[Pw_forum] Teter''extended norm conserving'' pseudotential
bahaareh tavakoli nejad
bahaartv at gmail.com
Mon Apr 4 20:48:02 CEST 2011
On Mon, Apr 4, 2011 at 9:29 AM, <pw_forum-request at pwscf.org> wrote:
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> 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
> *>*
> *>*
> *
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> ------------------------------
>
> 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
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>
> Hi dear users.
is there anybody who's know about Teter pseudopotential.I used it for
Sr.Sr has 38 electrons and valence electrons should be 4s2 4p6 5s2 4d0 in
ground state but in this pseudopotential zion=10 and the valence electrons
are 4s2 4p6 5s0 4d0!whate's the maning of it?can i use it for ground state
alculation?
Ok! this pseudopotential is used in abinit but i can't ask my question of
them.
thank's alot.
> ------------------------------
>
> _______________________________________________
> 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
> ****************************************
>
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