Hello Marcos,
Here is my arch.make and input file for the pseudopotential
arch.make,
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90
SIESTA_ARCH=x86_64-unknown-linux-gnu--Gfortran
FPP=
FPP_OUTPUT=
FC=gfortran
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)
FFLAGS=-g -O2
FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
LDFLAGS=
ARFLAGS_EXTRA=
FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=
BLAS_LIBS=-lblas
LAPACK_LIBS=-llapack
BLACS_LIBS=
SCALAPACK_LIBS=
COMP_LIBS=dc_lapack.a
NETCDF_LIBS=
NETCDF_INTERFACE=
LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS)
MPI_INTERFACE=
MPI_INCLUDE=
.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) $<
C.vdw.inp
pg C TM2 Pseudopotencial GS ref
tm2 3.00
C vw
0
1 3
2 0 2.00
2 1 2.00
3 2 0.00
1.50 1.54 1.54 0.0 0.0
12345678901234567890123456789012345678901234567890 Ruler
Thanks,
Zhengping
-----Original E-mail-----
> From: "Marcos Veríssimo Alves" <[email protected]>
> Sent time: 2009-10-25 04:44:12
> To: [email protected]
> CC:
> Subject: Re: Re: [SIESTA-L] VdW XC problem
>
> I would, but right now I don't have access to my computer where I have
> compiled siesta with gfortran. It's very weird that no matter which
> complier you use, no difference is seen. Instead, please send me:
>
> 1) your arch.make,
> 2) your input file for the pseudo
>
> so that I can see and try to check if anything is wrong at all.
>
> Cheers,
>
> Marcos
>
> On Sat, Oct 24, 2009 at 12:46 PM, ZhengPing Fu <[email protected]> wrote:
> > 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
> >
--
211 LRSM, 3231 Walnut Str., Philadelphia, PA 19104
215-573-8440
