--- trunk/OOPSE-3.0/make/Makefile.in	2005/12/30 00:18:28	2530
+++ trunk/OOPSE-3.0/make/Makefile.in	2006/07/26 21:45:19	2964
@@ -52,6 +52,7 @@ PackageLibs = \
 	selection \
 	restraints \
 	lattice \
+	hydrodynamics \
 	openbabel\
         antlr\
         mdParser
@@ -61,12 +62,29 @@ Applications = \
 	applications/dump2Xyz \
 	applications/staticProps \
 	applications/dynamicProps \
-        applications/simpleBuilder\
+	applications/simpleBuilder \
+	applications/randomBuilder \
 	applications/nanoRodBuilder \
-	applications/atom2mdin
+	applications/nanoparticleBuilder \
+	applications/atom2mdin \
+	applications/hydrodynamics \
+	applications/utilities
 
+
 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/thermoIntegration/liquid \
+	samples/thermoIntegration/solid \
         samples/water/dimer \
 	samples/water/spce \
 	samples/water/ssd \
@@ -75,33 +93,27 @@ Samples = \
 	samples/water/ssd-ion \
 	samples/water/tip3p_ice \
 	samples/water/tip4p \
-	samples/lipid \
-	samples/alkane \
-	samples/minimizer \
-	samples/metals \
-	samples/metals/EAM \
-	samples/metals/EAM/nanoparticle \
-	samples/metals/EAM/nanorod \
-	samples/metals/Sutton-Chen \
-	samples/thermoIntegration/liquid \
-	samples/thermoIntegration/solid \
-	samples/dipole \
-        samples/shape \
-	samples/zcons \
+	samples/zcons 
 
 IncludeDirs = \
+	@MPI_INC_DIR@ \
+	@FFTW_INC_DIR@ \
 	@CGAL_INC_DIR@ \
-	@MPI_INC_DIR@ 
+	@ZLIB_INC_DIR@ 
 
 LibraryDirs = \
+	@MPI_LIB_DIR@ \
+	@FFTW_LIB_DIR@ \
 	@CGAL_LIB_DIR@ \
-	@MPI_LIB_DIR@ 
+	@ZLIB_LIB_DIR@ 
 
 Libraries = \
 	@LIBS@ \
-	@CGAL_LIBS@ \
 	@MPI_LIB@ \
-	@MPI_F90_LIB@ 
+	@MPI_F90_LIB@ \
+	@FFTW_LIBS@ \
+	@CGAL_LIBS@ \
+	@ZLIB@ 
 
 OopseHome       = @OOPSE_HOME@
 ForceParamDir   = $(OopseHome)/share/forceFields
@@ -110,15 +122,27 @@ ParallelDeclare = -DIS_MPI
 DocDir          = $(OopseHome)/doc
 FrcDeclare      = -DFRC_PATH="$(ForceParamDir)"
 F90Declare      = -D__FORTRAN90
+UseSingle       = @USE_SINGLE_PRECISION@
+ifeq "$(UseSingle)" "yes"
+SingleDeclare   = -DSINGLE_PRECISION
+else
+SingleDeclare   = 
+endif
 ParallelDeclare = -DIS_MPI
+SinglePrecision = -DSINGLE_PRECISION
 UseMPI          = @USE_MPI@
 ModuleCase      = @F90_MODULE_NAMES@
 ModSuffix       = @MOD@
 LinkOptions = \
-	@F90LIBS@ 
+	@LDFLAGS@ \
+	@FCLIBS@ \
+	@CXXFLAGS@ 
+        
 
 ParallelLinkOptions = \
-	@F90LIBS@ 
+	@LDFLAGS@ \
+	@FCLIBS@ \
+	@CXXFLAGS@
 
 
 #---------------------------------------------------------------------------
@@ -351,7 +375,6 @@ 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
@@ -375,13 +398,17 @@ COptions               = $(FrcDeclare) @CFLAGS@
 JniOptions             =
 RmiOptions             = -d $(TargetDir) -classpath $(ClassPath) \
 			 -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)
+COptions               = $(FrcDeclare) $(SingleDeclare) @CFLAGS@
+CParallelOptions       = $(FrcDeclare) $(SingleDeclare) $(ParallelDeclare) @CFLAGS@
+CppOptions             = $(FrcDeclare) $(SingleDeclare) @CXXFLAGS@
+CppParallelOptions     = $(FrcDeclare) $(SingleDeclare) $(ParallelDeclare) @CXXFLAGS@
+ifeq "$(UseSingle)" "yes"
+FortranOptions         =  @FCFLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(TargetDir) @PREPDEFFLAG@$(SingleDeclare) @FCFLAGS_SRCEXT@
+FortranParallelOptions =  @FCFLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(ParallelTargetDir) @PREPDEFFLAG@$(SingleDeclare) @PREPDEFFLAG@$(ParallelDeclare) @FCFLAGS_SRCEXT@ 
+else
+FortranOptions         =  @FCFLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(TargetDir) @FCFLAGS_SRCEXT@
+FortranParallelOptions =  @FCFLAGS@ @MODDIRFLAG@$(SourceDir) @MODDIRFLAG@$(ParallelTargetDir) @PREPDEFFLAG@$(ParallelDeclare) @FCFLAGS_SRCEXT@ 
+endif
 JavaCompilerOptions    = -d $(TargetDir) -classpath $(ClassPath) \
 			 -sourcepath $(SourceDir) -deprecation
 JavaRunOptions         = -classpath $(ClassPath) 
@@ -418,6 +445,12 @@ ifneq "$(words $(Main))" "0"
   InstallCommand           = $(InstallData)
 endif
 
+ifneq "$(words $(ScriptFiles))" "0"
+  MyInstallDir             = $(InstallBinDir)
+  InstallFiles             = $(ScriptFiles)
+  InstallCommand           = $(InstallProgram)
+endif
+
 ifneq "$(words $(Main))" "0"
   MyInstallDir             = $(InstallBinDir)
   ifeq "$(UseMPI)" "yes"
@@ -517,13 +550,13 @@ $(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
@@ -657,7 +690,7 @@ all_lib_parallel_objs = $(patsubst %,$(TargetDir)/%,$(
 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))
+all_lib_parallel_objs = $(patsubst %,$(ParallelTargetDir)/%,$(call all_parallel_objs))
 
 $(CombinedStaticLib) : $(LibDir)/.stamp_UP
 	$(Print) creating $@     	
@@ -670,10 +703,16 @@ $(Executable) : $(CombinedStaticLib) $(ObjectFiles) $(
 	$(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