Analyses

PQAnalysis covers structural organization, translational dynamics, time-correlation spectra, molecular normal modes and conservation diagnostics. Choose the observable from the physical question and from the data recorded by the simulation.

Choose by input data

Analysis	Required physical data	Primary observable
RDF	Positions and periodic cell	\(g_{AB}(r)\) and cumulative coordination
MSD	Positions and periodic cell	\(\langle |\mathbf{r}(t)-\mathbf{r}(0)|^2\rangle\)
VACF	Velocities and frame time step	Normalized \(C_{vv}(t)\) and its spectrum
Vibrations	Structure, masses and Cartesian Hessian	Normal-mode wavenumbers and force constants
Momentum	Velocities and atomic masses	\(|\sum_i m_i\mathbf{v}_i|\) per frame

Each method page gives the estimator, a working input file, the output layout and a Python recipe. RDF, MSD, VACF and vibrations end with a checklist whose derivations sit on a “Theory and Validity” subpage. File columns and units are specified once in Analysis Output Files; the bundled fixture is Example data.