[Pw_forum] parallelization of phonon calculations
On Jul 25, 2012, at 16:13 , William Parker wrote: > Each image will output to its own output file labeled out.i_0 where > i runs from 1 to N_image - 1. The frequencies in these files will > be garbage unless all of the representations for a particular q- > point are contained in one image. After you run the image- > parallelized run, you must copy the data-file.*.*.xml files (not > the data-file.*.xml files) to the _ph0/(prefix).phsave/ directory > and run again on one image with recover=.true. in your input file. > This will produce the correct frequencies in the output file and > the (prefix).dyn* files. funny: "image" parallelization (the one done with MPI, not with separate calculations on a grid) should automatically perform the final step of collecting results. P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] pseudopotential
Dear all I have a question about pseudopotential in quantum espresso. Which pseudopotential better for describe "Van der Waals" bonding? Bani Adam Faculty of Science Egypt
[Pw_forum] pseudopotential
On Jul 25, 2012, at 18:32 , Emine Kucukbenli wrote: > for input_dft="vdW-DF2" use a revised-PW86 (the last commit on this > was some 5h ago so i would use w caution.) no need to be so cautious: today's commit was a correction to a comment > And follow the modifications to Modules/funct.f90 file with care for > addition of new vdW flavors :) here: http://qe-forge.org/scm/viewvc.php/trunk/espresso/Modules/funct.f90? root=q-e=log P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] pseudopotential
Perhaps knowing the physics behind it, the OP assumed that vdW-relevant distinguishing factor between pseudopotentials is the XC functionals they are generated with. In that case the question would be legit and the answer I suppose would go like the following: Choose a flavor of vdW you want to use, then for input_dft="vdW-DF" use a revPBE pseudo for input_dft="vdW-DF2" use a revised-PW86 (the last commit on this was some 5h ago so i would use w caution.) instead, input_dft="vdw-df-c09" or "vdw-df2-c09" should both be used with pseudos generated with c09x And follow the modifications to Modules/funct.f90 file with care for addition of new vdW flavors :) ciao emine Quoting Axel Kohlmeyer : > On Wed, Jul 25, 2012 at 5:00 PM, bf azi wrote: >> Dear all >> >> I have a question about pseudopotential in quantum espresso. >> Which pseudopotential better for describe "Van der Waals" bonding? > > please think about this for a little bit:
[Pw_forum] pseudopotential
On Wed, Jul 25, 2012 at 5:00 PM, bf azi wrote: > Dear all > > I have a question about pseudopotential in quantum espresso. > Which pseudopotential better for describe "Van der Waals" bonding? please think about this for a little bit: - in what range (i.e. distance from the atom core) does a pseudopotential modify an (atomic) wavefunction and what is it supposed to be like beyond that range? - in what range, i.e. distance between two atoms, do van der waals interactions matter? if you think this through, you should be able to come up with an answer to your question by yourself. cheers, axel. > > Bani Adam > Faculty of Science > Egypt > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
?Experimental results show that the stable ground stat? of oxygen molecule is triplet(2s+1=3). > > On Jul 25, 2012, at 12:20 , Franklin Zhan wrote: > >> since O2 is not a magnetic system > > I beg your pardon? > >> > 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. > > P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120725/adb5d138/attachment-0001.htm
[Pw_forum] parallelization of phonon calculations
Program PHONON v.4.3.2 On Wed, 25 Jul 2012 13:40:39 +0200, Paolo Giannozzi wrote: > Which version of the phonon code have you used? P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] Problem on runing espresso-4.3.2
On Jul 25, 2012, at 9:10 , Mahdi Faghih nasiri wrote: > "error while loading shared libraries: > /opt/intel/mkl/10.0.4.023/lib/em64t/libmkl_intel_lp64.so: > cannot open shared object file: No such file or directory You have to set up the correct LD_LIBRARY_PATH or whatever is needed, on all processors on which the code is running. Please have a look at the documentation of MKL libraries P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] parallelization of phonon calculations
Which version of the phonon code have you used? P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
Il 25/07/2012 12.41, Franklin Zhan ha scritto: > ...However, O2 molecule is not magnetic material, thus I do not > know why we need to take the spin polarization into consideration. You have to review some chemistry... Try to have a look here: http://www.youtube.com/watch?v=Isd9IEnR4bw Carlo Nervi -- Prof. Carlo Nervi carlo.nervi at unito.it Tel:+39 0116707507/8 Fax: +39 0116707855 - Dipartimento di Chimica, via P. Giuria 7, 10125 Torino, Italy.http://lem.ch.unito.it/
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
Dear Franklin You are making a bit of confusion between ferromagnetic systems (Fe, Ni, Co ,...), and paramagnetic systems (O2, among many others). Both kinds of system ARE magnetic, and generally require spin polarized calculations. Regarding k-points, molecules have electronic levels flat in the Brillouin zone (if you do not know what does such a statement mean and imply, a solid state physics textbook may help...). Thus, calculations of molecules do not depends on k-points, as long as the box is enough large to minimize the interaction between periodically repeated images of the molecule. Solids, like ZnO, are (in a quite rough manner of speaking...) characterized by dispersed electronic bands instead, and require to check the convergence with respect to the k-point mesh. HTH (another cup, please, and with cream...:-)) On Wednesday 25 July 2012 12:41:06 Franklin Zhan wrote: > Dear Prof. Giannozzi, > It is great to hear from you. > In my mind, only when we are dealing with some magnetic materials > calculation, such as Ni, iron, the spin polarization is taken into > account. However, O2 molecule is not magnetic material, thus I do not know > why we need to take the spin polarization into consideration. > > > > Best regards, > > > > > Franklin Zhan > > Ph.D student > School of Mechanical and Aerospace Engineering, > Nanyang Technological University, Singapore. > > > From: giannozz at democritos.it > > Date: Wed, 25 Jul 2012 12:25:51 +0200 > > To: pw_forum at pwscf.org > > Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface > > > > On Jul 25, 2012, at 12:20 , Franklin Zhan wrote: > > > since O2 is not a magnetic system > > > > I beg your pardon? > > > > > > 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. > > > > P. > > --- > > Paolo Giannozzi, Dept of Chemistry, > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > > > > ___ > > 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:
[Pw_forum] parallelization of phonon calculations
I agree that it should be automatic, but, in any case I've tried, ph.x doesn't find the other directories. --William On Jul 25, 2012, at 12:45 PM, Paolo Giannozzi wrote: > > On Jul 25, 2012, at 16:13 , William Parker wrote: > >> Each image will output to its own output file labeled out.i_0 where >> i runs from 1 to N_image - 1. The frequencies in these files will >> be garbage unless all of the representations for a particular q- >> point are contained in one image. After you run the image- >> parallelized run, you must copy the data-file.*.*.xml files (not >> the data-file.*.xml files) to the _ph0/(prefix).phsave/ directory >> and run again on one image with recover=.true. in your input file. >> This will produce the correct frequencies in the output file and >> the (prefix).dyn* files. > > funny: "image" parallelization (the one done with MPI, not with separate > calculations on a grid) should automatically perform the final step of > collecting results. > > P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum * William D. Parker phone: (630) 252-4834 Computational Postdoctoral Fellow fax: (630) 252-4798 MSD-212, Rm. C-215 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 *
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
On Jul 25, 2012, at 12:20 , Franklin Zhan wrote: > since O2 is not a magnetic system I beg your pardon? > > 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. P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] parallelization of phonon calculations
Dear all, I am planing to do a phonon calculation on a zeolite structure. The unit cell contains 37 atoms, the space group is P1, and the number of irreducible representations is therefore 3*37=111. Naturally I would like to parallelize this calculation as efficiently as possible. From the documentation of the Quantum Espresso web page I see that the irreducible representations can be grouped into "images" that can be computed largely independently. The following example is given: mpirun -np 64 ph.x -nimage 8 -npool 2 ... After a slight modification, I executed the following command line: mpirun -np 256 -npernode 8 ph.x -nimage 16 < struct0-phonon.inp > struct0-phonon.out The calculation terminates normally, but the result is not what I expected. Almost at the beginning of the output file the following it printed: Atomic displacements: There are 111 irreducible representations Representation 1 1 modes - To be done Representation 2 1 modes - To be done Representation 3 1 modes - To be done Representation 4 1 modes - To be done Representation 5 1 modes - To be done Representation 6 1 modes - To be done Representation 7 1 modes - Not done in this run Representation 8 1 modes - Not done in this run Representation 9 1 modes - Not done in this run - The message "Not done in this run" is printed for Representation 7 to 111. Towards the end of the output file the frequencies are printed. Frequencies 1 to 6 are slightly negative, frequencies 7 to 105 are virtually zero, and frequencies 106 to 111 are slightly positive. The first and last part of the mentioned output section are shown below: omega( 1) = -7.228419 [THz] =-241.114112 [cm-1] omega( 2) = -7.052563 [THz] =-235.248188 [cm-1] omega( 3) = -6.661820 [THz] =-222.214395 [cm-1] omega( 4) = -6.390946 [THz] =-213.179028 [cm-1] omega( 5) = -6.252886 [THz] =-208.573825 [cm-1] omega( 6) = -5.895227 [THz] =-196.643621 [cm-1] omega( 7) = -0.01 [THz] = -0.19 [cm-1] omega( 8) = -0.01 [THz] = -0.18 [cm-1] omega( 9) = -0.01 [THz] = -0.18 [cm-1] omega(10) = 0.00 [THz] = -0.17 [cm-1] omega(11) = 0.00 [THz] = -0.17 [cm-1] omega(12) = 0.00 [THz] = -0.15 [cm-1] omega(98) = 0.00 [THz] = 0.14 [cm-1] omega(99) = 0.00 [THz] = 0.14 [cm-1] omega(**) = 0.00 [THz] = 0.15 [cm-1] omega(**) = 0.00 [THz] = 0.16 [cm-1] omega(**) = 0.00 [THz] = 0.16 [cm-1] omega(**) = 0.00 [THz] = 0.16 [cm-1] omega(**) = 0.00 [THz] = 0.16 [cm-1] omega(**) = 0.01 [THz] = 0.17 [cm-1] omega(**) = 16.552716 [THz] = 552.139187 [cm-1] omega(**) = 16.683450 [THz] = 556.499976 [cm-1] omega(**) = 17.480012 [THz] = 583.070434 [cm-1] omega(**) = 17.635841 [THz] = 588.268333 [cm-1] omega(**) = 17.837822 [THz] = 595.005680 [cm-1] omega(**) = 18.630530 [THz] = 621.447600 [cm-1] ** I have a feeling that I have severely misunderstood some important concepts. I would therefore appreciate if someone could give an explanation on how to correctly perform a parallel phonon calculation. Thank you very much in advance for your help. Yours sincerely, Torstein Fjermestad University of Oslo Norway
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
Many thanks to you guys. I learned a lot today. Best regards, Franklin Zhan Ph.D student School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore. > Date: Wed, 25 Jul 2012 13:15:01 +0200 > From: carlo.nervi at unito.it > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface > > Il 25/07/2012 12.41, Franklin Zhan ha scritto: > > ...However, O2 molecule is not magnetic material, thus I do not > > know why we need to take the spin polarization into consideration. > > You have to review some chemistry... > Try to have a look here: > > http://www.youtube.com/watch?v=Isd9IEnR4bw > > Carlo Nervi > > -- > > Prof. Carlo Nervi carlo.nervi at unito.it Tel:+39 0116707507/8 > Fax: +39 0116707855 - Dipartimento di Chimica, via > P. Giuria 7, 10125 Torino, Italy.http://lem.ch.unito.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/b5d9d625/attachment.htm
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
Thanks for you reply. Best regards, Franklin Zhan Ph.D student School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore. Date: Wed, 25 Jul 2012 15:06:13 +0430 From: naz...@iasbs.ac.ir To: pw_forum at pwscf.org Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface Experimental results show that the stable ground stat of oxygen molecule is triplet(2s+1=3). > > On Jul 25, 2012, at 12:20 , Franklin Zhan wrote: > >> since O2 is not a magnetic system > > I beg your pardon? > >> > 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. > > P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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/20120725/0a9d63ee/attachment.htm
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
Dear Prof. Giannozzi, It is great to hear from you. In my mind, only when we are dealing with some magnetic materials calculation, such as Ni, iron, the spin polarization is taken into account. However, O2 molecule is not magnetic material, thus I do not know why we need to take the spin polarization into consideration. Best regards, Franklin Zhan Ph.D student School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore. > From: giannozz at democritos.it > Date: Wed, 25 Jul 2012 12:25:51 +0200 > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface > > > On Jul 25, 2012, at 12:20 , Franklin Zhan wrote: > > > since O2 is not a magnetic system > > I beg your pardon? > > > > 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. > > P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > 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/20120725/7eef446c/attachment.htm
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
s 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: > > > > > > > > > > > > prefix= 'O2' > > > outdir= '/scratch/zhan0273/PWSCF/O2/tmp' > > > > > > filplot = 'O2' > > > plot_num= 7 > > > spin_component=0 > > > ! kpoint=40 > > > kband=8 > > > / > > > > > > 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: > ___ > 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/20120725/7579356e/attachment.htm
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
Dear Giuseppe, Your are right, I am a physicist! Also, I completely forgot about the O2 fundamental state. Thank you for reply and for your correction! :-) Best regards all, Filipe On Wed, Jul 25, 2012 at 8:42 AM, Franklin Zhan wrote: > Many thanks to you guys. I learned a lot today. > > > Best regards, > -- > Franklin Zhan > > Ph.D student > School of Mechanical and Aerospace Engineering, > Nanyang Technological University, Singapore. > > > > > > > Date: Wed, 25 Jul 2012 13:15:01 +0200 > > From: carlo.nervi at unito.it > > > To: pw_forum at pwscf.org > > Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface > > > > Il 25/07/2012 12.41, Franklin Zhan ha scritto: > > > ...However, O2 molecule is not magnetic material, thus I do not > > > know why we need to take the spin polarization into consideration. > > > > You have to review some chemistry... > > Try to have a look here: > > > > http://www.youtube.com/watch?v=Isd9IEnR4bw > > > > Carlo Nervi > > > > -- > > > > Prof. Carlo Nervi carlo.nervi at unito.it Tel! :+39 0116707507/8 > > > Fax: +39 0116707855 - Dipartimento di Chimica, via > > P. Giuria 7, 10125 Torino, Italy. http://lem.ch.unito.it/ > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 8249-4628 (TIM) -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120725/4f5926cb/attachment.htm
[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
calculation = 'relax'
prefix='$FILE',
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/',
/
ibrav=1, celldm(1)=30.00,
nat=2, ntyp=1,
ecutwfc =35.0,
ecutrho =280.0,
occupations='smearing', degauss=0.01,
nspin=2,
starting_magnetization(1)=0.3,
/
mixing_mode='plain'
mixing_beta=0.3
conv_thr=1.0d-7
electron_maxstep=200
/
ion_dynamics='bfgs'
/
ATOMIC_SPECIES
O15.999 O_pbe.van.UPF
ATOMIC_POSITIONS {angstrom}
O5.000576334 5.029093041 5.029093041
O5.009423666 5.870906959 5.870906959
K_POINTS {gamma}
will provide a sufficient number of unoccupied orbitals for your purpose.
Then, remember that when you use nspin=2 and K_POINTS {gamma} you are formally
using two k points
(gamma up and gamma down) which are labelled as kpoint=1 and kpoint=2,
respectively. In your pw.x
output you should acknowledge (but you should already know it by molecular
orbital theory of
homonuclear diatomic molecules...) that both the HOMO in the up channel
(-9.1985 -9.1983) and the
LUMO in the down channel (-4.9925 -4.9924) are doubly degenerate. Thus, you
must plot the single-
electron orbitals and sum them.
-- SPIN UP
k = 0. 0. 0. ( 47171 PWs) bands (ev):
-34.3196 -21.0375 -17.4698 -17.4697 -14.7359 -9.1985 -9.1983 -0.6483
-0.1403 -0.0924
-- SPIN DOWN --
k = 0. 0. 0. ( 47171 PWs) bands (ev):
-33.1724 -19.2543 -13.7742 -12.6937 -12.6937 -4.9925 -4.9924 -0.5833
-0.0519 -0.0089
the Fermi energy is-8.4505 ev
This is quite easy, supposing that you read carefully the pp.x input guide...
But, as I said, you
won a free ride today...
prefix = '$FILEA'
outdir = '$TMP_DIR/'
filplot = '$FILEA-HOMOa.dat'
plot_num= 7
kpoint=1
kband=6
/
$PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
prefix = '$FILEA'
outdir = '$TMP_DIR/'
filplot = '$FILEA-HOMOb.dat'
plot_num= 7
kpoint=1
kband=7
/
$PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE
/
nfile = 2
filepp(1) = '$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:
> >
> >
> >
> > prefix= 'O2'
> > outdir= '/scratch/zhan0273/PWSCF/O2/tmp'
> >
> > filplot = 'O2'
> > plot_num= 7
> > spin_component=0
> > ! kpoint=40
> > kband=8
> > /
> >
> > 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,
> >
> > --
> >
[Pw_forum] parallelization of phonon calculations
Each image will output to its own output file labeled out.i_0 where i runs from 1 to N_image - 1. The frequencies in these files will be garbage unless all of the representations for a particular q-point are contained in one image. After you run the image-parallelized run, you must copy the data-file.*.*.xml files (not the data-file.*.xml files) to the _ph0/(prefix).phsave/ directory and run again on one image with recover=.true. in your input file. This will produce the correct frequencies in the output file and the (prefix).dyn* files. --William On Jul 25, 2012, at 7:37 AM, Torstein Fjermestad wrote: > Program PHONON v.4.3.2 > > On Wed, 25 Jul 2012 13:40:39 +0200, Paolo Giannozzi > wrote: >> Which version of the phonon code have you used? P. >> --- >> Paolo Giannozzi, Dept of Chemistry, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum * William D. Parker phone: (630) 252-4834 Computational Postdoctoral Fellow fax: (630) 252-4798 MSD-212, Rm. C-215 Argonne National Laboratory 9700 S. Cass Ave. Argonne, IL 60439 *
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
Hi Filipe, Thanks for you reply which makes me clearer a little bit. I will try to figure out it. Best regards, Franklin Zhan Ph.D student School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore. From: fl...@if.usp.br Date: Wed, 25 Jul 2012 03:43:30 -0300 To: pw_forum at pwscf.org Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface 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) andkdand=7 (to plot LUMO) I hope it will solve your problem, Best regards, -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 8249-4628 (TIM) On Wed, Jul 25, 2012 at 2:13 AM, Franklin Zhan wrote: 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: prefix= 'O2' outdir= '/scratch/zhan0273/PWSCF/O2/tmp' filplot = 'O2' plot_num= 7 spin_component=0 ! kpoint=40 kband=8 / 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 ___ 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/20120725/8b8ff8f9/attachment-0001.htm
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
t; 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: > > > > > > > > > > > > prefix= 'O2' > > > outdir= '/scratch/zhan0273/PWSCF/O2/tmp' > > > > > > filplot = 'O2' > > > plot_num= 7 > > > spin_component=0 > > > ! kpoint=40 > > > kband=8 > > > / > > > > > > 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: > ___ > 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
[Pw_forum] Problem on runing espresso-4.3.2
Dear all, When I tried to run espresso-4.3.2 with composer_xe_2011_sp1.6.233, the error "error while loading shared libraries: /opt/intel/mkl/10.0.4.023/lib/em64t/libmkl_intel_lp64.so: cannot open shared object file: No such file or directory" came out. Please help me to resolve it, thank you in advance! ? Mahdi Faghih nasiri MSC, Guilan University, Rasht, Iran. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120725/2b87793f/attachment.htm
