CLI reference

sqsgen

sqsgenerator - A CLI tool to find optimized SQS structures

sqsgen [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

analyse

Calculate SRO parameters of existing structures. Searches by default for a file named “sqs.result.yaml”.

sqsgen analyse [OPTIONS] [INPUT_FILES]...

Options

-s, --settings <settings>
-r, --reader <reader>

Backend for writing the structure files. Default is “None”

Options

ase | pymatgen

-of, --output-format <output_format>

Output format type

Options

yaml | json | pickle | native

Arguments

INPUT_FILES

Optional argument(s)

compute

Compute quantities to determine how computationally demanding you input file is

sqsgen compute [OPTIONS] COMMAND [ARGS]...

estimated-time

Estimate the runtime of your current settings

sqsgen compute estimated-time [OPTIONS] [FILENAME]

Options

-v, --verbose

Print very detailed infos

-if, --input-format <input_format>

The filetype of {filename}

Options

yaml | json | pickle

Arguments

FILENAME

Optional argument

rank

Calculate a unique number identifying the structure in the input file

sqsgen compute rank [OPTIONS] [FILENAME]

Options

-if, --input-format <input_format>

The filetype of {filename}

Options

yaml | json | pickle

Arguments

FILENAME

Optional argument

shell-distances

Calculate the default radii of the coordination shells

sqsgen compute shell-distances [OPTIONS] [FILENAME]

Options

-if, --input-format <input_format>

The filetype of {filename}

Options

yaml | json | pickle

Arguments

FILENAME

Optional argument

total-permutations

The number of iterations carried out. Useful for for “systematic” mode

sqsgen compute total-permutations [OPTIONS] [FILENAME]

Options

-if, --input-format <input_format>

The filetype of {filename}

Options

yaml | json | pickle

Arguments

FILENAME

Optional argument

export

Export sqsgenerator’s results into structure files

sqsgen export [OPTIONS] [FILENAME]

Options

-f, --format <format>

Output format for the structure file(s). The format must be supported by the specified backend

-w, --writer <writer>

Backend for writing the structure files. Default is “None”

Options

ase | pymatgen

-c, --compress <compress>

Gather the output structure files in an compressed archive

Options

zip | bz2 | gz | xz

-o, --output <output_file>

A file name prefix. The file extension is chosen automatically

-if, --input-format <input_format>

The filetype of {filename}

Options

yaml | json | pickle

Arguments

FILENAME

Optional argument

params

Utilities to check the parameters that are going to be used in the SQS iteration

sqsgen params [OPTIONS] COMMAND [ARGS]...

check

Check if your input settings will work

sqsgen params check [OPTIONS] [FILENAME]

Options

-if, --input-format <input_format>

The filetype of {filename}

Options

yaml | json | pickle

Arguments

FILENAME

Optional argument

show

Display all or certain input parameters

sqsgen params show [OPTIONS] [FILENAME]

Options

-p, --param <param>

Display only this input parameter(s)

Options

atol | rtol | mode | iterations | max_output_configurations | structure | which | composition | shell_distances | shell_weights | pair_weights | target_objective | prefactor_mode | prefactors | threads_per_rank

-of, --output-format <output_format>

Output format type

Options

yaml | json | pickle | native

--inplace

Dump the computed input parameters in the input settings file

-if, --input-format <input_format>

The filetype of {filename}

Options

yaml | json | pickle

Arguments

FILENAME

Optional argument

run

Perform a SQS iteration

sqsgen run [OPTIONS] COMMAND [ARGS]...

iteration

Perform a SQS iteration

sqsgen run iteration [OPTIONS] [FILENAME]

Options

-m, --minimal, -nm, --no-minimal

Include only configurations with minimum objective function in the results

-s, --similar, -ns, --no-similar

If the minimum objective is degenerate include also results with same parameters but different configuration

--log-level <log_level>

log level of the core extension. Should be “trace” used for error reporting

Options

trace | debug | info | warning | error

-d, --dump, -nd, --no-dump

Dump sqsgenerator’s results in a file

-e, --export

Export the results obtained from the SQS iteration as structure files

-dp, --dump-params

Dump input parameters - Append them to the newly generated output

-f, --format <format>

Output format for the structure file(s). The format must be supported by the specified backend

-w, --writer <writer>

Backend for writing the structure files. Default is “None”

Options

ase | pymatgen

-o, --output <output_file>

A file name prefix. The file extension is chosen automatically

-df, --dump-format <dump_format>

Format used to store sqsgenerator’s results

Options

yaml | json | pickle

-di, --dump-include <dump_include>

Include field in sqsgenerator’s results

Options

parameters | timings | objective

-c, --compress <compress>

Gather the output structure files in an compressed archive

Options

zip | bz2 | gz | xz

-if, --input-format <input_format>

The filetype of {filename}

Options

yaml | json | pickle

Arguments

FILENAME

Optional argument