Merged

python/_cosmo_cic.pyx

@@ -1,5 +1,6 @@
 from libcpp cimport bool
 from libcpp cimport string as cppstring
+from libcpp cimport vector as cppvector
 import numpy as np
 cimport numpy as np
 from cpython cimport PyObject, Py_INCREF
@@ -29,7 +30,7 @@ cdef extern from "cic.hpp" namespace "CosmoTool":
 @cython.cdivision(True)
 @cython.wraparound(False)
 def leanCic(float[:,:] particles, float L, int Resolution):
-  cdef CICParticles p
+  cdef cppvector.vector[CICParticles] *p
   cdef CICFilter *cic
   cdef np.uint64_t i
   cdef CICType *field
@@ -40,25 +41,34 @@ def leanCic(float[:,:] particles, float L, int Resolution):
   cdef np.uint64_t j
 
   cic = new CICFilter(Resolution, L)
+  print("Reset mesh")
   cic.resetMesh()
   
   if particles.shape[1] != 3:
     raise ValueError("Particles must be Nx3 array")
   
-  p.mass = 1
-  for i in xrange(particles.shape[0]):
-    p.coords[0] = particles[i,0]
-    p.coords[1] = particles[i,1]
-    p.coords[2] = particles[i,2]
-    cic.putParticles(&p, 1)
+  print("Inserting particles")
+#  p = new cppvector.vector[CICParticles](particles.shape[0])
+#  for i in xrange(particles.shape[0]):
+#    *p[i].mass = 1
+#    *p[i].coords[0] = particles[i,0]
+#    *p[i].coords[1] = particles[i,1]
+#    *p[i].coords[2] = particles[i,2]
+
+#  cic.putParticles(&p[0], particles.shape[0])
+  del p
     
+  print("Done")
   field = <CICType*>0
   dummyRes = 0
   cic.getDensityField(field, dummyRes)
+
+  print("Got to allocate a numpy %dx%dx%d" % (dummyRes, dummyRes,dummyRes))
   
   out_field = np.empty((dummyRes, dummyRes, dummyRes), dtype=np.float64)
   out_field0 = out_field.reshape(out_field.size)
   out_field_buf = out_field
+  print("Copy")
   for j in xrange(out_field_buf.size):
     out_field_buf[j] = field[j]
   

python/_cosmo_power.pyx

@@ -74,6 +74,9 @@ cdef class CosmologyPower:
     assert self.power.OMEGA_C > 0
     
     self.power.updateCosmology()
+
+  def setNormalization(self,A):
+    self.power.setNormalization(A)
     
   def normalize(self,s8,k_min=-1,k_max=-1):
     """normalize(self, sigma8)

src/cic.cpp

@@ -186,6 +186,11 @@ void CICFilter::putParticles(CICParticles *particles, uint32_t N)
     for (long p = tUsedMin[t]; p < tUsedMax[t]; p++)
       densityGrid[p] += threadedDensity[t][p];
   }
+
+  for (int t = 0; t < threadUsed; t++)
+  {
+    delete[] threadedDensity;
+  }
 }
   
 void CICFilter::getDensityField(CICType*& field, uint32_t& res)

src/cosmopower.cpp

@@ -90,7 +90,8 @@ static double powC(double q, double alpha_c)
 
 static double T_tilde_0(double q, double alpha_c, double beta_c)
 {
-  double a = log(M_E + 1.8 * beta_c * q);
+  static const double c_E = 2.718282; //M_E;
+  double a = log(c_E + 1.8 * beta_c * q);
   return a / ( a  + powC(q, alpha_c) * q * q);
 }
 
@@ -125,7 +126,7 @@ void CosmoPower::updateHuWigglesConsts()
 {
   double f_b = OMEGA_B / OMEGA_0;
   double f_c = OMEGA_C / OMEGA_0;
-  
+
   double k_silk = 1.6 * pow(OMEGA_B * h * h, 0.52) * pow(OmegaEff, 0.73) * (1 + pow(10.4 * OmegaEff, -0.95));
   double z_eq = 2.50e4 * OmegaEff * pow(Theta_27, -4);
   //double s = 44.5 * log(9.83 / OmegaEff) / (sqrt(1 + 10 * pow(OMEGA_B * h * h, 0.75)));
@@ -133,7 +134,7 @@ void CosmoPower::updateHuWigglesConsts()
 
   double b1_zd = 0.313 * pow(OmegaEff, -0.419) * (1 + 0.607 * pow(OmegaEff, 0.674));
   double b2_zd = 0.238 * pow(OmegaEff, 0.223);
-  double z_d = 1291 * pow(OmegaEff, 0.251) / (1 + 0.659 * pow(OmegaEff, 0.828)) * (1 + b1_zd * pow(OmegaEff, b2_zd));
+  double z_d = 1291 * pow(OmegaEff, 0.251) / (1 + 0.659 * pow(OmegaEff, 0.828)) * (1 + b1_zd * pow(OMEGA_B*h*h, b2_zd));
 
   double R_d = 31.5 * OMEGA_B * h * h * pow(Theta_27, -4) * 1e3 / z_d;
   double Req = 31.5 * OMEGA_B * h * h * pow(Theta_27, -4) * 1e3 / z_eq;
@@ -183,7 +184,10 @@ double CosmoPower::powerHuWiggles(double k)
   double q = k / (13.41 * k_eq);
   double T_c = f * T_tilde_0(q, 1, beta_c) + (1 - f) * T_tilde_0(q, alpha_c, beta_c);
 
-  double T_b = (T_tilde_0(q, 1, 1) / (1 + pow(k * s / 5.2, 2)) + alpha_b / (1 + pow(beta_b / (k * s), 3)) * exp(-pow(k/k_silk, 1.4))) * j_0(k * s_tilde);  
+  double T_b = ( 
+     T_tilde_0(q, 1, 1) / (1 + pow(xx / 5.2, 2)) + 
+     alpha_b / (1 + pow(beta_b / xx, 3)) * exp(-pow(k/k_silk, 1.4))
+     ) * j_0(k * s_tilde);  
 
   double T_k = OMEGA_B/OMEGA_0 * T_b + OMEGA_C/OMEGA_0 * T_c;  
 
@@ -286,7 +290,7 @@ void CosmoPower::normalize(double k_min, double k_max)
   ofstream ff("PP_k.txt");
   for (int i = 0; i < 100; i++)
     {
-       double k = pow(10.0, 4.0*i/100.-2);
+       double k = pow(10.0, 8.0*i/100.-4);
        ff << k << " " << power(k) << endl;
     }
 
@@ -376,5 +380,5 @@ void CosmoPower::setFunction(CosmoFunction f)
 
 void CosmoPower::setNormalization(double A_K)
 {
-  normPower = A_K/power(0.002);
+  normPower = A_K;///power(0.002);
 }