MOFUN
Installation
Requires Python > 3.8.
Command-line usage:
mofun --help Tue Jan 18 12:00:59 2022
Usage: mofun [OPTIONS] INPUTPATH OUTPUTPATH
Options:
-f, --find PATH
-r, --replace PATH
-p, --replace-fraction FLOAT
--atol FLOAT absolute tolerance in Angstroms for atom
posistions to be considered matching
-ap1, --axisp1-idx INTEGER index of first point on primary rotation axis
-ap2, --axisp2-idx INTEGER index of second point on primary rotation axis
-op, --opoint-idx INTEGER index of point that makes up secondary
rotation axis (between this point and the
primary rotation axis)
--dumppath PATH
-q, --chargefile FILENAME
--replicate INTEGER... replicate structure across x, y, and z
dimensions
--mic FLOAT enforce minimum image convention using a
cutoff of mic
--framework-element TEXT convert all atoms that are in group 0, the
framework group to a specific atom type to
make vizualizing the structure easier
--pp Assign UFF pair potentials to atoms
(sufficient for fixed force-field
calculations)
--help Show this message and exit.
Python documentation:
See Atoms for info on Atoms objects and how to use them.
See mofun for find_pattern_in_structure() and replace_pattern_in_structure().
See Examples for full examples on real systems, using both the command line and the Python interfaces.