Merge branch 'master' of bitbucket.org:glavaux/cosmotool

CMakeLists.txt

@@ -37,7 +37,7 @@ if (ENABLE_SHARP)
   ExternalProject_Add(sharp
     SOURCE_DIR ${SHARP_SOURCE}
     BUILD_IN_SOURCE 1 
-    CONFIGURE_COMMAND ${SHARP_SOURCE}/configure --prefix=${DEP_BUILD}
+    CONFIGURE_COMMAND ${SHARP_SOURCE}/configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD}
     BUILD_COMMAND ${CMAKE_MAKE_PROGRAM}
     INSTALL_COMMAND echo "No install"
   )
@@ -71,6 +71,18 @@ set(GSL_FIND_REQUIRED TRUE)
 FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH)
 FIND_PACKAGE_HANDLE_STANDARD_ARGS(GSL DEFAULT_MSG GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
 
+IF(ENABLE_OPENMP)
+
+  IF (NOT OPENMP_FOUND)
+    MESSAGE(ERROR "No known compiler option for enabling OpenMP")
+  ENDIF(NOT OPENMP_FOUND)
+
+  SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+  SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKED_FLAGS} ${OpenMP_C_FLAGS}")
+ENDIF(ENABLE_OPENMP)
+
+
 
 set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
 

sample/CMakeLists.txt

@@ -62,7 +62,7 @@ if (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
   include_directories(${SHARP_INCLUDE_PATH})
   add_executable(test_healpix_calls test_healpix_calls.cpp)
   target_link_libraries(test_healpix_calls ${tolink} ${SHARP_LIBRARIES})
-  set_target_properties(test_healpix_calls PROPERTIES COMPILE_FLAGS ${OpenMP_CXX_FLAGS} LINK_FLAGS ${OpenMP_CXX_FLAGS})
+  set_target_properties(test_healpix_calls PROPERTIES COMPILE_FLAGS "${OpenMP_CXX_FLAGS}" LINK_FLAGS "${OpenMP_CXX_FLAGS}")
   add_dependencies(test_healpix_calls sharp)
 endif (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
 

sample/testSmooth.cpp

@@ -85,14 +85,16 @@ int main()
   uint32_t dims[] = { NX, NX };
   ProgressiveOutput<ComputePrecision> out = 
     ProgressiveOutput<ComputePrecision>::saveArrayProgressive("out.nc", dims, 2);
+//#pragma omp parallel for schedule(static)
   for (uint32_t iy = 0; iy < NX; iy++)
     {
+      MySmooth::SPHState state;
       cout << "iy=" << iy << endl;
       for (uint32_t ix = 0; ix < NX; ix++)
         {
            MyTree::coords c = { 1.0*ix/NX, 1.0*iy/NX };
-           smooth.fetchNeighbours(c);
+           smooth.fetchNeighbours(c, &state);
-           out.put(smooth.computeSmoothedValue(c, unit_fun));
+           out.put(smooth.computeSmoothedValue(c, unit_fun, &state));
 
 	  
         }

src/fourier/base_types.hpp

@@ -55,6 +55,7 @@ namespace CosmoTool
   protected:
     SpectrumFunction() {}
   public:
+    typedef T type;
     typedef Eigen::Array<T, 1, Eigen::Dynamic> VecType;
     typedef Eigen::Map<VecType, Eigen::Aligned> MapType;
     typedef Eigen::Map<VecType const, Eigen::Aligned> ConstMapType;
@@ -88,6 +89,7 @@ namespace CosmoTool
     FourierMap() {}
     
   public:
+    typedef T type;
     typedef Eigen::Array<T, 1, Eigen::Dynamic> VecType;
     typedef Eigen::Map<VecType, Eigen::Aligned> MapType;
     typedef Eigen::Map<VecType const, Eigen::Aligned> ConstMapType;
@@ -190,6 +192,7 @@ namespace CosmoTool
   class MapUtilityFunction
   {
   public:
+    typedef T type;
     typedef SpectrumFunction<T> Spectrum;
     typedef boost::shared_ptr<Spectrum> Spectrum_ptr;
     typedef FourierMap<std::complex<T> > FMap;

src/fourier/details/euclidian_maps.hpp

@@ -36,6 +36,7 @@ knowledge of the CeCILL license and that you accept its terms.
 #ifndef __DETAILS_EUCLIDIAN_MAPS
 #define __DETAILS_EUCLIDIAN_MAPS
 
+#include <cmath>
 
 namespace CosmoTool
 {
@@ -246,7 +247,7 @@ namespace CosmoTool
 	    {
 	      long idx = q0+dims[0]*p;
 	      assert(idx < this->size());
-	      result += 2*(conj(d1[idx]) * d2[idx]).real();
+	      result += T(2)*(std::conj(d1[idx]) * d2[idx]).real();
 	    }
 	}
       if (even0)
@@ -254,8 +255,8 @@ namespace CosmoTool
 	  for (long p = 0; p < plane_size; p++)
 	    {
 	      long q0 = N0*p, q1 = (p+1)*N0-1;
-	      result += 2*conj(d1[q0]) * d2[q0];
+	      result += T(2)*std::conj(d1[q0]) * d2[q0];
-	      result += 2*conj(d1[q1]) * d2[q1];
+	      result += T(2)*std::conj(d1[q1]) * d2[q1];
 	    }
 	}
       return result;

src/fourier/details/euclidian_transform.hpp

@@ -122,12 +122,22 @@ namespace CosmoTool
       calls::execute(m_synthesis);
       realMap->scale(1/volume);
     }
+
+    void synthesis_unnormed()
+    {
+      calls::execute(m_synthesis);
+    }
     
     void analysis()
     {
       calls::execute(m_analysis);
       fourierMap->scale(volume/N);
     }
+
+    void analysis_unnormed()
+    {
+      calls::execute(m_analysis);
+    }
     
     void synthesis_conjugate()
     {

src/loadRamses.cpp

@@ -309,7 +309,7 @@ CosmoTool::SimuData *CosmoTool::loadRamsesSimu(const char *basename, int outputI
 
   double hubble = info.aexp*info.aexp/info.unit_t / (1e5/CM_IN_MPC);
   double L0 = info.boxSize*info.unitLength*hubble/100/CM_IN_MPC/info.aexp;
-  double unit_vel = L0*hubble/info.aexp;
+  double unit_vel = L0*100/info.aexp;
   
   while (1)
     {

src/sphSmooth.hpp

@@ -35,7 +35,7 @@ knowledge of the CeCILL license and that you accept its terms.
 
 #ifndef __COSMOTOOL_SPH_SMOOTH_HPP
 #define __COSMOTOOL_SPH_SMOOTH_HPP
-
+#include <boost/shared_ptr.hpp>
 #include "config.hpp"
 #include "mykdtree.hpp"
 
@@ -60,37 +60,48 @@ namespace CosmoTool
     typedef void (*runParticleValue)(ValType& t);
 
   public:
+    struct SPHState
+    {
+      boost::shared_ptr<SPHCell *[]> ngb;
+      boost::shared_ptr<CoordType[]> distances;
+      typename SPHTree::coords currentCenter;
+      int currentNgb;
+      ComputePrecision smoothRadius;
+    };
+    
+  
     SPHSmooth(SPHTree *tree, uint32_t Nsph);
     virtual ~SPHSmooth();   
 
-    void fetchNeighbours(const typename SPHTree::coords& c);
+    void fetchNeighbours(const typename SPHTree::coords& c, SPHState *state = 0);
+    
     void fetchNeighbours(const typename SPHTree::coords& c, uint32_t newNsph);
     void fetchNeighboursOnVolume(const typename SPHTree::coords& c, ComputePrecision radius);
     const typename SPHTree::coords& getCurrentCenter() const
     {
-      return currentCenter;
+      return internal.currentCenter;
     }
 
     ComputePrecision computeSmoothedValue(const typename SPHTree::coords& c,
-					  computeParticleValue fun);    
+					  computeParticleValue fun, SPHState *state = 0);    
     ComputePrecision computeInterpolatedValue(const typename SPHTree::coords& c,
-					      computeParticleValue fun);    
+					      computeParticleValue fun, SPHState *state = 0);    
     ComputePrecision getMaxDistance(const typename SPHTree::coords& c, 
 				    SPHNode *node) const;
 
     ComputePrecision getSmoothingLen() const
     {
-      return smoothRadius;
+      return internal.smoothRadius;
     }
 
     // TO USE WITH EXTREME CARE !
     void setSmoothingLen(ComputePrecision len)
     {
-      smoothRadius = len;
+      internal.smoothRadius = len;
     }
     // END
 
-    void runForEachNeighbour(runParticleValue fun);
+    void runForEachNeighbour(runParticleValue fun, SPHState *state = 0);
     void addGridSite(const typename SPHTree::coords& c);
 
     bool hasNeighbours() const;
@@ -100,32 +111,26 @@ namespace CosmoTool
     SPHTree *getTree() { return tree; }
 
     void changeNgb(uint32_t newMax) {
-      delete[] ngb;
+      internal.ngb = boost::shared_ptr<SPHCell *>(new SPHCell *[newMax]);
-      delete[] distances;
+      internal.distances = boost::shared_ptr<CoordType>(new CoordType[newMax]);
-      ngb = new SPHCell *[newMax];
-      distances = new CoordType[newMax];
       maxNgb = newMax;
     }
 
-    uint32_t getCurrent() const { return currentNgb; }
+    uint32_t getCurrent() const { return internal.currentNgb; }
 
     uint32_t getNgb() const { return maxNgb; }
  
   protected:
-    SPHCell **ngb;
+    SPHState internal;
-    CoordType *distances;
     uint32_t Nsph;
     uint32_t deltaNsph;
     uint32_t maxNgb;
-    uint32_t currentNgb;
     SPHTree *tree;
-    ComputePrecision smoothRadius;
-    typename SPHTree::coords currentCenter;
     
     ComputePrecision computeWValue(const typename SPHTree::coords & c,
 				   SPHCell& cell,
 				   CoordType d,
-				   computeParticleValue fun);
+				   computeParticleValue fun, SPHState *state);
     void runUnrollNode(SPHNode *node,
 		       runParticleValue fun);
   };

src/sphSmooth.tcc

@@ -1,4 +1,5 @@
 #include <cmath>
+#include "algo.hpp"
 
 namespace CosmoTool {
 
@@ -7,29 +8,27 @@ SPHSmooth<ValType,Ndims>::SPHSmooth(SPHTree *tree, uint32_t Nsph)
 {
   this->Nsph = Nsph;
   this->tree = tree;
-  this->currentNgb = 0;
+  internal.currentNgb = 0;
 
   this->maxNgb = Nsph;
-  ngb = new SPHCell *[maxNgb];  
+  internal.ngb = boost::shared_ptr<SPHCell *[]>(new SPHCell *[maxNgb]);  
-  distances = new CoordType[maxNgb];
+  internal.distances = boost::shared_ptr<CoordType[]>(new CoordType[maxNgb]);
 }
 
 template<typename ValType, int Ndims>
 SPHSmooth<ValType,Ndims>::~SPHSmooth()
 {
-  delete[] ngb;
-  delete[] distances;
 }
 
 template<typename ValType, int Ndims>
 ComputePrecision SPHSmooth<ValType,Ndims>::computeWValue(const typename SPHTree::coords& c,
 							 SPHCell& cell,
 							 CoordType d,
-							 computeParticleValue fun)
+							 computeParticleValue fun, SPHState *state)
 {
   CoordType weight;
 
-  d /= smoothRadius;
+  d /= state->smoothRadius;
   weight = getKernel(d);
 
   if (cell.val.weight != 0)
@@ -47,86 +46,91 @@ SPHSmooth<ValType,Ndims>::fetchNeighbours(const typename SPHTree::coords& c, uin
 
   if (requested > maxNgb)
     {
-      delete[] ngb;
-      delete[] distances;
-
       maxNgb = requested;
-      ngb = new SPHCell *[maxNgb];
+      internal.ngb = new SPHCell *[maxNgb];
-      distances = new CoordType[maxNgb];
+      internal.distances = new CoordType[maxNgb];
     }
 
-  memcpy(currentCenter, c, sizeof(c));
+  memcpy(internal.currentCenter, c, sizeof(c));
-  tree->getNearestNeighbours(c, requested, ngb, distances);
+  tree->getNearestNeighbours(c, requested, internal.ngb, internal.distances);
 
-  currentNgb = 0;
+  internal.currentNgb = 0;
-  for (uint32_t i = 0; i < requested && ngb[i] != 0; i++,currentNgb++)
+  for (uint32_t i = 0; i < requested && internal.ngb[i] != 0; i++,internal.currentNgb++)
     {
-      distances[i] = sqrt(distances[i]);
+      internal.distances[i] = sqrt(internal.distances[i]);
-      d2 = distances[i];
+      d2 = internal.distances[i];
       if (d2 > max_dist)
         max_dist = d2;
     }
 
-  smoothRadius = max_dist / 2;  
+  internal.smoothRadius = max_dist / 2;  
 }
 
 template<typename ValType, int Ndims>
-void
+void SPHSmooth<ValType,Ndims>::fetchNeighbours(const typename SPHTree::coords& c, SPHState *state)
-SPHSmooth<ValType,Ndims>::fetchNeighbours(const typename SPHTree::coords& c)
 {
   ComputePrecision d2, max_dist = 0;
   uint32_t requested = Nsph;
 
-  memcpy(currentCenter, c, sizeof(c));
+  if (state != 0) {
-  tree->getNearestNeighbours(c, requested, ngb, distances);
+    state->distances = boost::shared_ptr<CoordType[]>(new CoordType[Nsph]);
+    state->ngb = boost::shared_ptr<SPHCell *[]>(new SPHCell *[Nsph]);
+  } else
+    state = &internal;
+    
+  memcpy(state->currentCenter, c, sizeof(c));
+  
+  tree->getNearestNeighbours(c, requested, state->ngb.get(), state->distances.get());
 
-  currentNgb = 0;
+  state->currentNgb = 0;
-  for (uint32_t i = 0; i < requested && ngb[i] != 0; i++,currentNgb++)
+  for (uint32_t i = 0; i < requested && state->ngb[i] != 0; i++,state->currentNgb++)
     {
-      distances[i] = sqrt(distances[i]);
+      d2 = internal.distances[i] = sqrt(internal.distances[i]);
-      d2 = distances[i];
       if (d2 > max_dist)
-	max_dist = d2;
+        max_dist = d2;
     }
 
-  smoothRadius = max_dist / 2;  
+  state->smoothRadius = max_dist / 2;  
-}					
+}
+
 
 template<typename ValType, int Ndims>
 void
 SPHSmooth<ValType,Ndims>::fetchNeighboursOnVolume(const typename SPHTree::coords& c,
-						  ComputePrecision radius)
+                                                  ComputePrecision radius)
 {
   uint32_t numPart;
   ComputePrecision d2, max_dist = 0;
 
-  memcpy(currentCenter, c, sizeof(c));
+  memcpy(internal.currentCenter, c, sizeof(c));
 
-  currentNgb = tree->getIntersection(c, radius, ngb, distances,
+  internal.currentNgb = tree->getIntersection(c, radius, internal.ngb, internal.distances,
 				  maxNgb);
 
-  for (uint32_t i = 0; i < currentNgb; i++)
+  for (uint32_t i = 0; i < internal.currentNgb; i++)
     {
-      distances[i] = sqrt(distances[i]);
+      d2 = internal.distances[i] = sqrt(internal.distances[i]);
-      d2 = distances[i];
       if (d2 > max_dist)
-	max_dist = d2;
+        max_dist = d2;
     }
-  smoothRadius = max_dist / 2;  
+  internal.smoothRadius = max_dist / 2;  
 }				
 
 template<typename ValType, int Ndims>
 ComputePrecision 
 SPHSmooth<ValType,Ndims>::computeSmoothedValue(const typename SPHTree::coords& c,
-					       computeParticleValue fun)
+                                               computeParticleValue fun, SPHState *state)
 {
+  if (state == 0)
+    state = &internal;
+    
   ComputePrecision outputValue = 0;
   ComputePrecision max_dist = 0;
-  ComputePrecision r3 = smoothRadius * smoothRadius * smoothRadius;
+  ComputePrecision r3 = cube(state->smoothRadius);
 
-  for (uint32_t i = 0; i < currentNgb; i++)
+  for (uint32_t i = 0; i < state->currentNgb; i++)
     {
-      outputValue += computeWValue(c, *ngb[i], distances[i], fun);
+      outputValue += computeWValue(c, *state->ngb[i], state->distances[i], fun, state);
     }
 
   return outputValue / r3;
@@ -141,27 +145,33 @@ ComputePrecision interpolateOne(const ValType& t)
 // WARNING ! Cell's weight must be 1 !!!
 template<typename ValType, int Ndims>
 ComputePrecision SPHSmooth<ValType,Ndims>::computeInterpolatedValue(const typename SPHTree::coords& c,
-								    computeParticleValue fun)
+								    computeParticleValue fun, SPHState *state)
 {
+  if (state == 0)
+    state = &internal;
+    
   ComputePrecision outputValue = 0;
   ComputePrecision max_dist = 0;
   ComputePrecision weight = 0;
 
-  for (uint32_t i = 0; i < currentNgb; i++)
+  for (uint32_t i = 0; i < state->currentNgb; i++)
     {
-      outputValue += computeWValue(c, *ngb[i], distances[i], fun);
+      outputValue += computeWValue(c, *state->ngb[i], state->distances[i], fun);
-      weight += computeWValue(c, *ngb[i], distances[i], interpolateOne);
+      weight += computeWValue(c, *state->ngb[i], state->distances[i], interpolateOne);
     }
 
   return (outputValue == 0) ? 0 : (outputValue / weight);  
 }
 
 template<typename ValType, int Ndims>
-void SPHSmooth<ValType,Ndims>::runForEachNeighbour(runParticleValue fun)
+void SPHSmooth<ValType,Ndims>::runForEachNeighbour(runParticleValue fun, SPHState *state)
 {
-  for (uint32_t i = 0; i < currentNgb; i++)
+  if (state == 0)
+    state = &internal;
+    
+  for (uint32_t i = 0; i < state->currentNgb; i++)
     {
-      fun(ngb[i]);
+      fun(state->ngb[i]);
     }
 }
 
@@ -172,13 +182,13 @@ void SPHSmooth<ValType,Ndims>::addGridSite(const typename SPHTree::coords& c)
   ComputePrecision outputValue = 0;
   ComputePrecision max_dist = 0;
   
-  ComputePrecision r3 = smoothRadius * smoothRadius * smoothRadius;
+  ComputePrecision r3 = cube(internal.smoothRadius);
 
-  for (uint32_t i = 0; i < currentNgb; i++)
+  for (uint32_t i = 0; i < internal.currentNgb; i++)
     {
-      ComputePrecision d = distances[i];
+      ComputePrecision d = internal.distances[i];
-      SPHCell& cell = *ngb[i];
+      SPHCell& cell = *internal.ngb[i];
-      cell.val.weight += getKernel(d/smoothRadius) / r3;
+      cell.val.weight += getKernel(d/internal.smoothRadius) / r3;
 
     }
 }
@@ -202,7 +212,7 @@ SPHSmooth<ValType,Ndims>::getKernel(ComputePrecision x) const
 template<typename ValType, int Ndims>
 bool SPHSmooth<ValType,Ndims>::hasNeighbours() const
 {
-  return (currentNgb != 0);
+  return (internal.currentNgb != 0);
 }
 
 template<class ValType1, class ValType2, int Ndims>

src/yorick.hpp

@@ -218,7 +218,7 @@ namespace CosmoTool
 
   template<typename T>
   void saveArray(const std::string& fname,
-		 T *array, uint32_t *dimList, uint32_t rank);
+		 const T *array, uint32_t *dimList, uint32_t rank);
 
   template<typename T>
   void loadArray(const std::string& fname,

src/yorick_nc3.cpp

@@ -235,7 +235,7 @@ namespace CosmoTool {
 
   template<typename T>
   void saveArray(const std::string& fname,
-		 T *array, uint32_t *dimList, uint32_t rank)
+		 const T *array, uint32_t *dimList, uint32_t rank)
   {
     NcFile f(fname.c_str(), NcFile::Replace, 0, 0, NcFile::Netcdf4);
     
@@ -300,10 +300,10 @@ namespace CosmoTool {
 				  double*& array, uint32_t *&dimList, uint32_t& rank);
 
   template void saveArray<int>(const std::string& fname,
-			       int *array, uint32_t *dimList, uint32_t rank);
+			       const int *array, uint32_t *dimList, uint32_t rank);
   template void saveArray<float>(const std::string& fname,
-				 float *array, uint32_t *dimList, uint32_t rank);
+				 const float *array, uint32_t *dimList, uint32_t rank);
   template void saveArray<double>(const std::string& fname,
-				  double *array, uint32_t *dimList, uint32_t rank);
+				  const double *array, uint32_t *dimList, uint32_t rank);
   
 }

src/yorick_nc4.cpp

@@ -203,7 +203,7 @@ namespace CosmoTool {
 
   template<typename T>
   void saveArray(const std::string& fname,
-		 T *array, uint32_t *dimList, uint32_t rank)
+		 const T *array, uint32_t *dimList, uint32_t rank)
   {
     NcFile f(fname.c_str(), NcFile::replace);
     
@@ -263,10 +263,10 @@ namespace CosmoTool {
 				  double*& array, uint32_t *&dimList, uint32_t& rank);
 
   template void saveArray<int>(const std::string& fname,
-			       int *array, uint32_t *dimList, uint32_t rank);
+			       const int *array, uint32_t *dimList, uint32_t rank);
   template void saveArray<float>(const std::string& fname,
-				 float *array, uint32_t *dimList, uint32_t rank);
+				 const float *array, uint32_t *dimList, uint32_t rank);
   template void saveArray<double>(const std::string& fname,
-				  double *array, uint32_t *dimList, uint32_t rank);
+				  const double *array, uint32_t *dimList, uint32_t rank);
   
 }