From ymxiong at icpm.syb.ac.cn Sun Dec 1 03:44:18 2002 From: ymxiong at icpm.syb.ac.cn (Xiong Yuming) Date: Sun, 1 Dec 2002 10:44:18 +0800 Subject: [CPMD-list] run cpmd.x Message-ID: <200212010238.DAA08598@internet-fence.zurich.ihost.com> cpmd-listDear All Can anybody help me? Last time I compiled the cpmd source using lf95 compiler. But this time, when I run cpmd.x using LAM/MPI, it can not find some library files. so I decide recompile the source. In fact, when I compile the objects successfully, I can not make link all the objects because there are a lot of errors on my_para.o files. I dont know what library files I should apply to the compile. some advice will help me great. thanks.when I fail to compile the source, it gave me some suggestion as followed: make rm -f timetag.f /lib/cpp -P -C -traditional -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DPARALLEL -DMP_LIBRARY=__MPI -DMYRINET ./timetag.F ./timetag.f lf95 -c -I/usr/include ./timetag.f Encountered 0 errors, 0 warnings in file ./timetag.f. rm -f cpmd.x if [ "." != "." ]; then ln -s ./cpmd.x cpmd.x; fi lf95 -o ./cpmd.x timetag.o cpmd.o softex.o envir.o setcnst.o control.o control_def.o control_pri.o control_bcast.o control_test.o header.o inscan.o memory.o freem.o readsr.o timer.o ttimp.o timec.o stopgm.o util.o dftin.o sysin.o ratom.o recpnew.o ghermit.o detsp.o coninp.o prmem.o setsys.o genxc.o setsc.o numpw.o cry.o latgen.o recips.o functionals.o lsd_func.o rinit.o rinforce.o fftprp.o rggen.o formf.o rnlset.o ylmr.o glopar.o rnlin.o sort.o radin.o bessm.o ylmr2.o pbc.o ortho.o finalp.o forcep.o rhopri.o phfac.o wrener.o rrane.o ranp.o rinitwf.o mltfft.o wrgeo.o rnlsm1.o rnlsm2.o fft.o ffts.o fftsg.o forces.o lowdin.o rgs.o rgsvan.o atomwf.o atrho.o xcener.o graden.o gcener.o hesele.o noforce.o rhoofr.o vpsi.o nlforce.o rotate.o hnlmat.o ovlap.o dotp.o fnonloc.o gsize.o csize.o rscpot.o csmat.o ksmat.o vofrho.o vofrhoa.o vofrhob.o vofrhoh.o vofrhot.o initclust.o jacobi.o rnlrh.o rnlfor.o potfor.o ppener.o reigs.o geofile.o rpiiint.o eicalc.o testex.o densto.o proja.o atoms.o fitpack.o wv30.o rv30.o wr30wfn.o setbasis.o gfft.o fftchk.o nfunc.o gcxctbl.o rhoofr_c.o jacobi_c.o velocitinp.o setirec.o compress.o interp3d.o ptheory.o clinbcg.o elstpo.o exterp.o mulliken.o espchg.o atomc.o eextern.o interpt.o egointer.o fileopen.o scratch.o forcedr.o initrun.o ldos.o fnlalloc.o dqgalloc.o anneal.o ylmr3.o-o ./crnlsm.oimetagvofrhos.o softeget_addr.oo setcteststore.ool.o cloadse.oef.o crnlsmd.ori.o cwfnio.obcast.density_functionals.oer.o iwfopts.omemoryrwfopt.o.o reaupdwf.oimer.oodiis.oo timepcgrad.ogm.o ugmopts.otin.o rgmopt.oratom.fstart.ow.o ghstruc.o detspempfor.op.o prputtau.otsys.oconstr.o setscrrfo.opw.o crbfgs.otgen.orgdiis.oo funcsdion.o.o lsdhessin.orinit.hessout.oe.o ffhessup.oggen.odum2.o.o rnldetdof.omr.o gcnstfc.ornlin.fixcom.o radincnstpr.o.o ylmmoverho.oo orthelf.oinalp.lsd_elf.oo rhopmdpt.ohfac.omdmain.oo rrandynit.op.o rishake.o mltffrattle.oo.o rnresetac.olsm2.odispp.offts.onosalloc.oorces.noseinit.o rgs.onospinit.oatomwfnoseng.o.o xcenosepa.oaden.onoseup.oo heseenosmove.oce.o rpnosmove.osi.o nekinp printave.otp.o fprintp.o gsizerekine.o.o rscrinvel.omat.o rscvp.o vofrhrscve.orhoa.odeort.ob.o voquenbo.ovofrhovelupa.oclust.velupi.o.o rnlposupa.ofor.o posupi.o ppenerortog.os.o gerortv.o rpiiicrotwf.oalc.o noscinit.oensto.prpcnosmove.oms.o fprpcmove.ov30.o prpnosmove.ofn.o sprcnosmove.oft.o fddipo.o nfuncopeigr.obl.o rsample.oo jacosd_wannier.oitinp.wannier_ center.o wannier_print.o purge.o wc_dos.o fusion.o mdshop.o davidson.o ksdiag.o vgsortho.o hpsi.o spsi.o gsortho.o rhov1.o secdpt.o secder.o sdlinres.o sd_ii.o sd_loc2.o sd_nl2.o rnlsm_2d.o nl_res.o sd_loc.o sd_nl.o rho1ofr.o v1ofrho1.o lr_force.o opt_lr.o lr_upd.o dd_xc.o eind_ii.o eind_loc.o eind_nl.o lr_in.o lr_xcpot.o lr_ortho.o lr_pcg.o canon.o proppt.o prowfn.o dipo.o lodipo.o exdipo.o cmaos.o difrho.o conduct.o polarise.o calc_pij.o localize.o jrotation.o orbhard.o ohfd.o ohlr.o specpt.o td_dav.o td_nhdav.o lr_diag.o vhk.o gettrans.o rho1pri.o rw_linres.o td_force.o tdnlfor.o td_pcg.o orbrot.o vtd2.o stcop.o readvan.o aainit.o vdbinit.o rhov.o qvan1.o qvan2.o newd.o rnlfl.o augchg.o readvdb.o nlccset.o copot.o corec.o cofor.o nlccstr.o startpa.o loadpa.o sumfnl.o glosum.o summat.o my_para.o glomax.o glomin.o groups.o hipin.o hip.o mtin.o stress.o vlocst.o htrstr.o xcstr.o drhov.o nlsl.o nlsm1_s.o dqvan2.o dylmr.o ffsum.o qrada_s.o totstr.o putbet.o ranc.o newcell.o sdcell.o prpt.o prcpmd.o npt_md.o symmetry.o chksym.o symtrz.o multtb.o molsym.o lsfbtr.o friesner.o friesner_c.o ehpsi.o rrandd.o updrho.o anderson.o adjmu.o forces_diag.o mddiag.o extrap.o bogol.o calc_alm.o vbeta.o rhodiis.o rwswap.o frsblk.o frsblk_c.o mixing_r.o mixing_g.onnier_print.o purge.o wcbroyden.osion.oenbandpri.oavidson.o ksdiag.orkpnt.oho.o hpsi.o spsi.o gsortk290.ohov1.o secdpt.o sek290_2.odlinres.o sdkpclean.oloc2.opi_cntl.o rnlsmpi_init.ores.o pi_mdpt.osd_nl.pi_wf.ofr.o vpi_md.o.o lr_pi_diag.opt_lr.rreadf.o.o dd_repgen.od_ii.ofharm.ooc.o eglobal.o lr_instagetrans.oo lr_opinmtra cgetfu.opropptgetfnm.on.o digetgyr.oipo.o getcor.o cmaosprtgyr.oo.o coevirial.oolariswr_temps.oij.o lcl_init.o jrotamdclas.orbhardreadff.oo ohlrclas_force.otd_davh0psi1_p.ov.o lrv1ofrho_p.o.o getfnonloc_p.o1pri.odo_gga_p.o.o td_mddiag-interaction_p.ocg.o ogndstate_p.o.o stclegendre_p.o.o aaiinteraction_p.o rhov.rotate_my_wannier_p.od.o rnBYLM_p.ogchg.ohess_eta_p.olccsetinr_dr.o.o corlanc_phon_p.onlccstdmudn_p.opa.o lhesele_p.omfnl.odo_perturbation_p.omy_parpcgrad_p.o.o glornlsm_p.oups.o vpsi_p.ohip.o perturbation_p.ovlocsteigensystem_p.otr.o dphonons_p.o.o nlsrwfopt_p.oan2.o d_mat_p.ofsum.oupdwf_p.oo totsforces_p.ot.o rarhoofr_p.oll.o sraman_p.orpt.o opeigr_p.opt_md.nmr_p.otry.o nmr_util_p.otrz.o nmr_chi_p.olsym.onmr_shift_p.oesner.nmr_current_p.o ehpsinmr_para_p.o.o updhardness_p.oon.o arespin_p.oforcesrespo nse_p.o kdp_diag.o kdp_prep.o kdp_rho.o kdp_stress_kin.o kdpoints.o rhoofr_kdp.o mm_detsp.o mm_init.o mm_dim.o mm_qmmm_forcedr.o mm_mdmain.o mm_coninp.o mm_cpmd_add_MM_forces_f77.o mm_cpmd_esp_charges_f77.o mm_cpmd_ext_pot_f77.o sysdepend.o shmemory.o -I/usr/local/lf9560/lib -llapackmt -lblasmt -lmpi -lssl2mt --parallel my_para.o: In function `my_start_': my_para.o(.text+0xf): undefined reference to `mpi_init_' my_para.o: In function `my_end_': my_para.o(.text+0x689): undefined reference to `mpi_finalize_' my_para.o: In function `my_group_': my_para.o(.text+0x6be): undefined reference to `mpi_comm_group_' my_para.o(.text+0x6d7): undefined reference to `mpi_group_incl_' my_para.o(.text+0x6f0): undefined reference to `mpi_comm_create_' my_para.o: In function `my_stopall_': my_para.o(.text+0x738): undefined reference to `mpi_abort_' my_para.o: In function `my_sync_': my_para.o(.text+0x771): undefined reference to `mpi_barrier_' my_para.o: In function `my_environ_': my_para.o(.text+0x7dc): undefined reference to `mpi_comm_rank_' my_para.o(.text+0x7ee): undefined reference to `mpi_comm_size_' my_para.o: In function `my_bcast_': my_para.o(.text+0x8a0): undefined reference to `mpi_bcast_' my_para.o: In function `my_bsend_': my_para.o(.text+0xab4): undefined reference to `mpi_send_' my_para.o: In function `my_brecv_': my_para.o(.text+0xb68): undefined reference to `mpi_recv_' my_para.o: In function `my_concat_': my_para.o(.text+0xbfd): undefined reference to `mpi_allgather_' my_para.o: In function `my_trans_': my_para.o(.text+0xcdc): undefined reference to `mpi_alltoall_' my_para.o: In function `my_combine_': my_para.o(.text+0xdfa): undefined reference to `mpi_allreduce_' my_para.o(.text+0xe47): undefined reference to `mpi_allreduce_' my_para.o(.text+0xea9): undefined reference to `mpi_allreduce_' my_para.o(.text+0xf0b): undefined reference to `mpi_allreduce_' my_para.o(.text+0xf55): undefined reference to `mpi_allreduce_' my_para.o: In function `my_shift_': my_para.o(.text+0x1019): undefined reference to `mpi_comm_rank_' my_para.o(.text+0x1054): undefined reference to `mpi_comm_size_' my_para.o(.text+0x10ff): undefined reference to `mpi_isend_' my_para.o(.text+0x1151): undefined reference to `mpi_recv_' my_para.o(.data+0x8): undefined reference to `mpi_init_' my_para.o(.data+0xc): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0x10): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0x14): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0x18): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0x1c): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0x20): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0x24): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0x28): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0x2c): undefined reference to `mpi_dup_fn_' my_para.o(.data+0x30): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0x34): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0x38): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0x3c): undefined reference to `mpi_wtime_' my_para.o(.data+0x40): undefined reference to `mpi_wtick_' my_para.o(.data+0x44): undefined reference to `pmpi_wtime_' my_para.o(.data+0x48): undefined reference to `pmpi_wtick_' my_para.o(.data+0x98): undefined reference to `mpi_finalize_' my_para.o(.data+0x9c): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0xa0): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0xa4): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0xa8): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0xac): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0xb0): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0xb4): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0xb8): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0xbc): undefined reference to `mpi_dup_fn_' my_para.o(.data+0xc0): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0xc4): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0xc8): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0xcc): undefined reference to `mpi_wtime_' my_para.o(.data+0xd0): undefined reference to `mpi_wtick_' my_para.o(.data+0xd4): undefined reference to `pmpi_wtime_' my_para.o(.data+0xd8): undefined reference to `pmpi_wtick_' my_para.o(.data+0x914): undefined reference to `mpi_comm_create_' my_para.o(.data+0x918): undefined reference to `mpi_group_incl_' my_para.o(.data+0x91c): undefined reference to `mpi_comm_group_' my_para.o(.data+0x920): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0x924): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0x928): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0x92c): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0x930): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0x934): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0x938): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0x93c): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0x940): undefined reference to `mpi_dup_fn_' my_para.o(.data+0x944): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0x948): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0x94c): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0x950): undefined reference to `mpi_wtime_' my_para.o(.data+0x954): undefined reference to `mpi_wtick_' my_para.o(.data+0x958): undefined reference to `pmpi_wtime_' my_para.o(.data+0x95c): undefined reference to `pmpi_wtick_' my_para.o(.data+0x998): undefined reference to `mpi_abort_' my_para.o(.data+0x99c): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0x9a0): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0x9a4): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0x9a8): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0x9ac): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0x9b0): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0x9b4): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0x9b8): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0x9bc): undefined reference to `mpi_dup_fn_' my_para.o(.data+0x9c0): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0x9c4): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0x9c8): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0x9cc): undefined reference to `mpi_wtime_' my_para.o(.data+0x9d0): undefined reference to `mpi_wtick_' my_para.o(.data+0x9d4): undefined reference to `pmpi_wtime_' my_para.o(.data+0x9d8): undefined reference to `pmpi_wtick_' my_para.o(.data+0x9ec): undefined reference to `mpi_barrier_' my_para.o(.data+0xa34): undefined reference to `mpi_comm_size_' my_para.o(.data+0xa38): undefined reference to `mpi_comm_rank_' my_para.o(.data+0xa3c): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0xa40): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0xa44): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0xa48): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0xa4c): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0xa50): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0xa54): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0xa58): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0xa5c): undefined reference to `mpi_dup_fn_' my_para.o(.data+0xa60): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0xa64): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0xa68): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0xa6c): undefined reference to `mpi_wtime_' my_para.o(.data+0xa70): undefined reference to `mpi_wtick_' my_para.o(.data+0xa74): undefined reference to `pmpi_wtime_' my_para.o(.data+0xa78): undefined reference to `pmpi_wtick_' my_para.o(.data+0xab8): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0xabc): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0xac0): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0xac4): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0xac8): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0xacc): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0xad0): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0xad4): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0xad8): undefined reference to `mpi_dup_fn_' my_para.o(.data+0xadc): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0xae0): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0xae4): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0xae8): undefined reference to `mpi_wtime_' my_para.o(.data+0xaec): undefined reference to `mpi_wtick_' my_para.o(.data+0xaf0): undefined reference to `pmpi_wtime_' my_para.o(.data+0xaf4): undefined reference to `pmpi_wtick_' my_para.o(.data+0xb04): undefined reference to `mpi_bcast_' my_para.o(.data+0xb0c): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0xb10): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0xb14): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0xb18): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0xb1c): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0xb20): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0xb24): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0xb28): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0xb2c): undefined reference to `mpi_dup_fn_' my_para.o(.data+0xb30): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0xb34): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0xb38): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0xb3c): undefined reference to `mpi_wtime_' my_para.o(.data+0xb40): undefined reference to `mpi_wtick_' my_para.o(.data+0xb44): undefined reference to `pmpi_wtime_' my_para.o(.data+0xb48): undefined reference to `pmpi_wtick_' my_para.o(.data+0xc14): undefined reference to `mpi_send_' my_para.o(.data+0xc1c): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0xc20): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0xc24): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0xc28): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0xc2c): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0xc30): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0xc34): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0xc38): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0xc3c): undefined reference to `mpi_dup_fn_' my_para.o(.data+0xc40): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0xc44): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0xc48): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0xc4c): undefined reference to `mpi_wtime_' my_para.o(.data+0xc50): undefined reference to `mpi_wtick_' my_para.o(.data+0xc54): undefined reference to `pmpi_wtime_' my_para.o(.data+0xc58): undefined reference to `pmpi_wtick_' my_para.o(.data+0xcbc): undefined reference to `mpi_recv_' my_para.o(.data+0xcc4): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0xcc8): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0xccc): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0xcd0): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0xcd4): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0xcd8): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0xcdc): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0xce0): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0xce4): undefined reference to `mpi_dup_fn_' my_para.o(.data+0xce8): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0xcec): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0xcf0): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0xcf4): undefined reference to `mpi_wtime_' my_para.o(.data+0xcf8): undefined reference to `mpi_wtick_' my_para.o(.data+0xcfc): undefined reference to `pmpi_wtime_' my_para.o(.data+0xd00): undefined reference to `pmpi_wtick_' my_para.o(.data+0xd74): undefined reference to `mpi_allgather_' my_para.o(.data+0xd78): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0xd7c): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0xd80): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0xd84): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0xd88): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0xd8c): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0xd90): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0xd94): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0xd98): undefined reference to `mpi_dup_fn_' my_para.o(.data+0xd9c): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0xda0): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0xda4): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0xda8): undefined reference to `mpi_wtime_' my_para.o(.data+0xdac): undefined reference to `mpi_wtick_' my_para.o(.data+0xdb0): undefined reference to `pmpi_wtime_' my_para.o(.data+0xdb4): undefined reference to `pmpi_wtick_' my_para.o(.data+0xdf4): undefined reference to `mpi_alltoall_' my_para.o(.data+0xdfc): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0xe00): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0xe04): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0xe08): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0xe0c): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0xe10): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0xe14): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0xe18): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0xe1c): undefined reference to `mpi_dup_fn_' my_para.o(.data+0xe20): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0xe24): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0xe28): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0xe2c): undefined reference to `mpi_wtime_' my_para.o(.data+0xe30): undefined reference to `mpi_wtick_' my_para.o(.data+0xe34): undefined reference to `pmpi_wtime_' my_para.o(.data+0xe38): undefined reference to `pmpi_wtick_' my_para.o(.data+0xeb8): undefined reference to `mpi_allreduce_' my_para.o(.data+0xec0): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0xec4): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0xec8): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0xecc): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0xed0): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0xed4): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0xed8): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0xedc): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0xee0): undefined reference to `mpi_dup_fn_' my_para.o(.data+0xee4): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0xee8): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0xeec): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0xef0): undefined reference to `mpi_wtime_' my_para.o(.data+0xef4): undefined reference to `mpi_wtick_' my_para.o(.data+0xef8): undefined reference to `pmpi_wtime_' my_para.o(.data+0xefc): undefined reference to `pmpi_wtick_' my_para.o(.data+0xf90): undefined reference to `mpi_recv_' my_para.o(.data+0xf94): undefined reference to `mpi_isend_' my_para.o(.data+0xf98): undefined reference to `mpi_comm_size_' my_para.o(.data+0xfa0): undefined reference to `mpi_comm_rank_' my_para.o(.data+0xfa4): undefined reference to `mpi_null_copy_fn_' my_para.o(.data+0xfa8): undefined reference to `mpi_null_delete_fn_' my_para.o(.data+0xfac): undefined reference to `mpi_comm_null_copy_fn_' my_para.o(.data+0xfb0): undefined reference to `mpi_comm_null_delete_fn_' my_para.o(.data+0xfb4): undefined reference to `mpi_type_null_copy_fn_' my_para.o(.data+0xfb8): undefined reference to `mpi_type_null_delete_fn_' my_para.o(.data+0xfbc): undefined reference to `mpi_win_null_copy_fn_' my_para.o(.data+0xfc0): undefined reference to `mpi_win_null_delete_fn_' my_para.o(.data+0xfc4): undefined reference to `mpi_dup_fn_' my_para.o(.data+0xfc8): undefined reference to `mpi_comm_dup_fn_' my_para.o(.data+0xfcc): undefined reference to `mpi_type_dup_fn_' my_para.o(.data+0xfd0): undefined reference to `mpi_win_dup_fn_' my_para.o(.data+0xfd4): undefined reference to `mpi_wtime_' my_para.o(.data+0xfd8): undefined reference to `mpi_wtick_' my_para.o(.data+0xfdc): undefined reference to `pmpi_wtime_' my_para.o(.data+0xfe0): undefined reference to `pmpi_wtick_' ]0;yuming at station5:~/cpmd3.5.3/src[yuming at station5 src]$ exit best regards yours xiong ?????? ?????????????????????????????????????????????????? Institute of Metals Research of Chinese Academy of Science Shenyang Wencui Road 62#, PRC, 110016 Tel: 86-24-23904856 86-24-23847907 13032411835 ??????????????Xiong Yuming ??????mail to: ymxiong at icpm.syb.ac.cn ????????????????????2002-12-01 From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Sun Dec 1 09:58:50 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Sun, 01 Dec 2002 09:58:50 +0100 Subject: [CPMD-list] run cpmd.x In-Reply-To: <200212010238.DAA08598@internet-fence.zurich.ihost.com> Message-ID: <200212010858.gB18wom30723@yello.theochem.ruhr-uni-bochum.de> On Sun, 1 Dec 2002 10:44:18 +0800 "Xiong Yuming" wrote: > cpmd-listDear All > Can anybody help me? Last time I compiled the cpmd source using lf95 comp iler. But this time, when I run cpmd.x using LAM/MPI, it can not find some libr ary files. so I decide recompile the source. In fact, when I compile the object s successfully, I can not make link all the objects because there are a lot of errors on my_para.o files. I dont know what library files I should apply to the compile. some advice will help me great. thanks.when I fail to compile the sou rce, it gave me some suggestion as followed: [ lots of stuff deleted ] > my_para.o(.data+0xd84): undefined reference to `mpi_comm_null_delete_fn_' > > my_para.o(.data+0xd88): undefined reference to `mpi_type_null_copy_fn_' > > my_para.o(.data+0xd8c): undefined reference to `mpi_type_null_delete_fn_' > > my_para.o(.data+0xd90): undefined reference to `mpi_win_null_copy_fn_' > > my_para.o(.data+0xd94): undefined reference to `mpi_win_null_delete_fn_' > > my_para.o(.data+0xd98): undefined reference to `mpi_dup_fn_' > > my_para.o(.data+0xd9c): undefined reference to `mpi_comm_dup_fn_' > > my_para.o(.data+0xda0): undefined reference to `mpi_type_dup_fn_' > > my_para.o(.data+0xda4): undefined reference to `mpi_win_dup_fn_' > > my_para.o(.data+0xda8): undefined reference to `mpi_wtime_' > > my_para.o(.data+0xdac): undefined reference to `mpi_wtick_' > > my_para.o(.data+0xdb0): undefined reference to `pmpi_wtime_' > > my_para.o(.data+0xdb4): undefined reference to `pmpi_wtick_' > > my_para.o(.data+0xdf4): undefined reference to `mpi_alltoall_' > > my_para.o(.data+0xdfc): undefined reference to `mpi_null_copy_fn_' > > my_para.o(.data+0xe00): undefined reference to `mpi_null_delete_fn_' > > my_para.o(.data+0xe04): undefined reference to `mpi_comm_null_copy_fn_' > > my_para.o(.data+0xe08): undefined reference to `mpi_comm_null_delete_fn_' > > my_para.o(.data+0xe0c): undefined reference to `mpi_type_null_copy_fn_' > > my_para.o(.data+0xe10): undefined reference to `mpi_type_null_delete_fn_' > > my_para.o(.data+0xe14): undefined reference to `mpi_win_null_copy_fn_' > > my_para.o(.data+0xe18): undefined reference to `mpi_win_null_delete_fn_' hi, the mpi library you use has obviously been compiled for/with the g77 fortran compiler, which uses different rules to encode function/subroutine names into libraries than your fortran compiler does. you have to recompile the mpi libraries for/with your fortran compiler. alternatively you might check the documentation for your fortran compiler and search for a flag that turns on g77-style underscoring and then recompile cpmd. best regards, axel kohlmeyer. -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From pmignon at vub.ac.be Mon Dec 2 10:42:48 2002 From: pmignon at vub.ac.be (Pierre Mignon) Date: Mon, 2 Dec 2002 10:42:48 +0100 (MET) Subject: [CPMD-list] standard pseudopotential file format Message-ID: <200212020942.KAA00775@mach.vub.ac.be> Hello all, I want to use the Trouiller-Martins pseudopotential with CPMD. But i don't know what is the standard pseudopotential file format that is read by CPMD. I generated pseudopotential datas from the program of J.S. Martins and now i'd like to know which datas CPMD program needs to read in each atom's PP input. CAn someone help me ? Thank you in advance. Pierre Mignon. From audrius.alkauskas at unibas.ch Mon Dec 2 14:57:07 2002 From: audrius.alkauskas at unibas.ch (Audrius Alkauskas) Date: Mon, 02 Dec 2002 14:57:07 +0100 Subject: [CPMD-list] (no subject) Message-ID: <001701c29a0a$b3adaf90$51669883@audrius> Dear all 1. What are recommended cutoffs with Goedecker LDA pseudopotentials for: Ag (silver), B (boron), Cl (chlorine), N (nitrogen), C (carbon), H (hydrogen)? 2. I am doing now silver cluster intracting with big molecule. Is it wise to use finite-temperature methods for just 4 silver atoms? Audrius ================================ Audrius Alkauskas PhD student Condensed Matter Theory Group University of Basel Switzerland http://monet.physik.unibas.ch/~audrius/ ================================ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021202/e9f8f03a/attachment.html From audrius.alkauskas at unibas.ch Mon Dec 2 14:59:23 2002 From: audrius.alkauskas at unibas.ch (Audrius Alkauskas) Date: Mon, 02 Dec 2002 14:59:23 +0100 Subject: [CPMD-list] Goedecker psudopotential cutoffs Message-ID: <001e01c29a0b$049cfc30$51669883@audrius> Sorry for previous incorrect mail. Dear all 1. What are recommended cutoffs with Goedecker LDA pseudopotentials for: Ag (silver), B (boron), Cl (chlorine), N (nitrogen), C (carbon), H (hydrogen)? 2. I am doing now silver cluster intracting with big molecule. Is it wise to use finite-temperature methods for just 4 silver atoms? Audrius From ricardo at irsamc.ups-tlse.fr Mon Dec 2 15:01:50 2002 From: ricardo at irsamc.ups-tlse.fr (JOSE LUIS RICARDO-CHAVEZ) Date: Mon, 02 Dec 2002 15:01:50 +0100 Subject: [CPMD-list] Properties Message-ID: <3DEB67CE.9070305@irsamc.ups-tlse.fr> Dear CPMD community, I an using CPMD to perform LSD calculations on bimetallic magnetic clusters using ultrasoft pseudopotentials. The optimization of cluster geometry works fine but when I try to use the computed wavefunction to obtain the Mulliken charges using the default basis set it gives the following message: -------------------------------------------------------------- PROJECT WAVEFUNCTIONS ON ATOMIC PSEUDO-WAVEFUNCTIONS MULLIKEN POPULATION ANALYSIS AND MAYER BOND-ORDERS **************************************************************** * PROPERTY CALCULATIONS * **************************************************************** RESTART INFORMATION READ ON FILE ./RESTART *** PHFAC| THE NEW SIZE OF THE PROGRAM IS 11948 kBYTES *** LSCR= 100 MAX(LRNLSM1,LRNLSM2) = 20264 PROGRAM STOPS IN SUBROUTINE RNLSM| SCRATCH ARRAY TOO SMALL FORTRAN STOP 999 -------------------------------------------------------------- Does anybody knows how to correct this error? Thanks in advance, greetings. - Jos? Luis From krack at cscs.ch Tue Dec 3 11:35:12 2002 From: krack at cscs.ch (Matthias Krack (CSCS)) Date: Tue, 3 Dec 2002 11:35:12 +0100 (CET) Subject: [CPMD-list] CPMD2003 meeting (Monte Verita, Ascona, Switzerland) Message-ID: Dear CPMD User, Continuing the tradition of biannual CPMD meetings that we have started in Ringberg in 1999, we are organizing on the 13-16 March 2003 in the beautiful conference centre Stefano Franscini (http://www.csf-mv.ethz.ch) on Monte Verita (Ascona) close to Lugano (Switzerland) the third meeting in this series. Unfortunately, we will not be able to cover the full expenses and each participant will be asked to pay his own accommodation and travel costs. The expected fee will be in the order of 500 SFr depending on the amount of industrial funding. This will cover your full board accommodation at the centre. Those of you who are interested are requested to perform an online registration (http://www.cscs.ch/events/cpmd/form.html) or to complete and return the attached registration form giving a tentative title for a possible presentation before the 15th of January. At that time the funding situation will be clearer and instructions on how to pay the fee will be given. Unfortunately due to the space limitations there is a cap on the total number of participants. For that reason EARLY REGISTRATION IS RECOMMENDED. A number of oral contributions will be selected with special preference for young speakers below 35 years of age. M. Krack, M. Parrinello, U. Roethlisberger CPMD2003 March 13-16, 2003 Monte Verita, Ascona, Switzerland Registration Form First Name: Last Name: Institution: Street Address: Zip Code and City: Country: Phone: Fax: E-mail: WWW: I would like to present a poster and/or an oral presentation with the tentative title: ============================================================ Dr. Matthias Krack Phone: +41 (0)91 610-8214 ETH Zurich/CSCS FAX: +41 (0)91 610-8282 Via Cantonale - Galleria 2 E-mail: krack at cscs.ch CH-6928 Manno, Switzerland WWW: http://www.cscs.ch ============================================================ From vuilleum at lptl.jussieu.fr Tue Dec 3 18:19:52 2002 From: vuilleum at lptl.jussieu.fr (Rodolphe VUILLEUMIER) Date: Tue, 03 Dec 2002 18:19:52 +0100 Subject: [CPMD-list] cp2xvibs Message-ID: <3DECE7B8.6030507@lptl.jussieu.fr> Dear all, Some time ago I posted a little program cp2xvibs to the list. It converts the MOLVIB file generated by CPMD after a hessian calculation into a format readable by a personnaly modified version of xvibs.c to generate movies of the normal modes. Downloading these small programs from the list is actually not possible, so I have put them to download on my web page at http://www.jussieu.fr/users/vuilleum . I hope it can be of help to some of you. Regards, Rodolphe Vuilleumier -- Rodolphe Vuilleumier Laboratoire de Physique Theorique de Liquides Universite Pierre et Marie Curie - Tour 16-15 - 5eme etage 4 place Jussieu - 75005 Paris - France Tel: 33-(0)1-44-27-72-39 Fax: 33-(0)1-44-27-51-00 Email:vuilleum at lptl.jussieu.fr From vuilleum at lptl.jussieu.fr Tue Dec 3 18:30:23 2002 From: vuilleum at lptl.jussieu.fr (Rodolphe VUILLEUMIER) Date: Tue, 03 Dec 2002 18:30:23 +0100 Subject: [CPMD-list] cp2xvibs: correct web page Message-ID: <3DECEA2F.7050807@lptl.jussieu.fr> sorry, the correct address for cp2xvibs is http://www.lptl.jussieu.fr/users/vuilleum -- Rodolphe Vuilleumier Laboratoire de Physique Theorique de Liquides Universite Pierre et Marie Curie - Tour 16-15 - 5eme etage 4 place Jussieu - 75005 Paris - France Tel: 33-(0)1-44-27-72-39 Fax: 33-(0)1-44-27-51-00 Email:vuilleum at lptl.jussieu.fr From chesll at ccunix.ccu.edu.tw Wed Dec 4 02:27:33 2002 From: chesll at ccunix.ccu.edu.tw (ccunix) Date: Wed, 4 Dec 2002 09:27:33 +0800 Subject: [CPMD-list] Re: CPMD-list digest, Vol 1 #200 - 4 msgs References: <200212031101.MAA18000@cpmd.org> Message-ID: <001e01c29b34$526cc560$e53e7b8c@uaer> ----- Original Message ----- From: To: Sent: Tuesday, December 03, 2002 7:01 PM Subject: CPMD-list digest, Vol 1 #200 - 4 msgs > Send CPMD-list mailing list submissions to > cpmd-list at cpmd.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cpmd.org/mailman/listinfo/cpmd-list > or, via email, send a message with subject or body 'help' to > cpmd-list-request at cpmd.org > > You can reach the person managing the list at > cpmd-list-admin at cpmd.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of CPMD-list digest..." > > ---------------------------------------------------------------------------- ---- > Today's Topics: > > 1. (no subject) (Audrius Alkauskas) > 2. Goedecker psudopotential cutoffs (Audrius Alkauskas) > 3. Properties (JOSE LUIS RICARDO-CHAVEZ) > 4. CPMD2003 meeting (Monte Verita, Ascona, Switzerland) (Matthias Krack (CSCS)) > ---------------------------------------------------------------------------- ---- > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > > From rjsa at mail.shcnc.ac.cn Thu Dec 5 03:59:49 2002 From: rjsa at mail.shcnc.ac.cn (Rongjian Sa) Date: Thu, 5 Dec 2002 10:59:49 +0800 Subject: [CPMD-list] molecular orbital contours Message-ID: <200212050257.DAA32962@internet-fence.zurich.ihost.com> Dear CPMD users: I want to get the molecular orbital contours. But when I open the cpmd2cube transferred .cube files, I could find the molecular orbitals. So I want to know which keyword should I add to my input files? I wander if you can tell me an exmaple for this scheme. I will greatly appreciate your kind help! Sincerely yours, Rongjian Sa -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021205/096d9eeb/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 418 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20021205/096d9eeb/attachment.gif From niharc2002 at yahoo.com Thu Dec 5 07:40:31 2002 From: niharc2002 at yahoo.com (niharendu choudhury) Date: Wed, 4 Dec 2002 22:40:31 -0800 (PST) Subject: [CPMD-list] Liquid simulation using CPMD code Message-ID: <20021205064031.26518.qmail@web40501.mail.yahoo.com> Dear Prof./friends, I am trying to simulate bulk liquid sodium (Na) using CPMD with 108 particles and supposing that periodic boundary condition is in-built in the program. But after 20000 MD steps of 10 a.u. each, I found some particles are away from the central simulation box, which is originally ~16 Angstorm long. Why it is so if periodic boundary conditions (PBC) on particle coordinates are imposed in all the three directions? Also I found electron energy is increasing continuously and it is in the range of 0.07 a.u. at the end of 20000 steps. Is the dynamics running properly? Is the PBC autometically imposed by the program or I have to give some command in the input file to impose it? Your reply will be highly appreciated. Thank you. Dr. Niharendu Choudhury __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From hutter at pci.unizh.ch Thu Dec 5 09:28:08 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 5 Dec 2002 09:28:08 +0100 (MET) Subject: [CPMD-list] Liquid simulation using CPMD code In-Reply-To: <20021205064031.26518.qmail@web40501.mail.yahoo.com> Message-ID: Hi If you are not using the SYMMETRY 0 options your calculations are using periodic boundary conditions (PBC). PBC are imposed within CPMD for all calculations. However, the particle positions are not folded back to the original computational box. The reason for this is that most people prefer to have "smooth" trajectories without jumps of particles. This allows for easier tracking of special particles and nicer graphics. In addition it is easy (with a little script) to apply PBC yorself if needed. Sodium is a metal, and therefore missing an important feature that allows for stable CP dynamics: the band gap. Using Nose thermostats (on electrons and ions) it might still be possible to perform meaningfull CP simulations (see P. Blochl, M. Parrinello, PRB (45) 9413 (1992)). The choice of parameters for the thermostat will be nontrivial, highly system dependent and require extensive testing. Without thermostats you will have strong coupling between electronic degrees of freedom and ionic dof. Adiabaticity is not maintained and a steady increase of the ficticious kinetic energy will occur. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Wed, 4 Dec 2002, niharendu choudhury wrote: > > Dear Prof./friends, > I am trying to simulate bulk liquid sodium (Na) using > CPMD with 108 particles and supposing that periodic > boundary condition is in-built in the program. But > after 20000 MD steps of 10 a.u. each, I found some > particles are away from the central simulation box, > which is originally ~16 Angstorm long. > > Why it is so if periodic boundary conditions (PBC) on > particle coordinates are imposed in all the three > directions? > > Also I found electron energy is increasing > continuously and it is in the range of 0.07 a.u. at > the end of 20000 steps. > > Is the dynamics running properly? > Is the PBC autometically imposed by the program or I > have to give some command in the input file to impose > it? > Your reply will be highly appreciated. > Thank you. > Dr. Niharendu Choudhury > > > > > > __________________________________________________ > Do you Yahoo!? > Yahoo! Mail Plus - Powerful. Affordable. Sign up now. > http://mailplus.yahoo.com > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From hutter at pci.unizh.ch Thu Dec 5 09:32:30 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Thu, 5 Dec 2002 09:32:30 +0100 (MET) Subject: [CPMD-list] Properties In-Reply-To: <3DEB67CE.9070305@irsamc.ups-tlse.fr> Message-ID: Hi the same problem was reported by Julia Khalack on Nov 15. http://www.cpmd.org/pipermail/cpmd-list/2002-November/000521.html I posted a bug fix http://www.cpmd.org/pipermail/cpmd-list/2002-November/000522.html but there was another problem we haven't yet solved. Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Mon, 2 Dec 2002, JOSE LUIS RICARDO-CHAVEZ wrote: > Dear CPMD community, > > I an using CPMD to perform LSD calculations on bimetallic magnetic clusters > using ultrasoft pseudopotentials. The optimization of cluster geometry works > fine but when I try to use the computed wavefunction to obtain the Mulliken > charges using the default basis set it gives the following message: > > -------------------------------------------------------------- > PROJECT WAVEFUNCTIONS ON ATOMIC PSEUDO-WAVEFUNCTIONS > MULLIKEN POPULATION ANALYSIS AND MAYER BOND-ORDERS > > > **************************************************************** > * PROPERTY CALCULATIONS * > **************************************************************** > > > RESTART INFORMATION READ ON FILE ./RESTART > *** PHFAC| THE NEW SIZE OF THE PROGRAM IS 11948 kBYTES *** > LSCR= 100 MAX(LRNLSM1,LRNLSM2) = 20264 > > > PROGRAM STOPS IN SUBROUTINE RNLSM| SCRATCH ARRAY TOO SMALL > FORTRAN STOP 999 > -------------------------------------------------------------- > > Does anybody knows how to correct this error? > > Thanks in advance, greetings. > > - Jos? Luis > > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From jwh at science.uva.nl Thu Dec 5 09:49:53 2002 From: jwh at science.uva.nl (Jan-Willem Handgraaf) Date: Thu, 5 Dec 2002 09:49:53 +0100 Subject: [CPMD-list] Liquid simulation using CPMD code In-Reply-To: <20021205064031.26518.qmail@web40501.mail.yahoo.com> References: <20021205064031.26518.qmail@web40501.mail.yahoo.com> Message-ID: <200212050949.53365.jwh@science.uva.nl> On Thursday 05 December 2002 07:40, niharendu choudhury wrote: > Dear Prof./friends, > I am trying to simulate bulk liquid sodium (Na) using > CPMD with 108 particles and supposing that periodic > boundary condition is in-built in the program. But > after 20000 MD steps of 10 a.u. each, I found some > particles are away from the central simulation box, > which is originally ~16 Angstorm long. What program are you using to visualize your system? Check if it also takes into account periodic boundary conditions. > Also I found electron energy is increasing > continuously and it is in the range of 0.07 a.u. at > the end of 20000 steps. Did you consider using a thermostat for the electrons? Regards, Jan-Willem -- Jan-Willem Handgraaf Department of Chemical Engineering University of Amsterdam Nieuwe Achtergracht 166 1018 WV Amsterdam The Netherlands Room: C6.18 Tel: +31-20-5256492 Fax: +31-20-5255604 Email: jwh at science.uva.nl From yi_gao_cn at yahoo.com Thu Dec 5 11:45:59 2002 From: yi_gao_cn at yahoo.com (Yi Gao) Date: Thu, 5 Dec 2002 02:45:59 -0800 (PST) Subject: [CPMD-list] About thermostat Message-ID: <20021205104559.14962.qmail@web21305.mail.yahoo.com> Dear Sir, I'm now doing NVT and find that the temperature varies from 150K to 450K when the thermostat is 300K. I don't know how to decrease the variation around 300K. Please help me. Below is my input: &CPMD RESTART ALL LATEST MOLECULAR DYNAMICS QUENCH ELECTRONS BO TRAJECTORY SAMPLE 10 NOSE IONS 300 2000 NOSE ELECTRONS 0.0001 6000 NOSE PARAMETERS 8 8 4 40 125 1 EMASS 800 &END Yi Gao Institute of Theoretical and Computational Chemistry, Nanjing Univ. P.R.China http://itcc.nju.edu.cn __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From chenghuiqc at sina.com Mon Dec 9 15:11:00 2002 From: chenghuiqc at sina.com (chenghuiqc) Date: Mon, 09 Dec 2002 22:11:00 +0800 Subject: [CPMD-list] How to use Constraints in CPMD Message-ID: <20021209141100.3145.qmail@sina.com> Dear cpmd-list all, I have some question for the Shove option in &ATOMS section in CPMD input file.How can I change some coordinates during the MD run? The manual only says to use shove option and set the entry to -1,0,or 1. Can anyone tell me how to set the changing step and all about the shove option? thank you chenhui Chem Dept, Nanjing Univ P.R.China ______________________________________ =================================================================== ????????????15M???????? ?????????? (http://vip.sina.com/sol_mail/promotion/pro_men.html) ?????????????????????????????????????????? (http://classad.sina.com.cn/2shou/) ?????????????????????????????????????????????????? (http://sms.sina.com.cn/cgi-bin/sms/smspic.cgi) From hutter at pci.unizh.ch Mon Dec 9 18:32:09 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 9 Dec 2002 18:32:09 +0100 (MET) Subject: [CPMD-list] How to use Constraints in CPMD In-Reply-To: <20021209141100.3145.qmail@sina.com> Message-ID: Hi Constraints are fulfilled exactly within the MD. The SHOVE keyword allows to have one-sided constraints. This means the constraint value is allowed to shrink (or increase depending on the value of the SHOVE parameter). However, this option doesn't allow you to force a change in the constraint value. If you want to change the value of the constraint for example linearly you have to add a corresponding line of new code to the MD routine. This option is not available in the standard code. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Mon, 9 Dec 2002, chenghuiqc wrote: > Dear cpmd-list all, > I have some question for the Shove option in > &ATOMS section in CPMD input file.How can I change some > coordinates during the MD run? The manual only says > to use shove option and set the entry to -1,0,or 1. > Can anyone tell me how to set the changing step and > all about the shove option? > > thank you > > chenhui > Chem Dept, Nanjing Univ > P.R.China > > > ______________________________________ > > =================================================================== > ????????????15M???????? ?????????? (http://vip.sina.com/sol_mail/promotion/pro_men.html) > ?????????????????????????????????????????? (http://classad.sina.com.cn/2shou/) > ?????????????????????????????????????????????????? (http://sms.sina.com.cn/cgi-bin/sms/smspic.cgi) > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From andrea.fortini at mi.infn.it Tue Dec 10 00:54:55 2002 From: andrea.fortini at mi.infn.it (Andrea Fortini) Date: Mon, 9 Dec 2002 18:54:55 -0500 Subject: [CPMD-list] NLCC section Message-ID: <200212091854.55635.andrea.fortini@mi.infn.it> Dear all, I use a pseudopotential for sodium with analitic NLCC of this type &NLCC ANAL 0.020688 0.015611 0.685277 &END It works well with CPMD v3.5.2, but if I use CPMD v 3.5.3 I get this error UNKNOWN TYPE OF NLCC I would like to use this pseudo also with latest cpmd version: there some new option I have to add to input file or pseudo file, or I have to produce a new pseudo with numerical core correction? Thank you very much. Regards Andrea Fortini -- ************************************************************************* Andrea Fortini Universita' degli Studi di Milano Dipartimento di Fisica Via Celoria, 16 20135 Milano Italy Tel: (+39) 02 5031 7654 Fax: (+39) 02 5031 7487 Home page: www.mi.infn.it/~fortini ************************************************************************* From hutter at pci.unizh.ch Mon Dec 9 19:16:07 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Mon, 9 Dec 2002 19:16:07 +0100 (MET) Subject: [CPMD-list] NLCC section In-Reply-To: <200212091854.55635.andrea.fortini@mi.infn.it> Message-ID: Hi the update for USPP NLCC calculation introduced an error in the routine nlccset.F . You can fix this by replacing line 89 ELSEIF (NLCCT(IS).EQ.2) THEN by ELSEIF (NLCCT(IS).EQ.1) THEN regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Mon, 9 Dec 2002, Andrea Fortini wrote: > Dear all, > > I use a pseudopotential for sodium with analitic NLCC > of this type > > &NLCC > ANAL > 0.020688 0.015611 0.685277 > &END > > It works well with CPMD v3.5.2, but if I use CPMD v 3.5.3 I get this error > > UNKNOWN TYPE OF NLCC > > I would like to use this pseudo also with latest cpmd version: there some new > option I have to add to input file or pseudo file, or I have to produce a new > pseudo with numerical core correction? > > Thank you very much. > > Regards > Andrea Fortini > -- > ************************************************************************* > Andrea Fortini > Universita' degli Studi di Milano > Dipartimento di Fisica > Via Celoria, 16 > 20135 Milano > Italy > Tel: (+39) 02 5031 7654 > Fax: (+39) 02 5031 7487 > Home page: www.mi.infn.it/~fortini > ************************************************************************* > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From chenghuiqc at sina.com Fri Dec 13 15:33:32 2002 From: chenghuiqc at sina.com (chenghuiqc) Date: Fri, 13 Dec 2002 22:33:32 +0800 Subject: [CPMD-list] DIFFER keyword in CPMD Message-ID: <20021213143332.23870.qmail@sina.com> Dear cpmd-listers, I found that in the CPMD source file mm_coninp.F there are a parameter DIFFER. It should be one of the keyworks in the CONSTRAINTS part, but the manual do not introduce this parameter. In the source file there are a remark line that is DIFFER n1 n2 n3 dR0 [+1,-1,0] Who can tell me the meaning of this line? chenhui Dept Chem, Nanjing Univ P.R.China ______________________________________ =================================================================== ????????????15M???????? ?????????? (http://vip.sina.com/sol_mail/promotion/pro_men.html) ?????????????????????????????????????????? (http://classad.sina.com.cn/2shou/) ?????????????????????????????????????????????????? (http://sms.sina.com.cn/cgi-bin/sms/smspic.cgi) From hutter at pci.unizh.ch Wed Dec 18 13:27:35 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Wed, 18 Dec 2002 13:27:35 +0100 (MET) Subject: [CPMD-list] DIFFER keyword in CPMD In-Reply-To: <20021213143332.23870.qmail@sina.com> Message-ID: Hi with this Keyword R12-R23 is constraint to the value dR0. R12 = |R(n1)-R(n2)| and R23 = |R(n2)-R(n3)| regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Fri, 13 Dec 2002, chenghuiqc wrote: > Dear cpmd-listers, > > I found that in the CPMD source file > mm_coninp.F there are a parameter DIFFER. It > should be one of the keyworks in the CONSTRAINTS > part, but the manual do not introduce this parameter. > In the source file there are a remark line that is > > DIFFER n1 n2 n3 dR0 [+1,-1,0] > > Who can tell me the meaning of this line? > > > chenhui > Dept Chem, Nanjing Univ > P.R.China > ______________________________________ > > =================================================================== > ????????????15M???????? ?????????? (http://vip.sina.com/sol_mail/promotion/pro_men.html) > ?????????????????????????????????????????? (http://classad.sina.com.cn/2shou/) > ?????????????????????????????????????????????????? (http://sms.sina.com.cn/cgi-bin/sms/smspic.cgi) > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From krack at cscs.ch Fri Dec 20 17:22:24 2002 From: krack at cscs.ch (Matthias Krack (CSCS)) Date: Fri, 20 Dec 2002 17:22:24 +0100 (CET) Subject: [CPMD-list] REMINDER: CPMD2003 meeting (Monte Verita, Ascona, Switzerland) Message-ID: Dear CPMD User, Continuing the tradition of biannual CPMD meetings that we have started in Ringberg in 1999, we are organizing on the 13-16 March 2003 in the beautiful conference centre Stefano Franscini (http://www.csf-mv.ethz.ch) on Monte Verita (Ascona) close to Lugano (Switzerland) the third meeting in this series. Unfortunately, we will not be able to cover the full expenses and each participant will be asked to pay his own accommodation and travel costs. The expected fee will be in the order of 500 SFr depending on the amount of industrial funding. This will cover your full board accommodation at the centre (including lodging, all meals, coffee). Those of you who are interested are requested to perform an online registration (http://www.cscs.ch/events/cpmd/form.html) or to complete and return the attached registration form giving a tentative title for a possible presentation BEFORE THE 15TH OF JANUARY. At that time the funding situation will be clearer and instructions on how to pay the fee will be given. Unfortunately due to the space limitations there is a cap on the total number of participants. For that reason EARLY REGISTRATION IS RECOMMENDED. A number of oral contributions will be selected with special preference for young speakers below 35 years of age. M. Krack, M. Parrinello, U. Roethlisberger CPMD2003 March 13-16, 2003 Monte Verita, Ascona, Switzerland Registration Form First Name: Last Name: Institution: Street Address: Zip Code and City: Country: Phone: Fax: E-mail: WWW: I would like to present a poster and/or an oral presentation with the tentative title: ============================================================ Dr. Matthias Krack Phone: +41 (0)91 610-8214 ETH Zurich/CSCS FAX: +41 (0)91 610-8282 Via Cantonale - Galleria 2 E-mail: krack at cscs.ch CH-6928 Manno, Switzerland WWW: http://www.cscs.ch ============================================================ From M.A.Zwijnenburg at tnw.tudelft.nl Mon Dec 23 15:16:11 2002 From: M.A.Zwijnenburg at tnw.tudelft.nl (Martijn Zwijnenburg) Date: Mon, 23 Dec 2002 15:16:11 +0100 Subject: [CPMD-list] langevin molecular dynamics Message-ID: <3E0728AF.15304.399854B4@localhost> Hi, I have a somewhat more general question. I've recently found an article where they used ab initio langevin quantum molecular dynamics (lqmd) to study the time evolution of a condensed system of silicon clusters. Now I know from classical langevin md that you use a stochastic force to describe the influence of temperature and I guess the same holds for lqmd. Being in this sence somewhat comparable to thermostatted Car-Parinello MD. I would like to know if somebody can tell me how good one can expect the results of lqmd to be compared to say thermostatted Car- Parinello or Born-Oppenheimer MD? Cheers, Martijn ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg at tnw.tudelft.nl web page: http://come.to/tock From rjsa at mail.shcnc.ac.cn Mon Dec 23 15:53:19 2002 From: rjsa at mail.shcnc.ac.cn (Rongjian Sa) Date: Mon, 23 Dec 2002 22:53:19 +0800 Subject: [CPMD-list] Merry Christmas Message-ID: <200212240549.gBO5nZkd016814@mail.shcnc.ac.cn> Dear CPMD Devolper and Users: Thank you for you kind help! Christmas is coming, So Merry Christmas and with best wishes! Sincerely yours, Rongjian Sa -------------- next part -------------- An HTML attachment was scrubbed... URL: http://cpmd.org/pipermail/cpmd-list/attachments/20021223/59569e2a/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 418 bytes Desc: not available Url : http://cpmd.org/pipermail/cpmd-list/attachments/20021223/59569e2a/attachment.gif From yyteng at imr.ac.cn Wed Dec 25 14:51:58 2002 From: yyteng at imr.ac.cn (ÌÚÓ¢Ôª) Date: Wed, 25 Dec 2002 14:51:58 Subject: [CPMD-list] for helping Message-ID: <200212250643.HAA06762@internet-fence.zurich.ihost.com> dear F merry christmas!!! still the problem when I run the Ni fcc according to your advise I obtain the following message "ETOT=Inf" "DETOT=NaN" what is the meaning? another problem how I draw the dos curve created by cpmd? the two problem bother me long time thank you your chinese friend yyteng From yyteng at imr.ac.cn Wed Dec 25 14:52:04 2002 From: yyteng at imr.ac.cn (ÌÚÓ¢Ôª) Date: Wed, 25 Dec 2002 14:52:04 Subject: [CPMD-list] for helping Message-ID: <200212250643.HAA08490@internet-fence.zurich.ihost.com> dear F merry christmas!!! still the problem when I run the Ni fcc according to your advise I obtain the following message "ETOT=Inf" "DETOT=NaN" what is the meaning? another problem how I draw the dos curve created by cpmd? the two problem bother me long time thank you your chinese friend yyteng From yyteng at imr.ac.cn Wed Dec 25 14:52:11 2002 From: yyteng at imr.ac.cn (ÌÚÓ¢Ôª) Date: Wed, 25 Dec 2002 14:52:11 Subject: [CPMD-list] for helping Message-ID: <200212250643.HAA07760@internet-fence.zurich.ihost.com> dear all merry christmas!!! still the problem when I run the Ni fcc according to your advise I obtain the following message "ETOT=Inf" "DETOT=NaN" what is the meaning? another problem how I draw the dos curve created by cpmd? the two problem bother me long time thank you your chinese friend yyteng From Ari.P.Seitsonen at iki.fi Wed Dec 25 17:28:32 2002 From: Ari.P.Seitsonen at iki.fi (Ari.P.Seitsonen at iki.fi) Date: Wed, 25 Dec 2002 17:28:32 +0100 Subject: [CPMD-list] for helping In-Reply-To: <200212250643.HAA07760@internet-fence.zurich.ihost.com> (yyteng@imr.ac.cn) References: <200212250643.HAA07760@internet-fence.zurich.ihost.com> Message-ID: <200212251628.gBPGSWf23751@magadino.cscs.ch> Dear Yyteng, The output # "ETOT=Inf" # "DETOT=NaN" means that there is something very much wrong indeed in the job; could you please send us at least the input and the description for what you are trying to calculate? Greetings, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From chenghuiqc at sina.com Fri Dec 27 09:44:10 2002 From: chenghuiqc at sina.com (chenghuiqc) Date: Fri, 27 Dec 2002 16:44:10 +0800 Subject: [CPMD-list] constraint force in file CONSTRAINT Message-ID: <20021227084410.17053.qmail@sina.com> Dear cpmd-list all, I want to know does the file CONSTRAINT in cpmd contains any information about the force on the constraint, or are there other methods to produce the result the force on the constraint. chenhui Dept Chem, Nanjing Univ P.R.China ______________________________________ =================================================================== ????????????15M?????? ???????????????????? (http://vip.sina.com/sol_mail/promotion/pro_men.html) ?????????????????????????????????????????? (http://classad.sina.com.cn/2shou/) ????1???????????????????????? (http://sms.sina.com.cn/act/beautyxmas.html) From jwh at science.uva.nl Sat Dec 28 12:37:16 2002 From: jwh at science.uva.nl (Jan-Willem Handgraaf) Date: Sat, 28 Dec 2002 12:37:16 +0100 Subject: [CPMD-list] constraint force in file CONSTRAINT In-Reply-To: <20021227084410.17053.qmail@sina.com> References: <20021227084410.17053.qmail@sina.com> Message-ID: <200212281237.16354.jwh@science.uva.nl> On Friday 27 December 2002 09:44, chenghuiqc wrote: > Dear cpmd-list all, > I want to know does the file CONSTRAINT in cpmd contains any information > about the force on the constraint, or are there other methods to produce > the result the force on the constraint. Dear Chenhui, Yes, 'CONSTRAINT' contains the force and the value of the constraint both in a.u. Jan-Willem -- Jan-Willem Handgraaf Department of Chemical Engineering University of Amsterdam Nieuwe Achtergracht 166 1018 WV Amsterdam The Netherlands Room: C6.18 Tel: +31-20-5256492 Fax: +31-20-5255604 Email: jwh at science.uva.nl From chenghuiqc at sina.com Sat Dec 28 14:23:47 2002 From: chenghuiqc at sina.com (chenghuiqc) Date: Sat, 28 Dec 2002 21:23:47 +0800 Subject: [CPMD-list] problem of using USPP in cpmd Message-ID: <20021228132347.13075.qmail@sina.com> Dear cpmd-list all, I am now using a vanderbilt Vanderbilt USPP in cpmd for a Fe containing system. I found that if I include the Fe atom in my system we get the error **************************************************************** * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * * Fe 55.8470 1.2000 NO VANDERBILT * * C 12.0112 1.2000 NO VANDERBILT * * O 15.9994 1.2000 NO VANDERBILT * * N 14.0067 1.2000 NO VANDERBILT * * H 1.0080 1.2000 NO VANDERBILT * **************************************************************** PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES 0 7119 56911 24 454 1810 56 60 1 7117 56902 24 454 1812 56 60 2 7112 56849 24 453 1811 57 60 3 7116 56914 24 456 1812 56 60 G=0 COMPONENT ON PROCESSOR : 2 PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA *** LOADPA| THE NEW SIZE OF THE PROGRAM IS 76955 kBYTES *** *** RGGEN| THE NEW SIZE OF THE PROGRAM IS 78299 kBYTES *** !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 4 9 9 !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 4 9 9 !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 4 9 9 PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 2] Who can tell me what's wrong with my USPP for Fe and how to solve this problem? Thank you. chenhui Dept Chem,Nanjing Univ P.R.China ______________________________________ =================================================================== ????????????15M?????? ???????????????????? (http://vip.sina.com/sol_mail/promotion/pro_men.html) ?????????????????????????????????????????? (http://classad.sina.com.cn/2shou/) ????1???????????????????????? (http://sms.sina.com.cn/act/beautyxmas.html) From hutter at pci.unizh.ch Sat Dec 28 16:10:39 2002 From: hutter at pci.unizh.ch (Juerg Hutter) Date: Sat, 28 Dec 2002 16:10:39 +0100 (MET) Subject: [CPMD-list] problem of using USPP in cpmd In-Reply-To: <20021228132347.13075.qmail@sina.com> Message-ID: Hi you can try to change the following two lines in the file aainit.F 145c145 < CALL AZZERO(U,LX*MX*MX) --- > CALL AZZERO(U,2*LX*MX*MX) 228c228 < CALL AZZERO(AA,LIX*MIX*LIX*MIX*LX*MX) --- > CALL AZZERO(AA,2*LIX*MIX*LIX*MIX*LX*MX) This will most likely fix the problem. regards Juerg ---------------------------------------------------------- Juerg Hutter Phone : ++41 1 635 4491 Physical Chemistry Institute FAX : ++41 1 635 6838 University of Zurich E-mail: hutter at pci.unizh.ch Winterthurerstrasse 190 CH-8057 Zurich, Switzerland ---------------------------------------------------------- On Sat, 28 Dec 2002, chenghuiqc wrote: > Dear cpmd-list all, > I am now using a vanderbilt Vanderbilt USPP in cpmd for a Fe > containing system. I found that if I include the Fe atom in my > system we get the error **************************************************************** > * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL * > * Fe 55.8470 1.2000 NO VANDERBILT * > * C 12.0112 1.2000 NO VANDERBILT * > * O 15.9994 1.2000 NO VANDERBILT * > * N 14.0067 1.2000 NO VANDERBILT * > * H 1.0080 1.2000 NO VANDERBILT * > **************************************************************** > > > PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA > NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES > 0 7119 56911 24 454 1810 56 60 > 1 7117 56902 24 454 1812 56 60 > 2 7112 56849 24 453 1811 57 60 > 3 7116 56914 24 456 1812 56 60 > G=0 COMPONENT ON PROCESSOR : 2 > PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA > > *** LOADPA| THE NEW SIZE OF THE PROGRAM IS 76955 kBYTES *** > *** RGGEN| THE NEW SIZE OF THE PROGRAM IS 78299 kBYTES *** > !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 4 9 9 > !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 4 9 9 > !!! ERROR !!! AP(ILP,IL,IK) = 0.00000******** 4 9 9 > > > PROGRAM STOPS IN SUBROUTINE AAINIT| [PROC= 2] > > > Who can tell me what's wrong with my USPP for Fe and how to solve > this problem? Thank you. > > chenhui > Dept Chem,Nanjing Univ > P.R.China > ______________________________________ > > =================================================================== > ????????????15M?????? ???????????????????? (http://vip.sina.com/sol_mail/promotion/pro_men.html) > ?????????????????????????????????????????? (http://classad.sina.com.cn/2shou/) > ????1???????????????????????? (http://sms.sina.com.cn/act/beautyxmas.html) > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > From chenghuiqc at sina.com Mon Dec 30 04:18:34 2002 From: chenghuiqc at sina.com (chenghuiqc) Date: Mon, 30 Dec 2002 11:18:34 +0800 Subject: [CPMD-list] print force on the constraints Message-ID: <20021230031834.26828.qmail@sina.com> Dear cpmd-list all, I want to know which keywork in cpmd can print the force on constraints to the file CONSTRAINT chenhui Dept Chem,Nanjing univ P.R.China ______________________________________ =================================================================== ????????????15M?????? ???????????????????? (http://vip.sina.com/sol_mail/promotion/pro_men.html) ?????????????????????????????????????????? (http://classad.sina.com.cn/2shou/) ????1???????????????????????? (http://sms.sina.com.cn/act/beautyxmas.html) From niharc2002 at yahoo.com Wed Dec 4 06:22:33 2002 From: niharc2002 at yahoo.com (niharendu choudhury) Date: Tue, 3 Dec 2002 21:22:33 -0800 (PST) Subject: [CPMD-list] CPMD for bulk liquid simulation Message-ID: <20021204052233.89656.qmail@web40507.mail.yahoo.com> Dear Prof./friends, I am trying to simulate bulk liquid sodium (Na) using CPMD with 108 particles and supposing that periodic boundary condition is in-built in the program. But after 20000 MD steps of 10 au each, I found some particles are away from the central simulation box, which is originally ~16 Angstorm long. Why it is so if periodic boundary conditions (PBC) on particle coordinates are imposed in all the three directions? Also I found electron energy is increasing continuously and it is in the range of 0.02 a.u. Is the MD dynamics running properly? Is the PBC autometically imposed by the program or I have to give some command in the input file to impose it? Your reply will be highly appreciated. Thank you. Dr. Niharendu Choudhury __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From chenghuiqc at sina.com Thu Dec 5 12:39:29 2002 From: chenghuiqc at sina.com (chenghuiqc) Date: Thu, 05 Dec 2002 19:39:29 +0800 Subject: [CPMD-list] How to use Constraints in CPMD Message-ID: <20021205113929.24943.qmail@sina.com> Dear cpmd-list all, I have some question for the Shove option in &ATOMS section in CPMD input file.How can I change some coordinates during the MD run? The manual only says to use shove option and set the entry to -1,0,or 1. Can anyone tell me how to set the changing step and all about the shove option? thank you chenhui Chem Dept, Nanjing Univ P.R.China ______________________________________ =================================================================== ????????????15M???????? ?????????? (http://vip.sina.com/sol_mail/promotion/pro_men.html) ?????????????????????????????????????????? (http://classad.sina.com.cn/2shou/) ?????????????????????????????????????????????????? (http://sms.sina.com.cn/cgi-bin/sms/smspic.cgi) From kai.reichert at udo.edu Thu Dec 5 13:03:34 2002 From: kai.reichert at udo.edu (Kai Reichert) Date: Thu, 05 Dec 2002 13:03:34 +0100 Subject: [CPMD-list] cpmd-3.5.2 & ifc-6.0.1 Message-ID: <3DEF4096.4000408@udo.edu> Dear All, I'm not able to compile CPMD. As I own an Intel Fortran Compiler I issue the following command : Configure PC-IFC > Makefile I can then compile CPMD, but in the last linking stage I get dozens of undefined references. I tried to compile ATLAS on my own. But that did not work :-( In the newsgroups I found the hint, I should compile ATLAS also with ifc, instead of g77. Thats solve a lot of my undefined references, but it seems, that the liblapack library of ATLAS is insufficient ? I tried to compile the whole LAPACK distribution, but I failed. With my ifc, the compile process run in an infinite loop :-( I would really appreciate if someone could give detailed instructions on how to compile CPMD and all its required libraries on a standard redhat 7.3 linux system. Regards, Kai Reichert ----------------------------------------------- University of Dortmund Department of Chemical Engineering Campus Nord, Building G II, 5th floor Chair of Thermodynamics From cpmd-list at cpmd.org Thu Dec 5 14:26:52 2002 From: cpmd-list at cpmd.org (cpmd-list at cpmd.org) Date: Thu, 5 Dec 2002 14:26:52 +0100 Subject: [CPMD-list] About thermostat In-Reply-To: <20021205104559.14962.qmail@web21305.mail.yahoo.com> (message from Yi Gao on Thu, 5 Dec 2002 02:45:59 -0800 (PST)) References: <20021205104559.14962.qmail@web21305.mail.yahoo.com> Message-ID: <200212051326.gB5DQq631266@magadino.cscs.ch> Dear Dr Gao, > I'm now doing NVT and find that the temperature varies > from 150K to 450K when the thermostat is 300K. I don't > know how to decrease the variation around 300K. Please > help me. Below is my input: > > &CPMD > RESTART ALL LATEST > MOLECULAR DYNAMICS > QUENCH ELECTRONS BO > TRAJECTORY SAMPLE > 10 > NOSE IONS > 300 2000 > NOSE ELECTRONS > 0.0001 6000 > NOSE PARAMETERS > 8 8 4 40 125 1 > EMASS > 800 > &END > > Yi Gao > > Institute of Theoretical and Computational Chemistry, > Nanjing Univ. P.R.China > http://itcc.nju.edu.cn First of all, how many atoms do you have in your system? Like replied earlier on the list (http://www.cpmd.org/pipermail/cpmd-list/2002-November/000499.html), the intrinsic fluctuations (in NVE ensemble) depends on the number of degrees of freedom. Secondly, are you sure that there are ionic vibrations at 2000 cm^-1 to which the Nose thermostat can couple to? Hopefully you are aware of the possible implications caused by using thermostats, please see e.g. the books by Allen & Tildesley and Frenkel & Smit. Well, in metallic systems this might be the only possibility to conserve the total energy, I admit. Thirdly, many people on the list have sent inputs with a very small value for the target of the fictitious kinetic energy. Please notice that if it's too small the energy drift is INCREASED [see the paper by P. Blochl, M. Parrinello, PRB 45 (1992) 9413], so please be careful with these parameters. Greetings, apsi -- -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/ Tel +41 1 635 44 97 / Fax +41 1 635 68 38 / GSM +41 79 719 09 35 Anschrift: Physikalisch Chemisches Institut (PCI), Universit?t Z?rich (UniZh) Indirizzo: Winterthurerstra?e 190, CH-8057 Z?rich Address: Schweiz / Svizzera / Suisse / Svizra / Switzerland From kallies at zib.de Tue Dec 10 00:28:03 2002 From: kallies at zib.de (Bernd Kallies) Date: 10 Dec 2002 00:28:03 +0100 Subject: [CPMD-list] Problem with FFT_ESSL in CPMD353 on IBM p690 Message-ID: <1039476483.1166.280.camel@kallies> Dear all, I tried to compile/use CPMD 3.5.3 on an IBM p690 (Power4, AIX 5.1L, xlf8.1). I linked with my own LAPACK_CCI and IBM's ESSL. The preprocessor directives I used were -D__IBM -DESSL -DPARALLEL -DMP_LIBRARY=__MPI -DFFT_ESSL. Compiler flags for mpxlf_r were -O3 -qstrict -qmaxmem=-1 -qxlf77=leadzero -qintsize=4 -qrealsize=4 -qdpc=e -qarch=auto -qtune=auto I ran into problems when gradients of the density have to be calculated. Problems became clearly visible in geometry optimizations, when ZHEEV of LAPACK was entered with a matrix that contained NaNQ only, which caused crazy LANCZOS iterations with always the same results: ================================================================ == FORCES INITIALIZATION == ================================================================ EWALD SUM IN REAL SPACE OVER 9* 9* 9 CELLS << 1:10<<<<<<<<<<<< LANCZOS DIAGONALIZATION <<<<<<<<<<<<<<<<<<<< >> TIME FOR INITIAL SUBSPACE DIAGONALIZATION: 2.26 >> CYCLE NCONV B2MAX B2MIN #HPSI TIME 1 0 0.000E+00 1.000E+30 8.00 19.53 2 0 0.000E+00 1.000E+30 7.00 18.62 3 0 0.000E+00 1.000E+30 7.00 17.99 ... forever ... Problems disappear when I replace -DFFT_ESSL by -DFFT_DEFAULT. As far as I figured out, the problems begin already after the first call of INVFFT during the initialization of a run. An inspection of the in- and output of the first call of MLTFFT from INVFFT showed that it seems to return another and probably wrong FFT for the same input, when DCFT from IBM's ESSL is used. An example (ldax=81,lday=3281,n=80,m=3281,naux1=naux2=50000), result B at the end of the first call of MLTFFT: i j B(i,j) with -DFFT_DEFAULT B(i,j) with -DFFT_ESSL ( real imag ) ( real imag ) -------------------------------------------------------------- ... 473 1 ( .10164E+00 .70343E-17) ( .10164E+00 .70343E-17) 473 2 ( -.10241E+00 .15902E-16) ( -.10241E+00 -.70343E-17) 473 3 ( .10471E+00 -.16883E-16) ( .10471E+00 .70343E-17) 473 4 ( -.10865E+00 -.19796E-17) ( -.10865E+00 -.70343E-17) 473 5 ( .11441E+00 -.98143E-17) ( .11441E+00 .70343E-17) 473 6 ( -.12201E+00 -.54733E-17) ( -.12201E+00 -.70343E-17) 473 7 ( .13087E+00 -.13232E-16) ( .13087E+00 .70343E-17) 473 8 ( -.13966E+00 .19261E-16) ( -.13966E+00 -.70343E-17) 473 9 ( .14670E+00 -.22676E-17) ( .14670E+00 .70343E-17) 473 10 ( -.15089E+00 .14765E-16) ( -.15089E+00 -.70343E-17) 473 11 ( .15238E+00 .70343E-17) ( .15238E+00 .70343E-17) 473 12 ( -.15239E+00 .12665E-16) ( -.15239E+00 -.70343E-17) ... -------------------------------------------------------------- I'm not sure if this is caused by a bug in IBM's ESSL, or by a bug in CPMD regarding use of IBM's ESSL. Since CPMD is copyrighted by IBM, I believe the CPMD mailing list to be appropriate to post this problem to both the CPMD team and IBM. I'd like to know if or when there will be a fix available. An example CPMD input can be obtained from me on request, if this helps. In the meantime we'll not use ESSL for FFT's in any application. Best regards, B. Kallies -- Dr. Bernd Kallies Konrad-Zuse-Zentrum f?r Informationstechnik Berlin Takustr. 7 14195 Berlin Germany Tel: +49-30-84185-270 Fax: +49-30-84185-311 e-mail: kallies at zib.de From krack at cscs.ch Tue Dec 17 10:43:05 2002 From: krack at cscs.ch (Matthias Krack (CSCS)) Date: Tue, 17 Dec 2002 10:43:05 +0100 (CET) Subject: [CPMD-list] REMINDER: CPMD2003 meeting (Monte Verita, Ascona, Switzerland) Message-ID: Dear CPMD User, Continuing the tradition of biannual CPMD meetings that we have started in Ringberg in 1999, we are organizing on the 13-16 March 2003 in the beautiful conference centre Stefano Franscini (http://www.csf-mv.ethz.ch) on Monte Verita (Ascona) close to Lugano (Switzerland) the third meeting in this series. Unfortunately, we will not be able to cover the full expenses and each participant will be asked to pay his own accommodation and travel costs. The expected fee will be in the order of 500 SFr depending on the amount of industrial funding. This will cover your full board accommodation at the centre (including lodging, all meals, coffee). Those of you who are interested are requested to perform an online registration (http://www.cscs.ch/events/cpmd/form.html) or to complete and return the attached registration form giving a tentative title for a possible presentation BEFORE THE 15TH OF JANUARY. At that time the funding situation will be clearer and instructions on how to pay the fee will be given. Unfortunately due to the space limitations there is a cap on the total number of participants. For that reason EARLY REGISTRATION IS RECOMMENDED. A number of oral contributions will be selected with special preference for young speakers below 35 years of age. Buone feste! Merry Christmas and Happy New Year! M. Krack, M. Parrinello, U. Roethlisberger CPMD2003 March 13-16, 2003 Monte Verita, Ascona, Switzerland Registration Form First Name: Last Name: Institution: Street Address: Zip Code and City: Country: Phone: Fax: E-mail: WWW: I would like to present a poster and/or an oral presentation with the tentative title: ============================================================ Dr. Matthias Krack Phone: +41 (0)91 610-8214 ETH Zurich/CSCS FAX: +41 (0)91 610-8282 Via Cantonale - Galleria 2 E-mail: krack at cscs.ch CH-6928 Manno, Switzerland WWW: http://www.cscs.ch ============================================================ From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Mon Dec 30 23:15:27 2002 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Mon, 30 Dec 2002 23:15:27 +0100 Subject: [CPMD-list] cpmd-3.5.2 & ifc-6.0.1 In-Reply-To: <3DEF4096.4000408@udo.edu> Message-ID: <200212302215.gBUMFRp29971@yello.theochem.ruhr-uni-bochum.de> On Thu, 05 Dec 2002 13:03:34 +0100 Kai Reichert wrote: > Dear All, > > > I'm not able to compile CPMD. > > As I own an Intel Fortran Compiler I issue the following command : > > Configure PC-IFC > Makefile > > > I can then compile CPMD, but in the last linking stage I get dozens of > undefined references. > > > I tried to compile ATLAS on my own. > But that did not work :-( > > In the newsgroups I found the hint, I should compile ATLAS also with > ifc, instead of g77. you could also try 'g77 -fno-second-underscore' atlas. > > Thats solve a lot of my undefined references, but it seems, that the > liblapack library of ATLAS is insufficient ? > > I tried to compile the whole LAPACK distribution, but I failed. With my > ifc, the compile process run in an infinite loop :-( try compiling lapack with 'g77 -fno-second-underscore' and then link first atlas then your lapack and then (but only if you need it) -lg2c (you'll find the directory for the -L option with 'g77 -print-libgcc-file-name'. the speed for anything else than DGEMM/DGEMV (which is in atlas) does not really matter for cpmd. also compiling lapack with ifc but without optimization (-O0) is something you can try. as a last chance, you can ditch atlas completely an use the intel math kernel library (should be roughly as fast as atlas, depending on problem size). NOTE: the order of the -L and -l arguments _does_ matter. alternatively, i can offer you that i build a combined atlas/lapack for your platform (as i described to you in a previous, private email), but for that i need EXCLUSIVE access to a maschine of your architecture and a little bit of time (the complete atlas tuning run takes some time as do the manual library reassembly and the testing of the executables). to the cpmd.org maintainer(s): since building of cpmd on linux seems to be a recurring problem, how about putting a selection of precompiled executables (statically linked) into the contrib section? that would probably help a lot of people to get started and they don't have to fight with compilers and input file syntax at the same time. i can contribute binaries optimized for amd athlon xp (usable on thunderbird and later) cpus for that. cheers, axel kohlmeyer. > > I would really appreciate if someone could give detailed instructions on > how to compile CPMD and all its required libraries on a standard redhat > 7.3 linux system. > > > Regards, > > Kai Reichert > > > ----------------------------------------------- > University of Dortmund > Department of Chemical Engineering > Campus Nord, Building G II, 5th floor > Chair of Thermodynamics > > _______________________________________________ > CPMD-list mailing list > CPMD-list at cpmd.org > http://www.cpmd.org/mailman/listinfo/cpmd-list > -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot.