Search found 1726 matches

by graeme
Sun Aug 12, 2018 3:11 am
Forum: Bader
Topic: Cube File not working with Bader Analysis
Replies: 2
Views: 138

Re: Cube File not working with Bader Analysis

It is probably a memory issue. It runs fine on my laptop (see below). Either find a machine with more memory, or reduce the cell size, which appears to be ridiculously large. ------- GRID BASED BADER ANALYSIS (Version 1.03 11/13/17) OPEN ... chd.cube GAUSSIAN-STYLE INPUT FILE DENSITY-GRID: 432 x 432...
by graeme
Wed Aug 08, 2018 12:09 pm
Forum: VTSTTools
Topic: Is my neb calculations ok?
Replies: 1
Views: 40

Re: Is my neb calculations ok?

Make sure that you have our VTSTcode linked into the vasp binary that you used to run the NEB calculation. You should not see those zeros in the neb.dat file. You can grep any OUTCAR in the calculation for VTST to check.
by graeme
Thu Aug 02, 2018 8:54 pm
Forum: Bader
Topic: Cube File not working with Bader Analysis
Replies: 2
Views: 138

Re: Cube File not working with Bader Analysis

If you post the problem file, I can take a look.
by graeme
Mon Jul 23, 2018 9:12 pm
Forum: Bader
Topic: Very Large Charges From Bader
Replies: 3
Views: 391

Re: Very Large Charges From Bader

What you are looking at is not the net charge - it is the number of valence electrons associated with each atom. To get the net charge, you need to take the (positive) nuclear charge and subtract the charge in the ACF file. I can't see what atoms you have in your system, but let's say that the first...
by graeme
Fri Jul 20, 2018 7:09 pm
Forum: eOn
Topic: Missing false_boinc.h
Replies: 4
Views: 345

Re: Missing false_boinc.h

There are some tests in the examples directory, but not automatic unit tests. I know, we should have them.
by graeme
Fri Jul 20, 2018 1:54 am
Forum: eOn
Topic: Missing false_boinc.h
Replies: 4
Views: 345

Re: Missing false_boinc.h

This is my fault. I recently tried to remove all boinc dependencies in eon and I forgot some of the potentials.
Version 2366 should have fixed this problem.
by graeme
Wed Jul 11, 2018 2:14 pm
Forum: VTSTTools
Topic: the generated MODCAR is zero bit
Replies: 5
Views: 1131

Re: the generated MODCAR is zero bit

Neither of these are correct. 1. Run the neb calculation. 2. Run "vfin.pl subdir" where dir is the name of the directory to store the calculation. 3. Go into that directory "cd subdir" and make sure the calculation is sensible; you can run nebresults.pl and check the output 4. From that subdir (whic...
by graeme
Wed Jul 11, 2018 2:04 pm
Forum: VTSTTools
Topic: Problems with CNEB calculatios
Replies: 3
Views: 234

Re: Problems with CNEB calculatios

My guess is that you have not linked in our vtstcode into vasp. The graph that you show appears to have zero projected forces at each image, which is why the spline is so wiggly and you are getting extra extrema along the path. Start by greping your OUTCAR file for VTST - if you don't see a line say...
by graeme
Tue Jul 10, 2018 2:12 am
Forum: VTSTTools
Topic: the generated MODCAR is zero bit
Replies: 5
Views: 1131

Re: the generated MODCAR is zero bit

I can't see what is going on with this calculation. There are no OUTCARs in the 0? directories and the exts.dat file has energies of over 70 eV, which makes no sense. The way this should work is to run an NEB calculation and then simply run the neb2dim.pl script to set up a dimer calculation. There ...
by graeme
Fri Jul 06, 2018 8:59 pm
Forum: Bader
Topic: Bader charge analysis with -ref to CHGCAR_sum
Replies: 4
Views: 3272

Re: Bader charge analysis with -ref to CHGCAR_sum

The valence charge is normalized so that the sum of the values at the grid points in the CHGCAR file gives the total (valence) charge. There is no such normalization for the total charge. The integrated total charge is highly sensitive to the grid density because of the cusps at the nuclear centers....
by graeme
Fri Jul 06, 2018 8:49 pm
Forum: VTSTTools
Topic: Dynamical Matrix calc. gives different ZPE than when using IBRION = 5
Replies: 1
Views: 1753

Re: Dynamical Matrix calc. gives different ZPE than when using IBRION = 5

The first calculation does not make sense in terms of the number of negative modes. I would need to see that calculation to see what might be going wrong. The typical problems are related to the displacement size, which should be on the order of 0.01 - 0.001 Ang, accurate forces with ediff=1e-8, and...
by graeme
Thu Jul 05, 2018 3:23 am
Forum: VTSTTools
Topic: to prepare the MODECAR for a bond rotation TS
Replies: 2
Views: 2270

Re: to prepare the MODECAR for a bond rotation TS

If you have an NEB calculation (even a rough one) you can use our neb2dim.pl script to generate a dimer calculation with a MODECAR file aligned along the reaction coordinate at the interpolated saddle position.
by graeme
Wed Jul 04, 2018 3:43 am
Forum: Bader
Topic: Bader charge analysis with -ref to CHGCAR_sum
Replies: 4
Views: 3272

Re: Bader charge analysis with -ref to CHGCAR_sum

the command "bader CHGCAR -ref CHGCAR_sum" will determine the Bader volumes from the CHGCAR_sum file but then integrate the charge from the CHGCAR file in those Bader volumes. The total charge should be accurate, because the normalization of the CHGCAR file is based upon the sum of the charge densit...
by graeme
Tue Jul 03, 2018 1:22 pm
Forum: Bader
Topic: Bader code paused during an analysis
Replies: 8
Views: 4601

Re: Bader code paused during an analysis

There needs to be reasonable charge density files from vasp for this analysis to work. But again, I don't know what's going wrong with vasp or how to fix it - I've just seen this problem before (you can find similar posts on this forum). This problem needs to be addressed by the VASP folks - you can...
by graeme
Tue Jul 03, 2018 2:44 am
Forum: Bader
Topic: Bader code paused during an analysis
Replies: 8
Views: 4601

Re: Bader code paused during an analysis

It's a problem with the core charges written in the AECCAR files. In the snapshot, you can see lines of oscillating charge density leading from the atomic cores along the grid directions. I've seen this before, but I don't know the reason. Not only does this make the Bader analysis take a very long ...