VMD-L Mailing List

From: Arham Amouie (erham65t_at_yahoo.com)
Date: Tue Feb 18 2014 - 03:59:27 CST

Thank you for good explanations. Another feature of the new version of "vtfplugin" that is nice is the ability to have multiple atom lines for each atom. For systems containing many atoms that the number of atom types is small, this helps to reduce file size. Another possible way to reduce file size is to write coordinates in binary format.

Now my code can write in VTF format, and I tested it for an alloy-system of 2 million atoms.

Thanks again
Arham

--------------------------------------------
On Mon, 2/17/14, 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: Monday, February 17, 2014, 12:14 PM
 
 Hi!
 In principle,
 VMD is not really able to handle the case of time-dependent
 properties of the atoms.
 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 StuttgartPhone:
 +49-711-685-63607