UT theoretical chemistry code forum

Well, I guess this shows how little I do calculations any more. I also had trouble with vesta and vmd. I'll check with my group and see if they have tricks. I always use our xyz viewer (in tsase) and I know that the visualizer in ase will also load and play these movies.

The movie files are simply concatenated POSCAR files. You should be able to use visualizers including vesta, VMD, or there is a viewer in ase and in our tsase package.

You should get a BvAtxxxx.dat for each atom, if you use a command such as:

bader cubefile -p all_atom

If you want to print out the charge density for two atoms, you can use:

bader cubefile -p sel_atom 1-2

or

bader cubefile -p sel_atom 1
bader cubefile -p sel_atom 3

No, the difference between the excited state density vs the ground state density should, in general, change the size of the Bader volumes and the Bader charges of the atoms in the molecule.

That is surprising - the voronoi calculation trivially associates every point with the nearest atom. If the atoms are different, the integrated charges will be different but the volumes should be the same. If they are off by a small amount, that could be due to the discretization of the CHGCAR file....

Hm, I don't recall seeing that error before. If you can please post your CHGCAR and CHGCAR_sum, I will look into the problem.
Graeme

Yes, what you can do is make a small displacement along both directions of the unstable mode and minimize those structures. We have a small script, dimmins.pl which should set up those minimization calculations from a converged dimer calculation.

I'm looking at the dosanalyze.pl code and I see that the #-# format is accepted as an input, but there is no support for the #, # format when specifying atoms. So I'm not sure what the script is doing when you specify p 3,4. If you post a .tar.gz file of your calculation, I will be able to reproduce...

This depends a little bit upon what you are interested in. If you want to know about, for example, charge transfer between materials or anything that is based upon the absolute energy levels of the electrons, then you need a common energy reference, such as the vacuum level. If, however, you are wan...

Hi Jared, Sorry for the slow reply by email - I'll answer here. The dipole code simply integrates the charge density times a vector from the center of charge in each Bader volume. The issue is that we have never really used the code and I can not guarantee that it works. One issue that I would worry...

Yes, it is with respect to the Fermi level. In a periodic calculation, there is no simple absolute energy reference. One strategy is to use the energy of core electrons, which you can include with _pv or _sv potentials. More typical is to use a slab and explicitly calculate the vacuum level as a ref...

Check to see if the atoms with high forces are frozen. If so, those forces will be zeroed for the convergence test and the NEB force projections.

The TOTAL-FORCE is the NEB force. Below that, there is some NEB projection information, such as: NEB: Tangent ---------------------------------------------- 0.00000 0.00000 -0.00000 ..... NEB: forces: par spring, perp REAL, dneb 0.005906 0.023649 0.000000 NEB: distance to prev, next image, angle bet...

If the script is working properly, and you specify CONTCAR files (with a 1 flag), it should grab the POSCAR files from the endpoint directories and the CONTCAR file from the images in between.

The issue here is that the relevant forces for an NEB calculation is different from that of a normal minimization. For an NEB calculation, the force that is minimized is the projection of the real force perpendicular to the reaction path, plus a spring force that keeps the images equally spaced. Thi...