Thanks Dear M.V.Kondrin
On Tuesday, April 14, 2015, <[email protected]> wrote: > Send Pw_forum mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://pwscf.org/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. davcio problem again (loc duong ding) > 2. Re: force convergence in vc-relax (Tianli Feng) > 3. Re: force convergence in vc-relax (Paolo Giannozzi) > 4. Re: QE_Parallel (MKondrin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Apr 2015 13:08:28 +0000 (UTC) > From: loc duong ding <[email protected]> > Subject: [Pw_forum] davcio problem again > To: PWscf Forum <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="utf-8" > > Dear all, > I know this question is on the list of FAQ of QE but it seems strange in my case. I have an error while doing phonon calculation. The error is: > > ?Representation??? 10????? 2 modes -E??? L_3? To be done > > ???? Representation??? 11????? 2 modes -E??? L_3? To be done > > ???? Representation??? 12????? 2 modes -E??? L_3? To be done > > > > ???? Alpha used in Ewald sum =?? 2.8000 > > ???? negative rho (up, down):? 2.186E-03 0.000E+00 > ???? PHONON?????? :??? 47.79s CPU??????? 55.67s WALL > > > > ???? Representation #? 1 mode #?? 1 > > ???? Self-consistent Calculation > ? > ???? Pert. #? 1: Fermi energy shift (Ry) =??? -1.3453E+00??? -2.1176E-22 > > ????? iter #?? 1 total cpu time :?? 118.4 secs?? av.it.:? 11.8 > ????? thresh= 1.000E-02 alpha_mix =? 0.100 |ddv_scf|^2 =? 8.305E-04 > ? > ? Error in routine davcio (22): > ???? error while writing from file "/pfs/work3/workspace/scratch/se3624-TiSe2-doping-0/dispersion-bilayer2/0.001/charge0/./_ph0/TiSe2-bi.0.001.0.dwf17?This error is suddenly appear while ph.x is running. I have checked the disk space as well as permission of writing. All of these is not the problem because I can do pw.x for relax and scf calculation in the same folder. The error is only happened in phonon calculation. > > Do you know where is? the code (subroutine) that contains this read- or write-statement for phonon calculation? I would like to send this subroutine to the cluster admin but I can not find it. > Could you give me any hint to overcome this issue?? > With many thanks,Loc Duong > > Best regards, > ----------------------------------------------- > Dinh Loc Duong , Ph.D > Postdoctoral Researcher, Department of Nanoscience > Max Planck Institute for Solid State Research > Heisenbergstrasse 1, D-70569 Stuttgart, Germany? ? ? ? ? ?? > Email: [email protected], [email protected] > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://pwscf.org/pipermail/pw_forum/attachments/20150413/1312b4be/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 13 Apr 2015 12:19:58 -0400 > From: Tianli Feng <[email protected]> > Subject: Re: [Pw_forum] force convergence in vc-relax > To: PWSCF Forum <[email protected]> > Message-ID: > <CAAY= [email protected]> > Content-Type: text/plain; charset="utf-8" > > Hi Florian, I have not got the issue resolved yet. > > Hi Paolo, How can we find the explanation in that code? Many thanks. > > Best wishes, > Tianli > ------------ > Tianli Feng > Mechanical Engineering, Purdue University > ---The truth is not what you see, but what it is. > > On Mon, Apr 13, 2015 at 4:10 AM, Paolo Giannozzi <[email protected] > > wrote: > >> On Mon, 2015-04-13 at 00:16 -0700, Florian Altvater wrote: >> >> > did this issue ever get resolved/answered? I would also be very >> > interested in a solution/explanation of the behavior. >> >> The explanation is available in the part of code that perform the >> convergence check on forces >> >> P. >> > I also get relaxations where individual forces are higher than the >> > threshold, without the line stating that "SCF correction compared to >> > forces is large", in case that would be a reason here. Also happens in >> > regular "relax" calculations. >> > >> > Thanks so much, >> > Florian >> > >> > -- >> > Florian Brown-Altvater >> > PhD Candidate >> > Neaton group >> > UC Berkeley/LBNL >> > >> > Am 08.04.2015 um 12:07 schrieb Tianli Feng: >> > >> > > Dear All, >> > > >> > > >> > > I would really appreciate if anyone can help to explain a output in >> > > relaxing a structure. I used vc-relax to relax a lattice >> > > with forc_conv_thr set as 1.0D-9. After 44 steps, the results >> > > converge as following: >> > > >> > > >> > > Forces acting on atoms (Ry/au): >> > > >> > > >> > > atom 1 type 1 force = 0.00000638 0.00000000 >> > > 0.00000092 >> > > atom 2 type 1 force = 0.00000602 0.00000000 >> > > 0.00000671 >> > > atom 3 type 1 force = -0.00000074 0.00000000 >> > > 0.00000243 >> > > atom 4 type 1 force = 0.00000358 0.00000000 >> > > -0.00000082 >> > > atom 5 type 2 force = -0.00000821 0.00000000 >> > > -0.00000732 >> > > atom 6 type 2 force = -0.00000635 0.00000000 >> > > -0.00000202 >> > > atom 7 type 2 force = 0.00000337 0.00000000 >> > > -0.00000058 >> > > atom 8 type 2 force = -0.00000406 0.00000000 >> > > 0.00000068 >> > > >> > > >> > > Total force = 0.000018 Total SCF correction = >> > > 0.000002 >> > > SCF correction compared to forces is large: reduce conv_thr to >> > > get better values >> > > >> > > >> > > bfgs converged in 44 scf cycles and 43 bfgs steps >> > > (criteria: energy < 1.0E-04, force < 1.0E-09, cell < >> > > 5.0E-01) >> > > >> > > >> > > The last line says the relaxation converges with force <1.0E-9, but >> > > I saw the forces acting on each atom are not smaller than 1e-9. Does >> > > anyone has experience on relaxing a lattice and know what is >> > > happening? Many thanks!! >> > > >> > > >> > > Sincerely, >> > > Best wishes, >> > > Tianli >> > > ------------ >> > > Tianli Feng >> > > Mechanical Engineering, Purdue University >> > > ---The truth is not what you see, but what it is. >> > > >> > > >> > > _______________________________________________ >> > > Pw_forum mailing list >> > > [email protected] >> > > http://pwscf.org/mailman/listinfo/pw_forum >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > [email protected] >> > http://pwscf.org/mailman/listinfo/pw_forum >> >> -- >> Paolo Giannozzi, Dept. Chemistry&Physics&Environment, >> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> _______________________________________________ >> Pw_forum mailing list >> [email protected] >> http://pwscf.org/mailman/listinfo/pw_forum >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://pwscf.org/pipermail/pw_forum/attachments/20150413/9cee22a6/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Mon, 13 Apr 2015 19:48:22 +0000 > From: Paolo Giannozzi <[email protected]> > Subject: Re: [Pw_forum] force convergence in vc-relax > To: PWSCF Forum <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > $ grep -n 'bfgs converged in' */*.f90 */*/*.f90 > > Modules/bfgs_module.f90:912: & FMT = '(/,5X,"bfgs converged in ",I3," scf cycles and ", & > > > Around line 912 of Modules/bfgs_module.f90, you find > > IF ( conv_bfgs ) THEN > ! > WRITE( UNIT = stdout, & > & FMT = '(/,5X,"bfgs converged in ",I3," scf cycles and ", & > & I3," bfgs steps")' ) scf_iter, bfgs_iter > > > You search for "conv_bfgs" and you find > > ! > ! ... convergence is checked here > ! > energy_error = ABS( energy_p - energy ) > grad_error = MAXVAL( ABS( MATMUL( TRANSPOSE(hinv_block), grad(1:n-9)) ) ) > conv_bfgs = energy_error < energy_thr > conv_bfgs = conv_bfgs .AND. ( grad_error < grad_thr ) > > > "grad_error" is the largest component of the gradient (i.e. forces; the last 9 values are stresses). You should figure out the relation between forces as printed in the output and "grad_error", via variables "grad" (presumably the forces) and "hinv_block" (a transformation matrix from cartesian to crystal coordinates, I guess). > > > Anyway: 10^{-9} is an exceedingly small threshold for forces. > > > Paolo > > ________________________________ > From: [email protected] <[email protected]> on behalf of Tianli Feng <[email protected]> > Sent: Monday, April 13, 2015 18:19 > To: PWSCF Forum > Subject: Re: [Pw_forum] force convergence in vc-relax > > Hi Florian, I have not got the issue resolved yet. > > Hi Paolo, How can we find the explanation in that code? Many thanks. > > Best wishes, > Tianli > ------------ > Tianli Feng > Mechanical Engineering, Purdue University > ---The truth is not what you see, but what it is. > > On Mon, Apr 13, 2015 at 4:10 AM, Paolo Giannozzi <[email protected] <mailto:[email protected]>> wrote: > On Mon, 2015-04-13 at 00:16 -0700, Florian Altvater wrote: > >> did this issue ever get resolved/answered? I would also be very >> interested in a solution/explanation of the behavior. > > The explanation is available in the part of code that perform the > convergence check on forces > > P. >> I also get relaxations where individual forces are higher than the >> threshold, without the line stating that "SCF correction compared to >> forces is large", in case that would be a reason here. Also happens in >> regular "relax" calculations. >> >> Thanks so much, >> Florian >> >> -- >> Florian Brown-Altvater >> PhD Candidate >> Neaton group >> UC Berkeley/LBNL >> >> Am 08.04.2015 um 12:07 schrieb Tianli Feng: >> >> > Dear All, >> > >> > >> > I would really appreciate if anyone can help to explain a output in >> > relaxing a structure. I used vc-relax to relax a lattice >> > with forc_conv_thr set as 1.0D-9. After 44 steps, the results >> > converge as following: >> > >> > >> > Forces acting on atoms (Ry/au): >> > >> > >> > atom 1 type 1 force = 0.00000638 0.00000000 >> > 0.00000092 >> > atom 2 type 1 force = 0.00000602 0.00000000 >> > 0.00000671 >> > atom 3 type 1 force = -0.00000074 0.00000000 >> > 0.00000243 >> > atom 4 type 1 force = 0.00000358 0.00000000 >> > -0.00000082 >> > atom 5 type 2 force = -0.00000821 0.00000000 >> > -0.00000732 >> > atom 6 type 2 force = -0.00000635 0.00000000 >> > -0.00000202 >> > atom 7 type 2 force = 0.00000337 0.00000000 >> > -0.00000058 >> > atom 8 type 2 force = -0.00000406 0.00000000 >> > 0.00000068 >> > >> > >> > Total force = 0.000018 Total SCF correction = >> > 0.000002 >> > SCF correction compared to forces is large: reduce conv_thr to >> > get better values >> > >> > >> > bfgs converged in 44 scf cycles and 43 bfgs steps >> > (criteria: energy < 1.0E-04, force < 1.0E-09, cell < >> > 5.0E-01) >> > >> > >> > The last line says the relaxation converges with force <1.0E-9, but >> > I saw the forces acting on each atom are not smaller than 1e-9. Does >> > anyone has experience on relaxing a lattice and know what is >> > happening? Many thanks!! >> > >> > >> > Sincerely, >> > Best wishes, >> > Tianli >> > ------------ >> > Tianli Feng >> > Mechanical Engineering, Purdue University >> > ---The truth is not what you see, but what it is. >> > >> > >> > _______________________________________________ >> > Pw_forum mailing list >> > [email protected]<mailto:[email protected]> >> > http://pwscf.org/mailman/listinfo/pw_forum >> >> _______________________________________________ >> Pw_forum mailing list >> [email protected]<mailto:[email protected]> >> http://pwscf.org/mailman/listinfo/pw_forum > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216<tel:%2B39-0432-558216>, fax +39-0432-558222<tel:%2B39-0432-558222> > > _______________________________________________ > Pw_forum mailing list > [email protected]<mailto:[email protected]> > http://pwscf.org/mailman/listinfo/pw_forum > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://pwscf.org/pipermail/pw_forum/attachments/20150413/a104c36d/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Tue, 14 Apr 2015 12:38:40 +0300 > From: MKondrin <[email protected]> > Subject: Re: [Pw_forum] QE_Parallel > To: PWSCF Forum <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Gul Rahman wrote: >> Dear All, >> As I mentioned in my previous e-mail that my QE is very slow when I >> run it in parallel. >> I have no problem on the same machine if I use some other code, e.g., >> SIESTA. >> I probably missing something in my compilation of QE. Please, have a >> look into the attached sys.make file that I used to compile QE. >> Also, if some one can share the parallel sys.make file. >> After the compilation, I just use >> mpirun -np 32 --hostfile machines ./mpi_script.sh >> where mpi_script.sh file just contain the command for pw.x (./pw.x < >> myfile.scf.in <http://myfile.scf.in> >OUT) >> Thanks, >> Gul >> >> -- > Dear Prof. Gul, > > Usually good parallelization requires interaction between mpirun and > quantum espresso programs (pw.x for example). pw.x mostly benefits from > parallelization of fftw algorithm but there is one gotcha (because fftw > is not massively parallel task). Too fine granularity of this > algorithm requires too much of data transfer between nodes which in case > of the low speed network (like gigabit ethernet) produces too much > overhead. As a rule 4-8 parallel process in this circumstances is a > ceiling. However if you job requires summation over different k-points > you may introduce additional parallelization over k-points (which does > not require too much of data transfer and so network bottleneck is > avoided) which is done by adding command line option like pw.x -npool k > ... (where k is the number of slices in k-grid). As a result the whole > task consist of only 32/4=8 "fftw-parallel" processes (which is what you > usually want). This information is written in the beginning of the > output file. > > There are some other tricks to obtain further parallelization which is > discussed in PW help files. But this is the most general. > > Best wishes, > > M.V.Kondrin (High Pressure Physics Institute RAS) >> >> >> Dr. Gul Rahman >> Assistant Professor, >> Department of Physics, >> Quaid-i-Azam University, >> Islamabad, Pakistan >> >> http://www.qau.edu.pk/profile.php?id=818020 >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Pw_forum mailing list >> [email protected] >> http://pwscf.org/mailman/listinfo/pw_forum > > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > End of Pw_forum Digest, Vol 93, Issue 14 > **************************************** > -- Dr. Gul Rahman Assistant Professor, Department of Physics, Quaid-i-Azam University, Islamabad, Pakistan http://www.qau.edu.pk/profile.php?id=818020
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