[DFTB-Plus-User] Bader Charge Analysis

Tue Aug 25 15:07:00 CEST 2015

Firstly, it is best to post the things related to QE on QE forum. Experts
there can correct, if your input file is wrong.

Related to your question: As far as I can see, you are getting a charge
density file only (Not charge density difference). Then there will not be
any negative values.

********************************************************
*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 6:26 PM, Ozan Dernek <ozandernek at gmail.com> wrote:

> I guess I am missing a big part here. Starting form the very beginning:
>
>  -After executing a relax calculation in Quantum Espresso, i proceeded
> with partial density of states calculation.
>  - Then to obtain the .cube file, I executed the pp.x calculation as below;
> &inputpp
>       prefix='ca',
>    outdir='tmp-ngr-chexyl',
>   filplot='ngr-chexyl',
>   plot_num=0,
>   /
> &plot
>       iflag=3,
>       output_format=6,
>       fileout='charge-ngr-chexyl.cube',
> /
>
>   - The pp.x calculation returned the files ACF.dat, AVF.dat, BCF.dat and
> charge.cube files.
>   - Then I load the .cube file to VMD.
>
> If there should be another step before using VMD, I am not aware of that.
>
> PS: The problem here is there is no one using VM in my department, and I
> could not get a satisfying answer from the VMD-L mailing list. I genuinely
> appreciate your effort.
>
> Regards,
> Ozan
>
>
>
>
> 25 Ağu 2015 tarihinde 15:35 saatinde, Sharma SRK Chaitanya Yamijala <
> sharmajncasr at gmail.com> şunları yazdı:
>
> Could you please just tell me the steps what you have done to get charge
> difference plots (I just need commands, no need of description) before
> using vmd?
>
>
>
>
>
>
>
>
> ********************************************************
> *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 5:50 PM, Ozan Dernek <ozandernek at gmail.com> wrote:
>
>> 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.
>>
>>
>>
>>
>>
>>
>>
>>
>> ********************************************************
>> *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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