normal_modes_tool

Python tools helpful in working with normal modes.

Capabilities

• List normal modes and their frequencies

# Works only if the comment line in the xyz files has the following format
# 0. Vibration mode, 64.77 cm-1, B1
# i.e., frequency is the fourth whitespace-separated item of the comment line
python -m normal_modes_tool --list nmodes.xyz

• Displace the molecular geometry along a selected normal mode, see test/displace/displace.py.
• Compare two sets of normal modes and their harmonic frequencies, including building of the matrix of normal mode's overlaps, i.e., the Duszyński matrix test/sroph/build_duszynski.py.

python -m normal_modes_tool --compare new_nmodes.xyz old_nmodes.xyz

• Express the difference between two molecular geometries as displacement along normal modes, see test/pyrazine/find_dQ.py.
• Calculate the Huang-Rhys factors, see test/pyrazine/print_HRf.py or test/sroph/hrfs/huang_rhys_factors.py
• Find normal modes for molecule with isotope substitutions, see test/xsim/deuterate_nmodes.py.
• Transform gradients expressed in one set of normal modes to another, see test/xsim/deuterate_xsim_gradient.py.