conversion_api

A module containing API functions to convert between different file formats.

Summary

Functions:

gen2xyz

Converts a gen file to a xyz file and prints it to stdout or writes it to a file.

rst2xyz

Converts a restart file to a xyz file and prints it to stdout or writes it to a file.

traj2box

Converts multiple trajectory files to a box file and prints it to stdout or writes it to a file.

traj2qmcfc

Converts multiple trajectory files from a PQ format to a QMCFC format and prints it to stdout or writes it to a file.

xyz2gen

Converts a xyz file to a gen file and prints it to stdout or writes it to a file.

Reference

gen2xyz(
gen_file: str,
output: str | None = None,
md_format: MDEngineFormat | str = MDEngineFormat.PQ,
print_box: bool = True,
mode: FileWritingMode | str = 'w',
) → None[source]

Converts a gen file to a xyz file and prints it to stdout or writes it to a file.

Parameters:

  • gen_file (str) – The gen file to be converted.

  • output (str | None) – The output file. If not specified, the output is printed to stdout.

  • md_format (MDEngineFormat | str, optional) – The format of the md engine for the output file. The default is MDEngineFormat.PQ.

  • print_box (bool, optional) – If True, the box is not printed. If False, the box is printed. Default is False.

  • mode (FileWritingMode | str, optional) – The writing mode, by default “w”. The following modes are available: - “w”: write - “a”: append - “o”: overwrite

rst2xyz(
restart_file: str,
output: str | None = None,
print_box: bool = True,
md_format: MDEngineFormat | str = MDEngineFormat.PQ,
mode: FileWritingMode | str = 'w',
) → None[source]

Converts a restart file to a xyz file and prints it to stdout or writes it to a file.

When the print_box flag is set to True, the box is printed as well. This means that after the number of atoms the box is printed in the same line in the format a b c alpha beta gamma.

Parameters:

  • restart_file (str) – The restart file to be converted.

  • output (str | None) – The output file. If not specified, the output is printed to stdout.

  • print_box (bool) – If True, the box is printed. If False, the box is not printed. Default is True.

  • md_format (MDEngineFormat | str, optional) – The format of the md engine for the output file. The default is MDEngineFormat.PQ.

  • mode (FileWritingMode | str, optional) – The writing mode, by default “w”. The following modes are available: - “w”: write - “a”: append - “o”: overwrite

traj2box(
trajectory_files: list[str],
vmd: bool,
output: str | None = None,
mode: FileWritingMode | str = 'w',
) → None[source]

Converts multiple trajectory files to a box file and prints it to stdout or writes it to a file.

Without the vmd option the output is printed in a data file format. The first column represents the step starting from 1, the second to fourth column represent the box vectors a, b, c, the fifth to seventh column represent the box angles.

With the vmd option the output is printed in a VMD file format. Meaning the output is in xyz format with 8 particle entries representing the vertices of the box. The comment line contains the information about the box dimensions a, b and c and the box angles.

Parameters:

  • trajectory_files (list of str) – The trajectory file(s) to be converted.

  • vmd (bool) – Output in VMD format.

  • output (str | None, optional) – The output file. If not specified, the output is printed to stdout. Default is None.

  • mode (FileWritingMode | str, optional) – The writing mode, by default “w”. The following modes are available: - “w”: write - “a”: append - “o”: overwrite

traj2qmcfc(
trajectory_files: list[str],
output: str | None = None,
mode: FileWritingMode | str = 'w',
) → None[source]

Converts multiple trajectory files from a PQ format to a QMCFC format and prints it to stdout or writes it to a file.

Parameters:

  • trajectory_files (list of str) – The trajectory file(s) to be converted.

  • output (str, optional) – The output file. If not specified, the output is printed to stdout.

  • mode (FileWritingMode | str, optional) – The writing mode, by default “w”. The following modes are available: - “w”: write - “a”: append - “o”: overwrite

xyz2gen(
xyz_file: str,
output: str | None = None,
periodic: bool | None = None,
mode: FileWritingMode | str = 'w',
md_format: MDEngineFormat | str = MDEngineFormat.PQ,
) → None[source]

Converts a xyz file to a gen file and prints it to stdout or writes it to a file.

Parameters:

  • xyz_file (str) – The xyz file to be converted.

  • output (str | None) – The output file. If not specified, the output is printed to stdout.

  • periodic (bool | None, optional) – The periodicity of the system. If True, the system is considered periodic. If False, the system is considered non-periodic. If None, the periodicity is inferred from the system, by default None.

  • mode (FileWritingMode | str, optional) – The writing mode, by default “w”. The following modes are available: - “w”: write - “a”: append - “o”: overwrite

  • md_format (MDEngineFormat | str, optional) – The format of the md engine for the output file. The default is MDEngineFormat.PQ.