[Wien] [SPAM?] problem in mini for spinpolarized case
Laurence Marks
L-marks at northwestern.edu
Sun Dec 9 18:28:09 CET 2007
What is going on is the same as before, you no longer have
case.clmup/dn files. Why this is happening is not clear. One think I
note about your files is that new_super.clmsum is rather shorter than
your case.clmsum. Can you please check (by hand) that it has the same
number of LMs and plane wave coefficients. I am fairly sure that the
current clmaddsub will crash if these are different.
Maybe the clmaddsub code or the script clmextrapol is broken for
complex cases -- it works for non complex. I think Peter is rewriting
some of the logic in the min script so the -ex mode is safer so maybe
these issues will go away in the next release. One way around is to
recreate your case.clmup, case.clmdn and remove the -ex option from
when you run min.
On Dec 8, 2007 11:22 AM, Ravindran Ponniah
<ravindran.ponniah at kjemi.uio.no> wrote:
>
> Dear Wien users,
>
> As suggested by Laurence, I have now updated SRC_clmaddsub and still the
> mini job crash after 1 structural relaxation step. I will explain the
> problem in detail now.
>
> I have submitted a job as follows
>
> ###
> # Copy inpufiles to common scratch
> cp $WORK/*.in* $RUN
> cp $WORK/*.struct $RUN
> cp $WORK/*.klist* $RUN
> cp $WORK/*.kgen* $RUN
> cp $WORK/45k.clmsum $RUN/Mnsp1.clmsum
> cp $WORK/45k.clmup $RUN/Mnsp1.clmup
> cp $WORK/45k.clmdn $RUN/Mnsp1.clmdn
> cp $WORK/.min* $RUN
> cp $WORK/*.rsp* $RUN
>
> ###
> # Run program
> # Run program
> cp Mnsp1_15.struct Mnsp1.struct
> rm *super.clm*
> min -i 20 -s 1 -ex -j 'runsp_lapw -I -i 40 -fc 1.0 -it '
> save_lapw Mnsp1_15
> mv Mnsp1_15* $WORK
> ###
>
>
> The :log file looks
>
> > (min) options: -i 20 -s 1 -ex -j runsp_lapw -I -i 40 -fc 1.0 -it
> > (min) recover inm-file & call job runsp_lapw -I -i 40 -fc 1.0 -it
> > (runsp_lapw) options: -I -i 40 -fc 1.0 -it
> Sat Dec 8 01:56:35 CET 2007> (x) lapw0
> Sat Dec 8 01:56:54 CET 2007> (x) lapw1 -c -up
> Sat Dec 8 02:05:51 CET 2007> (x) lapw1 -c -dn
> Sat Dec 8 02:14:45 CET 2007> (x) lapw2 -c -up
> Sat Dec 8 02:16:43 CET 2007> (x) lapw2 -c -dn
> Sat Dec 8 02:18:26 CET 2007> (x) lcore -up
> Sat Dec 8 02:18:27 CET 2007> (x) lcore -dn
> ...
> ...
> Sat Dec 8 11:18:03 CET 2007> (x) lcore -up
> Sat Dec 8 11:18:04 CET 2007> (x) lcore -dn
> Sat Dec 8 11:18:05 CET 2007> (x) mixer
> Sat Dec 8 11:18:09 CET 2007> (x) mini Mnsp1 mini
> Sat Dec 8 11:18:10 CET 2007> (x) dstart -c
> Sat Dec 8 11:18:15 CET 2007> (x) dstart -c -up
> Sat Dec 8 11:18:18 CET 2007> (x) dstart -c -dn
> > (min) recover inm-file & call job runsp_lapw -I -i 40 -fc 1.0 -it
> > (runsp_lapw) options: -I -i 40 -fc 1.0 -it
> Sat Dec 8 11:18:22 CET 2007> (x) lapw0
> Sat Dec 8 11:18:36 CET 2007> (x) lapw1 -c -up
> >>> (min) status after runsp_lapw -I -i 40 -fc 1.0 -it \: 9 -> exit
> ######
>
> The dayfile is
>
> ###
> Calculating Mnsp1 in /global/work/ravi/92723.snowstorm.uit.no/Mnsp1
> on compute-9-7.local with PID 10908
>
> start (Sat Dec 8 11:18:22 CET 2007) with lapw0 (40/20 to go)
>
> cycle 1 (Sat Dec 8 11:18:22 CET 2007) (40/20 to go)
>
> > lapw0 (11:18:22) 11.420u 2.875s 0:14.38 99.3% 0+0k 0+0io 0pf+0w
> > lapw1 -c -up (11:18:36) 0.003u 0.010s 0:00.04 25.0% 0+0k 0+0io
> 2pf+0w
>
> > stop error
> ###
>
> The uplapw1.error is
>
> ###
> 'INILPW' - can't open unit: 18
> 'INILPW' - filename: Mnsp1.vspup
> 'INILPW' - status: old form: formatted
> 'LAPW1' - INILPW aborted unsuccessfully.
> ###
>
> It appears that the case.clmup/dn files are not created from dstart after
> one structural relaxation. ls -lt shows that
>
> ###
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 lapw0.error
> -rw-rw-r-- 1 ravi ravi 11990 Dec 8 11:18 :log
> -rw-rw-r-- 1 ravi ravi 398 Dec 8 11:18 Mnsp1.dayfile
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 Mnsp1.dmatdn_old
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 Mnsp1.dmatud_old
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 Mnsp1.dmatup_old
> -rw-rw-r-- 1 ravi ravi 61880 Dec 8 11:18 Mnsp1.output0
> -rw-rw-r-- 1 ravi ravi 764260 Dec 8 11:18 Mnsp1.vns
> -rw-rw-r-- 1 ravi ravi 31473 Dec 8 11:18 Mnsp1.vsp
> -rw-rw-r-- 1 ravi ravi 563 Dec 8 11:18 uplapw1.def
> -rw-rw-r-- 1 ravi ravi 282 Dec 8 11:18 uplapw1.error
> -rw-rw-r-- 1 ravi ravi 3535 Dec 8 11:18 Mnsp1.scf0
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 dndstart.error
> -rw-rw-r-- 1 ravi ravi 965 Dec 8 11:18 lapw0.def
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 Mnsp1.clmdn
> -rw-rw-r-- 1 ravi ravi 848898 Dec 8 11:18 Mnsp1.clmsum
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 Mnsp1.clmup
> -rw-rw-r-- 1 ravi ravi 453 Dec 8 11:18 Mnsp1.in2c
> -rw-rw-r-- 1 ravi ravi 177 Dec 8 11:18 Mnsp1.in2_ls
> -rw-rw-r-- 1 ravi ravi 453 Dec 8 11:18 Mnsp1.in2_st
> -rw-rw-r-- 1 ravi ravi 276 Dec 8 11:18 Mnsp1.in2_sy
> -rw-rw-r-- 1 ravi ravi 145524 Dec 8 11:18 Mnsp1.outputddn
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 Mnsp1.vnsdn
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 Mnsp1.vspdn
> -rw-rw-r-- 1 ravi ravi 795665 Dec 8 11:18 new_super.clmdn
> -rw-rw-r-- 1 ravi ravi 403 Dec 8 11:18 dndstart.def
> -rw-rw-r-- 1 ravi ravi 142 Dec 8 11:18 Mnsp1.in0_std
> -rw-rw-r-- 1 ravi ravi 145524 Dec 8 11:18 Mnsp1.outputdup
> -rw-rw-r-- 1 ravi ravi 848898 Dec 8 11:18 old.clmdn
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 updstart.error
> -rw-rw-r-- 1 ravi ravi 795665 Dec 8 11:18 new_super.clmup
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 dstart.error
> -rw-rw-r-- 1 ravi ravi 145524 Dec 8 11:18 Mnsp1.outputd
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 Mnsp1.test
> -rw-rw-r-- 1 ravi ravi 848898 Dec 8 11:18 old.clmup
> -rw-rw-r-- 1 ravi ravi 403 Dec 8 11:18 updstart.def
> -rw-rw-r-- 1 ravi ravi 795665 Dec 8 11:18 new_super.clmsum
> -rw-rw-r-- 1 ravi ravi 346 Dec 8 11:18 dstart.def
> -rw-rw-r-- 1 ravi ravi 0 Dec 8 11:18 mini.error
> -rw-rw-r-- 1 ravi ravi 848898 Dec 8 11:18 Mnsp1_1.clmdn
> -rw-rw-r-- 1 ravi ravi 848898 Dec 8 11:18 Mnsp1_1.clmsum
> -rw-rw-r-- 1 ravi ravi 848898 Dec 8 11:18 Mnsp1_1.clmup
> -rw-rw-r-- 1 ravi ravi 3159 Dec 8 11:18 Mnsp1_1.struct
> ###
>
> I am able to create case.clmup/dn files from dstart interactively after
> the job crash. I am unable to understand why case.clmup/dn files were not
> created after one structural relaxation (through mini) eventhough dstart
> -c -up and dstart -c -dn ran successfully (see dstart.error is empty). But, if I run
> dstart interactively after the job crash I am able to create case.clmup/dn
> files?!
>
> Could you kindly explain to me why mini crash after 1 structural
> relaxation step in spin-polarized cases?
>
> Best regards
> Ravi
>
>
> On Thu, 6 Dec 2007, Laurence Marks wrote:
>
> > The lapw0 program looks for non-zero case.clmup and case.clmdn
> > (MnCosp.clmup & dn) in order to know if it should run spin-polarized
> > or not. If spin-polarized then it creates the files case.vspup/dn for
> > the spherical parts of the potential, and case.vnsup/dn for the
> > non-spherical. If not spin polarized it will only create case.vsp and
> > case.vns. From the looks of it lapw0 ran non-polarized. Please check
> > if you have non-zero length case.clmup & clmdn. If they are zero
> > (which I suspect) have a look at the error files for dstart since this
> > probably crashed. You can then try running them by hand (x dstart -c ;
> > x dstart -c -up ; x dstart -c -dn) to see if this works or crashes for
> > some reason. If it crashes (which I suspect it will) you will have to
> > find out why -- perhaps rerun lstart (x lstart) again.
> >
> > If this works, copy them to new_super.clmsum, new_super.clmup,
> > new_super.clmdn and then copy your previous density files (probably
> > MnCosp_1.clmsum etc) to MnCosp.clmsum & clmup/clmdn. Then restart the
> > minimization but add "-NI" so it will keep going from the previous
> > cycle.
> >
> > This will put you back with appropriate files, although it might not
> > cure all the problems.
> >
> > N.B., as I may have mentioned earlier, check the directory
> > SRC_clmaddsub since the earliest version had a bug for spin-polarized
> > cases.
> >
> > On Dec 6, 2007 8:29 AM, Ravindran Ponniah
> > <ravindran.ponniah at kjemi.uio.no> wrote:
> >>
> >> Dear Wien users,
> >>
> >> As suggested by Peter Blaha I have now done structural relaxation by rm
> >> *super.clmsum/up/dn before the mini. i.e.
> >>
> >> ##
> >> rm *super.clm*
> >> cp MnCosp_15.struct MnCosp.struct
> >> min -i 20 -s 1 -ex -j 'runsp_lapw -I -i 40 -fc 1.0 -it '
> >> save_lapw MnCosp15
> >> mv MnCosp15* $WORK
> >> ###
> >>
> >> This time the mini compleated the one step in structural relaxation
> >>
> >>
> >> ##
> >>> (min) options: -i 20 -s 1 -ex -j runsp_lapw -I -i 40 -fc 1.0 -it
> >>> (min) recover inm-file & call job runsp_lapw -I -i 40 -fc 1.0 -it
> >>> (runsp_lapw) options: -I -i 40 -fc 1.0 -it
> >> Wed Dec 5 20:43:04 CET 2007> (x) lapw0
> >> Wed Dec 5 20:43:21 CET 2007> (x) lapw1 -c -up
> >> Wed Dec 5 20:51:03 CET 2007> (x) lapw1 -c -dn
> >> Wed Dec 5 20:58:41 CET 2007> (x) lapw2 -c -up
> >> Wed Dec 5 21:00:50 CET 2007> (x) lapw2 -c -dn
> >> Wed Dec 5 21:02:26 CET 2007> (x) lcore -up
> >> Wed Dec 5 21:02:27 CET 2007> (x) lcore -dn
> >> Wed Dec 5 21:02:28 CET 2007> (x) mixer
> >> ...
> >> ...
> >> Thu Dec 6 01:45:30 CET 2007> (x) lapw0
> >> Thu Dec 6 01:45:45 CET 2007> (x) lapw1 -it -c -up
> >> Thu Dec 6 01:52:03 CET 2007> (x) lapw1 -it -c -dn
> >> Thu Dec 6 01:58:17 CET 2007> (x) lapw2 -c -up
> >> Thu Dec 6 02:04:08 CET 2007> (x) lapw2 -c -dn
> >> Thu Dec 6 02:08:14 CET 2007> (x) lcore -up
> >> Thu Dec 6 02:08:15 CET 2007> (x) lcore -dn
> >> Thu Dec 6 02:08:17 CET 2007> (x) mixer
> >> Thu Dec 6 02:08:21 CET 2007> (x) mini MnCosp mini
> >> Thu Dec 6 02:08:24 CET 2007> (x) dstart -c
> >> Thu Dec 6 02:08:29 CET 2007> (x) dstart -c -up
> >> Thu Dec 6 02:08:32 CET 2007> (x) dstart -c -dn
> >>> (min) recover inm-file & call job runsp_lapw -I -i 40 -fc 1.0 -it
> >>> (runsp_lapw) options: -I -i 40 -fc 1.0 -it
> >> Thu Dec 6 02:08:36 CET 2007> (x) lapw0
> >> Thu Dec 6 02:08:51 CET 2007> (x) lapw1 -c -up
> >>>>> (min) status after runsp_lapw -I -i 40 -fc 1.0 -it \: 9 -> exit
> >> ####
> >>
> >> and then after lapw0 it crashed with the error message
> >>
> >> ##
> >> MIXER END
> >>>> (mini) arrived at end -> exit
> >> DSTART ENDS
> >> DSTART ENDS
> >> DSTART ENDS
> >> LAPW0 END
> >> LAPW1 - Error
> >> ...
> >> ##
> >>
> >> The uplapw1.error file show that
> >>
> >> ##
> >> 'INILPW' - can't open unit: 18
> >> 'INILPW' - filename: MnCosp.vspup
> >> 'INILPW' - status: old form: formatted
> >> 'LAPW1' - INILPW aborted unsuccessfully.
> >> ##
> >>
> >> I have no case.vaspup file in the working directory. see
> >>
> >> -rw-rw-r-- 1 ravi ravi 31473 MnCosp.vsp
> >> -rw-rw-r-- 1 ravi ravi 0 MnCosp.vspdn
> >> -rw-rw-r-- 1 ravi ravi 31473 MnCosp.vspdn_old
> >> -rw-rw-r-- 1 ravi ravi 31473 MnCosp.vspup_old
> >> -rw-rw-r-- 1 ravi ravi 31533 MnCosp.vspdn_st
> >> -rw-rw-r-- 1 ravi ravi 31533 MnCosp.vsp_st
> >>
> >> Do you know why lapw1 -up crashed in the second structural relaxation
> >> step? (I have no problem in structural relaxation for nonspinpolarized
> >> cases).
> >>
> >> Best regards
> >> Ravi
> >>
> >> On Tue, 4 Dec 2007, Peter Blaha wrote:
> >>
> >>> In the next version these problems will be fixed. (min_lapw will always
> >>> create with "x dstart -super" the necessary files automatically). I hope
> >>> to release this soon.
> >>>
> >>> In the present version, the required densities of superposed atoms is
> >>> done only at the end of init_lapw (and in clmextrapol for the new struct
> >>> file).
> >>> In your case, the new volume does not have a proper superposed density
> >>> and thus leads to the crash.
> >>>
> >>> At the moment I'd simply remove *super.clmsum/up/dn before the next
> >>> volume starts.
> >>>
> >> _______________________________________________
> >> Wien mailing list
> >> Wien at zeus.theochem.tuwien.ac.at
> >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> >>
> >
> >
> >
> > --
> > Laurence Marks
> > Department of Materials Science and Engineering
> > MSE Rm 2036 Cook Hall
> > 2220 N Campus Drive
> > Northwestern University
> > Evanston, IL 60208, USA
> > Tel: (847) 491-3996 Fax: (847) 491-7820
> > email: L-marks at northwestern dot edu
> > Web: www.numis.northwestern.edu
> > Commission on Electron Diffraction of IUCR
> > www.numis.northwestern.edu/IUCR_CED
> > _______________________________________________
> > Wien mailing list
> > Wien at zeus.theochem.tuwien.ac.at
> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> >
> _______________________________________________
> Wien mailing list
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>
--
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Commission on Electron Diffraction of IUCR
www.numis.northwestern.edu/IUCR_CED
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