--- trunk/OOPSE-3.0/make/Makefile.in	2004/10/06 21:22:43	1535
+++ trunk/OOPSE-3.0/make/Makefile.in	2004/10/11 21:13:46	1557
@@ -86,8 +86,10 @@ ForceParamDir   = @OOPSE_HOME@/share/forceFields/
 	@MPI_F90_LIB@
 
 OopseHome       = @OOPSE_HOME@
-ForceParamDir   = @OOPSE_HOME@/share/forceFields/
-SampleSimDir    = @OOPSE_HOME@/share/samples/
+ForceParamDir   = $(OopseHome)/share/forceFields
+SampleSimDir    = $(OopseHome)/share/samples
+InstallBinDir   = $(OopseHome)/bin
+DocDir          = $(OopseHome)/doc
 FrcDeclare      = -DFRC_PATH="$(ForceParamDir)"
 F90Declare      = -D__FORTRAN90
 ParallelDeclare = -DIS_MPI
@@ -223,6 +225,7 @@ endif
     ParallelStaticLibrary  = $(LibDir)/lib$(subst /,,$(patsubst %,oopse_%,$(Package)))_MPI.a
   endif
 endif
+
 #
 # Misc
 #
@@ -250,10 +253,10 @@ Install                = @INSTALL@
 CppCompiler            = @CXX@
 Linker                 = @CXX@
 MakeDepend             = makedepend
-Install                = @INSTALL@
+INSTALL                = @INSTALL@
 InstallProgram         = @INSTALL_PROGRAM@
 InstallData            = @INSTALL_DATA@
-MakeDir                = @MKINSTALLDIRS@
+MkDir                = @MKINSTALLDIRS@
 Delete                 = rm -fr
 StaticArchiver         = @AR@
 DynamicArchiver        = @CC@
@@ -272,8 +275,8 @@ Ranlib                 = @RANLIB@
 Yacc                   = @YACC@
 Lex                    = @LEX@
 Ranlib                 = @RANLIB@
+Doxygen                = @DOXYGEN@
 
-
 MakeOptions            = -k
 MakeDependOptions      = 
 StaticArchiverOptions  = rc
@@ -287,8 +290,8 @@ F90Options             =  @PREPFLAG@ @F90FLAGS@ @MODDI
 CppOptions             = $(FrcDeclare)
 CppParallelOptions     = $(FrcDeclare) $(ParallelDeclare)
 FortranOptions         =
-F90Options             =  @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(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) 
@@ -310,8 +313,47 @@ Space                  = $(Empty) $(Empty)
 
 Empty                  =
 Space                  = $(Empty) $(Empty)
+
+
+#---------------------------------------------------------------------------
+#
+#  Install
+#
+#---------------------------------------------------------------------------
+
+ifneq "$(words $(SampleFiles))" "0"
+  MySample                 = $(subst $(shell cd $(DEV_ROOT)/samples; pwd)/,,$(CurrentDir))
+  MyInstallDir             = $(SampleSimDir)/$(MySample)
+  InstallFiles             = $(SampleFiles)
+  InstallCommand           = $(InstallData)
+endif
+
+ifneq "$(words $(Main))" "0"
+  MyInstallDir             = $(InstallBinDir)
+  ifeq "$(UseMPI)" "yes"
+    InstallFiles             = $(Executable) $(ParallelExecutable)
+  else
+    InstallFiles             = $(Executable)
+  endif 
+  InstallCommand           = $(InstallProgram)
+endif
 
+ifneq "$(words $(ForcefieldFiles))" "0"
+  MyInstallDir             = $(ForceParamDir)
+  InstallFiles             = $(ForcefieldFiles)
+  InstallCommand           = $(InstallData)
+endif
 
+ifneq "$(words $(InstallFiles))" "0"
+  InstallList            =
+else
+  InstallList            = $(patsubst %,$(DEV_ROOT)/%,$(Samples)) $(DEV_ROOT)/forceFields $(patsubst %, $(SourceDir)/%,$(Applications)) 
+endif
+
+InstallListLoop          = $(patsubst %,$(SourceDir)/%/.install,$(PackageList))  $(patsubst %,%/.install,$(InstallList)) 
+
+
+
 #---------------------------------------------------------------------------
 #
 # Rules
@@ -379,17 +421,35 @@ $(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
 
 
@@ -486,6 +546,11 @@ $(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))
 extract_objs = $(shell $(StaticArchiver) -x $(1) $(call find_objs, $(1)))
@@ -521,6 +586,7 @@ ifeq "$(UseMPI)" "yes"
 
 _all : _buildall
 
+_buildall : 
 ifeq "$(UseMPI)" "yes"
 _buildall : \
 	$(DependencyFile) \
@@ -586,28 +652,42 @@ ifneq "$(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)
-	$(Delete) Make.cpptemp
+
+  ifeq "$(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)
-	$(Delete) Make.ctemp
+
+  ifeq "$(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 '$$(TargetDir)/' $(F90Declare)  $(F90Files) > Make.ftemp
-	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(ParallelTargetDir)/' $(ParallelDeclare) $(F90Declare)  $(F90Files) >> Make.ftemp
-	cat Make.ftemp >> $(DependencyFile)
-	$(Delete) 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
@@ -621,6 +701,24 @@ jarsign : $(JarFile)
 jarsign : $(JarFile)
 	$(JarSigner) -keystore GeoSoftKeystore $(JarFile) myself
 
+#make install
+%.install :
+	@$(MAKE) $(MakeOptions) -C $(subst .install,,$@) _installall 	
+
+install : $(InstallListLoop)
+	$(Print) Done Install
+
+_installall : _buildall _installdata
+
+$(MyInstallDir) : 
+	$(MkDir) $@
+
+_installdata :  $(MyInstallDir)
+	$(Print) $(InstallFiles) 
+ifneq "$(words $(InstallFiles))" "0"
+	$(InstallData) $(InstallFiles) $(MyInstallDir)
+endif	    
+	
 # make statistics
 _statisticsall :
 	@$(Print) $(patsubst %,$(CurrentDir)/%,$(SourceFiles)) >> $(DEV_ROOT)/files.tmp