[DFTB-Plus-User] Bader Charge Analysis

[Sharma SRK Chaitanya Yamijala]

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.








********************************************************
*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.
>
>
>
>
>
>
>
>
>
>
>
> ********************************************************
> *Chaitanya Sharma,*
> *Prof. Pati'*s group,
> Chemistry and Physics Materials unit,
> JNCASR, BANGLORE,
> Lab:: (080-2208) 2581, 2809
> https://sites.google.com/site/sharmasrkcyamijala/
> *********************************************************
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>
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