[DFTB-Plus-User] Bader Charge Analysis

[Ozan Dernek]

I have tried it, and after receiving your mail tried once more, but it gives nothing for the negative isovalue since the range starts with a positive value.  

Regards Ozan

25 Ağu 2015 tarihinde 14:41 saatinde, Sharma SRK Chaitanya Yamijala <sharmajncasr at gmail.com> şunları yazdı:

> You need to change one of the Iso-surface value to be negative. If you are using command line, see the below example:
> 
> mol selection all
> mol material Opaque
> mol addrep 0
> mol modstyle 1 0 Isosurface 0.000400 0 0 1 1 1         # positive value for Isosurface
> mol modmaterial 1 0 AOChalky
> mol modcolor 1 0 ColorID 31
> color change rgb 31 0.840000 0.420000 0.110000
> 
> mol selection all
> mol material AOChalky
> mol addrep 0
> mol modstyle 2 0 Isosurface -0.000400 0 0 1 1 1      # negative value for Isosurface
> mol modcolor 2 0 ColorID 23
> 
> HTH,
> Sharma.
> 
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> ********************************************************
> Chaitanya Sharma,
> Prof. Pati's group,
> Chemistry and Physics Materials unit,
> JNCASR, BANGLORE,
> Lab:: (080-2208) 2581, 2809
> https://sites.google.com/site/sharmasrkcyamijala/
> *********************************************************
> 
> On Tue, Aug 25, 2015 at 4:43 PM, Ozan Dernek <ozandernek at gmail.com> wrote:
> Hi, 
> 
> First of all, I would like to plot the difference in charge densities, but I can only see positive values . As you explained in the website, I first create a CPK rep, then make two isosurfaces, which only have positive isovalues. Is it because the code I am using to make the bader charge analysis, or should I do something via VMD ?
> 
> Thank you for your attention, 
> Regards, 
> Ozan Dernek
> 22 Ağu 2015 tarihinde 07:54 saatinde, Sharma SRK Chaitanya Yamijala <sharmajncasr at gmail.com> şunları yazdı:
> 
>> 
>> On Sat, Aug 22, 2015 at 4:47 AM, Ozan Dernek <ozandernek at gmail.com> wrote:
>> file from the structures that I am working on , the minimum isovalue is always bigger than zero.
>> 
>> Dear Ozan,
>> 
>> As you understood, if you want to plot charge density then it will be (should be) with all positive values. If you are plotting MOs or spin-densities or "difference in charge densities" etc. then you will be able to see a negative value in cube file. So, if you just would like to see the charge density on an atom, I guess, you should get all positive values. 
>> 
>> Also, though I am not sure, something like taking the difference between "full system's charge-density" and the "sum of charge-densities of all atoms (except for the one where you would like to see the charge)" may give you some hints about charge transfer from/to the atom of your interest (if this is what you are looking for!).
>> 
>> HTH,
>> Sharma.
>> 
>> P.S.: If you are dealing with systems with high charge fluctuations and if you haven't done the calculations with DFTB3, then my suggestion would be to stick to DFTB3 than SCC-DFTB. I guess you might have already started with DFTB3.
>> 
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>> 
>> ********************************************************
>> Chaitanya Sharma,
>> Prof. Pati's group,
>> Chemistry and Physics Materials unit,
>> JNCASR, BANGLORE,
>> Lab:: (080-2208) 2581, 2809
>> https://sites.google.com/site/sharmasrkcyamijala/
>> *********************************************************
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at mailman.zfn.uni-bremen.de
>> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> 
> 
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