Search found 2064 matches

by graeme
Sat Jan 22, 2022 11:25 pm
Forum: VTSTTools
Topic: NEB Calculation for MXene
Replies: 9
Views: 742

Re: NEB Calculation for MXene

I'm having a hard time making sense to this. This was run on dec. 6 with the error message:

/var/spool/pbs/mom_priv/jobs/120122.hn1-srmhpc03.SC: line 10: /opt/software/intel/parallel_studio_xe_2017.0.035/psxevars.sh: No such file or directory

This has nothing to do with the VTST code.
by graeme
Fri Jan 14, 2022 3:53 pm
Forum: VTSTTools
Topic: Convergence issue with NEB
Replies: 5
Views: 189

Re: Convergence issue with NEB

Yes, so for example, the 27th atom in your 00/POSCAR is a Na atom at: 1.14333094938690 2.24730915067498 0.89735201226803 0 27 which becomes the 28th atom in your 08/POCAR: 1.13079578641343 2.48871545028892 0.79269253138857 0 28 you need to reorder the atoms in one of these files so that their identi...
by graeme
Fri Jan 14, 2022 12:40 am
Forum: VTSTTools
Topic: Convergence issue with NEB
Replies: 5
Views: 189

Re: Convergence issue with NEB

If you look at the initial movie, you can see that there is a problem with the ordering of atoms between the initial and final states. See the attached movie, and how atoms are moving across the cell to take the place of identical atoms. You need to reorder the atoms between the initial states.
by graeme
Wed Jan 12, 2022 6:56 pm
Forum: VTSTTools
Topic: Forces cannot converge in NEB calculations
Replies: 6
Views: 560

Re: Forces cannot converge in NEB calculations

Yes, that is better. It is not required, but if you want to use subsequent neb-related scripts for determining saddle energies or plotting the minimum energy path, they need to know the energy of the endpoints and they get that from the OUTCAR files.
by graeme
Tue Jan 11, 2022 4:47 pm
Forum: VTSTTools
Topic: TST tools with vasp 6.2.1
Replies: 2
Views: 136

Re: TST tools with vasp 6.2.1

Look in the src/.objects file.
by graeme
Mon Jan 10, 2022 11:46 pm
Forum: VTSTTools
Topic: Forces cannot converge in NEB calculations
Replies: 6
Views: 560

Re: Forces cannot converge in NEB calculations

We have a script in the vtstscript package to help with this. For any vasp calculation, regular, dimer, or neb, you can use the vfin.pl script. This takes an input of a directory name. The script will then copy the calculation results to the specified directory as well as copying all the CONTCAR -> ...
by graeme
Fri Dec 10, 2021 8:35 pm
Forum: VTSTTools
Topic: NEB Calculation for MXene
Replies: 9
Views: 742

Re: NEB Calculation for MXene

if you run into any problems or want advice, the best thing is to tar/gz the entire calculation (without CHG* WAV* files) and post that.
by graeme
Fri Dec 10, 2021 3:23 am
Forum: VTSTTools
Topic: after CINEB run,the dimmer calculation cannot converge
Replies: 4
Views: 445

Re: after CINEB run,the dimmer calculation cannot converge

It is not a low barrier; there is no barrier. In the min1 calculation I posted, a careful relaxation of your initial state goes to the product state.
by graeme
Fri Dec 10, 2021 12:27 am
Forum: VTSTTools
Topic: after CINEB run,the dimmer calculation cannot converge
Replies: 4
Views: 445

Re: after CINEB run,the dimmer calculation cannot converge

I'm very glad that you posted this calculation because it is such a classical example of what we call a shoulder on the potential energy surface. These can be hard to picture, but in this case, it is pretty clear because the reaction coordinate largely involves just H-transfer. But first, I took you...
by graeme
Thu Dec 09, 2021 5:38 pm
Forum: VTSTTools
Topic: NEB Calculation for MXene
Replies: 9
Views: 742

Re: NEB Calculation for MXene

I would always recommend using cheap setting for the initial convergence of an NEB, including normal precision, a cutoff closer to 400 eV and a minimal KPOINT mesh. Once you have a converged path, it is easy to increase precision. But also, why ALGO=All? Anyway, I can't really tell more without seei...
by graeme
Tue Dec 07, 2021 4:09 pm
Forum: Bader
Topic: Molecular Dynamic CHGCAR AECCAR
Replies: 1
Views: 292

Re: Molecular Dynamic CHGCAR AECCAR

Hi Silvio, I do not know of a way to have vasp write the AECCAR files at each step along an MD trajectory. That said, I think it would be very easy to use a driver code, such as ASE, to do single energy point calculations in vasp, save the charge density files, and the MD steps in a loop. And yes, w...
by graeme
Tue Nov 23, 2021 3:05 pm
Forum: VTSTTools
Topic: Install VTST with vasp gpu
Replies: 2
Views: 503

Re: Install VTST with vasp gpu

If you look in /src/.objects, you will have to add the VTST code objects to the variable SOURCE_GPU in the same way that you did to SOURCE.
by graeme
Sun Nov 21, 2021 8:02 pm
Forum: VTSTTools
Topic: Forces cannot converge in NEB calculations
Replies: 6
Views: 560

Re: Forces cannot converge in NEB calculations

I did my standard calculation for problematic cases. I went to minimal precision settings and re-relaxed the endpoints. Then I did an 8 image band with IOPT=3 TIMESTEP=0.1. It seems to be converging just fine, to a barrier of about 0.77 eV with residual forces on the order of 0.03 eV/Ang. From this,...
by graeme
Wed Nov 17, 2021 4:12 pm
Forum: VTSTTools
Topic: CI-NEB convergence
Replies: 4
Views: 637

Re: CI-NEB convergence

Great to hear that things are working better. A few comments: If you have a converged NEB, you do not need to do a subsequent dimer calculations. The climbing image will be at the saddle if the NEB converges. For me to see what is happening between the NEB calculation and the Dimer calculations, it ...
by graeme
Tue Nov 16, 2021 9:28 pm
Forum: Bader
Topic: Bader error
Replies: 2
Views: 383

Re: Bader error

It looks like you ran the analysis properly using ./bader NaCl_valence.cube -ref NaCl_allelec.cube but I'm not sure what you are trying to do when you ran ./bader chargefile the argument, chargefile is supposed to be your charge density file, which is NaCl_valence.cube if you want to add additional ...