Search found 2255 matches

by graeme
Thu Jan 31, 2008 5:45 pm
Forum: VTSTTools
Topic: Abnormal NEB energy and Convergence problem
Replies: 9
Views: 23290

Re: Abnormal NEB energy and Convergence problem

Start by checking the initial geometries. You can make a movie of the unrelaxed calculation with nebmovie.pl. Try a single point energy calculation for one of the images - for example in the 01 directory. Does this calculation make sense? Why do you have IMAGES=1 when you have directories 01 and 04?...
by graeme
Thu Jan 31, 2008 5:40 pm
Forum: Bader
Topic: FFT grid
Replies: 3
Views: 11191

Re: FFT grid

Typically the default grid is somewhat course and a grid that is twice as fine is pretty good. But the best thing to do is to look for convergence of the Bader charges with respect to the grid density.
by graeme
Wed Jan 30, 2008 5:41 am
Forum: VTSTTools
Topic: dimer method can not start.
Replies: 8
Views: 21783

Re: dimer method can not start.

Strange, can we see your INCAR file?
by graeme
Tue Jan 29, 2008 2:44 am
Forum: VTSTTools
Topic: basic NEB run in VASP
Replies: 6
Views: 23463

Re: basic NEB run in VASP

It looks like there is a problem with one of the POSCAR files, perhaps in 02: 01/POSCAR found : 2 types and 33 ions LDA part: xc-table for Ceperly-Alder, standard interpolation 00/POSCAR found : 2 types and 33 ions No initial positions read in But anyways, this doesn't have anything to do with our c...
by graeme
Mon Jan 28, 2008 11:24 pm
Forum: VTSTTools
Topic: basic NEB run in VASP
Replies: 6
Views: 23463

Re: basic NEB run in VASP

There is not enough information to see what when wrong - there is no error message. Make sure that you can run a regular calculation on 12 nodes. Also, see if any error message is reported in the stdout (output to the screen) or from the queuing system.
by graeme
Mon Jan 21, 2008 4:39 pm
Forum: VTSTTools
Topic: about dynamical matrix calculation
Replies: 9
Views: 19874

Re: about dynamical matrix calculation

For slab calculations, we freeze one or two layers for all calculations (minimization, dimer, dynamical matrix, neb ... ). With frozen atoms, the slab is held in place, an you will avoid the low modes associated with rotation and translation - even when you include all non-frozen atoms in your dynam...
by graeme
Sat Jan 19, 2008 10:44 pm
Forum: VTSTTools
Topic: about dynamical matrix calculation
Replies: 9
Views: 19874

Re: about dynamical matrix calculation

Your initial state should not have negative modes (imaginary frequencies, marked with the 1 tag). Make sure that your initial state in fully optimized to a minimum. Check that your displacements are small enough that your calculated frequencies are insensitive to the displacement magnitude (typicall...
by graeme
Fri Jan 18, 2008 7:42 pm
Forum: VTSTTools
Topic: about dynamical matrix calculation
Replies: 9
Views: 19874

Re: about dynamical matrix calculation

The DISPLACECAR file requires only a list of 3xN numbers, indicating how much to displace each atom along each degree of freedom. Columns 4 and 5 are just for reference - they indicate the atom number and some distance, for example how much that atom has moved in a reaction. These two columns are no...
by graeme
Fri Jan 18, 2008 6:50 am
Forum: VTSTTools
Topic: about dynamical matrix calculation
Replies: 9
Views: 19874

Re: about dynamical matrix calculation

Your method does not sound quite right. The first step is correct - finding the minimum and saddle point. Now, do 2 separate (single image) dynamical matrix calculations, one for each of these states. You can use the dymseldsp.pl script to generate a DISPLACECAR, but since you do not have too many a...
by graeme
Thu Jan 10, 2008 4:33 pm
Forum: VTSTTools
Topic: What is the use of CENTCAR from the dimer run?
Replies: 1
Views: 6857

The CENTCAR contains the position of the center of the dimer, which is the current best estimation of the saddle. During the run, we make finite difference steps to evaluate curvatures. For these steps, the CONTCAR will be displaced from the CENTCAR by a small amount (DdR, or FDSTEP depending upon t...
by graeme
Wed Jan 09, 2008 7:25 pm
Forum: Bader
Topic: Bader analysis with all-electron charge density possible ?
Replies: 2
Views: 10809

This is a good question. We have never used this code, but here's a few thoughts: What is the normalization for the charge density? In the Bader code, the total charge is calculated as an integral of the charge density over the grid points. It looks like the EXCITING code is using a different normal...
by graeme
Mon Jan 07, 2008 4:32 am
Forum: VTSTTools
Topic: about neb sccripts
Replies: 7
Views: 17659

Ah, clearly I was wrong. Well, it's a little hard to tell what is causing this problem from the output. The nebbarrier.pl uses the dist.pl script to calculate the distance between the images. Do you have that in the same location as the nebbarrier.pl script? If not, this could result in zero values ...
by graeme
Mon Jan 07, 2008 1:35 am
Forum: VTSTTools
Topic: Tests for the VTST
Replies: 1
Views: 6831

There is no test suite, but this problem is also probably not due to the VTST code - I would be very surprised if it was. If you can run the normal vasp benchmarks, do a regular NEB calculation (without the VTST code), and get this error only when you link in the VTST code, then we would certainly l...
by graeme
Sun Jan 06, 2008 4:30 am
Forum: VTSTTools
Topic: about neb sccripts
Replies: 7
Views: 17659

I bet you have not compiled VASP with our NEB (VTST) code. Look in the OUTCAR for VTST - if you don't find it, this is the problem.
by graeme
Fri Jan 04, 2008 3:59 am
Forum: VTSTTools
Topic: about neb sccripts
Replies: 7
Views: 17659

Yes, just put the OUTCARs from your minimization in those directories. All the scripts do is grep those files for the energy.