VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 17 2014 - 06:45:42 CST

On Mon, Feb 17, 2014 at 6:36 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

>
>
> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Olaf Lenz
> *Gesendet:* Montag, 17. Februar 2014 09:44
> *An:* Arham Amouie
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Betreff:* Re: vmd-l: Simplest file format that includes atom color?
>
>
>
> Hi!
>
>
>
> In principle, VMD is not really able to handle the case of time-dependent
> properties of the atoms.
>
>
>
> Since when? What about the user defined coloring, with which you can set a
> value per atom per timestep.
>
>
what olaf means is that VMD currently has no mechanism to read per
timestep per atom data other than positions and velocities through molfile
plugins.

to make use of the user field, you need to feed the data into VMD through
some other means, e.g. by aliasing it into vx, vy, or vz and then copying
those fields to a user field with a script (as possible with the LAMMPS
plugin) or parse the trajectory file a second time from a tcl script and
then copy the data directly into the user field, or write the time
dependent data to a separate file and read that file from a tcl script and
assign the data to one of the 4 user fields.

olaf's plugin supports the second option by hooking part of the vtf molfile
plugin into the Tcl interpreter, so you don't have to write a Tcl parser.

axel.

>
>
> However, there is a workaround via Tcl-scripting. Via a Tcl script, you
> can modify any properties. If you now do this whenever the timestep
> changes, you can basically simulate time-dependent properties. Writing such
> a script is a bit tedious, however. You first need to load the
> time-dependent properties into Tcl, and then set up a hook that modifies
> the properties when the frame is changed.
>
>
>
> As you seem to have noted, the VTF plugin provides some support to
> simplify the first step: it allows to add "user data" to the timesteps in a
> VTF file and can load this data into Tcl via a single command. However, the
> corresponding plugin version is not yet in VMD 1.9.1, therefore you will
> have to compile it on your own, or you have to get an alpha-version of VMD
> 1.9.2 (via Biocore).
>
>
>
> To compile it, get it from
>
> https://github.com/olenz/vtfplugin
>
>
>
> and adapt the Makefile to your system. To be able to use the user data,
> you will have to compile Tcl-support, so you have to install Tcl including
> the developments files (tcl.h) on your system.
>
>
>
> Once you have done that and loaded the plugin (both the molfile reader
> plugin "vtfplugin" and the Tcl-plugin "vtftools"), have a look at the
> examples in samples/userdata/
>
>
>
> Olaf
>
>
>
>
>
> 2014-02-16 12:44 GMT+01:00 Arham Amouie <erham65t_at_yahoo.com>:
>
> Dear Dr. Olaf Lenz,
>
> As far as I understand, your nice file format assumes that the structure
> data is time-independent. In my case, the quantity which I use for coloring
> atoms changes with time, so I have to save each timestep in a seperate
> file. I don't exactly know how VMD works, but It would be more convenient
> if it was possible to update some data in each time step in addition to
> coordinates.
>
>
> Arham
> --------------------------------------------
> On Thu, 2/13/14, Olaf Lenz <olenz_at_icp.uni-stuttgart.de> wrote:
>
> Subject: Re: vmd-l: Simplest file format that includes atom color?
> To: "Arham Amouie" <erham65t_at_yahoo.com>
> Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Date: Thursday, February 13, 2014, 11:48 AM
>
>
> Hi!
> As
> Norman already wrote, it is hard to guess what you really
> want. I assume that you want to be able to choose the color
> of each atom individually.
> In VMD, the color of an atom is
> determined by the "Coloring Method", that you can
> choose in the dialog "Graphics ->
> Representations...". By default, it uses the
> "Name" coloring method, which determines the color
> of the atom by the first letters of the atom name and colors
> it accordings to the element (an atom with the name
> "C" is a carbon, so it is colored cyan,
> "H" is white, ...)
>
>
> Alternatively, you can
> color the atoms based on some property of the atom, e.g. the
> mass, the charge, beta, and the color scale. To be able to
> use that, you will have to set these properties somehow, and
> this is indeed something that you should do via the file
> format.
>
>
> For cases like yours, I
> have created the VTF file format, which can be visualized by
> VMD: https://github.com/olenz/vtfplugin/wiki/VTF-format
>
>
> When you already generate
> XYZ-files, then transforming them to VTF-files is simple. In
> a VTF file, you can modify any of the properties of the
> atoms.
> Olaf
>
>
>
>
> 2014-02-12 20:28 GMT+01:00
> Arham Amouie <erham65t_at_yahoo.com>:
>
>
>
>
> Hello
> I've
> written a MD code for EAM potentials. The typical number of
> atoms is of
> the order of 1 million. This code saves the positions in
> xyz files and I
> use VMD for visualization. Now, I'm going to change the
> output, so that
> each atom can have its particular color. I used csv format
> of ParaView
> for this reason, but ParaView doesn't work fast for me.
> What is the
> easiest solution in VMD?
>
> Thanks in advanceArham Amouei
>
>
>
>
>
> --
>
> Dr. rer. nat. Olaf
> Lenz
> Institut für
> Computerphysik, Allmandring 3, D-70569
> StuttgartPhone: +49-711-685-63607
>
>
>
>
>
>
>
> --
>
> Dr. rer. nat. Olaf Lenz
>
> Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
>
> Phone: +49-711-685-63607
>
>
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-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.