UT theoretical chemistry code forum

Within harmonic transition state theory (TST), the energy barrier can be used to derive the Arrhenius rate = A exp (-dE/kT) , where dE is the energy barrier. This is an approximation which gives a rate at all temperatures, but that is more accurate a low temperature. Here, the energy (enthalpy) barr...

There is a trade-off between the two approaches. In one, you can generate a guess at the saddle as being 1/2 way between initial and final states, and start a dimer search right away. If this is a bad assumption, even a crude NEB can give you a better approximation to the saddle with a few additiona...

Yes you can specify the position of the atoms manually, using the nebmake script, the interpolate script, or by first doing a short NEB calculation for a few iterations and then use the neb2dim script. Restart the dimer by first running the 'vfin.pl dir' , where dir is the directory into which the r...

Nice addition Johannes. We've added your cube reference file loading code to the current source and binaries.

v0.23 09/18/07

Johannes Voss added a cube file reference charge reading function.

I can't tell what is wrong from your INCAR. My guess is that this is due to a simple problem that is unrelated to our code. The NPAR=2 is not appropriate, but I don't think it will cause the problem. Another possible problem is that are that you are running a serial code. Look at the first few lines...

There are a couple of different ways to use the dimer method. One is to start from a guess at the saddle, and converge upon it. A second is to start from a minimum and find different possible saddles that lead to unknown final states. In you description, it sounds like you are mixing these two appro...

The simplest correction is to add hv/2 for each positive mode at stationary points. The frequencies, v, can be found using a dynamical matrix calculation. Once you have the eigenvalues, we do have a script called dymzpbar.pl, which will do this calculation. A better approximation is based upon the q...

The dimer is moving significantly every four ionic steps: 1. force at new position 2. displacement along the current lowest mode direction 3. small finite difference rotation to find a better lowest mode direction 4. finite difference step for conjugate gradient line optimization step Then the dimer...

It does not look like your vasp binary was built with our vtstcode. Instructions for doing this are at: http://theory.cm.utexas.edu/vtsttools/downloads/ You should be able to grep for VTST in the OUTCAR and find a line similar to: VTST: version 2.03b (08/01/07) if the vtstcode has been properly link...

There is not enough information here to know what's happening.

Can you make a .tar.gz file of the run, and send it to me?
(henkelman at mail.utexas.edu)

For all vasp jobs, you can run 'vfin.pl dir' where dir is the directory into which the job will be archived. The remaining files (in the original, parent directory) will be ready for continuation.

It's very important to use core charges when doing this analysis with vasp.

Follow the instructions at:

http://theory.cm.utexas.edu/bader/vasp.php

If you still have problems with zero charges, please write back.

V2.03c (08/15/07)
- Forces are zeroed on the frozen atoms after calls to NEB/dimer/Lanczos, which eliminates small values in the LBFGS inverse Hessian.

Many molecular viewers will play this kind of movie. Start with jmol or vmd.