UT theoretical chemistry code forum

I've updated the code to v1.04 with a bug fix for printing the Bader volumes.

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...

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 ...

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.

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.

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...

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)...

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.

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...

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.

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-...

Thanks for uplaoding the files. I see the problem and will adjust parameters to find a solution.

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...

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...

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.