On Mon, Apr 4, 2011 at 9:29 AM, <pw_forum-request at pwscf.org> wrote:
> Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Van der Waals (Adriano Mosca Conte) > 2. Shift of Energy (pari shok) > 3. Re: Shift of Energy (Duy Le) > 4. Re: 4.3 compile error. (?S) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 4 Apr 2011 15:27:08 +0200 (CEST) > From: "Adriano Mosca Conte" <Adriano.Mosca.Conte at roma2.infn.it> > Subject: [Pw_forum] Van der Waals > To: Pw_forum at pwscf.org > Message-ID: <59184.141.108.248.78.1301923628.squirrel at 141.108.248.78> > Content-Type: text/plain;charset=iso-8859-1 > > I have two questions about the calculations with VdW forces > (input_dft = 'vdW-DF'): > 1- Is it possible to perform VdW calculations with any kind of functional? > Or is it mandatory to use revPBE? > 2- I generated a VdW table on two different machines (sp6 of CINECA, > matrix of CASPUR). I got different numbers in the files vdW_kernel_table > (sign > and order of magnitude are different in many cases). Could it depend on the > modules I loaded on matrix? Which are the libraries used to generate > the table? > Adriano > > > -- > Universit? degli Studi Tor Vergata > via della Ricerca Scientifica 1 > 00133 Roma, Italia > Tel. +39 06 7259 4741 > Fax +39 06 2023507 > > > ------------------------------ > > Message: 2 > Date: Mon, 4 Apr 2011 10:32:53 -0400 > From: pari shok <parishok at gmail.com> > Subject: [Pw_forum] Shift of Energy > To: pw_forum at pwscf.org > Message-ID: <BANLkTi=EzJF-KgYL0Cf2Yxe45cWJte4y9g at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > Thank you very much for your help. > Please let me ask my final question w.r.t DOS shift of energy of SiC > supercell. > The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of > 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is > scaling > accordingly. > However, I still see the shift of energy in DOS diagram of two slabs (the > max and min of bandgap shifts, although the gap is almost 2.1 eV for both > 4H-SiC slabs). I was wondering whether this shift of energy is inevitable > or > it is as the result of my input file. > I kept k points (w.r.t. crystal), and cut off energy the same for both > structures. Should I scale the cut off energy as well. If positive, is > there > any relation between scaling the cell and cut off energy. > As you know, I need to find a reference for my further calculations. > I really really appreciate your help. > Yours > P Shok > > Dear All, > let me clarify a little point. > The potential (hence the eigenvalues) of any calculation in > periodic boundary conditions, not just a plane-wave one , is defined up > to an additive constant... In a finite system a reeference can be fixed > by requiring that the potential goes to zero at infinite distance but in > a periodic system this cannot be defined as there is nothing like a > point at infinite distance ... > In most codes (and in pw.x) this arbitrary constant is fixed by > setting the average electrostatic potential to zero. If the supercell is > properly constructed, with the properly scaled dimensions, the same > cutoff, equivalent k-points etc.. the two calculations should be > equivalent and the eigenvalues should be exactly mapped, the average > potential should be the same, the total energy should be an exact > multiple of the one of the original cell. > > If this does not happen one is NOT doing the supercell calculation > properly. > > So if when doing a supercell you do not get the scaled result check your > system definition. > > stefano > > > On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote: > >* Dear all > *>* I suspect that a a little misunderstanding has been going on here... > *>* I try to reformulate the question: in the case of a 8-atoms cell the > valence > *>* band maximum (VBM) has been found around 10 eV and the conduction band > *>* minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in > the > *>* position of VBM and CBM when calculated in a 72-atoms supercell, > but the band > *>* gap value is the same. Then, the answer to P Shok could be: plane wave > *>* pseudopotential calculations do not ensure an universal alignment of > *>* eigenvalues. You should use some "internal" reference, like the 1s > eigenvalue > *>* of an He atom, in your cell; or trust that the two VBM values are > aligned "de > *>* facto". > *>* HTH > *>* > *>* Giuseppe > *>* > *>* On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote: > *>>* Yes, > *>>* > *>>* I perfectly agree with Eyvaz! Moreover the experimental bandgap is > *>>* underestimated within LDA or GGA, and for 4H-SiC you would get about > *>>* 2.2-2.3 eV with LDA. > *>>* > *>>* How do you measure the bandgap? Beware that in the fundamental > cell the > *>>* bandgap is not a direct one, but it might become such when you use a > *>>* supercell (because of the refolding of the Brillouin zones). > *>>* > *>>* > *>>* HTH > *>>* > *>>* GS > *>>* > *>>* Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto: > *>>>* Hi, > *>>>* > *>>>>* The bandgap of 8-atoms is around 10-12 eV, > *>>>>* but that of 72-atom is around 5-7 eV. > *>>>* This is unbelievable, as SiC is an indirect band gap semiconductor > and > *>>>* the bandgap is around (2.5 - 3)eV depending on crystal modification > *>>>* (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.). > *>>>* See http://www.matprop.ru/SiC_bandstr > *>>>* > *>>>* So, check carefully your input/output files. > *>>>* > *>>>* Bests, > *>>>* Eyvaz. > *>>>* > *>>>* ------------------------------------------------------------------- > *>>>* Prof. Eyvaz Isaev, > *>>>* Department of Physics, Chemistry, and Biology (IFM), Linkoping > *>>>* University, Sweden Theoretical Physics Department, Moscow State > Institute > *>>>* of Steel& Alloys, Russia, isaev at ifm.liu.se > <http://www.democritos.it/mailman/listinfo/pw_forum>, eyvaz_isaev at > yahoo.com <http://www.democritos.it/mailman/listinfo/pw_forum> > *>>>* > *>>>* > *>>>* From: pari shok<parishok at gmail.com > <http://www.democritos.it/mailman/listinfo/pw_forum>> > *>>>* To: pw_forum at pwscf.org > <http://www.democritos.it/mailman/listinfo/pw_forum> > *>>>* Sent: Sun, April 3, 2011 1:34:51 AM > *>>>* Subject: [Pw_forum] shift of energy > *>>>* > *>>>* Dear Paolo, > *>>>* DOS of 72-atom SiC shows a shift of energy with respect to 8-atom > SiC.The > *>>>* bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around > 5-7 > *>>>* eV. Would you please help me to understand this shift. > *>>>* > *>>>* Thanks again. > *>>>* P Shok > *>>>* UMD > *>>>* > *>>>* On Apr 1, 2011, at 21:36 , pari shok wrote: > *>>>>* The DOS of 72-atom SiC (supercell) shows a shift of energy. > *>>>* a shift with respect to what? > *>>>* --- > *>>>* Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > *>>>* > *>>>* 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> > *>>>* http://www.democritos.it/mailman/listinfo/pw_forum > *>>* ? Gabriele Sclauzero, EPFL SB ITP CSEA > *>>* PH H2 462, Station 3, CH-1015 Lausanne > *>* > *>* > * > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110404/6c0c645c/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Mon, 4 Apr 2011 11:04:51 -0400 > From: Duy Le <ttduyle at gmail.com> > Subject: Re: [Pw_forum] Shift of Energy > To: PWSCF Forum <pw_forum at pwscf.org> > Cc: pari shok <parishok at gmail.com> > Message-ID: <BANLkTi=keZQ5tpRzvHs7t_d4x7V7Jrw7Qw at mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Mon, Apr 4, 2011 at 10:32 AM, pari shok <parishok at gmail.com> wrote: > > Dear All, > > Thank you very much for your help. > > Please let me ask my final question w.r.t DOS shift of energy of SiC > > supercell. > > The total energy of the 8-atom cell of SiC is: -76.276 Ry, while that of > > 72-atom SiC is -694 Ry. Neglecting almost -7 Ry, the total energy is > scaling > > accordingly. > If you are doing correctly, the results must be identical. So make > sure to check the structures, and the convergence of total energy vs. > cutoff energy and k-point sampling. > > However, I still see the shift of energy in DOS diagram of two slabs (the > > max and min of bandgap shifts, although the gap is almost 2.1 eV for both > > 4H-SiC slabs). I was wondering whether this shift of energy is inevitable > or > > it is as the result of my input file. > Slab? I though you are performing bulk calculation. Anyway, the shift > of energies' levels is normal. You should set the reference as center > of the gap (set it to be zero) then compare the DOS or band > structures. > By the way, if your bigger slab experiences the reconstruction, the > two slabs (8 atoms and 72 atoms) won't be identical => you should not > get the same results in this case. But 7Ry seems to be huge. > > I kept k points (w.r.t. crystal), and cut off energy the same for both > > structures. Should I scale the cut off energy as well. If positive, is > there > Okie, but you should scale the k-point sampling accordingly because > the BZ of 72 atoms cell is smaller. But this won't harm the results if > total energy is already converged vs. k-point sampling. > > any relation between scaling the cell and cut off energy. > No. Cut off energy depends on only pseudo potential. > > As you know, I need to find a reference for my further calculations. > > I really really appreciate your help. > > Yours > > P Shok > > > > -------------------------------------------------- > Duy Le > PhD Student > Department of Physics > University of Central Florida. > > "Men don't need hand to do things" > > Dear All, > > let me clarify a little point. > > The potential (hence the eigenvalues) of any calculation in > > periodic boundary conditions, not just a plane-wave one , is defined up > > > > to an additive constant... In a finite system a reeference can be fixed > > by requiring that the potential goes to zero at infinite distance but in > > a periodic system this cannot be defined as there is nothing like a > > > > point at infinite distance ... > > In most codes (and in pw.x) this arbitrary constant is fixed by > > setting the average electrostatic potential to zero. If the supercell is > > properly constructed, with the properly scaled dimensions, the same > > > > cutoff, equivalent k-points etc.. the two calculations should be > > equivalent and the eigenvalues should be exactly mapped, the average > > potential should be the same, the total energy should be an exact > > multiple of the one of the original cell. > > > > > > If this does not happen one is NOT doing the supercell calculation > properly. > > > > So if when doing a supercell you do not get the scaled result check your > > system definition. > > > > stefano > > > > > > On 04/04/2011 11:46 AM, Giuseppe Mattioli wrote: > > > >> Dear all > >> I suspect that a a little misunderstanding has been going on here... > >> I try to reformulate the question: in the case of a 8-atoms cell the > >> valence > >> band maximum (VBM) has been found around 10 eV and the conduction band > > > >> minimum (CBM) around 12 eV with a 2 eV band gap. So there is a shift in > >> the > >> position of VBM and CBM when calculated in a 72-atoms supercell, but the > >> band > >> gap value is the same. Then, the answer to P Shok could be: plane wave > > > >> pseudopotential calculations do not ensure an universal alignment of > >> eigenvalues. You should use some "internal" reference, like the 1s > >> eigenvalue > >> of an He atom, in your cell; or trust that the two VBM values are > aligned > >> "de > > > >> facto". > >> HTH > >> > >> Giuseppe > >> > >> On Monday 04 April 2011 09:39:18 Gabriele Sclauzero wrote: > >>> Yes, > >>> > >>> I perfectly agree with Eyvaz! Moreover the experimental bandgap is > > > >>> underestimated within LDA or GGA, and for 4H-SiC you would get about > >>> 2.2-2.3 eV with LDA. > >>> > >>> How do you measure the bandgap? Beware that in the fundamental cell > >>> the > > > >>> bandgap is not a direct one, but it might become such when you use a > >>> supercell (because of the refolding of the Brillouin zones). > >>> > >>> > >>> HTH > > > >>> > >>> GS > >>> > >>> Il giorno 03/apr/2011, alle ore 10.59, Eyvaz Isaev ha scritto: > >>>> Hi, > >>>> > >>>>> The bandgap of 8-atoms is around 10-12 eV, > > > >>>>> but that of 72-atom is around 5-7 eV. > >>>> This is unbelievable, as SiC is an indirect band gap semiconductor and > >>>> the bandgap is around (2.5 - 3)eV depending on crystal modification > > > >>>> (3C-SiC, 2H-SiC; 4H-SiC; 6H-SiC, etc.). > >>>> See http://www.matprop.ru/SiC_bandstr > >>>> > >>>> So, check carefully your input/output files. > > > >>>> > >>>> Bests, > >>>> Eyvaz. > >>>> > >>>> ------------------------------------------------------------------- > >>>> Prof. Eyvaz Isaev, > > > >>>> Department of Physics, Chemistry, and Biology (IFM), Linkoping > >>>> University, Sweden Theoretical Physics Department, Moscow State > >>>> Institute > >>>> of Steel& Alloys, Russia, isaev at ifm.liu.se, eyvaz_isaev at > yahoo.com > > > >>>> > >>>> > >>>> From: pari shok<parishok at gmail.com> > >>>> To: pw_forum at pwscf.org > > > >>>> Sent: Sun, April 3, 2011 1:34:51 AM > >>>> Subject: [Pw_forum] shift of energy > >>>> > >>>> Dear Paolo, > >>>> DOS of 72-atom SiC shows a shift of energy with respect to 8-atom > >>>> SiC.The > > > >>>> bandgap of 8-atoms is around 10-12 eV, but that of 72-atom is around > 5-7 > >>>> eV. Would you please help me to understand this shift. > >>>> > >>>> Thanks again. > > > >>>> P Shok > >>>> UMD > >>>> > >>>> On Apr 1, 2011, at 21:36 , pari shok wrote: > >>>>> The DOS of 72-atom SiC (supercell) shows a shift of energy. > > > >>>> a shift with respect to what? > >>>> --- > >>>> Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > >>>> > >>>> 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 > >>> ? Gabriele Sclauzero, EPFL SB ITP CSEA > >>> PH H2 462, Station 3, CH-1015 Lausanne > > > >> > >> > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > ------------------------------ > > Message: 4 > Date: Tue, 5 Apr 2011 00:14:21 +0800 (CST) > From: ?S <flux_ray12 at 163.com> > Subject: Re: [Pw_forum] 4.3 compile error. > To: "PWSCF Forum" <pw_forum at pwscf.org> > Message-ID: <174f5d1.7e22.12f214b1d61.Coremail.flux_ray12 at 163.com> > Content-Type: text/plain; charset="gbk" > > Hi, Vit. > I got the same problem like you. > > You can open the file TDDFPT/src/lr_main.f90 and find the line 252. It > should be written as: > IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR. > LR_iteration==itermax .OR. LR_iteration==1) ) CALL lr_write_restart() > Then, you can add a '&' after '==1) )' and put 'CALL lr_write_restart()' to > the next line. > Do not forget add enough space before 'CALL lr_write_restart()', otherwise > it would become annotate instead of code. > The modified one could like: > IF ( lr_io_level > 0 .and. (mod(LR_iteration,restart_step)==0 .OR. > LR_iteration==itermax .OR. LR_iteration==1) ) & > CALL lr_write_restart() > > > At 2011-04-03 19:41:28?Vit <vitruss at gmail.com> wrote: > > >Dear QE users! > >I'm having troubles compiling new release. I'm trying to use ACML where > >apllicable, but I'm getting the same error even with distro (debian 6.0.1) > >blas and lapack and internal fftw. > >Could you please help me resolving this issue? > > > >mpif90 -g -o turbo_lanczos.x \ > > lr_variables.o lr_charg_resp.o bcast_lr_input.o > lr_readin.o > >lr_alloc_init.o lr_calc_dens.o lr_dot.o lr_dealloc.o lr_ortho.o > lr_read_wf.o > >lr_normalise.o lr_lanczos.o lr_apply_liouvillian.o lr_main.o lr_dv_setup.o > >lr_setup_dgc.o lr_solve_e.o lr_dvpsi_e.o lr_ch_psi_all.o lr_cgsolve_all.o > >lr_h_psiq.o lr_sm1_psi.o stop_lr.o lr_read_d0psi.o lr_restart.o > >lr_write_restart.o print_clock_lr.o sd0psi.o lr_set_boxes_density.o > >lr_init_nfo.o ../../PH/libph.a ../../PW/libpw.a ../../Modules/libqemod.a > >../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a > >../../iotk/src/libiotk.a -L/opt/acml4.4.0/gfortran64/lib -lacml - > >L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib > -lacml > >lr_main.o: In function `lr_main': > >/opt/qe/4.3/TDDFPT/src/lr_main.f90:252: undefined reference to `lr_wri_' > >collect2: ld returned 1 exit status > >make[2]: *** [turbo_lanczos.x] Error 1 > >make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/src' > >make[2]: Entering directory `/opt/qe/4.3/TDDFPT/tools' > >test -n "" && ( cd ../.. ; make -w || exit 1) || : > >mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__ACML -D__MPI - > >D__PARA -I../../include -I../../iotk/src -I../../Modules -I. -c > >tddfpt_calculate_spectrum.f90 > >mpif90 -g -o turbo_spectrum.x \ > > tddfpt_calculate_spectrum.o ../../Modules/libqemod.a > ../../PW/libpw.a > >../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a > >../../iotk/src/libiotk.a -L/opt/acml4.4.0/gfortran64/lib -lacml - > >L/opt/acml4.4.0/gfortran64/lib -lacml -L/opt/acml4.4.0/gfortran64/lib > -lacml > >( cd ../../bin ; ln -fs ../TDDFPT/tools/turbo_spectrum.x . ) > >if [ -d ../bin ] ; then ( cd ../bin ; ln -fs ../tools/turbo_spectrum.x . > ); > >fi > >make[2]: Leaving directory `/opt/qe/4.3/TDDFPT/tools' > >make[1]: Leaving directory `/opt/qe/4.3/TDDFPT' > > > >With best regards, > >Koroteev Victor. > >_______________________________________________ > >Pw_forum mailing list > >Pw_forum at pwscf.org > >http://www.democritos.it/mailman/listinfo/pw_forum > -------------- nex t part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110405/a5f0eb48/attachment.htm > > ------------------------------ > > ___xx____________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 46, Issue 10 > **************************************** > Hi dear users is there anyone who knows about Teter pseudopotential?Sr has 38 electrons and valence electrons Should be 4s2 4p6 5s2 4d0 in ground state but in this pseudopotetial Zion=10 and the valence electrons are 4s2 4p6 5s0 4d0! what's the meaning of it? can i use it for ground state? Ok! this pseudopotential is used in abinit but i coulden't ask my question of them yet. thank's alot. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110404/4e89196e/attachment-0001.htm
