Transformed to CMake makefile

CMakeLists.txt

@@ -0,0 +1,16 @@
+cmake_minimum_required(VERSION 2.6)
+
+project(CosmoToolbox)
+
+find_path(NETCDF_INCLUDE_PATH NAMES netcdf.h)
+
+find_library(NETCDF_LIBRARY netcdf)
+find_library(NETCDFCPP_LIBRARY netcdf_c++)
+
+
+
+include(FindPackageHandleStandardArgs)
+set(NETCDF_FIND_REQUIRED TRUE)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH)
+
+add_subdirectory(src)

lib/Makefile

@@ -1,51 +0,0 @@
-SHLIBS= libCosmoTool.$(SOSUFFIX)
-SOURCES= loadRamses.cpp yorick.cpp miniargs.cpp  fortran.cpp interpolate.cpp load_data.cpp powerSpectrum.cpp octTree.cpp loadGadget.cpp
-LIBS= -lnetcdf_c++ -lnetcdf -lgsl -lgslcblas -lm
-
-include config.mk
-
-VPATH=../src
-
-all: $(SHLIBS)
-
-libCosmoTool.$(SOSUFFIX): loadRamses.o yorick.o miniargs.o fortran.o interpolate.o load_data.o powerSpectrum.o octTree.o loadGadget.o
-
-depend: $(SOURCES)
-	@echo "[DEPENDS] $^"
-	@$(CC) $(CPPFLAGS) -M -MM $^ > .mydepends
-
-install:
-	@mkdir -p ../install/lib
-	@mkdir -p ../install/include/CosmoTool
-	@echo "Copying libraries"
-	@cp libCosmoTool.$(SOSUFFIX) ../install/lib
-	@echo "Copying header files"
-	@cp ../src/*.hpp ../install/include/CosmoTool
-	@cp ../src/*.tcc ../install/include/CosmoTool
-
-distclean: clean
-	@rm -f .mydepends
-
-clean:
-	@rm -f *.o
-	@rm -f $(PROGS)
-
-.mydepends: depend Makefile config.mk
-
-%.$(SOSUFFIX):
-	@echo "[LINK SHARED] $@"
-	@$(CXX) $(SOFLAGS) -o $@ $^ $(LDFLAGS) $(LIBS)
-
-%.prog:
-	@echo "[L] $@"
-	@$(CXX) -o $@ $^ $(LDFLAGS) $(LIBS)
-
-%.o: %.c
-	@echo "[C] $< ..."
-	@$(CC) -c -fPIC -o  $@ $< $(CPPFLAGS) $(CFLAGS)
-
-%.o: %.cpp
-	@echo "[C++] $< ..."
-	@$(CXX) -c -fPIC -o $@ $< $(CPPFLAGS) $(CXXFLAGS)
-
-include .mydepends

lib/config.mk

@@ -1,9 +0,0 @@
-CC=gcc
-CXX=g++
-CFLAGS=-ggdb -O0
-CXXFLAGS=-ggdb -O0
-LDFLAGS=
-CPPFLAGS=
-
-SOSUFFIX=so
-SOFLAGS=-shared

src/CMakeLists.txt

@@ -0,0 +1,45 @@
+SET(CosmoTool_SRCS
+	fortran.cpp
+	interpolate.cpp
+	load_data.cpp
+	loadGadget.cpp
+	loadRamses.cpp
+	octTree.cpp
+	powerSpectrum.cpp
+	yorick.cpp
+)
+
+SET(CosmoTool_SRCS
+	bqueue.hpp
+	config.hpp
+	dinterpolate.hpp
+	field.hpp
+	fixArray.hpp
+	fortran.hpp
+	interpolate3d.hpp
+	interpolate.hpp
+	kdtree_leaf.hpp
+	linalg.hpp
+	load_data.hpp
+	loadGadget.hpp
+	loadRamses.hpp
+	loadSimu.hpp
+	miniargs.cpp
+	miniargs.hpp
+	mykdtree.hpp
+	octTree.hpp
+	powerSpectrum.hpp
+	sparseGrid.hpp
+	sphSmooth.hpp
+	yorick.hpp
+)
+
+add_library(CosmoTool SHARED  ${CosmoTool_SRCS})
+target_link_libraries(CosmoTool ${NETCDF_LIBRARY} ${NETCDFCPP_LIBRARY})
+
+install(TARGETS CosmoTool 
+	LIBRARY DESTINATION lib)
+install(DIRECTORY . DESTINATION include/CosmoTool
+	FILES_MATCHING PATTERN "*.hpp")
+install(DIRECTORY . DESTINATION include/CosmoTool
+	FILES_MATCHING PATTERN "*.tcc")

src/loadGadget.cpp

@@ -1,3 +1,4 @@
+#include <iostream>
 #include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
@@ -6,6 +7,7 @@
 #include "fortran.hpp"
 
 using namespace CosmoTool;
+using namespace std;
 
 PurePositionData *CosmoTool::loadGadgetPosition(const char *fname)
 {
@@ -93,33 +95,54 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
     return 0;
   }
 
-  f->beginCheckpoint();
-  for (int i = 0; i < 6; i++)
-    h.npart[i] = f->readInt32();
-  for (int i = 0; i < 6; i++)    
-    h.mass[i] = f->readReal64();
-  data->time = h.time = f->readReal64();
-  h.redshift = f->readReal64();
-  h.flag_sfr = f->readInt32();
-  h.flag_feedback = f->readInt32();
-  for (int i = 0; i < 6; i++)
-    h.npartTotal[i] = f->readInt32();
-  h.flag_cooling = f->readInt32();
-  h.num_files = f->readInt32();
-  data->BoxSize = h.BoxSize = f->readReal64();
-  h.Omega0 = f->readReal64();
-  h.OmegaLambda = f->readReal64();
-  h.HubbleParam = f->readReal64();
-  f->endCheckpoint(true);
-
   long NumPart = 0, NumPartTotal = 0;
-  for(int k=0; k<5; k++)
+
+  try
     {
-      NumPart += h.npart[k];
+      f->beginCheckpoint();
-      NumPartTotal += (id < 0) ? h.npart[k] : h.npartTotal[k];
+      for (int i = 0; i < 6; i++)
+	h.npart[i] = f->readInt32();
+      for (int i = 0; i < 6; i++)    
+	h.mass[i] = f->readReal64();
+      data->time = h.time = f->readReal64();
+      h.redshift = f->readReal64();
+      h.flag_sfr = f->readInt32();
+      h.flag_feedback = f->readInt32();
+      for (int i = 0; i < 6; i++)
+	h.npartTotal[i] = f->readInt32();
+      h.flag_cooling = f->readInt32();
+      h.num_files = f->readInt32();
+      data->BoxSize = h.BoxSize = f->readReal64();
+      h.Omega0 = f->readReal64();
+      h.OmegaLambda = f->readReal64();
+      h.HubbleParam = f->readReal64();
+      f->endCheckpoint(true);
+      
+      for(int k=0; k<6; k++)
+	{
+	  NumPart += h.npart[k];
+	  NumPartTotal += (id < 0) ? h.npart[k] : h.npartTotal[k];
+	}
+      data->NumPart = NumPart;
+      data->TotalNumPart = NumPartTotal;
+    }
+  catch (const InvalidUnformattedAccess& e)
+    {
+      cerr << "Invalid format while reading header" << endl;
+      delete data;
+      delete f;
+      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++)
+	  data->type[p] = k;
     }
-  data->NumPart = NumPart;
-  data->TotalNumPart = NumPartTotal;
 
   if (loadflags & NEED_POSITION) {
       
@@ -130,17 +153,27 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
 	return 0;
       }
     }
-
+    
-    f->beginCheckpoint();
+    try
-    for(int k = 0, p = 0; k < 5; k++) {
+      {
-      for(int n = 0; n < h.npart[k]; n++) {
+	f->beginCheckpoint();
-	data->Pos[0][p] = f->readReal32();
+	for(int k = 0, p = 0; k < 6; k++) {
-	data->Pos[1][p] = f->readReal32();
+	  for(int n = 0; n < h.npart[k]; n++) {
-	data->Pos[2][p] = f->readReal32();
+	    data->Pos[0][p] = f->readReal32();
-	p++;
+	    data->Pos[1][p] = f->readReal32();
+	    data->Pos[2][p] = f->readReal32();
+	    p++;
+	  }
+	}
+	f->endCheckpoint();
+      }
+    catch (const InvalidUnformattedAccess& e)
+      {
+	cerr << "Invalid format while reading positions" << endl;
+	delete f;
+	delete data;
+	return 0;
       }
-    }
-    f->endCheckpoint();
     
   } else {
     // Skip positions
@@ -153,21 +186,32 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
 	data->Vel[i] = new float[data->NumPart];
 	if (data->Vel[i] == 0) 
 	  {
+	    delete f;
 	    delete data;
 	    return 0;
 	  }
       }
-
+    
-    f->beginCheckpoint();
+    try
-    for(int k = 0, p = 0; k < 5; k++) {
+      {
-      for(int n = 0; n < h.npart[k]; n++) {
+	f->beginCheckpoint();
-	data->Vel[0][p] = f->readReal32();
+	for(int k = 0, p = 0; k < 6; k++) {
-	data->Vel[1][p] = f->readReal32();
+	  for(int n = 0; n < h.npart[k]; n++) {
-	data->Vel[2][p] = f->readReal32();
+	    data->Vel[0][p] = f->readReal32();
-	p++;
+	    data->Vel[1][p] = f->readReal32();
+	    data->Vel[2][p] = f->readReal32();
+	    p++;
+	  }
+	}
+	f->endCheckpoint();
+      }
+    catch (const InvalidUnformattedAccess& e)
+      {
+	cerr << "Invalid format while reading velocities" << endl;
+	delete f;
+	delete data;
+	return 0;
       }
-    }
-    f->endCheckpoint();
     
     // TODO: FIX THE UNITS OF THESE FUNKY VELOCITIES !!!
   } else {
@@ -177,23 +221,34 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
 
   // Skip ids
   if (loadflags & NEED_GADGET_ID) {
-    f->beginCheckpoint();
+    try
-    data->Id = new int[data->NumPart];
-    if (data->Id == 0)
       {
+	f->beginCheckpoint();
+	data->Id = new int[data->NumPart];
+	if (data->Id == 0)
+	  {
+	    delete f;
+	    delete data;
+	    return 0;
+	  }
+	
+	for(int k = 0, p = 0; k < 6; k++)
+	  {
+	    for(int n = 0; n < h.npart[k]; n++)
+	      {
+		data->Id[p] = f->readInt32();
+		p++;
+	      }
+	  }
+	f->endCheckpoint();
+      }
+    catch (const InvalidUnformattedAccess& e)
+      {
+	cerr << "Invalid formatted while reading ID" << endl;
+	delete f;
 	delete data;
 	return 0;
       }
-
-    for(int k = 0, p = 0; k < 6; k++)
-      {
-	for(int n = 0; n < h.npart[k]; n++)
-	  {
-	    data->Id[p] = f->readInt32();
-	    p++;
-	  }
-      }
-    f->endCheckpoint();
   } else {
     f->skip(2*4);
     for (int k = 0; k < 6; k++)

src/loadSimu.hpp

@@ -7,7 +7,7 @@ namespace CosmoTool
   static const int NEED_GADGET_ID = 1;
   static const int NEED_POSITION = 2;
   static const int NEED_VELOCITY = 4;
-  
+  static const int NEED_TYPE = 8;
 
   class SimuData 
   {
@@ -20,8 +20,9 @@ namespace CosmoTool
     int *Id;
     float *Pos[3];
     float *Vel[3];
+    int *type;
   public:
-    SimuData() : Id(0),NumPart(0)  { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; }
+    SimuData() : Id(0),NumPart(0),type(0)  { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; }
     ~SimuData() 
     {
       for (int j = 0; j < 3; j++)
@@ -31,6 +32,8 @@ namespace CosmoTool
 	  if (Vel[j])
 	    delete[] Vel[j];
 	}
+      if (type)
+	delete[] type;
       if (Id)
 	delete[] Id;
     }