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

CMakeLists.txt

@@ -22,11 +22,13 @@ option(INTERNAL_HDF5 "Build internal version of HDF5" OFF)
 option(INTERNAL_NETCDF "Build internal version of NETCDF" OFF)
 option(INTERNAL_BOOST "Build internal version of BOOST" OFF)
 
-IF(BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
+IF(NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
   SET(CosmoTool_local CosmoTool_static)
-ELSE(BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
+ELSE(NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
   SET(CosmoTool_local CosmoTool)
-ENDIF(BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
+ENDIF(NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
+
+MESSAGE(STATUS "Using the target ${CosmoTool_local} to build python module")
 
 include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
 
@@ -40,11 +42,10 @@ ENDIF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "
 
 find_program(CYTHON cython)
 
-set(HDF5_FIND_COMPONENTS HL CXX)
 if(HDF5_ROOTDIR)
   SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR})
 endif(HDF5_ROOTDIR)
-include(FindHDF5)
+find_package(HDF5 COMPONENTS HL CXX)
 
 
 set(NETCDF_FIND_REQUIRED TRUE)

doc/source/pythonmodule.rst

@@ -41,3 +41,13 @@ Timing
 .. autofunction:: time_block
 .. autofunction:: timeit
 .. autofunction:: timeit_quiet 
+
+
+Cosmology
+^^^^^^^^^
+
+Power spectrum
+--------------
+
+.. autoclass:: CosmologyPower
+   :members:

external/external_build.cmake

@@ -100,7 +100,7 @@ if (INTERNAL_NETCDF)
     CONFIGURE_COMMAND ${NETCDF_SOURCE_DIR}/configure
          --prefix=${NETCDF_BIN_DIR} --libdir=${NETCDF_BIN_DIR}/lib
          --enable-netcdf-4  --with-pic --disable-shared --disable-dap 
-         --disable-cdmremote --disable-rpc 
+         --disable-cdmremote --disable-rpc --enable-cxx-4 
          --disable-examples ${EXTRA_NC_FLAGS} CC=${CMAKE_C_COMPILER}
          CXX=${CMAKE_CXX_COMPILER}
     BUILD_IN_SOURCE 1
@@ -110,7 +110,7 @@ if (INTERNAL_NETCDF)
   SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_CPP_LDFLAGS})
   SET(cosmotool_DEPS ${cosmotool_DEPS} netcdf)
   SET(NETCDF_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf.a CACHE STRING "NetCDF lib" FORCE)
-  SET(NETCDFCPP_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf_c++.a CACHE STRING "NetCDF-C++ lib" FORCE)
+  SET(NETCDFCPP_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf_c++4.a CACHE STRING "NetCDF-C++ lib" FORCE)
   SET(NETCDF_INCLUDE_PATH ${NETCDF_BIN_DIR}/include CACHE STRING "NetCDF include" FORCE)
   SET(NETCDFCPP_INCLUDE_PATH ${NETCDF_INCLUDE_PATH} CACHE STRING "NetCDF C++ include path" FORCE)
 

python/_cosmo_power.pyx

@@ -49,11 +49,21 @@ cdef extern from "cosmopower.hpp" namespace "CosmoTool":
     double power(double)
  
 cdef class CosmologyPower:
+  """CosmologyPower(**cosmo)
+  
+  CosmologyPower manages and compute power spectra computation according to different
+  approximation given in the litterature.
+  
+  Keyword arguments:
+    omega_B_0 (float): relative baryon density
+    omega_M_0 (float): relative matter density
+    h (float): Hubble constant relative to 100 km/s/Mpc
+    ns (float): power law of the large scale inflation spectrum
+  """
 
   cdef CosmoPower power
 
   def __init__(self,**cosmo):    
-  
     self.power = CosmoPower()
     self.power.OMEGA_B = cosmo['omega_B_0']
     self.power.OMEGA_C = cosmo['omega_M_0']-cosmo['omega_B_0']
@@ -66,11 +76,26 @@ cdef class CosmologyPower:
     self.power.updateCosmology()
     
   def normalize(self,s8):
+    """normalize(self, sigma8)
+    
+    Compute the normalization of the power spectrum using sigma8.
+    
+    Arguments:
+      sigma8 (float): standard deviation of density field smoothed at 8 Mpc/h
+    """
     self.power.SIGMA8 = s8
     self.power.normalize()
     
     
   def setFunction(self,funcname):
+    """setFunction(self, funcname)
+    
+    Choose an approximation to use for the computation of the power spectrum
+    
+    Arguments:
+      funcname (str): the name of the approximation. It can be either
+                      EFSTATHIOU, HU_WIGGLES, HU_BARYON, BARDEEN or SUGIYAMA.
+    """
     cdef CosmoFunction f
     
     f = POWER_EFSTATHIOU
@@ -93,6 +118,19 @@ cdef class CosmologyPower:
     return self.power.power(k) * self.power.h**3
     
   def compute(self, k):
+    """compute(self, k)
+    
+    Compute the power spectrum for mode which length k.
+    
+    Arguments:
+      k (float): Mode for which to evaluate the power spectrum.
+                 It can be a scalar or a numpy array. 
+                 The units must be in 'h Mpc^{-1}'.
+    
+    Returns:
+      a scalar or a numpy array depending on the type of the k argument 
+    """
+    
     cdef np.ndarray out
     cdef double kval
     cdef tuple i

python/_project.pyx

@@ -808,7 +808,25 @@ def spherical_projection(int Nside,
                          npx.ndarray[DTYPE_t, ndim=3] density not None,
                          DTYPE_t min_distance,
                          DTYPE_t max_distance, int progress=1, int integrator_id=0, DTYPE_t[:] shifter = None, int booster=-1):
+    """
+    spherical_projection(Nside, density, min_distance, max_distance, progress=1, integrator_id=0, shifter=None, booster=-1)
     
+    Keyword arguments:
+      progress (int): show progress if it is equal to 1
+      integrator_id (int): specify the order of integration along the line of shift
+      shifter (DTYPE_t array): this is an array of size 3. It specifies the amount of shift to apply to the center, in unit of voxel
+      booster (int): what is the frequency of refreshment of the progress bar. Small number decreases performance by locking the GIL.
+      
+
+    Arguments:
+      Nside (int): Nside of the returned map
+      density (NxNxN array): this is the density field, expressed as a cubic array
+      min_distance (float): lower bound of the integration
+      max_distance (float): upper bound of the integration
+      
+    Returns:
+      an healpix map, as a 1-dimensional array.
+    """
     import healpy as hp
     import progressbar as pb
     cdef int i

python/cosmotool/borg.py

@@ -1,7 +1,7 @@
 ### 
 ### BORG code is from J. Jasche
 ###
-import StringIO
+import io
 import numpy as np
 from numpy import *
 import os.path
@@ -154,9 +154,11 @@ def get_grid_values(xx,data, ranges):
 def get_mean_density(fdir, smin, step):
     """ estimate ensemble mean
     """
-    print '-'*60
+    import progressbar as pb
-    print 'Get 3D ensemble mean density field'
+
-    print '-'*60
+    print('-'*60)
+    print('Get 3D ensemble mean density field')
+    print('-'*60)
 
     fname0 = fdir + 'initial_density_'+str(0)+'.dat'
     fname1 = fdir + 'final_density_'+str(0)+'.dat'
@@ -208,16 +210,20 @@ def get_mean_density(fdir, smin, step):
 def get_mean_density_fdir(fdir,init,steps):
     """ estimate ensemble mean
     """
-    print '-'*60
+    import progressbar as pb
-    print 'Get 3D ensemble mean density field'
+
-    print '-'*60
+    print('-'*60)
+    print('Get 3D ensemble mean density field')
+    print('-'*60)
 
     fname0,fname1=build_filelist(fdir)
     
     fname0=fname0[init::steps]
     fname1=fname1[init::steps]
     
-    MEAN0,ranges=read_borg_vol(fname0[0])
+    borg=read_borg_vol(fname0[0])
+    MEAN0 = borg.density
+    RANGES0 = borg.ranges
     MEAN0=MEAN0*0.;
     VAR0=copy(MEAN0)
     MEAN1=copy(MEAN0)
@@ -225,21 +231,23 @@ def get_mean_density_fdir(fdir,init,steps):
     norm0=0.
     norm1=0.
     
-    for fn in fname0:
+    for fn in pb.ProgressBar(len(fname0))(fname0):
-	auxdata0,auxranges0=read_borg_vol(fn)
+      auxborg=read_borg_vol(fn)
+      auxdata0 = auxborg.density
       MEAN0+=auxdata0
       VAR0+=auxdata0**2.
       norm0+=1.
-	del auxranges0
       del auxdata0
+      del auxborg
 
-    for fn in fname1:
+    for fn in pb.ProgressBar(len(fname1))(fname1):
-	auxdata1,auxranges1=read_borg_vol(fn)
+      auxborg1=read_borg_vol(fn)
+      auxdata1 = auxborg1.density
       MEAN1+=auxdata1
       VAR1+=auxdata1**2.
       norm1+=1.
-	del auxranges1
       del auxdata1
+      del auxborg1
 	
     MEAN0/=norm0
     VAR0/=norm0

python/cosmotool/cic.py

@@ -4,7 +4,7 @@ import numpy as np
 
 def cicParticles(particles, L, N):
 
-    if type(N) not in [int,long]:
+    if type(N) not in [int,int]:
       raise TypeError("N must be a numeric type")
 
     def shifted(i, t):
@@ -14,7 +14,7 @@ def cicParticles(particles, L, N):
 
     i =[]
     r = []
-    for d in xrange(3):
+    for d in range(3):
         q = ne.evaluate('(p%L)*N/L', local_dict={'p':particles[d], 'L':L, 'N':N })
         o = np.empty(q.size, dtype=np.int64)
         o[:] = np.floor(q)

python/cosmotool/cl_cic.py

@@ -163,8 +163,8 @@ class CIC_CL(object):
         # 2 dimensions
         translator['ndim'] = ndim
         translator['centered'] = '1' if centered else '0'
-        looperVariables = ','.join(['id%d' % d for d in xrange(ndim)])
+        looperVariables = ','.join(['id%d' % d for d in range(ndim)])
-        looperFor = '\n'.join(['for (int id{dim}=0; id{dim} < 2; id{dim}++) {{'.format(dim=d) for d in xrange(ndim)])
+        looperFor = '\n'.join(['for (int id{dim}=0; id{dim} < 2; id{dim}++) {{'.format(dim=d) for d in range(ndim)])
         looperForEnd = '}' * ndim
         
         kern = pragmas + CIC_PREKERNEL.format(**translator) + (CIC_KERNEL % {'looperVariables': looperVariables, 'looperFor': looperFor, 'looperForEnd':looperForEnd})

python/cosmotool/grafic.py

@@ -27,7 +27,7 @@ def readGrafic(filename):
         BoxSize = delta * Nx * h
         
         checkPoint = 4*Ny*Nz
-        for i in xrange(Nx):
+        for i in range(Nx):
             checkPoint = struct.unpack("I", f.read(4))[0]
             if checkPoint != 4*Ny*Nz:
               raise ValueError("Invalid unformatted access")
@@ -57,7 +57,7 @@ def writeGrafic(filename, field, BoxSize, scalefac, **cosmo):
                                           cosmo['omega_M_0'], cosmo['omega_lambda_0'], 100*cosmo['h'], checkPoint))
         checkPoint = 4*Ny*Nz
         field = field.reshape(field.shape, order='F')
-        for i in xrange(Nx):
+        for i in range(Nx):
             f.write(struct.pack("I", checkPoint))
             f.write(field[i].astype(np.float32).tostring())
             f.write(struct.pack("I", checkPoint))
@@ -73,7 +73,7 @@ def writeWhitePhase(filename, field):
         
         field = field.reshape(field.shape, order='F')
         checkPoint = struct.pack("I", 4*Nx*Ny)
-        for i in xrange(Nx):
+        for i in range(Nx):
             f.write(checkPoint)
             f.write(field[i].astype(np.float32).tostring())
             f.write(checkPoint)
@@ -87,7 +87,7 @@ def readWhitePhase(filename):
         
         checkPoint_ref = 4*Ny*Nz
         
-        for i in xrange(Nx):
+        for i in range(Nx):
             if struct.unpack("I", f.read(4))[0] != checkPoint_ref:
               raise ValueError("Invalid unformatted access")
               

python/cosmotool/timing.py

@@ -14,7 +14,7 @@ def time_block(name):
     yield
     te = time.time()
  
-    print ('%s %2.2f sec' %  (name, te-ts))
+    print('%s %2.2f sec' %  (name, te-ts))
 
 def timeit(method):
     """This decorator add a timing request for each call to the decorated function.
@@ -28,7 +28,7 @@ def timeit(method):
         result = method(*args, **kw)
         te = time.time()
 
-        print ('%r (%r, %r) %2.2f sec' % (method.__name__, args, kw, te-ts))
+        print('%r (%r, %r) %2.2f sec' % (method.__name__, args, kw, te-ts))
         return result
 
     return timed
@@ -46,7 +46,7 @@ def timeit_quiet(method):
         result = method(*args, **kw)
         te = time.time()
 
-        print ('%r %2.2f sec' % (method.__name__, te-ts))
+        print('%r %2.2f sec' % (method.__name__, te-ts))
         return result
 
     return timed

sample/simple3DFilter.cpp

@@ -1,3 +1,4 @@
+#include "openmp.hpp"
 #include "omptl/algorithm"
 #include <cassert>
 #include "yorick.hpp"
@@ -53,7 +54,7 @@ void computeInterpolatedField(MyTree *tree1, double boxsize, int Nres, double cx
       {
         double pz = (rz)*boxsize/Nres-cz;
 
-        cout << format("[%d] %d / %d") % omp_get_thread_num() % rz % Nres << endl;
+        cout << format("[%d] %d / %d") % smp_get_thread_id() % rz % Nres << endl;
         for (int ry = 0; ry < Nres; ry++)
           {
             double py = (ry)*boxsize/Nres-cy;

sample/testHDF5.cpp

@@ -38,10 +38,37 @@ knowledge of the CeCILL license and that you accept its terms.
 
 using namespace std;
 
+struct MyStruct
+{
+  int a;
+  double b;
+  char c;
+};
+
+struct MyStruct2
+{
+   MyStruct base;
+   int d;
+};
+
+
+CTOOL_STRUCT_TYPE(MyStruct, hdf5t_MyStruct,
+    ((int, a))
+    ((double, b))
+    ((char, c))
+)
+
+CTOOL_STRUCT_TYPE(MyStruct2, hdf5t_MyStruct2,
+    ((MyStruct, base))
+    ((int, d))
+)
+
 int main()
 {
   typedef  boost::multi_array<float, 2> array_type;
   typedef  boost::multi_array<float, 3> array3_type;
+  typedef  boost::multi_array<MyStruct, 1> array_mys_type;
+  typedef  boost::multi_array<MyStruct2, 1> array_mys2_type;
   typedef  boost::multi_array<std::complex<double>, 2> arrayc_type;
   typedef array_type::index index;
 
@@ -53,13 +80,27 @@ int main()
   array_type B;
   array3_type C(boost::extents[2][3][4]);
   arrayc_type D, E;
+  array_mys_type F(boost::extents[10]), G;
+  array_mys2_type H(boost::extents[10]);
   
   int values = 0;
   for (index i = 0; i != 2; i++)
     for (index j = 0; j != 3; j++)
       A[i][j] = values++;
       
+  for (index i = 0; i != 10; i++)
+    {
+        F[i].a = i;
+        F[i].b = double(i)/4.;
+        F[i].c = 'r'+i;
+        H[i].base = F[i];
+        H[i].d = 2*i;
+    } 
+  std::cout << " c = " << ((char *)&F[1])[offsetof(MyStruct, c)] << endl;
+    
   CosmoTool::hdf5_write_array(g, "test_data", A);
+  CosmoTool::hdf5_write_array(g, "test_struct", F);
+  CosmoTool::hdf5_write_array(g, "test_struct2", H);
   
   CosmoTool::hdf5_read_array(g, "test_data", B);
 
@@ -95,5 +136,12 @@ int main()
         abort();
       }
 
+  CosmoTool::hdf5_read_array(g, "test_struct", G);
+  for (index i = 0; i != 10; i++)
+    if (G[i].a != F[i].a || G[i].b != F[i].b || G[i].c != F[i].c) {
+        std::cout << "Invalid struct content" << endl;
+        abort();
+    }
+
   return 0;
 }

src/CMakeLists.txt

@@ -1,4 +1,3 @@
-add_definitions(-fPIC)
 
 SET(CosmoTool_SRCS
 	fortran.cpp
@@ -6,7 +5,6 @@ SET(CosmoTool_SRCS
 	load_data.cpp
 	loadGadget.cpp
 	loadRamses.cpp
-	octTree.cpp
 	powerSpectrum.cpp
 	miniargs.cpp
 	growthFactor.cpp
@@ -76,9 +74,11 @@ if (BUILD_SHARED_LIBS)
   target_link_libraries(CosmoTool ${CosmoTool_LIBS})
   if (BUILD_STATIC_LIBS)
      add_library(CosmoTool_static STATIC ${CosmoTool_SRCS})
+     set_target_properties(CosmoTool_static PROPERTIES COMPILE_FLAGS "${CMAKE_C_COMPILE_OPTIONS_PIC}")
   endif(BUILD_STATIC_LIBS)
 else (BUILD_SHARED_LIBS)
   add_library(CosmoTool STATIC ${CosmoTool_SRCS})
+  set_target_properties(CosmoTool PROPERTIES COMPILE_FLAGS "${CMAKE_C_COMPILE_OPTIONS_PIC}")
 endif (BUILD_SHARED_LIBS)
 
 install(TARGETS CosmoTool 

src/hdf5_array.hpp

@@ -44,6 +44,9 @@ knowledge of the CeCILL license and that you accept its terms.
 #include <boost/multi_array.hpp>
 #include <boost/type_traits/is_same.hpp> 
 #include <boost/type_traits/is_floating_point.hpp> 
+#include <boost/preprocessor/cat.hpp>
+#include <boost/preprocessor/stringize.hpp>
+#include <boost/preprocessor/seq/for_each.hpp>
 #include <vector>
 #include <H5Cpp.h>
 
@@ -59,7 +62,7 @@ namespace CosmoTool {
 
   template<typename T, class Enable = void> struct get_hdf5_data_type
   {
-    static H5::PredType type()  
+    static H5::DataType type()  
       {   
           BOOST_MPL_ASSERT_MSG(0, Unknown_HDF5_data_type, ()); 
           return H5::PredType::NATIVE_DOUBLE; 
@@ -68,7 +71,7 @@ namespace CosmoTool {
   
   #define HDF5_TYPE(tl, thdf5) \
   template<typename T> struct get_hdf5_data_type<T, typename boost::enable_if<boost::is_same<T, tl> >::type>  \
-    { static H5::PredType type() { return H5::PredType::thdf5; }; }
+    { static H5::DataType type() { return H5::PredType::thdf5; }; }
   
   HDF5_TYPE(char              , NATIVE_CHAR);
   HDF5_TYPE(long long         , NATIVE_LLONG);
@@ -202,6 +205,39 @@ namespace CosmoTool {
       hdf5_read_array(fg, data_set_name, data, hdf5_ComplexType<T>::ctype()->type);
   }
 
+
+#define CTOOL_HDF5_NAME(STRUCT) BOOST_PP_CAT(hdf5_,STRUCT)
+#define CTOOL_HDF5_INSERT_ELEMENT(r, STRUCT, element) \
+     { \
+       ::CosmoTool::get_hdf5_data_type<BOOST_PP_TUPLE_ELEM(2, 0, element)> t; \
+       position = HOFFSET(STRUCT, BOOST_PP_TUPLE_ELEM(2, 1, element)); \
+       const char *field_name = BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 1, element)); \
+       type.insertMember(field_name,  position, t.type()); \
+     } 
+  
+#define CTOOL_STRUCT_TYPE(STRUCT, TNAME, ATTRIBUTES) \
+namespace CosmoTool { \
+    class TNAME {  \
+    public:  \
+      H5::CompType type;  \
+  \
+      TNAME() : type(sizeof(STRUCT)) \
+      {  \
+        long position; \
+        BOOST_PP_SEQ_FOR_EACH(CTOOL_HDF5_INSERT_ELEMENT, STRUCT, ATTRIBUTES) \
+      }  \
+      \
+      static const TNAME *ctype() \
+      { \
+        static TNAME singleton; \
+        return &singleton; \
+      } \
+    }; \
+    template<> struct get_hdf5_data_type<STRUCT> { \
+        static H5::DataType type() { return TNAME::ctype()->type; }; \
+    }; \
+};
+
 };
 
 #endif

src/octTree.hpp

@@ -55,12 +55,20 @@ namespace CosmoTool
 
   typedef octCoordType OctCoords[3];
 
+  template<class T = void>
   struct OctCell
   {
     octPtr numberLeaves;
     octPtr children[8];
+    T data;
   };
 
+  template<typename T>
+  struct OctTree_defaultUpdater {
+    void operator()(T& d) { }
+  };
+
+  template<typename T_dataUpdater = OctTree_defaultUpdater<void>, class T = void>
   class OctTree
   {
   public:
@@ -103,9 +111,10 @@ namespace CosmoTool
     
 
   protected:
+    T_dataUpdater updater;
     const FCoordinates *particles;
     octPtr numParticles;
-    OctCell *cells;
+    OctCell<T> *cells;
     float Lbox;
     octPtr lastNode;
     octPtr numCells;  
@@ -177,4 +186,6 @@ namespace CosmoTool
 };
 
 
+#include "octTree.tcc"
+
 #endif

src/octTree.tcc

@@ -39,8 +39,9 @@ knowledge of the CeCILL license and that you accept its terms.
 #include "config.hpp"
 #include "octTree.hpp"
 
+namespace CosmoTool {
+
 using namespace std;
-using namespace CosmoTool;
 
 //#define VERBOSE
 
@@ -59,7 +60,8 @@ static uint32_t mypow(uint32_t i, uint32_t p)
     return j*j*i;  
 }
 
-OctTree::OctTree(const FCoordinates *particles, octPtr numParticles, 
+template<typename Updater, typename T>
+OctTree<Updater,T>::OctTree(const FCoordinates *particles, octPtr numParticles, 
 		 uint32_t maxMeanTreeDepth, uint32_t maxAbsoluteDepth,
 		 uint32_t threshold)
 {
@@ -94,7 +96,7 @@ OctTree::OctTree(const FCoordinates *particles, octPtr numParticles,
     }
   cout << xMin[0] << " " << xMin[1] << " " << xMin[2] << " lNorm=" << lenNorm << endl; 
 
-  cells = new OctCell[numCells];
+  cells = new OctCell<T>[numCells];
   Lbox = (float)(octCoordTypeNorm+1);
 
   cells[0].numberLeaves = 0;
@@ -110,12 +112,14 @@ OctTree::OctTree(const FCoordinates *particles, octPtr numParticles,
   //#endif
 }
 
-OctTree::~OctTree()
+template<typename Updater, typename T>
+OctTree<Updater,T>::~OctTree()
 {
   delete cells;
 }
 
-void OctTree::buildTree(uint32_t maxAbsoluteDepth)
+template<typename Updater, typename T>
+void OctTree<Updater,T>::buildTree(uint32_t maxAbsoluteDepth)
 {
   for (octPtr i = 0; i < numParticles; i++)
     {
@@ -129,7 +133,8 @@ void OctTree::buildTree(uint32_t maxAbsoluteDepth)
 }
 
 
-void OctTree::insertParticle(octPtr node, 
+template<typename Updater, typename T>
+void OctTree<Updater,T>::insertParticle(octPtr node, 
 			     const OctCoords& icoord,
 			     octCoordType halfNodeLength,
 			     octPtr particleId,
@@ -208,3 +213,5 @@ void OctTree::insertParticle(octPtr node,
   cells[node].children[octPos] = newNode;
 }
 
+
+};

src/openmp.hpp

@@ -0,0 +1,44 @@
+#ifndef __CTOOL_OPENMP_HPP
+#define __CTOOL_OPENMP_HPP
+
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+namespace CosmoTool {
+
+    static int smp_get_max_threads() {
+#ifdef _OPENMP
+        return omp_get_max_threads();
+#else
+        return 1;
+#endif
+    }
+    
+    static int smp_get_thread_id() {
+#ifdef _OPENMP
+        return omp_get_thread_num();
+#else
+        return 0;
+#endif
+    }
+
+    static int smp_get_num_threads() {
+#ifdef _OPENMP
+        return omp_get_num_threads();
+#else
+        return 1;
+#endif
+
+    }
+    
+    static void smp_set_nested(bool n) {
+#ifdef _OPENMP
+        omp_set_nested(n ? 1 : 0);
+#endif
+    }
+
+    
+};
+
+#endif

src/yorick_nc3.cpp

@@ -37,7 +37,7 @@ knowledge of the CeCILL license and that you accept its terms.
 #include "config.hpp"
 #ifdef NETCDFCPP4
 #include <netcdf>
-using namespace netCDF
+using namespace netCDF;
 #else
 #include <netcdfcpp.h>
 #endif