Update cosmotool 2nd part

external/cosmotool/sample/gadgetToArray.cpp

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+/*+
+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 <algorithm>
+#include <iostream>
+#include <cstdlib>
+#include "cic.hpp"
+#include "loadGadget.hpp"
+#include "miniargs.hpp"
+#include <H5Cpp.h>
+#include "hdf5_array.hpp"
+
+using namespace CosmoTool;
+using namespace std;
+
+int main(int argc, char **argv)
+{
+  typedef boost::multi_array<float, 2> array_type;
+  uint32_t res;
+  char *fname;
+  int id;
+  double MPC;
+
+  MiniArgDesc desc[] = {
+    { "SNAPSHOT", &fname, MINIARG_STRING },
+    { "MPC", &MPC, MINIARG_DOUBLE },
+    { 0, 0, MINIARG_NULL }
+  };
+
+  if (!parseMiniArgs(argc, argv, desc))
+    return 1;
+
+  H5::H5File f("density.h5", H5F_ACC_TRUNC);
+  
+
+  SimuData *p = loadGadgetMulti(fname, 0, 0);
+  double L0 = p->BoxSize/MPC;
+  cout << "Will read " << p->TotalNumPart << " particles" << endl;
+  array_type parts(boost::extents[p->TotalNumPart][7]);
+  uint64_t q = 0;
+  
+  try {
+    for (int cpuid=0;;cpuid++) {
+      cout << "  = CPU " << cpuid << " = " << endl;
+      p = loadGadgetMulti(fname, cpuid, NEED_POSITION|NEED_VELOCITY|NEED_MASS);
+      cout << "  = DONE LOAD, COPYING IN PLACE" << endl;
+      for (uint32_t i = 0; i < p->NumPart; i++)
+        {
+          for (int j = 0; j < 3; j++)
+            {
+              parts[q][j] = p->Pos[j][i]/MPC;
+              while (parts[q][j] < 0) parts[q][j] += L0;
+              while (parts[q][j] >= L0) parts[q][j] -= L0;
+              parts[q][j] -= L0/2;
+            }
+          parts[q][3] = p->Vel[0][i];
+          parts[q][4] = p->Vel[1][i];
+          parts[q][5] = p->Vel[2][i];
+          parts[q][6] = p->Mass[i];
+          q++;
+        }
+      cout << "  = DONE (q=" << q << ")" << endl;
+
+      delete p;
+    }
+  } catch (const NoSuchFileException& e) {}
+
+  cout << " ++ WRITING ++" << endl;
+  hdf5_write_array(f, "particles", parts);
+
+  return 0;
+}