Search found 1997 matches

by graeme
Thu Jul 15, 2021 8:21 pm
Forum: VTSTTools
Topic: How to find material's bonding strength by Bader charge analysis?
Replies: 1
Views: 97

Re: How to find material's bonding strength by Bader charge analysis?

There are people who would say yes, based upon accumulation or depletion of charge density at bond critical points, and maybe the curvatures of the charge density at those points. I would generally say no, not with any confidence. We only use it to see how charge has moved in a system, which may be ...
by graeme
Tue Jul 13, 2021 5:25 pm
Forum: VTSTTools
Topic: Identifying vib modes that contribute to entropy
Replies: 3
Views: 181

Re: Identifying vib modes that contribute to entropy

Hi Keerthan, You will have to be a little careful about how to convert these frequencies to the entropy of the system. First though, if you are at a temperature where you can consider all of these modes as harmonic, then you can calculate the harmonic vibrational entropy using all of the modes. Note...
by graeme
Tue Jul 13, 2021 1:40 am
Forum: VTSTTools
Topic: The influence of images used for CINEB
Replies: 2
Views: 330

Re: The influence of images used for CINEB

If you can attach a .tar.gz file of your calculation, I can help to debug the problem.
by graeme
Sun Jul 04, 2021 6:51 pm
Forum: VTSTTools
Topic: nebmake.pl problem
Replies: 1
Views: 218

Re: nebmake.pl problem

The structures in these two files look very different to me. I would be very surprised if there was a simple process connecting the two.
by graeme
Thu Jul 01, 2021 2:46 pm
Forum: VTSTTools
Topic: error message:(In vasp.pm::read_poscar, cannot open 'filename'
Replies: 2
Views: 193

Re: error message:(In vasp.pm::read_poscar, cannot open 'filename'

This may be related to how the script should be used. Make sure that you are including arguments of (1) the initial state POSCAR file; (2) the final state POSCAR file; and (3) the number of images. An example would be: nebmake.pl POSCAR_ini POSCAR_fin 6 Note: we should provide a sensible message if ...
by graeme
Thu Jun 24, 2021 3:17 am
Forum: VTSTTools
Topic: Solution of rate equation
Replies: 2
Views: 306

Re: Solution of rate equation

Dear Yu, Unfortunately, I think this is outside the scope of my support in this forum. I do deal with these issues with my own graduate students, but here, I just want to make sure that you can calculate barriers with our VTST methods. I hope that your advisor can provide some guidance in terms of s...
by graeme
Wed Jun 23, 2021 12:50 am
Forum: VTSTTools
Topic: multiple definition error
Replies: 5
Views: 468

Re: multiple definition error

Great to hear when things work out.
by graeme
Tue Jun 22, 2021 11:03 pm
Forum: VTSTTools
Topic: multiple definition error
Replies: 5
Views: 468

Re: multiple definition error

Ok, so first, you are right that bfgs.F is our file - I had forgotten about that! I think the problem is that you have somehow included the VTST objects twice. If you look at your link line, you can see: ... bfgs.o dynmat.o instanton.o lbfgs.o sd.o cg.o dimer.o bbm.o fire.o lanczos.o neb.o qm.o opt....
by graeme
Tue Jun 22, 2021 7:21 pm
Forum: Bader
Topic: CHGCAR file
Replies: 8
Views: 13164

Re: CHGCAR file

There is no post process or rearranging. A statement such as:

READ(IU,FORM) (((C(NX,NY,NZ),NX=1,NGXC),NY=1,NGYZ),NZ=1,NGZC)

will load all the data into the 64x64x64 array C.

Vesta will show either isosurfaces of the data or contour plot slices through the dataset.
by graeme
Tue Jun 22, 2021 4:44 pm
Forum: VTSTTools
Topic: multiple definition error
Replies: 5
Views: 468

Re: multiple definition error

Hm, this is a little strange. The file you mention, bfgs, is not a file in the vtst code. Let's just start with the basics - make sure that you got the code files from the vtstcode/vtstcode6.1 directory. Then add the vtst objects in the /src/.objects file. Importantly, do a "make clean". I...
by graeme
Tue Jun 22, 2021 3:48 pm
Forum: Bader
Topic: CHGCAR file
Replies: 8
Views: 13164

Re: CHGCAR file

If you look at my previous posts in the thread, you can see the format by which this data is written. It is a 64x64x64 data set written with 5 values per line. You could make a 64x64x64 array and read the values back in using the same type of format statement. But generally we read this data into a ...
by graeme
Sun Jun 20, 2021 2:33 pm
Forum: VTSTTools
Topic: CINEB Diverges in specific images
Replies: 5
Views: 573

Re: CINEB Diverges in specific images

Since this path has an intermediate minimum, it is really 2 paths, so having 8 images is resolving each with only 3-4. You do not need to do NEB before CINEB. I expect that the fluctuations of O2 are related to the intermediate minimum. If you minimize that and resolve the two reactions separately, ...
by graeme
Sun Jun 20, 2021 3:06 am
Forum: VTSTTools
Topic: CINEB Diverges in specific images
Replies: 5
Views: 573

Re: CINEB Diverges in specific images

Look at my standard go-to calculation using IOP=3 TIMESTEP=0.1 with 8 images. It seems to be converging, although with an intermediate minimum.
by graeme
Sat Jun 19, 2021 7:50 pm
Forum: VTSTTools
Topic: Nudged Elastic Band Calc.
Replies: 1
Views: 303

Re: Nudged Elastic Band Calc.

So, I don't believe this has to do with the VTST code. I'm actually not sure what is making the job stop, but I don't see anything related to VTST. Can you run single image calculations with the same settings? Also check for other trivial problems such as reaching your disk quota or a short time req...
by graeme
Sat Jun 19, 2021 7:43 pm
Forum: VTSTTools
Topic: Benchmark test cases for DFT program or VASP?
Replies: 1
Views: 222

Re: Benchmark test cases for DFT program or VASP?

In the recent versions of vasp, you can find a testsuite provided.