Add support for Python3.5, More bispectrum work

python/CMakeLists.txt

@@ -65,10 +65,10 @@ endif()
 
 # Discover where to put packages
 if (NOT PYTHON_SITE_PACKAGES)
-  execute_process (COMMAND ${PYTHON_EXECUTABLE} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()" OUTPUT_VARIABLE internal_PYTHON_SITE_PACKAGES OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process (COMMAND ${PYTHON_EXECUTABLE} -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())" OUTPUT_VARIABLE internal_PYTHON_SITE_PACKAGES OUTPUT_STRIP_TRAILING_WHITESPACE)
   SET(SYSTEM_PYTHON_SITE_PACKAGES ${internal_PYTHON_SITE_PACKAGES} CACHE PATH "Path to the target system-wide site-package where to install python modules")
 
-  execute_process (COMMAND ${PYTHON_EXECUTABLE} -c "from site import USER_SITE; print USER_SITE" OUTPUT_VARIABLE internal_PYTHON_SITE_PACKAGES OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process (COMMAND ${PYTHON_EXECUTABLE} -c "from site import USER_SITE; print(USER_SITE)" OUTPUT_VARIABLE internal_PYTHON_SITE_PACKAGES OUTPUT_STRIP_TRAILING_WHITESPACE)
   SET(USER_PYTHON_SITE_PACKAGES ${internal_PYTHON_SITE_PACKAGES} CACHE PATH "Path to the target user site-package where to install python modules")
 
   mark_as_advanced(USER_PYTHON_SITE_PACKAGES SYSTEM_PYTHON_SITE_PACKAGES)

python/_cosmo_bispectrum.cpp

@@ -4,54 +4,31 @@
 #include <boost/multi_array.hpp>
 #include <sys/types.h>
 #include <cmath>
+#include "symbol_visible.hpp"
+#include "algo.hpp"
 
 using std::cout;
 using std::endl;
 using boost::format;
-
+using CosmoTool::square;
-
-#if defined _WIN32 || defined __CYGWIN__
-  #ifdef BUILDING_DLL
-    #ifdef __GNUC__
-      #define DLL_PUBLIC __attribute__ ((dllexport))
-    #else
-      #define DLL_PUBLIC __declspec(dllexport) // Note: actually gcc seems to also supports this syntax.
-    #endif
-  #else
-    #ifdef __GNUC__
-      #define DLL_PUBLIC __attribute__ ((dllimport))
-    #else
-      #define DLL_PUBLIC __declspec(dllimport) // Note: actually gcc seems to also supports this syntax.
-    #endif
-  #endif
-  #define DLL_LOCAL
-#else
-  #if __GNUC__ >= 4
-    #define DLL_PUBLIC __attribute__ ((visibility ("default")))
-    #define DLL_LOCAL  __attribute__ ((visibility ("hidden")))
-  #else
-    #define DLL_PUBLIC
-    #define DLL_LOCAL
-  #endif
-#endif
-
 
 
 struct ModeSet
 {
-    size_t N1, N2, N3;
+    ssize_t N1, N2, N3;
-    bool omp;
+    bool half_copy;
     
     struct TriangleIterator
     {
         ssize_t i1, i2, i3;
-        size_t N1, N2, N3;
+        ssize_t N1, N2, N3;
+        ssize_t first_iteration;
         
         
         TriangleIterator& operator++() {
             i3++;
-            if (i3==N3) { i3 = 0; i2++; }
+            if (i3==(N3/2+1)) { i3 = first_iteration; i2++; }
-            if (i2==N2) { i2 = 0; i1++; }
+            if (i2==(N2/2+1)) { i2 = -N2/2; i1++; }
             return *this;
         }
     
@@ -62,7 +39,7 @@ struct ModeSet
         bool in_box() const {
             ssize_t hN1 = N1/2, hN2 = N2/2, hN3 = N3/2;
             
-            return (i1 >= -hN1) && (i1 < hN1) && (i2 >= -hN2) && (i2 < hN2) && (i3 >= -hN3) && (i3 < hN3);
+            return (i1 >= -hN1) && (i1 <= hN1) && (i2 >= -hN2) && (i2 <= hN2) && (i3 >= -hN3) && (i3 <= hN3);
         }
         
         TriangleIterator operator+(const TriangleIterator& other_t) const {
@@ -74,6 +51,23 @@ struct ModeSet
             return t;
         }
 
+        TriangleIterator& inp_array() {
+            if (i1 < 0)
+                i1 += N1;  
+            if (i2 < 0)
+                i2 += N2;  
+            if (i3 < 0)
+                i3 += N3;  
+            return *this;
+        }
+
+        TriangleIterator array() const {
+          TriangleIterator t = *this;
+          
+          t.inp_array();
+          return t;
+        }
+    
         TriangleIterator real() const {
             TriangleIterator t = *this;
             if (t.i1 >= N1/2)
@@ -86,7 +80,7 @@ struct ModeSet
         }
         
         double norm() const {
-            double r1 = i1, r2 = i3, r3 = i3;
+            double r1 = i1, r2 = i2, r3 = i3;
             return std::sqrt(r1*r1 + r2*r2 + r3*r3);
         }
         void reverse() { i1=-i1; i2=-i2; i3=-i3; }
@@ -94,23 +88,30 @@ struct ModeSet
         TriangleIterator& operator*() { return *this; }
     };
 
-    ModeSet(size_t N1_, size_t N2_, size_t N3_, bool do_openmp = false)
+    ModeSet(size_t N1_, size_t N2_, size_t N3_, bool _half_copy = false)
-        : N1(N1_), N2(N2_), N3(N3_),omp(do_openmp) {
+        : N1(N1_), N2(N2_), N3(N3_),half_copy(_half_copy) {
     } 
 
     TriangleIterator begin() const {
         TriangleIterator t;
-        t.i1 = t.i2 = t.i3 = 0;
+        t.i1 = -N1/2;
+        t.i2 = -N2/2;
+        if (half_copy)
+          t.first_iteration = t.i3 = 0;
+        else
+          t.first_iteration = t.i3 = -N3/2;
+        t.N1 = N1;
         t.N2 = N2;
         t.N3 = N3;
-        t.N1 = N1;
         return t;
     }
 
     TriangleIterator end() const {
         TriangleIterator t;
-        t.i2 = t.i3 = 0;
+        t.first_iteration = (half_copy ? 0 : (-N3/2));
-        t.i1 = N1;
+        t.i3 = t.first_iteration;
+        t.i2 = -N2/2;
+        t.i1 = N1/2+1;
         t.N1 = N1;
         t.N2 = N2;
         t.N3 = N3;
@@ -119,10 +120,50 @@ struct ModeSet
 
 };
 
+std::ostream& operator<<(std::ostream& o, const ModeSet::TriangleIterator& t)
+{
+  o << t.i1 << "," << t.i2 << "," << t.i3;
+  return o;
+}
+
 template<typename T>
 static T no_conj(const T& a) { return a; }
 
-extern "C" DLL_PUBLIC
+template<typename SubArrayB,typename SubArrayCnt,typename Delta>
+static inline void accum_bispec(const Delta& delta_mirror, SubArrayB b_Nt, SubArrayCnt b_B,
+    const typename Delta::element& v1, const typename Delta::element& v2,
+    const ModeSet::TriangleIterator& rm1, 
+    const ModeSet::TriangleIterator& rm2, 
+    const ModeSet::TriangleIterator& rm3,
+    double delta_k,
+    size_t Nk)
+{
+  typedef std::complex<double> CType;
+
+  size_t q1 = std::floor(rm1.norm()/delta_k);
+  if (q1 >= Nk)
+    return;
+    
+  size_t q2 = std::floor(rm2.norm()/delta_k);
+  if (q2 >= Nk)
+    return;
+
+  size_t q3 = std::floor(rm3.norm()/delta_k);
+  if (q3 >= Nk)
+    return;
+
+  CType prod = v1*v2;
+  ModeSet::TriangleIterator m3 = rm3;
+  // We use hermitic symmetry to get -m3, it is just the mode in m3 but conjugated.
+  m3.reverse();
+  m3.inp_array();
+  prod *= delta_mirror[m3.i1][m3.i2][m3.i3];
+
+  b_Nt[q1][q2][q3] ++;
+  b_B[q1][q2][q3] += prod;
+}
+
+extern "C" CTOOL_DLL_PUBLIC
 void CosmoTool_compute_bispectrum(
     double *delta_hat, size_t Nx, size_t Ny, size_t Nz,
     size_t *Ntriangles,
@@ -137,71 +178,68 @@ void CosmoTool_compute_bispectrum(
     boost::multi_array<std::complex<double>, 4> b_B(boost::extents[Ntasks][Nk][Nk][Nk]);
     boost::multi_array<size_t, 4> b_Nt(boost::extents[Ntasks][Nk][Nk][Nk]);
     typedef std::complex<double> CType;
+    boost::multi_array<std::complex<double>, 3> delta_mirror(boost::extents[Nx][Ny][Nz]); 
+    
+    // Add hermiticity
+    for (auto m : ModeSet(Nx, Ny, Nz, true)) {
+      auto n1 = m;
+      auto n2 = m.array();
+      n1.reverse();
+      n1.inp_array();
+      delta_mirror[n2.i1][n2.i2][n2.i3] = (a_delta[n2.i1][n2.i2][n2.i3]);
+      delta_mirror[n1.i1][n1.i2][n1.i3] = std::conj(delta_mirror[n2.i1][n2.i2][n2.i3]);
+    }
 
     // First loop over m1
 #pragma omp parallel
     {
 #pragma omp single
       {
-    for (auto m1 : ModeSet(Nx, Ny, Nz, true)) {
+        for (auto m1 : ModeSet(Nx, Ny, Nz)) {
+          auto am1 = m1.array();
+          CType v1 = delta_mirror[am1.i1][am1.i2][am1.i3];
           int tid = omp_get_thread_num();
+          
 #pragma omp task
           {
-        CType v1 = (m1.i3 >= kNz) ? std::conj(a_delta[m1.i1][m1.i2][(m1.N3-m1.i3)%m1.N3]) : a_delta[m1.i1][m1.i2][m1.i3];
             auto rm1 = m1.real();
             // Second mode m2
             for (auto m2 : ModeSet(Nx, Ny, Nz)) {
                 // Now derive m3
-            CType v2 = (m2.i3 >= kNz) ? std::conj(a_delta[m2.i1][m2.i2][(m2.N3-m2.i3)%m2.N3]) : a_delta[m2.i1][m2.i2][m2.i3];
+                auto am2 = m2.array();
-            auto rm2 = m2.real();
+                auto m3 = (m1+m2);
-            auto m3 = (rm1+rm2);
+                CType v2 = delta_mirror[am2.i1][am2.i2][am2.i3];
 
+                // Not in Fourier box, stop here     
                 if (!m3.in_box())
                     continue;
 
-            size_t q1 = std::floor(rm1.norm()/delta_k);
+                accum_bispec(delta_mirror, b_Nt[tid], b_B[tid], v1, v2, m1, m2, m3, delta_k, Nk);
-            size_t q2 = std::floor(rm2.norm()/delta_k);
-            size_t q3 = std::floor(m3.norm()/delta_k);
 
-            if (q1 >= Nk || q2 >= Nk || q3 >= Nk)
-                continue;
-
-            CType prod = v1*v2;
-            bool do_conj = false;
-            // We use hermitic symmetry to get -m3, it is just the mode in m3 but conjugated.
-            m3.reverse();
-            if (m3.i3 > 0) {
-               assert(m3.i3 < kNz);
-            } else {
-               m3.i3 = -m3.i3;
-               do_conj = !do_conj;
-            }
-            m3.i1 = (m3.N1 - m1.i1)%m3.N1;
-            m3.i2 = (m3.N2 - m3.i2)%m3.N2;
-            
-            if (do_conj)
-              prod *= std::conj(a_delta[m3.i1][m3.i2][m3.i3]);
-            else
-              prod *= (a_delta[m3.i1][m3.i2][m3.i3]);
-            
-            b_Nt[tid][q1][q2][q3] ++;
-            b_B[tid][q1][q2][q3] += prod;
             }
           }          
+
         }
       }
     }
 
-    for (int tid = 0; tid < Ntasks; tid++)
+#pragma omp taskwait
-      for (auto m1 : ModeSet(Nk, Nk, Nk)) {
+  for (int tid = 0; tid < Ntasks; tid++) {
-        a_Nt[m1.i1][m1.i2][m1.i3] += b_Nt[tid][m1.i1][m1.i2][m1.i3];
+    size_t *b_p = b_Nt[tid].origin();
-        a_B[m1.i1][m1.i2][m1.i3] += b_B[tid][m1.i1][m1.i2][m1.i3];
+    size_t *a_p = a_Nt.data();
+    std::complex<double> *b_B_p = b_B[tid].origin();
+    std::complex<double> *a_B_p = a_B.origin();
+//#pragma omp simd
+#pragma omp parallel for
+    for (size_t q = 0; q < Nk*Nk*Nk; q++) {
+      a_p[q] += b_p[q];
+      a_B_p[q] += b_B_p[q];
+    }
   }
-
 }
 
 
-extern "C" DLL_PUBLIC
+extern "C" CTOOL_DLL_PUBLIC
 void CosmoTool_compute_powerspectrum(
     double *delta_hat, size_t Nx, size_t Ny, size_t Nz,
     size_t *Ncounts,
@@ -215,10 +253,11 @@ void CosmoTool_compute_powerspectrum(
     typedef std::complex<double> CType;
 
     // First loop over m1
-    for (auto m1 : ModeSet(Nx, Ny, kNz)) {
+    for (auto m : ModeSet(Nx, Ny, kNz)) {
+        auto m1 = m.array();
         CType& v1 = a_delta[m1.i1][m1.i2][m1.i3];
 
-        size_t q1 = std::floor(m1.norm()/delta_k);
+        size_t q1 = std::floor(m.norm()/delta_k);
 
         if (q1 >= Nk)
             continue;

python/cosmotool/__init__.py

@@ -1,8 +1,8 @@
-from _cosmotool import *
+from ._cosmotool import *
-from _project import *
+from ._project import *
-from _cosmo_power import *
+from ._cosmo_power import *
-from _cosmo_cic import *
+from ._cosmo_cic import *
-from _fast_interp import *
+from ._fast_interp import *
 from .grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
 from .borg import read_borg_vol
 from .cic import cicParticles

python/cosmotool/bispectrum.py

@@ -124,4 +124,4 @@ if __name__=="__main__":
     delta[3,2,1]=1
     b = powerspectrum(delta, 1, 16, fourier=False)
     a = bispectrum(delta, 1, 16, fourier=False)
-    print a[0].max()
+    print(a[0].max())

python/cosmotool/borg.py

@@ -26,7 +26,6 @@ def build_filelist(fdir):
       fname_0=fname_0+glob.glob(fd+'initial_density_*')
       fname_1=fname_1+glob.glob(fd+'final_density_*')
 	   
-	   
     return fname_0, fname_1
 
 def read_borg_vol(BORGFILE):
@@ -57,13 +56,14 @@ def read_borg_vol(BORGFILE):
     
       if size(r)==5 : 
         if r[0] =="define":
-	  if r[1]=="Lattice" : N0=int(r[2])
+          if r[1]=="Lattice" :
+            N0=int(r[2])
             N1=int(r[3])
             N2=int(r[4])
             
-      
           if size(r)==11 :
-	if r[4] =="BoundingBox": xmin=float(r[5])
+            if r[4] =="BoundingBox":
+              xmin=float(r[5])
               xmax=float(r[6])
               ymin=float(r[7])
               ymax=float(r[8])

python_sample/test_bispectrum.py

@@ -3,23 +3,26 @@ import numpy as np
 import cosmotool as ct
 
 def myfun(N):
-  f=0.10
+  f=0.001
-  d=np.random.normal(size=(N,)*3)
+  L = 1.0
+  d=np.random.normal(size=(N,)*3)   * np.sqrt(float(N))**3 / L**3
   rho = d + f *(d*d - np.average(d*d))
+  delta = (L/N)**3
   
-  B = ct.bispectrum(rho, 1, N, fourier=False)
+  B = ct.bispectrum(rho * delta, 1, N, fourier=False)
-  P = ct.powerspectrum(rho, 1, N, fourier=False)
+  P = ct.powerspectrum(rho * delta, 1, N, fourier=False)
-  PP = P[1]/P[0]/N**3
+  PP = P[1]/P[0] / L**3 
   
   x = PP[:,None,None] * PP[None,:,None] + PP[:,None,None]*PP[None,None,:] + PP[None,:,None]*PP[None,None,:]
   
-  BB = B[1]/B[0]/N**6
+  BB = B[1]/B[0] / L**3
 
   y = BB/x
 
-  np.savez("bispec_%d.npz" % N, y=y, B_nt=B[0], B_r=B[1], P_n=P[0], P=P[1], rho=rho);
+  np.savez("bispec_%d.npz" % N, x=x, y=y, d=d,B_nt=B[0], B_r=B[1], P_n=P[0], P=P[1], BB=BB, rho=rho, PP=PP);
   
   
-print( timeit.timeit('from __main__ import myfun; myfun(16)', number=1) )
+#print( timeit.timeit('from __main__ import myfun; myfun(16)', number=1) )
+#print( timeit.timeit('from __main__ import myfun; myfun(24)', number=1) )
 print( timeit.timeit('from __main__ import myfun; myfun(32)', number=1) )
-print( timeit.timeit('from __main__ import myfun; myfun(64)', number=1) )
+#print( timeit.timeit('from __main__ import myfun; myfun(64)', number=1) )