Comments on: Bader analysis with SIESTA http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/ a scientific view on the purpose of life Sun, 05 Feb 2012 21:16:03 +0000 http://wordpress.org/?v=2.3.2 By: Kane http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1746 Kane Mon, 07 Nov 2011 14:37:58 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1746 hi Alex I'm new to use SIESTA, I want to get the wavefunctions, but I saw some reference says that use XCrySDen can get the 3D wavefun and rho , but my I get the wavefun like the classic wavefun , can get the coefficients ant take into the function to plot, thanks! hi Alex
I’m new to use SIESTA, I want to get the wavefunctions, but I saw some reference says that use XCrySDen can get the 3D wavefun and rho , but my I get the wavefun like the classic wavefun , can get the coefficients ant take into the function to plot, thanks!

]]> By: Alex http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1618 Alex Sat, 30 Apr 2011 22:22:39 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1618 Bader code was originally developed for full-potential calculations (i.e. all atoms with core). Basically, the algorithm requires a maximum of charge being centered on each atom (which is not the case for most pseudopotential calculations). Using TOCH (adding "artificial" core charge) instead of RHO solves this problem, except for the hydrogen where there is simply no core to add. So if you use TOCH, you have to correct manually only H. Bader code was originally developed for full-potential calculations (i.e. all atoms with core). Basically, the algorithm requires a maximum of charge being centered on each atom (which is not the case for most pseudopotential calculations).

Using TOCH (adding “artificial” core charge) instead of RHO solves this problem, except for the hydrogen where there is simply no core to add.

So if you use TOCH, you have to correct manually only H.

]]> By: Tanguy http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1595 Tanguy Fri, 29 Apr 2011 15:07:19 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1595 Alex, Thanks a lot for the complementary information. There is still one thing that I don't get. If I understand you correctly, it is enough to add a core charge for H only even if I have more atoms in my system? Or whould I do it for all the atoms I have in my system? Thanks ! Tanguy Alex,

Thanks a lot for the complementary information.

There is still one thing that I don’t get. If I understand you correctly, it is enough to add a core charge for H only even if I have more atoms in my system? Or whould I do it for all the atoms I have in my system?

Thanks !

Tanguy

]]> By: Alex http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1584 Alex Thu, 28 Apr 2011 22:04:47 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1584 It is in the rho2xsf.f, line 250. The charge=6 and sigma were for Ga (ii.eq.1 means the first atom in the unit cell), you need to change them. > If gaussian=0 at 4sigma, and sigma is approx. 3/4 of the covalent > radius, then I would suppose that for H we should take > sigma= 3/4 * 0.32 A / 4 = 0.06 A. That's the maximal value that you should use for sigma for H. Never make it bigger. If your grid is fine enough you can try to make it even smaller. People reported that charge values as small as 0.01 are enough to make the Bader program work. Try to use as small values as possible to reduce possible error. The idea is to make program find the maximum of charge centered on H. It is in the rho2xsf.f, line 250.

The charge=6 and sigma were for Ga (ii.eq.1 means the first atom in the unit cell), you need to change them.

> If gaussian=0 at 4sigma, and sigma is approx. 3/4 of the covalent
> radius, then I would suppose that for H we should take
> sigma= 3/4 * 0.32 A / 4 = 0.06 A.
That’s the maximal value that you should use for sigma for H. Never make it bigger.
If your grid is fine enough you can try to make it even smaller.

People reported that charge values as small as 0.01 are enough to make the Bader program work. Try to use as small values as possible to reduce possible error.
The idea is to make program find the maximum of charge centered on H.

]]> By: Tanguy http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1559 Tanguy Tue, 26 Apr 2011 17:47:07 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1559 Alex, Thanks for your answer. You say that "the code for H is there". Could you be more specific about the "there" you are referring to ? Regards, Tanguy Alex,

Thanks for your answer.

You say that “the code for H is there”. Could you be more specific about the “there” you are referring to ?

Regards,

Tanguy

]]> By: Alex http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1467 Alex Thu, 21 Apr 2011 00:09:18 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1467 Tanguy, please, see the updated procedure at the very top of the post. Try to see if Bader program finds H where it should be in your system. If it cannot, use my xsf2cube on TOCH file, plus, add an artificial extra core charge (Gaussian) to H - the code for H is there (though, commented out). Tanguy, please, see the updated procedure at the very top of the post.
Try to see if Bader program finds H where it should be in your system. If it cannot, use my xsf2cube on TOCH file, plus, add an artificial extra core charge (Gaussian) to H - the code for H is there (though, commented out).

]]> By: Tanguy http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1375 Tanguy Thu, 14 Apr 2011 14:41:22 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1375 Hello Alex, Thanks for the information. It really great job. I have some problem to understand what do I need to change in the code. You mentionned that if we are not working with the same atoms as your, we have some manual work to do. Could you specify what do we need to change (I am working with Zn, O, C, H and N) in the code to make it working? Thanks in advance for your help ! Tanguy Hello Alex,
Thanks for the information. It really great job.
I have some problem to understand what do I need to change in the code. You mentionned that if we are not working with the same atoms as your, we have some manual work to do.
Could you specify what do we need to change (I am working with Zn, O, C, H and N) in the code to make it working?
Thanks in advance for your help !
Tanguy

]]> By: Michael http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1264 Michael Thu, 07 Apr 2011 15:29:45 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-1264 Hello Alex, compiling your version of A.Postnikovs program with gfortran I Get following error message: " gfortran -o -g -O0 -c -o wraxsf1.o wraxsf1.f wraxsf1.f:30.72: open (is1, file='tmpfil',form='formatted',status='scratch') 1 Error: The STATUS specified in OPEN statement at (1) cannot have the value SCRATCH if a FILE specifier is present make: *** [wraxsf1.o] Error 1 " Whats worng? Hello Alex, compiling your version of A.Postnikovs program with gfortran I Get following error message:
”
gfortran -o -g -O0 -c -o wraxsf1.o wraxsf1.f
wraxsf1.f:30.72:

open (is1, file=’tmpfil’,form=’formatted’,status=’scratch’)
1
Error: The STATUS specified in OPEN statement at (1) cannot have the value SCRATCH if a FILE specifier is present
make: *** [wraxsf1.o] Error 1
”

Whats worng?

]]> By: Michael http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-540 Michael Fri, 07 Jan 2011 10:13:23 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-540 Hello I am Interestested in the XPS predictions stuff. Could you give me some informations about it? Another Question I am also interested in NMR-Paramters (e.g. shielding tensor). Is there some possibility to calculate them from siesta output? Hello I am Interestested in the XPS predictions stuff. Could you give me some informations about it?

Another Question I am also interested in NMR-Paramters (e.g. shielding tensor). Is there some possibility to calculate them from siesta output?

]]> By: Emma http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-468 Emma Fri, 20 Aug 2010 04:58:19 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-468 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. 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.

]]> By: Alex http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-466 Alex Fri, 20 Aug 2010 03:03:42 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-466 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. 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.

]]> By: Emma http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-460 Emma Thu, 19 Aug 2010 07:35:56 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-460 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! 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!

]]> By: Alex http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-234 Alex Tue, 07 Jul 2009 13:13:59 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-234 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. 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.

]]> By: Jeffei http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-233 Jeffei Tue, 07 Jul 2009 02:45:19 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-233 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 ? 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 ?

]]> By: Nguyen Ngoc Ha http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-232 Nguyen Ngoc Ha Tue, 07 Apr 2009 13:30:27 +0000 http://voznyy.elinity.com/blog/2008/01/bader-analysis-with-siesta/#comment-232 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. 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.

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