Contents

Command line interface

Contents

Command line interface#

orgdisord#

orgdisord [OPTIONS] COMMAND [ARGS]...

analyse#

Command line interface for orgdisord thermodynamics.

TODO energy units! TODO: slight numerical inconsistencies wrt to Jonas’ code

orgdisord analyse [OPTIONS] CSV_FILE

Options

--prefix <prefix>#: Prefix for output file names.

-q, --quiet#: Suppress output?

-l, --log <log>#: Log file name.

-t, --temperatures <temperatures>#: Temperature range in K (inclusive of end points).

-s, --steps <steps>#: Number of temperature steps.

--dt <dt>#: Temperature step size in K.

Arguments

CSV_FILE#: Required argument

enumerate#

Command line interface for orgdisord.

orgdisord enumerate [OPTIONS] [FILES]...

Options

-s, --supercell <supercell>#: Supercell size e.g. 2 1 1

-N, --maxiters <maxiters>#: Maximum number of configurations generated

--exclude_ordered#: Exclude ordered part of structure in output structures?

-r, --random#: Generate random configurations?

-m, --merge#: Merge equivalent structures?

-a, --algo <algo>#

Algorithm used for merging equivalent structures.

Options: symm | rematch | ewald

-d, --use_disordered_only#: Use only the disordered part of structure in merging?

-p, --symprec <symprec>#: Symmetry precision used for merging equivalent structures.

--no_write#: Suppress writing out structures?

--prefix <prefix>#: Prefix for output file names.

-f, --format <format>#

Format of output strucuture files.

Options: cif | xyz | poscar | cell

-q, --quiet#: Suppress output?

-l, --log <log>#: Log file name.

--view#: View structures using ASE gui?

--ox <ox>#: Specify oxidation states for each species e.g. –ox H 1 –ox O -2

--not_molecular_crystal#: Do not reload as molecular crystal?

-c, --correlated_assemblies#: Are the disorder assemblies correlated?i.e. are the disorder groups within each assembly to be selected with the same index? (The number of disorder groups in each assembly must be the same in such cases.)

--fix-ratio#: Fix the ratio of the disorder groups.

--ratio <ratio>#: Manually specify the ratio of the disorder groups. Must be used with –fix-ratio.e.g. –ratio 0.75 would constrain the ratios of disorder group 1 and 2 to be 3:1NOTE: This is only implemented for 1-assembly, 2-group structures.

--ratio-tol <ratio_tol>#: Tolerance for how close the ratio of disorder groups needs to be. See atol in numpy.isclose.Only used if –fix-ratio is specified.

--ignore-species#: Ignore species when merging structures?

Arguments

FILES#: Optional argument(s)