PQAnalysis¶

PQAnalysis provides command-line and Python tools for quantitative analysis of PQ molecular-dynamics simulations. It reads structures, trajectories, velocities and Hessians, then produces documented scientific tables for structural, transport and vibrational observables.

Quick start¶

PQAnalysis requires Python 3.12 or newer. Install it and run an analysis from its input file:

$ python -m pip install pqanalysis
$ pqanalysis rdf rdf.in

Getting Started walks through this run on the bundled example.

Analysis methods¶

Method	Required data	Reported quantity
Radial distribution	Positions and periodic cell	\(g_{AB}(r)\) and cumulative coordination
Mean square displacement	Positions and periodic cell	Cartesian MSD and diffusion fits
VACF and spectra	Velocities, sampling interval and optional charges	Normalized correlation and wavenumber spectrum
Vibrational analysis	Structure, masses and Cartesian Hessian	Normal modes, wavenumbers and optional IR intensities
Momentum diagnostic	Velocities and atomic masses	Frame-resolved total linear momentum

Python interface¶

The same input files and kernels are callable from Python; see Learn the Python API and the function index.

Development¶

New methods follow a documented path from estimator and validation evidence to the public API, CLI and schema-backed output. See Adding an Analysis for the required implementation steps and Architecture for package ownership boundaries.