TRAVIS: A Trajectory Analyzer and Visualizer¶
TRAVIS is a command line C++ program for analyzing and visualizing trajectories from all kinds of Molecular Dynamics or Monte Carlo simulations developed by M. Brehm (J. Chem. Inf. Model. 51(8) (2011)). TRAVIS is shipped with the Amsterdam Modeling Suite from on ADF2017.
The supported input formats of TRAVIS are:
- lmp (Lammps)
- HISTORY (DLPOLY)
- prmtop/mdcrd (Amber)
With ADF2017 the analysis of DFTB and ReaxFF trajectories is supported.
TRAVIS was designed with non-reactive trajectories in mind, thus one needs to make sure that:
- either the composition of the target species does not change, e.g. by analyzing only a suitable time-interval or running non-reactive dynamics
- or the analysis does not depend on the detection of a particular species, e.g. the diffusion of (inert) atoms
In order to run a TRAVIS analysis on your trajectory open a shell and navigate to the folder you ran your calculation in. Use the python script kf_to_xyz.py to convert your trajectory into a TRAVIS-compatible XYZ-format.
Assuming the trajectory is called traj.rxkf, run:
$ADFBIN/startpython $ADFHOME/scripting/trajectory_analysis/kf_to_xyz.py traj.rxkf
This step will create a file called traj_travis.xyz that contains the frames in XYZ format plus an additional 5th column containing the ReaxFF atomic charges.
Next, start TRAVIS to enter an interactive dialog:
$ADFBIN/travis.exe -p traj_travis.xyz
An example of how to use TRAVIS with ReaxFF can be found in the advanced Li-Batteries ReaxFF tutorial .