--- trunk/OOPSE-3.0/make/Makefile.in	2004/09/29 21:54:03	1512
+++ trunk/OOPSE-3.0/make/Makefile.in	2004/10/05 19:35:59	1525
@@ -33,59 +33,78 @@
 #  $<      - Current dependency
 #
 #---------------------------------------------------------------------------
-
-#---------------------------------------------------------------------------
-#
-#  Packages
-#
-#---------------------------------------------------------------------------
-
+IS_UNIX=1
 #packages to be made
 Packages = \
-        utils \
-        math \
-        types \
-        primitives \
-        visitors \
-        UseTheForce/DarkSide \
-        UseTheForce \
-        brains \
-        io \
-        integrators \
-        minimizers \
-        constraints \
-        profiling \
-        restraints \
-        applications 
+	utils \
+	math \
+	types \
+	primitives \
+	visitors \
+	UseTheForce/DarkSide \
+	UseTheForce \
+	brains \
+	io \
+	integrators \
+	minimizers \
+	constraints \
+	profiling \
+	restraints \
+	applications/oopse \
+	applications/dump2Xyz \
+	applications/simpleBuilder \
 
 #packages contain libraries
 PackageLibs = \
-	      utils \
-	      math \
-	      types \
-	      primitives \
-	      visitors \
-        UseTheForce/DarkSide \
-	      UseTheForce \
-        brains \
-	      io \
-	      integrators \
-	      minimizers \
-	      constraints \
-	      profiling \
-	      restraints 
+	utils \
+	math \
+	types \
+	primitives \
+	visitors \
+	UseTheForce/DarkSide \
+	UseTheForce \
+	brains \
+	io \
+	integrators \
+	minimizers \
+	constraints \
+	profiling \
+	restraints \
+
+IncludeDirs = \
+	@SPRNG_INC_DIR@ \
+	@MPI_INC_DIR@
+
+LibraryDirs = \
+	@SPRNG_LIB_DIR@ \
+	@MPI_LIB_DIR@ 
+
+Libraries = \
+	@SPRNG_LIB@ \
+	@MPI_LIB@ \
+	@MPI_F90_LIB@
+
+LinkOptions = \
+	@F90LIBS@
 
+OopseHome       = @OOPSE_HOME@
+ForceParamDir   = @OOPSE_HOME@/share/forceFields/
+SampleSimDir    = @OOPSE_HOME@/share/samples/
+FrcDeclare      = -DFRC_PATH="$(ForceParamDir)"
+ParallelDeclare = -DIS_MPI
+UseMPI          = @USE_MPI@
+
 #---------------------------------------------------------------------------
 #
 #  Directories
 #
 #---------------------------------------------------------------------------
 
-srcdir = @srcdir@
 SourceDir         = $(DEV_ROOT)/src
 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
@@ -155,23 +174,23 @@ ObjectFiles            = $(CFiles:%.c=        $(Packag
 JniHeaders             = $(JniSource:%.java=  $(PackageSourceDir)/%.h)
 ObjectFiles            = $(CFiles:%.c=        $(PackageTargetDir)/%.o)\
                          $(CppFiles:%.cpp=    $(PackageTargetDir)/%.o)\
-		                     $(FortranFiles:%.f=  $(PackageTargetDir)/%.o)\
-		                     $(F90Files:%.F90=    $(PackageTargetDir)/%.o)\
-		                     $(LexFiles:%.l=      $(PackageTargetDir)/%.o)\
-		                     $(YaccFiles:%.y=     $(PackageTargetDir)/%.o)
+		         $(FortranFiles:%.f=  $(PackageTargetDir)/%.o)\
+		         $(F90Files:%.F90=    $(PackageTargetDir)/%.o)\
+		         $(LexFiles:%.l=      $(PackageTargetDir)/%.o)\
+		         $(YaccFiles:%.y=     $(PackageTargetDir)/%.o)
 ParallelObjectFiles    = $(CFiles:%.c=        $(PackageParallelTargetDir)/%.o)\
-		                     $(CppFiles:%.cpp=    $(PackageParallelTargetDir)/%.o)\
-		                     $(FortranFiles:%.f=  $(PackageParallelTargetDir)/%.o)\
-		                     $(F90Files:%.F90=    $(PackageParallelTargetDir)/%.o)\
-		                     $(LexFiles:%.l=      $(PackageParallelTargetDir)/%.o)\
-		                     $(YaccFiles:%.y=     $(PackageParallelTargetDir)/%.o)
+		         $(CppFiles:%.cpp=    $(PackageParallelTargetDir)/%.o)\
+		         $(FortranFiles:%.f=  $(PackageParallelTargetDir)/%.o)\
+		         $(F90Files:%.F90=    $(PackageParallelTargetDir)/%.o)\
+		         $(LexFiles:%.l=      $(PackageParallelTargetDir)/%.o)\
+		         $(YaccFiles:%.y=     $(PackageParallelTargetDir)/%.o)
 
 DerivedSource          = $(YaccFiles:%.y=    %.h) \
-	                       $(YaccFiles:%.y=    %.c) \
-	                       $(LexFiles:%.l=     %.c)
+	                 $(YaccFiles:%.y=    %.c) \
+	                 $(LexFiles:%.l=     %.c)
 
 DerivedCFiles          = $(YaccFiles:%.y=    %.c) \
-	                       $(LexFiles:%.l=     %.c)
+	                 $(LexFiles:%.l=     %.c)
 
 OtherTargetFiles       = $(OtherSourceFiles:%=$(PackageTargetDir)/%)
 
@@ -190,10 +209,10 @@ ifneq  "$(words $(ObjectFiles) $(ParallelObjectFiles))
     Executable             = $(BinDir)/$(Main)
     ParallelExecutable     = $(BinDir)/$(Main)_MPI
   else
-    SharedLibrary          = $(LibDir)/lib$(subst /,,$(Package)).so 
-    StaticLibrary          = $(LibDir)/lib$(subst /,,$(Package)).a
-    ParallelSharedLibrary  = $(LibDir)/lib$(subst /,,$(Package))_MPI.so 
-    ParallelStaticLibrary  = $(LibDir)/lib$(subst /,,$(Package))_MPI.a
+    SharedLibrary          = $(LibDir)/lib$(subst /,,$(patsubst %,oopse_%,$(Package))).so
+    StaticLibrary          = $(LibDir)/lib$(subst /,,$(patsubst %,oopse_%,$(Package))).a
+    ParallelSharedLibrary  = $(ParallelLibDir)/lib$(subst /,,$(patsubst %,oopse_%,$(Package))).so
+    ParallelStaticLibrary  = $(ParallelLibDir)/lib$(subst /,,$(patsubst %,oopse_%,$(Package))).a
   endif
 endif
 #
@@ -203,8 +222,11 @@ LocalLibs        = $(subst /,,$(PackageLibs))
 JavaPackageNames = $(subst /,.,$(JavaPackages))
 IncludePath      = -I$(SourceDir) $(IncludeDirs:%=-I%)
 LibDirs          = -L$(LibDir)    $(LibraryDirs:%=-L%)
-LocalLibs        = $(subst /,,$(PackageLibs))
-LibList          = $(LocalLibs:%=-l%) $(Libraries:%=-l%)
+ParallelLibDirs  = -L$(ParallelLibDir)  $(LibraryDirs:%=-L%)
+LocalLibs        = $(subst /,,$(patsubst %, oopse_%, $(PackageLibs))) 
+ParallelLocalLibs= $(subst /,,$(patsubst %, oopse_%, $(PackageLibs))) 
+LibList          = $(LocalLibs:%=-l%) $(Libraries)
+ParallelLibList  = $(ParallelLocalLibs:%=-l%) $(Libraries)
 
 
 #---------------------------------------------------------------------------
@@ -242,7 +264,7 @@ MakeOptions            = -k -s
 Lex                    = @LEX@
 
 
-MakeOptions            = -k -s
+MakeOptions            = -k
 MakeDependOptions      = 
 StaticArchiverOptions  = rc
 DynamicArchiverOptions = -shared
@@ -250,8 +272,13 @@ FortranOptions         =
 JniOptions             =
 RmiOptions             = -d $(TargetDir) -classpath $(ClassPath) \
 			 -sourcepath $(SourceDir)
+COptions               = $(FrcDeclare)
+CParallelOptions       = $(FrcDeclare) $(ParallelDeclare)
+CppOptions             = $(FrcDeclare)
+CppParallelOptions     = $(FrcDeclare) $(ParallelDeclare)
 FortranOptions         =
-F90Options             =  -I$(SourceDir) -module $(TargetDir) 
+F90Options             =  @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(SourceDir) -module $(TargetDir) 
+F90ParallelOptions     =  @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(SourceDir) -module $(ParallelTargetDir)  @PREPDEFFLAG@$(ParallelDeclare)
 JavaCompilerOptions    = -d $(TargetDir) -classpath $(ClassPath) \
 			 -sourcepath $(SourceDir) -deprecation
 JavaRunOptions         = -classpath $(ClassPath) 
@@ -292,52 +319,79 @@ $(PackageTargetDir)/%.o : %.c
 # .c -> .o
 $(PackageTargetDir)/%.o : %.c
 	$(Print) $@
-	$(Print) $(CCompiler) $(COptions) -c $(IncludePath) $< -o $@
-	@$(CCompiler) $(COptions) -c $(IncludePath) $< -o $@
+	$(CCompiler) $(COptions) -c $(IncludePath) $< -o $@
 
+$(PackageParallelTargetDir)/%.o : %.c
+	$(Print) $@
+	$(CCompiler) $(CParallelOptions) -c $(IncludePath) $< -o $@
+
+ifeq "$(UseMPI)" "yes"
 %.o : %.c
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+	$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@
+else
+%.o : %.c
+	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+endif
 
 # .cpp -> .o
 $(PackageTargetDir)/%.o : %.cpp
-	$(Print) $@
-	$(Print) $(CppCompiler) $(CppOptions) -c $(IncludePath) $< -o $@
 	$(CppCompiler) $(CppOptions) -c $(IncludePath) $< -o $@
 
+$(PackageParallelTargetDir)/%.o : %.cpp
+	$(CppCompiler) $(CppParallelOptions) -c $(IncludePath) $< -o $@
+
+ifeq "$(UseMPI)" "yes"
 %.o : %.cpp
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+	$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@
+else
+%.o : %.cpp
+	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+endif
 
 # .f -> .o
 $(PackageTargetDir)/%.o : %.f
-	$(Print) $@
-	$(Print) $(FortranCompiler) $(FortranOptions) -c $< -o $@
-	@$(FortranCompiler) $(FortranOptions) -c $< -o $@
+	$(FortranCompiler) $(FortranOptions) -c $< -o $@
 
+$(PackageParallelTargetDir)/%.o : %.f
+	$(FortranCompiler) $(FortranParallelOptions) -c $< -o $@
+
+ifeq "$(UseMPI)" "yes"
 %.o : %.f
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+	$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@
+else
+%.o : %.f
+	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+endif
 
 # .F90 -> .o
 $(PackageTargetDir)/%.o : %.F90
-	$(Print) $@
-	$(Print) $(F90Compiler) $(F90Options) -c $< -o $@
-	@$(F90Compiler) $(F90Options) -c $< -o $@
+	$(F90Compiler) $(F90Options) $(IncludePath) -c $< -o $@
 
+$(PackageParallelTargetDir)/%.o : %.F90
+	$(F90Compiler) $(F90ParallelOptions) $(IncludePath) -c $< -o $@
+
+ifeq "$(UseMPI)" "yes"
 %.o : %.F90
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+	$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@
+else
+%.o : %.F90
+	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
+endif
 
+
 # .java -> .class
 $(PackageTargetDir)/%.class : $(PackageSourceDir)/%.java
-	$(Print) $@
-	$(Print) $(JavaCompiler) $(JavaCompilerOptions) $< 
-	@$(JavaCompiler) $(JavaCompilerOptions) $< 
+	$(JavaCompiler) $(JavaCompilerOptions) $< 
 
 %.class : $(PackageSourceDir)/%.java
 	@$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 
 # .class -> .h
 $(PackageSourceDir)/%.h : $(PackageTargetDir)/%.class
-	$(Print) $@
-	$(Print) $(JniCompiler) $(JniOptions) $(JavaPackageName).$*
 	$(JniCompiler) $(JniOptions) $(JavaPackageName).$*
 
 %.h : %.class
@@ -345,17 +399,13 @@ $(PackageSourceDir)/%.h : $(PackageTargetDir)/%.class
 
 #.y -> .h
 %.h : %.y
-	$(Print) $@
-	$(Print) @$(Yacc) -d $?
-	@$(Yacc) -d  $?
+	$(Yacc) -d  $?
 	@$(Move) y.tab.h $*.h
 	@$(Delete) y.tab.c
 
 #.y -> .c
 %.c : %.y
-	$(Print) $@
-	$(Print) $(Yacc) -d $?
-	@$(Yacc) -d  $?
+	$(Yacc) -d  $?
 	@$(Move) y.tab.c $*.c
 	@$(Delete) y.tab.h
 
@@ -366,43 +416,41 @@ $(LibDir)/%.a : $(ObjectFiles)
 	@$(Lex) -o$@ $?
 
 # .o -> .a
+
 $(LibDir)/%.a : $(ObjectFiles)
-	$(Print) $@
-	$(Print) $(StaticArchiver) $(StaticArchiverOptions) $@ $(ObjectFiles)
-	@$(StaticArchiver) $(StaticArchiverOptions) $@ $(ObjectFiles)
+	$(StaticArchiver) $(StaticArchiverOptions) $@ $(ObjectFiles)
 
+$(ParallelLibDir)/%.a: $(ParallelObjectFiles)
+	$(StaticArchiver) $(StaticArchiverOptions) $@ $(ParallelObjectFiles)
+
+ifeq "$(UseMPI)" "yes"
+%.a : $(ObjectFiles) $(ParallelObjectFiles)
+	$(MAKE) $(MakeOptions) $(LibDir)/$@
+	$(MAKE) $(MakeOptions) $(ParallelLibDir)/$@
+else
 %.a : $(ObjectFiles)
 	$(MAKE) $(MakeOptions) $(LibDir)/$@
+endif
 
-$(LibDir)/%_MPI.a : $(ParallelObjectFiles)
-	$(Print) $@
-	$(Print) $(StaticArchiver) $(StaticArchiverOptions) $@ $(ParallelObjectFiles)
-	@$(StaticArchiver) $(StaticArchiverOptions) $@ $(ParallelObjectFiles)
-
-%_MPI.a : $(ParallelObjectFiles)
-	$(MAKE) $(MakeOptions) $(LibDir)/$@
-
 # .o -> .so
 $(LibDir)/%.so : $(ObjectFiles)
-	$(Print) $@	
-	$(Print) $(DynamicArchiver) $(ObjectFiles) $(DynamicArchiverOptions) -o $@
 	$(DynamicArchiver) $(ObjectFiles) $(DynamicArchiverOptions) -o $@
 
-%.so : $(ObjectFiles)
-	$(MAKE) $(MakeOptions) $(LibDir)/$@
-
-$(LibDir)/%_MPI.so : $(ParallelObjectFiles)
-	$(Print) $@	
-	$(Print) $(DynamicArchiver) $(ParallelObjectFiles) $(DynamicArchiverOptions) -o $@
+$(ParallelLibDir)/%.so : $(ParallelObjectFiles)
 	$(DynamicArchiver) $(ParallelObjectFiles) $(DynamicArchiverOptions) -o $@
 
-%_MPI.so : $(ParallelObjectFiles)
+ifeq "$(UseMPI)" "yes"
+%.so : $(ObjectFiles) $(ParallelObjectFiles)
 	$(MAKE) $(MakeOptions) $(LibDir)/$@
+	$(MAKE) $(MakeOptions) $(ParallelLibDir)/$@
+else
+%.so : $(ObjectFiles)
+	$(MAKE) $(MakeOptions) $(LibDir)/$@
+endif
 
 # .class -> .jar
 $(LibDir)/%.jar : $(JavaClassFiles) $(OtherTargetFiles)
 	$(Print) $@
-	$(Print) $(JavaArchiver) -cf $@ $(JavaClassFilesRel) $(OtherTargetFiles)
 	@cd $(TargetDir); $(JavaArchiver) -cf $@ \
 	$(JavaClassFilesRel) $(OtherTargetFiles)
 
@@ -434,14 +482,10 @@ $(Executable) : $(ObjectFiles)
 
 # Executable
 $(Executable) : $(ObjectFiles)
-	$(Print) $@
-	$(Print) $(Linker) $(LinkOptions) $(LibDirs) $(LibList) $(ObjectFiles) -o $@
-	$(Linker) $(LinkOptions) $(LibDirs) $(LibList) $(ObjectFiles) -o $@
+	$(Linker) $(ObjectFiles) $(LinkOptions) $(LibDirs) $(LibList) $(LibList) $(LibList) -o $@
 
 $(ParallelExecutable) : $(ParallelObjectFiles)
-	$(Print) $@
-	$(Print) $(Linker) $(LinkOptions) $(LibDirs) $(LibList) $(ParallelObjectFiles) -o $@
-	$(Linker) $(LinkOptions) $(LibDirs) $(LibList) $(ParallelObjectFiles) -o $@
+	$(Linker) $(ParallelObjectFiles) $(LinkOptions) $(ParallelLibDirs) $(ParallelLibList) $(ParallelLibList) $(ParallelLibList) -o $@
 
 # Anything else is just copied from source to target
 $(PackageTargetDir)/% : $(PackageSourceDir)/%
@@ -454,18 +498,34 @@ _buildall : \
 
 _all : _buildall
 
+ifeq "$(UseMPI)" "yes"
 _buildall : \
 	$(DependencyFile) \
 	$(PackageTargetDir) \
 	$(ObjectFiles) \
+	$(ParallelObjectFiles) \
 	$(JavaClassFiles) \
 	$(RmiStubFiles) \
 	$(RmiSkeletonFiles) \
 	$(OtherTargetFiles) \
-	$(SharedLibrary) \
 	$(StaticLibrary) \
+	$(ParallelStaticLibrary) \
 	$(JarFile) \
-	$(Executable)
+	$(Executable) \
+	$(ParallelExecutable) 
+else
+_buildall : \
+	$(DependencyFile) \
+	$(PackageTargetDir) \
+	$(ObjectFiles) \
+	$(JavaClassFiles) \
+	$(RmiStubFiles) \
+	$(RmiSkeletonFiles) \
+	$(OtherTargetFiles) \
+	$(StaticLibrary) \
+	$(JarFile) \
+	$(Executable) 
+endif
 
 
 # make clean
@@ -473,12 +533,23 @@ _cleanall :
 	$(Print) Done clean.	
 
 _cleanall :
-	$(Delete) $(PackageTargetDir)/* \
-		  $(JarFile) \
+	$(Delete) $(ObjectFiles) $(ParallelObjectFiles)
+
+# make distclean
+distclean : $(PackageListLoop)
+	$(Print) Done clean.	
+
+_distcleanall :
+	$(Delete) $(ObjectFiles) \
+	          $(ParallelObjectFiles) \
+		        $(JarFile) \
 	          $(SharedLibrary) \
 	          $(StaticLibrary) \
+	          $(ParallelSharedLibrary) \
+	          $(ParallelStaticLibrary) \
 	          $(Executable) \
-	          $(DependencyFile)
+	          $(ParallelExecutable) \
+	          $(DependencyFile) 
 
 
 # make depend
@@ -491,20 +562,16 @@ $(DependencyFile) : $(DerivedSource)
 	$(Print) $@ 
 	@cd $(PackageSourceDir)
 
-	touch Make.ctemp
-	touch Make.ctemp
+	@touch Make.ctemp
+	@touch Make.ctemp
 
 ifneq "$(words $(CppFiles))" "0"
-	$(Print) Make dependencies for $(CppFiles)
-	$(Print) $(CppCompiler) $(IncludePath) -MM $(CppFiles)  > Make.cpptemp
 	$(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)
 endif
 
 ifneq "$(words $(CFiles))" "0" 
-	$(Print) Make dependencies for $(CFiles)
-	$(Print) $(CCompiler)   $(IncludePath) -MM $(CFiles) $(DerivedCFiles)   > Make.ctemp
 	$(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' >> $(DependencyFile)
@@ -512,8 +579,8 @@ ifneq "$(words $(F90Files))" "0"
 endif
 
 ifneq "$(words $(F90Files))" "0"
-	$(Print) Make dependencies for $(F90Files)
-	$(DEV_ROOT)/scripts/sfmakedepend  -I $(DEV_ROOT)/src -d '$$(DEV_ROOT)/obj' -f ./Make.ftemp -h *.F90
+	$(DEV_ROOT)/scripts/filepp  -I $(DEV_ROOT)/src -od '$$(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)
 endif
 	$(Delete) Make.cpptemp Make.ctemp Make.ftemp
@@ -545,6 +612,10 @@ pure : $(Executable).pure
 
 pure : $(Executable).pure
 
+#make cvslog
+cvslog:
+	$(DEV_ROOT)/scripts/cvs2cl.pl
+
 # Execute
 _runexe :
 	$(Executable) $(RunParameters)