Search found 1909 matches

by graeme
Wed Mar 01, 2006 8:55 am
Forum: VTSTTools
Topic: Some questions about NEB and CI-NEB
Replies: 8
Views: 18332

Right, vasp 4.6 has an old version of the NEB. The climbing image and new tangent modifications are not included. The code for the latest NEB method, including the climbing image can be downloaded from: http://theory.cm.utexas.edu/vtsttools/code/ If you put the 5 fortran files into your vasp.4.6 sou...
by graeme
Wed Mar 01, 2006 12:21 am
Forum: VTSTTools
Topic: Introduction of environment variables
Replies: 2
Views: 5094

Two variable can now be set to specify the

stdout: VTST_STDOUT
stderr: VTST_STDERR

The vfin.pl script uses these variables and copies the stdout file to the save directory, and the stderr file is erased.
by graeme
Tue Feb 28, 2006 8:30 am
Forum: Anouncements
Topic: Now you can read the web site eOn in Chinese
Replies: 1
Views: 16494

Ding_Cong,

You guys have done an amazing job with the chinese version. Thanks for all your help with the eon project!

-- Graeme
by graeme
Thu Feb 23, 2006 4:46 pm
Forum: Bader
Topic: Spurious bader charges
Replies: 13
Views: 17075

The molecule is in the center of the box, though, so isn't it unlikely that the boundaries are causing a problem?
by graeme
Fri Feb 17, 2006 4:52 am
Forum: VTSTTools
Topic: Stress effects in VASP
Replies: 2
Views: 5732

This is true, but if you were thinking about how the stress relates to finding transition states, we would all be interested in talking about it. This is a challanging problem that only a few groups are working on.
by graeme
Thu Feb 09, 2006 2:15 am
Forum: Bader
Topic: RCORE vs MIN DIST
Replies: 12
Views: 14903

I think that a bug in the minimum distance calculation is unlikely (although of course it's always possible). I checked the values given by the bader code against a manual measurement for several chgcar files, and found them to be consistent. Perhaps a few more checks would be in order, but I doubt ...
by graeme
Thu Feb 02, 2006 2:31 am
Forum: Bader
Topic: RCORE vs MIN DIST
Replies: 12
Views: 14903

Yes, that's right; you need to subtract the valance charge to find the net charge. I'm a little surprised that you are seeing many cases in which the distance from the atomic surfaces to the nuclei is within Rcore. The sum of Rcore for two bonding atoms should be less than the bonding distance. This...
by graeme
Thu Feb 02, 2006 1:17 am
Forum: Bader
Topic: RCORE vs MIN DIST
Replies: 12
Views: 14903

Hi Mark, Rcore is given in Bohr, and the minimum distance from a Bader surface to each atom should be larger than Rcore. The issue here is that the pseudopotentials alter the charge density inside of a radial cutoff, Rcore. In general, the charge density in the core region does not affect properties...
by graeme
Fri Jan 20, 2006 5:44 am
Forum: Bader
Topic: Spurious bader charges
Replies: 13
Views: 17075

Well, I think were stuck on this for now. Andri and I have tried a range of grid sizes and different INCAR parameters. I don't see a difference as large as you get. My biggest difference is 0.07e between C atoms, or 2%. Still, this is annoying. Which C atom has the larger charge also seems to depend...
by graeme
Wed Jan 18, 2006 8:46 pm
Forum: Bader
Topic: Spurious bader charges
Replies: 13
Views: 17075

The number of necessary grid point is related to the box size. It is really the density of grid points that matter. An 18x18x18 Ang box is quite large, so a large number of grid points could be appropriate. However, if you are looking at an isolated molecule, this is a very large box. You could use ...
by graeme
Wed Jan 18, 2006 3:35 pm
Forum: Bader
Topic: Spurious bader charges
Replies: 13
Views: 17075

360^3 is a pretty large data set, but I'm still surprised that it's causing a segmentation fault. Perhaps you are right about the memory. If you made the CHGCAR available I could try it on a large memory machine. You could also try one of your other suggestions. Reducing the cell size and the grid s...
by graeme
Tue Jan 17, 2006 3:22 pm
Forum: Bader
Topic: Spurious bader charges
Replies: 13
Views: 17075

The code does take into account boundary conditions. My first guess is that your fft grid needs to be finer. If the carbon atoms are lying in different positions with respect to the grid, the integrated charge for each atom will be different. I suggest that you look in the OUTCAR or the CHGCAR to fi...
by graeme
Sat Dec 31, 2005 11:24 pm
Forum: VTSTTools
Topic: Vasp.pm and diminit.pl changes
Replies: 1
Views: 4636

dimmins.pl

I've renamed the dimquench.pl script, written by Lijun, to dimmins.pl. I've changed it so it is like the diminit.pl script.

Both scripts are in cvs, along with the modifications to Vasp.pm. The vtsttools website documentation has been updated, as well as the tar file.
by graeme
Sat Dec 31, 2005 9:00 am
Forum: VTSTTools
Topic: Vasp.pm and diminit.pl changes
Replies: 1
Views: 4636

Vasp.pm and diminit.pl changes

Functions to make gaussian displacements, add coordinates, and multiply coordinates by a scalar have been added to vasp.pm. There is also a boundary condition function (set_bc) which uses the environmental variable VTST_BC to decide which condition should be applied. The read_othercar has been modif...
by graeme
Tue Dec 13, 2005 5:06 am
Forum: VTSTTools
Topic: density of states plotting routines
Replies: 2
Views: 5210

density of states plotting routines

Added two scripts, vdosplot.pl and vldosplot.pl. After some use and debugging, I'll add a sentence about them on the webpage. They scripts plot data generated using the split_dos.ksh and vp scripts from http://cst-www.nrl.navy.mil/~erwin/vasptips/