--- trunk/OOPSE-2.0/make/Makefile.in	2004/10/11 18:01:51	1553
+++ trunk/OOPSE-2.0/make/Makefile.in	2005/04/13 22:30:22	2190
@@ -38,25 +38,29 @@ PackageLibs = \
 #packages containing libraries
 PackageLibs = \
 	utils \
+	visitors \
 	math \
 	types \
 	primitives \
-	visitors \
 	UseTheForce/DarkSide \
 	UseTheForce \
 	brains \
 	io \
-	integrators \
-	minimizers \
+	integrators\
 	constraints \
-	profiling \
+	minimizers \
+	selection \
 	restraints \
+	lattice \
 
 #packages containing applications
 Applications = \
 	applications/oopse \
 	applications/dump2Xyz \
-	applications/simpleBuilder
+	applications/staticProps \
+	applications/dynamicProps \
+        applications/simpleBuilder\
+	applications/nanoRodBuilder \
 
 Samples = \
 	samples/argon \
@@ -73,17 +77,17 @@ IncludeDirs = \
 	samples/zcons \
 
 IncludeDirs = \
-	@SPRNG_INC_DIR@ \
-	@MPI_INC_DIR@
+	@CGAL_INC_DIR@ \
+	@MPI_INC_DIR@ 
 
 LibraryDirs = \
-	@SPRNG_LIB_DIR@ \
+	@CGAL_LIB_DIR@ \
 	@MPI_LIB_DIR@ 
 
 Libraries = \
-	@SPRNG_LIB@ \
+	@CGAL_LIBS@ \
 	@MPI_LIB@ \
-	@MPI_F90_LIB@
+	@MPI_F90_LIB@ 
 
 OopseHome       = @OOPSE_HOME@
 ForceParamDir   = $(OopseHome)/share/forceFields
@@ -125,7 +129,9 @@ Package          = $(subst $(shell cd $(SourceDir); pw
 # /home/maul/gezelter/src/code/src/UseTheForce/Darkside --> UseTheForce/Darkside
 #Package          = $(shell echo $(CurrentDir) | sed -e 's/^.*\/src\/\(.*\)/\1/g')
 #use shell script to get the absolute path and then rip it off from $(CurrentDir)
-Package          = $(subst $(shell cd $(SourceDir); pwd)/,,$(CurrentDir))
+#Package          = $(subst $(shell cd $(SourceDir); pwd)/,,$(CurrentDir))
+# REMINDER: We are now using the Package line in each subdir makefile.
+# This avoids the strange path problem and the subshell
 
 PackageList              = $(Package)
 PackageSourceDir         = $(SourceDir)/$(Package)
@@ -204,6 +210,70 @@ ThirdPartyJarsTmp = $(patsubst %,$(LibDir)/%,$(JavaLib
 
 OtherTargetFiles       = $(OtherSourceFiles:%=$(PackageTargetDir)/%)
 
+###########################################################################
+#
+# Figure out the names of the module files based on some work done by
+# configure.  The tr function below is from John Graham-Cumming
+# (http://www.jgc.org). 
+#
+# The tr function.   Has three arguments:
+#
+# $1   The list of characters to translate from
+# $2   The list of characters to translate to
+# $3   The text to translate
+#
+# For example, $(call tr,A B C,1 2 3,CAPITAL) becomes 21PIT1L.
+
+tr = $(eval __t := $3)                                                    \
+     $(foreach c,                                                         \
+         $(join $(addsuffix :,$1),$2),                                    \
+         $(eval __t :=                                                    \
+             $(subst $(word 1,$(subst :, ,$c)),$(word 2,$(subst :, ,$c)), \
+                 $(__t))))$(__t)
+
+# Common character classes for use with the tr function.  Each of
+# these is actually a variable declaration and must be wrapped with
+# $() or ${} to be used.
+
+[A-Z] := A B C D E F G H I J K L M N O P Q R S T U V W X Y Z #
+[a-z] := a b c d e f g h i j k l m n o p q r s t u v w x y z #
+[0-9] := 0 1 2 3 4 5 6 7 8 9 #
+[A-F] := A B C D E F #
+
+# Figure out whether we have $(eval) or not (GNU Make 3.80 and above)
+# if we do not then we need to use the shell version of tr, and not the
+# faster tr function above:
+
+__have_eval := $(false)
+__ignore := $(eval __have_eval := $(true))
+
+ifndef __have_eval
+  uc = $(shell echo $1 | tr "a-z" "A-Z")
+  lc = $(shell echo $1 | tr "A-Z" "a-z")
+else
+  uc = $(call tr,$([a-z]),$([A-Z]),$1)
+  lc = $(call tr,$([A-Z]),$([a-z]),$1)
+endif
+
+# OK, now we can actually use these functions to figure out the names
+# of the module files:
+
+ifneq "$(words $(Modules))" "0"
+ifeq "$(ModuleCase)" "UPPER"
+  MODULES = $(call uc,$(Modules))
+else
+  ifeq "$(ModuleCase)" "lower"
+    MODULES = $(call lc,$(Modules))
+  else
+    MODULES = $(Modules)
+  endif
+endif
+  ModuleFiles = $(MODULES:%= $(PackageTargetDir)/%.$(ModSuffix))
+  ParallelModuleFiles = $(MODULES:%= $(PackageParallelTargetDir)/%.$(ModSuffix))
+endif
+#
+###########################################################################
+
 ThirdPartyJarsTmp = $(patsubst %,$(LibDir)/%,$(JavaLibraries))
 ThirdPartyJars    = $(subst $(Space),$(X),$(ThirdPartyJarsTmp))
 
@@ -215,9 +285,11 @@ ifneq  "$(words $(ObjectFiles) $(ParallelObjectFiles))
 #if Main is defined, do not build library. It may not be true sometimes
 ifneq  "$(words $(ObjectFiles) $(ParallelObjectFiles))" "0"
   DependencyFile    = $(PackageSourceDir)/Makedepend
-  ifneq "$(Main)" ""
+  ifneq "$(words $(Main))" "0"
     Executable             = $(BinDir)/$(Main)
-    ParallelExecutable     = $(BinDir)/$(Main)_MPI
+    ifeq "$(BuiltParallelExe)" "1"
+      ParallelExecutable     = $(BinDir)/$(Main)_MPI
+    endif
   else
     SharedLibrary          = $(LibDir)/lib$(subst /,,$(patsubst %,oopse_%,$(Package)))_UP.so
     StaticLibrary          = $(LibDir)/lib$(subst /,,$(patsubst %,oopse_%,$(Package)))_UP.a
@@ -247,7 +319,7 @@ Move                   = mv
 #
 #---------------------------------------------------------------------------
 Print                  = @echo
-Move                   = mv
+Move                   = mv -f
 Copy                   = cp
 CCompiler              = @CC@
 CppCompiler            = @CXX@
@@ -255,8 +327,9 @@ InstallData            = @INSTALL_DATA@
 MakeDepend             = makedepend
 INSTALL                = @INSTALL@
 InstallProgram         = @INSTALL_PROGRAM@
+InstallScript          = @INSTALL_SCRIPT@
 InstallData            = @INSTALL_DATA@
-MkDir                = @MKINSTALLDIRS@
+MkDir                  = @MKINSTALLDIRS@
 Delete                 = rm -fr
 StaticArchiver         = @AR@
 DynamicArchiver        = @CC@
@@ -285,13 +358,13 @@ 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@ @OOPSE_TEMPLATE_FLAGS@
+CppParallelOptions     = $(FrcDeclare) $(ParallelDeclare) @CXXFLAGS@ @OOPSE_TEMPLATE_FLAGS@
 FortranOptions         =
-F90Options             =  @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(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) 
@@ -366,8 +439,11 @@ $(PackageTargetDir) :
 
 # Create target directory
 $(PackageTargetDir) :
-	$(MakeDir) $@
+	$(MkDir) $@
 
+$(BinDir) :
+	$(MkDir) $@
+
 # .c -> .o
 $(PackageTargetDir)/%.o : %.c
 	$(Print) $@
@@ -421,35 +497,34 @@ $(PackageTargetDir)/%.o : %.F90
 # .F90 -> .o
 $(PackageTargetDir)/%.o : %.F90
 	$(F90Compiler) $(F90Options) $(IncludePath) -c $< -o $@
-	if test -f *.$(ModSuffix); then \
-	  $(Move) *.$(ModSuffix) $(PackageTargetDir);\
+	if test -n "`ls *.$(ModSuffix)`"; then \
+	  $(Move) `ls *.$(ModSuffix)` $(PackageTargetDir);\
 	fi
 
 $(PackageParallelTargetDir)/%.o : %.F90
 	$(F90Compiler) $(F90ParallelOptions) $(IncludePath) -c $< -o $@
-	if test -f *.$(ModSuffix); then \
-	  $(Move) *.$(ModSuffix) $(PackageParallelTargetDir);\
+	if test -n "`ls *.$(ModSuffix)`"; then \
+	  $(Move) "`ls *.$(ModSuffix)`" $(PackageParallelTargetDir);\
 	fi
 
 ifeq "$(UseMPI)" "yes"
 %.o : %.F90
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
-	if test -f *.$(ModSuffix); then \
-	  $(Move) *.$(ModSuffix) $(PackageTargetDir);\
-	fi
+	if test -n "`ls *.$(ModSuffix)`"; then\
+          $(Move) "`ls *.$(ModSuffix)`" $(PackageTargetDir);\
+        fi
 
 	$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@
-	if test -f *.$(ModSuffix); then \
-	  $(Move) *.$(ModSuffix) $(PackageParallelTargetDir);\
+	if test -n "`ls *.$(ModSuffix)`"; then\
+	  $(Move) "`ls *.$(ModSuffix)`" $(PackageTargetDir);\
 	fi
 
 else
 %.o : %.F90
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
-	if test -f *.$(ModSuffix); then \
-	  $(Move) *.$(ModSuffix) $(PackageTargetDir);\
-	fi
-
+	if test -n "`ls *.$(ModSuffix)`"; then\
+          $(Move) "`ls *.$(ModSuffix)`" $(PackageTargetDir);\
+        fi
 endif
 
 
@@ -569,11 +644,11 @@ $(Executable) : $(CombinedStaticLib) $(ObjectFiles)
 	$(Ranlib) $(CombinedParallelStaticLib)
 
 # Executable
-$(Executable) : $(CombinedStaticLib) $(ObjectFiles)
-	$(Linker) $(ObjectFiles) $(LinkOptions) $(LibDirs) $(CombinedStaticLib) $(Libraries) -o $@
+$(Executable) : $(CombinedStaticLib) $(ObjectFiles) $(BinDir)
+	$(Linker) $(ObjectFiles) $(CombinedStaticLib) $(LinkOptions) $(LibDirs) $(Libraries) -o $@
 
-$(ParallelExecutable) : $(CombinedParallelStaticLib) $(ParallelObjectFiles)
-	$(Linker) $(ParallelObjectFiles) $(ParallelLinkOptions) $(LibDirs) $(CombinedParallelStaticLib) $(Libraries) -o $@
+$(ParallelExecutable) : $(CombinedParallelStaticLib) $(ParallelObjectFiles) $(BinDir)
+	$(Linker) $(ParallelObjectFiles) $(CombinedParallelStaticLib) $(ParallelLinkOptions) $(LibDirs) $(Libraries) -o $@
 
 # Anything else is just copied from source to target
 $(PackageTargetDir)/% : $(PackageSourceDir)/%
@@ -616,31 +691,39 @@ endif
 	$(Executable) 
 endif
 
+echo : $(PackageListLoop)
+	$(Print) Done echo.
 
+_echoall :
+	$(Print) $(Modules)
+
 # make clean
 clean : $(PackageListLoop)
 	$(Print) Done clean.	
 
 _cleanall :
-	$(Delete) $(ObjectFiles) $(ParallelObjectFiles)
+	$(Delete) \
+		$(ObjectFiles) \
+		$(ModuleFiles) \
+		$(ParallelObjectFiles) \
+		$(ParallelModuleFiles) \
+		$(JarFile) \
+		$(SharedLibrary) \
+		$(StaticLibrary) \
+		$(ParallelSharedLibrary) \
+		$(ParallelStaticLibrary) \
+		$(CombinedStaticLib) \
+		$(CombinedParallelStaticLib)
 
 # make distclean
 distclean : $(PackageListLoop)
 	$(Print) Done clean.	
 
-_distcleanall :
-	$(Delete) $(ObjectFiles) \
-	          $(ParallelObjectFiles) \
-		        $(JarFile) \
-	          $(SharedLibrary) \
-	          $(StaticLibrary) \
-	          $(ParallelSharedLibrary) \
-	          $(ParallelStaticLibrary) \
-	          $(Executable) \
+_distcleanall : _cleanall
+	$(Delete) $(Executable) \
 	          $(ParallelExecutable) \
 	          $(DependencyFile) 
 
-
 # make depend
 depend : $(PackageListLoop)
 	$(Print) Done dependencies.
@@ -652,28 +735,42 @@ ifneq "$(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
@@ -702,9 +799,9 @@ ifneq "$(words $(InstallFiles))" "0"
 _installdata :  $(MyInstallDir)
 	$(Print) $(InstallFiles) 
 ifneq "$(words $(InstallFiles))" "0"
-	$(InstallData) $(InstallFiles) $(MyInstallDir)
+	$(InstallCommand) $(InstallFiles) $(MyInstallDir)
 endif	    
-	
+
 # make statistics
 _statisticsall :
 	@$(Print) $(patsubst %,$(CurrentDir)/%,$(SourceFiles)) >> $(DEV_ROOT)/files.tmp