Hi Lammps’s user,
I visualize fix deposit dump file with VMD simple load file
dump 1 all xyz 10 tmp.deposit then set atom type.
VMD can recognize only frame with fixed number of particles. Then I have to extract dump file to piece of same particle=substract surface + n*adatoms and animate by VMD.
So I wonder could it be visualize a dump file (in xyz sequential) with varying number-of-atoms in one view?
many thanks and regards,
Tuoc Vu
Hi Lammps's user,
hi tuoc vu,
this is (another) vmd question and would be _much_ more suitable
to be asked on the VMD mailing list.
I visualize fix deposit dump file with VMD simple load file
dump 1 all xyz 10 tmp.deposit then set atom type.
VMD can recognize only frame with fixed number of particles. Then I have to
extract dump file to piece of same particle=substract surface + n*adatoms
and animate by VMD.
So I wonder could it be visualize a dump file (in xyz sequential) with
varying number-of-atoms in one view?
you have three options:
1) you can "explode" the .xyz file into multiple files (one per frame,
this can be done with a simple perl/awk/python/etc script) and then
load them (via a scripted loop) into separate "molecules" in VMD and
then use the MultiMolAnim plugin to loop/animate over them.
http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/
2) you can become a beta-tester for the latest version of
the topotools plugin. this adds support for a "topo readvarxyz"
command that will convert the .xyz file transparently into a
data set with a fixed number of atoms and then encode the
visibility into the "user" field. i.e. if you replace the default
"all" selection with "user > 0" then it should only show the
atoms that are present in a given frame.
http://sites.google.com/site/akohlmey/software/topotools
3) you can use a viewer that _can_ handle a variable number
of atoms per frame. i usually don't have to deal with this kind
of problem (the topotools hack was mostly done so that i don't
have to explain over and over again, _why_ vmd cannot handle
varying number of atom trajectories and that it can be worked
around with a little bit of effort. apparently, these days, even
a little bit of effort is too much...).
cheers,
axel.