[DFTB-Plus-User] Bader Charge Analysis
Ozan Dernek
ozandernek at gmail.com
Tue Aug 25 14:56:56 CEST 2015
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?
>
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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 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.
>>
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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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