mmml unwrap-traj¶
Unwrap periodic trajectories.
Usage¶
mmml unwrap-traj --help
Options¶
usage: mmml unwrap-traj [-h] -o OUTPUT [--format {auto,traj,xyz,extxyz,dcd}]
[--fast] [--index INDEX] [--cell CELL]
[--group-size GROUP_SIZE] [--n-groups N_GROUPS]
[--no-molecules] [--reference REFERENCE]
[--coord-key COORD_KEY] [--numbers-key NUMBERS_KEY]
[--cell-key CELL_KEY] [--quiet]
input
Unwrap periodic ASE trajectories or HDF5 coordinate files.
positional arguments:
input Input trajectory (.traj/.xyz/.extxyz/etc.) or .h5/.hdf5
file
Execution:
--n-groups N_GROUPS Number of equal contiguous molecule/groups for molecule-
wise unwrapping
Output & artifacts:
-o, --output OUTPUT Output file
Diagnostics & safety:
-h, --help show this help message and exit
--quiet Suppress summary output
Other options:
--format {auto,traj,xyz,extxyz,dcd}
Output format (default: infer from suffix)
--fast Use direct streaming writer for xyz/extxyz outputs
--index INDEX ASE input frame index/slice for non-HDF5 inputs
(default: :)
--cell CELL Override cell as 'a,b,c' or 9 matrix values
--group-size GROUP_SIZE
Atoms per contiguous molecule/group for molecule-wise
unwrapping
--no-molecules Disable automatic bonded-fragment grouping; unwrap atoms
independently
--reference REFERENCE
ASE-readable file supplying atomic numbers and fallback
cell for HDF5 inputs
--coord-key COORD_KEY
HDF5 coordinate dataset key (default:
R/positions/coordinates/coords/xyz)
--numbers-key NUMBERS_KEY
HDF5 atomic-number dataset key (default:
Z/atomic_numbers/numbers)
--cell-key CELL_KEY HDF5 cell dataset key (default:
cell/cells/lattice/lattices/box/boxes)
Unwrap periodic trajectories and write ASE/XYZ outputs. Examples: mmml unwrap-
traj in.traj -o unwrapped.traj mmml unwrap-traj in.traj -o unwrapped.xyz
--format xyz --fast mmml unwrap-traj coords.h5 -o unwrapped.extxyz --reference
wrapped.traj --fast