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

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This commit is contained in:
Guilhem Lavaux 2011-06-06 09:43:40 -04:00
commit 46a8ca36ae
9 changed files with 198 additions and 17 deletions
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7
CMakeLists.txt
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@ -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

104
GetGitRevisionDescription.cmake Normal file
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@ -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()

30
GetGitRevisionDescription.cmake.in Normal file
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@ -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)

28
src/loadGadget.cpp
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@ -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();
h.OmegaLambda = f->readReal64();
h.HubbleParam = f->readReal64();
data->Omega_M = h.Omega0 = f->readReal64();
data->Omega_Lambda = h.OmegaLambda = 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();
data->Vel[1][p] = f->readReal32();
data->Vel[2][p] = f->readReal32();
// THIS IS GADGET 1
data->Vel[0][p] = f->readReal32()*velmul;
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);

2
src/loadGadget.hpp
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@ -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);
};

1
src/loadRamses.cpp
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@ -243,7 +243,6 @@ int readInfoFile(const char *basename, int outputId, InfoData& info)
iss >> unitLength;
infoMap[keyword] = unitLength;
}
}

32
src/mykdtree.tcc
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@ -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)
{
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];

2
src/powerSpectrum.cpp
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@ -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 {

7
src/yorick.cpp
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@ -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>
{