[Pw_forum] Problem with concept of parameters in pseudopotentials

bahaareh tavakoli nejad bahaartv at gmail.com
Wed Apr 6 21:20:00 CEST 2011


On Tue, Apr 5, 2011 at 5:35 PM, <pw_forum-request at pwscf.org> wrote:

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> Today's Topics:
>
>   1. Problems with electrostatic corrections (Makov-Payne or
>      density counter charge) for aperiodic systems in 4.2 version
>      (Eduardo Ariel Menendez Proupin)
>   2. Re: Pw_forum Digest, Vol 46, Issue 12 (Stefano de Gironcoli)
>   3. Re: Problems with electrostatic corrections       (Makov-Payne    or
>      density counter charge) for aperiodic systems in 4.2 version
>      (Paolo Giannozzi)
>   4. Re: Problems with electrostatic corrections (Makov-Payne or
>      density counter charge) for aperiodic systems in 4.2 version
>      (Oliviero Andreussi)
>   5. Nonlinear scaling with pool parallelization (Markus Meinert)
>   6. Re: Nonlinear scaling with pool parallelization (Paolo Giannozzi)
>   7. Nonlinear scaling with pool parallelization (Markus Meinert)
>   8. Re: Nonlinear scaling with pool parallelization (Paolo Giannozzi)
>   9. Generating ultra soft pseudopotential (Tram Bui)
>  10. Re: Generating ultra soft pseudopotential (Duy Le)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 5 Apr 2011 10:44:10 -0300
> From: Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
> Subject: [Pw_forum] Problems with electrostatic corrections
>        (Makov-Payne or density counter charge) for aperiodic systems in 4.2
>        version
> To: pw_forum at pwscf.org
> Message-ID: <BANLkTinTEAmVsonPUjmefjCuQ3xfi0hZ3w at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 2) Why the DCC correction is disabled in version 4.2? Indeed when setting
> asume_isolated = 'dcc' and &EE input parameters to their default  values, I
> obtain an error message "DCC correction is disabled". Looking in the
> PW/input.f90 subroutine, one found that the dcc correction is disabled by
> an
> immediate call to errore subroutine.
>
> I guess some bug was discovered ans is not fixed yet.
> I take the occasion to ask if the DCC correction has been or will be
> available for slab calculations.
> --
>
>
> Eduardo Menendez
> Departamento de Fisica
> Facultad de Ciencias
> Universidad de Chile
> Phone: (56)(2)9787439
> URL: http://fisica.ciencias.uchile.cl/~emenendez
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> ------------------------------
>
> Message: 2
> Date: Tue, 05 Apr 2011 15:46:12 +0200
> From: Stefano de Gironcoli <degironc at sissa.it>
> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 46, Issue 12
> To: pw_forum at pwscf.org
> Message-ID: <20110405154612.xtjk8ix28ksw4cww at webmail.sissa.it>
> Content-Type: text/plain;       charset=ISO-8859-1;     DelSp="Yes";
>        format="flowed"
>
> Dear  bahaareh tavakoli nejad,
>
>   please make an effort to
>    1) provide a meaningful subject line
>    2) not reply including a full Digest email full of junk
>    3) provide your affiliation
>
>   In order to maximize your chance of getting an answer you should
> make it understandable and possibly sopecific.
>
>   HTH
>
>    stefano
>
> Quoting bahaareh tavakoli nejad <bahaartv at gmail.com>:
> .... AFTER TONS OF JUNK
> >
> > dear Gabriele
> > Ok!in this stage my question is about pseudopotentials in general no
> > software.
> > I guessed maybe one has information about various parameters in
> > pseudopotentials and know what are applications different kinds of them
> or
> > recommend me refrence.my question was'nt only Teter pseudopotential and
> are
> > general.it is irrational?
> >
>
>
>
> ----------------------------------------------------------------
>   SISSA Webmail https://webmail.sissa.it/
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>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 05 Apr 2011 16:35:15 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Problems with electrostatic corrections
>        (Makov-Payne    or density counter charge) for aperiodic systems in
> 4.2
>        version
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1302014115.6852.3.camel at fe12lx.fisica.uniud.it>
> Content-Type: text/plain
>
> On Tue, 2011-04-05 at 10:44 -0300, Eduardo Ariel Menendez Proupin wrote:
>
> > I guess some bug was discovered ans is not fixed yet.
>
> "bit-rotting" : if you leave a piece of code unattended, it will cease
> to work for no apparent reason.
>
> P.
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 05 Apr 2011 15:37:59 +0100
> From: Oliviero Andreussi <oliviero at MIT.EDU>
> Subject: Re: [Pw_forum] Problems with electrostatic corrections
>        (Makov-Payne or density counter charge) for aperiodic systems in 4.2
>        version
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4D9B2947.6020609 at mit.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> 1) Roughly speaking, eq. 15 of the original Makov-Payne paper express
> the energy of periodic system (E) in terms of the energy of the isolated
> system (E0) plus the energy of interaction between the periodic replicas
> (E11 and E12). Neglecting the fact that the E12 term has the wrong sing
> in the original equation (as it is stressed in a comment in the code),
> to obtain the energy of the isolated system you want to subtract E11 and
> E12 from your periodic total energy, as it is done in the code, i.e.
> E0=E-E11-E12.
>
> 2) The DCC correction was not bugged or bit-rotting, and, as far as I know,
> it was also working for 2D cases. It was removed from the code in order to
> clean it
> and make pw's compilation easier: this is because DCC required an external
> multigrid solver an a somehow cumbersome implementation. One of the
> developers of the original DCC code (Ismaila Dabo) is now working on a
> different version of the DCC that do not require multigrid solvers.
>
> Best,
>
> Oliviero Andreussi
>
> Postdoctoral Associate MIT-DMSE,
> 77 Massachusetts Ave, Office 13-4084,
> Cambridge, MA, 02139 USA
>
> Visiting Researcher, Oxford University,
> Departments of Materials, Rex Richards Building,
> Park Road, Oxford, Oxon, OX1 3PH, UK
>
> -------- Original Message --------
> >  Subject:     [Pw_forum] Problems with electrostatic corrections
> >  (Makov-Payne or density counter charge) for aperiodic systems in 4.2
> version
> >  Date:        Tue, 5 Apr 2011 13:33:22 +0100
> >  From:        ilyes hamdi<iiysidi at gmail.com>
> >  Reply-To:    PWSCF Forum<pw_forum at pwscf.org>
> >  To:  pw_forum at pwscf.org<pw_forum at pwscf.org>
> >
> >
> >
> >  Dear espresso users,
> >
> >  1) I'm a bit confused with the implementation of the Makov-Payne
> >  electrostatic corrections in PW/makov-payne.f90 in Version 4.2:
> >  - In their original paper, Makov and Payne define the first order
> >  correction E11 =  - \alpha * q^2/(2\epsilon* L). This quantity should be
> >  negative for cubic systems, however
> >  the writing statement in PW/makov-payne.f90 subroutine defines the
> >  correction to be -E11 (leading to a positive value).
> >  - The second order correction E12 is propertional to q Q/L^3 and is also
> >  defined as -E12 in the PW/makov-payne.f90 subroutine.
> >  - The total energy should be Etot = E0 + E11 + E12 = E0 - \alpha *
> >  q^2/(2\epsilon* L) + 2 \pi * q * Q / ( 3 \epsilon L^3), however it is
> >  implemented as E0-E11-E12.
> >
> >  2) Why the DCC correction is disabled in version 4.2? Indeed when
> >  setting asume_isolated = 'dcc' and&EE input parameters to their
> >  default  values, I obtain an error message "DCC correction is disabled".
> >  Looking in the PW/input.f90 subroutine, one found that the dcc
> >  correction is disabled by an immediate call to errore subroutine.
> >
> >  Please can any one verify if I'm correct or did I miss something.
> >
> >  Best regards
> >
> >
> >
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 05 Apr 2011 18:06:22 +0200
> From: Markus Meinert <meinert at physik.uni-bielefeld.de>
> Subject: [Pw_forum] Nonlinear scaling with pool parallelization
> To: pw_forum at pwscf.org
> Message-ID:
>        <
> 13591_1302019580_ZZh0n7G2X1ZlY.00_4D9B3DFE.9060400 at physik.uni-bielefeld.de
> >
>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> Dear QE users and developers,
>
> for some larger calculations I just obtained a small Beowulf type
> cluster, consisting of three machines with hexacore i7 CPUs, connected
> with gigabit ethernet. It runs Ubuntu 64bit, QE 4.2.1 is compiled with
> GCC 4.4, and I have compiled OpenMPI 1.4.3. The code is linked against
> the pre-compiled libatlas-corei7sse3 from Ubuntu.
>
> I want to perform calculations of quite large supercells for interface
> and surface studies of magnetic materials. Now, I'm testing the
> parallelization schemes. My understanding is that pool parallelization
> should scale approximately linearly with nodes. Indeed, the calculation
> of a bulk material scales nearly linearly with the number of nodes when
> I assign each node an individual pool. In contrast, if I do not assign
> pools, the calculations slow down extremely because of the communication
> overhead.
>
> Now we come to the strange part: the slab calculation. I did some quick
> timing tests which I would like to share with you. The times given in
> seconds are just the numbers the code provides when it runs (checked
> them however with htop).
>
> WITH pools:
> np      npool   setup   first iteration
> 6       1       108s    250s
> 12      2       78s     180s
> 18      3       69s     152s
>
> WITHOUT pools:
> np      setup   first iteration
> 6       108s    250s
> 12      75s     186s
> 18      59s     152s
>
> Without pools I have heavy load on the ethernet, but the calculations
> are about as fast as the ones with pools. With pools, there's almost no
> communication, apart from a few bursts. More importantly, the scaling of
> the calculation with pools is far from linear. With three machines, I
> get less than a factor of two in speed. The gain when going from two to
> three machines is just of the order of 25%.
>
> My program call is:
> mpirun -np 18 -hostfile ~/.mpi_hostfile
> ~/espresso/espresso-4.2.1/bin/pw.x -npool 3 -in pw.in | tee pw.out
>
> The pw.x program understands the call:
>
>      Parallel version (MPI), running on    18 processors
>      K-points division:     npool     =    3
>      R & G space division:  proc/pool =    6
>
> Can you explain this behavior? Is there anything I can tune to get a
> better scaling? Is there a known bottleneck for a setup like this? Can
> this be associated with the choice of k-point meshes? For bulk I have a
> shifted 8x8x8 mesh, for the slab I have a 8 8 1 1 1 0 setting.
>
> If you would like to have the input files to reproduce the problem,
> please tell me.
>
> With kind regards,
> Markus Meinert
>
>
> --
> Dipl.-Phys. Markus Meinert
>
> Thin Films and Physics of Nanostructures
> Department of Physics
> Bielefeld University
> Universit?tsstra?e 25
> 33615 Bielefeld
>
> Room D2-118
> e-mail: meinert at physik.uni-bielefeld.de
> Phone: +49 521 106 2661
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 05 Apr 2011 18:54:34 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Nonlinear scaling with pool parallelization
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1302022474.6852.36.camel at fe12lx.fisica.uniud.it>
> Content-Type: text/plain
>
> On Tue, 2011-04-05 at 18:06 +0200, Markus Meinert wrote:
>
> > For bulk I have a shifted 8x8x8 mesh, for the slab I have a 8 8 1 1 1 0
> setting.
>
> how many k-points? P.
> --
>  Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
>  Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>  Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 05 Apr 2011 19:54:35 +0200
> From: Markus Meinert <meinert at physik.uni-bielefeld.de>
> Subject: [Pw_forum] Nonlinear scaling with pool parallelization
> To: pw_forum at pwscf.org
> Message-ID:
>        <
> 17556_1302026072_ZZh0n0H4l0ks_.00_4D9B575B.4060208 at physik.uni-bielefeld.de
> >
>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> Sorry, I should go into a little bit more detail here. I used an
> _unshifted_ k-mesh. When I use a 8x8x8 mesh, yielding 58 points, I get a
> speedup of about 2 on three machines. With a 12x12x12 mesh with 144
> points the speedup becomes better (factor 2.6 for cpu time and 2.3 for
> WALL). I used to think that's because of communication. In the former
> case, an iteration takes less than a second. With more k points, the
> speedup converges slowly towards 3.
>
> The slab has 20 k points. But, since a single iteration takes about 100
> seconds, I do not see where the time is being spent, when the k points
> are independent.
>
> Regards,
> Markus
>
> --
> Dipl.-Phys. Markus Meinert
>
> Thin Films and Physics of Nanostructures
> Department of Physics
> Bielefeld University
> Universit?tsstra?e 25
> 33615 Bielefeld
>
> Room D2-118
> e-mail: meinert at physik.uni-bielefeld.de
> Phone: +49 521 106 2661
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 5 Apr 2011 21:54:02 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Nonlinear scaling with pool parallelization
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <65F016CA-33E7-47CA-A04B-3FCBCFCB143B at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
> On Apr 5, 2011, at 19:54 , Markus Meinert wrote:
>
> > I used an _unshifted_ k-mesh
>
> it doesn't matter if it is shifted or unshifted: only the number of k-
> points
> matters for k-point parallelization.
>
> > The slab has 20 k points.
>
> 20 k-points on 3 processors = 7+7+6: load balancing is not ideal.
> This is likely to be a minor factor, though.
>
> > But, since a single iteration takes about 100 seconds, I do not
> > see where the time is being spent, when the k points are independent.
>
> you do not see because you do not know where to look. Not that it
> is explained somewhere...have a look into the final report:
> * the time spent in "c_bands" and called routines is proportional to the
>   number of k-points, so it will scale linearly with the number of
> "k-point pools"
> * the time spent in "sum_band" is only in part proportional to the
> number
>   of k-points and will partially scale
> * the time spent in "v_of_rho", "newd", "mix_rho", is independent
> upon the
>   number of of k-points and will not scale at all
> * k-point parallelization does not reduce memory
> * The rest is usually irrelevant
> Also note that
> * FFT parallelization distributes most memory
> * FFT parallelization speeds up (with varying efficiency) almost all
> routines,
>   with the exception of "cdiaghg" or "rdiaghg"
> * linear-algebra parallelization (that you are not using) will (not
> always) speed
>   up   "cdiaghg" or "rdiaghg" and distribute more memory
> Alles klar?
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
>
> ------------------------------
>
> Message: 9
> Date: Tue, 5 Apr 2011 15:42:56 -0600
> From: Tram Bui <trambui at u.boisestate.edu>
> Subject: [Pw_forum] Generating ultra soft pseudopotential
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <BANLkTi=pmuBY4W3_84vsE_m1okCtMSg0rQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Folks,
>     I'm trying to build an input file for generating the Cs
> pseudopotential. when I run the ld1.x on my input file. I got an error
> message saying that i'm using the wrong core. would you help me with extra
> information of where I can find the help for how to choose the right core
> for some atoms such as in my case it is Cs.
>
> Thank you very much,
>
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
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> ------------------------------
>
> Message: 10
> Date: Tue, 5 Apr 2011 20:35:08 -0400
> From: Duy Le <ttduyle at gmail.com>
> Subject: Re: [Pw_forum] Generating ultra soft pseudopotential
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <BANLkTinwZhgYzbc+H_wsrxCPOO_SsJ=1tg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Some available PP of Cs can be found at
> http://charter.cnf.cornell.edu/psplist.php?element=Cs
> If you can not find what you need there, you can follow the
> instruction (videos and slides) July 25
> http://media.quantum-espresso.org/santa_barbara_2009_07/index.php
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Tue, Apr 5, 2011 at 5:42 PM, Tram Bui <trambui at u.boisestate.edu> wrote:
> > Dear Folks,
> > ???? I'm trying to build an input file for generating the Cs
> > pseudopotential. when I run the ld1.x on my input file. I got an error
> > message saying that i'm using the wrong core. would you help me with
> extra
> > information of where I can find the help for how to choose the right core
> > for some atoms such as in my case it is Cs.
> >
> > Thank you very much,
> > Tram Bui
> >
> > M.S. Materials Science & Engineering
> > trambui at u.boisestate.edu
> >
> >
> > _______________________________________________
> > 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
>
>
> End of Pw_forum Digest, Vol 46, Issue 15
> ****************************************
>
I'm trying calculate density of state and other quantities for SrS but i
have problems about concept of different parameters in pseudopotentials, for
example on top of Teter pseudopotential we have :


(Ar+3d10) + 4s2 4p6 5s0 4d0; rcs=rcp=rcd=1.7, no chem-hard, exnc(11);ecut
25/34
  38.00000  10.00000  950923      z,zion,pspdat
  4         3         2   2      2001    0
pspcod,pspxc,lmax,lloc,mmax,r2well
  0  0  0   2    1.69654886360351576          l,e99.0,e99.9,nproj,rcpsp
  .000 .000 .000 .000                         rms,ekb1,ekb2,epsatm
  1  0  0   2    1.69654886360351576          l,e99.0,e99.9,nproj,rcpsp
  .000 .000 .000 .000                         rms,ekb1,ekb2,epsatm
  2  0  0   0    1.69654886360351576          l,e99.0,e99.9,nproj,rcpsp
  .000 .000 .000 .000                         rms,ekb1,ekb2,epsatm
  .000   .000   .000                          rchrg,fchrg,qchrg
  0 = l
is the first line of this pseudopotenial means that only 8 valence electron
are used in calculations (for example calculation of density of states,
bandstructure....)and 4d and 5s orbitals are empty and don't participate in
calculation?

Thanks
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