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
>
