Metadata-Version: 2.4
Name: normal_modes_tools
Version: 1.0.5
Summary: Tools for working with normal modes
Project-URL: Homepage, https://github.com/the-pawel-wojcik/normal-modes-tools
Project-URL: Repository, https://github.com/the-pawel-wojcik/normal-modes-tools.git
Project-URL: Issues, https://github.com/the-pawel-wojcik/normal-modes-tools/issues
Author-email: Paweł Wójcik <pawel.wojcik5@gmail.com>
Keywords: chemistry
Requires-Python: >=3.13
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: xyz-parser
Description-Content-Type: text/markdown

# `normal_modes_tool`
Python tools helpful in working with normal modes.

## Capabilities
- 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`.
```bash
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`.


