--- trunk/SHAPES/Makefile	2004/06/15 20:24:51	1273
+++ trunk/SHAPES/Makefile	2004/06/24 19:06:47	1300
@@ -19,15 +19,15 @@ PREFIX=/usr/local
 # Path prefix for installation links
 PREFIX=/usr/local
 
-# Location of the oopse home
+# Location of the shapes home
 SHAPES_HOME=/usr/local/shapes
 VDW_PARAM_DIR=/usr/local/shapes/share/vdwFiles
 
 # C compiler
-CC=icc8
+CC=icc
 
 # C++ compiler
-CXX=icpc8
+CXX=icpc
 
 # ar
 AR=ar
@@ -47,14 +47,18 @@ MKINSTALLDIRS=@MKINSTALLDIRS@
 INSTALL_DATA=@INSTALL_DATA@
 MKINSTALLDIRS=@MKINSTALLDIRS@
 
+# fftw library and include files
+FFTWINC = -I/usr/local/include
+FFTWLIB = -L/usr/local/lib/ -lfftw3
+
 # CPP flags
 CPPFLAGS=
 
 # C flags
-CFLAGS_C=
+CFLAGS_C= -O3
 
 # C++ flags
-CXXFLAGS_C=
+CXXFLAGS_C= -O3
 
 # LDFLAGS
 LDFLAGS=
@@ -65,15 +69,16 @@ INCLUDES= -I..
 
 # include paths starting with "." are all relative to the SUBDIRS!!!
 
-INCLUDES= -I..
+INCLUDES= -I.. $(FFTWINC) 
 
-CFLAGS=$(CFLAGS_C) $(INCLUDES) $(DECLARE)
-CXXFLAGS=$(CXXFLAGS_C) $(INCLUDES) $(DECLARE)
-DEPFLAGS=$(CFLAGS_C) -I. 
+CFLAGS=$(CFLAGS_C) $(INCLUDES) $(DECLARE) 
+CXXFLAGS=$(CXXFLAGS_C) $(INCLUDES) $(DECLARE) 
+DEPFLAGS=$(CFLAGS_C) $(INCLUDES) -I. 
 
 SRC_DIR := ..
 
-FORCER=forcer$(EXE)
+SHAPER=shaper$(EXE)
+VISUALIZER=visualizer$(EXE)
 LDADD=-lz
 
 # Then do the compile rules:
@@ -86,16 +91,33 @@ C_FILES = \
 
 # Then list what we have to compile
 #
-C_FILES = \
-	$(DIR)/forcerCmd.c \
-	$(DIR)/MatVec3.c
+SHAPER_C_FILES = \
+	$(DIR)/shaperCmd.c \
+	$(DIR)/MatVec3.c \
+	$(DIR)/cospmls.c \
+	$(DIR)/makeweights.c \
+	$(DIR)/naive_synthesis.c \
+	$(DIR)/pmls.c \
+	$(DIR)/primitive.c \
+	$(DIR)/seminaive.c \
+	$(DIR)/FST_semi_memo.c 
 
-CXX_FILES = \
-	$(DIR)/forcer.cpp \
+VISUALIZER_C_FILES = \
+	$(DIR)/visualizerCmd.c 
+
+SHAPER_CXX_FILES = \
+	$(DIR)/shaper.cpp \
 	$(DIR)/PDBReader.cpp \
 	$(DIR)/RigidBody.cpp \
-	$(DIR)/VDWAtom.cpp
+	$(DIR)/VDWAtom.cpp \
+        $(DIR)/GridBuilder.cpp \
+	$(DIR)/SphereHarm.cpp 
 
+VISUALIZER_CXX_FILES = \
+	$(DIR)/SHFunc.cpp \
+	$(DIR)/SHAPE.cpp \
+	$(DIR)/visualizer.cpp 
+
 VDW_FILES= \
 	amber99.vdw \
 	charmm27.vdw \
@@ -104,27 +126,37 @@ C_SRCS   :=     $(C_FILES)
 	oplsaal.vdw 
 
 DIR:=.
-C_SRCS   :=     $(C_FILES)
-CXX_SRCS :=	$(CXX_FILES)
-SRCS     :=     $(C_SRCS) $(CXX_SRCS)
+SHAPER_C_SRCS   :=     $(SHAPER_C_FILES)
+SHAPER_CXX_SRCS :=	$(SHAPER_CXX_FILES)
+SHAPER_SRCS     :=     $(SHAPER_C_SRCS) $(SHAPER_CXX_SRCS)
+VISUALIZER_C_SRCS   :=     $(VISUALIZER_C_FILES)
+VISUALIZER_CXX_SRCS :=	$(VISUALIZER_CXX_FILES)
+VISUALIZER_SRCS     :=     $(VISUALIZER_C_SRCS) $(VISUALIZER_CXX_SRCS)
 
 DIR:=obj
-C_OBJS   :=     $(C_FILES:.c=.o)
-CXX_OBJS :=	$(CXX_FILES:.cpp=.o)
-OBJS     :=     $(C_OBJS) $(CXX_OBJS)
+SHAPER_C_OBJS   :=     $(SHAPER_C_FILES:.c=.o)
+SHAPER_CXX_OBJS :=	$(SHAPER_CXX_FILES:.cpp=.o)
+SHAPER_OBJS     :=     $(SHAPER_C_OBJS) $(SHAPER_CXX_OBJS)
+VISUALIZER_C_OBJS   :=     $(VISUALIZER_C_FILES:.c=.o)
+VISUALIZER_CXX_OBJS :=	$(VISUALIZER_CXX_FILES:.cpp=.o)
+VISUALIZER_OBJS     :=     $(VISUALIZER_C_OBJS) $(VISUALIZER_CXX_OBJS)
 
 SUBDIRS = obj
 
 # Possible make targets:
 
-all: forcer
+all: shaper visualizer
 
-forcer$(EXE) : $(OBJS)
-	$(CXX) $(CFLAGS) $(OBJS) -o $@ $(LDFLAGS) $(LDADD)
+shaper$(EXE) : $(SHAPER_OBJS)
+	$(CXX) $(CFLAGS) $(SHAPER_OBJS) -o $@ $(LDFLAGS) $(LDADD) $(FFTWLIB)
                                                                                                                                                             
-install : $(FORCER)
+visualizer$(EXE) : $(VISUALIZER_OBJS)
+	$(CXX) $(CFLAGS) $(VISUALIZER_OBJS) -o $@ $(LDFLAGS) $(LDADD)
+                                                                                                                                                            
+install : $(SHAPER) $(VISUALIZER)
 	$(MKINSTALLDIRS) $(SHAPES_HOME)/bin
-	$(INSTALL_PROGRAM) -s $(FORCER) $(SHAPES_HOME)/bin/$(FORCER)
+	$(INSTALL_PROGRAM) -s $(SHAPER) $(SHAPES_HOME)/bin/$(SHAPER)
+	$(INSTALL_PROGRAM) -s $(VISUALIZER) $(SHAPES_HOME)/bin/$(VISUALIZER)
 	$(MKINSTALLDIRS) $(VDW_PARAM_DIR)
 	for i in $(VDW_FILES); do \
 	  echo "Installing $$i in $(VDW_PARAM_DIR)\n"; \
@@ -138,22 +170,22 @@ clean : dummy
 	for i in $(SUBDIRS); do \
 	  (cd $$i; $(RM) *.o *.mod) || exit 1; \
 	done
-	$(RM) forcer *.o *.mod *~ Make.temp
+	$(RM) shaper visualizer *.o *.mod *~ Make.temp
 
 distclean : dummy
 	for i in $(SUBDIRS); do \
 	  (cd $$i; $(RM) *.o *.mod) || exit 1; \
 	done
-	$(RM) forcer *.o *.mod *~ Make.temp
+	$(RM) shaper visualizer *.o *.mod *~ Make.temp
 
 depend : Make.dep
 
 Make.dep :
 	echo "Only C dependencies are made automagically!"
 	echo "# DO NOT DELETE THIS LINE - used by make depend" > Make.dep
-	$(CC) $(DEPFLAGS) -MM $(C_SRCS) \
+	$(CC) $(DEPFLAGS) -MM $(SHAPER_C_SRCS) $(VISUALIZER_C_SRCS) \
 		| sed 's/\.o:/\$$(O)\ :/g' > Make.temp
-	$(CXX) $(DEPFLAGS) -MM $(CXX_SRCS) \
+	$(CXX) $(DEPFLAGS) -MM $(SHAPER_CXX_SRCS) $(VISUALIZER_CXX_SRCS) \
 		| sed 's/\.o:/\$$(O)\ :/g' >> Make.temp
 	cat Make.temp | sed 's/^[a-zA-Z0-9]/obj\/&/g' >> Make.dep
 	$(RM) Make.temp