[Pw_forum] Teter ''extended norm-conserving'' pseudopotential
bahaareh tavakoli nejad
bahaartv at gmail.com
Mon Apr 4 20:13:34 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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>
> 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.
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