Merge branch 'master' of https://bitbucket.org/cosmicvoids/vide_public

c_tools/mock/generateMock.cpp

@@ -695,7 +695,11 @@ int main(int argc, char **argv)
     }
   else if (args_info.gadget_given)
     {
-      loader = gadgetLoader(args_info.gadget_arg, 1/args_info.gadgetUnit_arg, NEED_POSITION|NEED_VELOCITY|NEED_GADGET_ID, preselector);
+      loader = gadgetLoader(args_info.gadget_arg, 1/args_info.gadgetUnit_arg, NEED_POSITION|NEED_VELOCITY|NEED_GADGET_ID, 1, preselector);
+    }
+  else if (args_info.gadget2_given)
+    {
+      loader = gadgetLoader(args_info.gadget2_arg, 1/args_info.gadgetUnit_arg, NEED_POSITION|NEED_VELOCITY|NEED_GADGET_ID, 2, preselector);
     }
   else if (args_info.flash_given)
     {

c_tools/mock/generateMock.ggo

@@ -8,6 +8,7 @@ option "ramsesBase" -	"Base directory for ramses" string optional
 option "ramsesId"   -   "Ramses snapshot id" int optional
 
 option "gadget"	    -	"Base name of gadget snapshot (without parallel writing extension)" string optional
+option "gadget2"	-	"Base name of gadget snapshot (version 2, without parallel writing extension)" string optional
 option "flash"	    -   "Base name for FLASH snapshot" string optional
 option "multidark"	    -   "Base name for multidark snapshot" string optional
 

c_tools/mock/loaders/gadget_loader.cpp

@@ -36,12 +36,13 @@ private:
   bool onefile;
   int _num_files;
   double unitMpc;
+  int gadgetFormat;
   SimuData *gadget_header;
   string snapshot_name;
   SimulationPreprocessor *preproc;
 public:
-  GadgetLoader(const string& basename, SimuData *header, int flags, bool singleFile, int _num, double unit, SimulationPreprocessor *p)
+  GadgetLoader(const string& basename, SimuData *header, int flags, bool singleFile, int _num, double unit, int gadgetFormat, SimulationPreprocessor *p)
-    : snapshot_name(basename), load_flags(flags), onefile(singleFile), _num_files(_num), unitMpc(1/unit), gadget_header(header), preproc(p)
+    : snapshot_name(basename), load_flags(flags), onefile(singleFile), _num_files(_num), unitMpc(1/unit), gadget_header(header), gadgetFormat(gadgetFormat), preproc(p)
   {
   }
   
@@ -67,9 +68,9 @@ public:
       return 0;
 
     if (onefile)
-      d = loadGadgetMulti(snapshot_name.c_str(), -1, load_flags);
+      d = loadGadgetMulti(snapshot_name.c_str(), -1, load_flags, gadgetFormat);
     else
-      d = loadGadgetMulti(snapshot_name.c_str(), id, load_flags);
+      d = loadGadgetMulti(snapshot_name.c_str(), id, load_flags, gadgetFormat);
 
     if (d->Id != 0)
       {
@@ -99,7 +100,7 @@ public:
 };
 
 
-SimulationLoader *gadgetLoader(const std::string& snapshot, double Mpc_unitLength, int flags, SimulationPreprocessor *p)
+SimulationLoader *gadgetLoader(const std::string& snapshot, double Mpc_unitLength, int flags, int gadgetFormat, SimulationPreprocessor *p)
 {
   bool singleFile = false;
   int num_files;
@@ -109,7 +110,7 @@ SimulationLoader *gadgetLoader(const std::string& snapshot, double Mpc_unitLengt
 
   try
     {
-      d = loadGadgetMulti(snapshot.c_str(), -1, 0);
+      d = loadGadgetMulti(snapshot.c_str(), -1, 0, gadgetFormat);
       singleFile = true;
       num_files = 1;
     }
@@ -117,7 +118,7 @@ SimulationLoader *gadgetLoader(const std::string& snapshot, double Mpc_unitLengt
     {
       try
         {
-          d = loadGadgetMulti(snapshot.c_str(), 0, 0);
+          d = loadGadgetMulti(snapshot.c_str(), 0, 0, gadgetFormat);
 	  num_files = 0;
         }
       catch(const NoSuchFileException& e)
@@ -135,7 +136,7 @@ SimulationLoader *gadgetLoader(const std::string& snapshot, double Mpc_unitLengt
     {
       try
 	{
-	  while ((d = loadGadgetMulti(snapshot.c_str(), num_files, 0)) != 0)
+	  while ((d = loadGadgetMulti(snapshot.c_str(), num_files, 0, gadgetFormat)) != 0)
 	    {
 	      num_files++;
 	      delete d;
@@ -146,5 +147,5 @@ SimulationLoader *gadgetLoader(const std::string& snapshot, double Mpc_unitLengt
 	}
     }
     
-  return new GadgetLoader(snapshot, header, flags, singleFile, num_files, Mpc_unitLength, p);
+  return new GadgetLoader(snapshot, header, flags, singleFile, num_files, Mpc_unitLength, gadgetFormat, p);
 }

c_tools/mock/loaders/simulation_loader.hpp

@@ -144,7 +144,7 @@ void delete_adaptor(void *ptr)
 
 
 // Unit length is the size of one Mpc in the simulation units
-SimulationLoader *gadgetLoader(const std::string& snapshot, double Mpc_unitLength, int flags, SimulationPreprocessor *p);
+SimulationLoader *gadgetLoader(const std::string& snapshot, double Mpc_unitLength, int flags, int gadgetFormat, SimulationPreprocessor *p);
 SimulationLoader *flashLoader(const std::string& snapshot, int flags, SimulationPreprocessor *p);
 SimulationLoader *multidarkLoader(const std::string& snapshot, SimulationPreprocessor *p);
 SimulationLoader *ramsesLoader(const std::string& snapshot, int baseid, bool double_precision, int flags, SimulationPreprocessor *p);

external/cosmotool/CMakeLists.txt

@@ -47,6 +47,10 @@ if (ENABLE_SHARP)
 endif (ENABLE_SHARP)
 
 
+find_package(Boost 1.53)
+mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES)
+
+
 set(HDF5_FIND_COMPONENTS HL CXX)
 if(HDF5_ROOTDIR)
   SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR})

external/cosmotool/src/CMakeLists.txt

@@ -55,7 +55,7 @@ SET(CosmoTool_SRCS ${CosmoTool_SRCS}
 	growthFactor.hpp
 )
 
-include_directories(${GSL_INCLUDE_PATH} ${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
+include_directories(${Boost_INCLUDE_DIRS} ${GSL_INCLUDE_PATH} ${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
 
 set(CosmoTool_LIBS  ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
 if (HDF5_FOUND)

external/cosmotool/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
 
@@ -71,6 +71,18 @@ UnformattedRead::~UnformattedRead()
   delete f;
 }
 
+int64_t UnformattedRead::position() const
+{
+ return f->tellg();
+}
+
+void UnformattedRead::seek(int64_t pos)
+{
+  f->clear();
+  f->seekg(pos, istream::beg);
+  checkPointRef = checkPointAccum = 0;
+}
+
 // Todo implement primitive description
 void UnformattedRead::setOrdering(Ordering o)
 {
@@ -112,7 +124,7 @@ void UnformattedRead::beginCheckpoint()
   checkPointRef = (cSize == Check_32bits) ? 4 : 8;
   checkPointAccum = 0;  
 
-  checkPointRef = (cSize == Check_32bits) ? readInt32() : readInt64();
+  checkPointRef = (cSize == Check_32bits) ? readUint32() : readInt64();
   checkPointAccum = 0;
 
   if (f->eof())
@@ -144,7 +156,7 @@ void UnformattedRead::endCheckpoint(bool autodrop)
 void UnformattedRead::readOrderedBuffer(void *buffer, int size)
       throw (InvalidUnformattedAccess)
 {
-  if ((checkPointAccum+size) > checkPointRef)
+  if ((checkPointAccum+(uint64_t)size) > checkPointRef)
        throw InvalidUnformattedAccess();
 
   f->read((char *)buffer, size);
@@ -186,6 +198,20 @@ float UnformattedRead::readReal32()
   return a.f;
 }
 
+uint32_t UnformattedRead::readUint32()
+  throw (InvalidUnformattedAccess)
+{
+  union
+  {
+    char b[4];
+    uint32_t i;
+  } a;
+
+  readOrderedBuffer(&a, 4);
+
+  return a.i;
+}
+
 int32_t UnformattedRead::readInt32()
   throw (InvalidUnformattedAccess)
 {

external/cosmotool/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
 
@@ -73,6 +73,8 @@ namespace CosmoTool
     // Todo implement primitive description
     void setOrdering(Ordering o);
     void setCheckpointSize(CheckpointSize cs);
+
+    uint64_t getBlockSize() const { return checkPointRef; }
     
     void beginCheckpoint()
       throw (InvalidUnformattedAccess,EndOfFileException);
@@ -83,6 +85,8 @@ namespace CosmoTool
       throw (InvalidUnformattedAccess);
     float readReal32()
       throw (InvalidUnformattedAccess);
+    uint32_t readUint32()
+      throw (InvalidUnformattedAccess);
     int32_t readInt32()
       throw (InvalidUnformattedAccess);
     int64_t readInt64()
@@ -91,6 +95,11 @@ namespace CosmoTool
     void skip(int64_t off)
       throw (InvalidUnformattedAccess);
 
+    int64_t position() const;
+    void seek(int64_t pos);
+
+    void readOrderedBuffer(void *buffer, int size)
+      throw (InvalidUnformattedAccess);
   protected:
     bool swapOrdering;
     CheckpointSize cSize;
@@ -98,8 +107,6 @@ namespace CosmoTool
     uint64_t checkPointAccum;
     std::ifstream *f;
 
-    void readOrderedBuffer(void *buffer, int size)
-      throw (InvalidUnformattedAccess);
   };
 
  class UnformattedWrite: public FortranTypes

external/cosmotool/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
 
@@ -38,6 +38,8 @@ knowledge of the CeCILL license and that you accept its terms.
 #include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
+#include <boost/function.hpp>
+#include <boost/bind.hpp>
 #include "load_data.hpp"
 #include "loadGadget.hpp"
 #include "fortran.hpp"
@@ -65,9 +67,16 @@ void loadGadgetHeader(UnformattedRead *f, GadgetHeader& h, SimuData *data, int i
   data->Omega_M = h.Omega0 = f->readReal64();
   data->Omega_Lambda = h.OmegaLambda = f->readReal64();
   data->Hubble = h.HubbleParam = f->readReal64();
+  (int)f->readInt32(); // stellarage
+  (int)f->readInt32(); // metals
+  for (int i = 0; i < 6; i++)
+    h.npartTotal[i] |= ((unsigned long)f->readInt32()) << 32;
+  (int)f->readInt32(); // entropy instead of u
+  h.flag_doubleprecision = f->readInt32();  
+
   f->endCheckpoint(true);
   
-  long NumPart = 0, NumPartTotal = 0;
+  ssize_t NumPart = 0, NumPartTotal = 0;
   for(int k=0; k<6; k++)
     {
       NumPart += h.npart[k];
@@ -77,6 +86,22 @@ void loadGadgetHeader(UnformattedRead *f, GadgetHeader& h, SimuData *data, int i
   data->TotalNumPart = NumPartTotal;
 }
 
+template<typename T>
+T myRead64(UnformattedRead *f) { return f->readReal64(); }
+
+template<typename T>
+T myRead32(UnformattedRead *f) { return f->readReal32(); }
+
+template<typename T>
+T myReadI64(UnformattedRead *f) { return f->readInt64(); }
+
+template<typename T>
+T myReadI32(UnformattedRead *f) { return f->readInt32(); }
+
+struct BlockInfo {
+   int64_t position, size;
+};
+
 SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
 				     int loadflags, int GadgetFormat, 
 				     SimuFilter filter)
@@ -86,6 +111,15 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
   UnformattedRead *f;
   GadgetHeader h;
   float velmul;
+  boost::function0<double> readToDouble;
+  boost::function0<float> readToSingle;
+  boost::function0<int64_t> readID;
+  long float_size;
+
+  if (GadgetFormat > 2) {
+     cerr << "Unknown gadget format" << endl;
+     return 0;
+  }
 
   if (id >= 0) {
     int k = snprintf(0, 0, "%s.%d", fname, id)+1;
@@ -96,7 +130,7 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
     if (f == 0)
       return 0;
 
-    delete out_fname;
+    delete[] out_fname;
 
   } else {
 
@@ -106,27 +140,72 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
 
   }
 
+  typedef std::map<std::string, BlockInfo> BlockMap;
+  BlockMap blockTable;
+  
+  if (GadgetFormat == 2) {
+    int64_t startBlock = 0;
+    char block[5];
+    int32_t blocksize;
+
+    try {
+      while (true) {
+        f->beginCheckpoint();
+        f->readOrderedBuffer(block, 4);
+        block[4] = 0;
+        blocksize = f->readInt32();
+        f->endCheckpoint();
+        blockTable[block].position = f->position();
+        blockTable[block].size = blocksize;
+        f->skip(blocksize);
+      }
+    } catch (EndOfFileException&) {}
+
+    f->seek(startBlock);
+  }
+
   data = new SimuData;
   if (data == 0) {
     delete f;
     return 0;
   }
 
-  long NumPart = 0, NumPartTotal = 0;
+  ssize_t NumPart = 0, NumPartTotal = 0;
+#define ENSURE2(name,out_sz) { \
+    if (GadgetFormat == 2) { \
+     BlockMap::iterator iter = blockTable.find(name); \
+     int64_t sz; \
+     if (iter == blockTable.end()) { \
+        std::cerr << "GADGET2: Cannot find block named '" << name << "'" << endl; \
+        if (data) delete data; \
+        delete f; \
+        return 0; \
+     } \
+     f->seek(iter->second.position); \
+     sz = iter->second.size; \
+     out_sz = sz;\
+    } \
+  } 
+#define ENSURE(name) ENSURE2(name,sz);
   
   try
     {
+      ENSURE("HEAD");
       loadGadgetHeader(f, h, data, id);
 
-      if (GadgetFormat == 1)
+      velmul = sqrt(h.time);
-        velmul = sqrt(h.time);
+      
-      else if (GadgetFormat == 2)
+      if (h.flag_doubleprecision) {
-        velmul = 1/(h.time);
+        //cout << "Gadget format with double precision" << endl;
-      else {
+        readToDouble = boost::bind(myRead64<double>, f);
-        cerr << "unknown gadget format" << endl;
+        readToSingle = boost::bind(myRead64<float>, f);
-	abort();
+        float_size = sizeof(double);
+      } else {
+        //cout << "Gadget format with single precision" << endl;
+        readToDouble = boost::bind(myRead32<double>, f);
+        readToSingle = boost::bind(myRead32<float>, f);
+        float_size = sizeof(float);
       }
-
       NumPart = data->NumPart;
       NumPartTotal = data->TotalNumPart;
     }
@@ -138,34 +217,47 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
       return 0;
     }
 
+
   if (loadflags & NEED_TYPE)
     {
       int p = 0;
-
+ 
       data->type = new int[data->NumPart];
       for (int k = 0; k < 6; k++)
-	for (int n = 0; n < h.npart[k]; n++,p++)
+        for (int n = 0; n < h.npart[k]; n++,p++)
-	  data->type[p] = k;
+            data->type[p] = k;
     }
 
   if (loadflags & NEED_POSITION) {
       
     for (int i = 0; i < 3; i++) {
-      data->Pos[i] = new float[data->NumPart];
+        data->Pos[i] = new float[data->NumPart];
-      if (data->Pos[i] == 0) {
+        if (data->Pos[i] == 0) {
-	delete data;
+        	delete data;
-	return 0;
+    	return 0;
-      }
     }
+  }
     
     try
       {
+        ENSURE("POS ");
 	f->beginCheckpoint();
+        if (f->getBlockSize() != NumPart*float_size*3) {
+          // Check that single would work
+          if (f->getBlockSize() == NumPart*sizeof(float)*3) {
+            // Change to single
+            cout << "Change back to single. Buggy header." << endl;
+            readToDouble = boost::bind(myRead32<double>, f);
+            readToSingle = boost::bind(myRead32<float>, f);
+            float_size = sizeof(float);
+          }
+        }
 	for(int k = 0, p = 0; k < 6; k++) {
 	  for(int n = 0; n < h.npart[k]; n++) {
-	    data->Pos[0][p] = f->readReal32();
+//            if ((n%1000000)==0) cout << n << endl;
-	    data->Pos[1][p] = f->readReal32();
+	    data->Pos[0][p] = readToSingle();
-	    data->Pos[2][p] = f->readReal32();
+	    data->Pos[1][p] = readToSingle();
+	    data->Pos[2][p] = readToSingle();
 	    p++;
 	  }
 	}
@@ -173,15 +265,16 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
       }
     catch (const InvalidUnformattedAccess& e)
       {
-	cerr << "Invalid format while reading positions" << endl;
+        cerr << "Invalid format while reading positions" << endl;
-	delete f;
+        delete f;
-	delete data;
+        delete data;
-	return 0;
+        return 0;
       }
     
   } else {
+    long float_size = (h.flag_doubleprecision) ? sizeof(double) : sizeof(float);
     // Skip positions
-    f->skip(NumPart * 3 * sizeof(float) + 2*4);
+    f->skip(NumPart * 3 * float_size + 2*4);
   }
   
   if (loadflags & NEED_VELOCITY) {
@@ -198,13 +291,15 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
     
     try
       {
+        ENSURE("VEL ");
 	f->beginCheckpoint();
 	for(int k = 0, p = 0; k < 6; k++) {
 	  for(int n = 0; n < h.npart[k]; n++) {
 	    // THIS IS GADGET 1
-	    data->Vel[0][p] = f->readReal32()*velmul;
+//            if ((n%1000000)==0) cout << n << endl;
-	    data->Vel[1][p] = f->readReal32()*velmul;
+	    data->Vel[0][p] = readToSingle()*velmul;
-	    data->Vel[2][p] = f->readReal32()*velmul;
+	    data->Vel[1][p] = readToSingle()*velmul;
+	    data->Vel[2][p] = readToSingle()*velmul;
 	    p++;
 	  }
 	}
@@ -222,13 +317,25 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
 ///    // TODO: FIX THE UNITS OF THESE FUNKY VELOCITIES !!!
   } else {
     // Skip velocities
-    f->skip(NumPart*3*sizeof(float)+2*4);
+    f->skip(NumPart*3*float_size+2*4);
   }
 
   // Skip ids
   if (loadflags & NEED_GADGET_ID) {
     try
       {
+        int64_t idSize;
+        ENSURE2("ID  ", idSize);
+
+        if (idSize / data->NumPart == 8) {
+          readID = boost::bind(myReadI64<int64_t>, f);
+        } else
+        if (idSize / data->NumPart == 4) {
+          readID = boost::bind(myReadI32<int64_t>, f);
+        } else {
+          throw InvalidUnformattedAccess();
+        }
+
 	f->beginCheckpoint();
 	data->Id = new long[data->NumPart];
 	if (data->Id == 0)
@@ -242,7 +349,7 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
 	  {
 	    for(int n = 0; n < h.npart[k]; n++)
 	      {
-		data->Id[p] = f->readInt32();
+		data->Id[p] = readID();
 		p++;
 	      }
 	  }
@@ -261,11 +368,66 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
       f->skip(h.npart[k]*4);
   }
 
+  if (loadflags & NEED_MASS) {
+    bool do_load = false;
+
+    for (int k = 0; k < 6; k++)
+      {
+         do_load = do_load || ((h.mass[k] == 0)&&(h.npart[k]>0));
+      }
+
+    try
+      {
+        long l = 0;
+	if (do_load) {
+          ENSURE("MASS");
+          f->beginCheckpoint();
+        }
+        data->Mass = new float[NumPart];
+        for (int k = 0; k < 6; k++)
+	  {
+            if (h.mass[k] == 0) {
+              for(int n = 0; n < h.npart[k]; n++)
+	        {
+//            if ((n%1000000)==0) cout << n << endl;
+                  data->Mass[l++] = readToSingle();
+                }
+            } else {
+              for(int n = 0; n < h.npart[k]; n++)
+	        {
+            if ((n%1000000)==0) cout << n << endl;
+                  data->Mass[l++] = h.mass[k];
+                }
+            }
+          }
+        if (do_load)
+          f->endCheckpoint();
+      }
+    catch (const InvalidUnformattedAccess& e)
+      {
+	cerr << "Invalid unformatted access while reading ID" << endl;
+	delete f;
+	delete data;
+	return 0;
+      }
+    catch (const EndOfFileException& e)
+      {
+        for (int k = 0; k < 6; k++)
+          cerr << "mass[" << k << "] = " << h.mass[k] << endl;
+      }
+  } else {
+    f->skip(2*4);
+    for (int k = 0; k < 6; k++)
+      if (h.mass[k] == 0)
+        f->skip(h.npart[k]*4);
+  }
+
   delete f;
 
   return data;
 }
 
+#undef ENSURE
 
 
 void CosmoTool::writeGadget(const std::string& fname, SimuData *data, int GadgetFormat)
@@ -274,12 +436,16 @@ void CosmoTool::writeGadget(const std::string& fname, SimuData *data, int Gadget
   int npart[6], npartTotal[6];
   float mass[6];
 
-  if (data->Pos[0] == 0 || data->Vel[0] == 0 || data->Id == 0)
+  if (data->Pos[0] == 0 || data->Vel[0] == 0 || data->Id == 0) {
+    cerr << "Invalid simulation data array" << endl;
     return;
+  }
 
   f = new UnformattedWrite(fname);
-  if (f == 0)
+  if (f == 0) {
+    cerr << "Cannot create file" << endl;
     return;
+  }
 
   for (int i = 0; i < 6; i++)
     {
@@ -321,8 +487,7 @@ void CosmoTool::writeGadget(const std::string& fname, SimuData *data, int Gadget
   f->endCheckpoint();
 
   float velmul = 1.0;
-  if (GadgetFormat == 1)
+  velmul = sqrt(data->time);
-    velmul = sqrt(data->time);
 
   f->beginCheckpoint();
   for(int n = 0; n < data->NumPart; n++) {

external/cosmotool/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
 

external/cosmotool/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
 
@@ -36,6 +36,7 @@ knowledge of the CeCILL license and that you accept its terms.
 #ifndef __COSMOTOOLBOX_HPP
 #define __COSMOTOOLBOX_HPP
 
+#include <sys/types.h>
 #include <map>
 #include <string>
 
@@ -45,6 +46,8 @@ namespace CosmoTool
   static const int NEED_POSITION = 2;
   static const int NEED_VELOCITY = 4;
   static const int NEED_TYPE = 8;
+  static const int NEED_MASS = 16;
+  static const int NEED_DOUBLE_PRECISION = 32;
 
   struct SimuParticle
   {
@@ -64,6 +67,8 @@ namespace CosmoTool
     typedef void (*FreeFunction)(void *);
     typedef std::map<std::string, std::pair<void *, FreeFunction> > AttributeMap;
 
+    bool noAuto;
+
     float BoxSize;
     float time;
     float Hubble;
@@ -71,59 +76,60 @@ namespace CosmoTool
     float Omega_M;
     float Omega_Lambda;
 
-    long NumPart;
+    ssize_t NumPart;
-    long TotalNumPart;
+    ssize_t TotalNumPart;
     long *Id;
     float *Pos[3];
     float *Vel[3];
+    float *Mass;
     int *type;
 
     AttributeMap attributes;
     
   public:
-    SimuData() : Id(0),NumPart(0),type(0)  { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; }
+    SimuData() : Mass(0), Id(0),NumPart(0),type(0),noAuto(false)  { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; }
     ~SimuData() 
     {
-      for (int j = 0; j < 3; j++)
+        if (!noAuto)  {
-	{
+            for (int j = 0; j < 3; j++) {
-	  if (Pos[j])
+                if (Pos[j])
-	    delete[] Pos[j];
+                    delete[] Pos[j];
-	  if (Vel[j])
+                if (Vel[j])
-	    delete[] Vel[j];
+                    delete[] Vel[j];
-	}
+            }
-      if (type)
+            if (type)
-	delete[] type;
+                delete[] type;
-      if (Id)
+            if (Id)
-	delete[] Id;
+                delete[] Id;
-
+            if (Mass)
-      for (AttributeMap::iterator i = attributes.begin();
+                delete[] Mass;
-	   i != attributes.end();
+        }
-	   ++i)
+        for (AttributeMap::iterator i = attributes.begin();
-	{
+             i != attributes.end();
-	  if (i->second.second)
+             ++i) {
-	    i->second.second(i->second.first);
+            if (i->second.second)
-	}
+                i->second.second(i->second.first);
+        }
     }    
     
     template<typename T>
     T *as(const std::string& n) 
     {
-      AttributeMap::iterator i = attributes.find(n);
+        AttributeMap::iterator i = attributes.find(n);
-      if (i == attributes.end())
+        if (i == attributes.end())
-	return 0;
+            return 0;
-      
+
-      return reinterpret_cast<T *>(i->second.first);
+        return reinterpret_cast<T *>(i->second.first);
     }
 
     void new_attribute(const std::string& n, void *p, FreeFunction free_func)
     {
-      AttributeMap::iterator i = attributes.find(n);
+        AttributeMap::iterator i = attributes.find(n);
-      if (i != attributes.end())
+        if (i != attributes.end()) {
-	{
+            if (i->second.second)
-	  if (i->second.second)
+                i->second.second(i->second.first);
-	    i->second.second(i->second.first);
+        }
-	}
+        attributes[n] = std::make_pair(p, free_func);
-      attributes[n] = std::make_pair(p, free_func);
     }
     
   };

external/cosmotool/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
 
@@ -55,7 +55,11 @@ namespace CosmoTool {
     double   Omega0;
     double   OmegaLambda;
     double   HubbleParam; 
-    char     fill[256- 6*4- 6*8- 2*8- 2*4- 6*4- 2*4 - 4*8];  /* fills to 256 Bytes */
+    int flag_doubleprecision;	
+    int flag_ic_info;            
+    float lpt_scalingfactor;
+    char fill[18];		/*!< fills to 256 Bytes */
+    char names[15][2];
   };
 
   struct ParticleState

external/external_build.cmake

@@ -241,6 +241,8 @@ ExternalProject_Add(cosmotool
 	-DNETCDF_LIBRARY=${NETCDF_LIBRARY}
 	-DNETCDFCPP_LIBRARY=${NETCDFCPP_LIBRARY}
   -DENABLE_SHARP=OFF
+  -DBOOST_INCLUDEDIR=${Boost_INCLUDE_DIRS}
+
 )
 SET(COSMOTOOL_LIBRARY ${CMAKE_BINARY_DIR}/ext_build/cosmotool/lib/libCosmoTool.a)
 set(COSMOTOOL_INCLUDE_PATH ${CMAKE_BINARY_DIR}/ext_build/cosmotool/include)

python_tools/void_python_tools/backend/launchers.py

@@ -165,6 +165,8 @@ def launchGenerate(sample, binPath, workDir=None, inputDataDir=None,
         dataFileLine = "multidark " + datafile
       elif sample.dataFormat == "gadget":
         dataFileLine = "gadget " + datafile
+      elif sample.dataFormat == "gadget2":
+        dataFileLine = "gadget2 " + datafile
       elif sample.dataFormat == "ahf":
         dataFileLine = "gadget " + datafile
       elif sample.dataFormat == "sdf":