MonomerFieldModel

Compute Raman and IR vibrational spectra of water molecules from local electric fields. Given the electric field projected along each O–H bond (e.g. sampled from an MD trajectory), the code solves the anharmonic vibrational Schrödinger equation on a 3D normal-mode grid and returns Raman transition polarizabilities and IR transition dipoles for the symmetric stretch, asymmetric stretch, and bend.

Installation

conda env create -f environment.yml
conda activate raman-spectra-water

Requires Python ≥ 3.10 with NumPy, SciPy, scikit-learn, joblib, and matplotlib (see environment.yml).

Usage

import numpy as np
from model import compute_frequencies

# (N, 2) array of electric-field projections along each O–H bond, in V/Å.
# Normally these come from MD; here is a small illustrative range.
example_fields = np.zeros([10, 2])
example_fields[:, 0] = np.linspace(0, -2, 10)

compute_frequencies(example_fields, "params/amoeba_params.json", seed=10)
# -> writes results.npz (freqs, activities, fields, eigenvalues)

See examples/examples.ipynb for a worked example showing the effect of the field on the symmetric stretch.

Parameters

compute_frequencies(projs, param_file, seed=10)

• projs — (N, 2) array of electric-field projections along the two O–H bonds (V/Å).
• param_file — JSON file of model parameters. Two water models are provided in params/:
  • params/amoeba_params.json — for the AMOEBA polarizable model.
  • params/spce_params.json — for the SPC/E model.
• seed — random seed for the bending-energy multipliers (default 10).

Results are written to results.npz containing freqs, activities, fields, and eigenvalues.

Module layout

File	Role
model.py	Main driver: compute_frequencies orchestrates the full calculation.
normal_modes.py	Harmonic normal-mode analysis and eigenvalue solver.
polarizability.py	Molecular polarizability model (onepol).
dipole.py	One-body and two-body dipole models (onedip, twodip).
potentials.py	Potential-energy surface (fastonebody).
basis.py	Vibrational basis functions and numerical derivatives.
geometry.py	Coordinate transforms between internal and Cartesian frames.
params/	Model parameters: constants.py (physical constants and equilibrium geometry) and the per-model JSON files (amoeba_params.json, spce_params.json).

Data

data/ holds the pre-trained models loaded at import time:

• polarizability_krr.joblib — kernel ridge model for the polarizability.
• one_body_ridge.joblib — ridge model for the one-body potential.
• one_body_shifts.npy — one-body energy shifts.

License

Copyright ©2026. The Regents of the University of California (Regents). All Rights Reserved. Permission to use, copy, modify, and distribute this software and its documentation is hereby granted, provided that the above copyright notice, this paragraph and the following two paragraphs appear in all copies, modifications, and distributions.

IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF REGENTS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.