Usage

Cosmochlore is a command line tool with one subcommand per analysis:

cosmochlore <COMMAND> <NAME> [OPTIONS]

Command	Description
cshm	Continuous shape measures calculation.
csom	Continuous symmetry operation measures calculation.
odis	Octahedral distortion analysis.
gidx	Geometry indices calculation.
help	Print the help or the help of the given subcommand(s).

<NAME> is the path to the input .xyz file with the structure to analyze.

Global options

Global options go before the command:

Flag	Description
-s, --silent	Print nothing to the terminal (banner, tables and progress messages). Files requested with flags are still written, and errors are still printed to stderr.
-h, --help	Print the help.
-V, --version	Print the version.

cosmochlore -s cshm FeHS.xyz -t

Warning

After the command, -s means something else: --sh for cshm and --seeds for csom.

Input files

Structures are read from standard .xyz files: the number of atoms, a comment line, then one label x y z line per atom.

FeHS.xyz

7
High-spin iron(ii) complex
Fe6 4.93013 10.3906 12.9236
N004 6.21021 10.6927 14.7824
N006 4.99632 8.50231 13.9489
N008 6.81046 10.0777 11.7691
N00B 5.46476 12.2907 12.1187
N00C 3.30099 11.3236 13.8608
N00D 3.74774 9.47633 11.4653

By default, the first atom is taken as the centre of the structure. Use -c/--center to pick another atom, or -n/--nc (where supported) when the file has no central atom.

Output files

Each command prints its results to the terminal. Extra files are only written when you ask for them with a flag, and they are named after the input file (FeHS.xyz gives FeHS_...).

Command	Flag	File written
cshm	-t, --table	name_cshm_table.csv: the table printed to the terminal.
	-i, --ideal	name_ideal.xyz: the reconstructed ideal structures for all the selected reference shapes.
csom	-t, --table	name_csom_table.csv: point group, deviation and refined rotation matrix.
	-f, --full	name_<PG>_details.csv, one per point group: the matrix and deviation of every symmetry operation.
	-o, --operated	name_<PG>_operated.xyz and name_<PG>_merged.mol2, one pair per point group.
odis	-t, --table	name_odis_table.csv: the distortion parameters. With --full, the cshm and csom tables are written too.
gidx	-t, --table	name_gidx_table.csv: the angles and indices.

For options of the specific commands, see modules.

Errors

Cosmochlore will always tell you if something went wrong at run-time. The program never crashes silently and never prints a number without letting you know that something failed.