[Pw_forum] Pw_forum Digest, Vol 93, Issue 14
Gul Rahman
gulrahman at qau.edu.pk
Tue Apr 14 16:23:03 CEST 2015
Thanks Dear
M.V.Kondrin
On Tuesday, April 14, 2015, <pw_forum-request at pwscf.org> wrote:
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> 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 <mambom1902 at yahoo.com>
> Subject: [Pw_forum] davcio problem again
> To: PWscf Forum <pw_forum at pwscf.org>
> Message-ID:
> <1765464840.2114723.1428930508286.JavaMail.yahoo at mail.yahoo.com>
> 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: mambom1902 at yahoo.com, l.duong at fkf.mpg.de
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> ------------------------------
>
> Message: 2
> Date: Mon, 13 Apr 2015 12:19:58 -0400
> From: Tianli Feng <tianli.feng2011 at gmail.com>
> Subject: Re: [Pw_forum] force convergence in vc-relax
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAAY=
65Ov7XcibYprcU2o6rWR+nAwnZkpaW62BNv3OvHY-_4D_A at mail.gmail.com>
> 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 <paolo.giannozzi at uniud.it
>
> 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
>> > > Pw_forum at pwscf.org
>> > > http://pwscf.org/mailman/listinfo/pw_forum
>> >
>> > _______________________________________________
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > 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
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
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> ------------------------------
>
> Message: 3
> Date: Mon, 13 Apr 2015 19:48:22 +0000
> From: Paolo Giannozzi <paolo.giannozzi at uniud.it>
> Subject: Re: [Pw_forum] force convergence in vc-relax
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1428954654934.11235 at uniud.it>
> 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: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf
of Tianli Feng <tianli.feng2011 at gmail.com>
> 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 <paolo.giannozzi at uniud.it
<mailto:paolo.giannozzi at uniud.it>> 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
>> > Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
>> > http://pwscf.org/mailman/listinfo/pw_forum
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
>> 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
> Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
> http://pwscf.org/mailman/listinfo/pw_forum
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> ------------------------------
>
> Message: 4
> Date: Tue, 14 Apr 2015 12:38:40 +0300
> From: MKondrin <mkondrin at hppi.troitsk.ru>
> Subject: Re: [Pw_forum] QE_Parallel
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <552CE020.1010406 at hppi.troitsk.ru>
> 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
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> ------------------------------
>
> _______________________________________________
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>
> 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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