--- trunk/OOPSE/libmdtools/Makefile.in	2003/12/19 17:25:00	887
+++ trunk/OOPSE/libmdtools/Makefile.in	2004/06/02 18:27:52	1224
@@ -49,9 +49,6 @@ MODDIRFLAG=@MODDIRFLAG@
 # MODDIRFLAG
 MODDIRFLAG=@MODDIRFLAG@
 
-# MPI F90 Module path
-MPI_F90_MODS=@MPI_F90_MODS@
-
 # Compiler dependent Fortran module
 FLIBS_EXTRA = @F90LIBS@
 
@@ -127,7 +124,7 @@ MPI_INCLUDES= -I$(MPI_INC) $(MODDIRFLAG)$(MPI_F90_MODS
 # include paths starting with "." are all relative to the SUBDIRS!!!
 
 INCLUDES= -I.. -I../../libBASS $(SPRNG_INC)
-MPI_INCLUDES= -I$(MPI_INC) $(MODDIRFLAG)$(MPI_F90_MODS)
+MPI_INCLUDES= -I$(MPI_INC)
 F90_INCLUDES= -I/usr/local/include
 
 CFLAGS=$(CFLAGS_C) $(INCLUDES) $(DECLARE) $(MPI_INCLUDES) $(FUNCWRAP)
@@ -166,64 +163,86 @@ C_FILES = \
 
 C_FILES = \
 	$(DIR)/mpiForceField.c \
+	$(DIR)/MatVec3.c \
 	$(DIR)/fInfo.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)/SimInfo.cpp \
-	$(DIR)/SimSetup.cpp \
-	$(DIR)/StatWriter.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)/mpiSimulation.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)/OOPSEMinimizer.cpp \
+	$(DIR)/OtherVisitor.cpp \
+	$(DIR)/PRCG.cpp \
+	$(DIR)/randomSPRNG.cpp \
+	$(DIR)/Restraints.cpp \
+	$(DIR)/RigidBody.cpp \
+	$(DIR)/RigidBodyVisitor.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)/ZConsWriter.cpp \
-	$(DIR)/mdProfile.cpp \
-	$(DIR)/GenericData.cpp
+	$(DIR)/ZconsVisitor.cpp \
+	$(DIR)/ZConsWriter.cpp
 
 F90_FILES= \
-	$(DIR)/definitions_module.F90 \
-	$(DIR)/status_module.F90 \
-	$(DIR)/atype_module.F90 \
+        $(DIR)/atype_module.F90 \
+	$(DIR)/calc_charge_charge.F90 \
 	$(DIR)/calc_dipole_dipole.F90 \
-	$(DIR)/calc_reaction_field.F90 \
-	$(DIR)/calc_LJ_FF.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)/oopseMPI_module.F90 \
+	$(DIR)/simulation_module.F90 \
+	$(DIR)/status_module.F90 \
+	$(DIR)/switch_module.F90 \
+	$(DIR)/timing.F90 \
+	$(DIR)/vector_class.F90 \
+	$(DIR)/wrappers.F90
 
 DIR:=.
 C_SRCS   :=     $(C_FILES)
@@ -340,11 +359,13 @@ obj/simulation_module$(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$(O)
@@ -354,6 +375,7 @@ obj/calc_reaction_field$(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$(O): ./calc_dipole_dipole.F90 \
@@ -361,11 +383,21 @@ obj/calc_dipole_dipole$(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$(O): ./calc_charge_charge.F90 \
+	obj/definitions_module$(O) \
+	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 \
 	obj/definitions_module$(O) \
 	obj/atype_module$(O) \
+	obj/switch_module$(O) \
 	obj/simulation_module$(O) \
 	obj/neighborLists$(O) \
 	obj/calc_LJ_FF$(O) \
@@ -374,6 +406,7 @@ 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$(O): ./notifyCutoffs.F90 \
@@ -383,6 +416,7 @@ obj/notifyCutoffs$(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$(O): ./wrappers.F90 \
@@ -394,11 +428,11 @@ obj/wrappers$(O): ./wrappers.F90 \
 	obj/do_Forces$(O) \
 	obj/notifyCutoffs$(O) 
 
+obj/timing$(O): ./timing.F90 \
+	obj/do_Forces$(O)
 
 
 
-
-
 #MPI dependencies:
 
 MPIobj/definitions_module$(O): ./definitions_module.F90
@@ -452,11 +486,13 @@ MPIobj/simulation_module$(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$(O) \
@@ -470,6 +506,7 @@ MPIobj/calc_reaction_field$(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$(O): ./calc_dipole_dipole.F90 \
@@ -478,12 +515,23 @@ MPIobj/calc_dipole_dipole$(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$(O): ./calc_charge_charge.F90 \
+	MPIobj/definitions_module$(O) \
+	MPIobj/atype_module$(O) \
+	MPIobj/simulation_module$(O) \
+	MPIobj/mpiSimulation_module$(O) \
+	MPIobj/force_globals$(O) \
+	MPIobj/status_module$(O) \
+	MPIobj/vector_class$(O)
+
 MPIobj/do_Forces$(O): ./do_Forces.F90 \
 	MPIobj/definitions_module$(O) \
 	MPIobj/mpiSimulation_module$(O) \
 	MPIobj/atype_module$(O) \
+	MPIobj/switch_module$(O) \
 	MPIobj/simulation_module$(O) \
 	MPIobj/neighborLists$(O) \
 	MPIobj/calc_LJ_FF$(O) \
@@ -492,6 +540,7 @@ 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$(O): ./notifyCutoffs.F90 \
@@ -501,6 +550,7 @@ MPIobj/notifyCutoffs$(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$(O): ./wrappers.F90 \
@@ -513,3 +563,6 @@ MPIobj/wrappers$(O): ./wrappers.F90 \
 	MPIobj/do_Forces$(O) \
 	MPIobj/notifyCutoffs$(O)  
 
+MPIobj/timing$(O): ./timing.F90 \
+	MPIobj/do_Forces$(O) \
+	MPIobj/mpiSimulation_module$(O)