Merged

CMakeLists.txt

@@ -7,6 +7,11 @@ include(GetGitRevisionDescription)
 include(ExternalProject)
 include(FindOpenMP)
 
+include(FindPythonLibs)
+set(NumPy_FIND_REQUIRED TRUE)
+include(${CMAKE_SOURCE_DIR}/FindNumPy.cmake)
+
+
 get_git_head_revision(HEAD GIT_VER)
 
 option(BUILD_SHARED_LIBS "Build shared libraries." OFF)
@@ -14,6 +19,12 @@ option(BUILD_STATIC_LIBS "Build static libraries." ON)
 option(ENABLE_OPENMP "Enable OpenMP support." OFF)
 option(ENABLE_SHARP "Enable SPHT support." ON)
 
+IF(BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
+  SET(CosmoTool_local CosmoTool_static)
+ELSE(BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
+  SET(CosmoTool_local CosmoTool)
+ENDIF(BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
+
 find_path(NETCDF_INCLUDE_PATH NAMES netcdf.h)
 find_path(NETCDFCPP_INCLUDE_PATH NAMES netcdfcpp.h netcdf)
 find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
@@ -31,6 +42,8 @@ find_library(NETCDF_LIBRARY netcdf)
 find_library(GSL_LIBRARY gsl)
 find_library(GSLCBLAS_LIBRARY gslcblas)
 
+find_program(CYTHON cython)
+
 find_package(Boost 1.53)
 
 if (ENABLE_SHARP)
@@ -50,6 +63,14 @@ if (ENABLE_SHARP)
   SET(SHARP_INCLUDE_PATH ${DEP_BUILD}/include)
 endif (ENABLE_SHARP)
 
+SET(OMPTL_BUILD_DIR ${CMAKE_BINARY_DIR}/omptl-prefix/src/omptl)
+ExternalProject_Add(omptl
+  URL ${CMAKE_SOURCE_DIR}/external/omptl-20120422.tar.bz2
+  CONFIGURE_COMMAND echo "No configure"
+  BUILD_COMMAND echo "No build"
+  INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${OMPTL_BUILD_DIR} ${CMAKE_BINARY_DIR}/external/stage/include/omptl
+)
+include_directories(${OMPTL_BUILD_DIR}/..)
 
 set(HDF5_FIND_COMPONENTS HL CXX)
 if(HDF5_ROOTDIR)
@@ -102,5 +123,6 @@ SET(CPACK_SOURCE_IGNORE_FILES
 
 add_subdirectory(src)
 add_subdirectory(sample)
+add_subdirectory(python)
 
 include(CPack)

FindNumPy.cmake

@@ -0,0 +1,102 @@
+# - Find the NumPy libraries
+# This module finds if NumPy is installed, and sets the following variables
+# indicating where it is.
+#
+# TODO: Update to provide the libraries and paths for linking npymath lib.
+#
+#  NUMPY_FOUND               - was NumPy found
+#  NUMPY_VERSION             - the version of NumPy found as a string
+#  NUMPY_VERSION_MAJOR       - the major version number of NumPy
+#  NUMPY_VERSION_MINOR       - the minor version number of NumPy
+#  NUMPY_VERSION_PATCH       - the patch version number of NumPy
+#  NUMPY_VERSION_DECIMAL     - e.g. version 1.6.1 is 10601
+#  NUMPY_INCLUDE_DIRS        - path to the NumPy include files
+
+#============================================================================
+# Copyright 2012 Continuum Analytics, Inc.
+#
+# MIT License
+#
+# Permission is hereby granted, free of charge, to any person obtaining
+# a copy of this software and associated documentation files
+# (the "Software"), to deal in the Software without restriction, including
+# without limitation the rights to use, copy, modify, merge, publish,
+# distribute, sublicense, and/or sell copies of the Software, and to permit
+# persons to whom the Software is furnished to do so, subject to
+# the following conditions:
+#
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+# OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+# OTHER DEALINGS IN THE SOFTWARE.
+#
+#============================================================================
+
+# Finding NumPy involves calling the Python interpreter
+if(NumPy_FIND_REQUIRED)
+    find_package(PythonInterp REQUIRED)
+else()
+    find_package(PythonInterp)
+endif()
+
+if(NOT PYTHONINTERP_FOUND)
+    set(NUMPY_FOUND FALSE)
+    return()
+endif()
+
+execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
+    "import numpy as n; print(n.__version__); print(n.get_include());"
+    RESULT_VARIABLE _NUMPY_SEARCH_SUCCESS
+    OUTPUT_VARIABLE _NUMPY_VALUES_OUTPUT
+    ERROR_VARIABLE _NUMPY_ERROR_VALUE
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+if(NOT _NUMPY_SEARCH_SUCCESS MATCHES 0)
+    if(NumPy_FIND_REQUIRED)
+        message(FATAL_ERROR
+            "NumPy import failure:\n${_NUMPY_ERROR_VALUE}")
+    endif()
+    set(NUMPY_FOUND FALSE)
+    return()
+endif()
+
+# Convert the process output into a list
+string(REGEX REPLACE ";" "\\\\;" _NUMPY_VALUES ${_NUMPY_VALUES_OUTPUT})
+string(REGEX REPLACE "\n" ";" _NUMPY_VALUES ${_NUMPY_VALUES})
+# Just in case there is unexpected output from the Python command.
+list(GET _NUMPY_VALUES -2 NUMPY_VERSION)
+list(GET _NUMPY_VALUES -1 NUMPY_INCLUDE_DIRS)
+
+string(REGEX MATCH "^[0-9]+\\.[0-9]+\\.[0-9]+" _VER_CHECK "${NUMPY_VERSION}")
+if("${_VER_CHECK}" STREQUAL "")
+    # The output from Python was unexpected. Raise an error always
+    # here, because we found NumPy, but it appears to be corrupted somehow.
+    message(FATAL_ERROR
+        "Requested version and include path from NumPy, got instead:\n${_NUMPY_VALUES_OUTPUT}\n")
+    return()
+endif()
+
+# Make sure all directory separators are '/'
+string(REGEX REPLACE "\\\\" "/" NUMPY_INCLUDE_DIRS ${NUMPY_INCLUDE_DIRS})
+
+# Get the major and minor version numbers
+string(REGEX REPLACE "\\." ";" _NUMPY_VERSION_LIST ${NUMPY_VERSION})
+list(GET _NUMPY_VERSION_LIST 0 NUMPY_VERSION_MAJOR)
+list(GET _NUMPY_VERSION_LIST 1 NUMPY_VERSION_MINOR)
+list(GET _NUMPY_VERSION_LIST 2 NUMPY_VERSION_PATCH)
+string(REGEX MATCH "[0-9]*" NUMPY_VERSION_PATCH ${NUMPY_VERSION_PATCH})
+math(EXPR NUMPY_VERSION_DECIMAL
+    "(${NUMPY_VERSION_MAJOR} * 10000) + (${NUMPY_VERSION_MINOR} * 100) + ${NUMPY_VERSION_PATCH}")
+
+find_package_message(NUMPY
+    "Found NumPy: version \"${NUMPY_VERSION}\" ${NUMPY_INCLUDE_DIRS}"
+    "${NUMPY_INCLUDE_DIRS}${NUMPY_VERSION}")
+
+set(NUMPY_FOUND TRUE)
+

build_tools/gather_sources.py

@@ -1,5 +1,5 @@
 #+
-# This is CosmoTool (./build_tools/gather_sources.py) -- Copyright (C) Guilhem Lavaux (2007-2013)
+# This is CosmoTool (./build_tools/gather_sources.py) -- Copyright (C) Guilhem Lavaux (2007-2014)
 #
 # guilhem.lavaux@gmail.com
 #
@@ -55,7 +55,7 @@ def apply_license(license, relimit, filename):
 
 def apply_python_license(filename):
   license="""#+
-# This is CosmoTool (@FILENAME@) -- Copyright (C) Guilhem Lavaux (2007-2013)
+# This is CosmoTool (@FILENAME@) -- Copyright (C) Guilhem Lavaux (2007-2014)
 #
 # guilhem.lavaux@gmail.com
 #
@@ -97,7 +97,7 @@ def apply_python_license(filename):
 
 def apply_cpp_license(filename):
   license="""/*+
-This is CosmoTool (@FILENAME@) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (@FILENAME@) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 
@@ -131,13 +131,14 @@ The fact that you are presently reading this means that you have had
 knowledge of the CeCILL license and that you accept its terms.
 +*/
 """
-  relimit = r'^(?s)/\*\+.*\+\*/'
+  relimit = r'^(?s)/\*\+.*\+\*/\n'
   print("C++ file: %s" % filename)
   apply_license(license, relimit, filename)
   
 
 def analyze_tree(prefix, t):
-  for ename,entry in t.items():
+  for entry in t:
+    ename = entry.name
     if ename == 'external' or ename == 'zobov':
       continue
     if type(entry) == Tree:

python/CMakeLists.txt

@@ -0,0 +1,49 @@
+set(CMAKE_SHARED_MODULE_PREFIX)
+
+include_directories(${NUMPY_INCLUDE_DIRS} ${PYTHON_INCLUDE_PATH} ${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src)
+
+IF(CYTHON)
+add_custom_command(
+  OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp
+  COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmotool.pyx
+  DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmotool.pyx) 
+
+ENDIF(CYTHON)
+
+
+add_library(_cosmotool MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp)
+
+SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Bsymbolic-functions")
+
+target_link_libraries(_cosmotool ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
+
+# Discover where to put packages
+if (NOT PYTHON_SITE_PACKAGES)
+  execute_process (COMMAND ${PYTHON_EXECUTABLE} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()" OUTPUT_VARIABLE internal_PYTHON_SITE_PACKAGES OUTPUT_STRIP_TRAILING_WHITESPACE)
+  SET(SYSTEM_PYTHON_SITE_PACKAGES ${internal_PYTHON_SITE_PACKAGES} CACHE PATH "Path to the target system-wide site-package where to install python modules")
+
+  execute_process (COMMAND ${PYTHON_EXECUTABLE} -c "from site import USER_SITE; print USER_SITE" OUTPUT_VARIABLE internal_PYTHON_SITE_PACKAGES OUTPUT_STRIP_TRAILING_WHITESPACE)
+  SET(USER_PYTHON_SITE_PACKAGES ${internal_PYTHON_SITE_PACKAGES} CACHE PATH "Path to the target user site-package where to install python modules")
+
+  mark_as_advanced(USER_PYTHON_SITE_PACKAGES SYSTEM_PYTHON_SITE_PACKAGES)
+endif (NOT PYTHON_SITE_PACKAGES)
+
+OPTION(INSTALL_PYTHON_LOCAL OFF)
+
+IF (NOT INSTALL_PYTHON_LOCAL)
+  SET(PYTHON_SITE_PACKAGES ${SYSTEM_PYTHON_SITE_PACKAGES})
+ELSE (NOT INSTALL_PYTHON_LOCAL)
+  SET(PYTHON_SITE_PACKAGES ${USER_PYTHON_SITE_PACKAGES})
+ENDIF(NOT INSTALL_PYTHON_LOCAL)
+
+
+if (WIN32 AND NOT CYGWIN)
+  SET_TARGET_PROPERTIES(_cosmotool PROPERTIES SUFFIX ".pyd")
+endif (WIN32 AND NOT CYGWIN)
+
+INSTALL(TARGETS _cosmotool
+  LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/cosmotool
+)
+
+INSTALL(DIRECTORY cosmotool DESTINATION ${PYTHON_SITE_PACKAGES} 
+        FILES_MATCHING PATTERN "*.py")

python/_cosmotool.pyx

@@ -0,0 +1,190 @@
+from libcpp cimport bool
+import numpy as np
+cimport numpy as np
+from cpython cimport PyObject, Py_INCREF
+
+np.import_array()
+
+
+cdef extern from "loadSimu.hpp" namespace "CosmoTool":
+
+  cdef cppclass SimuData:
+    np.float_t BoxSize
+    np.float_t time
+    np.float_t Hubble
+
+    np.float_t Omega_M
+    np.float_t Omega_Lambda
+    np.int64_t TotalNumPart
+    np.int64_t NumPart
+    np.int64_t *Id
+    float *Pos[3]
+    float *Vel[3]
+    int *type
+
+  cdef const int NEED_GADGET_ID 
+  cdef const int NEED_POSITION
+  cdef const int NEED_VELOCITY
+  cdef const int NEED_TYPE
+
+cdef extern from "loadGadget.hpp" namespace "CosmoTool":
+
+  SimuData *loadGadgetMulti(const char *fname, int id, int flags) except +
+
+cdef extern from "loadRamses.hpp" namespace "CosmoTool":
+  SimuData *loadRamsesSimu(const char *basename, int id, int cpuid, bool dp, int flags) except +
+
+cdef class Simulation:
+
+  cdef list positions
+  cdef list velocities
+  cdef object identifiers
+
+  cdef SimuData *data
+
+  property BoxSize:
+    def __get__(Simulation self):
+        return self.data.BoxSize
+        
+  property time:
+    def __get__(Simulation self):
+        return self.data.time
+
+  property Hubble:
+    def __get__(Simulation self):
+        return self.data.Hubble
+
+  property Omega_M:
+    def __get__(Simulation self):
+        return self.data.Omega_M
+        
+  property positions:
+    def __get__(Simulation self):
+        return self.positions
+        
+  property velocities:
+    def __get__(Simulation self):
+        return self.velocities
+        
+  property numParticles:
+    def __get__(Simulation self):
+        return self.data.NumPart
+
+  def __cinit__(Simulation self):
+    self.data = <SimuData *>0
+  
+  def __dealloc__(Simulation self):
+    if self.data != <SimuData *>0:
+      print("Clearing simulation data")
+      del self.data
+
+
+cdef class ArrayWrapper:
+    cdef void* data_ptr
+    cdef int size
+    cdef int type_array
+    
+    cdef set_data(self, int size, int type_array, void* data_ptr):
+        """ Set the data of the array
+
+This cannot be done in the constructor as it must recieve C-level
+arguments.
+
+Parameters:
+-----------
+size: int
+Length of the array.
+data_ptr: void*
+Pointer to the data
+
+    """
+        self.data_ptr = data_ptr
+        self.size = size
+        self.type_array = type_array
+     
+    def __array__(self):
+        """ Here we use the __array__ method, that is called when numpy
+tries to get an array from the object."""
+        cdef np.npy_intp shape[1]
+        
+        shape[0] = <np.npy_intp> self.size
+        # Create a 1D array, of length 'size'
+        ndarray = np.PyArray_SimpleNewFromData(1, shape, self.type_array, self.data_ptr)
+        return ndarray
+     
+    def __dealloc__(self):
+        """ Frees the array. This is called by Python when all the
+references to the object are gone. """
+        pass
+ 
+cdef object wrap_array(void *p, np.uint64_t s, int typ):
+    cdef np.ndarray ndarray
+    cdef ArrayWrapper wrapper
+
+    wrapper = ArrayWrapper()
+    wrapper.set_data(s, typ, p)
+    ndarray = np.array(wrapper, copy=False)
+    ndarray.base = <PyObject*> wrapper
+    Py_INCREF(wrapper)
+    
+    return ndarray
+
+
+cdef object wrap_float_array(float *p, np.uint64_t s):
+    return wrap_array(<void *>p, s, np.NPY_FLOAT)
+
+cdef object wrap_int64_array(np.int64_t* p, np.uint64_t s):
+    return wrap_array(<void *>p, s, np.NPY_INT64)
+
+cdef object wrap_simudata(SimuData *data, int flags):
+  cdef Simulation simu
+
+  simu = Simulation()
+  simu.data = data
+  if flags & NEED_POSITION:
+     simu.positions = [wrap_float_array(data.Pos[i], data.NumPart) for i in xrange(3)]
+  if flags & NEED_VELOCITY:
+     simu.velocities = [wrap_float_array(data.Vel[i], data.NumPart) for i in xrange(3)]
+  if flags & NEED_GADGET_ID:
+     simu.identifiers = wrap_int64_array(data.Id, data.NumPart)
+  return simu
+
+def loadGadget(str filename, int snapshot_id, bool loadPosition = True, bool loadVelocity = False, bool loadId = False):
+
+  cdef int flags
+  cdef SimuData *data
+  cdef Simulation simu
+
+  flags = 0
+  if loadPosition:
+     flags |= NEED_POSITION
+  if loadVelocity:
+     flags |= NEED_VELOCITY
+  if loadId:
+     flags |= NEED_GADGET_ID
+
+  data = loadGadgetMulti(filename, snapshot_id, flags)
+  if data == <SimuData*>0:
+    return None
+
+  return wrap_simudata(data, flags)
+
+def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = False, bool loadPosition = True, bool loadVelocity = False):
+  """ loadRamses(basepath, snapshot_id, cpu_id, doublePrecision=False, loadPosition=True, loadVelocity=False)
+  Loads the indicated snapshot based on the cpu id, snapshot id and basepath. It is important to specify the correct precision in doublePrecision.
+"""
+  cdef int flags
+  cdef SimuData *data
+  cdef Simulation simu
+
+  flags = 0
+  if loadPosition:
+     flags |= NEED_POSITION
+  if loadVelocity:
+     flags |= NEED_VELOCITY
+
+  data = loadRamsesSimu(basepath, snapshot_id, cpu_id, doublePrecision, flags)
+  if data == <SimuData*>0:
+    return None
+
+  return wrap_simudata(data, flags)

python/cosmotool/__init__.py

@@ -0,0 +1 @@
+from _cosmotool import *

sample/CMakeLists.txt

@@ -1,4 +1,4 @@
-SET(tolink ${GSL_LIBRARIES} CosmoTool ${CosmoTool_LIBS})
+SET(tolink ${GSL_LIBRARIES} ${CosmoTool_local} ${CosmoTool_LIBS})
 include_directories(${CMAKE_SOURCE_DIR}/src)
 include_directories(${FFTW3_INCLUDE_DIRS}
 ${EIGEN3_INCLUDE_DIRS} ${NETCDF_INCLUDE_PATH} ${GSL_INCLUDE_PATH})
@@ -33,7 +33,7 @@ add_executable(testPool testPool.cpp)
 target_link_libraries(testPool ${tolink})
 
 if (HDF5_FOUND)
-	  add_executable(testReadFlash testReadFlash.cpp)
+    add_executable(testReadFlash testReadFlash.cpp)
     target_link_libraries(testReadFlash ${tolink})
     
     add_executable(testHDF5 testHDF5.cpp)

sample/gadgetToArray.cpp

@@ -1,3 +1,37 @@
+/*+
+This is CosmoTool (./sample/gadgetToArray.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
+
+guilhem.lavaux@gmail.com
+
+This software is a computer program whose purpose is to provide a toolbox for cosmological
+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, 
+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". 
+
+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. 
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+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 
+data to be ensured and,  more generally, to use and operate it in the 
+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.
++*/
 #include <cmath>
 #include <iostream>
 #include <cstdlib>

sample/gadgetToDensity.cpp

@@ -1,3 +1,37 @@
+/*+
+This is CosmoTool (./sample/gadgetToDensity.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
+
+guilhem.lavaux@gmail.com
+
+This software is a computer program whose purpose is to provide a toolbox for cosmological
+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, 
+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". 
+
+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. 
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+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 
+data to be ensured and,  more generally, to use and operate it in the 
+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.
++*/
 #include <cmath>
 #include <iostream>
 #include <cstdlib>

sample/testAlgo.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testAlgo.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testAlgo.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testBQueue.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testBQueue.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testBQueue.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testBSP.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testBSP.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testBSP.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testDelaunay.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testDelaunay.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testDelaunay.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testEskow.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testEskow.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testEskow.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testHDF5.cpp

@@ -1,3 +1,37 @@
+/*+
+This is CosmoTool (./sample/testHDF5.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
+
+guilhem.lavaux@gmail.com
+
+This software is a computer program whose purpose is to provide a toolbox for cosmological
+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, 
+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". 
+
+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. 
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+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 
+data to be ensured and,  more generally, to use and operate it in the 
+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.
++*/
 #include <iostream>
 #include <H5Cpp.h>
 #include "hdf5_array.hpp"

sample/testInterpolate.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testInterpolate.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testInterpolate.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testNewton.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testNewton.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testNewton.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testPool.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testPool.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testPool.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testReadFlash.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testReadFlash.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testReadFlash.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testSmooth.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testSmooth.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testSmooth.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/test_cosmopower.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/test_cosmopower.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/test_cosmopower.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/test_fft_calls.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/test_fft_calls.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/test_fft_calls.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/test_healpix_calls.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/test_healpix_calls.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/test_healpix_calls.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testkd.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testkd.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testkd.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testkd2.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testkd2.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testkd2.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

sample/testkd3.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./sample/testkd3.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./sample/testkd3.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/CMakeLists.txt

@@ -1,3 +1,5 @@
+add_definitions(-fPIC)
+
 SET(CosmoTool_SRCS
 	fortran.cpp
 	interpolate.cpp
@@ -69,7 +71,6 @@ set(CosmoTool_LIBS ${CosmoTool_LIBS} PARENT_SCOPE)
 if (BUILD_SHARED_LIBS)
   add_library(CosmoTool SHARED ${CosmoTool_SRCS})
   target_link_libraries(CosmoTool ${CosmoTool_LIBS})
-
   if (BUILD_STATIC_LIBS)
      add_library(CosmoTool_static STATIC ${CosmoTool_SRCS})
   endif(BUILD_STATIC_LIBS)
@@ -89,5 +90,7 @@ endif (BUILD_SHARED_LIBS)
 
 install(DIRECTORY . DESTINATION include/CosmoTool
 	FILES_MATCHING PATTERN "*.hpp")
+install(DIRECTORY ${OMPTL_BUILD_DIR} 
+     DESTINATION include/CosmoTool/omptl)
 install(DIRECTORY . DESTINATION include/CosmoTool
 	FILES_MATCHING PATTERN "*.tcc")

src/algo.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/algo.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/algo.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/bqueue.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/bqueue.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/bqueue.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/bsp_simple.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/bsp_simple.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/bsp_simple.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/cic.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/cic.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/cic.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/cic.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/cic.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/cic.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 
@@ -36,7 +36,7 @@ knowledge of the CeCILL license and that you accept its terms.
 #ifndef __CICFILTER_HPP
 #define __CICFILTER_HPP
 
-#include "CosmoTool/config.hpp"
+#include "config.hpp"
 #include <inttypes.h>
 
 using namespace CosmoTool;

src/config.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/config.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/config.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 
@@ -39,6 +39,7 @@ knowledge of the CeCILL license and that you accept its terms.
 #include <string>
 #include <stdint.h>
 #include <exception>
+#include <stdexcept>
 #include <cstring>
 
 namespace CosmoTool
@@ -83,13 +84,13 @@ namespace CosmoTool
    * Base exception class for all exceptions handled by
    * this library.
    */
-  class Exception : public std::exception
+  class Exception : public std::runtime_error
   {
   public:
     Exception(const std::string& mess)
-      : msg(mess), msgok(true) {}
+      : std::runtime_error(mess), msg(mess), msgok(true) {}
     Exception()
-      : msgok(false) {}
+      : std::runtime_error("No message"), msgok(false) {}
 
     virtual ~Exception() throw () {}
 

src/cosmopower.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/cosmopower.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/cosmopower.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/cosmopower.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/cosmopower.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/cosmopower.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/dinterpolate.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/dinterpolate.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/dinterpolate.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/eskow.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/eskow.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/eskow.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/field.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/field.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/field.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fixArray.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fixArray.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fixArray.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fortran.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fortran.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fortran.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fortran.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fortran.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fortran.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/base_types.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/base_types.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/base_types.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/details/euclidian_maps.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/details/euclidian_maps.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/details/euclidian_maps.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/details/euclidian_spectrum_1d.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/details/euclidian_spectrum_1d.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/details/euclidian_spectrum_1d.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/details/euclidian_spectrum_1d_bin.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/details/euclidian_spectrum_1d_bin.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/details/euclidian_spectrum_1d_bin.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/details/euclidian_transform.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/details/euclidian_transform.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/details/euclidian_transform.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 
@@ -83,30 +83,30 @@ namespace CosmoTool
       Nc = 1;
       volume = 1;
       for (int i = 0; i < dims.size(); i++)
-	{
+        {
-	  N *= dims[i];
+          N *= dims[i];
           Nc *= m_dims_hc[i];
-	  volume *= L[i];
+          volume *= L[i];
-	  dk[i] = 2*M_PI/L[i];
+          dk[i] = 2*M_PI/L[i];
           swapped_dims[dims.size()-1-i] = dims[i];
-	}
+        }
 
       realMap = new EuclidianFourierMapReal<T>(
-		   boost::shared_ptr<T>(calls::alloc_real(N),
+                boost::shared_ptr<T>(calls::alloc_real(N),
-					std::ptr_fun(calls::free)),
+                                    std::ptr_fun(calls::free)),
-		   m_dims);
+                                    m_dims);
       fourierMap = new EuclidianFourierMapComplex<T>(
-		   boost::shared_ptr<std::complex<T> >((std::complex<T>*)calls::alloc_complex(Nc),
+                boost::shared_ptr<std::complex<T> >((std::complex<T>*)calls::alloc_complex(Nc),
-						       std::ptr_fun(calls::free)), 
+                                                    std::ptr_fun(calls::free)), 
-		   dims[0], m_dims_hc, dk);
+                dims[0], m_dims_hc, dk);
-     {
+      {
-      m_analysis = calls::plan_dft_r2c(dims.size(), &swapped_dims[0],
+        m_analysis = calls::plan_dft_r2c(dims.size(), &swapped_dims[0],
-				       realMap->data(), (typename calls::complex_type *)fourierMap->data(),
+                                        realMap->data(), (typename calls::complex_type *)fourierMap->data(),
-				       FFTW_DESTROY_INPUT|FFTW_MEASURE);
+                                        FFTW_DESTROY_INPUT|FFTW_MEASURE);
-      m_synthesis = calls::plan_dft_c2r(dims.size(), &swapped_dims[0],
+        m_synthesis = calls::plan_dft_c2r(dims.size(), &swapped_dims[0],
-					(typename calls::complex_type *)fourierMap->data(), realMap->data(),
+                                          (typename calls::complex_type *)fourierMap->data(), realMap->data(),
-					FFTW_DESTROY_INPUT|FFTW_MEASURE);
+                                          FFTW_DESTROY_INPUT|FFTW_MEASURE);
-     }
+      }
     }
     
     virtual ~EuclidianFourierTransform()

src/fourier/details/healpix_alms.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/details/healpix_alms.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/details/healpix_alms.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/details/healpix_map.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/details/healpix_map.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/details/healpix_map.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/details/healpix_spectrum.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/details/healpix_spectrum.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/details/healpix_spectrum.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/details/healpix_transform.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/details/healpix_transform.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/details/healpix_transform.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/details/healpix_utility.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/details/healpix_utility.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/details/healpix_utility.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/euclidian.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/euclidian.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/euclidian.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/fft/fftw_calls.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/fft/fftw_calls.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/fft/fftw_calls.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/fourier/healpix.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/fourier/healpix.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/fourier/healpix.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/growthFactor.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/growthFactor.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/growthFactor.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/growthFactor.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/growthFactor.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/growthFactor.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/h5_readFlash.cpp

@@ -1,11 +1,45 @@
 /*+
+This is CosmoTool (./src/h5_readFlash.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
+
+guilhem.lavaux@gmail.com
+
+This software is a computer program whose purpose is to provide a toolbox for cosmological
+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, 
+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". 
+
+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. 
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+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 
+data to be ensured and,  more generally, to use and operate it in the 
+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.
++*/
+/*+
 !!
 
 This file has been developped by P. M. Sutter
 
 !!
 
-+*/
+*/
 /* This file contains the functions that read the data from the HDF5 file
  * The functions accept the PARAMESH data through arguments.
  */

src/h5_readFlash.hpp

@@ -1,4 +1,38 @@
 /*+
+This is CosmoTool (./src/h5_readFlash.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
+
+guilhem.lavaux@gmail.com
+
+This software is a computer program whose purpose is to provide a toolbox for cosmological
+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, 
+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". 
+
+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. 
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+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 
+data to be ensured and,  more generally, to use and operate it in the 
+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.
++*/
+/*+
 
 !!! NOTE !!!
 
@@ -6,7 +40,7 @@ This file has been developped by P. M. Sutter.
 
 !!!!
 
-+*/
+*/
 /* This file contains the functions that read the data from the HDF5 file
  * The functions accept the PARAMESH data through arguments.
  */

src/hdf5_array.hpp

@@ -1,3 +1,37 @@
+/*+
+This is CosmoTool (./src/hdf5_array.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
+
+guilhem.lavaux@gmail.com
+
+This software is a computer program whose purpose is to provide a toolbox for cosmological
+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, 
+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". 
+
+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. 
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+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 
+data to be ensured and,  more generally, to use and operate it in the 
+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.
++*/
 #ifndef __COSMO_HDF5_ARRAY_HPP
 #define __COSMO_HDF5_ARRAY_HPP
 

src/hdf5_flash.h

@@ -1,9 +1,36 @@
 /*+
-!!
+This is CosmoTool (./src/hdf5_flash.h) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
-This particular file has been developped by P. M. Sutter
+guilhem.lavaux@gmail.com
 
-!!
+This software is a computer program whose purpose is to provide a toolbox for cosmological
+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, 
+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". 
+
+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. 
+
+In this respect, the user's attention is drawn to the risks associated
+with loading,  using,  modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+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 
+data to be ensured and,  more generally, to use and operate it in the 
+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.
 +*/
 /* general header file for the HDF 5 IO in FLASH */
 

src/interpolate.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/interpolate.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/interpolate.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/interpolate.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/interpolate.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/interpolate.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/interpolate3d.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/interpolate3d.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/interpolate3d.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/kdtree_leaf.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/kdtree_leaf.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/kdtree_leaf.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/kdtree_splitters.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/kdtree_splitters.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/kdtree_splitters.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/loadFlash.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/loadFlash.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/loadFlash.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/loadFlash.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/loadFlash.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/loadFlash.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/loadFlash_dummy.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/loadFlash_dummy.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/loadFlash_dummy.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/loadGadget.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/loadGadget.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/loadGadget.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 
@@ -96,7 +96,7 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
     if (f == 0)
       return 0;
 
-    delete out_fname;
+    delete[] out_fname;
 
   } else {
 

src/loadGadget.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/loadGadget.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/loadGadget.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/loadRamses.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/loadRamses.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/loadRamses.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/loadRamses.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/loadRamses.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/loadRamses.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/loadSimu.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/loadSimu.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/loadSimu.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/load_data.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/load_data.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/load_data.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/load_data.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/load_data.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/load_data.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/mach.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/mach.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/mach.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/miniargs.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/miniargs.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/miniargs.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/miniargs.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/miniargs.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/miniargs.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/mykdtree.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/mykdtree.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/mykdtree.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/mykdtree.tcc

@@ -1,5 +1,6 @@
 #include "replicateGenerator.hpp"
 #include <cstring>
+#include "omptl/omptl_algorithm"
 #include <algorithm>
 #include <limits>
 #include <iostream>

src/newton.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/newton.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/newton.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/octTree.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/octTree.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/octTree.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/octTree.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/octTree.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/octTree.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/pool.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/pool.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/pool.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/powerSpectrum.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/powerSpectrum.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/powerSpectrum.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/powerSpectrum.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/powerSpectrum.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/powerSpectrum.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/replicateGenerator.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/replicateGenerator.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/replicateGenerator.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/sparseGrid.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/sparseGrid.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/sparseGrid.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/sphSmooth.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/sphSmooth.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/sphSmooth.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/yorick.hpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/yorick.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/yorick.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/yorick_nc3.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/yorick_nc3.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/yorick_nc3.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com
 

src/yorick_nc4.cpp

@@ -1,5 +1,5 @@
 /*+
-This is CosmoTool (./src/yorick_nc4.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+This is CosmoTool (./src/yorick_nc4.cpp) -- Copyright (C) Guilhem Lavaux (2007-2014)
 
 guilhem.lavaux@gmail.com