diff --git a/cmake/AkantuMacros.cmake b/cmake/AkantuMacros.cmake
index ecdfd8127..e367913c8 100644
--- a/cmake/AkantuMacros.cmake
+++ b/cmake/AkantuMacros.cmake
@@ -1,160 +1,160 @@
#===============================================================================
# @file AkantuMacros.cmake
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date Thu Feb 17 17:28:21 2011
#
# @brief Set of macros used by akantu cmake files
#
# @section LICENSE
#
# Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
macro(check_for_isnan result)
include(CheckFunctionExists)
check_function_exists(std::isnan HAVE_STD_ISNAN)
if(HAVE_STD_ISNAN)
set(result "std::isnan(x)")
else()
check_function_exists(isnan HAVE_ISNAN)
if(HAVE_ISNAN)
set(result "(::isnan(x))")
else()
check_function_exists(_isnan HAVE_ISNAN_MATH_H)
if(HAVE_ISNAN_MATH_H)
set(result "(_isnan(x))")
else()
set(result (x == std::numeric_limits<Real>::quiet_NAN()))
endif()
endif()
endif()
endmacro()
#===============================================================================
macro(copy_files target_depend)
foreach(_file ${ARGN})
set(_target ${CMAKE_CURRENT_BINARY_DIR}/${_file})
set(_source ${CMAKE_CURRENT_SOURCE_DIR}/${_file})
add_custom_command(
OUTPUT ${_target}
COMMAND ${CMAKE_COMMAND} -E copy_if_different ${_source} ${_target}
DEPENDS ${_source}
)
set(_target_name ${target_depend}_${_file})
add_custom_target(${_target_name} DEPENDS ${_target})
add_dependencies(${target_depend} ${_target_name})
endforeach()
endmacro()
#===============================================================================
macro(add_akantu_definitions)
foreach(_definition ${AKANTU_DEFINITIONS})
add_definitions(-D${_definition})
endforeach()
endmacro()
macro(include_boost)
find_package(Boost REQUIRED)
mark_as_advanced(Boost_DIR)
if(Boost_FOUND)
- list(APPEND AKANTU_EXTERNAL_LIB_INCLUDE_DIR ${Boost_INCLUDE_DIRS})
+ list(APPEND AKANTU_EXTERNAL_LIB_INCLUDE_DIR ${Boost_INCLUDE_DIRS} ${Boost_INCLUDE_DIR})
endif()
message(STATUS "Looking for Boost liraries")
set(AKANTU_BOOST_COMPONENT_ALREADY_DONE)
foreach(_comp ${AKANTU_BOOST_COMPONENTS})
list(FIND AKANTU_BOOST_COMPONENT_ALREADY_DONE ${_comp} _res)
if(_res EQUAL -1)
find_package(Boost COMPONENTS ${_comp} QUIET)
string(TOUPPER ${_comp} _u_comp)
if(Boost_${_u_comp}_FOUND)
message(STATUS " ${_comp}: FOUND")
set(AKANTU_BOOST_${_u_comp} TRUE CACHE INTERNAL "" FORCE)
list(APPEND AKANTU_EXTERNAL_LIBRARIES ${Boost_${_u_comp}_LIBRARY})
else()
message(STATUS " ${_comp}: NOT FOUND")
endif()
list(APPEND AKANTU_BOOST_COMPONENT_ALREADY_DONE ${_comp})
endif()
endforeach()
endmacro()
#===============================================================================
if(__CMAKE_PARSE_ARGUMENTS_INCLUDED)
return()
endif()
set(__CMAKE_PARSE_ARGUMENTS_INCLUDED TRUE)
function(CMAKE_PARSE_ARGUMENTS prefix _optionNames _singleArgNames _multiArgNames)
# first set all result variables to empty/FALSE
foreach(arg_name ${_singleArgNames} ${_multiArgNames})
set(${prefix}_${arg_name})
endforeach(arg_name)
foreach(option ${_optionNames})
set(${prefix}_${option} FALSE)
endforeach(option)
set(${prefix}_UNPARSED_ARGUMENTS)
set(insideValues FALSE)
set(currentArgName)
# now iterate over all arguments and fill the result variables
foreach(currentArg ${ARGN})
list(FIND _optionNames "${currentArg}" optionIndex) # ... then this marks the end of the arguments belonging to this keyword
list(FIND _singleArgNames "${currentArg}" singleArgIndex) # ... then this marks the end of the arguments belonging to this keyword
list(FIND _multiArgNames "${currentArg}" multiArgIndex) # ... then this marks the end of the arguments belonging to this keyword
if(${optionIndex} EQUAL -1 AND ${singleArgIndex} EQUAL -1 AND ${multiArgIndex} EQUAL -1)
if(insideValues)
if("${insideValues}" STREQUAL "SINGLE")
set(${prefix}_${currentArgName} ${currentArg})
set(insideValues FALSE)
elseif("${insideValues}" STREQUAL "MULTI")
list(APPEND ${prefix}_${currentArgName} ${currentArg})
endif()
else(insideValues)
list(APPEND ${prefix}_UNPARSED_ARGUMENTS ${currentArg})
endif(insideValues)
else()
if(NOT ${optionIndex} EQUAL -1)
set(${prefix}_${currentArg} TRUE)
set(insideValues FALSE)
elseif(NOT ${singleArgIndex} EQUAL -1)
set(currentArgName ${currentArg})
set(${prefix}_${currentArgName})
set(insideValues "SINGLE")
elseif(NOT ${multiArgIndex} EQUAL -1)
set(currentArgName ${currentArg})
set(${prefix}_${currentArgName})
set(insideValues "MULTI")
endif()
endif()
endforeach(currentArg)
# propagate the result variables to the caller:
foreach(arg_name ${_singleArgNames} ${_multiArgNames} ${_optionNames})
set(${prefix}_${arg_name} ${${prefix}_${arg_name}} PARENT_SCOPE)
endforeach(arg_name)
set(${prefix}_UNPARSED_ARGUMENTS ${${prefix}_UNPARSED_ARGUMENTS} PARENT_SCOPE)
endfunction(CMAKE_PARSE_ARGUMENTS _options _singleArgs _multiArgs)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 752a64a5e..b3b41239f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,150 +1,153 @@
#===============================================================================
# @file CMakeLists.txt
#
# @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date Mon Nov 28 16:54:12 2011
#
# @brief CMake file for the library
#
# @section LICENSE
#
# Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
# Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
#
# Akantu is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with Akantu. If not, see <http://www.gnu.org/licenses/>.
#
#===============================================================================
#===============================================================================
# Package Management
#===============================================================================
generate_source_list_from_packages(${CMAKE_CURRENT_BINARY_DIR}
AKANTU_LIBRARY_SRCS
AKANTU_LIBRARY_INLINE_HDRS
AKANTU_LIBRARY_HDRS
AKANTU_LIBRARY_INCLUDE_DIRS)
#===========================================================================
# header for blas/lapack (any other fortran libraries)
#===========================================================================
if(AKANTU_LAPACK OR AKANTU_BLAS)
include(FortranCInterface)
FortranCInterface_HEADER(
${CMAKE_CURRENT_BINARY_DIR}/aka_fortran_mangling.hh
MACRO_NAMESPACE "AKA_FC_")
mark_as_advanced(CDEFS)
endif()
configure_file(common/aka_config.hh.in "${CMAKE_CURRENT_BINARY_DIR}/aka_config.hh" @ONLY)
list(APPEND AKANTU_LIBRARY_HDRS ${CMAKE_CURRENT_BINARY_DIR}/aka_config.hh)
#===========================================================================
# header precompilation
#===========================================================================
set(AKANTU_COMMON_HDR_TO_PRECOMPILE
common/aka_vector.hh
common/aka_math.hh
common/aka_types.hh
fem/element_class.hh
)
set(AKANTU_PRECOMPILE_HDR_INCLUDE_DIRS
${CMAKE_CURRENT_BINARY_DIR}/common/
${CMAKE_CURRENT_BINARY_DIR}/fem/
)
set(AKANTU_INCLUDE_DIRS
${CMAKE_CURRENT_BINARY_DIR} ${AKANTU_LIBRARY_INCLUDE_DIRS} ${AKANTU_PRECOMPILE_HDR_INCLUDE_DIRS}
CACHE INTERNAL "Internal include directories to link with Akantu as a subproject")
include_directories(${AKANTU_INCLUDE_DIRS} ${AKANTU_EXTERNAL_LIB_INCLUDE_DIR})
function(generate_material_list)
message(STATUS "Determining the list of recognized materials...")
+
+ set(_include_dirs ${AKANTU_INCLUDE_DIRS} ${AKANTU_EXTERNAL_LIB_INCLUDE_DIR})
+
try_run(_material_list_run _material_list_compile
${CMAKE_BINARY_DIR}
${PROJECT_SOURCE_DIR}/cmake/material_lister.cc
- CMAKE_FLAGS "-DINCLUDE_DIRECTORIES:STRING=${AKANTU_INCLUDE_DIRS}"
+ CMAKE_FLAGS "-DINCLUDE_DIRECTORIES:STRING=${_include_dirs}"
COMPILE_DEFINITIONS "-DAKANTU_CMAKE_LIST_MATERIALS"
COMPILE_OUTPUT_VARIABLE _compile_results
RUN_OUTPUT_VARIABLE _result_material_list)
if(_material_list_compile AND "${_material_list_run}" EQUAL 0)
message(STATUS "Materials included in Akantu:")
string(REPLACE "\n" ";" _material_list "${_result_material_list}")
foreach(_mat ${_material_list})
string(REPLACE ":" ";" _mat_key "${_mat}")
list(GET _mat_key 0 _key)
list(GET _mat_key 1 _class)
list(LENGTH _mat_key _l)
if("${_l}" GREATER 2)
list(REMOVE_AT _mat_key 0 1)
set(_opt " -- options: [")
foreach(_o ${_mat_key})
set(_opt "${_opt} ${_o}")
endforeach()
set(_opt "${_opt} ]")
else()
set(_opt "")
endif()
message(STATUS " ${_class} -- key: ${_key}${_opt}")
endforeach()
else()
message(STATUS "Could not determine the list of materials.")
message("${_compile_results}")
endif()
endfunction()
generate_material_list()
if(CMAKE_COMPILER_IS_GNUCXX)
include(PCHgcc)
foreach(_header ${AKANTU_COMMON_HDR_TO_PRECOMPILE})
add_pch_rule(${_header} AKANTU_LIBRARY_SRCS)
endforeach()
elseif(CMAKE_COMPILER_IS_GNUCXX)
endif()
#===============================================================================
# Library generation
#===============================================================================
add_library(akantu ${AKANTU_LIBRARY_SRCS})
target_link_libraries(akantu ${AKANTU_EXTERNAL_LIBRARIES})
list(APPEND AKANTU_PUBLIC_HDRS ${AKANTU_LIBRARY_HDRS} ${AKANTU_LIBRARY_INLINE_HDRS})
set_target_properties(akantu PROPERTIES ${AKANTU_LIBRARY_PROPERTIES})
set_target_properties(akantu PROPERTIES PUBLIC_HEADER "${AKANTU_PUBLIC_HDRS}")
list(APPEND AKANTU_EXPORT_LIST akantu)
install(TARGETS akantu
EXPORT ${AKANTU_TARGETS_EXPORT}
LIBRARY DESTINATION lib COMPONENT lib
ARCHIVE DESTINATION lib COMPONENT lib
PUBLIC_HEADER DESTINATION include/akantu/ COMPONENT dev
)
if("${AKANTU_TARGETS_EXPORT}" STREQUAL "AkantuLibraryDepends")
install(EXPORT AkantuLibraryDepends DESTINATION lib/akantu
COMPONENT dev)
endif()
#Export for build tree
export(TARGETS ${AKANTU_EXPORT_LIST}
FILE "${CMAKE_BINARY_DIR}/AkantuLibraryDepends.cmake")
export(PACKAGE Akantu)
diff --git a/src/io/parser/cppargparse/cppargparse.hh b/src/io/parser/cppargparse/cppargparse.hh
index 00e3bfabe..8a7d3da69 100644
--- a/src/io/parser/cppargparse/cppargparse.hh
+++ b/src/io/parser/cppargparse/cppargparse.hh
@@ -1,169 +1,169 @@
/**
* @file cppargparse.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Mar 28 14:07:02 2014
*
* @brief Get the commandline options and store them as short, long and others
*
* @section LICENSE
*
* Copyright (©) 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <map>
#include <string>
#include <iostream>
#include <vector>
#ifndef __CPPARGPARSE_HH__
#define __CPPARGPARSE_HH__
namespace cppargparse {
enum ArgumentType {
_string,
_integer,
_float,
_boolean
};
enum ArgumentNargs {
_one_if_possible = -1,
_at_least_one = -2,
_any = -3
};
enum ParseFlags {
_no_flags = 0x0,
_stop_on_not_parsed = 0x1,
_remove_parsed = 0x2
};
inline ParseFlags operator|(const ParseFlags & a, const ParseFlags & b) {
ParseFlags tmp = ParseFlags(int(a) | int(b));
return tmp;
}
class ArgumentParser {
public:
class Argument {
public:
Argument() : name(std::string()) {}
virtual ~Argument() {}
virtual void printself(std::ostream & stream) const = 0;
template<class T> operator T() const;
std::string name;
};
/// constructor
ArgumentParser();
/// destroy everything
~ArgumentParser();
/// add an argument with a description
void addArgument(const std::string & name_or_flag,
const std::string & help,
int nargs = 1,
ArgumentType type = _string);
/// add an argument with an help and a default value
template<class T>
void addArgument(const std::string & name_or_flag,
const std::string & help,
int nargs,
ArgumentType type,
T def);
/// add an argument with an help and a default + const value
template<class T>
void addArgument(const std::string & name_or_flag,
const std::string & help,
int nargs,
ArgumentType type,
T def,
T cons);
/// parse argc, argv
void parse(int & argc, char ** & argv,
int flags = _stop_on_not_parsed);
/// print the content in the stream
void printself(std::ostream & stream) const;
/// print the help text
void print_help(std::ostream & stream = std::cout) const;
/// print the usage text
void print_usage(std::ostream & stream = std::cout) const;
/// set an external function to replace the exit function from the stdlib
void setExternalExitFunction(void (*external_exit)(int)) {
this->external_exit = external_exit;
}
/// accessor for a registered argument that was parsed, throw an exception if
/// the argument does not exist or was not set (parsed or default value)
const Argument & operator[](const std::string & name) const;
-private:
+public:
class _Argument;
template<class T> class ArgumentStorage;
-
+private:
_Argument & _addArgument(const std::string & name_or_flag,
const std::string & description,
int nargs,
ArgumentType type);
void _exit(const std::string & msg = "", int status = 0);
bool checkType(ArgumentType type, const std::string & value) const;
void print_usage_nargs(std::ostream & stream, const _Argument & argument) const;
void print_help_argument(std::ostream & stream, const _Argument & argument) const;
private:
typedef std::map<std::string, _Argument *> _Arguments;
typedef std::map<std::string, Argument *> Arguments;
typedef std::map<std::string, _Argument *> ArgumentKeyMap;
typedef std::vector<_Argument *> PositionalArgument;
_Arguments arguments;
ArgumentKeyMap key_args;
PositionalArgument pos_args;
Arguments success_parsed;
std::string program_name;
void (*external_exit)(int);
};
}
inline std::ostream & operator<<(std::ostream & stream, const cppargparse::ArgumentParser & argparse) {
argparse.printself(stream);
return stream;
}
#endif /* __CPPARGPARSE_HH__ */
#include "cppargparse_tmpl.hh"
diff --git a/src/io/parser/cppargparse/cppargparse_tmpl.hh b/src/io/parser/cppargparse/cppargparse_tmpl.hh
index 9fbe094d6..d9bb0087f 100644
--- a/src/io/parser/cppargparse/cppargparse_tmpl.hh
+++ b/src/io/parser/cppargparse/cppargparse_tmpl.hh
@@ -1,214 +1,214 @@
/**
* @file cppargparse_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Mar 31 21:15:31 2014
*
* @brief
*
* @section LICENSE
*
* Copyright (©) 2010-2011 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include <stdexcept>
#ifndef __CPPARGPARSE_TMPL_HH__
#define __CPPARGPARSE_TMPL_HH__
namespace cppargparse {
/* -------------------------------------------------------------------------- */
/* Argument */
/* -------------------------------------------------------------------------- */
struct ArgumentParser::_Argument : public Argument {
_Argument() : Argument(),
help(std::string()),
nargs(1),
type(_string),
required(false),
parsed(false),
has_default(false),
has_const(false),
is_positional(false) {}
virtual ~_Argument() {}
void setValues(std::vector<std::string> & values) {
for (std::vector<std::string>::iterator it = values.begin();
it != values.end(); ++it) {
this->addValue(*it);
}
}
virtual void addValue(std::string & value) = 0;
virtual void setToDefault() = 0;
virtual void setToConst() = 0;
std::ostream & printDefault(std::ostream & stream) const {
stream << std::boolalpha;
if(has_default) {
stream << " (default: ";
this->_printDefault(stream);
stream << ")";
}
if(has_const) {
stream << " (const: ";
this->_printConst(stream);
stream << ")";
}
return stream;
}
virtual std::ostream & _printDefault(std::ostream & stream) const = 0;
virtual std::ostream & _printConst(std::ostream & stream) const = 0;
std::string help;
int nargs;
ArgumentType type;
bool required;
bool parsed;
bool has_default;
bool has_const;
std::vector<std::string> keys;
bool is_positional;
};
/* -------------------------------------------------------------------------- */
template<class T>
class ArgumentParser::ArgumentStorage : public ArgumentParser::_Argument {
public:
ArgumentStorage() : _default(T()), _const(T()), values(std::vector<T>()) {}
virtual void addValue(std::string & value) {
std::stringstream sstr(value);
T t;
sstr >> t;
values.push_back(t);
}
virtual void setToDefault() {
values.clear();
values.push_back(_default);
}
virtual void setToConst() {
values.clear();
values.push_back(_const);
}
void printself(std::ostream & stream) const {
stream << this->name << " =";
stream << std::boolalpha; // for boolean
for(typename std::vector<T>::const_iterator vit = this->values.begin();
vit != this->values.end(); ++vit) {
stream << " " << *vit;
}
}
virtual std::ostream & _printDefault(std::ostream & stream) const {
stream << _default;
return stream;
}
virtual std::ostream & _printConst(std::ostream & stream) const {
stream << _const;
return stream;
}
T _default;
T _const;
std::vector<T> values;
};
/* -------------------------------------------------------------------------- */
template<>
inline void ArgumentParser::ArgumentStorage<std::string>::addValue(std::string & value) {
values.push_back(value);
}
template<class T>
struct is_vector {
enum { value = false };
};
template<class T>
struct is_vector< std::vector<T> > {
enum { value = true };
};
-
+
/* -------------------------------------------------------------------------- */
-template<class T, bool is_vector = is_vector<T>::value>
+template<class T, bool is_vector = cppargparse::is_vector<T>::value>
struct cast_helper {
static T cast(const ArgumentParser::Argument & arg) {
const ArgumentParser::ArgumentStorage<T> & _arg =
dynamic_cast<const ArgumentParser::ArgumentStorage<T> &>(arg);
if(_arg.values.size() == 1) {
return _arg.values[0];
} else {
throw std::length_error("Not enougth or too many argument where passed for the command line argument: " + arg.name);
}
}
};
template<class T>
struct cast_helper<T, true> {
static T cast(const ArgumentParser::Argument & arg) {
const ArgumentParser::ArgumentStorage<T> & _arg =
dynamic_cast<const ArgumentParser::ArgumentStorage<T> &>(arg);
return _arg.values;
}
};
/* -------------------------------------------------------------------------- */
template<class T>
ArgumentParser::Argument::operator T() const{
return cast_helper<T>::cast(*this);
}
template<class T>
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help,
int nargs,
ArgumentType type,
T def) {
_Argument & arg = _addArgument(name_or_flag, help, nargs, type);
dynamic_cast<ArgumentStorage<T> &>(arg)._default = def;
arg.has_default = true;
}
template<class T>
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help,
int nargs,
ArgumentType type,
T def,
T cons) {
_Argument & arg = _addArgument(name_or_flag, help, nargs, type);
dynamic_cast<ArgumentStorage<T> &>(arg)._default = def;
arg.has_default = true;
dynamic_cast<ArgumentStorage<T> &>(arg)._const = cons;
arg.has_const = true;
}
}
#endif /* __AKANTU_CPPARGPARSE_TMPL_HH__ */