Search found 1810 matches

by graeme
Thu Feb 21, 2019 1:21 pm
Forum: VTSTTools
Topic: NEB calculation seems to be tremendously slow
Replies: 1
Views: 10

Re: NEB calculation seems to be tremendously slow

Probably. If you can post a .tar.gz file of the calculation, I can take a look.

Please remove any CHG* WAV* files. If it is too large, you can post a link to it.

Also, take a look back at the many posts about controlling convergence, and my suggestions.
by graeme
Wed Jan 30, 2019 1:24 pm
Forum: Bader
Topic: Error: Invalid decimal character . was detected
Replies: 2
Views: 949

Re: Error: Invalid decimal character . was detected

I'm not sure what is going wrong. I can run the analysis on my computer with your charge density file. Maybe build a clean version of the binary after removing all the object files. I'm puzzled about what could cause this error. Graeme ------------ bader CHGCAR GRID BASED BADER ANALYSIS (Version 1.0...
by graeme
Tue Jan 29, 2019 1:12 pm
Forum: Bader
Topic: bader anlaysis for charged vacancy defect
Replies: 5
Views: 3319

Re: bader anlaysis for charged vacancy defect

No, I'm just saying that you can find the charge state of the vacancy from the sum of the charge on the neighboring atoms. Any extra or missing charge can be associated with the vacancy.
by graeme
Mon Jan 28, 2019 5:39 pm
Forum: Bader
Topic: bader anlaysis for charged vacancy defect
Replies: 5
Views: 3319

Re: bader anlaysis for charged vacancy defect

Ah, yes, I see what you are asking about. It is quite possible that there will not be a charge density maximum at the vacancy site. If you are interested in the local charge of the vacancy as compared to the charge that may be delocalized throughout the crystal, you can look at the total charge of t...
by graeme
Sat Jan 26, 2019 3:58 pm
Forum: Bader
Topic: bader anlaysis for charged vacancy defect
Replies: 5
Views: 3319

Re: bader anlaysis for charged vacancy defect

Yes, for sure.
by graeme
Tue Jan 08, 2019 1:23 am
Forum: Bader
Topic: Questions on increase accuracy of Bader charges
Replies: 1
Views: 1544

Re: Questions on increase accuracy of Bader charges

Try using the "-b weight" flag for higher accuracy. This method, developed in the Trinkle group, divides cells on the boundary between atoms with a weight based upon linear interpolation.

Increase the grid density also improves accuracy for all methods.
by graeme
Thu Dec 20, 2018 9:17 pm
Forum: VTSTTools
Topic: Increasing K Points of Saddle Image from CINEB with Dimer Method
Replies: 1
Views: 2404

Re: Increasing K Points of Saddle Image from CINEB with Dimer Method

I took a look at your system and I think there are two complicating factors, neither of which really has to do with k-point sampling. First, I was able to reproduce your NEB calculation (see neba.tar.gz). I used a somewhat reduced z-axis to save some time. It has a barrier of about 0.9 eV and shows ...
by graeme
Thu Dec 20, 2018 3:27 am
Forum: VTSTTools
Topic: bond-boost method
Replies: 2
Views: 1811

Re: bond-boost method

This is a very good point - I didn't even realize that the bond boost method as implemented in the VTST code was not documented. We now use our EON code to run hyperdynamics with energy and forces from vasp. But anyway, it should be documented. From what I remember, the variables are consistent with...
by graeme
Tue Dec 18, 2018 6:29 pm
Forum: Bader
Topic: Charge Density Difference
Replies: 2
Views: 1911

Re: Charge Density Difference

If you can't get SIESTA to generate grids with the same number of points in your two calculations, then I would suggest looking for a script or math software to re-grid one of the data sets to be the same as the other. I did a quick search and found a free program as well as a python module which ha...
by graeme
Fri Dec 14, 2018 5:30 pm
Forum: VTSTTools
Topic: SSNEB failed
Replies: 2
Views: 1868

Re: SSNEB failed

Here are a few suggestions: First, make sure that your endpoints are minimized. Second, you need to think about a sensible mapping between the order of atoms in your initial and final structures. The ordering of the atoms determines which atom in the initial structure moves to which final state geom...
by graeme
Mon Dec 03, 2018 5:58 pm
Forum: VTSTTools
Topic: Vinyard formula in Arrhenius Eq. dymprefactor.pl
Replies: 3
Views: 2264

Re: Vinyard formula in Arrhenius Eq. dymprefactor.pl

800-1000K is almost for sure high-temperature. You really need to compare kT to hw for the highest frequencies in your system, but most phonons are excited at 1000K. Those two scripts do evaluate rates with the quantum partition function. I guess they were used to make Arrhenius-like plots, so you c...
by graeme
Mon Dec 03, 2018 2:21 pm
Forum: VTSTTools
Topic: Vinyard formula in Arrhenius Eq. dymprefactor.pl
Replies: 3
Views: 2264

Re: Vinyard formula in Arrhenius Eq. dymprefactor.pl

The Arrhenius expression uses the classical harmonic partition function q_cl = kT/hw. You can certainly replace this with the quantum partition function, which is close to what you wrote: q_qm = exp(-hw/2kT) / (1-exp(-hw/kT). At high temperature, this converges to the classes partition function and ...
by graeme
Mon Dec 03, 2018 2:45 am
Forum: VTSTTools
Topic: Hydrogen association dynamic matrix
Replies: 7
Views: 2797

Re: Hydrogen association dynamic matrix

I think that you just need to converge more precisely to the saddle. In the dim01 calculation, I reduced the force tolerance to 0.002 eV/Ang. You can see that the geometry moved significantly upon convergence. Then using the same settings as you, I see a single negative mode at the saddle, in the 0....
by graeme
Fri Nov 30, 2018 3:19 pm
Forum: VTSTTools
Topic: Convergence Problem
Replies: 3
Views: 2228

Re: Convergence Problem

The energy and forces are dropping steadily so you should be able to keep running. The slow convergence may be related to the fact that you have no frozen atoms, so there could be soft modes. But anyway, I don't see any problems with the convergence rate in this calculation.
by graeme
Fri Nov 30, 2018 4:05 am
Forum: VTSTTools
Topic: no TS found when the cNEB is over
Replies: 7
Views: 3051

Re: no TS found when the cNEB is over

onward!