Is there a file format and a suitable viz software that is capable of visualizing changeing dimensions of particles ?
I have particles that change their radius during the run, and i would like to actually see that in a movie.
VMD can’t do that unfortunately.
Thanks in advance,
Is there a file format and a suitable viz software that is capable of
visualizing changeing dimensions of particles ?
I have particles that change their radius during the run, and i would
like to actually see that in a movie.
VMD can't do that unfortunately.
i beg to differ. VMD _can_ do this. you probably
just don't know it well enough (and there is a lot
to know ). it is only that it is not something
that is directly available from a menu or directly
described in the user's guide.
there are currently two ways to go about this.
the traditional way is to write a little tcl script
that will load the radius information from an external
file into a tcl array with entries for each atom for
each fram and then change the radius for each atom
by placing a trace on the vmd_frame([molinfo top])
variable. you can find some explanations and examples
on how this works in a tutorial that i wrote long ago.
example scripts are deposited here:
this works for all VMD versions except from those
that were running on stone circles.
if you are more adventurous, you can try the latest
VMD alpha version. this version has code in it to do
this radius change automatically based on a per time
step property. it is not yet connected to a GUI element,
thus you have to set the environment variable
VMDMODULATERADIUS to a data field that you want to use
as the source of the radius. if you also set the environmet
variable LAMMPSREMAPFIELDS, e.g. to vx=radius
and then modulate by the vx field, you should get
exactly what you are asking for.
instructions on how to get VMD alpha releases are here:
The only thing I'll add is that you can use dump custom
from LAMMPS to add the radius of each particle to
the per-atom lines of output each snapshot.