Search found 1956 matches
- 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...
- 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.
- 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...
- 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.
- 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...
- 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.
- 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 ...
- 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.
- 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...
- 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...
- 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.
- 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.
- 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.
- 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.
It should be compatible with vasp 6 - I don't know of any changes to the format of the XDATCAR.
- 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...