--- trunk/OOPSE-2.0/make/Makefile.in	2004/10/08 23:15:07	1546
+++ trunk/OOPSE-2.0/make/Makefile.in	2004/11/05 21:04:12	1715
@@ -46,11 +46,10 @@ PackageLibs = \
 	UseTheForce \
 	brains \
 	io \
-	integrators \
-	minimizers \
 	constraints \
 	profiling \
 	restraints \
+	minimizers \
 
 #packages containing applications
 Applications = \
@@ -86,10 +85,10 @@ ForceParamDir   = @OOPSE_HOME@/share/forceFields
 	@MPI_F90_LIB@
 
 OopseHome       = @OOPSE_HOME@
-ForceParamDir   = @OOPSE_HOME@/share/forceFields
-SampleSimDir    = @OOPSE_HOME@/share/samples
-InstallBinDir   = @OOPSE_HOME@/bin
-DocDir          = @OOPSE_HOME@/doc
+ForceParamDir   = $(OopseHome)/share/forceFields
+SampleSimDir    = $(OopseHome)/share/samples
+InstallBinDir   = $(OopseHome)/bin
+DocDir          = $(OopseHome)/doc
 FrcDeclare      = -DFRC_PATH="$(ForceParamDir)"
 F90Declare      = -D__FORTRAN90
 ParallelDeclare = -DIS_MPI
@@ -253,7 +252,7 @@ Install                = @INSTALL@
 CppCompiler            = @CXX@
 Linker                 = @CXX@
 MakeDepend             = makedepend
-Install                = @INSTALL@
+INSTALL                = @INSTALL@
 InstallProgram         = @INSTALL_PROGRAM@
 InstallData            = @INSTALL_DATA@
 MkDir                = @MKINSTALLDIRS@
@@ -285,13 +284,13 @@ COptions               = $(FrcDeclare)
 JniOptions             =
 RmiOptions             = -d $(TargetDir) -classpath $(ClassPath) \
 			 -sourcepath $(SourceDir)
-COptions               = $(FrcDeclare)
-CParallelOptions       = $(FrcDeclare) $(ParallelDeclare)
-CppOptions             = $(FrcDeclare)
-CppParallelOptions     = $(FrcDeclare) $(ParallelDeclare)
+COptions               = $(FrcDeclare) @CFLAGS@
+CParallelOptions       = $(FrcDeclare) $(ParallelDeclare) @CFLAGS@
+CppOptions             = $(FrcDeclare) @CXXFLAGS@
+CppParallelOptions     = $(FrcDeclare) $(ParallelDeclare) @CXXFLAGS@
 FortranOptions         =
-F90Options             =  @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(SourceDir) -module $(TargetDir) 
-F90ParallelOptions     =  @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(SourceDir) -module $(ParallelTargetDir)  @PREPDEFFLAG@$(ParallelDeclare)
+F90Options             =  @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(TargetDir) 
+F90ParallelOptions     =  @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(ParallelTargetDir)  @PREPDEFFLAG@$(ParallelDeclare)
 JavaCompilerOptions    = -d $(TargetDir) -classpath $(ClassPath) \
 			 -sourcepath $(SourceDir) -deprecation
 JavaRunOptions         = -classpath $(ClassPath) 
@@ -421,17 +420,35 @@ $(PackageTargetDir)/%.o : %.F90
 # .F90 -> .o
 $(PackageTargetDir)/%.o : %.F90
 	$(F90Compiler) $(F90Options) $(IncludePath) -c $< -o $@
+	if test -f *.$(ModSuffix); then \
+	  $(Move) *.$(ModSuffix) $(PackageTargetDir);\
+	fi
 
 $(PackageParallelTargetDir)/%.o : %.F90
 	$(F90Compiler) $(F90ParallelOptions) $(IncludePath) -c $< -o $@
+	if test -f *.$(ModSuffix); then \
+	  $(Move) *.$(ModSuffix) $(PackageParallelTargetDir);\
+	fi
 
 ifeq "$(UseMPI)" "yes"
 %.o : %.F90
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+	if test -f *.$(ModSuffix); then \
+	  $(Move) *.$(ModSuffix) $(PackageTargetDir);\
+	fi
+
 	$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@
+	if test -f *.$(ModSuffix); then \
+	  $(Move) *.$(ModSuffix) $(PackageParallelTargetDir);\
+	fi
+
 else
 %.o : %.F90
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+	if test -f *.$(ModSuffix); then \
+	  $(Move) *.$(ModSuffix) $(PackageTargetDir);\
+	fi
+
 endif
 
 
@@ -634,28 +651,42 @@ ifneq "$(words $(CppFiles))" "0"
 	@cd $(PackageSourceDir)
 
 ifneq "$(words $(CppFiles))" "0"
-	$(CppCompiler) $(CppOptions) $(IncludePath) -MM $(CppFiles) > Make.cpptemp
-	@cat Make.cpptemp | sed 's/^[a-zA-Z0-9]/$$\(TargetDir\)\/&/g' >> $(DependencyFile)
+	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(TargetDir)/' -MM $(CppFiles)>> Make.cpptemp
+	@cat Make.cpptemp  >> $(DependencyFile)
 	$(Delete) Make.cpptemp
-	$(CppCompiler) $(CppParallelOptions) $(IncludePath) -MM $(CppFiles) > Make.cpptemp
-	@cat Make.cpptemp | sed 's/^[a-zA-Z0-9]/$$\(ParallelTargetDir\)\/&/g' >> $(DependencyFile)
+
+  ifeq "$(UseMPI)" "yes"
+	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(ParallelTargetDir)/' $(ParallelDeclare) -MM $(CppFiles)>> Make.cpptemp
+	@cat Make.cpptemp  >> $(DependencyFile)
 	@$(Delete) Make.cpptemp
+  endif
+
 endif
 
 ifneq "$(words $(CFiles))" "0" 
-	$(CCompiler) $(COptions) $(IncludePath) -MM $(CFiles) $(DerivedCFiles) > Make.ctemp
-	@cat Make.ctemp | sed 's/^[a-zA-Z0-9]/$$\(TargetDir\)\/&/g' >> $(DependencyFile)
+	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(TargetDir)/'  -MM $(CFiles) $(DerivedCFiles)  >> Make.ctemp
+	@cat Make.ctemp  >> $(DependencyFile)
 	$(Delete) Make.ctemp
-	$(CCompiler) $(CParallelOptions) $(IncludePath) -MM $(CFiles) $(DerivedCFiles) > Make.ctemp
-	@cat Make.ctemp | sed 's/^[a-zA-Z0-9]/$$\(ParallelTargetDir\)\/&/g' >> $(DependencyFile)
+
+  ifeq "$(UseMPI)" "yes"
+	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(ParallelTargetDir)/' $(ParallelDeclare) -MM $(CFiles) $(DerivedCFiles)  >> Make.ctemp
+	@cat Make.ctemp  >> $(DependencyFile)
 	@$(Delete) Make.ctemp
+  endif
+
 endif
 
 ifneq "$(words $(F90Files))" "0"
-	$(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
+	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(TargetDir)/' $(F90Declare) -MM -mc $(ModuleCase) -ms $(ModSuffix) $(F90Files) > Make.ftemp
 	@cat Make.ftemp >> $(DependencyFile)
 	@$(Delete) Make.ftemp
+
+  ifeq "$(UseMPI)" "yes"
+	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(ParallelTargetDir)/' $(ParallelDeclare) $(F90Declare) -MM -mc $(ModuleCase) -ms $(ModSuffix)  $(F90Files) >> Make.ftemp
+	@cat Make.ftemp >> $(DependencyFile)
+	@$(Delete) Make.ftemp
+  endif
+
 endif
 
 # make lib