UT theoretical chemistry code forum

You have probably already seen this page, but it does concisely describe the format of the chgcar file: http://cms.mpi.univie.ac.at/vasp/vasp/node66.html Basically, it has the simulation box, atomic coordinates, and then a grid of charge density values. Evaluating a plane averaged charge density is ...

I does not look like this script does deal with non-orthogonal boxes correctly. But it should. We'll post back when it's been done.

You should be pretty safe using the USPP for atoms with many electrons, such as gold. The core charge density maximum for Au should be well-represented with the valence electrons. But if the other atoms around the gold atom do not, there could be problems. The best way to access the error is to gene...

There looks to be some problem with the normalization or the input file. We'll need to know how the input file was generated, or see it. If it was from vasp, and you are using the core charge, make sure that you follow the instructions on this page carefully: http://theory.cm.utexas.edu/bader/vasp.p...

1) You can try a single intermediate image in a NEB calculation. However, if the path is curved, the vector between your initial and final states may not be a good approximation to the negative mode at the saddle. If the image does not converge to a saddle, try using 3 or 5 images. To the extent tha...

I can't tell from this information. The frequency calculations can be very sensitive to your choice of parameters. It is essential to use accurate forces (ediff=1e-8) and small finite displacements. Make sure that your frequencies do not change if you make your displacements smaller or your forces m...

The analysis is done on the valance density. There are 390 valance electrons so your sum looks fine. There are 6 valance electrons for O, so your charges on those atoms also looks fine. The total density is used to do the partitioning, but the sum over the Bader volumes is done for valance electrons...

It does look like the As has taken an electron from the 4 neighboring Si atoms. The output looks reasonable to me, even if the result it surprising. I'm not familiar enough with this system to know if the As charge should be 4 (giving 1 electron to the Si atoms, as you would expect if substitutional...

Yes, this is described in detail in this publication: http://theory.cm.utexas.edu/bader/download/tang08_bader.pdf Basically, the ongrid method is our original implementation. It's nice and simple, but was shown to have some bias with respect to the lattice orientation. The neargrid method is similar...

Once you have a saddle point you can displace the configuration by a small amount along the negative mode direction (both ways) and minimize to find the connecting minima. Using a conservative minimizer such as with damped dynamics will help to make sure that you don't skip over any local minima. If...

1) We have compared NEB images with a SD path. In the following paper: http://theory.cm.utexas.edu/henkelman/pubs/sheppard08_134106.pdf Section VIII and Figs. 9 and 10 show convergence to the minimum energy path (MEP) with a few different methods (NEB, string, and SD) These paths are mass un-weighte...

The endpoints must be converged with the same settings as the NEB to calculate energy barriers.

Make sure that your endpoints have been reoptimized using high precision in that run. There could be significant changes in the absolute energies, but it is unlikely that you will find significant changes in the relative energies (the barrier). We routinely reconverge NEB calculations using differen...

The charge density for the whole system is what you provide to the Bader analysis program. It is an input, not an output.

Are you asking if there is a way to graphically display the values of the Bader charges for each atom? If so, then the answer is no; we only give you the values.

The ACF.dat, BCF.dat and AVF.dat contain the results of run; the charge in each bader and atomic volumes, and a list of the bader volumes which make up the atomic volumes. None of these files can be visualized. If you want to view a particular volume, use the -p flag and choose to print either all o...