--- trunk/OOPSE/libmdtools/Makefile.in	2003/10/22 21:17:32	812
+++ trunk/OOPSE/libmdtools/Makefile.in	2003/12/19 20:36:35	891
@@ -46,6 +46,9 @@ MPI_INC=@MPI_INC@
 # MPICH include path
 MPI_INC=@MPI_INC@
 
+# MODDIRFLAG
+MODDIRFLAG=@MODDIRFLAG@
+
 # MPI F90 Module path
 MPI_F90_MODS=@MPI_F90_MODS@
 
@@ -95,6 +98,12 @@ CXXFLAGS_C=@CXXFLAGS@
 # C++ flags
 CXXFLAGS_C=@CXXFLAGS@
 
+# C++ template flags
+OOPSE_TEMPLATE_FLAGS=@OOPSE_TEMPLATE_FLAGS@
+
+# C++ namespace flags
+EXTRA_CC_FLAG=@EXTRA_CC_FLAG@
+
 # Preprocessor flag for fortran
 PREPFLAG=@PREPFLAG@
 
@@ -118,19 +127,20 @@ MPI_INCLUDES= -I$(MPI_INC) $(MPI_F90_MODS)
 # include paths starting with "." are all relative to the SUBDIRS!!!
 
 INCLUDES= -I.. -I../../libBASS $(SPRNG_INC)
-MPI_INCLUDES= -I$(MPI_INC) $(MPI_F90_MODS)
+MPI_INCLUDES= -I$(MPI_INC) $(MODDIRFLAG)$(MPI_F90_MODS)
+F90_INCLUDES= -I/usr/local/include
 
 CFLAGS=$(CFLAGS_C) $(INCLUDES) $(DECLARE) $(MPI_INCLUDES) $(FUNCWRAP)
-CXXFLAGS=$(CXXFLAGS_C) $(INCLUDES) $(DECLARE) $(FUNCWRAP)
+CXXFLAGS=$(CXXFLAGS_C) $(OOPSE_TEMPLATE_FLAGS) $(EXTRA_CC_FLAG) $(INCLUDES) $(DECLARE) $(FUNCWRAP)
 FFLAGS=$(PREPFLAG) $(FFLAGS_C) 
-F90FLAGS=$(PREPFLAG) $(F90FLAGS_C) 
+F90FLAGS=$(PREPFLAG) $(F90FLAGS_C) $(F90_INCLUDES)
 DEPFLAGS=$(CFLAGS_C) -I. -I../libBASS $(SPRNG_INC) $(MPI_INCLUDES)
 
 MPI_CFLAGS=$(CFLAGS) $(MPI_INCLUDES) $(MPI_DECLARE)
 MPI_CXXFLAGS=$(CXXFLAGS) $(MPI_INCLUDES) $(MPI_DECLARE)
 MPI_F90FLAGS=$(F90FLAGS) $(PREPDEFFLAG)$(MPI_DECLARE) $(MPI_INCLUDES)
 
-SRC_DIR := $(PWD)
+SRC_DIR := ..
 
 # Then do the compile rules:
 
@@ -192,6 +202,7 @@ CXX_FILES = \
 	$(DIR)/SimState.cpp \
 	$(DIR)/ZConstraint.cpp \
 	$(DIR)/ZConsWriter.cpp \
+	$(DIR)/mdProfile.cpp \
 	$(DIR)/GenericData.cpp
 
 F90_FILES= \
@@ -211,7 +222,9 @@ F90_FILES= \
 	$(DIR)/calc_gb.F90 \
 	$(DIR)/force_globals.F90 \
 	$(DIR)/mpiSimulation_module.F90 \
-	$(DIR)/notifyCutoffs.F90
+	$(DIR)/notifyCutoffs.F90 \
+	$(DIR)/oopseMPI_module.F90 \
+	$(DIR)/timing.F90
 
 DIR:=.
 C_SRCS   :=     $(C_FILES)
@@ -382,11 +395,11 @@ obj/wrappers$(O): ./wrappers.F90 \
 	obj/do_Forces$(O) \
 	obj/notifyCutoffs$(O) 
 
+obj/timing$(O): ./timing.F90 \
+	obj/do_Forces$(O)
 
 
 
-
-
 #MPI dependencies:
 
 MPIobj/definitions_module$(O): ./definitions_module.F90
@@ -395,8 +408,11 @@ MPIobj/mpiSimulation_module$(O): ./mpiSimulation_modul
 
 MPIobj/status_module$(O): ./status_module.F90
 
-MPIobj/mpiSimulation_module$(O): ./mpiSimulation_module.F90
+MPIobj/oopseMPI_module$(O): ./oopseMPI_module.F90
 
+MPIobj/mpiSimulation_module$(O): ./mpiSimulation_module.F90 \
+	MPIobj/oopseMPI_module$(O)
+
 MPIobj/force_globals$(O): ./force_globals.F90 \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/definitions_module$(O)
@@ -498,3 +514,6 @@ MPIobj/wrappers$(O): ./wrappers.F90 \
 	MPIobj/do_Forces$(O) \
 	MPIobj/notifyCutoffs$(O)  
 
+MPIobj/timing$(O): ./timing.F90 \
+	MPIobj/do_Forces$(O) \
+	MPIobj/mpiSimulation_module$(O)