VMD-L Mailing List

From: Dan Lussier (dtlussier_at_gmail.com)
Date: Tue Jul 14 2009 - 17:31:57 CDT

Thanks Axel. Just a couple of follow up questions:

1 - Would it be possible to fool the velocity parser into taking other
values by switching other columns (i.e. atom-wise potential energy,
coordination number) into the location identified by vx, vy, vz in the
header?

2 - If it isn't possible to get the other variables at load time is it
possible to inject them, for lack of a better word, into the frame
after the frames have been loaded by reading a column of a the ASCII
file manually using Tcl? Along these lines is there a typical free
user variable in VMD that can hold atom-wise values read in from files
or calculated by Tcl?

3 - Would the situation be any better or different when using DCD dump
files? From what I have gathered they only store the atom positions,
so I would need to manually load even velocities if this is possible.

Thanks again,

Dan

On 13-Jul-09, at 8:21 PM, Axel Kohlmeyer wrote:

> On Mon, 2009-07-13 at 19:44 +0100, Dan Lussier wrote:
>
> dan,
>
>> I had a question about using other data beyond just x,y,z from LAMMPS
>> ascii files produced by 'dump custom ...' command.
>
>
>> As it stands I am loading the LAMMPS ascii dump files using a loop
>> over a list of files like:
>>
>> set x 0
>> foreach filename [glob $search] {
>> set file_num [scan $filename "$filespec%d"]
>>
>> if { ($file_num >= $ilo) && ($file_num <= $ihi)} {
>> puts "Processing: $filename ($x)"
>>
>> if {$x == 0} {
>> mol new $filename type lammpstrj
>> set mol_name $filename
>> } else {
>> mol addfile $filename type lammpstrj
>> }
>> incr x
>> }
>> }
>>
>> This does a good job loading the system's geometry but as expected
>> leaves out the other values from the dump file.
>>
>> I'm interested in loading data from other columns of the dump files
>> (i.e. atom-wise potential energy, atom-wise coordination number,
>> etc.)
>> and was hoping there was a VMD friendly way to do this either as the
>> files are loaded or after the fact by looping over the frames.
>
> sorry, but as of the very latest version of the LAMMPS plugin in VMD,
> you can only retrieve the information about atom velocities.
>
> for everything else, the corresponding APIs are not yet available
> in the molfile plugin interface. the LAMMPS plugin parser does
> recognize a lot of entries, but has no way to pass this on.
>
> plans to adjust the API to have additional (and at some point
> arbitrary) properties passed along are underway, but will have
> to wait until after the release of 1.8.7 and then will need to
> be implemented on a case by case basis depending on demand,
> usefulness and ease of implementation.
>
> since for the increasing likelihood of multimillion particle
> simulations and the impracticality to do lots of analysis in
> postprocessing, i expect the demand and usefulness to increase
> steeply over the next couple of years...
> our group will definitely have demand along those lines.
>
> cheers,
> axel.
>> Any advice would be great.
>>
>> Many thanks.
>>
>> Dan
>
> --
> =
> ======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://
> www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =
> ======================================================================
> If you make something idiot-proof, the universe creates a better
> idiot.
>