Search found 1997 matches

by graeme
Wed Feb 03, 2021 3:20 am
Forum: Bader
Topic: The calculated charge is quite different from the given ACF.dat in example
Replies: 3
Views: 2390

Re: The calculated charge is quite different from the given ACF.dat in example

Make sure that you are doing the partitioning on the total charge density (CHGCAR_sum) and the integration on the valance charge (CHGCAR). The appropriate command is:

bader CHGCAR -ref CHGCAR_sum

This should reproduce the results in the ACF.dat file.
by graeme
Tue Feb 02, 2021 3:42 pm
Forum: VTSTTools
Topic: VASP 6.2 support
Replies: 6
Views: 4207

Re: VASP 6.2 support

Hi Adam, First, great to hear from you! We have not had any trouble with VTST and vasp 6.2 but I am eager to hear if anyone else does. Maybe start by greping the OUTCAR for VTST to see if the code was linked in. If not, there is likely a problem with how it was built. If you see a VTST statement in ...
by graeme
Thu Jan 28, 2021 9:23 pm
Forum: VTSTTools
Topic: Problems with VASP (Computational Materials)
Replies: 0
Views: 3723

Re: Problems with VASP (Computational Materials)

Looking at the structural change is a good idea. The xyz program that you mention is in our tsase package, and would need to be installed in your python distribution for that to work. I would suggest looking at the CONTCAR (the final configuration) as compared to the POSCAR (the initial configuratio...
by graeme
Wed Jan 27, 2021 4:01 pm
Forum: Bader
Topic: Bader charge on each atom is different?
Replies: 1
Views: 1827

Re: Bader charge on each atom is different?

If you can make your charge density files available to me, I can take a look.

Also, try adding the "-b weight" flag to see if that improves the precision of the calculations.
by graeme
Sat Jan 23, 2021 5:22 pm
Forum: eOn
Topic: Problems with Lammps and potential files
Replies: 3
Views: 2285

Re: Problems with Lammps and potential files

Great to hear that the problem was resolved. We do indeed need to add quite a bit of documentation.
by graeme
Fri Jan 22, 2021 6:36 pm
Forum: eOn
Topic: Problems with Lammps and potential files
Replies: 3
Views: 2285

Re: Problems with Lammps and potential files

Hi Sebastian, I think I would need to see the Fe.eam.alloy file, or better a .tar.gz file of the entire calculation, to debug this. But do check to see if this work in lammps directly. This reading of the lammps input file is done entirely in the lammps code, not in the eon code, and so I expect the...
by graeme
Tue Jan 12, 2021 11:17 pm
Forum: VTSTTools
Topic: What is considered a low frequency mode?
Replies: 2
Views: 2175

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: 3351

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: 2325

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: 3268

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: 3268

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: 1975

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: 5
Views: 3112

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: 2469

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: 2577

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...