from dynamics).

int_coor_multi.py

usage: int_coor_multi.py [-h] [-f FILENAME [FILENAME ...]] [--filetype FILETYPE] [-d DIST DIST]
                     [-b BEND BEND BEND] [-t TORS TORS TORS TORS] [-dg DIGITS]

Outputs the value of the speciefied internal coordinate

options:
-h, --help            show this help message and exit
-f FILENAME [FILENAME ...], --filename FILENAME [FILENAME ...]
--filetype FILETYPE
-d DIST DIST, --dist DIST DIST
                    The indices of atoms for distance
-b BEND BEND BEND, --bend BEND BEND BEND
                    The indices of atoms for bend angle
-t TORS TORS TORS TORS, --tors TORS TORS TORS TORS
                    The indices of atoms for dihedral angle
-dg DIGITS, --digits DIGITS
                    Number of decimal points

Example

int_coor_multi.py -d 1 2 -b 1 2 4 -t 5 1 2 6 -f dyn.xyz

Rotational constants

Computes the three rotational constants (in MHz) of a molecule from its cartesian coordinates. It can also accept multiple xyz files.

rot_const.py

usage: rot_const [-h] [-f FILENAME [FILENAME ...]] [--filetype FILETYPE]

Computes rotational constants (in MHz) of the molecule from geometry

options:
-h, --help            show this help message and exit
-f FILENAME [FILENAME ...], --filename FILENAME [FILENAME ...]
--filetype FILETYPE

Example

rot_const.py -f 1orca.xyz 2orca.xyz

Lanthanide complexes

The lanth_geo.py script provides functionality specifically for lanthanide complexes. Aside from bond lengths it computes the SAP/tSAP twisting angle for the main eight coordination sites.

To use this functionality, one needs to specify four BOTTOM_INDS defining the bottom square and four TOP_INDS defining the top square. Alternatively, one can specify 3 indices each to analyse a trigonal (anti)prism geometry.

lanth_geo.py

usage: lanth_geo.py [-h] [-f FILENAME] [--filetype FILETYPE] [-l LANTH_IND] [-b BOTTOM_INDS] [-t TOP_INDS]

Determine SAP or tSAP geomtry for lanthanide complex

options:
-h, --help            show this help message and exit
-f FILENAME, --filename FILENAME
--filetype FILETYPE
-l LANTH_IND, --lanth_ind LANTH_IND
                    index defining the lanthanide
-b BOTTOM_INDS, --bottom_inds BOTTOM_INDS
                    indices defining the bottom square
-t TOP_INDS, --top_inds TOP_INDS
                    indices defining the top square

Example

lanth_geo.py -f nucfid.xyz -b 2 23 16 9 -t 33 83 77 71