UT theoretical chemistry code forum

Graeme, it work fine now, but it seems to me there is still some error - file with valence charge is not calculated properly, i.e. even total amount of electrons (the first and last H atoms get about 6 electrons), however, if I use total=core+valence it works correctly.
I'm sending you the files ...

Thanks, Graeme.
Well, I wrote the export to CUBE myself, so I could make some errors as well.
But at least I can visualize it correctly in independent programs.
I'll try to look into it if you believe the error is there.

I've checked the newer version (only main.f90 is newer - from March 8th).

I still get same wrong distances.
I also see that the bigger cell that I take, the more and more charge appears on C atoms (for 1.5x1.5A cell I see charge only on S, for 3x3A I see charge on S and three C atoms, for even ...

Should I download a new version?

The wrong distances was not the main problem - I wouldn't care about them if the charges were correct.

Wenjie
- I've checked (visualized in 2 different programs) the densities before trying to get Bader charges - tehy are correct.
- there are six atoms with charges ...

I'm trying to analyze my CUBE files generated by SIESTA and have very strange behavior.

I've tested your H2O example it works fine.
My H2O file gave expected 0 on H and 8 on O.

Next I'm trying with simple thiol molecule HS-(CH2)4-CH3.
I've saved only partial core charges (used for NLCC) to make it ...

Graeme, I don't get how the added core charge can help the situation.
You say yourself that there is no maximum on H due to too smooth pseudopotential.
Core charge would add only core to oxygen, while H will still stay without maximum, so for Bader analysis nothing would changed.

Or, you want to ...

Hi,
I've just realized that the problem of wrong charges in water (and in other compounds with O-H, and probably with N-H bonds) in pseudopotential approach comes not from the absence of the core on the O as it is claimed in many places. Even without core one should get something on H, but we get 0 ...

Then I'm quite surprised that the program managed to calculate something for a part of the periodic slab.

I mean, I've cut it to make smaller to reduce memory usage, so that upper side of the slab ends up with 0 density, while from the bottom it is really cut through atoms.

If you say it assumes ...

Hi,
we need to add core electrons to our RHO, i.e. make all-electron density (the maximum of density should be on the atom), otherwise Bader analysis doesn't work correctly.

I'm trying to implement this right now for SIESTA, i.e. just add the core the CUBE file after all calculations done by SIESTA ...

I have some small propositions to improve the output of the program to make it a bit more convenient:

1. Along with the sequential number of the atom it would be nice to see also at least the atomic number of the species to speed up the process of atom identification (especially for big systems ...

Hi,
I'm trying to use your program for analysis of SIESTA densities.
I've made the conversion to CUBE format and checked in XCrysDen that it is done correctly.

However I still have a question concerning the grid on boundaries. CUBE itself has nothing to do with periodic cells and usually you will ...

I've just found in another thread that you propose to use PAW core, not all-electron core.

I also found that Abinit also has Bader analysis and as far as I understand, they use the original AIM program. And they propose to use the core from all electron calculations:
http://www.abinit.org/Infos/aim ...

Hi, I'm trying to use your program for analysis of densities from SIESTA. I've exported to CUBE and the analysis of H2O gives the expected for pseudopotential charges 0e and 2e on H and O respectively.
So, now I'm thinking about implementation of core charges.

You said that partial core can help ...

I've seen such a problem for my file if it was quite big.
I've compiled the newest version with intel fortran and the analysis crashed with segmentation error for a slab of 78 atoms after REASSIGNED POINTS: 0 was achieved in about 10 iterations (that were pseudopotential charges).
The I used about ...