--- trunk/OOPSE-2.0/make/Makefile.in	2005/11/18 17:50:17	2456
+++ trunk/OOPSE-2.0/make/Makefile.in	2006/01/12 20:19:18	2557
@@ -52,8 +52,9 @@ PackageLibs = \
 	selection \
 	restraints \
 	lattice \
-	openbabel
-
+	openbabel\
+        antlr\
+        mdParser
 #packages containing applications
 Applications = \
 	applications/oopse \
@@ -65,7 +66,20 @@ Samples = \
 	applications/atom2mdin
 
 Samples = \
+	samples/alkane \
 	samples/argon \
+	samples/cutoff \
+	samples/dipole \
+	samples/gbljtest \
+	samples/lipid \
+	samples/metals/EAM \
+	samples/metals/EAM/nanoparticle \
+	samples/metals/EAM/nanorod \
+	samples/metals/Sutton-Chen \
+	samples/minimizer \
+	samples/shape \
+	samples/thermoIntegration/liquid \
+	samples/thermoIntegration/solid \
         samples/water/dimer \
 	samples/water/spce \
 	samples/water/ssd \
@@ -74,15 +88,7 @@ Samples = \
 	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 \
+	samples/zcons 
 
 IncludeDirs = \
 	@CGAL_INC_DIR@ \
@@ -110,10 +116,10 @@ LinkOptions = \
 ModuleCase      = @F90_MODULE_NAMES@
 ModSuffix       = @MOD@
 LinkOptions = \
-	@F90LIBS@ 
+	@FCLIBS@ 
 
 ParallelLinkOptions = \
-	@F90LIBS@ 
+	@FCLIBS@ 
 
 
 #---------------------------------------------------------------------------
@@ -337,6 +343,7 @@ InstallProgram         = @INSTALL_PROGRAM@
 MakeDepend             = makedepend
 LN_S                   = @LN_S@
 INSTALL                = @INSTALL@
+EGREP                  = @EGREP@
 InstallProgram         = @INSTALL_PROGRAM@
 InstallScript          = @INSTALL_SCRIPT@
 InstallData            = @INSTALL_DATA@
@@ -345,7 +352,6 @@ F90Compiler            = @F90@
 StaticArchiver         = @AR@
 DynamicArchiver        = @CC@
 FortranCompiler        = @FC@
-F90Compiler            = @F90@
 JavaCompiler           = $(JAVA_HOME)/bin/javac
 JavaArchiver           = $(JAVA_HOME)/bin/jar
 JarSigner              = $(JAVA_HOME)/bin/jarsigner
@@ -371,11 +377,10 @@ CppOptions             = $(FrcDeclare) @CXXFLAGS@ @OOP
 			 -sourcepath $(SourceDir)
 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) @MODDIRFLAG@$(TargetDir) 
-F90ParallelOptions     =  @PREPFLAG@ @F90FLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(ParallelTargetDir)  @PREPDEFFLAG@$(ParallelDeclare)
+CppOptions             = $(FrcDeclare) @CXXFLAGS@
+CppParallelOptions     = $(FrcDeclare) $(ParallelDeclare) @CXXFLAGS@
+FortranOptions         =  @FCFLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(TargetDir) @FCFLAGS_SRCEXT@
+FortranParallelOptions =  @FCFLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(ParallelTargetDir) @PREPDEFFLAG@$(ParallelDeclar) @FCFLAGS_SRCEXT@ 
 JavaCompilerOptions    = -d $(TargetDir) -classpath $(ClassPath) \
 			 -sourcepath $(SourceDir) -deprecation
 JavaRunOptions         = -classpath $(ClassPath) 
@@ -420,6 +425,10 @@ endif
     InstallFiles             = $(Executable)
   endif 
   InstallCommand           = $(InstallProgram)
+  ifneq "$(words $(LinkTargets))" "0"
+    MyLinkSource = $(patsubst %, $(MyInstallDir)/%,$(Main)) 
+    MyLinkTargets = $(patsubst %, $(MyInstallDir)/%,$(LinkTargets))
+  endif
 endif
 
 ifneq "$(words $(ForcefieldFiles))" "0"
@@ -507,13 +516,13 @@ $(PackageTargetDir)/%.o : %.F90 $(MainMakefile)
 
 # .F90 -> .o
 $(PackageTargetDir)/%.o : %.F90 $(MainMakefile)
-	$(F90Compiler) $(F90Options) $(IncludePath) -c $< -o $@
+	$(FortranCompiler) $(FortranOptions) $(IncludePath) -c $< -o $@
 	if test -n "`ls *.$(ModSuffix)`"; then \
 	  $(Move) `ls *.$(ModSuffix)` $(PackageTargetDir);\
 	fi
 
 $(PackageParallelTargetDir)/%.o : %.F90 $(MainMakefile)
-	$(F90Compiler) $(F90ParallelOptions) $(IncludePath) -c $< -o $@
+	$(FortranCompiler) $(FortranParallelOptions) $(IncludePath) -c $< -o $@
 	if test -n "`ls *.$(ModSuffix)`"; then \
 	  $(Move) "`ls *.$(ModSuffix)`" $(PackageParallelTargetDir);\
 	fi
@@ -638,28 +647,38 @@ 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 = $(patsubst %,$(ParallelTargetDir)/%,$(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
-$(Executable) : $(CombinedStaticLib) $(ObjectFiles) $(BinDir)
+$(Executable) : $(CombinedStaticLib) $(ObjectFiles)
+	if test ! -d $(BinDir); then \
+		$(MkDir) $(BinDir) ;\
+	fi
 	$(Linker) $(ObjectFiles) $(CombinedStaticLib) $(LinkOptions) $(LibDirs) $(Libraries) -o $@
 
-$(ParallelExecutable) : $(CombinedParallelStaticLib) $(ParallelObjectFiles) $(BinDir)
+$(ParallelExecutable) : $(CombinedParallelStaticLib) $(ParallelObjectFiles)
+	if test ! -d $(BinDir); then \
+		$(MkDir) $(BinDir) ;\
+	fi
 	$(Linker) $(ParallelObjectFiles) $(CombinedParallelStaticLib) $(ParallelLinkOptions) $(LibDirs) $(Libraries) -o $@
 
 # Anything else is just copied from source to target
@@ -815,10 +834,9 @@ _installlinks :  $(MyInstallDir)
 endif	    
 
 _installlinks :  $(MyInstallDir)
-	$(Print) $(LinkTargets) 
-ifneq "$(words $(LinkTargets))" "0"
+ifneq "$(words $(MyLinkTargets))" "0"
 	@cd $(MyInstallDir)
-	$(foreach thisLink,$(LinkTargets),$(call do_link,$(Executable),$(thisLink)))
+	$(foreach thisLink,$(MyLinkTargets),$(call do_link,$(MyLinkSource),$(thisLink)))
 endif	    
 
 # make statistics