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 > > -- > ******************************************************** > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? l'oppression. > ******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM) > Tel + 39 06 90672836 - Fax +39 06 90672316 > E-mail: <giuseppe.mattioli at ism.cnr.it> > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120725/349bf0a8/attachment-0001.htm