--- trunk/OOPSE-2.0/make/Makefile.in	2005/03/21 19:22:55	2126
+++ trunk/OOPSE-2.0/make/Makefile.in	2005/11/18 17:50:17	2456
@@ -51,38 +51,52 @@ PackageLibs = \
 	minimizers \
 	selection \
 	restraints \
+	lattice \
+	openbabel
 
 #packages containing applications
 Applications = \
 	applications/oopse \
 	applications/dump2Xyz \
-        applications/simpleBuilder\
 	applications/staticProps \
 	applications/dynamicProps \
+        applications/simpleBuilder\
+	applications/nanoRodBuilder \
+	applications/atom2mdin
 
 Samples = \
 	samples/argon \
-	samples/water/dimer \
+        samples/water/dimer \
 	samples/water/spce \
 	samples/water/ssd \
 	samples/water/ssde \
+	samples/water/ssdrf \
+	samples/water/ssd-ion \
 	samples/water/tip3p_ice \
 	samples/water/tip4p \
 	samples/lipid \
 	samples/alkane \
 	samples/minimizer \
 	samples/metals \
+	samples/thermoIntegration/liquid \
+	samples/thermoIntegration/solid \
+	samples/dipole \
+        samples/shape \
 	samples/zcons \
 
 IncludeDirs = \
-	@MPI_INC_DIR@
+	@CGAL_INC_DIR@ \
+	@MPI_INC_DIR@ 
 
 LibraryDirs = \
+	@CGAL_LIB_DIR@ \
 	@MPI_LIB_DIR@ 
 
 Libraries = \
+	@LIBS@ \
+	@CGAL_LIBS@ \
 	@MPI_LIB@ \
-	@MPI_F90_LIB@
+	@MPI_F90_LIB@ 
 
 OopseHome       = @OOPSE_HOME@
 ForceParamDir   = $(OopseHome)/share/forceFields
@@ -113,6 +127,7 @@ BinDir            = $(DEV_ROOT)/bin
 ParallelTargetDir = $(DEV_ROOT)/MPIobj
 LibDir            = $(DEV_ROOT)/lib
 MakeDir           = $(DEV_ROOT)/make
+MainMakefile      = $(MakeDir)/Makefile
 BinDir            = $(DEV_ROOT)/bin
 DocsDir           = $(DEV_ROOT)/docs
 CurrentDir        = $(CURDIR)
@@ -205,6 +220,70 @@ 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))
 
@@ -218,7 +297,9 @@ 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
@@ -254,12 +335,13 @@ INSTALL                = @INSTALL@
 CppCompiler            = @CXX@
 Linker                 = @CXX@
 MakeDepend             = makedepend
+LN_S                   = @LN_S@
 INSTALL                = @INSTALL@
 InstallProgram         = @INSTALL_PROGRAM@
 InstallScript          = @INSTALL_SCRIPT@
 InstallData            = @INSTALL_DATA@
 MkDir                  = @MKINSTALLDIRS@
-Delete                 = rm -fr
+Delete                 = rm -f
 StaticArchiver         = @AR@
 DynamicArchiver        = @CC@
 FortranCompiler        = @FC@
@@ -374,70 +456,70 @@ $(PackageTargetDir)/%.o : %.c
 	$(MkDir) $@
 
 # .c -> .o
-$(PackageTargetDir)/%.o : %.c
+$(PackageTargetDir)/%.o : %.c $(MainMakefile)
 	$(Print) $@
 	$(CCompiler) $(COptions) -c $(IncludePath) $< -o $@
 
-$(PackageParallelTargetDir)/%.o : %.c
+$(PackageParallelTargetDir)/%.o : %.c $(MainMakefile)
 	$(Print) $@
 	$(CCompiler) $(CParallelOptions) -c $(IncludePath) $< -o $@
 
 ifeq "$(UseMPI)" "yes"
-%.o : %.c
+%.o : %.c $(MainMakefile)
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 	$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@
 else
-%.o : %.c
+%.o : %.c $(MainMakefile)
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 endif
 
 # .cpp -> .o
-$(PackageTargetDir)/%.o : %.cpp
+$(PackageTargetDir)/%.o : %.cpp $(MainMakefile)
 	$(CppCompiler) $(CppOptions) -c $(IncludePath) $< -o $@
 
-$(PackageParallelTargetDir)/%.o : %.cpp
+$(PackageParallelTargetDir)/%.o : %.cpp $(MainMakefile)
 	$(CppCompiler) $(CppParallelOptions) -c $(IncludePath) $< -o $@
 
 ifeq "$(UseMPI)" "yes"
-%.o : %.cpp
+%.o : %.cpp $(MainMakefile)
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 	$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@
 else
-%.o : %.cpp
+%.o : %.cpp $(MainMakefile)
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 endif
 
 # .f -> .o
-$(PackageTargetDir)/%.o : %.f
+$(PackageTargetDir)/%.o : %.f $(MainMakefile)
 	$(FortranCompiler) $(FortranOptions) -c $< -o $@
 
-$(PackageParallelTargetDir)/%.o : %.f
+$(PackageParallelTargetDir)/%.o : %.f $(MainMakefile)
 	$(FortranCompiler) $(FortranParallelOptions) -c $< -o $@
 
 ifeq "$(UseMPI)" "yes"
-%.o : %.f
+%.o : %.f $(MainMakefile)
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 	$(MAKE) $(MakeOptions) $(PackageParallelTargetDir)/$@
 else
-%.o : %.f
+%.o : %.f $(MainMakefile)
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 endif
 
 # .F90 -> .o
-$(PackageTargetDir)/%.o : %.F90
+$(PackageTargetDir)/%.o : %.F90 $(MainMakefile)
 	$(F90Compiler) $(F90Options) $(IncludePath) -c $< -o $@
 	if test -n "`ls *.$(ModSuffix)`"; then \
 	  $(Move) `ls *.$(ModSuffix)` $(PackageTargetDir);\
 	fi
 
-$(PackageParallelTargetDir)/%.o : %.F90
+$(PackageParallelTargetDir)/%.o : %.F90 $(MainMakefile)
 	$(F90Compiler) $(F90ParallelOptions) $(IncludePath) -c $< -o $@
 	if test -n "`ls *.$(ModSuffix)`"; then \
 	  $(Move) "`ls *.$(ModSuffix)`" $(PackageParallelTargetDir);\
 	fi
 
 ifeq "$(UseMPI)" "yes"
-%.o : %.F90
+%.o : %.F90 $(MainMakefile)
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 	if test -n "`ls *.$(ModSuffix)`"; then\
           $(Move) "`ls *.$(ModSuffix)`" $(PackageTargetDir);\
@@ -449,7 +531,7 @@ else
 	fi
 
 else
-%.o : %.F90
+%.o : %.F90 $(MainMakefile)
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 	if test -n "`ls *.$(ModSuffix)`"; then\
           $(Move) "`ls *.$(ModSuffix)`" $(PackageTargetDir);\
@@ -561,6 +643,7 @@ do_create = $(call extract_objs,$(1))$(call create_arc
 create_archive = $(shell  $(StaticArchiver) $(StaticArchiverOptions) $(2) $(call find_objs, $(1)))
 remove_objs = $(shell $(Delete) $(call find_objs, $(1)))
 do_create = $(call extract_objs,$(1))$(call create_archive,$(1),$(2))$(call remove_objs,$(1))  
+do_link = $(shell $(LN_S) $(1) $(2))
 
 $(CombinedStaticLib) : $(LibDir)/.stamp_UP
 	$(Print) create $@     	
@@ -620,7 +703,12 @@ endif
 	$(Executable) 
 endif
 
+echo : $(PackageListLoop)
+	$(Print) Done echo.
 
+_echoall :
+	$(Print) $(Modules)
+
 # make clean
 clean : $(PackageListLoop)
 	$(Print) Done clean.	
@@ -628,7 +716,9 @@ _cleanall :
 _cleanall :
 	$(Delete) \
 		$(ObjectFiles) \
+		$(ModuleFiles) \
 		$(ParallelObjectFiles) \
+		$(ParallelModuleFiles) \
 		$(JarFile) \
 		$(SharedLibrary) \
 		$(StaticLibrary) \
@@ -713,7 +803,7 @@ _installall : _buildall _installdata
 install : $(InstallListLoop)
 	$(Print) Done Install
 
-_installall : _buildall _installdata
+_installall : _buildall _installdata _installlinks
 
 $(MyInstallDir) : 
 	$(MkDir) $@
@@ -724,6 +814,13 @@ endif	    
 	$(InstallCommand) $(InstallFiles) $(MyInstallDir)
 endif	    
 
+_installlinks :  $(MyInstallDir)
+	$(Print) $(LinkTargets) 
+ifneq "$(words $(LinkTargets))" "0"
+	@cd $(MyInstallDir)
+	$(foreach thisLink,$(LinkTargets),$(call do_link,$(Executable),$(thisLink)))
+endif	    
+
 # make statistics
 _statisticsall :
 	@$(Print) $(patsubst %,$(CurrentDir)/%,$(SourceFiles)) >> $(DEV_ROOT)/files.tmp
@@ -734,15 +831,15 @@ $(Executable).pure :
 	$(Print) Done statistics.
 
 # make pure
-$(Executable).pure :
-	$(Purify) $(PurifyOptions) $(CppCompiler) $(LinkOptions) $(LibDirs) \
-	$(LibList) $(ObjectFiles) -o $@
+#$(Executable).pure :
+#	$(Purify) $(PurifyOptions) $(CppCompiler) $(LinkOptions) $(LibDirs) \
+#	$(LibList) $(ObjectFiles) -o $@
+#
+#pure : $(Executable).pure
 
-pure : $(Executable).pure
-
 #make cvslog
 cvslog:
-	$(DEV_ROOT)/scripts/cvs2cl.pl
+	$(DEV_ROOT)/scripts/cvs2cl
 
 # Execute
 _runexe :