# Some things to define for the compiler/linker
ROOT = /home/vdbedem/DEV/ModelBuildTool/MBT/

#I cannot find "clipper" files 
CLIPPER = /home/sdcsoftware/linux/CLIPPER_INTEL_1008_RHEL5/
CCPX=${CLIPPER}/ccp4-6.1.1

# Directories where we should search for #include'd files.
LOOPTK_INCLUDE = $(ROOT)/looptk/src/core $(ROOT)/looptk/src/utils
CGAL_INCLUDE = $(ROOT)/QFIT/CGAL-3.6.1/include/
CLIPPER_INCLUDE = $(CLIPPER)/clipper
CPLEX_INCLUDE = $(ROOT)/QFIT/ILOG/CPLEX_Studio122/cplex/include $(ROOT)/QFIT/ILOG/CPLEX_Studio122/concert/include

ICCPX=${CCPX}/include
GSL_INCLUDE = $(ROOT)/gsl-1.15/include
MKL_INCLUDE = /home/sw/intel/Compiler/11.1/072/mkl/include
GLUT_INCLUDE = $(ROOT)/looptk_helper/freeglut-2.6.0/include/
GLUI_INCLUDE = $(ROOT)/looptk_helper/glui-2.36/src/include/GL/
MY_INCLUDE = $(CGAL_INCLUDE) $(LOOPTK_INCLUDE) $(CLIPPER_INCLUDE) $(BONMIN_INCLUDE) $(ICCPX) $(MKL_INCLUDE) $(GSL_INCLUDE) $(CPLEX_INCLUDE) $(GLUT_INCLUDE) $(GLUI_INCLUDE)

# Directories where we should search for libraries.
CGAL_LIB = $(ROOT)/QFIT/CGAL-3.6.1/lib
CLIPPER_LIB = $(CLIPPER)/clipper/lib
CPLEX_LIBS = $(ROOT)/QFIT/ILOG/CPLEX_Studio122/concert/lib/x86-64_sles10_4.1/static_pic $(ROOT)/QFIT/ILOG/CPLEX_Studio122/cplex/lib/x86-64_sles10_4.1/static_pic
LCCPX=${CCPX}/lib
XLIBDIR = /usr/X11R6/lib /usr/X11R6/lib/modules/extensions /usr/X11R6/lib64
SYSLIBDIR = /lib /usr/lib64
GSLLIBDIR =$(ROOT)/gsl-1.15/lib
MKLLIBDIR = /home/sw/intel/Compiler/11.1/072/mkl/32
GLUTLIBDIR = $(ROOT)/looptk_helper/freeglut-2.6.0/lib
MYLIBDIR =  $(CLIPPER)/ccp4-onlylibs-dev/ $(CLIPPER)/ccp4-onlylibs-dev/lib $(CLIPPER_LIB) 
LIBDIRS = $(MYLIBDIR) $(XLIBDIR) $(SYSLIBDIR) $(GSLLIBDIR) $(MKLLIBDIR) $(LCCPX) $(CPLEX_LIBS) $(GLUTLIBDIR)

# Libraries the program will need.
GLUTLIBS = glut 
CLIPPERLIBS = clipper-ccp4 ccp4c clipper-minimol clipper-mmdb clipper-phs clipper-cif clipper-contrib clipper-core rfftw fftw mmdb m
MKLLIBS = mkl_lapack guide mkl_ia32 
GSLLIBS = gsl gslcblas
CPLEXLIBS = ilocplex cplex concert

SYSLIBS = Xi Xext X11 xml2 
#svml ifcore
LIBS = $(SYSLIBS) $(CLIPPERLIBS) $(CPLEXLIBS) $(GLUTLIBS)

# Variables determining optimization level and presence of
# debugging information in the output.  The default is to
# activate full optimization (-O3) and omit debugging symbols.
# For best debugging (e.g. with gdb or valgrind), override with
# DEBUG_VAR = -g and OPT_VAR = -O0.

DEBUG_VAR = -g 

OPT_VAR = -O2 -static-intel -axSSE4.2,SSE4.1,SSSE3 -msse2 -DMATH_DOUBLE -DIL_STD 

CG_LDFLAGS = \
          $(LONG_NAME_PROBLEM_LDFLAGS) \
          $(CGAL_LDFLAGS)

# The primary flags for the compiler and linker.
CPPFLAGS = $(DEBUG_VAR) $(OPT_VAR) $(CGAL_CXXFLAGS) $(addprefix -I,$(MY_INCLUDE)) -I/usr/include/libxml2/
CXX = icpc 
LDFLAGS = -pthread $(ROOT)/looptk/lib/looptk.a $(CGAL_LIB)/libCGAL.a $(CGAL_LIB)/libCGAL_Core.a $(GSLLIBDIR)/libgsl.a $(GSLLIBDIR)/libgslcblas.a /usr/lib64/libboost_thread.a $(addprefix -L, $(LIBDIRS)) $(addprefix -l,$(LIBS))
OBJECTS = $(patsubst src/%.cpp,src/%.o,$(wildcard src/*.cpp)) 
EXECUTABLE = qFit


# Build targets.

all: $(EXECUTABLE)

qFit : $(OBJECTS) 
	$(CXX) -o bin/$@ $(OBJECTS) $(LDFLAGS)

reDokkum_frag : $(OBJECTS)
	$(CXX) -o bin/$@ $(OBJECTS) $(LDFLAGS)
#MyMIQP.o: src/MyMIQP.cpp
#	g++ -c -I$(CPLEX_INCLUDE) -L$(CPLEX_LIBS) -lilocplex -lcplex -lconcert src/MyMIQP.cpp src/MyMIQP.o 
docs:
	./scandoc -i ./default.pl *.h
	mv *.html $(DOCDIR)

default: $(EXECUTABLE)
 
# Cleaning targets.

clean :
	rm -f *.o resolve

realclean : clean
	rm -f $(DOCDIR)/*.html