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  1. TOC {:toc}

pymatgen.cli package

This package contains various command line interfaces for common pymatgen functionality such as file conversion, etc. Entry points to these interfaces are defined in setup.py.

pymatgen.cli.feff_plot_cross_section module

Script for plotting cross sections generated by FEFF found in xmu.dat files.

main()

Main function.

pymatgen.cli.feff_plot_dos module

Script to plot density of states (DOS) generated by an FEFF run either by site, element, or orbital.

main()

Main function.

pymatgen.cli.get_environment module

Command line script to get the chemical environment of a structure.

main()

Main function for get_environment CLI.

pymatgen.cli.pmg module

A master convenience script with many tools for vasp and structure analysis.

diff_incar(args)

Handle diff commands.

  • Parameters

    args – Args from command.

main()

Handle main.

parse_view(args)

Handle view commands.

  • Parameters

    args – Args from command.

pymatgen.cli.pmg_analyze module

Implementation for pmg analyze CLI.

analyze(args)

Master function controlling which analysis to call.

  • Parameters

    args (dict) – args from argparse.

get_energies(rootdir, reanalyze, verbose, quick, sort, fmt)

Get energies of all vaspruns in directory (nested).

  • Parameters

    • rootdir (str) – Root directory.

    • reanalyze (bool) – Whether to ignore saved results and reanalyze

    • verbose (bool) – Verbose mode or not.

    • quick (bool) – Whether to perform a quick analysis (using OSZICAR instead of vasprun.xml

    • sort (bool) – Whether to sort the results in ascending order.

    • fmt (str) – tablefmt passed to tabulate.

get_magnetizations(dir: str, ion_list: list[int])

Get magnetization info from OUTCARs.

  • Parameters

    • dir (str) – Directory name

    • ion_list (list*[int]*) – List of ions to obtain magnetization information for.

  • Returns

    0 if successful.

  • Return type

    int

pymatgen.cli.pmg_config module

Implementation for pmg config CLI.

add_config_var(tokens: list[str], backup_suffix: str)

Add/update keys in .pmgrc.yaml config file.

build_bader(fortran_command='gfortran')

Build bader package.

  • Parameters

    fortran_command –

build_enum(fortran_command: str = 'gfortran')

Build enum.

  • Parameters

    fortran_command –

configure_pmg(args: Namespace)

Handle configure command.

install_software(install: Literal['enumlib', 'bader'])

Install all optional external software.

setup_cp2k_data(cp2k_data_dirs: list[str])

Setup CP2K basis and potential data directory.

setup_potcars(potcar_dirs: list[str])

Setup POTCAR directories.

pymatgen.cli.pmg_plot module

Implementation for pmg plot CLI.

get_chgint_plot(args, ax: Axes | None = None)

Plot integrated charge.

  • Parameters

    • args (dict) – args from argparse.

    • ax (plt.Axes) – Matplotlib Axes object for plotting.

  • Returns

    Matplotlib Axes object.

  • Return type

    plt.Axes

get_dos_plot(args)

Plot DOS.

  • Parameters

    args (dict) – Args from argparse.

get_xrd_plot(args)

Plot XRD.

  • Parameters

    args (dict) – Args from argparse

plot(args)

Master control method calling other plot methods based on args.

  • Parameters

    args (dict) – Args from argparse.

pymatgen.cli.pmg_potcar module

Implementation for pmg potcar CLI.

gen_potcar(dirname, filename)

Generate POTCAR from POTCAR.spec in directories.

  • Parameters

    • dirname (str) – Directory name.

    • filename (str) – Filename in directory.

generate_potcar(args)

Generate POTCAR.

  • Parameters

    args (dict) – Args from argparse.

proc_dir(dirname, procfilefunction)

Process a directory.

  • Parameters

    • dirname (str) – Directory name.

    • procfilefunction (callable) – Callable to execute on directory.

pymatgen.cli.pmg_query module

Implementation for pmg query CLI.

do_query(args)

Perform query to the Materials Project.

  • Parameters

    args (dict) – Args from argparse.

pymatgen.cli.pmg_structure module

Implementation for pmg structure CLI.

analyze_localenv(args)

Analyze local env of structures in files.

  • Parameters

    args (dict) – Args for argparse.

analyze_structures(args)

Master function to handle which operation to perform.

  • Parameters

    args (dict) – Args from argparse.

analyze_symmetry(args)

Analyze symmetry of structures in files.

  • Parameters

    args (dict) – Args from argparse.

compare_structures(args)

Compare structures in files for similarity using structure matcher.

  • Parameters

    args (dict) – Args from argparse.

convert_fmt(args)

Convert files from one format to another.

  • Parameters

    args (dict) – Args from argparse.