CNM post-processing CLI: lmodea-k-cnm

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CNM post-processing CLI: lmodea-k-cnm#

lmodea-k-cnm reads existing lmodea.h5 and dynmat.h5 files and computes alternative CNM amplitudes, including de-overlapped Konkoli-Cremer-style amplitudes for overlapping internal coordinates. This is a post-processing step for data generated by lmodea-k --cnm.

Usage#

lmodea-k-cnm [options]

Options#

--lmodea-h5 (default: lmodea.h5)

Path to the lmodea-k output file.

--dynmat-h5 (default: dynmat.h5)

Path to the standard dynamical-matrix input file.

-o / --output

Output HDF5 file. If omitted, the command updates lmodea.h5 according to the selected write mode.

--method (default: normalize_sum)

De-overlapping method. Supported values are normalize_sum, orthogonalise, project, and none.

--in-place

Modify lmodea.h5 in place.

-v / --verbose

Print more detailed progress information.

Output datasets#

The command writes CNM post-processing datasets to the selected output file, including:

  • CNM/amplitudes_deoverlapped

  • CNM/amplitudes_normalised

  • CNM/dominant_coord

  • CNM/max_amplitude

  • CNM/character_cumsum

  • CNM/coords_for_90_percent

  • local_modes/sym_keys

Examples#

lmodea-k-cnm --in-place
lmodea-k-cnm -o cnm_output.h5 --method orthogonalise