Command-Line Reference¶

pqanalysis dispatches all supported commands from one executable. Every subcommand also provides local help:

$ pqanalysis --help
$ pqanalysis rdf --help

The command tables on this page are validated against the command registry at build time: a missing, renamed or undocumented command fails the documentation build.

Analysis commands¶

Command	Purpose	Primary input
rdf	Radial distribution and cumulative coordination	Input file
msd	Mean square displacement and diffusion fits	Input file
vacf	Velocity or charge-flux correlation and spectra	Input file
vibrations	Hessian normal modes and optional IR intensities	Input file
check_momentum	Total linear momentum per velocity frame	Trajectory files
build_spectrum	Gaussian or Lorentzian broadening of discrete lines	Line table

Analysis commands accept --export FILE where applicable. Repeat the option to produce several output formats without repeating the calculation.

Table conversion¶

pqanalysis convert rewrites analysis tables between formats; see Analysis Output Files and the generated option reference.

Structure and trajectory conversion¶

Command	Purpose
rst2xyz	Convert a PQ restart structure to XYZ
xyz2rst	Convert XYZ coordinates to a PQ restart structure
xyz2gen	Convert XYZ to DFTB+ GEN
gen2xyz	Convert DFTB+ GEN to XYZ
traj2box	Extract periodic box data from trajectories
traj2extxyz	Write extended XYZ trajectories with selected metadata
traj2qmcfc	Convert trajectories to QMCFC conventions

Simulation-support commands¶

Command	Purpose
continue_input	Continue indexed PQ or QMCFC input/output sequences
add_molecules	Add molecular structures to an existing system
build_nep_traj	Build Neuroevolution Potential (NEP) training and test trajectories

Commands refuse unsafe output replacement by default. Consult each generated reference page for its supported writing modes and format-specific options.