pyqmmm.qm.neb_doubler

Module Contents

Functions

main(→ Dict[str, Any])

Double an ORCA NEB .allxyz trajectory by inserting NEB-IDPP midpoints between each pair.
pyqmmm.qm.neb_doubler.main(original: str = 'restart.allxyz', output_allxyz: str = 'restart_doubled.allxyz', output_xyz: str = 'restart_doubled.xyz', input_file: str = 'qmscript.in', module_load_cmd: str = 'module load orca/6.0.0', orca_path: str = '/data1/groups/HJKgroup/src/orca/orca6/6.0.0/orca', archive_dir: str = 'path_doubling_archive', nprocs: int = 1, maxcore: int = 3600, nimages: int = 3, strict_double: bool = True) → Dict[str, Any][source]

Double an ORCA NEB .allxyz trajectory by inserting NEB-IDPP midpoints between each pair.

Parameters:

  • original (str) – Input .allxyz (default: ‘restart.allxyz’)

  • output_allxyz (str) – Output .allxyz with ‘>’ separators (default: ‘restart_doubled.allxyz’)

  • output_xyz (str) – Output stacked .xyz (default: ‘restart_doubled.xyz’)

  • input_file (str) – Previous ORCA input to read charge/spin (default: ‘qmscript.in’)

  • module_load_cmd (str) – Module load command, empty to skip (default: ‘module load orca/6.0.0’)

  • orca_path (str) – Path to ORCA executable

  • archive_dir (str) – Directory to move temporary artifacts

  • nprocs (int) – PAL nprocs (default: 1)

  • maxcore (int) – Maxcore per process in MB (default: 3600)

  • nimages (int) – Total images for NEB-IDPP (odd >= 3): start + middle + end (default: 3)

  • strict_double (bool) – If True, pad with last frame to reach exactly 2*N frames (no extrapolation)

Returns:

Summary info with keys: [‘input_frames’,’output_frames’,’natoms’,’archived_items’,’output_allxyz’,’output_xyz’]

Return type:

dict