--- trunk/OOPSE-2.0/make/Makefile.in	2005/03/21 19:22:55	2126
+++ trunk/OOPSE-2.0/make/Makefile.in	2005/04/13 22:30:22	2190
@@ -51,14 +51,16 @@ PackageLibs = \
 	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 \
@@ -75,14 +77,17 @@ IncludeDirs = \
 	samples/zcons \
 
 IncludeDirs = \
-	@MPI_INC_DIR@
+	@CGAL_INC_DIR@ \
+	@MPI_INC_DIR@ 
 
 LibraryDirs = \
+	@CGAL_LIB_DIR@ \
 	@MPI_LIB_DIR@ 
 
 Libraries = \
+	@CGAL_LIBS@ \
 	@MPI_LIB@ \
-	@MPI_F90_LIB@
+	@MPI_F90_LIB@ 
 
 OopseHome       = @OOPSE_HOME@
 ForceParamDir   = $(OopseHome)/share/forceFields
@@ -204,6 +209,70 @@ 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),$(ThirdPartyJarsTmp))
@@ -218,7 +287,9 @@ ifneq  "$(words $(ObjectFiles) $(ParallelObjectFiles))
   DependencyFile    = $(PackageSourceDir)/Makedepend
   ifneq "$(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
@@ -620,7 +691,12 @@ endif
 	$(Executable) 
 endif
 
+echo : $(PackageListLoop)
+	$(Print) Done echo.
 
+_echoall :
+	$(Print) $(Modules)
+
 # make clean
 clean : $(PackageListLoop)
 	$(Print) Done clean.	
@@ -628,7 +704,9 @@ _cleanall :
 _cleanall :
 	$(Delete) \
 		$(ObjectFiles) \
+		$(ModuleFiles) \
 		$(ParallelObjectFiles) \
+		$(ParallelModuleFiles) \
 		$(JarFile) \
 		$(SharedLibrary) \
 		$(StaticLibrary) \