Search found 1947 matches

by graeme
Thu Jul 14, 2005 9:38 pm
Forum: VTSTTools
Topic: questions in relation to dynamical matrix method
Replies: 7
Views: 11554

A dynamical matrix (dynmat) calculation is done on a single POSCAR, which should be in the main directory, just as in a regular vasp run. You don't need any subdirectories for this calculation. You need to generate one DISPLACECAR, indicating which atoms are going to be displaced, and set NSW in you...
by graeme
Wed Jul 06, 2005 7:04 pm
Forum: VTSTTools
Topic: Transition State Calcu.
Replies: 2
Views: 7013

The settings of IBRION=3 and POTIM=0 are only appropriate if you are using one of our optimizers. If you have the default vasp code, you need to specify a non-zero POTIM to use IBRION=3 with the NEB. But this is not the problem you are seeing -- there is something else messed up. Are you running a p...
by graeme
Wed Jul 06, 2005 4:56 pm
Forum: Bader
Topic: questions about charge distribution
Replies: 3
Views: 9285

This is good to see. Yes, it is best to generate an accurate CHGCAR file before each Bader calculation. For elements with few valence electrons, additional electrons can be included at this point, by using the _pv or _sv pseudopotentials. This step, although tedious, is not overly time consuming. As...
by graeme
Tue Jul 05, 2005 7:46 pm
Forum: Bader
Topic: Can't Un-tar the Windows Archive
Replies: 1
Views: 5644

Thanks for the post. The bader_win.tar.gz file works with the unix style cygwin utilities on windows. We've added a bader.zip file which works with the standard winzip untilities on windows, and marked the old file as specifically for cygwin users.
by graeme
Tue Jul 05, 2005 7:16 pm
Forum: Bader
Topic: questions about charge distribution
Replies: 3
Views: 9285

The Bader charges of 0.9554 and 1.0053 on each hydrogen, resulting in an overall charge of +0.045 and -0.005, are likely different because of a limited resolution in the fft grid. If you look at the top of the CHGCAR file, or in the OUTCAR file, you can see the number of grid points used. To make su...
by graeme
Sun Jun 05, 2005 6:18 pm
Forum: Bader
Topic: bader - cube files
Replies: 3
Views: 10518

I don't know what's going on, but I bet a cube file visualizer might help. One guess is that the cube format is [-x/2 .. x/2] where as vasp is [0..x]. If Dacapo also has boundaries of [0..x] the charge values may need to be shifted by half a box so they line up with the atoms. An easy way to check t...
by graeme
Sun May 29, 2005 1:31 am
Forum: VTSTTools
Topic: Updated dimer.F
Replies: 3
Views: 7880

mail test

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by graeme
Thu May 26, 2005 11:35 pm
Forum: VTSTTools
Topic: xyz to poscar?
Replies: 1
Views: 10313

One issue with xyz->POSCAR is that there is no box in the standard xyz file. There is some jvasp file that is accepted by jmol, which is like an xyz file with a box. There is a script for getting to and from this file to POSCAR. Bill is a big fan of these files.
by graeme
Thu May 26, 2005 11:14 pm
Forum: Bader
Topic: pseudo-potential dependent charges
Replies: 4
Views: 13111

Another quick note about pseudopotentials -- this is clearly an area of concern for using the Bader analysis with vasp CHGCAR files. The vasp folk have said they will provide a way of getting proper core charges. The speed at which this happens is likely related to the interest of their users, so it...
by graeme
Thu May 26, 2005 11:05 pm
Forum: Bader
Topic: pseudo-potential dependent charges
Replies: 4
Views: 13111

The issue with Mg, and all elements on the left side of the periodic table is that the minimal number of valence electrons does not provide enough charge to capture the charge density maximum which should be at the Mg atomic center. For these elements you must use the _pv or _sv potentials to get an...
by graeme
Thu May 26, 2005 2:47 pm
Forum: VTSTTools
Topic: Updated dimer.F
Replies: 3
Views: 7880

The name of the main routine has changed over time, and the older names, such as chain_init, are still present as comments in the code. I've removed the old calls to clearify the code, leaving dimer_init and dimer_force. This is updated in cvs. These changes should not affect the building or running...
by graeme
Wed May 25, 2005 2:23 pm
Forum: VTSTTools
Topic: dimer reorientation
Replies: 1
Views: 5568

maintaining dimer orientation

As you suggest, copying the CONTCAR file to POSCAR in the 01 and 02 directories will be enough. If you have our scripts downloaded, there is a convenient way to archive a finished run and be ready to start a new one from where it left off, using: vfin.pl <archive dir name> This will work with regula...
by graeme
Tue May 24, 2005 2:34 am
Forum: VTSTTools
Topic: Web page and tar.gz file updates
Replies: 0
Views: 6897

Web page and tar.gz file updates

The web page and the vtstscripts.tar.gz has been updated to reflect the current scripts in cvs.
by graeme
Mon May 23, 2005 8:29 pm
Forum: VTSTTools
Topic: New scripts
Replies: 3
Views: 9196

changed names

I've change these script names, using the prefix chg: avgCHGCAR.pl -> chgavg.pl difffCHGCAR.pl -> chgdiff.pl avgPARCHG.pl -> chgparavg.pl I've also set the perl binary to be the general call which works on all platforms. Thanks again for these scripts, I think they will be very useful for visualizin...
by graeme
Mon May 23, 2005 8:26 pm
Forum: VTSTTools
Topic: Updated dimer.F
Replies: 3
Views: 7880

Updated dimer.F

Improved formatting for the out.dat file was checked into cvs. I also added a routine to deal with periodic boundaries into dimer.F.

Chain.F no longer prints that it is doing an NEB calculation for regular vasp runs.

I've updated the tar file.