Hi Marcos,
quite busy these days. It is a little disappointing to hear SIESTA
provide NEB function officially. NEB is quite useful and time consuming.
I used to think my NEB tasks could be accelerated by linear-scaling
feature. I just wondering whether there is any plan on implementation of
NEB/CI-NEB algorithm to SIESTA?
I compiled the Siesta with ifort 9.1. The ifort 11.1 is failed in
compiling SIESTA. I would like to share my arch.make file with all of
you. Please refer to below.
#
# 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=mpif90
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)
FFLAGS=-g
FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
LDFLAGS= -lpthread
ARFLAGS_EXTRA=
FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=
BLAS_LIBS=/opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_gf_lp64.a
/opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_def.so
/opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_blacs_intelmpi20_lp6
4.a /opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_intel_lp64.a
/opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_core.a
/opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_sequential.a /opt/intel
/mkl/10.1.0.015/lib/em64t/libmkl_intel_thread.a
/opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_intel_sp2dp.a
LAPACK_LIBS= /opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_lapack95.a
BLACS_LIBS=
SCALAPACK_LIBS= /opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_scalapack_lp64.a
COMP_LIBS=dc_lapack.a liblapack.a libblas.a
NETCDF_LIBS=
NETCDF_INTERFACE=
LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
$(NETCDF_LIBS)
#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=libmpi_f90.a
MPI_INCLUDE=/home/siesta/siesta/mpich2/include/
DEFS_MPI=-DMPI
#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:
On 2010-04-05 04:15, Marcos Veríssimo Alves wrote:
So, Vega, what exactly changed from your last email, where you had the
catastrophic compiler error, was it the compilation or the compiler
version? Could you please share it with us? If the compiler version is
still Intel 11: have you tested your compilation of siesta with the
examples and a real production system?
NEB is not yet implemented officially in siesta. Some people have
their own implementation, be it integrated in the code or using
scripts as drivers to siesta, however, but it's up to them to allow
you to use it.
Marcos
On Sun, Apr 4, 2010 at 4:16 PM, vega lew <[email protected]
<mailto:[email protected]>> wrote:
Dear all,
Finally I succeed in compiling parallel version of SIESTA. But I
wondering whether siesta could perform calculations like
NEB/CI-NEB to search transition state and estimate the energy
barrier for certain chemical reactions.
I found some work did by Zhipan Liu in Fudan University(china)
perform more efficient to locate the transition state and
estimate the energy barrier for chemical reactions.
The applications of the algorithm with SIESTA were reported in J.
AM. CHEM. SOC. 2007, 129, 2642, J. AM. CHEM. SOC. 2008, 130, 10996
etc. But I did not find it in Siesta 3.0b.
So how could I perform calculations to search transition state and
estimate the energy barrier for chemical reactions using this
version of siesta (3.0b).
thank you for reading
vega
--
================================================
Vega Lew ( weijia liu)
Graduate students
State Key Laboratory of Materials-oriented Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, China
***************************************************************
Email: [email protected] <mailto:[email protected]>
Office: Room A705, Technical Innovation Building,
Xinmofan Road 5#, Nanjing, China
***************************************************************
--
================================================
Vega Lew ( weijia liu)
Graduate students
State Key Laboratory of Materials-oriented Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, China
***************************************************************
Email: [email protected]
Office: Room A705, Technical Innovation Building,
Xinmofan Road 5#, Nanjing, China
***************************************************************
