Dear LAMMPS users,
I am running peri code from LAMMPS example folder recently. I apply dump
file into VMD and Paraview but find that the atoms that show in both post
proccessing is point or line, and when I want to change the graphical
representations (in VMD, I try to change the drawing method into VDW; and
in paraview, I try to change it into volume), the structure will disappear.
Does anyone have any idea about this situation? I will also like to know
how to make the picture looks like the below attachment:
yes. at least for VMD. the problem with VMD is, that it assumes you want
to process molecular data with MD units (e.g. length in angstrom).
VMD does not know that you use SI units. furthermore, VMD does not know
what the diameter of your particles is, so it guesses 1.5 (which is a
decent guess for atoms). if you switch to radius based visualization, you
cannot see the spheres because you are deep, deep inside them.
i just made a little experiment with the peri example from the LAMMPS
distribution.
after i uncomment the dump command and load the trajectory into VMD, i type
the following VMD/Tcl script commands into the console.
set sel [atomselect top all]
$sel set radius 0.0003
switching to VDW now works as expected, since i have reset the radius to a
value 5000x smaller, which is consistent with the distance between
particles.
now, to color code your atoms by an arbitrary per timestep property in VMD,
you have to use a hack. VMD can only read positions and velocities as
per-timestep per-atom data. the LAMMPS plugin for VMD has a remap function.
see https://sites.google.com/site/akohlmey/software/lammps-plugin
so if i launch VMD as follows:
env LAMMPSREMAPFIELDS=vx=c_1 vmd -lammpstrj dump.peri
the will read the data from compute 1 into the velocity x coordinate.
then do the same adjustment as above:
set sel [atomselect top all]
$sel set radius 0.0003
now switch to VDW representation and Coloring Method: Trajectory -> Velocity
and at the Trajectory tab activate "Update Color Every Frame", you should
get what you desire.
for a random mid-trajectory frame, i get the attached visualization...
axel.
