Search found 27 matches

by arosen
Wed Jun 01, 2022 5:46 pm
Forum: Bader
Topic: Question about voronoi flag in bader code
Replies: 2
Views: 10459

Re: Question about voronoi flag in bader code

Thanks for the reply. That's pretty much what I had figured but wanted to double-check.
by arosen
Wed Jun 01, 2022 4:40 pm
Forum: Bader
Topic: Question about voronoi flag in bader code
Replies: 2
Views: 10459

Question about voronoi flag in bader code

I know that you can calculate Voronoi charges via `-c voronoi` in the `bader` executable. However, I want to ask -- what precisely are these Voronoi charges? Are they Voronoi deformation density (VDD) charges, as discussed here (https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.10351), or are they...
by arosen
Sun May 16, 2021 8:31 pm
Forum: VTSTTools
Topic: Spin crossover with NEB
Replies: 0
Views: 34510

Spin crossover with NEB

Are there any plans to enable individual NUPDOWN keywords (and/or MAGMOM flags) for each image in an NEB run? Right now, the best I can do is copy a WAVECAR in each folder from a separate static run and hope that the spin state remains the same. If there's an easier way to approach this, please let ...
by arosen
Mon Oct 08, 2018 8:15 pm
Forum: VTSTTools
Topic: Transition state calculation for wealy bound molecules
Replies: 18
Views: 39866

Re: Transition state calculation for wealy bound molecules

Omran, The "negative" barrier is likely because what you have shown is not an elementary step. As Prof. Henkelman pointed out, your initial and final states do not involve H-abstraction at the same proposed active site. What I imagine happened is that the transition state you found is best...
by arosen
Thu May 03, 2018 4:12 am
Forum: VTSTTools
Topic: All atoms drift during dimer calculation
Replies: 2
Views: 11977

Re: All atoms drift during dimer calculation

Thanks for the helpful reply. When I noticed the curvature was pretty much 0, it was clear something was definitely off, and it makes sense that the translating atoms would only occur in these cases. Fortunately, when you set things up the right way, things tend to behave as you'd expect...
by arosen
Mon Apr 30, 2018 2:56 pm
Forum: VTSTTools
Topic: All atoms drift during dimer calculation
Replies: 2
Views: 11977

All atoms drift during dimer calculation

Occasionally when using the dimer method, all the atoms in the unit cell tend to drift in a certain direction despite the MODECAR only have one non-zero (x,y,z) entry. I don't think this impacts the rate of TS convergence since all the atoms seem to be translated by the same amount, but it's a bit p...
by arosen
Fri Feb 09, 2018 10:50 pm
Forum: VTSTTools
Topic: Dimer Method: High Torque When Restarting
Replies: 11
Views: 37594

Re: Dimer Method: High Torque When Restarting

Thanks for the reply. To prevent any unexpected errors, I think I'll just rerun the converged dimers using the updated VTST then. It shouldn't require many steps.
by arosen
Fri Feb 09, 2018 5:26 pm
Forum: VTSTTools
Topic: Dimer Method: High Torque When Restarting
Replies: 11
Views: 37594

Re: Dimer Method: High Torque When Restarting

If I wish to use `dimmins.pl` on dimer calculations that have finished on the prior version of VTST, is there any way to do this accurately without rerunning the converged dimer on the newest version of VTST? I'm not sure exactly what the issues were with the MODECAR. Also, I believe the documentati...
by arosen
Mon Feb 05, 2018 4:14 am
Forum: VTSTTools
Topic: EDWAV error only when using VTST (VASP 5.4.1)
Replies: 4
Views: 23188

Re: EDWAV error only when using VTST (VASP 5.4.1)

To anyone that may run into a similar issue, the issue was resolved when switching ALGO keywords. This is bizarre because the job runs fine with ALGO = 'All' with VASP 5.4.1 but switching to the VTST-enabled build resulted in EDWAV errors unless I switched ALGO. As previously noted, VTST should not ...
by arosen
Sun Feb 04, 2018 3:48 am
Forum: VTSTTools
Topic: Dimer Method: High Torque When Restarting
Replies: 11
Views: 37594

Re: Dimer Method: High Torque When Restarting

Fantastic, thank you for getting to that so promptly! Looking forward to the update, as I have a lot of dimer calculations in my near future!
by arosen
Fri Feb 02, 2018 1:40 am
Forum: VTSTTools
Topic: Dimer Method: High Torque When Restarting
Replies: 11
Views: 37594

Re: Dimer Method: High Torque When Restarting

Thanks for the workaround idea! I do use ASE, so this will likely be quite useful!
by arosen
Tue Jan 30, 2018 7:27 pm
Forum: VTSTTools
Topic: Dimer Method: High Torque When Restarting
Replies: 11
Views: 37594

Re: Dimer Method: High Torque When Restarting

Time flies! If any additional information would be helpful, let me know. I've attached the two DIMCARs, but it's just reiterating the prior post.
by arosen
Tue Jan 30, 2018 4:47 pm
Forum: VTSTTools
Topic: Dimer Method: High Torque When Restarting
Replies: 11
Views: 37594

Re: Dimer Method: High Torque When Restarting

Has this issue been resolved? I am finding identical behavior when I restart the dimer method using the `vfin.pl` script and VTST 3.1 (with VASP 5.4.1). The force continues off where the first job finished, but the torque/curvature/angle are all very high in the first iteration (with torque, curvatu...
by arosen
Tue Jan 30, 2018 4:12 am
Forum: VTSTTools
Topic: fix atomic position
Replies: 3
Views: 17395

Re: fix atomic position

You could use the Atomic Simulation Environment to set constraints using the `FixAtoms` class. It's pretty user-friendly (see here: https://wiki.fysik.dtu.dk/ase/ase/constraints.html)
by arosen
Mon Jan 22, 2018 4:56 pm
Forum: VTSTTools
Topic: EDWAV error only when using VTST (VASP 5.4.1)
Replies: 4
Views: 23188

Re: EDWAV error only when using VTST (VASP 5.4.1)

Thanks for the reply. That's what I figured as well but wanted to confirm. I'll continue trying to isolate the issue.