--- trunk/OOPSE/libmdtools/Makefile.in	2003/09/25 16:42:34	785
+++ trunk/OOPSE/libmdtools/Makefile.in	2003/10/29 14:29:12	840
@@ -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@
 
@@ -118,10 +127,10 @@ 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)
 
 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) $(F90FLAGS_C) 
 DEPFLAGS=$(CFLAGS_C) -I. -I../libBASS $(SPRNG_INC) $(MPI_INCLUDES)
@@ -130,7 +139,7 @@ SRC_DIR := $(PWD)
 MPI_CXXFLAGS=$(CXXFLAGS) $(MPI_INCLUDES) $(MPI_DECLARE)
 MPI_F90FLAGS=$(F90FLAGS) $(PREPDEFFLAG)$(MPI_DECLARE) $(MPI_INCLUDES)
 
-SRC_DIR := $(PWD)
+SRC_DIR := ..
 
 # Then do the compile rules:
 
@@ -166,6 +175,7 @@ CXX_FILES = \
 	$(DIR)/BondExtensions.cpp \
 	$(DIR)/DirectionalAtom.cpp \
 	$(DIR)/DumpWriter.cpp \
+	$(DIR)/DumpReader.cpp \
 	$(DIR)/Exclude.cpp \
 	$(DIR)/InitializeFromFile.cpp \
 	$(DIR)/LJFF.cpp \
@@ -186,8 +196,7 @@ CXX_FILES = \
 	$(DIR)/Molecule.cpp \
 	$(DIR)/NPTf.cpp \
 	$(DIR)/NPTi.cpp \
-	$(DIR)/NPTxym.cpp \
-	$(DIR)/NPTzm.cpp \
+	$(DIR)/NPTxyz.cpp \
 	$(DIR)/NVT.cpp \
 	$(DIR)/SimState.cpp \
 	$(DIR)/ZConstraint.cpp \