--- trunk/OOPSE-3.0/make/Makefile.in	2005/04/14 21:41:56	2199
+++ trunk/OOPSE-3.0/make/Makefile.in	2005/04/29 19:16:27	2217
@@ -64,16 +64,22 @@ Samples = \
 
 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 = \
@@ -118,6 +124,7 @@ 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)
@@ -330,7 +337,7 @@ Delete                 = rm -fr
 InstallScript          = @INSTALL_SCRIPT@
 InstallData            = @INSTALL_DATA@
 MkDir                  = @MKINSTALLDIRS@
-Delete                 = rm -fr
+Delete                 = rm -f
 StaticArchiver         = @AR@
 DynamicArchiver        = @CC@
 FortranCompiler        = @FC@
@@ -445,70 +452,70 @@ $(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 +527,7 @@ else
 	fi
 
 else
-%.o : %.F90
+%.o : %.F90 $(MainMakefile)
 	$(MAKE) $(MakeOptions) $(PackageTargetDir)/$@
 	if test -n "`ls *.$(ModSuffix)`"; then\
           $(Move) "`ls *.$(ModSuffix)`" $(PackageTargetDir);\