Added graficToDensity conversion. Added missing getBoxsize() method. Fixed grafic generation

python/_cosmotool.pyx

@@ -124,6 +124,9 @@ class _PySimulationAdaptor(PySimulationBase):
   
     self.simu = sim
 
+  def getBoxsize(self):
+    return self.simu.BoxSize
+    
   def getPositions(self):
     return self.simu.positions
     

python/cosmotool/grafic.py

@@ -7,7 +7,7 @@ def writeGrafic(filename, field, BoxSize, scalefac, **cosmo):
         checkPoint = 4*11
         
         Nx,Ny,Nz = field.shape
-        delta = BoxSize/Nx
+        delta = BoxSize/Nx/cosmo['h']
         bad = 0.0
         
         f.write(struct.pack("IIIIffffffffI", checkPoint, 

python_sample/icgen/borgicgen.py

@@ -49,13 +49,16 @@ def run_generation(input_borg, a_borg, a_ic, **cosmo):
         # Generate vel
         vel.append((psi*velmul).astype(np.float32)) 
 
-    return posx,vel,N,L,a_ic
+    density = np.fft.irfftn(density_hat*D1_0)*(N/L)**3
+
+    return posx,vel,density,N,L,a_ic
     
 def write_icfiles(*generated_ic, **cosmo):
     """Write the initial conditions from the tuple returned by run_generation"""
-    posx,vel,N,L,a_ic = generated_ic
+    posx,vel,density,N,L,a_ic = generated_ic
 
     ct.simpleWriteGadget("borg.gad", posx, velocities=vel, boxsize=L, Hubble=cosmo['h'], Omega_M=cosmo['omega_M_0'], time=a_ic) 
     for i,c in enumerate(['x','y','z']):
-        ct.writeGrafic("borg.ic_velc%s" % c, vel[i].reshape((N,N,N)), L, a_ic, **cosmo)
+        ct.writeGrafic("ic_velc%s" % c, vel[i].reshape((N,N,N)), L, a_ic, **cosmo)
 
+    ct.writeGrafic("ic_deltab", density, L, a_ic, **cosmo)

sample/CMakeLists.txt

@@ -42,6 +42,8 @@ if (HDF5_FOUND)
     add_executable(gadgetToArray gadgetToArray.cpp)
     target_link_libraries(gadgetToArray ${tolink})
 
+    add_executable(graficToDensity graficToDensity.cpp)
+    target_link_libraries(graficToDensity ${tolink})
 endif (HDF5_FOUND)
 
 
@@ -88,3 +90,4 @@ endif (Boost_FOUND)
 
 add_executable(gadgetToDensity gadgetToDensity.cpp)
 target_link_libraries(gadgetToDensity ${tolink})
+

sample/graficToDensity.cpp

@@ -0,0 +1,72 @@
+#include <cmath>
+#include <iostream>
+#include <cstdlib>
+#include <boost/multi_array.hpp>
+#include <H5Cpp.h>
+#include "hdf5_array.hpp"
+#include "miniargs.hpp"
+#include "fortran.hpp"
+
+using namespace std;
+using namespace CosmoTool;
+
+//#define GRAFIC_GUILHEM
+
+int main(int argc, char **argv)
+{
+  uint32_t res;
+  char *fname;
+  int id;
+
+  MiniArgDesc desc[] = {
+    { "GRAFIC", &fname, MINIARG_STRING },
+    { 0, 0, MINIARG_NULL }
+  };
+
+  if (!parseMiniArgs(argc, argv, desc))
+    return 1;
+
+  UnformattedRead ur(fname);
+
+  ur.beginCheckpoint();
+  int32_t nx = ur.readInt32();
+  int32_t ny = ur.readInt32();
+  int32_t nz = ur.readInt32();
+  float dx = ur.readReal32();
+  float xo = ur.readReal32();
+  float yo = ur.readReal32();
+  float zo = ur.readReal32();
+  float astart = ur.readReal32();
+  float omega_m = ur.readReal32();
+  float omega_nu = ur.readReal32();
+  float h0 = ur.readReal32();
+#ifdef GRAFIC_GUILHEM
+  float w0 = ur.readReal32();
+#endif
+  ur.endCheckpoint();
+
+  cout << "Grafic file: Nx=" << nx << " Ny=" << ny << " Nz=" << nz << endl;
+  cout << "a_start = " << astart << endl;
+  cout << "z_start = " << 1/astart - 1 << endl;
+  cout << "L = " << nx*dx << endl;
+
+  boost::multi_array<float, 3> density(boost::extents[nx][ny][nz]);
+
+  for (int32_t iz = 0; iz < nz; iz++)
+    {
+      ur.beginCheckpoint();
+      for (int32_t iy = 0; iy < ny; iy++)
+	{
+	  for (int32_t ix = 0; ix < nx; ix++)
+	    {
+	      density[ix][iy][iz] = ur.readReal32();
+	    }
+	}
+      ur.endCheckpoint();
+    }
+
+  H5::H5File f("density.h5", H5F_ACC_TRUNC);
+  hdf5_write_array(f, "density", density); 
+
+  return 0;
+}