Search found 1948 matches

by graeme
Mon Nov 30, 2020 2:53 am
Forum: VTSTTools
Topic: SSNEB with only Z relaxtion?
Replies: 3
Views: 40

Re: SSNEB with only Z relaxtion?

You can install ASE locally - it does not have to be installed system-wide. In regards to changing neb.F, stress is a 3x3 matrix. In our code it is an upper-diagonal matrix, which is why the following elements: stress(2,1)=0._q stress(3,1)=0._q stress(3,2)=0._q are set to zero. In your case, you can...
by graeme
Fri Nov 27, 2020 9:18 pm
Forum: VTSTTools
Topic: SSNEB with only Z relaxtion?
Replies: 3
Views: 40

Re: SSNEB with only Z relaxtion?

Hi Zhifenh, One option is to use the SSNEB through tsase. ASE provides the ability to apply such general constraints. You could also modify neb.F in a similar way to how you modified constr_cell_relax.F. For example, around line 236 you could zero all the elements of the stress except for the 3,3 te...
by graeme
Wed Nov 25, 2020 6:24 pm
Forum: VTSTTools
Topic: All zero forces in the neb.dat file
Replies: 5
Views: 141

Re: All zero forces in the neb.dat file

That is very likely correct.
by graeme
Mon Nov 23, 2020 2:33 pm
Forum: VTSTTools
Topic: All zero forces in the neb.dat file
Replies: 5
Views: 141

Re: All zero forces in the neb.dat file

Well, you would need to extract the forces and take a dot product with the tangent between images. I don't think that we have a script for doing this, but it wouldn't be too hard.
by graeme
Fri Nov 20, 2020 5:56 pm
Forum: VTSTTools
Topic: All zero forces in the neb.dat file
Replies: 5
Views: 141

Re: All zero forces in the neb.dat file

My guess is that you do not have our VTSTcode linked into your vasp binary. You can grep for VTST in the OUTCAR to check.
by graeme
Thu Nov 12, 2020 9:24 pm
Forum: VTSTTools
Topic: VASP-MD velocities and VACF
Replies: 15
Views: 27024

Re: VASP-MD velocities and VACF

You can download the scripts here: https://theory.cm.utexas.edu/vtsttools/download.html

It should be compatible with vasp 6 - I don't know of any changes to the format of the XDATCAR.
by graeme
Wed Nov 11, 2020 12:54 am
Forum: eOn
Topic: Question about running eOn with external potential
Replies: 1
Views: 975

Re: Question about running eOn with external potential

Hi Qian, I'm not really sure what cp2k does when it evaluates an empirical potential, but I could imagine that there is a significant overhead in running cp2k to evaluate a simple Morse interaction. To check this, you might just check the time to calculate a single point energy and force with cp2k a...
by graeme
Tue Nov 10, 2020 3:14 am
Forum: VTSTTools
Topic: SSNEB for 2D material
Replies: 5
Views: 368

Re: SSNEB for 2D material

Wow, yes, it is already implemented! This has to be thanks to Penghao Xiao.
by graeme
Mon Nov 09, 2020 8:50 pm
Forum: VTSTTools
Topic: SSNEB for 2D material
Replies: 5
Views: 368

Re: SSNEB for 2D material

Hi Leiwy, I think that the best approach might be to run vasp through the ASE code. Vasp can be used as a calculator in ASE and the SSNEB is implemented there as well. ASE has a great deal of flexibility in terms of constraints that be applied for the calculations. It would also not be difficult to ...
by graeme
Thu Nov 05, 2020 4:03 pm
Forum: VTSTTools
Topic: Transition State Search for Spin polarization Calculations
Replies: 2
Views: 267

Re: Transition State Search for Spin polarization Calculations

This is a tricky problem. Using MAGMOM is a good strategy. You can also do a single-point calculation for the problematic image, aiming to get the right electronic structure. Then, if you load that WAVECAR and CHGCAR in the NEB calculation, it will be more likely to be on the correct energy surface.
by graeme
Sat Oct 31, 2020 4:45 pm
Forum: VTSTTools
Topic: Two imaginary vib modes for TS
Replies: 3
Views: 373

Re: Two imaginary vib modes for TS

I see two possible issues. The first is that the initial electronic structure calculation is not converged; it reached the limit of 60 electronic steps and then moved on. This is normally not a problem in a calculation, but for the dynamical matrix, you need to have every iteration converged. You ca...
by graeme
Fri Oct 30, 2020 2:58 pm
Forum: Bader
Topic: Bader and voronoi analysis discrepancy
Replies: 6
Views: 660

Re: Bader and voronoi analysis discrepancy

From the data you sent for the ground state, the charge of 6.054571 on C 63 looks reasonable.

I'm not sure how much to trust Bader charges for a highly excited electronic state - I just don't have any experience with that.
by graeme
Fri Oct 30, 2020 2:44 am
Forum: Bader
Topic: Bader and voronoi analysis discrepancy
Replies: 6
Views: 660

Re: Bader and voronoi analysis discrepancy

You will have to tell me more about what you mean by 'deviant'. What is it in the analysis that you recognize as being wrong? I don't know enough about your calculation to know what makes sense. If you have included all of the electrons for C, then a Bader charge of ~6 would give a neutral atom, whi...
by graeme
Fri Oct 30, 2020 2:19 am
Forum: Bader
Topic: Bader and voronoi analysis discrepancy
Replies: 6
Views: 660

Re: Bader and voronoi analysis discrepancy

The Voronoi charges are not to be taken seriously. They just provide a sanity check on the charge distribution in a system.

You should rely on the Bader partitioning for your charge analysis.
by graeme
Thu Oct 22, 2020 3:08 pm
Forum: VTSTTools
Topic: How to view movie file generated by nebmovie.pl?
Replies: 4
Views: 669

Re: How to view movie file generated by nebmovie.pl?

Well, I guess this shows how little I do calculations any more. I also had trouble with vesta and vmd. I'll check with my group and see if they have tricks. I always use our xyz viewer (in tsase) and I know that the visualizer in ase will also load and play these movies.