pymatgen.cli package

Submodules

pymatgen.cli.feff_plot_cross_section module

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

main()[source]

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()[source]

Main function.

pymatgen.cli.get_environment module

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

main() → int[source]

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: Namespace) → int[source]

Handle diff commands.

Parameters:

args – Args from command.

main(argv: list[str] | None = None) → Any[source]

Entry point for the pmg CLI.

parse_view(args: Namespace) → int[source]

Handle view commands.

Parameters:

args – Args from command.

pymatgen.cli.pmg_analyze module

Implementation for pmg analyze CLI.

analyze(args: Namespace) → int[source]

Main function controlling which analysis to call.

Parameters:

args (Namespace) – args from argparse.

get_energies(rootdir: str, reanalyze: bool, verbose: bool, quick: bool, sort: bool, fmt: str) → int[source]

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(dirc: str, ion_list: list[int]) → int[source]

Get magnetization info from OUTCARs.

Parameters:

• dirc (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) → None[source]

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

build_bader(fortran_command='gfortran') → bool[source]

Build bader package.

Parameters:

fortran_command – The Fortran compiler command.

build_enum(fortran_command: str = 'gfortran') → bool[source]

Build enum.

Parameters:

fortran_command – The Fortran compiler command.

configure_pmg(args: Namespace)[source]

Handle configure command.

install_software(install: Literal['enumlib', 'bader']) → None[source]

Install all optional external software.

setup_cp2k_data(cp2k_data_dirs: list[str]) → None[source]

Setup CP2K basis and potential data directory.

setup_potcars(potcar_dirs: list[str]) → None[source]

Setup POTCAR directories.

pymatgen.cli.pmg_plot module

Implementation for pmg plot CLI.

get_chgint_plot(args: Namespace, ax: plt.Axes | None = None) → plt.Axes[source]

Plot integrated charge from CHGCAR file.

Parameters:

• args (Namespace) – args from argparse.

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

Returns:

Matplotlib Axes object.

Return type:

plt.Axes

get_dos_plot(args: Namespace) → plt.Axes[source]

Plot DOS from vasprun.xml file.

Parameters:

args (Namespace) – Args from argparse.

get_xrd_plot(args: Namespace) → plt.Axes[source]

Plot XRD from structure.

Parameters:

args (Namespace) – Args from argparse

plot(args: Namespace) → None[source]

Master control function calling other plot functions based on args.

Parameters:

args (Namespace) – Args from argparse.

pymatgen.cli.pmg_potcar module

Implementation for pmg potcar CLI.

gen_potcar(dirname: str, filename: str) → None[source]

Generate POTCAR from POTCAR.spec in directories.

Parameters:

• dirname (str) – Directory name.

• filename (str) – Filename in directory.

generate_potcar(args: Namespace) → None[source]

Generate POTCAR.

Parameters:

args (Namespace) – Args from argparse.

proc_dir(dirname: str, proc_file_function: Callable) → None[source]

Process a directory.

Parameters:

• dirname (str) – Directory name.

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

pymatgen.cli.pmg_structure module

Implementation for pmg structure CLI.

analyze_localenv(args: Namespace) → None[source]

Analyze local env of structures in files.

Parameters:

args (Namespace) – Args for argparse.

analyze_structures(args: Namespace) → None[source]

Main function to handle which operation to perform.

Parameters:

args (Namespace) – Args from argparse.

analyze_symmetry(args: Namespace) → None[source]

Analyze symmetry of structures in files.

Parameters:

args (Namespace) – Args from argparse.

compare_structures(args: Namespace) → None[source]

Compare structures in files for similarity using structure matcher.

Parameters:

args (Namespace) – Args from argparse.

convert_fmt(args: Namespace) → None[source]

Convert files from one format to another.

Parameters:

args (Namespace) – Args from argparse.