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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3168 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-09-24 16:30:58 +00:00
parent ad6d401806
commit c32f182546
49 changed files with 968 additions and 170 deletions
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11
src/MAKE/Makefile.altix
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@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -16,12 +17,14 @@ DEPFLAGS = -M
# one user needed icpc to link # one user needed icpc to link
LINK = icc LINK = icc
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O2 $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) USRLIB = $(PKGLIB)
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lmpi -lscs_mp $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.bgl
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@ -6,8 +6,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -18,17 +19,19 @@ CCFLAGS = $(PKGINC) -O3 -DFFT_FFTW -DMPICH_IGNORE_CXX_SEEK
DEPFLAGS = -M DEPFLAGS = -M
LINK = /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC LINK = /opt/ibmcmp/vacpp/7.0/bin/blrts_xlC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O3 -L/bgl/BlueLight/ppcfloor/bglsys/lib \ $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
-L/opt/ibmcmp/xlf/9.1/blrts_lib \ -L/opt/ibmcmp/xlf/9.1/blrts_lib \
-L/opt/ibmcmp/vacpp/7.0/blrts_lib \ -L/opt/ibmcmp/vacpp/7.0/blrts_lib \
-L/bgl/local/lib \ -L/bgl/local/lib \
-L/bgl/local/bglfftwgel-2.1.5.pre5/lib -L/bgl/local/bglfftwgel-2.1.5.pre5/lib
USRLIB = $(PKGLIB) -lxlopt -lxlomp_ser -lxl -lxlfmath -lm -lfftw \ USRLIB = $(PKGLIB) -lxlopt -lxlomp_ser -lxl -lxlfmath -lm -lfftw \
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
-lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lmassv -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lmassv
SYSLIB =$(FORTLIB) $(GPULIB) SYSLIB =$(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.cheetah
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@ -6,8 +6,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -16,12 +17,14 @@ CCFLAGS = $(PKGINC) -O4 -qnoipa -I/usr/apps/include -DFFT_FFTW
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpCC_r LINK = mpCC_r
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L/usr/apps/lib $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw USRLIB = $(PKGLIB) -lfftw
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.crockett
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@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -15,12 +16,14 @@ CCFLAGS = $(PKGINC) -g -O -DFFT_NONE -DLAMMPS_GZIP
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpiCC LINK = mpiCC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -g -O $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB =$(PKGLIB) USRLIB =$(PKGLIB)
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.cygwin
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@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -15,12 +16,14 @@ CCFLAGS = $(PKGINC) -O -g -I/cygdrive/c/cygwin/fftw/include -DFFT_FFTW -DMPICH_I
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpicxx LINK = mpicxx
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -g -L/cygdrive/c/cygwin/fftw/lib -L/cygdrive/c/cygwin/mpich2-1.0.4p1/lib $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw -lmpich USRLIB = $(PKGLIB) -lfftw -lmpich
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.debian
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@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -15,12 +16,14 @@ CCFLAGS = $(PKGINC) -g -O -I/usr/lib/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP
DEPFLAGS = -M DEPFLAGS = -M
LINK = g++ LINK = g++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -g -O -L/usr/lib/mpich/lib $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw -lmpich USRLIB = $(PKGLIB) -lfftw -lmpich
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB =$(FORTLIB) $(GPULIB) SYSLIB =$(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

11
src/MAKE/Makefile.diesel
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@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -15,12 +16,14 @@ CCFLAGS = $(PKGINC) -64 -O -mp -DFFT_SCSL
DEPFLAGS = -M DEPFLAGS = -M
LINK = CC LINK = CC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -64 $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) USRLIB = $(PKGLIB)
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm -lscs_mp -lmpi -lmpi++ $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.encanto
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@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -15,12 +16,14 @@ CCFLAGS = $(PKGINC) -O -DFFT_FFTW -I/home/jlane/fftw-2.1.5/fftw
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpicxx LINK = mpicxx
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L/home/jlane/fftw-2.1.5/fftw/.libs $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lstdc++ -lfftw USRLIB = $(PKGLIB) -lstdc++ -lfftw
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
ARCHIVE = ar ARCHIVE = ar

11
src/MAKE/Makefile.fink
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@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -14,12 +15,14 @@ CCFLAGS = $(PKGINC) -O -I../STUBS -I/sw/include -DFFT_FFTW
DEPFLAGS = -M DEPFLAGS = -M
LINK = c++ LINK = c++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L../STUBS -L/sw/lib $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw -lmpi USRLIB = $(PKGLIB) -lfftw -lmpi
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.freebsd
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@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -14,12 +15,14 @@ CCFLAGS = $(PKGINC) -O3 -DFFT_FFTW
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpic++ LINK = mpic++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O3 $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw -lmpi USRLIB = $(PKGLIB) -lfftw -lmpi
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

13
src/MAKE/Makefile.g++
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@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -14,12 +15,14 @@ CCFLAGS = -g -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK $(PKGINC)
DEPFLAGS = -M DEPFLAGS = -M
LINK = g++ LINK = g++
LINKFORT = -L/opt/intel/fce/10.0.023/lib LINKFORT = -L/opt/intel/fce/10.0.023/lib
LINKBLAS =
#LINKGPU = -L/usr/local/cuda/lib64 #LINKGPU = -L/usr/local/cuda/lib64
LINKFLAGS = -g -O $(PKGPATH) $(LINKFORT) $(LINKGPU) LINKFLAGS = -g -O $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = -lfftw -lmpich $(PKGLIB) USRLIB = -lfftw -lmpich $(PKGLIB)
FORTLIB = -lifcore -lsvml -lompstub -limf FORTLIB = -lifcore -lsvml -lompstub -limf
BLASLIB = -lblas -llapack
#GPULIB = -lcudart #GPULIB = -lcudart
SYSLIB = -lpthread $(FORTLIB) $(GPULIB) SYSLIB = -lpthread $(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size
@ -43,7 +46,7 @@ lib: $(OBJ)
%.d:%.cpp %.d:%.cpp
$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@ $(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
# Individual dependencies # Individual dependencie
DEPENDS = $(OBJ:.o=.d) DEPENDS = $(OBJ:.o=.d)
include $(DEPENDS) include $(DEPENDS)

11
src/MAKE/Makefile.glory
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@ -21,8 +21,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -31,12 +32,14 @@ CCFLAGS = $(PKGINC) -O -DFFT_FFTW -I${FFTW_INCLUDE}
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpicxx LINK = mpicxx
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L${FFTW_LIB} $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw -lstdc++ USRLIB = $(PKGLIB) -lfftw -lstdc++
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc

11
src/MAKE/Makefile.intel
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@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -17,12 +18,14 @@ NOALIAS = -fno-strict-aliasing
DEPFLAGS = -M DEPFLAGS = -M
LINK = icpc LINK = icpc
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -i-static $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -L../STUBS -lmpi -lfftw USRLIB = $(PKGLIB) -L../STUBS -lmpi -lfftw
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rcsv ARFLAGS = -rcsv
SIZE = size SIZE = size

11
src/MAKE/Makefile.intel_mkl
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@ -11,8 +11,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -21,12 +22,14 @@ CCFLAGS = $(PKGINC) -O3 -fno-alias -ip -unroll0 -g -DMPICH_IGNORE_CXX_SEEK -DLAM
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpiicc LINK = mpiicc
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -mt_mpi -L/opt/intel/mkl/10.0.011/lib/em64t $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) /opt/intel/mkl/10.0.011/lib/em64t/libfftw2xc_intel.a USRLIB = $(PKGLIB) /opt/intel/mkl/10.0.011/lib/em64t/libfftw2xc_intel.a
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lstdc++ -lpthread -lmkl_em64t -lguide $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

13
src/MAKE/Makefile.liberty
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@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -29,13 +30,15 @@ CCFLAGS = $(PKGINC) -O -DFFT_FFTW -I${FFTW_INCLUDE}
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpiCC LINK = mpiCC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
#LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L${FFTW}/fftw/.libs $(LINKGPU) #LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L${FFTW_LIB} $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw USRLIB = $(PKGLIB) -lfftw
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lstdc++ -lm $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.linux
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@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -14,12 +15,14 @@ CCFLAGS = -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK $(PKGINC)
DEPFLAGS = -M DEPFLAGS = -M
LINK = icc LINK = icc
LINKFORT = -L/opt/intel/fce/10.0.023/lib LINKFORT = -L/opt/intel/fce/10.0.023/lib
LINKBLAS =
#LINKGPU = -L/usr/local/cuda/lib64// #LINKGPU = -L/usr/local/cuda/lib64//
LINKFLAGS = -O $(PKGPATH) $(LINKFORT) $(LINKGPU) LINKFLAGS = -O $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = -lfftw -lmpich $(PKGLIB) USRLIB = -lfftw -lmpich $(PKGLIB)
FORTLIB = -lifcore -lsvml -lompstub -limf FORTLIB = -lifcore -lsvml -lompstub -limf
BLASLIB =
#GPULIB = -lcudart #GPULIB = -lcudart
SYSLIB = -lpthread -lstdc++ $(FORTLIB) $(GPULIB) SYSLIB = -lpthread -lstdc++ $(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

11
src/MAKE/Makefile.mac
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@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -14,12 +15,14 @@ CCFLAGS = -O -DFFT_FFTW -I../STUBS $(PKGINC)
DEPFLAGS = -M DEPFLAGS = -M
LINK = c++ LINK = c++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = -O $(PKGPATH) $(LINKFORT) $(LINKGPU) LINKFLAGS = -O $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = -lfftw ../STUBS/mpi.o $(PKGLIB) USRLIB = -lfftw ../STUBS/mpi.o $(PKGLIB)
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.mac_mpi
View File

@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -16,12 +17,14 @@ CCFLAGS = -O -MMD -MG -DFFT_FFTW \
-I${FFTW}/include -DOMPI_SKIP_MPICXX $(PKGINC) -I${FFTW}/include -DOMPI_SKIP_MPICXX $(PKGINC)
LINK = mpic++ LINK = mpic++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = -O -L${FFTW}/lib $(PKGPATH) $(LINKFORT) $(LINKGPU) LINKFLAGS = -O -L${FFTW}/lib $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = -lfftw $(PKGLIB) USRLIB = -lfftw $(PKGLIB)
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.odin
View File

@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -15,12 +16,14 @@ CCFLAGS = $(PKGINC) -O -I/opt/mpich-mx/include -DFFT_NONE -DLAMMPS_GZIP
DEPFLAGS = -M DEPFLAGS = -M
LINK = g++ LINK = g++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L/opt/mpich-mx/lib -L/opt/mx/lib $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lmpich -lmyriexpress USRLIB = $(PKGLIB) -lmpich -lmyriexpress
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB =$(FORTLIB) $(GPULIB) SYSLIB =$(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

11
src/MAKE/Makefile.openmpi
View File

@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -17,12 +18,14 @@ NOALIAS = -fno-strict-aliasing
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpic++ LINK = mpic++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw USRLIB = $(PKGLIB) -lfftw
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rcsv ARFLAGS = -rcsv
SIZE = size SIZE = size

11
src/MAKE/Makefile.opensuse
View File

@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -14,12 +15,14 @@ CCFLAGS = $(PKGINC) -O3 -I /opt/mpich/include/ -DFFT_FFTW -DLAMMPS_GZIP
DEPFLAGS = -M DEPFLAGS = -M
LINK = g++ LINK = g++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O3 -L /opt/mpich/ch-p4/lib64 $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -ldfftw -lmpich USRLIB = $(PKGLIB) -ldfftw -lmpich
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB =$(FORTLIB) $(GPULIB) SYSLIB =$(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

11
src/MAKE/Makefile.pg
View File

@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -17,13 +18,15 @@ CCFLAGS = $(PKGINC) -I/usr/local/mpich-1.2.6/pg/include \
DEPFLAGS = -M DEPFLAGS = -M
LINK = pgCC LINK = pgCC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -L/usr/local/mpich-1.2.6/pg/lib \ $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
-L/usr/local/lib -L/usr/local/lib
USRLIB = $(PKGLIB) -lfftw -lmpich USRLIB = $(PKGLIB) -lfftw -lmpich
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

11
src/MAKE/Makefile.power5
View File

@ -6,8 +6,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -17,12 +18,14 @@ CCFLAGS = $(PKGINC) -O3 -qnoipa -qlanglvl=oldmath \
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpCC_r LINK = mpCC_r
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -qnoipa -qlanglvl=oldmath -bmaxdata:0x70000000 $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -L/scr/oppe/LAMMPS/fftw-2.1.5/lib -lfftw USRLIB = $(PKGLIB) -L/scr/oppe/LAMMPS/fftw-2.1.5/lib -lfftw
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link target # Link target

11
src/MAKE/Makefile.qed
View File

@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -14,12 +15,14 @@ CCFLAGS = $(PKGINC) -O -I/usr/local/mpich-1.2.6-eth/include -DFFT_NONE
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpiCC LINK = mpiCC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L/usr/local/mpich-1.2.6-eth/lib $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lmpich USRLIB = $(PKGLIB) -lmpich
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

11
src/MAKE/Makefile.ross
View File

@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -15,12 +16,14 @@ CCFLAGS = $(PKGINC) -O -DFFT_DEC
DEPFLAGS = -M DEPFLAGS = -M
LINK = /usr/local/cplant/ross/current/bin/c++ LINK = /usr/local/cplant/ross/current/bin/c++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lmpi -lcxml USRLIB = $(PKGLIB) -lmpi -lcxml
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.sdsc
View File

@ -6,8 +6,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -20,15 +21,17 @@ NOALIAS = -qalias=noansi
DEPFLAGS = -M -qmakedep=gcc DEPFLAGS = -M -qmakedep=gcc
LINK = blrts_xlC LINK = blrts_xlC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O2 -L/bgl/BlueLight/ppcfloor/bglsys/lib \ $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
-L/opt/ibmcmp/xlf/bg/10.1/blrts_lib \ -L/opt/ibmcmp/xlf/bg/10.1/blrts_lib \
-L/opt/ibmcmp/vacpp/bg/8.0/blrts_lib \ -L/opt/ibmcmp/vacpp/bg/8.0/blrts_lib \
-L/usr/local/apps/V1R3/fftw-2.1.5d/lib -L/usr/local/apps/V1R3/fftw-2.1.5d/lib
USRLIB = $(PKGLIB) -lfftw -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lm USRLIB = $(PKGLIB) -lfftw -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -lm
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.seaborg
View File

@ -6,8 +6,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -16,12 +17,14 @@ CCFLAGS = $(PKGINC) -O2 -qnoipa -I/usr/common/usg/fftw/2.1.5/include -DFFT_FFTW
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpCC_r LINK = mpCC_r
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L/usr/lib -L/usr/common/usg/fftw/2.1.5/lib $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw -lfftw_mpi USRLIB = $(PKGLIB) -lfftw -lfftw_mpi
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.serial
View File

@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -14,12 +15,14 @@ CCFLAGS = -O -DFFT_NONE -I../STUBS $(PKGINC)
DEPFLAGS = -M DEPFLAGS = -M
LINK = g++ LINK = g++
LINKFORT = -L/opt/intel/fce/10.0.023/lib LINKFORT = -L/opt/intel/fce/10.0.023/lib
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = -O -L../STUBS $(PKGPATH) $(LINKFORT) $(LINKGPU) LINKFLAGS = -O -L../STUBS $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = -lmpi $(PKGLIB) USRLIB = -lmpi $(PKGLIB)
FORTLIB = -lifcore -lsvml -lompstub -limf FORTLIB = -lifcore -lsvml -lompstub -limf
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

11
src/MAKE/Makefile.serial_debug
View File

@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -17,12 +18,14 @@ NOALIAS = -fno-strict-aliasing
DEPFLAGS = -M DEPFLAGS = -M
LINK = g++ LINK = g++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -L../STUBS -lmpi -lfftw USRLIB = $(PKGLIB) -L../STUBS -lmpi -lfftw
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rcsv ARFLAGS = -rcsv
SIZE = size SIZE = size

11
src/MAKE/Makefile.serial_icc
View File

@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -14,12 +15,14 @@ CCFLAGS = $(PKGINC) -O -I../STUBS -DFFT_NONE
DEPFLAGS = -M DEPFLAGS = -M
LINK = icc LINK = icc
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L../STUBS $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lmpi USRLIB = $(PKGLIB) -lmpi
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lstdc++ $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

11
src/MAKE/Makefile.solaris
View File

@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -14,12 +15,14 @@ CCFLAGS = $(PKGINC) -O -I../STUBS -DFFT_NONE
DEPFLAGS = -M DEPFLAGS = -M
LINK = c++ LINK = c++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L../STUBS $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lmpi USRLIB = $(PKGLIB) -lmpi
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB =$(FORTLIB) $(GPULIB) SYSLIB =$(FORTLIB) $(BLASLIB) $(GPULIB)
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

11
src/MAKE/Makefile.spirit
View File

@ -11,8 +11,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -24,12 +25,14 @@ CCFLAGS = $(PKGINC) $(OPTIMIZE) -DFFT_FFTW -I$(FFTW)/include
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpicxx LINK = mpicxx
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) $(OPTIMIZE) -L$(FFTW)/lib $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw -lstdc++ USRLIB = $(PKGLIB) -lfftw -lstdc++
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.squall
View File

@ -12,8 +12,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -22,12 +23,14 @@ CCFLAGS = $(PKGINC) -DFFT_FFTW -I/home/athomps/tools/fftw-2.1.5/fftw
DEPFLAGS = -O2 -M DEPFLAGS = -O2 -M
LINK = mpiCC LINK = mpiCC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O2 -L/home/athomps/tools/fftw-2.1.5/fftw/.libs $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw -lmpi USRLIB = $(PKGLIB) -lfftw -lmpi
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.storm
View File

@ -6,8 +6,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -17,12 +18,14 @@ CCFLAGS = $(PKGINC) -fastsse -DFFT_FFTW -DMPICH_IGNORE_CXX_SEEK \
DEPFLAGS = -M DEPFLAGS = -M
LINK = CC LINK = CC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L/projects/fftw/fftw-2.1.5/lib $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw USRLIB = $(PKGLIB) -lfftw
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB =$(FORTLIB) $(GPULIB) SYSLIB =$(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.tacc
View File

@ -4,8 +4,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -17,12 +18,14 @@ CCFLAGS = -O -DFFT_FFTW -I${FFTW_INC} $(PKGINC)
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpiCC LINK = mpiCC
LINKFORT = -L/opt/apps/intel/10.1/fc/lib LINKFORT = -L/opt/apps/intel/10.1/fc/lib
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = -O -L${FFTW_LIB} $(PKGPATH) $(LINKFORT) $(LINKGPU) LINKFLAGS = -O -L${FFTW_LIB} $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = ${FFTW_LIB}/libfftw.a $(PKGLIB) USRLIB = ${FFTW_LIB}/libfftw.a $(PKGLIB)
FORTLIB = -lifcore FORTLIB = -lifcore
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
ARFLAGS = -rc ARFLAGS = -rc
SIZE = size SIZE = size

11
src/MAKE/Makefile.tbird
View File

@ -24,8 +24,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -34,12 +35,14 @@ CCFLAGS = -O -DFFT_FFTW -I$(FFTW_INCLUDE) $(PKGINC)
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpicxx LINK = mpicxx
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = -O $(PKGPATH) $(LINKFORT) $(LINKGPU) LINKFLAGS = -O $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(BLASLIB) $(FFTW_LINK_LINE) -lstdc++ $(PKGLIB) USRLIB = $(BLASLIB) $(FFTW_LINK_LINE) -lstdc++ $(PKGLIB)
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = -lm $(FORTLIB) $(GPULIB) SYSLIB = -lm $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
ARCHIVE = ar ARCHIVE = ar
ARFLAGS = -rc ARFLAGS = -rc

11
src/MAKE/Makefile.tesla
View File

@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -15,12 +16,14 @@ CCFLAGS = $(PKGINC) -O -I../STUBS -DFFT_SGI
DEPFLAGS = -M DEPFLAGS = -M
LINK = g++ LINK = g++
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L../STUBS $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lmpi USRLIB = $(PKGLIB) -lmpi
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm -lcomplib.sgimath $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.tflop
View File

@ -6,8 +6,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -16,12 +17,14 @@ CCFLAGS = $(PKGINC) -O4 -Knoieee -DFFT_INTEL
DEPFLAGS = -M DEPFLAGS = -M
LINK = ciCC LINK = ciCC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -Knoieee $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lmpi -lkmath USRLIB = $(PKGLIB) -lmpi -lkmath
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB =$(FORTLIB) $(GPULIB) SYSLIB =$(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = xsize SIZE = xsize
# Link rule # Link rule

11
src/MAKE/Makefile.valor
View File

@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -17,12 +18,14 @@ CCFLAGS = $(PKGINC) -O -DFFT_FFTW -I${FFTW}/include
DEPFLAGS = -M DEPFLAGS = -M
LINK = mpiCC LINK = mpiCC
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L${FFTW}/lib $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -lfftw -lstdc++ USRLIB = $(PKGLIB) -lfftw -lstdc++
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB = $(FORTLIB) -lm $(GPULIB) SYSLIB = $(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

11
src/MAKE/Makefile.xt3
View File

@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -18,12 +19,14 @@ NOALIAS = -fno-strict-aliasing
DEPFLAGS = -M DEPFLAGS = -M
LINK = CC --target=catamount LINK = CC --target=catamount
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -O -L$(FFTW_LIB) $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
USRLIB = $(PKGLIB) -ldfftw -lgmalloc USRLIB = $(PKGLIB) -ldfftw -lgmalloc
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB =$(FORTLIB) $(GPULIB) SYSLIB =$(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link target # Link target

11
src/MAKE/Makefile.ydl
View File

@ -5,8 +5,9 @@ SHELL = /bin/sh
# System-specific settings # System-specific settings
# LINKFORT & FORTLIB settings can be blank if not using LAMMPS Fortran libs # LINKFORT/FORTLIB settings can be removed if not using meam or reax packages
# LINKGPU & GPULIB settings can be blank if not using LAMMPS gpu lib # LINKBLAS/BLASLIB settings can be removed if not using user-atc package
# LINKGPU/GPULIB settings can be removed if not using gpu package
include Makefile.package include Makefile.package
@ -17,13 +18,15 @@ CCFLAGS = $(PKGINC) -g -O -I/opt/mpich/include \
DEPFLAGS = -M DEPFLAGS = -M
LINK = xlc -q64 LINK = xlc -q64
LINKFORT = LINKFORT =
LINKBLAS =
LINKGPU = LINKGPU =
LINKFLAGS = $(PKGPATH) $(LINKFORT) -g -O -L/opt/mpich/lib64 \ $(LINKGPU) LINKFLAGS = $(PKGPATH) $(LINKFORT) $(LINKBLAS) $(LINKGPU)
-L/usr/local/lib -lstdc++ -lc -L/usr/local/lib -lstdc++ -lc
USRLIB = $(PKGLIB) -lfftw -lmpich USRLIB = $(PKGLIB) -lfftw -lmpich
FORTLIB = FORTLIB =
BLASLIB =
GPULIB = GPULIB =
SYSLIB =$(FORTLIB) $(GPULIB) SYSLIB =$(FORTLIB) $(BLASLIB) $(GPULIB)
SIZE = size SIZE = size
# Link rule # Link rule

2
src/Makefile
View File

@ -16,7 +16,7 @@ OBJ = $(SRC:.cpp=.o)
PACKAGE = asphere class2 colloid dipole dpd gpu granular \ PACKAGE = asphere class2 colloid dipole dpd gpu granular \
kspace manybody meam molecule opt peri poems reax xtc kspace manybody meam molecule opt peri poems reax xtc
PACKUSER = user-ackland user-cg-cmm user-ewaldn user-smd PACKUSER = user-ackland user-atc user-cg-cmm user-ewaldn user-smd
PACKALL = $(PACKAGE) $(PACKUSER) PACKALL = $(PACKAGE) $(PACKUSER)

2
src/REAX/Install.csh
View File

@ -11,7 +11,6 @@ if ($1 == 1) then
cp style_reax.h .. cp style_reax.h ..
cp pair_reax.cpp .. cp pair_reax.cpp ..
cp pair_reax.h .. cp pair_reax.h ..
cp pair_reax_fortran.h .. cp pair_reax_fortran.h ..
@ -26,7 +25,6 @@ else if ($1 == 0) then
touch ../style_reax.h touch ../style_reax.h
rm ../pair_reax.cpp rm ../pair_reax.cpp
rm ../pair_reax.h rm ../pair_reax.h
rm ../pair_reax_fortran.h rm ../pair_reax_fortran.h

1
src/STUBS/mpi.h
View File

@ -30,6 +30,7 @@
#define MPI_MIN 3 #define MPI_MIN 3
#define MPI_MAXLOC 4 #define MPI_MAXLOC 4
#define MPI_MINLOC 5 #define MPI_MINLOC 5
#define MPI_LOR 6
#define MPI_ANY_SOURCE -1 #define MPI_ANY_SOURCE -1

27
src/USER-ATC/Install.csh Executable file
View File

@ -0,0 +1,27 @@
# Install/unInstall package classes in LAMMPS
# edit Makefile.package to include/exclude ATC library
if ($1 == 1) then
sed -i -e 's/[^ \t]*atc //' ../Makefile.package
sed -i -e 's|^PKGINC =[ \t]*|&-I../../lib/atc |' ../Makefile.package
sed -i -e 's|^PKGPATH =[ \t]*|&-L../../lib/atc |' ../Makefile.package
sed -i -e 's|^PKGLIB =[ \t]*|&-latc |' ../Makefile.package
cp style_user_atc.h ..
cp fix_atc.h ..
cp fix_atc.cpp ..
else if ($1 == 0) then
sed -i -e 's/[^ \t]*atc //' ../Makefile.package
rm ../style_user_atc.h
touch ../style_user_atc.h
rm ../fix_atc.h
rm ../fix_atc.cpp
endif

543
src/USER-ATC/fix_atc.cpp Normal file
View File

@ -0,0 +1,543 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Reese Jones, Jon Zimmerman, Jeremy Templeton (SNL)
------------------------------------------------------------------------- */
#include "stdio.h"
#include "string.h"
#include "fix_atc.h"
#include "ATC_TransferHardy.h"
#include "ATC_TransferThermal.h"
#include "ExtrinsicModel.h"
#include "LammpsInterface.h"
#include "fix_nve.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "neighbor.h"
#include "neigh_request.h"
#include "pointers.h"
#include "comm.h"
#include "error.h"
using namespace LAMMPS_NS;
// main page of doxygen documentation
/*! \mainpage AtC : Atom-to-Continuum methods
fix commands:
- \ref man_fix_atc (links to all related commands)
*/
/* ------------------------------------------------------------------------- */
FixATC::FixATC(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
// ID GROUP atc PHYSICSTYPE [PARAMETERFILE]
// can have either 4 or 5 args, only arg[3] and arg[4] are used by this class
if (narg > 5 || narg < 4) lmp->error->all("Illegal fix atc command");
// Set LAMMPS pointer on LammpsInterface
ATC::LammpsInterface::instance()->set_lammps(lmp);
/*! \page man_fix_atc fix atc command
\section syntax
fix AtC transfer <type> <parameter_file>
- type\n
= thermal : thermal coupling with fields: temperature \n
= two_temperature : electron-phonon coupling with field: temperature and electron_temperature \n
= hardy : Hardy on-the-fly post-processing (see "related" section for possible fields) \n
- parameter_file = name of the file with material parameters. \n
note: hardy does not require a parameter file
\section examples
<TT> fix_modify AtC transfer thermal Ar_thermal.dat </TT> \n
<TT> fix_modify AtC transfer hardy </TT>
\section description
This fix is the beginning to creating a coupled FE/MD simulation and/or
an on-the-fly estimation of continuum fields. The coupled versions of this
fix do Verlet integration and the Hardy/post-processing does not.
After instantiating this fix, several other fix_modify commands will be
needed to set up the problem, e.g. define the finite element mesh and
prescribe initial and boundary conditions.
The following coupling example is typical, but non-exhaustive:\n
<TT>
# ... commands to create and initialize the MD system \n
# initial fix to designate coupling type and group to apply it to \n
# tag group physics material_file \n
fix AtC internal atc thermal Ar_thermal.mat\n \n
# create a uniform 12 x 2 x 2 mesh that covers region contain the group \n
# nx ny nz region periodicity \n
fix_modify AtC fem create mesh 12 2 2 mdRegion f p p\n \n
# specify the control method for the type of coupling \n
# physics control_type \n
fix_modify AtC transfer thermal control flux \n \n
# specify the initial values for the empirical field "temperature" \n
# field node_group value \n
fix_modify AtC transfer initial temperature all 30.\n \n
# create an output stream for nodal fields \n
# filename output_frequency \n
fix_modify AtC transfer output atc_fe_output 100\n \n
run 1000 \n
</TT>
likewise for this post-processing example: \n
<TT>
# ... commands to create and initialize the MD system \n
# initial fix to designate post-processing and the group to apply it to \n
# no material file is allowed nor required \n
fix AtC internal atc hardy \n \n
# create a uniform 1 x 1 x 1 mesh that covers region contain the group \n
# with periodicity this effectively creats a system average \n
fix_modify AtC fem create mesh 1 1 1 box p p p \n\n
# change from default lagrangian map to eulerian \n
# refreshed every 100 steps \n
fix_modify AtC atom_element_map eulerian 100 \n \n
# start with no field defined \n
fix_modify AtC transfer fields none \n \n
# add mass density, potential energy density, stress and temperature \n
fix_modify AtC transfer fields add density energy stress temperature \n\n
# create an output stream for nodal fields \n
# filename output_frequency \n
fix_modify AtC transfer output nvtFE 100 text \n
run 1000 \n
</TT>
Note coupling and post-processing can be combined in the same simulations
using separate fixes.
\n
For detailed exposition of the theory and algorithms please see:\n
- Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA. <VAR> An
atomistic-to-continuum coupling method for heat transfer in solids. </VAR>
Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
- Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ,
<VAR> Calculation of stress in atomistic simulation </VAR>
Special Issue of Modelling and Simulation in Materials Science and
Engineering (2004), 12:S319
Please refer to the standard
finite element (FE) texts, e.g. T.J.R Hughes <VAR> The finite element
method </VAR>, Dover 2003, for the basics of FE simulation.
\section restrictions
Thermal and two_temperature (coupling) types use a Verlet time-integration
algorithm.
The hardy type does not contain its own time-integrator and must be used
with a separate fix that does contain one, e.g. nve, nvt, etc.
Currently,
- the coupling is restricted to thermal physics
- the FE computations are done in serial on each processor.
\section related
fix_modify commands for setup: \n
- \ref man_fem_mesh
- \ref man_mesh_nodeset
- \ref man_mesh_faceset
- \ref man_mesh_elemset
- \ref man_transfer_internal
- \ref man_transfer_boundary
- \ref man_internal_quadrature
- \ref man_time_integration
- \ref man_electron_integration
fix_modify commands for boundary and initial conditions:\n
- \ref man_initial
- \ref man_fix_nodes
- \ref man_unfix_nodes
- \ref man_fix_flux
- \ref man_unfix_flux
- \ref man_source
- \ref man_remove_source
fix_modify commands for control and filtering: \n
- \ref man_thermal_control
- \ref man_time_filter
- \ref man_filter_scale
- \ref man_equilibrium_start
- \ref man_extrinsic_exchange
fix_modify commands for output: \n
- \ref man_transfer_output
- \ref man_transfer_atomic_output
- \ref man_mesh_output
- \ref man_write_restart
- \ref man_read_restart
fix_modify commands for post-processing: \n
- \ref man_hardy_fields
- \ref man_hardy_gradients
- \ref man_hardy_rates
- \ref man_hardy_computes
- \ref man_hardy_set
- \ref man_hardy_on_the_fly
- \ref man_boundary_integral
- \ref man_contour_integral
miscellaneous fix_modify commands: \n
- \ref man_atom_element_map
- \ref man_neighbor_reset_frequency
Note: a set of example input files with the attendant material files are
included with this package
\section default
none
*/
// Construct new ATC_Transfer object
// note use "unfix" to destroy
int me = ATC::LammpsInterface::instance()->comm_rank();
string groupName(arg[1]);
// Postprocessing
try {
if (strcmp(arg[3],"hardy")==0)
{
if (narg < 5) {
if (me==0) printf("Constructing ATC transfer (hardy)\n");
atcTransfer_ = new ATC::ATC_TransferHardy(groupName);
}
else {
if (me==0) printf("Constructing ATC transfer (hardy) with parameter file %s\n",arg[4]);
std::string matParamFile = arg[4];
atcTransfer_ = new ATC::ATC_TransferHardy(groupName,matParamFile);
}
}
// PhysicsTypes
else if (strcmp(arg[3],"thermal")==0)
{
std::string matParamFile = arg[4];
if (me==0) printf("Constructing ATC transfer (thermal) with parameter file %s\n",arg[4]);
atcTransfer_ = new ATC::ATC_TransferThermal(groupName,matParamFile);
lmp->atom->add_callback(0); // NOTE what is this?
}
else if (strcmp(arg[3],"two_temperature")==0)
{
std::string matParamFile = arg[4];
if (me==0) printf("Constructing ATC transfer (two_temperature) with parameter file %s\n",arg[4]);
atcTransfer_ = new ATC::ATC_TransferThermal(groupName,matParamFile,
ATC::TWO_TEMPERATURE);
}
else
{
lmp->error->all("Unknown physics type in ATC");
}
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
lmp->atom->add_callback(0);
// Tell LAMMPS we want to write_restart to be called (writes fix state)
//restart_global = 1;
restart_global = 0; // NOTE : turning off ATC restart
// Tell LAMMPS we want to pack_restart to be called (writes per-atom data)
//restart_peratom = 1;
// Set output computation data based on transfer info
scalar_flag = atcTransfer_->scalar_flag();
vector_flag = atcTransfer_->vector_flag();
size_vector = atcTransfer_->size_vector();
scalar_vector_freq = atcTransfer_->scalar_vector_freq();
extscalar = atcTransfer_->extscalar();
extvector = atcTransfer_->extvector();
extlist = atcTransfer_->extlist();
// set comm size needed by this fix
comm_forward = 3;
}
/*----------------------------------------------------------------------- */
FixATC::~FixATC()
{
if (lmp->atom) lmp->atom->delete_callback(id,0);
if (atcTransfer_) delete atcTransfer_;
}
/* ---------------------------------------------------------------------- */
int FixATC::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= PRE_EXCHANGE;
mask |= MIN_PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
int FixATC::modify_param(int narg, char** arg)
{
bool match;
// pass on to transfer layer
try {
match = atcTransfer_->modify(narg,arg);
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
if (!match) return 0;
return narg;
}
/* ----------------------------------------------------------------------
create initial list of neighbor partners via call to neighbor->build()
must be done in setup (not init) since fix init comes before neigh init
------------------------------------------------------------------------- */
void FixATC::init()
{
// Guarantee construction of full neighborlist
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
void FixATC::setup(int vflag)
{
try {
atcTransfer_->initialize();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
groupbit = atcTransfer_->get_groupbit();
}
/* ----------------------------------------------------------------------
pass throughs to atc functions to handle swapping atom data on
when they move processors
------------------------------------------------------------------------- */
void FixATC::pre_exchange()
{
atcTransfer_->pre_exchange();
}
void FixATC::min_pre_exchange()
{
atcTransfer_->pre_exchange();
}
double FixATC::memory_usage()
{
double bytes = (double) atcTransfer_->memory_usage() * sizeof(double);
return bytes;
}
void FixATC::grow_arrays(int nmax)
{
atcTransfer_->grow_arrays(nmax);
}
void FixATC::copy_arrays(int i, int j)
{
atcTransfer_->copy_arrays(i,j);
}
int FixATC::pack_exchange(int i, double * buf)
{
int num = atcTransfer_->pack_exchange(i,buf);
return num;
}
int FixATC::unpack_exchange(int nlocal, double * buf)
{
int num = atcTransfer_->unpack_exchange(nlocal,buf);
return num;
}
int FixATC::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int num = atcTransfer_->pack_comm(n, list, buf, pbc_flag, pbc);
return num;
}
void FixATC::unpack_comm(int n, int first, double *buf)
{
atcTransfer_->unpack_comm(n, first, buf);
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixATC::pack_restart(int i, double *buf){
return 0;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixATC::unpack_restart(int nlocal, int nth){
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixATC::maxsize_restart(){
return 0;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixATC::size_restart(int nlocal){
return 0;
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixATC::write_restart(FILE *fp){
// hardcode filename for now
char ** args = new char*[2];
args[0] = new char[50];
args[1] = new char[50];
sprintf(args[0],"write_restart");
sprintf(args[1],"ATC.restart");
// Then call all objects I own to write their data
if (comm->me == 0) {
atcTransfer_->modify(2,args);
}
delete [] args[0];
delete [] args[1];
delete [] args;
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixATC::restart(char *buf){
// hardcode filename for now
char ** args = new char*[2];
args[0] = new char[50];
args[1] = new char[50];
sprintf(args[0],"read_restart");
sprintf(args[1],"ATC.restart");
// Then call all objects I own to write their data
if (comm->me == 0) {
atcTransfer_->modify(2,args);
}
delete [] args[0];
delete [] args[1];
delete [] args;
}
/* ----------------------------------------------------------------------
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
void FixATC::initial_integrate(int vflag)
{
try {
atcTransfer_->pre_init_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->init_integrate_velocity();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->mid_init_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->init_integrate_position();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->post_init_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
}
/* ---------------------------------------------------------------------- */
void FixATC::final_integrate()
{
// need updated ghost atom positions
comm->comm_fix(this);
try {
atcTransfer_->pre_final_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->final_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
try {
atcTransfer_->post_final_integrate();
}
catch (ATC::ATC_Error& atcError) {
cout << "ATC ERROR: " << atcError.get_error_description() << " processor: " << atcError.get_id() << endl;
throw;
}
}

86
src/USER-ATC/fix_atc.h Normal file
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@ -0,0 +1,86 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef FIX_ATC_H
#define FIX_ATC_H
#include "fix.h"
#include "pointers.h" // access to lammps pointers
// NOTE what is the correct way?
//class ATC::ATC_Transfer;
#include "ATC_Transfer.h"
#include "LammpsInterface.h"
namespace LAMMPS_NS {
// fwd decl
class NeighList;
class FixATC : public Fix {
public:
/** constructor & destructor */
FixATC(class LAMMPS *, int, char **);
~FixATC();
/** calls ATC_Transfer */
void init();
void init_list(int id, NeighList *ptr) {
ATC::LammpsInterface::instance()->init_list(id,ptr);
}
void setup(int vflag);
/** setmask: tell LAMMPS which fix methods to call */
int setmask();
/** initial_integrate: calls ATC_Transfer */
void initial_integrate(int vflag);
/** final_integrate: calls ATC_Transfer */
void final_integrate();
/** calls ATC_Transfer */
void pre_exchange();
void min_pre_exchange();
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
int pack_comm(int , int *, double *, int, int *);
void unpack_comm(int, int, double *);
/** modify atc parameters (parser) */
int modify_param(int narg, char** arg);
/** calls ATC_Transfer to handle restarting/checkpointing */
/** these four methods are for writing per-atom quantities */
int pack_restart(int, double *);
void unpack_restart(int, int);
int size_restart(int);
int maxsize_restart();
/** these two methods are for writing all other quantities */
void write_restart(FILE *);
void restart(char *);
protected:
/** functions for "thermo" output */
virtual double compute_scalar() {return atcTransfer_->compute_scalar();}
virtual double compute_vector(int n) {return atcTransfer_->compute_vector(n);}
double dtv,dtf;
ATC::ATC_Transfer *atcTransfer_;
};
}
#endif

20
src/USER-ATC/style_user_atc.h Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FixInclude
#include "fix_atc.h"
#endif
#ifdef FixClass
FixStyle(atc,FixATC)
#endif

2
src/style_user_packages.h
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@ -15,7 +15,7 @@
// see the README files in individual user-package directories for details // see the README files in individual user-package directories for details
#include "style_user_ackland.h" #include "style_user_ackland.h"
//#include "style_user_atc.h" #include "style_user_atc.h"
#include "style_user_cg_cmm.h" #include "style_user_cg_cmm.h"
#include "style_user_ewaldn.h" #include "style_user_ewaldn.h"
#include "style_user_smd.h" #include "style_user_smd.h"