VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 14 2013 - 11:59:37 CDT

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.