VMD-L Mailing List
From: Arham Amouie (erham65t_at_yahoo.com)
Date: Sun Feb 16 2014 - 05:44:20 CST
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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
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