UT theoretical chemistry code forum

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...

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...

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.

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...

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...

test

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.

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...

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...

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...

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...

The web page and the vtstscripts.tar.gz has been updated to reflect the current scripts in cvs.

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...

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.

The following scripts were modified:

neb_setup.pl -> nebsetup.pl
make_mode.pl -> modemake.pl
chenergy -> /dev/null

nebresults.pl: changed the output format, and called the internal scripts via $Bin/intscript.pl.