Search found 1909 matches

by graeme
Sun May 24, 2020 5:45 am
Forum: VTSTTools
Topic: DynamicMatrix_CH4
Replies: 4
Views: 192

Re: DynamicMatrix_CH4

Wait a sec. I just nicely and rapidly solved the problem that you posted and now you immediately post a different problem?!? No, take a minute to think about your calculation. With the frequencies that I sent, there are 6 zero-ish modes associated with translation and rotation. The others are vibrat...
by graeme
Sat May 23, 2020 5:18 pm
Forum: VTSTTools
Topic: VASP 6.1.0 support
Replies: 3
Views: 172

Re: VASP 6.1.0 support

Ok, I updated the tar file after writing to you - I realized that I did not update that.
by graeme
Sat May 23, 2020 5:17 pm
Forum: VTSTTools
Topic: DynamicMatrix_CH4
Replies: 4
Views: 192

Re: DynamicMatrix_CH4

The problem has to do with ISYM. In your calculation, vasp is detecting symmetry so that when you make a small displacement, it is zeroing the components of the force which break symmetry. Additionally, you have a tab instead of a space after your ISYM variable, so that even if you think you are set...
by graeme
Fri May 22, 2020 3:48 pm
Forum: VTSTTools
Topic: VASP 6.1.0 support
Replies: 3
Views: 172

Re: VASP 6.1.0 support

The most recent version of the VTST code is compatible with vasp.6.1.0. Note that I just recently made this update, so while we have not seen any problems, please let me know if you see any.
by graeme
Sat May 16, 2020 5:02 pm
Forum: Bader
Topic: bader tells different atomic charges of O2
Replies: 1
Views: 1251

Re: bader tells different atomic charges of O2

Try reducing the grid spacing using the NGXF, NGYF, and NGZF. Also try using the -b weight method.
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: 19
Views: 5671

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: 19
Views: 5671

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: 2
Views: 2361

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: 1218

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: 19
Views: 5671

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: 1947

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: 19
Views: 5671

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: 19
Views: 5671

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: 1947

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: 19
Views: 5671

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.