Search found 1956 matches

by graeme
Tue Jan 12, 2021 11:17 pm
Forum: VTSTTools
Topic: What is considered a low frequency mode?
Replies: 2
Views: 24

Re: What is considered a low frequency mode?

This is a good question, but one that I feel is a little difficult to answer. The reason that it is difficult is that it depends upon what information you want to extract from the frequencies. It is also a little complicated because it can depend upon if you have frozen atoms in the system. In the c...
by graeme
Sat Jan 02, 2021 6:07 pm
Forum: VTSTTools
Topic: Transition State Search for Spin polarization Calculations
Replies: 5
Views: 617

Re: Transition State Search for Spin polarization Calculations

If you are doing an NEB calculation, each image should read the wavecar (if present) in its own directory.
by graeme
Wed Dec 16, 2020 6:54 pm
Forum: eOn
Topic: How to Visualize EON output
Replies: 1
Views: 661

Re: How to Visualize EON output

Hi Abid, Yes, for sure, this is critical, and I think we have very limited documentation about visualization. First, there are a few scripts in the eon/tools directory which might help visualize the processes available from a particularly state, eon-prmov.sh, but the primary tool for making movies i...
by graeme
Mon Dec 07, 2020 2:02 am
Forum: Bader
Topic: Atomic Bader charge and charge transfer using Quantum Espresso
Replies: 4
Views: 735

Re: Atomic Bader charge and charge transfer using Quantum Espresso

I think that you want the all-electron (valence+core) but based upon the total charge in your calculation (248 e) it seems that you only have the valence density in your analysis.
by graeme
Fri Dec 04, 2020 10:01 pm
Forum: Bader
Topic: Atomic Bader charge and charge transfer using Quantum Espresso
Replies: 4
Views: 735

Re: Atomic Bader charge and charge transfer using Quantum Espresso

It looks to me like you don't have core charges included. Your N atoms has a charge over 8, which is including the charge on the 3 H atoms. You can still estimate the charge transfer from the Boron surface to the NH3 molecule as 8.1-8=0.1e, but you really need core charges to resolve the charge dens...
by graeme
Fri Dec 04, 2020 8:37 pm
Forum: VTSTTools
Topic: vacancy migration NEB
Replies: 1
Views: 301

Re: vacancy migration NEB

That is really a question about the science If you are trying to get an activation energy for a vacancy migration in a bulk material, I would recommend keeping both the cell size and shape fixed.
by graeme
Fri Dec 04, 2020 8:05 pm
Forum: VTSTTools
Topic: nebmake.pl bug?
Replies: 2
Views: 761

Re: nebmake.pl bug?

The script is working as it should. The issue is that you are moving almost exactly 1/2 way across the box in the y-direction between images 0 and 2. In our script, we find the shortest path between the initial and final states relative to the periodic boundary conditions. For the first atom, it is ...
by graeme
Thu Dec 03, 2020 11:48 pm
Forum: VTSTTools
Topic: Illegal division by 0 with dymmatrix_v5.4.pl
Replies: 3
Views: 356

Re: Illegal division by 0 with dymmatrix_v5.4.pl

It looks like you have 90 atoms in your DISPLACECAR and only 87 in your POSCAR.
by graeme
Mon Nov 30, 2020 2:53 am
Forum: VTSTTools
Topic: SSNEB with only Z relaxtion?
Replies: 3
Views: 459

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: 459

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: 613

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: 613

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: 613

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: 27708

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: 1283

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...