Search found 1947 matches

by graeme
Mon Oct 19, 2020 7:37 pm
Forum: Bader
Topic: Printing BV for multiple atoms in a single file & unable to print BV for all atoms
Replies: 1
Views: 912

Re: Printing BV for multiple atoms in a single file & unable to print BV for all atoms

You should get a BvAtxxxx.dat for each atom, if you use a command such as:

bader cubefile -p all_atom

If you want to print out the charge density for two atoms, you can use:

bader cubefile -p sel_atom 1-2

or

bader cubefile -p sel_atom 1
bader cubefile -p sel_atom 3
by graeme
Sat Oct 10, 2020 4:35 pm
Forum: Bader
Topic: Comparative charge analysis
Replies: 1
Views: 640

Re: Comparative charge analysis

No, the difference between the excited state density vs the ground state density should, in general, change the size of the Bader volumes and the Bader charges of the atoms in the molecule.
by graeme
Tue Sep 15, 2020 2:11 pm
Forum: Bader
Topic: Voronoi partition
Replies: 2
Views: 921

Re: Voronoi partition

That is surprising - the voronoi calculation trivially associates every point with the nearest atom. If the atoms are different, the integrated charges will be different but the volumes should be the same. If they are off by a small amount, that could be due to the discretization of the CHGCAR file....
by graeme
Mon Sep 14, 2020 2:17 pm
Forum: Bader
Topic: Error message "some volume not assigned"
Replies: 2
Views: 942

Re: Error message "some volume not assigned"

Hm, I don't recall seeing that error before. If you can please post your CHGCAR and CHGCAR_sum, I will look into the problem.
Graeme
by graeme
Thu Sep 10, 2020 5:01 pm
Forum: VTSTTools
Topic: how to check intrinsic reaction coordinate of optimized dimer method TS
Replies: 1
Views: 884

Re: how to check intrinsic reaction coordinate of optimized dimer method TS

Yes, what you can do is make a small displacement along both directions of the unstable mode and minimize those structures. We have a small script, dimmins.pl which should set up those minimization calculations from a converged dimer calculation.
by graeme
Wed Sep 09, 2020 11:45 pm
Forum: VTSTTools
Topic: Dosanalyze.pl script output question
Replies: 2
Views: 858

Re: Dosanalyze.pl script output question

I'm looking at the dosanalyze.pl code and I see that the #-# format is accepted as an input, but there is no support for the #, # format when specifying atoms. So I'm not sure what the script is doing when you specify p 3,4. If you post a .tar.gz file of your calculation, I will be able to reproduce...
by graeme
Wed Sep 09, 2020 2:21 pm
Forum: VTSTTools
Topic: d-band center from doslanalyze.pl
Replies: 4
Views: 1693

Re: d-band center from doslanalyze.pl

This depends a little bit upon what you are interested in. If you want to know about, for example, charge transfer between materials or anything that is based upon the absolute energy levels of the electrons, then you need a common energy reference, such as the vacuum level. If, however, you are wan...
by graeme
Sat Sep 05, 2020 1:07 am
Forum: Bader
Topic: Method behind calculating dipoles from Bader code
Replies: 1
Views: 1175

Re: Method behind calculating dipoles from Bader code

Hi Jared, Sorry for the slow reply by email - I'll answer here. The dipole code simply integrates the charge density times a vector from the center of charge in each Bader volume. The issue is that we have never really used the code and I can not guarantee that it works. One issue that I would worry...
by graeme
Tue Sep 01, 2020 1:08 am
Forum: VTSTTools
Topic: d-band center from doslanalyze.pl
Replies: 4
Views: 1693

Re: d-band center from doslanalyze.pl

Yes, it is with respect to the Fermi level. In a periodic calculation, there is no simple absolute energy reference. One strategy is to use the energy of core electrons, which you can include with _pv or _sv potentials. More typical is to use a slab and explicitly calculate the vacuum level as a ref...
by graeme
Sun Aug 30, 2020 2:55 pm
Forum: VTSTTools
Topic: nebefs.pl Forces
Replies: 6
Views: 1774

Re: nebefs.pl Forces

Check to see if the atoms with high forces are frozen. If so, those forces will be zeroed for the convergence test and the NEB force projections.
by graeme
Sat Aug 29, 2020 2:32 pm
Forum: VTSTTools
Topic: nebefs.pl Forces
Replies: 6
Views: 1774

Re: nebefs.pl Forces

The TOTAL-FORCE is the NEB force. Below that, there is some NEB projection information, such as: NEB: Tangent ---------------------------------------------- 0.00000 0.00000 -0.00000 ..... NEB: forces: par spring, perp REAL, dneb 0.005906 0.023649 0.000000 NEB: distance to prev, next image, angle bet...
by graeme
Sat Aug 29, 2020 2:39 am
Forum: VTSTTools
Topic: What is nebmovie.pl about?
Replies: 3
Views: 1126

Re: What is nebmovie.pl about?

If the script is working properly, and you specify CONTCAR files (with a 1 flag), it should grab the POSCAR files from the endpoint directories and the CONTCAR file from the images in between.
by graeme
Sat Aug 29, 2020 2:37 am
Forum: VTSTTools
Topic: nebefs.pl Forces
Replies: 6
Views: 1774

Re: nebefs.pl Forces

The issue here is that the relevant forces for an NEB calculation is different from that of a normal minimization. For an NEB calculation, the force that is minimized is the projection of the real force perpendicular to the reaction path, plus a spring force that keeps the images equally spaced. Thi...
by graeme
Thu Aug 27, 2020 9:52 pm
Forum: VTSTTools
Topic: What is nebmovie.pl about?
Replies: 3
Views: 1126

Re: What is nebmovie.pl about?

Hi Brendan, This is a simple script which concatenates either the POSCAR (initial) structures of an NEB calculations or the CONTCAR (final) structures. you can toggle which using a 0 (initial) or 1 (final) flag after the nebmovie.pl command. jmol should play this type of file if you look for the mov...
by graeme
Thu Aug 27, 2020 12:24 am
Forum: VTSTTools
Topic: VASP 6.1.0 support
Replies: 6
Views: 4179

Re: VASP 6.1.0 support

Hi Matt, you are right - I did not update the webpage. v180 should now be current and have compatibility for v6.1 as the default; v5.x files are in the vtstcode5 subdirectory.