VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 14 2013 - 13:11:16 CDT

If people felt it useful, I could add separate coloring for vx/vy/vz...
I didn't add it previously because there's something to be said for
keeping the VMD menus free of clutter, if it would be a very infrequently
used coloring mode.

Cheers,
  John

On Tue, May 14, 2013 at 06:59:37PM +0200, Axel Kohlmeyer wrote:
> On Tue, May 14, 2013 at 6:47 PM, Dave Schall <schalljd_at_gmail.com> wrote:
> > Axel,
> >
> > Your method sort of works, in that charge (now vx) does change dynamically;
> > however, there is one odd thing. The range for vx seems to be the absolute
> > value of the original q. My actual charge ranges from -0.62 to +0.22. Once I
> > ran your script, I have an autoscale values ranging from 0 to +0.62. So
> > there is something funny going on.
>
> nothing funny going on. you cannot color by vx, you color by velocity,
> which is sqrt(vx*vx + vy*vy + vz*vz) and thus gives you abs(vx).
>
> > I actually cheated (after trying your script) and did search and replace
> > with "perl -pi 's/q/vx/g' lammps.trj" to simply change all the q's to vx's
> > in the dump file. No additional scripts necessary (but I get the same range
> > issue).
>
> that is why i suggested to copy the vx field to user (or user2, user3, user4).
>
> axel.
>
> > Dave
> >
> >
> > On Tue, May 14, 2013 at 3:38 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> >>
> >> On Mon, May 13, 2013 at 10:20 PM, Dave Schall <schalljd_at_gmail.com> wrote:
> >> > Hello,
> >>
> >> hi dave,
> >>
> >> > I am trying to visualize results from a simulation where charge is a
> >> > dynamic
> >> > variable. I am using coordinate and charge data output from a LAMMPS
> >> > dump
> >> > command. The lammps trj file loads no problem into vmd, and I can color
> >> > atoms by charge, but I don't see the charges varying frame to frame (and
> >> > they are varying, I checked). I checked the "update colors every frame"
> >> > box
> >>
> >> this is due to the design decision in VMD. since its original target
> >> was visualize data from conventional bio force fields, properties that
> >> don't change (atom type, radius, number of atoms, charge and so on)
> >> were only stored once per molecule. only coordinates were stored per
> >> frame resulting in huge savings in memory consumption for long
> >> trajectories. there are some additional fields that can store per
> >> frame per atom data (user, user2, user3, user4, vx, vy, vz), but only
> >> the velocity fields are supported by the molfile plugin interface,
> >> which is used to read in trajectories. in the plugin for LAMMPS
> >> trajectories, i've included a little hack that allows you to remap
> >> fields, i.e. you can divert the charge field to the vx property and
> >> thus access the information inside of VMD.
> >>
> >> > as well. I seem to recall you need some sort of tcl script if you want
> >> > to
> >> > update charge for every frame. I have an old script that works for pdb
> >> > files
> >> > but I am not sure exactly where to start modifying the script to read a
> >> > lammps trj file. Can anybody point me towards a solution?
> >>
> >> that is a very cumbersome approach and i don't recommend that. i'd
> >> suggest you use something like this to load the charge information
> >> into the user field.
> >>
> >> global env
> >> set env(LAMMPSREMAPFIELDS) vx=q
> >> set mol [mol new lammps.trj type lammpstrj waitfor all]
> >> # insert "mol addfile command here, if needed"
> >> set nf [molinfo $mol get numframes]
> >> set sel [atomselect $mol all]
> >> for {set i 0} {$i < $nf} {incr i} {
> >> $sel frame 0
> >> $sel set user [$sel get vx]
> >> $sel set vx 0.0
> >> }
> >> $sel delete
> >> unset sel
> >> unset env(LAMMPSREMAPFIELDS)
> >>
> >> if you then set Coloring Method to Trajectory->User->User you should
> >> get the visualization you are looking for.
> >>
> >> for more info on the lammps molfile plugin, you can go to this page
> >>
> >> https://sites.google.com/site/akohlmey/software/lammps-icms#TOC-VMD-molfile-plugin
> >> and if you'd rather do it "the hard way", you can look up some
> >> examples and explanations in this pdf
> >>
> >> https://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1
> >>
> >> please let us know if you have any additional questions.
> >>
> >> cheers,
> >> axel.
> >>
> >>
> >> >
> >> > Thanks,
> >> >
> >> > Dave
> >> >
> >> >
> >> >
> >> > --
> >> > J. David Schall, Assistant Professor
> >> > Dept. of Mechanical Engineering, Oakland University
> >> > 130 DHE, Rochester, MI 48309
> >> > 248-370-2870
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
> >
> >
> > --
> > J. David Schall, Assistant Professor
> > Dept. of Mechanical Engineering, Oakland University
> > 130 DHE, Rochester, MI 48309
> > 248-370-2870
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
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