Xmovie

Hello,

I would like to visualize the dump file which has been recorded by this command : dump 1all dcd 40000 dump.mysiar

However, when I type " tools/xmovie/xmovie -scale dump.flow "

It gives " xmovie: Command not found. "

I had a look at to README file inside the xmovie file but I does not make sense to me.

Could you please help me about commands or any alternative programme? Actually I have check all programmes which are given on LAMMPS site.

Thank you in advance.

regards,

Selcuk

2011/10/21 Selçuk Atalay <[email protected]...>:

Hello,
I would like to visualize the dump file which has been recorded by this
command : dump 1all dcd 40000 dump.mysiar
However, when I type " tools/xmovie/xmovie -scale dump.flow "
It gives " xmovie: Command not found. "
I had a look at to README file inside the xmovie file but I does not make
sense to me.

xmovie has to be compiled before it can be used.
also it cannot read dcd format dump files.

Could you please help me about commands or any alternative programme?

Actually I have check all programmes which are given on LAMMPS site.

...and they all work, and very well, as is indicated by the many nice
pictures and movies on the LAMMPS home page. apparently, you
have to put a bit more effort into learning how to use those well.

an new option in recent lammps versions is to have lammps render
snapshot images directly. all you need is some kind of mpeg compression
software to combine those to a movie. that will look much better than
what xmovie will ever be able to provide. with current graphics and
computer hardware, xmovie is pretty much obsolete.

axel.

Hi,

My personal experience with xmovie was that I had to turn off the optimization in the makefile in order to compile the program. I compiled it on sabayon linux (a gentoo derivative) with gentoo gcc 4.5.2
There is also the pymol_asphere tool which converts dumps to pymol files. This one compiled out of the box.

Cheers,

Nikita

2011/10/21 Selçuk Atalay <selcukatalay@…8…>

Hello,

I would like to visualize the dump file which has been recorded by this command : dump 1all dcd 40000 dump.mysiar

I found out that it can be visualized via VMD, then I have installed the version of 1.9 for Windows. Windows OpenGL, CUDA (Windows XP/Vista/7 (32-bit) with OpenGL and CUDA

I have opened the prog. and from “file” I selected "It gives “load visualization state” then I uploaded my saved file from LAMMPS but it gives errors as all commands are invalid.

I have looked at some tutorial files but could not do.

Could you please help me?

Thank you in advance.

Regards,

Selcuk

2011/10/23 Selçuk Atalay <[email protected]...>:

Hello,
I would like to visualize the dump file which has been recorded by this
command : dump 1all dcd 40000 dump.mysiar
I found out that it can be visualized via VMD, then I have installed the

please post to the correct mailing list. what you
are describing is a VMD issue and in no way
LAMMPS related.

version of 1.9 for Windows. Windows OpenGL, CUDA (Windows XP/Vista/7
(32-bit) with OpenGL and CUDA
I have opened the prog. and from "file" I selected "It gives
"load visualization state" then I uploaded my saved file from LAMMPS but it
gives errors as all commands are invalid.
I have looked at some tutorial files but could not do.
Could you please help me?

no. read the VMD user's guide and tutorials properly
and you'll see. what you are doing is flat out nonsense,
and the resulting error messages are well deserved.
there are ain't no such thing as a free lunch.
if you don't pay attention, bad things happen.

please also note, that .dcd files _only_ contain
coordinate information and thus to visualize the
resulting trajectory you need some additional
information about the simulation system.

axel.

Perhaps I should not post this this reply. I don't know much about DCD files.

please also note, that .dcd files _only_ contain
coordinate information and thus to visualize the
resulting trajectory you need some additional
information about the simulation system.
axel.

I'm guessing that a ".PSF" file would contain the additional
information VMD needs in order to display the molecule. You can
generate a PSF file from your LAMMPS "DATA" file.

Instructions

1)

Axel (the guy who replied to your post before me) has written a nice
VMD plugin (toptools 1.2) that generates PSF files from lammps data
files.
If you already have topotools 1.2, you can skip this step.

a) Download topotool version 1.2 here:
http://sites.google.com/site/akohlmey/software/topotools
b) Unpack the file.
c) Copy the "topotools1.2" folder to the same folder where your
"topotools1.1" folder is located.
(On my linux machine it is located at
"/usr/local/lib/vmd/plugins/noarch/tcl/". I have no clue where this
would be located on a windows computer. I suspect that not so many
people use windows with lammps.)

2) Make a PSF file
(better instructions are also available in the topotools web page)
a) Start VMD
b) Menu Extensions->Tk Console
c) Enter:

(I assume that the the DATA file is called "system.data")

   topo readlammpsdata system.data molecular
   animate write psf system.psf

This generates "system.psf"

3) Visualise your trajectory in VMD
(Forgive me if you know how to do this step already.)

a) start VMD
b) From the "File" menu, load your PSF file by selecting "New
Molecule", then "Browse", then select your PSF file, and then select
"OK" and "Load". (Alternately if you loaded the PSF file already when
you started VMD, then in the "VMD Main" window, right click on the
molecule "system.psf", and in the pull-down menu, select "Load Data
Into Molecule".)
c) Click on the "Browse" button, and select your DCD file, click "OK",
and then "Load"

There are VMD tutorials to show you how to improve the visual
appearance of the molecules (such as using pcbtools to remove bonds
which stretch across the periodic boundary box).

I hope this helps
(In a hurry. I hope these instructions are accurate.)
Cheers
Andrew

2011/10/23 Andrew Jewett <[email protected]...>:

Perhaps I should not post this this reply. I don't know much about DCD files.

doesn't matter. it is good that more people
reply to questions and it is a very good way
to reaffirm and improve your own knowledge.
people always overestimate how much factual
knowledge and experience it takes to give
a meaningful answer. sometimes, all it takes
to help somebody is to repeat the same
question in a different way or to explain
something differently.

cheers,
    axel.