UT theoretical chemistry code forum

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 ...

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...

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...

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...

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 ...

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...

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...

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.

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...

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/

I've added the reading of the environmental variable VTST_BC to get the boundary conditions in the vasp2con.pl script. I think it's time to allow the boundary condition settings, along with optional printing styles to be controlled without having to modify the scripts. A variable can be read using t...

The potentials can now be built on osx by running the Gman/pot/build_osx_xlf script. This is nothing fancy, but it's better than it was. This requires that xlf, f2py, numeric, and scipy to be installed.

H-O bonds are definately a problem with pseudopotential codes, and possibly C-H. The results in our paper were generated using an all electron calculation with Gaussian. Even though H has 1 electron, the electrostatic repulsion is smoothed out with the pseudopotential, and as you have found, it can ...

Yeah, we have not implemented non-orthogonal cells yet. If enough people would find this valuable, this functionality could be added.

The amount of charge on each atom will be listed in the ACF.dat file, and in the output of the program if you choose option 4. In order to visualize the Bader volume around each atom, you can choose option 2, and specify which atom you are interested in. The BvAtxxxx.dat file has the same format as ...