API reference for command line tools

API reference for command line tools#

shry#

SHRY command line interface.

Quick use: shry STRUCTURE_CIF. See shry -h for more options.

usage: shry [-h] [--from-species [FROM_SPECIES ...]]
            [--to-species [TO_SPECIES ...]]
            [--scaling-matrix [SCALING_MATRIX ...]] [--count-only]
            [--mod-only] [--no-write] [--dir-size DIR_SIZE] [--write-symm]
            [--write-ewald] [--symmetrize] [--max-ewald MAX_EWALD]
            [--symprec SYMPREC] [--atol ATOL]
            [--angle-tolerance ANGLE_TOLERANCE] [--sample SAMPLE]
            [--seed SEED] [--disable-progressbar]
            input

Positional Arguments#

input

A CIF containing command line options as keys. (See $SHRY_INSTALLDIR/examples)

structure modification#

--from-species, -f

Replace FROM_SPECIES from the CIF file into TO_SPECIES. Matches either _atom_site_label or atom_site_type_symbol. Use comma or space (preferred) for multiple substitutions.

Default: ()

--to-species, -t

Final chemical formula of the replaced FROM_SPECIES. Accepts various formats for the concentration and oxidation states such as SmFe12, Sm0.5Fe0.5, Sm3+Sm2+2Fe3, etc. The number of entry must be the same as FROM_SPECIES.

Default: ()

--scaling-matrix, -s

Three (for diagonal supercells) or nine (for non-diagonal supercells) integers specifying the scaling matrix for constructing a supercell. One scalar value is also accepted, which is converted to three scalar values (e.g., 1 -> 1 1 1)

Default: '1 1 1'

input and output#

--count-only

Enumerate the total number of ordered configurations from the given CIF and quit.

Default: False

--mod-only

Write a modified CIF without generating the ordered structures.

Default: False

--no-write

Generate ordered structures, but do not store them into disk.

Default: False

--dir-size

Number of output CIFs written to each output directories.

Default: 10000

--write-symm

Write symmetries for all output CIFs (slower).

Default: False

--write-ewald

Write Ewald energy for all output CIFs.

Default: False

--symmetrize

Use Wyckoff labels from a symmetry search to label the input CIF’s sites. By default, the label given within the CIF is used.

Default: False

--max-ewald

Set maximum Ewald energy for the output CIFs

run configuration#

--symprec

Symmetry search precision (simulation cell fraction).

Default: 0.01

--atol

Discretization absolute tolerance (angstrom).

Default: 1e-05

--angle-tolerance

Symmetry search angle tolerance (degrees).

Default: 5.0

--sample

Sample N number of ordered structures.

--seed

Random seed for the random number generator. Used only when –sample is set. Defaults to the (integer rounded) unixtime.

Default: 1770947752

--disable-progressbar

Disable progress bar. May stabilize longer runs.

Default: False

SHRY version 0.1.dev1

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