added variable declarations

added BAO wiggle params in cosmo
minimally invasive approach
2023-11-03 11:05:52 +00:00 · 2022-12-09 21:53:03 +01:00 · 2022-12-09 16:17:48 +01:00 · 2022-12-02 12:36:41 +01:00 · 2022-12-01 18:52:18 +01:00 · 2022-12-01 17:03:02 +01:00
28 changed files with 459 additions and 4328 deletions
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@ -42,17 +42,6 @@ ENDIF(BUILD_PYTHON)
 MESSAGE(STATUS "Using the target ${CosmoTool_local} to build python module")
 find_library(ZLIB_LIBRARY z)
 find_library(DL_LIBRARY dl)
 find_library(RT_LIBRARY rt)
 if (RT_LIBRARY)
  SET(RT_DEP rt)
  message(STATUS "RT found, linking against it")
 else()
  SET(RT_DEP)
 endif()
 find_library(MATH_LIBRARY m)
 include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
 IF(YORICK_SUPPORT)
@ -66,6 +55,9 @@ IF(YORICK_SUPPORT)
 ENDIF(YORICK_SUPPORT)
 find_program(CYTHON NAMES cython3 cython)
 find_library(ZLIB_LIBRARY z)
 find_library(DL_LIBRARY dl)
 find_library(MATH_LIBRARY m)
 set(NETCDF_FIND_REQUIRED ${YORICK_SUPPORT})
 set(GSL_FIND_REQUIRED TRUE)
@ -79,7 +71,7 @@ SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
 SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "4${EXTRA_VERSION}")
+SET(CPACK_PACKAGE_VERSION_PATCH "1${EXTRA_VERSION}")
 SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")
 SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
 SET(CPACK_SOURCE_IGNORE_FILES 
--- a/MANIFEST.in
+++ b/MANIFEST.in
@ -1,5 +1,4 @@
 include  .gitignore
 include  pyproject.toml
 include  CMakeLists.txt
 include  FindNumPy.cmake
 include  FindPyLibs.cmake
@ -17,17 +16,14 @@ include  doc/source/cpplibrary.rst
 include  doc/source/index.rst
 include  doc/source/intro.rst
 include  doc/source/pythonmodule.rst
 include  external/config.guess
 include  external/config.sub
 include  external/external_build.cmake
-include  external/libsharp-8d51946.tar.gz
+include  external/libsharp-6077806.tar.gz
 include  external/omptl-20120422.tar.bz2
 include  external/patch-omptl
 include  python/CMakeLists.txt
 include  python/_cosmo_bispectrum.cpp
 include  python/_cosmo_cic.pyx
 include  python/_cosmo_power.pyx
 include  python/_cosmomath.pyx
 include  python/_cosmotool.pyx
 include  python/_fast_interp.pyx
 include  python/_project.pyx
@ -97,7 +93,6 @@ include  sample/testkd3.cpp
 include  setup.py
 include  src/CMakeLists.txt
 include  src/algo.hpp
 include  src/numpy_adaptors.hpp
 include  src/bqueue.hpp
 include  src/bqueue.tcc
 include  src/bsp_simple.hpp
--- a/builder/build-wheels.sh
+++ b/builder/build-wheels.sh
@ -8,15 +8,12 @@ export CC CXX
 # Install a system package required by our library
 #yum install -y atlas-devel
-yum install -y cmake3 gsl-devel zlib-devel fftw3-devel libffi-devel hdf5 hdf5-devel
+yum install -y cmake3 gsl-devel zlib-devel fftw3-devel
 ln -fs /usr/bin/cmake3 /usr/bin/cmake
-test -d /io/wheelhouse || mkdir /io/wheelhouse
+ALL_PYTHON="cp36-cp36m cp37-cp37m cp38-cp38 cp39-cp39" 
 test -d /io/wheelhouse/fix || mkdir /io/wheelhouse/fix
 ALL_PYTHON="cp39-cp39 cp310-cp310"
 # Compile wheels
 for pkg in $ALL_PYTHON; do
@ -24,12 +21,12 @@ for pkg in $ALL_PYTHON; do
 #    "${PYBIN}/pip" install -r /io/dev-requirements.txt
    "${PYBIN}/pip" install setuptools wheel Cython 
    "${PYBIN}/pip" install -r /io/requirements.txt
-    "${PYBIN}/pip" wheel -vvv /io/ -w /io/wheelhouse/
+    "${PYBIN}/pip" wheel -vvv /io/ -w wheelhouse/
 done
 # Bundle external shared libraries into the wheels
-for whl in /io/wheelhouse/cosmotool*linux*.whl; do
+for whl in wheelhouse/cosmotool*.whl; do
-    auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/fix
+    auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/
 done
 # Install packages and test
--- a/builder/start.sh
+++ b/builder/start.sh
@ -9,4 +9,4 @@ if ! [ -e ${d}/setup.py ] ; then
  exit 1
 fi
-podman run -ti  --rm -e PLAT=manylinux2014_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2014_x86_64 /io/builder/build-wheels.sh
+podman run -ti  --rm -e PLAT=manylinux2010_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2010_x86_64 /io/builder/build-wheels.sh
--- a/external/config.guess
+++ b/external/config.guess
--- a/external/config.sub
+++ b/external/config.sub
--- a/external/external_build.cmake
+++ b/external/external_build.cmake
@ -2,19 +2,16 @@ include(FindOpenMP)
 OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
 SET(SOURCE_PREFIX ${CMAKE_SOURCE_DIR})
 SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE STRING "URL to download FFTW from")
 SET(EIGEN_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2" CACHE STRING "URL to download Eigen from")
 SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from")
-SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.2/src/hdf5-1.12.2.tar.gz" CACHE STRING "URL to download HDF5 from")
+SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.bz2" CACHE STRING "URL to download HDF5 from")
-SET(NETCDF_URL "https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.tar.gz" CACHE STRING "URL to download NetCDF from")
+SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz" CACHE STRING "URL to download NetCDF from")
-SET(NETCDFCXX_URL "https://github.com/Unidata/netcdf-cxx4/archive/v4.3.1.tar.gz" CACHE STRING "URL to download NetCDF-C++ from")
+SET(NETCDFCXX_URL "https://github.com/Unidata/netcdf-cxx4/archive/v4.3.0.tar.gz" CACHE STRING "URL to download NetCDF-C++ from")
-SET(BOOST_URL "https://boostorg.jfrog.io/artifactory/main/release/1.82.0/source/boost_1_82_0.tar.gz" CACHE STRING "URL to download Boost from")
+SET(BOOST_URL "https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.bz2" CACHE STRING "URL to download Boost from")
-SET(GSL_URL "https://ftpmirror.gnu.org/gsl/gsl-2.7.tar.gz" CACHE STRING "URL to download GSL from ")
+SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to download GSL from ")
 mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL)
 file(MAKE_DIRECTORY ${SOURCE_PREFIX}/downloads)
 SET(all_deps)
 MACRO(CHECK_CHANGE_STATE VAR) 
@ -39,13 +36,12 @@ CHECK_CHANGE_STATE(INTERNAL_DLIB DLIB_INCLUDE_DIR DLIB_LIBRARIES)
 IF(ENABLE_OPENMP)
  IF (NOT OPENMP_FOUND)
-    MESSAGE(NOTICE "No known compiler option for enabling OpenMP")
+    MESSAGE(ERROR "No known compiler option for enabling OpenMP")
  ELSE()
    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
    SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_C_FLAGS}")
  ENDIF(NOT OPENMP_FOUND)
  SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
  SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_C_FLAGS}")
 ENDIF(ENABLE_OPENMP)
@ -59,25 +55,17 @@ if (ENABLE_SHARP)
  SET(DEP_BUILD ${BUILD_PREFIX}/sharp-prefix/src/sharp/auto)
  IF(NOT ENABLE_OPENMP)
    SET(SHARP_OPENMP --disable-openmp)
  ELSE()
    SET(SHARP_OPENMP)
  ENDIF()
  SET(CUTILS_LIBRARY ${DEP_BUILD}/lib/libc_utils.a)
  SET(FFTPACK_LIBRARY ${DEP_BUILD}/lib/libfftpack.a)
  SET(SHARP_LIBRARY ${DEP_BUILD}/lib/libsharp.a)
  SET(SHARP_LIBRARIES ${SHARP_LIBRARY} ${FFTPACK_LIBRARY} ${CUTILS_LIBRARY})
  SET(SHARP_INCLUDE_PATH ${DEP_BUILD}/include)
  message(STATUS "Flags: ${CMAKE_C_FLAGS}")
  ExternalProject_Add(sharp
-    URL ${CMAKE_SOURCE_DIR}/external/libsharp-8d51946.tar.gz
+    URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz
    PREFIX ${BUILD_PREFIX}/sharp-prefix
    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
    BUILD_IN_SOURCE 1 
-    CONFIGURE_COMMAND
+    CONFIGURE_COMMAND autoconf && ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP}
          cp -f ${CMAKE_SOURCE_DIR}/external/config.guess . &&
          cp -f ${CMAKE_SOURCE_DIR}/external/config.sub . &&
          autoconf &&
          ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" "CFLAGS=${CMAKE_C_FLAGS}" "LDFLAGS=${CMAKE_EXE_LINKER_FLAGS}" --prefix=${DEP_BUILD} ${SHARP_OPENMP}
    INSTALL_COMMAND echo "No install"
    BUILD_BYPRODUCTS ${SHARP_LIBRARIES}
  )
@ -94,23 +82,27 @@ if (INTERNAL_HDF5)
  ExternalProject_Add(hdf5
    PREFIX ${BUILD_PREFIX}/hdf5-prefix
    URL ${HDF5_URL}
-    URL_HASH MD5=30172c75e436d7f2180e274071a4ca97
+    URL_HASH MD5=29117bf488887f89888f9304c8ebea0b
-    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
+    CMAKE_ARGS
-    CONFIGURE_COMMAND
+       -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
-        ${HDF5_SOURCE_DIR}/configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" "CFLAGS=${CMAKE_C_FLAGS}" "LDFLAGS=${CMAKE_EXE_LINKER_FLAGS}" --prefix=${HDF5_BIN_DIR} --disable-shared  --enable-cxx --enable-hl --enable-tools --with-pic
+       -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-    INSTALL_COMMAND make install
+       -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
       -DHDF5_BUILD_CPP_LIB=ON
       -DHDF5_BUILD_TOOLS=ON
       -DHDF5_BUILD_HL_LIB=ON
       -DBUILD_SHARED_LIBS=OFF
  )
  SET(cosmotool_DEPS ${cosmotool_DEPS} hdf5)
  SET(hdf5_built hdf5)
  SET(ENV{HDF5_ROOT} ${HDF5_BIN_DIR})
  SET(HDF5_ROOTDIR ${HDF5_BIN_DIR})
  SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}/lib")
-  SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl ${RT_LIBRARY}")
+  SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl")
-  set(HDF5_C_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5.a)
+  set(HDF5_C_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5-static.a)
-  set(HDF5_HL_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl.a)
+  set(HDF5_HL_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl-static.a)
-  set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE)
+  set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5-static.a CACHE STRING "HDF5 lib" FORCE)
-  set(HDF5_HL_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_hl.a CACHE STRING "HDF5 HL lib" FORCE)
+  set(HDF5_HL_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_hl-static.a CACHE STRING "HDF5 HL lib" FORCE)
-  set(HDF5_CXX_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_cpp.a CACHE STRING "HDF5 C++ lib" FORCE)
+  set(HDF5_CXX_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_cpp-static.a CACHE STRING "HDF5 C++ lib" FORCE)
  SET(HDF5_INCLUDE_DIRS ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE)
  mark_as_advanced(HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIRS)
@ -168,52 +160,43 @@ if (INTERNAL_NETCDF)
  SET(NETCDF_CONFIG_COMMAND ${NETCDF_SOURCE_DIR}/configure
         --prefix=${NETCDF_BIN_DIR} --libdir=${NETCDF_BIN_DIR}/lib
         --enable-netcdf-4  --with-pic --disable-shared --disable-dap 
-         --disable-byterange --disable-cdmremote --disable-rpc --enable-cxx-4 
+         --disable-cdmremote --disable-rpc --enable-cxx-4 
         --disable-examples ${EXTRA_NC_FLAGS} CC=${CMAKE_C_COMPILER}
         CXX=${CMAKE_CXX_COMPILER})
  list(INSERT CMAKE_PREFIX_PATH 0 ${EXT_INSTALL})
  string(REPLACE ";" "|" CMAKE_PREFIX_PATH_ALT_SEP "${CMAKE_PREFIX_PATH}")
  ExternalProject_Add(netcdf
    DEPENDS ${hdf5_built}
    URL_HASH MD5=f48ee01534365006934f0c63d4055ea0
    PREFIX ${BUILD_PREFIX}/netcdf-prefix
    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
    URL ${NETCDF_URL}
-    LIST_SEPARATOR |
+  LIST_SEPARATOR |
-    CMAKE_ARGS
+	CMAKE_ARGS
 		-DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH_ALT_SEP}
 		-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
 		-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
                -DNC_EXTRA_DEPS=${RT_DEP}
 		-DBUILD_SHARED_LIBS=OFF
 		-DBUILD_TESTING=OFF
 		-DCMAKE_BUILD_TYPE=Release
 		-DENABLE_NETCDF4=ON
-                -DENABLE_BYTERANGE=FALSE
+    -DCMAKE_POSITION_INDEPENDENT_CODE=ON
-		-DCMAKE_POSITION_INDEPENDENT_CODE=ON
+    -DENABLE_DAP=OFF
 		-DENABLE_DAP=OFF
 		-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
                -DHDF5_C_LIBRARY=${HDF5_C_STATIC_LIBRARY}
                -DHDF5_HL_LIBRARY=${HDF5_HL_STATIC_LIBRARY}
                -DHDF5_INCLUDE_DIR=${HDF5_INCLUDE_DIRS}
-		-DCMAKE_INSTALL_LIBDIR=lib
+    -DCMAKE_INSTALL_LIBDIR=lib
  )
  SET(NETCDFCXX_SOURCE_DIR ${BUILD_PREFIX}/netcdf-c++-prefix/src/netcdf-c++)
  ExternalProject_Add(netcdf-c++
    DEPENDS ${hdf5_built} netcdf
    PREFIX ${BUILD_PREFIX}/netcdf-c++-prefix
    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
    URL ${NETCDFCXX_URL}
 	CMAKE_ARGS
 		-DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH_ALT_SEP}
 		-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
 		-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
 		-DBUILD_SHARED_LIBS=OFF
-                -DCMAKE_POSITION_INDEPENDENT_CODE=ON
+    -DCMAKE_POSITION_INDEPENDENT_CODE=ON
                -DHDF5_C_LIBRARY=${HDF5_C_STATIC_LIBRARY}
                -DHDF5_HL_LIBRARY=${HDF5_HL_STATIC_LIBRARY}
                -DHDF5_INCLUDE_DIR=${HDF5_INCLUDE_DIRS}
 		-DBUILD_TESTING=OFF
 		-DCMAKE_BUILD_TYPE=Release
 		-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
@ -251,8 +234,7 @@ if (INTERNAL_BOOST)
  ExternalProject_Add(boost
    URL ${BOOST_URL}
    PREFIX ${BUILD_PREFIX}/boost-prefix
-    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
+    URL_HASH MD5=da07ca30dd1c0d1fdedbd487efee01bd
    URL_HASH MD5=f7050f554a65f6a42ece221eaeec1660
    CONFIGURE_COMMAND 
           ${BOOST_SOURCE_DIR}/bootstrap.sh --prefix=${CMAKE_BINARY_DIR}/ext_build/boost
    BUILD_IN_SOURCE 1
@ -295,7 +277,6 @@ IF(INTERNAL_GSL)
  ExternalProject_Add(gsl
    URL ${GSL_URL}
    PREFIX ${BUILD_PREFIX}/gsl-prefix
    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
    CONFIGURE_COMMAND ${GSL_SOURCE_DIR}/configure
           --prefix=${EXT_INSTALL} --disable-shared
           --with-pic
@ -348,7 +329,6 @@ IF(INTERNAL_FFTW)
  ExternalProject_Add(fftw
     URL ${FFTW_URL}
     PREFIX ${BUILD_PREFIX}/fftw-prefix
    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
     CONFIGURE_COMMAND 
           ${FFTW_SOURCE}/configure
                 --prefix=${EXT_INSTALL}
@ -378,7 +358,6 @@ IF (INTERNAL_EIGEN)
  ExternalProject_Add(eigen
     URL ${EIGEN_URL}
     URL_HASH MD5=b9e98a200d2455f06db9c661c5610496
    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
     PREFIX ${BUILD_PREFIX}/eigen-prefix
     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
       -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
@ -411,7 +390,6 @@ SET(cosmotool_DEPS ${cosmotool_DEPS} omptl)
 SET(OMPTL_BUILD_DIR ${BUILD_PREFIX}/omptl-prefix/src/omptl)
 ExternalProject_Add(omptl
  PREFIX ${BUILD_PREFIX}/omptl-prefix
  DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
  URL ${CMAKE_SOURCE_DIR}/external/omptl-20120422.tar.bz2
  CONFIGURE_COMMAND echo "No configure"
  BUILD_COMMAND echo "No build"
--- a/external/libsharp-8d51946.tar.gz
+++ b/external/libsharp-8d51946.tar.gz
--- a/external/patch-omptl
+++ b/external/patch-omptl
@ -1,6 +1,6 @@
 diff -ur omptl.old/omptl_algorithm omptl/omptl_algorithm
--- omptl.old/omptl_algorithm	2022-06-19 08:21:39.815498672 +0200
+--- omptl.old/omptl_algorithm	2012-04-22 16:29:41.000000000 +0200
-+++ omptl/omptl_algorithm	2022-06-19 08:21:52.953544672 +0200
+++ omptl/omptl_algorithm	2021-06-20 15:40:29.000000000 +0200
@@ -20,7 +20,7 @@
 #define OMPTL_ALGORITHM 1
@ -23,13 +23,11 @@ diff -ur omptl.old/omptl_algorithm omptl/omptl_algorithm
 #endif /* OMPTL_ALGORITHM */
 diff -ur omptl.old/omptl_algorithm_par.h omptl/omptl_algorithm_par.h
--- omptl.old/omptl_algorithm_par.h	2022-06-19 08:21:39.816498675 +0200
+--- omptl.old/omptl_algorithm_par.h	2012-04-22 16:29:41.000000000 +0200
-+++ omptl/omptl_algorithm_par.h	2022-06-19 08:23:50.705956964 +0200
+++ omptl/omptl_algorithm_par.h	2021-06-20 15:40:50.000000000 +0200
-@@ -20,9 +20,10 @@
+@@ -21,8 +21,8 @@
 #include <utility>
 #include <cmath>
 #include <cstdlib>
 +#include <random>
 -#include <omptl/omptl_tools.h>
 -#include <omptl/omptl_numeric>
@ -38,78 +36,7 @@ diff -ur omptl.old/omptl_algorithm_par.h omptl/omptl_algorithm_par.h
 #include <iterator>
-@@ -510,7 +511,7 @@
+@@ -1700,7 +1700,7 @@
 		typename std::vector<Iterator>::iterator result =
 		    std::find_if(results.begin(),results.end(),
 -			std::bind2nd(std::not_equal_to<Iterator>(), last) );
 +			std::bind(std::not_equal_to<Iterator>(), std::placeholders::_1, last) );
 		if ( result != results.end() )
 			return *result;
@@ -569,7 +570,7 @@
 		const typename std::vector<Iterator>::iterator result
 			 = std::find_if(results.begin(), results.end(),
 -			std::bind2nd(std::not_equal_to<Iterator>(), last) );
 +			std::bind(std::not_equal_to<Iterator>(), std::placeholders::_1, last) );
 		if ( result != results.end() )
 			return *result;
@@ -654,7 +655,7 @@
 		const typename std::vector<Iterator>::iterator
 		result = std::find_if(results.begin(), results.end(),
 -					std::bind2nd(std::not_equal_to<Iterator>(), last1));
 +					std::bind(std::not_equal_to<Iterator>(), std::placeholders::_1, last1));
 		if ( result != results.end() )
 			return *result;
@@ -953,7 +954,7 @@
 		results[t] = std::lower_bound(partitions[t].first, partitions[t].second, value, comp);
 	const typename std::vector<ForwardIterator>::iterator result =
 -		std::find_if(results.begin(), results.end(), std::bind2nd(std::not_equal_to<ForwardIterator>(), last) );
 +		std::find_if(results.begin(), results.end(), std::bind(std::not_equal_to<ForwardIterator>(), std::placeholders::_1, last) );
 	if (result != results.end())
 		return *result;
@@ -1179,7 +1180,7 @@
 namespace detail
 {
 -	
 +
 template<typename Iterator, class StrictWeakOrdering>
 Iterator _pivot_range(Iterator first, Iterator last,
 	const typename std::iterator_traits<Iterator>::value_type pivot,
@@ -1309,14 +1310,14 @@
 void random_shuffle(RandomAccessIterator first, RandomAccessIterator last,
                     const unsigned P)
 {
 -	std::random_shuffle(first, last);
 +	std::shuffle(first, last, std::mt19937(std::random_device()()));
 }
 template <class RandomAccessIterator, class RandomNumberGenerator>
 void random_shuffle(RandomAccessIterator first, RandomAccessIterator last,
                     RandomNumberGenerator& rgen, const unsigned P)
 {
 -	std::random_shuffle(first, last, rgen);
 +	std::shuffle(first, last, std::mt19937(std::random_device()()));
 }
 // Not (yet) parallelized, not straightforward due to possible dependencies
@@ -1472,7 +1473,7 @@
                             const T& new_value, const unsigned P)
 {
 	return ::omptl::replace_copy_if(first, last, result,
 -			std::bind2nd(std::equal_to<T>(), old_value), new_value, P);
 +			std::bind(std::equal_to<T>(), std::placeholders::_1, old_value), new_value, P);
 }
 template <class ForwardIterator, class Predicate, class T>
@@ -1700,7 +1701,7 @@
 	std::vector<char> pivot_used(pivots.size(), false); // can't be bool due to parallel write
@ -118,56 +45,9 @@ diff -ur omptl.old/omptl_algorithm_par.h omptl/omptl_algorithm_par.h
 	assert(1u << max_depth <= P);
 	for (unsigned i = 0; i < max_depth; ++i)
 	{
@@ -1781,7 +1782,7 @@
 std::cout  << std::endl;
 std::cout << borders.size() << " " << partitions.size() << " " << P << std::endl;
 -*/	
 +*/
 	// Round one: sort final partitions, split remaining
 	#pragma omp parallel for
 	for (int i = 0; i < int(partitions.size()); ++i)
@@ -1814,7 +1815,7 @@
 			const RandomAccessIterator begin  = partitions[i].first;
 			const RandomAccessIterator end    = partitions[i].second;
 -			
 +
 			const RandomAccessIterator middle =
 				detail::_pivot_range(begin, end, pivots[pivot_index], comp);
 			partitions[i  ] = std::make_pair(begin, middle);
 diff -ur omptl.old/omptl_algorithm_ser.h omptl/omptl_algorithm_ser.h
 --- omptl.old/omptl_algorithm_ser.h	2022-06-19 08:21:39.815498672 +0200
 +++ omptl/omptl_algorithm_ser.h	2022-06-19 08:21:52.960544697 +0200
@@ -14,7 +14,7 @@
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 -
 +#include <random>
 namespace omptl
 {
@@ -463,14 +463,14 @@
 void random_shuffle(RandomAccessIterator first, RandomAccessIterator last,
       const unsigned P)
 {
 -	return ::std::random_shuffle(first, last);
 +	return ::std::shuffle(first, last, std::mt19937(std::random_device()()));
 }
 template <class RandomAccessIterator, class RandomNumberGenerator>
 void random_shuffle(RandomAccessIterator first, RandomAccessIterator last,
                     RandomNumberGenerator &rgen, const unsigned P)
 {
 -	return ::std::random_shuffle(first, last, rgen);
 +	return ::std::shuffle(first, last, std::mt19937(std::random_device()()));
 }
 template <class ForwardIterator, class T>
 diff -ur omptl.old/omptl_numeric omptl/omptl_numeric
--- omptl.old/omptl_numeric	2022-06-19 08:21:39.816498675 +0200
+--- omptl.old/omptl_numeric	2012-04-22 16:29:41.000000000 +0200
-+++ omptl/omptl_numeric	2022-06-19 08:21:52.955544679 +0200
+++ omptl/omptl_numeric	2021-06-20 15:40:29.000000000 +0200
@@ -19,7 +19,7 @@
 #define OMPTL_NUMERIC 1
@ -193,8 +73,8 @@ diff -ur omptl.old/omptl_numeric omptl/omptl_numeric
 #endif /* OMPTL_NUMERIC */
 diff -ur omptl.old/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h
--- omptl.old/omptl_numeric_extensions.h	2022-06-19 08:21:39.815498672 +0200
+--- omptl.old/omptl_numeric_extensions.h	2012-04-22 16:29:41.000000000 +0200
-+++ omptl/omptl_numeric_extensions.h	2022-06-19 08:21:52.956544683 +0200
+++ omptl/omptl_numeric_extensions.h	2021-06-20 15:40:29.000000000 +0200
@@ -51,9 +51,9 @@
 } // namespace
@ -208,8 +88,8 @@ diff -ur omptl.old/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h
 namespace omptl
 diff -ur omptl.old/omptl_numeric_par.h omptl/omptl_numeric_par.h
--- omptl.old/omptl_numeric_par.h	2022-06-19 08:21:39.816498675 +0200
+--- omptl.old/omptl_numeric_par.h	2012-04-22 16:29:41.000000000 +0200
-+++ omptl/omptl_numeric_par.h	2022-06-19 08:21:52.957544686 +0200
+++ omptl/omptl_numeric_par.h	2021-06-20 15:40:29.000000000 +0200
@@ -23,8 +23,8 @@
 #include <functional>
 #include <iterator>
@ -222,8 +102,8 @@ diff -ur omptl.old/omptl_numeric_par.h omptl/omptl_numeric_par.h
 namespace omptl
 {
 diff -ur omptl.old/omptl_tools.h omptl/omptl_tools.h
--- omptl.old/omptl_tools.h	2022-06-19 08:21:39.816498675 +0200
+--- omptl.old/omptl_tools.h	2012-04-22 16:29:41.000000000 +0200
-+++ omptl/omptl_tools.h	2022-06-19 08:21:52.957544686 +0200
+++ omptl/omptl_tools.h	2021-06-20 15:40:42.000000000 +0200
@@ -25,7 +25,7 @@
 #include <climits>
 #include <iterator>
--- a/pyproject.toml
+++ b/pyproject.toml
@ -1,4 +0,0 @@
 [build-system]
 requires = ["setuptools","wheel","cython"]
 build-backend = "setuptools.build_meta"
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@ -2,7 +2,7 @@ set(CMAKE_SHARED_MODULE_PREFIX)
 set(PYTHON_INCLUDES ${NUMPY_INCLUDE_DIRS} ${PYTHON_INCLUDE_PATH} ${CMAKE_SOURCE_DIR}/python)
-include_directories(${CMAKE_SOURCE_DIR}/python ${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src)
+include_directories(${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src)
 IF(CYTHON)
  add_custom_command(
@ -69,10 +69,13 @@ target_link_libraries(_fast_interp PRIVATE ${CosmoTool_local} )
 SET(ct_TARGETS   _cosmotool _project _cosmo_power _cosmo_cic _fast_interp _cosmomath)
 if (Boost_FOUND)
-  message(STATUS "Building bispectrum support")
+  message(STATUS "Building bispectrum support (path = ${Boost_INCLUDE_DIRS})")
  include_directories(${Boost_INCLUDE_DIRS})
  add_library(_cosmo_bispectrum MODULE _cosmo_bispectrum.cpp)
  target_link_libraries(_cosmo_bispectrum ${MATH_LIBRARY})
  if(ENABLE_OPENMP)
    set_target_properties(_cosmo_bispectrum PROPERTIES COMPILE_FLAGS "${OpenMP_CXX_FLAGS}" LINK_FLAGS "${OpenMP_CXX_FLAGS}")
  endif()
  if (Boost_DEP)
    add_dependencies(_cosmo_bispectrum ${Boost_DEP})
  endif()
--- a/python/_cosmo_power.pyx
+++ b/python/_cosmo_power.pyx
@ -39,10 +39,14 @@ cdef extern from "cosmopower.hpp" namespace "CosmoTool":
    double OmegaEff
    double Gamma0
    double normPower
    double A_BAO
    double r_BAO
    double k_D_BAO
    CosmoPower()
    void setFunction(CosmoFunction)
    void setFunction_BAO(CosmoFunction,double,double,double)
    void updateCosmology()
    void updatePhysicalCosmology()
    void normalize(double,double)
@ -101,8 +105,7 @@ cdef class CosmologyPower:
    """
    self.power.SIGMA8 = s8
    self.power.normalize(k_min, k_max)
-    
+   
  def setFunction(self,funcname):
    """setFunction(self, funcname)
--- a/python/_cosmomath.pyx
+++ b/python/_cosmomath.pyx
@ -12,7 +12,7 @@ cdef extern from "numpy/npy_common.h":
   ctypedef npy_intp
 cdef extern from "special_math.hpp" namespace "CosmoTool":
-   T log_modified_bessel_first_kind[T](T v, T z) except + nogil
+   T log_modified_bessel_first_kind[T](T v, T z) nogil except +
 cdef extern from "numpy_adaptors.hpp" namespace "CosmoTool":
   void parallel_ufunc_dd_d[T,IT](char **args, IT* dimensions, IT* steps, void *func)
--- a/python/_cosmotool.pyx
+++ b/python/_cosmotool.pyx
@ -39,7 +39,7 @@ cdef extern from "loadSimu.hpp" namespace "CosmoTool":
 cdef extern from "loadGadget.hpp" namespace "CosmoTool":
-  SimuData *loadGadgetMulti(const char *fname, int id, int flags, int gformat) except + nogil
+  SimuData *loadGadgetMulti(const char *fname, int id, int flags, int gformat) nogil except +
  void cxx_writeGadget "CosmoTool::writeGadget" (const char * s, SimuData *data) except +
 cdef extern from "safe_gadget.hpp":
@ -313,13 +313,6 @@ tries to get an array from the object."""
 references to the object are gone. """
        pass
 cdef extern from "numpy/arrayobject.h":
    # a little bit awkward: the reference to obj will be stolen
    # using PyObject*  to signal that Cython cannot handle it automatically
    int PyArray_SetBaseObject(np.ndarray arr, PyObject *obj) except -1 # -1 means there was an error
 cdef object wrap_array(void *p, np.uint64_t s, int typ):
    cdef np.ndarray ndarray
    cdef ArrayWrapper wrapper
@ -327,8 +320,7 @@ cdef object wrap_array(void *p, np.uint64_t s, int typ):
    wrapper = ArrayWrapper()
    wrapper.set_data(s, typ, p)
    ndarray = np.array(wrapper, copy=False)
-    #ndarray.base = <PyObject*> wrapper
+    ndarray.base = <PyObject*> wrapper
    PyArray_SetBaseObject(ndarray, <PyObject*> wrapper)
    Py_INCREF(wrapper)
    return ndarray
--- a/python/_project.pyx
+++ b/python/_project.pyx
@ -727,7 +727,7 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
    cdef int iu0[3]
    cdef int i
    cdef int N = density.shape[0]
-    cdef int half_N = density.shape[0]//2
+    cdef int half_N = density.shape[0]/2
    cdef int completed
    cdef DTYPE_t I0, d, dist2, delta, s, max_distance2
    cdef int jumper[1]
--- a/requirements.txt
+++ b/requirements.txt
@ -1,4 +1,5 @@
-numpy<1.22
+numpy<1.19
 cffi
 numexpr
-cython<3
+pyfftw
 cython
--- a/sample/CMakeLists.txt
+++ b/sample/CMakeLists.txt
@ -1,8 +1,4 @@
 SET(tolink  ${CosmoTool_local} ${CosmoTool_LIBS} ${GSL_LIBRARIES} ${DL_LIBRARY})
 if (RT_LIBRARY)
  SET(tolink ${tolink} ${RT_LIBRARY})
 endif()
 include_directories(${CMAKE_SOURCE_DIR}/src)
 include_directories(${FFTW3_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIRS} ${GSL_INCLUDE_PATH})
 if(YORICK_SUPPORT)
--- a/sample/simple3DFilter.cpp
+++ b/sample/simple3DFilter.cpp
@ -84,7 +84,6 @@ int main(int argc, char **argv) {
  char *fname1, *outFile;
  double rLimit, boxsize, rLimit2, cx, cy, cz;
  int Nres;
  int periodic;
  MiniArgDesc args[] = {{"INPUT DATA1", &fname1, MINIARG_STRING},
                        {"RADIUS LIMIT", &rLimit, MINIARG_DOUBLE},
@ -94,7 +93,6 @@ int main(int argc, char **argv) {
                        {"CY", &cy, MINIARG_DOUBLE},
                        {"CZ", &cz, MINIARG_DOUBLE},
                        {"OUTPUT FILE", &outFile, MINIARG_STRING},
                        {"PERIODIC", &periodic, MINIARG_INT},
                        {0, 0, MINIARG_NULL}};
  if (!parseMiniArgs(argc, argv, args))
@ -150,7 +148,6 @@ int main(int argc, char **argv) {
  cout << "Building trees..." << endl;
  MyTree tree1(allCells_1, N1_points);
  tree1.setPeriodic(periodic != 0, boxsize);
  cout << "Creating smoothing filter..." << endl;
--- a/setup.py
+++ b/setup.py
@ -2,7 +2,6 @@ import stat
 import os
 import sys
 import shutil
 from sysconfig import get_config_var
 from distutils.command.install_data import install_data
 import pathlib
 from setuptools import find_packages, setup, Extension
@ -77,9 +76,9 @@ class InstallCMakeLibs(install_lib):
 #        # your files are moved to the appropriate location when the installation
 #        # is run
 #
-#        libs = [os.path.join(bin_dir, _lib) for _lib in
+#        libs = [os.path.join(bin_dir, _lib) for _lib in 
-#                os.listdir(bin_dir) if
+#                os.listdir(bin_dir) if 
-#                os.path.isfile(os.path.join(bin_dir, _lib)) and
+#                os.path.isfile(os.path.join(bin_dir, _lib)) and 
 #                os.path.splitext(_lib)[1] in [".dll", ".so"]
 #                and not (_lib.startswith("python") or _lib.startswith(PACKAGE_NAME))]
 #
@ -88,16 +87,16 @@ class InstallCMakeLibs(install_lib):
 #            shutil.move(lib, os.path.join(self.build_dir,
 #                                          os.path.basename(lib)))
 #
-#        # Mark the libs for installation, adding them to
+#        # Mark the libs for installation, adding them to 
-#        # distribution.data_files seems to ensure that setuptools' record
+#        # distribution.data_files seems to ensure that setuptools' record 
 #        # writer appends them to installed-files.txt in the package's egg-info
 #        #
-#        # Also tried adding the libraries to the distribution.libraries list,
+#        # Also tried adding the libraries to the distribution.libraries list, 
-#        # but that never seemed to add them to the installed-files.txt in the
+#        # but that never seemed to add them to the installed-files.txt in the 
-#        # egg-info, and the online recommendation seems to be adding libraries
+#        # egg-info, and the online recommendation seems to be adding libraries 
-#        # into eager_resources in the call to setup(), which I think puts them
+#        # into eager_resources in the call to setup(), which I think puts them 
-#        # in data_files anyways.
+#        # in data_files anyways. 
-#        #
+#        # 
 #        # What is the best way?
 #
 #        # These are the additional installation files that should be
@ -105,7 +104,7 @@ class InstallCMakeLibs(install_lib):
 #        # step; depending on the files that are generated from your cmake
 #        # build chain, you may need to modify the below code
 #
-#        self.distribution.data_files = [os.path.join(self.install_dir,
+#        self.distribution.data_files = [os.path.join(self.install_dir, 
 #                                                     os.path.basename(lib))
 #                                        for lib in libs]
 #        print(self.distribution.data_files)
@ -168,24 +167,17 @@ class BuildCMakeExt(build_ext):
        # Change your cmake arguments below as necessary
        # Below is just an example set of arguments for building Blender as a Python module
        c_compiler=os.environ.get('CC', get_config_var("CC"))
        cxx_compiler=os.environ.get('CXX', get_config_var("CXX"))
        compilers=[]
        fill_up_settings=[
-              ("CMAKE_C_COMPILER", "CC", get_config_var("CC")),
+              ("CMAKE_C_COMPILER", "CC"),
-              ("CMAKE_CXX_COMPILER", "CXX", get_config_var("CXX")),
+              ("CMAKE_CXX_COMPILER", "CXX"),
-              ("CMAKE_C_FLAGS", "CFLAGS", None),
+              ("CMAKE_C_FLAGS", "CFLAGS"),
-              ("CMAKE_CXX_FLAGS", "CXXFLAGS", None),
+              ("CMAKE_EXE_LINKER_FLAGS_INIT", "LDFLAGS"),
-              ("CMAKE_EXE_LINKER_FLAGS_INIT", "LDFLAGS", None),
+              ("CMAKE_SHARED_LINKER_FLAGS_INIT", "LDFLAGS"),
-              ("CMAKE_SHARED_LINKER_FLAGS_INIT", "LDFLAGS", None),
+              ("CMAKE_MODULE_LINKER_FLAGS_INIT", "LDFLAGS")]
-              ("CMAKE_MODULE_LINKER_FLAGS_INIT", "LDFLAGS", None)]
+        for cmake_flag, os_flag in fill_up_settings:
-        for cmake_flag, os_flag, default_flag in fill_up_settings:
+          if os_flag in os.environ:
-          if os_flag in os.environ or default_flag is not None:
+             compilers.append(f"-D{cmake_flag}={os.environ[os_flag]}")
             c = os.environ.get(os_flag, default_flag)
             if not c is None:
               compilers.append(f"-D{cmake_flag}={c}")
        print(compilers)
        self.spawn(['cmake', '-H'+SOURCE_DIR, '-B'+self.build_temp,
                    '-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON',
@ -221,7 +213,7 @@ class BuildCMakeExt(build_ext):
               if  _pyd_top[0].startswith(PACKAGE_NAME):
                   if os.path.splitext(_pyd)[1] in [".pyd", ".so"] or _pyd_top[-1] == 'config.py':
                     pyd_path.append((_pyd_top,_pyd))
-
+               
        for top,p in pyd_path:
           _,n = os.path.split(p)
@ -237,10 +229,10 @@ class BuildCMakeExt(build_ext):
 CosmoTool_extension = CMakeExtension(name="cosmotool")
 setup(name='cosmotool',
-      version='1.3.6',
+      version='1.3.1',
      packages=["cosmotool"],
      package_dir={'cosmotool': 'python/cosmotool'},
-      install_requires=['cython','numpy','cffi','numexpr','h5py'],
+      install_requires=['numpy','cffi','numexpr','pyfftw','h5py'],
      setup_requires=['cython','cffi','numpy','numexpr'],
      ext_modules=[CosmoTool_extension],
      description='A small cosmotool box of useful functions',
--- a/src/cosmopower.cpp
+++ b/src/cosmopower.cpp
@ -212,30 +212,6 @@ double CosmoPower::powerHuWiggles(double k)
  return normPower * pow(k,n) * T_k * T_k;
 }
 double CosmoPower::BAO_Tk(double k){
  double no_wiggle_tk = noWiggleTk(k);
  double A = 0;
  double r_s = 10;
  double k_D = 2 * M_PI / 100;
  //sqrt as we want to make the parameterization part of the transfer function
  double param = sqrt(1 + A * sin(k * r_s) * exp(- k / k_D)); 
  return no_wiggle_tk * param;
 }
 double CosmoPower::sample_BAO(double k)
 {
  // BAO wiggle parameterization for reconstruction
  // Babic et al. 2022, https://arxiv.org/abs/2203.06177
  double T_k = BAO_Tk(k); 
  return normPower * pow(k,n) * T_k * T_k;
  }
 double CosmoPower::primordialPowerSpectrum(double k)
 {
  //Primordial power spectrum, needed for PNG
@ -481,18 +457,14 @@ void CosmoPower::setFunction(CosmoFunction f)
    case POWER_SUGIYAMA:
      eval = &CosmoPower::powerSugiyama;
      break;
    case SAMPLE_WIGGLES:
      eval = &CosmoPower::sample_BAO;
      break;
    case POWER_BDM:
      eval = &CosmoPower::powerBDM;
      break;
    case NOWIGGLE_TK:
      eval = &CosmoPower::noWiggleTk;
    case POWER_TEST:
      eval = &CosmoPower::powerTest;
      break;
    case BAO_TK:
      eval = &CosmoPower::BAO_Tk;
      break;
    default:
      abort();
    }
--- a/src/cosmopower.hpp
+++ b/src/cosmopower.hpp
@ -66,6 +66,10 @@ namespace CosmoTool {
    double Gamma0;
    double normPower;
    double A_BAO;
    double r_BAO;
    double k_D_BAO;
    struct EHuParams {
      double k_silk;
      double s;
@ -90,15 +94,13 @@ namespace CosmoTool {
      POWER_BDM,
      POWER_TEST,
      HU_WIGGLES_ORIGINAL,
-      SAMPLE_WIGGLES,
+      NOWIGGLE_TK
      BAO_TK
    };
    CosmoPower();
    ~CosmoPower();
    void setFunction(CosmoFunction f);
    void updateCosmology();
    void updatePhysicalCosmology();
    void normalize(double k_min = -1, double k_max = -1);
@ -110,6 +112,7 @@ namespace CosmoTool {
    double power(double k);
    double integrandNormalize(double k);
  private:
    double (CosmoPower::*eval)(double);
@ -124,9 +127,8 @@ namespace CosmoTool {
    double powerBDM(double k);
    double powerTest(double k);
    double powerHuWigglesOriginal(double k);
    double sample_BAO(double k);
    double noWiggleTk(double k);
-    double BAO_Tk(double k);
+
  };
 };
--- a/src/h5_readFlash.cpp
+++ b/src/h5_readFlash.cpp
@ -7,16 +7,16 @@ This software is a computer program whose purpose is to provide a toolbox for co
 data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...)
 This software is governed by the CeCILL license under French law and
-abiding by the rules of distribution of free software.  You can  use,
+abiding by the rules of distribution of free software.  You can  use, 
 modify and/ or redistribute the software under the terms of the CeCILL
 license as circulated by CEA, CNRS and INRIA at the following URL
-"http://www.cecill.info".
+"http://www.cecill.info". 
 As a counterpart to the access to the source code and  rights to copy,
 modify and redistribute granted by the license, users are provided only
 with a limited warranty  and the software's author,  the holder of the
 economic rights,  and the successive licensors  have only  limited
-liability.
+liability. 
 In this respect, the user's attention is drawn to the risks associated
 with loading,  using,  modifying and/or developing or reproducing the
@ -25,9 +25,9 @@ that may mean  that it is complicated to manipulate,  and  that  also
 therefore means  that it is reserved for developers  and  experienced
 professionals having in-depth computer knowledge. Users are therefore
 encouraged to load and test the software's suitability as regards their
-requirements in conditions enabling the security of their systems and/or
+requirements in conditions enabling the security of their systems and/or 
-data to be ensured and,  more generally, to use and operate it in the
+data to be ensured and,  more generally, to use and operate it in the 
-same conditions as regards security.
+same conditions as regards security. 
 The fact that you are presently reading this means that you have had
 knowledge of the CeCILL license and that you accept its terms.
@ -59,8 +59,8 @@ int ipvz_out   = 5;
 /* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx */
-/*  n*_runtime_parameters should be set by the caller to
+/*  n*_runtime_parameters should be set by the caller to 
-    the maximum number of runtime parameters to read.
+    the maximum number of runtime parameters to read. 
 */
 void h5_read_runtime_parameters
@ -100,12 +100,12 @@ void h5_read_runtime_parameters
  nreal_runtime_parameters = MAX_PARM;
  /* integer runtime parameters */
-  int_rt_parms = (int_runtime_params_t *) malloc(nint_runtime_parameters * sizeof(int_runtime_params_t));
+  int_rt_parms = (int_runtime_params_t *) malloc(nint_runtime_parameters * sizeof(int_runtime_params_t)); 
  rank = 1;
  DataSet dataset = file->openDataSet("integer runtime parameters");
-
+  
-  IntType int_rt_type = dataset.getIntType();
+  IntType int_rt_type = dataset.getIntType();  
  //int_rt_type = H5Dget_type(dataset);
  DataSpace dataspace = dataset.getSpace();
@ -123,7 +123,10 @@ void h5_read_runtime_parameters
  DataSpace memspace(rank, &dimens_1d);
  //memspace = H5Screate_simple(rank, &dimens_1d, NULL);
-  dataset.read(int_rt_parms, int_rt_type, memspace, dataspace);
+  dataset.read(int_rt_parms, int_rt_type, memspace, dataspace,
 		    H5P_DEFAULT);
  //status = H5Dread(dataset, int_rt_type, memspace, dataspace,
 	//	    H5P_DEFAULT, int_rt_parms);
  for (i = 0; i < nint_runtime_parameters; i++) {
@ -142,14 +145,14 @@ void h5_read_runtime_parameters
  /* reals */
-  real_rt_parms = (real_runtime_params_t *) malloc(nreal_runtime_parameters * sizeof(real_runtime_params_t));
+  real_rt_parms = (real_runtime_params_t *) malloc(nreal_runtime_parameters * sizeof(real_runtime_params_t)); 
-
+  
  rank = 1;
  dataset = file->openDataSet("real runtime parameters");
-  //dataset = H5Dopen(*file_identifier, "real runtime parameters");
+  //dataset = H5Dopen(*file_identifier, "real runtime parameters"); 
-
+  
  dataspace = dataset.getSpace();
-  FloatType real_rt_type = dataset.getFloatType();
+  FloatType real_rt_type = dataset.getFloatType();  
  ndims = dataspace.getSimpleExtentDims(&dimens_1d, NULL);
  //dataspace = H5Dget_space(dataset);
  //real_rt_type = H5Dget_type(dataset);
@ -164,7 +167,10 @@ void h5_read_runtime_parameters
   memspace = DataSpace(rank, &dimens_1d);
  //memspace = H5Screate_simple(rank, &dimens_1d, NULL);
-  dataset.read(real_rt_parms, real_rt_type, memspace, dataspace);
+  dataset.read(real_rt_parms, real_rt_type, memspace, dataspace,
 		    H5P_DEFAULT);
  //status = H5Dread(dataset, real_rt_type, memspace, dataspace,
 //		    H5P_DEFAULT, real_rt_parms);
  for (i = 0; i < nreal_runtime_parameters; i++) {
@ -187,7 +193,7 @@ void h5_read_runtime_parameters
      *LBox = real_runtime_parameter_values[i];
    }
    if (strncmp(real_runtime_parameter_names[i],"hubbleconstant", 14) == 0 ) {
-      *hubble = real_runtime_parameter_values[i];
+      *hubble = real_runtime_parameter_values[i];      
    }
    if (strncmp(real_runtime_parameter_names[i],"omegamatter", 11) == 0 ) {
      *omegam = real_runtime_parameter_values[i];
@ -199,7 +205,7 @@ void h5_read_runtime_parameters
      *omegalambda = real_runtime_parameter_values[i];
    }
  }
-
+  
  for (i = 0; i < nint_runtime_parameters; i++) {
    if (strncmp(int_runtime_parameter_names[i],"pt_numx",7) == 0 ) {
      *numPart = int_runtime_parameter_values[i];
@ -208,7 +214,7 @@ void h5_read_runtime_parameters
  }
 }
-
+     
 /* xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx*/
 void h5_read_flash3_particles (H5File* file,
                        int* totalparticles,
@ -235,8 +241,8 @@ void h5_read_flash3_particles (H5File* file,
  char     *propName;
  double   *partBuffer;
  char    part_names[50][OUTPUT_PROP_LENGTH];
-  int     string_size;
+  int     string_size;  
-
+         
 //  char part_names[NPART_PROPS][OUTPUT_PROP_LENGTH];
  hsize_t dimens_2d[2], maxdimens_2d[2];
  hsize_t start_2d[2], count_2d[2], stride_2d[2];
@ -259,12 +265,12 @@ void h5_read_flash3_particles (H5File* file,
  //total number of particle properties
  numProps = dimens_2d[0];
-
+  
  string_size = OUTPUT_PROP_LENGTH;
  StrType string_type = H5Tcopy(H5T_C_S1);
  string_type.setSize(string_size);
  //status = H5Tset_size(string_type, string_size);
-
+  
  rank = 2;
  start_2d[0] = 0;
@ -276,20 +282,22 @@ void h5_read_flash3_particles (H5File* file,
  count_2d[0] = dimens_2d[0];
  count_2d[1] = dimens_2d[1];
-  dataspace.selectHyperslab(H5S_SELECT_SET, count_2d, start_2d);
+  dataspace.selectHyperslab(H5S_SELECT_SET, count_2d, start_2d); 
  //status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start_2d,
  //                      stride_2d, count_2d, NULL);
  DataSpace memspace(rank, dimens_2d);
  //memspace = H5Screate_simple(rank, dimens_2d, NULL);
-  dataset.read(part_names, string_type);
+  dataset.read(part_names, string_type, H5S_ALL, H5S_ALL, H5P_DEFAULT);
-
+  //status = H5Dread(dataset, string_type, H5S_ALL, H5S_ALL,
  //              H5P_DEFAULT, part_names);
  string_type.close();
  memspace.close();
  dataspace.close();
-  dataset.close();
+  dataset.close(); 
  //H5Tclose(string_type);
  //H5Sclose(memspace);
  //H5Sclose(dataspace);
@ -305,7 +313,7 @@ void h5_read_flash3_particles (H5File* file,
    if (strncmp(part_names[i], "velz", 4) == 0) { ipvz = i+1; }
  }
-  if ((iptag < 0) || (ipx < 0) || (ipy < 0) || (ipz < 0) || (ipvx < 0) ||
+  if ((iptag < 0) || (ipx < 0) || (ipy < 0) || (ipz < 0) || (ipvx < 0) || 
       (ipvy < 0) || (ipvz < 0) ) {
    printf("One or more required particle attributes not found in file!\n");
    return;
@ -317,7 +325,7 @@ void h5_read_flash3_particles (H5File* file,
  //read particles
  dataset = file->openDataSet("tracer particles");
  //dataset = H5Dopen(*file_identifier, "tracer particles");
-
+  
  FloatType datatype = dataset.getFloatType();
  //datatype = H5Dget_type(dataset);
@ -330,7 +338,7 @@ void h5_read_flash3_particles (H5File* file,
  ndims = dataspace.getSimpleExtentDims(dimens_2d, NULL);
  //dataspace = H5Dget_space(dataset);
  //H5Sget_simple_extent_dims(dataspace, dimens_2d, maxdimens_2d);
-
+ 
  /*insert particle properties (numPartBuffer) particles at a time*/
  pstack = (*localnp);
  poffset = 0;
@ -358,7 +366,7 @@ void h5_read_flash3_particles (H5File* file,
    dimens_2d[0] = (pcount);
    dimens_2d[1] = (numProps);
-    dataspace.selectHyperslab(H5S_SELECT_SET, count_2d, start_2d);
+    dataspace.selectHyperslab(H5S_SELECT_SET, count_2d, start_2d); 
    //status     = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, start_2d,
    //                                 stride_2d, count_2d, NULL);
@ -366,7 +374,8 @@ void h5_read_flash3_particles (H5File* file,
    //memspace   = H5Screate_simple(rank, dimens_2d, maxdimens_2d);
    /* read data from the dataset */
-   dataset.read(partBuffer, datatype, memspace, dataspace);
+   dataset.read(partBuffer, datatype, memspace, dataspace, H5P_DEFAULT);
   //status = H5Dread(dataset, datatype, memspace, dataspace, H5P_DEFAULT, partBuffer);
    /* convert buffer into particle struct */
@ -382,8 +391,8 @@ void h5_read_flash3_particles (H5File* file,
      pos3[p+poffset]  = (float) *(partBuffer+ipz-1+p*numProps);
    }
    }
-
+   
-
+    
    if (vel1 && vel2 && vel3) {
    for(p=0; p < (pcount); p++) {
      vel1[p+poffset]  = (float) *(partBuffer+ipvx-1+p*numProps);
@ -414,7 +423,7 @@ void h5_read_flash3_particles (H5File* file,
  //status = H5Sclose(dataspace);
  //status = H5Dclose(dataset);
 }
-
+ 
 /*xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx*/
@ -442,7 +451,7 @@ void h5_read_flash3_header_info(H5File* file,
  H5std_string DATASET_NAME;
-  string_type = H5Tcopy(H5T_C_S1);
+  string_type = H5Tcopy(H5T_C_S1);  
  H5Tset_size(string_type, MAX_STRING_LENGTH);
  DataSet dataset = file->openDataSet("real scalars");
@ -458,13 +467,13 @@ void h5_read_flash3_header_info(H5File* file,
  /* malloc a pointer to a list of real_list_t's */
  real_list = (real_list_t *) malloc(dimens_1d * sizeof(real_list_t));
-  // create a new simple dataspace of 1 dimension and size of 'dimens_1d'
+  // create a new simple dataspace of 1 dimension and size of 'dimens_1d' 
  DataSpace memspace(1, &dimens_1d);
-  // create an empty vessel sized to hold one real_list_t's worth of data
+  // create an empty vessel sized to hold one real_list_t's worth of data 
  CompType real_list_type( sizeof(real_list_t) );
-  // subdivide the empty vessel into its component sections (name and value)
+  // subdivide the empty vessel into its component sections (name and value) 
  real_list_type.insertMember(
          "name",
          HOFFSET(real_list_t, name),
@ -475,8 +484,9 @@ void h5_read_flash3_header_info(H5File* file,
          HOFFSET(real_list_t, value),
          PredType::NATIVE_DOUBLE);
-  // read the data into 'real_list'
+  // read the data into 'real_list' 
-  dataset.read( real_list, real_list_type, memspace, dataspace);
+  dataset.read( real_list, real_list_type, memspace, dataspace,
                H5P_DEFAULT);
  if (status < 0) {
--- a/src/hdf5_array.hpp
+++ b/src/hdf5_array.hpp
@ -426,7 +426,7 @@ namespace CosmoTool {
 #define CTOOL_HDF5_INSERT_ELEMENT(r, STRUCT, element) \
     { \
       ::CosmoTool::get_hdf5_data_type<BOOST_PP_TUPLE_ELEM(2, 0, element)> t; \
-       long position = offsetof(STRUCT, BOOST_PP_TUPLE_ELEM(2, 1, element)); \
+       long 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()); \
     } 
--- a/src/interpolate.cpp
+++ b/src/interpolate.cpp
@ -157,7 +157,6 @@ const Interpolate& Interpolate::operator=(const Interpolate& a)
  gsl_spline_init(spline, a.spline->x, a.spline->y, a.spline->size);
  logx = a.logx;
  logy = a.logy;
  return *this;
 }
 double Interpolate::getMaxX() const
--- a/src/mykdtree.hpp
+++ b/src/mykdtree.hpp
@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/mykdtree.hpp) -- Copyright (C) Guilhem Lavaux (2007-2022)
+This is CosmoTool (./src/mykdtree.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 guilhem.lavaux@gmail.com
@ -7,16 +7,16 @@ This software is a computer program whose purpose is to provide a toolbox for co
 data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...)
 This software is governed by the CeCILL license under French law and
-abiding by the rules of distribution of free software.  You can  use,
+abiding by the rules of distribution of free software.  You can  use, 
 modify and/ or redistribute the software under the terms of the CeCILL
 license as circulated by CEA, CNRS and INRIA at the following URL
-"http://www.cecill.info".
+"http://www.cecill.info". 
 As a counterpart to the access to the source code and  rights to copy,
 modify and redistribute granted by the license, users are provided only
 with a limited warranty  and the software's author,  the holder of the
 economic rights,  and the successive licensors  have only  limited
-liability.
+liability. 
 In this respect, the user's attention is drawn to the risks associated
 with loading,  using,  modifying and/or developing or reproducing the
@ -25,9 +25,9 @@ that may mean  that it is complicated to manipulate,  and  that  also
 therefore means  that it is reserved for developers  and  experienced
 professionals having in-depth computer knowledge. Users are therefore
 encouraged to load and test the software's suitability as regards their
-requirements in conditions enabling the security of their systems and/or
+requirements in conditions enabling the security of their systems and/or 
-data to be ensured and,  more generally, to use and operate it in the
+data to be ensured and,  more generally, to use and operate it in the 
-same conditions as regards security.
+same conditions as regards security. 
 The fact that you are presently reading this means that you have had
 knowledge of the CeCILL license and that you accept its terms.
@ -48,13 +48,13 @@ namespace CosmoTool {
  typedef uint64_t NodeIntType;
-  template<int N, typename CType = ComputePrecision>
+  template<int N, typename CType = ComputePrecision> 
  struct KDDef
  {
    typedef CType CoordType;
    typedef float KDCoordinates[N];
  };
-
+  
  template<int N, typename ValType, typename CType = ComputePrecision>
  struct KDCell
  {
@ -102,7 +102,7 @@ namespace CosmoTool {
    uint64_t currentRank;
    uint64_t numCells;
  };
-
+  
  template<int N, typename ValType, typename CType = ComputePrecision>
  class RecursionMultipleInfo
@ -121,7 +121,7 @@ namespace CosmoTool {
    }
  };
-  template<int N, typename ValType, typename CType = ComputePrecision>
+  template<int N, typename ValType, typename CType = ComputePrecision> 
  struct KD_default_cell_splitter
  {
    void operator()(KDCell<N,ValType,CType> **cells, NodeIntType Ncells, NodeIntType& split_index, int axis, typename KDDef<N,CType>::KDCoordinates minBound, typename KDDef<N,CType>::KDCoordinates maxBound);
@ -135,7 +135,7 @@ namespace CosmoTool {
    typedef typename KDDef<N>::KDCoordinates coords;
    typedef KDCell<N,ValType,CType> Cell;
    typedef KDTreeNode<N,ValType,CType> Node;
-
+    
    CellSplitter splitter;
    KDTree(Cell *cells, NodeIntType Ncells);
@ -153,10 +153,10 @@ namespace CosmoTool {
       std::copy(replicate, replicate+N, this->replicate);
     }
-    uint64_t getIntersection(const coords& x, CoordType r,
+    uint64_t getIntersection(const coords& x, CoordType r, 
 			     Cell **cells,
 			     uint64_t numCells);
-    uint64_t getIntersection(const coords& x, CoordType r,
+    uint64_t getIntersection(const coords& x, CoordType r, 
 			     Cell **cells,
 			     CoordType *distances,
 			     uint64_t numCells);
@ -183,7 +183,7 @@ namespace CosmoTool {
    NodeIntType getNumberInNode(const Node *n) const { return n->numNodes; }
 #else
    NodeIntType getNumberInNode(const Node *n) const {
-      if (n == 0)
+      if (n == 0) 
        return 0;
      return 1+getNumberInNode(n->children[0])+getNumberInNode(n->children[1]);
    }
@ -211,7 +211,7 @@ namespace CosmoTool {
 		    uint32_t depth,
 		    coords minBound,
 		    coords maxBound);
-
+    
    template<bool justCount>
    void recursiveIntersectionCells(RecursionInfoCells<N,ValType, CType>& info,
 				    Node *node,
@ -224,7 +224,7 @@ namespace CosmoTool {
 			  CoordType& R2,
 			  Cell*& cell);
    void recursiveMultipleNearest(RecursionMultipleInfo<N,ValType,CType>& info, Node *node,
-				  int level);
+				  int level);    
  };
--- a/src/mykdtree.tcc
+++ b/src/mykdtree.tcc
@ -33,7 +33,7 @@ namespace CosmoTool {
  template<int N, typename ValType, typename CType, typename CellSplitter>
  KDTree<N,ValType,CType,CellSplitter>::KDTree(Cell *cells, NodeIntType Ncells)
  {
-    periodic = false;
+    periodic = false; 
    base_cell = cells;
    numNodes = Ncells;
@ -41,7 +41,7 @@ namespace CosmoTool {
    sortingHelper = new Cell *[Ncells];
    for (NodeIntType i = 0; i < Ncells; i++)
-	sortingHelper[i] = &cells[i];
+	sortingHelper[i] = &cells[i];    
    optimize();
  }
@ -73,14 +73,14 @@ namespace CosmoTool {
            absoluteMax[k] = cell->coord[k];
        }
      }
-
+    
    std::cout << "   rebuilding the tree..." << std::endl;
-    root = buildTree(sortingHelper, activeCells, 0, absoluteMin, absoluteMax);
+    root = buildTree(sortingHelper, activeCells, 0, absoluteMin, absoluteMax);    
    std::cout << "   done." << std::endl;
  }
  template<int N, typename ValType, typename CType, typename CellSplitter>
-  uint64_t KDTree<N,ValType,CType,CellSplitter>::getIntersection(const coords& x, CoordType r,
+  uint64_t KDTree<N,ValType,CType,CellSplitter>::getIntersection(const coords& x, CoordType r, 
 						    KDTree<N,ValType,CType,CellSplitter>::Cell **cells,
 						    uint64_t numCells)
  {
@ -112,7 +112,7 @@ namespace CosmoTool {
  }
  template<int N, typename ValType, typename CType, typename CellSplitter>
-  uint64_t KDTree<N,ValType,CType,CellSplitter>::getIntersection(const coords& x, CoordType r,
+  uint64_t KDTree<N,ValType,CType,CellSplitter>::getIntersection(const coords& x, CoordType r, 
 						    Cell **cells,
 						    CoordType *distances,
 						    uint64_t numCells)
@ -175,7 +175,7 @@ namespace CosmoTool {
  template<int N, typename ValType, typename CType, typename CellSplitter>
  template<bool justCount>
-  void KDTree<N,ValType,CType,CellSplitter>::recursiveIntersectionCells(RecursionInfoCells<N,ValType,CType>& info,
+  void KDTree<N,ValType,CType,CellSplitter>::recursiveIntersectionCells(RecursionInfoCells<N,ValType,CType>& info, 
 							   Node *node,
 							   int level)
  {
@ -183,7 +183,7 @@ namespace CosmoTool {
    CoordType d2 = 0;
 #if __KD_TREE_ACTIVE_CELLS == 1
-    if (node->value->active)
+    if (node->value->active) 
 #endif
      {
 	for (int j = 0; j < 3; j++)
@ -250,9 +250,9 @@ namespace CosmoTool {
  }
  template<int N, typename ValType, typename CType>
-  void KD_default_cell_splitter<N,ValType,CType>::operator()(KDCell<N,ValType,CType> **cells, NodeIntType Ncells,
+  void KD_default_cell_splitter<N,ValType,CType>::operator()(KDCell<N,ValType,CType> **cells, NodeIntType Ncells, 
                                                             NodeIntType& split_index, int axis,
-                                                             typename KDDef<N,CType>::KDCoordinates minBound,
+                                                             typename KDDef<N,CType>::KDCoordinates minBound, 
                                                             typename KDDef<N,CType>::KDCoordinates maxBound)
  {
    CellCompare<N,ValType,CType> compare(axis);
@ -279,9 +279,9 @@ namespace CosmoTool {
 //#pragma omp atomic capture
    nodeId = (this->lastNode)++;
-
+    
    node = &nodes[nodeId];
-
+    
    // Isolate the environment
    splitter(cell0, Ncells, mid, axis, minBound, maxBound);
@ -297,12 +297,12 @@ namespace CosmoTool {
    {
      node->children[0] = buildTree(cell0, mid, depth, minBound, tmpBound);
    }
-
+    
    memcpy(tmpBound, minBound, sizeof(coords));
    tmpBound[axis] = node->value->coord[axis];
 #pragma omp task private(tmpBound)
    {
-      node->children[1] = buildTree(cell0+mid+1, Ncells-mid-1, depth,
+      node->children[1] = buildTree(cell0+mid+1, Ncells-mid-1, depth, 
 				  tmpBound, maxBound);
    }
@ -391,17 +391,17 @@ namespace CosmoTool {
 	  }
 	return;
      }
-
+    
    // Check if current node is not the nearest
-    CoordType thisR2 =
+    CoordType thisR2 = 
      computeDistance(node->value, x);
-
+    
    if (thisR2 < R2)
      {
 	R2 = thisR2;
 	best = node->value;
-      }
+      }    
-
+    
    // Now we found the best. We check whether the hypersphere
    // intersect the hyperplane of the other branch
@ -435,11 +435,11 @@ namespace CosmoTool {
         {
           coords x_new;
           r.getPosition(x_new);
-           recursiveNearest(root, 0, x_new, R2, best);
+           recursiveNearest(root, 0, x_new, R2, best); 
         }
       while (r.next());
     }
-
+   
   return best;
 }
@ -474,15 +474,15 @@ namespace CosmoTool {
      {
 	recursiveMultipleNearest(info, go, level+1);
      }
-
+    
    // Check if current node is not the nearest
-    CoordType thisR2 =
+    CoordType thisR2 = 
      computeDistance(node->value, info.x);
    info.queue.push(node->value, thisR2);
    info.traversed++;
    //    if (go == 0)
    //      return;
-
+    
    // Now we found the best. We check whether the hypersphere
    // intersect the hyperplane of the other branch
@ -497,7 +497,7 @@ namespace CosmoTool {
 	  {
 	    recursiveMultipleNearest(info, other, level+1);
 	  }
-      }
+      }    
  }
 template<int N, typename ValType, typename CType, typename CellSplitter>
@ -505,7 +505,7 @@ namespace CosmoTool {
 						    Cell **cells)
 {
   RecursionMultipleInfo<N,ValType> info(x, cells, N2);
-
+   
   for (int i = 0; i < N2; i++)
     cells[i] = 0;
@ -532,7 +532,7 @@ namespace CosmoTool {
 						    CoordType *distances)
 {
   RecursionMultipleInfo<N,ValType> info(x, cells, N2);
-
+   
   for (int i = 0; i < N2; i++)
     cells[i] = 0;
@ -555,14 +555,14 @@ namespace CosmoTool {
 #ifdef __KD_TREE_SAVE_ON_DISK
 #define KDTREE_DISK_SIGNATURE "KDTREE"
 #define KDTREE_DISK_SIGNATURE_LEN 7
-
+  
  template<int N, typename CType>
  struct KDTreeOnDisk
  {
    long cell_id;
    long children_node[2];
    typename KDDef<N, CType>::KDCoordinates minBound, maxBound;
-  };
+  };  
  struct KDTreeHeader
  {
@ -619,7 +619,7 @@ namespace CosmoTool {
      {
         std::cerr << "KDTree Signature invalid" << std::endl;
         throw InvalidOnDiskKDTree();
-      }
+      } 
    if (h.numCells != Ncells || h.nodesUsed < 0) {
      std::cerr << "The number of cells has changed (" << h.numCells << " != " << Ncells << ") or nodesUsed=" << h.nodesUsed << std::endl;
@ -643,8 +643,8 @@ namespace CosmoTool {
           throw InvalidOnDiskKDTree();
        }
        if (node_on_disk.cell_id > numNodes || node_on_disk.cell_id < 0 ||
-	    (node_on_disk.children_node[0] >= 0 && node_on_disk.children_node[0] > lastNode) || node_on_disk.children_node[0] < -1 ||
+	    node_on_disk.children_node[0] > lastNode || node_on_disk.children_node[0] < -1 ||
-	    (node_on_disk.children_node[1] >= 0 && node_on_disk.children_node[1] > lastNode) || node_on_disk.children_node[1] < -1)
+	    node_on_disk.children_node[1] > lastNode || node_on_disk.children_node[1] < -1)
 	  {
 	    delete[] nodes;
            std::cerr << "Invalid cell id or children node id invalid" << std::endl;
@ -683,10 +683,10 @@ namespace CosmoTool {
      }
    root = &nodes[h.rootId];
-
+    
    sortingHelper = new Cell *[Ncells];
    for (NodeIntType i = 0; i < Ncells; i++)
-      sortingHelper[i] = &cells[i];
+      sortingHelper[i] = &cells[i];    
  }
 #endif
--- a/src/sphSmooth.hpp
+++ b/src/sphSmooth.hpp
@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/sphSmooth.hpp) -- Copyright (C) Guilhem Lavaux (2007-2022)
+This is CosmoTool (./src/sphSmooth.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 guilhem.lavaux@gmail.com
@ -7,16 +7,16 @@ This software is a computer program whose purpose is to provide a toolbox for co
 data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...)
 This software is governed by the CeCILL license under French law and
-abiding by the rules of distribution of free software.  You can  use,
+abiding by the rules of distribution of free software.  You can  use, 
 modify and/ or redistribute the software under the terms of the CeCILL
 license as circulated by CEA, CNRS and INRIA at the following URL
-"http://www.cecill.info".
+"http://www.cecill.info". 
 As a counterpart to the access to the source code and  rights to copy,
 modify and redistribute granted by the license, users are provided only
 with a limited warranty  and the software's author,  the holder of the
 economic rights,  and the successive licensors  have only  limited
-liability.
+liability. 
 In this respect, the user's attention is drawn to the risks associated
 with loading,  using,  modifying and/or developing or reproducing the
@ -25,9 +25,9 @@ that may mean  that it is complicated to manipulate,  and  that  also
 therefore means  that it is reserved for developers  and  experienced
 professionals having in-depth computer knowledge. Users are therefore
 encouraged to load and test the software's suitability as regards their
-requirements in conditions enabling the security of their systems and/or
+requirements in conditions enabling the security of their systems and/or 
-data to be ensured and,  more generally, to use and operate it in the
+data to be ensured and,  more generally, to use and operate it in the 
-same conditions as regards security.
+same conditions as regards security. 
 The fact that you are presently reading this means that you have had
 knowledge of the CeCILL license and that you accept its terms.
@ -39,89 +39,80 @@ knowledge of the CeCILL license and that you accept its terms.
 #include "config.hpp"
 #include "mykdtree.hpp"
-namespace CosmoTool {
+namespace CosmoTool
 {
  template <typename ValType, int Ndims = NUMDIMS>
-  class SPHSmooth {
+  class SPHSmooth
  {
  public:
-    typedef struct {
+    typedef struct
    {
      ComputePrecision weight;
      ValType pValue;
    } FullType;
-    typedef KDTree<Ndims, FullType> SPHTree;
+    typedef KDTree<Ndims,FullType> SPHTree;
-    typedef KDTreeNode<Ndims, FullType> SPHNode;
+    typedef KDTreeNode<Ndims,FullType> SPHNode;
-    typedef KDCell<Ndims, FullType> SPHCell;
+    typedef KDCell<Ndims,FullType>  SPHCell;
-    typedef typename KDTree<Ndims, FullType>::CoordType CoordType;
+    typedef typename KDTree<Ndims,FullType>::CoordType CoordType;
-    typedef ComputePrecision (*computeParticleValue)(const ValType &t);
+    typedef ComputePrecision (*computeParticleValue)(const ValType& t);
-    typedef void (*runParticleValue)(ValType &t);
+    typedef void (*runParticleValue)(ValType& t);
  public:
    typedef SPHCell *P_SPHCell;
-    struct SPHState {
+    struct SPHState
    {
      boost::shared_ptr<P_SPHCell[]> ngb;
      boost::shared_ptr<CoordType[]> distances;
      typename SPHTree::coords currentCenter;
      int currentNgb;
      ComputePrecision smoothRadius;
    };
-
+    
    SPHSmooth(SPHTree *tree, uint32_t Nsph);
-    virtual ~SPHSmooth();
+    virtual ~SPHSmooth();   
-    void
+    void fetchNeighbours(const typename SPHTree::coords& c, SPHState *state = 0);
-    fetchNeighbours(const typename SPHTree::coords &c, SPHState *state = 0);
+    
-
+    void fetchNeighbours(const typename SPHTree::coords& c, uint32_t newNsph);
-    void fetchNeighbours(
+    void fetchNeighboursOnVolume(const typename SPHTree::coords& c, ComputePrecision radius);
-        const typename SPHTree::coords &c, uint32_t newNsph,
+    const typename SPHTree::coords& getCurrentCenter() const
-        SPHState *state = 0);
+    {
    void fetchNeighboursOnVolume(
        const typename SPHTree::coords &c, ComputePrecision radius);
    const typename SPHTree::coords &getCurrentCenter() const {
      return internal.currentCenter;
    }
-    /** This is the pure SPH smoothing function. It does not reweight by the
+    template<typename FuncT>
-     * value computed at each grid site.
+    ComputePrecision computeSmoothedValue(const typename SPHTree::coords& c,
-     */
+					  FuncT fun, SPHState *state = 0);    
-    template <typename FuncT>
+	
-    ComputePrecision computeSmoothedValue(
+	template<typename FuncT>
-        const typename SPHTree::coords &c, FuncT fun, SPHState *state = 0);
+    ComputePrecision computeInterpolatedValue(const typename SPHTree::coords& c,
 					      FuncT fun, SPHState *state = 0);
    ComputePrecision getMaxDistance(const typename SPHTree::coords& c, 
 				    SPHNode *node) const;
-    /** This is the weighted SPH smoothing function. It does reweight by the
+    ComputePrecision getSmoothingLen() const
-     * value computed at each grid site. This ensures the total sum of the interpolated
+    {
-     * quantity is preserved by interpolating to the target mesh.
+      return internal.smoothRadius;
-     */
+    }
    template <typename FuncT>
    ComputePrecision computeInterpolatedValue(
        const typename SPHTree::coords &c, FuncT fun, SPHState *state = 0);
    /** This is the adjoint gradient of computeInterpolatedValue w.r.t. to the value
     * array. FuncT is expected to have the following prototype:
     *    void((CellValue defined by the user), ComputePrecision weighted_ag_value)
     */
    template <typename FuncT>
    void computeAdjointGradientSmoothedValue(
        const typename SPHTree::coords &c, ComputePrecision ag_value, FuncT fun,
        SPHState *state = 0);
    ComputePrecision
    getMaxDistance(const typename SPHTree::coords &c, SPHNode *node) const;
    ComputePrecision getSmoothingLen() const { return internal.smoothRadius; }
    // TO USE WITH EXTREME CARE !
-    void setSmoothingLen(ComputePrecision len) { internal.smoothRadius = len; }
+    void setSmoothingLen(ComputePrecision len)
    {
      internal.smoothRadius = len;
    }
    // END
-    template <typename FuncT>
+    template<typename FuncT>
    void runForEachNeighbour(FuncT fun, SPHState *state = 0);
-    void addGridSite(const typename SPHTree::coords &c, SPHState *state);
+    void addGridSite(const typename SPHTree::coords& c);
    void addGridSite(const typename SPHTree::coords &c);
    bool hasNeighbours() const;
-    virtual ComputePrecision getKernel(ComputePrecision d) const;
+    virtual ComputePrecision getKernel(ComputePrecision d) const;    
    SPHTree *getTree() { return tree; }
@ -134,29 +125,29 @@ namespace CosmoTool {
    uint32_t getCurrent() const { return internal.currentNgb; }
    uint32_t getNgb() const { return maxNgb; }
-
+ 
  protected:
    SPHState internal;
    uint32_t Nsph;
    uint32_t deltaNsph;
    uint32_t maxNgb;
    SPHTree *tree;
-
+    
-    template <typename FuncT>
+    template<typename FuncT>
-    ComputePrecision computeWValue(
+    ComputePrecision computeWValue(const typename SPHTree::coords & c,
-        const typename SPHTree::coords &c, SPHCell &cell, CoordType d,
+				   SPHCell& cell,
-        FuncT fun, SPHState *state);
+				   CoordType d,
-
+				   FuncT fun, SPHState *state);
-    template <typename FuncT>
+    
-    void runUnrollNode(SPHNode *node, FuncT fun);
+    template<typename FuncT>
    void runUnrollNode(SPHNode *node,
 		       FuncT fun);
  };
-  template <class ValType1, class ValType2, int Ndims>
+  template<class ValType1, class ValType2, int Ndims>
-  bool operator<(
+  bool operator<(const SPHSmooth<ValType1, Ndims>& s1, const SPHSmooth<ValType2, Ndims>& s2);
      const SPHSmooth<ValType1, Ndims> &s1,
      const SPHSmooth<ValType2, Ndims> &s2);
-}; // namespace CosmoTool
+};
 #include "sphSmooth.tcc"
--- a/src/sphSmooth.tcc
+++ b/src/sphSmooth.tcc
@ -3,248 +3,227 @@
 namespace CosmoTool {
-  template <typename ValType, int Ndims>
+template<typename ValType, int Ndims>
-  SPHSmooth<ValType, Ndims>::SPHSmooth(SPHTree *tree, uint32_t Nsph) {
+SPHSmooth<ValType,Ndims>::SPHSmooth(SPHTree *tree, uint32_t Nsph)
-    this->Nsph = Nsph;
+{
-    this->tree = tree;
+  this->Nsph = Nsph;
-    internal.currentNgb = 0;
+  this->tree = tree;
  internal.currentNgb = 0;
-    this->maxNgb = Nsph;
+  this->maxNgb = Nsph;
-    internal.ngb = boost::shared_ptr<SPHCell *[]>(new SPHCell *[maxNgb]);
+  internal.ngb = boost::shared_ptr<SPHCell *[]>(new SPHCell *[maxNgb]);  
-    internal.distances = boost::shared_ptr<CoordType[]>(new CoordType[maxNgb]);
+  internal.distances = boost::shared_ptr<CoordType[]>(new CoordType[maxNgb]);
-  }
+}
-  template <typename ValType, int Ndims>
+template<typename ValType, int Ndims>
-  SPHSmooth<ValType, Ndims>::~SPHSmooth() {}
+SPHSmooth<ValType,Ndims>::~SPHSmooth()
 {
 }
-  template <typename ValType, int Ndims>
+template<typename ValType, int Ndims>
-  template <typename FuncT>
+template<typename FuncT>
-  ComputePrecision SPHSmooth<ValType, Ndims>::computeWValue(
+ComputePrecision SPHSmooth<ValType,Ndims>::computeWValue(const typename SPHTree::coords& c,
-      const typename SPHTree::coords &c, SPHCell &cell, CoordType d, FuncT fun,
+							 SPHCell& cell,
-      SPHState *state) {
+							 CoordType d,
-    CoordType weight;
+							 FuncT fun, SPHState *state)
 {
  CoordType weight;
-    d /= state->smoothRadius;
+  d /= state->smoothRadius;
-    weight = getKernel(d);
+  weight = getKernel(d);
-    if (cell.val.weight != 0)
+  if (cell.val.weight != 0)
-      return weight * fun(cell.val.pValue) / cell.val.weight;
+    return weight * fun(cell.val.pValue) / cell.val.weight;
-    else
+  else
-      return 0;
+    return 0;
-  }
+}
-  template <typename ValType, int Ndims>
+template<typename ValType, int Ndims>
-  void SPHSmooth<ValType, Ndims>::fetchNeighbours(
+void
-      const typename SPHTree::coords &c, uint32_t newNngb, SPHState *state) {
+SPHSmooth<ValType,Ndims>::fetchNeighbours(const typename SPHTree::coords& c, uint32_t newNngb)
-    ComputePrecision d2, max_dist = 0;
+{
-    uint32_t requested = newNngb;
+  ComputePrecision d2, max_dist = 0;
  uint32_t requested = newNngb;
-    if (state != 0) {
+  if (requested > maxNgb)
-      state->distances = boost::shared_ptr<CoordType[]>(new CoordType[newNngb]);
+    {
-      state->ngb = boost::shared_ptr<SPHCell *[]>(new SPHCell *[newNngb]);
+      maxNgb = requested;
-    } else {
+      internal.ngb = boost::shared_ptr<P_SPHCell[]>(new P_SPHCell[maxNgb]);
-      state = &internal;
+      internal.distances = boost::shared_ptr<CoordType[]>(new CoordType[maxNgb]);
      if (requested > maxNgb) {
        maxNgb = requested;
        internal.ngb = boost::shared_ptr<P_SPHCell[]>(new P_SPHCell[maxNgb]);
        internal.distances =
            boost::shared_ptr<CoordType[]>(new CoordType[maxNgb]);
      }
    }
-    memcpy(state->currentCenter, c, sizeof(c));
+  memcpy(internal.currentCenter, c, sizeof(c));
-    tree->getNearestNeighbours(
+  tree->getNearestNeighbours(c, requested, (SPHCell **)internal.ngb.get(), (CoordType*)internal.distances.get());
        c, requested, (SPHCell **)state->ngb.get(),
        (CoordType *)state->distances.get());
-    state->currentNgb = 0;
+  internal.currentNgb = 0;
-    for (uint32_t i = 0; i < requested && (state->ngb)[i] != 0;
+  for (uint32_t i = 0; i < requested && (internal.ngb)[i] != 0; i++,internal.currentNgb++)
-         i++, state->currentNgb++) {
+    {
-      state->distances[i] = sqrt(state->distances[i]);
+      internal.distances[i] = sqrt(internal.distances[i]);
-      d2 = state->distances[i];
+      d2 = internal.distances[i];
      if (d2 > max_dist)
        max_dist = d2;
    }
-    state->smoothRadius = max_dist / 2;
+  internal.smoothRadius = max_dist / 2;  
-  }
+}
-  template <typename ValType, int Ndims>
+template<typename ValType, int Ndims>
-  void SPHSmooth<ValType, Ndims>::fetchNeighbours(
+void SPHSmooth<ValType,Ndims>::fetchNeighbours(const typename SPHTree::coords& c, SPHState *state)
-      const typename SPHTree::coords &c, SPHState *state) {
+{
-    ComputePrecision d2, max_dist = 0;
+  ComputePrecision d2, max_dist = 0;
-    uint32_t requested = Nsph;
+  uint32_t requested = Nsph;
-    if (state != 0) {
+  if (state != 0) {
-      state->distances = boost::shared_ptr<CoordType[]>(new CoordType[Nsph]);
+    state->distances = boost::shared_ptr<CoordType[]>(new CoordType[Nsph]);
-      state->ngb = boost::shared_ptr<SPHCell *[]>(new SPHCell *[Nsph]);
+    state->ngb = boost::shared_ptr<SPHCell *[]>(new SPHCell *[Nsph]);
-    } else
+  } else
-      state = &internal;
+    state = &internal;
  memcpy(state->currentCenter, c, sizeof(c));
  tree->getNearestNeighbours(c, requested, state->ngb.get(), state->distances.get());
-    memcpy(state->currentCenter, c, sizeof(c));
+  state->currentNgb = 0;
-
+  for (uint32_t i = 0; i < requested && state->ngb[i] != 0; i++,state->currentNgb++)
-    tree->getNearestNeighbours(
+    {
        c, requested, state->ngb.get(), state->distances.get());
    state->currentNgb = 0;
    for (uint32_t i = 0; i < requested && state->ngb[i] != 0;
         i++, state->currentNgb++) {
      d2 = state->distances[i] = sqrt(state->distances[i]);
      if (d2 > max_dist)
        max_dist = d2;
    }
    state->smoothRadius = max_dist / 2;
  }
  template <typename ValType, int Ndims>
  void SPHSmooth<ValType, Ndims>::fetchNeighboursOnVolume(
      const typename SPHTree::coords &c, ComputePrecision radius) {
    uint32_t numPart;
    ComputePrecision d2, max_dist = 0;
    memcpy(internal.currentCenter, c, sizeof(c));
    internal.currentNgb = tree->getIntersection(
        c, radius, internal.ngb, internal.distances, maxNgb);
    for (uint32_t i = 0; i < internal.currentNgb; i++) {
      d2 = internal.distances[i] = sqrt(internal.distances[i]);
      if (d2 > max_dist)
        max_dist = d2;
    }
    internal.smoothRadius = max_dist / 2;
  }
-  template <typename ValType, int Ndims>
+  state->smoothRadius = max_dist / 2;  
-  template <typename FuncT>
+}
  ComputePrecision SPHSmooth<ValType, Ndims>::computeSmoothedValue(
      const typename SPHTree::coords &c, FuncT fun, SPHState *state) {
    if (state == 0)
      state = &internal;
    ComputePrecision outputValue = 0;
    ComputePrecision max_dist = 0;
    ComputePrecision r3 = cube(state->smoothRadius);
-    for (uint32_t i = 0; i < state->currentNgb; i++) {
+template<typename ValType, int Ndims>
-      outputValue +=
+void
-          computeWValue(c, *state->ngb[i], state->distances[i], fun, state);
+SPHSmooth<ValType,Ndims>::fetchNeighboursOnVolume(const typename SPHTree::coords& c,
                                                  ComputePrecision radius)
 {
  uint32_t numPart;
  ComputePrecision d2, max_dist = 0;
  memcpy(internal.currentCenter, c, sizeof(c));
  internal.currentNgb = tree->getIntersection(c, radius, internal.ngb, internal.distances,
 				  maxNgb);
  for (uint32_t i = 0; i < internal.currentNgb; i++)
    {
      d2 = internal.distances[i] = sqrt(internal.distances[i]);
      if (d2 > max_dist)
        max_dist = d2;
    }
  internal.smoothRadius = max_dist / 2;  
 }				
 template<typename ValType, int Ndims>
 template<typename FuncT>
 ComputePrecision 
 SPHSmooth<ValType,Ndims>::computeSmoothedValue(const typename SPHTree::coords& c,
                                               FuncT fun, SPHState *state)
 {
  if (state == 0)
    state = &internal;
  ComputePrecision outputValue = 0;
  ComputePrecision max_dist = 0;
  ComputePrecision r3 = cube(state->smoothRadius);
  for (uint32_t i = 0; i < state->currentNgb; i++)
    {
      outputValue += computeWValue(c, *state->ngb[i], state->distances[i], fun, state);
    }
-    return outputValue / r3;
+  return outputValue / r3;
-  }
+}
-  template <typename ValType>
+template<typename ValType>
-  ComputePrecision interpolateOne(const ValType &t) {
+ComputePrecision interpolateOne(const ValType& t)
-    return 1.0;
+{
-  }
+  return 1.0;
 }
-  template <typename ValType, int Ndims>
+// WARNING ! Cell's weight must be 1 !!!
-  template <typename FuncT>
+template<typename ValType, int Ndims>
-  void SPHSmooth<ValType, Ndims>::computeAdjointGradientSmoothedValue(
+template<typename FuncT>
-      const typename SPHTree::coords &c, ComputePrecision ag_value, FuncT fun,
+ComputePrecision SPHSmooth<ValType,Ndims>::computeInterpolatedValue(const typename SPHTree::coords& c,
-      SPHState *state) {
+								    FuncT fun, SPHState *state)
-    if (state == 0)
+{
-      state = &internal;
+  if (state == 0)
    state = &internal;
  ComputePrecision outputValue = 0;
  ComputePrecision max_dist = 0;
  ComputePrecision weight = 0;
-    ComputePrecision outputValue = 0;
+  for (uint32_t i = 0; i < state->currentNgb; i++)
-    ComputePrecision max_dist = 0;
+    {
    ComputePrecision weight = 0;
    for (uint32_t i = 0; i < state->currentNgb; i++) {
      weight +=
          computeWValue(c, *state->ngb[i], state->distances[i], interpolateOne);
    }
    for (uint32_t i = 0; i < state->currentNgb; i++) {
      auto &cell = *state->ngb[i];
      double partial_ag =
          computeWValue(
              c, cell, state->distances[i],
              [ag_value](ComputePrecision) { return ag_value; }) /
          weight;
      fun(cell.val.pValue, ag_value);
    }
  }
  // WARNING ! Cell's weight must be 1 !!!
  template <typename ValType, int Ndims>
  template <typename FuncT>
  ComputePrecision SPHSmooth<ValType, Ndims>::computeInterpolatedValue(
      const typename SPHTree::coords &c, FuncT fun, SPHState *state) {
    if (state == 0)
      state = &internal;
    ComputePrecision outputValue = 0;
    ComputePrecision max_dist = 0;
    ComputePrecision weight = 0;
    for (uint32_t i = 0; i < state->currentNgb; i++) {
      outputValue += computeWValue(c, *state->ngb[i], state->distances[i], fun);
-      weight +=
+      weight += computeWValue(c, *state->ngb[i], state->distances[i], interpolateOne);
          computeWValue(c, *state->ngb[i], state->distances[i], interpolateOne);
    }
-    return (outputValue == 0) ? 0 : (outputValue / weight);
+  return (outputValue == 0) ? 0 : (outputValue / weight);  
-  }
+}
-  template <typename ValType, int Ndims>
+template<typename ValType, int Ndims>
-  template <typename FuncT>
+template<typename FuncT>
-  void
+void SPHSmooth<ValType,Ndims>::runForEachNeighbour(FuncT fun, SPHState *state)
-  SPHSmooth<ValType, Ndims>::runForEachNeighbour(FuncT fun, SPHState *state) {
+{
-    if (state == 0)
+  if (state == 0)
-      state = &internal;
+    state = &internal;
-
+    
-    for (uint32_t i = 0; i < state->currentNgb; i++) {
+  for (uint32_t i = 0; i < state->currentNgb; i++)
    {
      fun(state->ngb[i]);
    }
-  }
+}
  template <typename ValType, int Ndims>
  void SPHSmooth<ValType, Ndims>::addGridSite(
      const typename SPHTree::coords &c, SPHState *state) {
    ComputePrecision outputValue = 0;
    ComputePrecision max_dist = 0;
    ComputePrecision r3 = cube(state->smoothRadius);
-    for (uint32_t i = 0; i < state->currentNgb; i++) {
+template<typename ValType, int Ndims>
-      ComputePrecision d = state->distances[i];
+void SPHSmooth<ValType,Ndims>::addGridSite(const typename SPHTree::coords& c)
-      SPHCell &cell = *(state->ngb[i]);
+{
-      double kernel_value = getKernel(d / state->smoothRadius) / r3;
+  ComputePrecision outputValue = 0;
-#pragma omp atomic update
+  ComputePrecision max_dist = 0;
  ComputePrecision r3 = cube(internal.smoothRadius);
  for (uint32_t i = 0; i < internal.currentNgb; i++)
    {
      ComputePrecision d = internal.distances[i];
      SPHCell& cell = *(internal.ngb[i]);
      double kernel_value = getKernel(d/internal.smoothRadius) / r3;
 #pragma omp atomic
      cell.val.weight += kernel_value;
    }
-  }
+}
-  template <typename ValType, int Ndims>
+template<typename ValType, int Ndims>
-  void
+ComputePrecision 
-  SPHSmooth<ValType, Ndims>::addGridSite(const typename SPHTree::coords &c) {
+SPHSmooth<ValType,Ndims>::getKernel(ComputePrecision x) const
-    addGridSite(c, &internal);
+{
-  }
+  // WARNING !!! This is an unnormalized version of the kernel.
-
+  if (x < 1)
-  template <typename ValType, int Ndims>
+    return 1 - 1.5 * x * x + 0.75 * x * x * x;
-  ComputePrecision
+  else if (x < 2)
-  SPHSmooth<ValType, Ndims>::getKernel(ComputePrecision x) const {
+    {
    // WARNING !!! This is an unnormalized version of the kernel.
    if (x < 1)
      return 1 - 1.5 * x * x + 0.75 * x * x * x;
    else if (x < 2) {
      ComputePrecision d = 2 - x;
      return 0.25 * d * d * d;
-    } else
+    }
-      return 0;
+  else
-  }
+    return 0;
 }
-  template <typename ValType, int Ndims>
+template<typename ValType, int Ndims>
-  bool SPHSmooth<ValType, Ndims>::hasNeighbours() const {
+bool SPHSmooth<ValType,Ndims>::hasNeighbours() const
-    return (internal.currentNgb != 0);
+{
-  }
+  return (internal.currentNgb != 0);
 }
-  template <class ValType1, class ValType2, int Ndims>
+template<class ValType1, class ValType2, int Ndims>
-  bool operator<(
+bool operator<(const SPHSmooth<ValType1, Ndims>& s1, const SPHSmooth<ValType2, Ndims>& s2)
-      const SPHSmooth<ValType1, Ndims> &s1,
+{
-      const SPHSmooth<ValType2, Ndims> &s2) {
+  return (s1.getSmoothingLen() < s2.getSmoothingLen());
-    return (s1.getSmoothingLen() < s2.getSmoothingLen());
+}
-  }
+
-}; // namespace CosmoTool
+};
Author	SHA1	Message	Date
Eleni Tsaprazi	394472948a	added variable declarations	2023-11-03 11:05:52 +00:00
Eleni	1e4ced7c4d	added BAO wiggle params in cosmo	2022-12-09 21:53:03 +01:00
Eleni	e3ce2fbc41	minimally invasive approach	2022-12-09 16:17:48 +01:00
Eleni	a35e997ec8	moved param to transfer func	2022-12-02 12:36:41 +01:00
Eleni	17698dab5b	wiggle parameterization	2022-12-01 18:52:18 +01:00
Eleni	cd926a0834	added BAO wiggles	2022-12-01 17:03:02 +01:00