--- trunk/OOPSE-2.0/make/Makefile.in	2004/10/06 18:53:05	1530
+++ trunk/OOPSE-2.0/make/Makefile.in	2004/10/06 22:20:47	1539
@@ -57,6 +57,20 @@ Applications = \
 	applications/oopse \
 	applications/dump2Xyz \
 	applications/simpleBuilder
+
+Samples = \
+	samples/argon \
+	samples/water/dimer \
+	samples/water/spce \
+	samples/water/ssd \
+	samples/water/ssde \
+	samples/water/tip3p_ice \
+	samples/water/tip4p \
+	samples/lipid \
+	samples/alkane \
+	samples/minimizer \
+	samples/metals \
+	samples/zcons \
 
 IncludeDirs = \
 	@SPRNG_INC_DIR@ \
@@ -75,8 +89,11 @@ ParallelDeclare = -DIS_MPI
 ForceParamDir   = @OOPSE_HOME@/share/forceFields/
 SampleSimDir    = @OOPSE_HOME@/share/samples/
 FrcDeclare      = -DFRC_PATH="$(ForceParamDir)"
+F90Declare      = -D__FORTRAN90
 ParallelDeclare = -DIS_MPI
 UseMPI          = @USE_MPI@
+ModuleCase      = @F90_MODULE_NAMES@
+ModSuffix       = @MOD@
 LinkOptions = \
 	@F90LIBS@ 
 
@@ -94,7 +111,6 @@ ParallelLibDir    = $(DEV_ROOT)/MPIlib
 TargetDir         = $(DEV_ROOT)/obj
 ParallelTargetDir = $(DEV_ROOT)/MPIobj
 LibDir            = $(DEV_ROOT)/lib
-ParallelLibDir    = $(DEV_ROOT)/MPIlib
 MakeDir           = $(DEV_ROOT)/make
 BinDir            = $(DEV_ROOT)/bin
 DocsDir           = $(DEV_ROOT)/docs
@@ -256,8 +272,8 @@ Ranlib                 = @RANLIB@
 Yacc                   = @YACC@
 Lex                    = @LEX@
 Ranlib                 = @RANLIB@
+Doxygen                = @DOXYGEN@
 
-
 MakeOptions            = -k
 MakeDependOptions      = 
 StaticArchiverOptions  = rc
@@ -469,6 +485,11 @@ $(PackageTargetDir)/%_Skel.class : $(PackageTargetDir)
 
 %_Skel.class : %.class
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+
+document :
+	$(Print) Generate Documentation for OOPSE-2.0
+	@cd $(DEV_ROOT)/src	
+	$(Doxygen) $(DEV_ROOT)/make/Doxyfile
 
 #GUN make funtions to merge the libraries
 find_objs = $(shell $(StaticArchiver) -t $(1))
@@ -569,28 +590,30 @@ $(DependencyFile) : $(DerivedSource)
 	$(Print) $@ 
 	@cd $(PackageSourceDir)
 
-	@touch Make.ctemp
-	@touch Make.ctemp
-
 ifneq "$(words $(CppFiles))" "0"
-	$(CppCompiler) $(IncludePath) -MM $(CppFiles)  > Make.cpptemp
-	cat Make.cpptemp | sed 's/^[a-zA-Z0-9]/$$\(DEV_ROOT\)\/obj\/&/g' >> $(DependencyFile)
-	cat Make.cpptemp | sed 's/^[a-zA-Z0-9]/$$\(DEV_ROOT\)\/MPIobj\/&/g' >> $(DependencyFile)
+	$(CppCompiler) $(CppOptions) $(IncludePath) -MM $(CppFiles) > Make.cpptemp
+	@cat Make.cpptemp | sed 's/^[a-zA-Z0-9]/$$\(TargetDir\)\/&/g' >> $(DependencyFile)
+	$(Delete) Make.cpptemp
+	$(CppCompiler) $(CppParallelOptions) $(IncludePath) -MM $(CppFiles) > Make.cpptemp
+	@cat Make.cpptemp | sed 's/^[a-zA-Z0-9]/$$\(ParallelTargetDir\)\/&/g' >> $(DependencyFile)
+	@$(Delete) Make.cpptemp
 endif
 
 ifneq "$(words $(CFiles))" "0" 
-	$(CCompiler)   $(IncludePath) -MM $(CFiles) $(DerivedCFiles)   > Make.ctemp
-	cat Make.ctemp | sed 's/^[a-zA-Z0-9]/$$\(DEV_ROOT\)\/obj\/&/g' >> $(DependencyFile)
-	cat Make.ctemp | sed 's/^[a-zA-Z0-9]/$$\(DEV_ROOT\)\/MPIobj\/&/g' >> $(DependencyFile)
-
+	$(CCompiler) $(COptions) $(IncludePath) -MM $(CFiles) $(DerivedCFiles) > Make.ctemp
+	@cat Make.ctemp | sed 's/^[a-zA-Z0-9]/$$\(TargetDir\)\/&/g' >> $(DependencyFile)
+	$(Delete) Make.ctemp
+	$(CCompiler) $(CParallelOptions) $(IncludePath) -MM $(CFiles) $(DerivedCFiles) > Make.ctemp
+	@cat Make.ctemp | sed 's/^[a-zA-Z0-9]/$$\(ParallelTargetDir\)\/&/g' >> $(DependencyFile)
+	@$(Delete) Make.ctemp
 endif
 
 ifneq "$(words $(F90Files))" "0"
-	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(DEV_ROOT)/obj/' -D__FORTRAN90  $(F90Files) > Make.ftemp
-	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(DEV_ROOT)/MPIobj/' -DIS_MPI -D__FORTRAN90  $(F90Files) >> Make.ftemp
-	cat Make.ftemp >> $(DependencyFile)
+	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(TargetDir)/' $(F90Declare) -mc $(ModuleCase) -ms $(ModSuffix) $(F90Files) > Make.ftemp
+	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(ParallelTargetDir)/' $(ParallelDeclare) $(F90Declare) -mc $(ModuleCase) -ms $(ModSuffix)  $(F90Files) >> Make.ftemp
+	@cat Make.ftemp >> $(DependencyFile)
+	@$(Delete) Make.ftemp
 endif
-	$(Delete) Make.cpptemp Make.ctemp Make.ftemp
 
 # make lib
 lib    : $(PackageListLoop)