[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
Franklin Zhan
zhanhit at hotmail.com
Wed Jul 25 10:12:09 CEST 2012
Dear Giuseppe,
Deepest thanks for your advice.
Your suggestion is really helpful and inspiring.
If you are in Singapore, I would like to buy you a cup of coffee,
Cheers~,
Franklin
Franklin Zhan
Ph.D student
School of Mechanical and Aerospace Engineering,
Nanyang Technological University, Singapore.
> From: giuseppe.mattioli at ism.cnr.it
> To: pw_forum at pwscf.org
> Date: Wed, 25 Jul 2012 09:16:43 +0200
> Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface
>
>
> Dear Felipe
> You seem not to be a chemist...:-)
> The ground state of an O2 molecule is a triplet one, with 7 up valence electrons and 5 down.
>
> Dear Zhan
> This morning (morning in Italy, at least) you are lucky. I've done (almost) the same thing
> yesterday...
>
> Once the above is settled, first you should perform a relax calculation with K_POINTS (gamma). You do
> not need a nscf calculation if you use a bit of smearing. Something like
>
> &control
> calculation = 'relax'
> prefix='$FILE',
> pseudo_dir = '$PSEUDO_DIR/',
> outdir='$TMP_DIR/',
> /
> &system
> ibrav=1, celldm(1)=30.000000,
> nat=2, ntyp=1,
> ecutwfc =35.0,
> ecutrho =280.0,
> occupations='smearing', degauss=0.01,
> nspin=2,
> starting_magnetization(1)=0.3,
> /
> &electrons
> mixing_mode='plain'
> mixing_beta=0.3
> conv_thr=1.0d-7
> electron_maxstep=200
> /
> &ions
> ion_dynamics='bfgs'
> /
> ATOMIC_SPECIES
> O 15.999 O_pbe.van.UPF
> ATOMIC_POSITIONS {angstrom}
> O 5.000576334 5.029093041 5.029093041
> O 5.009423666 5.870906959 5.870906959
> K_POINTS {gamma}
>
> will provide a sufficient number of unoccupied orbitals for your purpose.
>
> Then, remember that when you use nspin=2 and K_POINTS {gamma} you are formally using two k points
> (gamma up and gamma down) which are labelled as kpoint=1 and kpoint=2, respectively. In your pw.x
> output you should acknowledge (but you should already know it by molecular orbital theory of
> homonuclear diatomic molecules...) that both the HOMO in the up channel (-9.1985 -9.1983) and the
> LUMO in the down channel (-4.9925 -4.9924) are doubly degenerate. Thus, you must plot the single-
> electron orbitals and sum them.
>
> ------ SPIN UP ------------
>
>
> k = 0.0000 0.0000 0.0000 ( 47171 PWs) bands (ev):
>
> -34.3196 -21.0375 -17.4698 -17.4697 -14.7359 -9.1985 -9.1983 -0.6483
> -0.1403 -0.0924
>
> ------ SPIN DOWN ----------
>
>
> k = 0.0000 0.0000 0.0000 ( 47171 PWs) bands (ev):
>
> -33.1724 -19.2543 -13.7742 -12.6937 -12.6937 -4.9925 -4.9924 -0.5833
> -0.0519 -0.0089
>
> the Fermi energy is -8.4505 ev
>
> This is quite easy, supposing that you read carefully the pp.x input guide... But, as I said, you
> won a free ride today...
>
> &inputpp
> prefix = '$FILEA'
> outdir = '$TMP_DIR/'
> filplot = '$FILEA-HOMOa.dat'
> plot_num= 7
> kpoint=1
> kband=6
> /
>
> $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
>
> &inputpp
> prefix = '$FILEA'
> outdir = '$TMP_DIR/'
> filplot = '$FILEA-HOMOb.dat'
> plot_num= 7
> kpoint=1
> kband=7
> /
>
> $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
>
>
> &inputpp
> /
> &plot
> nfile = 2
> filepp(1) = '$FILEA-HOMOa.dat'
> weight(1) = 1.0
> filepp(2) = '$FILEA-HOMOb.dat'
> weight(2) = 1.0
> iflag = 3
> output_format = 5
> fileout = '$FILEA-HOMO.plot'
> e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0,
> e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0,
> nx=56, ny=40
> /
>
> $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
>
> This will produce a nice .xsf file containing your HOMO orbital, which you can plot with xcrysden.
> You may also obtain a cube file, but I cannot remember the output format.
>
> As for the LUMO, use kpoint=2, and the correct kband numbers and do the same thing.
>
> I hope this really help... (in Italy I would have said: you owe me a cup of coffee...)
>
> Giuseppe
>
>
> On Wednesday 25 July 2012 08:43:30 Filipe Camargo Dalmatti Alves Lima wrote:
> > Dear Zhan,
> >
> > The number of electrons on your system determines the occupied bands and
> > consequently the HOMO level.
> >
> > So, What you need to do?
> >
> > First, check the number of electron that you are using. (If you are using
> > the O default pseudopotencials it should be 6 valence electrons)
> > Then, you'll have 12 electrons and 6 bands (each bands is occupied by 2
> > electrons).
> >
> > Now check your output file, which is generated using the pw.x code.
> > The band number 6 represents your HOMO level and the band number 7 is the
> > LUMO one.
> >
> > So, now you know your bands. Then you can obtain the wavefunction.
> >
> > You will need to run the pp.x twice: one for HOMO and another for LUMO.
> > kband=6 (to plot HOMO)
> > and
> > kdand=7 (to plot LUMO)
> >
> > I hope it will solve your problem,
> >
> > Best regards,
> >
> > > Dear PWSCF users,
> > >
> > > I am trying to calculate HOMO and LUMO levels and plot these isosurfaces
> > > for O2 molecule.
> > > I first relaxed the O2 and then did nscf calculation. then I used pp.x to
> > > calculate the HOMO and LUMO levels. but I can not find the HOMO or LUMO
> > > level in output files.
> > > the code for pp.x is pasted as following:
> > >
> > > &inputpp
> > >
> > > prefix= 'O2'
> > > outdir= '/scratch/zhan0273/PWSCF/O2/tmp'
> > >
> > > filplot = 'O2'
> > > plot_num= 7
> > > spin_component=0
> > > ! kpoint=40
> > > kband=8
> > > /
> > > &plot
> > > nfile = 1
> > > filepp(1) = 'O2'
> > > weight(1) = 1.0
> > > iflag = 3
> > > output_format = 5
> > > fileout = 'O2.orb.xsf'
> > > /
> > >
> > > So please give advice. Thank you all in advance!
> > >
> > > Best regards,
> > >
> > > ------------------------------
> > > Franklin Zhan
> > > Ph.D student
> > > School of Mechanical and Aerospace Engineering,
> > > Nanyang Technological University, Singapore.
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
>
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>
> Giuseppe Mattioli
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
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