Merge branch 'master' of file:///home/guilhem/Dropbox/gitRoot/CosmoToolbox

CMakeLists.txt

@@ -1,7 +1,12 @@
 cmake_minimum_required(VERSION 2.6)
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}")
 
 project(CosmoToolbox)
 
+include(GetGitRevisionDescription)
+
+get_git_head_revision(HEAD GIT_VER)
+
 option(BUILD_SHARED_LIBS "Build shared libraries." OFF)
 
 find_path(NETCDF_INCLUDE_PATH NAMES netcdf.h)
@@ -27,7 +32,7 @@ SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
 SET(CPACK_PACKAGE_VERSION_MINOR "0")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "0-${GIT_VER}")
 SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${GalaxExplorer_VERSION_MAJOR}.${GalaxExplorer_VERSION_MINOR}")
 SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
 SET(CPACK_SOURCE_IGNORE_FILES 

GetGitRevisionDescription.cmake

@@ -0,0 +1,104 @@
+# - Returns a version string from Git
+#
+# These functions force a re-configure on each git commit so that you can
+# trust the values of the variables in your build system.
+#
+#  get_git_head_revision(<refspecvar> <hashvar> [<additonal arguments to git describe> ...])
+#
+# Returns the refspec and sha hash of the current head revision
+#
+#  git_describe(<var> [<additonal arguments to git describe> ...])
+#
+# Returns the results of git describe on the source tree, and adjusting
+# the output so that it tests false if an error occurs.
+#
+#  git_get_exact_tag(<var> [<additonal arguments to git describe> ...])
+#
+# Returns the results of git describe --exact-match on the source tree,
+# and adjusting the output so that it tests false if there was no exact
+# matching tag.
+#
+# Requires CMake 2.6 or newer (uses the 'function' command)
+#
+# Original Author:
+# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
+# http://academic.cleardefinition.com
+# Iowa State University HCI Graduate Program/VRAC
+#
+# Copyright Iowa State University 2009-2010.
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+
+if(__get_git_revision_description)
+	return()
+endif()
+set(__get_git_revision_description YES)
+
+# We must run the following at "include" time, not at function call time,
+# to find the path to this module rather than the path to a calling list file
+get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH)
+
+function(get_git_head_revision _refspecvar _hashvar)
+	set(GIT_DIR "${CMAKE_SOURCE_DIR}/.git")
+	if(NOT EXISTS "${GIT_DIR}")
+		# not in git
+		set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
+		set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
+		return()
+	endif()
+	set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
+	if(NOT EXISTS "${GIT_DATA}")
+		file(MAKE_DIRECTORY "${GIT_DATA}")
+	endif()
+	set(HEAD_FILE "${GIT_DATA}/HEAD")
+	configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY)
+
+	configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in" "${GIT_DATA}/grabRef.cmake" @ONLY)
+	include("${GIT_DATA}/grabRef.cmake")
+
+	set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE)
+	set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE)
+endfunction()
+
+function(git_describe _var)
+	if(NOT GIT_FOUND)
+		find_package(Git QUIET)
+	endif()
+	get_git_head_revision(refspec hash)
+	if(NOT GIT_FOUND)
+		set(${_var} "GIT-NOTFOUND"  PARENT_SCOPE)
+		return()
+	endif()
+	if(NOT hash)
+		set(${_var} "HEAD-HASH-NOTFOUND"  PARENT_SCOPE)
+		return()
+	endif()
+
+	# TODO sanitize
+	#if((${ARGN}" MATCHES "&&") OR
+	#	(ARGN MATCHES "||") OR
+	#	(ARGN MATCHES "\\;"))
+	#	message("Please report the following error to the project!")
+	#	message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
+	#endif()
+
+	#message(STATUS "Arguments to execute_process: ${ARGN}")
+
+	execute_process(COMMAND "${GIT_EXECUTABLE}" describe ${hash} ${ARGN}
+		WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+		RESULT_VARIABLE res
+		OUTPUT_VARIABLE out
+		ERROR_QUIET
+		OUTPUT_STRIP_TRAILING_WHITESPACE)
+	if(NOT res EQUAL 0)
+		set(out "${out}-${res}-NOTFOUND")
+	endif()
+
+	set(${_var} "${out}" PARENT_SCOPE)
+endfunction()
+
+function(git_get_exact_tag _var)
+	git_describe(out --exact-match ${ARGN})
+	set(${_var} "${out}" PARENT_SCOPE)
+endfunction()

GetGitRevisionDescription.cmake.in

@@ -0,0 +1,30 @@
+# 
+# Internal file for GetGitRevisionDescription.cmake
+#
+# Requires CMake 2.6 or newer (uses the 'function' command)
+#
+# Original Author:
+# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
+# http://academic.cleardefinition.com
+# Iowa State University HCI Graduate Program/VRAC
+#
+# Copyright Iowa State University 2009-2010.
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+
+file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
+
+string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS)
+if(HEAD_CONTENTS MATCHES "ref")
+	# named branch
+	string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}")
+
+	configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
+else()
+	# detached HEAD
+	configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY)
+endif()
+
+file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024)
+string(STRIP "${HEAD_HASH}" HEAD_HASH)

src/loadGadget.cpp

@@ -1,3 +1,4 @@
+#include <cmath>
 #include <iostream>
 #include <assert.h>
 #include <stdio.h>
@@ -63,12 +64,13 @@ PurePositionData *CosmoTool::loadGadgetPosition(const char *fname)
 
 
 
-SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
+SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags, int GadgetFormat)
 {
   SimuData *data;
   int p, n;
   UnformattedRead *f;
   GadgetHeader h;
+  float velmul;
 
   if (id >= 0) {
     int k = snprintf(0, 0, "%s.%d", fname, id)+1;
@@ -113,9 +115,9 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
       h.flag_cooling = f->readInt32();
       h.num_files = f->readInt32();
       data->BoxSize = h.BoxSize = f->readReal64();
-      h.Omega0 = f->readReal64();
+      data->Omega_M = h.Omega0 = f->readReal64();
-      h.OmegaLambda = f->readReal64();
+      data->Omega_Lambda = h.OmegaLambda = f->readReal64();
-      h.HubbleParam = f->readReal64();
+      data->Hubble = h.HubbleParam = f->readReal64();
       f->endCheckpoint(true);
       
       for(int k=0; k<6; k++)
@@ -125,6 +127,14 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
 	}
       data->NumPart = NumPart;
       data->TotalNumPart = NumPartTotal;
+      if (GadgetFormat == 1)
+        velmul = sqrt(h.time);
+      else if (GadgetFormat == 2)
+        velmul = 1/(h.time);
+      else {
+        cerr << "unknown gadget format" << endl;
+	abort();
+      }
     }
   catch (const InvalidUnformattedAccess& e)
     {
@@ -197,9 +207,10 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
 	f->beginCheckpoint();
 	for(int k = 0, p = 0; k < 6; k++) {
 	  for(int n = 0; n < h.npart[k]; n++) {
-	    data->Vel[0][p] = f->readReal32();
+	    // THIS IS GADGET 1
-	    data->Vel[1][p] = f->readReal32();
+	    data->Vel[0][p] = f->readReal32()*velmul;
-	    data->Vel[2][p] = f->readReal32();
+	    data->Vel[1][p] = f->readReal32()*velmul;
+	    data->Vel[2][p] = f->readReal32()*velmul;
 	    p++;
 	  }
 	}
@@ -213,7 +224,8 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
 	return 0;
       }
     
-    // TODO: FIX THE UNITS OF THESE FUNKY VELOCITIES !!!
+    // THE VELOCITIES ARE IN PHYSICAL COORDINATES
+///    // TODO: FIX THE UNITS OF THESE FUNKY VELOCITIES !!!
   } else {
     // Skip velocities
     f->skip(NumPart*3*sizeof(float)+2*4);

src/loadGadget.hpp

@@ -8,7 +8,7 @@ namespace CosmoTool {
   
   PurePositionData *loadGadgetPosition(const char *fname);
 
-  SimuData *loadGadgetMulti(const char *fname, int id, int flags);
+  SimuData *loadGadgetMulti(const char *fname, int id, int flags, int GadgetFormat = 1);
   
 };
 

src/loadRamses.cpp

@@ -243,7 +243,6 @@ int readInfoFile(const char *basename, int outputId, InfoData& info)
 	  iss >> unitLength;
 
 	  infoMap[keyword] = unitLength;
-	  
 	}
     }
   

src/mykdtree.tcc

@@ -446,6 +446,7 @@ namespace CosmoTool {
   {
     char id[KDTREE_DISK_SIGNATURE_LEN];
     long nodesUsed, numCells;
+    long rootId;
   };
 
   template<int N, typename ValType, typename CType>
@@ -456,6 +457,7 @@ namespace CosmoTool {
     strncpy(h.id, KDTREE_DISK_SIGNATURE, KDTREE_DISK_SIGNATURE_LEN);
     h.nodesUsed = lastNode;
     h.numCells = numNodes;
+    h.rootId = root - nodes;
     o.write((char*)&h, sizeof(h));
 
     for (long i = 0; i < lastNode; i++)
@@ -464,13 +466,17 @@ namespace CosmoTool {
 
 	node_on_disk.cell_id = nodes[i].value - base_cell;
 	if (nodes[i].children[0] == 0)
-	  node_on_disk.children_node[0] = -1;
+	  node_on_disk.children_node[0] = -1L;
 	else
 	  node_on_disk.children_node[0] = nodes[i].children[0] - nodes;
+       assert((node_on_disk.children_node[0] == -1) || ((node_on_disk.children_node[0] >= 0) &&  (node_on_disk.children_node[0] < lastNode)));
+
 	if (nodes[i].children[1] == 0)
-	  node_on_disk.children_node[1] = -1;
+	  node_on_disk.children_node[1] = -1L;
 	else
 	  node_on_disk.children_node[1] = nodes[i].children[1] - nodes;
+       assert((node_on_disk.children_node[1] == -1) || ((node_on_disk.children_node[1] >= 0) &&  (node_on_disk.children_node[1] < lastNode)));
+
 	memcpy(node_on_disk.minBound, nodes[i].minBound, sizeof(coords));
 	memcpy(node_on_disk.maxBound, nodes[i].maxBound, sizeof(coords));
 
@@ -489,10 +495,15 @@ namespace CosmoTool {
 
     in.read((char *)&h, sizeof(h));
     if (!in || strncmp(h.id, KDTREE_DISK_SIGNATURE, KDTREE_DISK_SIGNATURE_LEN) != 0)
-      throw InvalidOnDiskKDTree();
+      {
+         std::cerr << "KDTree Signature invalid" << std::endl;
+         throw InvalidOnDiskKDTree();
+      } 
 
-    if (h.numCells != Ncells || h.nodesUsed < 0)
+    if (h.numCells != Ncells || h.nodesUsed < 0) {
+      std::cerr << "The number of cells has changed (" << h.numCells << " != " << Ncells << ") or nodesUsed=" << h.nodesUsed << std::endl;
       throw InvalidOnDiskKDTree();
+    }
 
     base_cell = cells;
     nodes = new Node[h.nodesUsed];
@@ -505,11 +516,18 @@ namespace CosmoTool {
 
 	in.read((char *)&node_on_disk, sizeof(node_on_disk));
 
-	if (!in || node_on_disk.cell_id > numNodes || node_on_disk.cell_id < 0 ||
+	if (!in) {
+           std::cerr << "End-of-file reached" << std::endl;
+           delete[] nodes;
+           throw InvalidOnDiskKDTree();
+        }
+        if (node_on_disk.cell_id > numNodes || node_on_disk.cell_id < 0 ||
 	    node_on_disk.children_node[0] > lastNode || node_on_disk.children_node[0] < -1 ||
 	    node_on_disk.children_node[1] > lastNode || node_on_disk.children_node[1] < -1)
 	  {
 	    delete[] nodes;
+            std::cerr << "Invalid cell id or children node id invalid" << std::endl;
+            std::cerr << node_on_disk.cell_id << std::endl << node_on_disk.children_node[0] << std::endl << node_on_disk.children_node[1] << std::endl;
 	    throw InvalidOnDiskKDTree();
 	  }
 
@@ -535,10 +553,16 @@ namespace CosmoTool {
 	if (c != N)
 	  {
 	    delete[] nodes;
+            std::cerr << "Coordinates of the cell inconsistent with the boundaries" << std::endl
+                      << "   X=" << nodes[i].value->coord[0] << " B=[" << nodes[i].minBound[0] << "," << nodes[i].maxBound[0] << "]" << std::endl
+                      << "   Y=" << nodes[i].value->coord[1] << " B=[" << nodes[i].minBound[1] << "," << nodes[i].maxBound[1] << "]" << std::endl
+                      << "   Z=" << nodes[i].value->coord[2] << " B=[" << nodes[i].minBound[2] << "," << nodes[i].maxBound[2] << "]" << std::endl;
 	    throw InvalidOnDiskKDTree();
 	  }
       }
 
+    root = &nodes[h.rootId];
+    
     sortingHelper = new Cell *[Ncells];
     for (uint32_t i = 0; i < Ncells; i++)
       sortingHelper[i] = &cells[i];    

src/powerSpectrum.cpp

@@ -21,7 +21,7 @@ using namespace std;
 #define POWER_BDM 7
 #define POWER_TEST 8
 
-#define POWER_SPECTRUM HU_WIGGLES
+#define POWER_SPECTRUM POWER_EFSTATHIOU
 
 namespace Cosmology {
 

src/yorick.cpp

@@ -118,6 +118,13 @@ public:
   static const NcType t = ncInt;
 };
 
+template<>
+class NetCDF_type<unsigned int>
+{
+public:
+  static const NcType t = ncInt;
+};
+
 template<>
 class NetCDF_type<float>
 {