Search found 1904 matches

by graeme
Sat Feb 08, 2020 4:21 pm
Forum: Bader
Topic: Atomic boundary trace or contours in a slice of a super-cell
Replies: 18
Views: 1357

Re: Atomic boundary trace or contours in a slice of a super-cell

I've updated the code to v1.04 with a bug fix for printing the Bader volumes.
by graeme
Thu Feb 06, 2020 9:15 pm
Forum: Bader
Topic: Atomic boundary trace or contours in a slice of a super-cell
Replies: 18
Views: 1357

Re: Atomic boundary trace or contours in a slice of a super-cell

I'm just not sure what you are asking for. I explained how to write the charge density in a Bader volume around a single atom. If you want to see a contour plot of the charge density inside that sphere, you can do that with a visualizer (see attached). But I don't really understand the words "draw c...
by graeme
Tue Feb 04, 2020 6:07 pm
Forum: VTSTTools
Topic: double negative imaginary frequency after dimer run
Replies: 1
Views: 419

Re: double negative imaginary frequency after dimer run

It's not clear to me how the vibrational modes were calculated. The modes in the VASPVIB.MOLF look a little strange in that they contain many zeros - were these calculated on a subset of coordinates? Anyway, frequency calculations at saddles do take some care. I would start by reducing the force in ...
by graeme
Fri Jan 31, 2020 3:56 pm
Forum: VTSTTools
Topic: from converged neb to dimer: ts goes away....
Replies: 2
Views: 203

Re: from converged neb to dimer: ts goes away....

I've been having trouble with the k221 dimer calculation using the gamma point saddle from the NEB. I'll try to figure out what's going on.

Nice to hear that the k221 NEB worked.
by graeme
Fri Jan 24, 2020 4:51 pm
Forum: Bader
Topic: Atomic boundary trace or contours in a slice of a super-cell
Replies: 18
Views: 1357

Re: Atomic boundary trace or contours in a slice of a super-cell

I get it. I was responding to what I thought was the larger question about how to plot a Bader volume. But yes, I see that we do have a bug in the code and I will try to fix it as soon as I can.
by graeme
Fri Jan 24, 2020 2:15 am
Forum: VTSTTools
Topic: H2O drifting away during NEB
Replies: 6
Views: 469

Re: H2O drifting away during NEB

I did a conservative relaxation of the NEB for the charged system and it looks ok (attached). You really have to be careful with IBRION=1 / IOPT=1. For IOPT=1, it is very important to set the INVCURV variable sufficiently small so as to ensure stable optimization. In your case, forces were spiking a...
by graeme
Thu Jan 23, 2020 4:36 pm
Forum: Bader
Topic: Atomic boundary trace or contours in a slice of a super-cell
Replies: 18
Views: 1357

Re: Atomic boundary trace or contours in a slice of a super-cell

I ran the following: bader CHGCAR -ref CHGCAR_sum -p sum_atom 1 and the code prints an output file called BvAt_summed.dat, which contains the charge density only in the Bader volume around Atom 1. I read this as a CHGCAR file into VESTA, and you can then see the Bader volume around atom 1 (attached)...
by graeme
Wed Jan 22, 2020 2:26 pm
Forum: Bader
Topic: Atomic boundary trace or contours in a slice of a super-cell
Replies: 18
Views: 1357

Re: Atomic boundary trace or contours in a slice of a super-cell

Something is not right. If you post your CHGCAR and CHGCAR_sum files, I'll take a look. There does seem to be a problem with our code - it should not be printing files with strange file names.
by graeme
Tue Jan 21, 2020 3:13 am
Forum: VTSTTools
Topic: H2O drifting away during NEB
Replies: 6
Views: 469

Re: H2O drifting away during NEB

I did my standard calculation for a problematic NEB and the results seem ok (attached). I used somewhat cheaper settings, which I think are appropriate for your system. In the first calculation (run1) I accidentally used built-in vasp CG because you specified this (IBRION=2) earlier in the INCAR fil...
by graeme
Wed Jan 15, 2020 11:00 pm
Forum: Bader
Topic: Atomic boundary trace or contours in a slice of a super-cell
Replies: 18
Views: 1357

Re: Atomic boundary trace or contours in a slice of a super-cell

you can do:
-p sel_atom 1,2,3
or
-p sel_atom 1-3
...
the term 'volume' means an atomic volume or a Bader volume. If you have core charge included, these should typically be identical.
by graeme
Wed Jan 15, 2020 4:24 pm
Forum: Bader
Topic: Atomic boundary trace or contours in a slice of a super-cell
Replies: 18
Views: 1357

Re: Atomic boundary trace or contours in a slice of a super-cell

The AtIndex.dat file will contain an integer for each grid point indicating the atom to which that grid point belongs. If you plot the region containing the value 1, that is the region associated with atom 1. Another way to plot that volume is to use the "-p sel_atom 1" which will give you a CHGCAR-...
by graeme
Wed Jan 15, 2020 3:12 am
Forum: VTSTTools
Topic: H2O drifting away during NEB
Replies: 6
Views: 469

Re: H2O drifting away during NEB

Thanks for uplaoding the files. I see the problem and will adjust parameters to find a solution.
by graeme
Thu Jan 02, 2020 3:07 pm
Forum: Bader
Topic: Atomic boundary trace or contours in a slice of a super-cell
Replies: 18
Views: 1357

Re: Atomic boundary trace or contours in a slice of a super-cell

If you use the -p atom_index flag, you will get a CHGCAR-like with integers indicating the locations of the atomic volumes. So then if you want to see the spatial location of the Bader volume around atom 1, you can load this file in a viewer and set your min and max contour values to only include th...
by graeme
Sun Dec 22, 2019 3:35 am
Forum: Bader
Topic: Atomic boundary trace or contours in a slice of a super-cell
Replies: 18
Views: 1357

Re: Atomic boundary trace or contours in a slice of a super-cell

The -p atom_index tag will give you a CHGCAR-like file with an integer indicating the locations of the atomic volumes. You can use any visualizer of CHGCAR files to see the surfaces between the atomic volumes. Vesta is a good option. I don't understand questions B or C; we provide the partitioning o...
by graeme
Wed Dec 18, 2019 2:21 am
Forum: Bader
Topic: Bader Charge analysis
Replies: 27
Views: 2276

Re: Bader Charge analysis

Ignore the results of the first command.

For the second two, you should see convergence with respect to the grid density, with the -b weight method converging faster than the regular method.