VMD-L Mailing List

From: Arham Amouie (erham65t_at_yahoo.com)
Date: Tue Feb 18 2014 - 04:52:20 CST

I use VMD 1.9.1 but upgraded "vtfplugin" to last version. Reading from compressed files is a good idea. I'll try. Thanks.

Arham

--------------------------------------------
On Tue, 2/18/14, 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: Tuesday, February 18, 2014, 1:51 PM
 
 Excellent! 
 One
 comment: the ability to have multiple atom lines for a
 single atom is broken in the plugin of VMD 1.9.1, so you
 have to use the current version, or VMD 1.9.
 
 
 However, to reduce the file size it is much simpler to
 compress the files: When the plugin is compiled with zlib
 support (_USE_ZLIB) you can simply gzip the files and the
 plugin can read the files still. To be able to do that, you
 have to install the zlib (including devel files).
 
 
 Olaf
 
 2014-02-18 10:59 GMT+01:00
 Arham Amouie <erham65t_at_yahoo.com>:
 
 
 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
 
 
 
 
 
 
 
 
 
 
 
 
 --
 Dr. rer. nat. Olaf Lenz
 Institut für Computerphysik,
 Allmandring 3, D-70569 StuttgartPhone:
 +49-711-685-63607