Dear list (and more specifically Axel):
IIn VMD, there are options to color atoms by user defined fields. I was hoping to store the kinetic energy per atom in the lammps trajectory file and read this into the user defined field in VMD. Has any one attempted this/know of an easy way to accomplish this?
Best,
Tamara
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Dear list (and more specifically Axel):
IIn VMD, there are options to color atoms by user defined fields. I was hoping to store the kinetic energy per atom in the lammps trajectory file and read this into the user defined field in VMD. Has any one attempted this/know of an easy way to accomplish this?
dear tamara,
the lammps trajectory reader plugin is already capable of doing this,
however, there is currently a limitation in VMD to pass this informatiiion
in the most flexible ways. the VMD molfile plugin API at the moment only
allows to pass the vx, vy, and vz fields, ie. the x-,y-,and z-component
of the velocity. since you want to pass the kinetic energy of each atom,
this would already be sufficient, as the difference would only be a
scaling factor. if you want to pass other information, there is currently
a workaround that would allow to map any field to one of the supported
fiields: you would have to set the environment variable LAMMPSREMAPFIELDS
to a list of A=B mappings. example
LAMMPSREMAPFIELDS=vx=fx,vy=radius,vz=q
this would store the x-direction force component in vx,
the radius in vy and the charge in vz.
for color by user applications, you would then have to
copy this information internally, but at least you don't
have to store it into an additional external file (with fix print)
and write your own reader/parser that would read and
store the information into a user field.
hope this helps,
axel.