[Wien] DOS and XANES
Dear Chikashi, Concerning your first question, you should check the parameters in param.inc of lapw1. These parameters are explained in the user guide p.87. Particularly, a maximum value of energy eigenvalues is defined in this file (NUME). If you want to calculate more states than the number specified in param.inc file by NUME, you will not be able to have it. If NUME is too small, you simply have to increase this value using siteconfig. Concerning the second question, in2 file is very nicely explained in the userguide p.93. Read carefully this part of the book and I believe that you will better understand how to use this file. With my best Regards Xavier ? a e'crit : Dear Wien2k users My name is Chikashi Suzuki, from Japan Atomic Energy Agency. I am running wien version WIEN2k 07.3. I calculate Am LIII Xay absoprtion spectra (XAS) of AmO2. I would like analyze this XAS considering the core-hole using the supercell (Am32O64). In order to analyze this XAS, I have to plot density of states (DOS) and XAS form Fermi level up to 70 eV. Howerver, usig the supercells of AmO2 (Am32O64) and CaF2 (Ca32O64), DOS and XAS can be plotted only up to 20-25 eV, though nband and emax in case.in1 are extended. Am32O64 nband:2000, emax:7.0 (Ry) Ca32O64 nband:1500, emax:7.0 (Ry) How should I do in order to plot DOS and XAS up to 70 eV? Or, cannot DOS and XAS be plotted up to 70 eV using WIEN2k 07.3? Or. can those be plotted up to 70 eV using WIEN2 of the latest version? In additon, in order to depict the charge density in the unoccupied range within the specific energy window (for example, 2 to 4.5 eV), case.in2 must be editted using WIEN2k 07.3 in addtion to run x lapw2 -all XX YY (where XX YY specifies the E-range) However, I don't know what is described in case.in2. Would you mind explainig what is described in case.in2 in detail, or sending the example for case in2 ? *** Dr. Chikashi Suzuki Research Group for Nuclear Materials Modeling Nuclear Science and Engineering Directorate Japan Atomic Energy Agency Tokai-mura, Naka-gun, Ibaraki-ken 319-1195, Japan Tel: +81-29-282-6373 Fax: +81-29-282-6122 Email: suzuki.chikashi at jaea.go.jp E-mail?suzuki.chikashi at jaea.go.jp *** ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] Surface states splitting
I've never explicitly shown the spin-splitting. What you can easily see is that when one adds SO, that the degenerate bands split. I'm not sure, but I think with the present WIEN2k implementation you cannot easily get this kind of spin-projection, since there is always some kind of symmetrization. Eventually it works when you break inversion symmetry and do spin-polarized calculations (putting M in the correct direction!?), but I'm not sure about that. In any case, the bandstructure and the SO splitting is perfectly ok with normal calculations. In Your paper PHYSICAL REVIEW B, VOLUME 65, 033407 in Fig. 1 you present two surface state dispersion curves for opposite spin projections. I am trying to repeat this for the W(110) surface. May I ask you to list the key points of your calculation? How is it possible to recognize the spin projection for surface states? Sincerely yours, Oleg Artamonov. ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ --
[Wien] Error during compilation
Do what it asks you to do: Check file compile.msg in the corresponding SRC_* directory for the compilation log and more info on any compilation problem. Look for instance in SRC_lapw1/compile.msg and read the detailed error messages there. Stefaan Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
[Wien] Surface states splitting
- Original Message - From: Oleg Artamonov To: A Mailing list for WIEN2k users Sent: Thursday, October 09, 2008 6:06 PM Subject: [Wien] Surface states splitting Dear Peter Blaha, In Your paper PHYSICAL REVIEW B, VOLUME 65, 033407 in Fig. 1 you present two surface state dispersion curves for opposite spin projections. I am trying to repeat this for the W(110) surface. May I ask you to list the key points of your calculation? How is it possible to recognize the spin projection for surface states? Sincerely yours, Oleg Artamonov. -- ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20081010/10e7133b/attachment-0001.html
[Wien] Compilation: how to specify a path to mpif.h?
Dear Robert and Laurence, Thank you for your advice, it did help. Now I have another question, let me post it here. I've successfully compiled lapw0 and lapw2 in parallel, but still have problems with lapw1 on the link stage: make PARALLEL='-DParallel' TYPE='REAL' TYPE_COMMENT='\!_REAL' \ ./lapw1_mpi FORT=/opt/mpich/pgi64/ch_p4/bin/mpif90 FFLAGS=' -Mfreeform -fast -Kieee '-DParallel'' make[1]: Entering directory `/home/users/natanzon/dvd/wien2k/SRC_lapw1' /opt/mpich/pgi64/ch_p4/bin/mpif90 -o ./lapw1_mpi abc.o atpar.o bandv1.o calkpt.o cbcomb.o coors.o cputim.o dblr2k.o dgeqrl.o dgewy.o dgewyg.o dlbrfg.o dsbein1.o dscgst.o dstebz2.o dsyevx2.o dsyr2m.o dsyrb4.o dsyrb5l.o dsyrdt4.o dsywyv.o dsyxev4.o dvbes1.o eisps.o errclr.o errflg.o forfhs.o gaunt1.o gaunt2.o gbass.o gtfnam.o hamilt.o hns.o horb.o inikpt.o inilpw.o lapw1.o latgen.o lmsort.o locdef.o lohns.o lopw.o matmm.o modules.o nn.o outerr.o outwin.o prtkpt.o prtres.o pzheevx16.o rdswar.o rint13.o rotate.o rotdef.o seclit.o seclr4.o seclr5.o select.o service.o setkpt.o setwar.o sphbes.o stern.o tapewf.o ustphx.o vectf.o warpin.o wfpnt.o wfpnt1.o ylm.o zhcgst.o zheevx2.o zher2m.o jacdavblock.o make_albl.o global2local.o par_syrk.o my_dsygst.o refblas_dtrsm.o seclit_par.o pdsyevx17.o pdstebz17.o -L/home/users/natanzon/acml/pgi64/lib -L/opt/pgi/linux86-64/7.1-4/libso/ -L/opt/pgi/linux86-64/7.1-4/libso -L/opt/mpich/pgi64/ch_p4/lib -L/home/banatanz/acml/pgi64_mp/lib -lpgmp -lpgbind -lacml_mp -lacml_mv -lmpich modules.o: In function `parallel_init_parallel_': modules_tmp_.F:(.text+0x1ea): undefined reference to `sl_init_' modules_tmp_.F:(.text+0x3b2): undefined reference to `sl_init_' modules.o: In function `parallel_init_parallelmatrices_': modules_tmp_.F:(.text+0x64f): undefined reference to `blacs_gridinfo_' modules_tmp_.F:(.text+0x694): undefined reference to `descinit_' modules_tmp_.F:(.text+0x6b3): undefined reference to `blacs_gridinfo_' modules_tmp_.F:(.text+0x6d1): undefined reference to `numroc_' modules_tmp_.F:(.text+0x6fe): undefined reference to `numroc_' modules_tmp_.F:(.text+0x72b): undefined reference to `numroc_' modules_tmp_.F:(.text+0x781): undefined reference to `descinit_' modules_tmp_.F:(.text+0x7c6): undefined reference to `descinit_' modules.o: In function `lapw_timer_init_all_timer_': modules_tmp_.F:(.text+0x865): undefined reference to `slboot_' ... and many more error messages like this. I suppose that this is because of lack of some libraries so I'be glad if you tell me which ones. The important lines of the Makefile for lapw1 are the following: FC = /opt/pgi/linux86-64/7.1-4/bin/pgf90 MPF = /opt/mpich/pgi64/ch_p4/bin/mpif90 CC = /opt/pgi/linux86-64/7.1-4/bin/pgcc FOPT = -Mfreeform -fast -Kieee FPOPT = -Mfreeform -fast -Kieee DParallel = '-DParallel' FGEN = $(PARALLEL) LDFLAGS = -L/home/users/natanzon/acml/pgi64/lib -L/opt/pgi/linux86-64/7.1-4/libso/ R_LIBS = -L/home/users/natanzon/acml/pgi64/lib -lacml C_LIBS = $(R_LIBS) RP_LIBS = -L/opt/pgi/linux86-64/7.1-4/libso -L/opt/mpich/pgi64/ch_p4/lib -L/home/banatanz/acml/pgi64_mp/lib -lpgmp -lpgbind -lacml_mp -lacml_mv -lmpich CP_LIBS = $(RP_LIBS) DESTDIR = . with kind regards, Yurko 2008/10/9 Robert Laskowski rolask at theochem.tuwien.ac.at: Hi, did you compiled it using mpif90 script, usually this should be set the enviroment for mpi during compilation. regards Robert On Wednesday 08 October 2008 17:04:37 Yurko Natanzon wrote: Dear wien2k users, I've successfully compiled Wien2k and now want to recompile it for parallel execution. I have everything required for this (mpich, scalapack). It seems, only lapw0, lapw1 and lapw2 should be recompiled, yes? So, I get the errors like this: PGF90-S-0017-Unable to open include file: mpif.h (rean0.F: 23) I know where mpif.h is located but how to specify a path? I've tried it in a different ways, but with no success. So i ended up in modifying .f files by hand replacing the code: #ifdef Parallel include 'mpif.h' #endif by the following: #ifdef Parallel include '/opt/mpich/pgi64/ch_p4/include/mpif.h' #endif It seems to work, but this is not convenient, especially if i want to install updates. So, could you propose me how to do it in siteconfig? My siteconfig settings for parralel execution are shown below: shared memory: yes compiler: /opt/pgi/linux86-64/7.0/bin/pgf95 RP RP_LIB(SCALAPACK+PBLAS): -L/home/users/natanzon/dvd/siesta/lib-pgf -L/opt/mpich/pgi64/ch_p4/lib -lblacs -lblacsF77init -lblacsCinit -lblacsF77init -lblacs -lscalapack -lmpich FP FPOPT(par.comp.options): -Mfreeform -fast -Kieee -Wl, -R/opt/mpich/pgi64/ch_p4/include I have a Linux cluster with AMD Opterons, pgf compiler, mpich and ACML libraries installed. regards, Yurko -- Dr Robert Laskowski Vienna University of Technology, Institute of Materials Chemistry, Getreidemarkt 9/165-TC, A-1060 Vienna tel. +43 1 58801 15686 Fax +43 1 58801 15698 ___ Wien
[Wien] Compilation: how to specify a path to mpif.h?
What you want to do for a problem such as this is use google (or some other search engine), then follow the path of links for an answer. A google search on blacs_gridinfo for instance will show that this is a scalapack routine (google scalapack as well if needed). This is a set of routines that you need in addition to an mpi compiler; a version of the lapack routines that works across many computers. (lapw0 does not need this, and I guess lapw2 does not as well although I have not checked in detail.) Best is an optimized library; I don't know exactly what you have so you might have to compile it yourself. On Fri, Oct 10, 2008 at 5:50 AM, Yurko Natanzon yurko.natanzon at gmail.com wrote: Dear Robert and Laurence, Thank you for your advice, it did help. Now I have another question, let me post it here. I've successfully compiled lapw0 and lapw2 in parallel, but still have problems with lapw1 on the link stage: make PARALLEL='-DParallel' TYPE='REAL' TYPE_COMMENT='\!_REAL' \ ./lapw1_mpi FORT=/opt/mpich/pgi64/ch_p4/bin/mpif90 FFLAGS=' -Mfreeform -fast -Kieee '-DParallel'' make[1]: Entering directory `/home/users/natanzon/dvd/wien2k/SRC_lapw1' /opt/mpich/pgi64/ch_p4/bin/mpif90 -o ./lapw1_mpi abc.o atpar.o bandv1.o calkpt.o cbcomb.o coors.o cputim.o dblr2k.o dgeqrl.o dgewy.o dgewyg.o dlbrfg.o dsbein1.o dscgst.o dstebz2.o dsyevx2.o dsyr2m.o dsyrb4.o dsyrb5l.o dsyrdt4.o dsywyv.o dsyxev4.o dvbes1.o eisps.o errclr.o errflg.o forfhs.o gaunt1.o gaunt2.o gbass.o gtfnam.o hamilt.o hns.o horb.o inikpt.o inilpw.o lapw1.o latgen.o lmsort.o locdef.o lohns.o lopw.o matmm.o modules.o nn.o outerr.o outwin.o prtkpt.o prtres.o pzheevx16.o rdswar.o rint13.o rotate.o rotdef.o seclit.o seclr4.o seclr5.o select.o service.o setkpt.o setwar.o sphbes.o stern.o tapewf.o ustphx.o vectf.o warpin.o wfpnt.o wfpnt1.o ylm.o zhcgst.o zheevx2.o zher2m.o jacdavblock.o make_albl.o global2local.o par_syrk.o my_dsygst.o refblas_dtrsm.o seclit_par.o pdsyevx17.o pdstebz17.o -L/home/users/natanzon/acml/pgi64/lib -L/opt/pgi/linux86-64/7.1-4/libso/ -L/opt/pgi/linux86-64/7.1-4/libso -L/opt/mpich/pgi64/ch_p4/lib -L/home/banatanz/acml/pgi64_mp/lib -lpgmp -lpgbind -lacml_mp -lacml_mv -lmpich modules.o: In function `parallel_init_parallel_': modules_tmp_.F:(.text+0x1ea): undefined reference to `sl_init_' modules_tmp_.F:(.text+0x3b2): undefined reference to `sl_init_' modules.o: In function `parallel_init_parallelmatrices_': modules_tmp_.F:(.text+0x64f): undefined reference to `blacs_gridinfo_' modules_tmp_.F:(.text+0x694): undefined reference to `descinit_' modules_tmp_.F:(.text+0x6b3): undefined reference to `blacs_gridinfo_' modules_tmp_.F:(.text+0x6d1): undefined reference to `numroc_' modules_tmp_.F:(.text+0x6fe): undefined reference to `numroc_' modules_tmp_.F:(.text+0x72b): undefined reference to `numroc_' modules_tmp_.F:(.text+0x781): undefined reference to `descinit_' modules_tmp_.F:(.text+0x7c6): undefined reference to `descinit_' modules.o: In function `lapw_timer_init_all_timer_': modules_tmp_.F:(.text+0x865): undefined reference to `slboot_' ... and many more error messages like this. I suppose that this is because of lack of some libraries so I'be glad if you tell me which ones. The important lines of the Makefile for lapw1 are the following: FC = /opt/pgi/linux86-64/7.1-4/bin/pgf90 MPF = /opt/mpich/pgi64/ch_p4/bin/mpif90 CC = /opt/pgi/linux86-64/7.1-4/bin/pgcc FOPT = -Mfreeform -fast -Kieee FPOPT = -Mfreeform -fast -Kieee DParallel = '-DParallel' FGEN = $(PARALLEL) LDFLAGS = -L/home/users/natanzon/acml/pgi64/lib -L/opt/pgi/linux86-64/7.1-4/libso/ R_LIBS = -L/home/users/natanzon/acml/pgi64/lib -lacml C_LIBS = $(R_LIBS) RP_LIBS = -L/opt/pgi/linux86-64/7.1-4/libso -L/opt/mpich/pgi64/ch_p4/lib -L/home/banatanz/acml/pgi64_mp/lib -lpgmp -lpgbind -lacml_mp -lacml_mv -lmpich CP_LIBS = $(RP_LIBS) DESTDIR = . with kind regards, Yurko 2008/10/9 Robert Laskowski rolask at theochem.tuwien.ac.at: Hi, did you compiled it using mpif90 script, usually this should be set the enviroment for mpi during compilation. regards Robert On Wednesday 08 October 2008 17:04:37 Yurko Natanzon wrote: Dear wien2k users, I've successfully compiled Wien2k and now want to recompile it for parallel execution. I have everything required for this (mpich, scalapack). It seems, only lapw0, lapw1 and lapw2 should be recompiled, yes? So, I get the errors like this: PGF90-S-0017-Unable to open include file: mpif.h (rean0.F: 23) I know where mpif.h is located but how to specify a path? I've tried it in a different ways, but with no success. So i ended up in modifying .f files by hand replacing the code: #ifdef Parallel include 'mpif.h' #endif by the following: #ifdef Parallel include '/opt/mpich/pgi64/ch_p4/include/mpif.h' #endif It seems to work, but this is not convenient, especially if i want to install updates. So, could you propose me how to do it in siteconfig? My
[Wien] lapw1 runs too slow for H2 molecule
Dear wien2k users, I'm running a simple exercise with H2 molecule located in the middle of a cubic box with a=15 Bohr. the H-H bond length is set to about 0.75 Ang and RMT radus is 0.71 (also the smaller values were tested). The problem is that the calculation is too long. It takes 40 minutes for LAPW1 to run: :log (runsp_lapw) options: Fri Oct 10 11:41:58 CEST 2008 (x) lapw0 Fri Oct 10 11:42:21 CEST 2008 (x) lapw1 -c -up Fri Oct 10 12:20:05 CEST 2008 (x) lapw1 -c -dn Fri Oct 10 12:58:24 CEST 2008 (x) lapw2 -c -up Fri Oct 10 12:58:28 CEST 2008 (x) lapw2 -c -dn Fri Oct 10 12:58:31 CEST 2008 (x) lcore -up Fri Oct 10 12:58:31 CEST 2008 (x) lcore -dn Fri Oct 10 12:58:31 CEST 2008 (x) mixer For comparison, the same calculation for one H atom in the box takes 3 seconds (lapw1), for CoO (a=8 Bohr) - just 12 seconds. I used init_lapw -numk 1 -vxc 13 I post my in0 and in1 files as well as a struct file: --in0 TOT 13(5...CA-LDA, 13...PBE-GGA, 11...WC-GGA) NR2V IFFT (R2V) -1 -1 -11.00min IFFT-parameters, enhancement factor #changed the default values because of IFFT errors ---in1c WFFIL(WFPRI, SUPWF) 7.00 104 (R-MT*K-MAX; MAX L IN WF, V-NMT 0.301 0 (GLOBAL E-PARAMETER WITH n OTHER CHOICES, global APW/LAPW) 00.30 0.000 CONT 1 0.301 0 (GLOBAL E-PARAMETER WITH n OTHER CHOICES, global APW/LAPW) 00.30 0.000 CONT 1 K-VECTORS FROM UNIT:4 -9.0 2.0 7 emin/emax/nband struct file h2 molecule P LATTICE,NONEQUIV.ATOMS: 2 MODE OF CALC=RELA unit=bohr 15.117815 15.117815 15.117815 90.00 90.00 90.00 ATOM -1: X=0.4530 Y=0.5000 Z=0.5000 MULT= 1 ISPLIT=-2 H 1NPT= 781 R0=0.0001 RMT=0.7100 Z: 1.0 LOCAL ROT MATRIX:0.000 0.000 1.000 0.000 1.000 0.000 -1.000 0.000 0.000 ATOM -2: X=0.5470 Y=0.5000 Z=0.5000 MULT= 1 ISPLIT=-2 H 1NPT= 781 R0=0.0001 RMT=0.7100 Z: 1.0 LOCAL ROT MATRIX:0.000 0.000 1.000 0.000 1.000 0.000 -1.000 0.000 0.000 8 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0-1 0 0. 0 0-1 0. 1 1 0 0 0. 0-1 0 0. 0 0 1 0. 2 1 0 0 0. 0 0-1 0. 0-1 0 0. 3 1 0 0 0. 0 0 1 0. 0-1 0 0. 4 1 0 0 0. 0 0-1 0. 0 1 0 0. 5 1 0 0 0. 0 0 1 0. 0 1 0 0. 6 1 0 0 0. 0 1 0 0. 0 0-1 0. 7 1 0 0 0. 0 1 0 0. 0 0 1 0. 8 With best regards, Yurko -- Yurko (aka Yuriy, Iurii, Jurij etc) Natanzon PhD Student Henryk Niewodniczan`ski Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Krako`w, Poland Email: Yurii.Natanzon at ifj.edu.pl, yurko.natanzon at gmail.com
[Wien] lapw1 runs too slow for H2 molecule
The reason is your value for RKMAX. To expand, the largest k-value in lapw1 is determined by RKMAX/min(RMT) which for H2 is 7/0.71. Probably when you did H you had a larger RMT (probably 2.0), so the largest k was 7/2.0 which is about 3 times smaller. Since the size of the matrix you are diagonalizing scales roughly as k**3, for H2 you have a matrix about 27 times larger so it will probably take at least 50 time longer. You can approximately use an RKMAX such that RKMAX/min(RMT) is about the same, i.e. for your H2 molecule use an RKMAX of 2 or 2.5. Unfortunately it is not quite as simple as this and larger RKMAX is better. Note as well that if you want to calculate the atomization energy of H2 you MUST use the same RMT and RKMAX for both H and H2, otherwise your energies are GIGO. N.B., running systems with small RMTs with Wien2k, e.g. for H, is not easy. On Fri, Oct 10, 2008 at 8:23 AM, Yurko Natanzon yurko.natanzon at gmail.com wrote: Dear wien2k users, I'm running a simple exercise with H2 molecule located in the middle of a cubic box with a=15 Bohr. the H-H bond length is set to about 0.75 Ang and RMT radus is 0.71 (also the smaller values were tested). The problem is that the calculation is too long. It takes 40 minutes for LAPW1 to run: :log (runsp_lapw) options: Fri Oct 10 11:41:58 CEST 2008 (x) lapw0 Fri Oct 10 11:42:21 CEST 2008 (x) lapw1 -c -up Fri Oct 10 12:20:05 CEST 2008 (x) lapw1 -c -dn Fri Oct 10 12:58:24 CEST 2008 (x) lapw2 -c -up Fri Oct 10 12:58:28 CEST 2008 (x) lapw2 -c -dn Fri Oct 10 12:58:31 CEST 2008 (x) lcore -up Fri Oct 10 12:58:31 CEST 2008 (x) lcore -dn Fri Oct 10 12:58:31 CEST 2008 (x) mixer For comparison, the same calculation for one H atom in the box takes 3 seconds (lapw1), for CoO (a=8 Bohr) - just 12 seconds. I used init_lapw -numk 1 -vxc 13 I post my in0 and in1 files as well as a struct file: --in0 TOT 13(5...CA-LDA, 13...PBE-GGA, 11...WC-GGA) NR2V IFFT (R2V) -1 -1 -11.00min IFFT-parameters, enhancement factor #changed the default values because of IFFT errors ---in1c WFFIL(WFPRI, SUPWF) 7.00 104 (R-MT*K-MAX; MAX L IN WF, V-NMT 0.301 0 (GLOBAL E-PARAMETER WITH n OTHER CHOICES, global APW/LAPW) 00.30 0.000 CONT 1 0.301 0 (GLOBAL E-PARAMETER WITH n OTHER CHOICES, global APW/LAPW) 00.30 0.000 CONT 1 K-VECTORS FROM UNIT:4 -9.0 2.0 7 emin/emax/nband struct file h2 molecule P LATTICE,NONEQUIV.ATOMS: 2 MODE OF CALC=RELA unit=bohr 15.117815 15.117815 15.117815 90.00 90.00 90.00 ATOM -1: X=0.4530 Y=0.5000 Z=0.5000 MULT= 1 ISPLIT=-2 H 1NPT= 781 R0=0.0001 RMT=0.7100 Z: 1.0 LOCAL ROT MATRIX:0.000 0.000 1.000 0.000 1.000 0.000 -1.000 0.000 0.000 ATOM -2: X=0.5470 Y=0.5000 Z=0.5000 MULT= 1 ISPLIT=-2 H 1NPT= 781 R0=0.0001 RMT=0.7100 Z: 1.0 LOCAL ROT MATRIX:0.000 0.000 1.000 0.000 1.000 0.000 -1.000 0.000 0.000 8 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0-1 0 0. 0 0-1 0. 1 1 0 0 0. 0-1 0 0. 0 0 1 0. 2 1 0 0 0. 0 0-1 0. 0-1 0 0. 3 1 0 0 0. 0 0 1 0. 0-1 0 0. 4 1 0 0 0. 0 0-1 0. 0 1 0 0. 5 1 0 0 0. 0 0 1 0. 0 1 0 0. 6 1 0 0 0. 0 1 0 0. 0 0-1 0. 7 1 0 0 0. 0 1 0 0. 0 0 1 0. 8 With best regards, Yurko -- Yurko (aka Yuriy, Iurii, Jurij etc) Natanzon PhD Student Henryk Niewodniczan`ski Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Krako`w, Poland Email: Yurii.Natanzon at ifj.edu.pl, yurko.natanzon at gmail.com ___ 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 Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering to study the structure of matter.
[Wien] did parallel calculation take effect?
You specified: Shared Memory Architecture? yes With this option it is assuming that your machine as a whole is a shared memory machine (eg. a single machine with dual quadcore cpus would qualify as 8-core shared memory), and thus does not use ssh to start the parallel jobs. You configure with siteconfig, that you have no shared memory machine and use ssh to connect to the different machines. vinct8954 schrieb: dear wien users: i met a confused about parallel calculation. i compile the wien2k codes in my clusters with out any errors.and the single calculation works well. but when i running programs in parallel mode, i met some puzzled problem. /the .machines file as followed:/ 1:console 1:c0101 1:c0102 1:c0103 1:c0104 1:c0105 1:c0106 1:c0107 ... granularity:1 extrafine:1 /the cycles seems to be nomal,which dayfile is :/ running lapw0 in single mode 15.949u 1.807s 0:19.06 93.0%0+0k 0+0io 29pf+0w lapw1 -p (22:31:08) starting parallel lapw1 at Wed Sep 17 22:31:08 CST 2008 - starting parallel LAPW1 jobs at Wed Sep 17 22:31:08 CST 2008 running LAPW1 in parallel mode (using .machines) 8 number_of_parallel_jobs console(79) 254.184u 16.657s 9:07.02 49.5% 0+0k 0+0io 38pf+0w c0101(79) 250.019u 16.482s 8:59.24 49.4% 0+0k 0+0io 27pf+0w c0102(79) 253.406u 16.350s 9:04.43 49.5% 0+0k 0+0io 9pf+0w c0103(79) 254.532u 17.161s 9:06.57 49.7% 0+0k 0+0io 0pf+0w c0104(79) 252.878u 15.813s 9:00.49 49.7% 0+0k 0+0io 0pf+0w c0105(79) 254.152u 15.739s 9:03.59 49.6% 0+0k 0+0io 0pf+0w c0106(79) 254.164u 15.906s 9:01.19 49.9% 0+0k 0+0io 0pf+0w c0107(79) 254.787u 16.461s 9:04.39 49.8% 0+0k 0+0io 0pf+0w c0101(1) 3.607u 0.272s 0:05.37 72.0% 0+0k 0+0io 0pf+0w c0102(1) 3.650u 0.242s 0:04.21 92.3% 0+0k 0+0io 0pf+0w c0104(1) 3.270u 0.225s 0:03.64 95.8% 0+0k 0+0io 0pf+0w Summary of lapw1para: console k=79user=254.184wallclock=547.02 c0101 k=80user=253.626wallclock=544.61 c0102 k=80user=257.056wallclock=548.64 c0103 k=79user=254.532wallclock=546.57 c0104 k=80user=256.148wallclock=544.13 c0105 k=79user=254.152wallclock=543.59 c0106 k=79user=254.164wallclock=541.19 c0107 k=79user=254.787wallclock=544.39 2039.101u 132.877s 9:14.54 391.6% 0+0k 0+0io 76pf+0w /but when i check the ps of every Compute Node , there is no lapw1 in other nodes at all. all the lapw1(or lapw2)_1.def lapw1(or lapw2)_2.def are running in master nodes. did the parallel calculation take effect? apparently , i used runsp_lapw -pfor parallel./ /long for some suggestions./ Appendix? the details of my clusters' environment as following? the system: fedora 8 and intel ifort 9.1 and the detail of compile options: Current settings: O Compiler options:-O3 -FR -w -mp1 -prec_div -pad -ip -xP L Linker Flags:-L/export/mathlib/cmkl81/lib/em64t -lguide -lpthread -lsvml P Preprocessor flags '-DParallel' R R_LIB (LAPACK+BLAS): -L/export/mathlib/cmkl81/lib/em64t -lmkl_lapack64 -lmkl_em64t -lguide -lpthread Shared Memory Architecture? yes the MPI and Scalapack options: RP RP_LIB(SCALAPACK+PBLAS): -L/export/mathlib/cmkl81/lib/em64t -lmkl_scalapack -lmkl_blacs_intelmpi20 -lmkl_lapack -lmkl_em64t -lguide -lpthread FP FPOPT(par.comp.options): -O3 -FR -w -mp1 -prec_div -pad -ip -xP MP MPIRUN commando: mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_ http://cn.mail.yahoo.com/ ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ --
[Wien] lapw1 runs too slow for H2 molecule
Dear Laurence, thank you for your explanation, it helped me a lot. Yes, I used larger RMT for H atom and smaller for H2 molecule. Now I see that it is necessary to run convergence tests of total energy vs RKmax each time I change RMt radii, is it? for example, when I want to optimize positions of lattice constants I have to reduce RMTs, so can I also reduce Rkmax proportionally in order to achieve better performance? regards, Yurko 2008/10/10 Laurence Marks L-marks at northwestern.edu: The reason is your value for RKMAX. To expand, the largest k-value in lapw1 is determined by RKMAX/min(RMT) which for H2 is 7/0.71. Probably when you did H you had a larger RMT (probably 2.0), so the largest k was 7/2.0 which is about 3 times smaller. Since the size of the matrix you are diagonalizing scales roughly as k**3, for H2 you have a matrix about 27 times larger so it will probably take at least 50 time longer. You can approximately use an RKMAX such that RKMAX/min(RMT) is about the same, i.e. for your H2 molecule use an RKMAX of 2 or 2.5. Unfortunately it is not quite as simple as this and larger RKMAX is better. Note as well that if you want to calculate the atomization energy of H2 you MUST use the same RMT and RKMAX for both H and H2, otherwise your energies are GIGO. N.B., running systems with small RMTs with Wien2k, e.g. for H, is not easy. On Fri, Oct 10, 2008 at 8:23 AM, Yurko Natanzon yurko.natanzon at gmail.com wrote: Dear wien2k users, I'm running a simple exercise with H2 molecule located in the middle of a cubic box with a=15 Bohr. the H-H bond length is set to about 0.75 Ang and RMT radus is 0.71 (also the smaller values were tested). The problem is that the calculation is too long. It takes 40 minutes for LAPW1 to run: :log (runsp_lapw) options: Fri Oct 10 11:41:58 CEST 2008 (x) lapw0 Fri Oct 10 11:42:21 CEST 2008 (x) lapw1 -c -up Fri Oct 10 12:20:05 CEST 2008 (x) lapw1 -c -dn Fri Oct 10 12:58:24 CEST 2008 (x) lapw2 -c -up Fri Oct 10 12:58:28 CEST 2008 (x) lapw2 -c -dn Fri Oct 10 12:58:31 CEST 2008 (x) lcore -up Fri Oct 10 12:58:31 CEST 2008 (x) lcore -dn Fri Oct 10 12:58:31 CEST 2008 (x) mixer For comparison, the same calculation for one H atom in the box takes 3 seconds (lapw1), for CoO (a=8 Bohr) - just 12 seconds. I used init_lapw -numk 1 -vxc 13 I post my in0 and in1 files as well as a struct file: --in0 TOT 13(5...CA-LDA, 13...PBE-GGA, 11...WC-GGA) NR2V IFFT (R2V) -1 -1 -11.00min IFFT-parameters, enhancement factor #changed the default values because of IFFT errors ---in1c WFFIL(WFPRI, SUPWF) 7.00 104 (R-MT*K-MAX; MAX L IN WF, V-NMT 0.301 0 (GLOBAL E-PARAMETER WITH n OTHER CHOICES, global APW/LAPW) 00.30 0.000 CONT 1 0.301 0 (GLOBAL E-PARAMETER WITH n OTHER CHOICES, global APW/LAPW) 00.30 0.000 CONT 1 K-VECTORS FROM UNIT:4 -9.0 2.0 7 emin/emax/nband struct file h2 molecule P LATTICE,NONEQUIV.ATOMS: 2 MODE OF CALC=RELA unit=bohr 15.117815 15.117815 15.117815 90.00 90.00 90.00 ATOM -1: X=0.4530 Y=0.5000 Z=0.5000 MULT= 1 ISPLIT=-2 H 1NPT= 781 R0=0.0001 RMT=0.7100 Z: 1.0 LOCAL ROT MATRIX:0.000 0.000 1.000 0.000 1.000 0.000 -1.000 0.000 0.000 ATOM -2: X=0.5470 Y=0.5000 Z=0.5000 MULT= 1 ISPLIT=-2 H 1NPT= 781 R0=0.0001 RMT=0.7100 Z: 1.0 LOCAL ROT MATRIX:0.000 0.000 1.000 0.000 1.000 0.000 -1.000 0.000 0.000 8 NUMBER OF SYMMETRY OPERATIONS 1 0 0 0. 0-1 0 0. 0 0-1 0. 1 1 0 0 0. 0-1 0 0. 0 0 1 0. 2 1 0 0 0. 0 0-1 0. 0-1 0 0. 3 1 0 0 0. 0 0 1 0. 0-1 0 0. 4 1 0 0 0. 0 0-1 0. 0 1 0 0. 5 1 0 0 0. 0 0 1 0. 0 1 0 0. 6 1 0 0 0. 0 1 0 0. 0 0-1 0. 7 1 0 0 0. 0 1 0 0. 0 0 1 0. 8 With best regards, Yurko -- Yurko (aka Yuriy, Iurii, Jurij etc) Natanzon PhD Student Henryk Niewodniczan`ski Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Krako`w, Poland Email: Yurii.Natanzon at ifj.edu.pl, yurko.natanzon at gmail.com ___ 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)
