Converts a LAMMPS 3d histogram to a cube file for visualization in VMD. The current way I compute histograms in LAMMPS is with the following commands in the input file:
compute cc1 TIP4P_Water chunk/atom bin/3d x 0.0 0.01 y 0.0 0.01 z 0.0 0.01 units reduced
fix 7 TIP4P_Water ave/chunk ${nevery} ${nrepeat} ${nfreq} cc1 density/number norm all file TIP4P.profile ave running overwrite
To understand these commands, please consult the LAMMPS website. Anything defined with the dollar sign followed by curly braces is a variable that can be defined earlier in the lammps input script.
note: the above command can change between different LAMMPS versions. This was working with LAMMPS-17Nov16.
| Authors: | Peter Boyd |
|---|---|
| Date: | 24/2/2018 |