diff --git a/src/MAKE/Makefile.serial b/src/MAKE/Makefile.serial index f5ef2d749..4685dbcc1 100644 --- a/src/MAKE/Makefile.serial +++ b/src/MAKE/Makefile.serial @@ -1,96 +1,96 @@ # serial = RedHat Linux box, g++4, no MPI, no FFTs SHELL = /bin/sh # --------------------------------------------------------------------- # compiler/linker settings # generally no need to edit this section # unless additional compiler/linker flags or libraries needed for your machine CC = g++ CCFLAGS = -O -g DEPFLAGS = -M LINK = g++ LINKFLAGS = -O -g -LIB = -ldl +LIB = ARCHIVE = ar ARFLAGS = -rc SIZE = size # --------------------------------------------------------------------- # LAMMPS-specific settings # specify settings for LAMMPS features you will use # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings, OPTIONAL # see possible settings in doc/Section_start.html#2_2 (step 4) LMP_INC = #-DLAMMPS_GZIP -DMALLOC_MEMALIGN=64 # MPI library, REQUIRED # see discussion in doc/Section_start.html#2_2 (step 5) # can point to dummy MPI library in src/STUBS as in Makefile.serial # INC = path for mpi.h, MPI compiler settings # PATH = path for MPI library # LIB = name of MPI library MPI_INC = -I../STUBS MPI_PATH = MPI_LIB = ../STUBS/libmpi.a # FFT library, OPTIONAL # see discussion in doc/Section_start.html#2_2 (step 6) # can be left blank to use provided KISS FFT library # INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = FFT_PATH = FFT_LIB = -lfftw3f # JPEG library, OPTIONAL # see discussion in doc/Section_start.html#2_2 (step 7) # only needed if -DLAMMPS_JPEG listed with LMP_INC # INC = path for jpeglib.h # PATH = path for JPEG library # LIB = name of JPEG library JPG_INC = JPG_PATH = JPG_LIB = # --------------------------------------------------------------------- # build rules and dependencies # no need to edit this section include Makefile.package.settings include Makefile.package EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) # Link target $(EXE): $(OBJ) $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) $(SIZE) $(EXE) # Library target lib: $(OBJ) $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) # Compilation rules %.o:%.cpp $(CC) $(CCFLAGS) $(EXTRA_INC) -c $< %.d:%.cpp $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ # Individual dependencies DEPENDS = $(OBJ:.o=.d) sinclude $(DEPENDS) diff --git a/src/MAKE/Makefile.serial-omp b/src/MAKE/Makefile.serial-omp index d6089ccaa..194d2911c 100755 --- a/src/MAKE/Makefile.serial-omp +++ b/src/MAKE/Makefile.serial-omp @@ -1,98 +1,98 @@ # serial = RedHat Linux box, g++4, no MPI, internal FFT, OpenMP SHELL = /bin/sh # --------------------------------------------------------------------- # compiler/linker settings # generally no need to edit this section # unless additional compiler/linker flags or libraries needed for your machine OPENMP=-fopenmp CC = g++ $(OPENMP) CCFLAGS = -O2 -fomit-frame-pointer -fno-rtti -fno-exceptions -g \ -march=native -ffast-math -mpc64 -finline-functions \ -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized DEPFLAGS = -M LINK = g++ $(OPENMP) LINKFLAGS = -O -g -fno-rtti -fno-exceptions -mpc64 -LIB = -ldl +LIB = ARCHIVE = ar ARFLAGS = -rcsv SIZE = size # --------------------------------------------------------------------- # LAMMPS-specific settings # specify settings for LAMMPS features you will use # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings, OPTIONAL # see possible settings in doc/Section_start.html#2_2 (step 4) LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=16 # MPI library, REQUIRED # see discussion in doc/Section_start.html#2_2 (step 5) # can point to dummy MPI library in src/STUBS as in Makefile.serial # INC = path for mpi.h, MPI compiler settings # PATH = path for MPI library # LIB = name of MPI library MPI_INC = -I../STUBS MPI_PATH = MPI_LIB = ../STUBS/libmpi.a # FFT library, OPTIONAL # see discussion in doc/Section_start.html#2_2 (step 6) # can be left blank to use provided KISS FFT library # INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = FFT_PATH = FFT_LIB = # JPEG library, OPTIONAL # see discussion in doc/Section_start.html#2_2 (step 7) # only needed if -DLAMMPS_JPEG listed with LMP_INC # INC = path for jpeglib.h # PATH = path for JPEG library # LIB = name of JPEG library JPG_INC = JPG_PATH = JPG_LIB = # --------------------------------------------------------------------- # build rules and dependencies # no need to edit this section include Makefile.package.settings include Makefile.package EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) # Link target $(EXE): $(OBJ) $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) $(SIZE) $(EXE) # Library target lib: $(OBJ) $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) # Compilation rules %.o:%.cpp $(CC) $(CCFLAGS) $(EXTRA_INC) -c $< %.d:%.cpp $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ # Individual dependencies DEPENDS = $(OBJ:.o=.d) sinclude $(DEPENDS) diff --git a/src/MAKE/Makefile.serial-opt b/src/MAKE/Makefile.serial-opt index 8292918dc..fe3004acc 100755 --- a/src/MAKE/Makefile.serial-opt +++ b/src/MAKE/Makefile.serial-opt @@ -1,98 +1,98 @@ # serial = RedHat Linux box, g++4, no MPI, internal FFT SHELL = /bin/sh # --------------------------------------------------------------------- # compiler/linker settings # generally no need to edit this section # unless additional compiler/linker flags or libraries needed for your machine CC = g++ CCFLAGS = -O2 -fomit-frame-pointer -fno-rtti -fno-exceptions -g \ -march=native -ffast-math -mpc64 -finline-functions \ -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized DEPFLAGS = -M LINK = g++ LINKFLAGS = -O -g -fno-rtti -fno-exceptions -mpc64 -LIB = -ldl +LIB = ARCHIVE = ar ARFLAGS = -rcsv SIZE = size # --------------------------------------------------------------------- # LAMMPS-specific settings # specify settings for LAMMPS features you will use # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings, OPTIONAL # see possible settings in doc/Section_start.html#2_2 (step 4) LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=16 # MPI library, REQUIRED # see discussion in doc/Section_start.html#2_2 (step 5) # can point to dummy MPI library in src/STUBS as in Makefile.serial # INC = path for mpi.h, MPI compiler settings # PATH = path for MPI library # LIB = name of MPI library MPI_INC = -I../STUBS MPI_PATH = MPI_LIB = ../STUBS/libmpi.a # FFT library, OPTIONAL # see discussion in doc/Section_start.html#2_2 (step 6) # can be left blank to use provided KISS FFT library # INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = FFT_PATH = FFT_LIB = # JPEG library, OPTIONAL # see discussion in doc/Section_start.html#2_2 (step 7) # only needed if -DLAMMPS_JPEG listed with LMP_INC # INC = path for jpeglib.h # PATH = path for JPEG library # LIB = name of JPEG library JPG_INC = JPG_PATH = JPG_LIB = # --------------------------------------------------------------------- # build rules and dependencies # no need to edit this section include Makefile.package.settings include Makefile.package EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) # Link target $(EXE): $(OBJ) $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) $(SIZE) $(EXE) # Library target lib: $(OBJ) $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) # Compilation rules %.o:%.cpp $(CC) $(CCFLAGS) $(EXTRA_INC) -c $< %.d:%.cpp $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ # Individual dependencies DEPENDS = $(OBJ:.o=.d) sinclude $(DEPENDS) diff --git a/src/MAKE/Makefile.serial_debug b/src/MAKE/Makefile.serial_debug index 8c40daae0..18898b3d3 100644 --- a/src/MAKE/Makefile.serial_debug +++ b/src/MAKE/Makefile.serial_debug @@ -1,95 +1,95 @@ # serial_debug = RedHat Linux box, g++4, no MPI, no FFTs SHELL = /bin/sh # --------------------------------------------------------------------- # compiler/linker settings # specify flags and libraries needed for your compiler CC = g++ CCFLAGS = -O0 -g -Wall -W -fstrict-aliasing DEPFLAGS = -M LINK = g++ LINKFLAGS = -O0 -g -LIB = -ldl +LIB = ARCHIVE = ar ARFLAGS = -rcsv SIZE = size # --------------------------------------------------------------------- # LAMMPS-specific settings # specify settings for LAMMPS features you will use # if you change any -D setting, do full re-compile after "make clean" # LAMMPS ifdef settings, OPTIONAL # see possible settings in doc/Section_start.html#2_2 (step 4) LMP_INC = -DLAMMPS_GZIP # MPI library, REQUIRED # see discussion in doc/Section_start.html#2_2 (step 5) # can point to dummy MPI library in src/STUBS as in Makefile.serial # INC = path for mpi.h, MPI compiler settings # PATH = path for MPI library # LIB = name of MPI library MPI_INC = -I../STUBS MPI_PATH = MPI_LIB = ../STUBS/libmpi.a # FFT library, OPTIONAL # see discussion in doc/Section_start.html#2_2 (step 6) # can be left blank to use provided KISS FFT library # INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings # PATH = path for FFT library # LIB = name of FFT library FFT_INC = -DFFT_NONE FFT_PATH = FFT_LIB = # JPEG library, OPTIONAL # see discussion in doc/Section_start.html#2_2 (step 7) # only needed if -DLAMMPS_JPEG listed with LMP_INC # INC = path for jpeglib.h # PATH = path for JPEG library # LIB = name of JPEG library JPG_INC = JPG_PATH = JPG_LIB = # --------------------------------------------------------------------- # build rules and dependencies # no need to edit this section include Makefile.package.settings include Makefile.package EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) # Link target $(EXE): $(OBJ) $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) $(SIZE) $(EXE) # Library target lib: $(OBJ) $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) # Compilation rules %.o:%.cpp $(CC) $(CCFLAGS) $(EXTRA_INC) -c $< %.d:%.cpp $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ # Individual dependencies DEPENDS = $(OBJ:.o=.d) sinclude $(DEPENDS) diff --git a/src/USER-MOLFILE/Install.sh b/src/USER-MOLFILE/Install.sh index f428d34af..57a6bb51d 100644 --- a/src/USER-MOLFILE/Install.sh +++ b/src/USER-MOLFILE/Install.sh @@ -1,24 +1,49 @@ # Install/unInstall package files in LAMMPS if (test $1 = 1) then cp molfile_interface.cpp .. cp dump_molfile.cpp .. cp molfile_interface.h .. cp dump_molfile.h .. cp molfile_plugin.h .. cp vmdplugin.h .. + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*molfile[^ \t]* //' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(molfile_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(molfile_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(molfile_SYSPATH) |' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*MOLFILE.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/USER-MOLFILE\/Makefile.lammps\ +' ../Makefile.package.settings + fi + elif (test $1 = 0) then rm -f ../molfile_interface.cpp rm -f ../dump_molfile.cpp rm -f ../molfile_interface.h rm -f ../dump_molfile.h rm -f ../molfile_plugin.h rm -f ../vmdplugin.h + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*molfile[^ \t]* //' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*MOLFILE.*$/d' ../Makefile.package.settings + fi + fi + diff --git a/src/USER-MOLFILE/Makefile.lammps b/src/USER-MOLFILE/Makefile.lammps new file mode 100644 index 000000000..cde5f34c6 --- /dev/null +++ b/src/USER-MOLFILE/Makefile.lammps @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package is used + +molfile_SYSINC = +molfile_SYSLIB = -ldl +molfile_SYSPATH =