--- trunk/OOPSE-2.0/make/Makefile.in	2005/02/14 23:26:25	2023
+++ trunk/OOPSE-2.0/make/Makefile.in	2005/04/13 22:30:22	2190
@@ -50,14 +50,17 @@ PackageLibs = \
 	constraints \
 	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 \
@@ -74,17 +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
@@ -206,7 +209,71 @@ OtherTargetFiles       = $(OtherSourceFiles:%=$(Packag
 	                 $(LexFiles:%.l=     %.c)
 
 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))
 
@@ -218,9 +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
@@ -258,6 +327,7 @@ InstallData            = @INSTALL_DATA@
 MakeDepend             = makedepend
 INSTALL                = @INSTALL@
 InstallProgram         = @INSTALL_PROGRAM@
+InstallScript          = @INSTALL_SCRIPT@
 InstallData            = @INSTALL_DATA@
 MkDir                  = @MKINSTALLDIRS@
 Delete                 = rm -fr
@@ -279,8 +349,6 @@ Ps                     = @PS@
 Lex                    = @LEX@
 Ranlib                 = @RANLIB@
 Doxygen                = @DOXYGEN@
-Ps                     = @PS@
-PsType                 = @PSTYPE@
 
 MakeOptions            = -k
 MakeDependOptions      = 
@@ -290,7 +358,7 @@ COptions               = $(FrcDeclare) @CFLAGS@ -DPS=$
 JniOptions             =
 RmiOptions             = -d $(TargetDir) -classpath $(ClassPath) \
 			 -sourcepath $(SourceDir)
-COptions               = $(FrcDeclare) @CFLAGS@ -DPS=$(Ps) -DPSTYPE=$(PsType)
+COptions               = $(FrcDeclare) @CFLAGS@
 CParallelOptions       = $(FrcDeclare) $(ParallelDeclare) @CFLAGS@
 CppOptions             = $(FrcDeclare) @CXXFLAGS@ @OOPSE_TEMPLATE_FLAGS@
 CppParallelOptions     = $(FrcDeclare) $(ParallelDeclare) @CXXFLAGS@ @OOPSE_TEMPLATE_FLAGS@
@@ -623,31 +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)
 	$(Print) Done dependencies.
@@ -723,7 +799,7 @@ ifneq "$(words $(InstallFiles))" "0"
 _installdata :  $(MyInstallDir)
 	$(Print) $(InstallFiles) 
 ifneq "$(words $(InstallFiles))" "0"
-	$(InstallData) $(InstallFiles) $(MyInstallDir)
+	$(InstallCommand) $(InstallFiles) $(MyInstallDir)
 endif	    
 
 # make statistics