Comments for Alex Voznyy

Comment on Bader analysis with SIESTA by Emma

Emma — Fri, 20 Aug 2010 04:58:19 +0000

Thanks for the swift reply! I am going to try out the TOCH file with the Bader program then.

As a matter of fact, I do have hydrogen in my system, but I’m gonna cross my fingers and hope that the problem with hydrogen is more severe for cases where the hydrogen is bonded electronegative species like oxygen and nitrogen. I have my hydrogens bonded to carbons.

Comment on Bader analysis with SIESTA by Alex

Alex — Fri, 20 Aug 2010 03:03:42 +0000

Thanks for the reminder, Emma, I completely forgot about TOCH.
At the time of that post I wasn’t sure about TOCH but I was recently working with it from a different perspective and now I think that TOCH is the perfect choice for Bader analysis with SIESTA.

You don’t have to modify anything, simply use TOCH instead of RHO when converting to CUBE.
By the way Utils/Grid/grid2cube might work even better than my modified rho2cube.

Unfortunately TOCH would still not help if you have hydrogen in your system.

Comment on Bader analysis with SIESTA by Emma

Emma — Thu, 19 Aug 2010 07:35:56 +0000

Hi Alex,

I noticed in this post in the SIESTA forum:
http://www.mail-archive.com/siesta-l@listserv.uam.es/msg01285.html

that you talked about the possibility of using the TOCH file generated by SIESTA with the Bader Analysis program. Did you explore that angle in the end?

Thank You!

Comment on Notepad++ language style for SIESTA FDF files by Alex

Alex — Fri, 18 Jun 2010 22:15:56 +0000

Hmmm… I’m not really sure what windows are you talking about.
Contact me via email, that would be faster.

Comment on Notepad++ language style for SIESTA FDF files by Alex

Alex — Wed, 16 Jun 2010 23:55:06 +0000

Check in the “User-Defined Dialogue…” that you have fdf (and maybe FDF, whatever) in the “Ext.” field, as well as “Ignore case” checkbox (however this is written in my XML file, so this should not be the reason of the problem).

I think, I had a bug once that Notepad did not pick up the style based on extension and I had to do it manually from Language list (see above).
Try to reinstall Notepad++ from scratch or ask on their support forum.

Comment on Notepad++ language style for SIESTA FDF files by ajnon dijua

ajnon dijua — Wed, 16 Jun 2010 20:58:59 +0000

It seems it is a very useful tool,thanks!
However, when i download your file and place in the C:\Documents and Settings\dijua\Application Data\Notepad++\, and find the FDF and SIESTA output in the User Language drop-down list, I do not find the windows like yours.

Comment on Bader analysis with SIESTA by Alex

Alex — Tue, 07 Jul 2009 13:13:59 +0000

Zero charge on H and 8 on Oxygen is due to the absence of charge peak on H (due to the use of pseudopotential) so Bader algorythm just doesn’t see an atom there at all. This is exactly the reason why partial or artificial core is required.

Yes, you can add the artificial core afterwards, just as a simple Gaussian, but then the atomic radii and core charges has to be provided for all atoms in your system. This is implemented in the rho2cube.f file only for H, but I haven’t done it for all periodic table to make the program usable out of the box for anybody.

You can try to work without any additional cores at all, in 90% cases it will work. The program won’t give the incorrect values as soon as it finds the atom positions correctly.

Comment on Bader analysis with SIESTA by Jeffei

Jeffei — Tue, 07 Jul 2009 02:45:19 +0000

Hi, Alex,
Can you just add the artificial core charge into the RHO file instead of recompile SIESTA?
You said: “One of the solutions is to save partial core charges used for NLCC calculations.”
How to do this ?

Comment on Bader analysis with SIESTA by Nguyen Ngoc Ha

Nguyen Ngoc Ha — Tue, 07 Apr 2009 13:30:27 +0000

Hi Alex,
Firstly, thanks for your modiffied code. But I have a problem to use it
- In your bader.zip from your website, there is only one atmfuncs.f file (and siesta2cube folder, bader folder), I used it to replace and then recompiled SIESTA but I never get the right results:
For example, H2O analysis, O: 8 electrons and H 0 electron!
Please let me know this,
Thank you so much.

Comment on Bader analysis with SIESTA by Alex

Alex — Wed, 21 May 2008 14:21:49 +0000

Spanning vector is the unit cell vector - origin and vectors are just to define the box in space for atoms in which you want to find the Bader charges.

Ideally you should choose the grid for Bader analysis exactly the same as was used by SIESTA (that’s what Denchar does) - just check the amount of grid points used by SIESTA in the .out file. No sense to make Bader grid denser if you used smaller cutoff in SIESTA itself.
For good accuracy of Bader analysis, the grid cutoff should be about ~300Ry in SIESTA. I believe 300Ry translates into about 10 grid points per 1A.

Comment on Bader analysis with SIESTA by Fei Gao

Fei Gao — Wed, 21 May 2008 01:14:04 +0000

Hi, Alex;

I am trying to use your flightly modifed rho2xsf for converting *.TOCH to CUBE format. I need to input the following;

(a) Enter origin point in Ang :
(b) Enter 1st spanning vetor in Ang:
(c) Enter 2nd spanning vetor in Ang:
(d) Enter 3rd spanning vetor in Ang:

Could you please share your experience with me how to chose these paramters from the calculations by SIESTA. Also, I am not sure the spanning vetor means.

The rho2xsf askes grid for three spanning vector. I just wonder how large the grid should be (say 200 200 200 or 300 300 300).

Many thanks,

Fei