--- trunk/OOPSE-2.0/make/Makefile.in	2004/10/06 18:53:05	1530
+++ trunk/OOPSE-2.0/make/Makefile.in	2004/10/11 15:43:16	1552
@@ -58,6 +58,20 @@ IncludeDirs = \
 	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@ \
 	@MPI_INC_DIR@
@@ -72,11 +86,16 @@ 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
 UseMPI          = @USE_MPI@
+ModuleCase      = @F90_MODULE_NAMES@
+ModSuffix       = @MOD@
 LinkOptions = \
 	@F90LIBS@ 
 
@@ -94,7 +113,6 @@ 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
@@ -207,6 +225,7 @@ endif
     ParallelStaticLibrary  = $(LibDir)/lib$(subst /,,$(patsubst %,oopse_%,$(Package)))_MPI.a
   endif
 endif
+
 #
 # Misc
 #
@@ -234,10 +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@
@@ -256,7 +275,7 @@ Ranlib                 = @RANLIB@
 Yacc                   = @YACC@
 Lex                    = @LEX@
 Ranlib                 = @RANLIB@
-
+Doxygen                = @DOXYGEN@
 
 MakeOptions            = -k
 MakeDependOptions      = 
@@ -294,8 +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
@@ -470,6 +528,11 @@ $(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, $(1)))
@@ -505,6 +568,7 @@ ifeq "$(UseMPI)" "yes"
 
 _all : _buildall
 
+_buildall : 
 ifeq "$(UseMPI)" "yes"
 _buildall : \
 	$(DependencyFile) \
@@ -568,29 +632,31 @@ $(DependencyFile) : $(DerivedSource)
 $(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)
@@ -603,6 +669,24 @@ 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