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

build_tools/gather_sources.py

@@ -5,7 +5,7 @@
 #
 # 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
@@ -61,7 +61,7 @@ def apply_python_license(filename):
 #
 # 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
@@ -143,6 +143,9 @@ def analyze_tree(prefix, t):
     if type(entry) == Tree:
       analyze_tree(prefix + "/" + ename, entry)
     elif type(entry) == Blob:
+      if ename == './src/hdf5_flash.h' or ename == './src/h5_readFlash.cpp' or ename == './src/h5_readFlash.hpp':
+        continue
+
       if re.match(".*\.(sh|py|pyx)$",ename) != None:
         fname=prefix+"/"+ename
         apply_python_license(fname)

sample/CMakeLists.txt

@@ -20,6 +20,9 @@ target_link_libraries(testkd ${tolink})
 add_executable(testkd2 testkd2.cpp)
 target_link_libraries(testkd2 ${tolink})
 
+add_executable(testkd3 testkd3.cpp)
+target_link_libraries(testkd3 ${tolink})
+
 add_executable(testDelaunay testDelaunay.cpp)
 target_link_libraries(testDelaunay ${tolink})
 

sample/testAlgo.cpp

@@ -32,6 +32,7 @@ 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 <stdio.h>
 #include "algo.hpp"

sample/testBQueue.cpp

@@ -32,6 +32,7 @@ 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 "bqueue.hpp"
 

sample/testBSP.cpp

@@ -32,6 +32,7 @@ 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.
 +*/
+
 #if 0
 #include "bsp_simple.hpp"
 

sample/testDelaunay.cpp

@@ -32,6 +32,7 @@ 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 <fstream>
 #include <iostream>
 #include "dinterpolate.hpp"

sample/testEskow.cpp

@@ -32,6 +32,7 @@ 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 <fstream>
 #include <cstring>
 #include <iostream>

sample/testInterpolate.cpp

@@ -32,6 +32,7 @@ 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 "interpolate3d.hpp"
 

sample/testNewton.cpp

@@ -32,6 +32,7 @@ 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 <cmath>
 

sample/testPool.cpp

@@ -32,6 +32,7 @@ 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 "pool.hpp"
 
 using namespace CosmoTool;

sample/testReadFlash.cpp

@@ -32,6 +32,7 @@ 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 <assert.h>
 #include <stdio.h>

sample/testSmooth.cpp

@@ -32,6 +32,7 @@ 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 "sphSmooth.hpp"
 #include "yorick.hpp"

sample/test_cosmopower.cpp

@@ -1,3 +1,37 @@
+/*+
+This is CosmoTool (./sample/test_cosmopower.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+
+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 "cosmopower.hpp"

sample/test_fft_calls.cpp

@@ -32,6 +32,7 @@ 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 <boost/format.hpp>
 #include "yorick.hpp"
 #include <gsl/gsl_rng.h>

sample/test_healpix_calls.cpp

@@ -32,6 +32,7 @@ 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 "fourier/healpix.hpp"
 

sample/testkd.cpp

@@ -32,6 +32,7 @@ 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.
 +*/
+
 #define __KD_TREE_SAVE_ON_DISK
 #include <ctime>
 #include <cassert>

sample/testkd2.cpp

@@ -32,6 +32,7 @@ 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 <ctime>
 #include <cassert>
 #include <cstdlib>

sample/testkd3.cpp

@@ -0,0 +1,187 @@
+/*+
+This is CosmoTool (./sample/testkd3.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+
+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 <ctime>
+#include <cassert>
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#define __KD_TREE_NUMNODES
+#include "mykdtree.hpp"
+#include "kdtree_splitters.hpp"
+#include <limits>
+
+#define NTRY 30
+#define NGB 24
+#define ND 3
+
+using namespace std;
+using namespace CosmoTool;
+
+typedef KDTree<ND,char,ComputePrecision,KD_homogeneous_cell_splitter<ND, char> > MyTree;
+//typedef KDTree<ND,char,ComputePrecision > MyTree;
+typedef KDCell<ND,char> MyCell;
+
+static double periodic(double a)
+{
+  while (a < -0.5)
+    a+=1;
+  while (a > 0.5)
+    a -= 1;
+  return a;
+}
+
+MyCell *findNearest(MyTree::coords& xc, MyCell *cells, uint32_t Ncells)
+{
+    MyCell *near2 = 0;
+    double R2 = INFINITY;
+    for (int i = 0; i < Ncells; i++)
+      {
+	double d2 = 0;
+	for (int j = 0; j < ND; j++)
+	  {
+	    double delta = periodic(xc[j]-cells[i].coord[j]);
+	    d2 += delta*delta;
+	  }
+	if (d2 < R2)
+	  {
+	    near2 = &cells[i];
+	    R2 = d2;
+	  }
+      }
+    return near2;
+}
+
+int main()
+{
+  uint32_t Ncells = 3000000;
+  MyCell *cells = new MyCell[Ncells];
+  
+  for (int i = 0; i < Ncells; i++)
+    {
+      cells[i].active = true;
+      for (int l = 0; l < ND; l++)
+	cells[i].coord[l] = drand48();
+    }
+  
+  // Check timing
+  clock_t startTimer = clock();
+  MyTree tree(cells, Ncells);
+  clock_t endTimer = clock();
+
+  tree.setPeriodic(true, 1.0);
+
+  clock_t delta = endTimer-startTimer;
+  double myTime = delta*1.0/CLOCKS_PER_SEC * 1.0;
+
+  cout << "KDTree build = " << myTime << " s" << endl;
+
+  MyTree::coords *xc = new MyTree::coords[NTRY];
+
+  cout << "Generating seeds..." << endl;
+  for (int k = 0; k < NTRY; k++)
+    {
+      for (int l = 0; l < ND; l++)
+	xc[k][l] = drand48();
+    }
+
+  // Check consistency
+  cout << "Check consistency..." << endl;
+  MyCell **ngb = new MyCell *[NGB];
+  double *distances = new double[NGB];
+  
+  ofstream fngb("nearest.txt");
+  for (int k = 0; k < NTRY; k++) {
+    cout << "Seed = " << xc[k][0] << " " << xc[k][1] << " " << xc[k][2] << endl;
+    tree.getNearestNeighbours(xc[k], NGB, ngb, distances);
+    int last = -1;
+
+    for (uint32_t i = 0; i < NGB; i++)
+      {
+	if (ngb[i] == 0)
+	  continue;
+
+	last = i;
+
+	double d2 = 0;
+	for (int l = 0; l < 3; l++)
+	  d2 += ({double delta = periodic(xc[k][l] - ngb[i]->coord[l]); delta*delta;});
+	fngb << ngb[i]->coord[0] << " " << ngb[i]->coord[1] << " " << ngb[i]->coord[2] << " " << sqrt(d2) << " " << sqrt(distances[i]) << endl;
+      }
+    fngb << endl << endl;
+    double farther_dist = distances[last];
+    for (uint32_t i = 0; i < Ncells; i++)
+      {
+         bool found = false;
+         // If the points is not in the list, it means it is farther than the farthest  point
+	 for (int j =0; j < NGB; j++)
+          {
+             if (&cells[i] == ngb[j]) {
+               found = true;
+               break;
+             }
+          } 
+	 double dist_to_seed = 0;
+	 for (int l = 0; l < 3; l++)
+	   {
+	     double delta = periodic(xc[k][l]-cells[i].coord[l]);
+	     dist_to_seed += delta*delta; 
+	   }
+	 double delta_epsilon = fabs(farther_dist/dist_to_seed-1);
+	 if (!found) 
+          { 
+	    if (dist_to_seed <= farther_dist &&
+		delta_epsilon > 1000*sqrt(numeric_limits<double>::epsilon()))
+	      {
+		cout << "SHOULD BE IN (d=" << dist_to_seed << "): Failed iteration " << k << " particle " << i << " (farthest=" << sqrt(farther_dist) << ")" << endl;
+		cout << "delta_epsilon = " << delta_epsilon << endl;
+		abort();
+	      }
+          }
+	 else
+	  {	    
+	    if (dist_to_seed > farther_dist && 
+		delta_epsilon > 1000*sqrt(numeric_limits<double>::epsilon())) 
+	      {	
+		cout << "SHOULD BE OUT (d=" << sqrt(dist_to_seed) << "): Failed iteration " << k << " particle " << i << " (farthest=" << sqrt(farther_dist) << ")" << endl;
+		cout << "delta_epsilon = " << delta_epsilon << " epsilon = " << 100*sqrt(numeric_limits<double>::epsilon()) << endl;
+		abort();
+	      }
+	  }
+      }
+  }
+
+  return 0;
+}

src/algo.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_ALGO_HPP
 #define __COSMOTOOL_ALGO_HPP
 

src/bqueue.hpp

@@ -32,6 +32,7 @@ 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_QUEUE_HPP
 #define __COSMO_QUEUE_HPP
 

src/bsp_simple.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_SIMPLE_BSP_HPP
 #define __COSMOTOOL_SIMPLE_BSP_HPP
 

src/cic.cpp

@@ -32,6 +32,7 @@ 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 <assert.h>
 #include <math.h>
 #include <inttypes.h>

src/cic.hpp

@@ -32,6 +32,7 @@ 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 __CICFILTER_HPP
 #define __CICFILTER_HPP
 

src/config.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_CONFIG_HPP
 #define __COSMOTOOL_CONFIG_HPP
 

src/cosmopower.cpp

@@ -32,6 +32,7 @@ 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 <cassert>
 #include <vector>
 #include <algorithm>

src/cosmopower.hpp

@@ -32,6 +32,7 @@ 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 _COSMOPOWER_HPP
 #define _COSMOPOWER_HPP
 

src/dinterpolate.hpp

@@ -32,6 +32,7 @@ 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_DINTERPOLATE_HPP
 #define __COSMO_DINTERPOLATE_HPP
 

src/eskow.hpp

@@ -32,6 +32,7 @@ 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 __ESKOW_CHOLESKY_HPP
 #define __ESKOW_CHOLESKY_HPP
 

src/field.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_FIELD
 #define __COSMOTOOL_FIELD
 

src/fixArray.hpp

@@ -32,6 +32,7 @@ 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 __FIX_ARRAY_HPP
 #define __FIX_ARRAY_HPP
 

src/fortran.cpp

@@ -32,6 +32,7 @@ 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 "config.hpp"
 #include <iostream>
 #include <fstream>

src/fortran.hpp

@@ -32,6 +32,7 @@ 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_FORTRAN_HPP
 #define __COSMO_FORTRAN_HPP
 

src/fourier/base_types.hpp

@@ -32,6 +32,7 @@ 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 __BASE_FOURIER_TYPES_HPP
 #define __BASE_FOURIER_TYPES_HPP
 

src/fourier/details/euclidian_maps.hpp

@@ -32,6 +32,7 @@ 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 __DETAILS_EUCLIDIAN_MAPS
 #define __DETAILS_EUCLIDIAN_MAPS
 

src/fourier/details/euclidian_spectrum_1d.hpp

@@ -32,6 +32,7 @@ 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 __DETAILS_EUCLIDIAN_SPECTRUM_1D
 #define __DETAILS_EUCLIDIAN_SPECTRUM_1D
 

src/fourier/details/euclidian_spectrum_1d_bin.hpp

@@ -32,6 +32,7 @@ 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 __DETAILS_EUCLIDIAN_SPECTRUM_1D_BIN
 #define __DETAILS_EUCLIDIAN_SPECTRUM_1D_BIN
 

src/fourier/details/euclidian_transform.hpp

@@ -32,6 +32,7 @@ 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 __DETAILS_EUCLIDIAN_TRANSFORM
 #define __DETAILS_EUCLIDIAN_TRANSFORM
 

src/fourier/details/healpix_alms.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_FOURIER_HEALPIX_DETAILS_ALM_HPP
 #define __COSMOTOOL_FOURIER_HEALPIX_DETAILS_ALM_HPP
 

src/fourier/details/healpix_map.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_FOURIER_HEALPIX_DETAILS_MAP_HPP
 #define __COSMOTOOL_FOURIER_HEALPIX_DETAILS_MAP_HPP
 

src/fourier/details/healpix_spectrum.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_FOURIER_HEALPIX_DETAILS_SPECTRUM_HPP
 #define __COSMOTOOL_FOURIER_HEALPIX_DETAILS_SPECTRUM_HPP
 

src/fourier/details/healpix_transform.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_FOURIER_HEALPIX_DETAILS_TRANSFORM_HPP
 #define __COSMOTOOL_FOURIER_HEALPIX_DETAILS_TRANSFORM_HPP
 

src/fourier/details/healpix_utility.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_FOURIER_HEALPIX_DETAILS_SPECTRUM_HP
 #define __COSMOTOOL_FOURIER_HEALPIX_DETAILS_SPECTRUM_HP
 

src/fourier/euclidian.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_FOURIER_EUCLIDIAN_HPP
 #define __COSMOTOOL_FOURIER_EUCLIDIAN_HPP
 

src/fourier/fft/fftw_calls.hpp

@@ -32,6 +32,7 @@ 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 __FFTW_UNIFIED_CALLS_HPP
 #define __FFTW_UNIFIED_CALLS_HPP
 

src/fourier/healpix.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_FOURIER_HEALPIX_HPP
 #define __COSMOTOOL_FOURIER_HEALPIX_HPP
 

src/growthFactor.cpp

@@ -32,6 +32,7 @@ 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 <gsl/gsl_integration.h>
 #include "interpolate.hpp"

src/growthFactor.hpp

@@ -32,6 +32,7 @@ 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_GROWTH_FACTOR_HPP
 #define COSMO_GROWTH_FACTOR_HPP
 

src/h5_readFlash.cpp

@@ -1,36 +1,10 @@
 /*+
-This is CosmoTool (./src/h5_readFlash.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+!!
 
-guilhem.lavaux@gmail.com
+This file has been developped by P. M. Sutter
 
-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 contains the functions that read the data from the HDF5 file
  * The functions accept the PARAMESH data through arguments.

src/h5_readFlash.hpp

@@ -1,36 +1,11 @@
 /*+
-This is CosmoTool (./src/h5_readFlash.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
 
-guilhem.lavaux@gmail.com
+!!! NOTE !!!
 
-This software is a computer program whose purpose is to provide a toolbox for cosmological
+This file has been developped by P. M. Sutter.
-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 contains the functions that read the data from the HDF5 file
  * The functions accept the PARAMESH data through arguments.

src/hdf5_flash.h

@@ -1,36 +1,9 @@
 /*+
-This is CosmoTool (./src/hdf5_flash.h) -- Copyright (C) Guilhem Lavaux (2007-2013)
+!!
 
-guilhem.lavaux@gmail.com
+This particular file has been developped by P. M. Sutter
 
-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

@@ -32,6 +32,7 @@ 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 <cassert>
 #include <cmath>
 #include <algorithm>

src/interpolate.hpp

@@ -32,6 +32,7 @@ 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 __CTOOL_INTERPOLATE_HPP
 #define __CTOOL_INTERPOLATE_HPP
 

src/interpolate3d.hpp

@@ -32,6 +32,7 @@ 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_INTERPOLATE3D_HPP
 #define __COSMO_INTERPOLATE3D_HPP
 

src/kdtree_leaf.hpp

@@ -32,6 +32,7 @@ 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 __LEAF_KDTREE_HPP
 #define __LEAF_KDTREE_HPP
 

src/kdtree_splitters.hpp

@@ -32,6 +32,7 @@ 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 __KDTREE_SPLITTERS_HPP
 #define __KDTREE_SPLITTERS_HPP
 

src/loadFlash.cpp

@@ -32,6 +32,7 @@ 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.
 +*/
+
 /* Reads in FLASH v3 files in HDF5 format */
 
 #include <iostream>

src/loadFlash.hpp

@@ -32,6 +32,7 @@ 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_LOAD_FLASH_HPP
 #define __COSMO_LOAD_FLASH_HPP
 

src/loadFlash_dummy.cpp

@@ -32,6 +32,7 @@ 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 "load_data.hpp"
 #include "loadFlash.hpp"
 

src/loadGadget.cpp

@@ -32,6 +32,7 @@ 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 <assert.h>
@@ -267,10 +268,10 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
 
 
 
-void CosmoTool::writeGadget(const char *fname, SimuData *data, int GadgetFormat)
+void CosmoTool::writeGadget(const std::string& fname, SimuData *data, int GadgetFormat)
 {
   UnformattedWrite *f;
-  int npart[6];
+  int npart[6], npartTotal[6];
   float mass[6];
 
   if (data->Pos[0] == 0 || data->Vel[0] == 0 || data->Id == 0)
@@ -282,12 +283,12 @@ void CosmoTool::writeGadget(const char *fname, SimuData *data, int GadgetFormat)
 
   for (int i = 0; i < 6; i++)
     {
-      npart[i] = 0;
+      npart[i] = npartTotal[i] = 0;
       mass[i] = 0;
     }
   mass[1] = 1.0;
-
   npart[1] = data->NumPart;
+  npartTotal[1] = data->TotalNumPart;
   
   f->beginCheckpoint();
   for (int i = 0; i < 6; i++)
@@ -301,7 +302,7 @@ void CosmoTool::writeGadget(const char *fname, SimuData *data, int GadgetFormat)
   f->writeInt32(0);
 
   for (int i = 0; i < 6; i++)
-    f->writeInt32(npart[i]);
+    f->writeInt32(npartTotal[i]);
   f->writeInt32(0);
   f->writeInt32(1);
   f->writeReal64(data->BoxSize);

src/loadGadget.hpp

@@ -32,9 +32,12 @@ 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_LOAD_GADGET_HPP
 #define __COSMO_LOAD_GADGET_HPP
 
+#include <string>
+
 #include "load_data.hpp"
 #include "loadSimu.hpp"
 
@@ -44,7 +47,7 @@ namespace CosmoTool {
 			    int GadgetFormat = 1, SimuFilter filter = 0);
  
   // Only single snapshot supported
-  void writeGadget(const char *fname, SimuData *data, int GadgetFormat = 1);
+  void writeGadget(const std::string& fname, SimuData *data, int GadgetFormat = 1);
  
 };
 

src/loadRamses.cpp

@@ -32,6 +32,7 @@ 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 <sys/types.h>
 #include <regex.h>
 #include <cmath>

src/loadRamses.hpp

@@ -32,6 +32,7 @@ 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 _LOAD_RAMSES_HPP
 #define _LOAD_RAMSES_HPP
 

src/loadSimu.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOLBOX_HPP
 #define __COSMOTOOLBOX_HPP
 

src/load_data.cpp

@@ -32,6 +32,7 @@ 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 <assert.h>
 #include <stdio.h>
 #include <stdlib.h>

src/load_data.hpp

@@ -32,6 +32,7 @@ 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 _LOAD_GADGET_DATA_HPP
 #define _LOAD_GADGET_DATA_HPP
 

src/mach.hpp

@@ -32,6 +32,7 @@ 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_MACHINE_TEST_HPP
 #define __COSMO_MACHINE_TEST_HPP
 

src/miniargs.cpp

@@ -32,6 +32,7 @@ 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 <cstdlib>
 #include <cstdio>
 #include <cstring>

src/miniargs.hpp

@@ -32,6 +32,7 @@ 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 _MAK_MINIARGS_HPP
 #define _MAK_MINIARGS_HPP
 

src/mykdtree.hpp

@@ -32,6 +32,7 @@ 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 __HV_KDTREE_HPP
 #define __HV_KDTREE_HPP
 
@@ -135,7 +136,13 @@ namespace CosmoTool {
     void setPeriodic(bool on, CoordType replicate)
      {
        periodic = on;
-       this->replicate = replicate;
+       std::fill(this->replicate, this->replicate+N, replicate);
+     }
+
+    void setPeriodic(bool on, const coords& replicate)
+     {
+       periodic = on;
+       std::copy(replicate, replicate+N, this->replicate);
      }
 
     uint32_t getIntersection(const coords& x, CoordType r, 
@@ -192,7 +199,7 @@ namespace CosmoTool {
     Cell *base_cell;
 
     bool periodic;
-    CoordType replicate;
+    coords replicate;
 
     Node *buildTree(Cell **cell0,
 		    uint32_t NumCells,

src/newton.hpp

@@ -32,6 +32,7 @@ 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 _COSMOTOOL_NEWTON_HPP
 #define _COSMOTOOL_NEWTON_HPP
 

src/octTree.cpp

@@ -32,6 +32,7 @@ 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 <cmath>
 #include <cassert>

src/octTree.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_AMR_HPP
 #define __COSMOTOOL_AMR_HPP
 

src/pool.hpp

@@ -32,6 +32,7 @@ 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_POOL_HPP
 #define __COSMO_POOL_HPP
 

src/powerSpectrum.cpp

@@ -32,6 +32,7 @@ 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 <cassert>
 #include <vector>
 #include <algorithm>

src/powerSpectrum.hpp

@@ -32,6 +32,7 @@ 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 _POWERSPECTRUM_HPP
 #define _POWERSPECTRUM_HPP
 

src/replicateGenerator.hpp

@@ -1,3 +1,37 @@
+/*+
+This is CosmoTool (./src/replicateGenerator.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
+
+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 __REPLICATE_GENERATOR_HPP
 #define __REPLICATE_GENERATOR_HPP
 
@@ -12,16 +46,29 @@ namespace CosmoTool
   {
   public:
     typedef Coord Coords[N];
-    Coord replicate;
+    Coords replicate;
 
     ReplicateGenerator(const Coords& x, Coord shift)
     {
       face = 0; 
-      replicate = shift;
+      std::fill(replicate, replicate+N, shift);
       numFaces = spower<N,long>(3);
       std::copy(x, x+N, x_base);
+      if (!next())
+	abort();
     }
 
+    ReplicateGenerator(const Coords& x, Coords& shift)
+    {
+      face = 0;
+      std::copy(shift, shift+N, replicate);
+      numFaces = spower<N,long>(3);
+      std::copy(x, x+N, x_base);
+      if (!next())
+        abort();
+    }
+
+
     bool next()
     {
       if (face == numFaces)
@@ -36,7 +83,7 @@ namespace CosmoTool
           int c_face;
           c_face = q_face % 3;
           q_face /= 3;
-          x_shifted[i] = x_base[i] + (c_face-1)*replicate;
+          x_shifted[i] = x_base[i] + (c_face-1)*replicate[i];
           no_move = no_move && (c_face == 1);
         }
       if (no_move)

src/sparseGrid.hpp

@@ -32,6 +32,7 @@ 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 __VOID_SPARSE_GRID_HPP
 #define __VOID_SPARSE_GRID_HPP
 

src/sphSmooth.hpp

@@ -32,6 +32,7 @@ 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 __COSMOTOOL_SPH_SMOOTH_HPP
 #define __COSMOTOOL_SPH_SMOOTH_HPP
 

src/yorick.hpp

@@ -32,6 +32,7 @@ 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 __YORICK_HELPERS_HPP
 #define __YORICK_HELPERS_HPP
 

src/yorick_nc3.cpp

@@ -32,6 +32,7 @@ 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 "ctool_netcdf_ver.hpp"
 #include "config.hpp"
 #ifdef NETCDFCPP4

src/yorick_nc4.cpp

@@ -32,6 +32,7 @@ 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 "ctool_netcdf_ver.hpp"
 #include "config.hpp"
 #include <netcdf>