[CPMD-list] Visualization of CPMD output properties
Axel Kohlmeyer
axel.kohlmeyer at theochem.ruhr-uni-bochum.de
Sat May 15 16:00:15 CEST 2004
On Sat, 15 May 2004, Dai Ling wrote:
DL> Dear Sirs:
DL>
hi,
DL> I have some question on visualization of CPMD output properties.
i have found that VMD is an excellent tool to visualize the results
from CPMD simulations, so many of your questions (and some you have
not asked yet) may be answered at
<http://www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html>
beginning with version 1.8.2 the VMD program allows you to read in
the coordinates from a TRAJECTORY file as format 'cpmd' if you have
loaded the matching GEOMETRY.xyz file first. there also is a (perl)
program to create an xyz file directly.
DL>
DL> 1. For the TRAJECTORY file, I have seen there is a perl script in the
DL> FAQ to transfer it to other formats. However, I don't know how to use
DL> the perl scripts. Or is there any other method to transfer TRAJECTORY
to use a perl script you either make them executable (chmod +x xxx.pl)
and use them like a regular executable './xxx.pl ...' or you run it
with 'perl xxx.pl ...'
DL> file to .cube or .pdb file?
cube files don't store trajectories and multi-step pdb file support is
also not as widespread as .xyz movie support.
DL> 2. For the MOVIE file, which software can visualize it?
AFAIK, this file is more-or-less obsolete. try using
'TRAJECTORY XYZ' to generated a .xyz file directly.
DL>
DL> 3. I tried to get density & band structure of Tantulum. I got DENSITY
DL> & ENERGYBANDS files. Which software can visualize the ENERGYBANDS
DL> file?
DL>
DL> 4. For item 3, I have installed cpmd2cube. It works well on
DL> transfering WANNIER file. However,when I use it to transfer DENSITY
DL> file, it fails with information:
DL>
DL> ****************************************************************
DL>
DL> .read input file ... done
DL> I think you stored a density (sum^2 = 0.85220979E-02)
DL> ERROR in file DENSITY
DL> Wannier-functions stored as density, you can not
DL> create a cube-file with the wavefunction
DL>
DL> ******************************************************************
DL>
DL> I am confusing because in my input file there is no command for Wannier function.
the current cpmd2cube sources at cpmd.org have several problems. many
of which have already been fixed in the developer version. i assume
there will be a new release of cpmd2cube along with the release of
cpmd-v3.9. in your specific case you got hit by a little think-o in the
commandline argument parsing/guessing. for a density you need to specify
the -rho or -dens flag explicitely (the program assumes -psi and the stops
if the sanity check fails) and it should work.
hope this helps,
axel kohlmeyer.
DL>
DL> The input file for item 3 & 4 is shown below. The pseudopotential for TA is created by fhi98PP.
DL>
DL> Any advice will be highly appreciated. Thanks in advance!
DL>
DL> Scott
DL>
DL> Input file:
DL>
DL> &CPMD
DL> OPTIMIZE WAVEFUNCTION
DL> FREE ENERGY FUNCTIONAL
DL> LANCZOS DIAGONALIZATION
DL> LANCZOS PARAMETERS N=1 ALL
DL> 50 8 0 1.D-8
DL> TROTTER FACTOR
DL> 0.001
DL> BOGOLIUBOV CORRECTION
DL> CONVERGENCE
DL> 5.D-5 5.D-4
DL> ELECTRON TEMPERATURE
DL> 300.D0
DL> MAXSTEP
DL> 1
DL> ENERGYBANDS
DL> &END
DL> &SYSTEM
DL> SYMMETRY
DL> BCC
DL> POINT GROUP
DL> AUTO
DL> SCALE
DL>
DL> TESR
DL> 10
DL> ANGSTROM
DL> CELL
DL> 3.3062 1.0 1.0 0.0 0.0 0.0
DL> SPHERICAL CUTOFF
DL> 63.
DL> density cutoff energy
DL> 6820
DL> KPOINTS BANDS block=50
DL> 51 0 0 0 0 0 1 Gamma to H
DL> 51 0 0 1 0 .5 .5 H to N
DL> 51 0 .5 .5 .5 .5 .5 N to P
DL> 51 .5 .5 .5 0 0 0 P to Gamma
DL> 51 0 0 0 .5 .5 0 Gamma to N
DL> 51 0 0 1 .5 .5 .5 H to P
DL> 0 0 0 0 0 0 0
DL> STATES
DL> 9
DL> &END
DL>
DL> &ATOMS
DL> *TA_MT_GIA_BLYP KLEIMAN-BYLANDER REGGIO=1.2
DL> LMAX=D LOC=P
DL> 1
DL> 0.00D0 0.00D0 0.00D0
DL> &END
DL>
DL>
DL>
DL>
DL>
DL>
DL>
DL> _______________________________________________
DL> CPMD-list mailing list
DL> CPMD-list at cpmd.org
DL> http://www.cpmd.org/mailman/listinfo/cpmd-list
DL>
DL>
--
=======================================================================
Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer at rub.de
Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
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