CPMD Plugin, Version 0.4
This plugin reads CPMD trajectories from the TRAJECTORY file. The file consists of many lines in the form
timestep x y z vx vy vzwhich contain the timestep number (NFI), the x-, y-, and z-positions and the x-, y-, and z-velocities respectively (in atomic units) for each atom. If a trajectory file is continued, CPMD will insert a line with the string <<<<<< NEW DATA >>>>>> which will be recognized and ignored by this plugin.
Notes:
Read-only
This plugin is used only to read files. VMD does not currently support
writing this file type. Saving in either binary DCD format (to reduce disk space
requirements and enable much faster loading) or XYZ format (to avoid having to load
a file with the atom name assignments first) instead is recommended.
Automatic File Format Detection
TRAJECTORY has no filename extension, so VMD will ask you to provide
a file type manually or try to read it as PDB as last resort (which will fail). However, if you rename the file to a name ending in
.cpmd VMD will atomatically detect the format.
Atom Names
The TRAJECTORY file does not contain any information about the
respective elements for the recorded positions. You have to
load a file containing that information in the same order,
e.g. the corresponding GEOMETRY.xyz file first and then
use Load Data Into Molecule....
Periodic Boundary Conditions
CPMD does not apply periodic boundary conditions before writing
to the TRAJECTORY file, so you may either preprocess the data
accordingly or use a script like the pbcswrap script from the VMD
script library to translate the atoms back into the unitcell.
