[DFTB-Plus-User] Bader Charge Analysis

Tue Aug 25 15:14:07 CEST 2015

I have just checked the pp.x input file reference and your flags are
perfectly alright to get a charge density (electron density) in a 3D form
in cube format. Once again, to remind you, you are getting charge density
not the difference (for that you need two such cube files and subtract them
using cubemanip.py from DFTB+ or cubman from gaussian or ...)

********************************************************
*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 6:40 PM, Ozan Dernek <ozandernek at gmail.com> wrote:

> Alright, thanks for your great attitude again,
>
> Regards
> Ozan
>
> 25 Ağu 2015 tarihinde 16:07 saatinde, Sharma SRK Chaitanya Yamijala <
> sharmajncasr at gmail.com> şunları yazdı:
>
> 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/
>>>> *********************************************************
>>>> _______________________________________________
>>>> 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
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>>
>>>>
>>> _______________________________________________
>>> 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
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>>>
>>>
>> _______________________________________________
>> 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
>>
>>
>>
>> _______________________________________________
>> 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
>>
>>
> _______________________________________________
> 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
>
>
>
> _______________________________________________
> 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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20150825/071b1bc8/attachment-0001.html>