--- trunk/OOPSE-4/make/Makefile.in	2005/04/14 21:41:56	2199
+++ trunk/OOPSE-4/make/Makefile.in	2005/12/02 20:10:30	2474
@@ -52,7 +52,9 @@ PackageLibs = \
 	selection \
 	restraints \
 	lattice \
-
+	openbabel\
+        antlr\
+        mdParser
 #packages containing applications
 Applications = \
 	applications/oopse \
@@ -61,19 +63,26 @@ Applications = \
 	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 = \
@@ -85,6 +94,7 @@ Libraries = \
 	@MPI_LIB_DIR@ 
 
 Libraries = \
+	@LIBS@ \
 	@CGAL_LIBS@ \
 	@MPI_LIB@ \
 	@MPI_F90_LIB@ 
@@ -118,6 +128,7 @@ 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)
@@ -325,12 +336,14 @@ INSTALL                = @INSTALL@
 CppCompiler            = @CXX@
 Linker                 = @CXX@
 MakeDepend             = makedepend
+LN_S                   = @LN_S@
 INSTALL                = @INSTALL@
+EGREP                  = @EGREP@
 InstallProgram         = @INSTALL_PROGRAM@
 InstallScript          = @INSTALL_SCRIPT@
 InstallData            = @INSTALL_DATA@
 MkDir                  = @MKINSTALLDIRS@
-Delete                 = rm -fr
+Delete                 = rm -f
 StaticArchiver         = @AR@
 DynamicArchiver        = @CC@
 FortranCompiler        = @FC@
@@ -409,6 +422,10 @@ endif
     InstallFiles             = $(Executable)
   endif 
   InstallCommand           = $(InstallProgram)
+  ifneq "$(words $(LinkTargets))" "0"
+    MyLinkSource = $(patsubst %, $(MyInstallDir)/%,$(Main)) 
+    MyLinkTargets = $(patsubst %, $(MyInstallDir)/%,$(LinkTargets))
+  endif
 endif
 
 ifneq "$(words $(ForcefieldFiles))" "0"
@@ -445,70 +462,70 @@ $(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);\
@@ -520,7 +537,7 @@ else
 	fi
 
 else
-%.o : %.F90
+%.o : %.F90 $(MainMakefile)
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 	if test -n "`ls *.$(ModSuffix)`"; then\
           $(Move) "`ls *.$(ModSuffix)`" $(PackageTargetDir);\
@@ -627,20 +644,25 @@ find_objs = $(shell $(StaticArchiver) -t $(1))
 	$(Doxygen) $(DEV_ROOT)/make/Doxyfile
 
 #GUN make funtions to merge the libraries
-find_objs = $(shell $(StaticArchiver) -t $(1))
+find_objs = $(shell $(StaticArchiver) -t $(1) | $(EGREP) -v "SYMDEF")
 extract_objs = $(shell $(StaticArchiver) -x $(1) $(call find_objs, $(1)))
 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))
+all_objs = $(foreach thisLib,$(LibNames), $(call find_objs, $(thisLib)))
+all_parallel_objs = $(foreach thisLib,$(ParallelLibNames), $(call find_objs, $(thisLib)))
+all_lib_objs = $(patsubst %,$(TargetDir)/%,$(call all_objs))
+all_lib_parallel_objs = $(patsubst %,$(TargetDir)/%,$(call all_parallel_objs))
 
 $(CombinedStaticLib) : $(LibDir)/.stamp_UP
-	$(Print) create $@     	
-	$(foreach thisLib,$(LibNames),$(call do_create,$(thisLib),$@))
+	$(Print) creating $@     	
+	$(StaticArchiver) $(StaticArchiverOptions) $@ $(call all_lib_objs)
 	$(Ranlib) $(CombinedStaticLib)
 
 $(CombinedParallelStaticLib) : $(LibDir)/.stamp_MPI
-	$(Print) create $@
-	$(foreach thisLib,$(ParallelLibNames), $(call do_create, $(thisLib), $@))
+	$(Print) creating $@
+	$(StaticArchiver) $(StaticArchiverOptions) $@ $(call all_lib_parallel_objs)
 	$(Ranlib) $(CombinedParallelStaticLib)
 
 # Executable
@@ -791,7 +813,7 @@ _installall : _buildall _installdata
 install : $(InstallListLoop)
 	$(Print) Done Install
 
-_installall : _buildall _installdata
+_installall : _buildall _installdata _installlinks
 
 $(MyInstallDir) : 
 	$(MkDir) $@
@@ -802,6 +824,12 @@ endif	    
 	$(InstallCommand) $(InstallFiles) $(MyInstallDir)
 endif	    
 
+_installlinks :  $(MyInstallDir)
+ifneq "$(words $(MyLinkTargets))" "0"
+	@cd $(MyInstallDir)
+	$(foreach thisLink,$(MyLinkTargets),$(call do_link,$(MyLinkSource),$(thisLink)))
+endif	    
+
 # make statistics
 _statisticsall :
 	@$(Print) $(patsubst %,$(CurrentDir)/%,$(SourceFiles)) >> $(DEV_ROOT)/files.tmp
@@ -812,12 +840,12 @@ $(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