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 < [email protected]> 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 <[email protected]> > 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 < >> [email protected]> 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 < >>> [email protected]> 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 >>>> [email protected] >>>> 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 >>> [email protected] >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> >> -- >> Regards, >> Arpan Kundu >> Doctoral Student >> Department of Mechanical Engineering >> Purdue University >> >> _______________________________________________ >> Pw_forum mailing list >> [email protected] >> 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 > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, Arpan Kundu Doctoral Student Department of Mechanical Engineering Purdue University
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