UT theoretical chemistry code forum

You are able to freeze atoms using the selective dynamics tags. Keep those same setting for the dynamical matrix calculation.

Within the harmonic approximation, you need to calculate the normal mode frequencies at the reactant and saddle point. Then the attempt frequency for hopping is given by: v = Prod v_rs / Prod v_ts , where Prod is the product of all the positive frequencies v = w/2pi, rs is the reactant state and ts ...

No, you can only run the NEB using vasp. The CI-NEB and G-SSNEB are provided with the vtstcode.

Yes, you can run the NEB with the code built into vasp. The VTSTcode add a few features including the climbing image, double nudging, and optimizers which are more efficient for the NEB. There are also some print statements which are needed to work with the VTSTscripts.

I would not recommend it. I would just use the standard Sb and Zn potentials. Zn, in particular, has plenty of valence electrons.

If your linux cluster has a queueing system, you can submit a large number of jobs and let the queueing system run the jobs as the resources are free. Another useful tool, which is implemented in most queueing systems is an array job. Here is some information about that for the sge: https://arc.liv....

I suggest using the default values of NG(X,Y,Z)F and then increase them by 50% to check for convergence. If you are integrating the valence charge, you will not need a super-fine grid. The total number of electrons should be precisely correct, independent of the grid density - this is a property of ...

It is very important to do the Bader partitioning based upon the total charge and the integration based upon the valence charge. From the Bader analysis webpage: By adding the LAECHG=.TRUE. to the INCAR file, the core charge is written to AECCAR0 and the valance charge to AECCAR2. These two charge d...

I'm attaching an example ssneb calculation for the perovskite work that you mentioned. Any detailed questions should be directed to the primary author of that work, Penghao Xiao. Your second question is a little harder to answer. The NEB is a good method to find the reaction pathway and barrier for ...

just the CHAIN+TOTAL

It is a problem with vasp, but again, I don't know what causes it. It would be nice if the vasp developers would look into it.

If you look in your AECCAR0 file, you will see that it is full of NaN (not a number) values. Vasp needs to output a proper AECCAR0 for the Bader analysis to work. I've seen this before but I'm not sure what causes it.

If you can make the charge density files available to me, I'll run tests.

Oh, because the script finds the shortest path between the initial and final state (the minimum image convention). In your case, atom 1 goes across one side of the box to the other, as allowed by the periodic boundary conditions.