run directory now separate from source directory

.gitignore

@@ -10,4 +10,5 @@ grapite-dev-exec-threshold
 phigrape
 *.h5
 .*
+CUDA
 .gitignore

Makefile

@@ -5,23 +5,24 @@ OPTIMIZATION ?= 3
 CUDAINC       = -I$(CUDAHOME)/include -I$(CUDAHOME)/samples/common/inc/
 CUDALIB       = -L$(CUDAHOME)/lib64 -lcudart -lcudadevrt -lcuda
 
-default grapite: GRAPEHOME = ../grapite
-default grapite: GRAPELIB  = -L$(GRAPEHOME) -lgrapite -fopenmp
+default: grapite
+grapite: GRAPEHOME = ../grapite
+grapite: GRAPELIB  = -L$(GRAPEHOME) -lgrapite
 yebisu:  GRAPEHOME = ../yebisu
 yebisu:  GRAPELIB  = -L$(GRAPEHOME) -lyebisug6
 sapporo: GRAPEHOME = ../sapporo2/lib
-sapporo: GRAPELIB  = -L$(GRAPEHOME) -lsapporo -fopenmp
+sapporo: GRAPELIB  = -L$(GRAPEHOME) -lsapporo
          GRAPEINC  = -I$(GRAPEHOME)
 
-CXXFLAGS     += -O$(OPTIMIZATION)
+CXXFLAGS     += -std=c++11 -O$(OPTIMIZATION)
 INC           = $(GRAPEINC) $(CUDAINC)
-LIB           = $(GRAPELIB) $(CUDALIB) -lm -fopenmp
+LIB           = $(GRAPELIB) $(CUDALIB) -lm
 MPICXX       ?= mpic++
 EXECUTABLE   ?= phigrape
 
 # HDF5
-CPPFLAGS     += -DHAS_HDF5
-LIB          += -lhdf5 -lz -ldl
+#CPPFLAGS     += -DHAS_HDF5
+#LIB          += -lhdf5 -lz -ldl
 
 default:
 	$(MPICXX) $(CPPFLAGS) $(CXXFLAGS) $(INC) black_holes.cpp external.cpp io.cpp config.cpp phigrape.cpp -o $(EXECUTABLE) $(LIB)

init.py

@@ -91,6 +91,8 @@ def gen_mask(particle_list, frac):
         mask = np.ones(N, dtype=int)
     elif frac==1:
         mask = np.zeros(N, dtype=int)
+    elif (frac < 0) or (1 < frac):
+        raise RuntimeError('Fraction has to be between 0 and 1')
     else:
         X = particle_list[:,:3]
         V = particle_list[:,3:]