[Pw_forum] On making a *.axsf file with XCrySDen

[Axel Kohlmeyer]

On Sun, 12 Oct 2008, Paul M. Grant wrote:

paul,

PG> Axel, thanks for getting back on this.  Let me think about your suggestion
PG> and see what others have to comment as well.

it is actually quite difficult to give a recommendation, 
since everybody uses a different nomenclature when it comes
to visualization and animations, based on background, software
being used and ability to put visual ideas in words (which i 
always found very difficult). 

PG> Reflecting on "animation" in general a little more, I wonder if there's a
PG> Linux screen capture tool available somewhere analogous to KDE Ksnapshot for
PG> jpeg images, but which could capture motion in addition resulting in an mpeg
PG> file.  Now that would be a handy and nifty gadget for lots of purposes!

there is a number of ways to do this and it depends on whether
you want a "realtime" capture or just "one frame per update"
type animations. the former could in principle be done on any 
x11 based machine with some smart shell scripting using the
xwd utility after figuring out the x window id of the display
window. the latter is a method that is been used by many "movie maker"
tools that are integrated into visualization programs.

in both cases you assemble a sequence of snapshots and then use
tools like ppmtompeg, mencoder, convert, gifsicle and so on 
to turn them into an mpeg, avi, or animated gif movie. 

please note that "realtime" capture (for mpeg) would require a 
screenshot frequency of up to 30 snapshots per second which is
probably beyond the capability of most hardware, not to mention
the limitations of the X protocol... but then again, it would
reduced the load and hardware requirements at playback time a lot.

it should be possible to write a proof-of-concept code based on
existing tools rather quickly. i'll put it on my (ever growing)
TODO list and will get back to you if i have something that is
worth trying out.

cheers,
   axel.

PG> 
PG> Paul M. Grant, PhD
PG> Principal, W2AGZ Technologies
PG> Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> EPRI Science Fellow (Retired)
PG> IBM Research Staff Member Emeritus
PG> w2agz at pacbell.net
PG> http://www.w2agz.com
PG>  
PG>  
PG> 
PG> 
PG> -----Original Message-----
PG> From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
PG> Behalf Of Axel Kohlmeyer
PG> Sent: Sunday, October 12, 2008 5:18 PM
PG> To: Paul M. Grant
PG> Cc: 'PWSCF Forum'
PG> Subject: Re: [Pw_forum] On making a *.axsf file with XCrySDen
PG> 
PG> On Sun, 12 Oct 2008, Paul M. Grant wrote:
PG> 
PG> hi paul,
PG> 
PG> not sure whether this is helpful, but i managed to do something
PG> similar to what you describe with VMD (granted VMD is still missing
PG> a lot of features for crystals etc. so it may not work as well for you).
PG> 
PG> the problem is that usually volumetric data sets are not associated
PG> with the individual time step of an animation. the VMD script works
PG> because it is loading a sequence of cube files with a 1:1 correlation
PG> of coordinate and volumetric data and then makes the correlation by
PG> replacing the volumetric data sets through a callback hook to the 
PG> animation loop frame number variable (standard tcl method). see:
PG> 
PG> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#c
PG> hap7_sect6
PG> 
PG> for more complicated scenarios (e.g. i have dome some nice movies of 
PG> the fluctuations of spin densities of electron pairs in the cavities 
PG> of an electride-like compound) one has to write more complicated tcl 
PG> scripts.
PG> 
PG> i would assume that there may be similar scripts possible with xcrysden, 
PG> provided the script API is flexible enough... (never tried it).
PG> 
PG> cheers,
PG>    axel.
PG> 
PG> 
PG> PG> How does one make an animated axsf file using XCrySDen directly?  For
PG> PG> example, suppose I want save in an axsf file the animation of an
PG> isosurface
PG> PG> of charge density moving through a given unit cell.  I can save the
PG> PG> "situation" as an .xcrysden script file for play back, but on loading it
PG> PG> doesn't raise the Modify -> Animation Controls option.  Only an .axsf
PG> file
PG> PG> apparently does this.  Do I have to go through the script file inserting
PG> PG> "ANIMSTEPS" by hand?
PG> PG> 
PG> PG> I note that the XCrySDen forum archives has had no entries since
PG> April.Is
PG> PG> PW_Forum now the appropriate target for XCrySDen issues?
PG> PG> 
PG> PG> Paul M. Grant, PhD
PG> PG> Principal, W2AGZ Technologies
PG> PG> Visiting Scholar, Applied Physics, Stanford (2005-2008)
PG> PG> EPRI Science Fellow (Retired)
PG> PG> IBM Research Staff Member Emeritus
PG> PG> w2agz at pacbell.net
PG> PG> http://www.w2agz.com <http://www.w2agz.com/> 
PG> PG>  
PG> PG>  
PG> PG> 
PG> PG> 
PG> PG> 
PG> 
PG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.