Hi, Marcos, I compiled serial version of siesta and atom with gfortran -c -g -O2, it make no difference. The error is
splint: ERROR: X out of range Stopping Program from Node: 0 ../../Utils/pg.sh: line 44: 32613 Aborted $prog cp: cannot stat `VPSOUT': No such file or directory cp: cannot stat `VPSFMT': No such file or directory no Pseudopotential are created. Would you mind to share your atm program with me? Thanks Zhengping -----Original E-mail----- > From: "Marcos Veríssimo Alves" <[email protected]> > Sent time: 2009-10-24 01:06:20 > To: [email protected] > CC: > Subject: Re: [SIESTA-L] VdW XC problem > > Zhengping, > > Some time ago I sent a long email about the use of compilers and maybe > this issue got diluted in the middle of the whole thing. Use either > g95 or gfortran to compile it serially, it'll work. > > Marcos > > On Fri, Oct 23, 2009 at 12:38 PM, ZhengPing Fu <[email protected]> wrote: > > Hi, Marcos > > > > I also try to create vdw pseudopotential of carbon. I use > > siesta-trunk-301/Tests/Pseudos/C.vdw.inp > > as the input file, and I get the error: splint: ERROR: X out of range. > > It make no difference whether I compile atom program with gcc, ifor, > > mpich2, openmpi or serial arch.make. > > I want to use the XC version because I am try to do some calc on double > > layer graphene, while the relaxation results with siesta2.02 and siesta3.0b > > give too small layer distance. Maybe it's due to the incorrect vdw force in > > siesta2.02 and siesta3.0b. > > > > cheers! > > > > zhengping > > > > -----Original E-mail----- > >> From: "Marcos Veríssimo Alves" <[email protected]> > >> Sent time: 2009-10-18 06:49:19 > >> To: [email protected] > >> CC: > >> Subject: [SIESTA-L] VdW XC problem > >> > >> Hi SIESTA developers, > >> > >> I have compiled the trunk version sucessfully (ifort 10.1.015, mkl > >> 10.0.1.014, gcc4.3.3-5ubuntu4 for all the libraries) and re-calculated > >> a relaxation (originally performed with SIESTA 0.12 - !!!!) with it, > >> with good agreement on the final geometries on GGA. Now I'd like to > >> perform the same relaxation but using the VdW functional included in > >> the trunk version. However, I am having trouble generating the pseudos > >> with the VdW functional, for C, H and O. Using the LDA input file in > >> the user-contributed pseudo database for SIESTA for H, the calculation > >> on ATOM starts but after some time (much longer than with the usual > >> generation times for LDA and GGA) I get the following error: > >> > >> ODEINT - Too many steps. > >> ODEINT - Too many steps. > >> forrtl: severe (174): SIGSEGV, segmentation fault occurred > >> Image PC Routine Line > >> Source > >> atm 00000000004DC594 Unknown Unknown Unknown > >> atm 00000000004DB656 Unknown Unknown Unknown > >> atm 00000000004DF815 Unknown Unknown Unknown > >> atm 000000000049B787 Unknown Unknown Unknown > >> atm 000000000043945C Unknown Unknown Unknown > >> atm 000000000041636A Unknown Unknown Unknown > >> atm 0000000000409459 Unknown Unknown Unknown > >> atm 000000000040108B Unknown Unknown Unknown > >> atm 00000000004002FE Unknown Unknown Unknown > >> atm 00000000005846E1 Unknown Unknown Unknown > >> atm 00000000004001E9 Unknown Unknown Unknown > >> ==> Output data in directory H.vdw > >> ==> Pseudopotential in H.vdw.vps and H.vdw.psf (and maybe in H.vdw.xml) > >> > >> Using a smaller rc (say 0.8 instead of 1.25) for the s channel, I get > >> a different error: "Stepsize not significant in RKQC". Since the > >> pseudo files are written nonetheless, I looked at H.vdw.psf and found > >> that the initial values for the pseudopotential are huge and positive: > >> > >> Down Pseudopotential follows (l on next line) > >> 0 > >> 0.549103214316E+39 0.117500146714E+40 0.166669234150E+40 > >> 0.237719184583E+40 > >> 0.285353560992E+40 0.353790433179E+40 0.410640166051E+40 > >> 0.473604557600E+40 > >> 0.535672527076E+40 0.598766945589E+40 0.662573971183E+40 > >> 0.727126597569E+40 > >> 0.792432802699E+40 0.858500612833E+40 0.925338124816E+40 > >> 0.992953500075E+40 > >> 0.106135495208E+41 0.113055080187E+41 0.120054936526E+41 > >> 0.127135908317E+41 > >> > >> and that at some point they converge to -2 (?): > >> > >> 0.456930826243E+43 0.101859895292E+42 0.314589853862E+41 > >> 0.116397450388E+41 > >> -0.629471476686E+40 0.760405662914E+39 0.341641877055E+38 > >> 0.196285512413E+35 > >> -0.101201540265E+31 -0.213016981113E+22 -6742.38640266 > >> -2.00000000052 > >> -2.00000000025 -2.00000000012 -2.00000000006 > >> -2.00000000003 > >> -2.00000000001 -2.00000000001 -2.00000000000 > >> -2.00000000000 > >> > >> As the compilation of atom is now related to that of siesta itself, I > >> am including the arch.make of my (serial) siesta-trunk at the end of > >> this email. In the references to the VdW functional I have not found > >> anything that could be useful to identify a possible source of error. > >> I applied the patch for the siesta trunk version before compiling it > >> as well. Is there a problem with the version of ATOM that comes with > >> it? > >> > >> Cheers, > >> > >> Marcos > >> > >> # > >> # This file is part of the SIESTA package. > >> # > >> # Copyright (c) Fundacion General Universidad Autonoma de Madrid: > >> # E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal > >> # and J.M.Soler, 1996- . > >> # > >> # Use of this software constitutes agreement with the full conditions > >> # given in the SIESTA license, as signed by all legitimate users. > >> # > >> .SUFFIXES: > >> .SUFFIXES: .f .F .o .a .f90 .F90 > >> > >> SIESTA_ARCH=x86_64-unknown-linux-gnu--Intel > >> > >> FPP= > >> FPP_OUTPUT= > >> FC=ifort > >> RANLIB=ranlib > >> > >> SYS=nag > >> > >> SP_KIND=4 > >> DP_KIND=8 > >> KINDS=$(SP_KIND) $(DP_KIND) > >> > >> #FFLAGS= -w -mp1 -tpp6 -O2 -prec_div -reentrancy none -prefetch > >> FFLAGS= -g -mp -O2 > >> FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT > >> LDFLAGS= -Vaxlib -i-static -static > >> > >> ARFLAGS_EXTRA= > >> > >> FCFLAGS_fixed_f= > >> FCFLAGS_free_f90= > >> FPPFLAGS_fixed_F= > >> FPPFLAGS_free_F90= > >> > >> BLAS_LIBS= -L/opt/intel/mkl/10.0.1.014/lib/em64t -lmkl_em64t > >> LAPACK_LIBS=-L/opt/intel/mkl/10.0.1.014/lib/em64t -lmkl_lapack > >> BLACS_LIBS= > >> SCALAPACK_LIBS= > >> > >> COMP_LIBS= > >> > >> NETCDF_LIBS=/usr/lib/libnetcdf.so.4.0.0 > >> NETCDF_INTERFACE= > >> > >> #LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) > >> $(NETCDF_LIBS) > >> LIBS= -lmkl_lapack -lmkl_em64t -lguide -lpthread -lmkl_core > >> > >> #SIESTA needs an F90 interface to MPI > >> #This will give you SIESTA's own implementation > >> #If your compiler vendor offers an alternative, you may change > >> #to it here. > >> MPI_INTERFACE= > >> MPI_INCLUDE= > >> MPI_LIBS= > >> DEFS_MPI= > >> > >> #Dependency rules are created by autoconf according to whether > >> #discrete preprocessing is necessary or not. > >> .F.o: > >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $< > >> .F90.o: > >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $< > >> .f.o: > >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $< > >> .f90.o: > >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $< > > > > > > -- > > > > 211 LRSM, 3231 Walnut Str., Philadelphia, PA 19104 > > 215-573-8440 > > -- 211 LRSM, 3231 Walnut Str., Philadelphia, PA 19104 215-573-8440
