On Tue, Apr 5, 2011 at 5:35 PM, <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. 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110405/a96b1f24/attachment-0001.htm > > ------------------------------ > > 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/ > Powered by Horde http://www.horde.org/ > > > > > ------------------------------ > > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110405/3dc4c2e3/attachment-0001.htm > > ------------------------------ > > 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? 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