--- trunk/OOPSE/libmdtools/Makefile.in	2004/05/07 21:35:05	1150
+++ trunk/OOPSE/libmdtools/Makefile.in	2004/06/04 14:35:59	1237
@@ -36,19 +36,16 @@ SPRNG_INC=@SPRNG_INC@
 
 # SPRNG include path
 SPRNG_INC=@SPRNG_INC@
+ 
+# Compile MPI code?
+USE_MPI=@USE_MPI@
+  
+# MPI include path
+MPI_INC_DIR=@MPI_INC_DIR@
 
-# MPICH library path
-MPI_LIBDIR=@MPI_LIBDIR@
+# MPI include path
+MPI_F90_INC=@MPI_F90_INC@
 
-# MPICH library
-MPI_LIB=@MPI_LIB@
-
-# MPICH include path
-MPI_INC=@MPI_INC@
-
-# MODDIRFLAG
-MODDIRFLAG=@MODDIRFLAG@
-
 # Compiler dependent Fortran module
 FLIBS_EXTRA = @F90LIBS@
 
@@ -124,18 +121,18 @@ MPI_INCLUDES= -I$(MPI_INC)
 # include paths starting with "." are all relative to the SUBDIRS!!!
 
 INCLUDES= -I.. -I../../libBASS $(SPRNG_INC)
-MPI_INCLUDES= -I$(MPI_INC)
-F90_INCLUDES= -I/usr/local/include
+MPI_INCLUDES= -I$(MPI_INC_DIR)
+MPI_F90_INCLUDES= -I$(MPI_F90_INC)
 
-CFLAGS=$(CFLAGS_C) $(INCLUDES) $(DECLARE) $(MPI_INCLUDES) $(FUNCWRAP)
-CXXFLAGS=$(CXXFLAGS_C) $(OOPSE_TEMPLATE_FLAGS) $(EXTRA_CC_FLAG) $(INCLUDES) $(DECLARE) $(FUNCWRAP)
+CFLAGS=$(CFLAGS_C) $(INCLUDES) $(DECLARE) 
+CXXFLAGS=$(CXXFLAGS_C) $(OOPSE_TEMPLATE_FLAGS) $(EXTRA_CC_FLAG) $(INCLUDES) $(DECLARE)
 FFLAGS=$(PREPFLAG) $(FFLAGS_C) 
-F90FLAGS=$(PREPFLAG) $(F90FLAGS_C) $(F90_INCLUDES)
+F90FLAGS=$(PREPFLAG) $(F90FLAGS_C) -I../../libBASS
 DEPFLAGS=$(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) $(MPI_INCLUDES)
+MPI_F90FLAGS=$(F90FLAGS) $(MPI_F90_INCLUDES) $(PREPDEFFLAG)$(MPI_DECLARE)
 
 SRC_DIR := ..
 
@@ -163,83 +160,93 @@ C_FILES = \
 
 C_FILES = \
 	$(DIR)/mpiForceField.c \
-	$(DIR)/MatVec3.c \
-	$(DIR)/fInfo.c
+	$(DIR)/MatVec3.c 
 
 CXX_FILES = \
-	$(DIR)/Atom.cpp \
+        $(DIR)/Atom.cpp \
+	$(DIR)/AtomVisitor.cpp \
 	$(DIR)/Bend.cpp \
 	$(DIR)/BendExtensions.cpp \
 	$(DIR)/Bond.cpp \
 	$(DIR)/BondExtensions.cpp \
+	$(DIR)/CGFamilyMinimizer.cpp \
+	$(DIR)/CompositeVisitor.cpp \
 	$(DIR)/DirectionalAtom.cpp \
-	$(DIR)/DumpWriter.cpp \
+	$(DIR)/DUFF.cpp \
 	$(DIR)/DumpReader.cpp \
+	$(DIR)/DumpWriter.cpp \
+	$(DIR)/EAM_FF.cpp \
 	$(DIR)/Exclude.cpp \
+	$(DIR)/ForceFields.cpp \
+	$(DIR)/fortranWrappers.cpp \
+	$(DIR)/GenericData.cpp \
+	$(DIR)/GhostBend.cpp \
 	$(DIR)/InitializeFromFile.cpp \
-	$(DIR)/LJFF.cpp \
-	$(DIR)/EAM_FF.cpp \
-	$(DIR)/WATER.cpp \
-	$(DIR)/RigidBody.cpp \
-	$(DIR)/SimInfo.cpp \
-	$(DIR)/SimSetup.cpp \
-	$(DIR)/StatWriter.cpp \
-	$(DIR)/StuntDouble.cpp \
 	$(DIR)/Integrator.cpp \
-	$(DIR)/Thermo.cpp \
-	$(DIR)/GhostBend.cpp \
-	$(DIR)/Torsion.cpp \
-	$(DIR)/TorsionExtensions.cpp \
-	$(DIR)/DUFF.cpp \
-	$(DIR)/randomSPRNG.cpp \
-	$(DIR)/fortranWrappers.cpp \
-	$(DIR)/ForceFields.cpp \
+	$(DIR)/LJFF.cpp \
+	$(DIR)/mdProfile.cpp \
 	$(DIR)/Molecule.cpp \
+	$(DIR)/mpiSimulation.cpp \
+	$(DIR)/NPT.cpp \
 	$(DIR)/NPTf.cpp \
 	$(DIR)/NPTi.cpp \
 	$(DIR)/NPTxyz.cpp \
 	$(DIR)/NVT.cpp \
-	$(DIR)/SimState.cpp \
-	$(DIR)/ZConstraint.cpp \
-	$(DIR)/ZConsWriter.cpp \
-	$(DIR)/mdProfile.cpp \
-	$(DIR)/GenericData.cpp \
-	$(DIR)/mpiSimulation.cpp \
-	$(DIR)/Utility.cpp \
 	$(DIR)/OOPSEMinimizer.cpp \
-	$(DIR)/CGFamilyMinimizer.cpp \
-	$(DIR)/PRCG.cpp \
-	$(DIR)/SDMinimizer.cpp \
-	$(DIR)/ZConsReader.cpp	\
-	$(DIR)/AtomVisitor.cpp \
-	$(DIR)/CompositeVisitor.cpp \
 	$(DIR)/OtherVisitor.cpp \
+	$(DIR)/PRCG.cpp \
+	$(DIR)/randomSPRNG.cpp \
+	$(DIR)/Restraints.cpp \
+	$(DIR)/RigidBody.cpp \
 	$(DIR)/RigidBodyVisitor.cpp \
-	$(DIR)/ZconsVisitor.cpp
+	$(DIR)/SDMinimizer.cpp \
+	$(DIR)/SimInfo.cpp \
+	$(DIR)/SimSetup.cpp \
+	$(DIR)/SimState.cpp \
+	$(DIR)/SkipList.cpp \
+	$(DIR)/StatWriter.cpp \
+	$(DIR)/StreamTokenizer.cpp \
+	$(DIR)/StuntDouble.cpp \
+	$(DIR)/Thermo.cpp \
+	$(DIR)/Torsion.cpp \
+	$(DIR)/TorsionExtensions.cpp \
+	$(DIR)/Utility.cpp \
+	$(DIR)/WATER.cpp \
+	$(DIR)/ZConsReader.cpp \
+	$(DIR)/ZConstraint.cpp \
+	$(DIR)/ZconsVisitor.cpp \
+	$(DIR)/Restraints.cpp	\
+	$(DIR)/ConstraintManager.cpp \
+	$(DIR)/ConstraintAlgorithm.cpp \
+	$(DIR)/Shake.cpp \
+	$(DIR)/Rattle.cpp \
+	$(DIR)/ShakeMin.cpp \
+	$(DIR)/CallbackFunctor.cpp \
+	$(DIR)/ConstraintElement.cpp \
+	$(DIR)/ZConsWriter.cpp
 
-
 F90_FILES= \
-	$(DIR)/definitions_module.F90 \
-	$(DIR)/status_module.F90 \
-	$(DIR)/atype_module.F90 \
-	$(DIR)/switch_module.F90 \
-	$(DIR)/calc_dipole_dipole.F90 \
+        $(DIR)/atype_module.F90 \
 	$(DIR)/calc_charge_charge.F90 \
-	$(DIR)/calc_reaction_field.F90 \
-	$(DIR)/calc_LJ_FF.F90 \
+	$(DIR)/calc_dipole_dipole.F90 \
 	$(DIR)/calc_eam.F90 \
+	$(DIR)/calc_gb.F90 \
+	$(DIR)/calc_LJ_FF.F90 \
+	$(DIR)/calc_reaction_field.F90 \
 	$(DIR)/calc_sticky_pair.F90 \
+	$(DIR)/definitions_module.F90 \
 	$(DIR)/do_Forces.F90 \
-	$(DIR)/vector_class.F90 \
-	$(DIR)/simulation_module.F90 \
-	$(DIR)/wrappers.F90 \
-	$(DIR)/neighborLists.F90 \
-	$(DIR)/calc_gb.F90 \
 	$(DIR)/force_globals.F90 \
 	$(DIR)/mpiSimulation_module.F90 \
+	$(DIR)/neighborLists.F90 \
 	$(DIR)/notifyCutoffs.F90 \
+	$(DIR)/oopseMPI_module.F90 \
+	$(DIR)/simulation_module.F90 \
+	$(DIR)/status_module.F90 \
+	$(DIR)/switch_module.F90 \
 	$(DIR)/timing.F90 \
-	$(DIR)/oopseMPI_module.F90
+	$(DIR)/vector_class.F90 \
+	$(DIR)/wrappers.F90
 
 DIR:=.
 C_SRCS   :=     $(C_FILES)
@@ -265,8 +272,13 @@ all: libmdtools.a libmdtools_MPI.a
 
 # Possible make targets:
 
+ifeq ($(USE_MPI),yes)
 all: libmdtools.a libmdtools_MPI.a
+else
+all: libmdtools.a
+endif
 
+
 libmdtools.a: $(OBJS)
 	$(RM) $@
 	$(AR) cr $@ $(OBJS)
@@ -356,11 +368,13 @@ obj/simulation_module$(O): ./simulation_module.F90 \
 	obj/vector_class$(O) \
 	obj/force_globals$(O) \
 	obj/atype_module$(O) \
+	obj/switch_module$(O) \
 	obj/neighborLists$(O)
 
 obj/calc_LJ_FF$(O): ./calc_LJ_FF.F90 \
 	obj/definitions_module$(O) \
 	obj/atype_module$(O) \
+	obj/switch_module$(O) \
 	obj/simulation_module$(O) \
 	obj/vector_class$(O) \
 	obj/force_globals$(O)
@@ -370,6 +384,7 @@ obj/calc_reaction_field$(O): ./calc_reaction_field.F90
 	obj/vector_class$(O) \
 	obj/atype_module$(O) \
 	obj/simulation_module$(O) \
+	obj/status_module$(O) \
 	obj/force_globals$(O)
 
 obj/calc_dipole_dipole$(O): ./calc_dipole_dipole.F90 \
@@ -377,6 +392,7 @@ obj/calc_dipole_dipole$(O): ./calc_dipole_dipole.F90 \
 	obj/atype_module$(O) \
 	obj/simulation_module$(O) \
 	obj/force_globals$(O) \
+	obj/status_module$(O) \
 	obj/vector_class$(O)
 
 obj/calc_charge_charge$(O): ./calc_charge_charge.F90 \
@@ -384,6 +400,7 @@ obj/calc_charge_charge$(O): ./calc_charge_charge.F90 \
 	obj/atype_module$(O) \
 	obj/simulation_module$(O) \
 	obj/force_globals$(O) \
+	obj/status_module$(O) \
 	obj/vector_class$(O)
 
 obj/do_Forces$(O): ./do_Forces.F90 \
@@ -398,6 +415,7 @@ obj/do_Forces$(O): ./do_Forces.F90 \
 	obj/calc_reaction_field$(O) \
 	obj/calc_gb$(O) \
 	obj/force_globals$(O) \
+	obj/status_module$(O) \
 	obj/vector_class$(O)
 
 obj/notifyCutoffs$(O): ./notifyCutoffs.F90 \
@@ -407,6 +425,7 @@ obj/notifyCutoffs$(O): ./notifyCutoffs.F90 \
 	obj/calc_eam$(O) \
 	obj/calc_dipole_dipole$(O) \
 	obj/calc_reaction_field$(O) \
+	obj/switch_module$(O) \
 	obj/do_Forces$(O) 
 
 obj/wrappers$(O): ./wrappers.F90 \
@@ -476,11 +495,13 @@ MPIobj/simulation_module$(O): ./simulation_module.F90 
 	MPIobj/force_globals$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/atype_module$(O) \
+	MPIobj/switch_module$(O) \
 	MPIobj/neighborLists$(O)
 
 MPIobj/calc_LJ_FF$(O): ./calc_LJ_FF.F90 \
 	MPIobj/definitions_module$(O) \
 	MPIobj/atype_module$(O) \
+	MPIobj/switch_module$(O) \
 	MPIobj/simulation_module$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/atype_module$(O) \
@@ -494,6 +515,7 @@ MPIobj/calc_reaction_field$(O): ./calc_reaction_field.
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/vector_class$(O) \
 	MPIobj/atype_module$(O) \
+	MPIobj/status_module$(O) \
 	MPIobj/force_globals$(O)
 
 MPIobj/calc_dipole_dipole$(O): ./calc_dipole_dipole.F90 \
@@ -502,6 +524,7 @@ MPIobj/calc_dipole_dipole$(O): ./calc_dipole_dipole.F9
 	MPIobj/simulation_module$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/force_globals$(O) \
+	MPIobj/status_module$(O) \
 	MPIobj/vector_class$(O)
 
 MPIobj/calc_charge_charge$(O): ./calc_charge_charge.F90 \
@@ -510,6 +533,7 @@ MPIobj/calc_charge_charge$(O): ./calc_charge_charge.F9
 	MPIobj/simulation_module$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/force_globals$(O) \
+	MPIobj/status_module$(O) \
 	MPIobj/vector_class$(O)
 
 MPIobj/do_Forces$(O): ./do_Forces.F90 \
@@ -525,6 +549,7 @@ MPIobj/do_Forces$(O): ./do_Forces.F90 \
 	MPIobj/calc_reaction_field$(O) \
 	MPIobj/calc_gb$(O) \
 	MPIobj/force_globals$(O) \
+	MPIobj/status_module$(O) \
 	MPIobj/vector_class$(O)
 
 MPIobj/notifyCutoffs$(O): ./notifyCutoffs.F90 \
@@ -534,6 +559,7 @@ MPIobj/notifyCutoffs$(O): ./notifyCutoffs.F90 \
 	MPIobj/calc_eam$(O) \
 	MPIobj/calc_dipole_dipole$(O) \
 	MPIobj/calc_reaction_field$(O) \
+	MPIobj/switch_module$(O) \
 	MPIobj/do_Forces$(O) 
 
 MPIobj/wrappers$(O): ./wrappers.F90 \