--- trunk/OOPSE/libmdtools/Makefile	2003/03/21 17:52:35	379
+++ trunk/OOPSE/libmdtools/Makefile	2003/04/04 22:22:30	460
@@ -12,13 +12,13 @@ DECLARES= -DFRC_PATH="$(OOPSE_HOME)/forcefields"
 
 # First do compile-time flags:
 
-DECLARES= -DFRC_PATH="$(OOPSE_HOME)/forcefields"
+DECLARES= -DFRC_PATH="$(FORCE_PARAM_DIR)"
 MPI_DECLARES= -DIS_MPI
 
 # include paths starting with "." are all relative to the SUBDIRS!!!
 
 INCLUDES= -I.. -I../../libBASS -I$(SPRNG_INC)
-MPI_INCLUDES= -I$(MPICH_INC) -I$(MPICH_INC)/mpi2c++ -I$(MPI_F90_MODS)
+MPI_INCLUDES= -I$(MPICH_INC) -I$(MPI_F90_MODS)
 
 CFLAGS=$(CFLAGS_C) $(INCLUDES) $(DECLARES) $(MPI_INCLUDES)
 CXXFLAGS=$(CXXFLAGS_C) $(INCLUDES) $(DECLARES)
@@ -54,13 +54,14 @@ CXX_FILES = \
 C_FILES = $(DIR)/mpiForceField.c
 
 CXX_FILES = \
+	$(DIR)/Atom.cpp \
 	$(DIR)/Bend.cpp \
 	$(DIR)/BendExtensions.cpp \
 	$(DIR)/Bond.cpp \
 	$(DIR)/BondExtensions.cpp \
-	$(DIR)/DipoleTestFF.cpp \
 	$(DIR)/DirectionalAtom.cpp \
 	$(DIR)/DumpWriter.cpp \
+	$(DIR)/Exclude.cpp \
 	$(DIR)/InitializeFromFile.cpp \
 	$(DIR)/LJ_FF.cpp \
 	$(DIR)/SimInfo.cpp \
@@ -72,12 +73,12 @@ CXX_FILES = \
 	$(DIR)/Torsion.cpp \
 	$(DIR)/TorsionExtensions.cpp \
 	$(DIR)/TraPPE_ExFF.cpp \
-	$(DIR)/TraPPEFF.cpp \
 	$(DIR)/Verlet.cpp \
 	$(DIR)/randomSPRNG.cpp \
 	$(DIR)/fortranWrappers.cpp \
 	$(DIR)/ForceFields.cpp \
-	$(DIR)/mpiSimulation.cpp
+	$(DIR)/mpiSimulation.cpp \
+	$(DIR)/Molecule.cpp
 
 
 F90_FILES= \
@@ -101,6 +102,7 @@ F90_SRCS :=	$(F90_FILES)
 C_SRCS   :=     $(C_FILES)
 CXX_SRCS :=	$(CXX_FILES)
 F90_SRCS :=	$(F90_FILES)
+SRCS     :=     $(C_SRCS) $(CXX_SRCS) $(F90_SRCS)
 
 DIR:=obj
 C_OBJS   :=     $(C_FILES:.c=.o)
@@ -144,19 +146,19 @@ distclean : dummy
 	for i in $(LIBSUBDIRS); do \
 	  (cd $$i; $(RM) *.o *.mod) || exit 1; \
 	done
-	$(RM) libmdtools.a libmdtools_MPI.a *.o *.mod *~ Make.temp Make.ftemp
+	$(RM) libmdtools.a libmdtools_MPI.a *.o *.mod *~ Make.temp Make.ftemp Make.dep
 
-Make.dep: depend
+depend : Make.dep
 
-depend :
+Make.dep : $(SRCS)
 	echo "Only C dependencies are made automagically!"
 	echo "# DO NOT DELETE THIS LINE - used by make depend" > Make.dep
 	$(CC) $(DEPFLAGS) -MM $(C_SRCS) $(CXX_SRCS) \
 		| sed 's/\.o:/\$$(O)\ :/g' > Make.temp
 	cat Make.temp | sed 's/^/obj\//' >> Make.dep
 	cat Make.temp | sed 's/^/MPIobj\//' >> Make.dep
-#	../utils/sfmakedepend -I $(MPI_F90_MODS) -d obj -f ./Make.ftemp -h *.F90
-#	../utils/sfmakedepend -I $(MPI_F90_MODS) -d MPIobj -f ./Make.ftemp -h *.F90
+#	../scripts/sfmakedepend -I $(MPI_F90_MODS) -d obj -f ./Make.ftemp -h *.F90
+#	../scripts/sfmakedepend -I $(MPI_F90_MODS) -d MPIobj -f ./Make.ftemp -h *.F90
 #	cat Make.ftemp | sed 's/\.o:/\$$(O)\ :/g' >> Make.dep
 	$(RM) Make.ftemp Make.temp
 
@@ -170,56 +172,61 @@ include Make.dep
 
 include Make.dep
 
-# known dependencies
+obj/$(F_MACH_DEFS): ./Linux_ifc_machdep.F90
 
-obj/$(F_MACH_DEFS): Linux_ifc_machdep.F90
+obj/vector_class$(O): ./vector_class.F90
 
-obj/vector_class$(O): vector_class.F90
-
-obj/force_globals$(O): force_globals.F90 \
+obj/force_globals$(O): ./force_globals.F90 \
 	obj/$(F_MACH_DEFS)
 
-obj/neighborLists$(O): neighborLists.F90 \
+obj/neighborLists$(O): ./neighborLists.F90 \
 	obj/$(F_MACH_DEFS) 
 
-obj/calc_sticky_pair$(O): calc_sticky_pair.F90 \
+obj/calc_sticky_pair$(O): ./calc_sticky_pair.F90 \
 	obj/$(F_MACH_DEFS) \
+	obj/simulation_module$(O) \
 	obj/force_globals$(O)
 
-obj/calc_gb$(O): calc_gb.F90 \
+obj/calc_gb$(O): ./calc_gb.F90 \
 	obj/$(F_MACH_DEFS) \
+	obj/simulation_module$(O) \
 	obj/force_globals$(O)
 
-obj/atype_module$(O): atype_module.F90 \
+obj/atype_module$(O): ./atype_module.F90 \
 	obj/$(F_MACH_DEFS) \
 	obj/vector_class$(O) \
 	obj/calc_sticky_pair$(O) \
 	obj/calc_gb$(O)
 
-obj/simulation_module$(O): simulation_module.F90 \
+obj/simulation_module$(O): ./simulation_module.F90 \
 	obj/$(F_MACH_DEFS) \
+	obj/vector_class$(O) \
+	obj/force_globals$(O) \
 	obj/atype_module$(O) \
 	obj/neighborLists$(O)
 
-obj/calc_LJ_FF$(O): calc_LJ_FF.F90 \
+obj/calc_LJ_FF$(O): ./calc_LJ_FF.F90 \
 	obj/$(F_MACH_DEFS) \
 	obj/atype_module$(O) \
+	obj/simulation_module$(O) \
 	obj/vector_class$(O) \
 	obj/force_globals$(O)
 
-obj/calc_reaction_field$(O): calc_reaction_field.F90 \
+obj/calc_reaction_field$(O): ./calc_reaction_field.F90 \
 	obj/$(F_MACH_DEFS) \
 	obj/vector_class$(O) \
+	obj/simulation_module$(O) \
 	obj/atype_module$(O) \
 	obj/force_globals$(O)
 
-obj/calc_dipole_dipole$(O): calc_dipole_dipole.F90 \
+obj/calc_dipole_dipole$(O): ./calc_dipole_dipole.F90 \
 	obj/$(F_MACH_DEFS) \
 	obj/atype_module$(O) \
+	obj/simulation_module$(O) \
 	obj/force_globals$(O) \
 	obj/vector_class$(O)
 
-obj/do_Forces$(O): do_Forces.F90 \
+obj/do_Forces$(O): ./do_Forces.F90 \
 	obj/$(F_MACH_DEFS) \
 	obj/simulation_module$(O) \
 	obj/atype_module$(O) \
@@ -231,7 +238,7 @@ obj/wrappers$(O): wrappers.F90 \
 	obj/calc_gb$(O) \
 	obj/force_globals$(O)
 
-obj/wrappers$(O): wrappers.F90 \
+obj/wrappers$(O): ./wrappers.F90 \
 	obj/$(F_MACH_DEFS) \
 	obj/simulation_module$(O) \
 	obj/atype_module$(O) \
@@ -239,64 +246,71 @@ MPIobj/$(F_MACH_DEFS): Linux_ifc_machdep.F90
 
 #MPI dependencies:
 
-MPIobj/$(F_MACH_DEFS): Linux_ifc_machdep.F90
+MPIobj/$(F_MACH_DEFS): ./Linux_ifc_machdep.F90
 
-MPIobj/vector_class$(O): vector_class.F90
+MPIobj/vector_class$(O): ./vector_class.F90
 
-MPIobj/mpiSimulation_module$(O): mpiSimulation_module.F90
+MPIobj/mpiSimulation_module$(O): ./mpiSimulation_module.F90
 
-MPIobj/force_globals$(O): force_globals.F90 \
+MPIobj/force_globals$(O): ./force_globals.F90 \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/$(F_MACH_DEFS)
 
-MPIobj/neighborLists$(O): neighborLists.F90 \
+MPIobj/neighborLists$(O): ./neighborLists.F90 \
 	MPIobj/$(F_MACH_DEFS) \
 	MPIobj/mpiSimulation_module$(O) 
 
-MPIobj/calc_sticky_pair$(O): calc_sticky_pair.F90 \
+MPIobj/calc_sticky_pair$(O): ./calc_sticky_pair.F90 \
 	MPIobj/$(F_MACH_DEFS) \
+	MPIobj/simulation_module$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/force_globals$(O)
 
-MPIobj/calc_gb$(O): calc_gb.F90 \
+MPIobj/calc_gb$(O): ./calc_gb.F90 \
 	MPIobj/$(F_MACH_DEFS) \
+	MPIobj/simulation_module$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/force_globals$(O)
 
-MPIobj/atype_module$(O): atype_module.F90 \
+MPIobj/atype_module$(O): ./atype_module.F90 \
 	MPIobj/$(F_MACH_DEFS) \
 	MPIobj/vector_class$(O) \
 	MPIobj/calc_sticky_pair$(O) \
 	MPIobj/calc_gb$(O)
 
-MPIobj/simulation_module$(O): simulation_module.F90 \
+MPIobj/simulation_module$(O): ./simulation_module.F90 \
 	MPIobj/$(F_MACH_DEFS) \
+	MPIobj/vector_class$(O) \
+	MPIobj/force_globals$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/atype_module$(O) \
 	MPIobj/neighborLists$(O)
 
-MPIobj/calc_LJ_FF$(O): calc_LJ_FF.F90 \
+MPIobj/calc_LJ_FF$(O): ./calc_LJ_FF.F90 \
 	MPIobj/$(F_MACH_DEFS) \
+	MPIobj/simulation_module$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/atype_module$(O) \
 	MPIobj/vector_class$(O) \
 	MPIobj/force_globals$(O)
 
-MPIobj/calc_reaction_field$(O): calc_reaction_field.F90 \
+MPIobj/calc_reaction_field$(O): ./calc_reaction_field.F90 \
 	MPIobj/$(F_MACH_DEFS) \
+	MPIobj/simulation_module$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/vector_class$(O) \
 	MPIobj/atype_module$(O) \
 	MPIobj/force_globals$(O)
 
-MPIobj/calc_dipole_dipole$(O): calc_dipole_dipole.F90 \
+MPIobj/calc_dipole_dipole$(O): ./calc_dipole_dipole.F90 \
 	MPIobj/$(F_MACH_DEFS) \
+	MPIobj/simulation_module$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/atype_module$(O) \
 	MPIobj/force_globals$(O) \
 	MPIobj/vector_class$(O)
 
-MPIobj/do_Forces$(O): do_Forces.F90 \
+MPIobj/do_Forces$(O): ./do_Forces.F90 \
 	MPIobj/$(F_MACH_DEFS) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/simulation_module$(O) \
@@ -309,11 +323,9 @@ MPIobj/wrappers$(O): wrappers.F90 \
 	MPIobj/calc_gb$(O) \
 	MPIobj/force_globals$(O)
 
-MPIobj/wrappers$(O): wrappers.F90 \
+MPIobj/wrappers$(O): ./wrappers.F90 \
 	MPIobj/$(F_MACH_DEFS) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/simulation_module$(O) \
 	MPIobj/atype_module$(O) \
 	MPIobj/do_Forces$(O) 
-
-