[Pw_forum] Plotting HOMO, LUMO wavefunction
Arpan Kundu
arpankundu18 at gmail.com
Wed Nov 5 05:48:09 CET 2014
Hi,
I think I figured out the problem. I was missing the 'lsign' parameter in
pp.x. 'lsign' basically gives |psi^2| * sign (psi). If 'lsign' is false, it
gives the magnitude of 'psi^2', which I was getting earlier. Now on putting
'lsign=true', I get the positive and negative values of the wavefunction
which I need. The HOMO and LUMO I got matches with the literature. Anyways,
thanks for the help.
On Tue, Nov 4, 2014 at 5:29 PM, Filipe Camargo Dalmatti Alves Lima <
flima at if.usp.br> wrote:
> Plot_num = 7 for wavefunction.
>
> This script was written in python. All it asks are the parameters you
> wrote in the input file provided in quantum espresso and options for pp.x.
> You must edit this file by hand using an editor of your preference. The
> prof. Kulik's script should make you life easier, as the python would do
> the hard job for you.
>
> If it is not helping you, I am attaching an example of input to be used on
> pp.x
>
> &inputpp
> prefix ='SAME_PREFIX_YOU_USE_ON_.IN_FILE',
> filplot = 'name of the output file. For each kpoint and kband there
> should be a DIFFERENTE NAME. Otherwise it will overwrite',
> plot_num = 7, #to plot wavefunctions. Are you using norm. conserving PPs?
> kpoint = 1, # If you are using monkhorst pack, you should first run a
> nscf calculation specifying the kpoints you are interested. Remember to
> backup your .save folder.
> kband = 4, # band you are plotting. Remember that bands = (number of
> electrons) / 2. If you have spin polarized you should check the up and down
> electrons.
> /
> &plot
> nfile= 1,
> filepp(1)='add a name here',
> weight(1)= 1.0,
> iflag= 3,
> output_format=6, # cube format
> fileout='wavefunction.X.Y.Z.cube'
> /
>
> all you need to do is prepare this file for your needs and run pp.x
>
>
> best regards,
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Tue, Nov 4, 2014 at 6:44 PM, Arpan Kundu <arpankundu18 at gmail.com>
> wrote:
>
>> Hi Filipe,
>>
>> Thanks a lot for your reply. The problem I am facing in plotting the
>> wavefunction is setting the appropriate parameters in pp.x. In the pp.x
>> manual, below are the options for plot_num. Which option should I select to
>> produce molecular orbitals? Also, I dont understand the method discussed
>> in the link that you provided:
>> http://hjklol.mit.edu/content/visualizing-molecular-orbitals . Where do
>> I edit the variables mentioned in the variables.py file ?
>>
>>
>> 0 = electron (pseudo-)charge density
>>
>> 1 = total potential V_bare + V_H + V_xc
>>
>> 2 = local ionic potential V_bare
>>
>> 3 = local density of states at e_fermi
>> (number of states per volume, in bohr^3,
>> per energy unit, in Ry)
>>
>> 4 = local density of electronic entropy
>>
>> 5 = STM images
>> Tersoff and Hamann, PRB 31, 805 (1985)
>>
>> 6 = spin polarization (rho(up)-rho(down))
>>
>> 7 = contribution of a selected wavefunction to the
>> (pseudo-)charge density. For norm-conserving PPs,
>> |psi|^2 (psi=selected wavefunction). Noncollinear case:
>> contribution of the given state to the charge or
>> to the magnetization along the direction indicated
>> by spin_component (0 = charge, 1 = x, 2 = y, 3 = z )
>>
>>
>>
>> On Tue, Nov 4, 2014 at 8:00 AM, Filipe Camargo Dalmatti Alves Lima <
>> flima at if.usp.br> wrote:
>>
>>> It might be a case that you should fine tuning the software you use to
>>> plot the wavefunction.
>>>
>>> I usually export as .cube and load the orbitals using the jmol for high
>>> quality image.
>>>
>>> Try typing these commands on the jmol console:
>>>
>>> load 'FILE.cube'
>>> background white
>>> isosurface NICKNAME_1 cutoff 0.009 color deepskyblue file ''
>>> isosurface NICKNAME_2 cutoff -0.0009 color red file ''
>>>
>>> As you can see, I can define different cutoff to drawn the "positive"
>>> and "negative" parts of the wavefunction.
>>> When you consider the figure is what you want, then type
>>>
>>> write povray 'ANYNAME.pov'
>>>
>>> It will generate a very good high quality image.
>>>
>>> I hope it helps you finding what you want.
>>>
>>> You might also consider study a very good tutorial (IMHO) provided by
>>> professor Heather Kulik, from MIT, at the link below:
>>> http://hjklol.mit.edu/content/visualizing-molecular-orbitals
>>>
>>> Best,
>>>
>>> Filipe
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Sat, Nov 1, 2014 at 7:33 PM, Lorenzo Paulatto <
>>> lorenzo.paulatto at impmc.upmc.fr> wrote:
>>>
>>>> On 10/31/2014 10:39 PM, Arpan Kundu wrote:
>>>> > Hi users,
>>>> >
>>>> > I want to plot the HOMO, LUMO wavefunction of H2O in QE. But the pp.x
>>>> > plots the charge density instead of the exact wavefunction. I mean the
>>>> > wavefunction should have a positive part and a negative part. But when
>>>> > I plot pp.x with a plot_num=7, it plots the contribution of the
>>>> > wavefunction to the charge density and it is mostly positive. Thanks a
>>>> > lot for your help.
>>>> >
>>>> >
>>>> Hi Arpan,
>>>> the manual of PP is only a couple of pages long, it's better to read it
>>>> to the end:
>>>> <
>>>> http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PP.html#idp42384
>>>> >
>>>>
>>>> kind regards
>>>>
>>>> --
>>>> Dr. Lorenzo Paulatto
>>>> IdR @ IMPMC -- CNRS & Université Paris 6
>>>> +33 (0)1 44 275 084 / skype: paulatz
>>>> http://www-int.impmc.upmc.fr/~paulatto/
>>>> 23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
>>>>
>>>> _______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>
>>>
>>>
>>>
>>> --
>>> _________________________________________
>>> Filipe Camargo Dalmatti Alves Lima
>>> PhD Student
>>> University of São Paulo, Physics Institute, Materials Physics
>>> Department, Nanomol Group, Brazil.
>>> Phones: (11) 3091-6881 (USP)
>>> (11) 97408-2755 (Vivo)
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>>
>> --
>> Regards,
>> Arpan Kundu
>> Doctoral Student
>> Department of Mechanical Engineering
>> Purdue University
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> _________________________________________
> Filipe Camargo Dalmatti Alves Lima
> PhD Student
> University of São Paulo, Physics Institute, Materials Physics Department,
> Nanomol Group, Brazil.
> Phones: (11) 3091-6881 (USP)
> (11) 97408-2755 (Vivo)
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
Regards,
Arpan Kundu
Doctoral Student
Department of Mechanical Engineering
Purdue University
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