VMD-L Mailing List

From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Tue Feb 18 2014 - 04:21:08 CST

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 Stuttgart
Phone: +49-711-685-63607