Search found 12 matches

by sinfire
Wed Apr 03, 2019 11:41 am
Forum: VTSTTools
Topic: Error in Dynamical Matrix run
Replies: 1
Views: 4144

Re: Error in Dynamical Matrix run

OK I think I solved the problem.

It turned out that I didn't read the dynmat page more carefully.


I had to set IBRION=3 but my calculation was set as IBRION=2.

Strange that other jobs worked fine though.
by sinfire
Wed Apr 03, 2019 8:59 am
Forum: VTSTTools
Topic: Error in Dynamical Matrix run
Replies: 1
Views: 4144

Error in Dynamical Matrix run

Hi all I'm trying run a dynamical matrix run to get the ZPE corrections. When running the job, I'm getting errors with NaNs appearing in the output. I'm running the job with 9 DOFs, 3 images with NSW=4. Could anyone explain why this error appears and suggest a way to avoid this error? I check the jo...
by sinfire
Tue Apr 02, 2019 4:39 am
Forum: VTSTTools
Topic: [DYNAMICAL MATRIX] Format of DISPLACECAR
Replies: 1
Views: 4059

[DYNAMICAL MATRIX] Format of DISPLACECAR

Hi all, I'm trying to do a zero-point energy evaluation on metal slab-adsorbant system. I'm trying to understand DISPLACECAR generation scripts. So I think I know what the first 4 numbers are in the DISPLACECAR file, but I'm not really sure what the last number means. Like: [dx] [dy] [dz] [atomnumbe...
by sinfire
Fri Oct 05, 2018 6:41 am
Forum: VTSTTools
Topic: NEB initial image construction
Replies: 5
Views: 9251

Re: NEB initial image construction

Thank you for the answer.

Regarding the distance, how close the distance between the images should be? (in other words, how many digits should I consider?)

Is 0.48 and 0.50 calculated from dist.pl close enough?
by sinfire
Thu Oct 04, 2018 3:51 am
Forum: VTSTTools
Topic: NEB initial image construction
Replies: 5
Views: 9251

Re: NEB initial image construction

Thank you Prof. Henkelman.

Could you elaborate on making a band out of two path segments?

I can't find any parameters defining a band. Do you mean constructing N images using the Initial state and the TS guess and construct Max_image - N images using the TS guess and Final state?
by sinfire
Wed Oct 03, 2018 6:37 am
Forum: VTSTTools
Topic: NEB initial image construction
Replies: 5
Views: 9251

NEB initial image construction

Hi all,

If the inital images constructed from nebmake.pl doesn't look right, would there be much problem if I tweak the constructed images manually to make a more reasonable path?

In that case, is there anything I need to consider when changing the images?

Thanks

M.-C.
by sinfire
Fri Aug 31, 2018 12:59 am
Forum: VTSTTools
Topic: NEB convergence
Replies: 3
Views: 7980

Re: NEB convergence

Thank you for the answer prof. Henkelman. Some additional questions: 1. What does exactly "run the FIRE calculation longer" mean? Are you suggesting lowering the time step and/or lowering the EDIFFG of the FIRE job? 2. As I look at the images, the distance between the starting geometry of ...
by sinfire
Thu Aug 30, 2018 6:19 am
Forum: VTSTTools
Topic: NEB convergence
Replies: 3
Views: 7980

NEB convergence

Hi all, I'm doing a CI-NEB calculation. Just wanted to check if this procedure makes sense. At first, I did a continuous FIRE(EDIFFG = -1.0) -> L-BFGS(EDIFF = -0.15) job using the default TIMESTEP parameters. The FIRE step was taking some time and when consulting the nebef.pl result, I noticed one o...
by sinfire
Mon Aug 27, 2018 10:27 am
Forum: VTSTTools
Topic: NEB energy oscillating
Replies: 3
Views: 7882

Re: NEB energy oscillating

Thank you for the reply. I noticed there's another executable and now it seems to be working. ====================================== ... VTST: version 3.1, (03/28/14) CHAIN: initializing optimizer OPT: Using VASP QUASI-newton optimizer CHAIN: Read ICHAIN 0 CHAIN: Running the NEB NEB: SPRING -5.00000...
by sinfire
Mon Aug 27, 2018 2:01 am
Forum: VTSTTools
Topic: NEB energy oscillating
Replies: 3
Views: 7882

NEB energy oscillating

Hi all, I'm doing a NEB calculation on oxygen dissociation. As I checked the energies, it seems to be oscillating(or 'stuck' I'd say). (The cnvg-f.txt file in the attachment is the result from grep "F=" stdout to look at E and dE) Is this or common thing or should I rerun the calculation w...
by sinfire
Thu Aug 23, 2018 12:20 am
Forum: VTSTTools
Topic: NEB optimizer choice
Replies: 3
Views: 8139

Re: NEB optimizer choice

Thank you for the answers. I'm trying to set up a queue submit file doing CI-NEB-FIRE with EDIFFG = --1.0 to CI-NEB-LBFGS with EDIFFG= -0.15 I changed the EDIFFG in the INCAR file after the FIRE run, and then runned LBFGS. Strangely the EDIFFG in the subdirecteries(01-0X) don't seem to change. Do I ...
by sinfire
Tue Aug 21, 2018 4:13 am
Forum: VTSTTools
Topic: NEB optimizer choice
Replies: 3
Views: 8139

NEB optimizer choice

Hi all: I'm doing a CI-NEB calculation. I'm currently testing the calculation using different optimizers, one with the default GDIIS optimizer and one with L-BFGS. In case the L-BFGS method fails to converge, is it reasonble to run CI-NEB with a more robust optimizer for several steps and continue t...