pimd-centroid

PIMD centroid and spread

Collapses a path-integral molecular dynamics bead trajectory to one con frame per sampled step. The positions are the centroid over the P beads; the readcon spreads section holds each atom’s root-mean-square displacement from the centroid along x, y and z in Angstrom. Needs readcon>=0.16.0.

rgpycrumbs eon pimd-centroid

Write the bead centroid and spread of TRAJECTORIES as a con file.

Usage

rgpycrumbs eon pimd-centroid [OPTIONS] TRAJECTORIES...

Options

--replicas <replicas>

Replicas in one file.

--every <every>

Default:

1

--reference <reference>

--symbols <symbols_file>

--cell <cell>

Box lengths a b c in Angstrom.

--time-average

One averaged frame.

-o, --out <out>

Default:

PosixPath('centroid.con')

Arguments

TRAJECTORIES

Required argument(s)

Inputs

CPMD TRAJECTORY text (step, x, y, z, vx, vy, vz per atom, positions in bohr) or extended xyz (Angstrom); the format follows from the first line.

• One file per replica, same frame and atom count:

  rgpycrumbs eon pimd-centroid TRAJECTORY_* --reference reactant.con -o centroid.con
  

• One file with P x N atoms per frame, replica-major:

  rgpycrumbs eon pimd-centroid TRAJECTORY --replicas 16 --every 10 --reference reactant.con
  

The trajectory has no cell, masses or fixed flags. --reference supplies symbols, masses, cell and fixed flags from the first frame of a con file; without it, --symbols (a whitespace-separated list, or the symbols of an xyz trajectory) and --cell A B C do.

Time average

--time-average writes one frame: the centroid averaged over the sampled frames (--every applies first). Its spread is the imaginary-time spread and the thermal spread of the centroid added in quadrature, and the frame metadata states both as spread_imaginary_time_rms and spread_thermal_rms (rms over atoms and components, Angstrom).

Per-frame metadata: replicas, frame_index (index in the input), spread_max.

API Reference

For developer details and source code see rgpycrumbs.eon.pimd_centroid.