CC=mpicxx
CFLAGS=-c -O3 -ffast-math -mfpmath=sse -funroll-loops -Wall
GMXINC=/opt/Bio/gromacs/include/gromacs/
GMXLIB=/opt/Bio/gromacs/lib/
#GMXINC=/home/kasson/include/gromacs
#GMXLIB=/home/kasson/lib

SOURCES=theobald_rmsd.cpp hierarchyclusterbalance.cpp assign.cpp assign_macro.cpp cleanup.cpp makestatefile.cpp findsnapshots.cpp

all: $(SOURCES) hierarchyclusterbalance assign assign_macro cleanup makestatefile findsnapshots

hierarchyclusterbalance: hierarchyclusterbalance.o theobald_rmsd.o
	$(CC) hierarchyclusterbalance.o theobald_rmsd.o -o $@ -L$(GMXLIB) -lgmx_mpi -lm

cleanup: cleanup.o
	$(CC) cleanup.o -o $@ -L$(GMXLIB) -lgmx_mpi -lm

assign: assign.o theobald_rmsd.o
	$(CC) assign.o theobald_rmsd.o -o $@ -L$(GMXLIB) -lgmx_mpi -lm

assign_macro: assign_macro.o theobald_rmsd.o
	$(CC) assign_macro.o theobald_rmsd.o -o $@ -L$(GMXLIB) -lgmx_mpi -lm

makestatefile: makestatefile.o
	$(CC) makestatefile.o -o $@ -L$(GMXLIB) -lgmx_mpi -lm

findsnapshots: findsnapshots.o
	$(CC) findsnapshots.o -o $@ -L$(GMXLIB) -lgmx_mpi -lm

.cpp.o:
	$(CC) $(CFLAGS) $< -o $@ -I$(GMXINC)

clean:
	rm *.o