Search found 1708 matches

by graeme
Wed Jun 20, 2018 4:46 pm
Forum: Bader
Topic: Points assigned to a maxima
Replies: 3
Views: 61

Re: Points assigned to a maxima

Every entry in that Atindex.dat file corresponds to a cell of charge density, just as would be specified in the CHGCAR file, but instead of the value of the charge density, it contains the atom number to which that cell was assigned by the Bader analysis.
by graeme
Wed Jun 20, 2018 3:08 pm
Forum: Bader
Topic: Points assigned to a maxima
Replies: 3
Views: 61

Re: Points assigned to a maxima

If you use the "-p atom_index" or "-p bader_index" the bader code will write a charge density like file with all the points assigned to each atom or each charge density maximum.
by graeme
Tue Jun 19, 2018 2:59 pm
Forum: Bader
Topic: Surface of maximum charge density
Replies: 5
Views: 127

Re: Surface of maximum charge density

Ah, no, it is a 1d plot of charge density (y-axis) vs distance (x-axis). The peaks in the charge density correspond to the location of the atomic centers (blue circles).
by graeme
Mon Jun 18, 2018 2:02 pm
Forum: Bader
Topic: Surface of maximum charge density
Replies: 5
Views: 127

Re: Surface of maximum charge density

The solution to the Schrodinger equation for a 1/r potential has a cusp (maximum) at the nuclei - just as in your illustration.
by graeme
Sun Jun 17, 2018 2:44 pm
Forum: VTSTTools
Topic: neb/cineb calculation problem
Replies: 1
Views: 78

Re: neb/cineb calculation problem

You need to have the vtstcode linked into your vasp binary for all the scripts to work.

But also, your initial and final states appear to be the same so that all three images have the same energy and there is no barrier.
by graeme
Fri Jun 15, 2018 4:52 pm
Forum: Bader
Topic: Surface of maximum charge density
Replies: 5
Views: 127

Re: Surface of maximum charge density

The Bader surfaces contain minima in the charge density along the direction perpendicular to the surface. In principle, I guess there should be surfaces for which the charge density is maximum along the surface normal. These would pass through the atomic cores. I have not seen these surfaces calcula...
by graeme
Thu Jun 14, 2018 6:59 pm
Forum: Bader
Topic: Determining the valence Charge on an atom
Replies: 2
Views: 62

Re: Determining the valence Charge on an atom

Oxygen has a valence of 8 and so if the total number of electrons on the O atom is 9.25 then it has a net charge of (-9.25) - (-8) = -1.25
by graeme
Wed Jun 13, 2018 2:04 pm
Forum: VTSTTools
Topic: Building the VTST code into VASP 5.4.4
Replies: 1
Views: 80

Re: Building the VTST code into VASP 5.4.4

Thanks for the note - I need to update those directions.

The relevant file is /src/.objects - you can add the vtst objects there as in the instructions.
by graeme
Wed Jun 13, 2018 1:59 pm
Forum: Bader
Topic: Do I need to compile Bader code into Vasp Code
Replies: 4
Views: 81

Re: Do I need to compile Bader code into Vasp Code

No, you can use it to post-process the charge density files that vasp writes.
by graeme
Tue Jun 12, 2018 3:46 pm
Forum: Bader
Topic: Visualising bader volumes
Replies: 2
Views: 91

Re: Visualising bader volumes

Yes, you can write a charge-density-like file containing the atomic volume numbers (-p all_atom) or for a single atom (-p sel_atom). Then you can visualize the volumes using an appropriate choice of your isosurface value.
by graeme
Thu Jun 07, 2018 3:01 am
Forum: VTSTTools
Topic: Dynamical Matrix Calculation Issue
Replies: 1
Views: 67

Re: Dynamical Matrix Calculation Issue

You do not have the vtstcode linked into your vasp binary.
by graeme
Thu Jun 07, 2018 2:58 am
Forum: VTSTTools
Topic: Perl script "vfin.pl" results in empty "Output" directory
Replies: 1
Views: 61

Re: Perl script "vfin.pl" results in empty "Output" directory

Make sure that you have downloaded all the vtstscripts and that they are in a directory that is in your path. Then, run "vfin.pl dir' where dir is the directory into which you want the calculations saved.
by graeme
Sat Jun 02, 2018 2:22 pm
Forum: Bader
Topic: Zero Charge even with LAECHG
Replies: 4
Views: 154

Re: Zero Charge even with LAECHG

Ah, my bad, I didn't read your post carefully.

Ok, I took a closer look and it seems that the atoms are not in the same locations in your AECCAR? files as in your CHGCAR file.
by graeme
Sat Jun 02, 2018 1:06 am
Forum: Bader
Topic: Zero Charge even with LAECHG
Replies: 4
Views: 154

Re: Zero Charge even with LAECHG

It looks fine to me. Here is ACF.dat from the command bader CHGCAR -ref CHGCAR_sum GRID BASED BADER ANALYSIS (Version 1.03 11/13/17) OPEN ... CHGCAR VASP5-STYLE INPUT FILE DENSITY-GRID: 80 x 80 x 336 CLOSE ... CHGCAR RUN TIME: 0.89 SECONDS OPEN ... CHGCAR_sum VASP5-STYLE INPUT FILE DENSITY-GRID: 80 ...