[Pw_forum] processing large charge_density and spin_density xml files

[Axel Kohlmeyer]

On Sun, 14 Jan 2007 stewart at cnf.cornell.edu wrote:

DS> Hi everyone, 

hi derek.

happy new year.

DS> I have been looking at a fairly large system (160 atoms) with a nanowire 
DS> between two (111) leads in PWscf.  I have converged the system, but now I 
DS> would like to plot out the charge density.  I have the xml files for charge 
DS> density and spin density.  However, I am running into insufficient virtual 
DS> memory complaints when running pp.x, even when I run the parallel version. 

hmm, you are running binaries compiled with intel fortran, right?
did you try increasing the stack size (using 'ulimit -s')?
what is the exact error message? could you try generating a core dump
(run 'ulimit -c unlimited', then pw.x as usual), then 'idb pw.x core.XXXX' 
and on the idb prompt type 'where' to generate a stack trace, so we
can see where it crashes.

DS> Does anyone know if it is possible to read the xml files directly with some 
DS> visualization packages (XCrysDens).  The xml files are fairly large (58 MB), 
DS> so I may be running into file size limit problems.  Is it always necessary 
DS> to run pp.x and then generate plot output? 

if the stack size 'trick' does not help, you can think about reducing
the number of grid points used for plotting. in CPMD using half the grid
in each direction (i.e. 1/8th of the data!) is the default and usually
is quite sufficient to get very nice pictures. you should be able to 
set the output grid in pp.x, but if that still is not sufficient, you
might want to try as a matter of last resort an NSCF calculation from 
a converged potential/wavefunction with a smaller real space density 
cutoff (and thus grid) and use that to get the output.

cheers,
   axel.

DS> 
DS> I have been using version 3.1.1 for these calculations. 
DS> 
DS> Thanks, 
DS> 
DS> Derek 
DS> 
DS> 
DS> ################################
DS> Derek Stewart, Ph. D.
DS> Scientific Computation Associate
DS> 250 Duffield Hall
DS> Cornell Nanoscale Facility (CNF)
DS> Ithaca, NY 14853
DS> stewart (at) cnf.cornell.edu
DS> (607) 255-2856
DS> _______________________________________________
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DS> Pw_forum at pwscf.org
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DS> 

-- 
=======================================================================
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.