UT theoretical chemistry code forum

Yes. One suggestion: it would be good to check where the excess or reduction in charge comes from. DFT tends to delocalize charge, and if the change in charge is not localized, it can be cancelled by the uniform background screening charge that is needed to maintain overall neutrality in the superce...

We'll have to make a few changes to this new code so that it is compatible with the different versions of vasp. Give us another week to get this sorted out.

I've made a few additional comments on that web page. First, yes, you put the same POSCAR in each of the image subdirectories. To construct the matrix, run: dymmatrix.pl 1 DISPLACECAR ??/OUTCAR which means that you have 1 DISPLACECAR file with force information in the ??/OUTCAR files. You can, of co...

The Bader definition of atomic volumes is very large for surface atoms. Unfortunately, there is no alternative definition within this theory. I think it would be better to integrate the density of states within the Bader volumes. A student in my group, Wenjie Tang, has the code for this and will pos...

The calculation is fine. In a Bader calculation, all space is assigned to atoms (or more precisely, charge density maxima). For a surface, all of the vacuum space is assigned to the surface atoms. The charges on these atoms look very reasonable.

The way you set this up is not quite right. I see that the instructions on the web page are not clear. I have modified the page:
http://theory.cm.utexas.edu/vtsttools/dynmat/
If it is still not understandable, let me know and I'll try again.

Yes, if you only care about the saddle point, you can stop the optimization when that image has converged.

Yes sure. It is good to use a small time step with a conservative optimizer until the forces on all images are < 1 eV/Ang.

You could try lowering the displacement to 0.002 in the second method and see if the frequencies change, or if they are converged with respect to the finite difference step size. Also, you should try to include some of the surface metal atoms. Again, check to see if the modes of the molecule are unc...

We would like to sort out problems with these charge density files. If you can send them to us, or make them available by posting them, we'll take a look.

If you post a link or send us the file, we'll take a look. Without a precise format definition, we would like to output a file that is as compatible with other tools as possible.

The problem might be different if the program is crashing on the initial energy calculation, or if it was able to calculate the energy of image 3 at least once. First though, I would start by making a movie of the initial band (e.g. with nebmovie.pl) so that you can see that the path makes sense. Th...

That's right, the NEWMODECAR should replace the MODECAR in the subsequent calculation.

You can select the atoms which have moved the most in your calculation, and displace those and their neighbors. We have a script for making this selection. Then you have to check that as you include more atoms (for example, with a smaller distance criteria) the prefactor converges. In practice thoug...

If you have our scripts, you can run nebef.pl in the neb directory to get a list of the final energies and forces for each image (the largest force on any atom).