diff --git a/cmake/AkantuCleaning.cmake b/cmake/AkantuCleaning.cmake
index f41eb399e..39202265c 100644
--- a/cmake/AkantuCleaning.cmake
+++ b/cmake/AkantuCleaning.cmake
@@ -1,77 +1,85 @@
#===============================================================================
# @file AkantuCleaning.cmake
#
# @author Nicolas Richart <nicolas.richart@epfl.ch>
#
# @date creation: Thu Jun 1, 2017
#
# @brief set of tools to clean the code
#
# @section LICENSE
#
# Copyright (©) 2010-2012, 2014, 2015 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/>.
#===============================================================================
# Adding clang-format target if executable is found
find_program(CLANG_FORMAT "clang-format")
mark_as_advanced(CLANG_FORMAT)
macro(register_code_to_format)
if(CLANG_FORMAT)
add_custom_target(
clang-format-all
COMMAND ${CLANG_FORMAT}
-i
-style=file
${ARGN}
)
endif()
endmacro()
# Adding clang-tidy target if executable is found
find_program(CLANG_TIDY "clang-tidy")
mark_as_advanced(CLANG_TIDY)
macro(register_target_to_tidy target)
if(CLANG_TIDY)
+ option(AKANTU_CLANG_TIDY_AUTOFIX OFF)
+ mark_as_advanced(AKANTU_CLANG_TIDY_AUTOFIX)
+
+ set(_autofix_option)
+ if(AKANTU_CLANG_TIDY_AUTOFIX)
+ set(_autofix_option -fix)
+ endif()
get_target_property(_sources ${target} SOURCES)
set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL
"Enable/Disable output of compile commands during generation" FORCE)
file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/clang-tidy)
set(_depends)
foreach(_src ${_sources})
get_filename_component(_src_dir ${_src} DIRECTORY)
file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/clang-tidy/${_src_dir})
add_custom_command(
OUTPUT ${PROJECT_BINARY_DIR}/clang-tidy/${_src}.yaml
COMMAND ${CLANG_TIDY}
-p=${PROJECT_BINARY_DIR}
-export-fixes=${PROJECT_BINARY_DIR}/clang-tidy/${_src}.yaml
+ ${_autofix_option}
${_src}
COMMENT "Tidying ${_src}"
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
)
list(APPEND _depends ${PROJECT_BINARY_DIR}/clang-tidy/${_src}.yaml)
endforeach()
add_custom_target(clang-tidy DEPENDS ${_depends})
endif()
endmacro()
diff --git a/python/swig/aka_array.i b/python/swig/aka_array.i
index cf4838547..117f261fb 100644
--- a/python/swig/aka_array.i
+++ b/python/swig/aka_array.i
@@ -1,250 +1,248 @@
/**
* @file aka_array.i
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Dec 12 2014
* @date last modification: Wed Nov 11 2015
*
* @brief wrapper for arrays
*
* @section LICENSE
*
* Copyright (©) 2015 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/>.
*
*/
%{
#define SWIG_FILE_WITH_INIT
#include "aka_array.hh"
#include "aka_types.hh"
%}
%include "typemaps.i"
namespace akantu {
%ignore Array::operator=;
%ignore Array::operator[];
%ignore Array::operator();
%ignore Array::set;
%ignore Array::begin;
%ignore Array::end;
%ignore Array::begin_reinterpret;
%ignore Array::end_reinterpret;
};
%include "aka_array.hh"
namespace akantu {
-
%ignore TensorProxy::operator=;
%ignore TensorProxy::operator[];
%ignore TensorProxy::operator();
%ignore Tensor3Proxy::operator=;
%ignore Tensor3Proxy::operator[];
%ignore Tensor3Proxy::operator();
%ignore TensorStorage::operator=;
%ignore TensorStorage::operator[];
%ignore TensorStorage::operator();
%ignore VectorProxy::operator=;
%ignore VectorProxy::operator[];
%ignore VectorProxy::operator();
%ignore MatrixProxy::operator=;
%ignore MatrixProxy::operator[];
%ignore MatrixProxy::operator();
%ignore Matrix::operator=;
%ignore Matrix::operator[];
%ignore Matrix::operator();
%ignore Tensor3::operator=;
%ignore Tensor3::operator[];
%ignore Tensor3::operator();
%ignore Vector::operator=;
%ignore Vector::operator[];
%ignore Vector::operator();
%ignore Vector::solve;
};
%include "aka_types.hh"
namespace akantu {
%template(RArray) Array<akantu::Real, true>;
%template(UArray) Array<akantu::UInt, true>;
%template(BArray) Array<bool, true>;
-
%template(RVector) Vector<akantu::Real>;
};
%include "numpy.i"
%init %{
import_array();
%}
%inline %{
namespace akantu{
template <typename T>
class ArrayForPython : public Array<T>{
public:
ArrayForPython(T * wrapped_memory,
UInt size = 0,
UInt nb_component = 1,
const ID & id = "")
: Array<T>(0,nb_component,id){
this->values = wrapped_memory;
this->size = size;
};
~ArrayForPython(){
this->values = NULL;
};
void resize(UInt new_size){
AKANTU_DEBUG_ASSERT(this->size == new_size,"cannot resize a temporary vector");
}
};
}
template <typename T> int getPythonDataTypeCode(){ AKANTU_EXCEPTION("undefined type");}
template <> int getPythonDataTypeCode<bool>(){
int data_typecode = NPY_NOTYPE;
size_t s = sizeof(bool);
switch(s) {
case 1: data_typecode = NPY_BOOL; break;
case 2: data_typecode = NPY_UINT16; break;
case 4: data_typecode = NPY_UINT32; break;
case 8: data_typecode = NPY_UINT64; break;
}
return data_typecode;
}
template <> int getPythonDataTypeCode<double>(){return NPY_DOUBLE;}
template <> int getPythonDataTypeCode<long double>(){return NPY_LONGDOUBLE;}
template <> int getPythonDataTypeCode<float>(){return NPY_FLOAT;}
template <> int getPythonDataTypeCode<unsigned long>(){
int data_typecode = NPY_NOTYPE;
size_t s = sizeof(unsigned long);
switch(s) {
case 2: data_typecode = NPY_UINT16; break;
case 4: data_typecode = NPY_UINT32; break;
case 8: data_typecode = NPY_UINT64; break;
}
return data_typecode;
}
template <> int getPythonDataTypeCode<akantu::UInt>(){
int data_typecode = NPY_NOTYPE;
size_t s = sizeof(akantu::UInt);
switch(s) {
case 2: data_typecode = NPY_UINT16; break;
case 4: data_typecode = NPY_UINT32; break;
case 8: data_typecode = NPY_UINT64; break;
}
return data_typecode;
}
template <> int getPythonDataTypeCode<int>(){
int data_typecode = NPY_NOTYPE;
size_t s = sizeof(int);
switch(s) {
case 2: data_typecode = NPY_INT16; break;
case 4: data_typecode = NPY_INT32; break;
case 8: data_typecode = NPY_INT64; break;
}
return data_typecode;
}
int getSizeOfPythonType(int type_num){
switch (type_num){
case NPY_INT16 : return 2;break;
case NPY_UINT16: return 2;break;
case NPY_INT32 : return 4;break;
case NPY_UINT32: return 4;break;
case NPY_INT64 : return 8;break;
case NPY_UINT64: return 8;break;
case NPY_FLOAT: return sizeof(float);break;
case NPY_DOUBLE: return sizeof(double);break;
case NPY_LONGDOUBLE: return sizeof(long double);break;
}
return 0;
}
std::string getPythonTypeName(int type_num){
switch (type_num){
case NPY_INT16 : return "NPY_INT16" ;break;
case NPY_UINT16: return "NPY_UINT16";break;
case NPY_INT32 : return "NPY_INT32" ;break;
case NPY_UINT32: return "NPY_UINT32";break;
case NPY_INT64 : return "NPY_INT64" ;break;
case NPY_UINT64: return "NPY_UINT64";break;
case NPY_FLOAT: return "NPY_FLOAT" ;break;
case NPY_DOUBLE: return "NPY_DOUBLE";break;
case NPY_LONGDOUBLE: return "NPY_LONGDOUBLE";break;
}
return 0;
}
template <typename T> void checkDataType(int type_num){
AKANTU_DEBUG_ASSERT(type_num == getPythonDataTypeCode<T>(),
"incompatible types between numpy and input function: " <<
type_num << " != " << getPythonDataTypeCode<T>() << std::endl <<
getSizeOfPythonType(type_num) << " != " << sizeof(T) <<
std::endl <<
"The numpy array is of type " << getPythonTypeName(type_num));
}
%}
%define %akantu_array_typemaps(DATA_TYPE)
%typemap(out, fragment="NumPy_Fragments") (akantu::Array< DATA_TYPE > &)
{
int data_typecode = getPythonDataTypeCode< DATA_TYPE >();
npy_intp dims[2] = {npy_intp($1->getSize()), npy_intp($1->getNbComponent())};
PyObject* obj = PyArray_SimpleNewFromData(2, dims, data_typecode, $1->storage());
PyArrayObject* array = (PyArrayObject*) obj;
if (!array) SWIG_fail;
$result = SWIG_Python_AppendOutput($result, obj);
}
%typemap(in) akantu::Array< DATA_TYPE > &
{
if (!PyArray_Check($input)) {
AKANTU_EXCEPTION("incompatible input which is not a numpy");
}
else {
PyArray_Descr * numpy_type = (PyArray_Descr*)PyArray_DESCR((PyArrayObject*)$input);
int type_num = numpy_type->type_num;
checkDataType< DATA_TYPE >(type_num);
UInt _n = PyArray_NDIM((PyArrayObject*)$input);
if (_n != 2) AKANTU_EXCEPTION("incompatible numpy dimension " << _n);
npy_intp * ndims = PyArray_DIMS((PyArrayObject*)$input);
akantu::UInt sz = ndims[0];
akantu::UInt nb_components = ndims[1];
PyArrayIterObject *iter = (PyArrayIterObject *)PyArray_IterNew($input);
if (iter == NULL) AKANTU_EXCEPTION("Python internal error");
$1 = new akantu::ArrayForPython< DATA_TYPE >((DATA_TYPE*)(iter->dataptr),sz,nb_components,"tmp_array_for_python");
}
}
%enddef
%akantu_array_typemaps(double )
%akantu_array_typemaps(float )
%akantu_array_typemaps(unsigned int)
%akantu_array_typemaps(unsigned long)
%akantu_array_typemaps(int )
%akantu_array_typemaps(bool )
diff --git a/src/common/aka_array.hh b/src/common/aka_array.hh
index 16a0ac321..646801a86 100644
--- a/src/common/aka_array.hh
+++ b/src/common/aka_array.hh
@@ -1,363 +1,365 @@
/**
* @file aka_array.hh
*
* @author Till Junge <till.junge@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Jan 22 2016
*
* @brief Array container for Akantu
* This container differs from the std::vector from the fact it as 2 dimensions
* a main dimension and the size stored per entries
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_VECTOR_HH__
#define __AKANTU_VECTOR_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <typeinfo>
#include <vector>
/* -------------------------------------------------------------------------- */
namespace akantu {
/// class that afford to store vectors in static memory
class ArrayBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit ArrayBase(ID id = "");
virtual ~ArrayBase();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the amount of space allocated in bytes
inline UInt getMemorySize() const;
/// set the size to zero without freeing the allocated space
inline void empty();
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the real size allocated in memory
AKANTU_GET_MACRO(AllocatedSize, allocated_size, UInt);
/// Get the Size of the Array
UInt getSize() const __attribute__((deprecated)) { return size_; }
UInt size() const { return size_; }
/// Get the number of components
AKANTU_GET_MACRO(NbComponent, nb_component, UInt);
/// Get the name of th array
AKANTU_GET_MACRO(ID, id, const ID &);
/// Set the name of th array
AKANTU_SET_MACRO(ID, id, const ID &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id of the vector
ID id;
/// the size allocated
UInt allocated_size{0};
/// the size used
UInt size_{0};
/// number of components
UInt nb_component{1};
/// size of the stored type
UInt size_of_type{0};
};
/* -------------------------------------------------------------------------- */
namespace {
template <std::size_t dim, typename T> struct IteratorHelper {};
template <typename T> struct IteratorHelper<0, T> { using type = T; };
template <typename T> struct IteratorHelper<1, T> { using type = Vector<T>; };
template <typename T> struct IteratorHelper<2, T> { using type = Matrix<T>; };
template <typename T> struct IteratorHelper<3, T> {
using type = Tensor3<T>;
};
template <std::size_t dim, typename T>
using IteratorHelper_t = typename IteratorHelper<dim, T>::type;
} // namespace
/* -------------------------------------------------------------------------- */
template <typename T, bool is_scal> class Array : public ArrayBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
using value_type = T;
using reference = value_type &;
using pointer_type = value_type *;
using const_reference = const value_type &;
/// Allocation of a new vector
explicit inline Array(UInt size = 0, UInt nb_component = 1,
const ID & id = "");
/// Allocation of a new vector with a default value
Array(UInt size, UInt nb_component, const value_type def_values[],
const ID & id = "");
/// Allocation of a new vector with a default value
Array(UInt size, UInt nb_component, const_reference value,
const ID & id = "");
/// Copy constructor (deep copy if deep=true)
Array(const Array<value_type, is_scal> & vect, bool deep = true,
const ID & id = "");
#ifndef SWIG
/// Copy constructor (deep copy)
explicit Array(const std::vector<value_type> & vect);
#endif
inline ~Array() override;
Array & operator=(const Array & a) {
/// this is to let STL allocate and copy arrays in the case of
/// std::vector::resize
AKANTU_DEBUG_ASSERT(this->size == 0, "Cannot copy akantu::Array");
return const_cast<Array &>(a);
}
+#ifndef SWIG
/* ------------------------------------------------------------------------ */
/* Iterator */
/* ------------------------------------------------------------------------ */
/// \todo protected: does not compile with intel check why
public:
template <class R, class it, class IR = R, bool is_tensor_ = is_tensor<R>{}>
class iterator_internal;
public:
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
template <typename R = T> class const_iterator;
template <typename R = T> class iterator;
/* ------------------------------------------------------------------------ */
/// iterator for Array of nb_component = 1
using scalar_iterator = iterator<T>;
/// const_iterator for Array of nb_component = 1
using const_scalar_iterator = const_iterator<T>;
/// iterator returning Vectors of size n on entries of Array with
/// nb_component = n
using vector_iterator = iterator<Vector<T>>;
/// const_iterator returning Vectors of n size on entries of Array with
/// nb_component = n
using const_vector_iterator = const_iterator<Vector<T>>;
/// iterator returning Matrices of size (m, n) on entries of Array with
/// nb_component = m*n
using matrix_iterator = iterator<Matrix<T>>;
/// const iterator returning Matrices of size (m, n) on entries of Array with
/// nb_component = m*n
using const_matrix_iterator = const_iterator<Matrix<T>>;
/// iterator returning Tensor3 of size (m, n, k) on entries of Array with
/// nb_component = m*n*k
using tensor3_iterator = iterator<Tensor3<T>>;
/// const iterator returning Tensor3 of size (m, n, k) on entries of Array
/// with nb_component = m*n*k
using const_tensor3_iterator = const_iterator<Tensor3<T>>;
/* ------------------------------------------------------------------------ */
template <typename... Ns> inline decltype(auto) begin(Ns&&... n);
template <typename... Ns> inline decltype(auto) end(Ns&&... n);
template <typename... Ns> inline decltype(auto) begin(Ns&&... n) const;
template <typename... Ns> inline decltype(auto) end(Ns&&... n) const;
template <typename... Ns> inline decltype(auto) begin_reinterpret(Ns&&... n);
template <typename... Ns> inline decltype(auto) end_reinterpret(Ns&&... n);
template <typename... Ns>
inline decltype(auto) begin_reinterpret(Ns&&... n) const;
template <typename... Ns>
inline decltype(auto) end_reinterpret(Ns&&... n) const;
+#endif // SWIG
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// append a tuple of size nb_component containing value
inline void push_back(const_reference value);
/// append a vector
// inline void push_back(const value_type new_elem[]);
/// append a Vector or a Matrix
template <template <typename> class C,
typename = std::enable_if_t<is_tensor<C<T>>{}>>
inline void push_back(const C<T> & new_elem);
/// append the value of the iterator
template <typename Ret> inline void push_back(const iterator<Ret> & it);
/// erase the value at position i
inline void erase(UInt i);
/// ask Nico, clarify
template <typename R> inline iterator<R> erase(const iterator<R> & it);
/// changes the allocated size but not the size
virtual void reserve(UInt size);
/// change the size of the Array
virtual void resize(UInt size);
/// change the size of the Array and initialize the values
virtual void resize(UInt size, const T & val);
/// change the number of components by interlacing data
/// @param multiplicator number of interlaced components add
/// @param block_size blocks of data in the array
/// Examaple for block_size = 2, multiplicator = 2
/// array = oo oo oo -> new array = oo nn nn oo nn nn oo nn nn
void extendComponentsInterlaced(UInt multiplicator, UInt stride);
/// search elem in the vector, return the position of the first occurrence or
/// -1 if not found
UInt find(const_reference elem) const;
/// @see Array::find(const_reference elem) const
UInt find(T elem[]) const;
/// @see Array::find(const_reference elem) const
template <template <typename> class C,
typename = std::enable_if_t<is_tensor<C<T>>{}>>
inline UInt find(const C<T> & elem);
/// set all entries of the array to 0
inline void clear() { std::fill_n(values, size_ * nb_component, T()); }
/// set all entries of the array to the value t
/// @param t value to fill the array with
inline void set(T t) { std::fill_n(values, size_ * nb_component, t); }
/// set all tuples of the array to a given vector or matrix
/// @param vm Matrix or Vector to fill the array with
template <template <typename> class C,
typename = std::enable_if_t<is_tensor<C<T>>{}>>
inline void set(const C<T> & vm);
/// Append the content of the other array to the current one
void append(const Array<T> & other);
/// copy another Array in the current Array, the no_sanity_check allows you to
/// force the copy in cases where you know what you do with two non matching
/// Arrays in terms of n
void copy(const Array<T, is_scal> & other, bool no_sanity_check = false);
/// give the address of the memory allocated for this vector
T * storage() const { return values; };
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
protected:
/// perform the allocation for the constructors
void allocate(UInt size, UInt nb_component = 1);
/// resize initializing with uninitialized_fill if fill is set
void resizeUnitialized(UInt new_size, bool fill, const T & val = T());
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
/// substraction entry-wise
Array<T, is_scal> & operator-=(const Array<T, is_scal> & other);
/// addition entry-wise
Array<T, is_scal> & operator+=(const Array<T, is_scal> & other);
/// multiply evry entry by alpha
Array<T, is_scal> & operator*=(const T & alpha);
/// check if the array are identical entry-wise
bool operator==(const Array<T, is_scal> & other) const;
/// @see Array::operator==(const Array<T, is_scal> & other) const
bool operator!=(const Array<T, is_scal> & other) const;
/// return a reference to the j-th entry of the i-th tuple
inline reference operator()(UInt i, UInt j = 0);
/// return a const reference to the j-th entry of the i-th tuple
inline const_reference operator()(UInt i, UInt j = 0) const;
/// return a reference to the ith component of the 1D array
inline reference operator[](UInt i);
/// return a const reference to the ith component of the 1D array
inline const_reference operator[](UInt i) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// array of values
T * values; // /!\ very dangerous
};
/* -------------------------------------------------------------------------- */
/* Inline Functions Array<T, is_scal> */
/* -------------------------------------------------------------------------- */
template <typename T, bool is_scal>
inline std::ostream & operator<<(std::ostream & stream,
const Array<T, is_scal> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
/* Inline Functions ArrayBase */
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream,
const ArrayBase & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "aka_array_tmpl.hh"
#include "aka_types.hh"
#endif /* __AKANTU_VECTOR_HH__ */
diff --git a/src/common/aka_array_tmpl.hh b/src/common/aka_array_tmpl.hh
index eb9b21b7e..9a2c7b0bb 100644
--- a/src/common/aka_array_tmpl.hh
+++ b/src/common/aka_array_tmpl.hh
@@ -1,1252 +1,1252 @@
/**
* @file aka_array_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jul 15 2010
* @date last modification: Fri Jan 22 2016
*
* @brief Inline functions of the classes Array<T> and ArrayBase
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
/* Inline Functions Array<T> */
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_ARRAY_TMPL_HH__
#define __AKANTU_AKA_ARRAY_TMPL_HH__
namespace akantu {
namespace debug {
struct ArrayException : public Exception {};
} // namespace debug
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline T & Array<T, is_scal>::operator()(UInt i, UInt j) {
AKANTU_DEBUG_ASSERT(size_ > 0, "The array \"" << id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < size_) && (j < nb_component),
"The value at position ["
<< i << "," << j << "] is out of range in array \""
<< id << "\"");
return values[i * nb_component + j];
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline const T & Array<T, is_scal>::operator()(UInt i, UInt j) const {
AKANTU_DEBUG_ASSERT(size_ > 0, "The array \"" << id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < size_) && (j < nb_component),
"The value at position ["
<< i << "," << j << "] is out of range in array \""
<< id << "\"");
return values[i * nb_component + j];
}
template <class T, bool is_scal>
inline T & Array<T, is_scal>::operator[](UInt i) {
AKANTU_DEBUG_ASSERT(size_ > 0, "The array \"" << id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < size_ * nb_component),
"The value at position ["
<< i << "] is out of range in array \"" << id
<< "\"");
return values[i];
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
inline const T & Array<T, is_scal>::operator[](UInt i) const {
AKANTU_DEBUG_ASSERT(size_ > 0, "The array \"" << id << "\" is empty");
AKANTU_DEBUG_ASSERT((i < size_ * nb_component),
"The value at position ["
<< i << "] is out of range in array \"" << id
<< "\"");
return values[i];
}
/* -------------------------------------------------------------------------- */
/**
* append a tuple to the array with the value value for all components
* @param value the new last tuple or the array will contain nb_component copies
* of value
*/
template <class T, bool is_scal>
inline void Array<T, is_scal>::push_back(const T & value) {
resizeUnitialized(size_ + 1, true, value);
}
/* -------------------------------------------------------------------------- */
/**
* append a tuple to the array
* @param new_elem a C-array containing the values to be copied to the end of
* the array */
// template <class T, bool is_scal>
// inline void Array<T, is_scal>::push_back(const T new_elem[]) {
// UInt pos = size_;
// resizeUnitialized(size_ + 1, false);
// T * tmp = values + nb_component * pos;
// std::uninitialized_copy(new_elem, new_elem + nb_component, tmp);
// }
/* -------------------------------------------------------------------------- */
/**
* append a matrix or a vector to the array
* @param new_elem a reference to a Matrix<T> or Vector<T> */
template <class T, bool is_scal>
template <template <typename> class C, typename>
inline void Array<T, is_scal>::push_back(const C<T> & new_elem) {
AKANTU_DEBUG_ASSERT(
nb_component == new_elem.size(),
"The vector("
<< new_elem.size()
<< ") as not a size compatible with the Array (nb_component="
<< nb_component << ").");
UInt pos = size_;
resizeUnitialized(size_ + 1, false);
T * tmp = values + nb_component * pos;
std::uninitialized_copy(new_elem.storage(), new_elem.storage() + nb_component,
tmp);
}
/* -------------------------------------------------------------------------- */
/**
* append a tuple to the array
* @param it an iterator to the tuple to be copied to the end of the array */
template <class T, bool is_scal>
template <class Ret>
inline void
Array<T, is_scal>::push_back(const Array<T, is_scal>::iterator<Ret> & it) {
UInt pos = size_;
resizeUnitialized(size_ + 1, false);
T * tmp = values + nb_component * pos;
T * new_elem = it.data();
std::uninitialized_copy(new_elem, new_elem + nb_component, tmp);
}
/* -------------------------------------------------------------------------- */
/**
* erase an element. If the erased element is not the last of the array, the
* last element is moved into the hole in order to maintain contiguity. This
* may invalidate existing iterators (For instance an iterator obtained by
* Array::end() is no longer correct) and will change the order of the
* elements.
* @param i index of element to erase
*/
template <class T, bool is_scal> inline void Array<T, is_scal>::erase(UInt i) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT((size_ > 0), "The array is empty");
AKANTU_DEBUG_ASSERT((i < size_), "The element at position ["
<< i << "] is out of range (" << i
<< ">=" << size_ << ")");
if (i != (size_ - 1)) {
for (UInt j = 0; j < nb_component; ++j) {
values[i * nb_component + j] = values[(size_ - 1) * nb_component + j];
}
}
resize(size_ - 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Subtract another array entry by entry from this array in place. Both arrays
* must
* have the same size and nb_component. If the arrays have different shapes,
* code compiled in debug mode will throw an expeption and optimised code
* will behave in an unpredicted manner
* @param other array to subtract from this
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> & Array<T, is_scal>::
operator-=(const Array<T, is_scal> & vect) {
AKANTU_DEBUG_ASSERT((size_ == vect.size_) &&
(nb_component == vect.nb_component),
"The too array don't have the same sizes");
T * a = values;
T * b = vect.storage();
for (UInt i = 0; i < size_ * nb_component; ++i) {
*a -= *b;
++a;
++b;
}
return *this;
}
/* -------------------------------------------------------------------------- */
/**
* Add another array entry by entry to this array in place. Both arrays must
* have the same size and nb_component. If the arrays have different shapes,
* code compiled in debug mode will throw an expeption and optimised code
* will behave in an unpredicted manner
* @param other array to add to this
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> & Array<T, is_scal>::
operator+=(const Array<T, is_scal> & vect) {
AKANTU_DEBUG_ASSERT((size_ == vect.size) &&
(nb_component == vect.nb_component),
"The too array don't have the same sizes");
T * a = values;
T * b = vect.storage();
for (UInt i = 0; i < size_ * nb_component; ++i) {
*a++ += *b++;
}
return *this;
}
/* -------------------------------------------------------------------------- */
/**
* Multiply all entries of this array by a scalar in place
* @param alpha scalar multiplicant
* @return reference to modified this
*/
template <class T, bool is_scal>
Array<T, is_scal> & Array<T, is_scal>::operator*=(const T & alpha) {
T * a = values;
for (UInt i = 0; i < size_ * nb_component; ++i) {
*a++ *= alpha;
}
return *this;
}
/* -------------------------------------------------------------------------- */
/**
* Compare this array element by element to another.
* @param other array to compare to
* @return true it all element are equal and arrays have the same shape, else
* false
*/
template <class T, bool is_scal>
bool Array<T, is_scal>::operator==(const Array<T, is_scal> & array) const {
bool equal = nb_component == array.nb_component && size_ == array.size_ &&
id == array.id;
if (!equal)
return false;
if (values == array.storage())
return true;
else
return std::equal(values, values + size_ * nb_component, array.storage());
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
bool Array<T, is_scal>::operator!=(const Array<T, is_scal> & array) const {
return !operator==(array);
}
/* -------------------------------------------------------------------------- */
/**
* set all tuples of the array to a given vector or matrix
* @param vm Matrix or Vector to fill the array with
*/
template <class T, bool is_scal>
template <template <typename> class C, typename>
inline void Array<T, is_scal>::set(const C<T> & vm) {
AKANTU_DEBUG_ASSERT(
nb_component == vm.size(),
"The size of the object does not match the number of components");
for (T * it = values; it < values + nb_component * size_;
it += nb_component) {
std::copy(vm.storage(), vm.storage() + nb_component, it);
}
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
void Array<T, is_scal>::append(const Array<T> & other) {
AKANTU_DEBUG_ASSERT(
nb_component == other.nb_component,
"Cannot append an array with a different number of component");
UInt old_size = this->size_;
this->resizeUnitialized(this->size_ + other.size(), false);
T * tmp = values + nb_component * old_size;
std::uninitialized_copy(other.storage(),
other.storage() + other.size() * nb_component, tmp);
}
/* -------------------------------------------------------------------------- */
/* Functions Array<T, is_scal> */
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(UInt size, UInt nb_component, const ID & id)
- : ArrayBase(id), values(NULL) {
+ : ArrayBase(id), values(nullptr) {
AKANTU_DEBUG_IN();
allocate(size, nb_component);
if (!is_scal) {
T val = T();
std::uninitialized_fill(values, values + size * nb_component, val);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(UInt size, UInt nb_component, const T def_values[],
const ID & id)
: ArrayBase(id), values(NULL) {
AKANTU_DEBUG_IN();
allocate(size, nb_component);
T * tmp = values;
for (UInt i = 0; i < size; ++i) {
tmp = values + nb_component * i;
std::uninitialized_copy(def_values, def_values + nb_component, tmp);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(UInt size, UInt nb_component, const T & value,
const ID & id)
- : ArrayBase(id), values(NULL) {
+ : ArrayBase(id), values(nullptr) {
AKANTU_DEBUG_IN();
allocate(size, nb_component);
std::uninitialized_fill_n(values, size * nb_component, value);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
Array<T, is_scal>::Array(const Array<T, is_scal> & vect, bool deep,
const ID & id)
: ArrayBase(vect) {
AKANTU_DEBUG_IN();
this->id = (id == "") ? vect.id : id;
if (deep) {
allocate(vect.size_, vect.nb_component);
T * tmp = values;
std::uninitialized_copy(vect.storage(),
vect.storage() + size_ * nb_component, tmp);
} else {
this->values = vect.storage();
this->size_ = vect.size_;
this->nb_component = vect.nb_component;
this->allocated_size = vect.allocated_size;
this->size_of_type = vect.size_of_type;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#ifndef SWIG
template <class T, bool is_scal>
Array<T, is_scal>::Array(const std::vector<T> & vect) {
AKANTU_DEBUG_IN();
this->id = "";
allocate(vect.size(), 1);
T * tmp = values;
std::uninitialized_copy(&(vect[0]), &(vect[size_ - 1]), tmp);
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal> Array<T, is_scal>::~Array() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG(dblAccessory,
"Freeing " << printMemorySize<T>(allocated_size * nb_component)
<< " (" << id << ")");
if (values) {
if (!is_scal)
for (UInt i = 0; i < size_ * nb_component; ++i) {
T * obj = values + i;
obj->~T();
}
free(values);
}
size_ = allocated_size = 0;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* perform the allocation for the constructors
* @param size is the size of the array
* @param nb_component is the number of component of the array
*/
template <class T, bool is_scal>
void Array<T, is_scal>::allocate(UInt size, UInt nb_component) {
AKANTU_DEBUG_IN();
if (size == 0) {
values = nullptr;
} else {
values = static_cast<T *>(malloc(nb_component * size * sizeof(T)));
AKANTU_DEBUG_ASSERT(values != nullptr,
"Cannot allocate "
<< printMemorySize<T>(size * nb_component) << " ("
<< id << ")");
}
- if (values == NULL) {
+ if (values == nullptr) {
this->size_ = this->allocated_size = 0;
} else {
AKANTU_DEBUG(dblAccessory, "Allocated "
<< printMemorySize<T>(size * nb_component)
<< " (" << id << ")");
this->size_ = this->allocated_size = size;
}
this->size_of_type = sizeof(T);
this->nb_component = nb_component;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
void Array<T, is_scal>::reserve(UInt new_size) {
UInt tmp_size = this->size_;
resizeUnitialized(new_size, false);
this->size_ = tmp_size;
}
/* -------------------------------------------------------------------------- */
/**
* change the size of the array and allocate or free memory if needed. If the
* size increases, the new tuples are filled with zeros
* @param new_size new number of tuples contained in the array */
template <class T, bool is_scal> void Array<T, is_scal>::resize(UInt new_size) {
resizeUnitialized(new_size, !is_scal);
}
/* -------------------------------------------------------------------------- */
/**
* change the size of the array and allocate or free memory if needed. If the
* size increases, the new tuples are filled with zeros
* @param new_size new number of tuples contained in the array */
template <class T, bool is_scal>
void Array<T, is_scal>::resize(UInt new_size, const T & val) {
this->resizeUnitialized(new_size, true, val);
}
/* -------------------------------------------------------------------------- */
/**
* change the size of the array and allocate or free memory if needed.
* @param new_size new number of tuples contained in the array */
template <class T, bool is_scal>
void Array<T, is_scal>::resizeUnitialized(UInt new_size, bool fill,
const T & val) {
// AKANTU_DEBUG_IN();
// free some memory
if (new_size <= allocated_size) {
if (!is_scal) {
T * old_values = values;
if (new_size < size_) {
for (UInt i = new_size * nb_component; i < size_ * nb_component; ++i) {
T * obj = old_values + i;
obj->~T();
}
}
}
if (allocated_size - new_size > AKANTU_MIN_ALLOCATION) {
AKANTU_DEBUG(dblAccessory,
"Freeing " << printMemorySize<T>((allocated_size - size_) *
nb_component)
<< " (" << id << ")");
// Normally there are no allocation problem when reducing an array
if (new_size == 0) {
free(values);
values = nullptr;
} else {
auto * tmp_ptr = static_cast<T *>(
realloc(values, new_size * nb_component * sizeof(T)));
if (tmp_ptr == nullptr) {
AKANTU_EXCEPTION("Cannot free data ("
<< id << ")"
<< " [current allocated size : " << allocated_size
<< " | "
<< "requested size : " << new_size << "]");
}
values = tmp_ptr;
}
allocated_size = new_size;
}
} else {
// allocate more memory
UInt size_to_alloc = (new_size - allocated_size < AKANTU_MIN_ALLOCATION)
? allocated_size + AKANTU_MIN_ALLOCATION
: new_size;
auto * tmp_ptr = static_cast<T *>(
realloc(values, size_to_alloc * nb_component * sizeof(T)));
AKANTU_DEBUG_ASSERT(
- tmp_ptr != NULL,
+ tmp_ptr != nullptr,
"Cannot allocate " << printMemorySize<T>(size_to_alloc * nb_component));
- if (tmp_ptr == NULL) {
+ if (tmp_ptr == nullptr) {
AKANTU_DEBUG_ERROR("Cannot allocate more data ("
<< id << ")"
<< " [current allocated size : " << allocated_size
<< " | "
<< "requested size : " << new_size << "]");
}
AKANTU_DEBUG(dblAccessory,
"Allocating " << printMemorySize<T>(
(size_to_alloc - allocated_size) * nb_component));
allocated_size = size_to_alloc;
values = tmp_ptr;
}
if (fill && this->size_ < new_size) {
std::uninitialized_fill(values + size_ * nb_component,
values + new_size * nb_component, val);
}
size_ = new_size;
// AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* change the number of components by interlacing data
* @param multiplicator number of interlaced components add
* @param block_size blocks of data in the array
* Examaple for block_size = 2, multiplicator = 2
* array = oo oo oo -> new array = oo nn nn oo nn nn oo nn nn */
template <class T, bool is_scal>
void Array<T, is_scal>::extendComponentsInterlaced(UInt multiplicator,
UInt block_size) {
AKANTU_DEBUG_IN();
if (multiplicator == 1)
return;
AKANTU_DEBUG_ASSERT(multiplicator > 1, "invalid multiplicator");
AKANTU_DEBUG_ASSERT(nb_component % block_size == 0,
"stride must divide actual number of components");
values = static_cast<T *>(
realloc(values, nb_component * multiplicator * size_ * sizeof(T)));
UInt new_component = nb_component / block_size * multiplicator;
for (UInt i = 0, k = size_ - 1; i < size_; ++i, --k) {
for (UInt j = 0; j < new_component; ++j) {
UInt m = new_component - j - 1;
UInt n = m / multiplicator;
for (UInt l = 0, p = block_size - 1; l < block_size; ++l, --p) {
values[k * nb_component * multiplicator + m * block_size + p] =
values[k * nb_component + n * block_size + p];
}
}
}
nb_component = nb_component * multiplicator;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* search elem in the array, return the position of the first occurrence or
* -1 if not found
* @param elem the element to look for
* @return index of the first occurrence of elem or -1 if elem is not present
*/
template <class T, bool is_scal>
UInt Array<T, is_scal>::find(const T & elem) const {
AKANTU_DEBUG_IN();
auto begin = this->begin();
auto end = this->end();
auto it = std::find(begin, end, elem);
AKANTU_DEBUG_OUT();
return (it != end) ? it - begin : UInt(-1);
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal> UInt Array<T, is_scal>::find(T elem[]) const {
AKANTU_DEBUG_IN();
T * it = values;
UInt i = 0;
for (; i < size_; ++i) {
if (*it == elem[0]) {
T * cit = it;
UInt c = 0;
for (; (c < nb_component) && (*cit == elem[c]); ++c, ++cit)
;
if (c == nb_component) {
AKANTU_DEBUG_OUT();
return i;
}
}
it += nb_component;
}
return UInt(-1);
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <template <typename> class C, typename>
inline UInt Array<T, is_scal>::find(const C<T> & elem) {
AKANTU_DEBUG_ASSERT(elem.size() == nb_component,
"Cannot find an element with a wrong size ("
<< elem.size() << ") != " << nb_component);
return this->find(elem.storage());
}
/* -------------------------------------------------------------------------- */
/**
* copy the content of another array. This overwrites the current content.
* @param other Array to copy into this array. It has to have the same
* nb_component as this. If compiled in debug mode, an incorrect other will
* result in an exception being thrown. Optimised code may result in
* unpredicted behaviour.
*/
template <class T, bool is_scal>
void Array<T, is_scal>::copy(const Array<T, is_scal> & vect,
bool no_sanity_check) {
AKANTU_DEBUG_IN();
if (!no_sanity_check)
if (vect.nb_component != nb_component)
AKANTU_DEBUG_ERROR(
"The two arrays do not have the same number of components");
resize((vect.size_ * vect.nb_component) / nb_component);
T * tmp = values;
std::uninitialized_copy(vect.storage(), vect.storage() + size_ * nb_component,
tmp);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool is_scal> class ArrayPrintHelper {
public:
template <typename T>
static void print_content(const Array<T> & vect, std::ostream & stream,
int indent) {
if (AKANTU_DEBUG_TEST(dblDump) || AKANTU_DEBUG_LEVEL_IS_TEST()) {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << " + values : {";
for (UInt i = 0; i < vect.size(); ++i) {
stream << "{";
for (UInt j = 0; j < vect.getNbComponent(); ++j) {
stream << vect(i, j);
if (j != vect.getNbComponent() - 1)
stream << ", ";
}
stream << "}";
if (i != vect.size() - 1)
stream << ", ";
}
stream << "}" << std::endl;
}
}
};
template <> class ArrayPrintHelper<false> {
public:
template <typename T>
static void print_content(__attribute__((unused)) const Array<T> & vect,
__attribute__((unused)) std::ostream & stream,
__attribute__((unused)) int indent) {}
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
void Array<T, is_scal>::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
std::streamsize prec = stream.precision();
std::ios_base::fmtflags ff = stream.flags();
stream.setf(std::ios_base::showbase);
stream.precision(2);
stream << space << "Array<" << debug::demangle(typeid(T).name()) << "> ["
<< std::endl;
stream << space << " + id : " << this->id << std::endl;
stream << space << " + size : " << this->size_ << std::endl;
stream << space << " + nb_component : " << this->nb_component << std::endl;
stream << space << " + allocated size : " << this->allocated_size
<< std::endl;
stream << space << " + memory size : "
<< printMemorySize<T>(allocated_size * nb_component) << std::endl;
if (!AKANTU_DEBUG_LEVEL_IS_TEST())
stream << space << " + address : " << std::hex << this->values
<< std::dec << std::endl;
stream.precision(prec);
stream.flags(ff);
ArrayPrintHelper<is_scal>::print_content(*this, stream, indent);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
/* Inline Functions ArrayBase */
/* -------------------------------------------------------------------------- */
inline UInt ArrayBase::getMemorySize() const {
return allocated_size * nb_component * size_of_type;
}
inline void ArrayBase::empty() { size_ = 0; }
/* -------------------------------------------------------------------------- */
/* Iterators */
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <class R, class daughter, class IR, bool is_tensor>
class Array<T, is_scal>::iterator_internal {
public:
using value_type = R;
using pointer = R *;
using reference = R &;
using proxy = typename R::proxy;
using const_proxy = const typename R::proxy;
using const_reference = const R &;
using internal_value_type = IR;
using internal_pointer = IR *;
using difference_type = std::ptrdiff_t;
using iterator_category = std::random_access_iterator_tag;
public:
iterator_internal() = default;
iterator_internal(pointer_type data, UInt _offset)
: _offset(_offset), initial(data), ret(nullptr), ret_ptr(data) {
AKANTU_DEBUG_ERROR(
"The constructor should never be called it is just an ugly trick...");
}
iterator_internal(std::unique_ptr<internal_value_type> && wrapped)
: _offset(wrapped->size()), initial(wrapped->storage()),
ret(std::move(wrapped)), ret_ptr(ret->storage()) {}
iterator_internal(const iterator_internal & it) {
if (this != &it) {
this->_offset = it._offset;
this->initial = it.initial;
this->ret_ptr = it.ret_ptr;
this->ret = std::make_unique<internal_value_type>(*it.ret, false);
}
}
iterator_internal(iterator_internal && it) = default;
virtual ~iterator_internal() = default;
inline iterator_internal & operator=(const iterator_internal & it) {
if (this != &it) {
this->_offset = it._offset;
this->initial = it.initial;
this->ret_ptr = it.ret_ptr;
if (this->ret)
this->ret->shallowCopy(*it.ret);
else
this->ret = std::make_unique<internal_value_type>(*it.ret, false);
}
return *this;
}
UInt getCurrentIndex() {
return (this->ret_ptr - this->initial) / this->_offset;
};
inline reference operator*() {
ret->values = ret_ptr;
return *ret;
};
inline const_reference operator*() const {
ret->values = ret_ptr;
return *ret;
};
inline pointer operator->() {
ret->values = ret_ptr;
return ret.get();
};
inline daughter & operator++() {
ret_ptr += _offset;
return static_cast<daughter &>(*this);
};
inline daughter & operator--() {
ret_ptr -= _offset;
return static_cast<daughter &>(*this);
};
inline daughter & operator+=(const UInt n) {
ret_ptr += _offset * n;
return static_cast<daughter &>(*this);
}
inline daughter & operator-=(const UInt n) {
ret_ptr -= _offset * n;
return static_cast<daughter &>(*this);
}
inline proxy operator[](const UInt n) {
ret->values = ret_ptr + n * _offset;
return proxy(*ret);
}
inline const_proxy operator[](const UInt n) const {
ret->values = ret_ptr + n * _offset;
return const_proxy(*ret);
}
inline bool operator==(const iterator_internal & other) const {
return this->ret_ptr == other.ret_ptr;
}
inline bool operator!=(const iterator_internal & other) const {
return this->ret_ptr != other.ret_ptr;
}
inline bool operator<(const iterator_internal & other) const {
return this->ret_ptr < other.ret_ptr;
}
inline bool operator<=(const iterator_internal & other) const {
return this->ret_ptr <= other.ret_ptr;
}
inline bool operator>(const iterator_internal & other) const {
return this->ret_ptr > other.ret_ptr;
}
inline bool operator>=(const iterator_internal & other) const {
return this->ret_ptr >= other.ret_ptr;
}
inline daughter operator+(difference_type n) {
daughter tmp(static_cast<daughter &>(*this));
tmp += n;
return tmp;
}
inline daughter operator-(difference_type n) {
daughter tmp(static_cast<daughter &>(*this));
tmp -= n;
return tmp;
}
inline difference_type operator-(const iterator_internal & b) {
return (this->ret_ptr - b.ret_ptr) / _offset;
}
inline pointer_type data() const { return ret_ptr; }
inline difference_type offset() const { return _offset; }
protected:
UInt _offset{0};
pointer_type initial{nullptr};
std::unique_ptr<internal_value_type> ret{nullptr};
pointer_type ret_ptr{nullptr};
};
/* -------------------------------------------------------------------------- */
/**
* Specialization for scalar types
*/
template <class T, bool is_scal>
template <class R, class daughter, class IR>
class Array<T, is_scal>::iterator_internal<R, daughter, IR, false> {
public:
using value_type = R;
using pointer = R *;
using reference = R &;
using const_reference = const R &;
using internal_value_type = IR;
using internal_pointer = IR *;
using difference_type = std::ptrdiff_t;
using iterator_category = std::random_access_iterator_tag;
public:
iterator_internal(pointer data = nullptr) : ret(data), initial(data){};
iterator_internal(const iterator_internal & it) = default;
iterator_internal(iterator_internal && it) = default;
virtual ~iterator_internal() = default;
inline iterator_internal & operator=(const iterator_internal & it) = default;
UInt getCurrentIndex() { return (this->ret - this->initial); };
inline reference operator*() { return *ret; };
inline const_reference operator*() const { return *ret; };
inline pointer operator->() { return ret; };
inline daughter & operator++() {
++ret;
return static_cast<daughter &>(*this);
};
inline daughter & operator--() {
--ret;
return static_cast<daughter &>(*this);
};
inline daughter & operator+=(const UInt n) {
ret += n;
return static_cast<daughter &>(*this);
}
inline daughter & operator-=(const UInt n) {
ret -= n;
return static_cast<daughter &>(*this);
}
inline reference operator[](const UInt n) { return ret[n]; }
inline bool operator==(const iterator_internal & other) const {
return ret == other.ret;
}
inline bool operator!=(const iterator_internal & other) const {
return ret != other.ret;
}
inline bool operator<(const iterator_internal & other) const {
return ret < other.ret;
}
inline bool operator<=(const iterator_internal & other) const {
return ret <= other.ret;
}
inline bool operator>(const iterator_internal & other) const {
return ret > other.ret;
}
inline bool operator>=(const iterator_internal & other) const {
return ret >= other.ret;
}
inline daughter operator-(difference_type n) { return daughter(ret - n); }
inline daughter operator+(difference_type n) { return daughter(ret + n); }
inline difference_type operator-(const iterator_internal & b) {
return ret - b.ret;
}
inline pointer data() const { return ret; }
protected:
pointer ret{nullptr};
pointer initial{nullptr};
};
/* -------------------------------------------------------------------------- */
/* Begin/End functions implementation */
/* -------------------------------------------------------------------------- */
namespace detail {
template <class Tuple, size_t... Is>
constexpr auto take_front_impl(Tuple && t, std::index_sequence<Is...>) {
return std::make_tuple(std::get<Is>(std::forward<Tuple>(t))...);
}
template <size_t N, class Tuple> constexpr auto take_front(Tuple && t) {
return take_front_impl(std::forward<Tuple>(t),
std::make_index_sequence<N>{});
}
template <typename... V>
constexpr auto product_all(V &&... v) ->
typename std::common_type<V...>::type {
typename std::common_type<V...>::type result = 1;
(void)std::initializer_list<int>{(result *= v, 0)...};
return result;
}
template <typename... T> std::string to_string_all(T &&... t) {
if (sizeof...(T) == 0)
return "";
std::stringstream ss;
bool noComma = true;
ss << "(";
(void)std::initializer_list<bool>{
(ss << (noComma ? "" : ", ") << t, noComma = false)...};
ss << ")";
return ss.str();
}
template <std::size_t N> struct InstantiationHelper {
template <typename type, typename T, typename... Ns>
static auto instantiate(T && data, Ns... ns) {
return std::make_unique<type>(data, ns...);
}
};
template <> struct InstantiationHelper<0> {
template <typename type, typename T> static auto instantiate(T && data) {
return data;
}
};
template <typename Arr, typename T, typename... Ns>
decltype(auto) get_iterator(Arr && array, T * data, Ns &&... ns) {
using type = IteratorHelper_t<sizeof...(Ns) - 1, T>;
using array_type = std::decay_t<Arr>;
using iterator =
std::conditional_t<std::is_const<Arr>::value,
typename array_type::template const_iterator<type>,
typename array_type::template iterator<type>>;
if (array.getNbComponent() * array.size() !=
product_all(std::forward<Ns>(ns)...)) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::ArrayException(),
"The iterator on Array "
<< to_string_all(array.size(), array.getNbComponent())
<< "is not compatible with the type "
<< debug::demangle(typeid(type).name()) << to_string_all(ns...));
}
auto && wrapped = aka::apply(
[&](auto... n) {
return InstantiationHelper<sizeof...(n)>::template instantiate<type>(
data, n...);
},
take_front<sizeof...(Ns) - 1>(std::make_tuple(ns...)));
return iterator(std::move(wrapped));
}
} // namespace detail
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin(Ns &&... ns) {
return detail::get_iterator(*this, values, std::forward<Ns>(ns)..., size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end(Ns &&... ns) {
return detail::get_iterator(*this, values + nb_component * size_,
std::forward<Ns>(ns)..., size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin(Ns &&... ns) const {
return detail::get_iterator(*this, values, std::forward<Ns>(ns)..., size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end(Ns &&... ns) const {
return detail::get_iterator(*this, values + nb_component * size_,
std::forward<Ns>(ns)..., size_);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin_reinterpret(Ns &&... ns) {
return detail::get_iterator(*this, values, std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end_reinterpret(Ns &&... ns) {
return detail::get_iterator(
*this, values + detail::product_all(std::forward<Ns>(ns)...),
std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::begin_reinterpret(Ns &&... ns) const {
return detail::get_iterator(*this, values, std::forward<Ns>(ns)...);
}
template <class T, bool is_scal>
template <typename... Ns>
inline decltype(auto) Array<T, is_scal>::end_reinterpret(Ns &&... ns) const {
return detail::get_iterator(
*this, values + detail::product_all(std::forward<Ns>(ns)...),
std::forward<Ns>(ns)...);
}
/* -------------------------------------------------------------------------- */
/* Views */
/* -------------------------------------------------------------------------- */
namespace detail {
template <typename Array, typename... Ns> class ArrayView {
using tuple = std::tuple<Ns...>;
public:
ArrayView(Array && array, Ns &&... ns)
: array(std::forward<Array>(array)),
sizes(std::forward<Ns>(ns)...){};
decltype(auto) begin() {
return aka::apply(
[&](auto &&... ns) { return array.begin_reinterpret(ns...); }, sizes);
}
decltype(auto) end() {
return aka::apply(
[&](auto &&... ns) { return array.end_reinterpret(ns...); }, sizes);
}
decltype(auto) size() {
return std::get<std::tuple_size<tuple>::value - 1>(sizes);
}
private:
Array array;
tuple sizes;
};
} // namespace detail
/* -------------------------------------------------------------------------- */
template <typename Array, typename... Ns>
decltype(auto) make_view(Array && array, Ns &&... ns) {
auto size = std::forward<decltype(array)>(array).size() *
std::forward<decltype(array)>(array).getNbComponent() /
detail::product_all(ns...);
return detail::ArrayView<Array, Ns..., decltype(size)>(
std::forward<Array>(array), std::forward<Ns>(ns)...,
std::forward<decltype(size)>(size));
}
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename R>
class Array<T, is_scal>::const_iterator
: public iterator_internal<const R, Array<T, is_scal>::const_iterator<R>,
R> {
public:
typedef iterator_internal<const R, const_iterator, R> parent;
using value_type = typename parent::value_type;
using pointer = typename parent::pointer;
using reference = typename parent::reference;
using difference_type = typename parent::difference_type;
using iterator_category = typename parent::iterator_category;
public:
const_iterator() : parent(){};
// const_iterator(pointer_type data, UInt offset) : parent(data, offset) {}
// const_iterator(pointer warped) : parent(warped) {}
// const_iterator(const parent & it) : parent(it) {}
const_iterator(const const_iterator & it) = default;
const_iterator(const_iterator && it) = default;
template <typename P, typename = std::enable_if_t<not is_tensor<P>{}>>
const_iterator(P * data) : parent(data) {}
template <typename UP_P, typename = std::enable_if_t<
is_tensor<typename UP_P::element_type>::value>>
const_iterator(UP_P && tensor) : parent(std::forward<UP_P>(tensor)) {}
const_iterator & operator=(const const_iterator & it) = default;
};
template <class T, class R, bool is_tensor_ = is_tensor<R>{}>
struct ConstConverterIteratorHelper {
using const_iterator = typename Array<T>::template const_iterator<R>;
using iterator = typename Array<T>::template iterator<R>;
static inline const_iterator convert(const iterator & it) {
return const_iterator(std::unique_ptr<R>(new R(*it, false)));
}
};
template <class T, class R> struct ConstConverterIteratorHelper<T, R, false> {
using const_iterator = typename Array<T>::template const_iterator<R>;
using iterator = typename Array<T>::template iterator<R>;
static inline const_iterator convert(const iterator & it) {
return const_iterator(it.data());
}
};
template <class T, bool is_scal>
template <typename R>
class Array<T, is_scal>::iterator
: public iterator_internal<R, Array<T, is_scal>::iterator<R>> {
public:
using parent = iterator_internal<R, iterator>;
using value_type = typename parent::value_type;
using pointer = typename parent::pointer;
using reference = typename parent::reference;
using difference_type = typename parent::difference_type;
using iterator_category = typename parent::iterator_category;
public:
iterator() : parent(){};
iterator(const iterator & it) = default;
iterator(iterator && it) = default;
template <typename P, typename = std::enable_if_t<not is_tensor<P>::value>>
iterator(P * data) : parent(data) {}
template <typename UP_P, typename = std::enable_if_t<
is_tensor<typename UP_P::element_type>::value>>
iterator(UP_P && tensor) : parent(std::forward<UP_P>(tensor)) {}
iterator & operator=(const iterator & it) = default;
operator const_iterator<R>() {
return ConstConverterIteratorHelper<T, R>::convert(*this);
}
};
/* -------------------------------------------------------------------------- */
template <class T, bool is_scal>
template <typename R>
inline typename Array<T, is_scal>::template iterator<R>
Array<T, is_scal>::erase(const iterator<R> & it) {
T * curr = it.data();
UInt pos = (curr - values) / nb_component;
erase(pos);
iterator<R> rit = it;
return --rit;
}
} // namespace akantu
#endif /* __AKANTU_AKA_ARRAY_TMPL_HH__ */
diff --git a/src/common/aka_common.cc b/src/common/aka_common.cc
index 7e61edc3b..9f42be2d3 100644
--- a/src/common/aka_common.cc
+++ b/src/common/aka_common.cc
@@ -1,155 +1,155 @@
/**
* @file aka_common.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Tue Jan 19 2016
*
* @brief Initialization of global variables
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "aka_static_memory.hh"
#include "communicator.hh"
#include "aka_random_generator.hh"
#include "parser.hh"
#include "cppargparse.hh"
#include "communication_tag.hh"
/* -------------------------------------------------------------------------- */
#include <ctime>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void initialize(int & argc, char **& argv) {
AKANTU_DEBUG_IN();
initialize("", argc, argv);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void initialize(const std::string & input_file, int & argc, char **& argv) {
AKANTU_DEBUG_IN();
StaticMemory::getStaticMemory();
Communicator & comm =
Communicator::getStaticCommunicator(argc, argv);
Tag::setMaxTag(comm.getMaxTag());
debug::debugger.setParallelContext(comm.whoAmI(), comm.getNbProc());
debug::setDebugLevel(dblError);
static_argparser.setParallelContext(comm.whoAmI(), comm.getNbProc());
static_argparser.setExternalExitFunction(debug::exit);
static_argparser.addArgument("--aka_input_file", "Akantu's input file", 1,
cppargparse::_string, std::string());
static_argparser.addArgument(
"--aka_debug_level",
std::string("Akantu's overall debug level") +
std::string(" (0: error, 1: exceptions, 4: warnings, 5: info, ..., "
"100: dump") +
std::string(" more info on levels can be foind in aka_error.hh)"),
1, cppargparse::_integer, int(dblWarning));
static_argparser.addArgument(
"--aka_print_backtrace",
"Should Akantu print a backtrace in case of error", 0,
cppargparse::_boolean, false, true);
static_argparser.parse(argc, argv, cppargparse::_remove_parsed);
std::string infile = static_argparser["aka_input_file"];
if (infile == "")
infile = input_file;
debug::debugger.printBacktrace(static_argparser["aka_print_backtrace"]);
if ("" != infile) {
readInputFile(infile);
}
long int seed;
try {
seed = static_parser.getParameter("seed", _ppsc_current_scope);
} catch (debug::Exception &) {
- seed = time(NULL);
+ seed = time(nullptr);
}
seed *= (comm.whoAmI() + 1);
RandomGenerator<UInt>::seed(seed);
int dbl_level = static_argparser["aka_debug_level"];
debug::setDebugLevel(DebugLevel(dbl_level));
AKANTU_DEBUG_INFO("Random seed set to " << seed);
std::atexit(finalize);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void finalize() {
AKANTU_DEBUG_IN();
// if (StaticCommunicator::isInstantiated()) {
// StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
// delete &comm;
// }
if (StaticMemory::isInstantiated()) {
delete &(StaticMemory::getStaticMemory());
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void readInputFile(const std::string & input_file) {
static_parser.parse(input_file);
}
/* -------------------------------------------------------------------------- */
cppargparse::ArgumentParser & getStaticArgumentParser() {
return static_argparser;
}
/* -------------------------------------------------------------------------- */
Parser & getStaticParser() { return static_parser; }
/* -------------------------------------------------------------------------- */
const ParserSection & getUserParser() {
return *(static_parser.getSubSections(_st_user).first);
}
std::unique_ptr<Communicator> Communicator::static_communicator;
} // akantu
diff --git a/src/common/aka_csr.hh b/src/common/aka_csr.hh
index e88f9a02c..2422d5b44 100644
--- a/src/common/aka_csr.hh
+++ b/src/common/aka_csr.hh
@@ -1,259 +1,259 @@
/**
* @file aka_csr.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Apr 20 2011
* @date last modification: Sun Oct 19 2014
*
* @brief A compresed sparse row structure based on akantu Arrays
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_array.hh"
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_CSR_HH__
#define __AKANTU_AKA_CSR_HH__
namespace akantu {
/**
* This class can be used to store the structure of a sparse matrix or for
* vectors with variable number of component per element
*
* @param nb_rows number of rows of a matrix or size of a vector.
*/
template <typename T> class CSR {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit CSR(UInt nb_rows = 0)
: nb_rows(nb_rows), rows_offsets(nb_rows + 1, 1, "rows_offsets"),
rows(0, 1, "rows") {
rows_offsets.clear();
};
virtual ~CSR(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// does nothing
inline void beginInsertions(){};
/// insert a new entry val in row row
inline UInt insertInRow(UInt row, const T & val) {
UInt pos = rows_offsets(row)++;
rows(pos) = val;
return pos;
}
/// access an element of the matrix
inline const T & operator()(UInt row, UInt col) const {
AKANTU_DEBUG_ASSERT(rows_offsets(row + 1) - rows_offsets(row) > col,
"This element is not present in this CSR");
return rows(rows_offsets(row) + col);
}
/// access an element of the matrix
inline T & operator()(UInt row, UInt col) {
AKANTU_DEBUG_ASSERT(rows_offsets(row + 1) - rows_offsets(row) > col,
"This element is not present in this CSR");
return rows(rows_offsets(row) + col);
}
inline void endInsertions() {
for (UInt i = nb_rows; i > 0; --i)
rows_offsets(i) = rows_offsets(i - 1);
rows_offsets(0) = 0;
}
inline void countToCSR() {
for (UInt i = 1; i < nb_rows; ++i)
rows_offsets(i) += rows_offsets(i - 1);
for (UInt i = nb_rows; i >= 1; --i)
rows_offsets(i) = rows_offsets(i - 1);
rows_offsets(0) = 0;
}
inline void clearRows() {
rows_offsets.clear();
rows.resize(0);
};
inline void resizeRows(UInt nb_rows) {
this->nb_rows = nb_rows;
rows_offsets.resize(nb_rows + 1);
rows_offsets.clear();
}
inline void resizeCols() { rows.resize(rows_offsets(nb_rows)); }
inline void copy(Array<UInt> & offsets, Array<T> & values) {
offsets.copy(rows_offsets);
values.copy(rows);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// returns the number of rows
inline UInt getNbRows() const { return rows_offsets.size() - 1; };
/// returns the number of non-empty columns in a given row
inline UInt getNbCols(UInt row) const {
return rows_offsets(row + 1) - rows_offsets(row);
};
/// returns the offset (start of columns) for a given row
inline UInt & rowOffset(UInt row) { return rows_offsets(row); };
/// iterator on a row
template <class R>
class iterator_internal
: public std::iterator<std::bidirectional_iterator_tag, R> {
public:
typedef std::iterator<std::bidirectional_iterator_tag, R> _parent;
typedef typename _parent::pointer pointer;
typedef typename _parent::reference reference;
- explicit iterator_internal(pointer x = NULL) : pos(x){};
+ explicit iterator_internal(pointer x = nullptr) : pos(x){};
iterator_internal(const iterator_internal & it) : pos(it.pos){};
iterator_internal & operator++() {
++pos;
return *this;
};
iterator_internal operator++(int) {
iterator tmp(*this);
operator++();
return tmp;
};
iterator_internal & operator--() {
--pos;
return *this;
};
iterator_internal operator--(int) {
iterator_internal tmp(*this);
operator--();
return tmp;
};
bool operator==(const iterator_internal & rhs) { return pos == rhs.pos; };
bool operator!=(const iterator_internal & rhs) { return pos != rhs.pos; };
reference operator*() { return *pos; };
pointer operator->() const { return pos; };
private:
pointer pos;
};
typedef iterator_internal<T> iterator;
typedef iterator_internal<const T> const_iterator;
inline iterator begin(UInt row) {
return iterator(rows.storage() + rows_offsets(row));
};
inline iterator end(UInt row) {
return iterator(rows.storage() + rows_offsets(row + 1));
};
inline const_iterator begin(UInt row) const {
return const_iterator(rows.storage() + rows_offsets(row));
};
inline const_iterator end(UInt row) const {
return const_iterator(rows.storage() + rows_offsets(row + 1));
};
inline iterator rbegin(UInt row) {
return iterator(rows.storage() + rows_offsets(row + 1) - 1);
};
inline iterator rend(UInt row) {
return iterator(rows.storage() + rows_offsets(row) - 1);
};
inline const Array<UInt> & getRowsOffset() const { return rows_offsets; };
inline const Array<T> & getRows() const { return rows; };
inline Array<T> & getRows() { return rows; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
UInt nb_rows;
/// array of size nb_rows containing the offset where the values are stored in
Array<UInt> rows_offsets;
/// compressed row values, values of row[i] are stored between rows_offsets[i]
/// and rows_offsets[i+1]
Array<T> rows;
};
/* -------------------------------------------------------------------------- */
/* Data CSR */
/* -------------------------------------------------------------------------- */
/**
* Inherits from CSR<UInt> and can contain information such as matrix values
* where the mother class would be a CSR structure for row and cols
*
* @return nb_rows
*/
template <class T> class DataCSR : public CSR<UInt> {
public:
DataCSR(UInt nb_rows = 0) : CSR<UInt>(nb_rows), data(0, 1){};
inline void resizeCols() {
CSR<UInt>::resizeCols();
data.resize(rows_offsets(nb_rows));
}
inline const Array<T> & getData() const { return data; };
private:
Array<T> data;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "aka_csr_inline_impl.cc"
/// standard output stream operator
// inline std::ostream & operator <<(std::ostream & stream, const CSR & _this)
// {
// _this.printself(stream);
// return stream;
// }
} // akantu
#endif /* __AKANTU_AKA_CSR_HH__ */
diff --git a/src/common/aka_error.cc b/src/common/aka_error.cc
index cb0346ce0..04209802d 100644
--- a/src/common/aka_error.cc
+++ b/src/common/aka_error.cc
@@ -1,355 +1,355 @@
/**
* @file aka_error.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Sep 06 2010
* @date last modification: Tue Jan 19 2016
*
* @brief handling of errors
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_error.hh"
#include "aka_common.hh"
#include "aka_config.hh"
/* -------------------------------------------------------------------------- */
#include <csignal>
#include <iostream>
#if (defined(READLINK_COMMAND) || defined(ADDR2LINE_COMMAND)) && \
(not defined(_WIN32))
#include <execinfo.h>
#include <sys/wait.h>
#endif
#include <cmath>
#include <cstring>
#include <cxxabi.h>
#include <fstream>
#include <iomanip>
#include <map>
#include <sys/types.h>
#include <unistd.h>
#if defined(AKANTU_CORE_CXX11)
#include <chrono>
#elif defined(AKANTU_USE_OBSOLETE_GETTIMEOFDAY)
#include <sys/time.h>
#else
#include <time.h>
#endif
#ifdef AKANTU_USE_MPI
#include <mpi.h>
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace debug {
static void printBacktraceAndExit(int) { std::terminate(); }
/* ------------------------------------------------------------------------ */
void initSignalHandler() { std::signal(SIGSEGV, &printBacktraceAndExit); }
/* ------------------------------------------------------------------------ */
std::string demangle(const char * symbol) {
int status;
std::string result;
char * demangled_name;
- if ((demangled_name = abi::__cxa_demangle(symbol, NULL, 0, &status)) !=
- NULL) {
+ if ((demangled_name = abi::__cxa_demangle(symbol, nullptr, nullptr,
+ &status)) != nullptr) {
result = demangled_name;
free(demangled_name);
} else {
result = symbol;
}
return result;
}
/* ------------------------------------------------------------------------ */
#if (defined(READLINK_COMMAND) || defined(ADDR2LINK_COMMAND)) && \
(not defined(_WIN32))
std::string exec(std::string cmd) {
FILE * pipe = popen(cmd.c_str(), "r");
if (!pipe)
return "";
char buffer[1024];
std::string result = "";
while (!feof(pipe)) {
- if (fgets(buffer, 128, pipe) != NULL)
+ if (fgets(buffer, 128, pipe) != nullptr)
result += buffer;
}
result = result.substr(0, result.size() - 1);
pclose(pipe);
return result;
}
#endif
/* ------------------------------------------------------------------------ */
void printBacktrace(__attribute__((unused)) int sig) {
AKANTU_DEBUG_INFO("Caught signal " << sig << "!");
#if not defined(_WIN32)
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
std::string me = "";
char buf[1024];
/* The manpage says it won't null terminate. Let's zero the buffer. */
memset(buf, 0, sizeof(buf));
/* Note we use sizeof(buf)-1 since we may need an extra char for NUL. */
if (readlink("/proc/self/exe", buf, sizeof(buf) - 1))
me = std::string(buf);
std::ifstream inmaps;
inmaps.open("/proc/self/maps");
std::map<std::string, size_t> addr_map;
std::string line;
while (inmaps.good()) {
std::getline(inmaps, line);
std::stringstream sstr(line);
size_t first = line.find('-');
std::stringstream sstra(line.substr(0, first));
size_t addr;
sstra >> std::hex >> addr;
std::string lib;
sstr >> lib; sstr >> lib;
sstr >> lib; sstr >> lib;
sstr >> lib; sstr >> lib;
if (lib != "" && addr_map.find(lib) == addr_map.end()) {
addr_map[lib] = addr;
}
}
if (me != "")
addr_map[me] = 0;
#endif
/// \todo for windows this part could be coded using CaptureStackBackTrace
/// and SymFromAddr
const size_t max_depth = 100;
size_t stack_depth;
void * stack_addrs[max_depth];
char ** stack_strings;
size_t i;
stack_depth = backtrace(stack_addrs, max_depth);
stack_strings = backtrace_symbols(stack_addrs, stack_depth);
std::cerr << "BACKTRACE : " << stack_depth << " stack frames."
<< std::endl;
size_t w = size_t(std::floor(log(double(stack_depth)) / std::log(10.)) + 1);
/// -1 to remove the call to the printBacktrace function
for (i = 1; i < stack_depth; i++) {
std::cerr << std::dec << " [" << std::setw(w) << i << "] ";
std::string bt_line(stack_strings[i]);
size_t first, second;
if ((first = bt_line.find('(')) != std::string::npos &&
(second = bt_line.find('+')) != std::string::npos) {
std::string location = bt_line.substr(0, first);
#if defined(READLINK_COMMAND)
location = exec(std::string(BOOST_PP_STRINGIZE(READLINK_COMMAND)) +
std::string(" -f ") + location);
#endif
std::string call =
demangle(bt_line.substr(first + 1, second - first - 1).c_str());
size_t f = bt_line.find('[');
size_t s = bt_line.find(']');
std::string address = bt_line.substr(f + 1, s - f - 1);
std::stringstream sstra(address);
size_t addr;
sstra >> std::hex >> addr;
std::cerr << location << " [" << call << "]";
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
std::map<std::string, size_t>::iterator it = addr_map.find(location);
if (it != addr_map.end()) {
std::stringstream syscom;
syscom << BOOST_PP_STRINGIZE(ADDR2LINE_COMMAND) << " 0x" << std::hex
<< (addr - it->second) << " -i -e " << location;
std::string line = exec(syscom.str());
std::cerr << " (" << line << ")" << std::endl;
} else {
#endif
std::cerr << " (0x" << std::hex << addr << ")" << std::endl;
#if defined(READLINK_COMMAND) && defined(ADDR2LINE_COMMAND)
}
#endif
} else {
std::cerr << bt_line << std::endl;
}
}
free(stack_strings);
std::cerr << "END BACKTRACE" << std::endl;
#endif
}
/* ------------------------------------------------------------------------ */
namespace {
void terminate_handler() {
auto eptr = std::current_exception();
auto t = abi::__cxa_current_exception_type();
auto name = t ? demangle(t->name()) : std::string("unknown");
try {
if (eptr)
std::rethrow_exception(eptr);
else
std::cerr << "!! Execution terminated for unknown reasons !!"
<< std::endl;
} catch (std::exception & e) {
std::cerr << "!! Uncaught exception of type " << name
<< " !!\nwhat(): \"" << e.what() << "\"" << std::endl;
} catch (...) {
std::cerr << "!! Something strange of type \"" << name
<< "\" was thrown.... !!" << std::endl;
}
if (debugger.printBacktrace())
printBacktrace(15);
}
} // namespace
/* ------------------------------------------------------------------------ */
/* ------------------------------------------------------------------------ */
Debugger::Debugger() {
cout = &std::cerr;
level = dblWarning;
parallel_context = "";
file_open = false;
print_backtrace = false;
initSignalHandler();
std::set_terminate(terminate_handler);
}
/* ------------------------------------------------------------------------ */
Debugger::~Debugger() {
if (file_open) {
dynamic_cast<std::ofstream *>(cout)->close();
delete cout;
}
}
/* ------------------------------------------------------------------------ */
void Debugger::exit(int status) {
if (status != 0)
std::terminate();
std::exit(0);
}
/*------------------------------------------------------------------------- */
void Debugger::throwException(const std::string & info,
const std::string & file, unsigned int line,
__attribute__((unused)) bool silent,
__attribute__((unused))
const std::string & location) const
noexcept(false) {
#if !defined(AKANTU_NDEBUG)
if (!silent) {
printMessage("###", dblWarning, info + location);
}
#endif
debug::Exception ex(info, file, line);
throw ex;
}
/* ------------------------------------------------------------------------ */
void Debugger::printMessage(const std::string & prefix,
const DebugLevel & level,
const std::string & info) const {
if (this->level >= level) {
#if defined(AKANTU_CORE_CXX11)
double timestamp =
std::chrono::duration_cast<std::chrono::duration<double, std::micro>>(
std::chrono::system_clock::now().time_since_epoch())
.count();
#elif defined(AKANTU_USE_OBSOLETE_GETTIMEOFDAY)
struct timeval time;
gettimeofday(&time, NULL);
double timestamp = time.tv_sec * 1e6 + time.tv_usec; /*in us*/
#else
struct timespec time;
clock_gettime(CLOCK_REALTIME_COARSE, &time);
double timestamp = time.tv_sec * 1e6 + time.tv_nsec * 1e-3; /*in us*/
#endif
*(cout) << parallel_context << "{" << (size_t)timestamp << "} " << prefix
<< " " << info << std::endl;
}
}
/* ------------------------------------------------------------------------ */
void Debugger::setDebugLevel(const DebugLevel & level) {
this->level = level;
}
/* ------------------------------------------------------------------------ */
const DebugLevel & Debugger::getDebugLevel() const { return this->level; }
/* ------------------------------------------------------------------------ */
void Debugger::setLogFile(const std::string & filename) {
if (file_open) {
dynamic_cast<std::ofstream *>(cout)->close();
delete cout;
}
std::ofstream * fileout = new std::ofstream(filename.c_str());
file_open = true;
cout = fileout;
}
std::ostream & Debugger::getOutputStream() { return *cout; }
/* ------------------------------------------------------------------------ */
void Debugger::setParallelContext(int rank, int size) {
std::stringstream sstr;
UInt pad = std::ceil(std::log10(size));
sstr << "<" << getpid() << ">[R" << std::setfill(' ') << std::right
<< std::setw(pad) << rank << "|S" << size << "] ";
parallel_context = sstr.str();
}
void setDebugLevel(const DebugLevel & level) {
debugger.setDebugLevel(level);
}
const DebugLevel & getDebugLevel() { return debugger.getDebugLevel(); }
/* --------------------------------------------------------------------------
*/
void exit(int status) { debugger.exit(status); }
} // namespace debug
} // namespace akantu
diff --git a/src/common/aka_random_generator.hh b/src/common/aka_random_generator.hh
index 3fada453f..73fa4952b 100644
--- a/src/common/aka_random_generator.hh
+++ b/src/common/aka_random_generator.hh
@@ -1,265 +1,268 @@
/**
* @file aka_random_generator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Nov 11 2015
*
* @brief generic random generator
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <random>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_RANDOM_GENERATOR_HH__
#define __AKANTU_AKA_RANDOM_GENERATOR_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* List of available distributions */
/* -------------------------------------------------------------------------- */
// clang-format off
#define AKANTU_RANDOM_DISTRIBUTION_TYPES \
((uniform , std::uniform_real_distribution )) \
((exponential , std::exponential_distribution )) \
((gamma , std::gamma_distribution )) \
((weibull , std::weibull_distribution )) \
((extreme_value, std::extreme_value_distribution)) \
((normal , std::normal_distribution )) \
((lognormal , std::lognormal_distribution )) \
((chi_squared , std::chi_squared_distribution )) \
((cauchy , std::cauchy_distribution )) \
((fisher_f , std::fisher_f_distribution )) \
((student_t , std::student_t_distribution ))
// clang-format on
#define AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(elem) BOOST_PP_CAT(_rdt_, elem)
#define AKANTU_RANDOM_DISTRIBUTION_PREFIX(s, data, elem) \
AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX(BOOST_PP_TUPLE_ELEM(2, 0, elem))
enum RandomDistributionType {
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_RANDOM_DISTRIBUTION_PREFIX, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)),
_rdt_not_defined
};
/* -------------------------------------------------------------------------- */
/* Generator */
/* -------------------------------------------------------------------------- */
template <typename T> class RandomGenerator {
/* ------------------------------------------------------------------------ */
public:
inline T operator()() { return generator(); }
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int) const {
stream << "RandGenerator [seed=" << _seed << "]";
}
/* ------------------------------------------------------------------------ */
public:
static void seed(long int s) {
_seed = s;
generator.seed(_seed);
}
static long int seed() { return _seed; }
static constexpr T min() { return generator.min(); }
static constexpr T max() { return generator.max(); }
/* ------------------------------------------------------------------------ */
private:
static long int _seed;
static std::default_random_engine generator;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#undef AKANTU_RANDOM_DISTRIBUTION_PREFIX
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE(r, data, elem) \
case AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem)): { \
stream << BOOST_PP_STRINGIZE(AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem))); \
break; \
}
inline std::ostream & operator<<(std::ostream & stream,
RandomDistributionType type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
default:
stream << UInt(type) << " not a RandomDistributionType";
break;
}
return stream;
}
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_PRINT_CASE
/* -------------------------------------------------------------------------- */
/* Some Helper */
/* -------------------------------------------------------------------------- */
template <typename T, class Distribution> class RandomDistributionTypeHelper {
enum { value = _rdt_not_defined };
};
/* -------------------------------------------------------------------------- */
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE(r, data, elem) \
template <typename T> \
struct RandomDistributionTypeHelper<T, BOOST_PP_TUPLE_ELEM(2, 1, elem) < \
T>> { \
enum { \
value = AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem)) \
}; \
\
static void printself(std::ostream & stream) { \
stream << BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 0, elem)); \
} \
};
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_GET_TYPE
/* -------------------------------------------------------------------------- */
template <class T> class RandomDistribution {
public:
+ virtual ~RandomDistribution() = default;
virtual T operator()(RandomGenerator<UInt> & gen) = 0;
virtual std::unique_ptr<RandomDistribution<T>> make_unique() const = 0;
virtual void printself(std::ostream & stream, int = 0) const = 0;
};
template <class T, class Distribution>
class RandomDistributionProxy : public RandomDistribution<T> {
public:
explicit RandomDistributionProxy(Distribution dist)
: distribution(std::move(dist)) {}
T operator()(RandomGenerator<UInt> & gen) override {
return distribution(gen);
}
std::unique_ptr<RandomDistribution<T>> make_unique() const override {
return std::make_unique<RandomDistributionProxy<T, Distribution>>(
distribution);
}
void printself(std::ostream & stream, int = 0) const override {
RandomDistributionTypeHelper<T, Distribution>::printself(stream);
stream << " [ " << distribution << " ]";
}
private:
Distribution distribution;
};
/* -------------------------------------------------------------------------- */
/* RandomParameter */
/* -------------------------------------------------------------------------- */
template <typename T> class RandomParameter {
public:
template <class Distribution>
explicit RandomParameter(T base_value, Distribution dist)
: base_value(base_value),
type(RandomDistributionType(
RandomDistributionTypeHelper<T, Distribution>::value)),
distribution_proxy(
std::make_unique<RandomDistributionProxy<T, Distribution>>(
std::move(dist))) {}
explicit RandomParameter(T base_value)
: base_value(base_value),
type(RandomDistributionType(
RandomDistributionTypeHelper<
T, std::uniform_real_distribution<T>>::value)),
distribution_proxy(
std::make_unique<
RandomDistributionProxy<T, std::uniform_real_distribution<T>>>(
std::uniform_real_distribution<T>(0., 0.))) {}
RandomParameter(const RandomParameter & other)
: base_value(other.base_value), type(other.type),
distribution_proxy(other.distribution_proxy->make_unique()) {}
RandomParameter & operator=(const RandomParameter & other) {
distribution_proxy = other.distribution_proxy->make_unique();
base_value = other.base_value;
type = other.type;
return *this;
}
+ virtual ~RandomParameter() = default;
+
inline void setBaseValue(const T & value) { this->base_value = value; }
inline T getBaseValue() const { return this->base_value; }
template <template <typename> class Generator, class iterator>
void setValues(iterator it, iterator end) {
RandomGenerator<UInt> gen;
for (; it != end; ++it)
*it = this->base_value + (*distribution_proxy)(gen);
}
virtual void printself(std::ostream & stream,
__attribute__((unused)) int indent = 0) const {
stream << base_value;
stream << " + " << *distribution_proxy;
}
private:
/// Value with no random variations
T base_value;
/// Random distribution type
RandomDistributionType type;
/// Proxy to store a std random distribution
std::unique_ptr<RandomDistribution<T>> distribution_proxy;
};
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
RandomDistribution<T> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
RandomParameter<T> & _this) {
_this.printself(stream);
return stream;
}
} // akantu
#endif /* __AKANTU_AKA_RANDOM_GENERATOR_HH__ */
diff --git a/src/common/aka_static_memory.cc b/src/common/aka_static_memory.cc
index 7d8709f47..d9d258834 100644
--- a/src/common/aka_static_memory.cc
+++ b/src/common/aka_static_memory.cc
@@ -1,156 +1,156 @@
/**
* @file aka_static_memory.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 06 2016
*
* @brief Memory management
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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>
#include <sstream>
/* -------------------------------------------------------------------------- */
#include "aka_static_memory.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
bool StaticMemory::is_instantiated = false;
-StaticMemory * StaticMemory::single_static_memory = NULL;
+StaticMemory * StaticMemory::single_static_memory = nullptr;
UInt StaticMemory::nb_reference = 0;
/* -------------------------------------------------------------------------- */
StaticMemory & StaticMemory::getStaticMemory() {
if(!single_static_memory) {
single_static_memory = new StaticMemory();
is_instantiated = true;
}
nb_reference++;
return *single_static_memory;
}
/* -------------------------------------------------------------------------- */
void StaticMemory::destroy() {
nb_reference--;
if(nb_reference == 0) {
delete single_static_memory;
}
}
/* -------------------------------------------------------------------------- */
StaticMemory::~StaticMemory() {
AKANTU_DEBUG_IN();
MemoryMap::iterator memory_it;
for(memory_it = memories.begin(); memory_it != memories.end(); ++memory_it) {
ArrayMap::iterator vector_it;
for(vector_it = (memory_it->second).begin();
vector_it != (memory_it->second).end();
++vector_it) {
delete vector_it->second;
}
(memory_it->second).clear();
}
memories.clear();
is_instantiated = false;
- StaticMemory::single_static_memory = NULL;
+ StaticMemory::single_static_memory = nullptr;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StaticMemory::sfree(const MemoryID & memory_id,
const ID & name) {
AKANTU_DEBUG_IN();
try {
ArrayMap & vectors = const_cast<ArrayMap &>(getMemory(memory_id));
ArrayMap::iterator vector_it;
vector_it = vectors.find(name);
if(vector_it != vectors.end()) {
AKANTU_DEBUG_INFO("Array " << name << " removed from the static memory number " << memory_id);
delete vector_it->second;
vectors.erase(vector_it);
AKANTU_DEBUG_OUT();
return;
}
} catch (debug::Exception e) {
AKANTU_EXCEPTION("The memory " << memory_id << " does not exist (perhaps already freed) ["
<< e.what() << "]");
AKANTU_DEBUG_OUT();
return;
}
AKANTU_DEBUG_INFO("The vector " << name << " does not exist (perhaps already freed)");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StaticMemory::printself(std::ostream & stream, int indent) const{
std::string space = "";
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
std::streamsize prec = stream.precision();
stream.precision(2);
stream << space << "StaticMemory [" << std::endl;
UInt nb_memories = memories.size();
stream << space << " + nb memories : " << nb_memories << std::endl;
Real tot_size = 0;
MemoryMap::const_iterator memory_it;
for(memory_it = memories.begin(); memory_it != memories.end(); ++memory_it) {
Real mem_size = 0;
stream << space << AKANTU_INDENT << "Memory [" << std::endl;
UInt mem_id = memory_it->first;
stream << space << AKANTU_INDENT << " + memory id : "
<< mem_id << std::endl;
UInt nb_vectors = (memory_it->second).size();
stream << space << AKANTU_INDENT << " + nb vectors : "
<< nb_vectors << std::endl;
stream.precision(prec);
ArrayMap::const_iterator vector_it;
for(vector_it = (memory_it->second).begin();
vector_it != (memory_it->second).end();
++vector_it) {
(vector_it->second)->printself(stream, indent + 2);
mem_size += (vector_it->second)->getMemorySize();
}
stream << space << AKANTU_INDENT << " + total size : " << printMemorySize<char>(mem_size) << std::endl;
stream << space << AKANTU_INDENT << "]" << std::endl;
tot_size += mem_size;
}
stream << space << " + total size : " << printMemorySize<char>(tot_size) << std::endl;
stream << space << "]" << std::endl;
stream.precision(prec);
}
/* -------------------------------------------------------------------------- */
} // akantu
diff --git a/src/common/aka_types.hh b/src/common/aka_types.hh
index bd65ef234..87eed2533 100644
--- a/src/common/aka_types.hh
+++ b/src/common/aka_types.hh
@@ -1,1263 +1,1263 @@
/**
* @file aka_types.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 17 2011
* @date last modification: Fri Jan 22 2016
*
* @brief description of the "simple" types
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_error.hh"
#include "aka_fwd.hh"
#include "aka_math.hh"
/* -------------------------------------------------------------------------- */
#include <initializer_list>
#include <iomanip>
#include <type_traits>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_TYPES_HH__
#define __AKANTU_AKA_TYPES_HH__
namespace akantu {
enum NormType { L_1 = 1, L_2 = 2, L_inf = UInt(-1) };
/**
* DimHelper is a class to generalize the setup of a dim array from 3
* values. This gives a common interface in the TensorStorage class
* independently of its derived inheritance (Vector, Matrix, Tensor3)
* @tparam dim
*/
template <UInt dim> struct DimHelper {
static inline void setDims(UInt m, UInt n, UInt p, UInt dims[dim]);
};
/* -------------------------------------------------------------------------- */
template <> struct DimHelper<1> {
static inline void setDims(UInt m, __attribute__((unused)) UInt n,
__attribute__((unused)) UInt p, UInt dims[1]) {
dims[0] = m;
}
};
/* -------------------------------------------------------------------------- */
template <> struct DimHelper<2> {
static inline void setDims(UInt m, UInt n, __attribute__((unused)) UInt p,
UInt dims[2]) {
dims[0] = m;
dims[1] = n;
}
};
/* -------------------------------------------------------------------------- */
template <> struct DimHelper<3> {
static inline void setDims(UInt m, UInt n, UInt p, UInt dims[3]) {
dims[0] = m;
dims[1] = n;
dims[2] = p;
}
};
/* -------------------------------------------------------------------------- */
template <typename T, UInt ndim, class RetType> class TensorStorage;
/* -------------------------------------------------------------------------- */
/* Proxy classes */
/* -------------------------------------------------------------------------- */
namespace tensors {
template <class A, class B> struct is_copyable {
enum : bool { value = false };
};
template <class A> struct is_copyable<A, A> {
enum : bool { value = true };
};
template <class A> struct is_copyable<A, typename A::RetType> {
enum : bool { value = true };
};
template <class A> struct is_copyable<A, typename A::RetType::proxy> {
enum : bool { value = true };
};
} // namespace tensors
/**
* @class TensorProxy aka_types.hh
* @desc The TensorProxy class is a proxy class to the TensorStorage it handles
* the
* wrapped case. That is to say if an accessor should give access to a Tensor
* wrapped on some data, like the Array<T>::iterator they can return a
* TensorProxy that will be automatically transformed as a TensorStorage wrapped
* on the same data
* @tparam T stored type
* @tparam ndim order of the tensor
* @tparam RetType real derived type
*/
template <typename T, UInt ndim, class _RetType> class TensorProxy {
protected:
using RetTypeProxy = typename _RetType::proxy;
TensorProxy(T * data, UInt m, UInt n, UInt p) {
DimHelper<ndim>::setDims(m, n, p, this->n);
this->values = data;
}
template <class Other, typename = std::enable_if_t<
tensors::is_copyable<TensorProxy, Other>::value>>
explicit TensorProxy(const Other & other) {
this->values = other.storage();
for (UInt i = 0; i < ndim; ++i)
this->n[i] = other.size(i);
}
public:
using RetType = _RetType;
//operator RetType() { return RetType(static_cast<RetTypeProxy &>(*this)); }
UInt size(UInt i) const {
AKANTU_DEBUG_ASSERT(i < ndim, "This tensor has only " << ndim
<< " dimensions, not "
<< (i + 1));
return n[i];
}
inline UInt size() const {
UInt _size = 1;
for (UInt d = 0; d < ndim; ++d)
_size *= this->n[d];
return _size;
}
T * storage() const { return values; }
template <class Other, typename = std::enable_if_t<
tensors::is_copyable<TensorProxy, Other>::value>>
inline TensorProxy & operator=(const Other & other) {
AKANTU_DEBUG_ASSERT(
other.size() == this->size(),
"You are trying to copy two tensors with different sizes");
memcpy(this->values, other.storage(), this->size() * sizeof(T));
return *this;
}
// template <class Other, typename = std::enable_if_t<
// tensors::is_copyable<TensorProxy, Other>::value>>
// inline TensorProxy & operator=(const Other && other) {
// AKANTU_DEBUG_ASSERT(
// other.size() == this->size(),
// "You are trying to copy two tensors with different sizes");
// memcpy(this->values, other.storage(), this->size() * sizeof(T));
// return *this;
// }
template <typename O> inline RetTypeProxy & operator*=(const O & o) {
RetType(*this) *= o;
return static_cast<RetTypeProxy &>(*this);
}
template <typename O> inline RetTypeProxy & operator/=(const O & o) {
RetType(*this) /= o;
return static_cast<RetTypeProxy &>(*this);
}
protected:
T * values;
UInt n[ndim];
};
/* -------------------------------------------------------------------------- */
template <typename T> class VectorProxy : public TensorProxy<T, 1, Vector<T>> {
using parent = TensorProxy<T, 1, Vector<T>>;
using type = Vector<T>;
public:
VectorProxy(T * data, UInt n) : parent(data, n, 0, 0) {}
template <class Other> explicit VectorProxy(Other & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline VectorProxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
// inline VectorProxy<T> & operator=(const VectorProxy && other) {
// parent::operator=(other);
// return *this;
// }
/* ------------------------------------------------------------------------ */
T & operator()(UInt index) { return this->values[index]; };
const T & operator()(UInt index) const { return this->values[index]; };
};
template <typename T> class MatrixProxy : public TensorProxy<T, 2, Matrix<T>> {
using parent = TensorProxy<T, 2, Matrix<T>>;
using type = Matrix<T>;
public:
MatrixProxy(T * data, UInt m, UInt n) : parent(data, m, n, 0) {}
template <class Other> explicit MatrixProxy(Other & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline MatrixProxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
};
template <typename T>
class Tensor3Proxy : public TensorProxy<T, 3, Tensor3<T>> {
typedef TensorProxy<T, 3, Tensor3<T>> parent;
using type = Tensor3<T>;
public:
Tensor3Proxy(T * data, UInt m, UInt n, UInt k) : parent(data, m, n, k) {}
Tensor3Proxy(const Tensor3Proxy & src) : parent(src) {}
Tensor3Proxy(const Tensor3<T> & src) : parent(src) {}
/* ---------------------------------------------------------------------- */
template <class Other>
inline Tensor3Proxy<T> & operator=(const Other & other) {
parent::operator=(other);
return *this;
}
};
/* -------------------------------------------------------------------------- */
/* Tensor base class */
/* -------------------------------------------------------------------------- */
template <typename T, UInt ndim, class RetType>
class TensorStorage : public TensorTrait {
public:
using value_type = T;
friend class Array<T>;
protected:
template <class TensorType> void copySize(const TensorType & src) {
for (UInt d = 0; d < ndim; ++d)
this->n[d] = src.size(d);
this->_size = src.size();
}
TensorStorage() : values(nullptr) {
for (UInt d = 0; d < ndim; ++d)
this->n[d] = 0;
_size = 0;
}
TensorStorage(const TensorProxy<T, ndim, RetType> & proxy) {
this->copySize(proxy);
this->values = proxy.storage();
this->wrapped = true;
}
protected:
TensorStorage(const TensorStorage & src) = delete;
public:
TensorStorage(const TensorStorage & src, bool deep_copy)
: values(nullptr), wrapped(false) {
if (deep_copy)
this->deepCopy(src);
else
this->shallowCopy(src);
}
protected:
TensorStorage(UInt m, UInt n, UInt p, const T & def) {
static_assert(std::is_trivially_constructible<T>{},
"Cannot create a tensor on non trivial types");
DimHelper<ndim>::setDims(m, n, p, this->n);
this->computeSize();
this->values = new T[this->_size];
this->set(def);
this->wrapped = false;
}
TensorStorage(T * data, UInt m, UInt n, UInt p) {
DimHelper<ndim>::setDims(m, n, p, this->n);
this->computeSize();
this->values = data;
this->wrapped = true;
}
public:
/* ------------------------------------------------------------------------ */
template <class TensorType> inline void shallowCopy(const TensorType & src) {
this->copySize(src);
if (!this->wrapped)
delete[] this->values;
this->values = src.storage();
this->wrapped = true;
}
/* ------------------------------------------------------------------------ */
template <class TensorType> inline void deepCopy(const TensorType & src) {
this->copySize(src);
if (!this->wrapped)
delete[] this->values;
static_assert(std::is_trivially_constructible<T>{},
"Cannot create a tensor on non trivial types");
this->values = new T[this->_size];
static_assert(std::is_trivially_copyable<T>{},
"Cannot copy a tensor on non trivial types");
memcpy((void *)this->values, (void *)src.storage(),
this->_size * sizeof(T));
this->wrapped = false;
}
virtual ~TensorStorage() {
if (!this->wrapped)
delete[] this->values;
}
/* ------------------------------------------------------------------------ */
inline TensorStorage & operator=(const TensorStorage & src) {
return this->operator=(dynamic_cast<RetType &>(src));
}
/* ------------------------------------------------------------------------ */
inline TensorStorage & operator=(const RetType & src) {
if (this != &src) {
if (this->wrapped) {
static_assert(std::is_trivially_copyable<T>{},
"Cannot copy a tensor on non trivial types");
// this test is not sufficient for Tensor of order higher than 1
AKANTU_DEBUG_ASSERT(this->_size == src.size(),
"Tensors of different size");
memcpy((void *)this->values, (void *)src.storage(),
this->_size * sizeof(T));
} else {
deepCopy(src);
}
}
return *this;
}
/* ------------------------------------------------------------------------ */
template <class R>
inline RetType & operator+=(const TensorStorage<T, ndim, R> & other) {
T * a = this->storage();
T * b = other.storage();
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be subtracted");
for (UInt i = 0; i < _size; ++i)
*(a++) += *(b++);
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
template <class R>
inline RetType & operator-=(const TensorStorage<T, ndim, R> & other) {
T * a = this->storage();
T * b = other.storage();
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be subtracted");
for (UInt i = 0; i < _size; ++i)
*(a++) -= *(b++);
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
inline RetType & operator+=(const T & x) {
T * a = this->values;
for (UInt i = 0; i < _size; ++i)
*(a++) += x;
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
inline RetType & operator-=(const T & x) {
T * a = this->values;
for (UInt i = 0; i < _size; ++i)
*(a++) -= x;
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
inline RetType & operator*=(const T & x) {
T * a = this->storage();
for (UInt i = 0; i < _size; ++i)
*(a++) *= x;
return *(static_cast<RetType *>(this));
}
/* ---------------------------------------------------------------------- */
inline RetType & operator/=(const T & x) {
T * a = this->values;
for (UInt i = 0; i < _size; ++i)
*(a++) /= x;
return *(static_cast<RetType *>(this));
}
/// Y = \alpha X + Y
inline RetType & aXplusY(const TensorStorage & other, const T & alpha = 1.) {
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be subtracted");
Math::aXplusY(this->_size, alpha, other.storage(), this->storage());
return *(static_cast<RetType *>(this));
}
/* ------------------------------------------------------------------------ */
T * storage() const { return values; }
UInt size() const { return _size; }
UInt size(UInt i) const {
AKANTU_DEBUG_ASSERT(i < ndim, "This tensor has only " << ndim
<< " dimensions, not "
<< (i + 1));
return n[i];
};
/* ------------------------------------------------------------------------ */
inline void clear() { memset(values, 0, _size * sizeof(T)); };
inline void set(const T & t) { std::fill_n(values, _size, t); };
template <class TensorType> inline void copy(const TensorType & other) {
AKANTU_DEBUG_ASSERT(
_size == other.size(),
"The two tensors do not have the same size, they cannot be copied");
memcpy(values, other.storage(), _size * sizeof(T));
}
bool isWrapped() const { return this->wrapped; }
protected:
inline void computeSize() {
_size = 1;
for (UInt d = 0; d < ndim; ++d)
_size *= this->n[d];
}
protected:
template <typename R, NormType norm_type> struct NormHelper {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
for (; it < end; ++it)
_norm += std::pow(std::abs(*it), norm_type);
return std::pow(_norm, 1. / norm_type);
}
};
template <typename R> struct NormHelper<R, L_1> {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
for (; it < end; ++it)
_norm += std::abs(*it);
return _norm;
}
};
template <typename R> struct NormHelper<R, L_2> {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
for (; it < end; ++it)
_norm += *it * *it;
return sqrt(_norm);
}
};
template <typename R> struct NormHelper<R, L_inf> {
template <class Ten> static R norm(const Ten & ten) {
R _norm = 0.;
R * it = ten.storage();
R * end = ten.storage() + ten.size();
for (; it < end; ++it)
_norm = std::max(std::abs(*it), _norm);
return _norm;
}
};
public:
/*----------------------------------------------------------------------- */
/// "Entrywise" norm norm<L_p> @f[ \|\boldsymbol{T}\|_p = \left(
/// \sum_i^{n[0]}\sum_j^{n[1]}\sum_k^{n[2]} |T_{ijk}|^p \right)^{\frac{1}{p}}
/// @f]
template <NormType norm_type> inline T norm() const {
return NormHelper<T, norm_type>::norm(*this);
}
protected:
UInt n[ndim];
UInt _size;
T * values;
bool wrapped{false};
};
/* -------------------------------------------------------------------------- */
/* Vector */
/* -------------------------------------------------------------------------- */
template <typename T> class Vector : public TensorStorage<T, 1, Vector<T>> {
typedef TensorStorage<T, 1, Vector<T>> parent;
public:
using value_type = typename parent::value_type;
using proxy = VectorProxy<T>;
public:
Vector() : parent() {}
explicit Vector(UInt n, const T & def = T()) : parent(n, 0, 0, def) {}
Vector(T * data, UInt n) : parent(data, n, 0, 0) {}
Vector(const Vector & src, bool deep_copy = true) : parent(src, deep_copy) {}
Vector(const TensorProxy<T, 1, Vector> & src) : parent(src) {}
Vector(std::initializer_list<T> list) : parent(list.size(), 0, 0, T()) {
UInt i = 0;
for (auto val : list) {
operator()(i++) = val;
}
}
public:
~Vector() override = default;
/* ------------------------------------------------------------------------ */
inline Vector & operator=(const Vector & src) {
parent::operator=(src);
return *this;
}
/* ------------------------------------------------------------------------ */
inline T & operator()(UInt i) {
AKANTU_DEBUG_ASSERT((i < this->n[0]),
"Access out of the vector! "
<< "Index (" << i
<< ") is out of the vector of size (" << this->n[0]
<< ")");
return *(this->values + i);
}
inline const T & operator()(UInt i) const {
AKANTU_DEBUG_ASSERT((i < this->n[0]),
"Access out of the vector! "
<< "Index (" << i
<< ") is out of the vector of size (" << this->n[0]
<< ")");
return *(this->values + i);
}
inline T & operator[](UInt i) { return this->operator()(i); }
inline const T & operator[](UInt i) const { return this->operator()(i); }
/* ------------------------------------------------------------------------ */
inline Vector<T> & operator*=(Real x) { return parent::operator*=(x); }
inline Vector<T> & operator/=(Real x) { return parent::operator/=(x); }
/* ------------------------------------------------------------------------ */
inline Vector<T> & operator*=(const Vector<T> & vect) {
T * a = this->storage();
T * b = vect.storage();
for (UInt i = 0; i < this->_size; ++i)
*(a++) *= *(b++);
return *this;
}
/* ------------------------------------------------------------------------ */
inline Real dot(const Vector<T> & vect) const {
return Math::vectorDot(this->values, vect.storage(), this->_size);
}
/* ------------------------------------------------------------------------ */
inline Real mean() const {
Real mean = 0;
T * a = this->storage();
for (UInt i = 0; i < this->_size; ++i)
mean += *(a++);
return mean / this->_size;
}
/* ------------------------------------------------------------------------ */
inline Vector & crossProduct(const Vector<T> & v1, const Vector<T> & v2) {
AKANTU_DEBUG_ASSERT(this->size() == 3,
"crossProduct is only defined in 3D (n=" << this->size()
<< ")");
AKANTU_DEBUG_ASSERT(
this->size() == v1.size() && this->size() == v2.size(),
"crossProduct is not a valid operation non matching size vectors");
Math::vectorProduct3(v1.storage(), v2.storage(), this->values);
return *this;
}
/* ------------------------------------------------------------------------ */
inline void solve(const Matrix<T> & A, const Vector<T> & b) {
AKANTU_DEBUG_ASSERT(
this->size() == A.rows() && this->_size == A.cols(),
"The size of the solution vector mismatches the size of the matrix");
AKANTU_DEBUG_ASSERT(
this->_size == b._size,
"The rhs vector has a mismatch in size with the matrix");
Math::solve(this->_size, A.storage(), this->values, b.storage());
}
/* ------------------------------------------------------------------------ */
template <bool tr_A>
inline void mul(const Matrix<T> & A, const Vector<T> & x, Real alpha = 1.0);
/* ------------------------------------------------------------------------ */
inline Real norm() const { return parent::template norm<L_2>(); }
template <NormType nt> inline Real norm() const {
return parent::template norm<nt>();
}
/* ------------------------------------------------------------------------ */
inline void normalize() {
Real n = norm();
operator/=(n);
}
/* ------------------------------------------------------------------------ */
/// norm of (*this - x)
inline Real distance(const Vector<T> & y) const {
Real * vx = this->values;
Real * vy = y.storage();
Real sum_2 = 0;
for (UInt i = 0; i < this->_size; ++i, ++vx, ++vy)
sum_2 += (*vx - *vy) * (*vx - *vy);
return sqrt(sum_2);
}
/* ------------------------------------------------------------------------ */
inline bool equal(const Vector<T> & v,
Real tolerance = Math::getTolerance()) const {
T * a = this->storage();
T * b = v.storage();
UInt i = 0;
while (i < this->_size && (std::abs(*(a++) - *(b++)) < tolerance))
++i;
return i == this->_size;
}
/* ------------------------------------------------------------------------ */
inline short compare(const Vector<T> & v,
Real tolerance = Math::getTolerance()) const {
T * a = this->storage();
T * b = v.storage();
for (UInt i(0); i < this->_size; ++i, ++a, ++b) {
if (std::abs(*a - *b) > tolerance)
return (((*a - *b) > tolerance) ? 1 : -1);
}
return 0;
}
/* ------------------------------------------------------------------------ */
inline bool operator==(const Vector<T> & v) const { return equal(v); }
inline bool operator!=(const Vector<T> & v) const { return !operator==(v); }
inline bool operator<(const Vector<T> & v) const { return compare(v) == -1; }
inline bool operator>(const Vector<T> & v) const { return compare(v) == 1; }
/* ------------------------------------------------------------------------ */
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << "[";
for (UInt i = 0; i < this->_size; ++i) {
if (i != 0)
stream << ", ";
stream << this->values[i];
}
stream << "]";
}
// friend class ::akantu::Array<T>;
};
using RVector = Vector<Real>;
/* ------------------------------------------------------------------------ */
template <>
inline bool Vector<UInt>::equal(const Vector<UInt> & v,
__attribute__((unused)) Real tolerance) const {
UInt * a = this->storage();
UInt * b = v.storage();
UInt i = 0;
while (i < this->_size && (*(a++) == *(b++)))
++i;
return i == this->_size;
}
/* ------------------------------------------------------------------------ */
/* Matrix */
/* ------------------------------------------------------------------------ */
template <typename T> class Matrix : public TensorStorage<T, 2, Matrix<T>> {
typedef TensorStorage<T, 2, Matrix<T>> parent;
public:
using value_type = typename parent::value_type;
using proxy = MatrixProxy<T>;
public:
Matrix() : parent() {}
Matrix(UInt m, UInt n, const T & def = T()) : parent(m, n, 0, def) {}
Matrix(T * data, UInt m, UInt n) : parent(data, m, n, 0) {}
Matrix(const Matrix & src, bool deep_copy = true) : parent(src, deep_copy) {}
Matrix(const MatrixProxy<T> & src) : parent(src) {}
Matrix(std::initializer_list<std::initializer_list<T>> list) {
static_assert(std::is_trivially_copyable<T>{},
"Cannot create a tensor on non trivial types");
std::size_t n = 0;
std::size_t m = list.size();
for (auto row : list) {
n = std::max(n, row.size());
}
DimHelper<2>::setDims(m, n, 0, this->n);
this->computeSize();
this->values = new T[this->_size];
this->set(0);
UInt i = 0, j = 0;
for (auto & row : list) {
for (auto & val : row) {
at(i, j++) = val;
}
++i;
j = 0;
}
}
- virtual ~Matrix() = default;
+ ~Matrix() override = default;
/* ------------------------------------------------------------------------ */
inline Matrix & operator=(const Matrix & src) {
parent::operator=(src);
return *this;
}
public:
/* ---------------------------------------------------------------------- */
UInt rows() const { return this->n[0]; }
UInt cols() const { return this->n[1]; }
/* ---------------------------------------------------------------------- */
inline T & at(UInt i, UInt j) {
AKANTU_DEBUG_ASSERT(((i < this->n[0]) && (j < this->n[1])),
"Access out of the matrix! "
<< "Index (" << i << ", " << j
<< ") is out of the matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return *(this->values + i + j * this->n[0]);
}
inline const T & at(UInt i, UInt j) const {
AKANTU_DEBUG_ASSERT(((i < this->n[0]) && (j < this->n[1])),
"Access out of the matrix! "
<< "Index (" << i << ", " << j
<< ") is out of the matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return *(this->values + i + j * this->n[0]);
}
/* ------------------------------------------------------------------------ */
inline T & operator()(UInt i, UInt j) { return this->at(i, j); }
inline const T & operator()(UInt i, UInt j) const { return this->at(i, j); }
/// give a line vector wrapped on the column i
inline VectorProxy<T> operator()(UInt j) {
AKANTU_DEBUG_ASSERT(j < this->n[1],
"Access out of the matrix! "
<< "You are trying to access the column vector "
<< j << " in a matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return VectorProxy<T>(this->values + j * this->n[0], this->n[0]);
}
inline const VectorProxy<T> operator()(UInt j) const {
AKANTU_DEBUG_ASSERT(j < this->n[1],
"Access out of the matrix! "
<< "You are trying to access the column vector "
<< j << " in a matrix of size (" << this->n[0]
<< ", " << this->n[1] << ")");
return VectorProxy<T>(this->values + j * this->n[0], this->n[0]);
}
inline T & operator[](UInt idx) { return *(this->values + idx); };
inline const T & operator[](UInt idx) const { return *(this->values + idx); };
/* ---------------------------------------------------------------------- */
inline Matrix operator*(const Matrix & B) {
Matrix C(this->rows(), B.cols());
C.mul<false, false>(*this, B);
return C;
}
/* ----------------------------------------------------------------------- */
inline Matrix & operator*=(const T & x) { return parent::operator*=(x); }
inline Matrix & operator*=(const Matrix & B) {
Matrix C(*this);
this->mul<false, false>(C, B);
return *this;
}
/* ---------------------------------------------------------------------- */
template <bool tr_A, bool tr_B>
inline void mul(const Matrix & A, const Matrix & B, T alpha = 1.0) {
UInt k = A.cols();
if (tr_A)
k = A.rows();
#ifndef AKANTU_NDEBUG
if (tr_B) {
AKANTU_DEBUG_ASSERT(k == B.cols(),
"matrices to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->cols() == B.rows(),
"matrices to multiply have no fit dimensions");
} else {
AKANTU_DEBUG_ASSERT(k == B.rows(),
"matrices to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->cols() == B.cols(),
"matrices to multiply have no fit dimensions");
}
if (tr_A) {
AKANTU_DEBUG_ASSERT(this->rows() == A.cols(),
"matrices to multiply have no fit dimensions");
} else {
AKANTU_DEBUG_ASSERT(this->rows() == A.rows(),
"matrices to multiply have no fit dimensions");
}
#endif // AKANTU_NDEBUG
Math::matMul<tr_A, tr_B>(this->rows(), this->cols(), k, alpha, A.storage(),
B.storage(), 0., this->storage());
}
/* ---------------------------------------------------------------------- */
inline void outerProduct(const Vector<T> & A, const Vector<T> & B) {
AKANTU_DEBUG_ASSERT(
A.size() == this->rows() && B.size() == this->cols(),
"A and B are not compatible with the size of the matrix");
for (UInt i = 0; i < this->rows(); ++i) {
for (UInt j = 0; j < this->cols(); ++j) {
this->values[i + j * this->rows()] += A[i] * B[j];
}
}
}
private:
class EigenSorter {
public:
EigenSorter(const Vector<T> & eigs) : eigs(eigs) {}
bool operator()(const UInt & a, const UInt & b) const {
return (eigs(a) > eigs(b));
}
private:
const Vector<T> & eigs;
};
public:
/* ---------------------------------------------------------------------- */
inline void eig(Vector<T> & eigenvalues, Matrix<T> & eigenvectors) const {
AKANTU_DEBUG_ASSERT(this->cols() == this->rows(),
"eig is not a valid operation on a rectangular matrix");
AKANTU_DEBUG_ASSERT(eigenvalues.size() == this->cols(),
"eigenvalues should be of size " << this->cols()
<< ".");
#ifndef AKANTU_NDEBUG
- if (eigenvectors.storage() != NULL)
+ if (eigenvectors.storage() != nullptr)
AKANTU_DEBUG_ASSERT((eigenvectors.rows() == eigenvectors.cols()) &&
(eigenvectors.rows() == this->cols()),
"Eigenvectors needs to be a square matrix of size "
<< this->cols() << " x " << this->cols() << ".");
#endif
Matrix<T> tmp = *this;
Vector<T> tmp_eigs(eigenvalues.size());
Matrix<T> tmp_eig_vects(eigenvectors.rows(), eigenvectors.cols());
if (tmp_eig_vects.rows() == 0 || tmp_eig_vects.cols() == 0)
Math::matrixEig(tmp.cols(), tmp.storage(), tmp_eigs.storage());
else
Math::matrixEig(tmp.cols(), tmp.storage(), tmp_eigs.storage(),
tmp_eig_vects.storage());
Vector<UInt> perm(eigenvalues.size());
for (UInt i = 0; i < perm.size(); ++i)
perm(i) = i;
std::sort(perm.storage(), perm.storage() + perm.size(),
EigenSorter(tmp_eigs));
for (UInt i = 0; i < perm.size(); ++i)
eigenvalues(i) = tmp_eigs(perm(i));
if (tmp_eig_vects.rows() != 0 && tmp_eig_vects.cols() != 0)
for (UInt i = 0; i < perm.size(); ++i) {
for (UInt j = 0; j < eigenvectors.rows(); ++j) {
eigenvectors(j, i) = tmp_eig_vects(j, perm(i));
}
}
}
/* ---------------------------------------------------------------------- */
inline void eig(Vector<T> & eigenvalues) const {
Matrix<T> empty;
eig(eigenvalues, empty);
}
/* ---------------------------------------------------------------------- */
inline void eye(T alpha = 1.) {
AKANTU_DEBUG_ASSERT(this->cols() == this->rows(),
"eye is not a valid operation on a rectangular matrix");
this->clear();
for (UInt i = 0; i < this->cols(); ++i) {
this->values[i + i * this->rows()] = alpha;
}
}
/* ---------------------------------------------------------------------- */
static inline Matrix<T> eye(UInt m, T alpha = 1.) {
Matrix<T> tmp(m, m);
tmp.eye(alpha);
return tmp;
}
/* ---------------------------------------------------------------------- */
inline T trace() const {
AKANTU_DEBUG_ASSERT(
this->cols() == this->rows(),
"trace is not a valid operation on a rectangular matrix");
T trace = 0.;
for (UInt i = 0; i < this->rows(); ++i) {
trace += this->values[i + i * this->rows()];
}
return trace;
}
/* ---------------------------------------------------------------------- */
inline Matrix transpose() const {
Matrix tmp(this->cols(), this->rows());
for (UInt i = 0; i < this->rows(); ++i) {
for (UInt j = 0; j < this->cols(); ++j) {
tmp(j, i) = operator()(i, j);
}
}
return tmp;
}
/* ---------------------------------------------------------------------- */
inline void inverse(const Matrix & A) {
AKANTU_DEBUG_ASSERT(A.cols() == A.rows(),
"inv is not a valid operation on a rectangular matrix");
AKANTU_DEBUG_ASSERT(this->cols() == A.cols(),
"the matrix should have the same size as its inverse");
if (this->cols() == 1)
*this->values = 1. / *A.storage();
else if (this->cols() == 2)
Math::inv2(A.storage(), this->values);
else if (this->cols() == 3)
Math::inv3(A.storage(), this->values);
else
Math::inv(this->cols(), A.storage(), this->values);
}
/* --------------------------------------------------------------------- */
inline T det() const {
AKANTU_DEBUG_ASSERT(this->cols() == this->rows(),
"inv is not a valid operation on a rectangular matrix");
if (this->cols() == 1)
return *(this->values);
else if (this->cols() == 2)
return Math::det2(this->values);
else if (this->cols() == 3)
return Math::det3(this->values);
else
return Math::det(this->cols(), this->values);
}
/* --------------------------------------------------------------------- */
inline T doubleDot(const Matrix<T> & other) const {
AKANTU_DEBUG_ASSERT(
this->cols() == this->rows(),
"doubleDot is not a valid operation on a rectangular matrix");
if (this->cols() == 1)
return *(this->values) * *(other.storage());
else if (this->cols() == 2)
return Math::matrixDoubleDot22(this->values, other.storage());
else if (this->cols() == 3)
return Math::matrixDoubleDot33(this->values, other.storage());
else
AKANTU_DEBUG_ERROR("doubleDot is not defined for other spatial dimensions"
<< " than 1, 2 or 3.");
return T();
}
/* ---------------------------------------------------------------------- */
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << "[";
for (UInt i = 0; i < this->n[0]; ++i) {
if (i != 0)
stream << ", ";
stream << "[";
for (UInt j = 0; j < this->n[1]; ++j) {
if (j != 0)
stream << ", ";
stream << operator()(i, j);
}
stream << "]";
}
stream << "]";
};
};
/* ------------------------------------------------------------------------ */
template <typename T>
template <bool tr_A>
inline void Vector<T>::mul(const Matrix<T> & A, const Vector<T> & x,
Real alpha) {
#ifndef AKANTU_NDEBUG
UInt n = x.size();
if (tr_A) {
AKANTU_DEBUG_ASSERT(n == A.rows(),
"matrix and vector to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->size() == A.cols(),
"matrix and vector to multiply have no fit dimensions");
} else {
AKANTU_DEBUG_ASSERT(n == A.cols(),
"matrix and vector to multiply have no fit dimensions");
AKANTU_DEBUG_ASSERT(this->size() == A.rows(),
"matrix and vector to multiply have no fit dimensions");
}
#endif
Math::matVectMul<tr_A>(A.rows(), A.cols(), alpha, A.storage(), x.storage(),
0., this->storage());
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const Matrix<T> & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const Vector<T> & _this) {
_this.printself(stream);
return stream;
}
/* ------------------------------------------------------------------------ */
/* Tensor3 */
/* ------------------------------------------------------------------------ */
template <typename T> class Tensor3 : public TensorStorage<T, 3, Tensor3<T>> {
typedef TensorStorage<T, 3, Tensor3<T>> parent;
public:
using value_type = typename parent::value_type;
using proxy = Tensor3Proxy<T>;
public:
Tensor3() : parent(){};
Tensor3(UInt m, UInt n, UInt p, const T & def = T()) : parent(m, n, p, def) {}
Tensor3(T * data, UInt m, UInt n, UInt p) : parent(data, m, n, p) {}
Tensor3(const Tensor3 & src, bool deep_copy = true)
: parent(src, deep_copy) {}
public:
/* ------------------------------------------------------------------------ */
inline Tensor3 & operator=(const Tensor3 & src) {
parent::operator=(src);
return *this;
}
/* ---------------------------------------------------------------------- */
inline T & operator()(UInt i, UInt j, UInt k) {
AKANTU_DEBUG_ASSERT(
(i < this->n[0]) && (j < this->n[1]) && (k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the element "
<< "(" << i << ", " << j << ", " << k << ") in a tensor of size ("
<< this->n[0] << ", " << this->n[1] << ", " << this->n[2] << ")");
return *(this->values + (k * this->n[0] + i) * this->n[1] + j);
}
inline const T & operator()(UInt i, UInt j, UInt k) const {
AKANTU_DEBUG_ASSERT(
(i < this->n[0]) && (j < this->n[1]) && (k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the element "
<< "(" << i << ", " << j << ", " << k << ") in a tensor of size ("
<< this->n[0] << ", " << this->n[1] << ", " << this->n[2] << ")");
return *(this->values + (k * this->n[0] + i) * this->n[1] + j);
}
inline MatrixProxy<T> operator()(UInt k) {
AKANTU_DEBUG_ASSERT((k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the slice " << k
<< " in a tensor3 of size (" << this->n[0] << ", "
<< this->n[1] << ", " << this->n[2] << ")");
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
inline const MatrixProxy<T> operator()(UInt k) const {
AKANTU_DEBUG_ASSERT((k < this->n[2]),
"Access out of the tensor3! "
<< "You are trying to access the slice " << k
<< " in a tensor3 of size (" << this->n[0] << ", "
<< this->n[1] << ", " << this->n[2] << ")");
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
inline MatrixProxy<T> operator[](UInt k) {
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
inline const MatrixProxy<T> operator[](UInt k) const {
return MatrixProxy<T>(this->values + k * this->n[0] * this->n[1],
this->n[0], this->n[1]);
}
};
/* -------------------------------------------------------------------------- */
// support operations for the creation of other vectors
/* -------------------------------------------------------------------------- */
template <typename T>
Vector<T> operator*(const T & scalar, const Vector<T> & a) {
Vector<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Vector<T> operator*(const Vector<T> & a, const T & scalar) {
Vector<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Vector<T> operator/(const Vector<T> & a, const T & scalar) {
Vector<T> r(a);
r /= scalar;
return r;
}
template <typename T>
Vector<T> operator*(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r *= b;
return r;
}
template <typename T>
Vector<T> operator+(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r += b;
return r;
}
template <typename T>
Vector<T> operator-(const Vector<T> & a, const Vector<T> & b) {
Vector<T> r(a);
r -= b;
return r;
}
template <typename T>
Vector<T> operator*(const Matrix<T> & A, const Vector<T> & b) {
Vector<T> r(b.size());
r.template mul<false>(A, b);
return r;
}
/* -------------------------------------------------------------------------- */
template <typename T>
Matrix<T> operator*(const T & scalar, const Matrix<T> & a) {
Matrix<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Matrix<T> operator*(const Matrix<T> & a, const T & scalar) {
Matrix<T> r(a);
r *= scalar;
return r;
}
template <typename T>
Matrix<T> operator/(const Matrix<T> & a, const T & scalar) {
Matrix<T> r(a);
r /= scalar;
return r;
}
template <typename T>
Matrix<T> operator+(const Matrix<T> & a, const Matrix<T> & b) {
Matrix<T> r(a);
r += b;
return r;
}
template <typename T>
Matrix<T> operator-(const Matrix<T> & a, const Matrix<T> & b) {
Matrix<T> r(a);
r -= b;
return r;
}
} // namespace akantu
#endif /* __AKANTU_AKA_TYPES_HH__ */
diff --git a/src/fe_engine/cohesive_element.cc b/src/fe_engine/cohesive_element.cc
index 97c4df49c..9a7073e13 100644
--- a/src/fe_engine/cohesive_element.cc
+++ b/src/fe_engine/cohesive_element.cc
@@ -1,151 +1,176 @@
/**
* @file cohesive_element.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Sun Sep 26 2010
* @date last modification: Mon Sep 14 2015
*
* @brief CohesiveElement implementation
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
-template<> UInt GeometricalElement<_gt_cohesive_2d_4>::spatial_dimension = 2;
-template<> UInt GeometricalElement<_gt_cohesive_2d_4>::nb_nodes_per_element = 4;
-template<> UInt GeometricalElement<_gt_cohesive_2d_4>::nb_facet_types = 1;
-template<> UInt GeometricalElement<_gt_cohesive_2d_4>::nb_facets[] = { 2 };
-template<> UInt GeometricalElement<_gt_cohesive_2d_4>::nb_nodes_per_facet[] = { 2 };
-template<> UInt GeometricalElement<_gt_cohesive_2d_4>::facet_connectivity_vect[] = {0, 2,
- 1, 3};
-template<> UInt * GeometricalElement<_gt_cohesive_2d_4>::facet_connectivity[] = { &facet_connectivity_vect[0] };
-
-template<> ElementType ElementClass<_cohesive_2d_4>::facet_type[] = { _segment_2 };
-template<> ElementType ElementClass<_cohesive_2d_4>::p1_type = _cohesive_2d_4;
+template <> UInt GeometricalElement<_gt_cohesive_2d_4>::spatial_dimension = 2;
+template <> UInt GeometricalElement<_gt_cohesive_2d_4>::nb_nodes_per_element = 4;
+template <> UInt GeometricalElement<_gt_cohesive_2d_4>::nb_facet_types = 1;
+template <> UInt GeometricalElement<_gt_cohesive_2d_4>::nb_facets[] = {2};
+template <>
+UInt GeometricalElement<_gt_cohesive_2d_4>::nb_nodes_per_facet[] = {2};
+template <>
+UInt GeometricalElement<_gt_cohesive_2d_4>::facet_connectivity_vect[] = {0, 2,
+ 1, 3};
+template <>
+UInt * GeometricalElement<_gt_cohesive_2d_4>::facet_connectivity[] = {
+ &facet_connectivity_vect[0]};
+
+template <>
+ElementType ElementClass<_cohesive_2d_4>::facet_type[] = {_segment_2};
+template <> ElementType ElementClass<_cohesive_2d_4>::p1_type = _cohesive_2d_4;
/* -------------------------------------------------------------------------- */
-template<> UInt GeometricalElement<_gt_cohesive_2d_6>::spatial_dimension = 2;
-template<> UInt GeometricalElement<_gt_cohesive_2d_6>::nb_nodes_per_element = 6;
-template<> UInt GeometricalElement<_gt_cohesive_2d_6>::nb_facet_types = 1;
-template<> UInt GeometricalElement<_gt_cohesive_2d_6>::nb_facets[] = { 2 };
-template<> UInt GeometricalElement<_gt_cohesive_2d_6>::nb_nodes_per_facet[] = { 3 };
-template<> UInt GeometricalElement<_gt_cohesive_2d_6>::facet_connectivity_vect[] = {0, 3,
- 1, 4,
- 2, 5};
-template<> UInt * GeometricalElement<_gt_cohesive_2d_6>::facet_connectivity[] = { &facet_connectivity_vect[0] };
-
-template<> ElementType ElementClass<_cohesive_2d_6>::facet_type[] = { _segment_3 };
-template<> ElementType ElementClass<_cohesive_2d_6>::p1_type = _cohesive_2d_4;
+template <> UInt GeometricalElement<_gt_cohesive_2d_6>::spatial_dimension = 2;
+template <>
+UInt GeometricalElement<_gt_cohesive_2d_6>::nb_nodes_per_element = 6;
+template <> UInt GeometricalElement<_gt_cohesive_2d_6>::nb_facet_types = 1;
+template <> UInt GeometricalElement<_gt_cohesive_2d_6>::nb_facets[] = {2};
+template <>
+UInt GeometricalElement<_gt_cohesive_2d_6>::nb_nodes_per_facet[] = {3};
+template <>
+UInt GeometricalElement<_gt_cohesive_2d_6>::facet_connectivity_vect[] = {
+ 0, 3, 1, 4, 2, 5};
+template <>
+UInt * GeometricalElement<_gt_cohesive_2d_6>::facet_connectivity[] = {
+ &facet_connectivity_vect[0]};
+
+template <>
+ElementType ElementClass<_cohesive_2d_6>::facet_type[] = {_segment_3};
+template <> ElementType ElementClass<_cohesive_2d_6>::p1_type = _cohesive_2d_4;
/* -------------------------------------------------------------------------- */
-template<> UInt GeometricalElement<_gt_cohesive_1d_2>::spatial_dimension = 1;
-template<> UInt GeometricalElement<_gt_cohesive_1d_2>::nb_nodes_per_element = 2;
-template<> UInt GeometricalElement<_gt_cohesive_1d_2>::nb_facet_types = 1;
-template<> UInt GeometricalElement<_gt_cohesive_1d_2>::nb_facets[] = { 2 };
-template<> UInt GeometricalElement<_gt_cohesive_1d_2>::nb_nodes_per_facet[] = { 1 };
-template<> UInt GeometricalElement<_gt_cohesive_1d_2>::facet_connectivity_vect[] = {0,
- 1};
-template<> UInt * GeometricalElement<_gt_cohesive_1d_2>::facet_connectivity[] = { &facet_connectivity_vect[0] };
-
-template<> ElementType ElementClass<_cohesive_1d_2>::facet_type[] = { _point_1 };
-template<> ElementType ElementClass<_cohesive_1d_2>::p1_type = _cohesive_1d_2;
+template <> UInt GeometricalElement<_gt_cohesive_1d_2>::spatial_dimension = 1;
+template <>
+UInt GeometricalElement<_gt_cohesive_1d_2>::nb_nodes_per_element = 2;
+template <> UInt GeometricalElement<_gt_cohesive_1d_2>::nb_facet_types = 1;
+template <> UInt GeometricalElement<_gt_cohesive_1d_2>::nb_facets[] = {2};
+template <>
+UInt GeometricalElement<_gt_cohesive_1d_2>::nb_nodes_per_facet[] = {1};
+template <>
+UInt GeometricalElement<_gt_cohesive_1d_2>::facet_connectivity_vect[] = {0, 1};
+template <>
+UInt * GeometricalElement<_gt_cohesive_1d_2>::facet_connectivity[] = {
+ &facet_connectivity_vect[0]};
+
+template <> ElementType ElementClass<_cohesive_1d_2>::facet_type[] = {_point_1};
+template <> ElementType ElementClass<_cohesive_1d_2>::p1_type = _cohesive_1d_2;
/* -------------------------------------------------------------------------- */
-template<> UInt GeometricalElement<_gt_cohesive_3d_6>::spatial_dimension = 3;
-template<> UInt GeometricalElement<_gt_cohesive_3d_6>::nb_nodes_per_element = 6;
-template<> UInt GeometricalElement<_gt_cohesive_3d_6>::nb_facet_types = 1;
-template<> UInt GeometricalElement<_gt_cohesive_3d_6>::nb_facets[] = { 2 };
-template<> UInt GeometricalElement<_gt_cohesive_3d_6>::nb_nodes_per_facet[] = { 3 };
-template<> UInt GeometricalElement<_gt_cohesive_3d_6>::facet_connectivity_vect[] = {0, 3,
- 1, 4,
- 2, 5};
-template<> UInt * GeometricalElement<_gt_cohesive_3d_6>::facet_connectivity[] = { &facet_connectivity_vect[0] };
-
-template<> ElementType ElementClass<_cohesive_3d_6>::facet_type[] = { _triangle_3 };
-template<> ElementType ElementClass<_cohesive_3d_6>::p1_type = _cohesive_3d_6;
+template <> UInt GeometricalElement<_gt_cohesive_3d_6>::spatial_dimension = 3;
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_6>::nb_nodes_per_element = 6;
+template <> UInt GeometricalElement<_gt_cohesive_3d_6>::nb_facet_types = 1;
+template <> UInt GeometricalElement<_gt_cohesive_3d_6>::nb_facets[] = {2};
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_6>::nb_nodes_per_facet[] = {3};
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_6>::facet_connectivity_vect[] = {
+ 0, 3, 1, 4, 2, 5};
+template <>
+UInt * GeometricalElement<_gt_cohesive_3d_6>::facet_connectivity[] = {
+ &facet_connectivity_vect[0]};
+
+template <>
+ElementType ElementClass<_cohesive_3d_6>::facet_type[] = {_triangle_3};
+template <> ElementType ElementClass<_cohesive_3d_6>::p1_type = _cohesive_3d_6;
/* -------------------------------------------------------------------------- */
-template<> UInt GeometricalElement<_gt_cohesive_3d_12>::spatial_dimension = 3;
-template<> UInt GeometricalElement<_gt_cohesive_3d_12>::nb_nodes_per_element = 12;
-template<> UInt GeometricalElement<_gt_cohesive_3d_12>::nb_facet_types = 1;
-template<> UInt GeometricalElement<_gt_cohesive_3d_12>::nb_facets[] = { 2 };
-template<> UInt GeometricalElement<_gt_cohesive_3d_12>::nb_nodes_per_facet[] = { 6 };
-template<> UInt GeometricalElement<_gt_cohesive_3d_12>::facet_connectivity_vect[] = {0, 6,
- 1, 7,
- 2, 8,
- 3, 9,
- 4, 10,
- 5, 11};
-template<> UInt * GeometricalElement<_gt_cohesive_3d_12>::facet_connectivity[] = { &facet_connectivity_vect[0] };
-
-template<> ElementType ElementClass<_cohesive_3d_12>::facet_type[] = { _triangle_6 };
-template<> ElementType ElementClass<_cohesive_3d_12>::p1_type = _cohesive_3d_6;
+template <> UInt GeometricalElement<_gt_cohesive_3d_12>::spatial_dimension = 3;
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_12>::nb_nodes_per_element = 12;
+template <> UInt GeometricalElement<_gt_cohesive_3d_12>::nb_facet_types = 1;
+template <> UInt GeometricalElement<_gt_cohesive_3d_12>::nb_facets[] = {2};
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_12>::nb_nodes_per_facet[] = {6};
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_12>::facet_connectivity_vect[] = {
+ 0, 6, 1, 7, 2, 8, 3, 9, 4, 10, 5, 11};
+template <>
+UInt * GeometricalElement<_gt_cohesive_3d_12>::facet_connectivity[] = {
+ &facet_connectivity_vect[0]};
+
+template <>
+ElementType ElementClass<_cohesive_3d_12>::facet_type[] = {_triangle_6};
+template <> ElementType ElementClass<_cohesive_3d_12>::p1_type = _cohesive_3d_6;
/* -------------------------------------------------------------------------- */
-template<> UInt GeometricalElement<_gt_cohesive_3d_8>::spatial_dimension = 3;
-template<> UInt GeometricalElement<_gt_cohesive_3d_8>::nb_nodes_per_element = 8;
-template<> UInt GeometricalElement<_gt_cohesive_3d_8>::nb_facet_types = 1;
-template<> UInt GeometricalElement<_gt_cohesive_3d_8>::nb_facets[] = { 2 };
-template<> UInt GeometricalElement<_gt_cohesive_3d_8>::nb_nodes_per_facet[] = { 4 };
-template<> UInt GeometricalElement<_gt_cohesive_3d_8>::facet_connectivity_vect[] = {0, 4,
- 1, 5,
- 2, 6,
- 3, 7};
-template<> UInt * GeometricalElement<_gt_cohesive_3d_8>::facet_connectivity[] = { &facet_connectivity_vect[0] };
-
-template<> ElementType ElementClass<_cohesive_3d_8>::facet_type[] = { _quadrangle_4 };
-template<> ElementType ElementClass<_cohesive_3d_8>::p1_type = _cohesive_3d_8;
+template <> UInt GeometricalElement<_gt_cohesive_3d_8>::spatial_dimension = 3;
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_8>::nb_nodes_per_element = 8;
+template <> UInt GeometricalElement<_gt_cohesive_3d_8>::nb_facet_types = 1;
+template <> UInt GeometricalElement<_gt_cohesive_3d_8>::nb_facets[] = {2};
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_8>::nb_nodes_per_facet[] = {4};
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_8>::facet_connectivity_vect[] = {
+ 0, 4, 1, 5, 2, 6, 3, 7};
+template <>
+UInt * GeometricalElement<_gt_cohesive_3d_8>::facet_connectivity[] = {
+ &facet_connectivity_vect[0]};
+
+template <>
+ElementType ElementClass<_cohesive_3d_8>::facet_type[] = {_quadrangle_4};
+template <> ElementType ElementClass<_cohesive_3d_8>::p1_type = _cohesive_3d_8;
/* -------------------------------------------------------------------------- */
-template<> UInt GeometricalElement<_gt_cohesive_3d_16>::spatial_dimension = 3;
-template<> UInt GeometricalElement<_gt_cohesive_3d_16>::nb_nodes_per_element = 16;
-template<> UInt GeometricalElement<_gt_cohesive_3d_16>::nb_facet_types = 1;
-template<> UInt GeometricalElement<_gt_cohesive_3d_16>::nb_facets[] = { 2 };
-template<> UInt GeometricalElement<_gt_cohesive_3d_16>::nb_nodes_per_facet[] = { 8 };
-template<> UInt GeometricalElement<_gt_cohesive_3d_16>::facet_connectivity_vect[] = {0, 8,
- 1, 9,
- 2, 10,
- 3, 11,
- 4, 12,
- 5, 13,
- 6, 14,
- 7, 15};
-template<> UInt * GeometricalElement<_gt_cohesive_3d_16>::facet_connectivity[] = { &facet_connectivity_vect[0] };
-
-template<> ElementType ElementClass<_cohesive_3d_16>::facet_type[] = { _quadrangle_8 };
-template<> ElementType ElementClass<_cohesive_3d_16>::p1_type = _cohesive_3d_8;
+template <> UInt GeometricalElement<_gt_cohesive_3d_16>::spatial_dimension = 3;
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_16>::nb_nodes_per_element = 16;
+template <> UInt GeometricalElement<_gt_cohesive_3d_16>::nb_facet_types = 1;
+template <> UInt GeometricalElement<_gt_cohesive_3d_16>::nb_facets[] = {2};
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_16>::nb_nodes_per_facet[] = {8};
+template <>
+UInt GeometricalElement<_gt_cohesive_3d_16>::facet_connectivity_vect[] = {
+ 0, 8, 1, 9, 2, 10, 3, 11, 4, 12, 5, 13, 6, 14, 7, 15};
+template <>
+UInt * GeometricalElement<_gt_cohesive_3d_16>::facet_connectivity[] = {
+ &facet_connectivity_vect[0]};
+
+template <>
+ElementType ElementClass<_cohesive_3d_16>::facet_type[] = {_quadrangle_8};
+template <> ElementType ElementClass<_cohesive_3d_16>::p1_type = _cohesive_3d_8;
/* -------------------------------------------------------------------------- */
-} // akantu
+} // namespace akantu
diff --git a/src/fe_engine/element_class.hh b/src/fe_engine/element_class.hh
index 188115a3d..6cb694cda 100644
--- a/src/fe_engine/element_class.hh
+++ b/src/fe_engine/element_class.hh
@@ -1,410 +1,408 @@
/**
* @file element_class.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Jan 21 2016
*
* @brief Declaration of the ElementClass main class and the
* Integration and Interpolation elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_CLASS_HH__
#define __AKANTU_ELEMENT_CLASS_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/// default element class structure
template <ElementType element_type> struct ElementClassProperty {
static const GeometricalType geometrical_type{_gt_not_defined};
static const InterpolationType interpolation_type{_itp_not_defined};
static const ElementKind element_kind{_ek_regular};
static const UInt spatial_dimension{0};
static const GaussIntegrationType gauss_integration_type{_git_not_defined};
static const UInt polynomial_degree{0};
};
/// Macro to generate the element class structures for different element types
#define AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(elem_type, geom_type, \
interp_type, elem_kind, sp, \
gauss_int_type, min_int_order) \
template <> struct ElementClassProperty<elem_type> { \
static const GeometricalType geometrical_type{geom_type}; \
static const InterpolationType interpolation_type{interp_type}; \
static const ElementKind element_kind{elem_kind}; \
static const UInt spatial_dimension{sp}; \
static const GaussIntegrationType gauss_integration_type{gauss_int_type}; \
static const UInt polynomial_degree{min_int_order}; \
}
/* -------------------------------------------------------------------------- */
/* Geometry */
/* -------------------------------------------------------------------------- */
/// Default GeometricalShape structure
template <GeometricalType geometrical_type> struct GeometricalShape {
static const GeometricalShapeType shape{_gst_point};
};
/// Templated GeometricalShape with function contains
template <GeometricalShapeType shape> struct GeometricalShapeContains {
/// Check if the point (vector in 2 and 3D) at natural coordinate coor
template <class vector_type>
static inline bool contains(const vector_type & coord);
};
/// Macro to generate the GeometricalShape structures for different geometrical
/// types
#define AKANTU_DEFINE_SHAPE(geom_type, geom_shape) \
template <> struct GeometricalShape<geom_type> { \
- static const GeometricalShapeType shape{geom_shape}; \
+ static const GeometricalShapeType shape{geom_shape}; \
}
AKANTU_DEFINE_SHAPE(_gt_hexahedron_20, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_hexahedron_8, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_pentahedron_15, _gst_prism);
AKANTU_DEFINE_SHAPE(_gt_pentahedron_6, _gst_prism);
AKANTU_DEFINE_SHAPE(_gt_point, _gst_point);
AKANTU_DEFINE_SHAPE(_gt_quadrangle_4, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_quadrangle_8, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_segment_2, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_segment_3, _gst_square);
AKANTU_DEFINE_SHAPE(_gt_tetrahedron_10, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_tetrahedron_4, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_triangle_3, _gst_triangle);
AKANTU_DEFINE_SHAPE(_gt_triangle_6, _gst_triangle);
/* -------------------------------------------------------------------------- */
/// Templated GeometricalElement with function getInradius
template <GeometricalType geometrical_type,
GeometricalShapeType shape =
GeometricalShape<geometrical_type>::shape>
class GeometricalElement {
public:
/// compute the in-radius
static inline Real getInradius(__attribute__((unused))
const Matrix<Real> & coord) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// true if the natural coordinates are in the element
template <class vector_type>
static inline bool contains(const vector_type & coord);
public:
static AKANTU_GET_MACRO_NOT_CONST(SpatialDimension, spatial_dimension, UInt);
static AKANTU_GET_MACRO_NOT_CONST(NbNodesPerElement, nb_nodes_per_element,
UInt);
static AKANTU_GET_MACRO_NOT_CONST(NbFacetTypes, nb_facet_types, UInt);
static inline UInt getNbFacetsPerElement(UInt t);
static inline UInt getNbFacetsPerElement();
static inline const MatrixProxy<UInt>
getFacetLocalConnectivityPerElement(UInt t = 0);
protected:
/// Number of nodes per element
static UInt nb_nodes_per_element;
/// spatial dimension of the element
static UInt spatial_dimension;
/// number of different facet types
static UInt nb_facet_types;
/// number of facets for element
static UInt nb_facets[];
+ /// Nb nodes per facets types
+ static UInt nb_nodes_per_facet[];
/// storage of the facet local connectivity
static UInt facet_connectivity_vect[];
/// local connectivity of facets
static UInt * facet_connectivity[];
-
-private:
- /// Type of the facet elements
- static UInt nb_nodes_per_facet[];
};
/* -------------------------------------------------------------------------- */
/* Interpolation */
/* -------------------------------------------------------------------------- */
/// default InterpolationProperty structure
template <InterpolationType interpolation_type> struct InterpolationProperty {
static const InterpolationKind kind{_itk_not_defined};
static const UInt nb_nodes_per_element{0};
static const UInt natural_space_dimension{0};
};
/// Macro to generate the InterpolationProperty structures for different
/// interpolation types
#define AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(itp_type, itp_kind, \
nb_nodes, ndim) \
template <> struct InterpolationProperty<itp_type> { \
static const InterpolationKind kind{itp_kind}; \
static const UInt nb_nodes_per_element{nb_nodes}; \
static const UInt natural_space_dimension{ndim}; \
}
/* -------------------------------------------------------------------------- */
/// Generic (templated by the enum InterpolationType which specifies the order
/// and the dimension of the interpolation) class handling the elemental
/// interpolation
template <InterpolationType interpolation_type,
InterpolationKind kind =
InterpolationProperty<interpolation_type>::kind>
class InterpolationElement {
public:
typedef InterpolationProperty<interpolation_type> interpolation_property;
/// compute the shape values for a given set of points in natural coordinates
static inline void computeShapes(const Matrix<Real> & natural_coord,
Matrix<Real> & N);
/// compute the shape values for a given point in natural coordinates
template <class vector_type>
static inline void computeShapes(const vector_type &, vector_type &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with variation of natural coordinates on a given set
* of points in natural coordinates
*/
static inline void computeDNDS(const Matrix<Real> & natural_coord,
Tensor3<Real> & dnds);
/**
* compute @f$ B_{ij} = \frac{\partial N_j}{\partial S_i} @f$ the variation of
* shape functions along with
* variation of natural coordinates on a given point in natural
* coordinates
*/
template <class vector_type, class matrix_type>
static inline void computeDNDS(const vector_type &, matrix_type &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// compute jacobian (or integration variable change factor) for a given point
/// in the case of spatial_dimension != natural_space_dimension
static inline void computeSpecialJacobian(const Matrix<Real> &, Real &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// interpolate a field given (arbitrary) natural coordinates
static inline void
interpolateOnNaturalCoordinates(const Vector<Real> & natural_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated);
/// interpolate a field given the shape functions on the interpolation point
static inline void interpolate(const Matrix<Real> & nodal_values,
const Vector<Real> & shapes,
Vector<Real> & interpolated);
/// interpolate a field given the shape functions on the interpolations points
static inline void interpolate(const Matrix<Real> & nodal_values,
const Matrix<Real> & shapes,
Matrix<Real> & interpolated);
/// compute the gradient of a given field on the given natural coordinates
static inline void
gradientOnNaturalCoordinates(const Vector<Real> & natural_coords,
const Matrix<Real> & f, Matrix<Real> & gradient);
public:
static AKANTU_GET_MACRO_NOT_CONST(
ShapeSize,
InterpolationProperty<interpolation_type>::nb_nodes_per_element, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
ShapeDerivativesSize,
(InterpolationProperty<interpolation_type>::nb_nodes_per_element *
InterpolationProperty<interpolation_type>::natural_space_dimension),
UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NaturalSpaceDimension,
InterpolationProperty<interpolation_type>::natural_space_dimension, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NbNodesPerInterpolationElement,
InterpolationProperty<interpolation_type>::nb_nodes_per_element, UInt);
};
/* -------------------------------------------------------------------------- */
/* Integration */
/* -------------------------------------------------------------------------- */
template <GaussIntegrationType git_class, UInt nb_points>
struct GaussIntegrationTypeData {
/// quadrature points in natural coordinates
static Real quad_positions[];
/// weights for the Gauss integration
static Real quad_weights[];
};
template <ElementType type,
UInt n = ElementClassProperty<type>::polynomial_degree>
class GaussIntegrationElement {
public:
static UInt getNbQuadraturePoints();
static const Matrix<Real> getQuadraturePoints();
static const Vector<Real> getWeights();
};
/* -------------------------------------------------------------------------- */
/* ElementClass */
/* -------------------------------------------------------------------------- */
template <ElementType element_type,
ElementKind element_kind =
ElementClassProperty<element_type>::element_kind>
class ElementClass
: public GeometricalElement<
ElementClassProperty<element_type>::geometrical_type>,
public InterpolationElement<
ElementClassProperty<element_type>::interpolation_type> {
protected:
typedef GeometricalElement<
ElementClassProperty<element_type>::geometrical_type>
geometrical_element;
typedef InterpolationElement<
ElementClassProperty<element_type>::interpolation_type>
interpolation_element;
typedef ElementClassProperty<element_type> element_property;
typedef typename interpolation_element::interpolation_property
interpolation_property;
public:
/**
* compute @f$ J = \frac{\partial x_j}{\partial s_i} @f$ the variation of real
* coordinates along with variation of natural coordinates on a given point in
* natural coordinates
*/
static inline void computeJMat(const Matrix<Real> & dnds,
const Matrix<Real> & node_coords,
Matrix<Real> & J);
/**
* compute the Jacobian matrix by computing the variation of real coordinates
* along with variation of natural coordinates on a given set of points in
* natural coordinates
*/
static inline void computeJMat(const Tensor3<Real> & dnds,
const Matrix<Real> & node_coords,
Tensor3<Real> & J);
/// compute the jacobians of a serie of natural coordinates
static inline void computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians);
/// compute jacobian (or integration variable change factor) for a set of
/// points
static inline void computeJacobian(const Tensor3<Real> & J,
Vector<Real> & jacobians);
/// compute jacobian (or integration variable change factor) for a given point
static inline void computeJacobian(const Matrix<Real> & J, Real & jacobians);
/// compute shape derivatives (input is dxds) for a set of points
static inline void computeShapeDerivatives(const Tensor3<Real> & J,
const Tensor3<Real> & dnds,
Tensor3<Real> & shape_deriv);
/// compute shape derivatives (input is dxds) for a given point
static inline void computeShapeDerivatives(const Matrix<Real> & J,
const Matrix<Real> & dnds,
Matrix<Real> & shape_deriv);
/// compute the normal of a surface defined by the function f
static inline void
computeNormalsOnNaturalCoordinates(const Matrix<Real> & coord,
Matrix<Real> & f, Matrix<Real> & normals);
/// get natural coordinates from real coordinates
static inline void inverseMap(const Vector<Real> & real_coords,
const Matrix<Real> & node_coords,
Vector<Real> & natural_coords,
Real tolerance = 1e-10);
/// get natural coordinates from real coordinates
static inline void inverseMap(const Matrix<Real> & real_coords,
const Matrix<Real> & node_coords,
Matrix<Real> & natural_coords,
Real tolerance = 1e-10);
public:
static AKANTU_GET_MACRO_NOT_CONST(Kind, element_kind, ElementKind);
static AKANTU_GET_MACRO_NOT_CONST(
SpatialDimension, ElementClassProperty<element_type>::spatial_dimension,
UInt);
static AKANTU_GET_MACRO_NOT_CONST(P1ElementType, p1_type,
const ElementType &);
static const ElementType & getFacetType(UInt t = 0) { return facet_type[t]; }
static ElementType * getFacetTypeInternal() { return facet_type; }
protected:
/// Type of the facet elements
static ElementType facet_type[];
/// type of element P1 associated
static ElementType p1_type;
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
/* -------------------------------------------------------------------------- */
#include "interpolation_element_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "element_class_tmpl.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
#include "element_class_pentahedron_6_inline_impl.cc"
/* keep order */
#include "element_class_hexahedron_20_inline_impl.cc"
#include "element_class_hexahedron_8_inline_impl.cc"
#include "element_class_pentahedron_15_inline_impl.cc"
#include "element_class_point_1_inline_impl.cc"
#include "element_class_quadrangle_4_inline_impl.cc"
#include "element_class_quadrangle_8_inline_impl.cc"
#include "element_class_segment_2_inline_impl.cc"
#include "element_class_segment_3_inline_impl.cc"
#include "element_class_tetrahedron_10_inline_impl.cc"
#include "element_class_tetrahedron_4_inline_impl.cc"
#include "element_class_triangle_3_inline_impl.cc"
#include "element_class_triangle_6_inline_impl.cc"
} // namespace akantu
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "element_class_structural.hh"
#endif
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "cohesive_element.hh"
#endif
#if defined(AKANTU_IGFEM)
#include "element_class_igfem.hh"
#endif
#endif /* __AKANTU_ELEMENT_CLASS_HH__ */
diff --git a/src/fe_engine/fe_engine.hh b/src/fe_engine/fe_engine.hh
index 2c6fffa42..9ca9a0343 100644
--- a/src/fe_engine/fe_engine.hh
+++ b/src/fe_engine/fe_engine.hh
@@ -1,384 +1,384 @@
/**
* @file fe_engine.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 22 2015
*
* @brief FEM class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_FE_ENGINE_HH__
#define __AKANTU_FE_ENGINE_HH__
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "element_type_map.hh"
#include "mesh_events.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Mesh;
class Integrator;
class ShapeFunctions;
class DOFManager;
class Element;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* The generic FEEngine class derived in a FEEngineTemplate class
* containing the
* shape functions and the integration method
*/
class FEEngine : protected Memory, public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FEEngine(Mesh & mesh, UInt spatial_dimension = _all_dimensions, ID id = "fem",
MemoryID memory_id = 0);
- virtual ~FEEngine();
+ ~FEEngine() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// pre-compute all the shape functions, their derivatives and the jacobians
virtual void
initShapeFunctions(const GhostType & ghost_type = _not_ghost) = 0;
/// extract the nodal values and store them per element
template <typename T>
static void extractNodalToElementField(
const Mesh & mesh, const Array<T> & nodal_f, Array<T> & elemental_f,
const ElementType & type, const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter);
/// filter a field
template <typename T>
static void
filterElementalData(const Mesh & mesh, const Array<T> & quad_f,
Array<T> & filtered_f, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter);
/* ------------------------------------------------------------------------ */
/* Integration method bridges */
/* ------------------------------------------------------------------------ */
/// integrate f for all elements of type "type"
virtual void
integrate(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate a scalar value f on all elements of type "type"
virtual Real
integrate(const Array<Real> & f, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate f for all integration points of type "type" but don't sum over
/// all integration points
virtual void integrateOnIntegrationPoints(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
const ElementType & type, const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// integrate one element scalar value on all elements of type "type"
virtual Real integrate(const Vector<Real> & f, const ElementType & type,
UInt index,
const GhostType & ghost_type = _not_ghost) const = 0;
/* ------------------------------------------------------------------------ */
/* compatibility with old FEEngine fashion */
/* ------------------------------------------------------------------------ */
#ifndef SWIG
/// get the number of integration points
virtual UInt
getNbIntegrationPoints(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const = 0;
/// get the precomputed shapes
const virtual Array<Real> &
getShapes(const ElementType & type, const GhostType & ghost_type = _not_ghost,
UInt id = 0) const = 0;
/// get the derivatives of shapes
const virtual Array<Real> &
getShapesDerivatives(const ElementType & type,
const GhostType & ghost_type = _not_ghost,
UInt id = 0) const = 0;
/// get integration points
const virtual Matrix<Real> &
getIntegrationPoints(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const = 0;
#endif
/* ------------------------------------------------------------------------ */
/* Shape method bridges */
/* ------------------------------------------------------------------------ */
/// Compute the gradient nablauq on the integration points of an element type
/// from nodal values u
virtual void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq,
const UInt nb_degree_of_freedom, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Interpolate a nodal field u at the integration points of an element type
/// -> uq
virtual void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
const ElementType & type, const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Interpolate a nodal field u at the integration points of many element
/// types -> uq
virtual void interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
- const ElementTypeMapArray<UInt> * filter_elements = NULL) const = 0;
+ const ElementTypeMapArray<UInt> * filter_elements = nullptr) const = 0;
/// Compute the interpolation point position in the global coordinates for
/// many element types
virtual void computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & integration_points_coordinates,
- const ElementTypeMapArray<UInt> * filter_elements = NULL) const = 0;
+ const ElementTypeMapArray<UInt> * filter_elements = nullptr) const = 0;
/// Compute the interpolation point position in the global coordinates for an
/// element type
virtual void computeIntegrationPointsCoordinates(
Array<Real> & integration_points_coordinates, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
virtual void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & integration_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// interpolate field at given position (interpolation_points) from given
/// values of this field at integration points (field)
virtual void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
virtual void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> &
integration_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const = 0;
/// interpolate on a phyiscal point inside an element
virtual void interpolate(const Vector<Real> & real_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const Element & element) const = 0;
/// compute the shape on a provided point
virtual void
computeShapes(const Vector<Real> & real_coords, UInt elem,
const ElementType & type, Vector<Real> & shapes,
const GhostType & ghost_type = _not_ghost) const = 0;
/// compute the shape derivatives on a provided point
virtual void
computeShapeDerivatives(const Vector<Real> & real__coords, UInt element,
const ElementType & type,
Matrix<Real> & shape_derivatives,
const GhostType & ghost_type = _not_ghost) const = 0;
/* ------------------------------------------------------------------------ */
/* Other methods */
/* ------------------------------------------------------------------------ */
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
const GhostType & ghost_type = _not_ghost) = 0;
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
__attribute__((unused)) const Array<Real> & field,
__attribute__((unused)) const GhostType & ghost_type = _not_ghost) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// pre-compute normals on integration points
virtual void computeNormalsOnIntegrationPoints(
__attribute__((unused)) const Array<Real> & field,
__attribute__((unused)) Array<Real> & normal,
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) const GhostType & ghost_type = _not_ghost) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
#ifdef AKANTU_STRUCTURAL_MECHANICS
/// assemble a field as a matrix for structural elements (ex. rho to mass
/// matrix)
virtual void assembleFieldMatrix(
__attribute__((unused)) const Array<Real> & field_1,
__attribute__((unused)) UInt nb_degree_of_freedom,
__attribute__((unused)) SparseMatrix & M,
__attribute__((unused)) Array<Real> * n,
__attribute__((unused)) ElementTypeMapArray<Real> & rotation_mat,
__attribute__((unused)) ElementType type,
__attribute__((unused)) const GhostType & ghost_type) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// compute shapes function in a matrix for structural elements
virtual void computeShapesMatrix(
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) UInt nb_degree_of_freedom,
__attribute__((unused)) UInt nb_nodes_per_element,
__attribute__((unused)) Array<Real> * n, __attribute__((unused)) UInt id,
__attribute__((unused)) UInt degree_to_interpolate,
__attribute__((unused)) UInt degree_interpolated,
__attribute__((unused)) const bool sign,
__attribute__((unused)) const GhostType & ghost_type) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
#endif
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
private:
/// initialise the class
void init();
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler interface */
/* ------------------------------------------------------------------------ */
public:
void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) final {}
void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) final {}
void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) override{};
void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) override {}
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override {}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
using ElementTypesIteratorHelper =
ElementTypeMapArray<Real, ElementType>::ElementTypesIteratorHelper;
ElementTypesIteratorHelper elementTypes(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const;
/// get the dimension of the element handeled by this fe_engine object
AKANTU_GET_MACRO(ElementDimension, element_dimension, UInt);
/// get the mesh contained in the fem object
AKANTU_GET_MACRO(Mesh, mesh, const Mesh &);
/// get the mesh contained in the fem object
AKANTU_GET_MACRO_NOT_CONST(Mesh, mesh, Mesh &);
/// get the in-radius of an element
static inline Real getElementInradius(const Matrix<Real> & coord,
const ElementType & type);
/// get the normals on integration points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(NormalsOnIntegrationPoints,
normals_on_integration_points, Real);
/// get cohesive element type for a given facet type
static inline ElementType
getCohesiveElementType(const ElementType & type_facet);
/// get igfem element type for a given regular type
static inline Vector<ElementType>
getIGFEMElementTypes(const ElementType & type);
/// get the interpolation element associated to an element type
static inline InterpolationType
getInterpolationType(const ElementType & el_type);
/// get the shape function class (probably useless: see getShapeFunction in
/// fe_engine_template.hh)
virtual const ShapeFunctions & getShapeFunctionsInterface() const = 0;
/// get the integrator class (probably useless: see getIntegrator in
/// fe_engine_template.hh)
virtual const Integrator & getIntegratorInterface() const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// spatial dimension of the problem
UInt element_dimension;
/// the mesh on which all computation are made
Mesh & mesh;
/// normals at integration points
ElementTypeMapArray<Real> normals_on_integration_points;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const FEEngine & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "fe_engine_inline_impl.cc"
#include "fe_engine_template.hh"
#endif /* __AKANTU_FE_ENGINE_HH__ */
diff --git a/src/fe_engine/fe_engine_template.hh b/src/fe_engine/fe_engine_template.hh
index 026963159..5b8c0e502 100644
--- a/src/fe_engine/fe_engine_template.hh
+++ b/src/fe_engine/fe_engine_template.hh
@@ -1,393 +1,395 @@
/**
* @file fe_engine_template.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief templated class that calls integration and shape objects
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_FE_ENGINE_TEMPLATE_HH__
#define __AKANTU_FE_ENGINE_TEMPLATE_HH__
/* -------------------------------------------------------------------------- */
#include "fe_engine.hh"
#include "integrator.hh"
#include "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManager;
namespace fe_engine {
namespace details {
template <ElementKind> struct AssembleLumpedTemplateHelper;
template <ElementKind> struct AssembleFieldMatrixHelper;
} // namespace details
} // namespace fe_engine
template <ElementKind, typename> struct AssembleFieldMatrixStructHelper;
struct DefaultIntegrationOrderFunctor {
template <ElementType type> static inline constexpr int getOrder() {
return ElementClassProperty<type>::polynomial_degree;
}
};
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind = _ek_regular,
class IntegrationOrderFunctor = DefaultIntegrationOrderFunctor>
class FEEngineTemplate : public FEEngine {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef I<kind, IntegrationOrderFunctor> Integ;
typedef S<kind> Shape;
FEEngineTemplate(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
ID id = "fem", MemoryID memory_id = 0);
- virtual ~FEEngineTemplate();
+ ~FEEngineTemplate() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// pre-compute all the shape functions, their derivatives and the jacobians
void initShapeFunctions(const GhostType & ghost_type = _not_ghost) override;
void initShapeFunctions(const Array<Real> & nodes,
const GhostType & ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
/* Integration method bridges */
/* ------------------------------------------------------------------------ */
/// integrate f for all elements of type "type"
void
integrate(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// integrate a scalar value on all elements of type "type"
Real
integrate(const Array<Real> & f, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// integrate one element scalar value on all elements of type "type"
- virtual Real
- integrate(const Vector<Real> & f, const ElementType & type, UInt index,
- const GhostType & ghost_type = _not_ghost) const override;
+ Real integrate(const Vector<Real> & f, const ElementType & type, UInt index,
+ const GhostType & ghost_type = _not_ghost) const override;
/// integrate partially around an integration point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
void integrateOnIntegrationPoints(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
const ElementType & type, const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate on a phyiscal point inside an element
void interpolate(const Vector<Real> & real_coords,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const Element & element) const override;
/// get the number of integration points
UInt getNbIntegrationPoints(
const ElementType & type,
const GhostType & ghost_type = _not_ghost) const override;
/// get shapes precomputed
const Array<Real> & getShapes(const ElementType & type,
const GhostType & ghost_type = _not_ghost,
UInt id = 0) const override;
/// get the derivatives of shapes
const Array<Real> &
getShapesDerivatives(const ElementType & type,
const GhostType & ghost_type = _not_ghost,
UInt id = 0) const override;
/// get integration points
const inline Matrix<Real> & getIntegrationPoints(
const ElementType & type,
const GhostType & ghost_type = _not_ghost) const override;
/* ------------------------------------------------------------------------ */
/* Shape method bridges */
/* ------------------------------------------------------------------------ */
/// compute the gradient of a nodal field on the integration points
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq,
const UInt nb_degree_of_freedom, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate a nodal field on the integration points
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
const ElementType & type, const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate a nodal field on the integration points given a
/// by_element_type
void interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
- const ElementTypeMapArray<UInt> * filter_elements = NULL) const override;
+ const ElementTypeMapArray<UInt> * filter_elements =
+ nullptr) const override;
/// compute the position of integration points given by an element_type_map
/// from nodes position
inline void computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
- const ElementTypeMapArray<UInt> * filter_elements = NULL) const override;
+ const ElementTypeMapArray<UInt> * filter_elements =
+ nullptr) const override;
/// compute the position of integration points from nodes position
inline void computeIntegrationPointsCoordinates(
Array<Real> & quadrature_points_coordinates, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const override;
/// interpolate field at given position (interpolation_points) from given
/// values of this field at integration points (field)
inline void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const override;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
inline void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const override;
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
inline void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
- const ElementTypeMapArray<UInt> * element_filter = NULL) const override;
+ const ElementTypeMapArray<UInt> * element_filter =
+ nullptr) const override;
/// find natural coords from real coords provided an element
void inverseMap(const Vector<Real> & real_coords, UInt element,
const ElementType & type, Vector<Real> & natural_coords,
const GhostType & ghost_type = _not_ghost) const;
/// return true if the coordinates provided are inside the element, false
/// otherwise
inline bool contains(const Vector<Real> & real_coords, UInt element,
const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/// compute the shape on a provided point
inline void
computeShapes(const Vector<Real> & real_coords, UInt element,
const ElementType & type, Vector<Real> & shapes,
const GhostType & ghost_type = _not_ghost) const override;
/// compute the shape derivatives on a provided point
inline void computeShapeDerivatives(
const Vector<Real> & real__coords, UInt element, const ElementType & type,
Matrix<Real> & shape_derivatives,
const GhostType & ghost_type = _not_ghost) const override;
/* ------------------------------------------------------------------------ */
/* Other methods */
/* ------------------------------------------------------------------------ */
/// pre-compute normals on integration points
void computeNormalsOnIntegrationPoints(
const GhostType & ghost_type = _not_ghost) override;
void computeNormalsOnIntegrationPoints(
const Array<Real> & field,
const GhostType & ghost_type = _not_ghost) override;
void computeNormalsOnIntegrationPoints(
const Array<Real> & field, Array<Real> & normal, const ElementType & type,
const GhostType & ghost_type = _not_ghost) const override;
template <ElementType type>
void computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
const GhostType & ghost_type) const;
private:
// To avoid a weird full specialization of a method in a non specalized class
void
computeNormalsOnIntegrationPointsPoint1(const Array<Real> &,
Array<Real> & normal,
const GhostType & ghost_type) const;
public:
/// function to print the contain of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// assemble a field as a lumped matrix (ex. rho in lumped mass)
template <class Functor>
void assembleFieldLumped(const Functor & field_funct, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
ElementType type,
const GhostType & ghost_type) const;
/// assemble a field as a matrix (ex. rho to mass matrix)
template <class Functor>
void assembleFieldMatrix(const Functor & field_funct, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
ElementType type,
const GhostType & ghost_type) const;
#ifdef AKANTU_STRUCTURAL_MECHANICS
/// assemble a field as a matrix (ex. rho to mass matrix)
void assembleFieldMatrix(const Array<Real> & field_1,
UInt nb_degree_of_freedom, SparseMatrix & M,
Array<Real> * n,
ElementTypeMapArray<Real> & rotation_mat,
const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/// compute shapes function in a matrix for structural elements
void computeShapesMatrix(const ElementType & type, UInt nb_degree_of_freedom,
UInt nb_nodes_per_element, Array<Real> * n, UInt id,
UInt degree_to_interpolate, UInt degree_interpolated,
const bool sign,
const GhostType & ghost_type = _not_ghost) const;
#endif
private:
friend struct fe_engine::details::AssembleLumpedTemplateHelper<kind>;
friend struct fe_engine::details::AssembleFieldMatrixHelper<kind>;
friend struct AssembleFieldMatrixStructHelper<kind, void>;
/// templated function to compute the scaling to assemble a lumped matrix
template <class Functor, ElementType type>
void assembleFieldLumped(const Functor & field_funct, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
const GhostType & ghost_type) const;
/// @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j
/// dV = \int \rho \varphi_i dV @f$
template <ElementType type>
void assembleLumpedRowSum(const Array<Real> & field, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
const GhostType & ghost_type) const;
/// @f$ \tilde{M}_{i} = c * M_{ii} = \int_{V_e} \rho dV @f$
template <ElementType type>
void assembleLumpedDiagonalScaling(const Array<Real> & field,
const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager,
const GhostType & ghost_type) const;
/// assemble a field as a matrix (ex. rho to mass matrix)
template <class Functor, ElementType type>
void assembleFieldMatrix(const Functor & field_funct, const ID & matrix_id,
const ID & dof_id, DOFManager & dof_manager,
const GhostType & ghost_type) const;
#ifdef AKANTU_STRUCTURAL_MECHANICS
/// assemble a field as a matrix for structural elements (ex. rho to mass
/// matrix)
template <ElementType type>
void assembleFieldMatrix(const Array<Real> & field_1,
UInt nb_degree_of_freedom, SparseMatrix & M,
Array<Real> * n,
ElementTypeMapArray<Real> & rotation_mat,
__attribute__((unused))
const GhostType & ghost_type) const;
#endif
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler interface */
/* ------------------------------------------------------------------------ */
public:
void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) override;
void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) override;
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the shape class (probably useless: see getShapeFunction)
const ShapeFunctions & getShapeFunctionsInterface() const override {
return shape_functions;
};
/// get the shape class
const Shape & getShapeFunctions() const { return shape_functions; };
/// get the integrator class (probably useless: see getIntegrator)
const Integrator & getIntegratorInterface() const override {
return integrator;
};
/// get the integrator class
const Integ & getIntegrator() const { return integrator; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
Integ integrator;
Shape shape_functions;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "fe_engine_template_tmpl.hh"
#include "fe_engine_template_tmpl_field.hh"
/* -------------------------------------------------------------------------- */
/* Shape Linked specialization */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "fe_engine_template_tmpl_struct.hh"
#endif
/* -------------------------------------------------------------------------- */
/* Shape IGFEM specialization */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_IGFEM)
#include "fe_engine_template_tmpl_igfem.hh"
#endif
#endif /* __AKANTU_FE_ENGINE_TEMPLATE_HH__ */
diff --git a/src/fe_engine/fe_engine_template_tmpl.hh b/src/fe_engine/fe_engine_template_tmpl.hh
index 48637bec3..83e0f168e 100644
--- a/src/fe_engine/fe_engine_template_tmpl.hh
+++ b/src/fe_engine/fe_engine_template_tmpl.hh
@@ -1,1301 +1,1301 @@
/**
* @file fe_engine_template_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Feb 15 2011
* @date last modification: Thu Nov 19 2015
*
* @brief Template implementation of FEEngineTemplate
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "dof_manager.hh"
#include "fe_engine_template.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::FEEngineTemplate(
Mesh & mesh, UInt spatial_dimension, ID id, MemoryID memory_id)
: FEEngine(mesh, spatial_dimension, id, memory_id),
integrator(mesh, id, memory_id), shape_functions(mesh, id, memory_id) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::~FEEngineTemplate() {}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GradientOnIntegrationPointsHelper {
template <class S>
static void call(const S &, Mesh &, const Array<Real> &, Array<Real> &,
const UInt, const ElementType &, const GhostType &,
const Array<UInt> &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
};
#define COMPUTE_GRADIENT(type) \
if (element_dimension == ElementClass<type>::getSpatialDimension()) \
shape_functions.template gradientOnIntegrationPoints<type>( \
u, nablauq, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GradientOnIntegrationPointsHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, Mesh & mesh, \
const Array<Real> & u, Array<Real> & nablauq, \
const UInt nb_degree_of_freedom, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
UInt element_dimension = mesh.getSpatialDimension(type); \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_GRADIENT, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER,
AKANTU_FE_ENGINE_LIST_GRADIENT_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_GRADIENT_ON_INTEGRATION_POINTS_HELPER
#undef COMPUTE_GRADIENT
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
gradientOnIntegrationPoints(const Array<Real> & u, Array<Real> & nablauq,
const UInt nb_degree_of_freedom,
const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
UInt nb_points =
shape_functions.getIntegrationPoints(type, ghost_type).cols();
#ifndef AKANTU_NDEBUG
UInt element_dimension = mesh.getSpatialDimension(type);
AKANTU_DEBUG_ASSERT(u.size() == mesh.getNbNodes(),
"The vector u(" << u.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(u.getNbComponent() == nb_degree_of_freedom,
"The vector u("
<< u.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(
nablauq.getNbComponent() == nb_degree_of_freedom * element_dimension,
"The vector nablauq(" << nablauq.getID()
<< ") has not the good number of component.");
// AKANTU_DEBUG_ASSERT(nablauq.size() == nb_element * nb_points,
// "The vector nablauq(" << nablauq.getID()
// << ") has not the good size.");
#endif
nablauq.resize(nb_element * nb_points);
fe_engine::details::GradientOnIntegrationPointsHelper<kind>::call(
shape_functions, mesh, u, nablauq, nb_degree_of_freedom, type, ghost_type,
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::initShapeFunctions(
const GhostType & ghost_type) {
initShapeFunctions(mesh.getNodes(), ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::initShapeFunctions(
const Array<Real> & nodes, const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
for (auto & type : mesh.elementTypes(element_dimension, ghost_type, kind)) {
integrator.initIntegrator(nodes, type, ghost_type);
const auto & control_points = getIntegrationPoints(type, ghost_type);
shape_functions.initShapeFunctions(nodes, control_points, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateHelper {};
#define INTEGRATE(type) \
integrator.template integrate<type>(f, intf, nb_degree_of_freedom, \
ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_HELPER(kind) \
template <> struct IntegrateHelper<kind> { \
template <class I> \
static void call(const I & integrator, const Array<Real> & f, \
Array<Real> & intf, UInt nb_degree_of_freedom, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_INTEGRATE_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & f, Array<Real> & intf, UInt nb_degree_of_freedom,
const ElementType & type, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
#ifndef AKANTU_NDEBUG
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
#endif
intf.resize(nb_element);
fe_engine::details::IntegrateHelper<kind>::call(integrator, f, intf,
nb_degree_of_freedom, type,
ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateScalarHelper {};
#define INTEGRATE(type) \
integral = \
integrator.template integrate<type>(f, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER(kind) \
template <> struct IntegrateScalarHelper<kind> { \
template <class I> \
static Real call(const I & integrator, const Array<Real> & f, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
Real integral = 0.; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
return integral; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_SCALAR_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
Real FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & f, const ElementType & type,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
// std::stringstream sstr; sstr << ghost_type;
// AKANTU_DEBUG_ASSERT(sstr.str() == nablauq.getTag(),
// "The vector " << nablauq.getID() << " is not taged " <<
// ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
UInt nb_quadrature_points = getNbIntegrationPoints(type, ghost_type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f("
<< f.getID() << ") has not the good size. ("
<< f.size()
<< "!=" << nb_quadrature_points * nb_element << ")");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == 1,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
#endif
Real integral = fe_engine::details::IntegrateScalarHelper<kind>::call(
integrator, f, type, ghost_type, filter_elements);
AKANTU_DEBUG_OUT();
return integral;
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateScalarOnOneElementHelper {};
#define INTEGRATE(type) \
res = integrator.template integrate<type>(f, index, ghost_type);
#define AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER(kind) \
template <> struct IntegrateScalarOnOneElementHelper<kind> { \
template <class I> \
static Real call(const I & integrator, const Vector<Real> & f, \
const ElementType & type, UInt index, \
const GhostType & ghost_type) { \
Real res = 0.; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
return res; \
} \
};
AKANTU_BOOST_ALL_KIND(
AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_SCALAR_ON_ONE_ELEMENT_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
Real FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::integrate(
const Vector<Real> & f, const ElementType & type, UInt index,
const GhostType & ghost_type) const {
Real res = fe_engine::details::IntegrateScalarOnOneElementHelper<kind>::call(
integrator, f, type, index, ghost_type);
return res;
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct IntegrateOnIntegrationPointsHelper {};
#define INTEGRATE(type) \
integrator.template integrateOnIntegrationPoints<type>( \
f, intf, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct IntegrateOnIntegrationPointsHelper<kind> { \
template <class I> \
static void call(const I & integrator, const Array<Real> & f, \
Array<Real> & intf, UInt nb_degree_of_freedom, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTEGRATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(
AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_INTEGRATE_ON_INTEGRATION_POINTS_HELPER
#undef INTEGRATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & f, Array<Real> & intf,
UInt nb_degree_of_freedom,
const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
UInt nb_quadrature_points = getNbIntegrationPoints(type);
#ifndef AKANTU_NDEBUG
// std::stringstream sstr; sstr << ghost_type;
// AKANTU_DEBUG_ASSERT(sstr.str() == nablauq.getTag(),
// "The vector " << nablauq.getID() << " is not taged " <<
// ghost_type);
AKANTU_DEBUG_ASSERT(f.size() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.size()
<< ") has not the good size ("
<< nb_element << ").");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(intf.getNbComponent() == nb_degree_of_freedom,
"The vector intf("
<< intf.getID()
<< ") has not the good number of component.");
#endif
intf.resize(nb_element * nb_quadrature_points);
fe_engine::details::IntegrateOnIntegrationPointsHelper<kind>::call(
integrator, f, intf, nb_degree_of_freedom, type, ghost_type,
filter_elements);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct InterpolateOnIntegrationPointsHelper {
template <class S>
static void call(const S &, const Array<Real> &, Array<Real> &,
const UInt, const ElementType &, const GhostType &,
const Array<UInt> &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
};
#define INTERPOLATE(type) \
shape_functions.template interpolateOnIntegrationPoints<type>( \
u, uq, nb_degree_of_freedom, ghost_type, filter_elements);
#define AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER(kind) \
template <> struct InterpolateOnIntegrationPointsHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, const Array<Real> & u, \
Array<Real> & uq, const UInt nb_degree_of_freedom, \
const ElementType & type, const GhostType & ghost_type, \
const Array<UInt> & filter_elements) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTERPOLATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER,
AKANTU_FE_ENGINE_LIST_INTERPOLATE_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_INTERPOLATE_ON_INTEGRATION_POINTS_HELPER
#undef INTERPOLATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateOnIntegrationPoints(const Array<Real> & u, Array<Real> & uq,
const UInt nb_degree_of_freedom,
const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_points =
shape_functions.getIntegrationPoints(type, ghost_type).cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.size();
#ifndef AKANTU_NDEBUG
AKANTU_DEBUG_ASSERT(u.size() == mesh.getNbNodes(),
"The vector u(" << u.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(u.getNbComponent() == nb_degree_of_freedom,
"The vector u("
<< u.getID()
<< ") has not the good number of component.");
AKANTU_DEBUG_ASSERT(uq.getNbComponent() == nb_degree_of_freedom,
"The vector uq("
<< uq.getID()
<< ") has not the good number of component.");
#endif
uq.resize(nb_element * nb_points);
fe_engine::details::InterpolateOnIntegrationPointsHelper<kind>::call(
shape_functions, u, uq, nb_degree_of_freedom, type, ghost_type,
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateOnIntegrationPoints(
const Array<Real> & u, ElementTypeMapArray<Real> & uq,
const ElementTypeMapArray<UInt> * filter_elements) const {
AKANTU_DEBUG_IN();
- const Array<UInt> * filter = NULL;
+ const Array<UInt> * filter = nullptr;
for (auto ghost_type : ghost_types) {
for (auto & type : uq.elementTypes(_all_dimensions, ghost_type, kind)) {
UInt nb_quad_per_element = getNbIntegrationPoints(type, ghost_type);
UInt nb_element = 0;
if (filter_elements) {
filter = &((*filter_elements)(type, ghost_type));
nb_element = filter->size();
} else {
filter = &empty_filter;
nb_element = mesh.getNbElement(type, ghost_type);
}
UInt nb_tot_quad = nb_quad_per_element * nb_element;
Array<Real> & quad = uq(type, ghost_type);
quad.resize(nb_tot_quad);
interpolateOnIntegrationPoints(u, quad, quad.getNbComponent(), type,
ghost_type, *filter);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeIntegrationPointsCoordinates(
ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * filter_elements) const {
const Array<Real> & nodes_coordinates = mesh.getNodes();
interpolateOnIntegrationPoints(
nodes_coordinates, quadrature_points_coordinates, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeIntegrationPointsCoordinates(
Array<Real> & quadrature_points_coordinates, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
const Array<Real> & nodes_coordinates = mesh.getNodes();
UInt spatial_dimension = mesh.getSpatialDimension();
interpolateOnIntegrationPoints(
nodes_coordinates, quadrature_points_coordinates, spatial_dimension, type,
ghost_type, filter_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<UInt> * element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
ElementTypeMapArray<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_for_interpolation", getID(),
getMemoryID());
quadrature_points_coordinates.initialize(*this,
_nb_component = spatial_dimension);
computeIntegrationPointsCoordinates(quadrature_points_coordinates,
element_filter);
shape_functions.initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates,
interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, quadrature_points_coordinates,
element_filter);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
ElementTypeMapArray<Real> interpolation_points_coordinates_matrices(
"interpolation_points_coordinates_matrices", id, memory_id);
ElementTypeMapArray<Real> quad_points_coordinates_inv_matrices(
"quad_points_coordinates_inv_matrices", id, memory_id);
initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates,
interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, element_filter);
interpolateElementalFieldFromIntegrationPoints(
field, interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, result, ghost_type, element_filter);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const {
shape_functions.interpolateElementalFieldFromIntegrationPoints(
field, interpolation_points_coordinates_matrices,
quad_points_coordinates_inv_matrices, result, ghost_type, element_filter);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct InterpolateHelper {
template <class S>
static void call(const S &, const Vector<Real> &, UInt,
const Matrix<Real> &, Vector<Real> &,
const ElementType &, const GhostType &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
};
#define INTERPOLATE(type) \
shape_functions.template interpolate<type>( \
real_coords, element, nodal_values, interpolated, ghost_type);
#define AKANTU_SPECIALIZE_INTERPOLATE_HELPER(kind) \
template <> struct InterpolateHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const Matrix<Real> & nodal_values, \
Vector<Real> & interpolated, const ElementType & type, \
const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INTERPOLATE, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_INTERPOLATE_HELPER,
AKANTU_FE_ENGINE_LIST_INTERPOLATE)
#undef AKANTU_SPECIALIZE_INTERPOLATE_HELPER
#undef INTERPOLATE
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::interpolate(
const Vector<Real> & real_coords, const Matrix<Real> & nodal_values,
Vector<Real> & interpolated, const Element & element) const {
AKANTU_DEBUG_IN();
fe_engine::details::InterpolateHelper<kind>::call(
shape_functions, real_coords, element.element, nodal_values, interpolated,
element.type, element.ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
computeNormalsOnIntegrationPoints(mesh.getNodes(), ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
// Real * coord = mesh.getNodes().storage();
UInt spatial_dimension = mesh.getSpatialDimension();
// allocate the normal arrays
for (auto & type : mesh.elementTypes(element_dimension, ghost_type, kind)) {
UInt size = mesh.getNbElement(type, ghost_type);
if (normals_on_integration_points.exists(type, ghost_type)) {
normals_on_integration_points(type, ghost_type).resize(size);
} else {
normals_on_integration_points.alloc(size, spatial_dimension, type,
ghost_type);
}
}
// loop over the type to build the normals
for (auto & type : mesh.elementTypes(element_dimension, ghost_type, kind)) {
Array<Real> & normals_on_quad =
normals_on_integration_points(type, ghost_type);
computeNormalsOnIntegrationPoints(field, normals_on_quad, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeNormalsOnIntegrationPoints {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
static void call(const FEEngineTemplate<I, S, k, IOF> &,
const Array<Real> &, Array<Real> &, const ElementType &,
const GhostType &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
};
#define COMPUTE_NORMALS_ON_INTEGRATION_POINTS(type) \
fem.template computeNormalsOnIntegrationPoints<type>(field, normal, \
ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS(kind) \
template <> struct ComputeNormalsOnIntegrationPoints<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF> \
static void call(const FEEngineTemplate<I, S, k, IOF> & fem, \
const Array<Real> & field, Array<Real> & normal, \
const ElementType & type, const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_NORMALS_ON_INTEGRATION_POINTS, \
kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS,
AKANTU_FE_ENGINE_LIST_COMPUTE_NORMALS_ON_INTEGRATION_POINTS)
#undef AKANTU_SPECIALIZE_COMPUTE_NORMALS_ON_INTEGRATION_POINTS
#undef COMPUTE_NORMALS_ON_INTEGRATION_POINTS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
const ElementType & type,
const GhostType & ghost_type) const {
fe_engine::details::ComputeNormalsOnIntegrationPoints<kind>::call(
*this, field, normal, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
if(type == _point_1) {
computeNormalsOnIntegrationPointsPoint1(field, normal, ghost_type);
return;
}
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_points = getNbIntegrationPoints(type, ghost_type);
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
normal.resize(nb_element * nb_points);
Array<Real>::matrix_iterator normals_on_quad =
normal.begin_reinterpret(spatial_dimension, nb_points, nb_element);
Array<Real> f_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, field, f_el, type, ghost_type);
const Matrix<Real> & quads =
integrator.template getIntegrationPoints<type>(ghost_type);
Array<Real>::matrix_iterator f_it =
f_el.begin(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem) {
ElementClass<type>::computeNormalsOnNaturalCoordinates(quads, *f_it,
*normals_on_quad);
++normals_on_quad;
++f_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
template <ElementKind kind> struct InverseMapHelper {
template <class S>
- static void call(const S & shape_functions, const Vector<Real> & real_coords,
- UInt element, const ElementType & type,
- Vector<Real> & natural_coords,
- const GhostType & ghost_type) {
+ static void call(const S & /*shape_functions*/, const Vector<Real> & /*real_coords*/,
+ UInt /*element*/, const ElementType & /*type*/,
+ Vector<Real> & /*natural_coords*/,
+ const GhostType & /*ghost_type*/) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
};
#define INVERSE_MAP(type) \
shape_functions.template inverseMap<type>(real_coords, element, \
natural_coords, ghost_type);
#define AKANTU_SPECIALIZE_INVERSE_MAP_HELPER(kind) \
template <> struct InverseMapHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType & type, Vector<Real> & natural_coords, \
const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INVERSE_MAP, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_INVERSE_MAP_HELPER,
AKANTU_FE_ENGINE_LIST_INVERSE_MAP)
#undef AKANTU_SPECIALIZE_INVERSE_MAP_HELPER
#undef INVERSE_MAP
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::inverseMap(
const Vector<Real> & real_coords, UInt element, const ElementType & type,
Vector<Real> & natural_coords, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
InverseMapHelper<kind>::call(shape_functions, real_coords, element, type,
natural_coords, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ContainsHelper {
template <class S>
static void call(const S &, const Vector<Real> &, UInt,
const ElementType &, const GhostType &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
};
#define CONTAINS(type) \
contain = shape_functions.template contains<type>(real_coords, element, \
ghost_type);
#define AKANTU_SPECIALIZE_CONTAINS_HELPER(kind) \
template <> struct ContainsHelper<kind> { \
template <template <ElementKind> class S, ElementKind k> \
static bool call(const S<k> & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType & type, const GhostType & ghost_type) { \
bool contain = false; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(CONTAINS, kind); \
return contain; \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_CONTAINS_HELPER,
AKANTU_FE_ENGINE_LIST_CONTAINS)
#undef AKANTU_SPECIALIZE_CONTAINS_HELPER
#undef CONTAINS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline bool FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::contains(
const Vector<Real> & real_coords, UInt element, const ElementType & type,
const GhostType & ghost_type) const {
return fe_engine::details::ContainsHelper<kind>::call(
shape_functions, real_coords, element, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeShapesHelper {
template <class S>
static void call(const S &, const Vector<Real> &, UInt, const ElementType,
Vector<Real> &, const GhostType &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
};
#define COMPUTE_SHAPES(type) \
shape_functions.template computeShapes<type>(real_coords, element, shapes, \
ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER(kind) \
template <> struct ComputeShapesHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType type, Vector<Real> & shapes, \
const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_SHAPES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER,
AKANTU_FE_ENGINE_LIST_COMPUTE_SHAPES)
#undef AKANTU_SPECIALIZE_COMPUTE_SHAPES_HELPER
#undef COMPUTE_SHAPES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapes(
const Vector<Real> & real_coords, UInt element, const ElementType & type,
Vector<Real> & shapes, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::ComputeShapesHelper<kind>::call(
shape_functions, real_coords, element, type, shapes, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct ComputeShapeDerivativesHelper {
template <class S>
static void call(__attribute__((unused)) const S & shape_functions,
__attribute__((unused)) const Vector<Real> & real_coords,
__attribute__((unused)) UInt element,
__attribute__((unused)) const ElementType type,
__attribute__((unused)) Matrix<Real> & shape_derivatives,
__attribute__((unused)) const GhostType & ghost_type) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
};
#define COMPUTE_SHAPE_DERIVATIVES(type) \
Matrix<Real> coords_mat(real_coords.storage(), shape_derivatives.rows(), 1); \
Tensor3<Real> shapesd_tensor(shape_derivatives.storage(), \
shape_derivatives.rows(), \
shape_derivatives.cols(), 1); \
shape_functions.template computeShapeDerivatives<type>( \
coords_mat, element, shapesd_tensor, ghost_type);
#define AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER(kind) \
template <> struct ComputeShapeDerivativesHelper<kind> { \
template <class S> \
static void call(const S & shape_functions, \
const Vector<Real> & real_coords, UInt element, \
const ElementType type, Matrix<Real> & shape_derivatives, \
const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(COMPUTE_SHAPE_DERIVATIVES, kind); \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(
AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER,
AKANTU_FE_ENGINE_LIST_COMPUTE_SHAPES_DERIVATIVES)
#undef AKANTU_SPECIALIZE_COMPUTE_SHAPE_DERIVATIVES_HELPER
#undef COMPUTE_SHAPE_DERIVATIVES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapeDerivatives(
const Vector<Real> & real_coords, UInt element, const ElementType & type,
Matrix<Real> & shape_derivatives, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
fe_engine::details::ComputeShapeDerivativesHelper<kind>::call(
shape_functions, real_coords, element, type, shape_derivatives,
ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetNbIntegrationPointsHelper {};
#define GET_NB_INTEGRATION_POINTS(type) \
nb_quad_points = integrator.template getNbIntegrationPoints<type>(ghost_type);
#define AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GetNbIntegrationPointsHelper<kind> { \
template <template <ElementKind, class> class I, ElementKind k, class IOF> \
static UInt call(const I<k, IOF> & integrator, const ElementType type, \
const GhostType & ghost_type) { \
UInt nb_quad_points = 0; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_NB_INTEGRATION_POINTS, kind); \
return nb_quad_points; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_GET_NB_INTEGRATION_POINTS_HELPER
#undef GET_NB_INTEGRATION
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline UInt
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getNbIntegrationPoints(
const ElementType & type, const GhostType & ghost_type) const {
return fe_engine::details::GetNbIntegrationPointsHelper<kind>::call(
integrator, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetShapesHelper {};
#define GET_SHAPES(type) ret = &(shape_functions.getShapes(type, ghost_type));
#define AKANTU_SPECIALIZE_GET_SHAPES_HELPER(kind) \
template <> struct GetShapesHelper<kind> { \
template <class S> \
static const Array<Real> & call(const S & shape_functions, \
const ElementType type, \
const GhostType & ghost_type) { \
const Array<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_SHAPES, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_SHAPES_HELPER)
#undef AKANTU_SPECIALIZE_GET_SHAPES_HELPER
#undef GET_SHAPES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Array<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getShapes(
const ElementType & type, const GhostType & ghost_type,
__attribute__((unused)) UInt id) const {
return fe_engine::details::GetShapesHelper<kind>::call(shape_functions, type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetShapesDerivativesHelper {
template <template <ElementKind> class S, ElementKind k>
static const Array<Real> & call(const S<k> &, const ElementType &,
const GhostType &, UInt) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
};
#define GET_SHAPES_DERIVATIVES(type) \
ret = &(shape_functions.getShapesDerivatives(type, ghost_type));
#define AKANTU_SPECIALIZE_GET_SHAPES_DERIVATIVES_HELPER(kind) \
template <> struct GetShapesDerivativesHelper<kind> { \
template <template <ElementKind> class S, ElementKind k> \
static const Array<Real> & \
call(const S<k> & shape_functions, const ElementType type, \
const GhostType & ghost_type, __attribute__((unused)) UInt id) { \
const Array<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_SHAPES_DERIVATIVES, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND_LIST(AKANTU_SPECIALIZE_GET_SHAPES_DERIVATIVES_HELPER,
AKANTU_FE_ENGINE_LIST_GET_SHAPES_DERIVATIVES)
#undef AKANTU_SPECIALIZE_GET_SHAPE_DERIVATIVES_HELPER
#undef GET_SHAPES_DERIVATIVES
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Array<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getShapesDerivatives(
const ElementType & type, const GhostType & ghost_type,
__attribute__((unused)) UInt id) const {
return fe_engine::details::GetShapesDerivativesHelper<kind>::call(
shape_functions, type, ghost_type, id);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
namespace fe_engine {
namespace details {
template <ElementKind kind> struct GetIntegrationPointsHelper {};
#define GET_INTEGRATION_POINTS(type) \
ret = &(integrator.template getIntegrationPoints<type>(ghost_type));
#define AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER(kind) \
template <> struct GetIntegrationPointsHelper<kind> { \
template <template <ElementKind, class> class I, ElementKind k, class IOF> \
static const Matrix<Real> & call(const I<k, IOF> & integrator, \
const ElementType type, \
const GhostType & ghost_type) { \
const Matrix<Real> * ret = NULL; \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(GET_INTEGRATION_POINTS, kind); \
return *ret; \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER)
#undef AKANTU_SPECIALIZE_GET_INTEGRATION_POINTS_HELPER
#undef GET_INTEGRATION_POINTS
} // namespace details
} // namespace fe_engine
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline const Matrix<Real> &
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::getIntegrationPoints(
const ElementType & type, const GhostType & ghost_type) const {
return fe_engine::details::GetIntegrationPointsHelper<kind>::call(
integrator, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::printself(
std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "FEEngineTemplate [" << std::endl;
stream << space << " + parent [" << std::endl;
FEEngine::printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << " + shape functions [" << std::endl;
shape_functions.printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << " + integrator [" << std::endl;
integrator.printself(stream, indent + 3);
stream << space << " ]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsAdded(
const Array<Element> & new_elements, const NewElementsEvent &) {
integrator.onElementsAdded(new_elements);
shape_functions.onElementsAdded(new_elements);
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsRemoved(
const Array<Element> &, const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::onElementsChanged(
const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &, const ChangedElementsEvent &) {}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
computeNormalsOnIntegrationPointsPoint1(
const Array<Real> &, Array<Real> & normal,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(mesh.getSpatialDimension() == 1,
"Mesh dimension must be 1 to compute normals on points!");
const ElementType type = _point_1;
UInt spatial_dimension = mesh.getSpatialDimension();
// UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_points = getNbIntegrationPoints(type, ghost_type);
UInt nb_element = mesh.getConnectivity(type, ghost_type).size();
normal.resize(nb_element * nb_points);
Array<Real>::matrix_iterator normals_on_quad =
normal.begin_reinterpret(spatial_dimension, nb_points, nb_element);
const Array<std::vector<Element>> & segments =
mesh.getElementToSubelement(type, ghost_type);
const Array<Real> & coords = mesh.getNodes();
const Mesh * mesh_segment;
if (mesh.isMeshFacets())
mesh_segment = &(mesh.getMeshParent());
else
mesh_segment = &mesh;
for (UInt elem = 0; elem < nb_element; ++elem) {
UInt nb_segment = segments(elem).size();
AKANTU_DEBUG_ASSERT(
nb_segment > 0,
"Impossible to compute a normal on a point connected to 0 segments");
Real normal_value = 1;
if (nb_segment == 1) {
const Element & segment = segments(elem)[0];
const Array<UInt> & segment_connectivity =
mesh_segment->getConnectivity(segment.type, segment.ghost_type);
// const Vector<UInt> & segment_points =
// segment_connectivity.begin(Mesh::getNbNodesPerElement(segment.type))[segment.element];
Real difference;
if (segment_connectivity(0) == elem) {
difference = coords(elem) - coords(segment_connectivity(1));
} else {
difference = coords(elem) - coords(segment_connectivity(0));
}
normal_value = difference / std::abs(difference);
}
for (UInt n(0); n < nb_points; ++n) {
(*normals_on_quad)(0, n) = normal_value;
}
++normals_on_quad;
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/fe_engine/integration_point.hh b/src/fe_engine/integration_point.hh
index b03973307..2e6314ce7 100644
--- a/src/fe_engine/integration_point.hh
+++ b/src/fe_engine/integration_point.hh
@@ -1,167 +1,168 @@
/**
* @file integration_point.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Jun 17 2015
* @date last modification: Sun Nov 15 2015
*
* @brief definition of the class IntegrationPoint
*
* @section LICENSE
*
* Copyright (©) 2015 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 "aka_types.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_QUADRATURE_POINT_H
#define AKANTU_QUADRATURE_POINT_H
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
class IntegrationPoint;
extern const IntegrationPoint IntegrationPointNull;
/* -------------------------------------------------------------------------- */
class IntegrationPoint : public Element {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef Vector<Real> position_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationPoint(const Element & element, UInt num_point = 0,
UInt nb_quad_per_element = 0)
: Element(element), num_point(num_point),
global_num(element.element * nb_quad_per_element + num_point),
position(nullptr, 0){};
IntegrationPoint(ElementType type = _not_defined, UInt element = 0,
UInt num_point = 0, GhostType ghost_type = _not_ghost)
: Element{type, element, ghost_type}, num_point(num_point), global_num(0),
position(nullptr, 0){};
IntegrationPoint(UInt element, UInt num_point, UInt global_num,
const position_type & position, ElementType type,
GhostType ghost_type = _not_ghost)
: Element{type, element, ghost_type}, num_point(num_point),
global_num(global_num), position(nullptr, 0) {
this->position.shallowCopy(position);
};
IntegrationPoint(const IntegrationPoint & quad)
: Element(quad), num_point(quad.num_point), global_num(quad.global_num),
position(nullptr, 0) {
position.shallowCopy(quad.position);
};
+ virtual ~IntegrationPoint() = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
inline bool operator==(const IntegrationPoint & quad) const {
return Element::operator==(quad) && this->num_point == quad.num_point;
}
inline bool operator!=(const IntegrationPoint & quad) const {
return Element::operator!=(quad) || (num_point != quad.num_point) || (global_num != quad.global_num);
}
bool operator<(const IntegrationPoint & rhs) const {
bool res = Element::operator<(rhs) ||
(Element::operator==(rhs) && this->num_point < rhs.num_point);
return res;
}
inline IntegrationPoint & operator=(const IntegrationPoint & q) {
if (this != &q) {
element = q.element;
type = q.type;
ghost_type = q.ghost_type;
num_point = q.num_point;
global_num = q.global_num;
position.shallowCopy(q.position);
}
return *this;
}
/// get the position of the integration point
AKANTU_GET_MACRO(Position, position, const position_type &);
/// set the position of the integration point
void setPosition(const position_type & position) {
this->position.shallowCopy(position);
}
/// deep copy of the position of the integration point
void copyPosition(const position_type & position) {
this->position.deepCopy(position);
}
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "IntegrationPoint [";
stream << *static_cast<const Element *>(this);
stream << ", " << num_point << "(" << global_num << ")"
<< "]";
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
/// number of quadrature point in the element
UInt num_point;
/// global number of the quadrature point
UInt global_num;
// TODO might be temporary: however this class should be tought maybe...
std::string material_id;
private:
/// position of the quadrature point
position_type position;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const IntegrationPoint & _this) {
_this.printself(stream);
return stream;
}
} // akantu
#endif /* AKANTU_QUADRATURE_POINT_H */
diff --git a/src/fe_engine/integrator.hh b/src/fe_engine/integrator.hh
index 8374f1415..5df11d185 100644
--- a/src/fe_engine/integrator.hh
+++ b/src/fe_engine/integrator.hh
@@ -1,137 +1,137 @@
/**
* @file integrator.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 22 2015
*
* @brief interface for integrator classes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
#ifndef __AKANTU_INTEGRATOR_HH__
#define __AKANTU_INTEGRATOR_HH__
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Integrator : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Integrator(const Mesh & mesh, const ID & id = "integrator",
const MemoryID & memory_id = 0)
: Memory(id, memory_id), mesh(mesh),
jacobians("jacobians", id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
- virtual ~Integrator(){};
+ ~Integrator() override{};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// empty method
template <ElementType type>
inline void precomputeJacobiansOnQuadraturePoints(__attribute__((unused))
GhostType ghost_type) {}
/// empty method
void integrateOnElement(__attribute__((unused)) const Array<Real> & f,
__attribute__((unused)) Real * intf,
__attribute__((unused)) UInt nb_degree_of_freedom,
__attribute__((unused)) const Element & elem,
__attribute__((unused))
GhostType ghost_type) const {};
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Integrator [" << std::endl;
jacobians.printself(stream, indent + 1);
stream << space << "]" << std::endl;
};
/* ------------------------------------------------------------------------ */
public:
virtual void onElementsAdded(const Array<Element> &) {}
virtual void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> & new_numbering) {
jacobians.onElementsRemoved(new_numbering);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// access to the jacobians
Array<Real> & getJacobians(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return jacobians(type, ghost_type);
};
/// access to the jacobians const
const Array<Real> &
getJacobians(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const {
return jacobians(type, ghost_type);
};
AKANTU_GET_MACRO(Jacobians, jacobians, const ElementTypeMapArray<Real> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// mesh associated to the integrator
const Mesh & mesh;
/// jacobians for all elements
ElementTypeMapArray<Real> jacobians;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "integrator_inline_impl.cc"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Integrator & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#endif /* __AKANTU_INTEGRATOR_HH__ */
diff --git a/src/fe_engine/integrator_gauss.hh b/src/fe_engine/integrator_gauss.hh
index d35db8ed3..b6f09fa1e 100644
--- a/src/fe_engine/integrator_gauss.hh
+++ b/src/fe_engine/integrator_gauss.hh
@@ -1,199 +1,199 @@
/**
* @file integrator_gauss.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 22 2015
*
* @brief Gauss integration facilities
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "integrator.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTEGRATOR_GAUSS_HH__
#define __AKANTU_INTEGRATOR_GAUSS_HH__
namespace akantu {
namespace integrator {
namespace details {
template <ElementKind> struct GaussIntegratorComputeJacobiansHelper;
} // namespace details
} // namespace fe_engine
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss : public Integrator {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegratorGauss(const Mesh & mesh, const ID & id = "integrator_gauss",
const MemoryID & memory_id = 0);
- virtual ~IntegratorGauss(){};
+ ~IntegratorGauss() override{};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initIntegrator(const Array<Real> & nodes, const ElementType & type,
const GhostType & ghost_type);
template <ElementType type>
inline void initIntegrator(const Array<Real> & nodes,
const GhostType & ghost_type);
/// integrate f on the element "elem" of type "type"
template <ElementType type>
inline void integrateOnElement(const Array<Real> & f, Real * intf,
UInt nb_degree_of_freedom, const UInt elem,
const GhostType & ghost_type) const;
/// integrate f for all elements of type "type"
template <ElementType type>
void integrate(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const;
/// integrate scalar field in_f
template <ElementType type, UInt polynomial_degree>
Real integrate(const Array<Real> & in_f,
const GhostType & ghost_type = _not_ghost) const;
/// integrate partially around a quadrature point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
template <ElementType type>
Real integrate(const Vector<Real> & in_f, UInt index,
const GhostType & ghost_type) const;
/// integrate scalar field in_f
template <ElementType type>
Real integrate(const Array<Real> & in_f, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const;
/// integrate a field without using the pre-computed values
template <ElementType type, UInt polynomial_degree>
void integrate(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom, const GhostType & ghost_type) const;
/// integrate partially around a quadrature point (@f$ intf_q = f_q * J_q *
/// w_q @f$)
template <ElementType type>
void integrateOnIntegrationPoints(const Array<Real> & in_f,
Array<Real> & intf,
UInt nb_degree_of_freedom,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const;
/// return a matrix with quadrature points natural coordinates
template <ElementType type>
const Matrix<Real> & getIntegrationPoints(const GhostType & ghost_type) const;
/// return number of quadrature points
template <ElementType type>
UInt getNbIntegrationPoints(const GhostType & ghost_type) const;
template <ElementType type, UInt n> Matrix<Real> getIntegrationPoints() const;
template <ElementType type, UInt n>
Vector<Real> getIntegrationWeights() const;
protected:
friend struct integrator::details::GaussIntegratorComputeJacobiansHelper<kind>;
template <ElementType type>
void computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeJacobiansOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & quad_points,
Array<Real> & jacobians, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// precompute jacobians on elements of type "type"
template <ElementType type>
void precomputeJacobiansOnQuadraturePoints(const Array<Real> & nodes,
const GhostType & ghost_type);
// multiply the jacobians by the integration weights and stores the results in
// jacobians
template <ElementType type, UInt polynomial_degree>
void multiplyJacobiansByWeights(Array<Real> & jacobians) const;
/// compute the vector of quadrature points natural coordinates
template <ElementType type>
void computeQuadraturePoints(const GhostType & ghost_type);
/// check that the jacobians are not negative
template <ElementType type>
void checkJacobians(const GhostType & ghost_type) const;
/// internal integrate partially around a quadrature point (@f$ intf_q = f_q *
/// J_q *
/// w_q @f$)
void integrateOnIntegrationPoints(const Array<Real> & in_f,
Array<Real> & intf,
UInt nb_degree_of_freedom,
const Array<Real> & jacobians,
UInt nb_element) const;
void integrate(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom, const Array<Real> & jacobians,
UInt nb_element) const;
public:
/// compute the jacobians on quad points for a given element
template <ElementType type>
void
computeJacobianOnQuadPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & integration_points,
Vector<Real> & jacobians) const;
public:
void onElementsAdded(const Array<Element> & elements) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// integrate the field f with the jacobian jac -> inte
inline void integrate(Real * f, Real * jac, Real * inte,
UInt nb_degree_of_freedom,
UInt nb_quadrature_points) const;
private:
/// ElementTypeMap of the quadrature points
ElementTypeMap<Matrix<Real>> quadrature_points;
};
} // namespace akantu
#include "integrator_gauss_inline_impl.cc"
#endif /* __AKANTU_INTEGRATOR_GAUSS_HH__ */
diff --git a/src/fe_engine/shape_cohesive.hh b/src/fe_engine/shape_cohesive.hh
index 38e512944..d214f7035 100644
--- a/src/fe_engine/shape_cohesive.hh
+++ b/src/fe_engine/shape_cohesive.hh
@@ -1,169 +1,169 @@
/**
* @file shape_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Feb 15 2011
* @date last modification: Thu Oct 22 2015
*
* @brief shape functions for cohesive elements description
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_array.hh"
#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_COHESIVE_HH__
#define __AKANTU_SHAPE_COHESIVE_HH__
namespace akantu {
struct CohesiveReduceFunctionMean {
inline Real operator()(Real u_plus, Real u_minus) {
return .5 * (u_plus + u_minus);
}
};
struct CohesiveReduceFunctionOpening {
inline Real operator()(Real u_plus, Real u_minus) {
return (u_plus - u_minus);
}
};
template <> class ShapeLagrange<_ek_cohesive> : public ShapeLagrangeBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, const ID & id = "shape_cohesive",
const MemoryID & memory_id = 0);
- virtual ~ShapeLagrange() = default;
+ ~ShapeLagrange() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
const ElementType & type,
const GhostType & ghost_type);
/// extract the nodal values and store them per element
template <ElementType type, class ReduceFunction>
void extractNodalToElementField(
const Array<Real> & nodal_f, Array<Real> & elemental_f,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// computes the shape functions derivatives for given interpolation points
template <ElementType type>
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const override;
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// pre compute all shape derivatives on the element integration points from
/// natural coordinates
template <ElementType type>
void precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
GhostType ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type, class ReduceFunction>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
const GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
const GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const {
interpolateOnIntegrationPoints<type, CohesiveReduceFunctionMean>(
u, uq, nb_degree_of_freedom, ghost_type, filter_elements);
}
/// compute the gradient of u on the integration points in the natural
/// coordinates
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const {
variationOnIntegrationPoints<type, CohesiveReduceFunctionMean>(
u, nablauq, nb_degree_of_freedom, ghost_type, filter_elements);
}
/// compute the gradient of u on the integration points
template <ElementType type, class ReduceFunction>
void variationOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// compute the normals to the field u on integration points
template <ElementType type, class ReduceFunction>
void computeNormalsOnIntegrationPoints(
const Array<Real> & u, Array<Real> & normals_u,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// multiply a field by shape functions
template <ElementType type>
void fieldTimesShapes(__attribute__((unused)) const Array<Real> & field,
__attribute__((unused))
Array<Real> & fiedl_times_shapes,
__attribute__((unused)) GhostType ghost_type) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
};
/// standard output stream operator
template <class ShapeFunction>
inline std::ostream & operator<<(std::ostream & stream,
const ShapeCohesive<ShapeFunction> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "shape_cohesive_inline_impl.cc"
#endif /* __AKANTU_SHAPE_COHESIVE_HH__ */
diff --git a/src/fe_engine/shape_functions.hh b/src/fe_engine/shape_functions.hh
index ccdac5dce..f7d130af6 100644
--- a/src/fe_engine/shape_functions.hh
+++ b/src/fe_engine/shape_functions.hh
@@ -1,214 +1,214 @@
/**
* @file shape_functions.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 22 2015
*
* @brief shape function class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_FUNCTIONS_HH__
#define __AKANTU_SHAPE_FUNCTIONS_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
class ShapeFunctions : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeFunctions(const Mesh & mesh, const ID & id = "shape",
const MemoryID & memory_id = 0);
- virtual ~ShapeFunctions() = default;
+ ~ShapeFunctions() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Shapes [" << std::endl;
integration_points.printself(stream, indent + 1);
stream << space << "]" << std::endl;
};
/// set the integration points for a given element
template <ElementType type>
void setIntegrationPointsByType(const Matrix<Real> & integration_points,
const GhostType & ghost_type);
/// Build pre-computed matrices for interpolation of field form integration
/// points at other given positions (interpolation_points)
void initElementalFieldInterpolationFromIntegrationPoints(
const ElementTypeMapArray<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const ElementTypeMapArray<Real> & quadrature_points_coordinates,
const ElementTypeMapArray<UInt> * element_filter) const;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
void interpolateElementalFieldFromIntegrationPoints(
const ElementTypeMapArray<Real> & field,
const ElementTypeMapArray<Real> &
interpolation_points_coordinates_matrices,
const ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType & ghost_type,
const ElementTypeMapArray<UInt> * element_filter) const;
protected:
/// interpolate nodal values stored by element on the integration points
template <ElementType type>
void interpolateElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & uq, const GhostType & ghost_type,
const Array<Real> & shapes,
const Array<UInt> & filter_elements = empty_filter) const;
/// gradient of nodal values stored by element on the control points
template <ElementType type>
void gradientElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & out_nablauq,
const GhostType & ghost_type, const Array<Real> & shapes_derivatives,
const Array<UInt> & filter_elements) const;
protected:
/// By element versions of non-templated eponym methods
template <ElementType type>
inline void interpolateElementalFieldFromIntegrationPoints(
const Array<Real> & field,
const Array<Real> & interpolation_points_coordinates_matrices,
const Array<Real> & quad_points_coordinates_inv_matrices,
ElementTypeMapArray<Real> & result, const GhostType & ghost_type,
const Array<UInt> & element_filter) const;
/// Interpolate field at given position from given values of this field at
/// integration points (field)
/// using matrices precomputed with
/// initElementalFieldInterplationFromIntegrationPoints
template <ElementType type>
inline void initElementalFieldInterpolationFromIntegrationPoints(
const Array<Real> & interpolation_points_coordinates,
ElementTypeMapArray<Real> & interpolation_points_coordinates_matrices,
ElementTypeMapArray<Real> & quad_points_coordinates_inv_matrices,
const Array<Real> & quadrature_points_coordinates,
const GhostType & ghost_type, const Array<UInt> & element_filter) const;
/// build matrix for the interpolation of field form integration points
template <ElementType type>
inline void buildElementalFieldInterpolationMatrix(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order =
ElementClassProperty<type>::polynomial_degree) const;
/// build the so called interpolation matrix (first collumn is 1, then the
/// other collumns are the traansposed coordinates)
inline void buildInterpolationMatrix(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix,
UInt integration_order) const;
public:
virtual void onElementsAdded(const Array<Element> &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
virtual void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the size of the shapes returned by the element class
static inline UInt getShapeSize(const ElementType & type);
/// get the size of the shapes derivatives returned by the element class
static inline UInt getShapeDerivativesSize(const ElementType & type);
inline const Matrix<Real> &
getIntegrationPoints(const ElementType & type,
const GhostType & ghost_type) const {
return integration_points(type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get a the shapes vector
inline const Array<Real> &
getShapes(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get a the shapes derivatives vector
inline const Array<Real> &
getShapesDerivatives(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// shape functions for all elements
ElementTypeMapArray<Real, InterpolationType> shapes;
/// shape functions derivatives for all elements
ElementTypeMapArray<Real, InterpolationType> shapes_derivatives;
/// associated mesh
const Mesh & mesh;
/// shape functions for all elements
ElementTypeMap<Matrix<Real>> integration_points;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ShapeFunctions & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "shape_functions_inline_impl.cc"
#endif /* __AKANTU_SHAPE_FUNCTIONS_HH__ */
diff --git a/src/fe_engine/shape_lagrange.hh b/src/fe_engine/shape_lagrange.hh
index 3973aeeb9..565a00f74 100644
--- a/src/fe_engine/shape_lagrange.hh
+++ b/src/fe_engine/shape_lagrange.hh
@@ -1,162 +1,162 @@
/**
* @file shape_lagrange.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
* @date last modification: Thu Nov 05 2015
*
* @brief lagrangian shape functions class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "shape_lagrange_base.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_LAGRANGE_HH__
#define __AKANTU_SHAPE_LAGRANGE_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Shape> class ShapeCohesive;
class ShapeIGFEM;
template <ElementKind kind> class ShapeLagrange : public ShapeLagrangeBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, const ID & id = "shape_lagrange",
const MemoryID & memory_id = 0);
- virtual ~ShapeLagrange() = default;
+ ~ShapeLagrange() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialization function for structural elements not yet implemented
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
const ElementType & type,
const GhostType & ghost_type);
/// computes the shape functions derivatives for given interpolation points
template <ElementType type>
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const override;
/// pre compute all shapes on the element integration points from natural
/// coordinates
template <ElementType type>
void precomputeShapesOnIntegrationPoints(const Array<Real> & nodes,
const GhostType & ghost_type);
/// pre compute all shape derivatives on the element integration points from
/// natural coordinates
template <ElementType type>
void
precomputeShapeDerivativesOnIntegrationPoints(const Array<Real> & nodes,
const GhostType & ghost_type);
/// interpolate nodal values on the integration points
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & u, Array<Real> & uq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
template <ElementType type>
void interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
const Array<Real> & shapes, GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// interpolate on physical point
template <ElementType type>
void interpolate(const Vector<Real> & real_coords, UInt elem,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const GhostType & ghost_type) const;
/// compute the gradient of u on the integration points
template <ElementType type>
void gradientOnIntegrationPoints(
const Array<Real> & u, Array<Real> & nablauq, UInt nb_degree_of_freedom,
GhostType ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter) const;
/// multiply a field by shape functions @f$ fts_{ij} = f_i * \varphi_j @f$
template <ElementType type>
void fieldTimesShapes(const Array<Real> & field,
Array<Real> & field_times_shapes,
GhostType ghost_type) const;
/// find natural coords from real coords provided an element
template <ElementType type>
void inverseMap(const Vector<Real> & real_coords, UInt element,
Vector<Real> & natural_coords,
const GhostType & ghost_type = _not_ghost) const;
/// return true if the coordinates provided are inside the element, false
/// otherwise
template <ElementType type>
bool contains(const Vector<Real> & real_coords, UInt elem,
const GhostType & ghost_type) const;
/// compute the shape on a provided point
template <ElementType type>
void computeShapes(const Vector<Real> & real_coords, UInt elem,
Vector<Real> & shapes, const GhostType & ghost_type) const;
/// compute the shape derivatives on a provided point
template <ElementType type>
void computeShapeDerivatives(const Matrix<Real> & real_coords, UInt elem,
Tensor3<Real> & shapes,
const GhostType & ghost_type) const;
protected:
/// compute the shape derivatives on integration points for a given element
template <ElementType type>
inline void
computeShapeDerivativesOnCPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & natural_coords,
Tensor3<Real> & shapesd) const;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_inline_impl.cc"
#endif /* __AKANTU_SHAPE_LAGRANGE_HH__ */
diff --git a/src/fe_engine/shape_lagrange_base.hh b/src/fe_engine/shape_lagrange_base.hh
index 2d3a0ab8c..08d915f7d 100644
--- a/src/fe_engine/shape_lagrange_base.hh
+++ b/src/fe_engine/shape_lagrange_base.hh
@@ -1,91 +1,91 @@
/**
* @file shape_lagrange_base.hh
*
* @author Nicolas Richart
*
* @date creation Thu Jul 27 2017
*
* @brief Base class for the shape lagrange
*
* @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 "shape_functions.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_LAGRANGE_BASE_HH__
#define __AKANTU_SHAPE_LAGRANGE_BASE_HH__
namespace akantu {
class ShapeLagrangeBase : public ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrangeBase(const Mesh & mesh, const ElementKind & kind,
const ID & id = "shape_lagrange",
const MemoryID & memory_id = 0);
- virtual ~ShapeLagrangeBase();
+ ~ShapeLagrangeBase() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// computes the shape functions for given interpolation points
virtual void computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
/// computes the shape functions derivatives for given interpolation points
virtual void computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const = 0;
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
template <ElementType type>
void computeShapesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shapes, const GhostType & ghost_type,
const Array<UInt> & filter_elements = empty_filter) const;
public:
void onElementsAdded(const Array<Element> & elements) override;
void
onElementsRemoved(const Array<Element> & elements,
const ElementTypeMapArray<UInt> & new_numbering) override;
protected:
/// The kind to consider
ElementKind _kind;
};
} // namespace akantu
#include "shape_lagrange_base_inline_impl.cc"
#endif /* __AKANTU_SHAPE_LAGRANGE_BASE_HH__ */
diff --git a/src/io/dumper/dumper_compute.hh b/src/io/dumper/dumper_compute.hh
index a55f37291..2f7931dd7 100644
--- a/src/io/dumper/dumper_compute.hh
+++ b/src/io/dumper/dumper_compute.hh
@@ -1,272 +1,272 @@
/**
* @file dumper_compute.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Tue Jan 19 2016
*
* @brief Field that map a function to another field
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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/>.
*
*/
#ifndef __AKANTU_DUMPER_COMPUTE_HH__
#define __AKANTU_DUMPER_COMPUTE_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dumper_iohelper.hh"
#include "dumper_type_traits.hh"
#include "dumper_field.hh"
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
class ComputeFunctorInterface {
public:
virtual ~ComputeFunctorInterface(){};
virtual UInt getDim() = 0;
virtual UInt getNbComponent(UInt old_nb_comp) = 0;
};
/* -------------------------------------------------------------------------- */
template <typename return_type>
class ComputeFunctorOutput : public ComputeFunctorInterface {
public:
ComputeFunctorOutput(){};
- virtual ~ComputeFunctorOutput(){};
+ ~ComputeFunctorOutput() override{};
};
/* -------------------------------------------------------------------------- */
template <typename input_type, typename return_type>
class ComputeFunctor : public ComputeFunctorOutput<return_type> {
public:
ComputeFunctor(){};
- virtual ~ComputeFunctor(){};
+ ~ComputeFunctor() override{};
virtual return_type func(const input_type & d, Element global_index) = 0;
};
/* -------------------------------------------------------------------------- */
template <typename SubFieldCompute, typename _return_type>
class FieldCompute : public Field {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef typename SubFieldCompute::iterator sub_iterator;
typedef typename SubFieldCompute::types sub_types;
typedef typename sub_types::return_type sub_return_type;
typedef _return_type return_type;
typedef typename sub_types::data_type data_type;
typedef TypeTraits<data_type, return_type, ElementTypeMapArray<data_type> >
types;
class iterator {
public:
iterator(const sub_iterator & it,
ComputeFunctor<sub_return_type, return_type> & func)
: it(it), func(func) {}
bool operator!=(const iterator & it) const { return it.it != this->it; }
iterator operator++() {
++this->it;
return *this;
}
UInt currentGlobalIndex() { return this->it.currentGlobalIndex(); }
return_type operator*() { return func.func(*it, it.getCurrentElement()); }
Element getCurrentElement() { return this->it.getCurrentElement(); }
UInt element_type() { return this->it.element_type(); }
protected:
sub_iterator it;
ComputeFunctor<sub_return_type, return_type> & func;
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FieldCompute(SubFieldCompute & cont, ComputeFunctorInterface & func)
: sub_field(cont),
func(dynamic_cast<ComputeFunctor<sub_return_type, return_type> &>(
func)) {
this->checkHomogeneity();
};
- ~FieldCompute() {
+ ~FieldCompute() override {
delete &(this->sub_field);
delete &(this->func);
}
- virtual void registerToDumper(const std::string & id,
- iohelper::Dumper & dumper) {
+ void registerToDumper(const std::string & id,
+ iohelper::Dumper & dumper) override {
dumper.addElemDataField(id, *this);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
iterator begin() { return iterator(sub_field.begin(), func); }
iterator end() { return iterator(sub_field.end(), func); }
UInt getDim() { return func.getDim(); }
UInt size() {
throw;
// return Functor::size();
return 0;
}
- virtual void checkHomogeneity() { this->homogeneous = true; };
+ void checkHomogeneity() override { this->homogeneous = true; };
iohelper::DataType getDataType() {
return iohelper::getDataType<data_type>();
}
/// get the number of components of the hosted field
- virtual ElementTypeMap<UInt>
+ ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
- ElementKind kind = _ek_not_defined) {
+ ElementKind kind = _ek_not_defined) override {
ElementTypeMap<UInt> nb_components;
const ElementTypeMap<UInt> & old_nb_components =
this->sub_field.getNbComponents(dim, ghost_type, kind);
ElementTypeMap<UInt>::type_iterator tit =
old_nb_components.firstType(dim, ghost_type, kind);
ElementTypeMap<UInt>::type_iterator end =
old_nb_components.lastType(dim, ghost_type, kind);
while (tit != end) {
UInt nb_comp = old_nb_components(*tit, ghost_type);
nb_components(*tit, ghost_type) = func.getNbComponent(nb_comp);
++tit;
}
return nb_components;
};
/// for connection to a FieldCompute
- inline virtual Field * connect(FieldComputeProxy & proxy);
+ inline Field * connect(FieldComputeProxy & proxy) override;
/// for connection to a FieldCompute
- virtual ComputeFunctorInterface * connect(HomogenizerProxy & proxy);
+ ComputeFunctorInterface * connect(HomogenizerProxy & proxy) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
SubFieldCompute & sub_field;
ComputeFunctor<sub_return_type, return_type> & func;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class FieldComputeProxy {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FieldComputeProxy(ComputeFunctorInterface & func) : func(func){};
inline static Field * createFieldCompute(Field * field,
ComputeFunctorInterface & func) {
/// that looks fishy an object passed as a ref and destroyed at their end of
/// the function
FieldComputeProxy compute_proxy(func);
return field->connect(compute_proxy);
}
template <typename T> Field * connectToField(T * ptr) {
if (dynamic_cast<ComputeFunctorOutput<Vector<Real> > *>(&func)) {
return this->connectToFunctor<Vector<Real> >(ptr);
} else if (dynamic_cast<ComputeFunctorOutput<Vector<UInt> > *>(&func)) {
return this->connectToFunctor<Vector<UInt> >(ptr);
}
else if (dynamic_cast<ComputeFunctorOutput<Matrix<UInt> > *>(&func)) {
return this->connectToFunctor<Matrix<UInt> >(ptr);
}
else if (dynamic_cast<ComputeFunctorOutput<Matrix<Real> > *>(&func)) {
return this->connectToFunctor<Matrix<Real> >(ptr);
}
else
throw;
}
template <typename output, typename T> Field * connectToFunctor(T * ptr) {
FieldCompute<T, output> * functor_ptr =
new FieldCompute<T, output>(*ptr, func);
return functor_ptr;
}
template <typename output, typename SubFieldCompute, typename return_type1,
typename return_type2>
Field * connectToFunctor(__attribute__((unused)) FieldCompute<
FieldCompute<SubFieldCompute, return_type1>, return_type2> * ptr) {
throw; // return new FieldCompute<T,output>(*ptr,func);
- return NULL;
+ return nullptr;
}
template <typename output, typename SubFieldCompute, typename return_type1,
typename return_type2, typename return_type3, typename return_type4>
Field * connectToFunctor(__attribute__((unused)) FieldCompute<
FieldCompute<FieldCompute<FieldCompute<SubFieldCompute, return_type1>,
return_type2>,
return_type3>,
return_type4> * ptr) {
throw; // return new FieldCompute<T,output>(*ptr,func);
- return NULL;
+ return nullptr;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
ComputeFunctorInterface & func;
};
/* -------------------------------------------------------------------------- */
/// for connection to a FieldCompute
template <typename SubFieldCompute, typename return_type>
inline Field *
FieldCompute<SubFieldCompute, return_type>::connect(FieldComputeProxy & proxy) {
return proxy.connectToField(this);
}
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
#endif /* __AKANTU_DUMPER_COMPUTE_HH__ */
diff --git a/src/io/dumper/dumper_element_partition.hh b/src/io/dumper/dumper_element_partition.hh
index ff8aa2654..79c8b9ced 100644
--- a/src/io/dumper/dumper_element_partition.hh
+++ b/src/io/dumper/dumper_element_partition.hh
@@ -1,124 +1,124 @@
/**
* @file dumper_element_partition.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Tue Jul 14 2015
*
* @brief ElementPartition field
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
#ifdef AKANTU_IGFEM
# include "dumper_igfem_element_partition.hh"
#endif
/* -------------------------------------------------------------------------- */
template<class types>
class element_partition_field_iterator
: public element_iterator<types, element_partition_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef element_iterator<types, dumper::element_partition_field_iterator> parent;
typedef typename types::return_type return_type;
typedef typename types::array_iterator array_iterator;
typedef typename types::field_type field_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
element_partition_field_iterator(const field_type & field,
const typename field_type::type_iterator & t_it,
const typename field_type::type_iterator & t_it_end,
const array_iterator & array_it,
const array_iterator & array_it_end,
const GhostType ghost_type = _not_ghost) :
parent(field, t_it, t_it_end, array_it, array_it_end, ghost_type) {
prank = Communicator::getStaticCommunicator().whoAmI();
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
return_type operator*() {
return return_type(1, prank);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
UInt prank;
};
/* -------------------------------------------------------------------------- */
template<bool filtered = false>
class ElementPartitionField :
public GenericElementalField<SingleType<UInt,Vector,filtered>,
element_partition_field_iterator> {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
typedef SingleType<UInt,Vector,filtered> types;
typedef element_partition_field_iterator<types> iterator;
typedef GenericElementalField<types,element_partition_field_iterator> parent;
typedef typename types::field_type field_type;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
ElementPartitionField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) :
parent(field, spatial_dimension, ghost_type, element_kind) {
this->homogeneous = true;
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
- UInt getDim() { return 1; }
+ UInt getDim() override { return 1; }
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
diff --git a/src/io/dumper/dumper_generic_elemental_field.hh b/src/io/dumper/dumper_generic_elemental_field.hh
index 383b8b575..ab5ee3886 100644
--- a/src/io/dumper/dumper_generic_elemental_field.hh
+++ b/src/io/dumper/dumper_generic_elemental_field.hh
@@ -1,224 +1,224 @@
/**
* @file dumper_generic_elemental_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Tue Jan 19 2016
*
* @brief Generic interface for elemental fields
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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/>.
*
*/
#ifndef __AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH__
#define __AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_field.hh"
#include "element_type_map_filter.hh"
#include "dumper_element_iterator.hh"
#include "dumper_homogenizing_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <class _types, template <class> class iterator_type>
class GenericElementalField : public Field {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
// check dumper_type_traits.hh for additional information over these types
typedef _types types;
typedef typename types::data_type data_type;
typedef typename types::it_type it_type;
typedef typename types::field_type field_type;
typedef typename types::array_type array_type;
typedef typename types::array_iterator array_iterator;
typedef typename field_type::type_iterator field_type_iterator;
typedef iterator_type<types> iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GenericElementalField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined)
: field(field), spatial_dimension(spatial_dimension),
ghost_type(ghost_type), element_kind(element_kind) {
this->checkHomogeneity();
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the number of components of the hosted field
- virtual ElementTypeMap<UInt>
+ ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
- ElementKind kind = _ek_not_defined) {
+ ElementKind kind = _ek_not_defined) override {
return this->field.getNbComponents(dim, ghost_type, kind);
};
/// return the size of the contained data: i.e. the number of elements ?
virtual UInt size() {
checkHomogeneity();
return this->nb_total_element;
}
/// return the iohelper datatype to be dumped
iohelper::DataType getDataType() {
return iohelper::getDataType<data_type>();
}
protected:
/// return the number of entries per element
UInt getNbDataPerElem(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const {
if (!nb_data_per_elem.exists(type, ghost_type))
return field(type, ghost_type).getNbComponent();
return nb_data_per_elem(type, this->ghost_type);
}
/// check if the same quantity of data for all element types
- virtual void checkHomogeneity();
+ void checkHomogeneity() override;
public:
- virtual void registerToDumper(const std::string & id,
- iohelper::Dumper & dumper) {
+ void registerToDumper(const std::string & id,
+ iohelper::Dumper & dumper) override {
dumper.addElemDataField(id, *this);
};
/// for connection to a FieldCompute
- inline virtual Field * connect(FieldComputeProxy & proxy) {
+ inline Field * connect(FieldComputeProxy & proxy) override {
return proxy.connectToField(this);
}
/// for connection to a Homogenizer
- inline virtual ComputeFunctorInterface * connect(HomogenizerProxy & proxy) {
+ inline ComputeFunctorInterface * connect(HomogenizerProxy & proxy) override {
return proxy.connectToField(this);
};
virtual iterator begin() {
field_type_iterator tit;
field_type_iterator end;
/// type iterators on the elemental field
tit = this->field.firstType(this->spatial_dimension, this->ghost_type,
this->element_kind);
end = this->field.lastType(this->spatial_dimension, this->ghost_type,
this->element_kind);
/// skip all types without data
ElementType type = *tit;
for (; tit != end && this->field(*tit, this->ghost_type).size() == 0;
++tit) {
}
type = *tit;
if (tit == end)
return this->end();
/// getting information for the field of the given type
const array_type & vect = this->field(type, this->ghost_type);
UInt nb_data_per_elem = this->getNbDataPerElem(type);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.size() * nb_component) / nb_data_per_elem;
/// define element-wise iterator
array_iterator it = vect.begin_reinterpret(nb_data_per_elem, size);
array_iterator it_end = vect.end_reinterpret(nb_data_per_elem, size);
/// define data iterator
iterator rit =
iterator(this->field, tit, end, it, it_end, this->ghost_type);
rit.setNbDataPerElem(this->nb_data_per_elem);
return rit;
}
virtual iterator end() {
field_type_iterator tit;
field_type_iterator end;
tit = this->field.firstType(this->spatial_dimension, this->ghost_type,
this->element_kind);
end = this->field.lastType(this->spatial_dimension, this->ghost_type,
this->element_kind);
ElementType type = *tit;
for (; tit != end; ++tit)
type = *tit;
const array_type & vect = this->field(type, this->ghost_type);
UInt nb_data = this->getNbDataPerElem(type);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.size() * nb_component) / nb_data;
array_iterator it = vect.end_reinterpret(nb_data, size);
iterator rit = iterator(this->field, end, end, it, it, this->ghost_type);
rit.setNbDataPerElem(this->nb_data_per_elem);
return rit;
}
virtual UInt getDim() {
if (this->homogeneous) {
field_type_iterator tit = this->field.firstType(
this->spatial_dimension, this->ghost_type, this->element_kind);
return this->getNbDataPerElem(*tit);
}
throw;
return 0;
}
- void setNbDataPerElem(const ElementTypeMap<UInt> & nb_data) {
+ void setNbDataPerElem(const ElementTypeMap<UInt> & nb_data) override {
nb_data_per_elem = nb_data;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the ElementTypeMapArray embedded in the field
const field_type & field;
/// total number of elements
UInt nb_total_element;
/// the spatial dimension of the problem
UInt spatial_dimension;
/// whether this is a ghost field or not (for type selection)
GhostType ghost_type;
/// The element kind to operate on
ElementKind element_kind;
/// The number of data per element type
ElementTypeMap<UInt> nb_data_per_elem;
};
/* -------------------------------------------------------------------------- */
#include "dumper_generic_elemental_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__ } // akantu
#endif /* __AKANTU_DUMPER_GENERIC_ELEMENTAL_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_homogenizing_field.hh b/src/io/dumper/dumper_homogenizing_field.hh
index ad50139dd..443468e72 100644
--- a/src/io/dumper/dumper_homogenizing_field.hh
+++ b/src/io/dumper/dumper_homogenizing_field.hh
@@ -1,217 +1,216 @@
/**
* @file dumper_homogenizing_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Tue Jul 14 2015
*
* @brief description of field homogenizing field
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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/>.
*
*/
#ifndef __AKANTU_DUMPER_HOMOGENIZING_FIELD_HH__
#define __AKANTU_DUMPER_HOMOGENIZING_FIELD_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_compute.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <typename type>
inline type typeConverter(const type & input,
- __attribute__((unused)) Vector<typename type::value_type> & res,
+ __attribute__((unused))
+ Vector<typename type::value_type> & res,
__attribute__((unused)) UInt nb_data) {
throw;
return input;
}
/* -------------------------------------------------------------------------- */
template <typename type>
inline Matrix<type> typeConverter(const Matrix<type> & input,
Vector<type> & res, UInt nb_data) {
Matrix<type> tmp(res.storage(), input.rows(), nb_data / input.rows());
Matrix<type> tmp2(tmp, true);
return tmp2;
}
/* -------------------------------------------------------------------------- */
template <typename type>
-inline Vector<type>
-typeConverter(__attribute__((unused)) const Vector<type> & input,
- __attribute__((unused)) Vector<type> & res,
- __attribute__((unused)) UInt nb_data) {
+inline Vector<type> typeConverter(__attribute__((unused))
+ const Vector<type> & input,
+ __attribute__((unused)) Vector<type> & res,
+ __attribute__((unused)) UInt nb_data) {
return res;
}
/* -------------------------------------------------------------------------- */
template <typename type>
class AvgHomogenizingFunctor : public ComputeFunctor<type, type> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
typedef typename type::value_type value_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
AvgHomogenizingFunctor(ElementTypeMap<UInt> & nb_datas) {
ElementTypeMap<UInt>::type_iterator tit = nb_datas.firstType();
ElementTypeMap<UInt>::type_iterator end = nb_datas.lastType();
nb_data = nb_datas(*tit);
for (; tit != end; ++tit)
if (nb_data != nb_datas(*tit))
throw;
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
- virtual type func(const type & d,
- __attribute__((unused)) Element global_index) {
-
+ type func(const type & d, Element /*global_index*/) {
Vector<value_type> res(this->nb_data);
if (d.size() % this->nb_data)
throw;
UInt nb_to_average = d.size() / this->nb_data;
value_type * ptr = d.storage();
for (UInt i = 0; i < nb_to_average; ++i) {
Vector<value_type> tmp(ptr, this->nb_data);
res += tmp;
ptr += this->nb_data;
}
res /= nb_to_average;
return typeConverter(d, res, this->nb_data);
};
- UInt getDim() { return nb_data; };
- UInt getNbComponent(__attribute__((unused)) UInt old_nb_comp) { throw; };
+ UInt getDim() override { return nb_data; };
+ UInt getNbComponent(UInt /*old_nb_comp*/) { throw; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// The size of data: i.e. the size of the vector to be returned
UInt nb_data;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class HomogenizerProxy {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
HomogenizerProxy(){};
public:
inline static ComputeFunctorInterface * createHomogenizer(Field & field);
template <typename T>
inline ComputeFunctorInterface * connectToField(T * field) {
ElementTypeMap<UInt> nb_components = field->getNbComponents();
typedef typename T::types::return_type ret_type;
return this->instantiateHomogenizer<ret_type>(nb_components);
}
template <typename ret_type>
inline ComputeFunctorInterface *
instantiateHomogenizer(ElementTypeMap<UInt> & nb_components);
};
/* -------------------------------------------------------------------------- */
template <typename ret_type>
inline ComputeFunctorInterface *
HomogenizerProxy::instantiateHomogenizer(ElementTypeMap<UInt> & nb_components) {
typedef dumper::AvgHomogenizingFunctor<ret_type> Homogenizer;
Homogenizer * foo = new Homogenizer(nb_components);
return foo;
}
template <>
inline ComputeFunctorInterface *
-HomogenizerProxy::instantiateHomogenizer<Vector<iohelper::ElemType> >(
+HomogenizerProxy::instantiateHomogenizer<Vector<iohelper::ElemType>>(
__attribute__((unused)) ElementTypeMap<UInt> & nb_components) {
throw;
- return NULL;
+ return nullptr;
}
/* -------------------------------------------------------------------------- */
/// for connection to a FieldCompute
template <typename SubFieldCompute, typename return_type>
inline ComputeFunctorInterface *
FieldCompute<SubFieldCompute, return_type>::connect(HomogenizerProxy & proxy) {
return proxy.connectToField(this);
}
/* -------------------------------------------------------------------------- */
inline ComputeFunctorInterface *
HomogenizerProxy::createHomogenizer(Field & field) {
HomogenizerProxy homogenizer_proxy;
return field.connect(homogenizer_proxy);
}
/* -------------------------------------------------------------------------- */
// inline ComputeFunctorInterface & createHomogenizer(Field & field){
// HomogenizerProxy::createHomogenizer(field);
// throw;
// ComputeFunctorInterface * ptr = NULL;
// return *ptr;
// }
// /* --------------------------------------------------------------------------
// */
__END_AKANTU_DUMPER__
-} // akantu
+} // namespace akantu
#endif /* __AKANTU_DUMPER_HOMOGENIZING_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_material_padders.hh b/src/io/dumper/dumper_material_padders.hh
index b19377c25..c5a0d1700 100644
--- a/src/io/dumper/dumper_material_padders.hh
+++ b/src/io/dumper/dumper_material_padders.hh
@@ -1,297 +1,298 @@
/**
* @file dumper_material_padders.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Fri Mar 27 2015
*
* @brief Material padders for plane stress/ plane strain
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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/>.
*
*/
#ifndef __AKANTU_DUMPER_MATERIAL_PADDERS_HH__
#define __AKANTU_DUMPER_MATERIAL_PADDERS_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_padding_helper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
class MaterialFunctor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialFunctor(const SolidMechanicsModel & model) :
model(model),
material_index(model.getMaterialByElement()),
nb_data_per_element("nb_data_per_element", model.getID(), model.getMemoryID()),
spatial_dimension(model.getSpatialDimension()){}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
/// return the material from the global element index
const Material & getMaterialFromGlobalIndex(Element global_index) {
UInt index = global_index.element;
UInt material_id = material_index(global_index.type)(index);
const Material & material = model.getMaterial(material_id);
return material;
}
/// return the type of the element from global index
ElementType getElementTypeFromGlobalIndex(Element global_index) {
return global_index.type;
}
protected:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// all material padders probably need access to solid mechanics model
const SolidMechanicsModel & model;
/// they also need an access to the map from global ids to material id and
/// local ids
const ElementTypeMapArray<UInt> & material_index;
/// the number of data per element
const ElementTypeMapArray<UInt> nb_data_per_element;
UInt spatial_dimension;
};
/* -------------------------------------------------------------------------- */
template <class T, class R>
class MaterialPadder : public MaterialFunctor,
public PadderGeneric<Vector<T>, R> {
public:
MaterialPadder(const SolidMechanicsModel & model) : MaterialFunctor(model) {}
};
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
class StressPadder : public MaterialPadder<Real, Matrix<Real> > {
public:
StressPadder(const SolidMechanicsModel & model)
: MaterialPadder<Real, Matrix<Real> >(model) {
this->setPadding(3, 3);
}
- inline Matrix<Real> func(const Vector<Real> & in, Element global_element_id) {
+ inline Matrix<Real> func(const Vector<Real> & in,
+ Element global_element_id) override {
UInt nrows = spatial_dimension;
UInt ncols = in.size() / nrows;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> stress = this->pad(in, nrows, ncols, nb_data);
const Material & material =
this->getMaterialFromGlobalIndex(global_element_id);
bool plane_strain = true;
if (spatial_dimension == 2)
plane_strain = !((bool) material.getParam("Plane_Stress"));
if (plane_strain) {
Real nu = material.getParam("nu");
for (UInt d = 0; d < nb_data; ++d) {
stress(2, 2 + 3 * d) =
nu * (stress(0, 0 + 3 * d) + stress(1, 1 + 3 * d));
}
}
return stress;
}
- UInt getDim() { return 9; };
+ UInt getDim() override { return 9; };
- UInt getNbComponent(__attribute__((unused)) UInt old_nb_comp) {
+ UInt getNbComponent(UInt /*old_nb_comp*/) {
return this->getDim();
};
};
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
class StrainPadder : public MaterialFunctor,
public PadderGeneric<Matrix<Real>, Matrix<Real> > {
public:
StrainPadder(const SolidMechanicsModel & model) : MaterialFunctor(model) {
this->setPadding(3, 3);
}
- inline Matrix<Real> func(const Matrix<Real> & in, Element global_element_id) {
+ inline Matrix<Real> func(const Matrix<Real> & in,
+ Element global_element_id) override {
UInt nrows = spatial_dimension;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> strain = this->pad(in, nb_data);
const Material & material =
this->getMaterialFromGlobalIndex(global_element_id);
bool plane_stress = material.getParam("Plane_Stress");
if (plane_stress) {
Real nu = material.getParam("nu");
for (UInt d = 0; d < nb_data; ++d) {
strain(2, 2 + 3 * d) =
nu / (nu - 1) * (strain(0, 0 + 3 * d) + strain(1, 1 + 3 * d));
}
}
return strain;
}
- UInt getDim() { return 9; };
+ UInt getDim() override { return 9; };
- UInt getNbComponent(__attribute__((unused)) UInt old_nb_comp) {
+ UInt getNbComponent(UInt /*old_nb_comp*/) {
return this->getDim();
};
};
/* -------------------------------------------------------------------------- */
template <bool green_strain>
class ComputeStrain : public MaterialFunctor,
public ComputeFunctor<Vector<Real>, Matrix<Real> > {
public:
ComputeStrain(const SolidMechanicsModel & model) : MaterialFunctor(model) {}
- inline Matrix<Real> func(const Vector<Real> & in,
- __attribute__((unused)) Element global_element_id) {
+ inline Matrix<Real> func(const Vector<Real> & in, Element /*global_element_id*/) {
UInt nrows = spatial_dimension;
UInt ncols = in.size() / nrows;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> ret_all_strain(nrows, ncols);
Tensor3<Real> all_grad_u(in.storage(), nrows, nrows, nb_data);
Tensor3<Real> all_strain(ret_all_strain.storage(), nrows, nrows, nb_data);
for (UInt d = 0; d < nb_data; ++d) {
Matrix<Real> grad_u = all_grad_u(d);
Matrix<Real> strain = all_strain(d);
if (spatial_dimension == 2) {
if (green_strain)
Material::gradUToGreenStrain<2>(grad_u, strain);
else
Material::gradUToEpsilon<2>(grad_u, strain);
} else if (spatial_dimension == 3) {
if (green_strain)
Material::gradUToGreenStrain<3>(grad_u, strain);
else
Material::gradUToEpsilon<3>(grad_u, strain);
}
}
return ret_all_strain;
}
- UInt getDim() { return spatial_dimension * spatial_dimension; };
+ UInt getDim() override { return spatial_dimension * spatial_dimension; };
- UInt getNbComponent(__attribute__((unused)) UInt old_nb_comp) {
+ UInt getNbComponent(UInt /*old_nb_comp*/) {
return this->getDim();
};
};
/* -------------------------------------------------------------------------- */
template <bool green_strain>
class ComputePrincipalStrain
: public MaterialFunctor,
public ComputeFunctor<Vector<Real>, Matrix<Real> > {
public:
ComputePrincipalStrain(const SolidMechanicsModel & model)
: MaterialFunctor(model) {}
inline Matrix<Real> func(const Vector<Real> & in,
- __attribute__((unused)) Element global_element_id) {
+ Element /*global_element_id*/) {
UInt nrows = spatial_dimension;
UInt nb_data = in.size() / (nrows * nrows);
Matrix<Real> ret_all_strain(nrows, nb_data);
Tensor3<Real> all_grad_u(in.storage(), nrows, nrows, nb_data);
Matrix<Real> strain(nrows, nrows);
for (UInt d = 0; d < nb_data; ++d) {
Matrix<Real> grad_u = all_grad_u(d);
if (spatial_dimension == 2) {
if (green_strain)
Material::gradUToGreenStrain<2>(grad_u, strain);
else
Material::gradUToEpsilon<2>(grad_u, strain);
} else if (spatial_dimension == 3) {
if (green_strain)
Material::gradUToGreenStrain<3>(grad_u, strain);
else
Material::gradUToEpsilon<3>(grad_u, strain);
}
Vector<Real> principal_strain(ret_all_strain(d));
strain.eig(principal_strain);
}
return ret_all_strain;
}
- UInt getDim() { return spatial_dimension; };
+ UInt getDim() override { return spatial_dimension; };
- UInt getNbComponent(__attribute__((unused)) UInt old_nb_comp) {
+ UInt getNbComponent(UInt /*old_nb_comp*/) {
return this->getDim();
};
};
/* -------------------------------------------------------------------------- */
class ComputeVonMisesStress
: public MaterialFunctor,
public ComputeFunctor<Vector<Real>, Vector<Real> > {
public:
ComputeVonMisesStress(const SolidMechanicsModel & model)
: MaterialFunctor(model) {}
inline Vector<Real> func(const Vector<Real> & in,
- __attribute__((unused)) Element global_element_id) {
+ Element /*global_element_id*/) {
UInt nrows = spatial_dimension;
UInt nb_data = in.size() / (nrows * nrows);
Vector<Real> von_mises_stress(nb_data);
Matrix<Real> deviatoric_stress(3, 3);
for (UInt d = 0; d < nb_data; ++d) {
Matrix<Real> cauchy_stress(in.storage() + d * nrows * nrows, nrows,
nrows);
von_mises_stress(d) = Material::stressToVonMises(cauchy_stress);
}
return von_mises_stress;
}
- UInt getDim() { return 1; };
+ UInt getDim() override { return 1; };
- UInt getNbComponent(__attribute__((unused)) UInt old_nb_comp) {
+ UInt getNbComponent(UInt /*old_nb_comp*/) {
return this->getDim();
};
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
} // akantu
#endif /* __AKANTU_DUMPER_MATERIAL_PADDERS_HH__ */
diff --git a/src/io/dumper/dumper_nodal_field.hh b/src/io/dumper/dumper_nodal_field.hh
index c462adc14..e01599dcf 100644
--- a/src/io/dumper/dumper_nodal_field.hh
+++ b/src/io/dumper/dumper_nodal_field.hh
@@ -1,240 +1,249 @@
/**
* @file dumper_nodal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Oct 26 2012
* @date last modification: Tue Jan 06 2015
*
* @brief Description of nodal fields
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
#ifndef __AKANTU_DUMPER_NODAL_FIELD_HH__
#define __AKANTU_DUMPER_NODAL_FIELD_HH__
#include "dumper_field.hh"
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
namespace akantu {
__BEGIN_AKANTU_DUMPER__
// This represents a iohelper compatible field
template<typename T, bool filtered = false,
class Container = Array<T>, class Filter = Array<UInt> >
class NodalField;
/* -------------------------------------------------------------------------- */
template<typename T, class Container, class Filter>
class NodalField<T, false, Container, Filter> : public dumper::Field {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
/// associated iterator with any nodal field (non filetered)
class iterator : public iohelper::iterator< T, iterator, Vector<T> > {
public:
iterator(T * vect, UInt offset, UInt n, UInt stride,
- __attribute__ ((unused)) const UInt * filter = NULL) :
+ __attribute__((unused)) const UInt * filter = nullptr)
+ :
- internal_it(vect), offset(offset), n(n), stride(stride) {}
+ internal_it(vect), offset(offset), n(n), stride(stride) {}
+
+ bool operator!=(const iterator & it) const override {
+ return internal_it != it.internal_it;
+ }
+ iterator & operator++() override {
+ internal_it += offset;
+ return *this;
+ };
+ Vector<T> operator*() override {
+ return Vector<T>(internal_it + stride, n);
+ };
- bool operator!=(const iterator & it) const { return internal_it != it.internal_it; }
- iterator & operator++() { internal_it += offset; return *this; };
- Vector<T> operator* (){ return Vector<T>(internal_it + stride, n); };
private:
T * internal_it;
UInt offset, n, stride;
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
NodalField(const Container & field, UInt n = 0, UInt stride = 0,
__attribute__ ((unused)) const Filter * filter = NULL) :
field(field), n(n), stride(stride), padding(0) {
- AKANTU_DEBUG_ASSERT(filter == NULL, "Filter passed to unfiltered NodalField!");
+ AKANTU_DEBUG_ASSERT(filter == nullptr,
+ "Filter passed to unfiltered NodalField!");
if(n == 0) { this->n = field.getNbComponent() - stride; }
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
-
- virtual void registerToDumper(const std::string & id,
- iohelper::Dumper & dumper) {
+
+ void registerToDumper(const std::string & id,
+ iohelper::Dumper & dumper) override {
dumper.addNodeDataField(id, *this);
}
inline iterator begin() {
return iterator(field.storage(), field.getNbComponent(), n, stride);
}
inline iterator end () {
return iterator(field.storage() + field.getNbComponent()*field.size(),
field.getNbComponent(), n, stride);
}
- bool isHomogeneous() { return true; }
- void checkHomogeneity() { this->homogeneous = true; }
+ bool isHomogeneous() override { return true; }
+ void checkHomogeneity() override { this->homogeneous = true; }
virtual UInt getDim() {
if(this->padding) return this->padding;
else return n;
}
void setPadding(UInt padding){this->padding = padding;}
UInt size() { return field.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Container & field;
UInt n, stride;
UInt padding;
};
/* -------------------------------------------------------------------------- */
template<typename T, class Container, class Filter>
class NodalField<T, true, Container, Filter> : public dumper::Field {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
class iterator : public iohelper::iterator< T, iterator, Vector<T> > {
public:
iterator(T * const vect, UInt _offset, UInt _n,
UInt _stride, const UInt * filter) :
internal_it(vect), offset(_offset), n(_n), stride(_stride),
filter(filter) {}
- bool operator!=(const iterator & it) const {
+ bool operator!=(const iterator & it) const override {
return filter != it.filter;
}
- iterator & operator++() {
+ iterator & operator++() override {
++filter;
return *this;
}
- Vector<T> operator* () {
+ Vector<T> operator*() override {
return Vector<T>(internal_it + *(filter)*offset + stride, n);
}
private:
T * const internal_it;
UInt offset, n, stride;
const UInt * filter;
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
NodalField(const Container & _field,
UInt _n = 0, UInt _stride = 0,
const Filter * filter = NULL)
: field(_field), n(_n), stride(_stride), filter(filter), padding(0) {
- AKANTU_DEBUG_ASSERT(this->filter != NULL,
- "No filter passed to filtered NodalField!");
+ AKANTU_DEBUG_ASSERT(this->filter != nullptr,
+ "No filter passed to filtered NodalField!");
AKANTU_DEBUG_ASSERT(this->filter->getNbComponent()==1,
"Multi-component filter given to NodalField ("
<< this->filter->getNbComponent()
<< " components detected, sould be 1");
if(n == 0) {
this->n = field.getNbComponent() - stride;
}
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
-
- virtual void registerToDumper(const std::string & id, iohelper::Dumper & dumper) {
+
+ void registerToDumper(const std::string & id,
+ iohelper::Dumper & dumper) override {
dumper.addNodeDataField(id, *this);
}
inline iterator begin() {
return iterator(field.storage(), field.getNbComponent(),
n, stride, filter->storage());
}
inline iterator end() {
return iterator(field.storage(), field.getNbComponent(),
n, stride, filter->storage()+filter->size());
}
- bool isHomogeneous() {
- return true;
- }
- void checkHomogeneity() { this->homogeneous = true; }
+ bool isHomogeneous() override { return true; }
+ void checkHomogeneity() override { this->homogeneous = true; }
virtual UInt getDim() {
if(this->padding) return this->padding;
else return n;
}
void setPadding(UInt padding){this->padding = padding;}
UInt size() {
return filter->size();
}
iohelper::DataType getDataType() {
return iohelper::getDataType<T>();
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Container & field;
UInt n, stride;
const Filter * filter;
UInt padding;
};
__END_AKANTU_DUMPER__
} // akantu
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_DUMPER_NODAL_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_paraview.hh b/src/io/dumper/dumper_paraview.hh
index 448fd2ee3..eabc41a88 100644
--- a/src/io/dumper/dumper_paraview.hh
+++ b/src/io/dumper/dumper_paraview.hh
@@ -1,74 +1,74 @@
/**
* @file dumper_paraview.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief Dumper Paraview using IOHelper
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DUMPER_PARAVIEW_HH__
#define __AKANTU_DUMPER_PARAVIEW_HH__
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class DumperParaview : public DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperParaview(const std::string & filename,
const std::string & directory = "./paraview",
bool parallel = true);
- virtual ~DumperParaview();
+ ~DumperParaview() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
// void dump();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
- void setBaseName(const std::string & basename);
+ void setBaseName(const std::string & basename) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // akantu
#endif /* __AKANTU_DUMPER_PARAVIEW_HH__ */
diff --git a/src/io/mesh_io/mesh_io_abaqus.hh b/src/io/mesh_io/mesh_io_abaqus.hh
index 877d87efc..0f6beec0a 100644
--- a/src/io/mesh_io/mesh_io_abaqus.hh
+++ b/src/io/mesh_io/mesh_io_abaqus.hh
@@ -1,60 +1,60 @@
/**
* @file mesh_io_abaqus.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
* @date last modification: Tue Jun 30 2015
*
* @brief read a mesh from an abaqus input file
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "mesh_io.hh"
#include "mesh_accessor.hh"
#ifndef __AKANTU_MESH_IO_ABAQUS_HH__
#define __AKANTU_MESH_IO_ABAQUS_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
class MeshIOAbaqus : public MeshIO {
public:
MeshIOAbaqus();
- virtual ~MeshIOAbaqus();
+ ~MeshIOAbaqus() override;
/// read a mesh from the file
- virtual void read(const std::string & filename, Mesh & mesh);
+ void read(const std::string & filename, Mesh & mesh) override;
/// write a mesh to a file
// virtual void write(const std::string & filename, const Mesh & mesh);
private:
/// correspondence between msh element types and akantu element types
std::map<std::string, ElementType> _abaqus_to_akantu_element_types;
};
} // akantu
#endif /* __AKANTU_MESH_IO_ABAQUS_HH__ */
diff --git a/src/io/mesh_io/mesh_io_diana.cc b/src/io/mesh_io/mesh_io_diana.cc
index bd32eed14..d2037f66c 100644
--- a/src/io/mesh_io/mesh_io_diana.cc
+++ b/src/io/mesh_io/mesh_io_diana.cc
@@ -1,604 +1,604 @@
/**
* @file mesh_io_diana.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
*
* @date creation: Sat Mar 26 2011
* @date last modification: Thu Jan 21 2016
*
* @brief handles diana meshes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_io_diana.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <string.h>
/* -------------------------------------------------------------------------- */
#include <stdio.h>
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIODiana::MeshIODiana() {
canReadSurface = true;
canReadExtendedData = true;
_diana_to_akantu_element_types["T9TM"] = _triangle_3;
_diana_to_akantu_element_types["CT6CM"] = _triangle_6;
_diana_to_akantu_element_types["Q12TM"] = _quadrangle_4;
_diana_to_akantu_element_types["CQ8CM"] = _quadrangle_8;
_diana_to_akantu_element_types["TP18L"] = _pentahedron_6;
_diana_to_akantu_element_types["CTP45"] = _pentahedron_15;
_diana_to_akantu_element_types["TE12L"] = _tetrahedron_4;
_diana_to_akantu_element_types["HX24L"] = _hexahedron_8;
_diana_to_akantu_element_types["CHX60"] = _hexahedron_20;
_diana_to_akantu_mat_prop["YOUNG"] = "E";
_diana_to_akantu_mat_prop["DENSIT"] = "rho";
_diana_to_akantu_mat_prop["POISON"] = "nu";
std::map<std::string, ElementType>::iterator it;
for (it = _diana_to_akantu_element_types.begin();
it != _diana_to_akantu_element_types.end(); ++it) {
UInt nb_nodes = Mesh::getNbNodesPerElement(it->second);
UInt * tmp = new UInt[nb_nodes];
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->second) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 8;
tmp[2] = 0;
tmp[3] = 6;
tmp[4] = 1;
tmp[5] = 7;
tmp[6] = 11;
tmp[7] = 9;
tmp[8] = 10;
tmp[9] = 5;
tmp[10] = 14;
tmp[11] = 3;
tmp[12] = 12;
tmp[13] = 4;
tmp[14] = 13;
break;
case _hexahedron_20:
tmp[0] = 5;
tmp[1] = 16;
tmp[2] = 4;
tmp[3] = 19;
tmp[4] = 7;
tmp[5] = 18;
tmp[6] = 6;
tmp[7] = 17;
tmp[8] = 13;
tmp[9] = 12;
tmp[10] = 15;
tmp[11] = 14;
tmp[12] = 1;
tmp[13] = 8;
tmp[14] = 0;
tmp[15] = 11;
tmp[16] = 3;
tmp[17] = 10;
tmp[18] = 2;
tmp[19] = 9;
break;
default:
// nothing to change
break;
}
_read_order[it->second] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIODiana::~MeshIODiana() {}
/* -------------------------------------------------------------------------- */
inline void my_getline(std::ifstream & infile, std::string & line) {
std::getline(infile, line); // read the line
size_t pos = line.find("\r"); /// remove the extra \r if needed
line = line.substr(0, pos);
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::read(const std::string & filename, Mesh & mesh) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt first_node_number = std::numeric_limits<UInt>::max();
diana_element_number_to_elements.clear();
if (!infile.good()) {
AKANTU_DEBUG_ERROR("Cannot open file " << filename);
}
while (infile.good()) {
my_getline(infile, line);
/// read all nodes
if (line == "'COORDINATES'") {
line = readCoordinates(infile, mesh, first_node_number);
}
/// read all elements
if (line == "'ELEMENTS'") {
line = readElements(infile, mesh, first_node_number);
}
/// read the material properties and write a .dat file
if (line == "'MATERIALS'") {
line = readMaterial(infile, filename);
}
/// read the material properties and write a .dat file
if (line == "'GROUPS'") {
line = readGroups(infile, mesh, first_node_number);
}
}
infile.close();
mesh_accessor.setNbGlobalNodes(mesh.getNbNodes());
MeshUtils::fillElementToSubElementsData(mesh);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshIODiana::write(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) const Mesh & mesh) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readCoordinates(std::ifstream & infile, Mesh & mesh,
UInt & first_node_number) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
std::string line;
UInt index;
Vector<Real> coord(3);
do {
my_getline(infile, line);
if ("'ELEMENTS'" == line)
break;
std::stringstream sstr_node(line);
sstr_node >> index >> coord(0) >> coord(1) >> coord(2);
first_node_number = first_node_number < index ? first_node_number : index;
nodes.push_back(coord);
} while (true);
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
UInt MeshIODiana::readInterval(std::stringstream & line,
std::set<UInt> & interval) {
UInt first;
line >> first;
if (line.fail()) {
return 0;
}
interval.insert(first);
UInt second;
int dash;
dash = line.get();
if (dash == '-') {
line >> second;
interval.insert(second);
return 2;
}
if (line.fail())
line.clear(std::ios::eofbit); // in case of get at end of the line
else
line.unget();
return 1;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readGroups(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
std::string line;
my_getline(infile, line);
bool reading_nodes_group = false;
while (line != "'SUPPORTS'") {
if (line == "NODES") {
reading_nodes_group = true;
my_getline(infile, line);
}
if (line == "ELEMEN") {
reading_nodes_group = false;
my_getline(infile, line);
}
std::stringstream * str = new std::stringstream(line);
UInt id;
std::string name;
char c;
*str >> id >> name >> c;
Array<UInt> * list_ids = new Array<UInt>(0, 1, name);
UInt s = 1;
bool end = false;
while (!end) {
while (!str->eof() && s != 0) {
std::set<UInt> interval;
s = readInterval(*str, interval);
std::set<UInt>::iterator it = interval.begin();
if (s == 1)
list_ids->push_back(*it);
if (s == 2) {
UInt first = *it;
++it;
UInt second = *it;
for (UInt i = first; i <= second; ++i) {
list_ids->push_back(i);
}
}
}
if (str->fail())
end = true;
else {
my_getline(infile, line);
delete str;
str = new std::stringstream(line);
}
}
delete str;
if (reading_nodes_group) {
NodeGroup & ng = mesh.createNodeGroup(name);
for (UInt i = 0; i < list_ids->size(); ++i) {
UInt node = (*list_ids)(i)-first_node_number;
ng.add(node, false);
}
delete list_ids;
} else {
ElementGroup & eg = mesh.createElementGroup(name);
for (UInt i = 0; i < list_ids->size(); ++i) {
Element & elem = diana_element_number_to_elements[(*list_ids)(i)];
if (elem.type != _not_defined)
eg.add(elem, false, false);
}
eg.optimize();
delete list_ids;
}
my_getline(infile, line);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readElements(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
std::string line;
my_getline(infile, line);
if ("CONNECTIVITY" == line) {
line = readConnectivity(infile, mesh, first_node_number);
}
/// read the line corresponding to the materials
if ("MATERIALS" == line) {
line = readMaterialElement(infile, mesh);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readConnectivity(std::ifstream & infile, Mesh & mesh,
UInt first_node_number) {
AKANTU_DEBUG_IN();
MeshAccessor mesh_accessor(mesh);
Int index;
std::string lline;
std::string diana_type;
ElementType akantu_type, akantu_type_old = _not_defined;
- Array<UInt> * connectivity = NULL;
+ Array<UInt> * connectivity = nullptr;
UInt node_per_element = 0;
Element elem;
- UInt * read_order = NULL;
+ UInt * read_order = nullptr;
while (1) {
my_getline(infile, lline);
// std::cerr << lline << std::endl;
std::stringstream sstr_elem(lline);
if (lline == "MATERIALS")
break;
/// traiter les coordonnees
sstr_elem >> index;
sstr_elem >> diana_type;
akantu_type = _diana_to_akantu_element_types[diana_type];
if (akantu_type == _not_defined)
continue;
if (akantu_type != akantu_type_old) {
connectivity = &(mesh_accessor.getConnectivity(akantu_type));
node_per_element = connectivity->getNbComponent();
akantu_type_old = akantu_type;
read_order = _read_order[akantu_type];
}
Vector<UInt> local_connect(node_per_element);
// used if element is written on two lines
UInt j_last = 0;
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
// check s'il y a pas plus rien après un certain point
if (sstr_elem.fail()) {
sstr_elem.clear();
sstr_elem.ignore();
break;
}
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
j_last = j;
}
// check if element is written in two lines
if (j_last != (node_per_element - 1)) {
// if this is the case, read on more line
my_getline(infile, lline);
std::stringstream sstr_elem(lline);
for (UInt j = (j_last + 1); j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
}
}
connectivity->push_back(local_connect);
elem.type = akantu_type;
elem.element = connectivity->size() - 1;
diana_element_number_to_elements[index] = elem;
akantu_number_to_diana_number[elem] = index;
}
AKANTU_DEBUG_OUT();
return lline;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readMaterialElement(std::ifstream & infile,
Mesh & mesh) {
AKANTU_DEBUG_IN();
std::string line;
std::stringstream sstr_tag_name;
sstr_tag_name << "tag_" << 0;
Mesh::type_iterator it = mesh.firstType();
Mesh::type_iterator end = mesh.lastType();
for (; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it);
mesh.getDataPointer<UInt>("material", *it, _not_ghost, 1)
.resize(nb_element);
}
my_getline(infile, line);
while (line != "'MATERIALS'") {
line =
line.substr(line.find('/') + 1,
std::string::npos); // erase the first slash / of the line
char tutu[250];
strcpy(tutu, line.c_str());
AKANTU_DEBUG_WARNING("reading line " << line);
Array<UInt> temp_id(0, 2);
UInt mat;
while (true) {
std::stringstream sstr_intervals_elements(line);
Vector<UInt> id(2);
char temp;
while (sstr_intervals_elements.good()) {
sstr_intervals_elements >> id(0) >> temp >> id(1); // >> "/" >> mat;
if (!sstr_intervals_elements.fail())
temp_id.push_back(id);
}
if (sstr_intervals_elements.fail()) {
sstr_intervals_elements.clear();
sstr_intervals_elements.ignore();
sstr_intervals_elements >> mat;
break;
}
my_getline(infile, line);
}
// loop over elements
// UInt * temp_id_val = temp_id.storage();
for (UInt i = 0; i < temp_id.size(); ++i)
for (UInt j = temp_id(i, 0); j <= temp_id(i, 1); ++j) {
Element & element = diana_element_number_to_elements[j];
if (element.type == _not_defined)
continue;
UInt elem = element.element;
ElementType type = element.type;
Array<UInt> & data =
mesh.getDataPointer<UInt>("material", type, _not_ghost);
data(elem) = mat;
}
my_getline(infile, line);
}
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
std::string MeshIODiana::readMaterial(std::ifstream & infile,
const std::string & filename) {
AKANTU_DEBUG_IN();
std::stringstream mat_file_name;
mat_file_name << "material_" << filename;
std::ofstream material_file;
material_file.open(mat_file_name.str().c_str()); // mat_file_name.str());
UInt mat_index;
std::string line;
bool first_mat = true;
bool end = false;
UInt mat_id = 0;
typedef std::map<std::string, Real> MatProp;
MatProp mat_prop;
do {
my_getline(infile, line);
std::stringstream sstr_material(line);
if (("'GROUPS'" == line) || ("'END'" == line)) {
if (!mat_prop.empty()) {
material_file << "material elastic [" << std::endl;
material_file << "\tname = material" << ++mat_id << std::endl;
for (MatProp::iterator it = mat_prop.begin(); it != mat_prop.end();
++it)
material_file << "\t" << it->first << " = " << it->second
<< std::endl;
material_file << "]" << std::endl;
mat_prop.clear();
}
end = true;
} else {
/// traiter les caractéristiques des matériaux
sstr_material >> mat_index;
if (!sstr_material.fail()) {
if (!first_mat) {
if (!mat_prop.empty()) {
material_file << "material elastic [" << std::endl;
material_file << "\tname = material" << ++mat_id << std::endl;
for (MatProp::iterator it = mat_prop.begin(); it != mat_prop.end();
++it)
material_file << "\t" << it->first << " = " << it->second
<< std::endl;
material_file << "]" << std::endl;
mat_prop.clear();
}
}
first_mat = false;
} else {
sstr_material.clear();
}
std::string prop_name;
sstr_material >> prop_name;
std::map<std::string, std::string>::iterator it;
it = _diana_to_akantu_mat_prop.find(prop_name);
if (it != _diana_to_akantu_mat_prop.end()) {
Real value;
sstr_material >> value;
mat_prop[it->second] = value;
} else {
AKANTU_DEBUG_INFO("In material reader, property " << prop_name
<< "not recognized");
}
}
} while (!end);
AKANTU_DEBUG_OUT();
return line;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_diana.hh b/src/io/mesh_io/mesh_io_diana.hh
index 7ddcbed5c..65004a5cc 100644
--- a/src/io/mesh_io/mesh_io_diana.hh
+++ b/src/io/mesh_io/mesh_io_diana.hh
@@ -1,107 +1,107 @@
/**
* @file mesh_io_diana.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Alodie Schneuwly <alodie.schneuwly@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Nov 19 2015
*
* @brief diana mesh reader description
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_IO_DIANA_HH__
#define __AKANTU_MESH_IO_DIANA_HH__
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIODiana : public MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIODiana();
- virtual ~MeshIODiana();
+ ~MeshIODiana() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
- virtual void read(const std::string & filename, Mesh & mesh);
+ void read(const std::string & filename, Mesh & mesh) override;
/// write a mesh to a file
- virtual void write(const std::string & filename, const Mesh & mesh);
+ void write(const std::string & filename, const Mesh & mesh) override;
private:
std::string readCoordinates(std::ifstream & infile, Mesh & mesh,
UInt & first_node_number);
std::string readElements(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readGroups(std::ifstream & infile, Mesh & mesh, UInt first_node_number);
std::string readConnectivity(std::ifstream & infile, Mesh & mesh,
UInt first_node_number);
std::string readMaterialElement(std::ifstream & infile, Mesh & mesh);
std::string readMaterial(std::ifstream & infile,
const std::string & filename);
UInt readInterval(std::stringstream & line, std::set<UInt> & interval);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
std::map<std::string, ElementType> _diana_to_akantu_element_types;
std::map<std::string, std::string> _diana_to_akantu_mat_prop;
/// order in witch element as to be read, akantu_node_order = _read_order[diana_node_order]
std::map<ElementType, UInt *> _read_order;
std::map<UInt, Element> diana_element_number_to_elements;
std::map<Element, UInt> akantu_number_to_diana_number;
};
} // akantu
#endif /* __AKANTU_MESH_IO_DIANA_HH__ */
diff --git a/src/io/mesh_io/mesh_io_msh.cc b/src/io/mesh_io/mesh_io_msh.cc
index 4fb0f54bc..c2b7287bf 100644
--- a/src/io/mesh_io/mesh_io_msh.cc
+++ b/src/io/mesh_io/mesh_io_msh.cc
@@ -1,971 +1,971 @@
/**
* @file mesh_io_msh.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Jan 21 2016
*
* @brief Read/Write for MSH files generated by gmsh
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -----------------------------------------------------------------------------
Version (Legacy) 1.0
$NOD
number-of-nodes
node-number x-coord y-coord z-coord
...
$ENDNOD
$ELM
number-of-elements
elm-number elm-type reg-phys reg-elem number-of-nodes node-number-list
...
$ENDELM
-----------------------------------------------------------------------------
Version 2.1
$MeshFormat
version-number file-type data-size
$EndMeshFormat
$Nodes
number-of-nodes
node-number x-coord y-coord z-coord
...
$EndNodes
$Elements
number-of-elements
elm-number elm-type number-of-tags < tag > ... node-number-list
...
$EndElements
$PhysicalNames
number-of-names
physical-dimension physical-number "physical-name"
...
$EndPhysicalNames
$NodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
node-number value ...
...
$EndNodeData
$ElementData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number value ...
...
$EndElementData
$ElementNodeData
number-of-string-tags
< "string-tag" >
...
number-of-real-tags
< real-tag >
...
number-of-integer-tags
< integer-tag >
...
elm-number number-of-nodes-per-element value ...
...
$ElementEndNodeData
-----------------------------------------------------------------------------
elem-type
1: 2-node line.
2: 3-node triangle.
3: 4-node quadrangle.
4: 4-node tetrahedron.
5: 8-node hexahedron.
6: 6-node prism.
7: 5-node pyramid.
8: 3-node second order line
9: 6-node second order triangle
10: 9-node second order quadrangle
11: 10-node second order tetrahedron
12: 27-node second order hexahedron
13: 18-node second order prism
14: 14-node second order pyramid
15: 1-node point.
16: 8-node second order quadrangle
17: 20-node second order hexahedron
18: 15-node second order prism
19: 13-node second order pyramid
20: 9-node third order incomplete triangle
21: 10-node third order triangle
22: 12-node fourth order incomplete triangle
23: 15-node fourth order triangle
24: 15-node fifth order incomplete triangle
25: 21-node fifth order complete triangle
26: 4-node third order edge
27: 5-node fourth order edge
28: 6-node fifth order edge
29: 20-node third order tetrahedron
30: 35-node fourth order tetrahedron
31: 56-node fifth order tetrahedron
-------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
// The boost spirit is a work on the way it does not compile so I kept the
// current code. The current code does not handle files generated on Windows
// <CRLF>
// #include <boost/config/warning_disable.hpp>
// #include <boost/spirit/include/qi.hpp>
// #include <boost/spirit/include/phoenix_core.hpp>
// #include <boost/spirit/include/phoenix_fusion.hpp>
// #include <boost/spirit/include/phoenix_object.hpp>
// #include <boost/spirit/include/phoenix_container.hpp>
// #include <boost/spirit/include/phoenix_operator.hpp>
// #include <boost/spirit/include/phoenix_bind.hpp>
// #include <boost/spirit/include/phoenix_stl.hpp>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
MeshIOMSH::MeshIOMSH() {
canReadSurface = true;
canReadExtendedData = true;
_msh_nodes_per_elem[_msh_not_defined] = 0;
_msh_nodes_per_elem[_msh_segment_2] = 2;
_msh_nodes_per_elem[_msh_triangle_3] = 3;
_msh_nodes_per_elem[_msh_quadrangle_4] = 4;
_msh_nodes_per_elem[_msh_tetrahedron_4] = 4;
_msh_nodes_per_elem[_msh_hexahedron_8] = 8;
_msh_nodes_per_elem[_msh_prism_1] = 6;
_msh_nodes_per_elem[_msh_pyramid_1] = 1;
_msh_nodes_per_elem[_msh_segment_3] = 3;
_msh_nodes_per_elem[_msh_triangle_6] = 6;
_msh_nodes_per_elem[_msh_quadrangle_9] = 9;
_msh_nodes_per_elem[_msh_tetrahedron_10] = 10;
_msh_nodes_per_elem[_msh_hexahedron_27] = 27;
_msh_nodes_per_elem[_msh_hexahedron_20] = 20;
_msh_nodes_per_elem[_msh_prism_18] = 18;
_msh_nodes_per_elem[_msh_prism_15] = 15;
_msh_nodes_per_elem[_msh_pyramid_14] = 14;
_msh_nodes_per_elem[_msh_point] = 1;
_msh_nodes_per_elem[_msh_quadrangle_8] = 8;
_msh_to_akantu_element_types[_msh_not_defined] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_2] = _segment_2;
_msh_to_akantu_element_types[_msh_triangle_3] = _triangle_3;
_msh_to_akantu_element_types[_msh_quadrangle_4] = _quadrangle_4;
_msh_to_akantu_element_types[_msh_tetrahedron_4] = _tetrahedron_4;
_msh_to_akantu_element_types[_msh_hexahedron_8] = _hexahedron_8;
_msh_to_akantu_element_types[_msh_prism_1] = _pentahedron_6;
_msh_to_akantu_element_types[_msh_pyramid_1] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_3] = _segment_3;
_msh_to_akantu_element_types[_msh_triangle_6] = _triangle_6;
_msh_to_akantu_element_types[_msh_quadrangle_9] = _not_defined;
_msh_to_akantu_element_types[_msh_tetrahedron_10] = _tetrahedron_10;
_msh_to_akantu_element_types[_msh_hexahedron_27] = _not_defined;
_msh_to_akantu_element_types[_msh_hexahedron_20] = _hexahedron_20;
_msh_to_akantu_element_types[_msh_prism_18] = _not_defined;
_msh_to_akantu_element_types[_msh_prism_15] = _pentahedron_15;
_msh_to_akantu_element_types[_msh_pyramid_14] = _not_defined;
_msh_to_akantu_element_types[_msh_point] = _point_1;
_msh_to_akantu_element_types[_msh_quadrangle_8] = _quadrangle_8;
_akantu_to_msh_element_types[_not_defined] = _msh_not_defined;
_akantu_to_msh_element_types[_segment_2] = _msh_segment_2;
_akantu_to_msh_element_types[_segment_3] = _msh_segment_3;
_akantu_to_msh_element_types[_triangle_3] = _msh_triangle_3;
_akantu_to_msh_element_types[_triangle_6] = _msh_triangle_6;
_akantu_to_msh_element_types[_tetrahedron_4] = _msh_tetrahedron_4;
_akantu_to_msh_element_types[_tetrahedron_10] = _msh_tetrahedron_10;
_akantu_to_msh_element_types[_quadrangle_4] = _msh_quadrangle_4;
_akantu_to_msh_element_types[_quadrangle_8] = _msh_quadrangle_8;
_akantu_to_msh_element_types[_hexahedron_8] = _msh_hexahedron_8;
_akantu_to_msh_element_types[_hexahedron_20] = _msh_hexahedron_20;
_akantu_to_msh_element_types[_pentahedron_6] = _msh_prism_1;
_akantu_to_msh_element_types[_pentahedron_15] = _msh_prism_15;
_akantu_to_msh_element_types[_point_1] = _msh_point;
#if defined(AKANTU_STRUCTURAL_MECHANICS)
_akantu_to_msh_element_types[_bernoulli_beam_2] = _msh_segment_2;
_akantu_to_msh_element_types[_bernoulli_beam_3] = _msh_segment_2;
_akantu_to_msh_element_types[_kirchhoff_shell] = _msh_triangle_3;
#endif
std::map<ElementType, MSHElementType>::iterator it;
for (it = _akantu_to_msh_element_types.begin();
it != _akantu_to_msh_element_types.end(); ++it) {
UInt nb_nodes = _msh_nodes_per_elem[it->second];
std::vector<UInt> tmp(nb_nodes);
for (UInt i = 0; i < nb_nodes; ++i) {
tmp[i] = i;
}
switch (it->first) {
case _tetrahedron_10:
tmp[8] = 9;
tmp[9] = 8;
break;
case _pentahedron_6:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
break;
case _pentahedron_15:
tmp[0] = 2;
tmp[1] = 0;
tmp[2] = 1;
tmp[3] = 5;
tmp[4] = 3;
tmp[5] = 4;
tmp[6] = 8;
tmp[8] = 11;
tmp[9] = 6;
tmp[10] = 9;
tmp[11] = 10;
tmp[12] = 14;
tmp[14] = 12;
break;
case _hexahedron_20:
tmp[9] = 11;
tmp[10] = 12;
tmp[11] = 9;
tmp[12] = 13;
tmp[13] = 10;
tmp[17] = 19;
tmp[18] = 17;
tmp[19] = 18;
break;
default:
// nothing to change
break;
}
_read_order[it->first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
MeshIOMSH::~MeshIOMSH() {}
/* -------------------------------------------------------------------------- */
/* Spirit stuff */
/* -------------------------------------------------------------------------- */
// namespace _parser {
// namespace spirit = ::boost::spirit;
// namespace qi = ::boost::spirit::qi;
// namespace ascii = ::boost::spirit::ascii;
// namespace lbs = ::boost::spirit::qi::labels;
// namespace phx = ::boost::phoenix;
// /* ------------------------------------------------------------------------
// */
// /* Lazy functors */
// /* ------------------------------------------------------------------------
// */
// struct _Element {
// int index;
// std::vector<int> tags;
// std::vector<int> connectivity;
// ElementType type;
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_get_nb_nodes_ {
// template <class elem_type> struct result { typedef int type; };
// template <class elem_type> bool operator()(elem_type et) {
// return MeshIOMSH::_msh_nodes_per_elem[et];
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_element_ {
// template <class id_t, class tags_t, class elem_type, class conn_t>
// struct result {
// typedef _Element type;
// };
// template <class id_t, class tags_t, class elem_type, class conn_t>
// _Element operator()(id_t id, const elem_type & et, const tags_t & t,
// const conn_t & c) {
// _Element tmp_el;
// tmp_el.index = id;
// tmp_el.tags = t;
// tmp_el.connectivity = c;
// tmp_el.type = et;
// return tmp_el;
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_check_value_ {
// template <class T> struct result { typedef void type; };
// template <class T> void operator()(T v1, T v2) {
// if (v1 != v2) {
// AKANTU_EXCEPTION("The msh parser expected a "
// << v2 << " in the header bug got a " << v1);
// }
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_node_read_ {
// template <class Mesh, class ID, class V, class size, class Map>
// struct result {
// typedef bool type;
// };
// template <class Mesh, class ID, class V, class size, class Map>
// bool operator()(Mesh & mesh, const ID & id, const V & pos, size max,
// Map & nodes_mapping) const {
// Vector<Real> tmp_pos(mesh.getSpatialDimension());
// UInt i = 0;
// for (typename V::const_iterator it = pos.begin();
// it != pos.end() || i < mesh.getSpatialDimension(); ++it)
// tmp_pos[i++] = *it;
// nodes_mapping[id] = mesh.getNbNodes();
// mesh.getNodes().push_back(tmp_pos);
// return (mesh.getNbNodes() < UInt(max));
// }
// };
// /* ------------------------------------------------------------------------
// */
// struct lazy_element_read_ {
// template <class Mesh, class EL, class size, class NodeMap, class ElemMap>
// struct result {
// typedef bool type;
// };
// template <class Mesh, class EL, class size, class NodeMap, class ElemMap>
// bool operator()(Mesh & mesh, const EL & element, size max,
// const NodeMap & nodes_mapping,
// ElemMap & elements_mapping) const {
// Vector<UInt> tmp_conn(Mesh::getNbNodesPerElement(element.type));
// AKANTU_DEBUG_ASSERT(element.connectivity.size() == tmp_conn.size(),
// "The element "
// << element.index
// << "in the MSH file has too many nodes.");
// mesh.addConnectivityType(element.type);
// Array<UInt> & connectivity = mesh.getConnectivity(element.type);
// UInt i = 0;
// for (std::vector<int>::const_iterator it =
// element.connectivity.begin();
// it != element.connectivity.end(); ++it) {
// typename NodeMap::const_iterator nit = nodes_mapping.find(*it);
// AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
// "There is an unknown node in the connectivity.");
// tmp_conn[i++] = nit->second;
// }
// ::akantu::Element el(element.type, connectivity.size());
// elements_mapping[element.index] = el;
// connectivity.push_back(tmp_conn);
// for (UInt i = 0; i < element.tags.size(); ++i) {
// std::stringstream tag_sstr;
// tag_sstr << "tag_" << i;
// Array<UInt> * data =
// mesh.template getDataPointer<UInt>(tag_sstr.str(), element.type,
// _not_ghost);
// data->push_back(element.tags[i]);
// }
// return (mesh.getNbElement() < UInt(max));
// }
// };
// /* ------------------------------------------------------------------------
// */
// template <class Iterator, typename Skipper = ascii::space_type>
// struct MshMeshGrammar : qi::grammar<Iterator, void(), Skipper> {
// public:
// MshMeshGrammar(Mesh & mesh)
// : MshMeshGrammar::base_type(start, "msh_mesh_reader"), mesh(mesh) {
// phx::function<lazy_element_> lazy_element;
// phx::function<lazy_get_nb_nodes_> lazy_get_nb_nodes;
// phx::function<lazy_check_value_> lazy_check_value;
// phx::function<lazy_node_read_> lazy_node_read;
// phx::function<lazy_element_read_> lazy_element_read;
// clang-format off
// start
// = *( known_section | unknown_section
// )
// ;
// known_section
// = qi::char_("$")
// >> sections [ lbs::_a = lbs::_1 ]
// >> qi::lazy(*lbs::_a)
// >> qi::lit("$End")
// //>> qi::lit(phx::ref(lbs::_a))
// ;
// unknown_section
// = qi::char_("$")
// >> qi::char_("") [ lbs::_a = lbs::_1 ]
// >> ignore_section
// >> qi::lit("$End")
// >> qi::lit(phx::val(lbs::_a))
// ;
// mesh_format // version followed by 0 or 1 for ascii or binary
// = version >> (
// ( qi::char_("0")
// >> qi::int_ [ lazy_check_value(lbs::_1, 8) ]
// )
// | ( qi::char_("1")
// >> qi::int_ [ lazy_check_value(lbs::_1, 8) ]
// >> qi::dword [ lazy_check_value(lbs::_1, 1) ]
// )
// )
// ;
// nodes
// = nodes_
// ;
// nodes_
// = qi::int_ [ lbs::_a = lbs::_1 ]
// > *(
// ( qi::int_ >> position ) [ lazy_node_read(phx::ref(mesh),
// lbs::_1,
// phx::cref(lbs::_2),
// lbs::_a,
// phx::ref(this->msh_nodes_to_akantu)) ]
// )
// ;
// element
// = elements_
// ;
// elements_
// = qi::int_ [ lbs::_a = lbs::_1 ]
// > qi::repeat(phx::ref(lbs::_a))[ element [ lazy_element_read(phx::ref(mesh),
// lbs::_1,
// phx::cref(lbs::_a),
// phx::cref(this->msh_nodes_to_akantu),
// phx::ref(this->msh_elemt_to_akantu)) ]]
// ;
// ignore_section
// = *(qi::char_ - qi::char_('$'))
// ;
// interpolation_scheme = ignore_section;
// element_data = ignore_section;
// node_data = ignore_section;
// version
// = qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ]
// >> *( qi::char_(".") >> qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ] )
// ;
// position
// = real [ phx::push_back(lbs::_val, lbs::_1) ]
// > real [ phx::push_back(lbs::_val, lbs::_1) ]
// > real [ phx::push_back(lbs::_val, lbs::_1) ]
// ;
// tags
// = qi::int_ [ lbs::_a = lbs::_1 ]
// > qi::repeat(phx::val(lbs::_a))[ qi::int_ [ phx::push_back(lbs::_val,
// lbs::_1) ] ]
// ;
// element
// = ( qi::int_ [ lbs::_a = lbs::_1 ]
// > msh_element_type [ lbs::_b = lazy_get_nb_nodes(lbs::_1) ]
// > tags [ lbs::_c = lbs::_1 ]
// > connectivity(lbs::_a) [ lbs::_d = lbs::_1 ]
// ) [ lbs::_val = lazy_element(lbs::_a,
// phx::cref(lbs::_b),
// phx::cref(lbs::_c),
// phx::cref(lbs::_d)) ]
// ;
// connectivity
// = qi::repeat(lbs::_r1)[ qi::int_ [ phx::push_back(lbs::_val,
// lbs::_1) ] ]
// ;
// sections.add
// ("MeshFormat", &mesh_format)
// ("Nodes", &nodes)
// ("Elements", &elements)
// ("PhysicalNames", &physical_names)
// ("InterpolationScheme", &interpolation_scheme)
// ("ElementData", &element_data)
// ("NodeData", &node_data);
// msh_element_type.add
// ("0" , _not_defined )
// ("1" , _segment_2 )
// ("2" , _triangle_3 )
// ("3" , _quadrangle_4 )
// ("4" , _tetrahedron_4 )
// ("5" , _hexahedron_8 )
// ("6" , _pentahedron_6 )
// ("7" , _not_defined )
// ("8" , _segment_3 )
// ("9" , _triangle_6 )
// ("10", _not_defined )
// ("11", _tetrahedron_10)
// ("12", _not_defined )
// ("13", _not_defined )
// ("14", _hexahedron_20 )
// ("15", _pentahedron_15)
// ("16", _not_defined )
// ("17", _point_1 )
// ("18", _quadrangle_8 );
// mesh_format .name("MeshFormat" );
// nodes .name("Nodes" );
// elements .name("Elements" );
// physical_names .name("PhysicalNames" );
// interpolation_scheme.name("InterpolationScheme");
// element_data .name("ElementData" );
// node_data .name("NodeData" );
// clang-format on
// }
// /* ----------------------------------------------------------------------
// */
// /* Rules */
// /* ----------------------------------------------------------------------
// */
// private:
// qi::symbols<char, ElementType> msh_element_type;
// qi::symbols<char, qi::rule<Iterator, void(), Skipper> *> sections;
// qi::rule<Iterator, void(), Skipper> start;
// qi::rule<Iterator, void(), Skipper, qi::locals<std::string> >
// unknown_section;
// qi::rule<Iterator, void(), Skipper, qi::locals<qi::rule<Iterator,
// Skipper> *> > known_section;
// qi::rule<Iterator, void(), Skipper> mesh_format, nodes, elements,
// physical_names, ignore_section,
// interpolation_scheme, element_data, node_data, any_line;
// qi::rule<Iterator, void(), Skipper, qi::locals<int> > nodes_;
// qi::rule<Iterator, void(), Skipper, qi::locals< int, int, vector<int>,
// vector<int> > > elements_;
// qi::rule<Iterator, std::vector<int>(), Skipper> version;
// qi::rule<Iterator, _Element(), Skipper, qi::locals<ElementType> >
// element;
// qi::rule<Iterator, std::vector<int>(), Skipper, qi::locals<int> > tags;
// qi::rule<Iterator, std::vector<int>(int), Skipper> connectivity;
// qi::rule<Iterator, std::vector<Real>(), Skipper> position;
// qi::real_parser<Real, qi::real_policies<Real> > real;
// /* ----------------------------------------------------------------------
// */
// /* Members */
// /* ----------------------------------------------------------------------
// */
// private:
// /// reference to the mesh to read
// Mesh & mesh;
// /// correspondance between the numbering of nodes in the abaqus file and
// in
// /// the akantu mesh
// std::map<UInt, UInt> msh_nodes_to_akantu;
// /// correspondance between the element number in the abaqus file and the
// /// Element in the akantu mesh
// std::map<UInt, Element> msh_elemt_to_akantu;
// };
// }
// /* --------------------------------------------------------------------------
// */
// void MeshIOAbaqus::read(const std::string& filename, Mesh& mesh) {
// namespace qi = boost::spirit::qi;
// namespace ascii = boost::spirit::ascii;
// std::ifstream infile;
// infile.open(filename.c_str());
// if(!infile.good()) {
// AKANTU_DEBUG_ERROR("Cannot open file " << filename);
// }
// std::string storage; // We will read the contents here.
// infile.unsetf(std::ios::skipws); // No white space skipping!
// std::copy(std::istream_iterator<char>(infile),
// std::istream_iterator<char>(),
// std::back_inserter(storage));
// typedef std::string::const_iterator iterator_t;
// typedef ascii::space_type skipper;
// typedef _parser::MshMeshGrammar<iterator_t, skipper> grammar;
// grammar g(mesh);
// skipper ws;
// iterator_t iter = storage.begin();
// iterator_t end = storage.end();
// qi::phrase_parse(iter, end, g, ws);
// this->setNbGlobalNodes(mesh, mesh.getNodes().size());
// MeshUtils::fillElementToSubElementsData(mesh);
// }
static void my_getline(std::ifstream & infile, std::string & str) {
std::string tmp_str;
std::getline(infile, tmp_str);
str = trim(tmp_str);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::read(const std::string & filename, Mesh & mesh) {
MeshAccessor mesh_accessor(mesh);
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt first_node_number = std::numeric_limits<UInt>::max(),
last_node_number = 0, file_format = 1, current_line = 0;
bool has_physical_names = false;
if (!infile.good()) {
AKANTU_DEBUG_ERROR("Cannot open file " << filename);
}
while (infile.good()) {
my_getline(infile, line);
current_line++;
/// read the header
if (line == "$MeshFormat") {
my_getline(infile, line); /// the format line
std::stringstream sstr(line);
std::string version;
sstr >> version;
Int format;
sstr >> format;
if (format != 0)
AKANTU_DEBUG_ERROR("This reader can only read ASCII files.");
my_getline(infile, line); /// the end of block line
current_line += 2;
file_format = 2;
}
/// read the physical names
if (line == "$PhysicalNames") {
has_physical_names = true;
my_getline(infile, line); /// the format line
std::stringstream sstr(line);
UInt num_of_phys_names;
sstr >> num_of_phys_names;
for (UInt k(0); k < num_of_phys_names; k++) {
my_getline(infile, line);
std::stringstream sstr_phys_name(line);
UInt phys_name_id;
UInt phys_dim;
sstr_phys_name >> phys_dim >> phys_name_id;
std::size_t b = line.find("\"");
std::size_t e = line.rfind("\"");
std::string phys_name = line.substr(b + 1, e - b - 1);
phys_name_map[phys_name_id] = phys_name;
}
}
/// read all nodes
if (line == "$Nodes" || line == "$NOD") {
UInt nb_nodes;
my_getline(infile, line);
std::stringstream sstr(line);
sstr >> nb_nodes;
current_line++;
Array<Real> & nodes = mesh_accessor.getNodes();
nodes.resize(nb_nodes);
mesh_accessor.setNbGlobalNodes(nb_nodes);
UInt index;
Real coord[3];
UInt spatial_dimension = nodes.getNbComponent();
/// for each node, read the coordinates
for (UInt i = 0; i < nb_nodes; ++i) {
UInt offset = i * spatial_dimension;
my_getline(infile, line);
std::stringstream sstr_node(line);
sstr_node >> index >> coord[0] >> coord[1] >> coord[2];
current_line++;
first_node_number = std::min(first_node_number, index);
last_node_number = std::max(last_node_number, index);
/// read the coordinates
for (UInt j = 0; j < spatial_dimension; ++j)
nodes.storage()[offset + j] = coord[j];
}
my_getline(infile, line); /// the end of block line
}
/// read all elements
if (line == "$Elements" || line == "$ELM") {
UInt nb_elements;
std::vector<UInt> read_order;
my_getline(infile, line);
std::stringstream sstr(line);
sstr >> nb_elements;
current_line++;
Int index;
UInt msh_type;
ElementType akantu_type, akantu_type_old = _not_defined;
- Array<UInt> * connectivity = NULL;
+ Array<UInt> * connectivity = nullptr;
UInt node_per_element = 0;
for (UInt i = 0; i < nb_elements; ++i) {
my_getline(infile, line);
std::stringstream sstr_elem(line);
current_line++;
sstr_elem >> index;
sstr_elem >> msh_type;
/// get the connectivity vector depending on the element type
akantu_type =
this->_msh_to_akantu_element_types[(MSHElementType)msh_type];
if (akantu_type == _not_defined) {
AKANTU_DEBUG_WARNING("Unsuported element kind "
<< msh_type << " at line " << current_line);
continue;
}
if (akantu_type != akantu_type_old) {
connectivity = &mesh_accessor.getConnectivity(akantu_type);
// connectivity->resize(0);
node_per_element = connectivity->getNbComponent();
akantu_type_old = akantu_type;
read_order = this->_read_order[akantu_type];
}
/// read tags informations
if (file_format == 2) {
UInt nb_tags;
sstr_elem >> nb_tags;
for (UInt j = 0; j < nb_tags; ++j) {
Int tag;
sstr_elem >> tag;
std::stringstream sstr_tag_name;
sstr_tag_name << "tag_" << j;
Array<UInt> & data = mesh.getDataPointer<UInt>(
sstr_tag_name.str(), akantu_type, _not_ghost);
data.push_back(tag);
}
} else if (file_format == 1) {
Int tag;
sstr_elem >> tag; // reg-phys
std::string tag_name = "tag_0";
Array<UInt> * data =
&mesh.getDataPointer<UInt>(tag_name, akantu_type, _not_ghost);
data->push_back(tag);
sstr_elem >> tag; // reg-elem
tag_name = "tag_1";
data = &mesh.getDataPointer<UInt>(tag_name, akantu_type, _not_ghost);
data->push_back(tag);
sstr_elem >> tag; // number-of-nodes
}
Vector<UInt> local_connect(node_per_element);
for (UInt j = 0; j < node_per_element; ++j) {
UInt node_index;
sstr_elem >> node_index;
AKANTU_DEBUG_ASSERT(node_index <= last_node_number,
"Node number not in range : line "
<< current_line);
node_index -= first_node_number;
local_connect(read_order[j]) = node_index;
}
connectivity->push_back(local_connect);
}
my_getline(infile, line); /// the end of block line
}
if ((line[0] == '$') && (line.find("End") == std::string::npos)) {
AKANTU_DEBUG_WARNING("Unsuported block_kind " << line << " at line "
<< current_line);
}
}
// mesh.updateTypesOffsets(_not_ghost);
infile.close();
this->constructPhysicalNames("tag_0", mesh);
if (has_physical_names)
mesh.createGroupsFromMeshData<std::string>("physical_names");
MeshUtils::fillElementToSubElementsData(mesh);
}
/* -------------------------------------------------------------------------- */
void MeshIOMSH::write(const std::string & filename, const Mesh & mesh) {
std::ofstream outfile;
const Array<Real> & nodes = mesh.getNodes();
outfile.open(filename.c_str());
outfile << "$MeshFormat" << std::endl;
outfile << "2.1 0 8" << std::endl;
outfile << "$EndMeshFormat" << std::endl;
outfile << std::setprecision(std::numeric_limits<Real>::digits10);
outfile << "$Nodes" << std::endl;
outfile << nodes.size() << std::endl;
outfile << std::uppercase;
for (UInt i = 0; i < nodes.size(); ++i) {
Int offset = i * nodes.getNbComponent();
outfile << i + 1;
for (UInt j = 0; j < nodes.getNbComponent(); ++j) {
outfile << " " << nodes.storage()[offset + j];
}
for (UInt p = nodes.getNbComponent(); p < 3; ++p)
outfile << " " << 0.;
outfile << std::endl;
;
}
outfile << std::nouppercase;
outfile << "$EndNodes" << std::endl;
;
outfile << "$Elements" << std::endl;
;
Int nb_elements = 0;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
nb_elements += connectivity.size();
}
outfile << nb_elements << std::endl;
UInt element_idx = 1;
for (auto && type :
mesh.elementTypes(_all_dimensions, _not_ghost, _ek_not_defined)) {
const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
UInt * tag[2] = {nullptr, nullptr};
if (mesh.hasData<UInt>("tag_0", type, _not_ghost)) {
const auto & data_tag_0 = mesh.getData<UInt>("tag_0", type, _not_ghost);
tag[0] = data_tag_0.storage();
}
if (mesh.hasData<UInt>("tag_1", type, _not_ghost)) {
const auto & data_tag_1 = mesh.getData<UInt>("tag_1", type, _not_ghost);
tag[1] = data_tag_1.storage();
}
for (UInt i = 0; i < connectivity.size(); ++i) {
UInt offset = i * connectivity.getNbComponent();
outfile << element_idx << " " << _akantu_to_msh_element_types[type]
<< " 2";
/// \todo write the real data in the file
for (UInt t = 0; t < 2; ++t)
if (tag[t])
outfile << " " << tag[t][i];
else
outfile << " 0";
for (UInt j = 0; j < connectivity.getNbComponent(); ++j) {
outfile << " " << connectivity.storage()[offset + j] + 1;
}
outfile << std::endl;
element_idx++;
}
}
outfile << "$EndElements" << std::endl;
;
outfile.close();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/io/mesh_io/mesh_io_msh.hh b/src/io/mesh_io/mesh_io_msh.hh
index 143bd095e..7c905705b 100644
--- a/src/io/mesh_io/mesh_io_msh.hh
+++ b/src/io/mesh_io/mesh_io_msh.hh
@@ -1,115 +1,115 @@
/**
* @file mesh_io_msh.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Dec 07 2015
*
* @brief Read/Write for MSH files
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_IO_MSH_HH__
#define __AKANTU_MESH_IO_MSH_HH__
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshIOMSH : public MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIOMSH();
- virtual ~MeshIOMSH();
+ ~MeshIOMSH() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
- virtual void read(const std::string & filename, Mesh & mesh);
+ void read(const std::string & filename, Mesh & mesh) override;
/// write a mesh to a file
- virtual void write(const std::string & filename, const Mesh & mesh);
+ void write(const std::string & filename, const Mesh & mesh) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// MSH element types
enum MSHElementType {
_msh_not_defined = 0,
_msh_segment_2 = 1, // 2-node line.
_msh_triangle_3 = 2, // 3-node triangle.
_msh_quadrangle_4 = 3, // 4-node quadrangle.
_msh_tetrahedron_4 = 4, // 4-node tetrahedron.
_msh_hexahedron_8 = 5, // 8-node hexahedron.
_msh_prism_1 = 6, // 6-node prism.
_msh_pyramid_1 = 7, // 5-node pyramid.
_msh_segment_3 = 8, // 3-node second order line
_msh_triangle_6 = 9, // 6-node second order triangle
_msh_quadrangle_9 = 10, // 9-node second order quadrangle
_msh_tetrahedron_10 = 11, // 10-node second order tetrahedron
_msh_hexahedron_27 = 12, // 27-node second order hexahedron
_msh_prism_18 = 13, // 18-node second order prism
_msh_pyramid_14 = 14, // 14-node second order pyramid
_msh_point = 15, // 1-node point.
_msh_quadrangle_8 = 16, // 8-node second order quadrangle
_msh_hexahedron_20 = 17, // 20-node second order hexahedron
_msh_prism_15 = 18 // 15-node second order prism
};
#define MAX_NUMBER_OF_NODE_PER_ELEMENT 10 // tetrahedron of second order
/// order in witch element as to be read
std::map< ElementType, std::vector<UInt> > _read_order;
/// number of nodes per msh element
std::map<MSHElementType, UInt> _msh_nodes_per_elem;
/// correspondence between msh element types and akantu element types
std::map<MSHElementType, ElementType> _msh_to_akantu_element_types;
/// correspondence between akantu element types and msh element types
std::map<ElementType, MSHElementType> _akantu_to_msh_element_types;
};
} // akantu
#endif /* __AKANTU_MESH_IO_MSH_HH__ */
diff --git a/src/io/parser/cppargparse/cppargparse.cc b/src/io/parser/cppargparse/cppargparse.cc
index f4a82dc00..acdc871a8 100644
--- a/src/io/parser/cppargparse/cppargparse.cc
+++ b/src/io/parser/cppargparse/cppargparse.cc
@@ -1,528 +1,531 @@
/**
* @file cppargparse.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
* @date last modification: Wed Nov 11 2015
*
* @brief implementation of the ArgumentParser
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "cppargparse.hh"
#include <cstdlib>
#include <cstring>
#include <libgen.h>
#include <iostream>
#include <iomanip>
#include <string>
#include <queue>
#include <sstream>
#include <algorithm>
#include <exception>
#include <stdexcept>
#include <string.h>
namespace cppargparse {
/* -------------------------------------------------------------------------- */
static inline std::string to_upper(const std::string & str) {
std::string lstr = str;
std::transform(lstr.begin(), lstr.end(), lstr.begin(),
(int (*)(int))std::toupper);
return lstr;
}
/* -------------------------------------------------------------------------- */
/* ArgumentParser */
/* -------------------------------------------------------------------------- */
-ArgumentParser::ArgumentParser() : external_exit(NULL), prank(0), psize(1) {
+ArgumentParser::ArgumentParser() : external_exit(nullptr), prank(0), psize(1) {
this->addArgument("-h;--help", "show this help message and exit", 0, _boolean,
false, true);
}
/* -------------------------------------------------------------------------- */
ArgumentParser::~ArgumentParser() {
for (_Arguments::iterator it = arguments.begin(); it != arguments.end();
++it) {
delete it->second;
}
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::setParallelContext(int prank, int psize) {
this->prank = prank;
this->psize = psize;
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::_exit(const std::string & msg, int status) {
if (prank == 0) {
if (msg != "") {
std::cerr << msg << std::endl;
std::cerr << std::endl;
}
this->print_help(std::cerr);
}
if (external_exit)
(*external_exit)(status);
else {
exit(status);
}
}
/* -------------------------------------------------------------------------- */
const ArgumentParser::Argument & ArgumentParser::
operator[](const std::string & name) const {
Arguments::const_iterator it = success_parsed.find(name);
if (it != success_parsed.end()) {
return *(it->second);
} else {
throw std::range_error("No argument named \'" + name +
"\' was found in the parsed argument," +
" make sur to specify it \'required\'" +
" or to give it a default value");
}
}
/* -------------------------------------------------------------------------- */
bool ArgumentParser::has(const std::string & name) const {
return (success_parsed.find(name) != success_parsed.end());
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::addArgument(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type) {
_addArgument(name_or_flag, help, nargs, type);
}
/* -------------------------------------------------------------------------- */
ArgumentParser::_Argument &
ArgumentParser::_addArgument(const std::string & name, const std::string & help,
int nargs, ArgumentType type) {
_Argument * arg = nullptr;
switch (type) {
case _string: {
arg = new ArgumentStorage<std::string>();
break;
}
case _float: {
arg = new ArgumentStorage<double>();
break;
}
case _integer: {
arg = new ArgumentStorage<int>();
break;
}
case _boolean: {
arg = new ArgumentStorage<bool>();
break;
}
}
arg->help = help;
arg->nargs = nargs;
arg->type = type;
std::stringstream sstr(name);
std::string item;
std::vector<std::string> tmp_keys;
while (std::getline(sstr, item, ';')) {
tmp_keys.push_back(item);
}
int long_key = -1;
int short_key = -1;
bool problem = (tmp_keys.size() > 2) || (name == "");
for (std::vector<std::string>::iterator it = tmp_keys.begin();
it != tmp_keys.end(); ++it) {
if (it->find("--") == 0) {
problem |= (long_key != -1);
long_key = it - tmp_keys.begin();
} else if (it->find("-") == 0) {
problem |= (long_key != -1);
short_key = it - tmp_keys.begin();
}
}
problem |= ((tmp_keys.size() == 2) && (long_key == -1 || short_key == -1));
if (problem) {
delete arg;
throw std::invalid_argument("Synthax of name or flags is not correct. "
"Possible synthax are \'-f\', \'-f;--foo\', "
"\'--foo\', \'bar\'");
}
if (long_key != -1) {
arg->name = tmp_keys[long_key];
arg->name.erase(0, 2);
} else if (short_key != -1) {
arg->name = tmp_keys[short_key];
arg->name.erase(0, 1);
} else {
arg->name = tmp_keys[0];
pos_args.push_back(arg);
arg->required = (nargs != _one_if_possible);
arg->is_positional = true;
}
arguments[arg->name] = arg;
if (!arg->is_positional) {
if (short_key != -1) {
std::string key = tmp_keys[short_key];
key_args[key] = arg;
arg->keys.push_back(key);
}
if (long_key != -1) {
std::string key = tmp_keys[long_key];
key_args[key] = arg;
arg->keys.push_back(key);
}
}
return *arg;
}
#if not HAVE_STRDUP
static char * strdup(const char * str) {
size_t len = strlen(str);
char *x = (char *)malloc(len+1); /* 1 for the null terminator */
- if(!x) return NULL; /* malloc could not allocate memory */
+ if(!x)
+ return nullptr; /* malloc could not allocate memory */
memcpy(x,str,len+1); /* copy the string into the new buffer */
return x;
}
#endif
/* -------------------------------------------------------------------------- */
void ArgumentParser::parse(int & argc, char **& argv, int flags,
bool parse_help) {
bool stop_in_not_parsed = flags & _stop_on_not_parsed;
bool remove_parsed = flags & _remove_parsed;
std::vector<std::string> argvs;
for (int i = 0; i < argc; ++i) {
argvs.push_back(std::string(argv[i]));
}
unsigned int current_position = 0;
if (this->program_name == "" && argc > 0) {
std::string prog = argvs[current_position];
const char * c_prog = prog.c_str();
char * c_prog_tmp = strdup(c_prog);
std::string base_prog(basename(c_prog_tmp));
this->program_name = base_prog;
std::free(c_prog_tmp);
}
std::queue<_Argument *> positional_queue;
for (PositionalArgument::iterator it = pos_args.begin(); it != pos_args.end();
++it)
positional_queue.push(*it);
std::vector<int> argvs_to_remove;
++current_position; // consume argv[0]
while (current_position < argvs.size()) {
std::string arg = argvs[current_position];
++current_position;
ArgumentKeyMap::iterator key_it = key_args.find(arg);
bool is_positional = false;
- _Argument * argument_ptr = NULL;
+ _Argument * argument_ptr = nullptr;
if (key_it == key_args.end()) {
if (positional_queue.empty()) {
if (stop_in_not_parsed)
this->_exit("Argument " + arg + " not recognized", EXIT_FAILURE);
continue;
} else {
argument_ptr = positional_queue.front();
is_positional = true;
--current_position;
}
} else {
argument_ptr = key_it->second;
}
if (remove_parsed && !is_positional && argument_ptr->name != "help") {
argvs_to_remove.push_back(current_position - 1);
}
_Argument & argument = *argument_ptr;
unsigned int min_nb_val = 0, max_nb_val = 0;
switch (argument.nargs) {
case _one_if_possible:
max_nb_val = 1;
break; // "?"
case _at_least_one:
min_nb_val = 1; // "+"
- // [[fallthrough]]; un-comment when compiler will get it
+ /* FALLTHRU */
+ /* [[fallthrough]]; un-comment when compiler will get it*/
case _any:
max_nb_val = argc - current_position;
break; // "*"
default:
min_nb_val = max_nb_val = argument.nargs; // "N"
}
std::vector<std::string> values;
unsigned int arg_consumed = 0;
if (max_nb_val <= (argc - current_position)) {
for (; arg_consumed < max_nb_val; ++arg_consumed) {
std::string v = argvs[current_position];
++current_position;
bool is_key = key_args.find(v) != key_args.end();
bool is_good_type = checkType(argument.type, v);
if (!is_key && is_good_type) {
values.push_back(v);
if (remove_parsed)
argvs_to_remove.push_back(current_position - 1);
} else {
// unconsume not parsed argument for optional
if (!is_positional || is_key)
--current_position;
break;
}
}
}
if (arg_consumed < min_nb_val) {
if (!is_positional) {
this->_exit("Not enought values for the argument " + argument.name +
" where provided",
EXIT_FAILURE);
} else {
if (stop_in_not_parsed)
this->_exit("Argument " + arg + " not recognized", EXIT_FAILURE);
}
} else {
if (is_positional)
positional_queue.pop();
if (!argument.parsed) {
success_parsed[argument.name] = &argument;
argument.parsed = true;
if ((argument.nargs == _one_if_possible || argument.nargs == 0) &&
arg_consumed == 0) {
if (argument.has_const)
argument.setToConst();
else if (argument.has_default)
argument.setToDefault();
} else {
argument.setValues(values);
}
} else {
this->_exit("Argument " + argument.name +
" already present in the list of argument",
EXIT_FAILURE);
}
}
}
for (_Arguments::iterator ait = arguments.begin(); ait != arguments.end();
++ait) {
_Argument & argument = *(ait->second);
if (!argument.parsed) {
if (argument.has_default) {
argument.setToDefault();
success_parsed[argument.name] = &argument;
}
if (argument.required) {
this->_exit("Argument " + argument.name + " required but not given!",
EXIT_FAILURE);
}
}
}
// removing the parsed argument if remove_parsed is true
if (argvs_to_remove.size()) {
std::vector<int>::const_iterator next_to_remove = argvs_to_remove.begin();
for (int i = 0, c = 0; i < argc; ++i) {
if (next_to_remove == argvs_to_remove.end() || i != *next_to_remove) {
argv[c] = argv[i];
++c;
} else {
if (next_to_remove != argvs_to_remove.end())
++next_to_remove;
}
}
argc -= argvs_to_remove.size();
}
this->argc = &argc;
this->argv = &argv;
if (this->arguments["help"]->parsed && parse_help) {
this->_exit();
}
}
/* -------------------------------------------------------------------------- */
bool ArgumentParser::checkType(ArgumentType type,
const std::string & value) const {
std::stringstream sstr(value);
switch (type) {
case _string: {
std::string s;
sstr >> s;
break;
}
case _float: {
double d;
sstr >> d;
break;
}
case _integer: {
int i;
sstr >> i;
break;
}
case _boolean: {
bool b;
sstr >> b;
break;
}
}
return (sstr.fail() == false);
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::printself(std::ostream & stream) const {
for (Arguments::const_iterator it = success_parsed.begin();
it != success_parsed.end(); ++it) {
const Argument & argument = *(it->second);
argument.printself(stream);
stream << std::endl;
}
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::print_usage(std::ostream & stream) const {
stream << "Usage: " << this->program_name;
// print shorten usage
for (_Arguments::const_iterator it = arguments.begin(); it != arguments.end();
++it) {
const _Argument & argument = *(it->second);
if (!argument.is_positional) {
if (!argument.required)
stream << " [";
stream << argument.keys[0];
this->print_usage_nargs(stream, argument);
if (!argument.required)
stream << "]";
}
}
for (PositionalArgument::const_iterator it = pos_args.begin();
it != pos_args.end(); ++it) {
const _Argument & argument = **it;
this->print_usage_nargs(stream, argument);
}
stream << std::endl;
}
/* -------------------------------------------------------------------------- */
void ArgumentParser::print_usage_nargs(std::ostream & stream,
const _Argument & argument) const {
std::string u_name = to_upper(argument.name);
switch (argument.nargs) {
case _one_if_possible:
stream << " [" << u_name << "]";
break;
case _at_least_one:
stream << " " << u_name;
- // [[fallthrough]]; un-comment when compiler will get it
+ /* FALLTHRU */
+ /* [[fallthrough]]; un-comment when compiler will get it */
case _any:
stream << " [" << u_name << " ...]";
break;
default:
for (int i = 0; i < argument.nargs; ++i) {
stream << " " << u_name;
}
}
}
void ArgumentParser::print_help(std::ostream & stream) const {
this->print_usage(stream);
if (!pos_args.empty()) {
stream << std::endl;
stream << "positional arguments:" << std::endl;
for (PositionalArgument::const_iterator it = pos_args.begin();
it != pos_args.end(); ++it) {
const _Argument & argument = **it;
this->print_help_argument(stream, argument);
}
}
if (!key_args.empty()) {
stream << std::endl;
stream << "optional arguments:" << std::endl;
for (_Arguments::const_iterator it = arguments.begin();
it != arguments.end(); ++it) {
const _Argument & argument = *(it->second);
if (!argument.is_positional) {
this->print_help_argument(stream, argument);
}
}
}
}
void ArgumentParser::print_help_argument(std::ostream & stream,
const _Argument & argument) const {
std::string key("");
if (argument.is_positional)
key = argument.name;
else {
std::stringstream sstr;
for (unsigned int i = 0; i < argument.keys.size(); ++i) {
if (i != 0)
sstr << ", ";
sstr << argument.keys[i];
this->print_usage_nargs(sstr, argument);
}
key = sstr.str();
}
stream << " " << std::left << std::setw(15) << key << " " << argument.help;
argument.printDefault(stream);
stream << std::endl;
}
}
diff --git a/src/io/parser/cppargparse/cppargparse_tmpl.hh b/src/io/parser/cppargparse/cppargparse_tmpl.hh
index 92a662404..d62452a05 100644
--- a/src/io/parser/cppargparse/cppargparse_tmpl.hh
+++ b/src/io/parser/cppargparse/cppargparse_tmpl.hh
@@ -1,245 +1,245 @@
/**
* @file cppargparse_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Apr 03 2014
* @date last modification: Tue Dec 08 2015
*
* @brief Implementation of the templated part of the commandline argument
* parser
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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>
#include <sstream>
#ifndef __CPPARGPARSE_TMPL_HH__
#define __CPPARGPARSE_TMPL_HH__
namespace cppargparse {
/* -------------------------------------------------------------------------- */
/* Argument */
/* -------------------------------------------------------------------------- */
/// internal description of arguments
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() {}
+ ~_Argument() override {}
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;
};
/* -------------------------------------------------------------------------- */
/// typed storage of the arguments
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) {
+ void addValue(std::string & value) override {
std::stringstream sstr(value);
T t;
sstr >> t;
values.push_back(t);
}
- virtual void setToDefault() {
+ void setToDefault() override {
values.clear();
values.push_back(_default);
}
- virtual void setToConst() {
+ void setToConst() override {
values.clear();
values.push_back(_const);
}
- void printself(std::ostream & stream) const {
+ void printself(std::ostream & stream) const override {
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 {
+ std::ostream & _printDefault(std::ostream & stream) const override {
stream << _default;
return stream;
}
- virtual std::ostream & _printConst(std::ostream & stream) const {
+ std::ostream & _printConst(std::ostream & stream) const override {
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 = 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 <> inline ArgumentParser::Argument::operator const char *() const {
return cast_helper<std::string>::cast(*this).c_str();
}
template <> inline ArgumentParser::Argument::operator unsigned int() const {
return cast_helper<int>::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;
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ArgumentParser::addArgument<const char *>(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, const char * def) {
this->addArgument<std::string>(name_or_flag, help, nargs, type, def);
}
template <>
inline void
ArgumentParser::addArgument<unsigned int>(const std::string & name_or_flag,
const std::string & help, int nargs,
ArgumentType type, unsigned int def) {
this->addArgument<int>(name_or_flag, help, nargs, type, def);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ArgumentParser::addArgument<const char *>(
const std::string & name_or_flag, const std::string & help, int nargs,
ArgumentType type, const char * def, const char * cons) {
this->addArgument<std::string>(name_or_flag, help, nargs, type, def, cons);
}
template <>
inline void ArgumentParser::addArgument<unsigned int>(
const std::string & name_or_flag, const std::string & help, int nargs,
ArgumentType type, unsigned int def, unsigned int cons) {
this->addArgument<int>(name_or_flag, help, nargs, type, def, cons);
}
}
#endif /* __AKANTU_CPPARGPARSE_TMPL_HH__ */
diff --git a/src/io/parser/parameter_registry.hh b/src/io/parser/parameter_registry.hh
index 913b81f80..5db930cb4 100644
--- a/src/io/parser/parameter_registry.hh
+++ b/src/io/parser/parameter_registry.hh
@@ -1,217 +1,217 @@
/**
* @file parameter_registry.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 09 2012
* @date last modification: Thu Dec 17 2015
*
* @brief Interface of the parameter registry
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PARAMETER_REGISTRY_HH__
#define __AKANTU_PARAMETER_REGISTRY_HH__
namespace akantu {
class ParserParameter;
}
namespace akantu {
/* -------------------------------------------------------------------------- */
/// Defines the access modes of parsable parameters
enum ParameterAccessType {
_pat_internal = 0x0001,
_pat_writable = 0x0010,
_pat_readable = 0x0100,
_pat_modifiable = 0x0110, //<_pat_readable | _pat_writable,
_pat_parsable = 0x1000,
_pat_parsmod = 0x1110 //< _pat_parsable | _pat_modifiable
};
/// Bit-wise operator between access modes
inline ParameterAccessType operator|(const ParameterAccessType & a,
const ParameterAccessType & b) {
ParameterAccessType tmp = ParameterAccessType(UInt(a) | UInt(b));
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T> class ParameterTyped;
/**
* Interface for the Parameter
*/
class Parameter {
public:
Parameter();
Parameter(std::string name, std::string description,
ParameterAccessType param_type);
virtual ~Parameter() = default;
/* ------------------------------------------------------------------------ */
bool isInternal() const;
bool isWritable() const;
bool isReadable() const;
bool isParsable() const;
void setAccessType(ParameterAccessType ptype);
/* ------------------------------------------------------------------------ */
template <typename T, typename V> void set(const V & value);
virtual void setAuto(const ParserParameter & param);
template <typename T> T & get();
template <typename T> const T & get() const;
virtual inline operator Real() const { throw std::bad_cast(); };
template <typename T> inline operator T() const;
/* ------------------------------------------------------------------------ */
virtual void printself(std::ostream & stream) const;
virtual const std::type_info& type() const = 0;
protected:
/// Returns const instance of templated sub-class ParameterTyped
template <typename T> const ParameterTyped<T> & getParameterTyped() const;
/// Returns instance of templated sub-class ParameterTyped
template <typename T> ParameterTyped<T> & getParameterTyped();
protected:
/// Name of parameter
std::string name;
private:
/// Description of parameter
std::string description;
/// Type of access
ParameterAccessType param_type;
};
/* -------------------------------------------------------------------------- */
/* Typed Parameter */
/* -------------------------------------------------------------------------- */
/**
* Type parameter transfering a ParserParameter (string: string) to a typed
* parameter in the memory of the p
*/
template <typename T> class ParameterTyped : public Parameter {
public:
ParameterTyped(std::string name, std::string description,
ParameterAccessType param_type, T & param);
/* ------------------------------------------------------------------------ */
template <typename V> void setTyped(const V & value);
- void setAuto(const ParserParameter & param);
+ void setAuto(const ParserParameter & param) override;
T & getTyped();
const T & getTyped() const;
- virtual void printself(std::ostream & stream) const;
+ void printself(std::ostream & stream) const override;
- inline operator Real() const;
+ inline operator Real() const override;
inline const std::type_info& type() const override { return typeid(T); }
private:
/// Value of parameter
T & param;
};
/* -------------------------------------------------------------------------- */
/* Parsable Interface */
/* -------------------------------------------------------------------------- */
/// Defines interface for classes to manipulate parsable parameters
class ParameterRegistry {
public:
ParameterRegistry();
virtual ~ParameterRegistry();
/* ------------------------------------------------------------------------ */
/// Add parameter to the params map
template <typename T>
void registerParam(std::string name, T & variable, ParameterAccessType type,
const std::string & description = "");
/// Add parameter to the params map (with default value)
template <typename T>
void registerParam(std::string name, T & variable, const T & default_value,
ParameterAccessType type,
const std::string & description = "");
/*------------------------------------------------------------------------- */
protected:
void registerSubRegistry(const ID & id, ParameterRegistry & registry);
/* ------------------------------------------------------------------------ */
public:
/// Set value to a parameter (with possible different type)
template <typename T, typename V>
void setMixed(const std::string & name, const V & value);
/// Set value to a parameter
template <typename T> void set(const std::string & name, const T & value);
/// Get value of a parameter
inline const Parameter & get(const std::string & name) const;
std::vector<ID> listParameters() const {
std::vector<ID> params;
for(auto & pair : this->params) params.push_back(pair.first);
return params;
}
std::vector<ID> listSubRegisteries() const {
std::vector<ID> subs;
for(auto & pair : this->sub_registries) subs.push_back(pair.first);
return subs;
}
protected:
template <typename T> T & get(const std::string & name);
protected:
void setParameterAccessType(const std::string & name,
ParameterAccessType ptype);
/* ------------------------------------------------------------------------ */
virtual void printself(std::ostream & stream, int indent) const;
protected:
/// Parameters map
typedef std::map<std::string, Parameter *> Parameters;
Parameters params;
/// list of sub-registries
typedef std::map<std::string, ParameterRegistry *> SubRegisteries;
SubRegisteries sub_registries;
/// should accessor check in sub registries
bool consisder_sub;
};
} // akantu
#include "parameter_registry_tmpl.hh"
#endif /* __AKANTU_PARAMETER_REGISTRY_HH__ */
diff --git a/src/io/parser/parsable.hh b/src/io/parser/parsable.hh
index 16dfab955..8911bddd2 100644
--- a/src/io/parser/parsable.hh
+++ b/src/io/parser/parsable.hh
@@ -1,76 +1,76 @@
/**
* @file parameter_registry.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 09 2012
* @date last modification: Thu Dec 17 2015
*
* @brief Interface of the parameter registry
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "parser.hh"
#include "parameter_registry.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PARSABLE_HH__
#define __AKANTU_PARSABLE_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Parsable Interface */
/* -------------------------------------------------------------------------- */
/// Defines interface for classes to manipulate parsable parameters
class Parsable : public ParameterRegistry {
public:
Parsable(const SectionType & section_type, const ID & id = std::string());
- virtual ~Parsable();
+ ~Parsable() override;
/// Add subsection to the sub_sections map
void registerSubSection(const SectionType & type, const std::string & name,
Parsable & sub_section);
/* ------------------------------------------------------------------------ */
public:
virtual void parseSection(const ParserSection & section);
virtual void parseSubSection(const ParserSection & section);
virtual void parseParam(const ParserParameter & parameter);
private:
SectionType section_type;
/// ID of parsable object
ID pid;
typedef std::pair<SectionType, std::string> SubSectionKey;
typedef std::map<SubSectionKey, Parsable *> SubSections;
/// Subsections map
SubSections sub_sections;
};
} // akantu
#include "parsable_tmpl.hh"
#endif /* __AKANTU_PARSABLE_HH__ */
diff --git a/src/io/parser/parser.hh b/src/io/parser/parser.hh
index 93f74edf7..ffe397dcc 100644
--- a/src/io/parser/parser.hh
+++ b/src/io/parser/parser.hh
@@ -1,515 +1,515 @@
/**
* @file parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Wed Jan 13 2016
*
* @brief File parser interface
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "aka_common.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PARSER_HH__
#define __AKANTU_PARSER_HH__
namespace akantu {
// clang-format off
#define AKANTU_SECTION_TYPES \
(global) \
(material) \
(model) \
(mesh) \
(heat) \
(contact) \
(friction) \
(embedded_interface) \
(rules) \
(non_local) \
(user) \
(solver) \
(neighborhoods) \
(neighborhood) \
(time_step_solver) \
(non_linear_solver) \
(model_solver) \
(integration_scheme) \
(weight_function) \
(not_defined)
// clang-format on
#define AKANTU_SECTION_TYPES_PREFIX(elem) BOOST_PP_CAT(_st_, elem)
#define AKANTU_SECT_PREFIX(s, data, elem) AKANTU_SECTION_TYPES_PREFIX(elem)
/// Defines the possible section types
enum SectionType {
BOOST_PP_SEQ_ENUM(
BOOST_PP_SEQ_TRANSFORM(AKANTU_SECT_PREFIX, _, AKANTU_SECTION_TYPES))
};
#undef AKANTU_SECT_PREFIX
#define AKANTU_SECTION_TYPE_PRINT_CASE(r, data, elem) \
case AKANTU_SECTION_TYPES_PREFIX(elem): { \
stream << BOOST_PP_STRINGIZE(AKANTU_SECTION_TYPES_PREFIX(elem)); \
break; \
}
inline std::ostream & operator<<(std::ostream & stream, SectionType type) {
switch (type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_SECTION_TYPE_PRINT_CASE, _,
AKANTU_SECTION_TYPES)
default:
stream << "not a SectionType";
break;
}
return stream;
}
#undef AKANTU_SECTION_TYPE_PRINT_CASE
/// Defines the possible search contexts/scopes (for parameter search)
enum ParserParameterSearchCxt {
_ppsc_current_scope = 0x1,
_ppsc_parent_scope = 0x2,
_ppsc_current_and_parent_scope = 0x3
};
/* ------------------------------------------------------------------------ */
/* Parameters Class */
/* ------------------------------------------------------------------------ */
class ParserSection;
/// @brief The ParserParameter objects represent the end of tree branches as
/// they
/// are the different informations contained in the input file.
class ParserParameter {
public:
ParserParameter()
- : parent_section(NULL), name(std::string()), value(std::string()),
+ : parent_section(nullptr), name(std::string()), value(std::string()),
dbg_filename(std::string()) {}
ParserParameter(const std::string & name, const std::string & value,
const ParserSection & parent_section)
: parent_section(&parent_section), name(name), value(value),
dbg_filename(std::string()) {}
ParserParameter(const ParserParameter & param)
: parent_section(param.parent_section), name(param.name),
value(param.value), dbg_filename(param.dbg_filename),
dbg_line(param.dbg_line), dbg_column(param.dbg_column) {}
virtual ~ParserParameter() {}
/// Get parameter name
const std::string & getName() const { return name; }
/// Get parameter value
const std::string & getValue() const { return value; }
/// Set info for debug output
void setDebugInfo(const std::string & filename, UInt line, UInt column) {
dbg_filename = filename;
dbg_line = line;
dbg_column = column;
}
template <typename T> inline operator T() const;
// template <typename T> inline operator Vector<T>() const;
// template <typename T> inline operator Matrix<T>() const;
/// Print parameter info in stream
void printself(std::ostream & stream,
__attribute__((unused)) unsigned int indent = 0) const {
stream << name << ": " << value << " (" << dbg_filename << ":" << dbg_line
<< ":" << dbg_column << ")";
}
private:
void setParent(const ParserSection & sect) { parent_section = § }
friend class ParserSection;
private:
/// Pointer to the parent section
const ParserSection * parent_section;
/// Name of the parameter
std::string name;
/// Value of the parameter
std::string value;
/// File for debug output
std::string dbg_filename;
/// Position of parameter in parsed file
UInt dbg_line, dbg_column;
};
/* ------------------------------------------------------------------------ */
/* Sections Class */
/* ------------------------------------------------------------------------ */
/// ParserSection represents a branch of the parsing tree.
class ParserSection {
public:
typedef std::multimap<SectionType, ParserSection> SubSections;
typedef std::map<std::string, ParserParameter> Parameters;
private:
typedef SubSections::const_iterator const_section_iterator_;
public:
/* ------------------------------------------------------------------------ */
/* SubSection iterator */
/* ------------------------------------------------------------------------ */
/// Iterator on sections
class const_section_iterator {
public:
const_section_iterator() {}
const_section_iterator(const const_section_iterator & other)
: it(other.it) {}
const_section_iterator(const const_section_iterator_ & it) : it(it) {}
const_section_iterator & operator=(const const_section_iterator & other) {
if (this != &other) {
it = other.it;
}
return *this;
}
const ParserSection & operator*() const { return it->second; }
const ParserSection * operator->() const { return &(it->second); }
bool operator==(const const_section_iterator & other) const {
return it == other.it;
}
bool operator!=(const const_section_iterator & other) const {
return it != other.it;
}
const_section_iterator & operator++() {
++it;
return *this;
}
const_section_iterator operator++(int) {
const_section_iterator tmp = *this;
operator++();
return tmp;
}
private:
const_section_iterator_ it;
};
/* ------------------------------------------------------------------------ */
/* Parameters iterator */
/* ------------------------------------------------------------------------ */
/// Iterator on parameters
class const_parameter_iterator {
public:
const_parameter_iterator(const const_parameter_iterator & other)
: it(other.it) {}
const_parameter_iterator(const Parameters::const_iterator & it) : it(it) {}
const_parameter_iterator &
operator=(const const_parameter_iterator & other) {
if (this != &other) {
it = other.it;
}
return *this;
}
const ParserParameter & operator*() const { return it->second; }
const ParserParameter * operator->() { return &(it->second); };
bool operator==(const const_parameter_iterator & other) const {
return it == other.it;
}
bool operator!=(const const_parameter_iterator & other) const {
return it != other.it;
}
const_parameter_iterator & operator++() {
++it;
return *this;
}
const_parameter_iterator operator++(int) {
const_parameter_iterator tmp = *this;
operator++();
return tmp;
}
private:
Parameters::const_iterator it;
};
/* ---------------------------------------------------------------------- */
ParserSection()
- : parent_section(NULL), name(std::string()), type(_st_not_defined) {}
+ : parent_section(nullptr), name(std::string()), type(_st_not_defined) {}
ParserSection(const std::string & name, SectionType type)
- : parent_section(NULL), name(name), type(type) {}
+ : parent_section(nullptr), name(name), type(type) {}
ParserSection(const std::string & name, SectionType type,
const std::string & option,
const ParserSection & parent_section)
: parent_section(&parent_section), name(name), type(type),
option(option) {}
ParserSection(const ParserSection & section)
: parent_section(section.parent_section), name(section.name),
type(section.type), option(section.option),
parameters(section.parameters),
sub_sections_by_type(section.sub_sections_by_type) {
setChldrenPointers();
}
ParserSection & operator=(const ParserSection & other) {
if (&other != this) {
parent_section = other.parent_section;
name = other.name;
type = other.type;
option = other.option;
parameters = other.parameters;
sub_sections_by_type = other.sub_sections_by_type;
setChldrenPointers();
}
return *this;
}
virtual ~ParserSection();
virtual void printself(std::ostream & stream, unsigned int indent = 0) const;
/* ---------------------------------------------------------------------- */
/* Creation functions */
/* ---------------------------------------------------------------------- */
public:
ParserParameter & addParameter(const ParserParameter & param);
ParserSection & addSubSection(const ParserSection & section);
protected:
/// Clean ParserSection content
void clean() {
parameters.clear();
sub_sections_by_type.clear();
}
private:
void setChldrenPointers() {
Parameters::iterator pit = this->parameters.begin();
for (; pit != this->parameters.end(); ++pit)
pit->second.setParent(*this);
SubSections::iterator sit = this->sub_sections_by_type.begin();
for (; sit != this->sub_sections_by_type.end(); ++sit)
sit->second.setParent(*this);
}
/* ---------------------------------------------------------------------- */
/* Accessors */
/* ---------------------------------------------------------------------- */
public:
/// Get begin and end iterators on subsections of certain type
std::pair<const_section_iterator, const_section_iterator>
getSubSections(SectionType type = _st_not_defined) const {
if (type != _st_not_defined) {
std::pair<const_section_iterator_, const_section_iterator_> range =
sub_sections_by_type.equal_range(type);
return std::pair<const_section_iterator, const_section_iterator>(
range.first, range.second);
} else {
return std::pair<const_section_iterator, const_section_iterator>(
sub_sections_by_type.begin(), sub_sections_by_type.end());
}
}
/// Get number of subsections of certain type
UInt getNbSubSections(SectionType type = _st_not_defined) const {
if (type != _st_not_defined) {
return this->sub_sections_by_type.count(type);
} else {
return this->sub_sections_by_type.size();
}
}
/// Get begin and end iterators on parameters
std::pair<const_parameter_iterator, const_parameter_iterator>
getParameters() const {
return std::pair<const_parameter_iterator, const_parameter_iterator>(
parameters.begin(), parameters.end());
}
/* ---------------------------------------------------------------------- */
/// Get parameter within specified context
const ParserParameter & getParameter(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
Parameters::const_iterator it;
if (search_ctx & _ppsc_current_scope)
it = parameters.find(name);
if (it == parameters.end()) {
if ((search_ctx & _ppsc_parent_scope) && parent_section)
return parent_section->getParameter(name, search_ctx);
else {
AKANTU_SILENT_EXCEPTION(
"The parameter " << name
<< " has not been found in the specified context");
}
}
return it->second;
}
/* ------------------------------------------------------------------------ */
/// Get parameter within specified context, with a default value in case the
/// parameter does not exists
template <class T>
const T getParameter(
const std::string & name, const T & default_value,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
try {
T tmp = this->getParameter(name, search_ctx);
return tmp;
} catch (debug::Exception &) {
return default_value;
}
}
/* ------------------------------------------------------------------------ */
/// Check if parameter exists within specified context
bool hasParameter(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
Parameters::const_iterator it;
if (search_ctx & _ppsc_current_scope)
it = parameters.find(name);
if (it == parameters.end()) {
if ((search_ctx & _ppsc_parent_scope) && parent_section)
return parent_section->hasParameter(name, search_ctx);
else {
return false;
}
}
return true;
}
/* --------------------------------------------------------------------------
*/
/// Get value of given parameter in context
template <class T>
T getParameterValue(
const std::string & name,
ParserParameterSearchCxt search_ctx = _ppsc_current_scope) const {
const ParserParameter & tmp_param = getParameter(name, search_ctx);
T t = tmp_param;
return t;
}
/* --------------------------------------------------------------------------
*/
/// Get section name
const std::string getName() const { return name; }
/// Get section type
SectionType getType() const { return type; }
/// Get section option
const std::string getOption(const std::string & def = "") const {
return option != "" ? option : def;
}
protected:
void setParent(const ParserSection & sect) { parent_section = § }
/* ---------------------------------------------------------------------- */
/* Members */
/* ---------------------------------------------------------------------- */
private:
/// Pointer to the parent section
const ParserSection * parent_section;
/// Name of section
std::string name;
/// Type of section, see AKANTU_SECTION_TYPES
SectionType type;
/// Section option
std::string option;
/// Map of parameters in section
Parameters parameters;
/// Multi-map of subsections
SubSections sub_sections_by_type;
};
/* ------------------------------------------------------------------------ */
/* Parser Class */
/* ------------------------------------------------------------------------ */
/// Root of parsing tree, represents the global ParserSection
class Parser : public ParserSection {
public:
Parser() : ParserSection("global", _st_global) {}
void parse(const std::string & filename);
std::string getLastParsedFile() const;
static bool isPermissive() { return permissive_parser; }
public:
/// Parse real scalar
static Real parseReal(const std::string & value,
const ParserSection & section);
/// Parse real vector
static Vector<Real> parseVector(const std::string & value,
const ParserSection & section);
/// Parse real matrix
static Matrix<Real> parseMatrix(const std::string & value,
const ParserSection & section);
/// Parse real random parameter
static RandomParameter<Real>
parseRandomParameter(const std::string & value,
const ParserSection & section);
protected:
/// General parse function
template <class T, class Grammar>
static T parseType(const std::string & value, Grammar & grammar);
protected:
// friend class Parsable;
static bool permissive_parser;
std::string last_parsed_file;
};
inline std::ostream & operator<<(std::ostream & stream,
const ParserParameter & _this) {
_this.printself(stream);
return stream;
}
inline std::ostream & operator<<(std::ostream & stream,
const ParserSection & section) {
section.printself(stream);
return stream;
}
} // akantu
#include "parser_tmpl.hh"
#endif /* __AKANTU_PARSER_HH__ */
diff --git a/src/mesh/element_type_map.hh b/src/mesh/element_type_map.hh
index 50ead8453..3a93260ad 100644
--- a/src/mesh/element_type_map.hh
+++ b/src/mesh/element_type_map.hh
@@ -1,437 +1,437 @@
/**
* @file element_type_map.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
* @date last modification: Fri Oct 02 2015
*
* @brief storage class by element type
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_array.hh"
#include "aka_memory.hh"
#include "aka_named_argument.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_TYPE_MAP_HH__
#define __AKANTU_ELEMENT_TYPE_MAP_HH__
namespace akantu {
class FEEngine;
} // namespace akantu
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(all_ghost_types);
DECLARE_NAMED_ARGUMENT(default_value);
DECLARE_NAMED_ARGUMENT(element_kind);
DECLARE_NAMED_ARGUMENT(ghost_type);
DECLARE_NAMED_ARGUMENT(nb_component);
DECLARE_NAMED_ARGUMENT(with_nb_element);
DECLARE_NAMED_ARGUMENT(with_nb_nodes_per_element);
DECLARE_NAMED_ARGUMENT(spatial_dimension);
DECLARE_NAMED_ARGUMENT(_do_not_default);
} // namespace
template <class Stored, typename SupportType = ElementType>
class ElementTypeMap;
/* -------------------------------------------------------------------------- */
/* ElementTypeMapBase */
/* -------------------------------------------------------------------------- */
/// Common non templated base class for the ElementTypeMap class
class ElementTypeMapBase {
public:
virtual ~ElementTypeMapBase() = default;
};
/* -------------------------------------------------------------------------- */
/* ElementTypeMap */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
class ElementTypeMap : public ElementTypeMapBase {
public:
ElementTypeMap();
- ~ElementTypeMap();
+ ~ElementTypeMap() override;
inline static std::string printType(const SupportType & type,
const GhostType & ghost_type);
/*! Tests whether a type is present in the object
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return true if the type is present. */
inline bool exists(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const;
/*! get the stored data corresponding to a type
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline const Stored &
operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const;
/*! get the stored data corresponding to a type
* @param type the type to check for
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline Stored & operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost);
/*! insert data of a new type (not yet present) into the map. THIS METHOD IS
* NOT ARRAY SAFE, when using ElementTypeMapArray, use setArray instead
* @param data to insert
* @param type type of data (if this type is already present in the map,
* an exception is thrown).
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @return stored data corresponding to type. */
inline Stored & operator()(const Stored & insert, const SupportType & type,
const GhostType & ghost_type = _not_ghost);
/// print helper
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
/*! iterator allows to iterate over type-data pairs of the map. The interface
* expects the SupportType to be ElementType. */
typedef std::map<SupportType, Stored> DataMap;
class type_iterator
: private std::iterator<std::forward_iterator_tag, const SupportType> {
public:
using value_type = const SupportType;
using pointer = const SupportType *;
using reference = const SupportType &;
protected:
using DataMapIterator =
typename ElementTypeMap<Stored>::DataMap::const_iterator;
public:
type_iterator(DataMapIterator & list_begin, DataMapIterator & list_end,
UInt dim, ElementKind ek);
type_iterator(const type_iterator & it);
type_iterator() {}
inline reference operator*();
inline reference operator*() const;
inline type_iterator & operator++();
type_iterator operator++(int);
inline bool operator==(const type_iterator & other) const;
inline bool operator!=(const type_iterator & other) const;
type_iterator & operator=(const type_iterator & other);
private:
DataMapIterator list_begin;
DataMapIterator list_end;
UInt dim;
ElementKind kind;
};
/// helper class to use in range for constructions
class ElementTypesIteratorHelper {
public:
using Container = ElementTypeMap<Stored, SupportType>;
using iterator = typename Container::type_iterator;
ElementTypesIteratorHelper(const Container & container, UInt dim,
GhostType ghost_type, ElementKind kind)
: container(std::cref(container)), dim(dim), ghost_type(ghost_type),
kind(kind) {}
template <typename... pack>
ElementTypesIteratorHelper(const Container & container, use_named_args_t,
pack &&... _pack)
: ElementTypesIteratorHelper(
container, OPTIONAL_NAMED_ARG(spatial_dimension, _all_dimensions),
OPTIONAL_NAMED_ARG(ghost_type, _not_ghost),
OPTIONAL_NAMED_ARG(element_kind, _ek_regular)) {}
ElementTypesIteratorHelper(const ElementTypesIteratorHelper &) = default;
ElementTypesIteratorHelper &
operator=(const ElementTypesIteratorHelper &) = default;
ElementTypesIteratorHelper &
operator=(ElementTypesIteratorHelper &&) = default;
iterator begin() {
return container.get().firstType(dim, ghost_type, kind);
}
iterator end() { return container.get().lastType(dim, ghost_type, kind); }
private:
std::reference_wrapper<const Container> container;
UInt dim;
GhostType ghost_type;
ElementKind kind;
};
private:
ElementTypesIteratorHelper
elementTypesImpl(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const;
template <typename... pack>
ElementTypesIteratorHelper
elementTypesImpl(const use_named_args_t & /*unused*/, pack &&... _pack) const;
template <typename... pack>
using named_argument_test =
aka::conjunction<aka::bool_constant<(sizeof...(pack) > 0)>,
is_named_argument<pack>...>;
public:
template <typename... pack>
std::enable_if_t<named_argument_test<pack...>{}, ElementTypesIteratorHelper>
elementTypes(pack &&... _pack) const {
return elementTypesImpl(use_named_args,
std::forward<decltype(_pack)>(_pack)...);
}
template <typename... pack>
std::enable_if_t<not named_argument_test<pack...>{},
ElementTypesIteratorHelper>
elementTypes(pack &&... _pack) const {
return elementTypesImpl(std::forward<decltype(_pack)>(_pack)...);
}
public:
/*! Get an iterator to the beginning of a subset datamap. This method expects
* the SupportType to be ElementType.
* @param dim optional: iterate over data of dimension dim (e.g. when
* iterating over (surface) facets of a 3D mesh, dim would be 2).
* by default, all dimensions are considered.
* @param ghost_type optional: by default, the data map for non-ghost
* elements is iterated over.
* @param kind optional: the kind of element to search for (see
* aka_common.hh), by default all kinds are considered
* @return an iterator to the first stored data matching the filters
* or an iterator to the end of the map if none match*/
inline type_iterator firstType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
/*! Get an iterator to the end of a subset datamap. This method expects
* the SupportType to be ElementType.
* @param dim optional: iterate over data of dimension dim (e.g. when
* iterating over (surface) facets of a 3D mesh, dim would be 2).
* by default, all dimensions are considered.
* @param ghost_type optional: by default, the data map for non-ghost
* elements is iterated over.
* @param kind optional: the kind of element to search for (see
* aka_common.hh), by default all kinds are considered
* @return an iterator to the last stored data matching the filters
* or an iterator to the end of the map if none match */
inline type_iterator lastType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const;
protected:
/*! Direct access to the underlying data map. for internal use by daughter
* classes only
* @param ghost_type whether to return the data map or the ghost_data map
* @return the raw map */
inline DataMap & getData(GhostType ghost_type);
/*! Direct access to the underlying data map. for internal use by daughter
* classes only
* @param ghost_type whether to return the data map or the ghost_data map
* @return the raw map */
inline const DataMap & getData(GhostType ghost_type) const;
/* ------------------------------------------------------------------------ */
protected:
DataMap data;
DataMap ghost_data;
};
/* -------------------------------------------------------------------------- */
/* Some typedefs */
/* -------------------------------------------------------------------------- */
template <typename T, typename SupportType>
class ElementTypeMapArray : public ElementTypeMap<Array<T> *, SupportType>,
public Memory {
public:
using type = T;
using array_type = Array<T>;
protected:
using parent = ElementTypeMap<Array<T> *, SupportType>;
using DataMap = typename parent::DataMap;
public:
using type_iterator = typename parent::type_iterator;
/// standard assigment (copy) operator
void operator=(const ElementTypeMapArray &) = delete;
ElementTypeMapArray(const ElementTypeMapArray &) = delete;
/*! Constructor
* @param id optional: identifier (string)
* @param parent_id optional: parent identifier. for organizational purposes
* only
* @param memory_id optional: choose a specific memory, defaults to memory 0
*/
ElementTypeMapArray(const ID & id = "by_element_type_array",
const ID & parent_id = "no_parent",
const MemoryID & memory_id = 0)
: parent(), Memory(parent_id + ":" + id, memory_id), name(id){};
/*! allocate memory for a new array
* @param size number of tuples of the new array
* @param nb_component tuple size
* @param type the type under which the array is indexed in the map
* @param ghost_type whether to add the field to the data map or the
* ghost_data map
* @return a reference to the allocated array */
inline Array<T> & alloc(UInt size, UInt nb_component,
const SupportType & type,
const GhostType & ghost_type,
const T & default_value = T());
/*! allocate memory for a new array in both the data and the ghost_data map
* @param size number of tuples of the new array
* @param nb_component tuple size
* @param type the type under which the array is indexed in the map*/
inline void alloc(UInt size, UInt nb_component, const SupportType & type,
const T & default_value = T());
/* get a reference to the array of certain type
* @param type data filed under type is returned
* @param ghost_type optional: by default the non-ghost map is searched
* @return a reference to the array */
inline const Array<T> &
operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const;
/// access the data of an element, this combine the map and array accessor
inline const T & operator()(const Element & element) const;
/// access the data of an element, this combine the map and array accessor
inline T & operator()(const Element & element);
/* get a reference to the array of certain type
* @param type data filed under type is returned
* @param ghost_type optional: by default the non-ghost map is searched
* @return a const reference to the array */
inline Array<T> & operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost);
/*! insert data of a new type (not yet present) into the map.
* @param type type of data (if this type is already present in the map,
* an exception is thrown).
* @param ghost_type optional: by default, the data map for non-ghost
* elements is searched
* @param vect the vector to include into the map
* @return stored data corresponding to type. */
inline void setArray(const SupportType & type, const GhostType & ghost_type,
const Array<T> & vect);
/*! frees all memory related to the data*/
inline void free();
/*! set all values in the ElementTypeMap to zero*/
inline void clear();
/*! deletes and reorders entries in the stored arrays
* @param new_numbering a ElementTypeMapArray of new indices. UInt(-1)
* indicates
* deleted entries. */
inline void
onElementsRemoved(const ElementTypeMapArray<UInt> & new_numbering);
/// text output helper
- virtual void printself(std::ostream & stream, int indent = 0) const;
+ void printself(std::ostream & stream, int indent = 0) const override;
/*! set the id
* @param id the new name
*/
inline void setID(const ID & id) { this->id = id; }
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
ElementTypeMap<UInt> nb_components;
for (auto & type : this->elementTypes(dim, ghost_type, kind)) {
UInt nb_comp = (*this)(type, ghost_type).getNbComponent();
nb_components(type, ghost_type) = nb_comp;
}
return nb_components;
}
/* ------------------------------------------------------------------------ */
/* more evolved allocators */
/* ------------------------------------------------------------------------ */
public:
/// initialize the arrays in accordance to a functor
template <class Func>
void initialize(const Func & f, const T & default_value, bool do_not_default);
/// initialize with sizes and number of components in accordance of a mesh
/// content
template <typename... pack>
void initialize(const Mesh & mesh, pack &&... _pack);
/// initialize with sizes and number of components in accordance of a fe
/// engine content (aka integration points)
template <typename... pack>
void initialize(const FEEngine & fe_engine, pack &&... _pack);
/* ------------------------------------------------------------------------ */
/* Accesssors */
/* ------------------------------------------------------------------------ */
public:
/// get the name of the internal field
AKANTU_GET_MACRO(Name, name, ID);
/// name of the elment type map: e.g. connectivity, grad_u
ID name;
};
/// to store data Array<Real> by element type
using ElementTypeMapReal = ElementTypeMapArray<Real>;
/// to store data Array<Int> by element type
using ElementTypeMapInt = ElementTypeMapArray<Int>;
/// to store data Array<UInt> by element type
using ElementTypeMapUInt = ElementTypeMapArray<UInt, ElementType>;
/// Map of data of type UInt stored in a mesh
using UIntDataMap = std::map<std::string, Array<UInt> *>;
using ElementTypeMapUIntDataMap = ElementTypeMap<UIntDataMap, ElementType>;
} // namespace akantu
#endif /* __AKANTU_ELEMENT_TYPE_MAP_HH__ */
diff --git a/src/mesh/group_manager.cc b/src/mesh/group_manager.cc
index 11ff31129..9899e747d 100644
--- a/src/mesh/group_manager.cc
+++ b/src/mesh/group_manager.cc
@@ -1,1040 +1,1040 @@
/**
* @file group_manager.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Mon Aug 17 2015
*
* @brief Stores information about ElementGroup and NodeGroup
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "group_manager.hh"
#include "aka_csr.hh"
#include "data_accessor.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iterator>
#include <list>
#include <numeric>
#include <queue>
#include <sstream>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
GroupManager::GroupManager(const Mesh & mesh, const ID & id,
const MemoryID & mem_id)
: id(id), memory_id(mem_id), mesh(mesh) {
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
GroupManager::~GroupManager() {
auto eit = element_groups.begin();
auto eend = element_groups.end();
for (; eit != eend; ++eit)
delete (eit->second);
auto nit = node_groups.begin();
auto nend = node_groups.end();
for (; nit != nend; ++nit)
delete (nit->second);
}
/* -------------------------------------------------------------------------- */
NodeGroup & GroupManager::createNodeGroup(const std::string & group_name,
bool replace_group) {
AKANTU_DEBUG_IN();
auto it = node_groups.find(group_name);
if (it != node_groups.end()) {
if (replace_group) {
it->second->empty();
AKANTU_DEBUG_OUT();
return *(it->second);
} else
AKANTU_EXCEPTION(
"Trying to create a node group that already exists:" << group_name);
}
std::stringstream sstr;
sstr << this->id << ":" << group_name << "_node_group";
NodeGroup * node_group =
new NodeGroup(group_name, mesh, sstr.str(), memory_id);
node_groups[group_name] = node_group;
AKANTU_DEBUG_OUT();
return *node_group;
}
/* -------------------------------------------------------------------------- */
template <typename T>
NodeGroup &
GroupManager::createFilteredNodeGroup(const std::string & group_name,
const NodeGroup & source_node_group,
T & filter) {
AKANTU_DEBUG_IN();
NodeGroup & node_group = this->createNodeGroup(group_name);
node_group.append(source_node_group);
if (T::type == FilterFunctor::_node_filter_functor) {
node_group.applyNodeFilter(filter);
} else {
AKANTU_DEBUG_ERROR("ElementFilter cannot be applied to NodeGroup yet."
<< " Needs to be implemented.");
}
AKANTU_DEBUG_OUT();
return node_group;
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyNodeGroup(const std::string & group_name) {
AKANTU_DEBUG_IN();
NodeGroups::iterator nit = node_groups.find(group_name);
NodeGroups::iterator nend = node_groups.end();
if (nit != nend) {
delete (nit->second);
node_groups.erase(nit);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
UInt dimension,
bool replace_group) {
AKANTU_DEBUG_IN();
NodeGroup & new_node_group =
createNodeGroup(group_name + "_nodes", replace_group);
auto it = element_groups.find(group_name);
if (it != element_groups.end()) {
if (replace_group) {
it->second->empty();
AKANTU_DEBUG_OUT();
return *(it->second);
} else
AKANTU_EXCEPTION("Trying to create a element group that already exists:"
<< group_name);
}
std::stringstream sstr;
sstr << this->id << ":" << group_name << "_element_group";
ElementGroup * element_group = new ElementGroup(
group_name, mesh, new_node_group, dimension, sstr.str(), memory_id);
std::stringstream sstr_nodes;
sstr_nodes << group_name << "_nodes";
node_groups[sstr_nodes.str()] = &new_node_group;
element_groups[group_name] = element_group;
AKANTU_DEBUG_OUT();
return *element_group;
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyElementGroup(const std::string & group_name,
bool destroy_node_group) {
AKANTU_DEBUG_IN();
auto eit = element_groups.find(group_name);
auto eend = element_groups.end();
if (eit != eend) {
if (destroy_node_group)
destroyNodeGroup(eit->second->getNodeGroup().getName());
delete (eit->second);
element_groups.erase(eit);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::destroyAllElementGroups(bool destroy_node_groups) {
AKANTU_DEBUG_IN();
auto eit = element_groups.begin();
auto eend = element_groups.end();
for (; eit != eend; ++eit) {
if (destroy_node_groups)
destroyNodeGroup(eit->second->getNodeGroup().getName());
delete (eit->second);
}
element_groups.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::createElementGroup(const std::string & group_name,
UInt dimension,
NodeGroup & node_group) {
AKANTU_DEBUG_IN();
if (element_groups.find(group_name) != element_groups.end())
AKANTU_EXCEPTION(
"Trying to create a element group that already exists:" << group_name);
ElementGroup * element_group =
new ElementGroup(group_name, mesh, node_group, dimension,
id + ":" + group_name + "_element_group", memory_id);
element_groups[group_name] = element_group;
AKANTU_DEBUG_OUT();
return *element_group;
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementGroup & GroupManager::createFilteredElementGroup(
const std::string & group_name, UInt dimension,
const NodeGroup & node_group, T & filter) {
AKANTU_DEBUG_IN();
- ElementGroup * element_group = NULL;
+ ElementGroup * element_group = nullptr;
if (T::type == FilterFunctor::_node_filter_functor) {
NodeGroup & filtered_node_group = this->createFilteredNodeGroup(
group_name + "_nodes", node_group, filter);
element_group =
&(this->createElementGroup(group_name, dimension, filtered_node_group));
} else if (T::type == FilterFunctor::_element_filter_functor) {
AKANTU_DEBUG_ERROR(
"Cannot handle an ElementFilter yet. Needs to be implemented.");
}
AKANTU_DEBUG_OUT();
return *element_group;
}
/* -------------------------------------------------------------------------- */
class ClusterSynchronizer : public DataAccessor<Element> {
using DistantIDs = std::set<std::pair<UInt, UInt>>;
public:
ClusterSynchronizer(GroupManager & group_manager, UInt element_dimension,
std::string cluster_name_prefix,
ElementTypeMapArray<UInt> & element_to_fragment,
const ElementSynchronizer & element_synchronizer,
UInt nb_cluster)
: group_manager(group_manager), element_dimension(element_dimension),
cluster_name_prefix(cluster_name_prefix),
element_to_fragment(element_to_fragment),
element_synchronizer(element_synchronizer), nb_cluster(nb_cluster) {}
UInt synchronize() {
Communicator & comm = Communicator::getStaticCommunicator();
UInt rank = comm.whoAmI();
UInt nb_proc = comm.getNbProc();
/// find starting index to renumber local clusters
Array<UInt> nb_cluster_per_proc(nb_proc);
nb_cluster_per_proc(rank) = nb_cluster;
comm.allGather(nb_cluster_per_proc);
starting_index = std::accumulate(nb_cluster_per_proc.begin(),
nb_cluster_per_proc.begin() + rank, 0);
UInt global_nb_fragment =
std::accumulate(nb_cluster_per_proc.begin() + rank,
nb_cluster_per_proc.end(), starting_index);
/// create the local to distant cluster pairs with neighbors
element_synchronizer.synchronizeOnce(*this, _gst_gm_clusters);
/// count total number of pairs
Array<int> nb_pairs(nb_proc); // This is potentially a bug for more than
// 2**31 pairs, but due to a all gatherv after
// it must be int to match MPI interfaces
nb_pairs(rank) = distant_ids.size();
comm.allGather(nb_pairs);
UInt total_nb_pairs = std::accumulate(nb_pairs.begin(), nb_pairs.end(), 0);
/// generate pairs global array
UInt local_pair_index =
std::accumulate(nb_pairs.storage(), nb_pairs.storage() + rank, 0);
Array<UInt> total_pairs(total_nb_pairs, 2);
for (auto & ids : distant_ids) {
total_pairs(local_pair_index, 0) = ids.first;
total_pairs(local_pair_index, 1) = ids.second;
++local_pair_index;
}
/// communicate pairs to all processors
nb_pairs *= 2;
comm.allGatherV(total_pairs, nb_pairs);
/// renumber clusters
/// generate fragment list
std::vector<std::set<UInt>> global_clusters;
UInt total_nb_cluster = 0;
Array<bool> is_fragment_in_cluster(global_nb_fragment, 1, false);
std::queue<UInt> fragment_check_list;
while (total_pairs.size() != 0) {
/// create a new cluster
++total_nb_cluster;
global_clusters.resize(total_nb_cluster);
std::set<UInt> & current_cluster = global_clusters[total_nb_cluster - 1];
UInt first_fragment = total_pairs(0, 0);
UInt second_fragment = total_pairs(0, 1);
total_pairs.erase(0);
fragment_check_list.push(first_fragment);
fragment_check_list.push(second_fragment);
while (!fragment_check_list.empty()) {
UInt current_fragment = fragment_check_list.front();
UInt * total_pairs_end =
total_pairs.storage() + total_pairs.size() * 2;
UInt * fragment_found =
std::find(total_pairs.storage(), total_pairs_end, current_fragment);
if (fragment_found != total_pairs_end) {
UInt position = fragment_found - total_pairs.storage();
UInt pair = position / 2;
UInt other_index = (position + 1) % 2;
fragment_check_list.push(total_pairs(pair, other_index));
total_pairs.erase(pair);
} else {
fragment_check_list.pop();
current_cluster.insert(current_fragment);
is_fragment_in_cluster(current_fragment) = true;
}
}
}
/// add to FragmentToCluster all local fragments
for (UInt c = 0; c < global_nb_fragment; ++c) {
if (!is_fragment_in_cluster(c)) {
++total_nb_cluster;
global_clusters.resize(total_nb_cluster);
std::set<UInt> & current_cluster =
global_clusters[total_nb_cluster - 1];
current_cluster.insert(c);
}
}
/// reorganize element groups to match global clusters
for (UInt c = 0; c < global_clusters.size(); ++c) {
/// create new element group corresponding to current cluster
std::stringstream sstr;
sstr << cluster_name_prefix << "_" << c;
ElementGroup & cluster =
group_manager.createElementGroup(sstr.str(), element_dimension, true);
std::set<UInt>::iterator it = global_clusters[c].begin();
std::set<UInt>::iterator end = global_clusters[c].end();
/// append to current element group all fragments that belong to
/// the same cluster if they exist
for (; it != end; ++it) {
Int local_index = *it - starting_index;
if (local_index < 0 || local_index >= Int(nb_cluster))
continue;
std::stringstream tmp_sstr;
tmp_sstr << "tmp_" << cluster_name_prefix << "_" << local_index;
auto eg_it = group_manager.element_group_find(tmp_sstr.str());
AKANTU_DEBUG_ASSERT(eg_it != group_manager.element_group_end(),
"Temporary fragment \"" << tmp_sstr.str()
<< "\" not found");
cluster.append(*(eg_it->second));
group_manager.destroyElementGroup(tmp_sstr.str(), true);
}
}
return total_nb_cluster;
}
private:
/// functions for parallel communications
inline UInt getNbData(const Array<Element> & elements,
- const SynchronizationTag & tag) const {
+ const SynchronizationTag & tag) const override {
if (tag == _gst_gm_clusters)
return elements.size() * sizeof(UInt);
return 0;
}
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
- const SynchronizationTag & tag) const {
+ const SynchronizationTag & tag) const override {
if (tag != _gst_gm_clusters)
return;
Array<Element>::const_iterator<> el_it = elements.begin();
Array<Element>::const_iterator<> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
const Element & el = *el_it;
/// for each element pack its global cluster index
buffer << element_to_fragment(el.type, el.ghost_type)(el.element) +
starting_index;
}
}
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
- const SynchronizationTag & tag) {
+ const SynchronizationTag & tag) override {
if (tag != _gst_gm_clusters)
return;
Array<Element>::const_iterator<> el_it = elements.begin();
Array<Element>::const_iterator<> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
UInt distant_cluster;
buffer >> distant_cluster;
const Element & el = *el_it;
UInt local_cluster =
element_to_fragment(el.type, el.ghost_type)(el.element) +
starting_index;
distant_ids.insert(std::make_pair(local_cluster, distant_cluster));
}
}
private:
GroupManager & group_manager;
UInt element_dimension;
std::string cluster_name_prefix;
ElementTypeMapArray<UInt> & element_to_fragment;
const ElementSynchronizer & element_synchronizer;
UInt nb_cluster;
DistantIDs distant_ids;
UInt starting_index;
};
/* -------------------------------------------------------------------------- */
/// \todo this function doesn't work in 1D
UInt GroupManager::createBoundaryGroupFromGeometry() {
UInt spatial_dimension = mesh.getSpatialDimension();
return createClusters(spatial_dimension - 1, "boundary");
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::createClusters(
UInt element_dimension, Mesh & mesh_facets, std::string cluster_name_prefix,
const GroupManager::ClusteringFilter & filter) {
return createClusters(element_dimension, cluster_name_prefix, filter, mesh_facets);
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::createClusters(
UInt element_dimension, std::string cluster_name_prefix,
const GroupManager::ClusteringFilter & filter) {
std::unique_ptr<Mesh> mesh_facets;
if (!mesh_facets && element_dimension > 0) {
MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
mesh_facets = std::make_unique<Mesh>(mesh.getSpatialDimension(),
mesh_accessor.getNodesSharedPtr(),
"mesh_facets_for_clusters");
mesh_facets->defineMeshParent(mesh);
MeshUtils::buildAllFacets(mesh, *mesh_facets, element_dimension,
element_dimension - 1);
}
return createClusters(element_dimension, cluster_name_prefix, filter, *mesh_facets);
}
/* -------------------------------------------------------------------------- */
//// \todo if needed element list construction can be optimized by
//// templating the filter class
UInt GroupManager::createClusters(UInt element_dimension,
std::string cluster_name_prefix,
const GroupManager::ClusteringFilter & filter,
Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
UInt nb_proc = mesh.getCommunicator().getNbProc();
std::string tmp_cluster_name_prefix = cluster_name_prefix;
ElementTypeMapArray<UInt> * element_to_fragment = nullptr;
if (nb_proc > 1 && mesh.isDistributed()) {
element_to_fragment =
new ElementTypeMapArray<UInt>("element_to_fragment", id, memory_id);
element_to_fragment->initialize(
mesh, _nb_component = 1, _spatial_dimension = element_dimension,
_element_kind = _ek_not_defined, _with_nb_element = true);
// mesh.initElementTypeMapArray(*element_to_fragment, 1, element_dimension,
// false, _ek_not_defined, true);
tmp_cluster_name_prefix = "tmp_" + tmp_cluster_name_prefix;
}
ElementTypeMapArray<bool> seen_elements("seen_elements", id, memory_id);
seen_elements.initialize(mesh, _spatial_dimension = element_dimension,
_element_kind = _ek_not_defined,
_with_nb_element = true);
// mesh.initElementTypeMapArray(seen_elements, 1, element_dimension, false,
// _ek_not_defined, true);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Element el;
el.ghost_type = ghost_type;
Mesh::type_iterator type_it =
mesh.firstType(element_dimension, ghost_type, _ek_not_defined);
Mesh::type_iterator type_end =
mesh.lastType(element_dimension, ghost_type, _ek_not_defined);
for (; type_it != type_end; ++type_it) {
el.type = *type_it;
UInt nb_element = mesh.getNbElement(*type_it, ghost_type);
Array<bool> & seen_elements_array = seen_elements(el.type, ghost_type);
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
if (!filter(el))
seen_elements_array(e) = true;
}
}
}
Array<bool> checked_node(mesh.getNbNodes(), 1, false);
UInt nb_cluster = 0;
/// keep looping until all elements are seen
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Element uns_el;
uns_el.ghost_type = ghost_type;
Mesh::type_iterator type_it =
mesh.firstType(element_dimension, ghost_type, _ek_not_defined);
Mesh::type_iterator type_end =
mesh.lastType(element_dimension, ghost_type, _ek_not_defined);
for (; type_it != type_end; ++type_it) {
uns_el.type = *type_it;
Array<bool> & seen_elements_vec =
seen_elements(uns_el.type, uns_el.ghost_type);
for (UInt e = 0; e < seen_elements_vec.size(); ++e) {
// skip elements that have been already seen
if (seen_elements_vec(e) == true)
continue;
// set current element
uns_el.element = e;
seen_elements_vec(e) = true;
/// create a new cluster
std::stringstream sstr;
sstr << tmp_cluster_name_prefix << "_" << nb_cluster;
ElementGroup & cluster =
createElementGroup(sstr.str(), element_dimension, true);
++nb_cluster;
// point element are cluster by themself
if (element_dimension == 0) {
cluster.add(uns_el);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(uns_el.type);
Vector<UInt> connect =
mesh.getConnectivity(uns_el.type, uns_el.ghost_type)
.begin(nb_nodes_per_element)[uns_el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
/// add element's nodes to the cluster
UInt node = connect[n];
if (!checked_node(node)) {
cluster.addNode(node);
checked_node(node) = true;
}
}
continue;
}
std::queue<Element> element_to_add;
element_to_add.push(uns_el);
/// keep looping until current cluster is complete (no more
/// connected elements)
while (!element_to_add.empty()) {
/// take first element and erase it in the queue
Element el = element_to_add.front();
element_to_add.pop();
/// if parallel, store cluster index per element
if (nb_proc > 1 && mesh.isDistributed())
(*element_to_fragment)(el.type, el.ghost_type)(el.element) =
nb_cluster - 1;
/// add current element to the cluster
cluster.add(el);
const Array<Element> & element_to_facet =
mesh_facets.getSubelementToElement(el.type, el.ghost_type);
UInt nb_facet_per_element = element_to_facet.getNbComponent();
for (UInt f = 0; f < nb_facet_per_element; ++f) {
const Element & facet = element_to_facet(el.element, f);
if (facet == ElementNull)
continue;
const std::vector<Element> & connected_elements =
mesh_facets.getElementToSubelement(
facet.type, facet.ghost_type)(facet.element);
for (UInt elem = 0; elem < connected_elements.size(); ++elem) {
const Element & check_el = connected_elements[elem];
// check if this element has to be skipped
if (check_el == ElementNull || check_el == el)
continue;
Array<bool> & seen_elements_vec_current =
seen_elements(check_el.type, check_el.ghost_type);
if (seen_elements_vec_current(check_el.element) == false) {
seen_elements_vec_current(check_el.element) = true;
element_to_add.push(check_el);
}
}
}
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(el.type);
Vector<UInt> connect = mesh.getConnectivity(el.type, el.ghost_type)
.begin(nb_nodes_per_element)[el.element];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
/// add element's nodes to the cluster
UInt node = connect[n];
if (!checked_node(node)) {
cluster.addNode(node, false);
checked_node(node) = true;
}
}
}
}
}
}
if (nb_proc > 1 && mesh.isDistributed()) {
ClusterSynchronizer cluster_synchronizer(
*this, element_dimension, cluster_name_prefix, *element_to_fragment,
this->mesh.getElementSynchronizer(), nb_cluster);
nb_cluster = cluster_synchronizer.synchronize();
delete element_to_fragment;
}
if (mesh.isDistributed())
this->synchronizeGroupNames();
AKANTU_DEBUG_OUT();
return nb_cluster;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void GroupManager::createGroupsFromMeshData(const std::string & dataset_name) {
std::set<std::string> group_names;
const ElementTypeMapArray<T> & datas = mesh.getData<T>(dataset_name);
typedef typename ElementTypeMapArray<T>::type_iterator type_iterator;
std::map<std::string, UInt> group_dim;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
type_iterator type_it = datas.firstType(_all_dimensions, *gt);
type_iterator type_end = datas.lastType(_all_dimensions, *gt);
for (; type_it != type_end; ++type_it) {
const Array<T> & dataset = datas(*type_it, *gt);
UInt nb_element = mesh.getNbElement(*type_it, *gt);
AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
"Not the same number of elements ("
<< *type_it << ":" << *gt
<< ") in the map from MeshData ("
<< dataset.size() << ") " << dataset_name
<< " and in the mesh (" << nb_element << ")!");
for (UInt e(0); e < nb_element; ++e) {
std::stringstream sstr;
sstr << dataset(e);
std::string gname = sstr.str();
group_names.insert(gname);
std::map<std::string, UInt>::iterator it = group_dim.find(gname);
if (it == group_dim.end()) {
group_dim[gname] = mesh.getSpatialDimension(*type_it);
} else {
it->second = std::max(it->second, mesh.getSpatialDimension(*type_it));
}
}
}
}
std::set<std::string>::iterator git = group_names.begin();
std::set<std::string>::iterator gend = group_names.end();
for (; git != gend; ++git)
createElementGroup(*git, group_dim[*git]);
if (mesh.isDistributed())
this->synchronizeGroupNames();
Element el;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
el.ghost_type = *gt;
type_iterator type_it = datas.firstType(_all_dimensions, *gt);
type_iterator type_end = datas.lastType(_all_dimensions, *gt);
for (; type_it != type_end; ++type_it) {
el.type = *type_it;
const Array<T> & dataset = datas(*type_it, *gt);
UInt nb_element = mesh.getNbElement(*type_it, *gt);
AKANTU_DEBUG_ASSERT(dataset.size() == nb_element,
"Not the same number of elements in the map from "
"MeshData and in the mesh!");
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(el.type);
Array<UInt>::const_iterator<Vector<UInt>> cit =
mesh.getConnectivity(*type_it, *gt).begin(nb_nodes_per_element);
for (UInt e(0); e < nb_element; ++e, ++cit) {
el.element = e;
std::stringstream sstr;
sstr << dataset(e);
ElementGroup & group = getElementGroup(sstr.str());
group.add(el, false, false);
const Vector<UInt> & connect = *cit;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connect[n];
group.addNode(node, false);
}
}
}
}
git = group_names.begin();
for (; git != gend; ++git) {
getElementGroup(*git).optimize();
}
}
template void GroupManager::createGroupsFromMeshData<std::string>(
const std::string & dataset_name);
template void
GroupManager::createGroupsFromMeshData<UInt>(const std::string & dataset_name);
/* -------------------------------------------------------------------------- */
void GroupManager::createElementGroupFromNodeGroup(
const std::string & name, const std::string & node_group_name,
UInt dimension) {
NodeGroup & node_group = getNodeGroup(node_group_name);
ElementGroup & group = createElementGroup(name, dimension, node_group);
group.fillFromNodeGroup();
}
/* -------------------------------------------------------------------------- */
void GroupManager::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "GroupManager [" << std::endl;
std::set<std::string> node_group_seen;
for (const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it) {
it->second->printself(stream, indent + 1);
node_group_seen.insert(it->second->getNodeGroup().getName());
}
for (const_node_group_iterator it(node_group_begin()); it != node_group_end();
++it) {
if (node_group_seen.find(it->second->getName()) == node_group_seen.end())
it->second->printself(stream, indent + 1);
}
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
UInt GroupManager::getNbElementGroups(UInt dimension) const {
if (dimension == _all_dimensions)
return element_groups.size();
ElementGroups::const_iterator it = element_groups.begin();
ElementGroups::const_iterator end = element_groups.end();
UInt count = 0;
for (; it != end; ++it)
count += (it->second->getDimension() == dimension);
return count;
}
/* -------------------------------------------------------------------------- */
void GroupManager::checkAndAddGroups(CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
UInt nb_node_group;
buffer >> nb_node_group;
AKANTU_DEBUG_INFO("Received " << nb_node_group << " node group names");
for (UInt ng = 0; ng < nb_node_group; ++ng) {
std::string node_group_name;
buffer >> node_group_name;
if (node_groups.find(node_group_name) == node_groups.end()) {
this->createNodeGroup(node_group_name);
}
AKANTU_DEBUG_INFO("Received node goup name: " << node_group_name);
}
UInt nb_element_group;
buffer >> nb_element_group;
AKANTU_DEBUG_INFO("Received " << nb_element_group << " element group names");
for (UInt eg = 0; eg < nb_element_group; ++eg) {
std::string element_group_name;
buffer >> element_group_name;
std::string node_group_name;
buffer >> node_group_name;
UInt dim;
buffer >> dim;
AKANTU_DEBUG_INFO("Received element group name: "
<< element_group_name << " corresponding to a "
<< Int(dim) << "D group with node group "
<< node_group_name);
NodeGroup & node_group = *node_groups[node_group_name];
if (element_groups.find(element_group_name) == element_groups.end()) {
this->createElementGroup(element_group_name, dim, node_group);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::fillBufferWithGroupNames(
DynamicCommunicationBuffer & comm_buffer) const {
AKANTU_DEBUG_IN();
// packing node group names;
UInt nb_groups = this->node_groups.size();
comm_buffer << nb_groups;
AKANTU_DEBUG_INFO("Sending " << nb_groups << " node group names");
NodeGroups::const_iterator nnames_it = node_groups.begin();
NodeGroups::const_iterator nnames_end = node_groups.end();
for (; nnames_it != nnames_end; ++nnames_it) {
std::string node_group_name = nnames_it->first;
comm_buffer << node_group_name;
AKANTU_DEBUG_INFO("Sending node goupe name: " << node_group_name);
}
// packing element group names with there associated node group name
nb_groups = this->element_groups.size();
comm_buffer << nb_groups;
AKANTU_DEBUG_INFO("Sending " << nb_groups << " element group names");
ElementGroups::const_iterator gnames_it = this->element_groups.begin();
ElementGroups::const_iterator gnames_end = this->element_groups.end();
for (; gnames_it != gnames_end; ++gnames_it) {
ElementGroup & element_group = *(gnames_it->second);
std::string element_group_name = gnames_it->first;
std::string node_group_name = element_group.getNodeGroup().getName();
UInt dim = element_group.getDimension();
comm_buffer << element_group_name;
comm_buffer << node_group_name;
comm_buffer << dim;
AKANTU_DEBUG_INFO("Sending element group name: "
<< element_group_name << " corresponding to a "
<< Int(dim) << "D group with the node group "
<< node_group_name);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GroupManager::synchronizeGroupNames() {
AKANTU_DEBUG_IN();
const Communicator & comm = mesh.getCommunicator();
Int nb_proc = comm.getNbProc();
Int my_rank = comm.whoAmI();
if (nb_proc == 1)
return;
if (my_rank == 0) {
for (Int p = 1; p < nb_proc; ++p) {
CommunicationStatus status;
comm.probe<char>(p, p, status);
AKANTU_DEBUG_INFO("Got " << printMemorySize<char>(status.size())
<< " from proc " << p);
CommunicationBuffer recv_buffer(status.size());
comm.receive(recv_buffer, p, p);
this->checkAndAddGroups(recv_buffer);
}
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
UInt buffer_size = comm_buffer.size();
comm.broadcast(buffer_size, 0);
AKANTU_DEBUG_INFO("Initiating broadcast with "
<< printMemorySize<char>(comm_buffer.size()));
comm.broadcast(comm_buffer, 0);
} else {
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
AKANTU_DEBUG_INFO("Sending " << printMemorySize<char>(comm_buffer.size())
<< " to proc " << 0);
comm.send(comm_buffer, 0, my_rank);
UInt buffer_size = 0;
comm.broadcast(buffer_size, 0);
AKANTU_DEBUG_INFO("Receiving broadcast with "
<< printMemorySize<char>(comm_buffer.size()));
CommunicationBuffer recv_buffer(buffer_size);
comm.broadcast(recv_buffer, 0);
this->checkAndAddGroups(recv_buffer);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
const ElementGroup &
GroupManager::getElementGroup(const std::string & name) const {
const_element_group_iterator it = element_group_find(name);
if (it == element_group_end()) {
AKANTU_EXCEPTION("There are no element groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
ElementGroup & GroupManager::getElementGroup(const std::string & name) {
element_group_iterator it = element_group_find(name);
if (it == element_group_end()) {
AKANTU_EXCEPTION("There are no element groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
const NodeGroup & GroupManager::getNodeGroup(const std::string & name) const {
const_node_group_iterator it = node_group_find(name);
if (it == node_group_end()) {
AKANTU_EXCEPTION("There are no node groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
NodeGroup & GroupManager::getNodeGroup(const std::string & name) {
node_group_iterator it = node_group_find(name);
if (it == node_group_end()) {
AKANTU_EXCEPTION("There are no node groups named "
<< name << " associated to the group manager: " << id);
}
return *(it->second);
}
} // namespace akantu
diff --git a/src/mesh/group_manager_inline_impl.cc b/src/mesh/group_manager_inline_impl.cc
index d6ebfbbf2..72f4946ff 100644
--- a/src/mesh/group_manager_inline_impl.cc
+++ b/src/mesh/group_manager_inline_impl.cc
@@ -1,207 +1,207 @@
/**
* @file group_manager_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Tue Dec 08 2015
*
* @brief Stores information relevent to the notion of domain boundary and
* surfaces.
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "dumper_field.hh"
#include "element_group.hh"
#include "element_type_map_filter.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_nodal_field.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, template <bool> class dump_type>
dumper::Field * GroupManager::createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
- if (field_ptr == NULL)
- return NULL;
+ if (field_ptr == nullptr)
+ return nullptr;
if (group_name == "all")
return this->createElementalField<dump_type<false> >(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
else
return this->createElementalFilteredField<dump_type<true> >(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <class> class T2,
template <class, template <class> class, bool> class dump_type>
dumper::Field * GroupManager::createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
- if (field_ptr == NULL)
- return NULL;
+ if (field_ptr == nullptr)
+ return nullptr;
if (group_name == "all")
return this->createElementalField<dump_type<T, T2, false> >(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
else
return this->createElementalFilteredField<dump_type<T, T2, true> >(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename T2, bool filtered>
class dump_type> ///< type of InternalMaterialField
dumper::Field *
GroupManager::createElementalField(const ElementTypeMapArray<T> & field,
const std::string & group_name,
UInt spatial_dimension,
const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const ElementTypeMapArray<T> * field_ptr = &field;
- if (field_ptr == NULL)
- return NULL;
+ if (field_ptr == nullptr)
+ return nullptr;
if (group_name == "all")
return this->createElementalField<dump_type<T, false> >(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
else
return this->createElementalFilteredField<dump_type<T, true> >(
field, group_name, spatial_dimension, kind, nb_data_per_elem);
}
/* -------------------------------------------------------------------------- */
template <typename dump_type, typename field_type>
dumper::Field * GroupManager::createElementalField(
const field_type & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const field_type * field_ptr = &field;
- if (field_ptr == NULL)
- return NULL;
+ if (field_ptr == nullptr)
+ return nullptr;
if (group_name != "all")
throw;
dumper::Field * dumper =
new dump_type(field, spatial_dimension, _not_ghost, kind);
dumper->setNbDataPerElem(nb_data_per_elem);
return dumper;
}
/* -------------------------------------------------------------------------- */
template <typename dump_type, typename field_type>
dumper::Field * GroupManager::createElementalFilteredField(
const field_type & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem) {
const field_type * field_ptr = &field;
- if (field_ptr == NULL)
- return NULL;
+ if (field_ptr == nullptr)
+ return nullptr;
if (group_name == "all")
throw;
typedef typename field_type::type T;
ElementGroup & group = this->getElementGroup(group_name);
UInt dim = group.getDimension();
if (dim != spatial_dimension)
throw;
const ElementTypeMapArray<UInt> & elemental_filter = group.getElements();
ElementTypeMapArrayFilter<T> * filtered = new ElementTypeMapArrayFilter<T>(
field, elemental_filter, nb_data_per_elem);
dumper::Field * dumper = new dump_type(*filtered, dim, _not_ghost, kind);
dumper->setNbDataPerElem(nb_data_per_elem);
return dumper;
}
/* -------------------------------------------------------------------------- */
template <typename type, bool flag, template <class, bool> class ftype>
dumper::Field * GroupManager::createNodalField(const ftype<type, flag> * field,
const std::string & group_name,
UInt padding_size) {
- if (field == NULL)
- return NULL;
+ if (field == nullptr)
+ return nullptr;
if (group_name == "all") {
typedef typename dumper::NodalField<type, false> DumpType;
- DumpType * dumper = new DumpType(*field, 0, 0, NULL);
+ DumpType * dumper = new DumpType(*field, 0, 0, nullptr);
dumper->setPadding(padding_size);
return dumper;
} else {
ElementGroup & group = this->getElementGroup(group_name);
const Array<UInt> * nodal_filter = &(group.getNodes());
typedef typename dumper::NodalField<type, true> DumpType;
DumpType * dumper = new DumpType(*field, 0, 0, nodal_filter);
dumper->setPadding(padding_size);
return dumper;
}
- return NULL;
+ return nullptr;
}
/* -------------------------------------------------------------------------- */
template <typename type, bool flag, template <class, bool> class ftype>
dumper::Field *
GroupManager::createStridedNodalField(const ftype<type, flag> * field,
const std::string & group_name, UInt size,
UInt stride, UInt padding_size) {
if (field == NULL)
- return NULL;
+ return nullptr;
if (group_name == "all") {
typedef typename dumper::NodalField<type, false> DumpType;
DumpType * dumper = new DumpType(*field, size, stride, NULL);
dumper->setPadding(padding_size);
return dumper;
} else {
ElementGroup & group = this->getElementGroup(group_name);
const Array<UInt> * nodal_filter = &(group.getNodes());
typedef typename dumper::NodalField<type, true> DumpType;
DumpType * dumper = new DumpType(*field, size, stride, nodal_filter);
dumper->setPadding(padding_size);
return dumper;
}
- return NULL;
+ return nullptr;
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif
diff --git a/src/mesh/mesh.cc b/src/mesh/mesh.cc
index a75f9b14a..a1c460a24 100644
--- a/src/mesh/mesh.cc
+++ b/src/mesh/mesh.cc
@@ -1,472 +1,476 @@
/**
* @file mesh.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Jan 22 2016
*
* @brief class handling meshes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 <sstream>
-
#include "aka_config.hh"
-
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
#include "group_manager_inline_impl.cc"
#include "mesh.hh"
#include "mesh_io.hh"
+#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "facet_synchronizer.hh"
#include "mesh_utils_distribution.hh"
#include "node_synchronizer.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_field.hh"
#include "dumper_internal_material_field.hh"
#endif
/* -------------------------------------------------------------------------- */
+#include <sstream>
+/* -------------------------------------------------------------------------- */
+
namespace akantu {
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id,
Communicator & communicator)
: Memory(id, memory_id),
GroupManager(*this, id + ":group_manager", memory_id),
nodes_type(0, 1, id + ":nodes_type"),
connectivities("connectivities", id, memory_id),
ghosts_counters("ghosts_counters", id, memory_id),
normals("normals", id, memory_id), spatial_dimension(spatial_dimension),
lower_bounds(spatial_dimension, 0.), upper_bounds(spatial_dimension, 0.),
size(spatial_dimension, 0.), local_lower_bounds(spatial_dimension, 0.),
local_upper_bounds(spatial_dimension, 0.),
mesh_data("mesh_data", id, memory_id), communicator(&communicator) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, Communicator & communicator,
const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id, communicator) {
AKANTU_DEBUG_IN();
this->nodes =
std::make_shared<Array<Real>>(0, spatial_dimension, id + ":coordinates");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, Communicator::getStaticCommunicator(), id,
memory_id) {}
/* -------------------------------------------------------------------------- */
Mesh::Mesh(UInt spatial_dimension, std::shared_ptr<Array<Real>> nodes,
const ID & id, const MemoryID & memory_id)
: Mesh(spatial_dimension, id, memory_id,
Communicator::getStaticCommunicator()) {
this->nodes = nodes;
this->nb_global_nodes = this->nodes->size();
this->nodes_to_elements.resize(nodes->size());
for (auto & node_set : nodes_to_elements) {
node_set = std::make_unique<std::set<Element>>();
}
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
Mesh & Mesh::initMeshFacets(const ID & id) {
AKANTU_DEBUG_IN();
if (!mesh_facets) {
mesh_facets = std::make_unique<Mesh>(spatial_dimension, this->nodes,
getID() + ":" + id, getMemoryID());
mesh_facets->mesh_parent = this;
mesh_facets->is_mesh_facets = true;
+
+ MeshUtils::buildAllFacets(*this, *mesh_facets, 0);
+
if (mesh.isDistributed()) {
mesh_facets->is_distributed = true;
mesh_facets->element_synchronizer = std::make_unique<FacetSynchronizer>(
*mesh_facets, mesh.getElementSynchronizer());
}
}
AKANTU_DEBUG_OUT();
return *mesh_facets;
}
/* -------------------------------------------------------------------------- */
void Mesh::defineMeshParent(const Mesh & mesh) {
AKANTU_DEBUG_IN();
this->mesh_parent = &mesh;
this->is_mesh_facets = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Mesh::~Mesh() = default;
/* -------------------------------------------------------------------------- */
void Mesh::read(const std::string & filename, const MeshIOType & mesh_io_type) {
MeshIO mesh_io;
mesh_io.read(filename, *this, mesh_io_type);
type_iterator it =
this->firstType(spatial_dimension, _not_ghost, _ek_not_defined);
type_iterator last =
this->lastType(spatial_dimension, _not_ghost, _ek_not_defined);
if (it == last)
AKANTU_EXCEPTION(
"The mesh contained in the file "
<< filename << " does not seem to be of the good dimension."
<< " No element of dimension " << spatial_dimension << " where read.");
this->nb_global_nodes = this->nodes->size();
this->computeBoundingBox();
this->nodes_to_elements.resize(nodes->size());
for (auto & node_set : nodes_to_elements) {
node_set = std::make_unique<std::set<Element>>();
}
}
/* -------------------------------------------------------------------------- */
void Mesh::write(const std::string & filename,
const MeshIOType & mesh_io_type) {
MeshIO mesh_io;
mesh_io.write(filename, *this, mesh_io_type);
}
/* -------------------------------------------------------------------------- */
void Mesh::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Mesh [" << std::endl;
stream << space << " + id : " << getID() << std::endl;
stream << space << " + spatial dimension : " << this->spatial_dimension
<< std::endl;
stream << space << " + nodes [" << std::endl;
nodes->printself(stream, indent + 2);
stream << space << " + connectivities [" << std::endl;
connectivities.printself(stream, indent + 2);
stream << space << " ]" << std::endl;
GroupManager::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void Mesh::computeBoundingBox() {
AKANTU_DEBUG_IN();
for (UInt k = 0; k < spatial_dimension; ++k) {
local_lower_bounds(k) = std::numeric_limits<double>::max();
local_upper_bounds(k) = -std::numeric_limits<double>::max();
}
for (UInt i = 0; i < nodes->size(); ++i) {
// if(!isPureGhostNode(i))
for (UInt k = 0; k < spatial_dimension; ++k) {
local_lower_bounds(k) = std::min(local_lower_bounds[k], (*nodes)(i, k));
local_upper_bounds(k) = std::max(local_upper_bounds[k], (*nodes)(i, k));
}
}
if (this->is_distributed) {
Matrix<Real> reduce_bounds(spatial_dimension, 2);
for (UInt k = 0; k < spatial_dimension; ++k) {
reduce_bounds(k, 0) = local_lower_bounds(k);
reduce_bounds(k, 1) = -local_upper_bounds(k);
}
communicator->allReduce(reduce_bounds, SynchronizerOperation::_min);
for (UInt k = 0; k < spatial_dimension; ++k) {
lower_bounds(k) = reduce_bounds(k, 0);
upper_bounds(k) = -reduce_bounds(k, 1);
}
} else {
this->lower_bounds = this->local_lower_bounds;
this->upper_bounds = this->local_upper_bounds;
}
size = upper_bounds - lower_bounds;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Mesh::initNormals() {
normals.initialize(*this, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_element_kind = _ek_not_defined);
}
/* -------------------------------------------------------------------------- */
void Mesh::getGlobalConnectivity(
ElementTypeMapArray<UInt> & global_connectivity) {
AKANTU_DEBUG_IN();
for (auto && ghost_type : ghost_types) {
for (auto type :
global_connectivity.elementTypes(_ghost_type = ghost_type)) {
if (not connectivities.exists(type, ghost_type))
continue;
auto & local_conn = connectivities(type, ghost_type);
auto & g_connectivity = global_connectivity(type, ghost_type);
UInt nb_nodes = local_conn.size() * local_conn.getNbComponent();
if (not nodes_global_ids && is_mesh_facets) {
std::transform(
local_conn.begin_reinterpret(nb_nodes),
local_conn.end_reinterpret(nb_nodes),
g_connectivity.begin_reinterpret(nb_nodes),
[& node_ids = *mesh_parent->nodes_global_ids](UInt l)->UInt {
return node_ids(l);
});
} else {
std::transform(local_conn.begin_reinterpret(nb_nodes),
local_conn.end_reinterpret(nb_nodes),
g_connectivity.begin_reinterpret(nb_nodes),
[& node_ids = *nodes_global_ids](UInt l)->UInt {
return node_ids(l);
});
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Mesh::getGroupDumper(const std::string & dumper_name,
const std::string & group_name) {
if (group_name == "all")
return this->getDumper(dumper_name);
else
return element_groups[group_name]->getDumper(dumper_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
ElementTypeMap<UInt> Mesh::getNbDataPerElem(ElementTypeMapArray<T> & arrays,
const ElementKind & element_kind) {
ElementTypeMap<UInt> nb_data_per_elem;
for (auto type : elementTypes(spatial_dimension, _not_ghost, element_kind)) {
UInt nb_elements = this->getNbElement(type);
auto & array = arrays(type);
nb_data_per_elem(type) = array.getNbComponent() * array.size();
nb_data_per_elem(type) /= nb_elements;
}
return nb_data_per_elem;
}
/* -------------------------------------------------------------------------- */
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<Real> & array,
const ElementKind & element_kind);
template ElementTypeMap<UInt>
Mesh::getNbDataPerElem(ElementTypeMapArray<UInt> & array,
const ElementKind & element_kind);
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
template <typename T>
dumper::Field *
Mesh::createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind) {
dumper::Field * field = nullptr;
ElementTypeMapArray<T> * internal = nullptr;
try {
internal = &(this->getData<T>(field_id));
} catch (...) {
return nullptr;
}
ElementTypeMap<UInt> nb_data_per_elem =
this->getNbDataPerElem(*internal, element_kind);
field = this->createElementalField<T, dumper::InternalMaterialField>(
*internal, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
return field;
}
template dumper::Field *
Mesh::createFieldFromAttachedData<Real>(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
template dumper::Field *
Mesh::createFieldFromAttachedData<UInt>(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
#endif
/* -------------------------------------------------------------------------- */
void Mesh::distribute() {
this->distribute(Communicator::getStaticCommunicator());
}
/* -------------------------------------------------------------------------- */
void Mesh::distribute(Communicator & communicator) {
AKANTU_DEBUG_ASSERT(is_distributed == false,
"This mesh is already distribute");
this->communicator = &communicator;
this->element_synchronizer = std::make_unique<ElementSynchronizer>(
*this, this->getID() + ":element_synchronizer", this->getMemoryID(),
true);
this->node_synchronizer = std::make_unique<NodeSynchronizer>(
*this, this->getID() + ":node_synchronizer", this->getMemoryID(), true);
Int psize = this->communicator->getNbProc();
#ifdef AKANTU_USE_SCOTCH
Int prank = this->communicator->whoAmI();
if (prank == 0) {
MeshPartitionScotch partition(*this, spatial_dimension);
partition.partitionate(psize);
MeshUtilsDistribution::distributeMeshCentralized(*this, 0, partition);
} else {
MeshUtilsDistribution::distributeMeshCentralized(*this, 0);
}
#else
if (!(psize == 1)) {
AKANTU_DEBUG_ERROR("Cannot distribute a mesh without a partitioning tool");
}
#endif
this->is_distributed = true;
this->computeBoundingBox();
}
/* -------------------------------------------------------------------------- */
void Mesh::getAssociatedElements(const Array<UInt> & node_list,
Array<Element> & elements) {
for (const auto & node : node_list)
for (const auto & element : *nodes_to_elements[node])
elements.push_back(element);
}
/* -------------------------------------------------------------------------- */
void Mesh::fillNodesToElements() {
Element e;
UInt nb_nodes = nodes->size();
for (UInt n = 0; n < nb_nodes; ++n) {
if (this->nodes_to_elements[n])
this->nodes_to_elements[n]->clear();
else
this->nodes_to_elements[n] = std::make_unique<std::set<Element>>();
}
for (auto ghost_type : ghost_types) {
e.ghost_type = ghost_type;
for (const auto & type :
elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
e.type = type;
UInt nb_element = this->getNbElement(type, ghost_type);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
connectivities(type, ghost_type)
.begin(Mesh::getNbNodesPerElement(type));
for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
e.element = el;
const Vector<UInt> & conn = *conn_it;
for (UInt n = 0; n < conn.size(); ++n)
nodes_to_elements[conn(n)]->insert(e);
}
}
}
}
/* -------------------------------------------------------------------------- */
void Mesh::eraseElements(const Array<Element> & elements) {
ElementTypeMap<UInt> last_element;
RemovedElementsEvent event(*this);
auto & remove_list = event.getList();
auto & new_numbering = event.getNewNumbering();
for (auto && el : elements) {
if (el.ghost_type != _not_ghost) {
auto & count = ghosts_counters(el);
--count;
if (count > 0)
continue;
}
remove_list.push_back(el);
if (not last_element.exists(el.type, el.ghost_type)) {
UInt nb_element = mesh.getNbElement(el.type, el.ghost_type);
last_element(nb_element - 1, el.type, el.ghost_type);
auto & numbering =
new_numbering.alloc(nb_element, 1, el.type, el.ghost_type);
for (auto && pair : enumerate(numbering)) {
std::get<1>(pair) = std::get<0>(pair);
}
}
UInt & pos = last_element(el.type, el.ghost_type);
auto & numbering = new_numbering(el.type, el.ghost_type);
numbering(el.element) = UInt(-1);
numbering(pos) = el.element;
--pos;
}
this->sendEvent(event);
}
} // namespace akantu
diff --git a/src/mesh/mesh.hh b/src/mesh/mesh.hh
index ffaa08a3b..a22dea521 100644
--- a/src/mesh/mesh.hh
+++ b/src/mesh/mesh.hh
@@ -1,602 +1,602 @@
/**
* @file mesh.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Jan 14 2016
*
* @brief the class representing the meshes
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_HH__
#define __AKANTU_MESH_HH__
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_event_handler_manager.hh"
#include "aka_memory.hh"
#include "dumpable.hh"
#include "element.hh"
#include "element_class.hh"
#include "element_type_map.hh"
#include "group_manager.hh"
#include "mesh_data.hh"
#include "mesh_events.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
class Communicator;
class ElementSynchronizer;
class NodeSynchronizer;
} // namespace akantu
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Mesh */
/* -------------------------------------------------------------------------- */
/**
* @class Mesh this contain the coordinates of the nodes in the Mesh.nodes
* Array, and the connectivity. The connectivity are stored in by element
* types.
*
* In order to loop on all element you have to loop on all types like this :
* @code{.cpp}
Mesh::type_iterator it = mesh.firstType(dim, ghost_type);
Mesh::type_iterator end = mesh.lastType(dim, ghost_type);
for(; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it);
const Array<UInt> & conn = mesh.getConnectivity(*it);
for(UInt e = 0; e < nb_element; ++e) {
...
}
}
@endcode
*/
class Mesh : protected Memory,
public EventHandlerManager<MeshEventHandler>,
public GroupManager,
public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
/// default constructor used for chaining, the last parameter is just to
/// differentiate constructors
Mesh(UInt spatial_dimension, const ID & id, const MemoryID & memory_id,
Communicator & communicator);
public:
/// constructor that create nodes coordinates array
Mesh(UInt spatial_dimension, const ID & id = "mesh",
const MemoryID & memory_id = 0);
/// mesh not distributed and not using the default communicator
Mesh(UInt spatial_dimension, Communicator & communicator,
const ID & id = "mesh", const MemoryID & memory_id = 0);
/// constructor that use an existing nodes coordinates array, by knowing its
/// ID
// Mesh(UInt spatial_dimension, const ID & nodes_id, const ID & id,
// const MemoryID & memory_id = 0);
/**
* constructor that use an existing nodes coordinates
* array, by getting the vector of coordinates
*/
Mesh(UInt spatial_dimension, std::shared_ptr<Array<Real>> nodes,
const ID & id = "mesh", const MemoryID & memory_id = 0);
- virtual ~Mesh();
+ ~Mesh() override;
/// @typedef ConnectivityTypeList list of the types present in a Mesh
typedef std::set<ElementType> ConnectivityTypeList;
/// read the mesh from a file
void read(const std::string & filename,
const MeshIOType & mesh_io_type = _miot_auto);
/// write the mesh to a file
void write(const std::string & filename,
const MeshIOType & mesh_io_type = _miot_auto);
private:
/// initialize the connectivity to NULL and other stuff
void init();
/// function that computes the bounding box (fills xmin, xmax)
void computeBoundingBox();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// patitionate the mesh among the processors involved in their computation
virtual void distribute(Communicator & communicator);
virtual void distribute();
/// function to print the containt of the class
- virtual void printself(std::ostream & stream, int indent = 0) const;
+ void printself(std::ostream & stream, int indent = 0) const override;
/// extract coordinates of nodes from an element
template <typename T>
inline void extractNodalValuesFromElement(const Array<T> & nodal_values,
T * elemental_values,
UInt * connectivity, UInt n_nodes,
UInt nb_degree_of_freedom) const;
// /// extract coordinates of nodes from a reversed element
// inline void extractNodalCoordinatesFromPBCElement(Real * local_coords,
// UInt * connectivity,
// UInt n_nodes);
/// convert a element to a linearized element
inline UInt elementToLinearized(const Element & elem) const;
/// convert a linearized element to an element
inline Element linearizedToElement(UInt linearized_element) const;
/// update the types offsets array for the conversions
// inline void updateTypesOffsets(const GhostType & ghost_type);
/// add a Array of connectivity for the type <type>.
inline void addConnectivityType(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
template <class Event> inline void sendEvent(Event & event) {
// if(event.getList().size() != 0)
EventHandlerManager<MeshEventHandler>::sendEvent<Event>(event);
}
/// prepare the event to remove the elements listed
void eraseElements(const Array<Element> & elements);
/* ------------------------------------------------------------------------ */
template <typename T>
inline void removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering);
/// initialize normals
void initNormals();
/// init facets' mesh
Mesh & initMeshFacets(const ID & id = "mesh_facets");
/// define parent mesh
void defineMeshParent(const Mesh & mesh);
/// get global connectivity array
void getGlobalConnectivity(ElementTypeMapArray<UInt> & global_connectivity);
public:
void getAssociatedElements(const Array<UInt> & node_list,
Array<Element> & elements);
private:
/// fills the nodes_to_elements structure
void fillNodesToElements();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the id of the mesh
AKANTU_GET_MACRO(ID, Memory::id, const ID &);
/// get the id of the mesh
AKANTU_GET_MACRO(MemoryID, Memory::memory_id, const MemoryID &);
/// get the spatial dimension of the mesh = number of component of the
/// coordinates
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the nodes Array aka coordinates
AKANTU_GET_MACRO(Nodes, *nodes, const Array<Real> &);
AKANTU_GET_MACRO_NOT_CONST(Nodes, *nodes, Array<Real> &);
/// get the normals for the elements
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Normals, normals, Real);
/// get the number of nodes
AKANTU_GET_MACRO(NbNodes, nodes->size(), UInt);
/// get the Array of global ids of the nodes (only used in parallel)
AKANTU_GET_MACRO(GlobalNodesIds, *nodes_global_ids, const Array<UInt> &);
AKANTU_GET_MACRO_NOT_CONST(GlobalNodesIds, *nodes_global_ids, Array<UInt> &);
/// get the global id of a node
inline UInt getNodeGlobalId(UInt local_id) const;
/// get the global id of a node
inline UInt getNodeLocalId(UInt global_id) const;
/// get the global number of nodes
inline UInt getNbGlobalNodes() const;
/// get the nodes type Array
AKANTU_GET_MACRO(NodesType, nodes_type, const Array<NodeType> &);
protected:
AKANTU_GET_MACRO_NOT_CONST(NodesType, nodes_type, Array<NodeType> &);
public:
inline NodeType getNodeType(UInt local_id) const;
/// say if a node is a pure ghost node
inline bool isPureGhostNode(UInt n) const;
/// say if a node is pur local or master node
inline bool isLocalOrMasterNode(UInt n) const;
inline bool isLocalNode(UInt n) const;
inline bool isMasterNode(UInt n) const;
inline bool isSlaveNode(UInt n) const;
AKANTU_GET_MACRO(LowerBounds, lower_bounds, const Vector<Real> &);
AKANTU_GET_MACRO(UpperBounds, upper_bounds, const Vector<Real> &);
AKANTU_GET_MACRO(LocalLowerBounds, local_lower_bounds, const Vector<Real> &);
AKANTU_GET_MACRO(LocalUpperBounds, local_upper_bounds, const Vector<Real> &);
/// get the connectivity Array for a given type
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Connectivity, connectivities, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Connectivity, connectivities, UInt);
AKANTU_GET_MACRO(Connectivities, connectivities,
const ElementTypeMapArray<UInt> &);
/// get the number of element of a type in the mesh
inline UInt getNbElement(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/// get the number of element for a given ghost_type and a given dimension
inline UInt getNbElement(const UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & kind = _ek_not_defined) const;
// /// get the connectivity list either for the elements or the ghost elements
// inline const ConnectivityTypeList &
// getConnectivityTypeList(const GhostType & ghost_type = _not_ghost) const;
/// compute the barycenter of a given element
inline void getBarycenter(UInt element, const ElementType & type,
Real * barycenter,
GhostType ghost_type = _not_ghost) const;
inline void getBarycenter(const Element & element,
Vector<Real> & barycenter) const;
/// get the element connected to a subelement
const Array<std::vector<Element>> &
getElementToSubelement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get the element connected to a subelement
Array<std::vector<Element>> &
getElementToSubelement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
/// get the subelement connected to an element
const Array<Element> &
getSubelementToElement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get the subelement connected to an element
Array<Element> &
getSubelementToElement(const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
/// register a new ElementalTypeMap in the MeshData
template <typename T>
inline ElementTypeMapArray<T> & registerData(const std::string & data_name);
template <typename T>
inline bool hasData(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get a name field associated to the mesh
template <typename T>
inline const Array<T> &
getData(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// get a name field associated to the mesh
template <typename T>
inline Array<T> & getData(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
/// get a name field associated to the mesh
template <typename T>
inline const ElementTypeMapArray<T> & getData(const ID & data_name) const;
/// get a name field associated to the mesh
template <typename T>
inline ElementTypeMapArray<T> & getData(const ID & data_name);
template <typename T>
ElementTypeMap<UInt> getNbDataPerElem(ElementTypeMapArray<T> & array,
const ElementKind & element_kind);
template <typename T>
dumper::Field * createFieldFromAttachedData(const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind);
/// templated getter returning the pointer to data in MeshData (modifiable)
template <typename T>
inline Array<T> &
getDataPointer(const std::string & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost,
UInt nb_component = 1, bool size_to_nb_element = true,
bool resize_with_parent = false);
/// Facets mesh accessor
inline const Mesh & getMeshFacets() const;
inline Mesh & getMeshFacets();
/// Parent mesh accessor
inline const Mesh & getMeshParent() const;
inline bool isMeshFacets() const { return this->is_mesh_facets; }
/// defines is the mesh is distributed or not
inline bool isDistributed() const { return this->is_distributed; }
#ifndef SWIG
/// return the dumper from a group and and a dumper name
DumperIOHelper & getGroupDumper(const std::string & dumper_name,
const std::string & group_name);
#endif
/* ------------------------------------------------------------------------ */
/* Wrappers on ElementClass functions */
/* ------------------------------------------------------------------------ */
public:
/// get the number of nodes per element for a given element type
static inline UInt getNbNodesPerElement(const ElementType & type);
/// get the number of nodes per element for a given element type considered as
/// a first order element
static inline ElementType getP1ElementType(const ElementType & type);
/// get the kind of the element type
static inline ElementKind getKind(const ElementType & type);
/// get spatial dimension of a type of element
static inline UInt getSpatialDimension(const ElementType & type);
/// get number of facets of a given element type
static inline UInt getNbFacetsPerElement(const ElementType & type);
/// get number of facets of a given element type
static inline UInt getNbFacetsPerElement(const ElementType & type, UInt t);
/// get local connectivity of a facet for a given facet type
static inline MatrixProxy<UInt>
getFacetLocalConnectivity(const ElementType & type, UInt t = 0);
/// get connectivity of facets for a given element
inline Matrix<UInt> getFacetConnectivity(const Element & element,
UInt t = 0) const;
/// get the number of type of the surface element associated to a given
/// element type
static inline UInt getNbFacetTypes(const ElementType & type, UInt t = 0);
/// get the type of the surface element associated to a given element
static inline ElementType getFacetType(const ElementType & type, UInt t = 0);
/// get all the type of the surface element associated to a given element
static inline VectorProxy<ElementType>
getAllFacetTypes(const ElementType & type);
/// get the number of nodes in the given element list
static inline UInt getNbNodesPerElementList(const Array<Element> & elements);
/* ------------------------------------------------------------------------ */
/* Element type Iterator */
/* ------------------------------------------------------------------------ */
using type_iterator = ElementTypeMapArray<UInt, ElementType>::type_iterator;
using ElementTypesIteratorHelper =
ElementTypeMapArray<UInt, ElementType>::ElementTypesIteratorHelper;
template <typename... pack>
ElementTypesIteratorHelper elementTypes(pack &&... _pack) const;
inline type_iterator firstType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.firstType(dim, ghost_type, kind);
}
inline type_iterator lastType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const {
return connectivities.lastType(dim, ghost_type, kind);
}
AKANTU_GET_MACRO(ElementSynchronizer, *element_synchronizer,
const ElementSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(ElementSynchronizer, *element_synchronizer,
ElementSynchronizer &);
AKANTU_GET_MACRO(NodeSynchronizer, *node_synchronizer,
const NodeSynchronizer &);
AKANTU_GET_MACRO_NOT_CONST(NodeSynchronizer, *node_synchronizer,
NodeSynchronizer &);
// AKANTU_GET_MACRO_NOT_CONST(Communicator, *communicator, StaticCommunicator
// &);
AKANTU_GET_MACRO(Communicator, *communicator, const auto &);
/* ------------------------------------------------------------------------ */
/* Private methods for friends */
/* ------------------------------------------------------------------------ */
private:
friend class MeshAccessor;
//#if defined(AKANTU_COHESIVE_ELEMENT)
// friend class CohesiveElementInserter;
//#endif
//#if defined(AKANTU_IGFEM)
// template <UInt dim> friend class MeshIgfemSphericalGrowingGel;
//#endif
AKANTU_GET_MACRO(NodesPointer, *nodes, Array<Real> &);
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
inline Array<UInt> & getNodesGlobalIdsPointer();
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline Array<NodeType> & getNodesTypePointer();
/// get a pointer to the connectivity Array for the given type and create it
/// if necessary
inline Array<UInt> &
getConnectivityPointer(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/// get the ghost element counter
inline Array<UInt> &
getGhostsCounters(const ElementType & type,
const GhostType & ghost_type = _ghost) {
AKANTU_DEBUG_ASSERT(ghost_type != _not_ghost,
"No ghost counter for _not_ghost elements");
return ghosts_counters(type, ghost_type);
}
/// get a pointer to the element_to_subelement Array for the given type and
/// create it if necessary
inline Array<std::vector<Element>> &
getElementToSubelementPointer(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/// get a pointer to the subelement_to_element Array for the given type and
/// create it if necessary
inline Array<Element> &
getSubelementToElementPointer(const ElementType & type,
const GhostType & ghost_type = _not_ghost);
AKANTU_GET_MACRO_NOT_CONST(MeshData, mesh_data, MeshData &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// array of the nodes coordinates
std::shared_ptr<Array<Real>> nodes;
/// global node ids
std::unique_ptr<Array<UInt>> nodes_global_ids;
/// node type, -3 pure ghost, -2 master for the node, -1 normal node, i in
/// [0-N] slave node and master is proc i
Array<NodeType> nodes_type;
/// global number of nodes;
UInt nb_global_nodes{0};
/// all class of elements present in this mesh (for heterogenous meshes)
ElementTypeMapArray<UInt> connectivities;
/// count the references on ghost elements
ElementTypeMapArray<UInt> ghosts_counters;
/// map to normals for all class of elements present in this mesh
ElementTypeMapArray<Real> normals;
/// list of all existing types in the mesh
// ConnectivityTypeList type_set;
/// the spatial dimension of this mesh
UInt spatial_dimension{0};
/// types offsets
// Array<UInt> types_offsets;
// /// list of all existing types in the mesh
// ConnectivityTypeList ghost_type_set;
// /// ghost types offsets
// Array<UInt> ghost_types_offsets;
/// min of coordinates
Vector<Real> lower_bounds;
/// max of coordinates
Vector<Real> upper_bounds;
/// size covered by the mesh on each direction
Vector<Real> size;
/// local min of coordinates
Vector<Real> local_lower_bounds;
/// local max of coordinates
Vector<Real> local_upper_bounds;
/// Extra data loaded from the mesh file
MeshData mesh_data;
/// facets' mesh
std::unique_ptr<Mesh> mesh_facets;
/// parent mesh (this is set for mesh_facets meshes)
const Mesh * mesh_parent{nullptr};
/// defines if current mesh is mesh_facets or not
bool is_mesh_facets{false};
/// defines if the mesh is centralized or distributed
bool is_distributed{false};
/// Communicator on which mesh is distributed
const Communicator * communicator;
/// Element synchronizer
std::unique_ptr<ElementSynchronizer> element_synchronizer;
/// Node synchronizer
std::unique_ptr<NodeSynchronizer> node_synchronizer;
using NodesToElements = std::vector<std::unique_ptr<std::set<Element>>>;
/// This info is stored to simplify the dynamic changes
NodesToElements nodes_to_elements;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Mesh & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Inline functions */
/* -------------------------------------------------------------------------- */
#include "element_type_map_tmpl.hh"
#include "mesh_inline_impl.cc"
#endif /* __AKANTU_MESH_HH__ */
diff --git a/src/mesh/mesh_data.hh b/src/mesh/mesh_data.hh
index 92f634eb6..41f2e445c 100644
--- a/src/mesh/mesh_data.hh
+++ b/src/mesh/mesh_data.hh
@@ -1,150 +1,150 @@
/**
* @file mesh_data.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Thu Nov 05 2015
*
* @brief Stores generic data loaded from the mesh file
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_DATA_HH__
#define __AKANTU_MESH_DATA_HH__
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "element_type_map.hh"
#include <map>
#include <string>
/* -------------------------------------------------------------------------- */
namespace akantu {
#define AKANTU_MESH_DATA_TYPES \
((_tc_int, Int))((_tc_uint, UInt))((_tc_real, Real))( \
(_tc_element, Element))((_tc_std_string, std::string))( \
(_tc_std_vector_element, std::vector<Element>))
#define AKANTU_MESH_DATA_TUPLE_FIRST_ELEM(s, data, elem) \
BOOST_PP_TUPLE_ELEM(2, 0, elem)
enum MeshDataTypeCode : int {
BOOST_PP_SEQ_ENUM(BOOST_PP_SEQ_TRANSFORM(AKANTU_MESH_DATA_TUPLE_FIRST_ELEM, ,
AKANTU_MESH_DATA_TYPES)),
_tc_unknown
};
class MeshData : public Memory {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
typedef MeshDataTypeCode TypeCode;
typedef std::map<std::string, ElementTypeMapBase *> ElementalDataMap;
typedef std::vector<std::string> StringVector;
typedef std::map<std::string, TypeCode> TypeCodeMap;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshData(const ID & id = "mesh_data", const ID & parent_id = "",
const MemoryID & memory_id = 0);
- ~MeshData();
+ ~MeshData() override;
/* ------------------------------------------------------------------------ */
/* Methods and accessors */
/* ------------------------------------------------------------------------ */
public:
/// Register new elemental data (and alloc data) with check if the name is
/// new
template <typename T> void registerElementalData(const ID & name);
inline void registerElementalData(const ID & name, TypeCode type);
/// Get an existing elemental data array
template <typename T>
bool hasDataArray(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// Get an existing elemental data array
template <typename T>
const Array<T> &
getElementalDataArray(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
template <typename T>
Array<T> & getElementalDataArray(const ID & data_name,
const ElementType & el_type,
const GhostType & ghost_type = _not_ghost);
/// Get an elemental data array, if it does not exist: allocate it
template <typename T>
Array<T> &
getElementalDataArrayAlloc(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost,
UInt nb_component = 1);
/// get the names of the data stored in elemental_data
inline void getTagNames(StringVector & tags, const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/// get the type of the data stored in elemental_data
template <typename T> TypeCode getTypeCode() const;
inline TypeCode getTypeCode(const ID & name) const;
template <typename T>
inline UInt getNbComponentTemplated(const ID & name,
const ElementType & el_type,
const GhostType & ghost_type) const;
inline UInt getNbComponent(const ID & name, const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
/// Get an existing elemental data
template <typename T>
const ElementTypeMapArray<T> & getElementalData(const ID & name) const;
template <typename T>
ElementTypeMapArray<T> & getElementalData(const ID & name);
private:
/// Register new elemental data (add alloc data)
template <typename T>
ElementTypeMapArray<T> * allocElementalData(const ID & name);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Map when elemental data is stored as ElementTypeMap
ElementalDataMap elemental_data;
/// Map when elementalType of the data stored in elemental_data
TypeCodeMap typecode_map;
};
} // akantu
#include "mesh_data_tmpl.hh"
#undef AKANTU_MESH_DATA_TUPLE_FIRST_ELEM
#endif /* __AKANTU_MESH_DATA_HH__ */
diff --git a/src/mesh/mesh_events.hh b/src/mesh/mesh_events.hh
index bb0cb2539..77dc78da3 100644
--- a/src/mesh/mesh_events.hh
+++ b/src/mesh/mesh_events.hh
@@ -1,187 +1,187 @@
/**
* @file mesh_events.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Feb 20 2015
* @date last modification: Mon Dec 07 2015
*
* @brief Classes corresponding to mesh events type
*
* @section LICENSE
*
* Copyright (©) 2015 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 "aka_array.hh"
#include "element.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_EVENTS_HH__
#define __AKANTU_MESH_EVENTS_HH__
namespace akantu {
/// akantu::MeshEvent is the base event for meshes
template <class Entity> class MeshEvent {
public:
virtual ~MeshEvent() {}
/// Get the list of entity modified by the event nodes or elements
const Array<Entity> & getList() const { return list; }
/// Get the list of entity modified by the event nodes or elements
Array<Entity> & getList() { return list; }
protected:
Array<Entity> list;
};
class Mesh;
/// akantu::MeshEvent related to new nodes in the mesh
class NewNodesEvent : public MeshEvent<UInt> {
public:
- virtual ~NewNodesEvent(){};
+ ~NewNodesEvent() override{};
};
/// akantu::MeshEvent related to nodes removed from the mesh
class RemovedNodesEvent : public MeshEvent<UInt> {
public:
- virtual ~RemovedNodesEvent(){};
+ ~RemovedNodesEvent() override{};
inline RemovedNodesEvent(const Mesh & mesh);
/// Get the new numbering following suppression of nodes from nodes arrays
AKANTU_GET_MACRO_NOT_CONST(NewNumbering, new_numbering, Array<UInt> &);
/// Get the new numbering following suppression of nodes from nodes arrays
AKANTU_GET_MACRO(NewNumbering, new_numbering, const Array<UInt> &);
private:
Array<UInt> new_numbering;
};
/// akantu::MeshEvent related to new elements in the mesh
class NewElementsEvent : public MeshEvent<Element> {
public:
- virtual ~NewElementsEvent(){};
+ ~NewElementsEvent() override{};
};
/// akantu::MeshEvent related to elements removed from the mesh
class RemovedElementsEvent : public MeshEvent<Element> {
public:
- virtual ~RemovedElementsEvent(){};
+ ~RemovedElementsEvent() override{};
inline RemovedElementsEvent(const Mesh & mesh,
ID new_numbering_id = "new_numbering");
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO(NewNumbering, new_numbering,
const ElementTypeMapArray<UInt> &);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_NOT_CONST(NewNumbering, new_numbering,
ElementTypeMapArray<UInt> &);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(NewNumbering, new_numbering, UInt);
/// Get the new numbering following suppression of elements from elements
/// arrays
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(NewNumbering, new_numbering, UInt);
protected:
ElementTypeMapArray<UInt> new_numbering;
};
/// akantu::MeshEvent for element that changed in some sort, can be seen as a
/// combination of removed and added elements
class ChangedElementsEvent : public RemovedElementsEvent {
public:
- virtual ~ChangedElementsEvent(){};
+ ~ChangedElementsEvent() override{};
inline ChangedElementsEvent(
const Mesh & mesh, ID new_numbering_id = "changed_event:new_numbering")
: RemovedElementsEvent(mesh, new_numbering_id){};
AKANTU_GET_MACRO(ListOld, list, const Array<Element> &);
AKANTU_GET_MACRO_NOT_CONST(ListOld, list, Array<Element> &);
AKANTU_GET_MACRO(ListNew, new_list, const Array<Element> &);
AKANTU_GET_MACRO_NOT_CONST(ListNew, new_list, Array<Element> &);
protected:
Array<Element> new_list;
};
/* -------------------------------------------------------------------------- */
class MeshEventHandler {
public:
virtual ~MeshEventHandler(){};
/* ------------------------------------------------------------------------ */
/* Internal code */
/* ------------------------------------------------------------------------ */
private:
/// send a akantu::NewNodesEvent
inline void sendEvent(const NewNodesEvent & event) {
onNodesAdded(event.getList(), event);
}
/// send a akantu::RemovedNodesEvent
inline void sendEvent(const RemovedNodesEvent & event) {
onNodesRemoved(event.getList(), event.getNewNumbering(), event);
}
/// send a akantu::NewElementsEvent
inline void sendEvent(const NewElementsEvent & event) {
onElementsAdded(event.getList(), event);
}
/// send a akantu::RemovedElementsEvent
inline void sendEvent(const RemovedElementsEvent & event) {
onElementsRemoved(event.getList(), event.getNewNumbering(), event);
}
/// send a akantu::ChangedElementsEvent
inline void sendEvent(const ChangedElementsEvent & event) {
onElementsChanged(event.getListOld(), event.getListNew(),
event.getNewNumbering(), event);
}
template <class EventHandler> friend class EventHandlerManager;
/* ------------------------------------------------------------------------ */
/* Interface */
/* ------------------------------------------------------------------------ */
public:
/// function to implement to react on akantu::NewNodesEvent
virtual void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) = 0;
/// function to implement to react on akantu::RemovedNodesEvent
virtual void onNodesRemoved(const Array<UInt> & nodes_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) = 0;
/// function to implement to react on akantu::NewElementsEvent
virtual void onElementsAdded(const Array<Element> & elements_list,
const NewElementsEvent & event) = 0;
/// function to implement to react on akantu::RemovedElementsEvent
virtual void
onElementsRemoved(const Array<Element> & elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) = 0;
/// function to implement to react on akantu::ChangedElementsEvent
virtual void
onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const ChangedElementsEvent & event) = 0;
};
} // akantu
#endif /* __AKANTU_MESH_EVENTS_HH__ */
diff --git a/src/mesh/mesh_inline_impl.cc b/src/mesh/mesh_inline_impl.cc
index a506bee50..df8fe3c66 100644
--- a/src/mesh/mesh_inline_impl.cc
+++ b/src/mesh/mesh_inline_impl.cc
@@ -1,635 +1,636 @@
/**
* @file mesh_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jul 15 2010
* @date last modification: Thu Jan 21 2016
*
* @brief Implementation of the inline functions of the mesh class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_iterators.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "cohesive_element.hh"
#endif
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_INLINE_IMPL_CC__
#define __AKANTU_MESH_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
inline ElementKind Element::kind() const { return Mesh::getKind(type); }
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename... pack>
Mesh::ElementTypesIteratorHelper Mesh::elementTypes(pack &&... _pack) const {
return connectivities.elementTypes(_pack...);
}
/* -------------------------------------------------------------------------- */
inline RemovedNodesEvent::RemovedNodesEvent(const Mesh & mesh)
: new_numbering(mesh.getNbNodes(), 1, "new_numbering") {}
/* -------------------------------------------------------------------------- */
inline RemovedElementsEvent::RemovedElementsEvent(const Mesh & mesh,
ID new_numbering_id)
: new_numbering(new_numbering_id, mesh.getID(), mesh.getMemoryID()) {}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<NewElementsEvent>(NewElementsEvent & event) {
this->nodes_to_elements.resize(nodes->size());
for (const auto & elem : event.getList()) {
const Array<UInt> & conn = connectivities(elem.type, elem.ghost_type);
UInt nb_nodes_per_elem = this->getNbNodesPerElement(elem.type);
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = conn(elem.element, n);
if (not nodes_to_elements[node])
nodes_to_elements[node] = std::make_unique<std::set<Element>>();
nodes_to_elements[node]->insert(elem);
}
}
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <> inline void Mesh::sendEvent<NewNodesEvent>(NewNodesEvent & event) {
this->computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
Mesh::sendEvent<RemovedElementsEvent>(RemovedElementsEvent & event) {
this->connectivities.onElementsRemoved(event.getNewNumbering());
this->fillNodesToElements();
this->computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<RemovedNodesEvent>(RemovedNodesEvent & event) {
const auto & new_numbering = event.getNewNumbering();
this->removeNodesFromArray(*nodes, new_numbering);
if (nodes_global_ids)
this->removeNodesFromArray(*nodes_global_ids, new_numbering);
if (nodes_type.size() != 0)
this->removeNodesFromArray(nodes_type, new_numbering);
if (not nodes_to_elements.empty()) {
std::vector<std::unique_ptr<std::set<Element>>> tmp(
nodes_to_elements.size());
auto it = nodes_to_elements.begin();
UInt new_nb_nodes = 0;
for (auto new_i : new_numbering) {
if (new_i != UInt(-1)) {
tmp[new_i] = std::move(*it);
++new_nb_nodes;
}
++it;
}
tmp.resize(new_nb_nodes);
std::move(tmp.begin(), tmp.end(), nodes_to_elements.begin());
}
computeBoundingBox();
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering) {
Array<T> tmp(vect.size(), vect.getNbComponent());
UInt nb_component = vect.getNbComponent();
UInt new_nb_nodes = 0;
for (UInt i = 0; i < new_numbering.size(); ++i) {
UInt new_i = new_numbering(i);
if (new_i != UInt(-1)) {
T * to_copy = vect.storage() + i * nb_component;
std::uninitialized_copy(to_copy, to_copy + nb_component,
tmp.storage() + new_i * nb_component);
++new_nb_nodes;
}
}
tmp.resize(new_nb_nodes);
vect.copy(tmp);
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> & Mesh::getNodesGlobalIdsPointer() {
AKANTU_DEBUG_IN();
if (not nodes_global_ids) {
nodes_global_ids = std::make_unique<Array<UInt>>(
nodes->size(), 1, getID() + ":nodes_global_ids");
for (auto && global_ids : enumerate(*nodes_global_ids)) {
std::get<1>(global_ids) = std::get<0>(global_ids);
}
}
AKANTU_DEBUG_OUT();
return *nodes_global_ids;
}
/* -------------------------------------------------------------------------- */
inline Array<NodeType> & Mesh::getNodesTypePointer() {
AKANTU_DEBUG_IN();
if (nodes_type.size() == 0) {
nodes_type.resize(nodes->size());
nodes_type.set(_nt_normal);
}
AKANTU_DEBUG_OUT();
return nodes_type;
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> &
Mesh::getConnectivityPointer(const ElementType & type,
const GhostType & ghost_type) {
if (connectivities.exists(type, ghost_type))
return connectivities(type, ghost_type);
if (ghost_type != _not_ghost) {
ghosts_counters.alloc(0, 1, type, ghost_type, 1);
}
AKANTU_DEBUG_INFO("The connectivity vector for the type " << type
<< " created");
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
return connectivities.alloc(0, nb_nodes_per_element, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline Array<std::vector<Element>> &
Mesh::getElementToSubelementPointer(const ElementType & type,
const GhostType & ghost_type) {
return getDataPointer<std::vector<Element>>("element_to_subelement", type,
ghost_type, 1, true);
}
/* -------------------------------------------------------------------------- */
inline Array<Element> &
Mesh::getSubelementToElementPointer(const ElementType & type,
const GhostType & ghost_type) {
auto & array = getDataPointer<Element>("subelement_to_element", type, ghost_type,
getNbFacetsPerElement(type), true,
is_mesh_facets);
array.set(ElementNull);
return array;
}
/* -------------------------------------------------------------------------- */
inline const Array<std::vector<Element>> &
Mesh::getElementToSubelement(const ElementType & type,
const GhostType & ghost_type) const {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline Array<std::vector<Element>> &
Mesh::getElementToSubelement(const ElementType & type,
const GhostType & ghost_type) {
return getData<std::vector<Element>>("element_to_subelement", type,
ghost_type);
}
/* -------------------------------------------------------------------------- */
inline const Array<Element> &
Mesh::getSubelementToElement(const ElementType & type,
const GhostType & ghost_type) const {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline Array<Element> &
Mesh::getSubelementToElement(const ElementType & type,
const GhostType & ghost_type) {
return getData<Element>("subelement_to_element", type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> &
Mesh::getDataPointer(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type, UInt nb_component,
bool size_to_nb_element, bool resize_with_parent) {
Array<T> & tmp = mesh_data.getElementalDataArrayAlloc<T>(
data_name, el_type, ghost_type, nb_component);
if (size_to_nb_element) {
if (resize_with_parent)
tmp.resize(mesh_parent->getNbElement(el_type, ghost_type));
else
tmp.resize(this->getNbElement(el_type, ghost_type));
} else {
tmp.resize(0);
}
return tmp;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline bool Mesh::hasData(const ID & data_name, const ElementType & el_type,
const GhostType & ghost_type) const {
return mesh_data.hasDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const Array<T> & Mesh::getData(const ID & data_name,
const ElementType & el_type,
const GhostType & ghost_type) const {
return mesh_data.getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline Array<T> & Mesh::getData(const ID & data_name,
const ElementType & el_type,
const GhostType & ghost_type) {
return mesh_data.getElementalDataArray<T>(data_name, el_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline const ElementTypeMapArray<T> &
Mesh::getData(const ID & data_name) const {
return mesh_data.getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> & Mesh::getData(const ID & data_name) {
return mesh_data.getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> & Mesh::registerData(const ID & data_name) {
this->mesh_data.registerElementalData<T>(data_name);
return this->getData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(const ElementType & type,
const GhostType & ghost_type) const {
try {
const Array<UInt> & conn = connectivities(type, ghost_type);
return conn.size();
} catch (...) {
return 0;
}
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbElement(const UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & kind) const {
AKANTU_DEBUG_ASSERT(spatial_dimension <= 3 || spatial_dimension == UInt(-1),
"spatial_dimension is " << spatial_dimension
<< " and is greater than 3 !");
UInt nb_element = 0;
for (auto type : elementTypes(spatial_dimension, ghost_type, kind))
nb_element += getNbElement(type, ghost_type);
return nb_element;
}
/* -------------------------------------------------------------------------- */
inline void Mesh::getBarycenter(UInt element, const ElementType & type,
Real * barycenter, GhostType ghost_type) const {
UInt * conn_val = getConnectivity(type, ghost_type).storage();
UInt nb_nodes_per_element = getNbNodesPerElement(type);
Real * local_coord = new Real[spatial_dimension * nb_nodes_per_element];
UInt offset = element * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
memcpy(local_coord + n * spatial_dimension,
nodes->storage() + conn_val[offset + n] * spatial_dimension,
spatial_dimension * sizeof(Real));
}
Math::barycenter(local_coord, nb_nodes_per_element, spatial_dimension,
barycenter);
delete[] local_coord;
}
/* -------------------------------------------------------------------------- */
inline void Mesh::getBarycenter(const Element & element,
Vector<Real> & barycenter) const {
getBarycenter(element.element, element.type, barycenter.storage(),
element.ghost_type);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElement(const ElementType & type) {
UInt nb_nodes_per_element = 0;
#define GET_NB_NODES_PER_ELEMENT(type) \
nb_nodes_per_element = ElementClass<type>::getNbNodesPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_NODES_PER_ELEMENT);
#undef GET_NB_NODES_PER_ELEMENT
return nb_nodes_per_element;
}
/* -------------------------------------------------------------------------- */
inline ElementType Mesh::getP1ElementType(const ElementType & type) {
ElementType p1_type = _not_defined;
#define GET_P1_TYPE(type) p1_type = ElementClass<type>::getP1ElementType()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_P1_TYPE);
#undef GET_P1_TYPE
return p1_type;
}
/* -------------------------------------------------------------------------- */
inline ElementKind Mesh::getKind(const ElementType & type) {
ElementKind kind = _ek_not_defined;
#define GET_KIND(type) kind = ElementClass<type>::getKind()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_KIND);
#undef GET_KIND
return kind;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getSpatialDimension(const ElementType & type) {
UInt spatial_dimension = 0;
#define GET_SPATIAL_DIMENSION(type) \
spatial_dimension = ElementClass<type>::getSpatialDimension()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SPATIAL_DIMENSION);
#undef GET_SPATIAL_DIMENSION
return spatial_dimension;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetTypes(const ElementType & type,
__attribute__((unused)) UInt t) {
UInt nb = 0;
#define GET_NB_FACET_TYPE(type) nb = ElementClass<type>::getNbFacetTypes()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET_TYPE);
#undef GET_NB_FACET_TYPE
return nb;
}
/* -------------------------------------------------------------------------- */
inline ElementType Mesh::getFacetType(const ElementType & type, UInt t) {
ElementType surface_type = _not_defined;
#define GET_FACET_TYPE(type) surface_type = ElementClass<type>::getFacetType(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_TYPE);
#undef GET_FACET_TYPE
return surface_type;
}
/* -------------------------------------------------------------------------- */
inline VectorProxy<ElementType>
Mesh::getAllFacetTypes(const ElementType & type) {
#define GET_FACET_TYPE(type) \
UInt nb = ElementClass<type>::getNbFacetTypes(); \
ElementType * elt_ptr = \
const_cast<ElementType *>(ElementClass<type>::getFacetTypeInternal()); \
return VectorProxy<ElementType>(elt_ptr, nb);
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_TYPE);
#undef GET_FACET_TYPE
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetsPerElement(const ElementType & type) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) n_facet = ElementClass<type>::getNbFacetsPerElement()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbFacetsPerElement(const ElementType & type, UInt t) {
AKANTU_DEBUG_IN();
UInt n_facet = 0;
#define GET_NB_FACET(type) \
n_facet = ElementClass<type>::getNbFacetsPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_NB_FACET);
#undef GET_NB_FACET
AKANTU_DEBUG_OUT();
return n_facet;
}
/* -------------------------------------------------------------------------- */
inline MatrixProxy<UInt>
Mesh::getFacetLocalConnectivity(const ElementType & type, UInt t) {
AKANTU_DEBUG_IN();
#define GET_FACET_CON(type) \
AKANTU_DEBUG_OUT(); \
return ElementClass<type>::getFacetLocalConnectivityPerElement(t)
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_FACET_CON);
#undef GET_FACET_CON
AKANTU_DEBUG_OUT();
return MatrixProxy<UInt>(
nullptr, 0, 0); // This avoid a compilation warning but will certainly
// also cause a segfault if reached
}
/* -------------------------------------------------------------------------- */
inline Matrix<UInt> Mesh::getFacetConnectivity(const Element & element,
UInt t) const {
AKANTU_DEBUG_IN();
Matrix<UInt> local_facets(getFacetLocalConnectivity(element.type, t), false);
Matrix<UInt> facets(local_facets.rows(), local_facets.cols());
const Array<UInt> & conn = connectivities(element.type, element.ghost_type);
for (UInt f = 0; f < facets.rows(); ++f) {
for (UInt n = 0; n < facets.cols(); ++n) {
facets(f, n) = conn(element.element, local_facets(f, n));
}
}
AKANTU_DEBUG_OUT();
return facets;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::extractNodalValuesFromElement(
const Array<T> & nodal_values, T * local_coord, UInt * connectivity,
UInt n_nodes, UInt nb_degree_of_freedom) const {
for (UInt n = 0; n < n_nodes; ++n) {
memcpy(local_coord + n * nb_degree_of_freedom,
nodal_values.storage() + connectivity[n] * nb_degree_of_freedom,
nb_degree_of_freedom * sizeof(T));
}
}
/* -------------------------------------------------------------------------- */
inline void Mesh::addConnectivityType(const ElementType & type,
const GhostType & ghost_type) {
getConnectivityPointer(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isPureGhostNode(UInt n) const {
return nodes_type.size() ? (nodes_type(n) == _nt_pure_gost) : false;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalOrMasterNode(UInt n) const {
return nodes_type.size()
? (nodes_type(n) == _nt_master) || (nodes_type(n) == _nt_normal)
: true;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalNode(UInt n) const {
return nodes_type.size() ? nodes_type(n) == _nt_normal : true;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isMasterNode(UInt n) const {
return nodes_type.size() ? nodes_type(n) == _nt_master : false;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isSlaveNode(UInt n) const {
return nodes_type.size() ? nodes_type(n) >= 0 : false;
}
/* -------------------------------------------------------------------------- */
inline NodeType Mesh::getNodeType(UInt local_id) const {
return nodes_type.size() ? nodes_type(local_id) : _nt_normal;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeGlobalId(UInt local_id) const {
return nodes_global_ids ? (*nodes_global_ids)(local_id) : local_id;
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNodeLocalId(UInt global_id) const {
- AKANTU_DEBUG_ASSERT(nodes_global_ids != NULL, "The global ids are note set.");
+ AKANTU_DEBUG_ASSERT(nodes_global_ids != nullptr,
+ "The global ids are note set.");
return nodes_global_ids->find(global_id);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbGlobalNodes() const {
return nodes_global_ids ? nb_global_nodes : nodes->size();
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbNodesPerElementList(const Array<Element> & elements) {
UInt nb_nodes_per_element = 0;
UInt nb_nodes = 0;
ElementType current_element_type = _not_defined;
Array<Element>::const_iterator<Element> el_it = elements.begin();
Array<Element>::const_iterator<Element> el_end = elements.end();
for (; el_it != el_end; ++el_it) {
const Element & el = *el_it;
if (el.type != current_element_type) {
current_element_type = el.type;
nb_nodes_per_element = Mesh::getNbNodesPerElement(current_element_type);
}
nb_nodes += nb_nodes_per_element;
}
return nb_nodes;
}
/* -------------------------------------------------------------------------- */
inline Mesh & Mesh::getMeshFacets() {
if (!this->mesh_facets)
AKANTU_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshFacets() const {
if (!this->mesh_facets)
AKANTU_EXCEPTION(
"No facet mesh is defined yet! check the buildFacets functions");
return *this->mesh_facets;
}
/* -------------------------------------------------------------------------- */
inline const Mesh & Mesh::getMeshParent() const {
if (!this->mesh_parent)
AKANTU_EXCEPTION(
"No parent mesh is defined! This is only valid in a mesh_facets");
return *this->mesh_parent;
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_MESH_INLINE_IMPL_CC__ */
diff --git a/src/mesh/node_group.hh b/src/mesh/node_group.hh
index 1003698b6..b8362db4f 100644
--- a/src/mesh/node_group.hh
+++ b/src/mesh/node_group.hh
@@ -1,141 +1,141 @@
/**
* @file node_group.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief Node group definition
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "aka_array.hh"
#include "aka_memory.hh"
#include "mesh_filter.hh"
#include "dumpable.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NODE_GROUP_HH__
#define __AKANTU_NODE_GROUP_HH__
namespace akantu {
class NodeGroup : public Memory, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NodeGroup(const std::string & name,
const Mesh & mesh,
const std::string & id = "node_group",
const MemoryID & memory_id = 0);
- virtual ~NodeGroup();
+ ~NodeGroup() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
typedef Array<UInt>::const_iterator<UInt> const_node_iterator;
/// empty the node group
void empty();
/// iterator to the beginning of the node group
inline const_node_iterator begin() const;
/// iterator to the end of the node group
inline const_node_iterator end() const;
/// add a node and give the local position through an iterator
inline const_node_iterator add(UInt node, bool check_for_duplicate = true);
/// remove a node
inline void remove(UInt node);
inline decltype(auto) find(UInt node) const {
return node_group.find(node);
}
/// remove duplicated nodes
void optimize();
/// append a group to current one
void append(const NodeGroup & other_group);
/// apply a filter on current node group
template <typename T>
void applyNodeFilter(T & filter);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_NOT_CONST(Nodes, node_group, Array<UInt> &);
AKANTU_GET_MACRO(Nodes, node_group, const Array<UInt> &);
AKANTU_GET_MACRO(Name, name, const std::string &);
/// give the number of nodes in the current group
inline UInt size() const;
UInt * storage(){return node_group.storage();};
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// name of the group
std::string name;
/// list of nodes in the group
Array<UInt> & node_group;
/// reference to the mesh in question
//const Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const NodeGroup & _this)
{
_this.printself(stream);
return stream;
}
} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "node_group_inline_impl.cc"
#endif /* __AKANTU_NODE_GROUP_HH__ */
diff --git a/src/mesh_utils/cohesive_element_inserter.cc b/src/mesh_utils/cohesive_element_inserter.cc
index 65ef1d158..e328de401 100644
--- a/src/mesh_utils/cohesive_element_inserter.cc
+++ b/src/mesh_utils/cohesive_element_inserter.cc
@@ -1,451 +1,449 @@
/**
* @file cohesive_element_inserter.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
* @date last modification: Sun Oct 04 2015
*
* @brief Cohesive element inserter functions
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "cohesive_element_inserter.hh"
#include "element_group.hh"
//#include "facet_synchronizer.hh"
#include "global_ids_updater.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <limits>
/* -------------------------------------------------------------------------- */
namespace akantu {
CohesiveElementInserter::CohesiveElementInserter(Mesh & mesh, bool is_extrinsic,
const ID & id)
: id(id), mesh(mesh), mesh_facets(mesh.initMeshFacets()),
insertion_facets("insertion_facets", id),
insertion_limits(mesh.getSpatialDimension(), 2),
check_facets("check_facets", id) {
-
- MeshUtils::buildAllFacets(mesh, mesh_facets, 0);
init(is_extrinsic);
}
/* -------------------------------------------------------------------------- */
CohesiveElementInserter::~CohesiveElementInserter() {
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
delete global_ids_updater;
#endif
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::init(bool is_extrinsic) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
MeshUtils::resetFacetToDouble(mesh_facets);
/// initialize facet insertion array
insertion_facets.initialize(mesh_facets,
_spatial_dimension = (spatial_dimension - 1),
_with_nb_element = true);
// mesh_facets.initElementTypeMapArray(
// insertion_facets, 1, spatial_dimension - 1, false, _ek_regular, true);
/// init insertion limits
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
insertion_limits(dim, 0) = std::numeric_limits<Real>::max() * (-1.);
insertion_limits(dim, 1) = std::numeric_limits<Real>::max();
}
if (is_extrinsic) {
check_facets.initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1);
// mesh_facets.initElementTypeMapArray(check_facets, 1, spatial_dimension -
// 1);
initFacetsCheck();
}
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
facet_synchronizer = NULL;
global_ids_updater = NULL;
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::initFacetsCheck() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType facet_gt = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, facet_gt);
Mesh::type_iterator last =
mesh_facets.lastType(spatial_dimension - 1, facet_gt);
for (; it != last; ++it) {
ElementType facet_type = *it;
Array<bool> & f_check = check_facets(facet_type, facet_gt);
const Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(facet_type, facet_gt);
UInt nb_facet = element_to_facet.size();
f_check.resize(nb_facet);
for (UInt f = 0; f < nb_facet; ++f) {
if (element_to_facet(f)[1] == ElementNull ||
(element_to_facet(f)[0].ghost_type == _ghost &&
element_to_facet(f)[1].ghost_type == _ghost)) {
f_check(f) = false;
} else
f_check(f) = true;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::limitCheckFacets() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> bary_facet(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, ghost_type);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, ghost_type);
for (; it != end; ++it) {
ElementType type = *it;
Array<bool> & f_check = check_facets(type, ghost_type);
UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);
for (UInt f = 0; f < nb_facet; ++f) {
if (f_check(f)) {
mesh_facets.getBarycenter(f, type, bary_facet.storage(), ghost_type);
UInt coord_in_limit = 0;
while (coord_in_limit < spatial_dimension &&
bary_facet(coord_in_limit) >
insertion_limits(coord_in_limit, 0) &&
bary_facet(coord_in_limit) <
insertion_limits(coord_in_limit, 1))
++coord_in_limit;
if (coord_in_limit != spatial_dimension)
f_check(f) = false;
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::setLimit(SpacialDirection axis, Real first_limit,
Real second_limit) {
AKANTU_DEBUG_ASSERT(
axis < mesh.getSpatialDimension(),
"You are trying to limit insertion in a direction that doesn't exist");
insertion_limits(axis, 0) = std::min(first_limit, second_limit);
insertion_limits(axis, 1) = std::max(first_limit, second_limit);
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::insertIntrinsicElements() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> bary_facet(spatial_dimension);
for (auto && ghost_type : ghost_types) {
for (const auto & type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, ghost_type)) {
auto & f_insertion = insertion_facets(type_facet, ghost_type);
auto & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, ghost_type);
UInt nb_facet = mesh_facets.getNbElement(type_facet, ghost_type);
for (UInt f = 0; f < nb_facet; ++f) {
if (element_to_facet(f)[1] == ElementNull)
continue;
mesh_facets.getBarycenter(f, type_facet, bary_facet.storage(),
ghost_type);
UInt coord_in_limit = 0;
while (coord_in_limit < spatial_dimension &&
bary_facet(coord_in_limit) >
insertion_limits(coord_in_limit, 0) &&
bary_facet(coord_in_limit) < insertion_limits(coord_in_limit, 1))
++coord_in_limit;
if (coord_in_limit == spatial_dimension)
f_insertion(f) = true;
}
}
}
AKANTU_DEBUG_OUT();
return insertElements();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::insertIntrinsicElements(std::string physname,
UInt material_index) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
ElementTypeMapArray<UInt> * phys_data;
try {
phys_data = &(mesh_facets.getData<UInt>("physical_names"));
} catch (...) {
phys_data = &(mesh_facets.registerData<UInt>("physical_names"));
phys_data->initialize(mesh_facets,
_spatial_dimension = spatial_dimension - 1,
_with_nb_element = true);
// mesh_facets.initElementTypeMapArray(*phys_data, 1, spatial_dimension - 1,
// false, _ek_regular, true);
}
Vector<Real> bary_facet(spatial_dimension);
mesh_facets.createElementGroup(physname);
GhostType ghost_type = _not_ghost;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, ghost_type);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, ghost_type);
for (; it != end; ++it) {
const ElementType type_facet = *it;
Array<bool> & f_insertion = insertion_facets(type_facet, ghost_type);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, ghost_type);
UInt nb_facet = mesh_facets.getNbElement(type_facet, ghost_type);
UInt coord_in_limit = 0;
ElementGroup & group = mesh.getElementGroup(physname);
ElementGroup & group_facet = mesh_facets.getElementGroup(physname);
Vector<Real> bary_physgroup(spatial_dimension);
Real norm_bary;
for (ElementGroup::const_element_iterator el_it(
group.begin(type_facet, ghost_type));
el_it != group.end(type_facet, ghost_type); ++el_it) {
UInt e = *el_it;
mesh.getBarycenter(e, type_facet, bary_physgroup.storage(), ghost_type);
#ifndef AKANTU_NDEBUG
bool find_a_partner = false;
#endif
norm_bary = bary_physgroup.norm();
Array<UInt> & material_id = (*phys_data)(type_facet, ghost_type);
for (UInt f = 0; f < nb_facet; ++f) {
if (element_to_facet(f)[1] == ElementNull)
continue;
mesh_facets.getBarycenter(f, type_facet, bary_facet.storage(),
ghost_type);
coord_in_limit = 0;
while (coord_in_limit < spatial_dimension &&
(std::abs(bary_facet(coord_in_limit) -
bary_physgroup(coord_in_limit)) /
norm_bary <
Math::getTolerance()))
++coord_in_limit;
if (coord_in_limit == spatial_dimension) {
f_insertion(f) = true;
#ifndef AKANTU_NDEBUG
find_a_partner = true;
#endif
group_facet.add(type_facet, f, ghost_type, false);
material_id(f) = material_index;
break;
}
}
AKANTU_DEBUG_ASSERT(find_a_partner,
"The element nO "
<< e << " of physical group " << physname
<< " did not find its associated facet!"
<< " Try to decrease math tolerance. "
<< std::endl);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt CohesiveElementInserter::insertElements(bool only_double_facets) {
CohesiveNewNodesEvent node_event;
NewElementsEvent element_event;
Array<UInt> new_pairs(0, 2);
UInt nb_new_elements = MeshUtils::insertCohesiveElements(
mesh, mesh_facets, insertion_facets, new_pairs, element_event.getList(),
only_double_facets);
UInt nb_new_nodes = new_pairs.size();
node_event.getList().reserve(nb_new_nodes);
node_event.getOldNodesList().reserve(nb_new_nodes);
for (UInt n = 0; n < nb_new_nodes; ++n) {
node_event.getList().push_back(new_pairs(n, 1));
node_event.getOldNodesList().push_back(new_pairs(n, 0));
}
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (mesh.isDistributed()) {
/// update nodes type
updateNodesType(mesh, node_event);
updateNodesType(mesh_facets, node_event);
/// update global ids
nb_new_nodes = this->updateGlobalIDs(node_event);
/// compute total number of new elements
const auto & comm = mesh.getCommunicator();
comm.allReduce(nb_new_elements, _so_sum);
}
#endif
if (nb_new_nodes > 0)
mesh.sendEvent(node_event);
if (nb_new_elements > 0) {
updateInsertionFacets();
// mesh.updateTypesOffsets(_not_ghost);
mesh.sendEvent(element_event);
MeshUtils::resetFacetToDouble(mesh_facets);
}
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (mesh.isDistributed()) {
/// update global ids
this->synchronizeGlobalIDs(node_event);
}
#endif
return nb_new_elements;
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::updateInsertionFacets() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType facet_gt = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, facet_gt);
Mesh::type_iterator last =
mesh_facets.lastType(spatial_dimension - 1, facet_gt);
for (; it != last; ++it) {
ElementType facet_type = *it;
Array<bool> & ins_facets = insertion_facets(facet_type, facet_gt);
// this is the extrinsic case
if (check_facets.exists(facet_type, facet_gt)) {
Array<bool> & f_check = check_facets(facet_type, facet_gt);
UInt nb_facets = f_check.size();
for (UInt f = 0; f < ins_facets.size(); ++f) {
if (ins_facets(f)) {
++nb_facets;
ins_facets(f) = false;
f_check(f) = false;
}
}
f_check.resize(nb_facets);
}
// and this the intrinsic one
else {
ins_facets.resize(mesh_facets.getNbElement(facet_type, facet_gt));
ins_facets.set(false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void CohesiveElementInserter::printself(std::ostream & stream,
int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "CohesiveElementInserter [" << std::endl;
stream << space << " + mesh [" << std::endl;
mesh.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + mesh_facets [" << std::endl;
mesh_facets.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
} // namespace akantu
diff --git a/src/mesh_utils/cohesive_element_inserter.hh b/src/mesh_utils/cohesive_element_inserter.hh
index decc1fc45..f220d71f9 100644
--- a/src/mesh_utils/cohesive_element_inserter.hh
+++ b/src/mesh_utils/cohesive_element_inserter.hh
@@ -1,204 +1,204 @@
/**
* @file cohesive_element_inserter.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Dec 04 2013
* @date last modification: Fri Oct 02 2015
*
* @brief Cohesive element inserter
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "data_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
#define __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
namespace akantu {
class GlobalIdsUpdater;
class FacetSynchronizer;
} // akantu
namespace akantu {
class CohesiveElementInserter : public DataAccessor<Element> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
CohesiveElementInserter(Mesh & mesh, bool is_extrinsic = false,
const ID & id = "cohesive_element_inserter");
- virtual ~CohesiveElementInserter();
+ ~CohesiveElementInserter() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// init function
void init(bool is_extrinsic);
/// set range limitation for intrinsic cohesive element insertion
void setLimit(SpacialDirection axis, Real first_limit, Real second_limit);
/// insert intrinsic cohesive elements in a predefined range
UInt insertIntrinsicElements();
/// preset insertion of intrinsic cohesive elements along
/// a predefined group of facet and assign them a defined material index.
/// insertElement() method has to be called to finalize insertion.
void insertIntrinsicElements(std::string physname, UInt material_index);
/// insert extrinsic cohesive elements (returns the number of new
/// cohesive elements)
UInt insertElements(bool only_double_facets = false);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// limit check facets to match given insertion limits
void limitCheckFacets();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
/// init parallel variables
void initParallel(FacetSynchronizer * facet_synchronizer,
ElementSynchronizer * element_synchronizer);
#endif
protected:
/// init facets check
void initFacetsCheck();
/// update facet insertion arrays after facets doubling
void updateInsertionFacets();
/// update nodes type and global ids for parallel simulations
/// (locally, within each processor)
UInt updateGlobalIDs(NewNodesEvent & node_event);
/// synchronize the global ids among the processors in parallel simulations
void synchronizeGlobalIDs(NewNodesEvent & node_event);
/// update nodes type
void updateNodesType(Mesh & mesh, NewNodesEvent & node_event);
/// functions for parallel communications
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
template <bool pack_mode>
inline void
packUnpackGlobalConnectivity(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
template <bool pack_mode>
inline void
packUnpackGroupedInsertionData(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_NOT_CONST(InsertionFacetsByElement, insertion_facets,
ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO(InsertionFacetsByElement, insertion_facets,
const ElementTypeMapArray<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(InsertionFacets, insertion_facets, bool);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(CheckFacets, check_facets, bool);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(CheckFacets, check_facets, bool);
AKANTU_GET_MACRO(MeshFacets, mesh_facets, const Mesh &);
AKANTU_GET_MACRO_NOT_CONST(MeshFacets, mesh_facets, Mesh &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// object id
ID id;
/// main mesh where to insert cohesive elements
Mesh & mesh;
/// mesh containing facets
Mesh & mesh_facets;
/// list of facets where to insert elements
ElementTypeMapArray<bool> insertion_facets;
/// limits for element insertion
Array<Real> insertion_limits;
/// vector containing facets in which extrinsic cohesive elements can be
/// inserted
ElementTypeMapArray<bool> check_facets;
// /// facet synchronizer
// FacetSynchronizer & facet_synchronizer;
/// global connectivity ids updater
std::unique_ptr<GlobalIdsUpdater> global_ids_updater;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const CohesiveElementInserter & _this) {
_this.printself(stream);
return stream;
}
class CohesiveNewNodesEvent : public NewNodesEvent{
public:
CohesiveNewNodesEvent() = default;
- virtual ~CohesiveNewNodesEvent() = default;
+ ~CohesiveNewNodesEvent() override = default;
AKANTU_GET_MACRO_NOT_CONST(OldNodesList, old_nodes, Array<UInt> &);
AKANTU_GET_MACRO(OldNodesList, old_nodes, const Array<UInt> &);
private:
Array<UInt> old_nodes;
};
} // akantu
#include "cohesive_element_inserter_inline_impl.cc"
#endif /* __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__ */
diff --git a/src/mesh_utils/cohesive_element_inserter_inline_impl.cc b/src/mesh_utils/cohesive_element_inserter_inline_impl.cc
index 350049797..0837a19ec 100644
--- a/src/mesh_utils/cohesive_element_inserter_inline_impl.cc
+++ b/src/mesh_utils/cohesive_element_inserter_inline_impl.cc
@@ -1,106 +1,106 @@
/**
* @file cohesive_element_inserter_inline_impl.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief Cohesive element inserter inline functions
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "cohesive_element_inserter.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_CC__
#define __AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt CohesiveElementInserter::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
if (tag == _gst_ce_groups) {
size = elements.size() * (sizeof(bool) + sizeof(unsigned int));
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
inline void CohesiveElementInserter::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
if (tag == _gst_ce_groups)
packUnpackGroupedInsertionData<true>(buffer, elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void CohesiveElementInserter::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (tag == _gst_ce_groups)
packUnpackGroupedInsertionData<false>(buffer, elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool pack_mode>
inline void CohesiveElementInserter::packUnpackGroupedInsertionData(
CommunicationBuffer & buffer, const Array<Element> & elements) const {
AKANTU_DEBUG_IN();
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
ElementTypeMapArray<UInt> & physical_names =
mesh_facets.registerData<UInt>("physical_names");
- Array<bool> * vect = NULL;
- Array<unsigned int> * vect2 = NULL;
+ Array<bool> * vect = nullptr;
+ Array<unsigned int> * vect2 = nullptr;
Array<Element>::const_iterator<Element> it = elements.begin();
Array<Element>::const_iterator<Element> end = elements.end();
for (; it != end; ++it) {
const Element & el = *it;
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
vect =
&const_cast<Array<bool> &>(insertion_facets(el.type, el.ghost_type));
vect2 = &(physical_names(el.type, el.ghost_type));
}
Vector<bool> data(vect->storage() + el.element, 1);
Vector<unsigned int> data2(vect2->storage() + el.element, 1);
if (pack_mode) {
buffer << data;
buffer << data2;
} else {
buffer >> data;
buffer >> data2;
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
#endif /* __AKANTU_COHESIVE_ELEMENT_INSERTER_INLINE_IMPL_CC__ */
diff --git a/src/mesh_utils/global_ids_updater.hh b/src/mesh_utils/global_ids_updater.hh
index 6cbe5e79e..eadc66eb0 100644
--- a/src/mesh_utils/global_ids_updater.hh
+++ b/src/mesh_utils/global_ids_updater.hh
@@ -1,100 +1,100 @@
/**
* @file global_ids_updater.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Oct 02 2015
*
* @brief Class that updates the global ids of new nodes that are
* inserted in the mesh. The functions in this class must be called
* after updating the node types
*
* @section LICENSE
*
* Copyright (©) 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GLOBAL_IDS_UPDATER_HH__
#define __AKANTU_GLOBAL_IDS_UPDATER_HH__
/* -------------------------------------------------------------------------- */
#include "data_accessor.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer;
} // akantu
namespace akantu {
class GlobalIdsUpdater : public DataAccessor<Element> {
public:
GlobalIdsUpdater(Mesh & mesh, ElementSynchronizer * synchronizer)
: mesh(mesh), synchronizer(synchronizer) {}
/// function to update and synchronize the global connectivity of
/// new inserted nodes. It must be called after updating the node
/// types. (It calls in sequence the functions
/// updateGlobalIDsLocally and synchronizeGlobalIDs)
UInt updateGlobalIDs(UInt old_nb_nodes);
/// function to update the global connectivity (only locally) of new
/// inserted nodes. It must be called after updating the node types.
UInt updateGlobalIDsLocally(UInt old_nb_nodes);
/// function to synchronize the global connectivity of new inserted
/// nodes among the processors. It must be called after updating the
/// node types.
void synchronizeGlobalIDs();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
- inline virtual UInt getNbData(const Array<Element> & elements,
- const SynchronizationTag & tag) const;
+ inline UInt getNbData(const Array<Element> & elements,
+ const SynchronizationTag & tag) const override;
- inline virtual void packData(CommunicationBuffer & buffer,
- const Array<Element> & elements,
- const SynchronizationTag & tag) const;
+ inline void packData(CommunicationBuffer & buffer,
+ const Array<Element> & elements,
+ const SynchronizationTag & tag) const override;
- inline virtual void unpackData(CommunicationBuffer & buffer,
- const Array<Element> & elements,
- const SynchronizationTag & tag);
+ inline void unpackData(CommunicationBuffer & buffer,
+ const Array<Element> & elements,
+ const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
template <bool pack_mode>
inline void
packUnpackGlobalConnectivity(CommunicationBuffer & buffer,
const Array<Element> & elements) const;
/* ------------------------------------------------------------------------ */
/* Members */
/* ------------------------------------------------------------------------ */
private:
/// Reference to the mesh to update
Mesh & mesh;
/// distributed synchronizer to communicate the connectivity
ElementSynchronizer * synchronizer;
};
} // akantu
#include "global_ids_updater_inline_impl.cc"
#endif /* __AKANTU_GLOBAL_IDS_UPDATER_HH__ */
diff --git a/src/mesh_utils/mesh_partition.hh b/src/mesh_utils/mesh_partition.hh
index 7f834ce03..cb2caacb3 100644
--- a/src/mesh_utils/mesh_partition.hh
+++ b/src/mesh_utils/mesh_partition.hh
@@ -1,151 +1,151 @@
/**
* @file mesh_partition.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Sep 01 2015
*
* @brief tools to partitionate a mesh
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_PARTITION_HH__
#define __AKANTU_MESH_PARTITION_HH__
/* -------------------------------------------------------------------------- */
#include "aka_csr.hh"
#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartition : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshPartition(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "MeshPartitioner",
const MemoryID & memory_id = 0);
- virtual ~MeshPartition();
+ ~MeshPartition() override;
class EdgeLoadFunctor {
public:
virtual Int operator()(const Element & el1, const Element & el2) const
noexcept = 0;
};
class ConstEdgeLoadFunctor : public EdgeLoadFunctor {
public:
- virtual inline Int operator()(const Element &, const Element &) const
- noexcept {
+ inline Int operator()(const Element &, const Element &) const
+ noexcept override {
return 1;
}
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// define a partition of the mesh
virtual void
partitionate(UInt nb_part,
const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
const Array<UInt> & pairs = Array<UInt>()) = 0;
/// reorder the nodes to reduce the filling during the factorization of a
/// matrix that has a profil based on the connectivity of the mesh
virtual void reorder() = 0;
/// fill the partitions array with a given linearized partition information
void fillPartitionInformation(const Mesh & mesh,
const Int * linearized_partitions);
protected:
/// build the dual graph of the mesh, for all element of spatial_dimension
void buildDualGraph(Array<Int> & dxadj, Array<Int> & dadjncy,
Array<Int> & edge_loads,
const EdgeLoadFunctor & edge_load_func);
/// tweak the mesh to handle the PBC pairs
void tweakConnectivity(const Array<UInt> & pairs);
/// restore the mesh that has been tweaked
void restoreConnectivity();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
bool hasPartitions(const ElementType & type, const GhostType & ghost_type);
AKANTU_GET_MACRO(Partitions, partitions, const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Partition, partitions, UInt);
AKANTU_GET_MACRO(GhostPartitionCSR, ghost_partitions_csr,
const ElementTypeMap<CSR<UInt>> &);
AKANTU_GET_MACRO(NbPartition, nb_partitions, UInt);
AKANTU_SET_MACRO(NbPartition, nb_partitions, UInt);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id
std::string id;
/// the mesh to partition
const Mesh & mesh;
/// dimension of the elements to consider in the mesh
UInt spatial_dimension;
/// number of partitions
UInt nb_partitions;
/// partition numbers
ElementTypeMapArray<UInt> partitions;
ElementTypeMap<CSR<UInt>> ghost_partitions_csr;
ElementTypeMapArray<UInt> ghost_partitions;
ElementTypeMapArray<UInt> ghost_partitions_offset;
Array<UInt> * permutation;
ElementTypeMapArray<UInt> saved_connectivity;
Array<Element> lin_to_element;
};
} // namespace akantu
#ifdef AKANTU_USE_SCOTCH
#include "mesh_partition_scotch.hh"
#endif
#endif /* __AKANTU_MESH_PARTITION_HH__ */
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
index bfb340547..a8f44b91a 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
+++ b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.hh
@@ -1,98 +1,98 @@
/**
* @file mesh_partition_mesh_data.hh
*
* @author Dana Christen <dana.christen@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief mesh partitioning based on data provided in the mesh
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_PARTITION_MESH_DATA_HH__
#define __AKANTU_MESH_PARTITION_MESH_DATA_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_partition.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartitionMeshData : public MeshPartition {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshPartitionMeshData(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "MeshPartitionerMeshData",
const MemoryID & memory_id = 0);
MeshPartitionMeshData(const Mesh & mesh,
const ElementTypeMapArray<UInt> & mapping,
UInt spatial_dimension,
const ID & id = "MeshPartitionerMeshData",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
+ void
+ partitionate(UInt nb_part,
+ const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
+ const Array<UInt> & pairs = Array<UInt>()) override;
- virtual void partitionate(UInt nb_part,
- const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
- const Array<UInt> & pairs = Array<UInt>());
-
- virtual void reorder();
+ void reorder() override;
void setPartitionMapping(const ElementTypeMapArray<UInt> & mapping);
void setPartitionMappingFromMeshData(const std::string & data_name);
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const ElementTypeMapArray<UInt> * partition_mapping;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_MESH_PARTITION_MESH_DATA_HH__ */
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh b/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
index 81eb819b3..e96865878 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
+++ b/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
@@ -1,81 +1,81 @@
/**
* @file mesh_partition_scotch.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief mesh partitioning based on libScotch
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_PARTITION_SCOTCH_HH__
#define __AKANTU_MESH_PARTITION_SCOTCH_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_partition.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshPartitionScotch : public MeshPartition {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshPartitionScotch(const Mesh & mesh, UInt spatial_dimension,
const ID & id = "mesh_partition_scotch",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
+ void
+ partitionate(UInt nb_part,
+ const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
+ const Array<UInt> & pairs = Array<UInt>()) override;
- virtual void partitionate(UInt nb_part,
- const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
- const Array<UInt> & pairs = Array<UInt>());
-
- virtual void reorder();
+ void reorder() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // akantu
#endif /* __AKANTU_MESH_PARTITION_SCOTCH_HH__ */
diff --git a/src/mesh_utils/mesh_utils.cc b/src/mesh_utils/mesh_utils.cc
index 7ee541f65..d4378f2b7 100644
--- a/src/mesh_utils/mesh_utils.cc
+++ b/src/mesh_utils/mesh_utils.cc
@@ -1,2172 +1,2172 @@
/**
* @file mesh_utils.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Aug 20 2010
* @date last modification: Fri Jan 22 2016
*
* @brief All mesh utils necessary for various tasks
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "mesh_utils.hh"
#include "element_synchronizer.hh"
#include "fe_engine.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#include <limits>
#include <numeric>
#include <queue>
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void MeshUtils::buildNode2Elements(const Mesh & mesh,
CSR<Element> & node_to_elem,
UInt spatial_dimension) {
AKANTU_DEBUG_IN();
if (spatial_dimension == _all_dimensions)
spatial_dimension = mesh.getSpatialDimension();
/// count number of occurrence of each node
UInt nb_nodes = mesh.getNbNodes();
/// array for the node-element list
node_to_elem.resizeRows(nb_nodes);
node_to_elem.clearRows();
AKANTU_DEBUG_ASSERT(
mesh.firstType(spatial_dimension) != mesh.lastType(spatial_dimension),
"Some elements must be found in right dimension to compute facets!");
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first =
mesh.firstType(spatial_dimension, *gt, _ek_not_defined);
Mesh::type_iterator last =
mesh.lastType(spatial_dimension, *gt, _ek_not_defined);
for (; first != last; ++first) {
ElementType type = *first;
UInt nb_element = mesh.getNbElement(type, *gt);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
mesh.getConnectivity(type, *gt).begin(
Mesh::getNbNodesPerElement(type));
for (UInt el = 0; el < nb_element; ++el, ++conn_it)
for (UInt n = 0; n < conn_it->size(); ++n)
++node_to_elem.rowOffset((*conn_it)(n));
}
}
node_to_elem.countToCSR();
node_to_elem.resizeCols();
/// rearrange element to get the node-element list
Element e;
node_to_elem.beginInsertions();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first =
mesh.firstType(spatial_dimension, *gt, _ek_not_defined);
Mesh::type_iterator last =
mesh.lastType(spatial_dimension, *gt, _ek_not_defined);
e.ghost_type = *gt;
for (; first != last; ++first) {
ElementType type = *first;
e.type = type;
UInt nb_element = mesh.getNbElement(type, *gt);
Array<UInt>::const_iterator<Vector<UInt>> conn_it =
mesh.getConnectivity(type, *gt).begin(
Mesh::getNbNodesPerElement(type));
for (UInt el = 0; el < nb_element; ++el, ++conn_it) {
e.element = el;
for (UInt n = 0; n < conn_it->size(); ++n)
node_to_elem.insertInRow((*conn_it)(n), e);
}
}
}
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* This function should disappear in the future (used in mesh partitioning)
*/
// void MeshUtils::buildNode2Elements(const Mesh & mesh, CSR<UInt> &
// node_to_elem,
// UInt spatial_dimension) {
// AKANTU_DEBUG_IN();
// if (spatial_dimension == _all_dimensions)
// spatial_dimension = mesh.getSpatialDimension();
// UInt nb_nodes = mesh.getNbNodes();
// const Mesh::ConnectivityTypeList & type_list =
// mesh.getConnectivityTypeList(); Mesh::ConnectivityTypeList::const_iterator
// it;
// UInt nb_types = type_list.size();
// UInt nb_good_types = 0;
// Vector<UInt> nb_nodes_per_element(nb_types);
// UInt ** conn_val = new UInt *[nb_types];
// Vector<UInt> nb_element(nb_types);
// for (it = type_list.begin(); it != type_list.end(); ++it) {
// ElementType type = *it;
// if (Mesh::getSpatialDimension(type) != spatial_dimension)
// continue;
// nb_nodes_per_element[nb_good_types] = Mesh::getNbNodesPerElement(type);
// conn_val[nb_good_types] = mesh.getConnectivity(type,
// _not_ghost).storage(); nb_element[nb_good_types] =
// mesh.getConnectivity(type, _not_ghost).size();
// nb_good_types++;
// }
// AKANTU_DEBUG_ASSERT(
// nb_good_types != 0,
// "Some elements must be found in right dimension to compute facets!");
// /// array for the node-element list
// node_to_elem.resizeRows(nb_nodes);
// node_to_elem.clearRows();
// /// count number of occurrence of each node
// for (UInt t = 0; t < nb_good_types; ++t) {
// for (UInt el = 0; el < nb_element[t]; ++el) {
// UInt el_offset = el * nb_nodes_per_element[t];
// for (UInt n = 0; n < nb_nodes_per_element[t]; ++n) {
// ++node_to_elem.rowOffset(conn_val[t][el_offset + n]);
// }
// }
// }
// node_to_elem.countToCSR();
// node_to_elem.resizeCols();
// node_to_elem.beginInsertions();
// /// rearrange element to get the node-element list
// for (UInt t = 0, linearized_el = 0; t < nb_good_types; ++t)
// for (UInt el = 0; el < nb_element[t]; ++el, ++linearized_el) {
// UInt el_offset = el * nb_nodes_per_element[t];
// for (UInt n = 0; n < nb_nodes_per_element[t]; ++n)
// node_to_elem.insertInRow(conn_val[t][el_offset + n], linearized_el);
// }
// node_to_elem.endInsertions();
// delete[] conn_val;
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void MeshUtils::buildNode2ElementsElementTypeMap(const Mesh & mesh,
CSR<UInt> & node_to_elem,
const ElementType & type,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_elements = mesh.getConnectivity(type, ghost_type).size();
UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();
/// array for the node-element list
node_to_elem.resizeRows(nb_nodes);
node_to_elem.clearRows();
/// count number of occurrence of each node
for (UInt el = 0; el < nb_elements; ++el) {
UInt el_offset = el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n)
++node_to_elem.rowOffset(conn_val[el_offset + n]);
}
/// convert the occurrence array in a csr one
node_to_elem.countToCSR();
node_to_elem.resizeCols();
node_to_elem.beginInsertions();
/// save the element index in the node-element list
for (UInt el = 0; el < nb_elements; ++el) {
UInt el_offset = el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
node_to_elem.insertInRow(conn_val[el_offset + n], el);
}
}
node_to_elem.endInsertions();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacets(Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end = mesh.lastType(spatial_dimension - 1, gt_facet);
for (; it != end; ++it) {
mesh.getConnectivity(*it, *gt).resize(0);
// \todo inform the mesh event handler
}
}
buildFacetsDimension(mesh, mesh, true, spatial_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt to_dimension) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
buildAllFacets(mesh, mesh_facets, spatial_dimension, to_dimension);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt from_dimension, UInt to_dimension) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(
mesh_facets.isMeshFacets(),
"The mesh_facets should be initialized with initMeshFacets");
/// generate facets
buildFacetsDimension(mesh, mesh_facets, false, from_dimension);
/// copy nodes type
MeshAccessor mesh_accessor_facets(mesh_facets);
mesh_accessor_facets.getNodesType().copy(mesh.getNodesType());
/// sort facets and generate sub-facets
for (UInt i = from_dimension - 1; i > to_dimension; --i) {
buildFacetsDimension(mesh_facets, mesh_facets, false, i);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacetsDimension(const Mesh & mesh, Mesh & mesh_facets,
bool boundary_only, UInt dimension) {
AKANTU_DEBUG_IN();
// save the current parent of mesh_facets and set it temporarly to mesh since
// mesh is the one containing the elements for which mesh_facets has the
// sub-elements
// example: if the function is called with mesh = mesh_facets
const Mesh * mesh_facets_parent = nullptr;
try {
mesh_facets_parent = &mesh_facets.getMeshParent();
} catch (...) {
}
mesh_facets.defineMeshParent(mesh);
MeshAccessor mesh_accessor(mesh_facets);
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<Real> & mesh_facets_nodes = mesh_facets.getNodes();
const Array<Real>::const_vector_iterator mesh_facets_nodes_it =
mesh_facets_nodes.begin(spatial_dimension);
CSR<Element> node_to_elem;
buildNode2Elements(mesh, node_to_elem, dimension);
Array<UInt> counter;
std::vector<Element> connected_elements;
// init the SubelementToElement data to improve performance
for (auto && ghost_type : ghost_types) {
for (auto && type : mesh.elementTypes(dimension, ghost_type)) {
mesh_accessor.getSubelementToElement(type, ghost_type);
Vector<ElementType> facet_types = mesh.getAllFacetTypes(type);
for (auto && ft : arange(facet_types.size())) {
ElementType facet_type = facet_types(ft);
mesh_accessor.getElementToSubelement(facet_type, ghost_type);
mesh_accessor.getConnectivity(facet_type, ghost_type);
}
}
}
const ElementSynchronizer * synchronizer = nullptr;
if (mesh.isDistributed()) {
synchronizer = &(mesh.getElementSynchronizer());
}
Element current_element;
for (auto && ghost_type : ghost_types) {
GhostType facet_ghost_type = ghost_type;
current_element.ghost_type = ghost_type;
for (auto && type : mesh.elementTypes(dimension, ghost_type)) {
auto facet_types = mesh.getAllFacetTypes(type);
current_element.type = type;
for (auto && ft : arange(facet_types.size())) {
auto facet_type = facet_types(ft);
auto nb_element = mesh.getNbElement(type, ghost_type);
auto element_to_subelement =
&mesh_facets.getElementToSubelement(facet_type, ghost_type);
auto connectivity_facets =
&mesh_facets.getConnectivity(facet_type, ghost_type);
auto nb_facet_per_element = mesh.getNbFacetsPerElement(type, ft);
const auto & element_connectivity =
mesh.getConnectivity(type, ghost_type);
const Matrix<UInt> facet_local_connectivity =
mesh.getFacetLocalConnectivity(type, ft);
auto nb_nodes_per_facet = connectivity_facets->getNbComponent();
Vector<UInt> facet(nb_nodes_per_facet);
for (UInt el = 0; el < nb_element; ++el) {
current_element.element = el;
for (UInt f = 0; f < nb_facet_per_element; ++f) {
for (UInt n = 0; n < nb_nodes_per_facet; ++n)
facet(n) =
element_connectivity(el, facet_local_connectivity(f, n));
UInt first_node_nb_elements = node_to_elem.getNbCols(facet(0));
counter.resize(first_node_nb_elements);
counter.clear();
// loop over the other nodes to search intersecting elements,
// which are the elements that share another node with the
// starting element after first_node
UInt local_el = 0;
auto first_node_elements = node_to_elem.begin(facet(0));
auto first_node_elements_end = node_to_elem.end(facet(0));
for (; first_node_elements != first_node_elements_end;
++first_node_elements, ++local_el) {
for (UInt n = 1; n < nb_nodes_per_facet; ++n) {
auto node_elements_begin = node_to_elem.begin(facet(n));
auto node_elements_end = node_to_elem.end(facet(n));
counter(local_el) +=
std::count(node_elements_begin, node_elements_end,
*first_node_elements);
}
}
// counting the number of elements connected to the facets and
// taking the minimum element number, because the facet should
// be inserted just once
UInt nb_element_connected_to_facet = 0;
Element minimum_el = ElementNull;
connected_elements.clear();
for (UInt el_f = 0; el_f < first_node_nb_elements; el_f++) {
Element real_el = node_to_elem(facet(0), el_f);
if (not(counter(el_f) == nb_nodes_per_facet - 1))
continue;
++nb_element_connected_to_facet;
minimum_el = std::min(minimum_el, real_el);
connected_elements.push_back(real_el);
}
if (minimum_el != current_element)
continue;
bool full_ghost_facet = false;
UInt n = 0;
while (n < nb_nodes_per_facet && mesh.isPureGhostNode(facet(n)))
++n;
if (n == nb_nodes_per_facet)
full_ghost_facet = true;
if (full_ghost_facet)
continue;
if (boundary_only and nb_element_connected_to_facet != 1)
continue;
std::vector<Element> elements;
// build elements_on_facets: linearized_el must come first
// in order to store the facet in the correct direction
// and avoid to invert the sign in the normal computation
elements.push_back(current_element);
if (nb_element_connected_to_facet == 1) { /// boundary facet
elements.push_back(ElementNull);
} else if (nb_element_connected_to_facet == 2) { /// internal facet
elements.push_back(connected_elements[1]);
/// check if facet is in between ghost and normal
/// elements: if it's the case, the facet is either
/// ghost or not ghost. The criterion to decide this
/// is arbitrary. It was chosen to check the processor
/// id (prank) of the two neighboring elements. If
/// prank of the ghost element is lower than prank of
/// the normal one, the facet is not ghost, otherwise
/// it's ghost
GhostType gt[2] = {_not_ghost, _not_ghost};
for (UInt el = 0; el < connected_elements.size(); ++el)
gt[el] = connected_elements[el].ghost_type;
if (gt[0] != gt[1] and
(gt[0] == _not_ghost or gt[1] == _not_ghost)) {
UInt prank[2];
for (UInt el = 0; el < 2; ++el) {
prank[el] = synchronizer->getRank(connected_elements[el]);
}
// ugly trick from Marco detected :P
bool ghost_one = (gt[0] != _ghost);
if (prank[ghost_one] > prank[!ghost_one])
facet_ghost_type = _not_ghost;
else
facet_ghost_type = _ghost;
connectivity_facets =
&mesh_facets.getConnectivity(facet_type, facet_ghost_type);
element_to_subelement = &mesh_facets.getElementToSubelement(
facet_type, facet_ghost_type);
}
} else { /// facet of facet
for (UInt i = 1; i < nb_element_connected_to_facet; ++i) {
elements.push_back(connected_elements[i]);
}
}
element_to_subelement->push_back(elements);
connectivity_facets->push_back(facet);
/// current facet index
UInt current_facet = connectivity_facets->size() - 1;
/// loop on every element connected to current facet and
/// insert current facet in the first free spot of the
/// subelement_to_element vector
for (UInt elem = 0; elem < elements.size(); ++elem) {
Element loc_el = elements[elem];
if (loc_el.type == _not_defined)
continue;
Array<Element> & subelement_to_element =
mesh_facets.getSubelementToElement(loc_el.type,
loc_el.ghost_type);
UInt nb_facet_per_loc_element =
subelement_to_element.getNbComponent();
for (UInt f_in = 0; f_in < nb_facet_per_loc_element; ++f_in) {
auto & el = subelement_to_element(loc_el.element, f_in);
if (el.type != _not_defined)
continue;
el.type = facet_type;
el.element = current_facet;
el.ghost_type = facet_ghost_type;
break;
}
}
/// reset connectivity in case a facet was found in
/// between ghost and normal elements
if (facet_ghost_type != ghost_type) {
facet_ghost_type = ghost_type;
connectivity_facets =
&mesh_accessor.getConnectivity(facet_type, facet_ghost_type);
element_to_subelement = &mesh_accessor.getElementToSubelement(
facet_type, facet_ghost_type);
}
}
}
}
}
}
// restore the parent of mesh_facet
if (mesh_facets_parent)
mesh_facets.defineMeshParent(*mesh_facets_parent);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberMeshNodes(Mesh & mesh,
Array<UInt> & local_connectivities,
UInt nb_local_element, UInt nb_ghost_element,
ElementType type,
Array<UInt> & old_nodes_numbers) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
std::map<UInt, UInt> renumbering_map;
for (UInt i = 0; i < old_nodes_numbers.size(); ++i) {
renumbering_map[old_nodes_numbers(i)] = i;
}
/// renumber the nodes
renumberNodesInConnectivity(local_connectivities,
(nb_local_element + nb_ghost_element) *
nb_nodes_per_element,
renumbering_map);
old_nodes_numbers.resize(renumbering_map.size());
for (auto & renumber_pair : renumbering_map) {
old_nodes_numbers(renumber_pair.second) = renumber_pair.first;
}
renumbering_map.clear();
MeshAccessor mesh_accessor(mesh);
/// copy the renumbered connectivity to the right place
auto & local_conn = mesh_accessor.getConnectivity(type);
local_conn.resize(nb_local_element);
memcpy(local_conn.storage(), local_connectivities.storage(),
nb_local_element * nb_nodes_per_element * sizeof(UInt));
auto & ghost_conn = mesh_accessor.getConnectivity(type, _ghost);
ghost_conn.resize(nb_ghost_element);
std::memcpy(ghost_conn.storage(),
local_connectivities.storage() +
nb_local_element * nb_nodes_per_element,
nb_ghost_element * nb_nodes_per_element * sizeof(UInt));
auto & ghost_counter = mesh_accessor.getGhostsCounters(type, _ghost);
ghost_counter.resize(nb_ghost_element, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::renumberNodesInConnectivity(
Array<UInt> & list_nodes, UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map) {
AKANTU_DEBUG_IN();
UInt * connectivity = list_nodes.storage();
UInt new_node_num = renumbering_map.size();
for (UInt n = 0; n < nb_nodes; ++n, ++connectivity) {
UInt & node = *connectivity;
std::map<UInt, UInt>::iterator it = renumbering_map.find(node);
if (it == renumbering_map.end()) {
UInt old_node = node;
renumbering_map[old_node] = new_node_num;
node = new_node_num;
++new_node_num;
} else {
node = it->second;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::purifyMesh(Mesh & mesh) {
AKANTU_DEBUG_IN();
std::map<UInt, UInt> renumbering_map;
RemovedNodesEvent remove_nodes(mesh);
Array<UInt> & nodes_removed = remove_nodes.getList();
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType)gt;
Mesh::type_iterator it =
mesh.firstType(_all_dimensions, ghost_type, _ek_not_defined);
Mesh::type_iterator end =
mesh.lastType(_all_dimensions, ghost_type, _ek_not_defined);
for (; it != end; ++it) {
ElementType type(*it);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_element(connectivity.size());
renumberNodesInConnectivity(
connectivity, nb_element * nb_nodes_per_element, renumbering_map);
}
}
Array<UInt> & new_numbering = remove_nodes.getNewNumbering();
std::fill(new_numbering.begin(), new_numbering.end(), UInt(-1));
std::map<UInt, UInt>::iterator it = renumbering_map.begin();
std::map<UInt, UInt>::iterator end = renumbering_map.end();
for (; it != end; ++it) {
new_numbering(it->first) = it->second;
}
for (UInt i = 0; i < new_numbering.size(); ++i) {
if (new_numbering(i) == UInt(-1))
nodes_removed.push_back(i);
}
mesh.sendEvent(remove_nodes);
AKANTU_DEBUG_OUT();
}
#if defined(AKANTU_COHESIVE_ELEMENT)
/* -------------------------------------------------------------------------- */
UInt MeshUtils::insertCohesiveElements(
Mesh & mesh, Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion,
Array<UInt> & doubled_nodes, Array<Element> & new_elements,
bool only_double_facets) {
UInt spatial_dimension = mesh.getSpatialDimension();
UInt elements_to_insert = updateFacetToDouble(mesh_facets, facet_insertion);
if (elements_to_insert > 0) {
if (spatial_dimension == 1) {
doublePointFacet(mesh, mesh_facets, doubled_nodes);
} else {
doubleFacet(mesh, mesh_facets, spatial_dimension - 1, doubled_nodes,
true);
findSubfacetToDouble<false>(mesh, mesh_facets);
if (spatial_dimension == 2) {
doubleSubfacet<2>(mesh, mesh_facets, doubled_nodes);
} else if (spatial_dimension == 3) {
doubleFacet(mesh, mesh_facets, 1, doubled_nodes, false);
findSubfacetToDouble<true>(mesh, mesh_facets);
doubleSubfacet<3>(mesh, mesh_facets, doubled_nodes);
}
}
if (!only_double_facets)
updateCohesiveData(mesh, mesh_facets, new_elements);
}
return elements_to_insert;
}
#endif
/* -------------------------------------------------------------------------- */
void MeshUtils::doubleNodes(Mesh & mesh, const std::vector<UInt> & old_nodes,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
Array<Real> & position = mesh.getNodes();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt old_nb_nodes = position.size();
UInt new_nb_nodes = old_nb_nodes + old_nodes.size();
UInt old_nb_doubled_nodes = doubled_nodes.size();
UInt new_nb_doubled_nodes = old_nb_doubled_nodes + old_nodes.size();
position.resize(new_nb_nodes);
doubled_nodes.resize(new_nb_doubled_nodes);
Array<Real>::iterator<Vector<Real>> position_begin =
position.begin(spatial_dimension);
for (UInt n = 0; n < old_nodes.size(); ++n) {
UInt new_node = old_nb_nodes + n;
/// store doubled nodes
doubled_nodes(old_nb_doubled_nodes + n, 0) = old_nodes[n];
doubled_nodes(old_nb_doubled_nodes + n, 1) = new_node;
/// update position
std::copy(position_begin + old_nodes[n], position_begin + old_nodes[n] + 1,
position_begin + new_node);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::doubleFacet(Mesh & mesh, Mesh & mesh_facets,
UInt facet_dimension, Array<UInt> & doubled_nodes,
bool facet_mode) {
AKANTU_DEBUG_IN();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it = mesh_facets.firstType(facet_dimension, gt_facet);
Mesh::type_iterator end = mesh_facets.lastType(facet_dimension, gt_facet);
for (; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.size();
if (nb_facet_to_double == 0)
continue;
ElementType type_subfacet = Mesh::getFacetType(type_facet);
const UInt nb_subfacet_per_facet =
Mesh::getNbFacetsPerElement(type_facet);
GhostType gt_subfacet = _casper;
- Array<std::vector<Element>> * f_to_subfacet = NULL;
+ Array<std::vector<Element>> * f_to_subfacet = nullptr;
Array<Element> & subfacet_to_facet =
mesh_facets.getSubelementToElement(type_facet, gt_facet);
Array<UInt> & conn_facet =
mesh_facets.getConnectivity(type_facet, gt_facet);
UInt nb_nodes_per_facet = conn_facet.getNbComponent();
UInt old_nb_facet = conn_facet.size();
UInt new_nb_facet = old_nb_facet + nb_facet_to_double;
conn_facet.resize(new_nb_facet);
subfacet_to_facet.resize(new_nb_facet);
UInt new_facet = old_nb_facet - 1;
Element new_facet_el{type_facet, 0, gt_facet};
Array<Element>::iterator<Vector<Element>> subfacet_to_facet_begin =
subfacet_to_facet.begin(nb_subfacet_per_facet);
Array<UInt>::iterator<Vector<UInt>> conn_facet_begin =
conn_facet.begin(nb_nodes_per_facet);
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
++new_facet;
/// adding a new facet by copying original one
/// copy connectivity in new facet
std::copy(conn_facet_begin + old_facet,
conn_facet_begin + old_facet + 1,
conn_facet_begin + new_facet);
/// update subfacet_to_facet
std::copy(subfacet_to_facet_begin + old_facet,
subfacet_to_facet_begin + old_facet + 1,
subfacet_to_facet_begin + new_facet);
new_facet_el.element = new_facet;
/// loop on every subfacet
for (UInt sf = 0; sf < nb_subfacet_per_facet; ++sf) {
Element & subfacet = subfacet_to_facet(old_facet, sf);
if (subfacet == ElementNull)
continue;
if (gt_subfacet != subfacet.ghost_type) {
gt_subfacet = subfacet.ghost_type;
f_to_subfacet = &mesh_facets.getElementToSubelement(
type_subfacet, subfacet.ghost_type);
}
/// update facet_to_subfacet array
(*f_to_subfacet)(subfacet.element).push_back(new_facet_el);
}
}
/// update facet_to_subfacet and _segment_3 facets if any
if (!facet_mode) {
updateSubfacetToFacet(mesh_facets, type_facet, gt_facet, true);
updateFacetToSubfacet(mesh_facets, type_facet, gt_facet, true);
updateQuadraticSegments<true>(mesh, mesh_facets, type_facet, gt_facet,
doubled_nodes);
} else
updateQuadraticSegments<false>(mesh, mesh_facets, type_facet, gt_facet,
doubled_nodes);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt MeshUtils::updateFacetToDouble(
Mesh & mesh_facets, const ElementTypeMapArray<bool> & facet_insertion) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
UInt nb_facets_to_double = 0.;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, gt_facet);
for (; it != end; ++it) {
ElementType type_facet = *it;
const Array<bool> & f_insertion = facet_insertion(type_facet, gt_facet);
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
ElementType el_type = _not_defined;
GhostType el_gt = _casper;
UInt nb_facet_per_element = 0;
Element old_facet_el{type_facet, 0, gt_facet};
- Array<Element> * facet_to_element = NULL;
+ Array<Element> * facet_to_element = nullptr;
for (UInt f = 0; f < f_insertion.size(); ++f) {
if (f_insertion(f) == false)
continue;
++nb_facets_to_double;
if (element_to_facet(f)[1].type == _not_defined
#if defined(AKANTU_COHESIVE_ELEMENT)
|| element_to_facet(f)[1].kind() == _ek_cohesive
#endif
) {
AKANTU_DEBUG_WARNING("attempt to double a facet on the boundary");
continue;
}
f_to_double.push_back(f);
UInt new_facet = mesh_facets.getNbElement(type_facet, gt_facet) +
f_to_double.size() - 1;
old_facet_el.element = f;
/// update facet_to_element vector
Element & elem_to_update = element_to_facet(f)[1];
UInt el = elem_to_update.element;
if (elem_to_update.ghost_type != el_gt ||
elem_to_update.type != el_type) {
el_type = elem_to_update.type;
el_gt = elem_to_update.ghost_type;
facet_to_element =
&mesh_facets.getSubelementToElement(el_type, el_gt);
nb_facet_per_element = facet_to_element->getNbComponent();
}
Element * f_update =
std::find(facet_to_element->storage() + el * nb_facet_per_element,
facet_to_element->storage() + el * nb_facet_per_element +
nb_facet_per_element,
old_facet_el);
AKANTU_DEBUG_ASSERT(
facet_to_element->storage() + el * nb_facet_per_element !=
facet_to_element->storage() + el * nb_facet_per_element +
nb_facet_per_element,
"Facet not found");
f_update->element = new_facet;
/// update elements connected to facet
std::vector<Element> first_facet_list = element_to_facet(f);
element_to_facet.push_back(first_facet_list);
/// set new and original facets as boundary facets
element_to_facet(new_facet)[0] = element_to_facet(new_facet)[1];
element_to_facet(f)[1] = ElementNull;
element_to_facet(new_facet)[1] = ElementNull;
}
}
}
AKANTU_DEBUG_OUT();
return nb_facets_to_double;
}
/* -------------------------------------------------------------------------- */
void MeshUtils::resetFacetToDouble(Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
Mesh::type_iterator it = mesh_facets.firstType(_all_dimensions, gt);
Mesh::type_iterator end = mesh_facets.lastType(_all_dimensions, gt);
for (; it != end; ++it) {
ElementType type = *it;
mesh_facets.getDataPointer<UInt>("facet_to_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element>>(
"facets_to_subfacet_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element>>(
"elements_to_subfacet_double", type, gt, 1, false);
mesh_facets.getDataPointer<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type, gt, 1, false);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool subsubfacet_mode>
void MeshUtils::findSubfacetToDouble(Mesh & mesh, Mesh & mesh_facets) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
if (spatial_dimension == 1)
return;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, gt_facet);
for (; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.size();
if (nb_facet_to_double == 0)
continue;
ElementType type_subfacet = Mesh::getFacetType(type_facet);
GhostType gt_subfacet = _casper;
ElementType type_subsubfacet = Mesh::getFacetType(type_subfacet);
GhostType gt_subsubfacet = _casper;
- Array<UInt> * conn_subfacet = NULL;
- Array<UInt> * sf_to_double = NULL;
- Array<std::vector<Element>> * sf_to_subfacet_double = NULL;
- Array<std::vector<Element>> * f_to_subfacet_double = NULL;
- Array<std::vector<Element>> * el_to_subfacet_double = NULL;
+ Array<UInt> * conn_subfacet = nullptr;
+ Array<UInt> * sf_to_double = nullptr;
+ Array<std::vector<Element>> * sf_to_subfacet_double = nullptr;
+ Array<std::vector<Element>> * f_to_subfacet_double = nullptr;
+ Array<std::vector<Element>> * el_to_subfacet_double = nullptr;
UInt nb_subfacet = Mesh::getNbFacetsPerElement(type_facet);
UInt nb_subsubfacet;
UInt nb_nodes_per_sf_el;
if (subsubfacet_mode) {
nb_nodes_per_sf_el = Mesh::getNbNodesPerElement(type_subsubfacet);
nb_subsubfacet = Mesh::getNbFacetsPerElement(type_subfacet);
} else
nb_nodes_per_sf_el = Mesh::getNbNodesPerElement(type_subfacet);
Array<Element> & subfacet_to_facet =
mesh_facets.getSubelementToElement(type_facet, gt_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
- Array<Element> * subsubfacet_to_subfacet = NULL;
+ Array<Element> * subsubfacet_to_subfacet = nullptr;
UInt old_nb_facet = subfacet_to_facet.size() - nb_facet_to_double;
Element current_facet{type_facet, 0, gt_facet};
std::vector<Element> element_list;
std::vector<Element> facet_list;
std::vector<Element> * subfacet_list;
if (subsubfacet_mode)
subfacet_list = new std::vector<Element>;
/// map to filter subfacets
- Array<std::vector<Element>> * facet_to_subfacet = NULL;
+ Array<std::vector<Element>> * facet_to_subfacet = nullptr;
/// this is used to make sure that both new and old facets are
/// checked
UInt facets[2];
/// loop on every facet
for (UInt f_index = 0; f_index < 2; ++f_index) {
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
facets[bool(f_index)] = f_to_double(facet);
facets[!bool(f_index)] = old_nb_facet + facet;
UInt old_facet = facets[0];
UInt new_facet = facets[1];
Element & starting_element = element_to_facet(new_facet)[0];
current_facet.element = old_facet;
/// loop on every subfacet
for (UInt sf = 0; sf < nb_subfacet; ++sf) {
Element & subfacet = subfacet_to_facet(old_facet, sf);
if (subfacet == ElementNull)
continue;
if (gt_subfacet != subfacet.ghost_type) {
gt_subfacet = subfacet.ghost_type;
if (subsubfacet_mode) {
subsubfacet_to_subfacet = &mesh_facets.getSubelementToElement(
type_subfacet, gt_subfacet);
} else {
conn_subfacet =
&mesh_facets.getConnectivity(type_subfacet, gt_subfacet);
sf_to_double = &mesh_facets.getData<UInt>(
"facet_to_double", type_subfacet, gt_subfacet);
f_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subfacet,
gt_subfacet);
el_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_subfacet,
gt_subfacet);
facet_to_subfacet = &mesh_facets.getElementToSubelement(
type_subfacet, gt_subfacet);
}
}
if (subsubfacet_mode) {
/// loop on every subsubfacet
for (UInt ssf = 0; ssf < nb_subsubfacet; ++ssf) {
Element & subsubfacet =
(*subsubfacet_to_subfacet)(subfacet.element, ssf);
if (subsubfacet == ElementNull)
continue;
if (gt_subsubfacet != subsubfacet.ghost_type) {
gt_subsubfacet = subsubfacet.ghost_type;
conn_subfacet = &mesh_facets.getConnectivity(type_subsubfacet,
gt_subsubfacet);
sf_to_double = &mesh_facets.getData<UInt>(
"facet_to_double", type_subsubfacet, gt_subsubfacet);
sf_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subsubfacet,
gt_subsubfacet);
f_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subsubfacet,
gt_subsubfacet);
el_to_subfacet_double =
&mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_subsubfacet,
gt_subsubfacet);
facet_to_subfacet = &mesh_facets.getElementToSubelement(
type_subsubfacet, gt_subsubfacet);
}
UInt global_ssf = subsubfacet.element;
Vector<UInt> subsubfacet_connectivity(
conn_subfacet->storage() + global_ssf * nb_nodes_per_sf_el,
nb_nodes_per_sf_el);
/// check if subsubfacet is to be doubled
if (findElementsAroundSubfacet<true>(
mesh, mesh_facets, starting_element, current_facet,
subsubfacet_connectivity, element_list, facet_list,
subfacet_list) == false &&
removeElementsInVector(*subfacet_list,
(*facet_to_subfacet)(global_ssf)) ==
false) {
sf_to_double->push_back(global_ssf);
sf_to_subfacet_double->push_back(*subfacet_list);
f_to_subfacet_double->push_back(facet_list);
el_to_subfacet_double->push_back(element_list);
}
}
} else {
const UInt global_sf = subfacet.element;
Vector<UInt> subfacet_connectivity(
conn_subfacet->storage() + global_sf * nb_nodes_per_sf_el,
nb_nodes_per_sf_el);
/// check if subfacet is to be doubled
if (findElementsAroundSubfacet<false>(
mesh, mesh_facets, starting_element, current_facet,
subfacet_connectivity, element_list,
facet_list) == false &&
removeElementsInVector(
facet_list, (*facet_to_subfacet)(global_sf)) == false) {
sf_to_double->push_back(global_sf);
f_to_subfacet_double->push_back(facet_list);
el_to_subfacet_double->push_back(element_list);
}
}
}
}
}
if (subsubfacet_mode)
delete subfacet_list;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
void MeshUtils::updateCohesiveData(Mesh & mesh, Mesh & mesh_facets,
Array<Element> & new_elements) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
bool third_dimension = spatial_dimension == 3;
MeshAccessor mesh_facets_accessor(mesh_facets);
for (auto gt_facet : ghost_types) {
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.size();
if (nb_facet_to_double == 0)
continue;
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
auto & facet_to_coh_element =
mesh_facets_accessor.getSubelementToElement(type_cohesive, gt_facet);
auto & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
auto & conn_cohesive = mesh.getConnectivity(type_cohesive, gt_facet);
UInt nb_nodes_per_facet = Mesh::getNbNodesPerElement(type_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
UInt old_nb_cohesive_elements = conn_cohesive.size();
UInt new_nb_cohesive_elements = conn_cohesive.size() + nb_facet_to_double;
UInt old_nb_facet = element_to_facet.size() - nb_facet_to_double;
facet_to_coh_element.resize(new_nb_cohesive_elements);
conn_cohesive.resize(new_nb_cohesive_elements);
UInt new_elements_old_size = new_elements.size();
new_elements.resize(new_elements_old_size + nb_facet_to_double);
Element c_element{type_cohesive, 0, gt_facet};
Element f_element{type_facet, 0, gt_facet};
UInt facets[2];
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
/// (in 3D cohesive elements connectivity is inverted)
facets[third_dimension] = f_to_double(facet);
facets[!third_dimension] = old_nb_facet + facet;
UInt cohesive_element = old_nb_cohesive_elements + facet;
/// store doubled facets
f_element.element = facets[0];
facet_to_coh_element(cohesive_element, 0) = f_element;
f_element.element = facets[1];
facet_to_coh_element(cohesive_element, 1) = f_element;
/// modify cohesive elements' connectivity
for (UInt n = 0; n < nb_nodes_per_facet; ++n) {
conn_cohesive(cohesive_element, n) = conn_facet(facets[0], n);
conn_cohesive(cohesive_element, n + nb_nodes_per_facet) =
conn_facet(facets[1], n);
}
/// update element_to_facet vectors
c_element.element = cohesive_element;
element_to_facet(facets[0])[1] = c_element;
element_to_facet(facets[1])[1] = c_element;
/// add cohesive element to the element event list
new_elements(new_elements_old_size + facet) = c_element;
}
}
}
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
void MeshUtils::doublePointFacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
if (spatial_dimension != 1)
return;
Array<Real> & position = mesh.getNodes();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_facet = *gt;
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, gt_facet);
for (; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & conn_facet =
mesh_facets.getConnectivity(type_facet, gt_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
const Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.size();
UInt old_nb_facet = element_to_facet.size() - nb_facet_to_double;
UInt new_nb_facet = element_to_facet.size();
UInt old_nb_nodes = position.size();
UInt new_nb_nodes = old_nb_nodes + nb_facet_to_double;
position.resize(new_nb_nodes);
conn_facet.resize(new_nb_facet);
UInt old_nb_doubled_nodes = doubled_nodes.size();
doubled_nodes.resize(old_nb_doubled_nodes + nb_facet_to_double);
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt new_facet = old_nb_facet + facet;
ElementType type = element_to_facet(new_facet)[0].type;
UInt el = element_to_facet(new_facet)[0].element;
GhostType gt = element_to_facet(new_facet)[0].ghost_type;
UInt old_node = conn_facet(old_facet);
UInt new_node = old_nb_nodes + facet;
/// update position
position(new_node) = position(old_node);
conn_facet(new_facet) = new_node;
Array<UInt> & conn_segment = mesh.getConnectivity(type, gt);
UInt nb_nodes_per_segment = conn_segment.getNbComponent();
/// update facet connectivity
UInt i;
for (i = 0;
conn_segment(el, i) != old_node && i <= nb_nodes_per_segment; ++i)
;
conn_segment(el, i) = new_node;
doubled_nodes(old_nb_doubled_nodes + facet, 0) = old_node;
doubled_nodes(old_nb_doubled_nodes + facet, 1) = new_node;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool third_dim_segments>
void MeshUtils::updateQuadraticSegments(Mesh & mesh, Mesh & mesh_facets,
ElementType type_facet,
GhostType gt_facet,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
if (type_facet != _segment_3)
return;
Array<UInt> & f_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_facet, gt_facet);
UInt nb_facet_to_double = f_to_double.size();
UInt old_nb_facet =
mesh_facets.getNbElement(type_facet, gt_facet) - nb_facet_to_double;
Array<UInt> & conn_facet = mesh_facets.getConnectivity(type_facet, gt_facet);
Array<std::vector<Element>> & element_to_facet =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
/// this ones matter only for segments in 3D
- Array<std::vector<Element>> * el_to_subfacet_double = NULL;
- Array<std::vector<Element>> * f_to_subfacet_double = NULL;
+ Array<std::vector<Element>> * el_to_subfacet_double = nullptr;
+ Array<std::vector<Element>> * f_to_subfacet_double = nullptr;
if (third_dim_segments) {
el_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_facet, gt_facet);
f_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_facet, gt_facet);
}
std::vector<UInt> middle_nodes;
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt node = conn_facet(old_facet, 2);
if (!mesh.isPureGhostNode(node))
middle_nodes.push_back(node);
}
UInt n = doubled_nodes.size();
doubleNodes(mesh, middle_nodes, doubled_nodes);
for (UInt facet = 0; facet < nb_facet_to_double; ++facet) {
UInt old_facet = f_to_double(facet);
UInt old_node = conn_facet(old_facet, 2);
if (mesh.isPureGhostNode(old_node))
continue;
UInt new_node = doubled_nodes(n, 1);
UInt new_facet = old_nb_facet + facet;
conn_facet(new_facet, 2) = new_node;
if (third_dim_segments) {
updateElementalConnectivity(mesh_facets, old_node, new_node,
element_to_facet(new_facet));
updateElementalConnectivity(mesh, old_node, new_node,
(*el_to_subfacet_double)(facet),
&(*f_to_subfacet_double)(facet));
} else {
updateElementalConnectivity(mesh, old_node, new_node,
element_to_facet(new_facet));
}
++n;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateSubfacetToFacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode) {
AKANTU_DEBUG_IN();
Array<UInt> & sf_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_subfacet, gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.size();
/// update subfacet_to_facet vector
ElementType type_facet = _not_defined;
GhostType gt_facet = _casper;
- Array<Element> * subfacet_to_facet = NULL;
+ Array<Element> * subfacet_to_facet = nullptr;
UInt nb_subfacet_per_facet = 0;
UInt old_nb_subfacet = mesh_facets.getNbElement(type_subfacet, gt_subfacet) -
nb_subfacet_to_double;
- Array<std::vector<Element>> * facet_list = NULL;
+ Array<std::vector<Element>> * facet_list = nullptr;
if (facet_mode)
facet_list = &mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subfacet, gt_subfacet);
else
facet_list = &mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subfacet, gt_subfacet);
Element old_subfacet_el{type_subfacet, 0, gt_subfacet};
Element new_subfacet_el{type_subfacet, 0, gt_subfacet};
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
old_subfacet_el.element = sf_to_double(sf);
new_subfacet_el.element = old_nb_subfacet + sf;
for (UInt f = 0; f < (*facet_list)(sf).size(); ++f) {
Element & facet = (*facet_list)(sf)[f];
if (facet.type != type_facet || facet.ghost_type != gt_facet) {
type_facet = facet.type;
gt_facet = facet.ghost_type;
subfacet_to_facet =
&mesh_facets.getSubelementToElement(type_facet, gt_facet);
nb_subfacet_per_facet = subfacet_to_facet->getNbComponent();
}
Element * sf_update = std::find(
subfacet_to_facet->storage() + facet.element * nb_subfacet_per_facet,
subfacet_to_facet->storage() + facet.element * nb_subfacet_per_facet +
nb_subfacet_per_facet,
old_subfacet_el);
AKANTU_DEBUG_ASSERT(subfacet_to_facet->storage() +
facet.element * nb_subfacet_per_facet !=
subfacet_to_facet->storage() +
facet.element * nb_subfacet_per_facet +
nb_subfacet_per_facet,
"Subfacet not found");
*sf_update = new_subfacet_el;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateFacetToSubfacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode) {
AKANTU_DEBUG_IN();
Array<UInt> & sf_to_double =
mesh_facets.getData<UInt>("facet_to_double", type_subfacet, gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.size();
Array<std::vector<Element>> & facet_to_subfacet =
mesh_facets.getElementToSubelement(type_subfacet, gt_subfacet);
- Array<std::vector<Element>> * facet_to_subfacet_double = NULL;
+ Array<std::vector<Element>> * facet_to_subfacet_double = nullptr;
if (facet_mode) {
facet_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"facets_to_subfacet_double", type_subfacet, gt_subfacet);
} else {
facet_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subfacet, gt_subfacet);
}
UInt old_nb_subfacet = facet_to_subfacet.size();
facet_to_subfacet.resize(old_nb_subfacet + nb_subfacet_to_double);
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf)
facet_to_subfacet(old_nb_subfacet + sf) = (*facet_to_subfacet_double)(sf);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MeshUtils::doubleSubfacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes) {
AKANTU_DEBUG_IN();
if (spatial_dimension == 1)
return;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType gt_subfacet = *gt;
Mesh::type_iterator it = mesh_facets.firstType(0, gt_subfacet);
Mesh::type_iterator end = mesh_facets.lastType(0, gt_subfacet);
for (; it != end; ++it) {
ElementType type_subfacet = *it;
Array<UInt> & sf_to_double = mesh_facets.getData<UInt>(
"facet_to_double", type_subfacet, gt_subfacet);
UInt nb_subfacet_to_double = sf_to_double.size();
if (nb_subfacet_to_double == 0)
continue;
AKANTU_DEBUG_ASSERT(
type_subfacet == _point_1,
"Only _point_1 subfacet doubling is supported at the moment");
Array<UInt> & conn_subfacet =
mesh_facets.getConnectivity(type_subfacet, gt_subfacet);
UInt old_nb_subfacet = conn_subfacet.size();
UInt new_nb_subfacet = old_nb_subfacet + nb_subfacet_to_double;
conn_subfacet.resize(new_nb_subfacet);
std::vector<UInt> nodes_to_double;
UInt old_nb_doubled_nodes = doubled_nodes.size();
/// double nodes
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt old_subfacet = sf_to_double(sf);
nodes_to_double.push_back(conn_subfacet(old_subfacet));
}
doubleNodes(mesh, nodes_to_double, doubled_nodes);
/// add new nodes in connectivity
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt new_subfacet = old_nb_subfacet + sf;
UInt new_node = doubled_nodes(old_nb_doubled_nodes + sf, 1);
conn_subfacet(new_subfacet) = new_node;
}
/// update facet and element connectivity
Array<std::vector<Element>> & f_to_subfacet_double =
mesh_facets.getData<std::vector<Element>>("facets_to_subfacet_double",
type_subfacet, gt_subfacet);
Array<std::vector<Element>> & el_to_subfacet_double =
mesh_facets.getData<std::vector<Element>>(
"elements_to_subfacet_double", type_subfacet, gt_subfacet);
- Array<std::vector<Element>> * sf_to_subfacet_double = NULL;
+ Array<std::vector<Element>> * sf_to_subfacet_double = nullptr;
if (spatial_dimension == 3)
sf_to_subfacet_double = &mesh_facets.getData<std::vector<Element>>(
"subfacets_to_subsubfacet_double", type_subfacet, gt_subfacet);
for (UInt sf = 0; sf < nb_subfacet_to_double; ++sf) {
UInt old_node = doubled_nodes(old_nb_doubled_nodes + sf, 0);
UInt new_node = doubled_nodes(old_nb_doubled_nodes + sf, 1);
updateElementalConnectivity(mesh, old_node, new_node,
el_to_subfacet_double(sf),
&f_to_subfacet_double(sf));
updateElementalConnectivity(mesh_facets, old_node, new_node,
f_to_subfacet_double(sf));
if (spatial_dimension == 3)
updateElementalConnectivity(mesh_facets, old_node, new_node,
(*sf_to_subfacet_double)(sf));
}
if (spatial_dimension == 2) {
updateSubfacetToFacet(mesh_facets, type_subfacet, gt_subfacet, true);
updateFacetToSubfacet(mesh_facets, type_subfacet, gt_subfacet, true);
} else if (spatial_dimension == 3) {
updateSubfacetToFacet(mesh_facets, type_subfacet, gt_subfacet, false);
updateFacetToSubfacet(mesh_facets, type_subfacet, gt_subfacet, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::flipFacets(
Mesh & mesh_facets, const ElementTypeMapArray<UInt> & global_connectivity,
GhostType gt_facet) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh_facets.getSpatialDimension();
/// get global connectivity for local mesh
ElementTypeMapArray<UInt> global_connectivity_tmp("global_connectivity_tmp",
mesh_facets.getID(),
mesh_facets.getMemoryID());
global_connectivity_tmp.initialize(
mesh_facets, _spatial_dimension = spatial_dimension - 1,
_with_nb_nodes_per_element = true, _with_nb_element = true);
mesh_facets.getGlobalConnectivity(global_connectivity_tmp);
/// loop on every facet
for (auto type_facet :
mesh_facets.elementTypes(spatial_dimension - 1, gt_facet)) {
auto & connectivity = mesh_facets.getConnectivity(type_facet, gt_facet);
const auto & g_connectivity = global_connectivity(type_facet, gt_facet);
auto & el_to_f = mesh_facets.getElementToSubelement(type_facet, gt_facet);
auto & subfacet_to_facet =
mesh_facets.getSubelementToElement(type_facet, gt_facet);
UInt nb_subfacet_per_facet = subfacet_to_facet.getNbComponent();
UInt nb_nodes_per_facet = connectivity.getNbComponent();
UInt nb_facet = connectivity.size();
UInt nb_nodes_per_P1_facet =
Mesh::getNbNodesPerElement(Mesh::getP1ElementType(type_facet));
auto & global_conn_tmp = global_connectivity_tmp(type_facet, gt_facet);
auto conn_it = connectivity.begin(nb_nodes_per_facet);
auto gconn_tmp_it = global_conn_tmp.begin(nb_nodes_per_facet);
auto conn_glob_it = g_connectivity.begin(nb_nodes_per_facet);
auto subf_to_f = subfacet_to_facet.begin(nb_subfacet_per_facet);
UInt * conn_tmp_pointer = new UInt[nb_nodes_per_facet];
Vector<UInt> conn_tmp(conn_tmp_pointer, nb_nodes_per_facet);
Element el_tmp;
Element * subf_tmp_pointer = new Element[nb_subfacet_per_facet];
Vector<Element> subf_tmp(subf_tmp_pointer, nb_subfacet_per_facet);
for (UInt f = 0; f < nb_facet;
++f, ++conn_it, ++gconn_tmp_it, ++subf_to_f, ++conn_glob_it) {
Vector<UInt> & gconn_tmp = *gconn_tmp_it;
const Vector<UInt> & conn_glob = *conn_glob_it;
Vector<UInt> & conn_local = *conn_it;
/// skip facet if connectivities are the same
if (gconn_tmp == conn_glob)
continue;
/// re-arrange connectivity
conn_tmp = conn_local;
UInt * begin = conn_glob.storage();
UInt * end = conn_glob.storage() + nb_nodes_per_facet;
for (UInt n = 0; n < nb_nodes_per_facet; ++n) {
UInt * new_node = std::find(begin, end, gconn_tmp(n));
AKANTU_DEBUG_ASSERT(new_node != end, "Node not found");
UInt new_position = new_node - begin;
conn_local(new_position) = conn_tmp(n);
}
/// if 3D, check if facets are just rotated
if (spatial_dimension == 3) {
/// find first node
UInt * new_node = std::find(begin, end, gconn_tmp(0));
AKANTU_DEBUG_ASSERT(new_node != end, "Node not found");
UInt new_position = new_node - begin;
UInt n = 1;
/// count how many nodes in the received connectivity follow
/// the same order of those in the local connectivity
for (; n < nb_nodes_per_P1_facet &&
gconn_tmp(n) ==
conn_glob((new_position + n) % nb_nodes_per_P1_facet);
++n)
;
/// skip the facet inversion if facet is just rotated
if (n == nb_nodes_per_P1_facet)
continue;
}
/// update data to invert facet
el_tmp = el_to_f(f)[0];
el_to_f(f)[0] = el_to_f(f)[1];
el_to_f(f)[1] = el_tmp;
subf_tmp = (*subf_to_f);
(*subf_to_f)(0) = subf_tmp(1);
(*subf_to_f)(1) = subf_tmp(0);
}
delete[] subf_tmp_pointer;
delete[] conn_tmp_pointer;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::fillElementToSubElementsData(Mesh & mesh) {
AKANTU_DEBUG_IN();
if (mesh.getNbElement(mesh.getSpatialDimension() - 1) == 0) {
AKANTU_DEBUG_INFO("There are not facets, add them in the mesh file or call "
"the buildFacet method.");
return;
}
UInt spatial_dimension = mesh.getSpatialDimension();
ElementTypeMapArray<Real> barycenters("barycenter_tmp", mesh.getID(),
mesh.getMemoryID());
barycenters.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = _all_dimensions);
// mesh.initElementTypeMapArray(barycenters, spatial_dimension,
// _all_dimensions);
Element element;
for (auto ghost_type : ghost_types) {
element.ghost_type = ghost_type;
for (auto & type : mesh.elementTypes(_all_dimensions, ghost_type)) {
element.type = type;
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<Real> & barycenters_arr = barycenters(type, ghost_type);
barycenters_arr.resize(nb_element);
auto bary = barycenters_arr.begin(spatial_dimension);
auto bary_end = barycenters_arr.end(spatial_dimension);
for (UInt el = 0; bary != bary_end; ++bary, ++el) {
element.element = el;
mesh.getBarycenter(element, *bary);
}
}
}
MeshAccessor mesh_accessor(mesh);
for (Int sp(spatial_dimension); sp >= 1; --sp) {
if (mesh.getNbElement(sp) == 0)
continue;
for (auto ghost_type : ghost_types) {
for (auto & type : mesh.elementTypes(sp, ghost_type)) {
mesh_accessor.getSubelementToElement(type, ghost_type)
.resize(mesh.getNbElement(type, ghost_type));
mesh_accessor.getSubelementToElement(type, ghost_type).clear();
}
for (auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
mesh_accessor.getElementToSubelement(type, ghost_type)
.resize(mesh.getNbElement(type, ghost_type));
mesh.getElementToSubelement(type, ghost_type).clear();
}
}
CSR<Element> nodes_to_elements;
buildNode2Elements(mesh, nodes_to_elements, sp);
Element facet_element;
for (auto ghost_type : ghost_types) {
facet_element.ghost_type = ghost_type;
for (auto & type : mesh.elementTypes(sp - 1, ghost_type)) {
facet_element.type = type;
auto & element_to_subelement =
mesh.getElementToSubelement(type, ghost_type);
const auto & connectivity = mesh.getConnectivity(type, ghost_type);
auto fit = connectivity.begin(mesh.getNbNodesPerElement(type));
auto fend = connectivity.end(mesh.getNbNodesPerElement(type));
UInt fid = 0;
for (; fit != fend; ++fit, ++fid) {
const Vector<UInt> & facet = *fit;
facet_element.element = fid;
std::map<Element, UInt> element_seen_counter;
UInt nb_nodes_per_facet =
mesh.getNbNodesPerElement(Mesh::getP1ElementType(type));
for (UInt n(0); n < nb_nodes_per_facet; ++n) {
auto eit = nodes_to_elements.begin(facet(n));
auto eend = nodes_to_elements.end(facet(n));
for (; eit != eend; ++eit) {
auto & elem = *eit;
auto cit = element_seen_counter.find(elem);
if (cit != element_seen_counter.end()) {
cit->second++;
} else {
element_seen_counter[elem] = 1;
}
}
}
std::vector<Element> connected_elements;
auto cit = element_seen_counter.begin();
auto cend = element_seen_counter.end();
for (; cit != cend; ++cit) {
if (cit->second == nb_nodes_per_facet)
connected_elements.push_back(cit->first);
}
auto ceit = connected_elements.begin();
auto ceend = connected_elements.end();
for (; ceit != ceend; ++ceit)
element_to_subelement(fid).push_back(*ceit);
for (UInt ce = 0; ce < connected_elements.size(); ++ce) {
Element & elem = connected_elements[ce];
Array<Element> & subelement_to_element =
mesh_accessor.getSubelementToElement(elem.type,
elem.ghost_type);
UInt f(0);
for (; f < mesh.getNbFacetsPerElement(elem.type) &&
subelement_to_element(elem.element, f) != ElementNull;
++f)
;
AKANTU_DEBUG_ASSERT(
f < mesh.getNbFacetsPerElement(elem.type),
"The element " << elem << " seems to have too many facets!! ("
<< f << " < "
<< mesh.getNbFacetsPerElement(elem.type) << ")");
subelement_to_element(elem.element, f) = facet_element;
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <bool third_dim_points>
bool MeshUtils::findElementsAroundSubfacet(
const Mesh & mesh, const Mesh & mesh_facets,
const Element & starting_element, const Element & end_facet,
const Vector<UInt> & subfacet_connectivity,
std::vector<Element> & elem_list, std::vector<Element> & facet_list,
std::vector<Element> * subfacet_list) {
AKANTU_DEBUG_IN();
/// preallocated stuff before starting
bool facet_matched = false;
elem_list.clear();
facet_list.clear();
if (third_dim_points)
subfacet_list->clear();
elem_list.push_back(starting_element);
- const Array<UInt> * facet_connectivity = NULL;
- const Array<UInt> * sf_connectivity = NULL;
- const Array<Element> * facet_to_element = NULL;
- const Array<Element> * subfacet_to_facet = NULL;
+ const Array<UInt> * facet_connectivity = nullptr;
+ const Array<UInt> * sf_connectivity = nullptr;
+ const Array<Element> * facet_to_element = nullptr;
+ const Array<Element> * subfacet_to_facet = nullptr;
ElementType current_type = _not_defined;
GhostType current_ghost_type = _casper;
ElementType current_facet_type = _not_defined;
GhostType current_facet_ghost_type = _casper;
ElementType current_subfacet_type = _not_defined;
GhostType current_subfacet_ghost_type = _casper;
- const Array<std::vector<Element>> * element_to_facet = NULL;
+ const Array<std::vector<Element>> * element_to_facet = nullptr;
- const Element * opposing_el = NULL;
+ const Element * opposing_el = nullptr;
std::queue<Element> elements_to_check;
elements_to_check.push(starting_element);
/// keep going until there are elements to check
while (!elements_to_check.empty()) {
/// check current element
Element & current_el = elements_to_check.front();
if (current_el.type != current_type ||
current_el.ghost_type != current_ghost_type) {
current_type = current_el.type;
current_ghost_type = current_el.ghost_type;
facet_to_element =
&mesh_facets.getSubelementToElement(current_type, current_ghost_type);
}
/// loop over each facet of the element
for (UInt f = 0; f < facet_to_element->getNbComponent(); ++f) {
const Element & current_facet =
(*facet_to_element)(current_el.element, f);
if (current_facet == ElementNull)
continue;
if (current_facet_type != current_facet.type ||
current_facet_ghost_type != current_facet.ghost_type) {
current_facet_type = current_facet.type;
current_facet_ghost_type = current_facet.ghost_type;
element_to_facet = &mesh_facets.getElementToSubelement(
current_facet_type, current_facet_ghost_type);
facet_connectivity = &mesh_facets.getConnectivity(
current_facet_type, current_facet_ghost_type);
if (third_dim_points)
subfacet_to_facet = &mesh_facets.getSubelementToElement(
current_facet_type, current_facet_ghost_type);
}
/// check if end facet is reached
if (current_facet == end_facet)
facet_matched = true;
/// add this facet if not already passed
if (std::find(facet_list.begin(), facet_list.end(), current_facet) ==
facet_list.end() &&
hasElement(*facet_connectivity, current_facet,
subfacet_connectivity)) {
facet_list.push_back(current_facet);
if (third_dim_points) {
/// check subfacets
for (UInt sf = 0; sf < subfacet_to_facet->getNbComponent(); ++sf) {
const Element & current_subfacet =
(*subfacet_to_facet)(current_facet.element, sf);
if (current_subfacet == ElementNull)
continue;
if (current_subfacet_type != current_subfacet.type ||
current_subfacet_ghost_type != current_subfacet.ghost_type) {
current_subfacet_type = current_subfacet.type;
current_subfacet_ghost_type = current_subfacet.ghost_type;
sf_connectivity = &mesh_facets.getConnectivity(
current_subfacet_type, current_subfacet_ghost_type);
}
if (std::find(subfacet_list->begin(), subfacet_list->end(),
current_subfacet) == subfacet_list->end() &&
hasElement(*sf_connectivity, current_subfacet,
subfacet_connectivity))
subfacet_list->push_back(current_subfacet);
}
}
} else
continue;
/// consider opposing element
if ((*element_to_facet)(current_facet.element)[0] == current_el)
opposing_el = &(*element_to_facet)(current_facet.element)[1];
else
opposing_el = &(*element_to_facet)(current_facet.element)[0];
/// skip null elements since they are on a boundary
if (*opposing_el == ElementNull)
continue;
/// skip this element if already added
if (std::find(elem_list.begin(), elem_list.end(), *opposing_el) !=
elem_list.end())
continue;
/// only regular elements have to be checked
if (opposing_el->kind() == _ek_regular)
elements_to_check.push(*opposing_el);
elem_list.push_back(*opposing_el);
#ifndef AKANTU_NDEBUG
const Array<UInt> & conn_elem =
mesh.getConnectivity(opposing_el->type, opposing_el->ghost_type);
AKANTU_DEBUG_ASSERT(
hasElement(conn_elem, *opposing_el, subfacet_connectivity),
"Subfacet doesn't belong to this element");
#endif
}
/// erased checked element from the list
elements_to_check.pop();
}
AKANTU_DEBUG_OUT();
return facet_matched;
}
/* -------------------------------------------------------------------------- */
UInt MeshUtils::updateLocalMasterGlobalConnectivity(Mesh & mesh,
UInt local_nb_new_nodes) {
const auto & comm = mesh.getCommunicator();
Int rank = comm.whoAmI();
Int nb_proc = comm.getNbProc();
if (nb_proc == 1)
return local_nb_new_nodes;
/// resize global ids array
Array<UInt> & nodes_global_ids = mesh.getGlobalNodesIds();
UInt old_nb_nodes = mesh.getNbNodes() - local_nb_new_nodes;
nodes_global_ids.resize(mesh.getNbNodes());
/// compute the number of global nodes based on the number of old nodes
Vector<UInt> old_local_master_nodes(nb_proc);
for (UInt n = 0; n < old_nb_nodes; ++n)
if (mesh.isLocalOrMasterNode(n))
++old_local_master_nodes(rank);
comm.allGather(old_local_master_nodes);
UInt old_global_nodes =
std::accumulate(old_local_master_nodes.storage(),
old_local_master_nodes.storage() + nb_proc, 0);
/// compute amount of local or master doubled nodes
Vector<UInt> local_master_nodes(nb_proc);
for (UInt n = old_nb_nodes; n < mesh.getNbNodes(); ++n)
if (mesh.isLocalOrMasterNode(n))
++local_master_nodes(rank);
comm.allGather(local_master_nodes);
/// update global number of nodes
UInt total_nb_new_nodes = std::accumulate(
local_master_nodes.storage(), local_master_nodes.storage() + nb_proc, 0);
if (total_nb_new_nodes == 0)
return 0;
/// set global ids of local and master nodes
UInt starting_index =
std::accumulate(local_master_nodes.storage(),
local_master_nodes.storage() + rank, old_global_nodes);
for (UInt n = old_nb_nodes; n < mesh.getNbNodes(); ++n) {
if (mesh.isLocalOrMasterNode(n)) {
nodes_global_ids(n) = starting_index;
++starting_index;
}
}
MeshAccessor mesh_accessor(mesh);
mesh_accessor.setNbGlobalNodes(old_global_nodes + total_nb_new_nodes);
return total_nb_new_nodes;
}
/* -------------------------------------------------------------------------- */
void MeshUtils::updateElementalConnectivity(
Mesh & mesh, UInt old_node, UInt new_node,
const std::vector<Element> & element_list,
__attribute__((unused)) const std::vector<Element> * facet_list) {
AKANTU_DEBUG_IN();
ElementType el_type = _not_defined;
GhostType gt_type = _casper;
- Array<UInt> * conn_elem = NULL;
+ Array<UInt> * conn_elem = nullptr;
#if defined(AKANTU_COHESIVE_ELEMENT)
- const Array<Element> * cohesive_facets = NULL;
+ const Array<Element> * cohesive_facets = nullptr;
#endif
UInt nb_nodes_per_element = 0;
- UInt * n_update = NULL;
+ UInt * n_update = nullptr;
for (UInt el = 0; el < element_list.size(); ++el) {
const Element & elem = element_list[el];
if (elem.type == _not_defined)
continue;
if (elem.type != el_type || elem.ghost_type != gt_type) {
el_type = elem.type;
gt_type = elem.ghost_type;
conn_elem = &mesh.getConnectivity(el_type, gt_type);
nb_nodes_per_element = conn_elem->getNbComponent();
#if defined(AKANTU_COHESIVE_ELEMENT)
if (elem.kind() == _ek_cohesive)
cohesive_facets =
&mesh.getMeshFacets().getSubelementToElement(el_type, gt_type);
#endif
}
#if defined(AKANTU_COHESIVE_ELEMENT)
if (elem.kind() == _ek_cohesive) {
AKANTU_DEBUG_ASSERT(
- facet_list != NULL,
+ facet_list != nullptr,
"Provide a facet list in order to update cohesive elements");
/// loop over cohesive element's facets
for (UInt f = 0, n = 0; f < 2; ++f, n += nb_nodes_per_element / 2) {
const Element & facet = (*cohesive_facets)(elem.element, f);
/// skip facets if not present in the list
if (std::find(facet_list->begin(), facet_list->end(), facet) ==
facet_list->end())
continue;
n_update = std::find(
conn_elem->storage() + elem.element * nb_nodes_per_element + n,
conn_elem->storage() + elem.element * nb_nodes_per_element + n +
nb_nodes_per_element / 2,
old_node);
AKANTU_DEBUG_ASSERT(n_update !=
conn_elem->storage() +
elem.element * nb_nodes_per_element + n +
nb_nodes_per_element / 2,
"Node not found in current element");
/// update connectivity
*n_update = new_node;
}
} else {
#endif
n_update =
std::find(conn_elem->storage() + elem.element * nb_nodes_per_element,
conn_elem->storage() + elem.element * nb_nodes_per_element +
nb_nodes_per_element,
old_node);
AKANTU_DEBUG_ASSERT(n_update != conn_elem->storage() +
elem.element * nb_nodes_per_element +
nb_nodes_per_element,
"Node not found in current element");
/// update connectivity
*n_update = new_node;
#if defined(AKANTU_COHESIVE_ELEMENT)
}
#endif
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/mesh_utils/mesh_utils.hh b/src/mesh_utils/mesh_utils.hh
index b7ed40928..4d9ff8267 100644
--- a/src/mesh_utils/mesh_utils.hh
+++ b/src/mesh_utils/mesh_utils.hh
@@ -1,244 +1,244 @@
/**
* @file mesh_utils.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Oct 02 2015
*
* @brief All mesh utils necessary for various tasks
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "mesh.hh"
#include "aka_csr.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_UTILS_HH__
#define __AKANTU_MESH_UTILS_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class MeshUtils {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build a CSR<UInt> that contains for each node the linearized number of
/// the connected elements of a given spatial dimension
// static void buildNode2Elements(const Mesh & mesh, CSR<UInt> & node_to_elem,
// UInt spatial_dimension = _all_dimensions);
/// build a CSR<Element> that contains for each node the list of connected
/// elements of a given spatial dimension
static void buildNode2Elements(const Mesh & mesh, CSR<Element> & node_to_elem,
UInt spatial_dimension = _all_dimensions);
/// build a CSR<UInt> that contains for each node the number of
/// the connected elements of a given ElementType
static void
buildNode2ElementsElementTypeMap(const Mesh & mesh, CSR<UInt> & node_to_elem,
const ElementType & type,
const GhostType & ghost_type = _not_ghost);
/// build the facets elements on the boundaries of a mesh
static void buildFacets(Mesh & mesh);
/// build all the facets elements: boundary and internals and store them in
/// the mesh_facets for element of dimension from_dimension to to_dimension
static void buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt from_dimension, UInt to_dimension);
/// build all the facets elements: boundary and internals and store them in
/// the mesh_facets
static void buildAllFacets(const Mesh & mesh, Mesh & mesh_facets,
UInt to_dimension = 0);
/// build facets for a given spatial dimension
static void buildFacetsDimension(
const Mesh & mesh, Mesh & mesh_facets, bool boundary_only, UInt dimension);
/// take the local_connectivity array as the array of local and ghost
/// connectivity, renumber the nodes and set the connectivity of the mesh
static void renumberMeshNodes(Mesh & mesh, Array<UInt> & local_connectivities,
UInt nb_local_element, UInt nb_ghost_element,
ElementType type, Array<UInt> & old_nodes);
/// compute pbc pair for a given direction
static void computePBCMap(const Mesh & mymesh, const UInt dir,
std::map<UInt, UInt> & pbc_pair);
/// compute pbc pair for a surface pair
static void computePBCMap(const Mesh & mymesh,
const std::pair<Surface, Surface> & surface_pair,
std::map<UInt, UInt> & pbc_pair);
/// remove not connected nodes /!\ this functions renumbers the nodes.
static void purifyMesh(Mesh & mesh);
#if defined(AKANTU_COHESIVE_ELEMENT)
/// function to insert cohesive elements on the selected facets
/// @return number of facets that have been doubled
static UInt
insertCohesiveElements(Mesh & mesh, Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion,
Array<UInt> & doubled_nodes,
Array<Element> & new_elements,
bool only_double_facets);
#endif
/// fill the subelement to element and the elements to subelements data
static void fillElementToSubElementsData(Mesh & mesh);
/// flip facets based on global connectivity
static void flipFacets(Mesh & mesh_facets,
const ElementTypeMapArray<UInt> & global_connectivity,
GhostType gt_facet);
/// provide list of elements around a node and check if a given
/// facet is reached
template <bool third_dim_points>
static bool findElementsAroundSubfacet(
const Mesh & mesh, const Mesh & mesh_facets,
const Element & starting_element, const Element & end_facet,
const Vector<UInt> & subfacet_connectivity,
std::vector<Element> & elem_list, std::vector<Element> & facet_list,
std::vector<Element> * subfacet_list = nullptr);
/// function to check if a node belongs to a given element
static inline bool hasElement(const Array<UInt> & connectivity,
const Element & el, const Vector<UInt> & nodes);
/// reset facet_to_double arrays in the Mesh
static void resetFacetToDouble(Mesh & mesh_facets);
/// associate a node type to each segment in the mesh
// static void buildSegmentToNodeType(const Mesh & mesh, Mesh & mesh_facets);
/// update local and master global connectivity when new nodes are added
static UInt updateLocalMasterGlobalConnectivity(Mesh & mesh,
UInt old_nb_nodes);
private:
/// match pairs that are on the associated pbc's
static void matchPBCPairs(const Mesh & mymesh, const UInt dir,
Array<UInt> & selected_left,
Array<UInt> & selected_right,
std::map<UInt, UInt> & pbc_pair);
/// function used by all the renumbering functions
static void
renumberNodesInConnectivity(Array<UInt> & list_nodes, UInt nb_nodes,
std::map<UInt, UInt> & renumbering_map);
/// update facet_to_subfacet
static void updateFacetToSubfacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode);
/// update subfacet_to_facet
static void updateSubfacetToFacet(Mesh & mesh_facets,
ElementType type_subfacet,
GhostType gt_subfacet, bool facet_mode);
/// function to double a given facet and update the list of doubled
/// nodes
static void doubleFacet(Mesh & mesh, Mesh & mesh_facets, UInt facet_dimension,
Array<UInt> & doubled_nodes, bool facet_mode);
/// function to double a subfacet given start and end index for
/// local facet_to_subfacet vector, and update the list of doubled
/// nodes
template <UInt spatial_dimension>
static void doubleSubfacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes);
/// double a node
static void doubleNodes(Mesh & mesh, const std::vector<UInt> & old_nodes,
Array<UInt> & doubled_nodes);
/// fill facet_to_double array in the mesh
/// returns the number of facets to be doubled
static UInt
updateFacetToDouble(Mesh & mesh_facets,
const ElementTypeMapArray<bool> & facet_insertion);
/// find subfacets to be doubled
template <bool subsubfacet_mode>
static void findSubfacetToDouble(Mesh & mesh, Mesh & mesh_facets);
/// double facets (points) in 1D
static void doublePointFacet(Mesh & mesh, Mesh & mesh_facets,
Array<UInt> & doubled_nodes);
#if defined(AKANTU_COHESIVE_ELEMENT)
/// update cohesive element data
static void updateCohesiveData(Mesh & mesh, Mesh & mesh_facets,
Array<Element> & new_elements);
#endif
/// update elemental connectivity after doubling a node
- inline static void
- updateElementalConnectivity(Mesh & mesh, UInt old_node, UInt new_node,
- const std::vector<Element> & element_list,
- const std::vector<Element> * facet_list = NULL);
+ inline static void updateElementalConnectivity(
+ Mesh & mesh, UInt old_node, UInt new_node,
+ const std::vector<Element> & element_list,
+ const std::vector<Element> * facet_list = nullptr);
/// double middle nodes if facets are _segment_3
template <bool third_dim_segments>
static void updateQuadraticSegments(Mesh & mesh, Mesh & mesh_facets,
ElementType type_facet,
GhostType gt_facet,
Array<UInt> & doubled_nodes);
/// remove elements on a vector
inline static bool
removeElementsInVector(const std::vector<Element> & elem_to_remove,
std::vector<Element> & elem_list);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "mesh_utils_inline_impl.cc"
} // akantu
#endif /* __AKANTU_MESH_UTILS_HH__ */
diff --git a/src/model/boundary_condition.hh b/src/model/boundary_condition.hh
index ed18419b2..65a09e0a1 100644
--- a/src/model/boundary_condition.hh
+++ b/src/model/boundary_condition.hh
@@ -1,106 +1,108 @@
/**
* @file boundary_condition.hh
*
* @author Dana Christen <dana.christen@gmail.com>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Dec 18 2015
*
* @brief XXX
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BOUNDARY_CONDITION_HH__
#define __AKANTU_BOUNDARY_CONDITION_HH__
#include "aka_common.hh"
#include "boundary_condition_functor.hh"
#include "mesh.hh"
#include "fe_engine.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
namespace akantu {
template <class ModelType>
class BoundaryCondition {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
/* ------------------------------------------------------------------------ */
/* Constructors / Destructors / Initializers */
/* ------------------------------------------------------------------------ */
public:
- BoundaryCondition() : model(NULL), primal(NULL), dual(NULL), primal_increment(NULL) {}
+ BoundaryCondition()
+ : model(nullptr), primal(nullptr), dual(nullptr),
+ primal_increment(nullptr) {}
///Initialize the boundary conditions
void initBC(ModelType & ptr, Array<Real> & primal, Array<Real> & dual);
void initBC(ModelType & ptr, Array<Real> & primal,
Array<Real> & primal_increment, Array<Real> & dual);
/* ------------------------------------------------------------------------ */
/* Methods and accessors */
/* ------------------------------------------------------------------------ */
public:
//inline void initBoundaryCondition();
template<typename FunctorType>
///Apply the boundary conditions
inline void applyBC(const FunctorType & func);
template<class FunctorType>
inline void applyBC(const FunctorType & func, const std::string & group_name);
template<class FunctorType>
inline void applyBC(const FunctorType & func, const ElementGroup & element_group);
AKANTU_GET_MACRO_NOT_CONST(Model, *model, ModelType &);
AKANTU_GET_MACRO_NOT_CONST(Primal,*primal, Array<Real> &);
AKANTU_GET_MACRO_NOT_CONST(Dual, *dual, Array<Real> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
template<class FunctorType, BC::Functor::Type type = FunctorType::type>
struct TemplateFunctionWrapper;
private:
ModelType * model;
Array<Real> * primal;
Array<Real> * dual;
Array<Real> * primal_increment;
};
} // akantu
#include "boundary_condition_tmpl.hh"
#endif /* __AKANTU_BOUNDARY_CONDITION_HH__ */
diff --git a/src/model/boundary_condition_functor.hh b/src/model/boundary_condition_functor.hh
index cbc7358d8..776fa1514 100644
--- a/src/model/boundary_condition_functor.hh
+++ b/src/model/boundary_condition_functor.hh
@@ -1,197 +1,197 @@
/**
* @file boundary_condition_functor.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Thu Oct 15 2015
*
* @brief Definitions of the functors to apply boundary conditions
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "aka_common.hh"
#include "fe_engine.hh"
#include "integration_point.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__
#define __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
namespace BC {
typedef ::akantu::SpacialDirection Axis;
struct Functor {
enum Type { _dirichlet, _neumann };
};
/* ------------------------------------------------------------------------ */
/* Dirichlet */
/* ------------------------------------------------------------------------ */
namespace Dirichlet {
/* ---------------------------------------------------------------------- */
class DirichletFunctor : public Functor {
protected:
DirichletFunctor() : axis(_x) {}
explicit DirichletFunctor(Axis ax) : axis(ax) {}
public:
void operator()(__attribute__((unused)) UInt node,
__attribute__((unused)) Vector<bool> & flags,
__attribute__((unused)) Vector<Real> & primal,
__attribute__((unused)) const Vector<Real> & coord) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
public:
static const Type type = _dirichlet;
protected:
Axis axis;
};
/* ---------------------------------------------------------------------- */
class FlagOnly : public DirichletFunctor {
public:
explicit FlagOnly(Axis ax = _x) : DirichletFunctor(ax) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const;
};
/* ---------------------------------------------------------------------- */
class FreeBoundary : public DirichletFunctor {
public:
explicit FreeBoundary(Axis ax = _x) : DirichletFunctor(ax) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const;
};
/* ---------------------------------------------------------------------- */
class FixedValue : public DirichletFunctor {
public:
FixedValue(Real val, Axis ax = _x) : DirichletFunctor(ax), value(val) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const;
protected:
Real value;
};
/* ---------------------------------------------------------------------- */
class IncrementValue : public DirichletFunctor {
public:
IncrementValue(Real val, Axis ax = _x) : DirichletFunctor(ax), value(val) {}
public:
inline void operator()(UInt node, Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const;
inline void setIncrement(Real val) { this->value = val; }
protected:
Real value;
};
} // end namespace Dirichlet
/* ------------------------------------------------------------------------ */
/* Neumann */
/* ------------------------------------------------------------------------ */
namespace Neumann {
/* ---------------------------------------------------------------------- */
class NeumannFunctor : public Functor {
protected:
NeumannFunctor() {}
public:
virtual void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const = 0;
virtual ~NeumannFunctor() {}
public:
static const Type type = _neumann;
};
/* ---------------------------------------------------------------------- */
class FromHigherDim : public NeumannFunctor {
public:
explicit FromHigherDim(const Matrix<Real> & mat) : bc_data(mat) {}
- virtual ~FromHigherDim() {}
+ ~FromHigherDim() override {}
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
- const Vector<Real> & normals) const;
+ const Vector<Real> & normals) const override;
protected:
Matrix<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FromSameDim : public NeumannFunctor {
public:
explicit FromSameDim(const Vector<Real> & vec) : bc_data(vec) {}
- virtual ~FromSameDim() {}
+ ~FromSameDim() override {}
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
- const Vector<Real> & normals) const;
+ const Vector<Real> & normals) const override;
protected:
Vector<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FreeBoundary : public NeumannFunctor {
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
- const Vector<Real> & normals) const;
+ const Vector<Real> & normals) const override;
};
} // end namespace Neumann
} // end namespace BC
} // akantu
#include "boundary_condition_functor_inline_impl.cc"
#endif /* __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__ */
diff --git a/src/model/common/neighborhood_base.hh b/src/model/common/neighborhood_base.hh
index 73e5fcb22..b6f365edc 100644
--- a/src/model/common/neighborhood_base.hh
+++ b/src/model/common/neighborhood_base.hh
@@ -1,151 +1,151 @@
/**
* @file neighborhood_base.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Wed Nov 25 2015
*
* @brief Generic neighborhood of quadrature points
*
* @section LICENSE
*
* Copyright (©) 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NEIGHBORHOOD_BASE_HH__
#define __AKANTU_NEIGHBORHOOD_BASE_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_memory.hh"
#include "data_accessor.hh"
#include "integration_point.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
template <class T> class SpatialGrid;
class GridSynchronizer;
class RemovedElementsEvent;
} // namespace akantu
namespace akantu {
class NeighborhoodBase : protected Memory,
public DataAccessor<Element>,
public SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NeighborhoodBase(Model & model,
const ElementTypeMapArray<Real> & quad_coordinates,
const ID & id = "neighborhood",
const MemoryID & memory_id = 0);
- virtual ~NeighborhoodBase();
+ ~NeighborhoodBase() override;
typedef std::vector<std::pair<IntegrationPoint, IntegrationPoint>> PairList;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// intialize the neighborhood
virtual void initNeighborhood();
// /// create a synchronizer registry
// void createSynchronizerRegistry(DataAccessor * data_accessor);
/// initialize the material computed parameter
inline void insertIntegrationPoint(const IntegrationPoint & quad,
const Vector<Real> & coords);
/// create the pairs of quadrature points
void updatePairList();
/// save the pairs of quadrature points in a file
void savePairs(const std::string & filename) const;
/// save the coordinates of all neighbors of a quad
void saveNeighborCoords(const std::string & filename) const;
/// create grid synchronizer and exchange ghost cells
virtual void createGridSynchronizer() = 0;
virtual void synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) = 0;
/// inherited function from MeshEventHandler
virtual void
onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
protected:
/// create the grid
void createGrid();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
AKANTU_GET_MACRO(Model, model, const Model &);
/// return the object handling synchronizers
AKANTU_GET_MACRO(PairLists, pair_list, const PairList *);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the model to which the neighborhood belongs
Model & model;
/// Radius of impact: to determine if two quadrature points influence each
/// other
Real neighborhood_radius;
/**
* the pairs of quadrature points
* 0: not ghost to not ghost
* 1: not ghost to ghost
*/
PairList pair_list[2];
/// the regular grid to construct/update the pair lists
std::unique_ptr<SpatialGrid<IntegrationPoint>> spatial_grid;
bool is_creating_grid;
/// the grid synchronizer for parallel computations
std::unique_ptr<GridSynchronizer> grid_synchronizer;
/// the quadrature point positions
const ElementTypeMapArray<Real> & quad_coordinates;
/// the spatial dimension of the problem
const UInt spatial_dimension;
};
} // namespace akantu
#include "neighborhood_base_inline_impl.cc"
#endif /* __AKANTU_NEIGHBORHOOD_BASE_HH__ */
diff --git a/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh b/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
index 3ea9e3e94..67b7f51c9 100644
--- a/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
+++ b/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.hh
@@ -1,117 +1,117 @@
/**
* @file neighborhood_max_criterion.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Thu Oct 15 2015
*
* @brief Neighborhood to find a maximum value in a neighborhood
*
* @section LICENSE
*
* Copyright (©) 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH__
#define __AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH__
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class NeighborhoodMaxCriterion : public NeighborhoodBase, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NeighborhoodMaxCriterion(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & criterion_id,
const ID & id = "neighborhood_max_criterion",
const MemoryID & memory_id = 0);
- virtual ~NeighborhoodMaxCriterion();
+ ~NeighborhoodMaxCriterion() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the neighborhood
- virtual void initNeighborhood();
+ void initNeighborhood() override;
/// create grid synchronizer and exchange ghost cells
- virtual void createGridSynchronizer();
+ void createGridSynchronizer() override;
/// find the quads which have the maximum criterion in their neighborhood
void findMaxQuads(std::vector<IntegrationPoint> & max_quads);
protected:
/// remove unneccessary ghost elements
void
cleanupExtraGhostElements(const ElementTypeMap<UInt> & nb_ghost_protected);
/// insert the quadrature points in the grid
void insertAllQuads(const GhostType & ghost_type);
/// compare criterion with neighbors
void checkNeighbors(const GhostType & ghost_type);
/* --------------------------------------------------------------------------
*/
/* DataAccessor inherited members */
/* --------------------------------------------------------------------------
*/
public:
virtual inline UInt getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const;
virtual inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const;
virtual inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag);
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// a boolean to store the information if a quad has the max
/// criterion in the neighborhood
ElementTypeMapArray<bool> is_highest;
/// an element type map to store the flattened internal of the criterion
ElementTypeMapReal criterion;
};
} // akantu
#include "neighborhood_max_criterion_inline_impl.cc"
#endif /* __AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH__ */
diff --git a/src/model/common/non_local_toolbox/base_weight_function.hh b/src/model/common/non_local_toolbox/base_weight_function.hh
index 47252eec9..59bc32172 100644
--- a/src/model/common/non_local_toolbox/base_weight_function.hh
+++ b/src/model/common/non_local_toolbox/base_weight_function.hh
@@ -1,169 +1,169 @@
/**
* @file base_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
* @date last modification: Thu Oct 15 2015
*
* @brief Base weight function for non local materials
*
* @section LICENSE
*
* Copyright (©) 2015 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 "data_accessor.hh"
#include "model.hh"
#include "non_local_manager.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BASE_WEIGHT_FUNCTION_HH__
#define __AKANTU_BASE_WEIGHT_FUNCTION_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Normal weight function */
/* -------------------------------------------------------------------------- */
class BaseWeightFunction : public Parsable, public DataAccessor<Element> {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
BaseWeightFunction(NonLocalManager & manager,
const std::string & type = "base")
: Parsable(_st_weight_function, "weight_function:" + type),
manager(manager), type(type),
spatial_dimension(manager.getModel().getMesh().getSpatialDimension()) {
this->registerParam("update_rate", update_rate, 1U, _pat_parsmod,
"Update frequency");
}
- virtual ~BaseWeightFunction() {}
+ ~BaseWeightFunction() override {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
/// initialize the weight function
virtual inline void init();
/// update the internal parameters
virtual void updateInternals(){};
/* ------------------------------------------------------------------------ */
/// set the non-local radius
inline void setRadius(Real radius);
/* ------------------------------------------------------------------------ */
/// compute the weight for a given distance between two quadrature points
inline Real operator()(Real r, const IntegrationPoint & q1,
const IntegrationPoint & q2);
/// print function
void printself(std::ostream & stream, int indent = 0) const override {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "WeightFunction " << type << " [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
}
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
/// get the radius
Real getRadius() { return R; }
/// get the update rate
UInt getUpdateRate() { return update_rate; }
public:
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
UInt getNbData(const Array<Element> &,
const SynchronizationTag &) const override {
return 0;
}
inline void packData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) const override {}
inline void unpackData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) override {}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Type, type, const ID &);
protected:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// reference to the non-local manager
NonLocalManager & manager;
/// the non-local radius
Real R;
/// the non-local radius squared
Real R2;
/// the update rate
UInt update_rate;
/// name of the type of weight function
const std::string type;
/// the spatial dimension
UInt spatial_dimension;
};
inline std::ostream & operator<<(std::ostream & stream,
const BaseWeightFunction & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "base_weight_function_inline_impl.cc"
/* -------------------------------------------------------------------------- */
/* Include all other weight function types */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_DAMAGE_NON_LOCAL)
#include "damaged_weight_function.hh"
#include "remove_damaged_weight_function.hh"
#include "remove_damaged_with_damage_rate_weight_function.hh"
#include "stress_based_weight_function.hh"
#endif
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_BASE_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager.hh b/src/model/common/non_local_toolbox/non_local_manager.hh
index 458182e59..f249eac9c 100644
--- a/src/model/common/non_local_toolbox/non_local_manager.hh
+++ b/src/model/common/non_local_toolbox/non_local_manager.hh
@@ -1,288 +1,288 @@
/**
* @file non_local_manager.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief Classes that manages all the non-local neighborhoods
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "communication_buffer.hh"
#include "data_accessor.hh"
#include "mesh_events.hh"
#include "non_local_manager_callback.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_MANAGER_HH__
#define __AKANTU_NON_LOCAL_MANAGER_HH__
namespace akantu {
class Model;
class NonLocalNeighborhoodBase;
class GridSynchronizer;
class SynchronizerRegistry;
class IntegrationPoint;
template <typename T> class SpatialGrid;
class FEEngine;
} // namespace akantu
namespace akantu {
class NonLocalManager : protected Memory,
public MeshEventHandler,
public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalManager(Model & model, NonLocalManagerCallback & callback,
const ID & id = "non_local_manager",
const MemoryID & memory_id = 0);
- virtual ~NonLocalManager();
+ ~NonLocalManager() override;
using NeighborhoodMap =
std::map<ID, std::unique_ptr<NonLocalNeighborhoodBase>>;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ----------------------------------------------------------------------- */
public:
/// register a new internal needed for the weight computations
ElementTypeMapReal & registerWeightFunctionInternal(const ID & field_name);
/// register a non-local variable
void registerNonLocalVariable(const ID & variable_name,
const ID & nl_variable_name, UInt nb_component);
/// register non-local neighborhood
inline void registerNeighborhood(const ID & neighborhood,
const ID & weight_func_id);
// void registerNonLocalManagerCallback(NonLocalManagerCallback & callback);
/// average the internals and compute the non-local stresses
virtual void computeAllNonLocalStresses();
/// initialize the non-local manager: compute pair lists and weights for all
/// neighborhoods
virtual void initialize();
/// synchronize once on a given tag using the neighborhoods synchronizer
void synchronize(DataAccessor<Element> & data_accessor, const SynchronizationTag &);
protected:
/// create the grid synchronizers for each neighborhood
void createNeighborhoodSynchronizers();
/// compute the weights in each neighborhood for non-local averaging
void computeWeights();
/// compute the weights in each neighborhood for non-local averaging
void updatePairLists();
/// average the non-local variables
void averageInternals(const GhostType & ghost_type = _not_ghost);
/// update the flattened version of the weight function internals
void updateWeightFunctionInternals();
protected:
/// create a new neighborhood for a given domain ID
void createNeighborhood(const ID & weight_func, const ID & neighborhood);
/// set the values of the jacobians
void setJacobians(const FEEngine & fe_engine, const ElementKind & kind);
/// allocation of eelment type maps
// void initElementTypeMap(UInt nb_component,
// ElementTypeMapReal & element_map,
// const FEEngine & fe_engine,
// const ElementKind el_kind = _ek_regular);
/// resizing of element type maps
void resizeElementTypeMap(UInt nb_component, ElementTypeMapReal & element_map,
const FEEngine & fee,
const ElementKind el_kind = _ek_regular);
/// remove integration points from element type maps
void removeIntegrationPointsFromMap(
const ElementTypeMapArray<UInt> & new_numbering, UInt nb_component,
ElementTypeMapReal & element_map, const FEEngine & fee,
const ElementKind el_kind = _ek_regular);
/// allocate the non-local variables
void initNonLocalVariables();
/// cleanup unneccessary ghosts
void cleanupExtraGhostElements();//ElementTypeMap<UInt> & nb_ghost_protected);
/* ------------------------------------------------------------------------ */
/* DataAccessor kind of interface */
/* ------------------------------------------------------------------------ */
public:
/// get Nb data for synchronization in parallel
UInt getNbData(const Array<Element> & elements, const ID & id) const;
/// pack data for synchronization in parallel
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const ID & id) const;
/// unpack data for synchronization in parallel
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const ID & id) const;
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) override;
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override {}
void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override {}
void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) override{};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
AKANTU_GET_MACRO(Model, model, const Model &);
AKANTU_GET_MACRO_NOT_CONST(Model, model, Model &);
AKANTU_GET_MACRO_NOT_CONST(Volumes, volumes, ElementTypeMapReal &)
AKANTU_GET_MACRO(NbStressCalls, compute_stress_calls, UInt);
/// return the fem object associated with a provided name
inline NonLocalNeighborhoodBase & getNeighborhood(const ID & name) const;
inline const Array<Real> & getJacobians(const ElementType & type,
const GhostType & ghost_type) {
return *jacobians(type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the spatial dimension
const UInt spatial_dimension;
protected:
/// the non-local neighborhoods present
NeighborhoodMap neighborhoods;
/// list of all the non-local materials in the model
// std::vector<ID> non_local_materials;
struct NonLocalVariable {
NonLocalVariable(const ID & variable_name, const ID & nl_variable_name,
const ID & id, UInt nb_component)
: local(variable_name, id, 0), non_local(nl_variable_name, id, 0),
nb_component(nb_component) {}
ElementTypeMapReal local;
ElementTypeMapReal non_local;
UInt nb_component;
};
/// the non-local variables associated to a certain neighborhood
std::map<ID, std::unique_ptr<NonLocalVariable>> non_local_variables;
/// reference to the model
Model & model;
/// jacobians for all the elements in the mesh
ElementTypeMap<const Array<Real> *> jacobians;
/// store the position of the quadrature points
ElementTypeMapReal integration_points_positions;
/// store the volume of each quadrature point for the non-local weight
/// normalization
ElementTypeMapReal volumes;
/// counter for computeStress calls
UInt compute_stress_calls;
/// map to store weight function types from input file
std::map<ID, ParserSection> weight_function_types;
/// map to store the internals needed by the weight functions
std::map<ID, std::unique_ptr<ElementTypeMapReal>> weight_function_internals;
/* --------------------------------------------------------------------------
*/
/// the following are members needed to make this processor participate in the
/// grid creation of neighborhoods he doesn't own as a member. For details see
/// createGridSynchronizers function
/// synchronizer registry for dummy grid synchronizers
std::unique_ptr<SynchronizerRegistry> dummy_registry;
/// map of dummy synchronizers
std::map<ID, std::unique_ptr<GridSynchronizer>> dummy_synchronizers;
/// dummy spatial grid
std::unique_ptr<SpatialGrid<IntegrationPoint>> dummy_grid;
/// create a set of all neighborhoods present in the simulation
std::set<ID> global_neighborhoods;
class DummyDataAccessor : public DataAccessor<Element> {
public:
inline UInt getNbData(const Array<Element> &,
const SynchronizationTag &) const override {
return 0;
};
inline void packData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) const override{};
inline void unpackData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) override{};
};
DummyDataAccessor dummy_accessor;
/* ------------------------------------------------------------------------ */
NonLocalManagerCallback * callback;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "non_local_manager_inline_impl.cc"
#endif /* __AKANTU_NON_LOCAL_MANAGER_HH__ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood.hh b/src/model/common/non_local_toolbox/non_local_neighborhood.hh
index e8f134948..b92eb3e3c 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood.hh
@@ -1,135 +1,135 @@
/**
* @file non_local_neighborhood.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 25 2015
*
* @brief Non-local neighborhood for non-local averaging based on
* weight function
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_HH__
#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_HH__
/* -------------------------------------------------------------------------- */
#include "base_weight_function.hh"
#include "non_local_neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class NonLocalManager;
class BaseWeightFunction;
} // namespace akantu
namespace akantu {
template <class WeightFunction = BaseWeightFunction>
class NonLocalNeighborhood : public NonLocalNeighborhoodBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalNeighborhood(NonLocalManager & manager,
const ElementTypeMapReal & quad_coordinates,
const ID & id = "neighborhood",
const MemoryID & memory_id = 0);
- virtual ~NonLocalNeighborhood();
+ ~NonLocalNeighborhood() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// compute the weights for non-local averaging
- void computeWeights();
+ void computeWeights() override;
/// save the pair of weights in a file
void saveWeights(const std::string & filename) const override;
/// compute the non-local counter part for a given element type map
// compute the non-local counter part for a given element type map
void weightedAverageOnNeighbours(const ElementTypeMapReal & to_accumulate,
ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom,
const GhostType & ghost_type2) const override;
/// update the weights based on the weight function
- void updateWeights();
+ void updateWeights() override;
/// register a new non-local variable in the neighborhood
//void registerNonLocalVariable(const ID & id);
protected:
template <class Func>
inline void foreach_weight(const GhostType & ghost_type, Func && func);
template <class Func>
inline void foreach_weight(const GhostType & ghost_type, Func && func) const;
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(NonLocalManager, non_local_manager, const NonLocalManager &);
AKANTU_GET_MACRO_NOT_CONST(NonLocalManager, non_local_manager,
NonLocalManager &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Pointer to non-local manager class
NonLocalManager & non_local_manager;
/// the weights associated to the pairs
std::array<std::unique_ptr<Array<Real>>, 2> pair_weight;
/// weight function
std::unique_ptr<WeightFunction> weight_function;
};
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* Implementation of template functions */
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "non_local_neighborhood_inline_impl.cc"
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_HH__ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh b/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
index 185a3ae6a..547766016 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_base.hh
@@ -1,130 +1,130 @@
/**
* @file non_local_neighborhood_base.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Wed Nov 25 2015
*
* @brief Non-local neighborhood base class
*
* @section LICENSE
*
* Copyright (©) 2015 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 "neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__
#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__
namespace akantu {
class Model;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class NonLocalNeighborhoodBase : public NeighborhoodBase, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalNeighborhoodBase(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id = "non_local_neighborhood",
const MemoryID & memory_id = 0);
- virtual ~NonLocalNeighborhoodBase();
+ ~NonLocalNeighborhoodBase() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create grid synchronizer and exchange ghost cells
void createGridSynchronizer() override;
void synchronize(DataAccessor<Element> & data_accessor,
const SynchronizationTag & tag) override;
/// compute weights, for instance needed for non-local damage computation
virtual void computeWeights(){};
// compute the non-local counter part for a given element type map
virtual void
weightedAverageOnNeighbours(const ElementTypeMapReal & to_accumulate,
ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom,
const GhostType & ghost_type2) const = 0;
/// update the weights for the non-local averaging
virtual void updateWeights() = 0;
/// update the weights for the non-local averaging
virtual void saveWeights(const std::string &) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// register a new non-local variable in the neighborhood
virtual void registerNonLocalVariable(const ID & id);
/// clean up the unneccessary ghosts
void cleanupExtraGhostElements(std::set<Element> & relevant_ghost_elements);
protected:
/// create the grid
void createGrid();
/* --------------------------------------------------------------------------
*/
/* DataAccessor inherited members */
/* --------------------------------------------------------------------------
*/
public:
inline UInt getNbData(const Array<Element> &,
const SynchronizationTag &) const override {
return 0;
}
inline void packData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) const override {}
inline void unpackData(CommunicationBuffer &, const Array<Element> &,
const SynchronizationTag &) override {}
/* --------------------------------------------------------------------------
*/
/* Accessors */
/* --------------------------------------------------------------------------
*/
public:
AKANTU_GET_MACRO(NonLocalVariables, non_local_variables,
const std::set<ID> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// list of non-local variables associated to the neighborhood
std::set<ID> non_local_variables;
};
} // namespace akantu
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh b/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
index 780c3e002..aa4f9a31d 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_tmpl.hh
@@ -1,280 +1,280 @@
/**
* @file non_local_neighborhood_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Sep 28 2015
* @date last modification: Wed Nov 25 2015
*
* @brief Implementation of class non-local neighborhood
*
* @section LICENSE
*
* Copyright (©) 2015 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 "non_local_manager.hh"
#include "non_local_neighborhood.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH__
#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
template <class Func>
inline void NonLocalNeighborhood<WeightFunction>::foreach_weight(
const GhostType & ghost_type, Func && func) {
auto weight_it =
pair_weight[ghost_type]->begin(pair_weight[ghost_type]->getNbComponent());
for (auto & pair : pair_list[ghost_type]) {
std::forward<decltype(func)>(func)(pair.first, pair.second, *weight_it);
++weight_it;
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
template <class Func>
inline void NonLocalNeighborhood<WeightFunction>::foreach_weight(
const GhostType & ghost_type, Func && func) const {
auto weight_it =
pair_weight[ghost_type]->begin(pair_weight[ghost_type]->getNbComponent());
for (auto & pair : pair_list[ghost_type]) {
std::forward<decltype(func)>(func)(pair.first, pair.second, *weight_it);
++weight_it;
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
NonLocalNeighborhood<WeightFunction>::NonLocalNeighborhood(
NonLocalManager & manager, const ElementTypeMapReal & quad_coordinates,
const ID & id, const MemoryID & memory_id)
: NonLocalNeighborhoodBase(manager.getModel(), quad_coordinates, id,
memory_id),
non_local_manager(manager) {
AKANTU_DEBUG_IN();
this->weight_function = std::make_unique<WeightFunction>(manager);
this->registerSubSection(_st_weight_function, "weight_parameter",
*weight_function);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
NonLocalNeighborhood<WeightFunction>::~NonLocalNeighborhood() = default;
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::computeWeights() {
AKANTU_DEBUG_IN();
this->weight_function->setRadius(this->neighborhood_radius);
Vector<Real> q1_coord(this->spatial_dimension);
Vector<Real> q2_coord(this->spatial_dimension);
UInt nb_weights_per_pair = 2; /// w1: q1->q2, w2: q2->q1
/// get the elementtypemap for the neighborhood volume for each quadrature
/// point
ElementTypeMapReal & quadrature_points_volumes =
this->non_local_manager.getVolumes();
/// update the internals of the weight function if applicable (not
/// all the weight functions have internals and do noting in that
/// case)
weight_function->updateInternals();
for (auto ghost_type : ghost_types) {
/// allocate the array to store the weight, if it doesn't exist already
if (!(pair_weight[ghost_type])) {
pair_weight[ghost_type] =
std::make_unique<Array<Real>>(0, nb_weights_per_pair);
}
/// resize the array to the correct size
pair_weight[ghost_type]->resize(pair_list[ghost_type].size());
/// set entries to zero
pair_weight[ghost_type]->clear();
/// loop over all pairs in the current pair list array and their
/// corresponding weights
PairList::const_iterator first_pair = pair_list[ghost_type].begin();
PairList::const_iterator last_pair = pair_list[ghost_type].end();
Array<Real>::vector_iterator weight_it =
pair_weight[ghost_type]->begin(nb_weights_per_pair);
// Compute the weights
for (; first_pair != last_pair; ++first_pair, ++weight_it) {
Vector<Real> & weight = *weight_it;
const IntegrationPoint & q1 = first_pair->first;
const IntegrationPoint & q2 = first_pair->second;
/// get the coordinates for the given pair of quads
Array<Real>::const_vector_iterator coords_type_1_it =
this->quad_coordinates(q1.type, q1.ghost_type)
.begin(this->spatial_dimension);
q1_coord = coords_type_1_it[q1.global_num];
Array<Real>::const_vector_iterator coords_type_2_it =
this->quad_coordinates(q2.type, q2.ghost_type)
.begin(this->spatial_dimension);
q2_coord = coords_type_2_it[q2.global_num];
Array<Real> & quad_volumes_1 =
quadrature_points_volumes(q1.type, q1.ghost_type);
const Array<Real> & jacobians_2 =
this->non_local_manager.getJacobians(q2.type, q2.ghost_type);
const Real & q2_wJ = jacobians_2(q2.global_num);
/// compute distance between the two quadrature points
Real r = q1_coord.distance(q2_coord);
/// compute the weight for averaging on q1 based on the distance
Real w1 = this->weight_function->operator()(r, q1, q2);
weight(0) = q2_wJ * w1;
quad_volumes_1(q1.global_num) += weight(0);
if (q2.ghost_type != _ghost && q1.global_num != q2.global_num) {
const Array<Real> & jacobians_1 =
this->non_local_manager.getJacobians(q1.type, q1.ghost_type);
Array<Real> & quad_volumes_2 =
quadrature_points_volumes(q2.type, q2.ghost_type);
/// compute the weight for averaging on q2
const Real & q1_wJ = jacobians_1(q1.global_num);
Real w2 = this->weight_function->operator()(r, q2, q1);
weight(1) = q1_wJ * w2;
quad_volumes_2(q2.global_num) += weight(1);
} else
weight(1) = 0.;
}
}
/// normalize the weights
for (auto ghost_type : ghost_types) {
- foreach_weight(ghost_type, [this, &quadrature_points_volumes](
+ foreach_weight(ghost_type, [&](
const auto & q1, const auto & q2,
auto & weight) {
auto & quad_volumes_1 = quadrature_points_volumes(q1.type, q1.ghost_type);
auto & quad_volumes_2 = quadrature_points_volumes(q2.type, q2.ghost_type);
Real q1_volume = quad_volumes_1(q1.global_num);
auto ghost_type2 = q2.ghost_type;
weight(0) *= 1. / q1_volume;
if (ghost_type2 != _ghost) {
Real q2_volume = quad_volumes_2(q2.global_num);
weight(1) *= 1. / q2_volume;
}
});
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::saveWeights(
const std::string & filename) const {
std::ofstream pout;
std::stringstream sstr;
const Communicator & comm = model.getMesh().getCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
pout.open(sstr.str().c_str());
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType)gt;
AKANTU_DEBUG_ASSERT((pair_weight[ghost_type]),
"the weights have not been computed yet");
Array<Real> & weights = *(pair_weight[ghost_type]);
Array<Real>::const_vector_iterator weights_it = weights.begin(2);
for (UInt i = 0; i < weights.size(); ++i, ++weights_it)
pout << "w1: " << (*weights_it)(0) << " w2: " << (*weights_it)(1)
<< std::endl;
}
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::weightedAverageOnNeighbours(
const ElementTypeMapReal & to_accumulate, ElementTypeMapReal & accumulated,
UInt nb_degree_of_freedom, const GhostType & ghost_type2) const {
auto it = non_local_variables.find(accumulated.getName());
// do averaging only for variables registered in the neighborhood
if (it == non_local_variables.end())
return;
foreach_weight(
ghost_type2,
[ghost_type2, nb_degree_of_freedom, &to_accumulate,
&accumulated](const auto & q1, const auto & q2, auto & weight) {
const Vector<Real> to_acc_1 =
to_accumulate(q1.type, q1.ghost_type)
.begin(nb_degree_of_freedom)[q1.global_num];
const Vector<Real> to_acc_2 =
to_accumulate(q2.type, q2.ghost_type)
.begin(nb_degree_of_freedom)[q2.global_num];
Vector<Real> acc_1 = accumulated(q1.type, q1.ghost_type)
.begin(nb_degree_of_freedom)[q1.global_num];
Vector<Real> acc_2 = accumulated(q2.type, q2.ghost_type)
.begin(nb_degree_of_freedom)[q2.global_num];
acc_1 += weight(0) * to_acc_2;
if (ghost_type2 != _ghost) {
acc_2 += weight(1) * to_acc_1;
}
});
}
/* -------------------------------------------------------------------------- */
template <class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::updateWeights() {
// Update the weights for the non local variable averaging
if (this->weight_function->getUpdateRate() &&
(this->non_local_manager.getNbStressCalls() %
this->weight_function->getUpdateRate() ==
0)) {
SynchronizerRegistry::synchronize(_gst_mnl_weight);
this->computeWeights();
}
}
} // namespace akantu
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL__ */
diff --git a/src/model/dof_manager.cc b/src/model/dof_manager.cc
index 4a33ef9ea..c7db77db8 100644
--- a/src/model/dof_manager.cc
+++ b/src/model/dof_manager.cc
@@ -1,595 +1,595 @@
/**
* @file dof_manager.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Aug 12 09:52:30 2015
*
* @brief Implementation of the common parts of the DOFManagers
*
* @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 "dof_manager.hh"
#include "element_group.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include "node_group.hh"
#include "non_linear_solver.hh"
#include "sparse_matrix.hh"
#include "communicator.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
DOFManager::DOFManager(const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), mesh(nullptr), local_system_size(0),
pure_local_system_size(0), system_size(0),
communicator(Communicator::getStaticCommunicator()) {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFManager(Mesh & mesh, const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), mesh(&mesh), local_system_size(0),
pure_local_system_size(0), system_size(0),
communicator(mesh.getCommunicator()) {
this->mesh->registerEventHandler(*this, _ehp_dof_manager);
}
/* -------------------------------------------------------------------------- */
DOFManager::~DOFManager() = default;
/* -------------------------------------------------------------------------- */
// void DOFManager::getEquationsNumbers(const ID &, Array<UInt> &) {
// AKANTU_DEBUG_TO_IMPLEMENT();
// }
/* -------------------------------------------------------------------------- */
std::vector<ID> DOFManager::getDOFIDs() const {
std::vector<ID> keys;
for (const auto & dof_data : this->dofs)
keys.push_back(dof_data.first);
return keys;
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayLocalArray(
const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
const ElementType & type, const GhostType & ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_element;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
- UInt * filter_it = NULL;
+ UInt * filter_it = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filter_it = filter_elements.storage();
} else {
nb_element = this->mesh->getNbElement(type, ghost_type);
}
AKANTU_DEBUG_ASSERT(elementary_vect.size() == nb_element,
"The vector elementary_vect("
<< elementary_vect.getID()
<< ") has not the good size.");
const Array<UInt> & connectivity =
this->mesh->getConnectivity(type, ghost_type);
// Array<UInt>::const_vector_iterator conn_begin =
// connectivity.begin(nb_nodes_per_element);
// Array<UInt>::const_vector_iterator conn_it = conn_begin;
Array<Real>::const_matrix_iterator elem_it =
elementary_vect.begin(nb_degree_of_freedom, nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el, ++elem_it) {
UInt element = el;
- if (filter_it != NULL) {
+ if (filter_it != nullptr) {
// conn_it = conn_begin + *filter_it;
element = *filter_it;
}
// const Vector<UInt> & conn = *conn_it;
const Matrix<Real> & elemental_val = *elem_it;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt offset_node = connectivity(element, n) * nb_degree_of_freedom;
Vector<Real> assemble(array_assembeled.storage() + offset_node,
nb_degree_of_freedom);
Vector<Real> elem_val = elemental_val(n);
assemble.aXplusY(elem_val, scale_factor);
}
- if (filter_it != NULL)
+ if (filter_it != nullptr)
++filter_it;
// else
// ++conn_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayToResidual(
const ID & dof_id, const Array<Real> & elementary_vect,
const ElementType & type, const GhostType & ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
Array<Real> array_localy_assembeled(this->mesh->getNbNodes(),
nb_degree_of_freedom);
array_localy_assembeled.clear();
this->assembleElementalArrayLocalArray(
elementary_vect, array_localy_assembeled, type, ghost_type, scale_factor,
filter_elements);
this->assembleToResidual(dof_id, array_localy_assembeled, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManager::assembleElementalArrayToLumpedMatrix(
const ID & dof_id, const Array<Real> & elementary_vect,
const ID & lumped_mtx, const ElementType & type,
const GhostType & ghost_type, Real scale_factor,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom =
elementary_vect.getNbComponent() / nb_nodes_per_element;
Array<Real> array_localy_assembeled(this->mesh->getNbNodes(),
nb_degree_of_freedom);
array_localy_assembeled.clear();
this->assembleElementalArrayLocalArray(
elementary_vect, array_localy_assembeled, type, ghost_type, scale_factor,
filter_elements);
this->assembleToLumpedMatrix(dof_id, array_localy_assembeled, lumped_mtx, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData::DOFData(const ID & dof_id)
- : support_type(_dst_generic), group_support("__mesh__"), dof(NULL),
- blocked_dofs(NULL), increment(NULL), previous(NULL),
+ : support_type(_dst_generic), group_support("__mesh__"), dof(nullptr),
+ blocked_dofs(nullptr), increment(nullptr), previous(nullptr),
solution(0, 1, dof_id + ":solution"),
local_equation_number(0, 1, dof_id + ":local_equation_number") {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData::~DOFData() {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData & DOFManager::getNewDOFData(const ID & dof_id) {
DOFStorage::iterator it = this->dofs.find(dof_id);
if (it != this->dofs.end()) {
AKANTU_EXCEPTION("This dof array has already been registered");
}
std::unique_ptr<DOFData> dofs_storage = std::make_unique<DOFData>(dof_id);
this->dofs[dof_id] = std::move(dofs_storage);
return *dofs_storage;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsInternal(const ID & dof_id,
Array<Real> & dofs_array) {
DOFData & dofs_storage = this->getDOFData(dof_id);
dofs_storage.dof = &dofs_array;
UInt nb_local_dofs = 0;
UInt nb_pure_local = 0;
const DOFSupportType & support_type = dofs_storage.support_type;
switch (support_type) {
case _dst_nodal: {
UInt nb_nodes = 0;
const ID & group = dofs_storage.group_support;
- NodeGroup * node_group = NULL;
+ NodeGroup * node_group = nullptr;
if (group == "__mesh__") {
nb_nodes = this->mesh->getNbNodes();
} else {
node_group = &this->mesh->getElementGroup(group).getNodeGroup();
nb_nodes = node_group->size();
}
nb_local_dofs = nb_nodes;
AKANTU_DEBUG_ASSERT(
dofs_array.size() == nb_local_dofs,
"The array of dof is too shot to be associated to nodes.");
for (UInt n = 0; n < nb_nodes; ++n) {
UInt node = n;
if (node_group)
node = node_group->getNodes()(n);
nb_pure_local += this->mesh->isLocalOrMasterNode(node) ? 1 : 0;
}
nb_pure_local *= dofs_array.getNbComponent();
nb_local_dofs *= dofs_array.getNbComponent();
break;
}
case _dst_generic: {
nb_local_dofs = nb_pure_local =
dofs_array.size() * dofs_array.getNbComponent();
break;
}
default: { AKANTU_EXCEPTION("This type of dofs is not handled yet."); }
}
this->pure_local_system_size += nb_pure_local;
this->local_system_size += nb_local_dofs;
communicator.allReduce(nb_pure_local, SynchronizerOperation::_sum);
this->system_size += nb_pure_local;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type) {
DOFData & dofs_storage = this->getNewDOFData(dof_id);
dofs_storage.support_type = support_type;
this->registerDOFsInternal(dof_id, dofs_array);
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & support_group) {
DOFData & dofs_storage = this->getNewDOFData(dof_id);
dofs_storage.support_type = _dst_nodal;
dofs_storage.group_support = support_group;
this->registerDOFsInternal(dof_id, dofs_array);
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsPrevious(const ID & dof_id, Array<Real> & array) {
DOFData & dof = this->getDOFData(dof_id);
- if (dof.previous != NULL) {
+ if (dof.previous != nullptr) {
AKANTU_EXCEPTION("The previous dofs array for "
<< dof_id << " has already been registered");
}
dof.previous = &array;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsIncrement(const ID & dof_id, Array<Real> & array) {
DOFData & dof = this->getDOFData(dof_id);
- if (dof.increment != NULL) {
+ if (dof.increment != nullptr) {
AKANTU_EXCEPTION("The dofs increment array for "
<< dof_id << " has already been registered");
}
dof.increment = &array;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerDOFsDerivative(const ID & dof_id, UInt order,
Array<Real> & dofs_derivative) {
DOFData & dof = this->getDOFData(dof_id);
std::vector<Array<Real> *> & derivatives = dof.dof_derivatives;
if (derivatives.size() < order) {
- derivatives.resize(order, NULL);
+ derivatives.resize(order, nullptr);
} else {
- if (derivatives[order - 1] != NULL) {
+ if (derivatives[order - 1] != nullptr) {
AKANTU_EXCEPTION("The dof derivatives of order "
<< order << " already been registered for this dof ("
<< dof_id << ")");
}
}
derivatives[order - 1] = &dofs_derivative;
}
/* -------------------------------------------------------------------------- */
void DOFManager::registerBlockedDOFs(const ID & dof_id,
Array<bool> & blocked_dofs) {
DOFData & dof = this->getDOFData(dof_id);
- if (dof.blocked_dofs != NULL) {
+ if (dof.blocked_dofs != nullptr) {
AKANTU_EXCEPTION("The blocked dofs array for "
<< dof_id << " has already been registered");
}
dof.blocked_dofs = &blocked_dofs;
}
/* -------------------------------------------------------------------------- */
void DOFManager::splitSolutionPerDOFs() {
DOFStorage::iterator it = this->dofs.begin();
DOFStorage::iterator end = this->dofs.end();
for (; it != end; ++it) {
DOFData & dof_data = *it->second;
dof_data.solution.resize(dof_data.dof->size() *
dof_data.dof->getNbComponent());
this->getSolutionPerDOFs(it->first, dof_data.solution);
}
}
/* -------------------------------------------------------------------------- */
SparseMatrix &
DOFManager::registerSparseMatrix(const ID & matrix_id,
std::unique_ptr<SparseMatrix> & matrix) {
SparseMatricesMap::const_iterator it = this->matrices.find(matrix_id);
if (it != this->matrices.end()) {
AKANTU_EXCEPTION("The matrix " << matrix_id << " already exists in "
<< this->id);
}
SparseMatrix & ret = *matrix;
this->matrices[matrix_id] = std::move(matrix);
return ret;
}
/* -------------------------------------------------------------------------- */
/// Get an instance of a new SparseMatrix
Array<Real> & DOFManager::getNewLumpedMatrix(const ID & id) {
ID matrix_id = this->id + ":lumped_mtx:" + id;
LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(matrix_id);
if (it != this->lumped_matrices.end()) {
AKANTU_EXCEPTION("The lumped matrix " << matrix_id << " already exists in "
<< this->id);
}
auto mtx =
std::make_unique<Array<Real>>(this->local_system_size, 1, matrix_id);
this->lumped_matrices[matrix_id] = std::move(mtx);
return *this->lumped_matrices[matrix_id];
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & DOFManager::registerNonLinearSolver(
const ID & non_linear_solver_id,
std::unique_ptr<NonLinearSolver> & non_linear_solver) {
NonLinearSolversMap::const_iterator it =
this->non_linear_solvers.find(non_linear_solver_id);
if (it != this->non_linear_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << non_linear_solver_id
<< " already exists in "
<< this->id);
}
NonLinearSolver & ret = *non_linear_solver;
this->non_linear_solvers[non_linear_solver_id] = std::move(non_linear_solver);
return ret;
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManager::registerTimeStepSolver(
const ID & time_step_solver_id,
std::unique_ptr<TimeStepSolver> & time_step_solver) {
TimeStepSolversMap::const_iterator it =
this->time_step_solvers.find(time_step_solver_id);
if (it != this->time_step_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << time_step_solver_id
<< " already exists in "
<< this->id);
}
TimeStepSolver & ret = *time_step_solver;
this->time_step_solvers[time_step_solver_id] = std::move(time_step_solver);
return ret;
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManager::getMatrix(const ID & id) {
ID matrix_id = this->id + ":mtx:" + id;
SparseMatricesMap::const_iterator it = this->matrices.find(matrix_id);
if (it == this->matrices.end()) {
AKANTU_SILENT_EXCEPTION("The matrix " << matrix_id << " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasMatrix(const ID & id) const {
ID mtx_id = this->id + ":mtx:" + id;
SparseMatricesMap::const_iterator it = this->matrices.find(mtx_id);
return it != this->matrices.end();
}
/* -------------------------------------------------------------------------- */
Array<Real> & DOFManager::getLumpedMatrix(const ID & id) {
ID matrix_id = this->id + ":lumped_mtx:" + id;
LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(matrix_id);
if (it == this->lumped_matrices.end()) {
AKANTU_SILENT_EXCEPTION("The lumped matrix "
<< matrix_id << " does not exists in " << this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
const Array<Real> & DOFManager::getLumpedMatrix(const ID & id) const {
ID matrix_id = this->id + ":lumped_mtx:" + id;
LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(matrix_id);
if (it == this->lumped_matrices.end()) {
AKANTU_SILENT_EXCEPTION("The lumped matrix "
<< matrix_id << " does not exists in " << this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasLumpedMatrix(const ID & id) const {
ID mtx_id = this->id + ":lumped_mtx:" + id;
LumpedMatricesMap::const_iterator it = this->lumped_matrices.find(mtx_id);
return it != this->lumped_matrices.end();
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & DOFManager::getNonLinearSolver(const ID & id) {
ID non_linear_solver_id = this->id + ":nls:" + id;
NonLinearSolversMap::const_iterator it =
this->non_linear_solvers.find(non_linear_solver_id);
if (it == this->non_linear_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << non_linear_solver_id
<< " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasNonLinearSolver(const ID & id) const {
ID solver_id = this->id + ":nls:" + id;
NonLinearSolversMap::const_iterator it =
this->non_linear_solvers.find(solver_id);
return it != this->non_linear_solvers.end();
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & DOFManager::getTimeStepSolver(const ID & id) {
ID time_step_solver_id = this->id + ":tss:" + id;
TimeStepSolversMap::const_iterator it =
this->time_step_solvers.find(time_step_solver_id);
if (it == this->time_step_solvers.end()) {
AKANTU_EXCEPTION("The non linear solver " << time_step_solver_id
<< " does not exists in "
<< this->id);
}
return *(it->second);
}
/* -------------------------------------------------------------------------- */
bool DOFManager::hasTimeStepSolver(const ID & solver_id) const {
ID time_step_solver_id = this->id + ":tss:" + solver_id;
TimeStepSolversMap::const_iterator it =
this->time_step_solvers.find(time_step_solver_id);
return it != this->time_step_solvers.end();
}
/* -------------------------------------------------------------------------- */
void DOFManager::savePreviousDOFs(const ID & dofs_id) {
this->getPreviousDOFs(dofs_id).copy(this->getDOFs(dofs_id));
}
/* -------------------------------------------------------------------------- */
/* Mesh Events */
/* -------------------------------------------------------------------------- */
std::pair<UInt, UInt>
DOFManager::updateNodalDOFs(const ID & dof_id, const Array<UInt> & nodes_list) {
auto & dof_data = this->getDOFData(dof_id);
UInt nb_new_local_dofs = 0;
UInt nb_new_pure_local = 0;
nb_new_local_dofs = nodes_list.size();
for (const auto & node : nodes_list) {
nb_new_pure_local += this->mesh->isLocalOrMasterNode(node) ? 1 : 0;
}
const auto & dof_array = *dof_data.dof;
nb_new_pure_local *= dof_array.getNbComponent();
nb_new_local_dofs *= dof_array.getNbComponent();
this->pure_local_system_size += nb_new_pure_local;
this->local_system_size += nb_new_local_dofs;
UInt nb_new_global = nb_new_pure_local;
communicator.allReduce(nb_new_global, SynchronizerOperation::_sum);
this->system_size += nb_new_global;
return std::make_pair(nb_new_local_dofs, nb_new_pure_local);
}
/* -------------------------------------------------------------------------- */
void DOFManager::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent &) {
for (auto & pair : this->dofs) {
const auto & dof_id = pair.first;
auto & dof_data = this->getDOFData(dof_id);
if (dof_data.support_type != _dst_nodal)
continue;
const auto & group = dof_data.group_support;
if (group == "__mesh__") {
this->updateNodalDOFs(dof_id, nodes_list);
} else {
const auto & node_group =
this->mesh->getElementGroup(group).getNodeGroup();
Array<UInt> new_nodes_list;
for (const auto & node : nodes_list) {
if (node_group.find(node) != UInt(-1))
new_nodes_list.push_back(node);
}
this->updateNodalDOFs(dof_id, new_nodes_list);
}
}
}
/* -------------------------------------------------------------------------- */
void DOFManager::onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) {}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsAdded(const Array<Element> &,
const NewElementsEvent &) {}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) {}
/* -------------------------------------------------------------------------- */
void DOFManager::onElementsChanged(const Array<Element> &,
const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) {}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/dof_manager.hh b/src/model/dof_manager.hh
index 23b76fc4c..fd22976d7 100644
--- a/src/model/dof_manager.hh
+++ b/src/model/dof_manager.hh
@@ -1,465 +1,463 @@
/**
* @file dof_manager.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Jul 22 11:43:43 2015
*
* @brief Class handling the different types of dofs
*
* @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 "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_MANAGER_HH__
#define __AKANTU_DOF_MANAGER_HH__
namespace akantu {
class TermsToAssemble;
class NonLinearSolver;
class TimeStepSolver;
class SparseMatrix;
} // namespace akantu
namespace akantu {
class DOFManager : protected Memory, protected MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFManager(const ID & id = "dof_manager", const MemoryID & memory_id = 0);
DOFManager(Mesh & mesh, const ID & id = "dof_manager",
const MemoryID & memory_id = 0);
- virtual ~DOFManager();
+ ~DOFManager() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
/// common function to help registering dofs
void registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array);
public:
/// register an array of degree of freedom
virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type);
/// the dof as an implied type of _dst_nodal and is defined only on a subset
/// of nodes
virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & group_support);
/// register an array of previous values of the degree of freedom
virtual void registerDOFsPrevious(const ID & dof_id,
Array<Real> & dofs_array);
/// register an array of increment of degree of freedom
virtual void registerDOFsIncrement(const ID & dof_id,
Array<Real> & dofs_array);
/// register an array of derivatives for a particular dof array
virtual void registerDOFsDerivative(const ID & dof_id, UInt order,
Array<Real> & dofs_derivative);
/// register array representing the blocked degree of freedoms
virtual void registerBlockedDOFs(const ID & dof_id,
Array<bool> & blocked_dofs);
/// Assemble an array to the global residual array
virtual void assembleToResidual(const ID & dof_id,
const Array<Real> & array_to_assemble,
Real scale_factor = 1.) = 0;
/// Assemble an array to the global lumped matrix array
virtual void assembleToLumpedMatrix(const ID & dof_id,
const Array<Real> & array_to_assemble,
const ID & lumped_mtx,
Real scale_factor = 1.) = 0;
/**
* Assemble elementary values to a local array of the size nb_nodes *
* nb_dof_per_node. The dof number is implicitly considered as
* conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayLocalArray(
const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
const ElementType & type, const GhostType & ghost_type,
Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayToResidual(
const ID & dof_id, const Array<Real> & elementary_vect,
const ElementType & type, const GhostType & ghost_type,
Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to a global array corresponding to a lumped
* matrix
*/
virtual void assembleElementalArrayToLumpedMatrix(
const ID & dof_id, const Array<Real> & elementary_vect,
const ID & lumped_mtx, const ElementType & type,
const GhostType & ghost_type, Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d. With 0 <
* n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id,
const Array<Real> & elementary_mat, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const MatrixType & elemental_matrix_type = _symmetric,
const Array<UInt> & filter_elements = empty_filter) = 0;
/// multiply a vector by a matrix and assemble the result to the residual
virtual void assembleMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) = 0;
/// multiply a vector by a lumped matrix and assemble the result to the
/// residual
virtual void assembleLumpedMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) = 0;
/// assemble coupling terms between to dofs
virtual void assemblePreassembledMatrix(const ID & dof_id_m,
const ID & dof_id_n,
const ID & matrix_id,
const TermsToAssemble & terms) = 0;
/// sets the residual to 0
virtual void clearResidual() = 0;
/// sets the matrix to 0
virtual void clearMatrix(const ID & mtx) = 0;
/// sets the lumped matrix to 0
virtual void clearLumpedMatrix(const ID & mtx) = 0;
/// splits the solution storage from a global view to the per dof storages
void splitSolutionPerDOFs();
/// extract a lumped matrix part corresponding to a given dof
virtual void getLumpedMatrixPerDOFs(const ID & dof_id, const ID & lumped_mtx,
Array<Real> & lumped) = 0;
protected:
/// minimum functionality to implement per derived version of the DOFManager
/// to allow the splitSolutionPerDOFs function to work
virtual void getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array) = 0;
protected:
/* ------------------------------------------------------------------------ */
/// register a matrix
SparseMatrix & registerSparseMatrix(const ID & matrix_id,
std::unique_ptr<SparseMatrix> & matrix);
/// register a non linear solver instantiated by a derived class
NonLinearSolver &
registerNonLinearSolver(const ID & non_linear_solver_id,
std::unique_ptr<NonLinearSolver> & non_linear_solver);
/// register a time step solver instantiated by a derived class
TimeStepSolver &
registerTimeStepSolver(const ID & time_step_solver_id,
std::unique_ptr<TimeStepSolver> & time_step_solver);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the equation numbers corresponding to a dof_id. This might be used to
/// access the matrix.
inline const Array<UInt> & getEquationsNumbers(const ID & dof_id) const;
/// Global number of dofs
AKANTU_GET_MACRO(SystemSize, this->system_size, UInt);
/// Local number of dofs
AKANTU_GET_MACRO(LocalSystemSize, this->local_system_size, UInt);
/// Retrieve all the registered DOFs
std::vector<ID> getDOFIDs() const;
/* ------------------------------------------------------------------------ */
/* DOFs and derivatives accessors */
/* ------------------------------------------------------------------------ */
/// Get a reference to the registered dof array for a given id
inline Array<Real> & getDOFs(const ID & dofs_id);
/// Get the support type of a given dof
inline DOFSupportType getSupportType(const ID & dofs_id) const;
/// are the dofs registered
inline bool hasDOFs(const ID & dofs_id) const;
/// Get a reference to the registered dof derivatives array for a given id
inline Array<Real> & getDOFsDerivatives(const ID & dofs_id, UInt order);
/// Does the dof has derivatives
inline bool hasDOFsDerivatives(const ID & dofs_id, UInt order) const;
/// Get a reference to the blocked dofs array registered for the given id
inline const Array<bool> & getBlockedDOFs(const ID & dofs_id) const;
/// Does the dof has a blocked array
inline bool hasBlockedDOFs(const ID & dofs_id) const;
/// Get a reference to the registered dof increment array for a given id
inline Array<Real> & getDOFsIncrement(const ID & dofs_id);
/// Does the dof has a increment array
inline bool hasDOFsIncrement(const ID & dofs_id) const;
/// Does the dof has a previous array
inline Array<Real> & getPreviousDOFs(const ID & dofs_id);
/// Get a reference to the registered dof array for previous step values a
/// given id
inline bool hasPreviousDOFs(const ID & dofs_id) const;
/// saves the values from dofs to previous dofs
virtual void savePreviousDOFs(const ID & dofs_id);
/// Get a reference to the solution array registered for the given id
inline const Array<Real> & getSolution(const ID & dofs_id) const;
/* ------------------------------------------------------------------------ */
/* Matrices accessors */
/* ------------------------------------------------------------------------ */
/// Get an instance of a new SparseMatrix
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) = 0;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) = 0;
/// Get the reference of an existing matrix
SparseMatrix & getMatrix(const ID & matrix_id);
/// check if the given matrix exists
bool hasMatrix(const ID & matrix_id) const;
/// Get an instance of a new lumped matrix
virtual Array<Real> & getNewLumpedMatrix(const ID & matrix_id);
/// Get the lumped version of a given matrix
const Array<Real> & getLumpedMatrix(const ID & matrix_id) const;
/// Get the lumped version of a given matrix
Array<Real> & getLumpedMatrix(const ID & matrix_id);
/// check if the given matrix exists
bool hasLumpedMatrix(const ID & matrix_id) const;
/* ------------------------------------------------------------------------ */
/* Non linear system solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a non linear solver
virtual NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & _non_linear_solver_type) = 0;
/// get instance of a non linear solver
virtual NonLinearSolver & getNonLinearSolver(const ID & nls_solver_id);
/// check if the given solver exists
bool hasNonLinearSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
/* Time-Step Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a time step solver
virtual TimeStepSolver &
getNewTimeStepSolver(const ID & time_step_solver_id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver) = 0;
/// get instance of a time step solver
virtual TimeStepSolver & getTimeStepSolver(const ID & time_step_solver_id);
/// check if the given solver exists
bool hasTimeStepSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
const Mesh & getMesh() {
if (mesh) {
return *mesh;
} else {
AKANTU_EXCEPTION("No mesh registered in this dof manager");
}
}
/* ------------------------------------------------------------------------ */
AKANTU_GET_MACRO(Communicator, communicator, const auto &);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler interface */
/* ------------------------------------------------------------------------ */
protected:
/// helper function for the DOFManager::onNodesAdded method
virtual std::pair<UInt, UInt> updateNodalDOFs(const ID & dof_id,
const Array<UInt> & nodes_list);
public:
/// function to implement to react on akantu::NewNodesEvent
- virtual void onNodesAdded(const Array<UInt> & nodes_list,
- const NewNodesEvent & event);
+ void onNodesAdded(const Array<UInt> & nodes_list,
+ const NewNodesEvent & event) override;
/// function to implement to react on akantu::RemovedNodesEvent
- virtual void onNodesRemoved(const Array<UInt> & nodes_list,
- const Array<UInt> & new_numbering,
- const RemovedNodesEvent & event);
+ void onNodesRemoved(const Array<UInt> & nodes_list,
+ const Array<UInt> & new_numbering,
+ const RemovedNodesEvent & event) override;
/// function to implement to react on akantu::NewElementsEvent
- virtual void onElementsAdded(const Array<Element> & elements_list,
- const NewElementsEvent & event);
+ void onElementsAdded(const Array<Element> & elements_list,
+ const NewElementsEvent & event) override;
/// function to implement to react on akantu::RemovedElementsEvent
- virtual void
- onElementsRemoved(const Array<Element> & elements_list,
- const ElementTypeMapArray<UInt> & new_numbering,
- const RemovedElementsEvent & event);
+ void onElementsRemoved(const Array<Element> & elements_list,
+ const ElementTypeMapArray<UInt> & new_numbering,
+ const RemovedElementsEvent & event) override;
/// function to implement to react on akantu::ChangedElementsEvent
- virtual void
- onElementsChanged(const Array<Element> & old_elements_list,
- const Array<Element> & new_elements_list,
- const ElementTypeMapArray<UInt> & new_numbering,
- const ChangedElementsEvent & event);
+ void onElementsChanged(const Array<Element> & old_elements_list,
+ const Array<Element> & new_elements_list,
+ const ElementTypeMapArray<UInt> & new_numbering,
+ const ChangedElementsEvent & event) override;
protected:
struct DOFData;
inline DOFData & getDOFData(const ID & dof_id);
inline const DOFData & getDOFData(const ID & dof_id) const;
template <class _DOFData>
inline _DOFData & getDOFDataTyped(const ID & dof_id);
template <class _DOFData>
inline const _DOFData & getDOFDataTyped(const ID & dof_id) const;
virtual DOFData & getNewDOFData(const ID & dof_id);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// dof representations in the dof manager
struct DOFData {
DOFData() = delete;
explicit DOFData(const ID & dof_id);
virtual ~DOFData();
/// DOF support type (nodal, general) this is needed to determine how the
/// dof are shared among processors
DOFSupportType support_type;
ID group_support;
/// Degree of freedom array
Array<Real> * dof;
/// Blocked degree of freedoms array
Array<bool> * blocked_dofs;
/// Degree of freedoms increment
Array<Real> * increment;
/// Degree of freedoms at previous step
Array<Real> * previous;
/// Solution associated to the dof
Array<Real> solution;
/// local numbering equation numbers
Array<UInt> local_equation_number;
/* ---------------------------------------------------------------------- */
/* data for dynamic simulations */
/* ---------------------------------------------------------------------- */
/// Degree of freedom derivatives arrays
std::vector<Array<Real> *> dof_derivatives;
};
/// type to store dofs information
using DOFStorage = std::map<ID, std::unique_ptr<DOFData>>;
/// type to store all the matrices
using SparseMatricesMap = std::map<ID, std::unique_ptr<SparseMatrix>>;
/// type to store all the lumped matrices
using LumpedMatricesMap = std::map<ID, std::unique_ptr<Array<Real>>>;
/// type to store all the non linear solver
using NonLinearSolversMap = std::map<ID, std::unique_ptr<NonLinearSolver>>;
/// type to store all the time step solver
using TimeStepSolversMap = std::map<ID, std::unique_ptr<TimeStepSolver>>;
/// store a reference to the dof arrays
DOFStorage dofs;
/// list of sparse matrices that where created
SparseMatricesMap matrices;
/// list of lumped matrices
LumpedMatricesMap lumped_matrices;
/// non linear solvers storage
NonLinearSolversMap non_linear_solvers;
/// time step solvers storage
TimeStepSolversMap time_step_solvers;
/// reference to the underlying mesh
Mesh * mesh;
/// Total number of degrees of freedom (size with the ghosts)
UInt local_system_size;
/// Number of purely local dofs (size without the ghosts)
UInt pure_local_system_size;
/// Total number of degrees of freedom
UInt system_size;
/// Communicator used for this manager, should be the same as in the mesh if a
/// mesh is registered
const Communicator & communicator;
};
} // namespace akantu
#include "dof_manager_inline_impl.cc"
#endif /* __AKANTU_DOF_MANAGER_HH__ */
diff --git a/src/model/dof_manager_default.cc b/src/model/dof_manager_default.cc
index 6944e7da6..8c7d95689 100644
--- a/src/model/dof_manager_default.cc
+++ b/src/model/dof_manager_default.cc
@@ -1,913 +1,912 @@
/**
* @file dof_manager_default.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 11 16:21:01 2015
*
* @brief Implementation of the default DOFManager
*
* @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 "dof_manager_default.hh"
#include "dof_synchronizer.hh"
#include "element_group.hh"
#include "node_synchronizer.hh"
#include "non_linear_solver_default.hh"
#include "sparse_matrix_aij.hh"
#include "communicator.hh"
#include "terms_to_assemble.hh"
#include "time_step_solver_default.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <memory>
#include <numeric>
#include <unordered_map>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::addSymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & elementary_mat,
const Vector<UInt> & equation_numbers, UInt max_size) {
for (UInt i = 0; i < elementary_mat.rows(); ++i) {
UInt c_irn = equation_numbers(i);
if (c_irn < max_size) {
for (UInt j = i; j < elementary_mat.cols(); ++j) {
UInt c_jcn = equation_numbers(j);
if (c_jcn < max_size) {
matrix(c_irn, c_jcn) += elementary_mat(i, j);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::addUnsymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & elementary_mat,
const Vector<UInt> & equation_numbers, UInt max_size) {
for (UInt i = 0; i < elementary_mat.rows(); ++i) {
UInt c_irn = equation_numbers(i);
if (c_irn < max_size) {
for (UInt j = 0; j < elementary_mat.cols(); ++j) {
UInt c_jcn = equation_numbers(j);
if (c_jcn < max_size) {
if (c_jcn >= c_irn) {
matrix(c_irn, c_jcn) += elementary_mat(i, j);
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::addElementalMatrixToUnsymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & elementary_mat,
const Vector<UInt> & equation_numbers, UInt max_size) {
for (UInt i = 0; i < elementary_mat.rows(); ++i) {
UInt c_irn = equation_numbers(i);
if (c_irn < max_size) {
for (UInt j = 0; j < elementary_mat.cols(); ++j) {
UInt c_jcn = equation_numbers(j);
if (c_jcn < max_size) {
matrix(c_irn, c_jcn) += elementary_mat(i, j);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(const ID & id, const MemoryID & memory_id)
: DOFManager(id, memory_id), residual(0, 1, std::string(id + ":residual")),
global_residual(nullptr),
global_solution(0, 1, std::string(id + ":global_solution")),
global_blocked_dofs(0, 1, std::string(id + ":global_blocked_dofs")),
previous_global_blocked_dofs(
0, 1, std::string(id + ":previous_global_blocked_dofs")),
dofs_type(0, 1, std::string(id + ":dofs_type")),
data_cache(0, 1, std::string(id + ":data_cache_array")),
jacobian_release(0),
global_equation_number(0, 1, "global_equation_number"),
first_global_dof_id(0), synchronizer(nullptr) {}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFManagerDefault(Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: DOFManager(mesh, id, memory_id),
residual(0, 1, std::string(id + ":residual")), global_residual(nullptr),
global_solution(0, 1, std::string(id + ":global_solution")),
global_blocked_dofs(0, 1, std::string(id + ":global_blocked_dofs")),
previous_global_blocked_dofs(
0, 1, std::string(id + ":previous_global_blocked_dofs")),
dofs_type(0, 1, std::string(id + ":dofs_type")),
data_cache(0, 1, std::string(id + ":data_cache_array")),
jacobian_release(0),
global_equation_number(0, 1, "global_equation_number"),
first_global_dof_id(0), synchronizer(nullptr) {
if (this->mesh->isDistributed())
this->synchronizer = std::make_unique<DOFSynchronizer>(
*this, this->id + ":dof_synchronizer", this->memory_id, communicator);
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::~DOFManagerDefault() = default;
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFManagerDefault::assembleToGlobalArray(
const ID & dof_id, const Array<T> & array_to_assemble,
Array<T> & global_array, T scale_factor) {
AKANTU_DEBUG_IN();
const Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
UInt nb_degree_of_freedoms =
array_to_assemble.size() * array_to_assemble.getNbComponent();
AKANTU_DEBUG_ASSERT(equation_number.size() == nb_degree_of_freedoms,
"The array to assemble does not have a correct size."
<< " (" << array_to_assemble.getID() << ")");
typename Array<T>::const_scalar_iterator arr_it =
array_to_assemble.begin_reinterpret(nb_degree_of_freedoms);
Array<UInt>::const_scalar_iterator equ_it = equation_number.begin();
for (UInt d = 0; d < nb_degree_of_freedoms; ++d, ++arr_it, ++equ_it) {
global_array(*equ_it) += scale_factor * (*arr_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
DOFManagerDefault::DOFDataDefault::DOFDataDefault(const ID & dof_id)
: DOFData(dof_id), associated_nodes(0, 1, dof_id + "associated_nodes") {}
/* -------------------------------------------------------------------------- */
DOFManager::DOFData & DOFManagerDefault::getNewDOFData(const ID & dof_id) {
this->dofs[dof_id] = std::make_unique<DOFDataDefault>(dof_id);
return *this->dofs[dof_id];
}
/* -------------------------------------------------------------------------- */
class GlobalDOFInfoDataAccessor : public DataAccessor<UInt> {
public:
typedef
typename std::unordered_map<UInt, std::vector<UInt>>::size_type size_type;
GlobalDOFInfoDataAccessor() = default;
void addDOFToNode(UInt node, UInt dof) { dofs_per_node[node].push_back(dof); }
UInt getNthDOFForNode(UInt nth_dof, UInt node) const {
return dofs_per_node.find(node)->second[nth_dof];
}
- virtual UInt getNbData(const Array<UInt> & nodes,
- const SynchronizationTag & tag) const {
+ UInt getNbData(const Array<UInt> & nodes,
+ const SynchronizationTag & tag) const override {
if (tag == _gst_size) {
return nodes.size() * sizeof(size_type);
}
if (tag == _gst_update) {
UInt total_size = 0;
for (auto node : nodes) {
auto it = dofs_per_node.find(node);
if (it != dofs_per_node.end())
total_size += CommunicationBuffer::sizeInBuffer(it->second);
}
return total_size;
}
return 0;
}
- virtual void packData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
- const SynchronizationTag & tag) const {
+ void packData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
+ const SynchronizationTag & tag) const override {
for (auto node : nodes) {
auto it = dofs_per_node.find(node);
if (tag == _gst_size) {
if (it != dofs_per_node.end()) {
buffer << it->second.size();
} else {
buffer << 0;
}
} else if (tag == _gst_update) {
if (it != dofs_per_node.end())
buffer << it->second;
}
}
}
- virtual void unpackData(CommunicationBuffer & buffer,
- const Array<UInt> & nodes,
- const SynchronizationTag & tag) {
+ void unpackData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
+ const SynchronizationTag & tag) override {
for (auto node : nodes) {
auto it = dofs_per_node.find(node);
if (tag == _gst_size) {
size_type size;
buffer >> size;
if (size != 0)
dofs_per_node[node].resize(size);
} else if (tag == _gst_update) {
if (it != dofs_per_node.end())
buffer >> it->second;
}
}
}
protected:
std::unordered_map<UInt, std::vector<UInt>> dofs_per_node;
};
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerDOFsInternal(const ID & dof_id, UInt nb_dofs,
UInt nb_pure_local_dofs) {
// auto prank = this->communicator.whoAmI();
// auto psize = this->communicator.getNbProc();
// access the relevant data to update
auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
const auto & support_type = dof_data.support_type;
const auto & group = dof_data.group_support;
if (support_type == _dst_nodal and group != "__mesh__") {
auto & support_nodes =
this->mesh->getElementGroup(group).getNodeGroup().getNodes();
this->updateDOFsData(
dof_data, nb_dofs, nb_pure_local_dofs,
[&support_nodes](UInt node) -> UInt { return support_nodes[node]; });
} else {
this->updateDOFsData(dof_data, nb_dofs, nb_pure_local_dofs,
[](UInt node) -> UInt { return node; });
}
// update the synchronizer if needed
if (this->synchronizer)
this->synchronizer->registerDOFs(dof_id);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerDOFs(const ID & dof_id,
Array<Real> & dofs_array,
const DOFSupportType & support_type) {
// stores the current numbers of dofs
UInt nb_dofs_old = this->local_system_size;
UInt nb_pure_local_dofs_old = this->pure_local_system_size;
// update or create the dof_data
DOFManager::registerDOFs(dof_id, dofs_array, support_type);
UInt nb_dofs = this->local_system_size - nb_dofs_old;
UInt nb_pure_local_dofs =
this->pure_local_system_size - nb_pure_local_dofs_old;
this->registerDOFsInternal(dof_id, nb_dofs, nb_pure_local_dofs);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::registerDOFs(const ID & dof_id,
Array<Real> & dofs_array,
const ID & group_support) {
// stores the current numbers of dofs
UInt nb_dofs_old = this->local_system_size;
UInt nb_pure_local_dofs_old = this->pure_local_system_size;
// update or create the dof_data
DOFManager::registerDOFs(dof_id, dofs_array, group_support);
UInt nb_dofs = this->local_system_size - nb_dofs_old;
UInt nb_pure_local_dofs =
this->pure_local_system_size - nb_pure_local_dofs_old;
this->registerDOFsInternal(dof_id, nb_dofs, nb_pure_local_dofs);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
const MatrixType & matrix_type) {
ID matrix_id = this->id + ":mtx:" + id;
std::unique_ptr<SparseMatrix> sm =
std::make_unique<SparseMatrixAIJ>(*this, matrix_type, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
/* -------------------------------------------------------------------------- */
SparseMatrix & DOFManagerDefault::getNewMatrix(const ID & id,
const ID & matrix_to_copy_id) {
ID matrix_id = this->id + ":mtx:" + id;
SparseMatrixAIJ & sm_to_copy = this->getMatrix(matrix_to_copy_id);
std::unique_ptr<SparseMatrix> sm =
std::make_unique<SparseMatrixAIJ>(sm_to_copy, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ & DOFManagerDefault::getMatrix(const ID & id) {
SparseMatrix & matrix = DOFManager::getMatrix(id);
return dynamic_cast<SparseMatrixAIJ &>(matrix);
}
/* -------------------------------------------------------------------------- */
NonLinearSolver &
DOFManagerDefault::getNewNonLinearSolver(const ID & id,
const NonLinearSolverType & type) {
ID non_linear_solver_id = this->id + ":nls:" + id;
std::unique_ptr<NonLinearSolver> nls;
switch (type) {
#if defined(AKANTU_IMPLICIT)
case _nls_newton_raphson:
case _nls_newton_raphson_modified: {
nls = std::make_unique<NonLinearSolverNewtonRaphson>(
*this, type, non_linear_solver_id, this->memory_id);
break;
}
case _nls_linear: {
nls = std::make_unique<NonLinearSolverLinear>(
*this, type, non_linear_solver_id, this->memory_id);
break;
}
#endif
case _nls_lumped: {
nls = std::make_unique<NonLinearSolverLumped>(
*this, type, non_linear_solver_id, this->memory_id);
break;
}
default:
AKANTU_EXCEPTION("The asked type of non linear solver is not supported by "
"this dof manager");
}
return this->registerNonLinearSolver(non_linear_solver_id, nls);
}
/* -------------------------------------------------------------------------- */
TimeStepSolver &
DOFManagerDefault::getNewTimeStepSolver(const ID & id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver) {
ID time_step_solver_id = this->id + ":tss:" + id;
std::unique_ptr<TimeStepSolver> tss = std::make_unique<TimeStepSolverDefault>(
*this, type, non_linear_solver, time_step_solver_id, this->memory_id);
return this->registerTimeStepSolver(time_step_solver_id, tss);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::clearResidual() {
this->residual.resize(this->local_system_size);
this->residual.clear();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::clearMatrix(const ID & mtx) {
this->getMatrix(mtx).clear();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::clearLumpedMatrix(const ID & mtx) {
this->getLumpedMatrix(mtx).clear();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::updateGlobalBlockedDofs() {
DOFStorage::iterator it = this->dofs.begin();
DOFStorage::iterator end = this->dofs.end();
this->previous_global_blocked_dofs.copy(this->global_blocked_dofs);
this->global_blocked_dofs.resize(this->local_system_size);
this->global_blocked_dofs.clear();
for (; it != end; ++it) {
if (!this->hasBlockedDOFs(it->first))
continue;
DOFData & dof_data = *it->second;
this->assembleToGlobalArray(it->first, *dof_data.blocked_dofs,
this->global_blocked_dofs, true);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void DOFManagerDefault::getArrayPerDOFs(const ID & dof_id,
const Array<T> & global_array,
Array<T> & local_array) const {
AKANTU_DEBUG_IN();
const Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
UInt nb_degree_of_freedoms = equation_number.size();
local_array.resize(nb_degree_of_freedoms / local_array.getNbComponent());
auto loc_it = local_array.begin_reinterpret(nb_degree_of_freedoms);
auto equ_it = equation_number.begin();
for (UInt d = 0; d < nb_degree_of_freedoms; ++d, ++loc_it, ++equ_it) {
(*loc_it) = global_array(*equ_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
// void DOFManagerDefault::getEquationsNumbers(const ID & dof_id,
// Array<UInt> & equation_numbers) {
// AKANTU_DEBUG_IN();
// this->getArrayPerDOFs(dof_id, this->global_equation_number,
// equation_numbers); AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->global_solution, solution_array);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::getLumpedMatrixPerDOFs(const ID & dof_id,
const ID & lumped_mtx,
Array<Real> & lumped) {
AKANTU_DEBUG_IN();
this->getArrayPerDOFs(dof_id, this->getLumpedMatrix(lumped_mtx), lumped);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleToResidual(
const ID & dof_id, const Array<Real> & array_to_assemble,
Real scale_factor) {
AKANTU_DEBUG_IN();
this->assembleToGlobalArray(dof_id, array_to_assemble, this->residual,
scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleToLumpedMatrix(
const ID & dof_id, const Array<Real> & array_to_assemble,
const ID & lumped_mtx, Real scale_factor) {
AKANTU_DEBUG_IN();
Array<Real> & lumped = this->getLumpedMatrix(lumped_mtx);
this->assembleToGlobalArray(dof_id, array_to_assemble, lumped, scale_factor);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor) {
SparseMatrixAIJ & A = this->getMatrix(A_id);
// Array<Real> data_cache(this->local_system_size, 1, 0.);
this->data_cache.resize(this->local_system_size);
this->data_cache.clear();
this->assembleToGlobalArray(dof_id, x, data_cache, 1.);
A.matVecMul(data_cache, this->residual, scale_factor, 1.);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleLumpedMatMulVectToResidual(
const ID & dof_id, const ID & A_id, const Array<Real> & x,
Real scale_factor) {
const Array<Real> & A = this->getLumpedMatrix(A_id);
// Array<Real> data_cache(this->local_system_size, 1, 0.);
this->data_cache.resize(this->local_system_size);
this->data_cache.clear();
this->assembleToGlobalArray(dof_id, x, data_cache, scale_factor);
Array<Real>::const_scalar_iterator A_it = A.begin();
Array<Real>::const_scalar_iterator A_end = A.end();
Array<Real>::const_scalar_iterator x_it = data_cache.begin();
Array<Real>::scalar_iterator r_it = this->residual.begin();
for (; A_it != A_end; ++A_it, ++x_it, ++r_it) {
*r_it += *A_it * *x_it;
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id, const Array<Real> & elementary_mat,
const ElementType & type, const GhostType & ghost_type,
const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
DOFData & dof_data = this->getDOFData(dof_id);
AKANTU_DEBUG_ASSERT(dof_data.support_type == _dst_nodal,
"This function applies only on Nodal dofs");
this->addToProfile(matrix_id, dof_id, type, ghost_type);
const Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
SparseMatrixAIJ & A = this->getMatrix(matrix_id);
UInt nb_element;
if (ghost_type == _not_ghost) {
nb_element = this->mesh->getNbElement(type);
} else {
AKANTU_DEBUG_TO_IMPLEMENT();
}
UInt * filter_it = nullptr;
if (filter_elements != empty_filter) {
nb_element = filter_elements.size();
filter_it = filter_elements.storage();
} else {
if (dof_data.group_support != "__mesh__") {
const Array<UInt> & group_elements =
this->mesh->getElementGroup(dof_data.group_support)
.getElements(type, ghost_type);
nb_element = group_elements.size();
filter_it = group_elements.storage();
} else {
nb_element = this->mesh->getNbElement(type, ghost_type);
}
}
AKANTU_DEBUG_ASSERT(elementary_mat.size() == nb_element,
"The vector elementary_mat("
<< elementary_mat.getID()
<< ") has not the good size.");
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = dof_data.dof->getNbComponent();
const Array<UInt> & connectivity =
this->mesh->getConnectivity(type, ghost_type);
auto conn_begin = connectivity.begin(nb_nodes_per_element);
auto conn_it = conn_begin;
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom;
Vector<UInt> element_eq_nb(nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::const_matrix_iterator el_mat_it =
elementary_mat.begin(size_mat, size_mat);
for (UInt e = 0; e < nb_element; ++e, ++el_mat_it) {
if (filter_it)
conn_it = conn_begin + *filter_it;
this->extractElementEquationNumber(equation_number, *conn_it,
nb_degree_of_freedom, element_eq_nb);
std::transform(element_eq_nb.storage(),
element_eq_nb.storage() + element_eq_nb.size(),
element_eq_nb.storage(), [&](UInt & local) -> UInt {
return this->localToGlobalEquationNumber(local);
});
if (filter_it)
++filter_it;
else
++conn_it;
if (A.getMatrixType() == _symmetric)
if (elemental_matrix_type == _symmetric)
this->addSymmetricElementalMatrixToSymmetric(
A, *el_mat_it, element_eq_nb, A.size());
else
this->addUnsymmetricElementalMatrixToSymmetric(
A, *el_mat_it, element_eq_nb, A.size());
else
this->addElementalMatrixToUnsymmetric(A, *el_mat_it, element_eq_nb,
A.size());
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::assemblePreassembledMatrix(
const ID & dof_id_m, const ID & dof_id_n, const ID & matrix_id,
const TermsToAssemble & terms) {
const Array<UInt> & equation_number_m =
this->getLocalEquationNumbers(dof_id_m);
const Array<UInt> & equation_number_n =
this->getLocalEquationNumbers(dof_id_n);
SparseMatrixAIJ & A = this->getMatrix(matrix_id);
for (const auto & term : terms) {
UInt gi = this->localToGlobalEquationNumber(equation_number_m(term.i()));
UInt gj = this->localToGlobalEquationNumber(equation_number_n(term.j()));
A.add(gi, gj, term);
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::addToProfile(const ID & matrix_id, const ID & dof_id,
const ElementType & type,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
const DOFData & dof_data = this->getDOFData(dof_id);
if (dof_data.support_type != _dst_nodal)
return;
auto mat_dof = std::make_pair(matrix_id, dof_id);
auto type_pair = std::make_pair(type, ghost_type);
auto prof_it = this->matrix_profiled_dofs.find(mat_dof);
if (prof_it != this->matrix_profiled_dofs.end() &&
std::find(prof_it->second.begin(), prof_it->second.end(), type_pair) !=
prof_it->second.end())
return;
UInt nb_degree_of_freedom_per_node = dof_data.dof->getNbComponent();
const Array<UInt> & equation_number = this->getLocalEquationNumbers(dof_id);
SparseMatrixAIJ & A = this->getMatrix(matrix_id);
UInt size = A.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const auto & connectivity = this->mesh->getConnectivity(type, ghost_type);
auto cbegin = connectivity.begin(nb_nodes_per_element);
auto cit = cbegin;
UInt nb_elements = connectivity.size();
UInt * ge_it = nullptr;
if (dof_data.group_support != "__mesh__") {
const Array<UInt> & group_elements =
this->mesh->getElementGroup(dof_data.group_support)
.getElements(type, ghost_type);
ge_it = group_elements.storage();
nb_elements = group_elements.size();
}
UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom_per_node;
Vector<UInt> element_eq_nb(size_mat);
for (UInt e = 0; e < nb_elements; ++e) {
if (ge_it)
cit = cbegin + *ge_it;
this->extractElementEquationNumber(
equation_number, *cit, nb_degree_of_freedom_per_node, element_eq_nb);
std::transform(element_eq_nb.storage(),
element_eq_nb.storage() + element_eq_nb.size(),
element_eq_nb.storage(), [&](UInt & local) -> UInt {
return this->localToGlobalEquationNumber(local);
});
if (ge_it)
++ge_it;
else
++cit;
for (UInt i = 0; i < size_mat; ++i) {
UInt c_irn = element_eq_nb(i);
if (c_irn < size) {
for (UInt j = 0; j < size_mat; ++j) {
UInt c_jcn = element_eq_nb(j);
if (c_jcn < size) {
A.add(c_irn, c_jcn);
}
}
}
}
}
this->matrix_profiled_dofs[mat_dof].push_back(type_pair);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::applyBoundary(const ID & matrix_id) {
SparseMatrixAIJ & J = this->getMatrix(matrix_id);
if (this->jacobian_release == J.getValueRelease()) {
auto are_equal =
std::equal(global_blocked_dofs.begin(), global_blocked_dofs.end(),
previous_global_blocked_dofs.begin());
if (are_equal)
J.applyBoundary();
previous_global_blocked_dofs.copy(global_blocked_dofs);
} else {
J.applyBoundary();
}
this->jacobian_release = J.getValueRelease();
}
/* -------------------------------------------------------------------------- */
const Array<Real> & DOFManagerDefault::getGlobalResidual() {
if (this->synchronizer) {
if (not this->global_residual) {
this->global_residual =
std::make_unique<Array<Real>>(0, 1, "global_residual");
}
if (this->synchronizer->getCommunicator().whoAmI() == 0) {
this->global_residual->resize(this->system_size);
this->synchronizer->gather(this->residual, *this->global_residual);
} else {
this->synchronizer->gather(this->residual);
}
return *this->global_residual;
} else {
return this->residual;
}
}
/* -------------------------------------------------------------------------- */
const Array<Real> & DOFManagerDefault::getResidual() const {
return this->residual;
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::setGlobalSolution(const Array<Real> & solution) {
if (this->synchronizer) {
if (this->synchronizer->getCommunicator().whoAmI() == 0) {
this->synchronizer->scatter(this->global_solution, solution);
} else {
this->synchronizer->scatter(this->global_solution);
}
} else {
AKANTU_DEBUG_ASSERT(solution.size() == this->global_solution.size(),
"Sequential call to this function needs the solution "
"to be the same size as the global_solution");
this->global_solution.copy(solution);
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) {
DOFManager::onNodesAdded(nodes_list, event);
if (this->synchronizer)
this->synchronizer->onNodesAdded(nodes_list);
}
/* -------------------------------------------------------------------------- */
std::pair<UInt, UInt>
DOFManagerDefault::updateNodalDOFs(const ID & dof_id,
const Array<UInt> & nodes_list) {
UInt nb_new_local_dofs, nb_new_pure_local;
std::tie(nb_new_local_dofs, nb_new_pure_local) =
DOFManager::updateNodalDOFs(dof_id, nodes_list);
auto & dof_data = this->getDOFDataTyped<DOFDataDefault>(dof_id);
updateDOFsData(dof_data, nb_new_local_dofs, nb_new_pure_local,
[&nodes_list](UInt pos) -> UInt { return nodes_list[pos]; });
return std::make_pair(nb_new_local_dofs, nb_new_pure_local);
}
/* -------------------------------------------------------------------------- */
void DOFManagerDefault::updateDOFsData(DOFDataDefault & dof_data,
UInt nb_new_local_dofs,
UInt nb_new_pure_local,
std::function<UInt(UInt)> getNode) {
auto prank = this->communicator.whoAmI();
auto psize = this->communicator.getNbProc();
// access the relevant data to update
const auto & support_type = dof_data.support_type;
GlobalDOFInfoDataAccessor data_accessor;
// resize all relevant arrays
this->residual.resize(this->local_system_size);
this->dofs_type.resize(this->local_system_size);
this->global_solution.resize(this->local_system_size);
this->global_blocked_dofs.resize(this->local_system_size);
this->previous_global_blocked_dofs.resize(this->local_system_size);
this->global_equation_number.resize(this->local_system_size);
for (auto & lumped_matrix : lumped_matrices)
lumped_matrix.second->resize(this->local_system_size);
dof_data.local_equation_number.reserve(
dof_data.local_equation_number.size() + nb_new_local_dofs);
// determine the first local/global dof id to use
Array<UInt> nb_dofs_per_proc(psize);
nb_dofs_per_proc(prank) = nb_new_pure_local;
this->communicator.allGather(nb_dofs_per_proc);
this->first_global_dof_id += std::accumulate(
nb_dofs_per_proc.begin(), nb_dofs_per_proc.begin() + prank, 0);
UInt first_dof_id = this->local_system_size - nb_new_local_dofs;
if (support_type == _dst_nodal) {
dof_data.associated_nodes.reserve(dof_data.associated_nodes.size() +
nb_new_local_dofs);
}
// update per dof info
for (UInt d = 0; d < nb_new_local_dofs; ++d) {
UInt local_eq_num = first_dof_id + d;
dof_data.local_equation_number.push_back(local_eq_num);
bool is_local_dof = true;
// determine the dof type
switch (support_type) {
case _dst_nodal: {
UInt node = getNode(d / dof_data.dof->getNbComponent());
this->dofs_type(local_eq_num) = this->mesh->getNodeType(node);
dof_data.associated_nodes.push_back(node);
is_local_dof = this->mesh->isLocalOrMasterNode(node);
if (is_local_dof) {
data_accessor.addDOFToNode(node, first_global_dof_id);
}
break;
}
case _dst_generic: {
this->dofs_type(local_eq_num) = _nt_normal;
break;
}
default: { AKANTU_EXCEPTION("This type of dofs is not handled yet."); }
}
// update global id for local dofs
if (is_local_dof) {
this->global_equation_number(local_eq_num) = this->first_global_dof_id;
this->global_to_local_mapping[this->first_global_dof_id] = local_eq_num;
++this->first_global_dof_id;
} else {
this->global_equation_number(local_eq_num) = 0;
}
}
// synchronize the global numbering for slaves
if (support_type == _dst_nodal && this->synchronizer) {
auto nb_dofs_per_node = dof_data.dof->getNbComponent();
auto & node_synchronizer = this->mesh->getNodeSynchronizer();
node_synchronizer.synchronizeOnce(data_accessor, _gst_size);
node_synchronizer.synchronizeOnce(data_accessor, _gst_update);
std::vector<UInt> counters(nb_new_local_dofs / nb_dofs_per_node);
for (UInt d = 0; d < nb_new_local_dofs; ++d) {
UInt local_eq_num = first_dof_id + d;
if (not this->isSlaveDOF(local_eq_num))
continue;
UInt node = d / nb_dofs_per_node;
UInt dof_count = counters[node]++;
node = getNode(node);
UInt global_dof_id = data_accessor.getNthDOFForNode(dof_count, node);
this->global_equation_number(local_eq_num) = global_dof_id;
this->global_to_local_mapping[global_dof_id] = local_eq_num;
}
}
}
} // namespace akantu
// LocalWords: dof dofs
diff --git a/src/model/dof_manager_default.hh b/src/model/dof_manager_default.hh
index 2cb8a89b8..6a70ac77f 100644
--- a/src/model/dof_manager_default.hh
+++ b/src/model/dof_manager_default.hh
@@ -1,360 +1,360 @@
/**
* @file dof_manager_default.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 11 14:06:18 2015
*
* @brief Default implementation of the dof manager
*
* @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 "dof_manager.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
#include <functional>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_MANAGER_DEFAULT_HH__
#define __AKANTU_DOF_MANAGER_DEFAULT_HH__
namespace akantu {
class SparseMatrixAIJ;
class NonLinearSolverDefault;
class TimeStepSolverDefault;
class DOFSynchronizer;
} // namespace akantu
namespace akantu {
class DOFManagerDefault : public DOFManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFManagerDefault(const ID & id = "dof_manager_default",
const MemoryID & memory_id = 0);
DOFManagerDefault(Mesh & mesh, const ID & id = "dof_manager_default",
const MemoryID & memory_id = 0);
- virtual ~DOFManagerDefault();
+ ~DOFManagerDefault() override;
protected:
struct DOFDataDefault : public DOFData {
explicit DOFDataDefault(const ID & dof_id);
/// associated node for _dst_nodal dofs only
Array<UInt> associated_nodes;
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
void registerDOFsInternal(const ID & dof_id, UInt nb_dofs,
UInt nb_pure_local_dofs);
public:
/// register an array of degree of freedom
void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type) override;
/// the dof as an implied type of _dst_nodal and is defined only on a subset
/// of nodes
void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & group_support) override;
/// Assemble an array to the global residual array
void assembleToResidual(const ID & dof_id,
const Array<Real> & array_to_assemble,
Real scale_factor = 1.) override;
/// Assemble an array to the global lumped matrix array
void assembleToLumpedMatrix(const ID & dof_id,
const Array<Real> & array_to_assemble,
const ID & lumped_mtx,
Real scale_factor = 1.) override;
/**
* Assemble elementary values to the global matrix. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
void assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id,
const Array<Real> & elementary_mat, const ElementType & type,
const GhostType & ghost_type, const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements) override;
/// multiply a vector by a matrix and assemble the result to the residual
void assembleMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) override;
/// multiply a vector by a lumped matrix and assemble the result to the
/// residual
void assembleLumpedMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) override;
/// assemble coupling terms between to dofs
void assemblePreassembledMatrix(const ID & dof_id_m, const ID & dof_id_n,
const ID & matrix_id,
const TermsToAssemble & terms) override;
protected:
/// Assemble an array to the global residual array
template <typename T>
void assembleToGlobalArray(const ID & dof_id,
const Array<T> & array_to_assemble,
Array<T> & global_array, T scale_factor);
public:
/// clear the residual
void clearResidual() override;
/// sets the matrix to 0
void clearMatrix(const ID & mtx) override;
/// sets the lumped matrix to 0
void clearLumpedMatrix(const ID & mtx) override;
/// update the global dofs vector
virtual void updateGlobalBlockedDofs();
/// apply boundary conditions to jacobian matrix
virtual void applyBoundary(const ID & matrix_id = "J");
// void getEquationsNumbers(const ID & dof_id,
// Array<UInt> & equation_numbers) override;
protected:
/// Get local part of an array corresponding to a given dofdata
template <typename T>
void getArrayPerDOFs(const ID & dof_id, const Array<T> & global_array,
Array<T> & local_array) const;
/// Get the part of the solution corresponding to the dof_id
void getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array) override;
/// fill a Vector with the equation numbers corresponding to the given
/// connectivity
inline void extractElementEquationNumber(
const Array<UInt> & equation_numbers, const Vector<UInt> & connectivity,
UInt nb_degree_of_freedom, Vector<UInt> & local_equation_number);
public:
/// extract a lumped matrix part corresponding to a given dof
void getLumpedMatrixPerDOFs(const ID & dof_id, const ID & lumped_mtx,
Array<Real> & lumped) override;
private:
/// Add a symmetric matrices to a symmetric sparse matrix
void addSymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<UInt> & equation_numbers, UInt max_size);
/// Add a unsymmetric matrices to a symmetric sparse matrix (i.e. cohesive
/// elements)
void addUnsymmetricElementalMatrixToSymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<UInt> & equation_numbers, UInt max_size);
/// Add a matrices to a unsymmetric sparse matrix
void addElementalMatrixToUnsymmetric(SparseMatrixAIJ & matrix,
const Matrix<Real> & element_mat,
const Vector<UInt> & equation_numbers,
UInt max_size);
void addToProfile(const ID & matrix_id, const ID & dof_id,
const ElementType & type, const GhostType & ghost_type);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler interface */
/* ------------------------------------------------------------------------ */
protected:
std::pair<UInt, UInt>
updateNodalDOFs(const ID & dof_id, const Array<UInt> & nodes_list) override;
private:
void updateDOFsData(DOFDataDefault & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local,
std::function<UInt(UInt)> getNode);
public:
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get an instance of a new SparseMatrix
SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) override;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) override;
/// Get the reference of an existing matrix
SparseMatrixAIJ & getMatrix(const ID & matrix_id);
/* ------------------------------------------------------------------------ */
/* Non Linear Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a non linear solver
NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & _non_linear_solver_type) override;
/* ------------------------------------------------------------------------ */
/* Time-Step Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a time step solver
TimeStepSolver &
getNewTimeStepSolver(const ID & id, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver) override;
/* ------------------------------------------------------------------------ */
/// Get the solution array
AKANTU_GET_MACRO_NOT_CONST(GlobalSolution, global_solution, Array<Real> &);
/// Set the global solution array
void setGlobalSolution(const Array<Real> & solution);
/// Get the global residual array across processors (SMP call)
const Array<Real> & getGlobalResidual();
/// Get the residual array
const Array<Real> & getResidual() const;
/// Get the blocked dofs array
AKANTU_GET_MACRO(GlobalBlockedDOFs, global_blocked_dofs, const Array<bool> &);
/// Get the blocked dofs array
AKANTU_GET_MACRO(PreviousGlobalBlockedDOFs, previous_global_blocked_dofs,
const Array<bool> &);
/// Get the location type of a given dof
inline bool isLocalOrMasterDOF(UInt local_dof_num);
/// Answer to the question is a dof a slave dof ?
inline bool isSlaveDOF(UInt local_dof_num);
/// get the equation numbers (in local numbering) corresponding to a dof ID
inline const Array<UInt> & getLocalEquationNumbers(const ID & dof_id) const;
/// tells if the dof manager knows about a global dof
bool hasGlobalEquationNumber(UInt global) const;
/// return the local index of the global equation number
inline UInt globalToLocalEquationNumber(UInt global) const;
/// converts local equation numbers to global equation numbers;
inline UInt localToGlobalEquationNumber(UInt local) const;
/// get the array of dof types (use only if you know what you do...)
inline Int getDOFType(UInt local_id) const;
/// get the array of dof types (use only if you know what you do...)
inline const Array<UInt> & getDOFsAssociatedNodes(const ID & dof_id) const;
/// access the internal dof_synchronizer
AKANTU_GET_MACRO_NOT_CONST(Synchronizer, *synchronizer, DOFSynchronizer &);
/// access the internal dof_synchronizer
bool hasSynchronizer() const { return synchronizer != nullptr; }
protected:
DOFData & getNewDOFData(const ID & dof_id) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
// using AIJMatrixMap = std::map<ID, std::unique_ptr<SparseMatrixAIJ>>;
// using DefaultNonLinearSolversMap =
// std::map<ID, std::unique_ptr<NonLinearSolverDefault>>;
// using DefaultTimeStepSolversMap =
// std::map<ID, std::unique_ptr<TimeStepSolverDefault>>;
using DOFToMatrixProfile =
std::map<std::pair<ID, ID>,
std::vector<std::pair<ElementType, GhostType>>>;
/// contains the the dofs that where added to the profile of a given matrix.
DOFToMatrixProfile matrix_profiled_dofs;
/// rhs to the system of equation corresponding to the residual linked to the
/// different dofs
Array<Real> residual;
/// rhs used only on root proc in case of parallel computing, this is the full
/// gathered rhs array
std::unique_ptr<Array<Real>> global_residual;
/// solution of the system of equation corresponding to the different dofs
Array<Real> global_solution;
/// blocked degree of freedom in the system equation corresponding to the
/// different dofs
Array<bool> global_blocked_dofs;
/// blocked degree of freedom in the system equation corresponding to the
/// different dofs
Array<bool> previous_global_blocked_dofs;
/// define the dofs type, local, shared, ghost
Array<Int> dofs_type;
/// Map of the different matrices stored in the dof manager
//AIJMatrixMap aij_matrices;
/// Map of the different time step solvers stored with there real type
//DefaultTimeStepSolversMap default_time_step_solver_map;
/// Memory cache, this is an array to keep the temporary memory needed for
/// some operations, it is meant to be resized or cleared when needed
Array<Real> data_cache;
/// Release at last apply boundary on jacobian
UInt jacobian_release;
/// equation number in global numbering
Array<UInt> global_equation_number;
using equation_numbers_map = std::unordered_map<UInt, UInt>;
/// dual information of global_equation_number
equation_numbers_map global_to_local_mapping;
/// accumulator to know what would be the next global id to use
UInt first_global_dof_id;
/// synchronizer to maintain coherency in dof fields
std::unique_ptr<DOFSynchronizer> synchronizer;
};
} // namespace akantu
#include "dof_manager_default_inline_impl.cc"
#endif /* __AKANTU_DOF_MANAGER_DEFAULT_HH__ */
diff --git a/src/model/dof_manager_inline_impl.cc b/src/model/dof_manager_inline_impl.cc
index 0a035af4a..d9dab0b49 100644
--- a/src/model/dof_manager_inline_impl.cc
+++ b/src/model/dof_manager_inline_impl.cc
@@ -1,154 +1,154 @@
/**
* @file dof_manager_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Aug 12 11:07:01 2015
*
* @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 "dof_manager.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_MANAGER_INLINE_IMPL_CC__
#define __AKANTU_DOF_MANAGER_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFs(const ID & dof_id) const {
DOFStorage::const_iterator it = this->dofs.find(dof_id);
return it != this->dofs.end();
}
/* -------------------------------------------------------------------------- */
inline DOFManager::DOFData & DOFManager::getDOFData(const ID & dof_id) {
DOFStorage::iterator it = this->dofs.find(dof_id);
if (it == this->dofs.end()) {
AKANTU_EXCEPTION("The dof " << dof_id << " does not exists in "
<< this->id);
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
const DOFManager::DOFData & DOFManager::getDOFData(const ID & dof_id) const {
DOFStorage::const_iterator it = this->dofs.find(dof_id);
if (it == this->dofs.end()) {
AKANTU_EXCEPTION("The dof " << dof_id << " does not exists in "
<< this->id);
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
const Array<UInt> & DOFManager::getEquationsNumbers(const ID & dof_id) const {
return getDOFData(dof_id).local_equation_number;
}
/* -------------------------------------------------------------------------- */
template <class _DOFData>
inline _DOFData & DOFManager::getDOFDataTyped(const ID & dof_id) {
return dynamic_cast<_DOFData &>(this->getDOFData(dof_id));
}
/* -------------------------------------------------------------------------- */
template <class _DOFData>
inline const _DOFData & DOFManager::getDOFDataTyped(const ID & dof_id) const {
return dynamic_cast<const _DOFData &>(this->getDOFData(dof_id));
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFs(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).dof);
}
/* -------------------------------------------------------------------------- */
inline DOFSupportType DOFManager::getSupportType(const ID & dofs_id) const {
return this->getDOFData(dofs_id).support_type;
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getPreviousDOFs(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).previous);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasPreviousDOFs(const ID & dofs_id) const {
- return (this->getDOFData(dofs_id).previous != NULL);
+ return (this->getDOFData(dofs_id).previous != nullptr);
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFsIncrement(const ID & dofs_id) {
return *(this->getDOFData(dofs_id).increment);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFsIncrement(const ID & dofs_id) const {
- return (this->getDOFData(dofs_id).increment != NULL);
+ return (this->getDOFData(dofs_id).increment != nullptr);
}
/* -------------------------------------------------------------------------- */
inline Array<Real> & DOFManager::getDOFsDerivatives(const ID & dofs_id,
UInt order) {
std::vector<Array<Real> *> & derivatives =
this->getDOFData(dofs_id).dof_derivatives;
- if ((order > derivatives.size()) || (derivatives[order - 1] == NULL))
+ if ((order > derivatives.size()) || (derivatives[order - 1] == nullptr))
AKANTU_EXCEPTION("No derivatives of order " << order << " present in "
<< this->id << " for dof "
<< dofs_id);
return *derivatives[order - 1];
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasDOFsDerivatives(const ID & dofs_id,
UInt order) const{
const std::vector<Array<Real> *> & derivatives =
this->getDOFData(dofs_id).dof_derivatives;
- return ((order < derivatives.size()) && (derivatives[order - 1] != NULL));
+ return ((order < derivatives.size()) && (derivatives[order - 1] != nullptr));
}
/* -------------------------------------------------------------------------- */
inline const Array<Real> & DOFManager::getSolution(const ID & dofs_id) const {
return this->getDOFData(dofs_id).solution;
}
/* -------------------------------------------------------------------------- */
inline const Array<bool> &
DOFManager::getBlockedDOFs(const ID & dofs_id) const {
return *(this->getDOFData(dofs_id).blocked_dofs);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManager::hasBlockedDOFs(const ID & dofs_id) const {
return (this->getDOFData(dofs_id).blocked_dofs != nullptr);
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_DOF_MANAGER_INLINE_IMPL_CC__ */
diff --git a/src/model/integration_scheme/integration_scheme.hh b/src/model/integration_scheme/integration_scheme.hh
index a13051f22..024313073 100644
--- a/src/model/integration_scheme/integration_scheme.hh
+++ b/src/model/integration_scheme/integration_scheme.hh
@@ -1,111 +1,111 @@
/**
* @file integration_scheme.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Sep 28 10:43:18 2015
*
* @brief This class is just a base class for the integration schemes
*
* @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 "aka_common.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTEGRATION_SCHEME_HH__
#define __AKANTU_INTEGRATION_SCHEME_HH__
namespace akantu {
class DOFManager;
}
namespace akantu {
class IntegrationScheme : public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
enum SolutionType {
_not_defined = -1,
_displacement = 0,
_temperature = 0,
_velocity = 1,
_temperature_rate = 1,
_acceleration = 2,
};
IntegrationScheme(DOFManager & dof_manager, const ID & dof_id, UInt order);
- virtual ~IntegrationScheme() = default;
+ ~IntegrationScheme() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// generic interface of a predictor
virtual void predictor(Real delta_t) = 0;
/// generic interface of a corrector
virtual void corrector(const SolutionType & type, Real delta_t) = 0;
/// assemble the jacobian matrix
virtual void assembleJacobian(const SolutionType & type, Real delta_t) = 0;
/// assemble the residual
virtual void assembleResidual(bool is_lumped) = 0;
/// returns a list of needed matrices
virtual std::vector<std::string> getNeededMatrixList() = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the order of the integration scheme
UInt getOrder() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// The underlying DOFManager
DOFManager & dof_manager;
/// The id of the dof treated by this integration scheme.
ID dof_id;
/// The order of the integrator
UInt order;
};
/* -------------------------------------------------------------------------- */
// std::ostream & operator<<(std::ostream & stream,
// const IntegrationScheme::SolutionType & type);
std::istream & operator>>(std::istream & stream,
IntegrationScheme::SolutionType & type);
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_INTEGRATION_SCHEME_HH__ */
diff --git a/src/model/integration_scheme/integration_scheme_2nd_order.hh b/src/model/integration_scheme/integration_scheme_2nd_order.hh
index 220fbe50b..d60ee5777 100644
--- a/src/model/integration_scheme/integration_scheme_2nd_order.hh
+++ b/src/model/integration_scheme/integration_scheme_2nd_order.hh
@@ -1,108 +1,108 @@
/**
* @file integration_scheme_2nd_order.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Oct 23 2015
*
* @brief Interface of the integrator of second order
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_array.hh"
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH__
#define __AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH__
namespace akantu {
class SparseMatrix;
}
namespace akantu {
class IntegrationScheme2ndOrder : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationScheme2ndOrder(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 2){};
- virtual ~IntegrationScheme2ndOrder() = default;
+ ~IntegrationScheme2ndOrder() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get list of needed matrices
std::vector<std::string> getNeededMatrixList() override;
/// generic interface of a predictor
void predictor(Real delta_t) override;
/// generic interface of a corrector
void corrector(const SolutionType & type, Real delta_t) override;
void assembleResidual(bool is_lumped) override;
protected:
/// generic interface of a predictor of 2nd order
virtual void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const = 0;
/// generic interface of a corrector of 2nd order
virtual void corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
virtual Real getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getVelocityCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // akantu
#include "newmark-beta.hh"
#endif /* __AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH__ */
diff --git a/src/model/integration_scheme/newmark-beta.hh b/src/model/integration_scheme/newmark-beta.hh
index 795e24125..7373c56a9 100644
--- a/src/model/integration_scheme/newmark-beta.hh
+++ b/src/model/integration_scheme/newmark-beta.hh
@@ -1,196 +1,196 @@
/**
* @file newmark-beta.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 05 2010
* @date last modification: Fri Oct 23 2015
*
* @brief implementation of the newmark-@f$\beta@f$ integration scheme. This
* implementation is taken from Méthodes numériques en mécanique des solides by
* Alain Curnier \note{ISBN: 2-88074-247-1}
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NEWMARK_BETA_HH__
#define __AKANTU_NEWMARK_BETA_HH__
/* -------------------------------------------------------------------------- */
#include "integration_scheme_2nd_order.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/**
* The three differentiate equations (dynamic and cinematic) are :
* @f{eqnarray*}{
* M \ddot{u}_{n+1} + C \dot{u}_{n+1} + K u_{n+1} &=& q_{n+1} \\
* u_{n+1} &=& u_{n} + (1 - \alpha) \Delta t \dot{u}_{n} + \alpha \Delta t
*\dot{u}_{n+1} + (1/2 - \alpha) \Delta t^2 \ddot{u}_n \\
* \dot{u}_{n+1} &=& \dot{u}_{n} + (1 - \beta) \Delta t \ddot{u}_{n} + \beta
*\Delta t \ddot{u}_{n+1}
* @f}
*
* Predictor:
* @f{eqnarray*}{
* u^{0}_{n+1} &=& u_{n} + \Delta t \dot{u}_n + \frac{\Delta t^2}{2}
*\ddot{u}_n \\
* \dot{u}^{0}_{n+1} &=& \dot{u}_{n} + \Delta t \ddot{u}_{n} \\
* \ddot{u}^{0}_{n+1} &=& \ddot{u}_{n}
* @f}
*
* Solve :
* @f[ (c M + d C + e K^i_{n+1}) w = = q_{n+1} - f^i_{n+1} - C \dot{u}^i_{n+1}
*- M \ddot{u}^i_{n+1} @f]
*
* Corrector :
* @f{eqnarray*}{
* \ddot{u}^{i+1}_{n+1} &=& \ddot{u}^{i}_{n+1} + c w \\
* \dot{u}^{i+1}_{n+1} &=& \dot{u}^{i}_{n+1} + d w \\
* u^{i+1}_{n+1} &=& u^{i}_{n+1} + e w
* @f}
*
* c, d and e are parameters depending on the method used to solve the equations
*@n
* For acceleration : @f$ w = \delta \ddot{u}, e = \alpha \beta \Delta t^2, d =
*\beta \Delta t, c = 1 @f$ @n
* For velocity : @f$ w = \delta \dot{u}, e = 1/\beta \Delta t, d =
*1, c = \alpha \Delta t @f$ @n
* For displacement : @f$ w = \delta u, e = 1, d =
*1/\alpha \Delta t, c = 1/\alpha \beta \Delta t^2 @f$
*/
class NewmarkBeta : public IntegrationScheme2ndOrder {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NewmarkBeta(DOFManager & dof_manager, const ID & dof_id, Real alpha = 0.,
Real beta = 0.);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const override;
void corrector(const SolutionType & type, Real delta_t, Array<Real> & u,
Array<Real> & u_dot, Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const override;
void assembleJacobian(const SolutionType & type, Real delta_t) override;
public:
Real getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const override;
Real getVelocityCoefficient(const SolutionType & type,
Real delta_t) const override;
Real getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const override;
private:
template <SolutionType type>
void allCorrector(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot, const Array<bool> & blocked_dofs,
const Array<Real> & delta) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Beta, beta, Real);
AKANTU_GET_MACRO(Alpha, alpha, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the @f$\beta@f$ parameter
Real beta;
/// the @f$\alpha@f$ parameter
Real alpha;
Real k;
Real h;
/// last release of M matrix
UInt m_release;
/// last release of K matrix
UInt k_release;
/// last release of C matrix
UInt c_release;
};
/**
* central difference method (explicit)
* undamped stability condition :
* @f$ \Delta t = \alpha \Delta t_{crit} = \frac{2}{\omega_{max}} \leq \min_{e}
*\frac{l_e}{c_e}
*
*/
class CentralDifference : public NewmarkBeta {
public:
CentralDifference(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 0., 1. / 2.){};
- std::vector<std::string> getNeededMatrixList() { return {"M", "C"}; }
+ std::vector<std::string> getNeededMatrixList() override { return {"M", "C"}; }
};
//#include "integration_scheme/central_difference.hh"
/// undamped trapezoidal rule (implicit)
class TrapezoidalRule2 : public NewmarkBeta {
public:
TrapezoidalRule2(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 2., 1. / 2.){};
};
/// Fox-Goodwin rule (implicit)
class FoxGoodwin : public NewmarkBeta {
public:
FoxGoodwin(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 6., 1. / 2.){};
};
/// Linear acceleration (implicit)
class LinearAceleration : public NewmarkBeta {
public:
LinearAceleration(DOFManager & dof_manager, const ID & dof_id)
: NewmarkBeta(dof_manager, dof_id, 1. / 3., 1. / 2.){};
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_NEWMARK_BETA_HH__ */
diff --git a/src/model/model.cc b/src/model/model.cc
index 1a17d7ed9..a9ffb9eb7 100644
--- a/src/model/model.cc
+++ b/src/model/model.cc
@@ -1,350 +1,350 @@
/**
* @file model.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Oct 03 2011
* @date last modification: Thu Nov 19 2015
*
* @brief implementation of model common parts
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "model.hh"
#include "communicator.hh"
#include "data_accessor.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Model::Model(Mesh & mesh, UInt dim, const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), ModelSolver(mesh, id, memory_id), mesh(mesh),
spatial_dimension(dim == _all_dimensions ? mesh.getSpatialDimension()
: dim),
is_pbc_slave_node(0, 1, "is_pbc_slave_node"), parser(getStaticParser()) {
AKANTU_DEBUG_IN();
this->mesh.registerEventHandler(*this, _ehp_model);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Model::~Model() = default;
/* -------------------------------------------------------------------------- */
// void Model::setParser(Parser & parser) { this->parser = &parser; }
/* -------------------------------------------------------------------------- */
void Model::initFull(const ModelOptions & options) {
AKANTU_DEBUG_IN();
method = options.analysis_method;
if (!this->hasDefaultSolver()) {
this->initNewSolver(this->method);
}
initModel();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Model::initNewSolver(const AnalysisMethod & method) {
ID solver_name;
TimeStepSolverType tss_type;
std::tie(solver_name, tss_type) = this->getDefaultSolverID(method);
if (!this->hasSolver(solver_name)) {
ModelSolverOptions options = this->getDefaultSolverOptions(tss_type);
this->getNewSolver(solver_name, tss_type, options.non_linear_solver_type);
this->setIntegrationScheme(solver_name, "displacement",
options.integration_scheme_type["displacement"],
options.solution_type["displacement"]);
}
this->method = method;
this->setDefaultSolver(solver_name);
}
/* -------------------------------------------------------------------------- */
void Model::initPBC() {
std::map<UInt, UInt>::iterator it = pbc_pair.begin();
std::map<UInt, UInt>::iterator end = pbc_pair.end();
is_pbc_slave_node.resize(mesh.getNbNodes());
#ifndef AKANTU_NDEBUG
Array<Real>::const_vector_iterator coord_it =
mesh.getNodes().begin(this->spatial_dimension);
#endif
while (it != end) {
UInt i1 = (*it).first;
is_pbc_slave_node(i1) = true;
#ifndef AKANTU_NDEBUG
UInt i2 = (*it).second;
UInt slave = mesh.isDistributed() ? mesh.getGlobalNodesIds()(i1) : i1;
UInt master = mesh.isDistributed() ? mesh.getGlobalNodesIds()(i2) : i2;
AKANTU_DEBUG_INFO("pairing " << slave << " (" << Vector<Real>(coord_it[i1])
<< ") with " << master << " ("
<< Vector<Real>(coord_it[i2]) << ")");
#endif
++it;
}
}
/* -------------------------------------------------------------------------- */
void Model::dumpGroup(const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.dump();
}
/* -------------------------------------------------------------------------- */
void Model::dumpGroup(const std::string & group_name,
const std::string & dumper_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.dump(dumper_name);
}
/* -------------------------------------------------------------------------- */
void Model::dumpGroup() {
GroupManager::element_group_iterator bit = mesh.element_group_begin();
GroupManager::element_group_iterator bend = mesh.element_group_end();
for (; bit != bend; ++bit) {
bit->second->dump();
}
}
/* -------------------------------------------------------------------------- */
void Model::setGroupDirectory(const std::string & directory) {
GroupManager::element_group_iterator bit = mesh.element_group_begin();
GroupManager::element_group_iterator bend = mesh.element_group_end();
for (; bit != bend; ++bit) {
bit->second->setDirectory(directory);
}
}
/* -------------------------------------------------------------------------- */
void Model::setGroupDirectory(const std::string & directory,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.setDirectory(directory);
}
/* -------------------------------------------------------------------------- */
void Model::setGroupBaseName(const std::string & basename,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.setBaseName(basename);
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Model::getGroupDumper(const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
return group.getDumper();
}
/* -------------------------------------------------------------------------- */
// DUMPER stuff
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & field_id,
dumper::Field * field,
DumperIOHelper & dumper) {
#ifdef AKANTU_USE_IOHELPER
dumper.registerField(field_id, field);
#endif
}
/* -------------------------------------------------------------------------- */
void Model::addDumpField(const std::string & field_id) {
this->addDumpFieldToDumper(mesh.getDefaultDumperName(), field_id);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldVector(const std::string & field_id) {
this->addDumpFieldVectorToDumper(mesh.getDefaultDumperName(), field_id);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldTensor(const std::string & field_id) {
this->addDumpFieldTensorToDumper(mesh.getDefaultDumperName(), field_id);
}
/* -------------------------------------------------------------------------- */
void Model::setBaseName(const std::string & field_id) {
mesh.setBaseName(field_id);
}
/* -------------------------------------------------------------------------- */
void Model::setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
mesh.setBaseNameToDumper(dumper_name, basename);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, "all", _ek_regular,
false);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupField(const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
this->addDumpGroupFieldToDumper(group.getDefaultDumperName(), field_id,
group_name, _ek_regular, false);
}
/* -------------------------------------------------------------------------- */
void Model::removeDumpGroupField(const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
this->removeDumpGroupFieldFromDumper(group.getDefaultDumperName(), field_id,
group_name);
}
/* -------------------------------------------------------------------------- */
void Model::removeDumpGroupFieldFromDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
group.removeDumpFieldFromDumper(dumper_name, field_id);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, "all", _ek_regular, 3);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldVector(const std::string & field_id,
const std::string & group_name) {
ElementGroup & group = mesh.getElementGroup(group_name);
this->addDumpGroupFieldVectorToDumper(group.getDefaultDumperName(), field_id,
group_name);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, group_name,
_ek_regular, true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, "all", _ek_regular,
true);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind,
bool padding_flag) {
this->addDumpGroupFieldToDumper(dumper_name, field_id, group_name,
this->spatial_dimension, element_kind,
padding_flag);
}
/* -------------------------------------------------------------------------- */
void Model::addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
UInt spatial_dimension,
const ElementKind & element_kind,
bool padding_flag) {
#ifdef AKANTU_USE_IOHELPER
- dumper::Field * field = NULL;
+ dumper::Field * field = nullptr;
if (!field)
field = this->createNodalFieldReal(field_id, group_name, padding_flag);
if (!field)
field = this->createNodalFieldUInt(field_id, group_name, padding_flag);
if (!field)
field = this->createNodalFieldBool(field_id, group_name, padding_flag);
if (!field)
field = this->createElementalField(field_id, group_name, padding_flag,
spatial_dimension, element_kind);
if (!field)
field = this->mesh.createFieldFromAttachedData<UInt>(field_id, group_name,
element_kind);
if (!field)
field = this->mesh.createFieldFromAttachedData<Real>(field_id, group_name,
element_kind);
if (!field)
AKANTU_DEBUG_WARNING("No field could be found based on name: " << field_id);
if (field) {
DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name, group_name);
this->addDumpGroupFieldToDumper(field_id, field, dumper);
}
#endif
}
/* -------------------------------------------------------------------------- */
void Model::dump() { mesh.dump(); }
/* -------------------------------------------------------------------------- */
void Model::setDirectory(const std::string & directory) {
mesh.setDirectory(directory);
}
/* -------------------------------------------------------------------------- */
void Model::setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
mesh.setDirectoryToDumper(dumper_name, directory);
}
/* -------------------------------------------------------------------------- */
void Model::setTextModeToDumper() { mesh.setTextModeToDumper(); }
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/model.hh b/src/model/model.hh
index 8036a5bef..35a359e98 100644
--- a/src/model/model.hh
+++ b/src/model/model.hh
@@ -1,349 +1,349 @@
/**
* @file model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Oct 16 2015
*
* @brief Interface of a model
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "aka_memory.hh"
#include "fe_engine.hh"
#include "mesh.hh"
#include "model_solver.hh"
#include "aka_named_argument.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MODEL_HH__
#define __AKANTU_MODEL_HH__
namespace akantu {
class SynchronizerRegistry;
class Parser;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
namespace {
DECLARE_NAMED_ARGUMENT(analysis_method);
}
struct ModelOptions {
explicit ModelOptions(AnalysisMethod analysis_method = _static)
: analysis_method(analysis_method) {}
template <typename... pack>
ModelOptions(use_named_args_t, pack &&... _pack)
: ModelOptions(OPTIONAL_NAMED_ARG(analysis_method, _static)) {}
virtual ~ModelOptions() = default;
AnalysisMethod analysis_method;
};
class DumperIOHelper;
class Model : public Memory, public ModelSolver, public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Model(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const ID & id = "model", const MemoryID & memory_id = 0);
- virtual ~Model();
+ ~Model() override;
typedef std::map<std::string, std::unique_ptr<FEEngine>> FEEngineMap;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void initFull(const ModelOptions & options);
template <typename P, typename T, typename... pack>
void initFull(named_argument::param_t<P, T &&> && first, pack &&... _pack) {
this->initFull(ModelOptions{use_named_args, first, _pack...});
}
/// initialize a new solver if needed
void initNewSolver(const AnalysisMethod & method);
protected:
/// get some default values for derived classes
virtual std::tuple<ID, TimeStepSolverType> getDefaultSolverID(const AnalysisMethod & method) = 0;
virtual void initModel() = 0;
// /// change local equation number so that PBC is assembled properly
// void changeLocalEquationNumberForPBC(std::map<UInt, UInt> & pbc_pair,
// UInt dimension);
/// function to print the containt of the class
- virtual void printself(std::ostream &, int = 0) const {};
+ void printself(std::ostream &, int = 0) const override{};
// /// initialize the model for PBC
// void setPBC(UInt x, UInt y, UInt z);
// void setPBC(SurfacePairList & surface_pairs);
public:
virtual void initPBC();
/// set the parser to use
//void setParser(Parser & parser);
/* ------------------------------------------------------------------------ */
/* Access to the dumpable interface of the boundaries */
/* ------------------------------------------------------------------------ */
/// Dump the data for a given group
void dumpGroup(const std::string & group_name);
void dumpGroup(const std::string & group_name,
const std::string & dumper_name);
/// Dump the data for all boundaries
void dumpGroup();
/// Set the directory for a given group
void setGroupDirectory(const std::string & directory,
const std::string & group_name);
/// Set the directory for all boundaries
void setGroupDirectory(const std::string & directory);
/// Set the base name for a given group
void setGroupBaseName(const std::string & basename,
const std::string & group_name);
/// Get the internal dumper of a given group
DumperIOHelper & getGroupDumper(const std::string & group_name);
/* ------------------------------------------------------------------------ */
/* Function for non local capabilities */
/* ------------------------------------------------------------------------ */
virtual void updateDataForNonLocalCriterion(__attribute__((unused))
ElementTypeMapReal & criterion) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
protected:
template <typename T>
void allocNodalField(Array<T> *& array, UInt nb_component, const ID & name);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get id of model
AKANTU_GET_MACRO(ID, id, const ID)
/// get the number of surfaces
AKANTU_GET_MACRO(Mesh, mesh, Mesh &)
/// synchronize the boundary in case of parallel run
virtual void synchronizeBoundaries(){};
/// return the fem object associated with a provided name
inline FEEngine & getFEEngine(const ID & name = "") const;
/// return the fem boundary object associated with a provided name
virtual FEEngine & getFEEngineBoundary(const ID & name = "");
/// register a fem object associated with name
template <typename FEEngineClass>
inline void registerFEEngineObject(const std::string & name, Mesh & mesh,
UInt spatial_dimension);
/// unregister a fem object associated with name
inline void unRegisterFEEngineObject(const std::string & name);
/// return the synchronizer registry
SynchronizerRegistry & getSynchronizerRegistry();
/// return the fem object associated with a provided name
template <typename FEEngineClass>
inline FEEngineClass & getFEEngineClass(std::string name = "") const;
/// return the fem boundary object associated with a provided name
template <typename FEEngineClass>
inline FEEngineClass & getFEEngineClassBoundary(std::string name = "");
/// get the pbc pairs
std::map<UInt, UInt> & getPBCPairs() { return pbc_pair; };
/// returns if node is slave in pbc
inline bool isPBCSlaveNode(const UInt) const {
throw;
return false; /* TODO repair PBC*/
}
/// returns the array of pbc slave nodes (boolean information)
AKANTU_GET_MACRO(IsPBCSlaveNode, is_pbc_slave_node, const Array<bool> &)
/// Get the type of analysis method used
AKANTU_GET_MACRO(AnalysisMethod, method, AnalysisMethod);
/* ------------------------------------------------------------------------ */
/* Pack and unpack helper functions */
/* ------------------------------------------------------------------------ */
public:
inline UInt getNbIntegrationPoints(const Array<Element> & elements,
const ID & fem_id = ID()) const;
/* ------------------------------------------------------------------------ */
/* Dumpable interface (kept for convenience) and dumper relative functions */
/* ------------------------------------------------------------------------ */
void setTextModeToDumper();
virtual void addDumpGroupFieldToDumper(const std::string & field_id,
dumper::Field * field,
DumperIOHelper & dumper);
virtual void addDumpField(const std::string & field_id);
virtual void addDumpFieldVector(const std::string & field_id);
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldTensor(const std::string & field_id);
virtual void setBaseName(const std::string & basename);
virtual void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename);
virtual void addDumpGroupField(const std::string & field_id,
const std::string & group_name);
virtual void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind,
bool padding_flag);
virtual void addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
UInt spatial_dimension,
const ElementKind & element_kind,
bool padding_flag);
virtual void removeDumpGroupField(const std::string & field_id,
const std::string & group_name);
virtual void removeDumpGroupFieldFromDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name);
virtual void addDumpGroupFieldVector(const std::string & field_id,
const std::string & group_name);
virtual void addDumpGroupFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name);
virtual dumper::Field *
createNodalFieldReal(__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
- return NULL;
+ return nullptr;
}
virtual dumper::Field *
createNodalFieldUInt(__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
- return NULL;
+ return nullptr;
}
virtual dumper::Field *
createNodalFieldBool(__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
- return NULL;
+ return nullptr;
}
virtual dumper::Field *
createElementalField(__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag,
__attribute__((unused)) const UInt & spatial_dimension,
__attribute__((unused)) const ElementKind & kind) {
- return NULL;
+ return nullptr;
}
void setDirectory(const std::string & directory);
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory);
virtual void dump();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
friend std::ostream & operator<<(std::ostream &, const Model &);
/// analysis method check the list in akantu::AnalysisMethod
AnalysisMethod method;
/// Mesh
Mesh & mesh;
/// Spatial dimension of the problem
UInt spatial_dimension;
/// the main fem object present in all models
FEEngineMap fems;
/// the fem object present in all models for boundaries
FEEngineMap fems_boundary;
/// default fem object
std::string default_fem;
/// pbc pairs
std::map<UInt, UInt> pbc_pair;
/// flag per node to know is pbc slave
Array<bool> is_pbc_slave_node;
/// parser to the pointer to use
Parser & parser;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream, const Model & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "model_inline_impl.cc"
#endif /* __AKANTU_MODEL_HH__ */
diff --git a/src/model/model_inline_impl.cc b/src/model/model_inline_impl.cc
index 9d5568242..ef491704e 100644
--- a/src/model/model_inline_impl.cc
+++ b/src/model/model_inline_impl.cc
@@ -1,215 +1,215 @@
/**
* @file model_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 25 2010
* @date last modification: Wed Nov 11 2015
*
* @brief inline implementation of the model class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MODEL_INLINE_IMPL_CC__
#define __AKANTU_MODEL_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline FEEngineClass & Model::getFEEngineClassBoundary(std::string name) {
AKANTU_DEBUG_IN();
if (name == "")
name = default_fem;
FEEngineMap::const_iterator it_boun = fems_boundary.find(name);
if (it_boun == fems_boundary.end()) {
AKANTU_DEBUG_INFO("Creating FEEngine boundary " << name);
FEEngineMap::const_iterator it = fems.find(name);
AKANTU_DEBUG_ASSERT(it != fems.end(), "The FEEngine "
<< name << " is not registered");
UInt spatial_dimension = it->second->getElementDimension();
std::stringstream sstr;
sstr << id << ":fem_boundary:" << name;
fems_boundary[name] = std::make_unique<FEEngineClass>(
it->second->getMesh(), spatial_dimension - 1, sstr.str(), memory_id);
}
AKANTU_DEBUG_OUT();
return dynamic_cast<FEEngineClass &>(*fems_boundary[name]);
}
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline FEEngineClass & Model::getFEEngineClass(std::string name) const {
AKANTU_DEBUG_IN();
if (name == "")
name = default_fem;
FEEngineMap::const_iterator it = fems.find(name);
AKANTU_DEBUG_ASSERT(it != fems.end(), "The FEEngine "
<< name << " is not registered");
AKANTU_DEBUG_OUT();
return dynamic_cast<FEEngineClass &>(*(it->second));
}
/* -------------------------------------------------------------------------- */
inline void Model::unRegisterFEEngineObject(const std::string & name) {
FEEngineMap::iterator it = fems.find(name);
AKANTU_DEBUG_ASSERT(it != fems.end(), "FEEngine object with name "
<< name << " was not found");
fems.erase(it);
if (!fems.empty())
default_fem = (*fems.begin()).first;
}
/* -------------------------------------------------------------------------- */
template <typename FEEngineClass>
inline void Model::registerFEEngineObject(const std::string & name, Mesh & mesh,
UInt spatial_dimension) {
if (fems.size() == 0)
default_fem = name;
#ifndef AKANTU_NDEBUG
FEEngineMap::iterator it = fems.find(name);
AKANTU_DEBUG_ASSERT(it == fems.end(), "FEEngine object with name "
<< name << " was already created");
#endif
std::stringstream sstr;
sstr << id << ":fem:" << name << memory_id;
fems[name] = std::make_unique<FEEngineClass>(mesh, spatial_dimension, sstr.str(), memory_id);
}
/* -------------------------------------------------------------------------- */
inline FEEngine & Model::getFEEngine(const ID & name) const {
AKANTU_DEBUG_IN();
ID tmp_name = name;
if (name == "")
tmp_name = default_fem;
FEEngineMap::const_iterator it = fems.find(tmp_name);
AKANTU_DEBUG_ASSERT(it != fems.end(),
"The FEEngine " << tmp_name << " is not registered");
AKANTU_DEBUG_OUT();
return *(it->second);\
}
/* -------------------------------------------------------------------------- */
inline FEEngine & Model::getFEEngineBoundary(const ID & name) {
AKANTU_DEBUG_IN();
ID tmp_name = name;
if (name == "")
tmp_name = default_fem;
FEEngineMap::const_iterator it = fems_boundary.find(tmp_name);
AKANTU_DEBUG_ASSERT(it != fems_boundary.end(), "The FEEngine boundary "
<< tmp_name
<< " is not registered");
- AKANTU_DEBUG_ASSERT(it->second != NULL, "The FEEngine boundary "
- << tmp_name
- << " was not created");
+ AKANTU_DEBUG_ASSERT(it->second != nullptr, "The FEEngine boundary "
+ << tmp_name
+ << " was not created");
AKANTU_DEBUG_OUT();
return *(it->second);
}
// /* --------------------------------------------------------------------------
// */
// /// @todo : should merge with a single function which handles local and
// global
// inline void Model::changeLocalEquationNumberForPBC(std::map<UInt,UInt> &
// pbc_pair,
// UInt dimension){
// for (std::map<UInt,UInt>::iterator it = pbc_pair.begin();
// it != pbc_pair.end();++it) {
// Int node_master = (*it).second;
// Int node_slave = (*it).first;
// for (UInt i = 0; i < dimension; ++i) {
// (*dof_synchronizer->getLocalDOFEquationNumbersPointer())
// (node_slave*dimension+i) = dimension*node_master+i;
// (*dof_synchronizer->getGlobalDOFEquationNumbersPointer())
// (node_slave*dimension+i) = dimension*node_master+i;
// }
// }
// }
// /* --------------------------------------------------------------------------
// */
// inline bool Model::isPBCSlaveNode(const UInt node) const {
// // if no pbc is defined, is_pbc_slave_node is of size zero
// if (is_pbc_slave_node.size() == 0)
// return false;
// else
// return is_pbc_slave_node(node);
// }
/* -------------------------------------------------------------------------- */
template <typename T>
void Model::allocNodalField(Array<T> *& array, UInt nb_component, const ID & name) {
if (array == nullptr) {
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_disp;
sstr_disp << id << ":" << name;
array =
&(alloc<T>(sstr_disp.str(), nb_nodes, nb_component, T()));
}
}
/* -------------------------------------------------------------------------- */
inline UInt Model::getNbIntegrationPoints(const Array<Element> & elements,
const ID & fem_id) const {
UInt nb_quad = 0;
Array<Element>::const_iterator<Element> it = elements.begin();
Array<Element>::const_iterator<Element> end = elements.end();
for (; it != end; ++it) {
const Element & el = *it;
nb_quad +=
getFEEngine(fem_id).getNbIntegrationPoints(el.type, el.ghost_type);
}
return nb_quad;
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_MODEL_INLINE_IMPL_CC__ */
diff --git a/src/model/model_solver.cc b/src/model/model_solver.cc
index 678ae42cb..1225ea251 100644
--- a/src/model/model_solver.cc
+++ b/src/model/model_solver.cc
@@ -1,359 +1,359 @@
/**
* @file model_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Aug 12 13:31:56 2015
*
* @brief Implementation of ModelSolver
*
* @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 "model_solver.hh"
#include "dof_manager.hh"
#include "dof_manager_default.hh"
#include "mesh.hh"
#include "non_linear_solver.hh"
#include "time_step_solver.hh"
#if defined(AKANTU_USE_PETSC)
#include "dof_manager_petsc.hh"
#endif
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
ModelSolver::ModelSolver(Mesh & mesh, const ID & id, UInt memory_id)
: Parsable(_st_model_solver, id), SolverCallback(), parent_id(id),
- parent_memory_id(memory_id), mesh(mesh), dof_manager(NULL),
+ parent_memory_id(memory_id), mesh(mesh), dof_manager(nullptr),
default_solver_id("") {}
/* -------------------------------------------------------------------------- */
ModelSolver::~ModelSolver() { delete this->dof_manager; }
/* -------------------------------------------------------------------------- */
void ModelSolver::initDOFManager() {
std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
sub_sect = getStaticParser().getSubSections(_st_model_solver);
// default without external solver activated at compilation same as mumps that
// is the historical solver but with only the lumped solver
ID solver_type = "explicit";
#if defined(AKANTU_USE_MUMPS)
solver_type = "mumps";
#elif defined(AKANTU_USE_PETSC)
solver_type = "petsc";
#endif
- const ParserSection * section = NULL;
+ const ParserSection * section = nullptr;
Parser::const_section_iterator it;
- for (it = sub_sect.first; it != sub_sect.second && section == NULL; ++it) {
+ for (it = sub_sect.first; it != sub_sect.second && section == nullptr; ++it) {
if (it->getName() == this->parent_id) {
section = &(*it);
solver_type = section->getOption(solver_type);
}
}
if (section) {
this->initDOFManager(*section, solver_type);
} else {
this->initDOFManager(solver_type);
}
}
/* -------------------------------------------------------------------------- */
void ModelSolver::initDOFManager(const ID & solver_type) {
if (solver_type == "explicit") {
ID id = this->parent_id + ":dof_manager_default";
this->dof_manager = new DOFManagerDefault(mesh, id, this->parent_memory_id);
} else if (solver_type == "petsc") {
#if defined(AKANTU_USE_PETSC)
ID id = this->parent_id + ":dof_manager_petsc";
this->dof_manager = new DOFManagerPETSc(mesh, id, this->parent_memory_id);
#else
AKANTU_EXCEPTION(
"To use PETSc you have to activate it in the compilations options");
#endif
} else if (solver_type == "mumps") {
#if defined(AKANTU_USE_MUMPS)
ID id = this->parent_id + ":dof_manager_default";
this->dof_manager = new DOFManagerDefault(mesh, id, this->parent_memory_id);
#else
AKANTU_EXCEPTION(
"To use MUMPS you have to activate it in the compilations options");
#endif
} else {
AKANTU_EXCEPTION(
"To use the solver "
<< solver_type
<< " you will have to code it. This is an unknown solver type.");
}
this->setDOFManager(*this->dof_manager);
}
/* -------------------------------------------------------------------------- */
template <typename T> static T getOptionToType(const std::string & opt_str) {
std::stringstream sstr(opt_str);
T opt;
sstr >> opt;
return opt;
}
/* -------------------------------------------------------------------------- */
void ModelSolver::initDOFManager(const ParserSection & section,
const ID & solver_type) {
this->initDOFManager(solver_type);
std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
sub_sect = section.getSubSections(_st_time_step_solver);
Parser::const_section_iterator it;
for (it = sub_sect.first; it != sub_sect.second; ++it) {
ID solver_id = it->getName();
// std::string str = it->getOption();
TimeStepSolverType tss_type =
it->getParameter("type", this->getDefaultSolverType());
ModelSolverOptions tss_options = this->getDefaultSolverOptions(tss_type);
std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
sub_solvers_sect = it->getSubSections(_st_non_linear_solver);
Parser::const_section_iterator sub_it;
UInt nb_non_linear_solver_section =
it->getNbSubSections(_st_non_linear_solver);
NonLinearSolverType nls_type = tss_options.non_linear_solver_type;
if (nb_non_linear_solver_section == 1) {
const ParserSection & nls_section = *(sub_solvers_sect.first);
nls_type = getOptionToType<NonLinearSolverType>(nls_section.getName());
} else if (nb_non_linear_solver_section > 0) {
AKANTU_EXCEPTION("More than one non linear solver are provided for the "
"time step solver "
<< solver_id);
}
this->getNewSolver(solver_id, tss_type, nls_type);
if (nb_non_linear_solver_section == 1) {
const ParserSection & nls_section = *(sub_solvers_sect.first);
this->dof_manager->getNonLinearSolver(solver_id).parseSection(
nls_section);
}
std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
sub_integrator_sect = it->getSubSections(_st_integration_scheme);
for (sub_it = sub_integrator_sect.first;
sub_it != sub_integrator_sect.second; ++sub_it) {
const ParserSection & is_section = *sub_it;
const ID & dof_id = is_section.getName();
IntegrationSchemeType it_type = is_section.getParameter(
"type", tss_options.integration_scheme_type[dof_id]);
IntegrationScheme::SolutionType s_type = is_section.getParameter(
"solution_type", tss_options.solution_type[dof_id]);
this->setIntegrationScheme(solver_id, dof_id, it_type, s_type);
}
std::map<ID, IntegrationSchemeType>::const_iterator it =
tss_options.integration_scheme_type.begin();
std::map<ID, IntegrationSchemeType>::const_iterator end =
tss_options.integration_scheme_type.end();
for (; it != end; ++it) {
if (!this->hasIntegrationScheme(solver_id, it->first)) {
this->setIntegrationScheme(solver_id, it->first, it->second,
tss_options.solution_type[it->first]);
}
}
}
if (section.hasParameter("default_solver")) {
ID default_solver = section.getParameter("default_solver");
this->setDefaultSolver(default_solver);
}
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & ModelSolver::getSolver(const ID & solver_id) {
ID tmp_solver_id = solver_id;
if (tmp_solver_id == "")
tmp_solver_id = this->default_solver_id;
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(tmp_solver_id);
return tss;
}
/* -------------------------------------------------------------------------- */
const TimeStepSolver & ModelSolver::getSolver(const ID & solver_id) const {
ID tmp_solver_id = solver_id;
if (solver_id == "")
tmp_solver_id = this->default_solver_id;
const TimeStepSolver & tss =
this->dof_manager->getTimeStepSolver(tmp_solver_id);
return tss;
}
/* -------------------------------------------------------------------------- */
TimeStepSolver & ModelSolver::getTimeStepSolver(const ID & solver_id) {
return this->getSolver(solver_id);
}
/* -------------------------------------------------------------------------- */
const TimeStepSolver &
ModelSolver::getTimeStepSolver(const ID & solver_id) const {
return this->getSolver(solver_id);
}
/* -------------------------------------------------------------------------- */
NonLinearSolver & ModelSolver::getNonLinearSolver(const ID & solver_id) {
return this->getSolver(solver_id).getNonLinearSolver();
}
/* -------------------------------------------------------------------------- */
const NonLinearSolver &
ModelSolver::getNonLinearSolver(const ID & solver_id) const {
return this->getSolver(solver_id).getNonLinearSolver();
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasSolver(const ID & solver_id) const {
ID tmp_solver_id = solver_id;
if (solver_id == "")
tmp_solver_id = this->default_solver_id;
return this->dof_manager->hasTimeStepSolver(tmp_solver_id);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setDefaultSolver(const ID & solver_id) {
AKANTU_DEBUG_ASSERT(
this->hasSolver(solver_id),
"Cannot set the default solver to a solver that does not exists");
this->default_solver_id = solver_id;
}
/* -------------------------------------------------------------------------- */
void ModelSolver::solveStep(const ID & solver_id) {
AKANTU_DEBUG_IN();
TimeStepSolver & tss = this->getSolver(solver_id);
// make one non linear solve
tss.solveStep(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ModelSolver::getNewSolver(const ID & solver_id,
TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) {
if (this->default_solver_id == "") {
this->default_solver_id = solver_id;
}
if (non_linear_solver_type == _nls_auto) {
switch (time_step_solver_type) {
case _tsst_dynamic:
case _tsst_static:
non_linear_solver_type = _nls_newton_raphson;
break;
case _tsst_dynamic_lumped:
non_linear_solver_type = _nls_lumped;
break;
case _tsst_not_defined:
AKANTU_EXCEPTION(time_step_solver_type
<< " is not a valid time step solver type");
break;
}
}
this->initSolver(time_step_solver_type, non_linear_solver_type);
NonLinearSolver & nls = this->dof_manager->getNewNonLinearSolver(
solver_id, non_linear_solver_type);
this->dof_manager->getNewTimeStepSolver(solver_id, time_step_solver_type,
nls);
}
/* -------------------------------------------------------------------------- */
Real ModelSolver::getTimeStep(const ID & solver_id) const {
const TimeStepSolver & tss = this->getSolver(solver_id);
return tss.getTimeStep();
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setTimeStep(Real time_step, const ID & solver_id) {
TimeStepSolver & tss = this->getSolver(solver_id);
return tss.setTimeStep(time_step);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::setIntegrationScheme(
const ID & solver_id, const ID & dof_id,
const IntegrationSchemeType & integration_scheme_type,
IntegrationScheme::SolutionType solution_type) {
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(solver_id);
tss.setIntegrationScheme(dof_id, integration_scheme_type, solution_type);
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasDefaultSolver() const {
return (this->default_solver_id != "");
}
/* -------------------------------------------------------------------------- */
bool ModelSolver::hasIntegrationScheme(const ID & solver_id,
const ID & dof_id) const {
TimeStepSolver & tss = this->dof_manager->getTimeStepSolver(solver_id);
return tss.hasIntegrationScheme(dof_id);
}
/* -------------------------------------------------------------------------- */
void ModelSolver::predictor() {}
/* -------------------------------------------------------------------------- */
void ModelSolver::corrector() {}
/* -------------------------------------------------------------------------- */
TimeStepSolverType ModelSolver::getDefaultSolverType() const {
return _tsst_dynamic_lumped;
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions
ModelSolver::getDefaultSolverOptions(__attribute__((unused))
const TimeStepSolverType & type) const {
ModelSolverOptions options;
options.non_linear_solver_type = _nls_auto;
return options;
}
} // namespace akantu
diff --git a/src/model/model_solver.hh b/src/model/model_solver.hh
index e6f0aef79..fe6ae060b 100644
--- a/src/model/model_solver.hh
+++ b/src/model/model_solver.hh
@@ -1,185 +1,185 @@
/**
* @file model_solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Jul 22 10:53:10 2015
*
* @brief Class regrouping the common solve interface to the different models
*
* @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 "aka_common.hh"
#include "integration_scheme.hh"
#include "parsable.hh"
#include "solver_callback.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MODEL_SOLVER_HH__
#define __AKANTU_MODEL_SOLVER_HH__
namespace akantu {
class Mesh;
class DOFManager;
class TimeStepSolver;
class NonLinearSolver;
struct ModelSolverOptions;
}
namespace akantu {
class ModelSolver : public Parsable,
public SolverCallback,
public SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ModelSolver(Mesh & mesh, const ID & id, UInt memory_id);
- virtual ~ModelSolver();
+ ~ModelSolver() override;
/// initialize the dof manager based on solver type passed in the input file
void initDOFManager();
/// initialize the dof manager based on the used chosen solver type
void initDOFManager(const ID & solver_type);
protected:
/// initialize the dof manager based on the used chosen solver type
void initDOFManager(const ParserSection & section, const ID & solver_type);
/// Callback for the model to instantiate the matricees when needed
virtual void initSolver(__attribute__((unused)) TimeStepSolverType time_step_solver_type,
__attribute__((unused)) NonLinearSolverType non_linear_solver_type) {
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solve a step using a given pre instantiated time step solver and
/// nondynamic linear solver
virtual void solveStep(const ID & solver_id = "");
/// Initialize a time solver that can be used afterwards with its id
void getNewSolver(const ID & solver_id,
TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type = _nls_auto);
/// set an integration scheme for a given dof and a given solver
void
setIntegrationScheme(const ID & solver_id, const ID & dof_id,
const IntegrationSchemeType & integration_scheme_type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
/// set an externally instantiated integration scheme
void setIntegrationScheme(const ID & solver_id, const ID & dof_id,
IntegrationScheme & integration_scheme,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined);
/* ------------------------------------------------------------------------ */
/* SolverCallback interface */
/* ------------------------------------------------------------------------ */
public:
/// Predictor interface for the callback
void predictor() override;
/// Corrector interface for the callback
void corrector() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Default time step solver to instantiate for this model
virtual TimeStepSolverType getDefaultSolverType() const;
/// Default configurations for a given time step solver
virtual ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const;
/// get access to the internal dof manager
DOFManager & getDOFManager() { return *this->dof_manager; }
/// get the time step of a given solver
Real getTimeStep(const ID & solver_id = "") const;
/// set the time step of a given solver
virtual void setTimeStep(Real time_step, const ID & solver_id = "");
/// set the parameter 'param' of the solver 'solver_id'
template <typename T>
void set(const ID & param, const T & value, const ID & solver_id = "");
/// get the parameter 'param' of the solver 'solver_id'
const Parameter & get(const ID & param, const ID & solver_id = "") const;
/// answer to the question "does the solver exists ?"
bool hasSolver(const ID & solver_id) const;
/// changes the current default solver
void setDefaultSolver(const ID & solver_id);
/// is a default solver defined
bool hasDefaultSolver() const;
/// is an integration scheme set for a given solver and a given dof
bool hasIntegrationScheme(const ID & solver_id, const ID & dof_id) const;
TimeStepSolver & getTimeStepSolver(const ID & solver_id = "");
NonLinearSolver & getNonLinearSolver(const ID & solver_id = "");
const TimeStepSolver & getTimeStepSolver(const ID & solver_id = "") const;
const NonLinearSolver & getNonLinearSolver(const ID & solver_id = "") const;
private:
TimeStepSolver & getSolver(const ID & solver_id);
const TimeStepSolver & getSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
ID parent_id;
UInt parent_memory_id;
/// Underlying mesh
Mesh & mesh;
/// Underlying dof_manager (the brain...)
DOFManager * dof_manager;
/// Default time step solver to use
ID default_solver_id;
};
struct ModelSolverOptions {
NonLinearSolverType non_linear_solver_type;
std::map<ID, IntegrationSchemeType> integration_scheme_type;
std::map<ID, IntegrationScheme::SolutionType> solution_type;
};
} // akantu
#endif /* __AKANTU_MODEL_SOLVER_HH__ */
diff --git a/src/model/non_linear_solver.hh b/src/model/non_linear_solver.hh
index 750e0536d..f476b5f02 100644
--- a/src/model/non_linear_solver.hh
+++ b/src/model/non_linear_solver.hh
@@ -1,96 +1,96 @@
/**
* @file non_linear_solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Aug 24 23:48:41 2015
*
* @brief Non linear solver interface
*
* @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 "aka_common.hh"
#include "aka_memory.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_HH__
#define __AKANTU_NON_LINEAR_SOLVER_HH__
namespace akantu {
class DOFManager;
class SolverCallback;
}
namespace akantu {
class NonLinearSolver : Memory, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolver(DOFManager & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver", UInt memory_id = 0);
- virtual ~NonLinearSolver();
+ ~NonLinearSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solve the system described by the jacobian matrix, and rhs contained in
/// the dof manager
virtual void solve(SolverCallback & callback) = 0;
protected:
void checkIfTypeIsSupported();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
DOFManager & _dof_manager;
/// type of non linear solver
NonLinearSolverType non_linear_solver_type;
/// list of supported non linear solver types
std::set<NonLinearSolverType> supported_type;
};
namespace debug {
class NLSNotConvergedException : public Exception {
public:
NLSNotConvergedException(Real threshold, UInt niter, Real error)
: Exception("The non linear solver did not converge."),
threshold(threshold), niter(niter), error(error) {}
Real threshold;
UInt niter;
Real error;
};
}
} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_HH__ */
diff --git a/src/model/non_linear_solver_linear.hh b/src/model/non_linear_solver_linear.hh
index c52b5a693..289fff390 100644
--- a/src/model/non_linear_solver_linear.hh
+++ b/src/model/non_linear_solver_linear.hh
@@ -1,78 +1,78 @@
/**
* @file non_linear_solver_linear.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 25 00:48:07 2015
*
* @brief Default implementation of NonLinearSolver, in case no external library
* is there to do the job
*
* @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 "non_linear_solver.hh"
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_LINEAR_HH__
#define __AKANTU_NON_LINEAR_SOLVER_LINEAR_HH__
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class NonLinearSolverLinear : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverLinear(DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_linear",
UInt memory_id = 0);
- virtual ~NonLinearSolverLinear();
+ ~NonLinearSolverLinear() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
- virtual void solve(SolverCallback & solver_callback);
+ void solve(SolverCallback & solver_callback) override;
AKANTU_GET_MACRO_NOT_CONST(Solver, solver, SparseSolverMumps &);
AKANTU_GET_MACRO(Solver, solver, const SparseSolverMumps &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
DOFManagerDefault & dof_manager;
/// Sparse solver used for the linear solves
SparseSolverMumps solver;
};
} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_LINEAR_HH__ */
diff --git a/src/model/non_linear_solver_lumped.hh b/src/model/non_linear_solver_lumped.hh
index 834791c3c..9916dcb93 100644
--- a/src/model/non_linear_solver_lumped.hh
+++ b/src/model/non_linear_solver_lumped.hh
@@ -1,82 +1,82 @@
/**
* @file non_linear_solver_lumped.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 25 00:48:07 2015
*
* @brief Default implementation of NonLinearSolver, in case no external library
* is there to do the job
*
* @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 "non_linear_solver.hh"
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_LUMPED_HH__
#define __AKANTU_NON_LINEAR_SOLVER_LUMPED_HH__
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class NonLinearSolverLumped : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverLumped(DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_lumped",
UInt memory_id = 0);
- virtual ~NonLinearSolverLumped();
+ ~NonLinearSolverLumped() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
- virtual void solve(SolverCallback & solver_callback);
+ void solve(SolverCallback & solver_callback) override;
static void solveLumped(const Array<Real> & A,
Array<Real> & x,
const Array<Real> & b,
const Array<bool> & blocked_dofs,
Real alpha);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// Coefficient to apply between x and A^{-1} b
Real alpha;
};
} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_LUMPED_HH__ */
diff --git a/src/model/non_linear_solver_newton_raphson.hh b/src/model/non_linear_solver_newton_raphson.hh
index 1b07a299d..e1e6539de 100644
--- a/src/model/non_linear_solver_newton_raphson.hh
+++ b/src/model/non_linear_solver_newton_raphson.hh
@@ -1,104 +1,104 @@
/**
* @file non_linear_solver_newton_raphson.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 25 00:48:07 2015
*
* @brief Default implementation of NonLinearSolver, in case no external library
* is there to do the job
*
* @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 "non_linear_solver.hh"
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH__
#define __AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH__
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class NonLinearSolverNewtonRaphson : public NonLinearSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLinearSolverNewtonRaphson(DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type,
const ID & id = "non_linear_solver_newton_raphson",
UInt memory_id = 0);
- virtual ~NonLinearSolverNewtonRaphson();
+ ~NonLinearSolverNewtonRaphson() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Function that solve the non linear system described by the dof manager and
/// the solver callback functions
- virtual void solve(SolverCallback & solver_callback);
+ void solve(SolverCallback & solver_callback) override;
AKANTU_GET_MACRO_NOT_CONST(Solver, solver, SparseSolverMumps &);
AKANTU_GET_MACRO(Solver, solver, const SparseSolverMumps &);
protected:
/// test the convergence compare norm of array to convergence_criteria
bool testConvergence(const Array<Real> & array);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// Sparse solver used for the linear solves
SparseSolverMumps solver;
/// Type of convergence criteria
SolveConvergenceCriteria convergence_criteria_type;
/// convergence threshold
Real convergence_criteria;
/// Max number of iterations
int max_iterations;
/// Number of iterations at last solve call
int n_iter;
/// Convergence error at last solve call
Real error;
/// Did the last call to solve reached convergence
bool converged;
/// Force a re-computation of the jacobian matrix
bool force_linear_recompute;
};
} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_NEWTON_RAPHSON_HH__ */
diff --git a/src/model/solid_mechanics/material.cc b/src/model/solid_mechanics/material.cc
index 66fff0841..dd99cdfa8 100644
--- a/src/model/solid_mechanics/material.cc
+++ b/src/model/solid_mechanics/material.cc
@@ -1,1606 +1,1606 @@
/**
* @file material.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Tue Nov 24 2015
*
* @brief Implementation of the common part of the material class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "material.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
Material::Material(SolidMechanicsModel & model, const ID & id)
: Memory(id, model.getMemoryID()), Parsable(_st_material, id),
is_init(false), fem(model.getFEEngine()), finite_deformation(false),
name(""), model(model),
spatial_dimension(this->model.getSpatialDimension()),
element_filter("element_filter", id, this->memory_id),
stress("stress", *this), eigengradu("eigen_grad_u", *this),
gradu("grad_u", *this), green_strain("green_strain", *this),
piola_kirchhoff_2("piola_kirchhoff_2", *this),
potential_energy("potential_energy", *this), is_non_local(false),
use_previous_stress(false), use_previous_gradu(false),
interpolation_inverse_coordinates("interpolation inverse coordinates",
*this),
interpolation_points_matrices("interpolation points matrices", *this) {
AKANTU_DEBUG_IN();
/// for each connectivity types allocate the element filer array of the
/// material
element_filter.initialize(model.getMesh(),
_spatial_dimension = spatial_dimension);
// model.getMesh().initElementTypeMapArray(element_filter, 1,
// spatial_dimension,
// false, _ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Material::Material(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id)
: Memory(id, model.getMemoryID()), Parsable(_st_material, id),
is_init(false), fem(model.getFEEngine()), finite_deformation(false),
name(""), model(model), spatial_dimension(dim),
element_filter("element_filter", id, this->memory_id),
stress("stress", *this, dim, fe_engine, this->element_filter),
eigengradu("eigen_grad_u", *this, dim, fe_engine, this->element_filter),
gradu("gradu", *this, dim, fe_engine, this->element_filter),
green_strain("green_strain", *this, dim, fe_engine, this->element_filter),
piola_kirchhoff_2("poila_kirchhoff_2", *this, dim, fe_engine,
this->element_filter),
potential_energy("potential_energy", *this, dim, fe_engine,
this->element_filter),
is_non_local(false), use_previous_stress(false),
use_previous_gradu(false),
interpolation_inverse_coordinates("interpolation inverse_coordinates",
*this, dim, fe_engine,
this->element_filter),
interpolation_points_matrices("interpolation points matrices", *this, dim,
fe_engine, this->element_filter) {
AKANTU_DEBUG_IN();
element_filter.initialize(mesh, _spatial_dimension = spatial_dimension);
// mesh.initElementTypeMapArray(element_filter, 1, spatial_dimension, false,
// _ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Material::~Material() = default;
/* -------------------------------------------------------------------------- */
void Material::initialize() {
registerParam("rho", rho, Real(0.), _pat_parsable | _pat_modifiable,
"Density");
registerParam("name", name, std::string(), _pat_parsable | _pat_readable);
registerParam("finite_deformation", finite_deformation, false,
_pat_parsable | _pat_readable, "Is finite deformation");
registerParam("inelastic_deformation", inelastic_deformation, false,
_pat_internal, "Is inelastic deformation");
/// allocate gradu stress for local elements
eigengradu.initialize(spatial_dimension * spatial_dimension);
gradu.initialize(spatial_dimension * spatial_dimension);
stress.initialize(spatial_dimension * spatial_dimension);
potential_energy.initialize(1);
this->model.registerEventHandler(*this);
}
/* -------------------------------------------------------------------------- */
void Material::initMaterial() {
AKANTU_DEBUG_IN();
if (finite_deformation) {
this->piola_kirchhoff_2.initialize(spatial_dimension * spatial_dimension);
if (use_previous_stress)
this->piola_kirchhoff_2.initializeHistory();
this->green_strain.initialize(spatial_dimension * spatial_dimension);
}
if (use_previous_stress)
this->stress.initializeHistory();
if (use_previous_gradu)
this->gradu.initializeHistory();
for (std::map<ID, InternalField<Real> *>::iterator it =
internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it)
it->second->resize();
for (std::map<ID, InternalField<UInt> *>::iterator it =
internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it)
it->second->resize();
for (std::map<ID, InternalField<bool> *>::iterator it =
internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it)
it->second->resize();
is_init = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::savePreviousState() {
AKANTU_DEBUG_IN();
for (std::map<ID, InternalField<Real> *>::iterator it =
internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it) {
if (it->second->hasHistory())
it->second->saveCurrentValues();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the residual by assembling @f$\int_{e} \sigma_e \frac{\partial
* \varphi}{\partial X} dX @f$
*
* @param[in] displacements nodes displacements
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
// void Material::updateResidual(GhostType ghost_type) {
// AKANTU_DEBUG_IN();
// computeAllStresses(ghost_type);
// assembleResidual(ghost_type);
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void Material::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
if (!finite_deformation) {
Array<Real> & internal_force =
const_cast<Array<Real> &>(model.getInternalForce());
Mesh & mesh = fem.getMesh();
Mesh::type_iterator it =
element_filter.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type =
element_filter.lastType(spatial_dimension, ghost_type);
for (; it != last_type; ++it) {
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element) {
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(*it, ghost_type);
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(*it, ghost_type);
/// compute @f$\sigma \frac{\partial \varphi}{\partial X}@f$ by
/// @f$\mathbf{B}^t \mathbf{\sigma}_q@f$
Array<Real> * sigma_dphi_dx =
new Array<Real>(nb_element * nb_quadrature_points,
size_of_shapes_derivatives, "sigma_x_dphi_/_dX");
Array<Real> * shapesd_filtered =
new Array<Real>(0, size_of_shapes_derivatives, "filtered shapesd");
FEEngine::filterElementalData(mesh, shapes_derivatives,
*shapesd_filtered, *it, ghost_type,
elem_filter);
Array<Real> & stress_vect = this->stress(*it, ghost_type);
Array<Real>::matrix_iterator sigma =
stress_vect.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator B =
shapesd_filtered->begin(spatial_dimension, nb_nodes_per_element);
Array<Real>::matrix_iterator Bt_sigma_it =
sigma_dphi_dx->begin(spatial_dimension, nb_nodes_per_element);
for (UInt q = 0; q < nb_element * nb_quadrature_points;
++q, ++sigma, ++B, ++Bt_sigma_it)
Bt_sigma_it->mul<false, false>(*sigma, *B);
delete shapesd_filtered;
/**
* compute @f$\int \sigma * \frac{\partial \varphi}{\partial X}dX@f$ by
* @f$ \sum_q \mathbf{B}^t
* \mathbf{\sigma}_q \overline w_q J_q@f$
*/
Array<Real> * int_sigma_dphi_dx = new Array<Real>(
nb_element, nb_nodes_per_element * spatial_dimension,
"int_sigma_x_dphi_/_dX");
fem.integrate(*sigma_dphi_dx, *int_sigma_dphi_dx,
size_of_shapes_derivatives, *it, ghost_type, elem_filter);
delete sigma_dphi_dx;
/// assemble
model.getDOFManager().assembleElementalArrayLocalArray(
*int_sigma_dphi_dx, internal_force, *it, ghost_type, -1,
elem_filter);
delete int_sigma_dphi_dx;
}
}
} else {
switch (spatial_dimension) {
case 1:
this->assembleInternalForces<1>(ghost_type);
break;
case 2:
this->assembleInternalForces<2>(ghost_type);
break;
case 3:
this->assembleInternalForces<3>(ghost_type);
break;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the stress from the gradu
*
* @param[in] current_position nodes postition + displacements
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void Material::computeAllStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
for (const auto & type :
element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
if (elem_filter.size() == 0)
continue;
Array<Real> & gradu_vect = gradu(type, ghost_type);
/// compute @f$\nabla u@f$
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect,
spatial_dimension, type, ghost_type,
elem_filter);
gradu_vect -= eigengradu(type, ghost_type);
/// compute @f$\mathbf{\sigma}_q@f$ from @f$\nabla u@f$
computeStress(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computeAllCauchyStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(finite_deformation, "The Cauchy stress can only be "
"computed if you are working in "
"finite deformation.");
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
switch (spatial_dimension) {
case 1:
this->computeCauchyStress<1>(type, ghost_type);
break;
case 2:
this->computeCauchyStress<2>(type, ghost_type);
break;
case 3:
this->computeCauchyStress<3>(type, ghost_type);
break;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::computeCauchyStress(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real>::matrix_iterator gradu_it =
this->gradu(el_type, ghost_type).begin(dim, dim);
Array<Real>::matrix_iterator gradu_end =
this->gradu(el_type, ghost_type).end(dim, dim);
Array<Real>::matrix_iterator piola_it =
this->piola_kirchhoff_2(el_type, ghost_type).begin(dim, dim);
Array<Real>::matrix_iterator stress_it =
this->stress(el_type, ghost_type).begin(dim, dim);
Matrix<Real> F_tensor(dim, dim);
for (; gradu_it != gradu_end; ++gradu_it, ++piola_it, ++stress_it) {
Matrix<Real> & grad_u = *gradu_it;
Matrix<Real> & piola = *piola_it;
Matrix<Real> & sigma = *stress_it;
gradUToF<dim>(grad_u, F_tensor);
this->computeCauchyStressOnQuad<dim>(F_tensor, piola, sigma);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::setToSteadyState(GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & displacement = model.getDisplacement();
// resizeInternalArray(gradu);
UInt spatial_dimension = model.getSpatialDimension();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
/// compute @f$\nabla u@f$
fem.gradientOnIntegrationPoints(displacement, gradu_vect, spatial_dimension,
type, ghost_type, elem_filter);
setToSteadyState(type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the stiffness matrix by assembling @f$\int_{\omega} B^t \times D
* \times B d\omega @f$
*
* @param[in] current_position nodes postition + displacements
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void Material::assembleStiffnessMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
if (finite_deformation) {
switch (spatial_dimension) {
case 1: {
assembleStiffnessMatrixNL<1>(type, ghost_type);
assembleStiffnessMatrixL2<1>(type, ghost_type);
break;
}
case 2: {
assembleStiffnessMatrixNL<2>(type, ghost_type);
assembleStiffnessMatrixL2<2>(type, ghost_type);
break;
}
case 3: {
assembleStiffnessMatrixNL<3>(type, ghost_type);
assembleStiffnessMatrixL2<3>(type, ghost_type);
break;
}
}
} else {
switch (spatial_dimension) {
case 1: {
assembleStiffnessMatrix<1>(type, ghost_type);
break;
}
case 2: {
assembleStiffnessMatrix<2>(type, ghost_type);
break;
}
case 3: {
assembleStiffnessMatrix<3>(type, ghost_type);
break;
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleStiffnessMatrix(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> & elem_filter = element_filter(type, ghost_type);
if (elem_filter.size()) {
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect, dim,
type, ghost_type, elem_filter);
UInt tangent_size = getTangentStiffnessVoigtSize(dim);
Array<Real> * tangent_stiffness_matrix = new Array<Real>(
nb_element * nb_quadrature_points, tangent_size * tangent_size,
"tangent_stiffness_matrix");
tangent_stiffness_matrix->clear();
computeTangentModuli(type, *tangent_stiffness_matrix, ghost_type);
Array<Real> * shapesd_filtered = new Array<Real>(
nb_element, dim * nb_nodes_per_element, "filtered shapesd");
FEEngine::filterElementalData(fem.getMesh(), shapes_derivatives,
*shapesd_filtered, type, ghost_type,
elem_filter);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = dim * nb_nodes_per_element;
Array<Real> * bt_d_b =
new Array<Real>(nb_element * nb_quadrature_points,
bt_d_b_size * bt_d_b_size, "B^t*D*B");
Matrix<Real> B(tangent_size, dim * nb_nodes_per_element);
Matrix<Real> Bt_D(dim * nb_nodes_per_element, tangent_size);
Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator Bt_D_B_it =
bt_d_b->begin(dim * nb_nodes_per_element, dim * nb_nodes_per_element);
Array<Real>::matrix_iterator D_it =
tangent_stiffness_matrix->begin(tangent_size, tangent_size);
Array<Real>::matrix_iterator D_end =
tangent_stiffness_matrix->end(tangent_size, tangent_size);
for (; D_it != D_end;
++D_it, ++Bt_D_B_it, ++shapes_derivatives_filtered_it) {
Matrix<Real> & D = *D_it;
Matrix<Real> & Bt_D_B = *Bt_D_B_it;
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
*shapes_derivatives_filtered_it, B, nb_nodes_per_element);
Bt_D.mul<true, false>(B, D);
Bt_D_B.mul<false, false>(Bt_D, B);
}
delete tangent_stiffness_matrix;
delete shapesd_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
Array<Real> * K_e =
new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");
fem.integrate(*bt_d_b, *K_e, bt_d_b_size * bt_d_b_size, type, ghost_type,
elem_filter);
delete bt_d_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleStiffnessMatrixNL(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
// Array<Real> & gradu_vect = delta_gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
// gradu_vect.resize(nb_quadrature_points * nb_element);
// fem.gradientOnIntegrationPoints(model.getIncrement(), gradu_vect,
// dim, type, ghost_type, &elem_filter);
Array<Real> * shapes_derivatives_filtered = new Array<Real>(
nb_element * nb_quadrature_points, dim * nb_nodes_per_element,
"shapes derivatives filtered");
Array<Real>::const_matrix_iterator shapes_derivatives_it =
shapes_derivatives.begin(spatial_dimension, nb_nodes_per_element);
Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
shapes_derivatives_filtered->begin(spatial_dimension,
nb_nodes_per_element);
UInt * elem_filter_val = elem_filter.storage();
for (UInt e = 0; e < nb_element; ++e, ++elem_filter_val)
for (UInt q = 0; q < nb_quadrature_points;
++q, ++shapes_derivatives_filtered_it)
*shapes_derivatives_filtered_it =
shapes_derivatives_it[*elem_filter_val * nb_quadrature_points + q];
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_s_b_size = dim * nb_nodes_per_element;
Array<Real> * bt_s_b = new Array<Real>(nb_element * nb_quadrature_points,
bt_s_b_size * bt_s_b_size, "B^t*D*B");
UInt piola_matrix_size = getCauchyStressMatrixSize(dim);
Matrix<Real> B(piola_matrix_size, bt_s_b_size);
Matrix<Real> Bt_S(bt_s_b_size, piola_matrix_size);
Matrix<Real> S(piola_matrix_size, piola_matrix_size);
shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(
spatial_dimension, nb_nodes_per_element);
Array<Real>::matrix_iterator Bt_S_B_it =
bt_s_b->begin(bt_s_b_size, bt_s_b_size);
Array<Real>::matrix_iterator Bt_S_B_end =
bt_s_b->end(bt_s_b_size, bt_s_b_size);
Array<Real>::matrix_iterator piola_it =
piola_kirchhoff_2(type, ghost_type).begin(dim, dim);
for (; Bt_S_B_it != Bt_S_B_end;
++Bt_S_B_it, ++shapes_derivatives_filtered_it, ++piola_it) {
Matrix<Real> & Bt_S_B = *Bt_S_B_it;
Matrix<Real> & Piola_kirchhoff_matrix = *piola_it;
setCauchyStressMatrix<dim>(Piola_kirchhoff_matrix, S);
VoigtHelper<dim>::transferBMatrixToBNL(*shapes_derivatives_filtered_it, B,
nb_nodes_per_element);
Bt_S.mul<true, false>(B, S);
Bt_S_B.mul<false, false>(Bt_S, B);
}
delete shapes_derivatives_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
Array<Real> * K_e =
new Array<Real>(nb_element, bt_s_b_size * bt_s_b_size, "K_e");
fem.integrate(*bt_s_b, *K_e, bt_s_b_size * bt_s_b_size, type, ghost_type,
elem_filter);
delete bt_s_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleStiffnessMatrixL2(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
fem.gradientOnIntegrationPoints(model.getDisplacement(), gradu_vect, dim,
type, ghost_type, elem_filter);
UInt tangent_size = getTangentStiffnessVoigtSize(dim);
Array<Real> * tangent_stiffness_matrix =
new Array<Real>(nb_element * nb_quadrature_points,
tangent_size * tangent_size, "tangent_stiffness_matrix");
tangent_stiffness_matrix->clear();
computeTangentModuli(type, *tangent_stiffness_matrix, ghost_type);
Array<Real> * shapes_derivatives_filtered = new Array<Real>(
nb_element * nb_quadrature_points, dim * nb_nodes_per_element,
"shapes derivatives filtered");
Array<Real>::const_matrix_iterator shapes_derivatives_it =
shapes_derivatives.begin(spatial_dimension, nb_nodes_per_element);
Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
shapes_derivatives_filtered->begin(spatial_dimension,
nb_nodes_per_element);
UInt * elem_filter_val = elem_filter.storage();
for (UInt e = 0; e < nb_element; ++e, ++elem_filter_val)
for (UInt q = 0; q < nb_quadrature_points;
++q, ++shapes_derivatives_filtered_it)
*shapes_derivatives_filtered_it =
shapes_derivatives_it[*elem_filter_val * nb_quadrature_points + q];
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = dim * nb_nodes_per_element;
Array<Real> * bt_d_b = new Array<Real>(nb_element * nb_quadrature_points,
bt_d_b_size * bt_d_b_size, "B^t*D*B");
Matrix<Real> B(tangent_size, dim * nb_nodes_per_element);
Matrix<Real> B2(tangent_size, dim * nb_nodes_per_element);
Matrix<Real> Bt_D(dim * nb_nodes_per_element, tangent_size);
shapes_derivatives_filtered_it = shapes_derivatives_filtered->begin(
spatial_dimension, nb_nodes_per_element);
Array<Real>::matrix_iterator Bt_D_B_it =
bt_d_b->begin(dim * nb_nodes_per_element, dim * nb_nodes_per_element);
Array<Real>::matrix_iterator grad_u_it = gradu_vect.begin(dim, dim);
Array<Real>::matrix_iterator D_it =
tangent_stiffness_matrix->begin(tangent_size, tangent_size);
Array<Real>::matrix_iterator D_end =
tangent_stiffness_matrix->end(tangent_size, tangent_size);
for (; D_it != D_end;
++D_it, ++Bt_D_B_it, ++shapes_derivatives_filtered_it, ++grad_u_it) {
Matrix<Real> & grad_u = *grad_u_it;
Matrix<Real> & D = *D_it;
Matrix<Real> & Bt_D_B = *Bt_D_B_it;
// transferBMatrixToBL1<dim > (*shapes_derivatives_filtered_it, B,
// nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
*shapes_derivatives_filtered_it, B, nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToBL2(*shapes_derivatives_filtered_it,
grad_u, B2, nb_nodes_per_element);
B += B2;
Bt_D.mul<true, false>(B, D);
Bt_D_B.mul<false, false>(Bt_D, B);
}
delete tangent_stiffness_matrix;
delete shapes_derivatives_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
Array<Real> * K_e =
new Array<Real>(nb_element, bt_d_b_size * bt_d_b_size, "K_e");
fem.integrate(*bt_d_b, *K_e, bt_d_b_size * bt_d_b_size, type, ghost_type,
elem_filter);
delete bt_d_b;
model.getDOFManager().assembleElementalMatricesToMatrix(
"K", "displacement", *K_e, type, ghost_type, _symmetric, elem_filter);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & internal_force = model.getInternalForce();
Mesh & mesh = fem.getMesh();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
if (elem_filter.size() == 0)
continue;
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_element = elem_filter.size();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
Array<Real> * shapesd_filtered = new Array<Real>(
nb_element, size_of_shapes_derivatives, "filtered shapesd");
FEEngine::filterElementalData(mesh, shapes_derivatives, *shapesd_filtered,
type, ghost_type, elem_filter);
Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
// Set stress vectors
UInt stress_size = getTangentStiffnessVoigtSize(dim);
// Set matrices B and BNL*
UInt bt_s_size = dim * nb_nodes_per_element;
Array<Real> * bt_s =
new Array<Real>(nb_element * nb_quadrature_points, bt_s_size, "B^t*S");
Array<Real>::matrix_iterator grad_u_it =
this->gradu(type, ghost_type).begin(dim, dim);
Array<Real>::matrix_iterator grad_u_end =
this->gradu(type, ghost_type).end(dim, dim);
Array<Real>::matrix_iterator stress_it =
this->piola_kirchhoff_2(type, ghost_type).begin(dim, dim);
shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator bt_s_it = bt_s->begin(bt_s_size, 1);
Matrix<Real> S_vect(stress_size, 1);
Matrix<Real> B_tensor(stress_size, bt_s_size);
Matrix<Real> B2_tensor(stress_size, bt_s_size);
for (; grad_u_it != grad_u_end; ++grad_u_it, ++stress_it,
++shapes_derivatives_filtered_it,
++bt_s_it) {
Matrix<Real> & grad_u = *grad_u_it;
Matrix<Real> & r_it = *bt_s_it;
Matrix<Real> & S_it = *stress_it;
setCauchyStressArray<dim>(S_it, S_vect);
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
*shapes_derivatives_filtered_it, B_tensor, nb_nodes_per_element);
VoigtHelper<dim>::transferBMatrixToBL2(*shapes_derivatives_filtered_it,
grad_u, B2_tensor,
nb_nodes_per_element);
B_tensor += B2_tensor;
r_it.mul<true, false>(B_tensor, S_vect);
}
delete shapesd_filtered;
/// compute @f$ k_e = \int_e \mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
Array<Real> * r_e = new Array<Real>(nb_element, bt_s_size, "r_e");
fem.integrate(*bt_s, *r_e, bt_s_size, type, ghost_type, elem_filter);
delete bt_s;
model.getDOFManager().assembleElementalArrayLocalArray(
*r_e, internal_force, type, ghost_type, -1., elem_filter);
delete r_e;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computeAllStressesFromTangentModuli(GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
switch (spatial_dimension) {
case 1: {
computeAllStressesFromTangentModuli<1>(type, ghost_type);
break;
}
case 2: {
computeAllStressesFromTangentModuli<2>(type, ghost_type);
break;
}
case 3: {
computeAllStressesFromTangentModuli<3>(type, ghost_type);
break;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void Material::computeAllStressesFromTangentModuli(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
const Array<Real> & shapes_derivatives =
fem.getShapesDerivatives(type, ghost_type);
Array<UInt> & elem_filter = element_filter(type, ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
UInt nb_element = elem_filter.size();
if (nb_element) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
gradu_vect.resize(nb_quadrature_points * nb_element);
Array<Real> & disp = model.getDisplacement();
fem.gradientOnIntegrationPoints(disp, gradu_vect, dim, type, ghost_type,
elem_filter);
UInt tangent_moduli_size = getTangentStiffnessVoigtSize(dim);
Array<Real> * tangent_moduli_tensors = new Array<Real>(
nb_element * nb_quadrature_points,
tangent_moduli_size * tangent_moduli_size, "tangent_moduli_tensors");
tangent_moduli_tensors->clear();
computeTangentModuli(type, *tangent_moduli_tensors, ghost_type);
Array<Real> * shapesd_filtered = new Array<Real>(
nb_element, dim * nb_nodes_per_element, "filtered shapesd");
FEEngine::filterElementalData(fem.getMesh(), shapes_derivatives,
*shapesd_filtered, type, ghost_type,
elem_filter);
Array<Real> filtered_u(nb_element,
nb_nodes_per_element * spatial_dimension);
FEEngine::extractNodalToElementField(fem.getMesh(), disp, filtered_u, type,
ghost_type, elem_filter);
/// compute @f$\mathbf{D} \mathbf{B} \mathbf{u}@f$
Array<Real>::matrix_iterator shapes_derivatives_filtered_it =
shapesd_filtered->begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator D_it =
tangent_moduli_tensors->begin(tangent_moduli_size, tangent_moduli_size);
Array<Real>::matrix_iterator sigma_it =
stress(type, ghost_type).begin(spatial_dimension, spatial_dimension);
Array<Real>::vector_iterator u_it =
filtered_u.begin(spatial_dimension * nb_nodes_per_element);
Matrix<Real> B(tangent_moduli_size,
spatial_dimension * nb_nodes_per_element);
Vector<Real> Bu(tangent_moduli_size);
Vector<Real> DBu(tangent_moduli_size);
for (UInt e = 0; e < nb_element; ++e, ++u_it) {
for (UInt q = 0; q < nb_quadrature_points;
++q, ++D_it, ++shapes_derivatives_filtered_it, ++sigma_it) {
Vector<Real> & u = *u_it;
Matrix<Real> & sigma = *sigma_it;
Matrix<Real> & D = *D_it;
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(
*shapes_derivatives_filtered_it, B, nb_nodes_per_element);
Bu.mul<false>(B, u);
DBu.mul<false>(D, Bu);
// Voigt notation to full symmetric tensor
for (UInt i = 0; i < dim; ++i)
sigma(i, i) = DBu(i);
if (dim == 2) {
sigma(0, 1) = sigma(1, 0) = DBu(2);
} else if (dim == 3) {
sigma(1, 2) = sigma(2, 1) = DBu(3);
sigma(0, 2) = sigma(2, 0) = DBu(4);
sigma(0, 1) = sigma(1, 0) = DBu(5);
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computePotentialEnergyByElements() {
AKANTU_DEBUG_IN();
for (auto type : element_filter.elementTypes(spatial_dimension, _not_ghost)) {
computePotentialEnergy(type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::computePotentialEnergy(ElementType, GhostType) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real Material::getPotentialEnergy() {
AKANTU_DEBUG_IN();
Real epot = 0.;
computePotentialEnergyByElements();
/// integrate the potential energy for each type of elements
for (auto type : element_filter.elementTypes(spatial_dimension, _not_ghost)) {
epot += fem.integrate(potential_energy(type, _not_ghost), type, _not_ghost,
element_filter(type, _not_ghost));
}
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
Real Material::getPotentialEnergy(ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
Real epot = 0.;
Vector<Real> epot_on_quad_points(fem.getNbIntegrationPoints(type));
computePotentialEnergyByElement(type, index, epot_on_quad_points);
epot = fem.integrate(epot_on_quad_points, type, element_filter(type)(index));
AKANTU_DEBUG_OUT();
return epot;
}
/* -------------------------------------------------------------------------- */
Real Material::getEnergy(std::string type) {
AKANTU_DEBUG_IN();
if (type == "potential")
return getPotentialEnergy();
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
Real Material::getEnergy(std::string energy_id, ElementType type, UInt index) {
AKANTU_DEBUG_IN();
if (energy_id == "potential")
return getPotentialEnergy(type, index);
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
void Material::initElementalFieldInterpolation(
const ElementTypeMapArray<Real> & interpolation_points_coordinates) {
AKANTU_DEBUG_IN();
this->fem.initElementalFieldInterpolationFromIntegrationPoints(
interpolation_points_coordinates, this->interpolation_points_matrices,
this->interpolation_inverse_coordinates, &(this->element_filter));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::interpolateStress(ElementTypeMapArray<Real> & result,
const GhostType ghost_type) {
this->fem.interpolateElementalFieldFromIntegrationPoints(
this->stress, this->interpolation_points_matrices,
this->interpolation_inverse_coordinates, result, ghost_type,
&(this->element_filter));
}
/* -------------------------------------------------------------------------- */
void Material::interpolateStressOnFacets(
ElementTypeMapArray<Real> & result,
ElementTypeMapArray<Real> & by_elem_result, const GhostType ghost_type) {
interpolateStress(by_elem_result, ghost_type);
UInt stress_size = this->stress.getNbComponent();
const Mesh & mesh = this->model.getMesh();
const Mesh & mesh_facets = mesh.getMeshFacets();
for (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_fil = element_filter(type, ghost_type);
Array<Real> & by_elem_res = by_elem_result(type, ghost_type);
UInt nb_element = elem_fil.size();
UInt nb_element_full = this->model.getMesh().getNbElement(type, ghost_type);
UInt nb_interpolation_points_per_elem =
by_elem_res.size() / nb_element_full;
const Array<Element> & facet_to_element =
mesh_facets.getSubelementToElement(type, ghost_type);
ElementType type_facet = Mesh::getFacetType(type);
UInt nb_facet_per_elem = facet_to_element.getNbComponent();
UInt nb_quad_per_facet =
nb_interpolation_points_per_elem / nb_facet_per_elem;
Element element_for_comparison{type, 0, ghost_type};
- const Array<std::vector<Element>> * element_to_facet = NULL;
+ const Array<std::vector<Element>> * element_to_facet = nullptr;
GhostType current_ghost_type = _casper;
- Array<Real> * result_vec = NULL;
+ Array<Real> * result_vec = nullptr;
Array<Real>::const_matrix_iterator result_it =
by_elem_res.begin_reinterpret(
stress_size, nb_interpolation_points_per_elem, nb_element_full);
for (UInt el = 0; el < nb_element; ++el) {
UInt global_el = elem_fil(el);
element_for_comparison.element = global_el;
for (UInt f = 0; f < nb_facet_per_elem; ++f) {
Element facet_elem = facet_to_element(global_el, f);
UInt global_facet = facet_elem.element;
if (facet_elem.ghost_type != current_ghost_type) {
current_ghost_type = facet_elem.ghost_type;
element_to_facet = &mesh_facets.getElementToSubelement(
type_facet, current_ghost_type);
result_vec = &result(type_facet, current_ghost_type);
}
bool is_second_element =
(*element_to_facet)(global_facet)[0] != element_for_comparison;
for (UInt q = 0; q < nb_quad_per_facet; ++q) {
Vector<Real> result_local(result_vec->storage() +
(global_facet * nb_quad_per_facet + q) *
result_vec->getNbComponent() +
is_second_element * stress_size,
stress_size);
const Matrix<Real> & result_tmp(result_it[global_el]);
result_local = result_tmp(f * nb_quad_per_facet + q);
}
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
const Array<T> &
Material::getArray(__attribute__((unused)) const ID & vect_id,
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) const GhostType & ghost_type) const {
AKANTU_DEBUG_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <typename T>
Array<T> & Material::getArray(__attribute__((unused)) const ID & vect_id,
__attribute__((unused)) const ElementType & type,
__attribute__((unused))
const GhostType & ghost_type) {
AKANTU_DEBUG_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <>
const Array<Real> & Material::getArray(const ID & vect_id,
const ElementType & type,
const GhostType & ghost_type) const {
std::stringstream sstr;
std::string ghost_id = "";
if (ghost_type == _ghost)
ghost_id = ":ghost";
sstr << getID() << ":" << vect_id << ":" << type << ghost_id;
ID fvect_id = sstr.str();
try {
return Memory::getArray<Real>(fvect_id);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << "(" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <>
Array<Real> & Material::getArray(const ID & vect_id, const ElementType & type,
const GhostType & ghost_type) {
std::stringstream sstr;
std::string ghost_id = "";
if (ghost_type == _ghost)
ghost_id = ":ghost";
sstr << getID() << ":" << vect_id << ":" << type << ghost_id;
ID fvect_id = sstr.str();
try {
return Memory::getArray<Real>(fvect_id);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << "(" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <>
const Array<UInt> & Material::getArray(const ID & vect_id,
const ElementType & type,
const GhostType & ghost_type) const {
std::stringstream sstr;
std::string ghost_id = "";
if (ghost_type == _ghost)
ghost_id = ":ghost";
sstr << getID() << ":" << vect_id << ":" << type << ghost_id;
ID fvect_id = sstr.str();
try {
return Memory::getArray<UInt>(fvect_id);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << "(" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <>
Array<UInt> & Material::getArray(const ID & vect_id, const ElementType & type,
const GhostType & ghost_type) {
std::stringstream sstr;
std::string ghost_id = "";
if (ghost_type == _ghost)
ghost_id = ":ghost";
sstr << getID() << ":" << vect_id << ":" << type << ghost_id;
ID fvect_id = sstr.str();
try {
return Memory::getArray<UInt>(fvect_id);
} catch (debug::Exception & e) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain a vector "
<< vect_id << "(" << fvect_id
<< ") [" << e << "]");
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
const InternalField<T> & Material::getInternal(__attribute__((unused))
const ID & int_id) const {
AKANTU_DEBUG_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T> & Material::getInternal(__attribute__((unused))
const ID & int_id) {
AKANTU_DEBUG_TO_IMPLEMENT();
return NULL;
}
/* -------------------------------------------------------------------------- */
template <>
const InternalField<Real> & Material::getInternal(const ID & int_id) const {
std::map<ID, InternalField<Real> *>::const_iterator it =
internal_vectors_real.find(getID() + ":" + int_id);
if (it == internal_vectors_real.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <> InternalField<Real> & Material::getInternal(const ID & int_id) {
std::map<ID, InternalField<Real> *>::iterator it =
internal_vectors_real.find(getID() + ":" + int_id);
if (it == internal_vectors_real.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <>
const InternalField<UInt> & Material::getInternal(const ID & int_id) const {
std::map<ID, InternalField<UInt> *>::const_iterator it =
internal_vectors_uint.find(getID() + ":" + int_id);
if (it == internal_vectors_uint.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
template <> InternalField<UInt> & Material::getInternal(const ID & int_id) {
std::map<ID, InternalField<UInt> *>::iterator it =
internal_vectors_uint.find(getID() + ":" + int_id);
if (it == internal_vectors_uint.end()) {
AKANTU_SILENT_EXCEPTION("The material " << name << "(" << getID()
<< ") does not contain an internal "
<< int_id << " ("
<< (getID() + ":" + int_id) << ")");
}
return *it->second;
}
/* -------------------------------------------------------------------------- */
void Material::addElements(const Array<Element> & elements_to_add) {
AKANTU_DEBUG_IN();
UInt mat_id = model.getInternalIndexFromID(getID());
Array<Element>::const_iterator<Element> el_begin = elements_to_add.begin();
Array<Element>::const_iterator<Element> el_end = elements_to_add.end();
for (; el_begin != el_end; ++el_begin) {
const Element & element = *el_begin;
Array<UInt> & mat_indexes =
model.getMaterialByElement(element.type, element.ghost_type);
Array<UInt> & mat_loc_num =
model.getMaterialLocalNumbering(element.type, element.ghost_type);
UInt index =
this->addElement(element.type, element.element, element.ghost_type);
mat_indexes(element.element) = mat_id;
mat_loc_num(element.element) = index;
}
this->resizeInternals();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::removeElements(const Array<Element> & elements_to_remove) {
AKANTU_DEBUG_IN();
Array<Element>::const_iterator<Element> el_begin = elements_to_remove.begin();
Array<Element>::const_iterator<Element> el_end = elements_to_remove.end();
if (el_begin == el_end)
return;
ElementTypeMapArray<UInt> material_local_new_numbering(
"remove mat filter elem", getID(), getMemoryID());
Element element;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
element.ghost_type = ghost_type;
ElementTypeMapArray<UInt>::type_iterator it =
element_filter.firstType(_all_dimensions, ghost_type, _ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end =
element_filter.lastType(_all_dimensions, ghost_type, _ek_not_defined);
for (; it != end; ++it) {
ElementType type = *it;
element.type = type;
Array<UInt> & elem_filter = this->element_filter(type, ghost_type);
Array<UInt> & mat_loc_num =
this->model.getMaterialLocalNumbering(type, ghost_type);
if (!material_local_new_numbering.exists(type, ghost_type))
material_local_new_numbering.alloc(elem_filter.size(), 1, type,
ghost_type);
Array<UInt> & mat_renumbering =
material_local_new_numbering(type, ghost_type);
UInt nb_element = elem_filter.size();
Array<UInt> elem_filter_tmp;
UInt new_id = 0;
for (UInt el = 0; el < nb_element; ++el) {
element.element = elem_filter(el);
if (std::find(el_begin, el_end, element) == el_end) {
elem_filter_tmp.push_back(element.element);
mat_renumbering(el) = new_id;
mat_loc_num(element.element) = new_id;
++new_id;
} else {
mat_renumbering(el) = UInt(-1);
}
}
elem_filter.resize(elem_filter_tmp.size());
elem_filter.copy(elem_filter_tmp);
}
}
for (std::map<ID, InternalField<Real> *>::iterator it =
internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
for (std::map<ID, InternalField<UInt> *>::iterator it =
internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
for (std::map<ID, InternalField<bool> *>::iterator it =
internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::resizeInternals() {
AKANTU_DEBUG_IN();
for (std::map<ID, InternalField<Real> *>::iterator it =
internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it)
it->second->resize();
for (std::map<ID, InternalField<UInt> *>::iterator it =
internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it)
it->second->resize();
for (std::map<ID, InternalField<bool> *>::iterator it =
internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it)
it->second->resize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Material::onElementsAdded(const Array<Element> &,
const NewElementsEvent &) {
this->resizeInternals();
}
/* -------------------------------------------------------------------------- */
void Material::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
UInt my_num = model.getInternalIndexFromID(getID());
ElementTypeMapArray<UInt> material_local_new_numbering(
"remove mat filter elem", getID(), getMemoryID());
Array<Element>::const_iterator<Element> el_begin = element_list.begin();
Array<Element>::const_iterator<Element> el_end = element_list.end();
for (ghost_type_t::iterator g = ghost_type_t::begin();
g != ghost_type_t::end(); ++g) {
GhostType gt = *g;
ElementTypeMapArray<UInt>::type_iterator it =
new_numbering.firstType(_all_dimensions, gt, _ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end =
new_numbering.lastType(_all_dimensions, gt, _ek_not_defined);
for (; it != end; ++it) {
ElementType type = *it;
if (element_filter.exists(type, gt) && element_filter(type, gt).size()) {
Array<UInt> & elem_filter = element_filter(type, gt);
Array<UInt> & mat_indexes = this->model.getMaterialByElement(*it, gt);
Array<UInt> & mat_loc_num =
this->model.getMaterialLocalNumbering(*it, gt);
UInt nb_element = this->model.getMesh().getNbElement(type, gt);
// all materials will resize of the same size...
mat_indexes.resize(nb_element);
mat_loc_num.resize(nb_element);
if (!material_local_new_numbering.exists(type, gt))
material_local_new_numbering.alloc(elem_filter.size(), 1, type, gt);
Array<UInt> & mat_renumbering = material_local_new_numbering(type, gt);
const Array<UInt> & renumbering = new_numbering(type, gt);
Array<UInt> elem_filter_tmp;
UInt ni = 0;
Element el{type, 0, gt};
for (UInt i = 0; i < elem_filter.size(); ++i) {
el.element = elem_filter(i);
if (std::find(el_begin, el_end, el) == el_end) {
UInt new_el = renumbering(el.element);
AKANTU_DEBUG_ASSERT(
new_el != UInt(-1),
"A not removed element as been badly renumbered");
elem_filter_tmp.push_back(new_el);
mat_renumbering(i) = ni;
mat_indexes(new_el) = my_num;
mat_loc_num(new_el) = ni;
++ni;
} else {
mat_renumbering(i) = UInt(-1);
}
}
elem_filter.resize(elem_filter_tmp.size());
elem_filter.copy(elem_filter_tmp);
}
}
}
for (std::map<ID, InternalField<Real> *>::iterator it =
internal_vectors_real.begin();
it != internal_vectors_real.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
for (std::map<ID, InternalField<UInt> *>::iterator it =
internal_vectors_uint.begin();
it != internal_vectors_uint.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
for (std::map<ID, InternalField<bool> *>::iterator it =
internal_vectors_bool.begin();
it != internal_vectors_bool.end(); ++it)
it->second->removeIntegrationPoints(material_local_new_numbering);
}
/* -------------------------------------------------------------------------- */
void Material::beforeSolveStep() { this->savePreviousState(); }
/* -------------------------------------------------------------------------- */
void Material::afterSolveStep() {
for (auto & type : element_filter.elementTypes(_all_dimensions, _not_ghost,
_ek_not_defined)) {
this->updateEnergies(type, _not_ghost);
}
}
/* -------------------------------------------------------------------------- */
void Material::onDamageIteration() { this->savePreviousState(); }
/* -------------------------------------------------------------------------- */
void Material::onDamageUpdate() {
ElementTypeMapArray<UInt>::type_iterator it = this->element_filter.firstType(
_all_dimensions, _not_ghost, _ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end =
element_filter.lastType(_all_dimensions, _not_ghost, _ek_not_defined);
for (; it != end; ++it) {
this->updateEnergiesAfterDamage(*it, _not_ghost);
}
}
/* -------------------------------------------------------------------------- */
void Material::onDump() {
if (this->isFiniteDeformation())
this->computeAllCauchyStresses(_not_ghost);
}
/* -------------------------------------------------------------------------- */
void Material::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
std::string type = getID().substr(getID().find_last_of(":") + 1);
stream << space << "Material " << type << " [" << std::endl;
Parsable::printself(stream, indent);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
/// extrapolate internal values
void Material::extrapolateInternal(const ID & id, const Element & element,
__attribute__((unused))
const Matrix<Real> & point,
Matrix<Real> & extrapolated) {
if (this->isInternal<Real>(id, element.kind())) {
UInt nb_element =
this->element_filter(element.type, element.ghost_type).size();
const ID name = this->getID() + ":" + id;
UInt nb_quads =
this->internal_vectors_real[name]->getFEEngine().getNbIntegrationPoints(
element.type, element.ghost_type);
const Array<Real> & internal =
this->getArray<Real>(id, element.type, element.ghost_type);
UInt nb_component = internal.getNbComponent();
Array<Real>::const_matrix_iterator internal_it =
internal.begin_reinterpret(nb_component, nb_quads, nb_element);
Element local_element = this->convertToLocalElement(element);
/// instead of really extrapolating, here the value of the first GP
/// is copied into the result vector. This works only for linear
/// elements
/// @todo extrapolate!!!!
AKANTU_DEBUG_WARNING("This is a fix, values are not truly extrapolated");
const Matrix<Real> & values = internal_it[local_element.element];
UInt index = 0;
Vector<Real> tmp(nb_component);
for (UInt j = 0; j < values.cols(); ++j) {
tmp = values(j);
if (tmp.norm() > 0) {
index = j;
break;
}
}
for (UInt i = 0; i < extrapolated.size(); ++i) {
extrapolated(i) = values(index);
}
} else {
Matrix<Real> default_values(extrapolated.rows(), extrapolated.cols(), 0.);
extrapolated = default_values;
}
}
/* -------------------------------------------------------------------------- */
void Material::applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const GhostType ghost_type) {
for (auto && type : element_filter.elementTypes(_all_dimensions, _not_ghost,
_ek_not_defined)) {
if (!element_filter(type, ghost_type).size())
continue;
auto eigen_it = this->eigengradu(type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto eigen_end = this->eigengradu(type, ghost_type)
.end(spatial_dimension, spatial_dimension);
for (; eigen_it != eigen_end; ++eigen_it) {
auto & current_eigengradu = *eigen_it;
current_eigengradu = prescribed_eigen_grad_u;
}
}
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/material.hh b/src/model/solid_mechanics/material.hh
index 311e68a66..db578d06c 100644
--- a/src/model/solid_mechanics/material.hh
+++ b/src/model/solid_mechanics/material.hh
@@ -1,683 +1,681 @@
/**
* @file material.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Nov 25 2015
*
* @brief Mother class for all materials
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_factory.hh"
#include "aka_voigthelper.hh"
#include "data_accessor.hh"
#include "integration_point.hh"
#include "parsable.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
#include "internal_field.hh"
#include "random_internal_field.hh"
/* -------------------------------------------------------------------------- */
#include "mesh_events.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_HH__
#define __AKANTU_MATERIAL_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class Model;
class SolidMechanicsModel;
} // namespace akantu
namespace akantu {
/**
* Interface of all materials
* Prerequisites for a new material
* - inherit from this class
* - implement the following methods:
* \code
* virtual Real getStableTimeStep(Real h, const Element & element =
* ElementNull);
*
* virtual void computeStress(ElementType el_type,
* GhostType ghost_type = _not_ghost);
*
* virtual void computeTangentStiffness(const ElementType & el_type,
* Array<Real> & tangent_matrix,
* GhostType ghost_type = _not_ghost);
* \endcode
*
*/
class Material : public Memory,
public DataAccessor<Element>,
public Parsable,
public MeshEventHandler,
protected SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
#if __cplusplus > 199711L
Material(const Material & mat) = delete;
Material & operator=(const Material & mat) = delete;
#endif
/// Initialize material with defaults
Material(SolidMechanicsModel & model, const ID & id = "");
/// Initialize material with custom mesh & fe_engine
Material(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
/// Destructor
- virtual ~Material();
+ ~Material() override;
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Function that materials can/should reimplement */
/* ------------------------------------------------------------------------ */
protected:
/// constitutive law
virtual void computeStress(__attribute__((unused)) ElementType el_type,
__attribute__((unused))
GhostType ghost_type = _not_ghost) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// compute the tangent stiffness matrix
virtual void computeTangentModuli(__attribute__((unused))
const ElementType & el_type,
__attribute__((unused))
Array<Real> & tangent_matrix,
__attribute__((unused))
GhostType ghost_type = _not_ghost) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// compute the potential energy
virtual void computePotentialEnergy(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// compute the potential energy for an element
virtual void
computePotentialEnergyByElement(__attribute__((unused)) ElementType type,
__attribute__((unused)) UInt index,
__attribute__((unused))
Vector<Real> & epot_on_quad_points) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
virtual void updateEnergies(__attribute__((unused)) ElementType el_type,
__attribute__((unused))
GhostType ghost_type = _not_ghost) {}
virtual void updateEnergiesAfterDamage(__attribute__((unused))
ElementType el_type,
__attribute__((unused))
GhostType ghost_type = _not_ghost) {}
/// set the material to steady state (to be implemented for materials that
/// need it)
virtual void setToSteadyState(__attribute__((unused)) ElementType el_type,
__attribute__((unused))
GhostType ghost_type = _not_ghost) {}
/// function called to update the internal parameters when the modifiable
/// parameters are modified
virtual void updateInternalParameters() {}
public:
/// extrapolate internal values
virtual void extrapolateInternal(const ID & id, const Element & element,
const Matrix<Real> & points,
Matrix<Real> & extrapolated);
/// compute the p-wave speed in the material
virtual Real getPushWaveSpeed(__attribute__((unused))
const Element & element) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// compute the s-wave speed in the material
virtual Real getShearWaveSpeed(__attribute__((unused))
const Element & element) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// get a material celerity to compute the stable time step (default: is the
/// push wave speed)
virtual Real getCelerity(const Element & element) const {
return getPushWaveSpeed(element);
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <typename T>
void registerInternal(__attribute__((unused)) InternalField<T> & vect) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
template <typename T>
void unregisterInternal(__attribute__((unused)) InternalField<T> & vect) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// initialize the material computed parameter
virtual void initMaterial();
/// compute the residual for this material
// virtual void updateResidual(GhostType ghost_type = _not_ghost);
/// assemble the residual for this material
virtual void assembleInternalForces(GhostType ghost_type);
/// save the stress in the previous_stress if needed
virtual void savePreviousState();
/// compute the stresses for this material
virtual void computeAllStresses(GhostType ghost_type = _not_ghost);
virtual void
computeAllStressesFromTangentModuli(GhostType ghost_type = _not_ghost);
virtual void computeAllCauchyStresses(GhostType ghost_type = _not_ghost);
/// set material to steady state
void setToSteadyState(GhostType ghost_type = _not_ghost);
/// compute the stiffness matrix
virtual void assembleStiffnessMatrix(GhostType ghost_type);
/// add an element to the local mesh filter
inline UInt addElement(const ElementType & type, UInt element,
const GhostType & ghost_type);
inline UInt addElement(const Element & element);
/// add many elements at once
void addElements(const Array<Element> & elements_to_add);
/// remove many element at once
void removeElements(const Array<Element> & elements_to_remove);
/// function to print the contain of the class
- virtual void printself(std::ostream & stream, int indent = 0) const;
+ void printself(std::ostream & stream, int indent = 0) const override;
/**
* interpolate stress on given positions for each element by means
* of a geometrical interpolation on quadrature points
*/
void interpolateStress(ElementTypeMapArray<Real> & result,
const GhostType ghost_type = _not_ghost);
/**
* interpolate stress on given positions for each element by means
* of a geometrical interpolation on quadrature points and store the
* results per facet
*/
void interpolateStressOnFacets(ElementTypeMapArray<Real> & result,
ElementTypeMapArray<Real> & by_elem_result,
const GhostType ghost_type = _not_ghost);
/**
* function to initialize the elemental field interpolation
* function by inverting the quadrature points' coordinates
*/
void initElementalFieldInterpolation(
const ElementTypeMapArray<Real> & interpolation_points_coordinates);
/* ------------------------------------------------------------------------ */
/* Common part */
/* ------------------------------------------------------------------------ */
protected:
/* ------------------------------------------------------------------------ */
inline UInt getTangentStiffnessVoigtSize(UInt spatial_dimension) const;
/// compute the potential energy by element
void computePotentialEnergyByElements();
/// resize the intenals arrays
virtual void resizeInternals();
/* ------------------------------------------------------------------------ */
/* Finite deformation functions */
/* This functions area implementing what is described in the paper of Bathe */
/* et al, in IJNME, Finite Element Formulations For Large Deformation */
/* Dynamic Analysis, Vol 9, 353-386, 1975 */
/* ------------------------------------------------------------------------ */
protected:
/// assemble the residual
template <UInt dim> void assembleInternalForces(GhostType ghost_type);
/// Computation of Cauchy stress tensor in the case of finite deformation from
/// the 2nd Piola-Kirchhoff for a given element type
template <UInt dim>
void computeCauchyStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// Computation the Cauchy stress the 2nd Piola-Kirchhoff and the deformation
/// gradient
template <UInt dim>
inline void computeCauchyStressOnQuad(const Matrix<Real> & F,
const Matrix<Real> & S,
Matrix<Real> & cauchy,
const Real & C33 = 1.0) const;
template <UInt dim>
void computeAllStressesFromTangentModuli(const ElementType & type,
GhostType ghost_type);
template <UInt dim>
void assembleStiffnessMatrix(const ElementType & type, GhostType ghost_type);
/// assembling in finite deformation
template <UInt dim>
void assembleStiffnessMatrixNL(const ElementType & type,
GhostType ghost_type);
template <UInt dim>
void assembleStiffnessMatrixL2(const ElementType & type,
GhostType ghost_type);
/// Size of the Stress matrix for the case of finite deformation see: Bathe et
/// al, IJNME, Vol 9, 353-386, 1975
inline UInt getCauchyStressMatrixSize(UInt spatial_dimension) const;
/// Sets the stress matrix according to Bathe et al, IJNME, Vol 9, 353-386,
/// 1975
template <UInt dim>
inline void setCauchyStressMatrix(const Matrix<Real> & S_t,
Matrix<Real> & sigma);
/// write the stress tensor in the Voigt notation.
template <UInt dim>
inline void setCauchyStressArray(const Matrix<Real> & S_t,
Matrix<Real> & sigma_voight);
/* ------------------------------------------------------------------------ */
/* Conversion functions */
/* ------------------------------------------------------------------------ */
public:
template <UInt dim>
static inline void gradUToF(const Matrix<Real> & grad_u, Matrix<Real> & F);
static inline void rightCauchy(const Matrix<Real> & F, Matrix<Real> & C);
static inline void leftCauchy(const Matrix<Real> & F, Matrix<Real> & B);
template <UInt dim>
static inline void gradUToEpsilon(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon);
template <UInt dim>
static inline void gradUToGreenStrain(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon);
static inline Real stressToVonMises(const Matrix<Real> & stress);
protected:
/// converts global element to local element
inline Element convertToLocalElement(const Element & global_element) const;
/// converts local element to global element
inline Element convertToGlobalElement(const Element & local_element) const;
/// converts global quadrature point to local quadrature point
inline IntegrationPoint
convertToLocalPoint(const IntegrationPoint & global_point) const;
/// converts local quadrature point to global quadrature point
inline IntegrationPoint
convertToGlobalPoint(const IntegrationPoint & local_point) const;
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
- virtual inline UInt getNbData(const Array<Element> & elements,
- const SynchronizationTag & tag) const;
+ inline UInt getNbData(const Array<Element> & elements,
+ const SynchronizationTag & tag) const override;
- virtual inline void packData(CommunicationBuffer & buffer,
- const Array<Element> & elements,
- const SynchronizationTag & tag) const;
+ inline void packData(CommunicationBuffer & buffer,
+ const Array<Element> & elements,
+ const SynchronizationTag & tag) const override;
- virtual inline void unpackData(CommunicationBuffer & buffer,
- const Array<Element> & elements,
- const SynchronizationTag & tag);
+ inline void unpackData(CommunicationBuffer & buffer,
+ const Array<Element> & elements,
+ const SynchronizationTag & tag) override;
template <typename T>
inline void packElementDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & fem_id = ID()) const;
template <typename T>
inline void unpackElementDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
const ID & fem_id = ID());
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
- virtual void onNodesAdded(const Array<UInt> &, const NewNodesEvent &){};
- virtual void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
- const RemovedNodesEvent &){};
+ void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override{};
+ void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
+ const RemovedNodesEvent &) override{};
- virtual void onElementsAdded(const Array<Element> & element_list,
- const NewElementsEvent & event);
+ void onElementsAdded(const Array<Element> & element_list,
+ const NewElementsEvent & event) override;
- virtual void
- onElementsRemoved(const Array<Element> & element_list,
- const ElementTypeMapArray<UInt> & new_numbering,
- const RemovedElementsEvent & event);
+ void onElementsRemoved(const Array<Element> & element_list,
+ const ElementTypeMapArray<UInt> & new_numbering,
+ const RemovedElementsEvent & event) override;
- virtual void onElementsChanged(const Array<Element> &, const Array<Element> &,
- const ElementTypeMapArray<UInt> &,
- const ChangedElementsEvent &){};
+ void onElementsChanged(const Array<Element> &, const Array<Element> &,
+ const ElementTypeMapArray<UInt> &,
+ const ChangedElementsEvent &) override{};
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
virtual void beforeSolveStep();
virtual void afterSolveStep();
-
- virtual void onDamageIteration();
- virtual void onDamageUpdate();
- virtual void onDump();
+ void onDamageIteration() override;
+ void onDamageUpdate() override;
+ void onDump() override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Name, name, const std::string &);
AKANTU_GET_MACRO(Model, model, const SolidMechanicsModel &)
AKANTU_GET_MACRO(ID, Memory::getID(), const ID &);
AKANTU_GET_MACRO(Rho, rho, Real);
AKANTU_SET_MACRO(Rho, rho, Real);
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// return the potential energy for the subset of elements contained by the
/// material
Real getPotentialEnergy();
/// return the potential energy for the provided element
Real getPotentialEnergy(ElementType & type, UInt index);
/// return the energy (identified by id) for the subset of elements contained
/// by the material
virtual Real getEnergy(std::string energy_id);
/// return the energy (identified by id) for the provided element
virtual Real getEnergy(std::string energy_id, ElementType type, UInt index);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ElementFilter, element_filter, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(GradU, gradu, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Stress, stress, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(PotentialEnergy, potential_energy,
Real);
AKANTU_GET_MACRO(GradU, gradu, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(Stress, stress, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(ElementFilter, element_filter,
const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO(FEEngine, fem, FEEngine &);
bool isNonLocal() const { return is_non_local; }
template <typename T>
const Array<T> & getArray(const ID & id, const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
template <typename T>
Array<T> & getArray(const ID & id, const ElementType & type,
const GhostType & ghost_type = _not_ghost);
template <typename T>
const InternalField<T> & getInternal(const ID & id) const;
template <typename T> InternalField<T> & getInternal(const ID & id);
template <typename T>
inline bool isInternal(const ID & id, const ElementKind & element_kind) const;
template <typename T>
ElementTypeMap<UInt>
getInternalDataPerElem(const ID & id, const ElementKind & element_kind) const;
bool isFiniteDeformation() const { return finite_deformation; }
bool isInelasticDeformation() const { return inelastic_deformation; }
template <typename T> inline void setParam(const ID & param, T value);
inline const Parameter & getParam(const ID & param) const;
template <typename T>
void flattenInternal(const std::string & field_id,
ElementTypeMapArray<T> & internal_flat,
const GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) const;
/// apply a constant eigengrad_u everywhere in the material
virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const GhostType = _not_ghost);
/// specify if the matrix need to be recomputed for this material
virtual bool hasStiffnessMatrixChanged() { return true; }
protected:
bool isInit() const { return is_init; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// boolean to know if the material has been initialized
bool is_init;
std::map<ID, InternalField<Real> *> internal_vectors_real;
std::map<ID, InternalField<UInt> *> internal_vectors_uint;
std::map<ID, InternalField<bool> *> internal_vectors_bool;
protected:
/// Link to the fem object in the model
FEEngine & fem;
/// Finite deformation
bool finite_deformation;
/// Finite deformation
bool inelastic_deformation;
/// material name
std::string name;
/// The model to witch the material belong
SolidMechanicsModel & model;
/// density : rho
Real rho;
/// spatial dimension
UInt spatial_dimension;
/// list of element handled by the material
ElementTypeMapArray<UInt> element_filter;
/// stresses arrays ordered by element types
InternalField<Real> stress;
/// eigengrad_u arrays ordered by element types
InternalField<Real> eigengradu;
/// grad_u arrays ordered by element types
InternalField<Real> gradu;
/// Green Lagrange strain (Finite deformation)
InternalField<Real> green_strain;
/// Second Piola-Kirchhoff stress tensor arrays ordered by element types
/// (Finite deformation)
InternalField<Real> piola_kirchhoff_2;
/// potential energy by element
InternalField<Real> potential_energy;
/// tell if using in non local mode or not
bool is_non_local;
/// tell if the material need the previous stress state
bool use_previous_stress;
/// tell if the material need the previous strain state
bool use_previous_gradu;
/// elemental field interpolation coordinates
InternalField<Real> interpolation_inverse_coordinates;
/// elemental field interpolation points
InternalField<Real> interpolation_points_matrices;
/// vector that contains the names of all the internals that need to
/// be transferred when material interfaces move
std::vector<ID> internals_to_transfer;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Material & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "material_inline_impl.cc"
#include "internal_field_tmpl.hh"
#include "random_internal_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
/* Auto loop */
/* -------------------------------------------------------------------------- */
/// This can be used to automatically write the loop on quadrature points in
/// functions such as computeStress. This macro in addition to write the loop
/// provides two tensors (matrices) sigma and grad_u
#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type) \
Array<Real>::matrix_iterator gradu_it = \
this->gradu(el_type, ghost_type) \
.begin(this->spatial_dimension, this->spatial_dimension); \
Array<Real>::matrix_iterator gradu_end = \
this->gradu(el_type, ghost_type) \
.end(this->spatial_dimension, this->spatial_dimension); \
\
this->stress(el_type, ghost_type) \
.resize(this->gradu(el_type, ghost_type).size()); \
\
Array<Real>::iterator<Matrix<Real>> stress_it = \
this->stress(el_type, ghost_type) \
.begin(this->spatial_dimension, this->spatial_dimension); \
\
if (this->isFiniteDeformation()) { \
this->piola_kirchhoff_2(el_type, ghost_type) \
.resize(this->gradu(el_type, ghost_type).size()); \
stress_it = this->piola_kirchhoff_2(el_type, ghost_type) \
.begin(this->spatial_dimension, this->spatial_dimension); \
} \
\
for (; gradu_it != gradu_end; ++gradu_it, ++stress_it) { \
Matrix<Real> & __attribute__((unused)) grad_u = *gradu_it; \
Matrix<Real> & __attribute__((unused)) sigma = *stress_it
#define MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END }
/// This can be used to automatically write the loop on quadrature points in
/// functions such as computeTangentModuli. This macro in addition to write the
/// loop provides two tensors (matrices) sigma_tensor, grad_u, and a matrix
/// where the elemental tangent moduli should be stored in Voigt Notation
#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_mat) \
Array<Real>::matrix_iterator gradu_it = \
this->gradu(el_type, ghost_type) \
.begin(this->spatial_dimension, this->spatial_dimension); \
Array<Real>::matrix_iterator gradu_end = \
this->gradu(el_type, ghost_type) \
.end(this->spatial_dimension, this->spatial_dimension); \
Array<Real>::matrix_iterator sigma_it = \
this->stress(el_type, ghost_type) \
.begin(this->spatial_dimension, this->spatial_dimension); \
\
tangent_mat.resize(this->gradu(el_type, ghost_type).size()); \
\
UInt tangent_size = \
this->getTangentStiffnessVoigtSize(this->spatial_dimension); \
Array<Real>::matrix_iterator tangent_it = \
tangent_mat.begin(tangent_size, tangent_size); \
\
for (; gradu_it != gradu_end; ++gradu_it, ++sigma_it, ++tangent_it) { \
Matrix<Real> & __attribute__((unused)) grad_u = *gradu_it; \
Matrix<Real> & __attribute__((unused)) sigma_tensor = *sigma_it; \
Matrix<Real> & tangent = *tangent_it
#define MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END }
/* -------------------------------------------------------------------------- */
namespace akantu {
using MaterialFactory =
Factory<Material, UInt, const ID &, SolidMechanicsModel &, const ID &>;
} // namespace akantu
#define INSTANTIATE_MATERIAL_ONLY(mat_name) \
template class mat_name<1>; \
template class mat_name<2>; \
template class mat_name<3>
#define MATERIAL_DEFAULT_PER_DIM_ALLOCATOR(id, mat_name) \
[](UInt dim, const ID &, SolidMechanicsModel & model, \
const ID & id) -> std::unique_ptr<Material> { \
switch (dim) { \
case 1: \
return std::make_unique<mat_name<1>>(model, id); \
case 2: \
return std::make_unique<mat_name<2>>(model, id); \
case 3: \
return std::make_unique<mat_name<3>>(model, id); \
default: \
AKANTU_EXCEPTION("The dimension " \
<< dim << "is not a valid dimension for the material " \
<< #id); \
} \
}
#define INSTANTIATE_MATERIAL(id, mat_name) \
INSTANTIATE_MATERIAL_ONLY(mat_name); \
static bool material_is_alocated_##id = \
MaterialFactory::getInstance().registerAllocator( \
#id, MATERIAL_DEFAULT_PER_DIM_ALLOCATOR(id, mat_name))
#endif /* __AKANTU_MATERIAL_HH__ */
diff --git a/src/model/solid_mechanics/material_selector.hh b/src/model/solid_mechanics/material_selector.hh
index d49b9e4f8..6759d1967 100644
--- a/src/model/solid_mechanics/material_selector.hh
+++ b/src/model/solid_mechanics/material_selector.hh
@@ -1,142 +1,142 @@
/**
* @file material_selector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Dec 17 2015
*
* @brief class describing how to choose a material for a given element
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "aka_common.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_SELECTOR_HH__
#define __AKANTU_MATERIAL_SELECTOR_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModel;
/**
* main class to assign same or different materials for different
* elements
*/
class MaterialSelector {
public:
MaterialSelector() : fallback_value(0) {}
virtual ~MaterialSelector() {}
virtual UInt operator()(__attribute__((unused)) const Element & element) {
return fallback_value;
}
void setFallback(UInt f) { fallback_value = f; }
protected:
UInt fallback_value;
};
/* -------------------------------------------------------------------------- */
/**
* class that assigns the first material to regular elements by default
*/
class DefaultMaterialSelector : public MaterialSelector {
public:
explicit DefaultMaterialSelector(const ElementTypeMapArray<UInt> & material_index)
: material_index(material_index) {}
- UInt operator()(const Element & element) {
+ UInt operator()(const Element & element) override {
if (not material_index.exists(element.type, element.ghost_type))
return fallback_value;
const auto & mat_indexes = material_index(element.type, element.ghost_type);
if (element.element < mat_indexes.size()) {
auto && tmp_mat = mat_indexes(element.element);
if (tmp_mat != UInt(-1))
return tmp_mat;
}
return fallback_value;
}
private:
const ElementTypeMapArray<UInt> & material_index;
};
/* -------------------------------------------------------------------------- */
/**
* Use elemental data to assign materials
*/
template <typename T>
class ElementDataMaterialSelector : public MaterialSelector {
public:
ElementDataMaterialSelector(const ElementTypeMapArray<T> & element_data,
const SolidMechanicsModel & model,
UInt first_index = 1)
: element_data(element_data), model(model), first_index(first_index) {}
inline T elementData(const Element & element) {
DebugLevel dbl = debug::getDebugLevel();
debug::setDebugLevel(dblError);
T data = element_data(element.type, element.ghost_type)(element.element);
debug::setDebugLevel(dbl);
return data;
}
- inline UInt operator()(const Element & element) {
+ inline UInt operator()(const Element & element) override {
return MaterialSelector::operator()(element);
}
protected:
/// list of element with the specified data (i.e. tag value)
const ElementTypeMapArray<T> & element_data;
/// the model that the materials belong
const SolidMechanicsModel & model;
/// first material index: equal to 1 if none specified
UInt first_index;
};
/* -------------------------------------------------------------------------- */
/**
* class to use mesh data information to assign different materials
* where name is the tag value: tag_0, tag_1
*/
template <typename T>
class MeshDataMaterialSelector : public ElementDataMaterialSelector<T> {
public:
MeshDataMaterialSelector(const std::string & name,
const SolidMechanicsModel & model,
UInt first_index = 1);
};
} // namespace akantu
#endif /* __AKANTU_MATERIAL_SELECTOR_HH__ */
diff --git a/src/model/solid_mechanics/materials/internal_field.hh b/src/model/solid_mechanics/materials/internal_field.hh
index 25cd18f86..96df05f34 100644
--- a/src/model/solid_mechanics/materials/internal_field.hh
+++ b/src/model/solid_mechanics/materials/internal_field.hh
@@ -1,257 +1,257 @@
/**
* @file internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief Material internal properties
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTERNAL_FIELD_HH__
#define __AKANTU_INTERNAL_FIELD_HH__
namespace akantu {
class Material;
class FEEngine;
/**
* class for the internal fields of materials
* to store values for each quadrature
*/
template <typename T> class InternalField : public ElementTypeMapArray<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
InternalField(const ID & id, Material & material);
- virtual ~InternalField();
+ ~InternalField() override;
/// This constructor is only here to let cohesive elements compile
InternalField(const ID & id, Material & material, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter);
/// More general constructor
InternalField(const ID & id, Material & material, UInt dim, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter);
InternalField(const ID & id, const InternalField<T> & other);
private:
InternalField operator=(__attribute__((unused))
const InternalField & other){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// function to reset the FEEngine for the internal field
virtual void setFEEngine(FEEngine & fe_engine);
/// function to reset the element kind for the internal
virtual void setElementKind(ElementKind element_kind);
/// initialize the field to a given number of component
virtual void initialize(UInt nb_component);
/// activate the history of this field
virtual void initializeHistory();
/// resize the arrays and set the new element to 0
virtual void resize();
/// set the field to a given value v
virtual void setDefaultValue(const T & v);
/// reset all the fields to the default value
virtual void reset();
/// save the current values in the history
virtual void saveCurrentValues();
/// remove the quadrature points corresponding to suppressed elements
virtual void
removeIntegrationPoints(const ElementTypeMapArray<UInt> & new_numbering);
/// print the content
- virtual void printself(std::ostream & stream, int indent = 0) const;
+ void printself(std::ostream & stream, int indent = 0) const override;
/// get the default value
inline operator T() const;
virtual FEEngine & getFEEngine() { return *fem; }
virtual const FEEngine & getFEEngine() const { return *fem; }
/// AKANTU_GET_MACRO(FEEngine, *fem, FEEngine &);
protected:
/// initialize the arrays in the ElementTypeMapArray<T>
void internalInitialize(UInt nb_component);
/// set the values for new internals
virtual void setArrayValues(T * begin, T * end);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
typedef typename ElementTypeMapArray<T>::type_iterator type_iterator;
typedef typename ElementTypeMapArray<UInt>::type_iterator filter_type_iterator;
/// get the type iterator on all types contained in the internal field
type_iterator firstType(const GhostType & ghost_type = _not_ghost) const {
return ElementTypeMapArray<T>::firstType(this->spatial_dimension, ghost_type,
this->element_kind);
}
/// get the type iterator on the last type contained in the internal field
type_iterator lastType(const GhostType & ghost_type = _not_ghost) const {
return ElementTypeMapArray<T>::lastType(this->spatial_dimension, ghost_type,
this->element_kind);
}
/// get the type iterator on all types contained in the internal field
filter_type_iterator filterFirstType(const GhostType & ghost_type = _not_ghost) const {
return this->element_filter.firstType(this->spatial_dimension, ghost_type,
this->element_kind);
}
/// get the type iterator on the last type contained in the internal field
filter_type_iterator filterLastType(const GhostType & ghost_type = _not_ghost) const {
return this->element_filter.lastType(this->spatial_dimension, ghost_type,
this->element_kind);
}
/// get the array for a given type of the element_filter
const Array<UInt> getFilter(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const {
return this->element_filter(type, ghost_type);
}
/// get the Array corresponding to the type en ghost_type specified
virtual Array<T> & operator()(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return ElementTypeMapArray<T>::operator()(type, ghost_type);
}
virtual const Array<T> &
operator()(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const {
return ElementTypeMapArray<T>::operator()(type, ghost_type);
}
virtual Array<T> & previous(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
- AKANTU_DEBUG_ASSERT(previous_values != NULL,
+ AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return this->previous_values->operator()(type, ghost_type);
}
virtual const Array<T> &
previous(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const {
- AKANTU_DEBUG_ASSERT(previous_values != NULL,
+ AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return this->previous_values->operator()(type, ghost_type);
}
virtual InternalField<T> & previous() {
- AKANTU_DEBUG_ASSERT(previous_values != NULL,
+ AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return *(this->previous_values);
}
virtual const InternalField<T> & previous() const {
- AKANTU_DEBUG_ASSERT(previous_values != NULL,
+ AKANTU_DEBUG_ASSERT(previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
return *(this->previous_values);
}
/// check if the history is used or not
- bool hasHistory() const { return (previous_values != NULL); }
+ bool hasHistory() const { return (previous_values != nullptr); }
/// get the kind treated by the internal
const ElementKind & getElementKind() const { return element_kind; }
/// return the number of components
UInt getNbComponent() const { return nb_component; }
/// return the spatial dimension corresponding to the internal element type
/// loop filter
UInt getSpatialDimension() const { return this->spatial_dimension; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the material for which this is an internal parameter
Material & material;
/// the fem containing the mesh and the element informations
FEEngine * fem;
/// Element filter if needed
const ElementTypeMapArray<UInt> & element_filter;
/// default value
T default_value;
/// spatial dimension of the element to consider
UInt spatial_dimension;
/// ElementKind of the element to consider
ElementKind element_kind;
/// Number of component of the internal field
UInt nb_component;
/// Is the field initialized
bool is_init;
/// previous values
InternalField<T> * previous_values;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const InternalField<T> & _this) {
_this.printself(stream);
return stream;
}
} // akantu
#endif /* __AKANTU_INTERNAL_FIELD_HH__ */
diff --git a/src/model/solid_mechanics/materials/internal_field_tmpl.hh b/src/model/solid_mechanics/materials/internal_field_tmpl.hh
index 88d2b2539..85147ea95 100644
--- a/src/model/solid_mechanics/materials/internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/materials/internal_field_tmpl.hh
@@ -1,320 +1,320 @@
/**
* @file internal_field_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Tue Dec 08 2015
*
* @brief Material internal properties
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTERNAL_FIELD_TMPL_HH__
#define __AKANTU_INTERNAL_FIELD_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(const ID & id, Material & material)
: ElementTypeMapArray<T>(id, material.getID(), material.getMemoryID()),
material(material), fem(&(material.getModel().getFEEngine())),
element_filter(material.getElementFilter()), default_value(T()),
spatial_dimension(material.getModel().getSpatialDimension()),
element_kind(_ek_regular), nb_component(0), is_init(false),
- previous_values(NULL) {}
+ previous_values(nullptr) {}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(
const ID & id, Material & material, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter)
: ElementTypeMapArray<T>(id, material.getID(), material.getMemoryID()),
material(material), fem(&fem), element_filter(element_filter),
default_value(T()), spatial_dimension(material.getSpatialDimension()),
element_kind(_ek_regular), nb_component(0), is_init(false),
- previous_values(NULL) {}
+ previous_values(nullptr) {}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(
const ID & id, Material & material, UInt dim, FEEngine & fem,
const ElementTypeMapArray<UInt> & element_filter)
: ElementTypeMapArray<T>(id, material.getID(), material.getMemoryID()),
material(material), fem(&fem), element_filter(element_filter),
default_value(T()), spatial_dimension(dim), element_kind(_ek_regular),
- nb_component(0), is_init(false), previous_values(NULL) {}
+ nb_component(0), is_init(false), previous_values(nullptr) {}
/* -------------------------------------------------------------------------- */
template <typename T>
InternalField<T>::InternalField(const ID & id, const InternalField<T> & other)
: ElementTypeMapArray<T>(id, other.material.getID(),
other.material.getMemoryID()),
material(other.material), fem(other.fem),
element_filter(other.element_filter), default_value(other.default_value),
spatial_dimension(other.spatial_dimension),
element_kind(other.element_kind), nb_component(other.nb_component),
- is_init(false), previous_values(NULL) {
+ is_init(false), previous_values(nullptr) {
AKANTU_DEBUG_ASSERT(other.is_init,
"Cannot create a copy of a non initialized field");
this->internalInitialize(this->nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T> InternalField<T>::~InternalField() {
if (this->is_init) {
this->material.unregisterInternal(*this);
}
delete previous_values;
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::setFEEngine(FEEngine & fe_engine) {
this->fem = &fe_engine;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::setElementKind(ElementKind element_kind) {
this->element_kind = element_kind;
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::initialize(UInt nb_component) {
internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::initializeHistory() {
if (!previous_values)
previous_values = new InternalField<T>("previous_" + this->getID(), *this);
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::resize() {
if (!this->is_init)
return;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
filter_type_iterator it = this->filterFirstType(*gt);
filter_type_iterator end = this->filterLastType(*gt);
for (; it != end; ++it) {
UInt nb_element = this->element_filter(*it, *gt).size();
UInt nb_quadrature_points = this->fem->getNbIntegrationPoints(*it, *gt);
UInt new_size = nb_element * nb_quadrature_points;
UInt old_size = 0;
- Array<T> * vect = NULL;
+ Array<T> * vect = nullptr;
if (this->exists(*it, *gt)) {
vect = &(this->operator()(*it, *gt));
old_size = vect->size();
vect->resize(new_size);
} else {
vect = &(this->alloc(nb_element * nb_quadrature_points, nb_component,
*it, *gt));
}
this->setArrayValues(vect->storage() + old_size * vect->getNbComponent(),
vect->storage() + new_size * vect->getNbComponent());
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::setDefaultValue(const T & value) {
this->default_value = value;
this->reset();
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::reset() {
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
type_iterator it = this->firstType(*gt);
type_iterator end = this->lastType(*gt);
for (; it != end; ++it) {
Array<T> & vect = this->operator()(*it, *gt);
vect.clear();
this->setArrayValues(vect.storage(),
vect.storage() +
vect.size() * vect.getNbComponent());
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::internalInitialize(UInt nb_component) {
if (!this->is_init) {
this->nb_component = nb_component;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
filter_type_iterator it = this->filterFirstType(*gt);
filter_type_iterator end = this->filterLastType(*gt);
for (; it != end; ++it) {
UInt nb_element = this->element_filter(*it, *gt).size();
UInt nb_quadrature_points = this->fem->getNbIntegrationPoints(*it, *gt);
if (this->exists(*it, *gt))
this->operator()(*it, *gt).resize(nb_element * nb_quadrature_points);
else
this->alloc(nb_element * nb_quadrature_points, nb_component, *it,
*gt);
}
}
this->material.registerInternal(*this);
this->is_init = true;
}
this->reset();
if (this->previous_values)
this->previous_values->internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::setArrayValues(T * begin, T * end) {
for (; begin < end; ++begin)
*begin = this->default_value;
}
/* -------------------------------------------------------------------------- */
template <typename T> void InternalField<T>::saveCurrentValues() {
- AKANTU_DEBUG_ASSERT(this->previous_values != NULL,
+ AKANTU_DEBUG_ASSERT(this->previous_values != nullptr,
"The history of the internal "
<< this->getID() << " has not been activated");
if (!this->is_init)
return;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
type_iterator it = this->firstType(*gt);
type_iterator end = this->lastType(*gt);
for (; it != end; ++it) {
this->previous_values->operator()(*it, *gt)
.copy(this->operator()(*it, *gt));
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::removeIntegrationPoints(
const ElementTypeMapArray<UInt> & new_numbering) {
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
ElementTypeMapArray<UInt>::type_iterator it =
new_numbering.firstType(_all_dimensions, *gt, _ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end =
new_numbering.lastType(_all_dimensions, *gt, _ek_not_defined);
for (; it != end; ++it) {
ElementType type = *it;
if (this->exists(type, *gt)) {
Array<T> & vect = this->operator()(type, *gt);
if (!vect.size())
continue;
const Array<UInt> & renumbering = new_numbering(type, *gt);
UInt nb_quad_per_elem = fem->getNbIntegrationPoints(type, *gt);
UInt nb_component = vect.getNbComponent();
Array<T> tmp(renumbering.size() * nb_quad_per_elem, nb_component);
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created from nowhere!!");
AKANTU_DEBUG_ASSERT(
tmp.size() == vect.size(),
"Something strange append some mater was created or disappeared in "
<< vect.getID() << "(" << vect.size()
<< "!=" << tmp.size() << ") "
"!!");
UInt new_size = 0;
for (UInt i = 0; i < renumbering.size(); ++i) {
UInt new_i = renumbering(i);
if (new_i != UInt(-1)) {
memcpy(tmp.storage() + new_i * nb_component * nb_quad_per_elem,
vect.storage() + i * nb_component * nb_quad_per_elem,
nb_component * nb_quad_per_elem * sizeof(T));
++new_size;
}
}
tmp.resize(new_size * nb_quad_per_elem);
vect.copy(tmp);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void InternalField<T>::printself(std::ostream & stream, int indent) const {
stream << "InternalField [ " << this->getID();
#if !defined(AKANTU_NDEBUG)
if (AKANTU_DEBUG_TEST(dblDump)) {
stream << std::endl;
ElementTypeMapArray<T>::printself(stream, indent + 3);
} else {
#endif
stream << " {" << this->getData(_not_ghost).size() << " types - "
<< this->getData(_ghost).size() << " ghost types"
<< "}";
#if !defined(AKANTU_NDEBUG)
}
#endif
stream << " ]";
}
/* -------------------------------------------------------------------------- */
template <>
inline void ParameterTyped<InternalField<Real> >::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Real r = in_param;
param.setDefaultValue(r);
}
/* -------------------------------------------------------------------------- */
template <typename T> inline InternalField<T>::operator T() const {
return default_value;
}
} // akantu
#endif /* __AKANTU_INTERNAL_FIELD_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_elastic.hh b/src/model/solid_mechanics/materials/material_elastic.hh
index f28f92293..791043bf6 100644
--- a/src/model/solid_mechanics/materials/material_elastic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic.hh
@@ -1,158 +1,158 @@
/**
* @file material_elastic.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Nov 15 2015
*
* @brief Material isotropic elastic
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "material_thermal.hh"
#include "plane_stress_toolbox.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_ELASTIC_HH__
#define __AKANTU_MATERIAL_ELASTIC_HH__
namespace akantu {
/**
* Material elastic isotropic
*
* parameters in the material files :
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - Plane_Stress : if 0: plane strain, else: plane stress (default: 0)
*/
template <UInt spatial_dimension>
class MaterialElastic
: public PlaneStressToolbox<spatial_dimension,
MaterialThermal<spatial_dimension>> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
typedef PlaneStressToolbox<spatial_dimension,
MaterialThermal<spatial_dimension>>
Parent;
public:
MaterialElastic(SolidMechanicsModel & model, const ID & id = "");
MaterialElastic(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
- virtual ~MaterialElastic() {}
+ ~MaterialElastic() override {}
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
- virtual void initMaterial();
+ void initMaterial() override;
/// constitutive law for all element of a type
void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost) override;
/// compute the elastic potential energy
void computePotentialEnergy(ElementType el_type,
GhostType ghost_type = _not_ghost) override;
- virtual void
+ void
computePotentialEnergyByElement(ElementType type, UInt index,
- Vector<Real> & epot_on_quad_points);
+ Vector<Real> & epot_on_quad_points) override;
/// compute the p-wave speed in the material
Real getPushWaveSpeed(const Element & element) const override;
/// compute the s-wave speed in the material
- virtual Real getShearWaveSpeed(const Element & element) const;
+ Real getShearWaveSpeed(const Element & element) const override;
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma,
const Real sigma_th = 0) const;
/// compute the tangent stiffness matrix for an element
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent) const;
/// recompute the lame coefficient if E or nu changes
- virtual void updateInternalParameters();
+ void updateInternalParameters() override;
static inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & sigma,
Real & epot);
- virtual bool hasStiffnessMatrixChanged() {
+ bool hasStiffnessMatrixChanged() override {
return (! was_stiffness_assembled);
}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get first Lame constant
AKANTU_GET_MACRO(Lambda, lambda, Real);
/// get second Lame constant
AKANTU_GET_MACRO(Mu, mu, Real);
/// get bulk modulus
AKANTU_GET_MACRO(Kappa, kpa, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// Bulk modulus
Real kpa;
/// defines if the stiffness was computed
bool was_stiffness_assembled;
};
} // akantu
#include "material_elastic_inline_impl.cc"
#endif /* __AKANTU_MATERIAL_ELASTIC_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_thermal.hh b/src/model/solid_mechanics/materials/material_thermal.hh
index 792d6097a..c9aad9194 100644
--- a/src/model/solid_mechanics/materials/material_thermal.hh
+++ b/src/model/solid_mechanics/materials/material_thermal.hh
@@ -1,106 +1,106 @@
/**
* @file material_thermal.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Aug 18 2015
*
* @brief Material isotropic thermo-elastic
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_THERMAL_HH__
#define __AKANTU_MATERIAL_THERMAL_HH__
namespace akantu {
template<UInt spatial_dimension>
class MaterialThermal : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialThermal(SolidMechanicsModel & model, const ID & id = "");
MaterialThermal(SolidMechanicsModel & model,
UInt dim,
const Mesh & mesh,
FEEngine & fe_engine,
const ID & id = "");
- virtual ~MaterialThermal() {};
+ ~MaterialThermal() override{};
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
- virtual void initMaterial();
+ void initMaterial() override;
/// constitutive law for all element of a type
- virtual void computeStress(ElementType el_type, GhostType ghost_type);
+ void computeStress(ElementType el_type, GhostType ghost_type) override;
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Young modulus
Real E;
/// Poisson ratio
Real nu;
/// Thermal expansion coefficient
/// TODO : implement alpha as a matrix
Real alpha;
/// Temperature field
InternalField<Real> delta_T;
/// Current thermal stress
InternalField<Real> sigma_th;
/// Tell if we need to use the previous thermal stress
bool use_previous_stress_thermal;
};
} // akantu
#endif /* __AKANTU_MATERIAL_THERMAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/plane_stress_toolbox.hh b/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
index 4a5e0c45b..3eb0ee11b 100644
--- a/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
+++ b/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
@@ -1,106 +1,106 @@
/**
* @file plane_stress_toolbox.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 16 2014
* @date last modification: Tue Aug 18 2015
*
* @brief Tools to implement the plane stress behavior in a material
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PLANE_STRESS_TOOLBOX_HH__
#define __AKANTU_PLANE_STRESS_TOOLBOX_HH__
namespace akantu {
class SolidMechanicsModel;
class FEEngine;
} // akantu
namespace akantu {
/**
* Empty class in dimensions different from 2
* This class is only specialized for 2D in the tmpl file
*/
template <UInt dim, class ParentMaterial = Material>
class PlaneStressToolbox : public ParentMaterial {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PlaneStressToolbox(SolidMechanicsModel & model, const ID & id = "")
: ParentMaterial(model, id) {}
PlaneStressToolbox(SolidMechanicsModel & model, UInt spatial_dimension,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "")
: ParentMaterial(model, spatial_dimension, mesh, fe_engine, id) {}
- virtual ~PlaneStressToolbox() {}
+ ~PlaneStressToolbox() override {}
protected:
void initialize();
public:
- virtual void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) {
+ void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) override {
AKANTU_DEBUG_IN();
ParentMaterial::computeAllCauchyStresses(ghost_type);
AKANTU_DEBUG_OUT();
}
virtual void computeCauchyStressPlaneStress(__attribute__((unused))
ElementType el_type,
__attribute__((unused))
GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ERROR("The function \"computeCauchyStressPlaneStress\" can "
"only be used in 2D Plane stress problems, which means "
"that you made a mistake somewhere!! ");
AKANTU_DEBUG_OUT();
}
protected:
bool initialize_third_axis_deformation;
};
#define AKANTU_PLANE_STRESS_TOOL_SPEC(dim) \
template <> \
inline PlaneStressToolbox<dim, Material>::PlaneStressToolbox( \
SolidMechanicsModel & model, const ID & id) \
: Material(model, id) {}
AKANTU_PLANE_STRESS_TOOL_SPEC(1)
AKANTU_PLANE_STRESS_TOOL_SPEC(3)
} // namespace akantu
#include "plane_stress_toolbox_tmpl.hh"
#endif /* __AKANTU_PLANE_STRESS_TOOLBOX_HH__ */
diff --git a/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh b/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
index ecf88c1f4..e31099310 100644
--- a/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
+++ b/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
@@ -1,169 +1,169 @@
/**
* @file plane_stress_toolbox_tmpl.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Tue Sep 16 2014
* @date last modification: Tue Aug 18 2015
*
* @brief 2D specialization of the akantu::PlaneStressToolbox class
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH__
#define __AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class ParentMaterial>
class PlaneStressToolbox<2, ParentMaterial> : public ParentMaterial {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PlaneStressToolbox(SolidMechanicsModel & model, const ID & id = "");
PlaneStressToolbox(SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id = "");
- virtual ~PlaneStressToolbox() {}
+ ~PlaneStressToolbox() override {}
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ThirdAxisDeformation,
third_axis_deformation, Real);
protected:
void initialize() {
this->registerParam("Plane_Stress", plane_stress, false, _pat_parsmod,
"Is plane stress");
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
- virtual void initMaterial() {
+ void initMaterial() override {
ParentMaterial::initMaterial();
if (this->plane_stress && this->initialize_third_axis_deformation) {
this->third_axis_deformation.initialize(1);
this->third_axis_deformation.resize();
}
}
/* ------------------------------------------------------------------------ */
- virtual void computeStress(ElementType el_type, GhostType ghost_type) {
+ void computeStress(ElementType el_type, GhostType ghost_type) override {
ParentMaterial::computeStress(el_type, ghost_type);
if (this->plane_stress)
computeThirdAxisDeformation(el_type, ghost_type);
}
/* ------------------------------------------------------------------------ */
virtual void computeThirdAxisDeformation(ElementType, GhostType) {}
/// Computation of Cauchy stress tensor in the case of finite deformation
- virtual void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) {
+ void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) override {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
AKANTU_DEBUG_ASSERT(this->finite_deformation,
"The Cauchy stress can only be computed if you are "
"working in finite deformation.");
// resizeInternalArray(stress);
Mesh::type_iterator it = this->fem.getMesh().firstType(2, ghost_type);
Mesh::type_iterator last_type =
this->fem.getMesh().lastType(2, ghost_type);
for (; it != last_type; ++it)
this->computeCauchyStressPlaneStress(*it, ghost_type);
} else
ParentMaterial::computeAllCauchyStresses(ghost_type);
AKANTU_DEBUG_OUT();
}
virtual void
computeCauchyStressPlaneStress(__attribute__((unused)) ElementType el_type,
__attribute__((unused))
GhostType ghost_type = _not_ghost){};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// third axis strain measure value
InternalField<Real> third_axis_deformation;
/// Plane stress or plane strain
bool plane_stress;
/// For non linear materials, the \epsilon_{zz} might be required
bool initialize_third_axis_deformation;
};
template <class ParentMaterial>
inline PlaneStressToolbox<2, ParentMaterial>::PlaneStressToolbox(
SolidMechanicsModel & model, const ID & id)
: ParentMaterial(model, id),
third_axis_deformation("third_axis_deformation", *this),
plane_stress(false), initialize_third_axis_deformation(false) {
/// @todo Plane_Stress should not be possible to be modified after
/// initMaterial (but before)
this->initialize();
}
template <class ParentMaterial>
inline PlaneStressToolbox<2, ParentMaterial>::PlaneStressToolbox(
SolidMechanicsModel & model, UInt dim, const Mesh & mesh,
FEEngine & fe_engine, const ID & id)
: ParentMaterial(model, dim, mesh, fe_engine, id),
third_axis_deformation("third_axis_deformation", *this, dim, fe_engine,
this->element_filter),
plane_stress(false), initialize_third_axis_deformation(false) {
this->initialize();
}
template <>
inline PlaneStressToolbox<2, Material>::PlaneStressToolbox(
SolidMechanicsModel & model, const ID & id)
: Material(model, id),
third_axis_deformation("third_axis_deformation", *this),
plane_stress(false), initialize_third_axis_deformation(false) {
/// @todo Plane_Stress should not be possible to be modified after
/// initMaterial (but before)
this->registerParam("Plane_Stress", plane_stress, false, _pat_parsmod,
"Is plane stress");
}
} // namespace akantu
#endif /* __AKANTU_PLANE_STRESS_TOOLBOX_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/random_internal_field.hh b/src/model/solid_mechanics/materials/random_internal_field.hh
index 66ee3d1a9..f3e6decda 100644
--- a/src/model/solid_mechanics/materials/random_internal_field.hh
+++ b/src/model/solid_mechanics/materials/random_internal_field.hh
@@ -1,108 +1,108 @@
/**
* @file random_internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief Random internal material parameter
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "aka_random_generator.hh"
#include "internal_field.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_RANDOM_INTERNAL_FIELD_HH__
#define __AKANTU_RANDOM_INTERNAL_FIELD_HH__
namespace akantu {
/**
* class for the internal fields of materials with a random
* distribution
*/
template<typename T,
template<typename> class BaseField = InternalField,
template<typename> class Generator = RandomGenerator>
class RandomInternalField : public BaseField<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
RandomInternalField(const ID & id, Material & material);
- virtual ~RandomInternalField();
+ ~RandomInternalField() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
RandomInternalField operator=(const RandomInternalField &) = delete;
public:
AKANTU_GET_MACRO(RandomParameter, random_parameter, const RandomParameter<T>);
/// initialize the field to a given number of component
- virtual void initialize(UInt nb_component);
+ void initialize(UInt nb_component) override;
/// set the field to a given value
- void setDefaultValue(const T & value);
+ void setDefaultValue(const T & value) override;
/// set the specified random distribution to a given parameter
void setRandomDistribution(const RandomParameter<T> & param);
/// print the content
- virtual void printself(std::ostream & stream, int indent = 0) const;
+ void printself(std::ostream & stream, int indent = 0) const override;
protected:
- virtual void setArrayValues(T * begin, T * end);
+ void setArrayValues(T * begin, T * end) override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
inline operator Real() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// random parameter containing the distribution and base value
RandomParameter<T> random_parameter;
};
/// standard output stream operator
template<typename T>
inline std::ostream & operator <<(std::ostream & stream, const RandomInternalField<T> & _this)
{
_this.printself(stream);
return stream;
}
} // akantu
#endif /* __AKANTU_RANDOM_INTERNAL_FIELD_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
index 2ef20c741..7ffbfdbf3 100644
--- a/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/damaged_weight_function.hh
@@ -1,82 +1,82 @@
/**
* @file damaged_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 15 2015
*
* @brief Damaged weight function for non local materials
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DAMAGED_WEIGHT_FUNCTION_HH__
#define __AKANTU_DAMAGED_WEIGHT_FUNCTION_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Damage weight function */
/* -------------------------------------------------------------------------- */
class DamagedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
DamagedWeightFunction(NonLocalManager & manager)
- : BaseWeightFunction(manager, "damaged"), damage(NULL) {
+ : BaseWeightFunction(manager, "damaged"), damage(nullptr) {
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
/// set the pointers of internals to the right flattend version
- virtual void init();
+ void init() override;
inline Real operator()(Real r,
const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2);
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// internal pointer to the current damage vector
ElementTypeMapReal * damage;
};
#if defined(AKANTU_INCLUDE_INLINE_IMPL)
#include "damaged_weight_function_inline_impl.cc"
#endif
} // namespace akantu
#endif /* __AKANTU_DAMAGED_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
index 54b9c49b7..3a5ca0524 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_weight_function.hh
@@ -1,96 +1,96 @@
/**
* @file remove_damaged_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
* @date last modification: Thu Oct 15 2015
*
* @brief Removed damaged weight function for non local materials
*
* @section LICENSE
*
* Copyright (©) 2015 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 "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH__
#define __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Remove damaged weight function */
/* -------------------------------------------------------------------------- */
class RemoveDamagedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
RemoveDamagedWeightFunction(NonLocalManager & manager)
- : BaseWeightFunction(manager, "remove_damaged"), damage(NULL) {
+ : BaseWeightFunction(manager, "remove_damaged"), damage(nullptr) {
this->registerParam("damage_limit", this->damage_limit, 1., _pat_parsable,
"Damage Threshold");
this->init();
}
/* --------------------------------------------------------------------------
*/
/* Base Weight Function inherited methods */
/* --------------------------------------------------------------------------
*/
- virtual inline void init();
+ inline void init() override;
inline Real operator()(Real r, const IntegrationPoint & q1,
const IntegrationPoint & q2);
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
inline UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) override;
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// limit at which a point is considered as complitely broken
Real damage_limit;
/// internal pointer to the current damage vector
ElementTypeMapReal * damage;
};
} // namespace akantu
#include "remove_damaged_weight_function_inline_impl.cc"
#endif /* __AKANTU_REMOVE_DAMAGED_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
index dca670cba..31eb2dbc8 100644
--- a/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/remove_damaged_with_damage_rate_weight_function.hh
@@ -1,82 +1,83 @@
/**
* @file remove_damaged_with_damage_rate_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 15 2015
*
* @brief Removed damaged weight function for non local materials
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_RATE_WEIGHT_FUNCTION_HH__
#define __AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_RATE_WEIGHT_FUNCTION_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Remove damaged with damage rate weight function */
/* -------------------------------------------------------------------------- */
class RemoveDamagedWithDamageRateWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
- RemoveDamagedWithDamageRateWeightFunction(NonLocalManager & manager) : BaseWeightFunction(manager, "remove_damage_with_damage_rate"),
- damage_with_damage_rate(NULL) {
+ RemoveDamagedWithDamageRateWeightFunction(NonLocalManager & manager)
+ : BaseWeightFunction(manager, "remove_damage_with_damage_rate"),
+ damage_with_damage_rate(nullptr) {
this->registerParam<Real>("damage_limit", this->damage_limit_with_damage_rate, 1, _pat_parsable, "Damage Threshold");
this->init();
}
/* -------------------------------------------------------------------------- */
/* Base Weight Function inherited methods */
/* -------------------------------------------------------------------------- */
inline Real operator()(Real r,
const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2);
- virtual inline void init();
+ inline void init() override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// limit at which a point is considered as complitely broken
Real damage_limit_with_damage_rate;
/// internal pointer to the current damage vector
ElementTypeMapReal * damage_with_damage_rate;
};
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "remove_damaged_with_damage_rate_weight_function_inline_impl.cc"
#endif
} // akantu
#endif /* __AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
index fd3e0744e..07a742faa 100644
--- a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.hh
@@ -1,104 +1,104 @@
/**
* @file stress_based_weight_function.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Cyprien Wolff <cyprien.wolff@epfl.ch>
*
* @date creation: Mon Aug 24 2015
* @date last modification: Thu Oct 15 2015
*
* @brief Removed damaged weight function for non local materials
*
* @section LICENSE
*
* Copyright (©) 2015 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 "base_weight_function.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH__
#define __AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Stress Based Weight */
/* -------------------------------------------------------------------------- */
/// based on based on Giry et al.: Stress-based nonlocal damage model,
/// IJSS, 48, 2011
class StressBasedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
StressBasedWeightFunction(NonLocalManager & manager);
/* -------------------------------------------------------------------------- */
/* Base Weight Function inherited methods */
/* -------------------------------------------------------------------------- */
- void init();
+ void init() override;
- virtual inline void updateInternals();
+ inline void updateInternals() override;
void updatePrincipalStress(GhostType ghost_type);
inline void updateQuadraturePointsCoordinates(ElementTypeMapArray<Real> & quadrature_points_coordinates);
inline Real operator()(Real r,
const IntegrationPoint & q1,
const IntegrationPoint & q2);
/// computation of ellipsoid
inline Real computeRhoSquare(Real r,
Vector<Real> & eigs,
Matrix<Real> & eigenvects,
Vector<Real> & x_s);
protected:
inline void setInternal();
private:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
/// tensile strength
Real ft;
/// prinicipal stresses
ElementTypeMapReal * stress_diag;
/// for preselection of types (optimization)
ElementTypeMapReal * selected_stress_diag;
/// principal directions
ElementTypeMapReal * stress_base;
/// lenght intrinisic to the material
ElementTypeMapReal * characteristic_size;
};
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "stress_based_weight_function_inline_impl.cc"
#endif
} // akantu
#endif /* __AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model.hh b/src/model/solid_mechanics/solid_mechanics_model.hh
index c0f013d23..495e28103 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model.hh
@@ -1,581 +1,581 @@
/**
* @file solid_mechanics_model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Tue Jan 19 2016
*
* @brief Model of Solid Mechanics
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "boundary_condition.hh"
#include "data_accessor.hh"
#include "fe_engine.hh"
#include "model.hh"
#include "non_local_manager.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
//#include "integrator_gauss.hh"
//#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_HH__
namespace akantu {
class Material;
class MaterialSelector;
class DumperIOHelper;
class NonLocalManager;
template <ElementKind kind, class IntegrationOrderFunctor>
class IntegratorGauss;
template <ElementKind kind> class ShapeLagrange;
} // namespace akantu
/* -------------------------------------------------------------------------- */
namespace akantu {
struct SolidMechanicsModelOptions : public ModelOptions {
explicit SolidMechanicsModelOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass);
template <typename... pack>
SolidMechanicsModelOptions(use_named_args_t, pack &&... _pack);
};
/* -------------------------------------------------------------------------- */
class SolidMechanicsModel
: public Model,
public DataAccessor<Element>,
public DataAccessor<UInt>,
public BoundaryCondition<SolidMechanicsModel>,
public NonLocalManagerCallback,
public EventHandlerManager<SolidMechanicsModelEventHandler> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
class NewMaterialElementsEvent : public NewElementsEvent {
public:
AKANTU_GET_MACRO_NOT_CONST(MaterialList, material, Array<UInt> &);
AKANTU_GET_MACRO(MaterialList, material, const Array<UInt> &);
protected:
Array<UInt> material;
};
using MyFEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
protected:
using EventManager = EventHandlerManager<SolidMechanicsModelEventHandler>;
public:
SolidMechanicsModel(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const ID & id = "solid_mechanics_model",
const MemoryID & memory_id = 0);
- virtual ~SolidMechanicsModel();
+ ~SolidMechanicsModel() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <typename P, typename T, typename... pack>
void initFull(named_argument::param_t<P, T &&> && first, pack &&... _pack) {
this->initFull(SolidMechanicsModelOptions{use_named_args, first, _pack...});
}
/// initialize completely the model
void initFull(
const ModelOptions & options = SolidMechanicsModelOptions()) override;
/// initialize the fem object needed for boundary conditions
void initFEEngineBoundary();
protected:
/// initialize all internal arrays for materials
virtual void initMaterials();
/// initialize the model
void initModel() override;
/// function to print the containt of the class
void printself(std::ostream & stream, int indent = 0) const override;
/// get some default values for derived classes
std::tuple<ID, TimeStepSolverType>
getDefaultSolverID(const AnalysisMethod & method) override;
/* ------------------------------------------------------------------------ */
/* Solver interface */
/* ------------------------------------------------------------------------ */
public:
/// assembles the stiffness matrix,
virtual void assembleStiffnessMatrix();
/// assembles the internal forces in the array internal_forces
virtual void assembleInternalForces();
protected:
/// callback for the solver, this adds f_{ext} - f_{int} to the residual
void assembleResidual() override;
/// get the type of matrix needed
MatrixType getMatrixType(const ID & matrix_id) override;
/// callback for the solver, this assembles different matrices
void assembleMatrix(const ID & matrix_id) override;
/// callback for the solver, this assembles the stiffness matrix
void assembleLumpedMatrix(const ID & matrix_id) override;
/// callback for the solver, this is called at beginning of solve
void predictor() override;
/// callback for the solver, this is called at end of solve
void corrector() override;
/// callback for the solver, this is called at beginning of solve
void beforeSolveStep() override;
/// callback for the solver, this is called at end of solve
void afterSolveStep() override;
/// Callback for the model to instantiate the matricees when needed
void initSolver(TimeStepSolverType time_step_solver_type,
NonLinearSolverType non_linear_solver_type) override;
protected:
/* ------------------------------------------------------------------------ */
TimeStepSolverType getDefaultSolverType() const override;
/* ------------------------------------------------------------------------ */
ModelSolverOptions
getDefaultSolverOptions(const TimeStepSolverType & type) const override;
public:
bool isDefaultSolverExplicit() {
return method == _explicit_lumped_mass ||
method == _explicit_consistent_mass;
}
protected:
/// update the current position vector
void updateCurrentPosition();
/* ------------------------------------------------------------------------ */
/* Materials (solid_mechanics_model_material.cc) */
/* ------------------------------------------------------------------------ */
public:
/// register an empty material of a given type
Material & registerNewMaterial(const ID & mat_name, const ID & mat_type,
const ID & opt_param);
/// reassigns materials depending on the material selector
virtual void reassignMaterial();
/// apply a constant eigen_grad_u on all quadrature points of a given material
virtual void applyEigenGradU(const Matrix<Real> & prescribed_eigen_grad_u,
const ID & material_name,
const GhostType ghost_type = _not_ghost);
protected:
/// register a material in the dynamic database
Material & registerNewMaterial(const ParserSection & mat_section);
/// read the material files to instantiate all the materials
void instantiateMaterials();
/// set the element_id_by_material and add the elements to the good materials
void
- assignMaterialToElements(const ElementTypeMapArray<UInt> * filter = NULL);
+ assignMaterialToElements(const ElementTypeMapArray<UInt> * filter = nullptr);
/* ------------------------------------------------------------------------ */
/* Mass (solid_mechanics_model_mass.cc) */
/* ------------------------------------------------------------------------ */
public:
/// assemble the lumped mass matrix
void assembleMassLumped();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
protected:
/// assemble the lumped mass matrix for local and ghost elements
void assembleMassLumped(GhostType ghost_type);
/// assemble the mass matrix for either _ghost or _not_ghost elements
void assembleMass(GhostType ghost_type);
/// fill a vector of rho
void computeRho(Array<Real> & rho, ElementType type, GhostType ghost_type);
/// compute the kinetic energy
Real getKineticEnergy();
Real getKineticEnergy(const ElementType & type, UInt index);
/// compute the external work (for impose displacement, the velocity should be
/// given too)
Real getExternalWork();
/* ------------------------------------------------------------------------ */
/* NonLocalManager inherited members */
/* ------------------------------------------------------------------------ */
protected:
void initializeNonLocal() override;
void updateDataForNonLocalCriterion(ElementTypeMapReal & criterion) override;
void computeNonLocalStresses(const GhostType & ghost_type) override;
void
insertIntegrationPointsInNeighborhoods(const GhostType & ghost_type) override;
/// update the values of the non local internal
void updateLocalInternal(ElementTypeMapReal & internal_flat,
const GhostType & ghost_type,
const ElementKind & kind) override;
/// copy the results of the averaging in the materials
void updateNonLocalInternal(ElementTypeMapReal & internal_flat,
const GhostType & ghost_type,
const ElementKind & kind) override;
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) override;
UInt getNbData(const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void packData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) override;
protected:
void
splitElementByMaterial(const Array<Element> & elements,
std::vector<Array<Element>> & elements_per_mat) const;
template <typename Operation>
void splitByMaterial(const Array<Element> & elements, Operation && op) const;
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
void onNodesRemoved(const Array<UInt> & element_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) override;
void onElementsAdded(const Array<Element> & nodes_list,
const NewElementsEvent & event) override;
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override{};
/* ------------------------------------------------------------------------ */
/* Dumpable interface (kept for convenience) and dumper relative functions */
/* ------------------------------------------------------------------------ */
public:
virtual void onDump();
//! decide wether a field is a material internal or not
bool isInternal(const std::string & field_name,
const ElementKind & element_kind);
#ifndef SWIG
//! give the amount of data per element
virtual ElementTypeMap<UInt>
getInternalDataPerElem(const std::string & field_name,
const ElementKind & kind);
//! flatten a given material internal field
ElementTypeMapArray<Real> &
flattenInternal(const std::string & field_name, const ElementKind & kind,
const GhostType ghost_type = _not_ghost);
//! flatten all the registered material internals
void flattenAllRegisteredInternals(const ElementKind & kind);
#endif
dumper::Field * createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
dumper::Field * createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag) override;
dumper::Field * createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
const UInt & spatial_dimension,
const ElementKind & kind) override;
virtual void dump(const std::string & dumper_name);
virtual void dump(const std::string & dumper_name, UInt step);
virtual void dump(const std::string & dumper_name, Real time, UInt step);
void dump() override;
virtual void dump(UInt step);
virtual void dump(Real time, UInt step);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the dimension of the system space
AKANTU_GET_MACRO(SpatialDimension, Model::spatial_dimension, UInt);
/// set the value of the time step
void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// get the value of the conversion from forces/ mass to acceleration
AKANTU_GET_MACRO(F_M2A, f_m2a, Real);
/// set the value of the conversion from forces/ mass to acceleration
AKANTU_SET_MACRO(F_M2A, f_m2a, Real);
/// get the SolidMechanicsModel::displacement vector
AKANTU_GET_MACRO(Displacement, *displacement, Array<Real> &);
/// get the SolidMechanicsModel::previous_displacement vector
AKANTU_GET_MACRO(PreviousDisplacement, *previous_displacement, Array<Real> &);
/// get the SolidMechanicsModel::current_position vector \warn only consistent
/// after a call to SolidMechanicsModel::updateCurrentPosition
const Array<Real> & getCurrentPosition();
/// get the SolidMechanicsModel::increment vector \warn only consistent if
/// SolidMechanicsModel::setIncrementFlagOn has been called before
AKANTU_GET_MACRO(Increment, *displacement_increment, Array<Real> &);
/// get the lumped SolidMechanicsModel::mass vector
AKANTU_GET_MACRO(Mass, *mass, Array<Real> &);
/// get the SolidMechanicsModel::velocity vector
AKANTU_GET_MACRO(Velocity, *velocity, Array<Real> &);
/// get the SolidMechanicsModel::acceleration vector, updated by
/// SolidMechanicsModel::updateAcceleration
AKANTU_GET_MACRO(Acceleration, *acceleration, Array<Real> &);
/// get the SolidMechanicsModel::force vector (external forces)
AKANTU_GET_MACRO(Force, *external_force, Array<Real> &);
/// get the SolidMechanicsModel::internal_force vector (internal forces)
AKANTU_GET_MACRO(InternalForce, *internal_force, Array<Real> &);
/// get the SolidMechanicsModel::blocked_dofs vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<bool> &);
/// get the value of the SolidMechanicsModel::increment_flag
AKANTU_GET_MACRO(IncrementFlag, increment_flag, bool);
/// get a particular material (by material index)
inline Material & getMaterial(UInt mat_index);
/// get a particular material (by material index)
inline const Material & getMaterial(UInt mat_index) const;
/// get a particular material (by material name)
inline Material & getMaterial(const std::string & name);
/// get a particular material (by material name)
inline const Material & getMaterial(const std::string & name) const;
/// get a particular material id from is name
inline UInt getMaterialIndex(const std::string & name) const;
/// give the number of materials
inline UInt getNbMaterials() const { return materials.size(); }
inline void setMaterialSelector(MaterialSelector & selector);
/// give the material internal index from its id
Int getInternalIndexFromID(const ID & id) const;
/// compute the stable time step
Real getStableTimeStep();
/// get the energies
Real getEnergy(const std::string & energy_id);
/// compute the energy for energy
Real getEnergy(const std::string & energy_id, const ElementType & type,
UInt index);
/// get the FEEngine object to integrate or interpolate on the boundary
FEEngine & getFEEngineBoundary(const ID & name = "") override;
AKANTU_GET_MACRO(MaterialByElement, material_index,
const ElementTypeMapArray<UInt> &);
/// vectors containing local material element index for each global element
/// index
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(MaterialByElement, material_index,
UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(MaterialByElement, material_index, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(MaterialLocalNumbering,
material_local_numbering, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(MaterialLocalNumbering,
material_local_numbering, UInt);
/// Access the non_local_manager interface
AKANTU_GET_MACRO(NonLocalManager, *non_local_manager, NonLocalManager &);
protected:
friend class Material;
protected:
/// compute the stable time step
Real getStableTimeStep(const GhostType & ghost_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// conversion coefficient form force/mass to acceleration
Real f_m2a;
/// displacements array
Array<Real> * displacement;
UInt displacement_release{0};
/// displacements array at the previous time step (used in finite deformation)
Array<Real> * previous_displacement{nullptr};
/// increment of displacement
Array<Real> * displacement_increment{nullptr};
/// lumped mass array
Array<Real> * mass{nullptr};
/// Check if materials need to recompute the mass array
bool need_to_reassemble_lumped_mass{true};
/// Check if materials need to recompute the mass matrix
bool need_to_reassemble_mass{true};
/// velocities array
Array<Real> * velocity{nullptr};
/// accelerations array
Array<Real> * acceleration{nullptr};
/// accelerations array
// Array<Real> * increment_acceleration;
/// external forces array
Array<Real> * external_force{nullptr};
/// internal forces array
Array<Real> * internal_force{nullptr};
/// array specifing if a degree of freedom is blocked or not
Array<bool> * blocked_dofs{nullptr};
/// array of current position used during update residual
Array<Real> * current_position{nullptr};
UInt current_position_release{0};
/// Arrays containing the material index for each element
ElementTypeMapArray<UInt> material_index;
/// Arrays containing the position in the element filter of the material
/// (material's local numbering)
ElementTypeMapArray<UInt> material_local_numbering;
#ifdef SWIGPYTHON
public:
#endif
/// list of used materials
std::vector<std::unique_ptr<Material>> materials;
/// mapping between material name and material internal id
std::map<std::string, UInt> materials_names_to_id;
#ifdef SWIGPYTHON
protected:
#endif
/// class defining of to choose a material
MaterialSelector * material_selector;
/// define if it is the default selector or not
bool is_default_material_selector;
/// flag defining if the increment must be computed or not
bool increment_flag;
/// tells if the material are instantiated
bool are_materials_instantiated;
typedef std::map<std::pair<std::string, ElementKind>,
ElementTypeMapArray<Real> *>
flatten_internal_map;
/// map a registered internals to be flattened for dump purposes
flatten_internal_map registered_internals;
/// non local manager
std::unique_ptr<NonLocalManager> non_local_manager;
};
/* -------------------------------------------------------------------------- */
namespace BC {
namespace Neumann {
typedef FromHigherDim FromStress;
typedef FromSameDim FromTraction;
} // namespace Neumann
} // namespace BC
} // namespace akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "parser.hh"
#include "solid_mechanics_model_inline_impl.cc"
#include "solid_mechanics_model_tmpl.hh"
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
index 80bd758d2..1d001ff32 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.cc
@@ -1,615 +1,615 @@
/**
* @file fragment_manager.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Thu Jan 23 2014
* @date last modification: Mon Dec 14 2015
*
* @brief Group manager to handle fragments
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "fragment_manager.hh"
#include "aka_iterators.hh"
#include "material_cohesive.hh"
#include "mesh_iterators.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <functional>
#include <numeric>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
FragmentManager::FragmentManager(SolidMechanicsModelCohesive & model,
bool dump_data, const ID & id,
const MemoryID & memory_id)
: GroupManager(model.getMesh(), id, memory_id), model(model),
mass_center(0, model.getSpatialDimension(), "mass_center"),
mass(0, model.getSpatialDimension(), "mass"),
velocity(0, model.getSpatialDimension(), "velocity"),
inertia_moments(0, model.getSpatialDimension(), "inertia_moments"),
principal_directions(
0, model.getSpatialDimension() * model.getSpatialDimension(),
"principal_directions"),
quad_coordinates("quad_coordinates", id),
mass_density("mass_density", id),
nb_elements_per_fragment(0, 1, "nb_elements_per_fragment"),
dump_data(dump_data) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
/// compute quadrature points' coordinates
quad_coordinates.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost);
// mesh.initElementTypeMapArray(quad_coordinates, spatial_dimension,
// spatial_dimension, _not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getMesh().getNodes(),
quad_coordinates);
/// store mass density per quadrature point
mass_density.initialize(mesh, _spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost);
// mesh.initElementTypeMapArray(mass_density, 1, spatial_dimension,
// _not_ghost);
storeMassDensityPerIntegrationPoint();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
class CohesiveElementFilter : public GroupManager::ClusteringFilter {
public:
CohesiveElementFilter(const SolidMechanicsModelCohesive & model,
const Real max_damage = 1.)
: model(model), is_unbroken(max_damage) {}
- bool operator()(const Element & el) const {
+ bool operator()(const Element & el) const override {
if (Mesh::getKind(el.type) == _ek_regular)
return true;
const Array<UInt> & mat_indexes =
model.getMaterialByElement(el.type, el.ghost_type);
const Array<UInt> & mat_loc_num =
model.getMaterialLocalNumbering(el.type, el.ghost_type);
const MaterialCohesive & mat = static_cast<const MaterialCohesive &>(
model.getMaterial(mat_indexes(el.element)));
UInt el_index = mat_loc_num(el.element);
UInt nb_quad_per_element =
model.getFEEngine("CohesiveFEEngine")
.getNbIntegrationPoints(el.type, el.ghost_type);
const Array<Real> & damage_array = mat.getDamage(el.type, el.ghost_type);
AKANTU_DEBUG_ASSERT(nb_quad_per_element * el_index < damage_array.size(),
"This quadrature point is out of range");
const Real * element_damage =
damage_array.storage() + nb_quad_per_element * el_index;
UInt unbroken_quads = std::count_if(
element_damage, element_damage + nb_quad_per_element, is_unbroken);
if (unbroken_quads > 0)
return true;
return false;
}
private:
struct IsUnbrokenFunctor {
IsUnbrokenFunctor(const Real & max_damage) : max_damage(max_damage) {}
bool operator()(const Real & x) { return x < max_damage; }
const Real max_damage;
};
const SolidMechanicsModelCohesive & model;
const IsUnbrokenFunctor is_unbroken;
};
/* -------------------------------------------------------------------------- */
void FragmentManager::buildFragments(Real damage_limit) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
ElementSynchronizer * cohesive_synchronizer =
const_cast<ElementSynchronizer *>(model.getCohesiveSynchronizer());
if (cohesive_synchronizer) {
cohesive_synchronizer->computeBufferSize(model, _gst_smmc_damage);
cohesive_synchronizer->asynchronousSynchronize(model, _gst_smmc_damage);
cohesive_synchronizer->waitEndSynchronize(model, _gst_smmc_damage);
}
#endif
auto & mesh_facets = const_cast<Mesh &>(mesh.getMeshFacets());
UInt spatial_dimension = model.getSpatialDimension();
std::string fragment_prefix("fragment");
/// generate fragments
global_nb_fragment =
createClusters(spatial_dimension, mesh_facets, fragment_prefix,
CohesiveElementFilter(model, damage_limit));
nb_fragment = getNbElementGroups(spatial_dimension);
fragment_index.resize(nb_fragment);
UInt * fragment_index_it = fragment_index.storage();
/// loop over fragments
for (const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
/// get fragment index
std::string fragment_index_string =
it->first.substr(fragment_prefix.size() + 1);
std::stringstream sstr(fragment_index_string.c_str());
sstr >> *fragment_index_it;
AKANTU_DEBUG_ASSERT(!sstr.fail(), "fragment_index is not an integer");
}
/// compute fragments' mass
computeMass();
if (dump_data) {
createDumpDataArray(fragment_index, "fragments", true);
createDumpDataArray(mass, "fragments mass");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeMass() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
/// create a unit field per quadrature point, since to compute mass
/// it's neccessary to integrate only density
ElementTypeMapArray<Real> unit_field("unit_field", id);
unit_field.initialize(model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost, _default_value = 1.);
// mesh.initElementTypeMapArray(unit_field, spatial_dimension,
// spatial_dimension,
// _not_ghost);
// ElementTypeMapArray<Real>::type_iterator it =
// unit_field.firstType(spatial_dimension, _not_ghost, _ek_regular);
// ElementTypeMapArray<Real>::type_iterator end =
// unit_field.lastType(spatial_dimension, _not_ghost, _ek_regular);
// for (; it != end; ++it) {
// ElementType type = *it;
// Array<Real> & field_array = unit_field(type);
// UInt nb_element = mesh.getNbElement(type);
// UInt nb_quad_per_element =
// model.getFEEngine().getNbIntegrationPoints(type);
// field_array.resize(nb_element * nb_quad_per_element);
// field_array.set(1.);
// }
integrateFieldOnFragments(unit_field, mass);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeCenterOfMass() {
AKANTU_DEBUG_IN();
/// integrate position multiplied by density
integrateFieldOnFragments(quad_coordinates, mass_center);
/// divide it by the fragments' mass
Real * mass_storage = mass.storage();
Real * mass_center_storage = mass_center.storage();
UInt total_components = mass_center.size() * mass_center.getNbComponent();
for (UInt i = 0; i < total_components; ++i)
mass_center_storage[i] /= mass_storage[i];
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeVelocity() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
/// compute velocity per quadrature point
ElementTypeMapArray<Real> velocity_field("velocity_field", id);
velocity_field.initialize(
model.getFEEngine(), _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension, _ghost_type = _not_ghost);
// mesh.initElementTypeMapArray(velocity_field, spatial_dimension,
// spatial_dimension, _not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getVelocity(),
velocity_field);
/// integrate on fragments
integrateFieldOnFragments(velocity_field, velocity);
/// divide it by the fragments' mass
Real * mass_storage = mass.storage();
Real * velocity_storage = velocity.storage();
UInt total_components = velocity.size() * velocity.getNbComponent();
for (UInt i = 0; i < total_components; ++i)
velocity_storage[i] /= mass_storage[i];
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Given the distance @f$ \mathbf{r} @f$ between a quadrature point
* and its center of mass, the moment of inertia is computed as \f[
* I_\mathrm{CM} = \mathrm{tr}(\mathbf{r}\mathbf{r}^\mathrm{T})
* \mathbf{I} - \mathbf{r}\mathbf{r}^\mathrm{T} \f] for more
* information check Wikipedia
* (http://en.wikipedia.org/wiki/Moment_of_inertia#Identities_for_a_skew-symmetric_matrix)
*
*/
void FragmentManager::computeInertiaMoments() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
computeCenterOfMass();
/// compute local coordinates products with respect to the center of match
ElementTypeMapArray<Real> moments_coords("moments_coords", id);
moments_coords.initialize(model.getFEEngine(),
_nb_component =
spatial_dimension * spatial_dimension,
_spatial_dimension = spatial_dimension,
_ghost_type = _not_ghost, _default_value = 1.);
// mesh.initElementTypeMapArray(moments_coords,
// spatial_dimension * spatial_dimension,
// spatial_dimension, _not_ghost);
// /// resize the by element type
// ElementTypeMapArray<Real>::type_iterator it =
// moments_coords.firstType(spatial_dimension, _not_ghost, _ek_regular);
// ElementTypeMapArray<Real>::type_iterator end =
// moments_coords.lastType(spatial_dimension, _not_ghost, _ek_regular);
// for (; it != end; ++it) {
// ElementType type = *it;
// Array<Real> & field_array = moments_coords(type);
// UInt nb_element = mesh.getNbElement(type);
// UInt nb_quad_per_element =
// model.getFEEngine().getNbIntegrationPoints(type);
// field_array.resize(nb_element * nb_quad_per_element);
// }
/// compute coordinates
Array<Real>::const_vector_iterator mass_center_it =
mass_center.begin(spatial_dimension);
/// loop over fragments
for (const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++mass_center_it) {
const ElementTypeMapArray<UInt> & el_list = it->second->getElements();
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_quad_per_element =
model.getFEEngine().getNbIntegrationPoints(type);
Array<Real> & moments_coords_array = moments_coords(type);
const Array<Real> & quad_coordinates_array = quad_coordinates(type);
const Array<UInt> & el_list_array = el_list(type);
Array<Real>::matrix_iterator moments_begin =
moments_coords_array.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_vector_iterator quad_coordinates_begin =
quad_coordinates_array.begin(spatial_dimension);
Vector<Real> relative_coords(spatial_dimension);
for (UInt el = 0; el < el_list_array.size(); ++el) {
UInt global_el = el_list_array(el);
/// loop over quadrature points
for (UInt q = 0; q < nb_quad_per_element; ++q) {
UInt global_q = global_el * nb_quad_per_element + q;
Matrix<Real> moments_matrix = moments_begin[global_q];
const Vector<Real> & quad_coord_vector =
quad_coordinates_begin[global_q];
/// to understand this read the documentation written just
/// before this function
relative_coords = quad_coord_vector;
relative_coords -= *mass_center_it;
moments_matrix.outerProduct(relative_coords, relative_coords);
Real trace = moments_matrix.trace();
moments_matrix *= -1.;
moments_matrix += Matrix<Real>::eye(spatial_dimension, trace);
}
}
}
}
/// integrate moments
Array<Real> integrated_moments(global_nb_fragment,
spatial_dimension * spatial_dimension);
integrateFieldOnFragments(moments_coords, integrated_moments);
/// compute and store principal moments
inertia_moments.resize(global_nb_fragment);
principal_directions.resize(global_nb_fragment);
Array<Real>::matrix_iterator integrated_moments_it =
integrated_moments.begin(spatial_dimension, spatial_dimension);
Array<Real>::vector_iterator inertia_moments_it =
inertia_moments.begin(spatial_dimension);
Array<Real>::matrix_iterator principal_directions_it =
principal_directions.begin(spatial_dimension, spatial_dimension);
for (UInt frag = 0; frag < global_nb_fragment; ++frag,
++integrated_moments_it, ++inertia_moments_it,
++principal_directions_it) {
integrated_moments_it->eig(*inertia_moments_it, *principal_directions_it);
}
if (dump_data)
createDumpDataArray(inertia_moments, "moments of inertia");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeAllData() {
AKANTU_DEBUG_IN();
buildFragments();
computeVelocity();
computeInertiaMoments();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::storeMassDensityPerIntegrationPoint() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator end = mesh.lastType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
Array<Real> & mass_density_array = mass_density(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
mass_density_array.resize(nb_element * nb_quad_per_element);
const Array<UInt> & mat_indexes = model.getMaterialByElement(type);
Real * mass_density_it = mass_density_array.storage();
/// store mass_density for each element and quadrature point
for (UInt el = 0; el < nb_element; ++el) {
Material & mat = model.getMaterial(mat_indexes(el));
for (UInt q = 0; q < nb_quad_per_element; ++q, ++mass_density_it)
*mass_density_it = mat.getRho();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::integrateFieldOnFragments(
ElementTypeMapArray<Real> & field, Array<Real> & output) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
UInt nb_component = output.getNbComponent();
/// integration part
output.resize(global_nb_fragment);
output.clear();
UInt * fragment_index_it = fragment_index.storage();
Array<Real>::vector_iterator output_begin = output.begin(nb_component);
/// loop over fragments
for (const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
const ElementTypeMapArray<UInt> & el_list = it->second->getElements();
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_quad_per_element =
model.getFEEngine().getNbIntegrationPoints(type);
const Array<Real> & density_array = mass_density(type);
Array<Real> & field_array = field(type);
const Array<UInt> & elements = el_list(type);
UInt nb_element = elements.size();
/// generate array to be integrated by filtering fragment's elements
Array<Real> integration_array(elements.size() * nb_quad_per_element,
nb_component);
Array<Real>::matrix_iterator int_array_it =
integration_array.begin_reinterpret(nb_quad_per_element, nb_component,
nb_element);
Array<Real>::matrix_iterator int_array_end =
integration_array.end_reinterpret(nb_quad_per_element, nb_component,
nb_element);
Array<Real>::matrix_iterator field_array_begin =
field_array.begin_reinterpret(nb_quad_per_element, nb_component,
field_array.size() /
nb_quad_per_element);
Array<Real>::const_vector_iterator density_array_begin =
density_array.begin_reinterpret(nb_quad_per_element,
density_array.size() /
nb_quad_per_element);
for (UInt el = 0; int_array_it != int_array_end; ++int_array_it, ++el) {
UInt global_el = elements(el);
*int_array_it = field_array_begin[global_el];
/// multiply field by density
const Vector<Real> & density_vector = density_array_begin[global_el];
for (UInt i = 0; i < nb_quad_per_element; ++i) {
for (UInt j = 0; j < nb_component; ++j) {
(*int_array_it)(i, j) *= density_vector(i);
}
}
}
/// integrate the field over the fragment
Array<Real> integrated_array(elements.size(), nb_component);
model.getFEEngine().integrate(integration_array, integrated_array,
nb_component, type, _not_ghost, elements);
/// sum over all elements and store the result
Vector<Real> output_tmp(output_begin[*fragment_index_it]);
output_tmp += std::accumulate(integrated_array.begin(nb_component),
integrated_array.end(nb_component),
Vector<Real>(nb_component));
}
}
/// sum output over all processors
const Communicator & comm = mesh.getCommunicator();
comm.allReduce(output, SynchronizerOperation::_sum);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FragmentManager::computeNbElementsPerFragment() {
AKANTU_DEBUG_IN();
UInt spatial_dimension = model.getSpatialDimension();
nb_elements_per_fragment.resize(global_nb_fragment);
nb_elements_per_fragment.clear();
UInt * fragment_index_it = fragment_index.storage();
/// loop over fragments
for (const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
const ElementTypeMapArray<UInt> & el_list = it->second->getElements();
/// loop over elements of the fragment
for (auto type :
el_list.elementTypes(spatial_dimension, _not_ghost, _ek_regular)) {
UInt nb_element = el_list(type).size();
nb_elements_per_fragment(*fragment_index_it) += nb_element;
}
}
/// sum values over all processors
const auto & comm = mesh.getCommunicator();
comm.allReduce(nb_elements_per_fragment, SynchronizerOperation::_sum);
if (dump_data)
createDumpDataArray(nb_elements_per_fragment, "elements per fragment");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void FragmentManager::createDumpDataArray(Array<T> & data, std::string name,
bool fragment_index_output) {
AKANTU_DEBUG_IN();
if (data.size() == 0)
return;
auto & mesh_not_const = const_cast<Mesh &>(mesh);
auto && spatial_dimension = mesh.getSpatialDimension();
auto && nb_component = data.getNbComponent();
auto && data_begin = data.begin(nb_component);
auto fragment_index_it = fragment_index.begin();
/// loop over fragments
for (const auto & fragment : ElementGroupsIterable(*this)) {
const auto & fragment_idx = *fragment_index_it;
/// loop over cluster types
for (auto & type : fragment.elementTypes(spatial_dimension)) {
/// init mesh data
auto & mesh_data = mesh_not_const.getDataPointer<T>(
name, type, _not_ghost, nb_component);
auto mesh_data_begin = mesh_data.begin(nb_component);
/// fill mesh data
for (const auto & elem : fragment.getElements(type)) {
Vector<T> md_tmp = mesh_data_begin[elem];
if (fragment_index_output) {
md_tmp(0) = fragment_idx;
} else {
md_tmp = data_begin[fragment_idx];
}
}
}
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
index 84b18a443..269fdd115 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.hh
@@ -1,75 +1,76 @@
/**
* @file material_selector_cohesive.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Dec 11 2015
* @date last modification: Mon Dec 14 2015
*
* @brief Material selectors for cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2015 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 "material_selector.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
#ifndef __AKANTU_MATERIAL_SELECTOR_COHESIVE_HH__
#define __AKANTU_MATERIAL_SELECTOR_COHESIVE_HH__
/* -------------------------------------------------------------------------- */
/**
* class that assigns the first cohesive material by default to the
* cohesive elements
*/
class DefaultMaterialCohesiveSelector : public DefaultMaterialSelector {
public:
DefaultMaterialCohesiveSelector(const SolidMechanicsModelCohesive & model);
- virtual UInt operator()(const Element & element);
+ UInt operator()(const Element & element) override;
private:
const ElementTypeMapArray<UInt> & facet_material;
const Mesh & mesh;
};
/* -------------------------------------------------------------------------- */
/// To be used with intrinsic elements inserted along mesh physical surfaces
class MeshDataMaterialCohesiveSelector
: public MeshDataMaterialSelector<std::string> {
public:
MeshDataMaterialCohesiveSelector(const SolidMechanicsModelCohesive & model);
- virtual UInt operator()(const Element & element);
+ UInt operator()(const Element & element) override;
+
protected:
const Mesh &mesh_facets;
const ElementTypeMapArray<UInt> & material_index;
bool third_dimension;
};
#endif /* __AKANTU_MATERIAL_SELECTOR_COHESIVE_HH__ */
} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
index 241604669..946884013 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/cohesive_internal_field.hh
@@ -1,70 +1,71 @@
/**
* @file cohesive_internal_field.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 08 2015
*
* @brief Internal field for cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "internal_field.hh"
#ifndef __AKANTU_COHESIVE_INTERNAL_FIELD_HH__
#define __AKANTU_COHESIVE_INTERNAL_FIELD_HH__
namespace akantu {
/// internal field class for cohesive materials
template<typename T>
class CohesiveInternalField : public InternalField<T> {
public:
CohesiveInternalField(const ID & id, Material & material);
- virtual ~CohesiveInternalField();
+ ~CohesiveInternalField() override;
/// initialize the field to a given number of component
- void initialize(UInt nb_component);
+ void initialize(UInt nb_component) override;
+
private:
CohesiveInternalField operator=(__attribute__((unused)) const CohesiveInternalField & other) {};
};
/* -------------------------------------------------------------------------- */
/* Facet Internal Field */
/* -------------------------------------------------------------------------- */
template<typename T>
class FacetInternalField : public InternalField<T> {
public:
FacetInternalField(const ID & id, Material & material);
- virtual ~FacetInternalField();
+ ~FacetInternalField() override;
/// initialize the field to a given number of component
- void initialize(UInt nb_component);
+ void initialize(UInt nb_component) override;
};
} // akantu
#endif /* __AKANTU_COHESIVE_INTERNAL_FIELD_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
index 52c228a0d..ee1d80f9d 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/materials/material_cohesive.hh
@@ -1,261 +1,256 @@
/**
* @file material_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Jan 12 2016
*
* @brief Specialization of the material class for cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "material.hh"
/* -------------------------------------------------------------------------- */
#include "cohesive_internal_field.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_HH__
#define __AKANTU_MATERIAL_COHESIVE_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelCohesive;
}
namespace akantu {
class MaterialCohesive : public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive>
MyFEEngineCohesiveType;
public:
MaterialCohesive(SolidMechanicsModel & model, const ID & id = "");
- virtual ~MaterialCohesive();
+ ~MaterialCohesive() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
- virtual void initMaterial();
+ void initMaterial() override;
/// compute tractions (including normals and openings)
void computeTraction(GhostType ghost_type = _not_ghost);
/// assemble residual
- void assembleInternalForces(GhostType ghost_type = _not_ghost);
+ void assembleInternalForces(GhostType ghost_type = _not_ghost) override;
/// compute reversible and total energies by element
void computeEnergies();
/// check stress for cohesive elements' insertion, by default it
/// also updates the cohesive elements' data
- virtual void checkInsertion(__attribute__((unused)) bool check_only = false) {
+ virtual void checkInsertion(bool /*check_only*/ = false) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// check delta_max for cohesive elements in case of no convergence
/// in the solveStep (only for extrinsic-implicit)
- virtual void checkDeltaMax(__attribute__((unused))
- GhostType ghost_type = _not_ghost) {
+ virtual void checkDeltaMax(GhostType /*ghost_type*/ = _not_ghost) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// reset variables when convergence is reached (only for
/// extrinsic-implicit)
- virtual void resetVariables(__attribute__((unused))
- GhostType ghost_type = _not_ghost) {
+ virtual void resetVariables(GhostType /*ghost_type*/ = _not_ghost) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// interpolate stress on given positions for each element (empty
/// implemantation to avoid the generic call to be done on cohesive elements)
- virtual void interpolateStress(__attribute__((unused)) const ElementType type,
- __attribute__((unused))
- Array<Real> & result){};
+ virtual void interpolateStress(const ElementType /*type*/,
+
+ Array<Real> & /*result*/){};
/// compute the stresses
- virtual void computeAllStresses(__attribute__((unused))
- GhostType ghost_type = _not_ghost){};
+ void computeAllStresses(GhostType /*ghost_type*/ = _not_ghost) override{};
// add the facet to be handled by the material
UInt addFacet(const Element & element);
protected:
- virtual void
- computeTangentTraction(__attribute__((unused)) const ElementType & el_type,
- __attribute__((unused)) Array<Real> & tangent_matrix,
- __attribute__((unused)) const Array<Real> & normal,
- __attribute__((unused))
- GhostType ghost_type = _not_ghost) {
+ virtual void computeTangentTraction(const ElementType & /*el_type*/,
+ Array<Real> & /*tangent_matrix*/,
+ const Array<Real> & /*normal*/,
+ GhostType /*ghost_type*/ = _not_ghost) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// compute the normal
void computeNormal(const Array<Real> & position, Array<Real> & normal,
ElementType type, GhostType ghost_type);
/// compute the opening
void computeOpening(const Array<Real> & displacement, Array<Real> & opening,
ElementType type, GhostType ghost_type);
template <ElementType type>
void computeNormal(const Array<Real> & position, Array<Real> & normal,
GhostType ghost_type);
/// assemble stiffness
- void assembleStiffnessMatrix(GhostType ghost_type);
+ void assembleStiffnessMatrix(GhostType ghost_type) override;
/// constitutive law
virtual void computeTraction(const Array<Real> & normal, ElementType el_type,
GhostType ghost_type = _not_ghost) = 0;
/// parallelism functions
inline UInt getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const;
inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const;
inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the opening
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Opening, opening, Real);
/// get the traction
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Traction, tractions, Real);
/// get damage
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real);
/// get facet filter
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(FacetFilter, facet_filter, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(FacetFilter, facet_filter, UInt);
AKANTU_GET_MACRO(FacetFilter, facet_filter,
const ElementTypeMapArray<UInt> &);
// AKANTU_GET_MACRO(ElementFilter, element_filter, const
// ElementTypeMapArray<UInt> &);
/// compute reversible energy
Real getReversibleEnergy();
/// compute dissipated energy
Real getDissipatedEnergy();
/// compute contact energy
Real getContactEnergy();
/// get energy
- virtual Real getEnergy(std::string type);
+ Real getEnergy(std::string type) override;
/// return the energy (identified by id) for the provided element
- virtual Real getEnergy(std::string energy_id, ElementType type, UInt index) {
+ Real getEnergy(std::string energy_id, ElementType type, UInt index) override {
return Material::getEnergy(energy_id, type, index);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// list of facets assigned to this material
ElementTypeMapArray<UInt> facet_filter;
/// Link to the cohesive fem object in the model
FEEngine & fem_cohesive;
private:
/// reversible energy by quadrature point
CohesiveInternalField<Real> reversible_energy;
/// total energy by quadrature point
CohesiveInternalField<Real> total_energy;
protected:
/// opening in all elements and quadrature points
CohesiveInternalField<Real> opening;
/// opening in all elements and quadrature points (previous time step)
CohesiveInternalField<Real> opening_old;
/// traction in all elements and quadrature points
CohesiveInternalField<Real> tractions;
/// traction in all elements and quadrature points (previous time step)
CohesiveInternalField<Real> tractions_old;
/// traction due to contact
CohesiveInternalField<Real> contact_tractions;
/// normal openings for contact tractions
CohesiveInternalField<Real> contact_opening;
/// maximum displacement
CohesiveInternalField<Real> delta_max;
/// tell if the previous delta_max state is needed (in iterative schemes)
bool use_previous_delta_max;
/// tell if the previous opening state is needed (in iterative schemes)
bool use_previous_opening;
/// damage
CohesiveInternalField<Real> damage;
/// pointer to the solid mechanics model for cohesive elements
SolidMechanicsModelCohesive * model;
/// critical stress
RandomInternalField<Real, FacetInternalField> sigma_c;
/// critical displacement
Real delta_c;
/// array to temporarily store the normals
Array<Real> normal;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_cohesive_inline_impl.cc"
} // namespace akantu
#include "cohesive_internal_field_tmpl.hh"
#endif /* __AKANTU_MATERIAL_COHESIVE_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
index 551bd967e..7dbc2a198 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_parallel.cc
@@ -1,397 +1,397 @@
/**
* @file solid_mechanics_model_cohesive_parallel.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief Functions for parallel cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "solid_mechanics_model_tmpl.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::synchronizeGhostFacetsConnectivity() {
AKANTU_DEBUG_IN();
const Communicator & comm = mesh.getCommunicator();
Int psize = comm.getNbProc();
if (psize > 1) {
/// get global connectivity for not ghost facets
global_connectivity =
new ElementTypeMapArray<UInt>("global_connectivity", id);
auto & mesh_facets = inserter->getMeshFacets();
global_connectivity->initialize(
mesh_facets, _spatial_dimension = spatial_dimension - 1,
_with_nb_element = true, _with_nb_nodes_per_element = true,
_element_kind = _ek_regular,
_ghost_type = _not_ghost);
mesh_facets.getGlobalConnectivity(*global_connectivity);
/// communicate
synchronize(_gst_smmc_facets_conn);
/// flip facets
MeshUtils::flipFacets(mesh_facets, *global_connectivity, _ghost);
delete global_connectivity;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateCohesiveSynchronizers() {
/// update synchronizers if needed
if (not mesh.isDistributed())
return;
auto & mesh_facets = inserter->getMeshFacets();
auto & facet_synchronizer = mesh_facets.getElementSynchronizer();
const auto & cfacet_synchronizer = facet_synchronizer;
// update the cohesive element synchronizer
cohesive_synchronizer->updateSchemes(
[&](auto && scheme, auto && proc, auto && direction) {
auto & facet_scheme =
cfacet_synchronizer.getCommunications().getScheme(proc, direction);
for (auto && facet : facet_scheme) {
const auto & connected_elements = mesh_facets.getElementToSubelement(
facet.type,
facet.ghost_type)(facet.element); // slow access here
const auto & cohesive_element = connected_elements[1];
auto && cohesive_type = FEEngine::getCohesiveElementType(facet.type);
auto old_nb_cohesive_elements =
mesh.getNbElement(cohesive_type, facet.ghost_type);
old_nb_cohesive_elements -=
mesh.getData<UInt>("facet_to_double", facet.type,
facet.ghost_type).size();
if (cohesive_element.kind() == _ek_cohesive and
cohesive_element.element >= old_nb_cohesive_elements) {
scheme.push_back(cohesive_element);
}
}
});
const auto & comm = mesh.getCommunicator();
auto && my_rank = comm.whoAmI();
// update the facet stress synchronizer
facet_stress_synchronizer->updateSchemes([&](auto && scheme, auto && proc,
auto && /*direction*/) {
auto it_element = scheme.begin();
for (auto && element : scheme) {
auto && facet_check = inserter->getCheckFacets(
element.type, element.ghost_type)(element.element); // slow access
// here
if (facet_check) {
auto && connected_elements = mesh_facets.getElementToSubelement(
element.type, element.ghost_type)(element.element); // slow access
// here
auto && rank_left = facet_synchronizer.getRank(connected_elements[0]);
auto && rank_right = facet_synchronizer.getRank(connected_elements[1]);
// keep element if the element is still a boundary element between two
// processors
if ((rank_left == Int(proc) and rank_right == my_rank) or
(rank_left == my_rank and rank_right == Int(proc))) {
*it_element = element;
++it_element;
}
}
}
scheme.resize(it_element - scheme.begin());
});
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SolidMechanicsModelCohesive::packFacetStressDataHelper(
const ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
packUnpackFacetStressDataHelper<T, true>(
const_cast<ElementTypeMapArray<T> &>(data_to_pack), buffer, elements);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SolidMechanicsModelCohesive::unpackFacetStressDataHelper(
ElementTypeMapArray<T> & data_to_unpack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
packUnpackFacetStressDataHelper<T, false>(data_to_unpack, buffer, elements);
}
/* -------------------------------------------------------------------------- */
template <typename T, bool pack_helper>
void SolidMechanicsModelCohesive::packUnpackFacetStressDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements) const {
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
UInt nb_quad_per_elem = 0;
UInt sp2 = spatial_dimension * spatial_dimension;
UInt nb_component = sp2 * 2;
bool element_rank = 0;
Mesh & mesh_facets = inserter->getMeshFacets();
- Array<T> * vect = NULL;
- Array<std::vector<Element>> * element_to_facet = NULL;
+ Array<T> * vect = nullptr;
+ Array<std::vector<Element>> * element_to_facet = nullptr;
auto & fe_engine = this->getFEEngine("FacetsFEEngine");
for (auto && el : elements) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
vect = &data_to_pack(el.type, el.ghost_type);
element_to_facet =
&(mesh_facets.getElementToSubelement(el.type, el.ghost_type));
nb_quad_per_elem =
fe_engine.getNbIntegrationPoints(el.type, el.ghost_type);
}
if (pack_helper)
element_rank =
(*element_to_facet)(el.element)[0].ghost_type != _not_ghost;
else
element_rank =
(*element_to_facet)(el.element)[0].ghost_type == _not_ghost;
for (UInt q = 0; q < nb_quad_per_elem; ++q) {
Vector<T> data(vect->storage() +
(el.element * nb_quad_per_elem + q) * nb_component +
element_rank * sp2,
sp2);
if (pack_helper)
buffer << data;
else
buffer >> data;
}
}
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::getNbQuadsForFacetCheck(
const Array<Element> & elements) const {
UInt nb_quads = 0;
UInt nb_quad_per_facet = 0;
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
auto & fe_engine = this->getFEEngine("FacetsFEEngine");
for(auto & el : elements) {
if (el.type != current_element_type ||
el.ghost_type != current_ghost_type) {
current_element_type = el.type;
current_ghost_type = el.ghost_type;
nb_quad_per_facet = fe_engine
.getNbIntegrationPoints(el.type, el.ghost_type);
}
nb_quads += nb_quad_per_facet;
}
return nb_quads;
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::getNbData(
const Array<Element> & elements, const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
UInt size = 0;
if (elements.size() == 0)
return 0;
/// regular element case
if (elements(0).kind() == _ek_regular) {
switch (tag) {
case _gst_smmc_facets: {
size += elements.size() * sizeof(bool);
break;
}
case _gst_smmc_facets_conn: {
UInt nb_nodes = Mesh::getNbNodesPerElementList(elements);
size += nb_nodes * sizeof(UInt);
break;
}
case _gst_smmc_facets_stress: {
UInt nb_quads = getNbQuadsForFacetCheck(elements);
size += nb_quads * spatial_dimension * spatial_dimension * sizeof(Real);
break;
}
default: { size += SolidMechanicsModel::getNbData(elements, tag); }
}
}
/// cohesive element case
else if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case _gst_material_id: {
size += elements.size() * sizeof(UInt);
break;
}
case _gst_smm_boundary: {
UInt nb_nodes_per_element = 0;
for (auto && el : elements) {
nb_nodes_per_element += Mesh::getNbNodesPerElement(el.type);
}
// force, displacement, boundary
size += nb_nodes_per_element * spatial_dimension *
(2 * sizeof(Real) + sizeof(bool));
break;
}
default:
break;
}
if (tag != _gst_material_id && tag != _gst_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
size += mat.getNbData(elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
return size;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::packData(
CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
AKANTU_DEBUG_IN();
if (elements.size() == 0)
return;
if (elements(0).kind() == _ek_regular) {
switch (tag) {
case _gst_smmc_facets: {
packElementalDataHelper(inserter->getInsertionFacetsByElement(), buffer,
elements, false, getFEEngine());
break;
}
case _gst_smmc_facets_conn: {
packElementalDataHelper(*global_connectivity, buffer, elements, false,
getFEEngine());
break;
}
case _gst_smmc_facets_stress: {
packFacetStressDataHelper(facet_stress, buffer, elements);
break;
}
default: { SolidMechanicsModel::packData(buffer, elements, tag); }
}
} else if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case _gst_material_id: {
packElementalDataHelper(material_index, buffer, elements, false,
getFEEngine("CohesiveFEEngine"));
break;
}
case _gst_smm_boundary: {
packNodalDataHelper(*internal_force, buffer, elements, mesh);
packNodalDataHelper(*velocity, buffer, elements, mesh);
packNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {}
}
if (tag != _gst_material_id && tag != _gst_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.packData(buffer, elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
AKANTU_DEBUG_IN();
if (elements.size() == 0)
return;
if (elements(0).kind() == _ek_regular) {
switch (tag) {
case _gst_smmc_facets: {
unpackElementalDataHelper(inserter->getInsertionFacetsByElement(), buffer,
elements, false, getFEEngine());
break;
}
case _gst_smmc_facets_conn: {
unpackElementalDataHelper(*global_connectivity, buffer, elements, false,
getFEEngine());
break;
}
case _gst_smmc_facets_stress: {
unpackFacetStressDataHelper(facet_stress, buffer, elements);
break;
}
default: { SolidMechanicsModel::unpackData(buffer, elements, tag); }
}
} else if (elements(0).kind() == _ek_cohesive) {
switch (tag) {
case _gst_material_id: {
unpackElementalDataHelper(material_index, buffer, elements, false,
getFEEngine("CohesiveFEEngine"));
break;
}
case _gst_smm_boundary: {
unpackNodalDataHelper(*internal_force, buffer, elements, mesh);
unpackNodalDataHelper(*velocity, buffer, elements, mesh);
unpackNodalDataHelper(*blocked_dofs, buffer, elements, mesh);
break;
}
default: {}
}
if (tag != _gst_material_id && tag != _gst_smmc_facets) {
splitByMaterial(elements, [&](auto && mat, auto && elements) {
mat.unpackData(buffer, elements, tag);
});
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_mass.cc b/src/model/solid_mechanics/solid_mechanics_model_mass.cc
index b44d2e995..9cce541a0 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_mass.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_mass.cc
@@ -1,159 +1,159 @@
/**
* @file solid_mechanics_model_mass.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 05 2010
* @date last modification: Fri Oct 16 2015
*
* @brief function handling mass computation
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "integrator_gauss.hh"
#include "material.hh"
#include "model_solver.hh"
#include "shape_lagrange.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class ComputeRhoFunctor {
public:
explicit ComputeRhoFunctor(const SolidMechanicsModel & model)
: model(model){};
void operator()(Matrix<Real> & rho, const Element & element) const {
const Array<UInt> & mat_indexes =
model.getMaterialByElement(element.type, element.ghost_type);
Real mat_rho =
model.getMaterial(mat_indexes(element.element)).getParam("rho");
rho.set(mat_rho);
}
private:
const SolidMechanicsModel & model;
};
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMassLumped() {
AKANTU_DEBUG_IN();
if(not need_to_reassemble_lumped_mass) return;
UInt nb_nodes = mesh.getNbNodes();
- if (this->mass == NULL) {
+ if (this->mass == nullptr) {
std::stringstream sstr_mass;
sstr_mass << id << ":mass";
mass =
&(alloc<Real>(sstr_mass.str(), nb_nodes, Model::spatial_dimension, 0));
} else {
mass->clear();
}
if (!this->getDOFManager().hasLumpedMatrix("M")) {
this->getDOFManager().getNewLumpedMatrix("M");
}
this->getDOFManager().clearLumpedMatrix("M");
assembleMassLumped(_not_ghost);
assembleMassLumped(_ghost);
this->getDOFManager().getLumpedMatrixPerDOFs("displacement", "M",
*(this->mass));
/// for not connected nodes put mass to one in order to avoid
#if !defined(AKANTU_NDEBUG)
bool has_unconnected_nodes = false;
auto mass_it =
mass->begin_reinterpret(mass->size() * mass->getNbComponent());
auto mass_end =
mass->end_reinterpret(mass->size() * mass->getNbComponent());
for (; mass_it != mass_end; ++mass_it) {
if (std::abs(*mass_it) < std::numeric_limits<Real>::epsilon() ||
Math::isnan(*mass_it)) {
has_unconnected_nodes = true;
break;
}
}
if (has_unconnected_nodes)
AKANTU_DEBUG_WARNING("There are nodes that seem to not be connected to any "
"elements, beware that they have lumped mass of 0.");
#endif
this->synchronize(_gst_smm_mass);
need_to_reassemble_lumped_mass = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMass() {
AKANTU_DEBUG_IN();
if(not need_to_reassemble_mass) return;
this->getDOFManager().clearMatrix("M");
assembleMass(_not_ghost);
need_to_reassemble_mass = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMassLumped(GhostType ghost_type) {
AKANTU_DEBUG_IN();
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctor compute_rho(*this);
for (auto type : mesh.elementTypes(Model::spatial_dimension, ghost_type)) {
fem.assembleFieldLumped(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMass(GhostType ghost_type) {
AKANTU_DEBUG_IN();
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctor compute_rho(*this);
for (auto type : mesh.elementTypes(Model::spatial_dimension, ghost_type)) {
fem.assembleFieldMatrix(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
} // namespace akantu
diff --git a/src/model/time_step_solver.hh b/src/model/time_step_solver.hh
index c1d44e7d4..fab8342e3 100644
--- a/src/model/time_step_solver.hh
+++ b/src/model/time_step_solver.hh
@@ -1,132 +1,132 @@
/**
* @file time_step_solver.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Aug 24 12:42:04 2015
*
* @brief This corresponding to the time step evolution solver
*
* @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 "aka_array.hh"
#include "aka_memory.hh"
#include "integration_scheme.hh"
#include "parameter_registry.hh"
#include "solver_callback.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TIME_STEP_SOLVER_HH__
#define __AKANTU_TIME_STEP_SOLVER_HH__
namespace akantu {
class DOFManager;
class NonLinearSolver;
}
namespace akantu {
class TimeStepSolver : public Memory,
public ParameterRegistry,
public SolverCallback {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolver(DOFManager & dof_manager, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, const ID & id,
UInt memory_id);
- virtual ~TimeStepSolver();
+ ~TimeStepSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// solves on step
virtual void solveStep(SolverCallback & solver_callback) = 0;
/// register an integration scheme for a given dof
virtual void
setIntegrationScheme(const ID & dof_id, const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined) = 0;
/// replies if a integration scheme has been set
virtual bool hasIntegrationScheme(const ID & dof_id) const = 0;
/* ------------------------------------------------------------------------ */
/* Solver Callback interface */
/* ------------------------------------------------------------------------ */
public:
/// implementation of the SolverCallback::getMatrixType()
- MatrixType getMatrixType(const ID &) override final { return _mt_not_defined; }
+ MatrixType getMatrixType(const ID &) final { return _mt_not_defined; }
/// implementation of the SolverCallback::predictor()
void predictor() override;
/// implementation of the SolverCallback::corrector()
void corrector() override;
/// implementation of the SolverCallback::assembleJacobian()
void assembleMatrix(const ID & matrix_id) override;
/// implementation of the SolverCallback::assembleJacobian()
- void assembleLumpedMatrix(const ID & matrix_id) override final;
+ void assembleLumpedMatrix(const ID & matrix_id) final;
/// implementation of the SolverCallback::assembleResidual()
void assembleResidual() override;
void beforeSolveStep() override;
void afterSolveStep() override;
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(TimeStep, time_step, Real);
AKANTU_SET_MACRO(TimeStep, time_step, Real);
AKANTU_GET_MACRO(NonLinearSolver, non_linear_solver, const NonLinearSolver &);
AKANTU_GET_MACRO_NOT_CONST(NonLinearSolver, non_linear_solver,
NonLinearSolver &);
protected:
MatrixType getCommonMatrixType();
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Underlying dof manager containing the dof to treat
DOFManager & _dof_manager;
/// Type of solver
TimeStepSolverType type;
/// The time step for this solver
Real time_step;
/// Temporary storage for solver callback
SolverCallback * solver_callback;
/// NonLinearSolver used by this tome step solver
NonLinearSolver & non_linear_solver;
/// List of required matrices
std::map<std::string, MatrixType> needed_matrices;
};
} // akantu
#endif /* __AKANTU_TIME_STEP_SOLVER_HH__ */
diff --git a/src/model/time_step_solvers/time_step_solver_default.cc b/src/model/time_step_solvers/time_step_solver_default.cc
index dcf576d46..747378f1d 100644
--- a/src/model/time_step_solvers/time_step_solver_default.cc
+++ b/src/model/time_step_solvers/time_step_solver_default.cc
@@ -1,282 +1,282 @@
/**
* @file time_step_solver_default.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Sep 16 10:20:55 2015
*
* @brief Default implementation of the time step solver
*
* @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 "time_step_solver_default.hh"
#include "dof_manager_default.hh"
#include "integration_scheme_1st_order.hh"
#include "integration_scheme_2nd_order.hh"
#include "mesh.hh"
#include "non_linear_solver.hh"
#include "pseudo_time.hh"
#include "sparse_matrix_aij.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
TimeStepSolverDefault::TimeStepSolverDefault(
DOFManagerDefault & dof_manager, const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, const ID & id, UInt memory_id)
: TimeStepSolver(dof_manager, type, non_linear_solver, id, memory_id),
dof_manager(dof_manager), is_mass_lumped(false) {
switch (type) {
case _tsst_dynamic:
break;
case _tsst_dynamic_lumped:
this->is_mass_lumped = true;
break;
case _tsst_static:
/// initialize a static time solver for callback dofs
break;
default:
AKANTU_DEBUG_TO_IMPLEMENT();
}
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::setIntegrationScheme(
const ID & dof_id, const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type) {
if (this->integration_schemes.find(dof_id) !=
this->integration_schemes.end()) {
AKANTU_EXCEPTION("Their DOFs "
<< dof_id
<< " have already an integration scheme associated");
}
std::unique_ptr<IntegrationScheme> integration_scheme;
if (this->is_mass_lumped) {
switch (type) {
case _ist_forward_euler: {
integration_scheme = std::make_unique<ForwardEuler>(dof_manager, dof_id);
break;
}
case _ist_central_difference: {
integration_scheme =
std::make_unique<CentralDifference>(dof_manager, dof_id);
break;
}
default:
AKANTU_EXCEPTION(
"This integration scheme cannot be used in lumped dynamic");
}
} else {
switch (type) {
case _ist_pseudo_time: {
integration_scheme = std::make_unique<PseudoTime>(dof_manager, dof_id);
break;
}
case _ist_forward_euler: {
integration_scheme = std::make_unique<ForwardEuler>(dof_manager, dof_id);
break;
}
case _ist_trapezoidal_rule_1: {
integration_scheme =
std::make_unique<TrapezoidalRule1>(dof_manager, dof_id);
break;
}
case _ist_backward_euler: {
integration_scheme = std::make_unique<BackwardEuler>(dof_manager, dof_id);
break;
}
case _ist_central_difference: {
integration_scheme =
std::make_unique<CentralDifference>(dof_manager, dof_id);
break;
}
case _ist_fox_goodwin: {
integration_scheme = std::make_unique<FoxGoodwin>(dof_manager, dof_id);
break;
}
case _ist_trapezoidal_rule_2: {
integration_scheme =
std::make_unique<TrapezoidalRule2>(dof_manager, dof_id);
break;
}
case _ist_linear_acceleration: {
integration_scheme =
std::make_unique<LinearAceleration>(dof_manager, dof_id);
break;
}
case _ist_generalized_trapezoidal: {
integration_scheme =
std::make_unique<GeneralizedTrapezoidal>(dof_manager, dof_id);
break;
}
case _ist_newmark_beta:
integration_scheme = std::make_unique<NewmarkBeta>(dof_manager, dof_id);
break;
}
}
AKANTU_DEBUG_ASSERT(integration_scheme,
"No integration scheme was found for the provided types");
auto && matrices_names = integration_scheme->getNeededMatrixList();
for (auto && name : matrices_names) {
needed_matrices.insert({name, _mt_not_defined});
}
this->integration_schemes[dof_id] = std::move(integration_scheme);
this->solution_types[dof_id] = solution_type;
this->integration_schemes_owner.insert(dof_id);
}
/* -------------------------------------------------------------------------- */
bool TimeStepSolverDefault::hasIntegrationScheme(const ID & dof_id) const {
return this->integration_schemes.find(dof_id) !=
this->integration_schemes.end();
}
/* -------------------------------------------------------------------------- */
TimeStepSolverDefault::~TimeStepSolverDefault() = default;
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::solveStep(SolverCallback & solver_callback) {
this->solver_callback = &solver_callback;
this->solver_callback->beforeSolveStep();
this->non_linear_solver.solve(*this);
this->solver_callback->afterSolveStep();
- this->solver_callback = NULL;
+ this->solver_callback = nullptr;
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::predictor() {
AKANTU_DEBUG_IN();
TimeStepSolver::predictor();
for (auto & pair : this->integration_schemes) {
auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
if (this->dof_manager.hasPreviousDOFs(dof_id)) {
this->dof_manager.savePreviousDOFs(dof_id);
}
/// integrator predictor
integration_scheme->predictor(this->time_step);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::corrector() {
AKANTU_DEBUG_IN();
TimeStepSolver::corrector();
for (auto & pair : this->integration_schemes) {
auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
const auto & solution_type = this->solution_types[dof_id];
integration_scheme->corrector(solution_type, this->time_step);
/// computing the increment of dof if needed
if (this->dof_manager.hasDOFsIncrement(dof_id)) {
if (!this->dof_manager.hasPreviousDOFs(dof_id)) {
AKANTU_DEBUG_WARNING("In order to compute the increment of "
<< dof_id << " a 'previous' has to be registered");
continue;
}
Array<Real> & increment = this->dof_manager.getDOFsIncrement(dof_id);
Array<Real> & previous = this->dof_manager.getPreviousDOFs(dof_id);
UInt dof_array_comp = this->dof_manager.getDOFs(dof_id).getNbComponent();
auto prev_dof_it = previous.begin(dof_array_comp);
auto incr_it = increment.begin(dof_array_comp);
auto incr_end = increment.end(dof_array_comp);
increment.copy(this->dof_manager.getDOFs(dof_id));
for (; incr_it != incr_end; ++incr_it, ++prev_dof_it) {
*incr_it -= *prev_dof_it;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleMatrix(const ID & matrix_id) {
AKANTU_DEBUG_IN();
TimeStepSolver::assembleMatrix(matrix_id);
if (matrix_id != "J")
return;
for (auto & pair : this->integration_schemes) {
auto & dof_id = pair.first;
auto & integration_scheme = pair.second;
const auto & solution_type = this->solution_types[dof_id];
integration_scheme->assembleJacobian(solution_type, this->time_step);
}
this->dof_manager.applyBoundary("J");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::assembleResidual() {
AKANTU_DEBUG_IN();
if (this->needed_matrices.find("M") != needed_matrices.end()) {
if (this->is_mass_lumped) {
this->assembleLumpedMatrix("M");
} else {
this->assembleMatrix("M");
}
}
TimeStepSolver::assembleResidual();
for (auto & pair : this->integration_schemes) {
auto & integration_scheme = pair.second;
integration_scheme->assembleResidual(this->is_mass_lumped);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/model/time_step_solvers/time_step_solver_default.hh b/src/model/time_step_solvers/time_step_solver_default.hh
index fd7cfc201..e77633ca1 100644
--- a/src/model/time_step_solvers/time_step_solver_default.hh
+++ b/src/model/time_step_solvers/time_step_solver_default.hh
@@ -1,111 +1,111 @@
/**
* @file time_step_solver_default.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Aug 24 17:10:29 2015
*
* @brief Default implementation for the time stepper
*
* @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 "integration_scheme.hh"
#include "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__
#define __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__
namespace akantu {
class DOFManagerDefault;
}
namespace akantu {
class TimeStepSolverDefault : public TimeStepSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolverDefault(DOFManagerDefault & dof_manager,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver, const ID & id,
UInt memory_id);
- virtual ~TimeStepSolverDefault();
+ ~TimeStepSolverDefault() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// registers an integration scheme for a given dof
void setIntegrationScheme(const ID & dof_id,
const IntegrationSchemeType & type,
IntegrationScheme::SolutionType solution_type =
IntegrationScheme::_not_defined) override;
bool hasIntegrationScheme(const ID & dof_id) const override;
/// implementation of the TimeStepSolver::predictor()
void predictor() override;
/// implementation of the TimeStepSolver::corrector()
void corrector() override;
/// implementation of the TimeStepSolver::assembleMatrix()
void assembleMatrix(const ID & matrix_id) override;
/// implementation of the TimeStepSolver::assembleResidual()
void assembleResidual() override;
/// implementation of the generic TimeStepSolver::solveStep()
void solveStep(SolverCallback & solver_callback) override;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
typedef std::map<ID, std::unique_ptr<IntegrationScheme>>
DOFsIntegrationSchemes;
typedef std::map<ID, IntegrationScheme::SolutionType>
DOFsIntegrationSchemesSolutionTypes;
typedef std::set<ID> DOFsIntegrationSchemesOwner;
/// DOFManager with its real type
DOFManagerDefault & dof_manager;
/// Underlying integration scheme per dof, \todo check what happens in dynamic
/// in case of coupled equations
DOFsIntegrationSchemes integration_schemes;
/// defines if the solver is owner of the memory or not
DOFsIntegrationSchemesOwner integration_schemes_owner;
/// Type of corrector to use
DOFsIntegrationSchemesSolutionTypes solution_types;
/// define if the mass matrix is lumped or not
bool is_mass_lumped;
};
} // namespace akantu
#endif /* __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__ */
diff --git a/src/python/python_functor.hh b/src/python/python_functor.hh
index 970419e0a..7516baeea 100644
--- a/src/python/python_functor.hh
+++ b/src/python/python_functor.hh
@@ -1,127 +1,129 @@
/**
* @file python_functor.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Nov 15 2015
*
* @brief Python Functor interface
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 <Python.h>
-/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
+#include <Python.h>
#include <map>
+#include <vector>
/* -------------------------------------------------------------------------- */
+
+#ifndef __AKANTU_PYTHON_FUNCTOR_HH__
+#define __AKANTU_PYTHON_FUNCTOR_HH__
+
namespace akantu {
-/* -------------------------------------------------------------------------- */
class PythonFunctor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PythonFunctor(PyObject * obj);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// call the python functor
PyObject * callFunctor(PyObject * functor, PyObject * args,
PyObject * kwargs) const;
/// call the python functor from variadic types
template <typename return_type, typename... Params>
return_type callFunctor(const std::string & functor_name,
Params &... parameters) const;
/// empty function to cose the recursive template loop
inline void packArguments(std::vector<PyObject *> & pArgs) const;
/// get the python function object
inline PyObject * getPythonFunction(const std::string & functor_name) const;
/// variadic template for unknown number of arguments to unpack
template <typename T, typename... Args>
inline void packArguments(std::vector<PyObject *> & pArgs, T & p,
Args &... params) const;
/// convert an akantu object to python
template <typename T>
inline PyObject * convertToPython(const T & akantu_obj) const;
/// convert a stl vector to python
template <typename T>
inline PyObject * convertToPython(const std::vector<T> & akantu_obj) const;
/// convert a stl vector to python
template <typename T>
inline PyObject * convertToPython(const std::vector<Array<T> *> & akantu_obj) const;
/// convert a stl vector to python
template <typename T1, typename T2>
inline PyObject * convertToPython(const std::map<T1, T2> & akantu_obj) const;
/// convert an akantu vector to python
template <typename T>
inline PyObject * convertToPython(const Vector<T> & akantu_obj) const;
/// convert an akantu vector to python
template <typename T>
inline PyObject * convertToPython(const Array<T> & akantu_obj) const;
/// convert an akantu vector to python
template <typename T>
inline PyObject * convertToPython(Array<T> * akantu_obj) const;
/// convert a akantu matrix to python
template <typename T>
inline PyObject * convertToPython(const Matrix<T> & akantu_obj) const;
/// convert a python object to an akantu object
template <typename return_type>
inline return_type convertToAkantu(PyObject * python_obj) const;
/// convert a python object to an akantu object
template <typename T>
inline std::vector<T> convertListToAkantu(PyObject * python_obj) const;
/// returns the numpy data type code
template <typename T> inline int getPythonDataTypeCode() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
PyObject * python_obj;
};
-/* -------------------------------------------------------------------------- */
+
} // akantu
-/* -------------------------------------------------------------------------- */
-#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
-#include "python_functor_inline_impl.cc"
#endif /* __AKANTU_PYTHON_FUNCTOR_HH__ */
+
+#include "python_functor_inline_impl.cc"
diff --git a/src/python/python_functor_inline_impl.cc b/src/python/python_functor_inline_impl.cc
index a652c938c..ad679181d 100644
--- a/src/python/python_functor_inline_impl.cc
+++ b/src/python/python_functor_inline_impl.cc
@@ -1,316 +1,319 @@
/**
* @file python_functor_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Nov 13 2015
* @date last modification: Wed Nov 18 2015
*
* @brief Python functor interface
*
* @section LICENSE
*
* Copyright (©) 2015 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 "integration_point.hh"
/* -------------------------------------------------------------------------- */
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <numpy/arrayobject.h>
#include <typeinfo>
/* -------------------------------------------------------------------------- */
+#ifndef __AKANTU_PYTHON_FUNCTOR_INLINE_IMPL_CC__
+#define __AKANTU_PYTHON_FUNCTOR_INLINE_IMPL_CC__
+
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> inline int PythonFunctor::getPythonDataTypeCode() const {
AKANTU_EXCEPTION("undefined type: " << debug::demangle(typeid(T).name()));
}
/* -------------------------------------------------------------------------- */
template <> inline int PythonFunctor::getPythonDataTypeCode<bool>() const {
int data_typecode = NPY_NOTYPE;
size_t s = sizeof(bool);
switch (s) {
case 1:
data_typecode = NPY_BOOL;
break;
case 2:
data_typecode = NPY_UINT16;
break;
case 4:
data_typecode = NPY_UINT32;
break;
case 8:
data_typecode = NPY_UINT64;
break;
}
return data_typecode;
}
/* -------------------------------------------------------------------------- */
template <> inline int PythonFunctor::getPythonDataTypeCode<double>() const {
return NPY_DOUBLE;
}
/* -------------------------------------------------------------------------- */
template <typename T>
PyObject * PythonFunctor::convertToPython(const T &) const {
AKANTU_DEBUG_ERROR(
__func__ << " : not implemented yet !" << std::endl
<< debug::demangle(typeid(T).name()));
}
/* -------------------------------------------------------------------------- */
template <>
inline PyObject *
PythonFunctor::convertToPython<double>(const double & akantu_object) const {
return PyFloat_FromDouble(akantu_object);
}
/* -------------------------------------------------------------------------- */
template <>
inline PyObject *
PythonFunctor::convertToPython<UInt>(const UInt & akantu_object) const {
return PyInt_FromLong(akantu_object);
}
/* -------------------------------------------------------------------------- */
template <>
inline PyObject *
PythonFunctor::convertToPython<bool>(const bool & akantu_object) const {
return PyBool_FromLong(long(akantu_object));
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline PyObject *
PythonFunctor::convertToPython(const std::vector<T> & array) const {
int data_typecode = getPythonDataTypeCode<T>();
npy_intp dims[1] = {int(array.size())};
PyObject * obj = PyArray_SimpleNewFromData(1, dims, data_typecode,
const_cast<T *>(&array[0]));
PyArrayObject * res = (PyArrayObject *)obj;
return (PyObject *)res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline PyObject *
PythonFunctor::convertToPython(const std::vector<Array<T> *> & array) const {
PyObject * res = PyDict_New();
for (auto a : array) {
PyObject * obj = this->convertToPython(*a);
PyObject * name = this->convertToPython(a->getID());
PyDict_SetItem(res, name, obj);
}
return (PyObject *)res;
}
/* -------------------------------------------------------------------------- */
template <typename T1, typename T2>
inline PyObject *
PythonFunctor::convertToPython(const std::map<T1, T2> & map) const {
PyObject * res = PyDict_New();
for (auto a : map) {
PyObject * key = this->convertToPython(a.first);
PyObject * value = this->convertToPython(a.second);
PyDict_SetItem(res, key, value);
}
return (PyObject *)res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
PyObject * PythonFunctor::convertToPython(const Vector<T> & array) const {
int data_typecode = getPythonDataTypeCode<T>();
npy_intp dims[1] = {array.size()};
PyObject * obj =
PyArray_SimpleNewFromData(1, dims, data_typecode, array.storage());
PyArrayObject * res = (PyArrayObject *)obj;
return (PyObject *)res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
PyObject * PythonFunctor::convertToPython(const Array<T> & array) const {
int data_typecode = getPythonDataTypeCode<T>();
npy_intp dims[2] = {array.size(), array.getNbComponent()};
PyObject * obj =
PyArray_SimpleNewFromData(2, dims, data_typecode, array.storage());
PyArrayObject * res = (PyArrayObject *)obj;
return (PyObject *)res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
PyObject * PythonFunctor::convertToPython(Array<T> * array) const {
return this->convertToPython(*array);
}
/* -------------------------------------------------------------------------- */
template <typename T>
PyObject * PythonFunctor::convertToPython(const Matrix<T> & mat) const {
int data_typecode = getPythonDataTypeCode<T>();
npy_intp dims[2] = {mat.size(0), mat.size(1)};
PyObject * obj =
PyArray_SimpleNewFromData(2, dims, data_typecode, mat.storage());
PyArrayObject * res = (PyArrayObject *)obj;
return (PyObject *)res;
}
/* -------------------------------------------------------------------------- */
template <>
inline PyObject *
PythonFunctor::convertToPython<std::string>(const std::string & str) const {
return PyString_FromString(str.c_str());
}
/* -------------------------------------------------------------------------- */
template <>
inline PyObject * PythonFunctor::convertToPython<IntegrationPoint>(
const IntegrationPoint & qp) const {
PyObject * input = PyDict_New();
PyObject * num_point = this->convertToPython(qp.num_point);
PyObject * global_num = this->convertToPython(qp.global_num);
PyObject * material_id = this->convertToPython(qp.material_id);
PyObject * position = this->convertToPython(qp.getPosition());
PyDict_SetItemString(input, "num_point", num_point);
PyDict_SetItemString(input, "global_num", global_num);
PyDict_SetItemString(input, "material_id", material_id);
PyDict_SetItemString(input, "position", position);
return input;
}
/* -------------------------------------------------------------------------- */
inline PyObject *
PythonFunctor::getPythonFunction(const std::string & functor_name) const {
if (!PyInstance_Check(this->python_obj))
AKANTU_EXCEPTION("Python object is not an instance");
PyObject * pFunctor =
PyObject_GetAttrString(this->python_obj, functor_name.c_str());
if (!pFunctor)
AKANTU_EXCEPTION("Python dictionary has no " << functor_name << " entry");
return pFunctor;
}
/* -------------------------------------------------------------------------- */
inline void
PythonFunctor::packArguments(__attribute__((unused))
std::vector<PyObject *> & p_args) const {}
/* -------------------------------------------------------------------------- */
template <typename T, typename... Args>
inline void PythonFunctor::packArguments(std::vector<PyObject *> & p_args,
T & p, Args &... params) const {
p_args.push_back(this->convertToPython(p));
if (sizeof...(params) != 0)
this->packArguments(p_args, params...);
}
/* -------------------------------------------------------------------------- */
template <typename return_type, typename... Params>
return_type PythonFunctor::callFunctor(const std::string & functor_name,
Params &... parameters) const {
_import_array();
std::vector<PyObject *> arg_vector;
this->packArguments(arg_vector, parameters...);
PyObject * pArgs = PyTuple_New(arg_vector.size());
for (UInt i = 0; i < arg_vector.size(); ++i) {
PyTuple_SetItem(pArgs, i, arg_vector[i]);
}
PyObject * kwargs = PyDict_New();
PyObject * pFunctor = getPythonFunction(functor_name);
PyObject * res = this->callFunctor(pFunctor, pArgs, kwargs);
Py_XDECREF(pArgs);
Py_XDECREF(kwargs);
return this->convertToAkantu<return_type>(res);
}
/* -------------------------------------------------------------------------- */
template <typename return_type>
inline return_type PythonFunctor::convertToAkantu(PyObject * python_obj) const {
if (PyList_Check(python_obj)) {
return this->convertListToAkantu<typename return_type::value_type>(
python_obj);
}
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
inline void PythonFunctor::convertToAkantu<void>(PyObject * python_obj) const {
if (python_obj != Py_None)
AKANTU_DEBUG_WARNING(
"functor return a value while none was expected: ignored");
}
/* -------------------------------------------------------------------------- */
template <>
inline std::string
PythonFunctor::convertToAkantu<std::string>(PyObject * python_obj) const {
if (!PyString_Check(python_obj))
AKANTU_EXCEPTION("cannot convert object to string");
return PyString_AsString(python_obj);
}
/* -------------------------------------------------------------------------- */
template <>
inline Real PythonFunctor::convertToAkantu<Real>(PyObject * python_obj) const {
if (!PyFloat_Check(python_obj))
AKANTU_EXCEPTION("cannot convert object to float");
return PyFloat_AsDouble(python_obj);
}
/* -------------------------------------------------------------------------- */
template <>
inline UInt PythonFunctor::convertToAkantu<UInt>(PyObject * python_obj) const {
if (!PyInt_Check(python_obj))
AKANTU_EXCEPTION("cannot convert object to integer");
return PyInt_AsLong(python_obj);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::vector<T>
PythonFunctor::convertListToAkantu(PyObject * python_obj) const {
std::vector<T> res;
UInt size = PyList_Size(python_obj);
for (UInt i = 0; i < size; ++i) {
PyObject * item = PyList_GET_ITEM(python_obj, i);
res.push_back(this->convertToAkantu<T>(item));
}
return res;
}
/* -------------------------------------------------------------------------- */
} // akantu
#endif /* __AKANTU_PYTHON_FUNCTOR_INLINE_IMPL_CC__ */
diff --git a/src/solver/sparse_matrix_aij.hh b/src/solver/sparse_matrix_aij.hh
index 3b015e8aa..11d04b448 100644
--- a/src/solver/sparse_matrix_aij.hh
+++ b/src/solver/sparse_matrix_aij.hh
@@ -1,179 +1,179 @@
/**
* @file sparse_matrix_aij.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Aug 17 21:22:57 2015
*
* @brief AIJ implementation of the SparseMatrix (this the format used by Mumps)
*
* @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 "aka_array.hh"
#include "aka_common.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SPARSE_MATRIX_AIJ_HH__
#define __AKANTU_SPARSE_MATRIX_AIJ_HH__
namespace akantu {
class DOFManagerDefault;
class TermsToAssemble;
}
namespace akantu {
class SparseMatrixAIJ : public SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrixAIJ(DOFManagerDefault & dof_manager,
const MatrixType & matrix_type,
const ID & id = "sparse_matrix_aij");
SparseMatrixAIJ(const SparseMatrixAIJ & matrix,
const ID & id = "sparse_matrix_aij");
- virtual ~SparseMatrixAIJ();
+ ~SparseMatrixAIJ() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// remove the existing profile
inline void clearProfile() override;
/// add a non-zero element
inline UInt add(UInt i, UInt j) override;
/// set the matrix to 0
void clear() override;
/// assemble a local matrix in the sparse one
inline void add(UInt i, UInt j, Real value) override;
/// set the size of the matrix
void resize(UInt size) { this->size_ = size; }
/// modify the matrix to "remove" the blocked dof
void applyBoundary(Real block_val = 1.) override;
/// save the profil in a file using the MatrixMarket file format
void saveProfile(const std::string & filename) const override;
/// save the matrix in a file using the MatrixMarket file format
void saveMatrix(const std::string & filename) const override;
/// copy assuming the profile are the same
virtual void copyContent(const SparseMatrix & matrix);
/// multiply the matrix by a scalar
void mul(Real alpha) override;
/// add matrix *this += B
// virtual void add(const SparseMatrix & matrix, Real alpha);
/// Equivalent of *gemv in blas
void matVecMul(const Array<Real> & x, Array<Real> & y,
Real alpha = 1., Real beta = 0.) const override;
/* ------------------------------------------------------------------------ */
/// accessor to A_{ij} - if (i, j) not present it returns 0
inline Real operator()(UInt i, UInt j) const override;
/// accessor to A_{ij} - if (i, j) not present it fails, (i, j) should be
/// first added to the profile
inline Real & operator()(UInt i, UInt j) override;
protected:
/// This is the revert of add B += \alpha * *this;
void addMeTo(SparseMatrix & B, Real alpha) const override;
private:
/// This is just to inline the addToMatrix function
template <class MatrixType>
void addMeToTemplated(MatrixType & B, Real alpha) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(IRN, irn, const Array<Int> &);
AKANTU_GET_MACRO(JCN, jcn, const Array<Int> &);
AKANTU_GET_MACRO(A, a, const Array<Real> &);
/// The release changes at each call of a function that changes the profile,
/// it in increasing but could overflow so it should be checked as
/// (my_release != release) and not as (my_release < release)
AKANTU_GET_MACRO(ProfileRelease, profile_release, UInt);
AKANTU_GET_MACRO(ValueRelease, value_release, UInt);
UInt getRelease() const override { return value_release; }
protected:
using KeyCOO = std::pair<UInt, UInt>;
using coordinate_list_map = std::unordered_map<KeyCOO, UInt>;
/// get the pair corresponding to (i, j)
inline KeyCOO key(UInt i, UInt j) const {
if (this->matrix_type == _symmetric && (i > j))
return std::make_pair(j, i);
return std::make_pair(i, j);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
DOFManagerDefault & dof_manager;
/// row indexes
Array<Int> irn;
/// column indexes
Array<Int> jcn;
/// values : A[k] = Matrix[irn[k]][jcn[k]]
Array<Real> a;
/// Profile release
UInt profile_release{1};
/// Value release
UInt value_release{1};
/// map for (i, j) -> k correspondence
coordinate_list_map irn_jcn_k;
};
} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij_inline_impl.cc"
#endif /* __AKANTU_SPARSE_MATRIX_AIJ_HH__ */
diff --git a/src/solver/sparse_solver.hh b/src/solver/sparse_solver.hh
index dbdbf4f8f..8ac558ef3 100644
--- a/src/solver/sparse_solver.hh
+++ b/src/solver/sparse_solver.hh
@@ -1,122 +1,122 @@
/**
* @file sparse_solver.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Jan 19 2016
*
* @brief interface for solvers
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_memory.hh"
//#include "data_accessor.hh"
#include "parsable.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLVER_HH__
#define __AKANTU_SOLVER_HH__
namespace akantu {
enum SolverParallelMethod {
_not_parallel,
_fully_distributed,
_master_slave_distributed
};
class DOFManager;
}
namespace akantu {
class SparseSolver : protected Memory,
public Parsable,
public CommunicatorEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseSolver(DOFManager & dof_manager, const ID & matrix_id,
const ID & id = "solver", const MemoryID & memory_id = 0);
- virtual ~SparseSolver();
+ ~SparseSolver() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the solver
virtual void initialize() = 0;
virtual void analysis(){};
virtual void factorize(){};
virtual void solve(){};
protected:
virtual void destroyInternalData(){};
public:
virtual void beforeStaticSolverDestroy();
void createSynchronizerRegistry();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
- virtual void onCommunicatorFinalize();
+ void onCommunicatorFinalize() override;
-// inline virtual UInt getNbDataForDOFs(const Array<UInt> & dofs,
+ // inline virtual UInt getNbDataForDOFs(const Array<UInt> & dofs,
// SynchronizationTag tag) const;
// inline virtual void packDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag) const;
// inline virtual void unpackDOFData(CommunicationBuffer & buffer,
// const Array<UInt> & dofs,
// SynchronizationTag tag);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// manager handling the dofs for this SparseMatrix solver
DOFManager & _dof_manager;
/// The id of the associated matrix
ID matrix_id;
/// How to parallelize the solve
SolverParallelMethod parallel_method;
/// Communicator used by the solver
const Communicator & communicator;
};
} // akantu
#endif /* __AKANTU_SOLVER_HH__ */
diff --git a/src/solver/sparse_solver_mumps.cc b/src/solver/sparse_solver_mumps.cc
index 4be72ba7a..5f5313299 100644
--- a/src/solver/sparse_solver_mumps.cc
+++ b/src/solver/sparse_solver_mumps.cc
@@ -1,440 +1,441 @@
/**
* @file sparse_solver_mumps.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Tue Jan 19 2016
*
* @brief implem of SparseSolverMumps class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
* @section DESCRIPTION
*
* @subsection Ctrl_param Control parameters
*
* ICNTL(1),
* ICNTL(2),
* ICNTL(3) : output streams for error, diagnostics, and global messages
*
* ICNTL(4) : verbose level : 0 no message - 4 all messages
*
* ICNTL(5) : type of matrix, 0 assembled, 1 elementary
*
* ICNTL(6) : control the permutation and scaling(default 7) see mumps doc for
* more information
*
* ICNTL(7) : determine the pivot order (default 7) see mumps doc for more
* information
*
* ICNTL(8) : describe the scaling method used
*
* ICNTL(9) : 1 solve A x = b, 0 solve At x = b
*
* ICNTL(10) : number of iterative refinement when NRHS = 1
*
* ICNTL(11) : > 0 return statistics
*
* ICNTL(12) : only used for SYM = 2, ordering strategy
*
* ICNTL(13) :
*
* ICNTL(14) : percentage of increase of the estimated working space
*
* ICNTL(15-17) : not used
*
* ICNTL(18) : only used if ICNTL(5) = 0, 0 matrix centralized, 1 structure on
* host and mumps give the mapping, 2 structure on host and distributed matrix
* for facto, 3 distributed matrix
*
* ICNTL(19) : > 0, Shur complement returned
*
* ICNTL(20) : 0 rhs dense, 1 rhs sparse
*
* ICNTL(21) : 0 solution in rhs, 1 solution distributed in ISOL_loc and SOL_loc
* allocated by user
*
* ICNTL(22) : 0 in-core, 1 out-of-core
*
* ICNTL(23) : maximum memory allocatable by mumps pre proc
*
* ICNTL(24) : controls the detection of "null pivot rows"
*
* ICNTL(25) :
*
* ICNTL(26) :
*
* ICNTL(27) :
*
* ICNTL(28) : 0 automatic choice, 1 sequential analysis, 2 parallel analysis
*
* ICNTL(29) : 0 automatic choice, 1 PT-Scotch, 2 ParMetis
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
#include "sparse_matrix_aij.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_communicator_data.hh"
#endif
#include "sparse_solver_mumps.hh"
/* -------------------------------------------------------------------------- */
// static std::ostream & operator <<(std::ostream & stream, const DMUMPS_STRUC_C
// & _this) {
// stream << "DMUMPS Data [" << std::endl;
// stream << " + job : " << _this.job << std::endl;
// stream << " + par : " << _this.par << std::endl;
// stream << " + sym : " << _this.sym << std::endl;
// stream << " + comm_fortran : " << _this.comm_fortran << std::endl;
// stream << " + nz : " << _this.nz << std::endl;
// stream << " + irn : " << _this.irn << std::endl;
// stream << " + jcn : " << _this.jcn << std::endl;
// stream << " + nz_loc : " << _this.nz_loc << std::endl;
// stream << " + irn_loc : " << _this.irn_loc << std::endl;
// stream << " + jcn_loc : " << _this.jcn_loc << std::endl;
// stream << "]";
// return stream;
// }
namespace akantu {
/* -------------------------------------------------------------------------- */
SparseSolverMumps::SparseSolverMumps(DOFManagerDefault & dof_manager,
const ID & matrix_id, const ID & id,
const MemoryID & memory_id)
: SparseSolver(dof_manager, matrix_id, id, memory_id),
dof_manager(dof_manager),
master_rhs_solution(0, 1) {
AKANTU_DEBUG_IN();
this->prank = communicator.whoAmI();
#ifdef AKANTU_USE_MPI
this->parallel_method = _fully_distributed;
#else // AKANTU_USE_MPI
this->parallel_method = _not_parallel;
#endif // AKANTU_USE_MPI
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseSolverMumps::~SparseSolverMumps() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::destroyInternalData() {
if (this->is_initialized) {
this->mumps_data.job = _smj_destroy; // destroy
dmumps_c(&this->mumps_data);
this->is_initialized = false;
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::checkInitialized() {
if (this->is_initialized) return;
this->initialize();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::setOutputLevel() {
// Output setup
icntl(1) = 0; // error output
icntl(2) = 0; // diagnostics output
icntl(3) = 0; // information
icntl(4) = 0;
#if !defined(AKANTU_NDEBUG)
DebugLevel dbg_lvl = debug::debugger.getDebugLevel();
if (AKANTU_DEBUG_TEST(dblDump)) {
strcpy(this->mumps_data.write_problem, "mumps_matrix.mtx");
}
// clang-format off
icntl(1) = (dbg_lvl >= dblWarning) ? 6 : 0;
icntl(3) = (dbg_lvl >= dblInfo) ? 6 : 0;
icntl(2) = (dbg_lvl >= dblTrace) ? 6 : 0;
icntl(4) =
dbg_lvl >= dblDump ? 4 :
dbg_lvl >= dblTrace ? 3 :
dbg_lvl >= dblInfo ? 2 :
dbg_lvl >= dblWarning ? 1 :
0;
// clang-format on
#endif
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::initMumpsData() {
auto & A = dof_manager.getMatrix(matrix_id);
// Default Scaling
icntl(8) = 77;
// Assembled matrix
icntl(5) = 0;
/// Default centralized dense second member
icntl(20) = 0;
icntl(21) = 0;
// automatic choice for analysis
icntl(28) = 0;
UInt size = A.size();
if (prank == 0) {
this->master_rhs_solution.resize(size);
}
this->mumps_data.nz_alloc = 0;
this->mumps_data.n = size;
switch (this->parallel_method) {
case _fully_distributed:
icntl(18) = 3; // fully distributed
this->mumps_data.nz_loc = A.getNbNonZero();
this->mumps_data.irn_loc = A.getIRN().storage();
this->mumps_data.jcn_loc = A.getJCN().storage();
break;
case _not_parallel:
case _master_slave_distributed:
icntl(18) = 0; // centralized
if (prank == 0) {
this->mumps_data.nz = A.getNbNonZero();
this->mumps_data.irn = A.getIRN().storage();
this->mumps_data.jcn = A.getJCN().storage();
} else {
this->mumps_data.nz = 0;
this->mumps_data.irn = NULL;
this->mumps_data.jcn = NULL;
}
break;
default:
AKANTU_DEBUG_ERROR("This case should not happen!!");
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::initialize() {
AKANTU_DEBUG_IN();
this->mumps_data.par = 1; // The host is part of computations
switch (this->parallel_method) {
case _not_parallel:
break;
case _master_slave_distributed:
this->mumps_data.par = 0; // The host is not part of the computations
- // [[fallthrough]]; un-comment when compiler will get it
+ /* FALLTHRU */
+ /* [[fallthrough]]; un-comment when compiler will get it */
case _fully_distributed:
#ifdef AKANTU_USE_MPI
const MPICommunicatorData & mpi_data =
dynamic_cast<const MPICommunicatorData &>(
communicator.getCommunicatorData());
MPI_Comm mpi_comm = mpi_data.getMPICommunicator();
this->mumps_data.comm_fortran = MPI_Comm_c2f(mpi_comm);
#else
AKANTU_DEBUG_ERROR(
"You cannot use parallel method to solve without activating MPI");
#endif
break;
}
const auto & A = dof_manager.getMatrix(matrix_id);
this->mumps_data.sym = 2 * (A.getMatrixType() == _symmetric);
this->prank = communicator.whoAmI();
this->setOutputLevel();
this->mumps_data.job = _smj_initialize; // initialize
dmumps_c(&this->mumps_data);
this->setOutputLevel();
this->is_initialized = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::analysis() {
AKANTU_DEBUG_IN();
initMumpsData();
this->mumps_data.job = _smj_analyze; // analyze
dmumps_c(&this->mumps_data);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::factorize() {
AKANTU_DEBUG_IN();
auto & A = dof_manager.getMatrix(matrix_id);
if (parallel_method == _fully_distributed)
this->mumps_data.a_loc = A.getA().storage();
else {
if (prank == 0)
this->mumps_data.a = A.getA().storage();
}
this->mumps_data.job = _smj_factorize; // factorize
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solve(Array<Real> & x, const Array<Real> & b) {
auto & synch = this->dof_manager.getSynchronizer();
if (this->prank == 0) {
this->master_rhs_solution.resize(this->dof_manager.getSystemSize());
synch.gather(b, this->master_rhs_solution);
} else {
synch.gather(b);
}
this->solveInternal();
if (this->prank == 0) {
synch.scatter(x, this->master_rhs_solution);
} else {
synch.scatter(x);
}
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solve() {
this->master_rhs_solution.copy(this->dof_manager.getGlobalResidual());
this->solveInternal();
this->dof_manager.setGlobalSolution(this->master_rhs_solution);
this->dof_manager.splitSolutionPerDOFs();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::solveInternal() {
AKANTU_DEBUG_IN();
this->checkInitialized();
const auto & A = dof_manager.getMatrix(matrix_id);
this->setOutputLevel();
if (this->last_profile_release != A.getProfileRelease()) {
this->analysis();
this->last_profile_release = A.getProfileRelease();
}
if (AKANTU_DEBUG_TEST(dblDump)) {
std::stringstream sstr;
sstr << prank << ".mtx";
A.saveMatrix("solver_mumps" + sstr.str());
}
if (this->last_value_release != A.getValueRelease()) {
this->factorize();
this->last_value_release = A.getValueRelease();
}
if (prank == 0) {
this->mumps_data.rhs = this->master_rhs_solution.storage();
}
this->mumps_data.job = _smj_solve; // solve
dmumps_c(&this->mumps_data);
this->printError();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::printError() {
Vector<Int> _info_v(2);
_info_v[0] = info(1); // to get errors
_info_v[1] = -info(1); // to get warnings
dof_manager.getCommunicator().allReduce(_info_v, SynchronizerOperation::_min);
_info_v[1] = -_info_v[1];
if (_info_v[0] < 0) { // < 0 is an error
switch (_info_v[0]) {
case -10:
AKANTU_DEBUG_ERROR("The matrix is singular");
break;
case -9: {
icntl(14) += 10;
if (icntl(14) != 90) {
// std::cout << "Dynamic memory increase of 10%" << std::endl;
AKANTU_DEBUG_WARNING("MUMPS dynamic memory is insufficient it will be "
"increased allowed to use 10% more");
// change releases to force a recompute
this->last_value_release--;
this->last_profile_release--;
this->solve();
} else {
AKANTU_DEBUG_ERROR("The MUMPS workarray is too small INFO(2)="
<< info(2) << "No further increase possible");
}
break;
}
default:
AKANTU_DEBUG_ERROR("Error in mumps during solve process, check mumps "
"user guide INFO(1) = "
<< _info_v[1]);
}
} else if (_info_v[1] > 0) {
AKANTU_DEBUG_WARNING("Warning in mumps during solve process, check mumps "
"user guide INFO(1) = "
<< _info_v[1]);
}
}
} // akantu
diff --git a/src/solver/sparse_solver_mumps.hh b/src/solver/sparse_solver_mumps.hh
index 1787f52c3..f200333b5 100644
--- a/src/solver/sparse_solver_mumps.hh
+++ b/src/solver/sparse_solver_mumps.hh
@@ -1,157 +1,157 @@
/**
* @file sparse_solver_mumps.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Jan 19 2016
*
* @brief Solver class implementation for the mumps solver
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "sparse_solver.hh"
/* -------------------------------------------------------------------------- */
#include <dmumps_c.h>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLVER_MUMPS_HH__
#define __AKANTU_SOLVER_MUMPS_HH__
namespace akantu {
class DOFManagerDefault;
class SparseMatrixAIJ;
}
namespace akantu {
class SparseSolverMumps : public SparseSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseSolverMumps(DOFManagerDefault & dof_manager,
const ID & matrix_id,
const ID & id = "sparse_solver_mumps",
const MemoryID & memory_id = 0);
- virtual ~SparseSolverMumps();
+ ~SparseSolverMumps() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build the profile and do the analysis part
- virtual void initialize();
+ void initialize() override;
/// analysis (symbolic facto + permutations)
- virtual void analysis();
+ void analysis() override;
/// factorize the matrix
- virtual void factorize();
+ void factorize() override;
/// solve the system
virtual void solve(Array<Real> & x, const Array<Real> & b);
/// solve using residual and solution from the dof_manager
- virtual void solve();
+ void solve() override;
private:
/// print the error if any happened in mumps
void printError();
/// solve the system with master_rhs_solution as b and x
void solveInternal();
/// set internal values;
void initMumpsData();
/// set the level of verbosity of mumps based on the debug level of akantu
void setOutputLevel();
protected:
/// de-initialize the internal data
- virtual void destroyInternalData();
+ void destroyInternalData() override;
/// check if initialized and except if it is not the case
void checkInitialized();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
private:
/// access the control variable
inline Int & icntl(UInt i) { return mumps_data.icntl[i - 1]; }
/// access the results info
inline Int & info(UInt i) { return mumps_data.info[i - 1]; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// DOFManager used by the Mumps implementation of the SparseSolver
DOFManagerDefault & dof_manager;
/// Full right hand side on the master processors and solution after solve
Array<Real> master_rhs_solution;
/// mumps data
DMUMPS_STRUC_C mumps_data;
/// Rank of the current process
UInt prank;
/// matrix release at last solve
UInt last_profile_release{UInt(-1)};
/// matrix release at last solve
UInt last_value_release{UInt(-1)};
/// check if the solver data are initialized
bool is_initialized{false};
/* ------------------------------------------------------------------------ */
/* Local types */
/* ------------------------------------------------------------------------ */
private:
SolverParallelMethod parallel_method;
// bool rhs_is_local;
enum SolverMumpsJob {
_smj_initialize = -1,
_smj_analyze = 1,
_smj_factorize = 2,
_smj_solve = 3,
_smj_analyze_factorize = 4,
_smj_factorize_solve = 5,
_smj_complete = 6, // analyze, factorize, solve
_smj_destroy = -2
};
};
} // akantu
#endif /* __AKANTU_SOLVER_MUMPS_HH__ */
diff --git a/src/synchronizer/communication_request.hh b/src/synchronizer/communication_request.hh
index ba9c858cb..f93ba330c 100644
--- a/src/synchronizer/communication_request.hh
+++ b/src/synchronizer/communication_request.hh
@@ -1,111 +1,113 @@
/**
* @file real_static_communicator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Wed Jan 13 2016
*
* @brief empty class just for inheritance
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <memory>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_REAL_STATIC_COMMUNICATOR_HH__
#define __AKANTU_REAL_STATIC_COMMUNICATOR_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
class InternalCommunicationRequest {
public:
InternalCommunicationRequest(UInt source, UInt dest);
virtual ~InternalCommunicationRequest();
virtual void printself(std::ostream & stream, int indent = 0) const;
AKANTU_GET_MACRO(Source, source, UInt);
AKANTU_GET_MACRO(Destination, destination, UInt);
private:
UInt source;
UInt destination;
UInt id;
static UInt counter;
};
/* -------------------------------------------------------------------------- */
class CommunicationRequest {
public:
CommunicationRequest(
std::shared_ptr<InternalCommunicationRequest> request = nullptr)
: request(std::move(request)) {}
+ virtual ~CommunicationRequest() = default;
+
virtual void free() { request.reset(); }
void printself(std::ostream & stream, int indent = 0) const {
request->printself(stream, indent);
};
UInt getSource() const { return request->getSource(); }
UInt getDestination() const { return request->getDestination(); }
bool isFreed() const { return request.get() == nullptr; }
InternalCommunicationRequest & getInternal() { return *request; }
private:
std::shared_ptr<InternalCommunicationRequest> request;
};
/* -------------------------------------------------------------------------- */
class CommunicationStatus {
public:
AKANTU_GET_MACRO(Source, source, Int);
UInt size() const { return size_; }
AKANTU_GET_MACRO(Tag, tag, Int);
AKANTU_SET_MACRO(Source, source, Int);
AKANTU_SET_MACRO(Size, size_, UInt);
AKANTU_SET_MACRO(Tag, tag, Int);
private:
Int source{0};
UInt size_{0};
Int tag{0};
};
/* -------------------------------------------------------------------------- */
/// Datatype to pack pairs for MPI_{MIN,MAX}LOC
template <typename T1, typename T2> struct SCMinMaxLoc {
T1 min_max;
T2 loc;
};
} // akantu
#endif /* __AKANTU_REAL_STATIC_COMMUNICATOR_HH__ */
diff --git a/src/synchronizer/communications_tmpl.hh b/src/synchronizer/communications_tmpl.hh
index 6b07dae12..badefca03 100644
--- a/src/synchronizer/communications_tmpl.hh
+++ b/src/synchronizer/communications_tmpl.hh
@@ -1,560 +1,560 @@
/**
* @file communications_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Sep 6 17:14:06 2016
*
* @brief Implementation of Communications
*
* @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 "communications.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COMMUNICATIONS_TMPL_HH__
#define __AKANTU_COMMUNICATIONS_TMPL_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications<Entity>::iterator {
typedef
typename std::map<UInt, Communication>::iterator communication_iterator;
public:
- iterator() : communications(NULL) {}
+ iterator() : communications(nullptr) {}
iterator(scheme_iterator scheme_it, communication_iterator comm_it,
Communications<Entity> & communications,
const SynchronizationTag & tag)
: scheme_it(scheme_it), comm_it(comm_it), communications(&communications),
tag(tag) {}
iterator & operator=(const iterator & other) {
if (this != &other) {
this->scheme_it = other.scheme_it;
this->comm_it = other.comm_it;
this->communications = other.communications;
this->tag = other.tag;
}
return *this;
}
iterator & operator++() {
++scheme_it;
++comm_it;
return *this;
}
CommunicationDescriptor<Entity> operator*() {
AKANTU_DEBUG_ASSERT(
scheme_it->first == comm_it->first,
"The two iterators are not in phase, something wrong"
<< " happened, time to take out your favorite debugger ("
<< scheme_it->first << " != " << comm_it->first << ")");
return CommunicationDescriptor<Entity>(comm_it->second, scheme_it->second,
*communications, tag,
scheme_it->first);
}
bool operator==(const iterator & other) const {
return scheme_it == other.scheme_it && comm_it == other.comm_it;
}
bool operator!=(const iterator & other) const {
return scheme_it != other.scheme_it || comm_it != other.comm_it;
}
private:
scheme_iterator scheme_it;
communication_iterator comm_it;
Communications<Entity> * communications;
SynchronizationTag tag;
};
/* -------------------------------------------------------------------------- */
template <class Entity> class Communications<Entity>::tag_iterator {
typedef std::map<SynchronizationTag, UInt>::const_iterator internal_iterator;
public:
tag_iterator(const internal_iterator & it) : it(it) {}
tag_iterator & operator++() {
++it;
return *this;
}
SynchronizationTag operator*() { return it->first; }
bool operator==(const tag_iterator & other) const { return it == other.it; }
bool operator!=(const tag_iterator & other) const { return it != other.it; }
private:
internal_iterator it;
};
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::CommunicationPerProcs &
Communications<Entity>::getCommunications(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto comm_it = this->communications[sr].find(tag);
if (comm_it == this->communications[sr].end())
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No known communications for the tag: " << tag);
return comm_it->second;
}
/* ---------------------------------------------------------------------- */
template <class Entity>
UInt Communications<Entity>::getPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) const {
const std::map<SynchronizationTag, UInt> & pending =
pending_communications[sr];
auto it = pending.find(tag);
if (it == pending.end())
return 0;
return it->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
bool Communications<Entity>::hasPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) const {
return this->hasCommunication(tag) && (this->getPending(tag, sr) != 0);
}
/* ---------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::begin(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
return iterator(this->schemes[sr].begin(), comms.begin(), *this, tag);
}
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::end(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
return iterator(this->schemes[sr].end(), comms.end(), *this, tag);
}
/* ---------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAny(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
auto it = comms.begin();
auto end = comms.end();
std::vector<CommunicationRequest> requests;
for (; it != end; ++it) {
auto & request = it->second.request();
if (!request.isFreed())
requests.push_back(request);
}
UInt req_id = communicator.waitAny(requests);
if (req_id != UInt(-1)) {
auto & request = requests[req_id];
UInt proc = sr == _recv ? request.getSource() : request.getDestination();
return iterator(this->schemes[sr].find(proc), comms.find(proc), *this, tag);
} else {
return this->end(tag, sr);
}
}
/* ---------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::waitAll(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
auto & comms = this->getCommunications(tag, sr);
auto it = comms.begin();
auto end = comms.end();
std::vector<CommunicationRequest> requests;
for (; it != end; ++it) {
requests.push_back(it->second.request());
}
communicator.waitAll(requests);
}
template <class Entity>
void Communications<Entity>::incrementPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) {
++(pending_communications[sr][tag]);
}
template <class Entity>
void Communications<Entity>::decrementPending(
const SynchronizationTag & tag, const CommunicationSendRecv & sr) {
--(pending_communications[sr][tag]);
}
template <class Entity>
void Communications<Entity>::freeRequests(const SynchronizationTag & tag,
const CommunicationSendRecv & sr) {
iterator it = this->begin(tag, sr);
iterator end = this->end(tag, sr);
for (; it != end; ++it) {
(*it).freeRequest();
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createScheme(UInt proc,
const CommunicationSendRecv & sr) {
// scheme_iterator it = schemes[sr].find(proc);
// if (it != schemes[sr].end()) {
// AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
// "Communication scheme("
// << sr
// << ") already created for proc: " <<
// proc);
// }
return schemes[sr][proc];
}
template <class Entity>
void Communications<Entity>::resetSchemes(const CommunicationSendRecv & sr) {
scheme_iterator it = this->schemes[sr].begin();
scheme_iterator end = this->schemes[sr].end();
for (; it != end; ++it) {
it->second.resize(0);
}
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::setCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size,
const CommunicationSendRecv & sr) {
// accessor that fails if it does not exists
comm_size_computed[tag] = true; // TODO: need perhaps to be split based on sr
auto & comms = this->communications[sr];
auto & comms_per_tag = comms.at(tag);
comms_per_tag.at(proc).resize(size);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::initializeCommunications(
const SynchronizationTag & tag) {
for (auto t = send_recv_t::begin(); t != send_recv_t::end(); ++t) {
pending_communications[*t].insert(std::make_pair(tag, 0));
auto & comms = this->communications[*t];
auto & comms_per_tag =
comms.insert(std::make_pair(tag, CommunicationPerProcs()))
.first->second;
for (auto pair : this->schemes[*t]) {
comms_per_tag.emplace(std::piecewise_construct,
std::forward_as_tuple(pair.first),
std::forward_as_tuple(*t));
}
}
comm_counter.insert(std::make_pair(tag, 0));
}
/* -------------------------------------------------------------------------- */
template <class Entity>
Communications<Entity>::Communications(const Communicator & communicator)
: communicator(communicator) {}
/* ---------------------------------------------------------------------- */
// template <class Entity>
// typename Communications<Entity>::iterator
// Communications<Entity>::begin_send(const SynchronizationTag & tag) {
// return this->begin(tag, _send);
// }
// template <class Entity>
// typename Communications<Entity>::iterator
// Communications<Entity>::end_send(const SynchronizationTag & tag) {
// return this->end(tag, _send);
// }
// /* ---------------------------------------------------------------------- */
// template <class Entity>
// typename Communications<Entity>::iterator
// Communications<Entity>::begin_recv(const SynchronizationTag & tag) {
// return this->begin(tag, _recv);
// }
// template <class Entity>
// typename Communications<Entity>::iterator
// Communications<Entity>::end_recv(const SynchronizationTag & tag) {
// return this->end(tag, _recv);
// }
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::tag_iterator
Communications<Entity>::begin_tag() {
return tag_iterator(comm_counter.begin());
}
template <class Entity>
typename Communications<Entity>::tag_iterator
Communications<Entity>::end_tag() {
return tag_iterator(comm_counter.end());
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_scheme(const CommunicationSendRecv & sr) {
return this->schemes[sr].begin();
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_scheme(const CommunicationSendRecv & sr) {
return this->schemes[sr].end();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_scheme(const CommunicationSendRecv & sr) const {
return this->schemes[sr].begin();
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_scheme(const CommunicationSendRecv & sr) const {
return this->schemes[sr].end();
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_send_scheme() {
return this->begin_scheme(_send);
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_send_scheme() {
return this->end_scheme(_send);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_send_scheme() const {
return this->begin_scheme(_send);
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_send_scheme() const {
return this->end_scheme(_send);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::begin_recv_scheme() {
return this->begin_scheme(_recv);
}
template <class Entity>
typename Communications<Entity>::scheme_iterator
Communications<Entity>::end_recv_scheme() {
return this->end_scheme(_recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::begin_recv_scheme() const {
return this->begin_scheme(_recv);
}
template <class Entity>
typename Communications<Entity>::const_scheme_iterator
Communications<Entity>::end_recv_scheme() const {
return this->end_scheme(_recv);
}
/* ------------------------------------------------------------------------ */
template <class Entity>
bool Communications<Entity>::hasCommunication(
const SynchronizationTag & tag) const {
return (communications[_send].find(tag) != communications[_send].end());
}
template <class Entity>
void Communications<Entity>::incrementCounter(const SynchronizationTag & tag) {
auto it = comm_counter.find(tag);
if (it == comm_counter.end()) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No counter initialized in communications for the tags: " << tag);
}
++(it->second);
}
template <class Entity>
UInt Communications<Entity>::getCounter(const SynchronizationTag & tag) const {
auto it = comm_counter.find(tag);
if (it == comm_counter.end()) {
AKANTU_CUSTOM_EXCEPTION_INFO(
debug::CommunicationException(),
"No counter initialized in communications for the tags: " << tag);
}
return it->second;
}
template <class Entity>
bool Communications<Entity>::hasCommunicationSize(
const SynchronizationTag & tag) const {
auto it = comm_size_computed.find(tag);
if (it == comm_size_computed.end()) {
return false;
}
return it->second;
}
template <class Entity> void Communications<Entity>::invalidateSizes() {
for (auto && pair : comm_size_computed) {
pair.second = true;
}
}
template <class Entity>
bool Communications<Entity>::hasPendingRecv(
const SynchronizationTag & tag) const {
return this->hasPending(tag, _recv);
}
template <class Entity>
bool Communications<Entity>::hasPendingSend(
const SynchronizationTag & tag) const {
return this->hasPending(tag, _send);
}
template <class Entity>
const auto & Communications<Entity>::getCommunicator() const {
return communicator;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAnyRecv(const SynchronizationTag & tag) {
return this->waitAny(tag, _recv);
}
template <class Entity>
typename Communications<Entity>::iterator
Communications<Entity>::waitAnySend(const SynchronizationTag & tag) {
return this->waitAny(tag, _send);
}
template <class Entity>
void Communications<Entity>::waitAllRecv(const SynchronizationTag & tag) {
this->waitAll(tag, _recv);
}
template <class Entity>
void Communications<Entity>::waitAllSend(const SynchronizationTag & tag) {
this->waitAll(tag, _send);
}
template <class Entity>
void Communications<Entity>::freeSendRequests(const SynchronizationTag & tag) {
this->freeRequests(tag, _send);
}
template <class Entity>
void Communications<Entity>::freeRecvRequests(const SynchronizationTag & tag) {
this->freeRequests(tag, _recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createSendScheme(UInt proc) {
return createScheme(proc, _send);
}
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::createRecvScheme(UInt proc) {
return createScheme(proc, _recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity> void Communications<Entity>::resetSchemes() {
resetSchemes(_send);
resetSchemes(_recv);
}
/* -------------------------------------------------------------------------- */
template <class Entity>
typename Communications<Entity>::Scheme &
Communications<Entity>::getScheme(UInt proc, const CommunicationSendRecv & sr) {
return this->schemes[sr].find(proc)->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
const typename Communications<Entity>::Scheme &
Communications<Entity>::getScheme(UInt proc,
const CommunicationSendRecv & sr) const {
return this->schemes[sr].find(proc)->second;
}
/* -------------------------------------------------------------------------- */
template <class Entity>
void Communications<Entity>::setSendCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size) {
this->setCommunicationSize(tag, proc, size, _send);
}
template <class Entity>
void Communications<Entity>::setRecvCommunicationSize(
const SynchronizationTag & tag, UInt proc, UInt size) {
this->setCommunicationSize(tag, proc, size, _recv);
}
} // namespace akantu
#endif /* __AKANTU_COMMUNICATIONS_TMPL_HH__ */
diff --git a/src/synchronizer/communicator.hh b/src/synchronizer/communicator.hh
index 4ece11d46..900b6b0dd 100644
--- a/src/synchronizer/communicator.hh
+++ b/src/synchronizer/communicator.hh
@@ -1,456 +1,456 @@
/**
* @file static_communicator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Jan 19 2016
*
* @brief Class handling the parallel communications
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_array.hh"
#include "aka_common.hh"
#include "aka_event_handler_manager.hh"
#include "communication_buffer.hh"
#include "communication_request.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STATIC_COMMUNICATOR_HH__
#define __AKANTU_STATIC_COMMUNICATOR_HH__
namespace akantu {
namespace debug {
class CommunicationException : public Exception {
public:
CommunicationException()
: Exception("An exception happen during a communication process.") {}
};
} // namespace debug
/// @enum SynchronizerOperation reduce operation that the synchronizer can
/// perform
enum class SynchronizerOperation {
_sum,
_min,
_max,
_prod,
_land,
_band,
_lor,
_bor,
_lxor,
_bxor,
_min_loc,
_max_loc,
_null
};
enum class CommunicationMode { _auto, _synchronous, _ready };
namespace {
int _any_source = -1;
}
} // namespace akantu
namespace akantu {
struct CommunicatorInternalData {
virtual ~CommunicatorInternalData() = default;
};
class Communicator;
struct FinalizeCommunicatorEvent {
explicit FinalizeCommunicatorEvent(const Communicator & comm)
: communicator(comm) {}
const Communicator & communicator;
};
class CommunicatorEventHandler {
public:
virtual ~CommunicatorEventHandler() {}
virtual void onCommunicatorFinalize() {}
private:
inline void sendEvent(const FinalizeCommunicatorEvent &) {
onCommunicatorFinalize();
}
template <class EventHandler> friend class EventHandlerManager;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
class Communicator : public EventHandlerManager<CommunicatorEventHandler> {
struct private_member {};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Communicator(int & argc, char **& argv, const private_member &);
- virtual ~Communicator();
+ ~Communicator() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Point to Point */
/* ------------------------------------------------------------------------ */
template <typename T>
inline void receive(Array<T> & values, Int sender, Int tag) const {
return this->receiveImpl(
values.storage(), values.size() * values.getNbComponent(), sender, tag);
}
template <typename Tensor>
inline void
receive(Tensor & values, Int sender, Int tag,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
return this->receiveImpl(values.storage(), values.size(), sender, tag);
}
template <bool is_static>
inline void receive(CommunicationBufferTemplated<is_static> & values,
Int sender, Int tag) const {
return this->receiveImpl(values.storage(), values.size(), sender, tag);
}
template <typename T>
inline void
receive(T & values, Int sender, Int tag,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
return this->receiveImpl(&values, 1, sender, tag);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void
send(const Array<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->sendImpl(values.storage(),
values.size() * values.getNbComponent(), receiver,
tag, mode);
}
template <typename Tensor>
inline void
send(const Tensor & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
return this->sendImpl(values.storage(), values.size(), receiver, tag, mode);
}
template <bool is_static>
inline void
send(const CommunicationBufferTemplated<is_static> & values, Int receiver,
Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->sendImpl(values.storage(), values.size(), receiver, tag, mode);
}
template <typename T>
inline void
send(const T & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
return this->sendImpl(&values, 1, receiver, tag, mode);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline CommunicationRequest
asyncSend(const Array<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.storage(),
values.size() * values.getNbComponent(),
receiver, tag, mode);
}
template <typename T>
inline CommunicationRequest
asyncSend(const std::vector<T> & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.data(), values.size(), receiver, tag,
mode);
}
template <typename Tensor>
inline CommunicationRequest
asyncSend(const Tensor & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
return this->asyncSendImpl(values.storage(), values.size(), receiver, tag,
mode);
}
template <bool is_static>
inline CommunicationRequest
asyncSend(const CommunicationBufferTemplated<is_static> & values,
Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const {
return this->asyncSendImpl(values.storage(), values.size(), receiver, tag,
mode);
}
template <typename T>
inline CommunicationRequest
asyncSend(const T & values, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
return this->asyncSendImpl(&values, 1, receiver, tag, mode);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline CommunicationRequest asyncReceive(Array<T> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(
values.storage(), values.size() * values.getNbComponent(), sender, tag);
}
template <typename T>
inline CommunicationRequest asyncReceive(std::vector<T> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.data(), values.size(), sender, tag);
}
template <typename Tensor,
typename = std::enable_if_t<is_tensor<Tensor>::value>>
inline CommunicationRequest asyncReceive(Tensor & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.storage(), values.size(), sender, tag);
}
template <bool is_static>
inline CommunicationRequest
asyncReceive(CommunicationBufferTemplated<is_static> & values, Int sender,
Int tag) const {
return this->asyncReceiveImpl(values.storage(), values.size(), sender, tag);
}
/* ------------------------------------------------------------------------ */
template <typename T>
void probe(Int sender, Int tag, CommunicationStatus & status) const;
template <typename T>
bool asyncProbe(Int sender, Int tag, CommunicationStatus & status) const;
/* ------------------------------------------------------------------------ */
/* Collectives */
/* ------------------------------------------------------------------------ */
template <typename T>
inline void allReduce(Array<T> & values,
const SynchronizerOperation & op) const {
this->allReduceImpl(values.storage(),
values.size() * values.getNbComponent(), op);
}
template <typename Tensor>
inline void
allReduce(Tensor & values, const SynchronizerOperation & op,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
this->allReduceImpl(values.storage(), values.size(), op);
}
template <typename T>
inline void
allReduce(T & values, const SynchronizerOperation & op,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
this->allReduceImpl(&values, 1, op);
}
/* ------------------------------------------------------------------------ */
template <typename T> inline void allGather(Array<T> & values) const {
AKANTU_DEBUG_ASSERT(UInt(psize) == values.size(),
"The array size is not correct");
this->allGatherImpl(values.storage(), values.getNbComponent());
}
template <typename Tensor,
typename = std::enable_if_t<is_tensor<Tensor>::value>>
inline void allGather(Tensor & values) const {
AKANTU_DEBUG_ASSERT(UInt(psize) == values.size(),
"The vector size is not correct");
this->allGatherImpl(values.storage(), 1);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void allGatherV(Array<T> & values, Array<Int> sizes) const {
this->allGatherVImpl(values.storage(), sizes.storage());
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void reduce(Array<T> & values, const SynchronizerOperation & op,
int root = 0) const {
this->reduceImpl(values.storage(), values.size() * values.getNbComponent(),
op, root);
}
/* ------------------------------------------------------------------------ */
template <typename Tensor>
inline void
gather(Tensor & values, int root = 0,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
this->gatherImpl(values.storage(), values.getNbComponent(), root);
}
template <typename T>
inline void
gather(T values, int root = 0,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
this->gatherImpl(&values, 1, root);
}
/* ------------------------------------------------------------------------ */
template <typename Tensor, typename T>
inline void
gather(Tensor & values, Array<T> & gathered,
std::enable_if_t<is_tensor<Tensor>::value> * = nullptr) const {
AKANTU_DEBUG_ASSERT(values.size() == gathered.getNbComponent(),
"The array size is not correct");
gathered.resize(psize);
this->gatherImpl(values.data(), values.size(), gathered.storage(),
gathered.getNbComponent());
}
template <typename T>
inline void
gather(T values, Array<T> & gathered,
std::enable_if_t<std::is_arithmetic<T>::value> * = nullptr) const {
this->gatherImpl(&values, 1, gathered.storage(), 1);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void gatherV(Array<T> & values, Array<Int> sizes, int root = 0) const {
this->gatherVImpl(values.storage(), sizes.storage(), root);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void broadcast(Array<T> & values, int root = 0) const {
this->broadcastImpl(values.storage(),
values.size() * values.getNbComponent(), root);
}
template <bool is_static>
inline void broadcast(CommunicationBufferTemplated<is_static> & values,
int root = 0) const {
this->broadcastImpl(values.storage(), values.size(), root);
}
template <typename T> inline void broadcast(T & values, int root = 0) const {
this->broadcastImpl(&values, 1, root);
}
/* ------------------------------------------------------------------------ */
void barrier() const;
CommunicationRequest asyncBarrier() const;
/* ------------------------------------------------------------------------ */
/* Request handling */
/* ------------------------------------------------------------------------ */
bool test(CommunicationRequest & request) const;
bool testAll(std::vector<CommunicationRequest> & request) const;
void wait(CommunicationRequest & request) const;
void waitAll(std::vector<CommunicationRequest> & requests) const;
UInt waitAny(std::vector<CommunicationRequest> & requests) const;
inline void freeCommunicationRequest(CommunicationRequest & request) const;
inline void
freeCommunicationRequest(std::vector<CommunicationRequest> & requests) const;
template <typename T, typename MsgProcessor, typename TagGen>
inline void
receiveAnyNumber(std::vector<CommunicationRequest> & send_requests,
Array<T> receive_buffer, MsgProcessor && processor,
TagGen && tag_gen) const;
protected:
template <typename T>
void
sendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const;
template <typename T>
void receiveImpl(T * buffer, Int size, Int sender, Int tag) const;
template <typename T>
CommunicationRequest asyncSendImpl(
const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode = CommunicationMode::_auto) const;
template <typename T>
CommunicationRequest asyncReceiveImpl(T * buffer, Int size, Int sender,
Int tag) const;
template <typename T>
void allReduceImpl(T * values, int nb_values,
const SynchronizerOperation & op) const;
template <typename T> void allGatherImpl(T * values, int nb_values) const;
template <typename T> void allGatherVImpl(T * values, int * nb_values) const;
template <typename T>
void reduceImpl(T * values, int nb_values, const SynchronizerOperation & op,
int root = 0) const;
template <typename T>
void gatherImpl(T * values, int nb_values, int root = 0) const;
template <typename T>
void gatherImpl(T * values, int nb_values, T * gathered,
int nb_gathered = 0) const;
template <typename T>
void gatherVImpl(T * values, int * nb_values, int root = 0) const;
template <typename T>
void broadcastImpl(T * values, int nb_values, int root = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
Int getNbProc() const { return psize; };
Int whoAmI() const { return prank; };
static Communicator & getStaticCommunicator();
static Communicator & getStaticCommunicator(int & argc, char **& argv);
int getMaxTag() const;
int getMinTag() const;
AKANTU_GET_MACRO(CommunicatorData, (*communicator_data), decltype(auto));
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
static std::unique_ptr<Communicator> static_communicator;
protected:
Int prank{0};
Int psize{1};
std::unique_ptr<CommunicatorInternalData> communicator_data;
};
inline std::ostream & operator<<(std::ostream & stream,
const CommunicationRequest & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "communicator_inline_impl.hh"
#endif /* __AKANTU_STATIC_COMMUNICATOR_HH__ */
diff --git a/src/synchronizer/communicator_mpi_inline_impl.cc b/src/synchronizer/communicator_mpi_inline_impl.cc
index a5e72fe98..9c3cf04ee 100644
--- a/src/synchronizer/communicator_mpi_inline_impl.cc
+++ b/src/synchronizer/communicator_mpi_inline_impl.cc
@@ -1,465 +1,465 @@
/**
* @file static_communicator_mpi.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
* @date last modification: Thu Jan 21 2016
*
* @brief StaticCommunicatorMPI implementation
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_iterators.hh"
#include "communicator.hh"
#include "mpi_communicator_data.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
#include <unordered_map>
#include <vector>
#include <memory>
/* -------------------------------------------------------------------------- */
#include <mpi.h>
/* -------------------------------------------------------------------------- */
#if (defined(__GNUC__) || defined(__GNUG__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION < 60000
namespace std {
template <> struct hash<akantu::SynchronizerOperation> {
using argument_type = akantu::SynchronizerOperation;
size_t operator()(const argument_type & e) const noexcept {
auto ue = underlying_type_t<argument_type>(e);
return uh(ue);
}
private:
const hash<underlying_type_t<argument_type>> uh{};
};
} // namespace std
#endif
#endif
namespace akantu {
class CommunicationRequestMPI : public InternalCommunicationRequest {
public:
CommunicationRequestMPI(UInt source, UInt dest)
: InternalCommunicationRequest(source, dest),
request(std::make_unique<MPI_Request>()) {}
MPI_Request & getMPIRequest() { return *request; };
private:
std::unique_ptr<MPI_Request> request;
};
namespace {
template <typename T> inline MPI_Datatype getMPIDatatype();
MPI_Op getMPISynchronizerOperation(const SynchronizerOperation & op) {
std::unordered_map<SynchronizerOperation, MPI_Op> _operations{
{SynchronizerOperation::_sum, MPI_SUM},
{SynchronizerOperation::_min, MPI_MIN},
{SynchronizerOperation::_max, MPI_MAX},
{SynchronizerOperation::_prod, MPI_PROD},
{SynchronizerOperation::_land, MPI_LAND},
{SynchronizerOperation::_band, MPI_BAND},
{SynchronizerOperation::_lor, MPI_LOR},
{SynchronizerOperation::_bor, MPI_BOR},
{SynchronizerOperation::_lxor, MPI_LXOR},
{SynchronizerOperation::_bxor, MPI_BXOR},
{SynchronizerOperation::_min_loc, MPI_MINLOC},
{SynchronizerOperation::_max_loc, MPI_MAXLOC},
{SynchronizerOperation::_null, MPI_OP_NULL}};
return _operations[op];
}
template <typename T> MPI_Datatype inline getMPIDatatype() {
return MPI_DATATYPE_NULL;
}
#define SPECIALIZE_MPI_DATATYPE(type, mpi_type) \
template <> MPI_Datatype inline getMPIDatatype<type>() { return mpi_type; }
#define COMMA ,
SPECIALIZE_MPI_DATATYPE(char, MPI_CHAR)
SPECIALIZE_MPI_DATATYPE(float, MPI_FLOAT)
SPECIALIZE_MPI_DATATYPE(double, MPI_DOUBLE)
SPECIALIZE_MPI_DATATYPE(long double, MPI_LONG_DOUBLE)
SPECIALIZE_MPI_DATATYPE(signed int, MPI_INT)
SPECIALIZE_MPI_DATATYPE(NodeType, getMPIDatatype<Int>())
SPECIALIZE_MPI_DATATYPE(unsigned int, MPI_UNSIGNED)
SPECIALIZE_MPI_DATATYPE(signed long int, MPI_LONG)
SPECIALIZE_MPI_DATATYPE(unsigned long int, MPI_UNSIGNED_LONG)
SPECIALIZE_MPI_DATATYPE(signed long long int, MPI_LONG_LONG)
SPECIALIZE_MPI_DATATYPE(unsigned long long int, MPI_UNSIGNED_LONG_LONG)
SPECIALIZE_MPI_DATATYPE(SCMinMaxLoc<double COMMA int>, MPI_DOUBLE_INT)
SPECIALIZE_MPI_DATATYPE(SCMinMaxLoc<float COMMA int>, MPI_FLOAT_INT)
SPECIALIZE_MPI_DATATYPE(bool, MPI_CXX_BOOL)
inline int getMPISource(int src) {
if (src == _any_source)
return MPI_ANY_SOURCE;
return src;
}
decltype(auto) convertRequests(std::vector<CommunicationRequest> & requests) {
std::vector<MPI_Request> mpi_requests(requests.size());
for (auto && request_pair : zip(requests, mpi_requests)) {
auto && req = std::get<0>(request_pair);
auto && mpi_req = std::get<1>(request_pair);
mpi_req = dynamic_cast<CommunicationRequestMPI &>(req.getInternal())
.getMPIRequest();
}
return mpi_requests;
}
} // namespace
// this is ugly but shorten the code a lot
#define MPIDATA \
(*reinterpret_cast<MPICommunicatorData *>(communicator_data.get()))
/* -------------------------------------------------------------------------- */
/* Implementation */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
Communicator::Communicator(int & /*argc*/, char **& /*argv*/,
const private_member & /*unused*/)
: communicator_data(std::make_unique<MPICommunicatorData>()) {
prank = MPIDATA.rank();
psize = MPIDATA.size();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::sendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
switch (mode) {
case CommunicationMode::_auto:
MPI_Send(buffer, size, type, receiver, tag, communicator);
break;
case CommunicationMode::_synchronous:
MPI_Ssend(buffer, size, type, receiver, tag, communicator);
break;
case CommunicationMode::_ready:
MPI_Rsend(buffer, size, type, receiver, tag, communicator);
break;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::receiveImpl(T * buffer, Int size, Int sender,
Int tag) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status status;
MPI_Datatype type = getMPIDatatype<T>();
MPI_Recv(buffer, size, type, getMPISource(sender), tag, communicator,
&status);
}
/* -------------------------------------------------------------------------- */
template <typename T>
CommunicationRequest
Communicator::asyncSendImpl(const T * buffer, Int size, Int receiver, Int tag,
const CommunicationMode & mode) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
CommunicationRequestMPI * request =
new CommunicationRequestMPI(prank, receiver);
MPI_Request & req = request->getMPIRequest();
MPI_Datatype type = getMPIDatatype<T>();
switch (mode) {
case CommunicationMode::_auto:
MPI_Isend(buffer, size, type, receiver, tag, communicator, &req);
break;
case CommunicationMode::_synchronous:
MPI_Issend(buffer, size, type, receiver, tag, communicator, &req);
break;
case CommunicationMode::_ready:
MPI_Irsend(buffer, size, type, receiver, tag, communicator, &req);
break;
}
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
CommunicationRequest Communicator::asyncReceiveImpl(T * buffer, Int size,
Int sender, Int tag) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
CommunicationRequestMPI * request =
new CommunicationRequestMPI(sender, prank);
MPI_Datatype type = getMPIDatatype<T>();
MPI_Request & req = request->getMPIRequest();
MPI_Irecv(buffer, size, type, getMPISource(sender), tag, communicator, &req);
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::probe(Int sender, Int tag,
CommunicationStatus & status) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status mpi_status;
MPI_Probe(getMPISource(sender), tag, communicator, &mpi_status);
MPI_Datatype type = getMPIDatatype<T>();
int count;
MPI_Get_count(&mpi_status, type, &count);
status.setSource(mpi_status.MPI_SOURCE);
status.setTag(mpi_status.MPI_TAG);
status.setSize(count);
}
/* -------------------------------------------------------------------------- */
template <typename T>
bool Communicator::asyncProbe(Int sender, Int tag,
CommunicationStatus & status) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Status mpi_status;
int test;
MPI_Iprobe(getMPISource(sender), tag, communicator, &test, &mpi_status);
if (not test)
return false;
MPI_Datatype type = getMPIDatatype<T>();
int count;
MPI_Get_count(&mpi_status, type, &count);
status.setSource(mpi_status.MPI_SOURCE);
status.setTag(mpi_status.MPI_TAG);
status.setSize(count);
return true;
}
/* -------------------------------------------------------------------------- */
bool Communicator::test(CommunicationRequest & request) const {
MPI_Status status;
int flag;
CommunicationRequestMPI & req_mpi =
dynamic_cast<CommunicationRequestMPI &>(request.getInternal());
MPI_Request & req = req_mpi.getMPIRequest();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Test(&req, &flag, &status);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Test.");
return (flag != 0);
}
/* -------------------------------------------------------------------------- */
bool Communicator::testAll(std::vector<CommunicationRequest> & requests) const {
int are_finished;
auto && mpi_requests = convertRequests(requests);
MPI_Testall(mpi_requests.size(), mpi_requests.data(), &are_finished,
MPI_STATUSES_IGNORE);
return are_finished != 0 ? true : false;
}
/* -------------------------------------------------------------------------- */
void Communicator::wait(CommunicationRequest & request) const {
MPI_Status status;
CommunicationRequestMPI & req_mpi =
dynamic_cast<CommunicationRequestMPI &>(request.getInternal());
MPI_Request & req = req_mpi.getMPIRequest();
MPI_Wait(&req, &status);
}
/* -------------------------------------------------------------------------- */
void Communicator::waitAll(std::vector<CommunicationRequest> & requests) const {
auto && mpi_requests = convertRequests(requests);
MPI_Waitall(mpi_requests.size(), mpi_requests.data(), MPI_STATUSES_IGNORE);
}
/* -------------------------------------------------------------------------- */
UInt Communicator::waitAny(std::vector<CommunicationRequest> & requests) const {
auto && mpi_requests = convertRequests(requests);
int pos;
MPI_Waitany(mpi_requests.size(), mpi_requests.data(), &pos,
MPI_STATUSES_IGNORE);
if (pos != MPI_UNDEFINED) {
return pos;
} else {
return UInt(-1);
}
}
/* -------------------------------------------------------------------------- */
void Communicator::barrier() const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Barrier(communicator);
}
/* -------------------------------------------------------------------------- */
CommunicationRequest Communicator::asyncBarrier() const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
CommunicationRequestMPI * request = new CommunicationRequestMPI(0, 0);
MPI_Request & req = request->getMPIRequest();
MPI_Ibarrier(communicator, &req);
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::reduceImpl(T * values, int nb_values,
const SynchronizerOperation & op,
int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Reduce(MPI_IN_PLACE, values, nb_values, type,
getMPISynchronizerOperation(op), root, communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allReduceImpl(T * values, int nb_values,
const SynchronizerOperation & op) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allreduce(MPI_IN_PLACE, values, nb_values, type,
getMPISynchronizerOperation(op), communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allGatherImpl(T * values, int nb_values) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allgather(MPI_IN_PLACE, nb_values, type, values, nb_values, type,
communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::allGatherVImpl(T * values, int * nb_values) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
std::vector<int> displs(psize);
displs[0] = 0;
for (int i = 1; i < psize; ++i) {
displs[i] = displs[i - 1] + nb_values[i - 1];
}
MPI_Datatype type = getMPIDatatype<T>();
MPI_Allgatherv(MPI_IN_PLACE, *nb_values, type, values, nb_values,
displs.data(), type, communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherImpl(T * values, int nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
- T *send_buf = NULL, *recv_buf = NULL;
+ T *send_buf = nullptr, *recv_buf = nullptr;
if (prank == root) {
send_buf = (T *)MPI_IN_PLACE;
recv_buf = values;
} else {
send_buf = values;
}
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gather(send_buf, nb_values, type, recv_buf, nb_values, type, root,
communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherImpl(T * values, int nb_values, T * gathered,
int nb_gathered) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
T * send_buf = values;
T * recv_buf = gathered;
if (nb_gathered == 0)
nb_gathered = nb_values;
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gather(send_buf, nb_values, type, recv_buf, nb_gathered, type,
this->prank, communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::gatherVImpl(T * values, int * nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
int * displs = nullptr;
if (prank == root) {
displs = new int[psize];
displs[0] = 0;
for (int i = 1; i < psize; ++i) {
displs[i] = displs[i - 1] + nb_values[i - 1];
}
}
- T *send_buf = NULL, *recv_buf = NULL;
+ T *send_buf = nullptr, *recv_buf = nullptr;
if (prank == root) {
send_buf = (T *)MPI_IN_PLACE;
recv_buf = values;
} else
send_buf = values;
MPI_Datatype type = getMPIDatatype<T>();
MPI_Gatherv(send_buf, *nb_values, type, recv_buf, nb_values, displs, type,
root, communicator);
if (prank == root) {
delete[] displs;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Communicator::broadcastImpl(T * values, int nb_values, int root) const {
MPI_Comm communicator = MPIDATA.getMPICommunicator();
MPI_Datatype type = getMPIDatatype<T>();
MPI_Bcast(values, nb_values, type, root, communicator);
}
/* -------------------------------------------------------------------------- */
int Communicator::getMaxTag() const { return MPIDATA.getMaxTag(); }
int Communicator::getMinTag() const { return 0; }
/* -------------------------------------------------------------------------- */
} // namespace akantu
diff --git a/src/synchronizer/data_accessor.hh b/src/synchronizer/data_accessor.hh
index 6ef63932a..16cfab1e9 100644
--- a/src/synchronizer/data_accessor.hh
+++ b/src/synchronizer/data_accessor.hh
@@ -1,281 +1,279 @@
/**
* @file data_accessor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Tue Dec 08 2015
*
* @brief Interface of accessors for pack_unpack system
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "communication_buffer.hh"
#include "element.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DATA_ACCESSOR_HH__
#define __AKANTU_DATA_ACCESSOR_HH__
namespace akantu {
class FEEngine;
} // akantu
namespace akantu {
class DataAccessorBase {
public:
DataAccessorBase() {}
virtual ~DataAccessorBase() {}
};
template <class T> class DataAccessor : public virtual DataAccessorBase {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DataAccessor() {}
- virtual ~DataAccessor() {}
+ ~DataAccessor() override {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
* @brief get the number of data to exchange for a given array of T
* (elements or dofs) and a given akantu::SynchronizationTag
*/
virtual UInt getNbData(const Array<T> & elements,
const SynchronizationTag & tag) const = 0;
/**
* @brief pack the data for a given array of T (elements or dofs) and a given
* akantu::SynchronizationTag
*/
virtual void packData(CommunicationBuffer & buffer, const Array<T> & element,
const SynchronizationTag & tag) const = 0;
/**
* @brief unpack the data for a given array of T (elements or dofs) and a
* given akantu::SynchronizationTag
*/
virtual void unpackData(CommunicationBuffer & buffer,
const Array<T> & element,
const SynchronizationTag & tag) = 0;
};
/* -------------------------------------------------------------------------- */
/* Specialization */
/* -------------------------------------------------------------------------- */
template <> class DataAccessor<Element> : public virtual DataAccessorBase {
public:
DataAccessor() {}
- virtual ~DataAccessor() {}
+ ~DataAccessor() override {}
virtual UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const = 0;
virtual void packData(CommunicationBuffer & buffer,
const Array<Element> & element,
const SynchronizationTag & tag) const = 0;
virtual void unpackData(CommunicationBuffer & buffer,
const Array<Element> & element,
const SynchronizationTag & tag) = 0;
/* ------------------------------------------------------------------------ */
public:
template <typename T, bool pack_helper>
static void
packUnpackNodalDataHelper(Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh);
/* ------------------------------------------------------------------------ */
template <typename T, bool pack_helper>
static void packUnpackElementalDataHelper(
ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & element, bool per_quadrature_point_data,
const FEEngine & fem);
/* ------------------------------------------------------------------------ */
template <typename T>
static void
packNodalDataHelper(const Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
packUnpackNodalDataHelper<T, true>(const_cast<Array<T> &>(data), buffer,
elements, mesh);
}
template <typename T>
static inline void
unpackNodalDataHelper(Array<T> & data, CommunicationBuffer & buffer,
const Array<Element> & elements, const Mesh & mesh) {
packUnpackNodalDataHelper<T, false>(data, buffer, elements, mesh);
}
/* ------------------------------------------------------------------------ */
template <typename T>
static inline void
packElementalDataHelper(const ElementTypeMapArray<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
bool per_quadrature_point, const FEEngine & fem) {
packUnpackElementalDataHelper<T, true>(
const_cast<ElementTypeMapArray<T> &>(data_to_pack), buffer, elements,
per_quadrature_point, fem);
}
template <typename T>
static inline void
unpackElementalDataHelper(ElementTypeMapArray<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<Element> & elements,
bool per_quadrature_point, const FEEngine & fem) {
packUnpackElementalDataHelper<T, false>(data_to_unpack, buffer, elements,
per_quadrature_point, fem);
}
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <> class DataAccessor<UInt> : public virtual DataAccessorBase {
public:
DataAccessor() {}
- virtual ~DataAccessor() {}
+ ~DataAccessor() override {}
virtual UInt getNbData(const Array<UInt> & elements,
const SynchronizationTag & tag) const = 0;
virtual void packData(CommunicationBuffer & buffer,
const Array<UInt> & element,
const SynchronizationTag & tag) const = 0;
virtual void unpackData(CommunicationBuffer & buffer,
const Array<UInt> & element,
const SynchronizationTag & tag) = 0;
/* ------------------------------------------------------------------------ */
public:
template <typename T, bool pack_helper>
static void packUnpackDOFDataHelper(Array<T> & data,
CommunicationBuffer & buffer,
const Array<UInt> & dofs);
template <typename T>
static inline void packDOFDataHelper(const Array<T> & data_to_pack,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
packUnpackDOFDataHelper<T, true>(const_cast<Array<T> &>(data_to_pack),
buffer, dofs);
}
template <typename T>
static inline void unpackDOFDataHelper(Array<T> & data_to_unpack,
CommunicationBuffer & buffer,
const Array<UInt> & dofs) {
packUnpackDOFDataHelper<T, false>(data_to_unpack, buffer, dofs);
}
};
/* -------------------------------------------------------------------------- */
template <typename T> class AddOperation {
public:
inline T operator()(T & a, T & b) { return a + b; };
};
template <typename T> class IdentityOperation {
public:
inline T & operator()(T &, T & b) { return b; };
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <template <class> class Op, class T>
class ReduceUIntDataAccessor : public virtual DataAccessor<UInt> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ReduceUIntDataAccessor(Array<T> & data, const SynchronizationTag & tag)
: data(data), tag(tag) {}
- virtual ~ReduceUIntDataAccessor() {}
+ ~ReduceUIntDataAccessor() override {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
- virtual UInt getNbData(const Array<UInt> & elements,
- const SynchronizationTag & tag) const {
+ UInt getNbData(const Array<UInt> & elements,
+ const SynchronizationTag & tag) const override {
if (tag != this->tag)
return 0;
Vector<T> tmp(data.getNbComponent());
return elements.size() * CommunicationBuffer::sizeInBuffer(tmp);
}
/* ------------------------------------------------------------------------ */
- virtual void packData(CommunicationBuffer & buffer,
- const Array<UInt> & elements,
- const SynchronizationTag & tag) const {
+ void packData(CommunicationBuffer & buffer, const Array<UInt> & elements,
+ const SynchronizationTag & tag) const override {
if (tag != this->tag)
return;
auto data_it = data.begin(data.getNbComponent());
for (auto el : elements) {
buffer << Vector<T>(data_it[el]);
}
}
/* ------------------------------------------------------------------------ */
- virtual void unpackData(CommunicationBuffer & buffer,
- const Array<UInt> & elements,
- const SynchronizationTag & tag) {
+ void unpackData(CommunicationBuffer & buffer, const Array<UInt> & elements,
+ const SynchronizationTag & tag) override {
if (tag != this->tag)
return;
auto data_it = data.begin(data.getNbComponent());
for (auto el : elements) {
Vector<T> unpacked(data.getNbComponent());
Vector<T> vect(data_it[el]);
buffer >> unpacked;
vect = oper(vect, unpacked);
}
}
protected:
/// data to (un)pack
Array<T> & data;
/// Tag to consider
SynchronizationTag tag;
/// reduction operator
Op<Vector<T>> oper;
};
/* -------------------------------------------------------------------------- */
template <class T>
using SimpleUIntDataAccessor = ReduceUIntDataAccessor<IdentityOperation, T>;
} // akantu
#endif /* __AKANTU_DATA_ACCESSOR_HH__ */
diff --git a/src/synchronizer/dof_synchronizer.hh b/src/synchronizer/dof_synchronizer.hh
index 9e1eeb9a7..da02089fe 100644
--- a/src/synchronizer/dof_synchronizer.hh
+++ b/src/synchronizer/dof_synchronizer.hh
@@ -1,113 +1,116 @@
/**
* @file dof_synchronizer.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
* @date last modification: Tue Dec 08 2015
*
* @brief Synchronize Array of DOFs
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_array.hh"
#include "aka_common.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Mesh;
class DOFManagerDefault;
}
#ifndef __AKANTU_DOF_SYNCHRONIZER_HH__
#define __AKANTU_DOF_SYNCHRONIZER_HH__
namespace akantu {
class DOFSynchronizer : public SynchronizerImpl<UInt> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFSynchronizer(
DOFManagerDefault & dof_manager, const ID & id = "dof_synchronizer",
MemoryID memory_id = 0,
const Communicator & comm = Communicator::getStaticCommunicator());
- virtual ~DOFSynchronizer();
+ ~DOFSynchronizer() override;
virtual void registerDOFs(const ID & dof_id);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <typename T>
/// Gather the DOF value on the root proccessor
void gather(const Array<T> & to_gather, Array<T> & gathered);
/// Gather the DOF value on the root proccessor
template <typename T> void gather(const Array<T> & to_gather);
/// Scatter a DOF Array form root to all processors
template <typename T>
void scatter(Array<T> & scattered, const Array<T> & to_scatter);
/// Scatter a DOF Array form root to all processors
template <typename T> void scatter(Array<T> & scattered);
template <typename T> void synchronize(Array<T> & vector) const;
template <template <class> class Op, typename T>
void reduceSynchronize(Array<T> & vector) const;
void onNodesAdded(const Array<UInt> & nodes);
protected:
/// check if dof changed set on at least one processor
bool hasChanged();
/// init the scheme for scatter and gather operation, need extra memory
void initScatterGatherCommunicationScheme();
- Int getRank(const UInt & /*node*/) const override final { AKANTU_DEBUG_TO_IMPLEMENT(); }
+ Int getRank(const UInt & /*node*/) const final {
+ AKANTU_DEBUG_TO_IMPLEMENT();
+ }
+
private:
/// Root processor for scatter/gather operations
Int root;
/// information on the dofs
DOFManagerDefault & dof_manager;
/// dofs from root
Array<UInt> root_dofs;
/// Dofs received from slaves proc (only on master)
std::map<UInt, Array<UInt>> master_receive_dofs;
bool dof_changed;
};
} // akantu
#include "dof_synchronizer_inline_impl.cc"
#endif /* __AKANTU_DOF_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/element_synchronizer.hh b/src/synchronizer/element_synchronizer.hh
index 55d838646..103ddd79e 100644
--- a/src/synchronizer/element_synchronizer.hh
+++ b/src/synchronizer/element_synchronizer.hh
@@ -1,210 +1,210 @@
/**
* @file element_synchronizer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Dana Christen <dana.christen@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief Main element synchronizer
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_SYNCHRONIZER_HH__
#define __AKANTU_ELEMENT_SYNCHRONIZER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "mesh_partition.hh"
#include "synchronizer_impl.hh"
namespace akantu {
class Mesh;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementSynchronizer : public SynchronizerImpl<Element>,
public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementSynchronizer(Mesh & mesh, const ID & id = "element_synchronizer",
MemoryID memory_id = 0,
bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
public:
- virtual ~ElementSynchronizer();
+ ~ElementSynchronizer() override;
friend class ElementInfoPerProc;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/// mesh event handler onElementsChanged
void onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const ChangedElementsEvent & event) override;
/// mesh event handler onRemovedElement
void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
/// mesh event handler onNodesAdded
void onNodesAdded(const Array<UInt> & /* nodes_list*/,
const NewNodesEvent & /*event*/) override{};
/// mesh event handler onRemovedNodes
void onNodesRemoved(const Array<UInt> & /*nodes_list*/,
const Array<UInt> & /*new_numbering*/,
const RemovedNodesEvent & /*event*/) override{};
/// mesh event handler onElementsAdded
void onElementsAdded(const Array<Element> & /*elements_list*/,
const NewElementsEvent & /*event*/) override{};
protected:
/// reset send and recv element lists
void reset();
/// remove elements from the synchronizer without renumbering them
void removeElements(const Array<Element> & element_to_remove);
/// renumber the elements in the synchronizer
void renumberElements(const ElementTypeMapArray<UInt> & new_numbering);
/// build processor to element correspondence
void buildElementToPrank();
protected:
/// fill the nodes type vector
void fillNodesType(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name, const ElementType & el_type,
const Array<UInt> & partition_num);
template <typename T>
void fillTagBufferTemplated(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name,
const ElementType & el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition);
void fillTagBuffer(const MeshData & mesh_data,
DynamicCommunicationBuffer * buffers,
const std::string & tag_name, const ElementType & el_type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition);
/// function that handels the MeshData to be split (root side)
static void synchronizeTagsSend(ElementSynchronizer & communicator, UInt root,
Mesh & mesh, UInt nb_tags,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_local_element, UInt nb_ghost_element);
/// function that handles the MeshData to be split (other nodes)
static void synchronizeTagsRecv(ElementSynchronizer & communicator, UInt root,
Mesh & mesh, UInt nb_tags,
const ElementType & type,
UInt nb_local_element, UInt nb_ghost_element);
/// function that handles the preexisting groups in the mesh
static void synchronizeElementGroups(ElementSynchronizer & communicator,
UInt root, Mesh & mesh,
const ElementType & type,
const Array<UInt> & partition_num,
const CSR<UInt> & ghost_partition,
UInt nb_element);
/// function that handles the preexisting groups in the mesh
static void synchronizeElementGroups(ElementSynchronizer & communicator,
UInt root, Mesh & mesh,
const ElementType & type);
/// function that handles the preexisting groups in the mesh
static void synchronizeNodeGroupsMaster(ElementSynchronizer & communicator,
UInt root, Mesh & mesh);
/// function that handles the preexisting groups in the mesh
static void synchronizeNodeGroupsSlaves(ElementSynchronizer & communicator,
UInt root, Mesh & mesh);
template <class CommunicationBuffer>
static void fillNodeGroupsFromBuffer(ElementSynchronizer & communicator,
Mesh & mesh,
CommunicationBuffer & buffer);
/// substitute elements in the send and recv arrays
void
substituteElements(const std::map<Element, Element> & old_to_new_elements);
/* ------------------------------------------------------------------------ */
/* Sanity checks */
/* ------------------------------------------------------------------------ */
- virtual UInt sanityCheckDataSize(const Array<Element> & elements,
- const SynchronizationTag & tag) const;
+ UInt sanityCheckDataSize(const Array<Element> & elements,
+ const SynchronizationTag & tag) const override;
/* ------------------------------------------------------------------------ */
- virtual void
- packSanityCheckData(CommunicationDescriptor<Element> & comm_desc) const;
+ void
+ packSanityCheckData(CommunicationDescriptor<Element> & comm_desc) const override;
/* ------------------------------------------------------------------------ */
- virtual void
- unpackSanityCheckData(CommunicationDescriptor<Element> & comm_desc) const;
+ void
+ unpackSanityCheckData(CommunicationDescriptor<Element> & comm_desc) const override;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Mesh, mesh, Mesh &);
- Int getRank(const Element & element) const override final;
+ Int getRank(const Element & element) const final;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// reference to the underlying mesh
Mesh & mesh;
friend class FilteredSynchronizer;
friend class FacetSynchronizer;
ElementTypeMapArray<Int> element_to_prank;
};
/* -------------------------------------------------------------------------- */
} // namespace akantu
#endif /* __AKANTU_ELEMENT_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/grid_synchronizer.hh b/src/synchronizer/grid_synchronizer.hh
index 379e017d4..1005d0654 100644
--- a/src/synchronizer/grid_synchronizer.hh
+++ b/src/synchronizer/grid_synchronizer.hh
@@ -1,103 +1,103 @@
/**
* @file grid_synchronizer.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief Synchronizer based on spatial grid
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "element_synchronizer.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GRID_SYNCHRONIZER_HH__
#define __AKANTU_GRID_SYNCHRONIZER_HH__
namespace akantu {
class Mesh;
template <class T> class SpatialGrid;
class GridSynchronizer : public ElementSynchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
template <typename E>
GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
const ID & id = "grid_synchronizer", MemoryID memory_id = 0,
const bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
template <typename E>
GridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
SynchronizerRegistry & synchronizer_registry,
const std::set<SynchronizationTag> & tags_to_register,
const ID & id = "grid_synchronizer", MemoryID memory_id = 0,
const bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
- virtual ~GridSynchronizer() = default;
+ ~GridSynchronizer() override = default;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
/**
*Create the Grid Synchronizer:
*Compute intersection and send info to neighbours that will be stored in
*ghosts elements
*/
template <typename E>
void createGridSynchronizer(const SpatialGrid<E> & grid);
protected:
/// Define the tags that will be used in the send and receive instructions
enum CommTags {
SIZE_TAG = 0,
DATA_TAG = 1,
ASK_NODES_TAG = 2,
SEND_NODES_TAG = 3
};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
} // namespace akantu
#include "grid_synchronizer_tmpl.hh"
#endif /* __AKANTU_GRID_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/mpi_communicator_data.hh b/src/synchronizer/mpi_communicator_data.hh
index 2a2b2e6bc..2b0222e90 100644
--- a/src/synchronizer/mpi_communicator_data.hh
+++ b/src/synchronizer/mpi_communicator_data.hh
@@ -1,136 +1,136 @@
/**
* @file mpi_type_wrapper.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Wed Oct 07 2015
*
* @brief Wrapper on MPI types to have a better separation between libraries
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#if __cplusplus > 199711L
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wliteral-suffix"
#endif
#endif
#include <mpi.h>
#if defined(__INTEL_COMPILER)
//#pragma warning ( disable : 383 )
#elif defined(__clang__) // test clang to be sure that when we test for gnu it
// is only gnu
#elif (defined(__GNUC__) || defined(__GNUG__))
#if __cplusplus > 199711L
#pragma GCC diagnostic pop
#endif
#endif
/* -------------------------------------------------------------------------- */
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MPI_TYPE_WRAPPER_HH__
#define __AKANTU_MPI_TYPE_WRAPPER_HH__
namespace akantu {
class MPICommunicatorData : public CommunicatorInternalData {
public:
MPICommunicatorData() {
int is_initialized = false;
MPI_Initialized(&is_initialized);
if (!is_initialized) {
- MPI_Init(NULL, NULL); // valid according to the spec
+ MPI_Init(nullptr, nullptr); // valid according to the spec
}
MPI_Comm_create_errhandler(MPICommunicatorData::errorHandler, &error_handler);
setMPICommunicator(MPI_COMM_WORLD);
is_externaly_initialized = is_initialized;
}
- ~MPICommunicatorData() {
+ ~MPICommunicatorData() override {
if (not is_externaly_initialized) {
MPI_Finalize();
}
}
inline void setMPICommunicator(MPI_Comm comm) {
MPI_Comm_set_errhandler(communicator, save_error_handler);
communicator = comm;
MPI_Comm_get_errhandler(comm, &save_error_handler);
MPI_Comm_set_errhandler(comm, error_handler);
}
inline int rank() const {
int prank;
MPI_Comm_rank(communicator, &prank);
return prank;
}
inline int size() const {
int psize;
MPI_Comm_size(communicator, &psize);
return psize;
}
inline MPI_Comm getMPICommunicator() const { return communicator; }
inline int getMaxTag() const {
int flag;
int * value;
MPI_Comm_get_attr(communicator, MPI_TAG_UB, &value, &flag);
AKANTU_DEBUG_ASSERT(flag, "No attribute MPI_TAG_UB.");
return *value;
}
private:
MPI_Comm communicator{MPI_COMM_WORLD};
MPI_Errhandler save_error_handler{MPI_ERRORS_ARE_FATAL};
bool is_externaly_initialized{false};
/* ------------------------------------------------------------------------ */
MPI_Errhandler error_handler;
static void errorHandler(MPI_Comm * /*comm*/, int * error_code, ...) {
char error_string[MPI_MAX_ERROR_STRING];
int str_len;
MPI_Error_string(*error_code, error_string, &str_len);
AKANTU_CUSTOM_EXCEPTION_INFO(debug::CommunicationException(),
"MPI failed with the error code "
<< *error_code << ": \"" << error_string
<< "\"");
}
};
} // namespace akantu
#endif /* __AKANTU_MPI_TYPE_WRAPPER_HH__ */
diff --git a/src/synchronizer/node_info_per_processor.hh b/src/synchronizer/node_info_per_processor.hh
index 9a28d965b..e75fcafd7 100644
--- a/src/synchronizer/node_info_per_processor.hh
+++ b/src/synchronizer/node_info_per_processor.hh
@@ -1,110 +1,110 @@
/**
* @file node_info_per_processor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Mar 11 14:45:15 2016
*
* @brief Helper classes to create the distributed synchronizer and distribute
* a mesh
*
* @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 "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NODE_INFO_PER_PROCESSOR_HH__
#define __AKANTU_NODE_INFO_PER_PROCESSOR_HH__
namespace akantu {
class NodeSynchronizer;
class Communicator;
}
/* -------------------------------------------------------------------------- */
namespace akantu {
class NodeInfoPerProc : protected MeshAccessor {
public:
NodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt,
UInt root);
virtual void synchronizeNodes() = 0;
virtual void synchronizeTypes() = 0;
virtual void synchronizeGroups() = 0;
protected:
template <class CommunicationBuffer>
void fillNodeGroupsFromBuffer(CommunicationBuffer & buffer);
void fillNodesType();
void fillCommunicationScheme(const Array<UInt> &);
protected:
NodeSynchronizer & synchronizer;
const Communicator & comm;
UInt rank;
UInt nb_proc;
UInt root;
Mesh & mesh;
UInt spatial_dimension;
UInt message_count;
};
/* -------------------------------------------------------------------------- */
class MasterNodeInfoPerProc : protected NodeInfoPerProc {
public:
MasterNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt,
UInt root);
- void synchronizeNodes();
- void synchronizeTypes();
- void synchronizeGroups();
+ void synchronizeNodes() override;
+ void synchronizeTypes() override;
+ void synchronizeGroups() override;
private:
/// get the list of nodes to send and send them
std::vector<Array<UInt> > nodes_per_proc;
Array<UInt> nb_nodes_per_proc;
};
/* -------------------------------------------------------------------------- */
class SlaveNodeInfoPerProc : protected NodeInfoPerProc {
public:
SlaveNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt,
UInt root);
- void synchronizeNodes();
- void synchronizeTypes();
- void synchronizeGroups();
+ void synchronizeNodes() override;
+ void synchronizeTypes() override;
+ void synchronizeGroups() override;
private:
};
} // akantu
#endif /* __AKANTU_NODE_INFO_PER_PROCESSOR_HH__ */
diff --git a/src/synchronizer/node_synchronizer.hh b/src/synchronizer/node_synchronizer.hh
index 45d42b786..8bfd76044 100644
--- a/src/synchronizer/node_synchronizer.hh
+++ b/src/synchronizer/node_synchronizer.hh
@@ -1,86 +1,88 @@
/**
* @file node_synchronizer.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Sep 23 11:45:24 2016
*
* @brief Synchronizer for nodal information
*
* @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 "mesh_events.hh"
#include "synchronizer_impl.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NODE_SYNCHRONIZER_HH__
#define __AKANTU_NODE_SYNCHRONIZER_HH__
namespace akantu {
class NodeSynchronizer : public MeshEventHandler,
public SynchronizerImpl<UInt> {
public:
NodeSynchronizer(Mesh & mesh, const ID & id = "element_synchronizer",
MemoryID memory_id = 0,
const bool register_to_event_manager = true,
EventHandlerPriority event_priority = _ehp_synchronizer);
- virtual ~NodeSynchronizer();
+ ~NodeSynchronizer() override;
friend class NodeInfoPerProc;
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override;
/// function to implement to react on akantu::RemovedNodesEvent
void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) override {}
/// function to implement to react on akantu::NewElementsEvent
void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) override {}
/// function to implement to react on akantu::RemovedElementsEvent
void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) override {}
/// function to implement to react on akantu::ChangedElementsEvent
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override {}
public:
AKANTU_GET_MACRO(Mesh, mesh, Mesh &);
protected:
- Int getRank(const UInt & /*node*/) const override final { AKANTU_DEBUG_TO_IMPLEMENT(); }
+ Int getRank(const UInt & /*node*/) const final {
+ AKANTU_DEBUG_TO_IMPLEMENT();
+ }
protected:
Mesh & mesh;
//std::unordered_map<UInt, Int> node_to_prank;
};
} // namespace akantu
#endif /* __AKANTU_NODE_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/synchronizer.hh b/src/synchronizer/synchronizer.hh
index 1f15397f1..2fad3305a 100644
--- a/src/synchronizer/synchronizer.hh
+++ b/src/synchronizer/synchronizer.hh
@@ -1,130 +1,130 @@
/**
* @file synchronizer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Dec 10 2015
*
* @brief Common interface for synchronizers
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_memory.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SYNCHRONIZER_HH__
#define __AKANTU_SYNCHRONIZER_HH__
namespace akantu {
/* -------------------------------------------------------------------------- */
/* Base class for synchronizers */
/* -------------------------------------------------------------------------- */
class Synchronizer : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Synchronizer(const ID & id = "synchronizer", MemoryID memory_id = 0,
const Communicator & comm =
Communicator::getStaticCommunicator());
- virtual ~Synchronizer(){};
+ ~Synchronizer() override{};
virtual void printself(__attribute__((unused)) std::ostream & stream,
__attribute__((unused)) int indent = 0) const {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronize ghosts without state
template <class DataAccessor>
void synchronizeOnce(DataAccessor & data_accessor,
const SynchronizationTag & tag) const;
/// synchronize ghosts
template <class DataAccessor>
void synchronize(DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// asynchronous synchronization of ghosts
template <class DataAccessor>
void asynchronousSynchronize(const DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// wait end of asynchronous synchronization of ghosts
template <class DataAccessor>
void waitEndSynchronize(DataAccessor & data_accessor,
const SynchronizationTag & tag);
/// compute buffer size for a given tag and data accessor
template <class DataAccessor>
void computeBufferSize(const DataAccessor & data_accessor,
const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Communicator, communicator, const Communicator &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id of the synchronizer
ID id;
/// hashed version of the id
int hash_id;
/// message counter per tag
std::map<SynchronizationTag, UInt> tag_counter;
/// the static memory instance
const Communicator & communicator;
/// nb processors in the communicator
UInt nb_proc;
/// rank in the communicator
UInt rank;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const Synchronizer & _this) {
_this.printself(stream);
return stream;
}
} // akantu
#include "synchronizer_tmpl.hh"
#endif /* __AKANTU_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/synchronizer_impl.hh b/src/synchronizer/synchronizer_impl.hh
index a8cfdfea4..1b28e3583 100644
--- a/src/synchronizer/synchronizer_impl.hh
+++ b/src/synchronizer/synchronizer_impl.hh
@@ -1,122 +1,122 @@
/**
* @file synchronizer_impl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Aug 24 13:26:47 2016
*
* @brief Implementation of the generic part of synchronizers
*
* @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 "communications.hh"
#include "synchronizer.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SYNCHRONIZER_IMPL_HH__
#define __AKANTU_SYNCHRONIZER_IMPL_HH__
namespace akantu {
template <class Entity> class SynchronizerImpl : public Synchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SynchronizerImpl(
const ID & id = "synchronizer", MemoryID memory_id = 0,
const Communicator & comm = Communicator::getStaticCommunicator());
- virtual ~SynchronizerImpl(){};
+ ~SynchronizerImpl() override{};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// synchronous synchronization without state
virtual void synchronizeOnceImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) const;
/// asynchronous synchronization of ghosts
virtual void
asynchronousSynchronizeImpl(const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/// wait end of asynchronous synchronization of ghosts
virtual void waitEndSynchronizeImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/// compute all buffer sizes
virtual void computeAllBufferSizes(const DataAccessor<Entity> & data_accessor);
/// compute buffer size for a given tag and data accessor
virtual void computeBufferSizeImpl(const DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
virtual void synchronizeImpl(DataAccessor<Entity> & data_accessor,
const SynchronizationTag & tag) {
this->asynchronousSynchronizeImpl(data_accessor, tag);
this->waitEndSynchronizeImpl(data_accessor, tag);
}
/* ------------------------------------------------------------------------ */
/// extract the elements that have a true predicate from in_synchronizer and
/// store them in the current synchronizer
template <typename Pred>
void split(SynchronizerImpl & in_synchronizer, Pred && pred);
/// update schemes in a synchronizer
template <typename Updater>
void updateSchemes(Updater && scheme_updater);
/* ------------------------------------------------------------------------ */
virtual UInt sanityCheckDataSize(const Array<Entity> & elements,
const SynchronizationTag & tag) const;
virtual void
packSanityCheckData(CommunicationDescriptor<Entity> & comm_desc) const;
virtual void
unpackSanityCheckData(CommunicationDescriptor<Entity> & comm_desc) const;
public:
AKANTU_GET_MACRO(Communications, communications, const Communications<Entity> &);
protected:
AKANTU_GET_MACRO_NOT_CONST(Communications, communications, Communications<Entity> &);
virtual Int getRank(const Entity & entity) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// information on the communications
Communications<Entity> communications;
};
} // akantu
#include "synchronizer_impl_tmpl.hh"
#endif /* __AKANTU_SYNCHRONIZER_IMPL_HH__ */
diff --git a/src/synchronizer/synchronizer_registry.cc b/src/synchronizer/synchronizer_registry.cc
index 0c8ce1398..38c318c89 100644
--- a/src/synchronizer/synchronizer_registry.cc
+++ b/src/synchronizer/synchronizer_registry.cc
@@ -1,139 +1,139 @@
/**
* @file synchronizer_registry.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 16 2011
* @date last modification: Thu Oct 08 2015
*
* @brief Registry of synchronizers
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "synchronizer_registry.hh"
#include "synchronizer.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
/* -------------------------------------------------------------------------- */
SynchronizerRegistry::SynchronizerRegistry() : data_accessor(nullptr) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SynchronizerRegistry::~SynchronizerRegistry() {
AKANTU_DEBUG_IN();
synchronizers.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::registerDataAccessor(
DataAccessorBase & data_accessor) {
this->data_accessor = &data_accessor;
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::synchronize(SynchronizationTag tag) {
AKANTU_DEBUG_IN();
- AKANTU_DEBUG_ASSERT(data_accessor != NULL, "No data accessor set.");
+ AKANTU_DEBUG_ASSERT(data_accessor != nullptr, "No data accessor set.");
std::pair<Tag2Sync::iterator, Tag2Sync::iterator> range =
synchronizers.equal_range(tag);
for (Tag2Sync::iterator it = range.first; it != range.second; ++it) {
it->second->synchronize(*data_accessor, tag);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::asynchronousSynchronize(SynchronizationTag tag) {
AKANTU_DEBUG_IN();
- AKANTU_DEBUG_ASSERT(data_accessor != NULL, "No data accessor set.");
+ AKANTU_DEBUG_ASSERT(data_accessor != nullptr, "No data accessor set.");
std::pair<Tag2Sync::iterator, Tag2Sync::iterator> range =
synchronizers.equal_range(tag);
for (Tag2Sync::iterator it = range.first; it != range.second; ++it) {
(*it).second->asynchronousSynchronize(*data_accessor, tag);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::waitEndSynchronize(SynchronizationTag tag) {
AKANTU_DEBUG_IN();
- AKANTU_DEBUG_ASSERT(data_accessor != NULL, "No data accessor set.");
+ AKANTU_DEBUG_ASSERT(data_accessor != nullptr, "No data accessor set.");
std::pair<Tag2Sync::iterator, Tag2Sync::iterator> range =
synchronizers.equal_range(tag);
for (Tag2Sync::iterator it = range.first; it != range.second; ++it) {
(*it).second->waitEndSynchronize(*data_accessor, tag);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::registerSynchronizer(Synchronizer & synchronizer,
SynchronizationTag tag) {
AKANTU_DEBUG_IN();
synchronizers.insert(
std::pair<SynchronizationTag, Synchronizer *>(tag, &synchronizer));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SynchronizerRegistry::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "SynchronizerRegistry [" << std::endl;
Tag2Sync::const_iterator it;
for (it = synchronizers.begin(); it != synchronizers.end(); it++) {
stream << space << " + Synchronizers for tag " << (*it).first << " ["
<< std::endl;
(*it).second->printself(stream, indent + 1);
stream << space << " ]" << std::endl;
}
stream << space << "]" << std::endl;
}
} // akantu
diff --git a/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc b/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc
index bdd4aece5..8c696153e 100644
--- a/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc
+++ b/test/test_mesh_utils/test_segment_nodetype/test_segment_nodetype.cc
@@ -1,97 +1,97 @@
/**
* @file test_segment_nodetype.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Sep 18 2015
*
* @brief Test to verify that the node type is correctly associated to
* the segments in parallel
*
* @section LICENSE
*
* Copyright (©) 2015 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 "element_synchronizer.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
// partition the mesh
if (prank == 0) {
mesh.read("mesh.msh");
}
mesh.distribute();
// compute the node types for each segment
Mesh & mesh_facets = mesh.initMeshFacets();
MeshUtils::buildSegmentToNodeType(mesh, mesh_facets);
// verify that the number of segments per node type makes sense
std::map<Int, UInt> nb_facets_per_nodetype;
UInt nb_segments = 0;
for (auto ghost_type : ghost_types) {
const Array<Int> & segment_to_nodetype =
mesh_facets.getData<Int>("segment_to_nodetype", _segment_2, ghost_type);
// count the number of segments per node type
for (auto & stn : segment_to_nodetype) {
if (nb_facets_per_nodetype.find(stn) == nb_facets_per_nodetype.end())
nb_facets_per_nodetype[stn] = 1;
else
++nb_facets_per_nodetype[stn];
}
nb_segments += segment_to_nodetype.size();
}
// checking the solution
if (nb_segments != 24)
AKANTU_DEBUG_ERROR("The number of segments is wrong");
if (prank == 0) {
if (nb_facets_per_nodetype[-1] != 3 || nb_facets_per_nodetype[-2] != 9 ||
nb_facets_per_nodetype[-3] != 12)
AKANTU_DEBUG_ERROR(
"The segments of processor 0 have the wrong node type");
if (nb_facets_per_nodetype.size() > 3)
AKANTU_DEBUG_ERROR("Processor 0 cannot have any slave segment");
}
if (prank == psize - 1 &&
nb_facets_per_nodetype.find(-2) != nb_facets_per_nodetype.end())
AKANTU_DEBUG_ERROR("The last processor must not have any master facets");
finalize();
return 0;
}
diff --git a/test/test_model/test_model_solver/test_model_solver_my_model.hh b/test/test_model/test_model_solver/test_model_solver_my_model.hh
index 58fc2a0e9..9490b1a10 100644
--- a/test/test_model/test_model_solver/test_model_solver_my_model.hh
+++ b/test/test_model/test_model_solver/test_model_solver_my_model.hh
@@ -1,468 +1,468 @@
/**
* @file test_dof_manager_default.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Feb 24 12:28:44 2016
*
* @brief Test default dof manager
*
* @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 "aka_iterators.hh"
#include "data_accessor.hh"
#include "dof_manager_default.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "model_solver.hh"
#include "sparse_matrix.hh"
#include "communicator.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
#ifndef __AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH__
#define __AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH__
/**
* =\o-----o-----o-> F
* | |
* |---- L ----|
*/
class MyModel : public ModelSolver, public DataAccessor<Element> {
public:
MyModel(Real F, Mesh & mesh, bool lumped)
: ModelSolver(mesh, "model_solver", 0), nb_dofs(mesh.getNbNodes()),
nb_elements(mesh.getNbElement()), E(1.), A(1.), rho(1.), lumped(lumped),
mesh(mesh), displacement(nb_dofs, 1, "disp"),
velocity(nb_dofs, 1, "velo"), acceleration(nb_dofs, 1, "accel"),
blocked(nb_dofs, 1, "blocked"), forces(nb_dofs, 1, "force_ext"),
internal_forces(nb_dofs, 1, "force_int"),
stresses(nb_elements, 1, "stress"), strains(nb_elements, 1, "strain"),
initial_lengths(nb_elements, 1, "L0") {
this->initDOFManager();
this->getDOFManager().registerDOFs("disp", displacement, _dst_nodal);
this->getDOFManager().registerDOFsDerivative("disp", 1, velocity);
this->getDOFManager().registerDOFsDerivative("disp", 2, acceleration);
this->getDOFManager().registerBlockedDOFs("disp", blocked);
displacement.set(0.);
velocity.set(0.);
acceleration.set(0.);
forces.set(0.);
blocked.set(false);
UInt global_nb_nodes = mesh.getNbGlobalNodes();
for (auto && n : arange(nb_dofs)) {
auto global_id = mesh.getNodeGlobalId(n);
if (global_id == (global_nb_nodes - 1))
forces(n, _x) = F;
if (global_id == 0)
blocked(n, _x) = true;
}
auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2).end(2);
auto L_it = this->initial_lengths.begin();
for (; cit != cend; ++cit, ++L_it) {
const Vector<UInt> & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
*L_it = std::abs(p2 - p1);
}
this->registerDataAccessor(*this);
this->registerSynchronizer(
const_cast<ElementSynchronizer &>(this->mesh.getElementSynchronizer()),
_gst_user_1);
}
void assembleLumpedMass() {
Array<Real> & M = this->getDOFManager().getLumpedMatrix("M");
M.clear();
this->assembleLumpedMass(_not_ghost);
if (this->mesh.getNbElement(_segment_2, _ghost) > 0)
this->assembleLumpedMass(_ghost);
is_lumped_mass_assembled = true;
}
void assembleLumpedMass(const GhostType & ghost_type) {
Array<Real> & M = this->getDOFManager().getLumpedMatrix("M");
Array<Real> m_all_el(this->mesh.getNbElement(_segment_2, ghost_type), 2);
Array<Real>::vector_iterator m_it = m_all_el.begin(2);
auto cit = this->mesh.getConnectivity(_segment_2, ghost_type).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2, ghost_type).end(2);
for (; cit != cend; ++cit, ++m_it) {
const Vector<UInt> & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
Real M_n = rho * A * L / 2;
(*m_it)(0) = (*m_it)(1) = M_n;
}
this->getDOFManager().assembleElementalArrayLocalArray(
m_all_el, M, _segment_2, ghost_type);
}
void assembleMass() {
SparseMatrix & M = this->getDOFManager().getMatrix("M");
M.clear();
Array<Real> m_all_el(this->nb_elements, 4);
Array<Real>::matrix_iterator m_it = m_all_el.begin(2, 2);
auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2).end(2);
Matrix<Real> m(2, 2);
m(0, 0) = m(1, 1) = 2;
m(0, 1) = m(1, 0) = 1;
// under integrated
// m(0, 0) = m(1, 1) = 3./2.;
// m(0, 1) = m(1, 0) = 3./2.;
// lumping the mass matrix
// m(0, 0) += m(0, 1);
// m(1, 1) += m(1, 0);
// m(0, 1) = m(1, 0) = 0;
for (; cit != cend; ++cit, ++m_it) {
const Vector<UInt> & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
Matrix<Real> & m_el = *m_it;
m_el = m;
m_el *= rho * A * L / 6.;
}
this->getDOFManager().assembleElementalMatricesToMatrix(
"M", "disp", m_all_el, _segment_2);
is_mass_assembled = true;
}
MatrixType getMatrixType(const ID &) { return _symmetric; }
void assembleMatrix(const ID & matrix_id) {
if (matrix_id == "K") {
if (not is_stiffness_assembled)
this->assembleStiffness();
} else if (matrix_id == "M") {
if (not is_mass_assembled)
this->assembleMass();
} else if (matrix_id == "C") {
// pass, no damping matrix
} else {
AKANTU_EXCEPTION("This solver does not know what to do with a matrix "
<< matrix_id);
}
}
void assembleLumpedMatrix(const ID & matrix_id) {
if (matrix_id == "M") {
if (not is_lumped_mass_assembled)
this->assembleLumpedMass();
} else {
AKANTU_EXCEPTION("This solver does not know what to do with a matrix "
<< matrix_id);
}
}
void assembleStiffness() {
SparseMatrix & K = this->getDOFManager().getMatrix("K");
K.clear();
Matrix<Real> k(2, 2);
k(0, 0) = k(1, 1) = 1;
k(0, 1) = k(1, 0) = -1;
Array<Real> k_all_el(this->nb_elements, 4);
auto k_it = k_all_el.begin(2, 2);
auto cit = this->mesh.getConnectivity(_segment_2).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2).end(2);
for (; cit != cend; ++cit, ++k_it) {
const auto & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real p1 = this->mesh.getNodes()(n1, _x);
Real p2 = this->mesh.getNodes()(n2, _x);
Real L = std::abs(p2 - p1);
auto & k_el = *k_it;
k_el = k;
k_el *= E * A / L;
}
this->getDOFManager().assembleElementalMatricesToMatrix(
"K", "disp", k_all_el, _segment_2);
is_stiffness_assembled = true;
}
void assembleResidual() {
this->getDOFManager().assembleToResidual("disp", forces);
internal_forces.clear();
this->assembleResidual(_not_ghost);
this->synchronize(_gst_user_1);
this->getDOFManager().assembleToResidual("disp", internal_forces, -1.);
- // auto & comm = StaticCommunicator::getStaticCommunicator();
+ // auto & comm = Communicator::getStaticCommunicator();
// const auto & dof_manager_default =
// dynamic_cast<DOFManagerDefault &>(this->getDOFManager());
// const auto & residual = dof_manager_default.getResidual();
// int prank = comm.whoAmI();
// int psize = comm.getNbProc();
// for (int p = 0; p < psize; ++p) {
// if (prank == p) {
// UInt local_dof = 0;
// for (auto res : residual) {
// UInt global_dof =
// dof_manager_default.localToGlobalEquationNumber(local_dof);
// std::cout << local_dof << " [" << global_dof << " - "
// << dof_manager_default.getDOFType(local_dof) << "]: " <<
// res
// << std::endl;
// ++local_dof;
// }
// std::cout << std::flush;
// }
// comm.barrier();
// }
// comm.barrier();
// if(prank == 0) std::cout << "===========================" << std::endl;
}
void assembleResidual(const GhostType & ghost_type) {
Array<Real> forces_internal_el(
this->mesh.getNbElement(_segment_2, ghost_type), 2);
auto cit = this->mesh.getConnectivity(_segment_2, ghost_type).begin(2);
auto cend = this->mesh.getConnectivity(_segment_2, ghost_type).end(2);
auto f_it = forces_internal_el.begin(2);
auto strain_it = this->strains.begin();
auto stress_it = this->stresses.begin();
auto L_it = this->initial_lengths.begin();
for (; cit != cend; ++cit, ++f_it, ++strain_it, ++stress_it, ++L_it) {
const auto & conn = *cit;
UInt n1 = conn(0);
UInt n2 = conn(1);
Real u1 = this->displacement(n1, _x);
Real u2 = this->displacement(n2, _x);
*strain_it = (u2 - u1) / *L_it;
*stress_it = E * *strain_it;
Real f_n = A * *stress_it;
Vector<Real> & f = *f_it;
f(0) = -f_n;
f(1) = f_n;
}
this->getDOFManager().assembleElementalArrayLocalArray(
forces_internal_el, internal_forces, _segment_2, ghost_type);
}
Real getPotentialEnergy() {
Real res = 0;
if (!lumped) {
res = this->mulVectMatVect(this->displacement,
this->getDOFManager().getMatrix("K"),
this->displacement);
} else {
auto strain_it = this->strains.begin();
auto stress_it = this->stresses.begin();
auto strain_end = this->strains.end();
auto L_it = this->initial_lengths.begin();
for (; strain_it != strain_end; ++strain_it, ++stress_it, ++L_it) {
res += *strain_it * *stress_it * A * *L_it;
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
}
return res / 2.;
}
Real getKineticEnergy() {
Real res = 0;
if (!lumped) {
res = this->mulVectMatVect(
this->velocity, this->getDOFManager().getMatrix("M"), this->velocity);
} else {
auto & m = this->getDOFManager().getLumpedMatrix("M");
auto it = velocity.begin();
auto end = velocity.end();
auto m_it = m.begin();
for (UInt node = 0; it != end; ++it, ++m_it, ++node) {
if (mesh.isLocalOrMasterNode(node))
res += *m_it * *it * *it;
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
}
return res / 2.;
}
Real getExternalWorkIncrement() {
Real res = 0;
auto it = velocity.begin();
auto end = velocity.end();
auto if_it = internal_forces.begin();
auto ef_it = forces.begin();
auto b_it = blocked.begin();
for (UInt node = 0; it != end; ++it, ++if_it, ++ef_it, ++b_it, ++node) {
if (mesh.isLocalOrMasterNode(node))
res += (*b_it ? -*if_it : *ef_it) * *it;
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
return res * this->getTimeStep();
}
Real mulVectMatVect(const Array<Real> & x, const SparseMatrix & A,
const Array<Real> & y) {
Array<Real> Ay(this->nb_dofs, 1, 0.);
A.matVecMul(y, Ay);
Real res = 0.;
Array<Real>::const_scalar_iterator it = Ay.begin();
Array<Real>::const_scalar_iterator end = Ay.end();
Array<Real>::const_scalar_iterator x_it = x.begin();
for (UInt node = 0; it != end; ++it, ++x_it, ++node) {
if (mesh.isLocalOrMasterNode(node))
res += *x_it * *it;
}
mesh.getCommunicator().allReduce(res, SynchronizerOperation::_sum);
return res;
}
void predictor() {}
void corrector() {}
/* ------------------------------------------------------------------------ */
UInt getNbData(const Array<Element> & elements,
const SynchronizationTag &) const {
return elements.size() * sizeof(Real);
}
void packData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_user_1) {
for (const auto & el : elements) {
buffer << this->stresses(el.element);
}
}
}
void unpackData(CommunicationBuffer & buffer, const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == _gst_user_1) {
auto cit = this->mesh.getConnectivity(_segment_2, _ghost).begin(2);
for (const auto & el : elements) {
Real stress;
buffer >> stress;
Real f = A * stress;
Vector<UInt> conn = cit[el.element];
this->internal_forces(conn(0), _x) += -f;
this->internal_forces(conn(1), _x) += f;
}
}
}
private:
UInt nb_dofs;
UInt nb_elements;
Real E, A, rho;
bool lumped;
bool is_stiffness_assembled{false};
bool is_mass_assembled{false};
bool is_lumped_mass_assembled{false};
public:
Mesh & mesh;
Array<Real> displacement;
Array<Real> velocity;
Array<Real> acceleration;
Array<bool> blocked;
Array<Real> forces;
Array<Real> internal_forces;
Array<Real> stresses;
Array<Real> strains;
Array<Real> initial_lengths;
};
#endif /* __AKANTU_TEST_MODEL_SOLVER_MY_MODEL_HH__ */
} // akantu
diff --git a/test/test_model/test_non_local_toolbox/my_model.hh b/test/test_model/test_non_local_toolbox/my_model.hh
index 458712eae..6304cf19c 100644
--- a/test/test_model/test_non_local_toolbox/my_model.hh
+++ b/test/test_model/test_non_local_toolbox/my_model.hh
@@ -1,118 +1,122 @@
/**
* @file my_model.hh
*
* @author Nicolas Richart
*
* @date creation Sun Sep 10 2017
*
* @brief A Documented file.
*
* @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 "integrator_gauss.hh"
#include "model.hh"
#include "non_local_manager.hh"
#include "non_local_manager_callback.hh"
#include "non_local_neighborhood_base.hh"
#include "shape_lagrange.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
class MyModel : public Model, public NonLocalManagerCallback {
using MyFEEngineType = FEEngineTemplate<IntegratorGauss, ShapeLagrange>;
public:
MyModel(Mesh & mesh, UInt spatial_dimension)
: Model(mesh, spatial_dimension), manager(*this, *this) {
registerFEEngineObject<MyFEEngineType>("FEEngine", mesh, spatial_dimension);
manager.registerNeighborhood("test_region", "test_region");
getFEEngine().initShapeFunctions();
manager.initialize();
}
void initModel() override {}
MatrixType getMatrixType(const ID &) override { return _mt_not_defined; }
+ std::tuple<ID, TimeStepSolverType>
+ getDefaultSolverID(const AnalysisMethod & /*method*/) {
+ return {"test", _tsst_static};
+ }
+
void assembleMatrix(const ID &) override {}
void assembleLumpedMatrix(const ID &) override {}
void assembleResidual() override {}
void onNodesAdded(const Array<UInt> &, const NewNodesEvent &) override {}
void onNodesRemoved(const Array<UInt> &, const Array<UInt> &,
const RemovedNodesEvent &) override {}
void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) override {}
void onElementsRemoved(const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const RemovedElementsEvent &) override {}
void onElementsChanged(const Array<Element> &, const Array<Element> &,
const ElementTypeMapArray<UInt> &,
const ChangedElementsEvent &) override {}
void insertIntegrationPointsInNeighborhoods(
const GhostType & ghost_type) override {
ElementTypeMapArray<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_tmp_nl", this->id, this->memory_id);
quadrature_points_coordinates.initialize(this->getFEEngine(),
_nb_component = spatial_dimension,
_ghost_type = ghost_type);
IntegrationPoint q;
q.ghost_type = ghost_type;
- q.kind = _ek_regular;
q.global_num = 0;
auto & neighborhood = manager.getNeighborhood("test_region");
for (auto & type : quadrature_points_coordinates.elementTypes(
spatial_dimension, ghost_type)) {
q.type = type;
auto & quads = quadrature_points_coordinates(type, ghost_type);
this->getFEEngine().computeIntegrationPointsCoordinates(quads, type,
ghost_type);
auto quad_it = quads.begin(quads.getNbComponent());
auto quad_end = quads.end(quads.getNbComponent());
q.num_point = 0;
for (; quad_it != quad_end; ++quad_it) {
neighborhood.insertIntegrationPoint(q, *quad_it);
++q.num_point;
++q.global_num;
}
}
}
void computeNonLocalStresses(const GhostType &) override {}
void updateLocalInternal(ElementTypeMapReal &, const GhostType &,
const ElementKind &) override {}
void updateNonLocalInternal(ElementTypeMapReal &, const GhostType &,
const ElementKind &) override {}
const auto & getNonLocalManager() const { return manager; }
private:
NonLocalManager manager;
};
diff --git a/test/test_model/test_non_local_toolbox/test_build_neighborhood_parallel.cc b/test/test_model/test_non_local_toolbox/test_build_neighborhood_parallel.cc
index 756685754..c199735a3 100644
--- a/test/test_model/test_non_local_toolbox/test_build_neighborhood_parallel.cc
+++ b/test/test_model/test_non_local_toolbox/test_build_neighborhood_parallel.cc
@@ -1,191 +1,191 @@
/**
* @file test_build_neighborhood_parallel.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Sat Sep 26 2015
* @date last modification: Wed Nov 25 2015
*
* @brief test in parallel for the class NonLocalNeighborhood
*
* @section LICENSE
*
* Copyright (©) 2015 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 "dumper_paraview.hh"
#include "non_local_neighborhood_base.hh"
#include "solid_mechanics_model.hh"
#include "test_material.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
akantu::initialize("material_parallel_test.dat", argc, argv);
- auto & comm = akantu::StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
// some configuration variables
const UInt spatial_dimension = 2;
// mesh creation and read
Mesh mesh(spatial_dimension);
if (prank == 0) {
mesh.read("parallel_test.msh");
}
mesh.distribute();
/// model creation
SolidMechanicsModel model(mesh);
/// dump the ghost elements before the non-local part is intialized
DumperParaview dumper_ghost("ghost_elements");
dumper_ghost.registerMesh(mesh, spatial_dimension, _ghost);
if (psize > 1) {
dumper_ghost.dump();
}
/// creation of material selector
MeshDataMaterialSelector<std::string> mat_selector("physical_names", model);
model.setMaterialSelector(mat_selector);
/// dump material index in paraview
model.addDumpField("partitions");
model.dump();
/// model initialization changed to use our material
model.initFull();
/// dump the ghost elements after ghosts for non-local have been added
if (psize > 1)
dumper_ghost.dump();
model.addDumpField("grad_u");
model.addDumpField("grad_u non local");
model.addDumpField("material_index");
/// apply constant strain field everywhere in the plate
Matrix<Real> applied_strain(spatial_dimension, spatial_dimension);
applied_strain.clear();
for (UInt i = 0; i < spatial_dimension; ++i)
applied_strain(i, i) = 2.;
ElementType element_type = _triangle_3;
GhostType ghost_type = _not_ghost;
/// apply constant grad_u field in all elements
for (UInt m = 0; m < model.getNbMaterials(); ++m) {
auto & mat = model.getMaterial(m);
auto & grad_u = const_cast<Array<Real> &>(
mat.getInternal<Real>("grad_u")(element_type, ghost_type));
auto grad_u_it = grad_u.begin(spatial_dimension, spatial_dimension);
auto grad_u_end = grad_u.end(spatial_dimension, spatial_dimension);
for (; grad_u_it != grad_u_end; ++grad_u_it)
(*grad_u_it) = -1. * applied_strain;
}
/// double the strain in the center: find the closed gauss point to the center
/// compute the quadrature points
ElementTypeMapReal quad_coords("quad_coords");
quad_coords.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_with_nb_element = true);
model.getFEEngine().computeIntegrationPointsCoordinates(quad_coords);
Vector<Real> center(spatial_dimension, 0.);
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, _not_ghost, _ek_regular);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, _not_ghost, _ek_regular);
Real min_distance = 2;
IntegrationPoint q_min;
for (; it != last_type; ++it) {
ElementType type = *it;
UInt nb_elements = mesh.getNbElement(type, _not_ghost);
UInt nb_quads = model.getFEEngine().getNbIntegrationPoints(type);
Array<Real> & coords = quad_coords(type, _not_ghost);
Array<Real>::const_vector_iterator coord_it =
coords.begin(spatial_dimension);
for (UInt e = 0; e < nb_elements; ++e) {
for (UInt q = 0; q < nb_quads; ++q, ++coord_it) {
Real dist = center.distance(*coord_it);
if (dist < min_distance) {
min_distance = dist;
q_min.element = e;
q_min.num_point = q;
q_min.global_num = nb_elements * nb_quads + q;
q_min.type = type;
}
}
}
}
Real global_min = min_distance;
- comm.allReduce(global_min, _so_min);
+ comm.allReduce(global_min, SynchronizerOperation::_min);
if (Math::are_float_equal(global_min, min_distance)) {
UInt mat_index = model.getMaterialByElement(q_min.type, _not_ghost)
.begin()[q_min.element];
Material & mat = model.getMaterial(mat_index);
UInt nb_quads = model.getFEEngine().getNbIntegrationPoints(q_min.type);
UInt local_el_index =
model.getMaterialLocalNumbering(q_min.type, _not_ghost)
.begin()[q_min.element];
UInt local_num = (local_el_index * nb_quads) + q_min.num_point;
Array<Real> & grad_u = const_cast<Array<Real> &>(
mat.getInternal<Real>("grad_u")(q_min.type, _not_ghost));
Array<Real>::iterator<Matrix<Real>> grad_u_it =
grad_u.begin(spatial_dimension, spatial_dimension);
grad_u_it += local_num;
Matrix<Real> & g_u = *grad_u_it;
g_u += applied_strain;
}
/// compute the non-local strains
model.assembleInternalForces();
model.dump();
/// damage the element with higher grad_u completely, so that it is
/// not taken into account for the averaging
if (Math::are_float_equal(global_min, min_distance)) {
UInt mat_index = model.getMaterialByElement(q_min.type, _not_ghost)
.begin()[q_min.element];
Material & mat = model.getMaterial(mat_index);
UInt nb_quads = model.getFEEngine().getNbIntegrationPoints(q_min.type);
UInt local_el_index =
model.getMaterialLocalNumbering(q_min.type, _not_ghost)
.begin()[q_min.element];
UInt local_num = (local_el_index * nb_quads) + q_min.num_point;
Array<Real> & damage = const_cast<Array<Real> &>(
mat.getInternal<Real>("damage")(q_min.type, _not_ghost));
Real * dam_ptr = damage.storage();
dam_ptr += local_num;
*dam_ptr = 0.9;
}
/// compute the non-local strains
model.assembleInternalForces();
model.dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_non_local_toolbox/test_pair_computation.cc b/test/test_model/test_non_local_toolbox/test_pair_computation.cc
index 84207e7cb..d88839d3a 100644
--- a/test/test_model/test_non_local_toolbox/test_pair_computation.cc
+++ b/test/test_model/test_non_local_toolbox/test_pair_computation.cc
@@ -1,227 +1,224 @@
/**
* @file test_pair_computation.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Wed Nov 25 2015
*
* @brief test the weight computation with and without grid
*
* @section LICENSE
*
* Copyright (©) 2015 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 "dumper_paraview.hh"
#include "non_local_manager.hh"
#include "non_local_neighborhood.hh"
#include "solid_mechanics_model.hh"
#include "test_material_damage.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
typedef std::vector<std::pair<IntegrationPoint, IntegrationPoint>> PairList;
/* -------------------------------------------------------------------------- */
void computePairs(SolidMechanicsModel & model, PairList * pair_list);
int main(int argc, char * argv[]) {
akantu::initialize("material_remove_damage.dat", argc, argv);
// some configuration variables
const UInt spatial_dimension = 2;
- StaticCommunicator & comm =
- akantu::StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
// mesh creation and read
Mesh mesh(spatial_dimension);
if (prank == 0) {
mesh.read("pair_test.msh");
}
mesh.distribute();
/// model creation
SolidMechanicsModel model(mesh);
/// creation of material selector
MeshDataMaterialSelector<std::string> mat_selector("physical_names", model);
model.setMaterialSelector(mat_selector);
/// model initialization changed to use our material
model.initFull();
/// dump material index in paraview
model.addDumpField("material_index");
model.dump();
/// compute the pairs by looping over all the quadrature points
PairList pair_list[2];
computePairs(model, pair_list);
const PairList * pairs_mat_1 = model.getNonLocalManager().getNeighborhood("mat_1").getPairLists();
const PairList * pairs_mat_2 = model.getNonLocalManager().getNeighborhood("mat_2").getPairLists();
/// compare the number of pairs
UInt nb_not_ghost_pairs_grid = pairs_mat_1[0].size() + pairs_mat_2[0].size();
UInt nb_ghost_pairs_grid = pairs_mat_1[1].size() + pairs_mat_2[1].size();
UInt nb_not_ghost_pairs_no_grid = pair_list[0].size();
UInt nb_ghost_pairs_no_grid = pair_list[1].size();
if ((nb_not_ghost_pairs_grid != nb_not_ghost_pairs_no_grid) ||
(nb_ghost_pairs_grid != nb_ghost_pairs_no_grid)) {
std::cout << "The number of pairs is not correct: TEST FAILED!!!"
<< std::endl;
finalize();
return EXIT_FAILURE;
}
for (UInt i = 0; i < pairs_mat_1[0].size(); ++i) {
PairList::const_iterator it = std::find(
pair_list[0].begin(), pair_list[0].end(), (pairs_mat_1[0])[i]);
if (it == pair_list[0].end()) {
std::cout << "The pairs are not correct" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
for (UInt i = 0; i < pairs_mat_2[0].size(); ++i) {
PairList::const_iterator it = std::find(
pair_list[0].begin(), pair_list[0].end(), (pairs_mat_2[0])[i]);
if (it == pair_list[0].end()) {
std::cout << "The pairs are not correct" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
for (UInt i = 0; i < pairs_mat_1[1].size(); ++i) {
PairList::const_iterator it = std::find(
pair_list[1].begin(), pair_list[1].end(), (pairs_mat_1[1])[i]);
if (it == pair_list[1].end()) {
std::cout << "The pairs are not correct" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
for (UInt i = 0; i < pairs_mat_2[1].size(); ++i) {
PairList::const_iterator it = std::find(
pair_list[1].begin(), pair_list[1].end(), (pairs_mat_2[1])[i]);
if (it == pair_list[1].end()) {
std::cout << "The pairs are not correct" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
finalize();
return 0;
}
/* -------------------------------------------------------------------------- */
void computePairs(SolidMechanicsModel & model, PairList * pair_list) {
ElementKind kind = _ek_regular;
Mesh & mesh = model.getMesh();
UInt spatial_dimension = model.getSpatialDimension();
/// compute the quadrature points
ElementTypeMapReal quad_coords("quad_coords");
quad_coords.initialize(mesh, _nb_component = spatial_dimension,
_spatial_dimension = spatial_dimension,
_with_nb_element = true);
model.getFEEngine().computeIntegrationPointsCoordinates(quad_coords);
/// loop in a n^2 way over all the quads to generate the pairs
Real neighborhood_radius = 0.5;
Mesh::type_iterator it_1 =
mesh.firstType(spatial_dimension, _not_ghost, kind);
Mesh::type_iterator last_type_1 =
mesh.lastType(spatial_dimension, _not_ghost, kind);
IntegrationPoint q1;
IntegrationPoint q2;
- q1.kind = kind;
- q2.kind = kind;
GhostType ghost_type_1 = _not_ghost;
q1.ghost_type = ghost_type_1;
Vector<Real> q1_coords(spatial_dimension);
Vector<Real> q2_coords(spatial_dimension);
for (; it_1 != last_type_1; ++it_1) {
ElementType type_1 = *it_1;
q1.type = type_1;
UInt nb_elements_1 = mesh.getNbElement(type_1, ghost_type_1);
UInt nb_quads_1 = model.getFEEngine().getNbIntegrationPoints(type_1);
Array<Real> & quad_coords_1 = quad_coords(q1.type, q1.ghost_type);
Array<Real>::const_vector_iterator coord_it_1 =
quad_coords_1.begin(spatial_dimension);
for (UInt e_1 = 0; e_1 < nb_elements_1; ++e_1) {
q1.element = e_1;
UInt mat_index_1 = model.getMaterialByElement(q1.type, q1.ghost_type)
.begin()[q1.element];
for (UInt q_1 = 0; q_1 < nb_quads_1; ++q_1) {
q1.global_num = nb_quads_1 * e_1 + q_1;
q1.num_point = q_1;
q1_coords = coord_it_1[q1.global_num];
/// loop over all other quads and create pairs for this given quad
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type_2 = *gt;
q2.ghost_type = ghost_type_2;
Mesh::type_iterator it_2 =
mesh.firstType(spatial_dimension, ghost_type_2, kind);
Mesh::type_iterator last_type_2 =
mesh.lastType(spatial_dimension, ghost_type_2, kind);
for (; it_2 != last_type_2; ++it_2) {
ElementType type_2 = *it_2;
q2.type = type_2;
UInt nb_elements_2 = mesh.getNbElement(type_2, ghost_type_2);
UInt nb_quads_2 =
model.getFEEngine().getNbIntegrationPoints(type_2);
Array<Real> & quad_coords_2 = quad_coords(q2.type, q2.ghost_type);
Array<Real>::const_vector_iterator coord_it_2 =
quad_coords_2.begin(spatial_dimension);
for (UInt e_2 = 0; e_2 < nb_elements_2; ++e_2) {
q2.element = e_2;
UInt mat_index_2 =
model.getMaterialByElement(q2.type, q2.ghost_type)
.begin()[q2.element];
for (UInt q_2 = 0; q_2 < nb_quads_2; ++q_2) {
q2.global_num = nb_quads_2 * e_2 + q_2;
q2.num_point = q_2;
q2_coords = coord_it_2[q2.global_num];
Real distance = q1_coords.distance(q2_coords);
if (mat_index_1 != mat_index_2)
continue;
else if (distance <=
neighborhood_radius + Math::getTolerance() &&
(q2.ghost_type == _ghost ||
(q2.ghost_type == _not_ghost &&
q1.global_num <=
q2.global_num))) { // storing only half lists
pair_list[q2.ghost_type].push_back(std::make_pair(q1, q2));
}
}
}
}
}
}
}
}
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/test_cohesive_facet_stress_synchronizer.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/test_cohesive_facet_stress_synchronizer.cc
index 1a32681bf..a9a04a914 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/test_cohesive_facet_stress_synchronizer.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_facet_stress_synchronizer/test_cohesive_facet_stress_synchronizer.cc
@@ -1,205 +1,205 @@
/**
* @file test_cohesive_facet_stress_synchronizer.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief Test for facet stress synchronizer
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include <limits>
#include <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real function(Real constant, Real x, Real y, Real z) {
return constant + 2. * x + 3. * y + 4 * z;
}
int main(int argc, char *argv[]) {
initialize("material.dat", argc, argv);
const UInt spatial_dimension = 3;
ElementType type = _tetrahedron_10;
ElementType type_facet = Mesh::getFacetType(type);
Math::setTolerance(1.e-11);
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if(prank == 0) {
// Read the mesh
mesh.read("tetrahedron.msh");
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition, NULL, true);
model.initFull(SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
Array<Real> & position = mesh.getNodes();
/* ------------------------------------------------------------------------ */
/* Facet part */
/* ------------------------------------------------------------------------ */
/// compute quadrature points positions on facets
const Mesh & mesh_facets = model.getMeshFacets();
UInt nb_facet = mesh_facets.getNbElement(type_facet);
UInt nb_quad_per_facet = model.getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
UInt nb_tot_quad = nb_quad_per_facet * nb_facet;
Array<Real> quad_facets(nb_tot_quad, spatial_dimension);
model.getFEEngine("FacetsFEEngine").interpolateOnIntegrationPoints(position,
quad_facets,
spatial_dimension,
type_facet);
/* ------------------------------------------------------------------------ */
/* End of facet part */
/* ------------------------------------------------------------------------ */
/// compute quadrature points position of the elements
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_tot_quad_el = nb_quad_per_element * nb_element;
Array<Real> quad_elements(nb_tot_quad_el, spatial_dimension);
model.getFEEngine().interpolateOnIntegrationPoints(position,
quad_elements,
spatial_dimension,
type);
/// assign some values to stresses
Array<Real> & stress
= const_cast<Array<Real>&>(model.getMaterial(0).getStress(type));
Array<Real>::iterator<Matrix<Real> > stress_it
= stress.begin(spatial_dimension, spatial_dimension);
for (UInt q = 0; q < nb_tot_quad_el; ++q, ++stress_it) {
/// compute values
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = i; j < spatial_dimension; ++j) {
UInt index = i * spatial_dimension + j;
(*stress_it)(i, j) = function(index,
quad_elements(q, 0),
quad_elements(q, 1),
quad_elements(q, 2));
}
}
/// fill symmetrical part
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < i; ++j) {
(*stress_it)(i, j) = (*stress_it)(j, i);
}
}
// stress_it->clear();
// for (UInt i = 0; i < spatial_dimension; ++i)
// (*stress_it)(i, i) = sigma_c * 5;
}
/// compute and communicate stress on facets
model.checkCohesiveStress();
/* ------------------------------------------------------------------------ */
/* Check facet stress */
/* ------------------------------------------------------------------------ */
const Array<Real> & facet_stress = model.getStressOnFacets(type_facet);
const Array<bool> & facet_check
= model.getElementInserter().getCheckFacets(type_facet);
const Array<std::vector<Element> > & elements_to_facet
= model.getMeshFacets().getElementToSubelement(type_facet);
Array<Real>::iterator<Vector<Real> > quad_facet_it
= quad_facets.begin(spatial_dimension);
Array<Real>::const_iterator<Matrix<Real> > facet_stress_it
= facet_stress.begin(spatial_dimension, spatial_dimension * 2);
Matrix<Real> current_stress(spatial_dimension, spatial_dimension);
for (UInt f = 0; f < nb_facet; ++f) {
if (!facet_check(f) ||
(elements_to_facet(f)[0].ghost_type == _not_ghost &&
elements_to_facet(f)[1].ghost_type == _not_ghost)) {
quad_facet_it += nb_quad_per_facet;
facet_stress_it += nb_quad_per_facet;
continue;
}
for (UInt q = 0; q < nb_quad_per_facet; ++q, ++quad_facet_it, ++facet_stress_it) {
/// compute current_stress
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = i; j < spatial_dimension; ++j) {
UInt index = i * spatial_dimension + j;
current_stress(i, j) = function(index,
(*quad_facet_it)(0),
(*quad_facet_it)(1),
(*quad_facet_it)(2));
}
}
/// fill symmetrical part
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < i; ++j) {
current_stress(i, j) = current_stress(j, i);
}
}
/// compare it to interpolated one
for (UInt s = 0; s < 2; ++s) {
Matrix<Real> stress_to_check(facet_stress_it->storage()
+ s * spatial_dimension * spatial_dimension,
spatial_dimension,
spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
if (!Math::are_float_equal(stress_to_check(i, j), current_stress(i, j))) {
std::cout << "Stress doesn't match" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
}
}
}
}
finalize();
if (prank == 0)
std::cout << "OK: test_cohesive_facet_stress_synchronizer passed!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc
index 0484a2351..f80e75f54 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_buildfragments/test_cohesive_parallel_buildfragments.cc
@@ -1,432 +1,432 @@
/**
* @file test_cohesive_parallel_buildfragments.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief Test to build fragments in parallel
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include <limits>
#include <fstream>
#include <iostream>
#include <algorithm>
#include <functional>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
#include "material_cohesive.hh"
#include "fragment_manager.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
void verticalInsertionLimit(SolidMechanicsModelCohesive &);
void displaceElements(SolidMechanicsModelCohesive &, const Real, const Real);
bool isInertiaEqual(const Vector<Real> &, const Vector<Real> &);
void rotateArray(Array<Real> & array, Real angle);
UInt getNbBigFragments(FragmentManager &, UInt);
const UInt spatial_dimension = 3;
const UInt total_nb_fragment = 4;
const Real rotation_angle = M_PI / 4.;
const Real global_tolerance = 1.e-9;
int main(int argc, char *argv[]) {
initialize("material.dat", argc, argv);
Math::setTolerance(global_tolerance);
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if(prank == 0) {
// Read the mesh
mesh.read("mesh.msh");
/// partition the mesh
MeshUtils::purifyMesh(mesh);
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition, NULL, true);
delete partition;
/// model initialization
model.initFull(SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
mesh.computeBoundingBox();
Real L = mesh.getUpperBounds()(0) - mesh.getLowerBounds()(0);
Real h = mesh.getUpperBounds()(1) - mesh.getLowerBounds()(1);
Real rho = model.getMaterial("bulk").getParam<Real>("rho");
Real theoretical_mass = L * h * h * rho;
Real frag_theo_mass = theoretical_mass / total_nb_fragment;
UInt nb_element = mesh.getNbElement(spatial_dimension, _not_ghost, _ek_regular);
comm.allReduce(&nb_element, 1, _so_sum);
UInt nb_element_per_fragment = nb_element / total_nb_fragment;
FragmentManager fragment_manager(model);
fragment_manager.computeAllData();
getNbBigFragments(fragment_manager, nb_element_per_fragment + 1);
model.setBaseName("extrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity");
model.addDumpField("stress");
model.addDumpField("partitions");
model.addDumpField("fragments");
model.addDumpField("fragments mass");
model.addDumpField("moments of inertia");
model.addDumpField("elements per fragment");
model.dump();
model.setBaseNameToDumper("cohesive elements", "cohesive_elements_test");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
/// set check facets
verticalInsertionLimit(model);
model.assembleMassLumped();
model.synchronizeBoundaries();
/// impose initial displacement
Array<Real> & displacement = model.getDisplacement();
Array<Real> & velocity = model.getVelocity();
const Array<Real> & position = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes; ++n) {
displacement(n, 0) = position(n, 0) * 0.1;
velocity(n, 0) = position(n, 0);
}
rotateArray(mesh.getNodes(), rotation_angle);
// rotateArray(displacement, rotation_angle);
// rotateArray(velocity, rotation_angle);
model.updateResidual();
model.checkCohesiveStress();
model.dump();
model.dump("cohesive elements");
const Array<Real> & fragment_mass = fragment_manager.getMass();
const Array<Real> & fragment_center = fragment_manager.getCenterOfMass();
Real el_size = L / total_nb_fragment;
Real lim = -L/2 + el_size * 0.99;
/// define theoretical inertia moments
Vector<Real> small_frag_inertia(spatial_dimension);
small_frag_inertia(0) = frag_theo_mass * (h*h + h*h) / 12.;
small_frag_inertia(1) = frag_theo_mass * (el_size*el_size + h*h) / 12.;
small_frag_inertia(2) = frag_theo_mass * (el_size*el_size + h*h) / 12.;
std::sort(small_frag_inertia.storage(),
small_frag_inertia.storage() + spatial_dimension,
std::greater<Real>());
const Array<Real> & inertia_moments = fragment_manager.getMomentsOfInertia();
Array<Real>::const_iterator< Vector<Real> > inertia_moments_begin
= inertia_moments.begin(spatial_dimension);
/// displace one fragment each time
for (UInt frag = 1; frag <= total_nb_fragment; ++frag) {
if (prank == 0)
std::cout << "Generating fragment: " << frag << std::endl;
fragment_manager.computeAllData();
/// check number of big fragments
UInt nb_big_fragment = getNbBigFragments(fragment_manager,
nb_element_per_fragment + 1);
model.dump();
model.dump("cohesive elements");
if (frag < total_nb_fragment) {
if (nb_big_fragment != 1) {
AKANTU_DEBUG_ERROR("The number of big fragments is wrong: " << nb_big_fragment);
return EXIT_FAILURE;
}
}
else {
if (nb_big_fragment != 0) {
AKANTU_DEBUG_ERROR("The number of big fragments is wrong: " << nb_big_fragment);
return EXIT_FAILURE;
}
}
/// check number of fragments
UInt nb_fragment_num = fragment_manager.getNbFragment();
if (nb_fragment_num != frag) {
AKANTU_DEBUG_ERROR("The number of fragments is wrong! Numerical: " << nb_fragment_num << " Theoretical: " << frag);
return EXIT_FAILURE;
}
/// check mass computation
if (frag < total_nb_fragment) {
Real total_mass = 0.;
UInt small_fragments = 0;
for (UInt f = 0; f < nb_fragment_num; ++f) {
const Vector<Real> & current_inertia = inertia_moments_begin[f];
if (Math::are_float_equal(fragment_mass(f, 0), frag_theo_mass)) {
/// check center of mass
if (fragment_center(f, 0) > (L * frag / total_nb_fragment - L / 2)) {
AKANTU_DEBUG_ERROR("Fragment center is wrong!");
return EXIT_FAILURE;
}
/// check moment of inertia
if (!isInertiaEqual(current_inertia, small_frag_inertia)) {
AKANTU_DEBUG_ERROR("Inertia moments are wrong");
return EXIT_FAILURE;
}
++small_fragments;
total_mass += frag_theo_mass;
}
else {
/// check the moment of inertia for the biggest fragment
Real big_frag_mass = frag_theo_mass * (total_nb_fragment - frag + 1);
Real big_frag_size = el_size * (total_nb_fragment - frag + 1);
Vector<Real> big_frag_inertia(spatial_dimension);
big_frag_inertia(0) = big_frag_mass * (h*h + h*h) / 12.;
big_frag_inertia(1)
= big_frag_mass * (big_frag_size*big_frag_size + h*h) / 12.;
big_frag_inertia(2)
= big_frag_mass * (big_frag_size*big_frag_size + h*h) / 12.;
std::sort(big_frag_inertia.storage(),
big_frag_inertia.storage() + spatial_dimension,
std::greater<Real>());
if (!isInertiaEqual(current_inertia, big_frag_inertia)) {
AKANTU_DEBUG_ERROR("Inertia moments are wrong");
return EXIT_FAILURE;
}
}
}
if (small_fragments != nb_fragment_num - 1) {
AKANTU_DEBUG_ERROR("The number of small fragments is wrong!");
return EXIT_FAILURE;
}
if (!Math::are_float_equal(total_mass,
small_fragments * frag_theo_mass)) {
AKANTU_DEBUG_ERROR("The mass of small fragments is wrong!");
return EXIT_FAILURE;
}
}
/// displace fragments
rotateArray(mesh.getNodes(), -rotation_angle);
// rotateArray(displacement, -rotation_angle);
displaceElements(model, lim, el_size * 2);
rotateArray(mesh.getNodes(), rotation_angle);
// rotateArray(displacement, rotation_angle);
model.updateResidual();
lim += el_size;
}
model.dump();
model.dump("cohesive elements");
/// check centers
const Array<Real> & fragment_velocity = fragment_manager.getVelocity();
Real initial_position = -L / 2. + el_size / 2.;
for (UInt frag = 0; frag < total_nb_fragment; ++frag) {
Real theoretical_center = initial_position + el_size * frag;
UInt f_index = 0;
while (f_index < total_nb_fragment &&
!Math::are_float_equal(fragment_center(f_index, 0), theoretical_center))
++f_index;
if (f_index == total_nb_fragment) {
AKANTU_DEBUG_ERROR("The fragments' center is wrong!");
return EXIT_FAILURE;
}
f_index = 0;
while (f_index < total_nb_fragment &&
!Math::are_float_equal(fragment_velocity(f_index, 0),
theoretical_center))
++f_index;
if (f_index == total_nb_fragment) {
AKANTU_DEBUG_ERROR("The fragments' velocity is wrong!");
return EXIT_FAILURE;
}
}
finalize();
if (prank == 0)
std::cout << "OK: test_cohesive_buildfragments was passed!" << std::endl;
return EXIT_SUCCESS;
}
void verticalInsertionLimit(SolidMechanicsModelCohesive & model) {
UInt spatial_dimension = model.getSpatialDimension();
const Mesh & mesh_facets = model.getMeshFacets();
const Array<Real> & position = mesh_facets.getNodes();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end();
++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1, ghost_type);
Mesh::type_iterator end = mesh_facets.lastType(spatial_dimension - 1, ghost_type);
for(; it != end; ++it) {
ElementType type = *it;
Array<bool> & check_facets
= model.getElementInserter().getCheckFacets(type, ghost_type);
const Array<UInt> & connectivity = mesh_facets.getConnectivity(type, ghost_type);
UInt nb_nodes_per_facet = connectivity.getNbComponent();
for (UInt f = 0; f < check_facets.getSize(); ++f) {
if (!check_facets(f)) continue;
UInt nb_aligned_nodes = 1;
Real first_node_pos = position(connectivity(f, 0), 0);
for (; nb_aligned_nodes < nb_nodes_per_facet; ++nb_aligned_nodes) {
Real other_node_pos = position(connectivity(f, nb_aligned_nodes), 0);
if (! Math::are_float_equal(first_node_pos, other_node_pos))
break;
}
if (nb_aligned_nodes != nb_nodes_per_facet) {
check_facets(f) = false;
}
}
}
}
}
void displaceElements(SolidMechanicsModelCohesive & model,
const Real lim,
const Real amount) {
UInt spatial_dimension = model.getSpatialDimension();
Array<Real> & displacement = model.getDisplacement();
Mesh & mesh = model.getMesh();
UInt nb_nodes = mesh.getNbNodes();
Array<bool> displaced(nb_nodes);
displaced.clear();
Vector<Real> barycenter(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end();
++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, ghost_type);
for(; it != end; ++it) {
ElementType type = *it;
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_element = connectivity.getSize();
UInt nb_nodes_per_element = connectivity.getNbComponent();
Array<UInt>::const_vector_iterator conn_el
= connectivity.begin(nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter(el, type, barycenter.storage(), ghost_type);
if (barycenter(0) < lim) {
const Vector<UInt> & conn = conn_el[el];
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = conn(n);
if (!displaced(node)) {
displacement(node, 0) -= amount;
displaced(node) = true;
}
}
}
}
}
}
}
bool isInertiaEqual(const Vector<Real> & a, const Vector<Real> & b) {
UInt nb_terms = a.size();
UInt equal_terms = 0;
while (equal_terms < nb_terms &&
std::abs(a(equal_terms) - b(equal_terms)) / a(equal_terms) < Math::getTolerance())
++equal_terms;
return equal_terms == nb_terms;
}
void rotateArray(Array<Real> & array, Real angle) {
UInt spatial_dimension = array.getNbComponent();
Real rotation_values[] = {std::cos(angle), std::sin(angle), 0,
-std::sin(angle), std::cos(angle), 0,
0, 0, 1};
Matrix<Real> rotation(rotation_values, spatial_dimension, spatial_dimension);
RVector displaced_node(spatial_dimension);
Array<Real>::vector_iterator node_it = array.begin(spatial_dimension);
Array<Real>::vector_iterator node_end = array.end(spatial_dimension);
for (; node_it != node_end; ++node_it) {
displaced_node.mul<false>(rotation, *node_it);
*node_it = displaced_node;
}
}
UInt getNbBigFragments(FragmentManager & fragment_manager,
UInt minimum_nb_elements) {
fragment_manager.computeNbElementsPerFragment();
const Array<UInt> & nb_elements_per_fragment
= fragment_manager.getNbElementsPerFragment();
UInt nb_fragment = fragment_manager.getNbFragment();
UInt nb_big_fragment = 0;
for (UInt frag = 0; frag < nb_fragment; ++frag) {
if (nb_elements_per_fragment(frag) >= minimum_nb_elements) {
++nb_big_fragment;
}
}
return nb_big_fragment;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic.cc
index f5b83daac..ece21b065 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic.cc
@@ -1,172 +1,172 @@
/**
* @file test_cohesive_parallel_extrinsic.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief parallel test for cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
#include "dumper_paraview.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize("material.dat", argc, argv);
const UInt max_steps = 500;
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if(prank == 0) {
// Read the mesh
mesh.read("mesh.msh");
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
// debug::setDebugLevel(dblDump);
partition->partitionate(psize);
// debug::setDebugLevel(dblWarning);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition, NULL, true);
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// debug::setDebugLevel(dblWarning);
model.initFull(SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
model.limitInsertion(_y, -0.30, -0.20);
model.updateAutomaticInsertion();
// debug::setDebugLevel(dblDump);
// std::cout << mesh_facets << std::endl;
// debug::setDebugLevel(dblWarning);
Real time_step = model.getStableTimeStep()*0.1;
model.setTimeStep(time_step);
std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & displacement = model.getDisplacement();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
/// boundary conditions
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
boundary(n, 1) = true;
if (position(n, 0) > 0.99 || position(n, 0) < -0.99)
boundary(n, 0) = true;
}
/// initial conditions
Real loading_rate = 0.5;
Real disp_update = loading_rate * time_step;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 1) = loading_rate * position(n, 1);
}
model.synchronizeBoundaries();
model.updateResidual();
model.setBaseName("extrinsic_parallel");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity" );
model.addDumpField("acceleration");
model.addDumpField("residual" );
model.addDumpField("stress");
model.addDumpField("grad_u");
model.addDumpField("partitions");
// model.getDumper().getDumper().setMode(iohelper::BASE64);
model.dump();
model.setBaseNameToDumper("cohesive elements",
"extrinsic_parallel_cohesive_elements");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
/// update displacement on extreme nodes
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99 || position(n, 1) < -0.99)
displacement(n, 1) += disp_update * position(n, 1);
}
model.checkCohesiveStress();
model.solveStep();
// model.dump();
if(s % 10 == 0) {
if(prank == 0) std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
// // update displacement
// for (UInt n = 0; n < nb_nodes; ++n) {
// if (position(n, 1) + displacement(n, 1) > 0) {
// displacement(n, 0) -= 0.01;
// }
// }
// Real Ed = dynamic_cast<MaterialCohesive&> (model.getMaterial(1)).getDissipatedEnergy();
// Real Er = dynamic_cast<MaterialCohesive&> (model.getMaterial(1)).getReversibleEnergy();
// edis << s << " "
// << Ed << std::endl;
// erev << s << " "
// << Er << std::endl;
}
model.dump();
model.dump("cohesive elements");
// edis.close();
// erev.close();
Real Ed = model.getEnergy("dissipated");
Real Edt = 200 * sqrt(2);
if(prank == 0) {
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.999 || Ed > Edt * 1.001 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron.cc
index 05e10df9c..256c12b66 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron.cc
@@ -1,230 +1,230 @@
/**
* @file test_cohesive_parallel_extrinsic_tetrahedron.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief 3D extrinsic cohesive elements test
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
Real function(Real constant, Real x, Real y, Real z) {
return constant + 2. * x + 3. * y + 4 * z;
}
int main(int argc, char *argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
// const UInt max_steps = 1000;
// Real increment = 0.005;
const UInt spatial_dimension = 3;
Math::setTolerance(1.e-12);
ElementType type = _tetrahedron_10;
ElementType type_facet = Mesh::getFacetType(type);
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if(prank == 0) {
// Read the mesh
mesh.read("tetrahedron.msh");
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initParallel(partition, NULL, true);
model.initFull(SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
const MaterialCohesiveLinear<3> & mat_cohesive
= dynamic_cast < const MaterialCohesiveLinear<3> & > (model.getMaterial(1));
const Real sigma_c = mat_cohesive.getParam< RandomInternalField<Real, FacetInternalField> >("sigma_c");
const Real beta = mat_cohesive.getParam<Real>("beta");
// const Real G_cI = mat_cohesive.getParam<Real>("G_cI");
Array<Real> & position = mesh.getNodes();
/* ------------------------------------------------------------------------ */
/* Facet part */
/* ------------------------------------------------------------------------ */
/// compute quadrature points positions on facets
const Mesh & mesh_facets = model.getMeshFacets();
UInt nb_facet = mesh_facets.getNbElement(type_facet);
UInt nb_quad_per_facet = model.getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
UInt nb_tot_quad = nb_quad_per_facet * nb_facet;
Array<Real> quad_facets(nb_tot_quad, spatial_dimension);
model.getFEEngine("FacetsFEEngine").interpolateOnIntegrationPoints(position,
quad_facets,
spatial_dimension,
type_facet);
/* ------------------------------------------------------------------------ */
/* End of facet part */
/* ------------------------------------------------------------------------ */
/// compute quadrature points position of the elements
UInt nb_quad_per_element = model.getFEEngine().getNbIntegrationPoints(type);
UInt nb_element = mesh.getNbElement(type);
UInt nb_tot_quad_el = nb_quad_per_element * nb_element;
Array<Real> quad_elements(nb_tot_quad_el, spatial_dimension);
model.getFEEngine().interpolateOnIntegrationPoints(position,
quad_elements,
spatial_dimension,
type);
/// assign some values to stresses
Array<Real> & stress
= const_cast<Array<Real>&>(model.getMaterial(0).getStress(type));
Array<Real>::iterator<Matrix<Real> > stress_it
= stress.begin(spatial_dimension, spatial_dimension);
for (UInt q = 0; q < nb_tot_quad_el; ++q, ++stress_it) {
/// compute values
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = i; j < spatial_dimension; ++j) {
UInt index = i * spatial_dimension + j;
(*stress_it)(i, j) = index * function(sigma_c * 5,
quad_elements(q, 0),
quad_elements(q, 1),
quad_elements(q, 2));
}
}
/// fill symmetrical part
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < i; ++j) {
(*stress_it)(i, j) = (*stress_it)(j, i);
}
}
}
/// compute stress on facet quads
Array<Real> stress_facets(nb_tot_quad, spatial_dimension * spatial_dimension);
Array<Real>::iterator<Matrix<Real> > stress_facets_it
= stress_facets.begin(spatial_dimension, spatial_dimension);
for (UInt q = 0; q < nb_tot_quad; ++q, ++stress_facets_it) {
/// compute values
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = i; j < spatial_dimension; ++j) {
UInt index = i * spatial_dimension + j;
(*stress_facets_it)(i, j) = index * function(sigma_c * 5,
quad_facets(q, 0),
quad_facets(q, 1),
quad_facets(q, 2));
}
}
/// fill symmetrical part
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < i; ++j) {
(*stress_facets_it)(i, j) = (*stress_facets_it)(j, i);
}
}
}
/// insert cohesive elements
model.checkCohesiveStress();
/// check insertion stress
const Array<Real> & normals =
model.getFEEngine("FacetsFEEngine").getNormalsOnIntegrationPoints(type_facet);
const Array<Real> & tangents = model.getTangents(type_facet);
const Array<Real> & sigma_c_eff = mat_cohesive.getInsertionTraction(type_cohesive);
Vector<Real> normal_stress(spatial_dimension);
const Array<std::vector<Element> > & coh_element_to_facet
= mesh_facets.getElementToSubelement(type_facet);
Array<Real>::iterator<Matrix<Real> > quad_facet_stress
= stress_facets.begin(spatial_dimension, spatial_dimension);
Array<Real>::const_iterator<Vector<Real> > quad_normal
= normals.begin(spatial_dimension);
Array<Real>::const_iterator<Vector<Real> > quad_tangents
= tangents.begin(tangents.getNbComponent());
for (UInt f = 0; f < nb_facet; ++f) {
const Element & cohesive_element = coh_element_to_facet(f)[1];
for (UInt q = 0; q < nb_quad_per_facet; ++q, ++quad_facet_stress,
++quad_normal, ++quad_tangents) {
if (cohesive_element == ElementNull) continue;
normal_stress.mul<false>(*quad_facet_stress, *quad_normal);
Real normal_contrib = normal_stress.dot(*quad_normal);
Real first_tangent_contrib = 0;
for (UInt dim = 0; dim < spatial_dimension; ++dim)
first_tangent_contrib += normal_stress(dim) * (*quad_tangents)(dim);
Real second_tangent_contrib = 0;
for (UInt dim = 0; dim < spatial_dimension; ++dim)
second_tangent_contrib
+= normal_stress(dim) * (*quad_tangents)(dim + spatial_dimension);
Real tangent_contrib = std::sqrt(first_tangent_contrib * first_tangent_contrib +
second_tangent_contrib * second_tangent_contrib);
normal_contrib = std::max(0., normal_contrib);
Real effective_norm = std::sqrt(normal_contrib * normal_contrib
+ tangent_contrib * tangent_contrib / beta / beta);
if (effective_norm < sigma_c) continue;
if (!Math::are_float_equal(effective_norm,
sigma_c_eff(cohesive_element.element
* nb_quad_per_facet + q))) {
std::cout << "Insertion tractions do not match" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
}
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
index 2abbd0b12..70404b8ef 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic/test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
@@ -1,395 +1,395 @@
/**
* @file test_cohesive_parallel_extrinsic_tetrahedron_displacement.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief Displacement test for 3D cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
#include "dumper_paraview.hh"
#include "material_cohesive_linear.hh"
#ifdef AKANTU_USE_IOHELPER
# include "dumper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
using namespace akantu;
bool checkDisplacement(SolidMechanicsModelCohesive & model,
ElementType type,
std::ofstream & error_output,
UInt step,
bool barycenters);
int main(int argc, char *argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
const UInt max_steps = 500;
Math::setTolerance(1.e-12);
UInt spatial_dimension = 3;
ElementType type = _tetrahedron_10;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if(prank == 0) {
// Read the mesh
mesh.read("tetrahedron.msh");
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
// debug::setDebugLevel(dblDump);
partition->partitionate(psize);
// debug::setDebugLevel(dblWarning);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition, NULL, true);
// debug::setDebugLevel(dblDump);
// std::cout << mesh << std::endl;
// debug::setDebugLevel(dblWarning);
model.initFull(SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true));
/* ------------------------------------------------------------------------ */
/* Facet part */
/* ------------------------------------------------------------------------ */
// Array<Real> limits(spatial_dimension, 2);
// limits(0, 0) = -0.01;
// limits(0, 1) = 0.01;
// limits(1, 0) = -100;
// limits(1, 1) = 100;
// limits(2, 0) = -100;
// limits(2, 1) = 100;
// model.enableFacetsCheckOnArea(limits);
/* ------------------------------------------------------------------------ */
/* End of facet part */
/* ------------------------------------------------------------------------ */
// debug::setDebugLevel(dblDump);
// std::cout << mesh_facets << std::endl;
// debug::setDebugLevel(dblWarning);
Real time_step = model.getStableTimeStep()*0.1;
model.setTimeStep(time_step);
std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & displacement = model.getDisplacement();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
/// boundary conditions
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 0) > 0.99 || position(n, 0) < -0.99) {
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
boundary(n, dim) = true;
}
}
if (position(n, 0) > 0.99 || position(n, 0) < -0.99) {
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
boundary(n, dim) = true;
}
}
}
// #if defined (AKANTU_DEBUG_TOOLS)
// Vector<Real> facet_center(spatial_dimension);
// facet_center(0) = 0;
// facet_center(1) = -0.16666667;
// facet_center(2) = 0.5;
// debug::element_manager.setMesh(mesh);
// debug::element_manager.addModule(debug::_dm_material_cohesive);
// debug::element_manager.addModule(debug::_dm_debug_tools);
// //debug::element_manager.addModule(debug::_dm_integrator);
// #endif
/// initial conditions
Real loading_rate = 1;
Real disp_update = loading_rate * time_step;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 0) = loading_rate * position(n, 0);
velocity(n, 1) = loading_rate * position(n, 0);
}
model.synchronizeBoundaries();
model.updateResidual();
std::stringstream paraview_output;
paraview_output << "extrinsic_parallel_tetrahedron_" << psize;
model.setBaseName(paraview_output.str());
model.addDumpFieldVector("displacement");
model.addDumpFieldVector("velocity" );
model.addDumpFieldVector("acceleration");
model.addDumpFieldVector("residual" );
model.addDumpFieldTensor("stress");
model.addDumpFieldTensor("grad_u");
model.addDumpField("partitions");
// model.getDumper().getDumper().setMode(iohelper::BASE64);
model.dump();
model.setBaseNameToDumper("cohesive elements",
paraview_output.str()+"_cohesive_elements");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump("cohesive elements");
std::stringstream error_stream;
error_stream << "error" << ".csv";
std::ofstream error_output;
error_output.open(error_stream.str().c_str());
error_output << "# Step, Average, Max, Min" << std::endl;
if (checkDisplacement(model, type, error_output, 0, true)) {}
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
/// update displacement on extreme nodes
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (position(n, 0) > 0.99 || position(n, 0) < -0.99) {
displacement(n, 0) += disp_update * position(n, 0);
displacement(n, 1) += disp_update * position(n, 0);
}
}
model.checkCohesiveStress();
model.solveStep();
if(s % 100 == 0) {
if(prank == 0) std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
}
model.dump();
model.dump("cohesive elements");
if (!checkDisplacement(model, type, error_output, max_steps, false)) {
finalize();
return EXIT_FAILURE;
}
finalize();
return EXIT_SUCCESS;
}
bool checkDisplacement(SolidMechanicsModelCohesive & model,
ElementType type,
std::ofstream & error_output,
UInt step,
bool barycenters) {
Mesh & mesh = model.getMesh();
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<UInt> & connectivity = mesh.getConnectivity(type);
const Array<Real> & displacement = model.getDisplacement();
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_elem = Mesh::getNbNodesPerElement(type);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
if (psize == 1) {
std::stringstream displacement_file;
displacement_file << "displacement/displacement_"
<< std::setfill('0') << std::setw(6)
<< step;
std::ofstream displacement_output;
displacement_output.open(displacement_file.str().c_str());
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = connectivity(el, n);
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
displacement_output << std::setprecision(15)
<< displacement(node, dim) << " ";
}
displacement_output << std::endl;
}
}
displacement_output.close();
if (barycenters) {
std::stringstream barycenter_file;
barycenter_file << "displacement/barycenters";
std::ofstream barycenter_output;
barycenter_output.open(barycenter_file.str().c_str());
Element element(type, 0);
Vector<Real> bary(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
mesh.getBarycenter(element, bary);
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
barycenter_output << std::setprecision(15)
<< bary(dim) << " ";
}
barycenter_output << std::endl;
}
barycenter_output.close();
}
}
else {
if (barycenters) return true;
/// read data
std::stringstream displacement_file;
displacement_file << "displacement/displacement_"
<< std::setfill('0') << std::setw(6)
<< step;
std::ifstream displacement_input;
displacement_input.open(displacement_file.str().c_str());
Array<Real> displacement_serial(0, spatial_dimension);
Vector<Real> disp_tmp(spatial_dimension);
while (displacement_input.good()) {
for (UInt i = 0; i < spatial_dimension; ++i)
displacement_input >> disp_tmp(i);
displacement_serial.push_back(disp_tmp);
}
std::stringstream barycenter_file;
barycenter_file << "displacement/barycenters";
std::ifstream barycenter_input;
barycenter_input.open(barycenter_file.str().c_str());
Array<Real> barycenter_serial(0, spatial_dimension);
while (barycenter_input.good()) {
for (UInt dim = 0; dim < spatial_dimension; ++dim)
barycenter_input >> disp_tmp(dim);
barycenter_serial.push_back(disp_tmp);
}
Element element(type, 0);
Vector<Real> bary(spatial_dimension);
Array<Real>::iterator<Vector<Real> > it;
Array<Real>::iterator<Vector<Real> > begin
= barycenter_serial.begin(spatial_dimension);
Array<Real>::iterator<Vector<Real> > end
= barycenter_serial.end(spatial_dimension);
Array<Real>::const_iterator<Vector<Real> > disp_it;
Array<Real>::iterator<Vector<Real> > disp_serial_it;
Vector<Real> difference(spatial_dimension);
Array<Real> error;
/// compute error
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
mesh.getBarycenter(element, bary);
/// find element
for (it = begin; it != end; ++it) {
UInt matched_dim = 0;
while (matched_dim < spatial_dimension &&
Math::are_float_equal(bary(matched_dim), (*it)(matched_dim)))
++matched_dim;
if (matched_dim == spatial_dimension) break;
}
if (it == end) {
std::cout << "Element barycenter not found!" << std::endl;
return false;
}
UInt matched_el = it - begin;
disp_serial_it = displacement_serial.begin(spatial_dimension)
+ matched_el * nb_nodes_per_elem;
for (UInt n = 0; n < nb_nodes_per_elem; ++n, ++disp_serial_it) {
UInt node = connectivity(el, n);
if (!mesh.isLocalOrMasterNode(node)) continue;
disp_it = displacement.begin(spatial_dimension) + node;
difference = *disp_it;
difference -= *disp_serial_it;
error.push_back(difference.norm());
}
}
/// compute average error
Real average_error = std::accumulate(error.begin(), error.end(), 0.);
comm.allReduce(&average_error, 1, _so_sum);
UInt error_size = error.getSize();
comm.allReduce(&error_size, 1, _so_sum);
average_error /= error_size;
/// compute maximum and minimum
Real max_error = *std::max_element(error.begin(), error.end());
comm.allReduce(&max_error, 1, _so_max);
Real min_error = *std::min_element(error.begin(), error.end());
comm.allReduce(&min_error, 1, _so_min);
/// output data
if (prank == 0) {
error_output << step << ", "
<< average_error << ", "
<< max_error << ", "
<< min_error << std::endl;
}
if (max_error > 1.e-9) {
std::cout << "Displacement error is too big!" << std::endl;
return false;
}
}
return true;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/test_cohesive_parallel_extrinsic_IG_TG.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/test_cohesive_parallel_extrinsic_IG_TG.cc
index 84d56d478..e5aba2874 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/test_cohesive_parallel_extrinsic_IG_TG.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_extrinsic_IG_TG/test_cohesive_parallel_extrinsic_IG_TG.cc
@@ -1,295 +1,295 @@
/**
* @file test_cohesive_parallel_extrinsic_IG_TG.cc
*
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief Test for considering different cohesive properties for
* intergranular (IG) and transgranular (TG) fractures in extrinsic
* cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include <limits>
#include <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
#include "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
class MultiGrainMaterialSelector : public DefaultMaterialCohesiveSelector {
public:
MultiGrainMaterialSelector(const SolidMechanicsModelCohesive & model, const ID & transgranular_id, const ID & intergranular_id) :
DefaultMaterialCohesiveSelector(model),
transgranular_id(transgranular_id),
intergranular_id(intergranular_id),
model(model),
mesh(model.getMesh()),
mesh_facets(model.getMeshFacets()),
spatial_dimension(model.getSpatialDimension()),
nb_IG(0), nb_TG(0) {
}
UInt operator()(const Element & element) {
if(mesh_facets.getSpatialDimension(element.type) == (spatial_dimension - 1)) {
const std::vector<Element> & element_to_subelement = mesh_facets.getElementToSubelement(element.type, element.ghost_type)(element.element);
const Element & el1 = element_to_subelement[0];
const Element & el2 = element_to_subelement[1];
UInt grain_id1 = mesh.getData<UInt>("tag_0", el1.type, el1.ghost_type)(el1.element);
if(el2 != ElementNull) {
UInt grain_id2 = mesh.getData<UInt>("tag_0", el2.type, el2.ghost_type)(el2.element);
if (grain_id1 == grain_id2){
//transgranular = 0 indicator
nb_TG++;
return model.getMaterialIndex(transgranular_id);
} else {
//intergranular = 1 indicator
nb_IG++;
return model.getMaterialIndex(intergranular_id);
}
} else {
//transgranular = 0 indicator
nb_TG++;
return model.getMaterialIndex(transgranular_id);
}
} else {
return DefaultMaterialCohesiveSelector::operator()(element);
}
}
private:
ID transgranular_id, intergranular_id;
const SolidMechanicsModelCohesive & model;
const Mesh & mesh;
const Mesh & mesh_facets;
UInt spatial_dimension;
UInt nb_IG;
UInt nb_TG;
};
/* -------------------------------------------------------------------------- */
void limitInsertion(SolidMechanicsModelCohesive & model) {
Real tolerance = 0.1;
const Mesh & mesh = model.getMesh();
const Mesh & mesh_facets = model.getMeshFacets();
CohesiveElementInserter & inserter = model.getElementInserter();
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> bary_facet(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end();
++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1, ghost_type);
Mesh::type_iterator end = mesh_facets.lastType(spatial_dimension - 1, ghost_type);
for(; it != end; ++it) {
ElementType type = *it;
Array<bool> & f_check = inserter.getCheckFacets(type, ghost_type);
UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);
for (UInt f = 0; f < nb_facet; ++f) {
if (f_check(f)) {
mesh_facets.getBarycenter(f, type, bary_facet.storage(), ghost_type);
if ( !(bary_facet(0) > -tolerance && bary_facet(0) < tolerance) &&
!(bary_facet(1) > -tolerance && bary_facet(1) < tolerance) )
f_check(f) = false;
}
}
}
}
model.updateAutomaticInsertion();
}
int main(int argc, char *argv[]) {
initialize("material.dat", argc, argv);
debug::setDebugLevel(dblWarning);
const UInt spatial_dimension = 2;
const UInt max_steps = 600;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if(prank == 0) {
mesh.read("square.msh");
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
/// model initialization
model.initParallel(partition, NULL, true);
delete partition;
MultiGrainMaterialSelector material_selector(model, "TG_cohesive", "IG_cohesive");
model.setMaterialSelector(material_selector);
model.initFull(SolidMechanicsModelCohesiveOptions(_explicit_lumped_mass, true, false));
Real time_step = model.getStableTimeStep()*0.1;
model.setTimeStep(time_step);
// std::cout << "Time step: " << time_step << std::endl;
limitInsertion(model);
// std::cout << mesh << std::endl;
Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
Array<Real> & displacement = model.getDisplacement();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
/// boundary conditions
for (UInt n = 0; n < nb_nodes; ++n) {
if (position(n, 1) > 0.99|| position(n, 1) < -0.99)
boundary(n, 1) = true;
if (position(n, 0) > 0.99 || position(n, 0) < -0.99)
boundary(n, 0) = true;
}
model.synchronizeBoundaries();
model.updateResidual();
model.setBaseName("extrinsic");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity" );
model.addDumpField("acceleration");
model.addDumpField("residual" );
model.addDumpField("stress");
model.addDumpField("strain");
model.addDumpField("partitions");
model.setBaseNameToDumper("cohesive elements", "extrinsic_cohesive");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.addDumpFieldToDumper("cohesive elements", "damage");
model.dump();
model.dump("cohesive elements");
/// initial conditions
Real loading_rate = 0.1;
// bar_height = 2
Real VI = loading_rate * 2* 0.5;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 1) = loading_rate * position(n, 1);
velocity(n, 0) = loading_rate * position(n, 0);
}
// std::ofstream edis("edis.txt");
// std::ofstream erev("erev.txt");
// Array<Real> & residual = model.getResidual();
// model.dump();
// const Array<Real> & stress = model.getMaterial(0).getStress(type);
Real dispy = 0;
// UInt nb_coh_elem = 0;
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
dispy += VI * time_step;
/// update displacement on extreme nodes
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (position(n, 1) > 0.99){
displacement(n, 1) = dispy;
velocity(n,1) = VI;}
if (position(n, 1) < -0.99){
displacement(n, 1) = -dispy;
velocity(n,1) = -VI;}
if (position(n, 0) > 0.99){
displacement(n, 0) = dispy;
velocity(n,0) = VI;}
if (position(n, 0) < -0.99){
displacement(n, 0) = -dispy;
velocity(n,0) = -VI;}
}
model.checkCohesiveStress();
model.solveStep();
if(s % 10 == 0) {
if(prank == 0)
std::cout << "passing step " << s << "/" << max_steps << std::endl;
// model.dump();
// model.dump("cohesive elements");
}
// Real Ed = model.getEnergy("dissipated");
// edis << s << " "
// << Ed << std::endl;
// erev << s << " "
// << Er << std::endl;
}
model.dump();
model.dump("cohesive elements");
// edis.close();
// erev.close();
// mesh.write("mesh_final.msh");
Real Ed = model.getEnergy("dissipated");
Real Edt = 40;
if(prank == 0)
std::cout << Ed << " " << Edt << std::endl;
if (Ed < Edt * 0.99 || Ed > Edt * 1.01 || std::isnan(Ed)) {
if(prank == 0)
std::cout << "The dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
// for (UInt n = 0; n < position.getSize(); ++n) {
// for (UInt s = 0; s < spatial_dimension; ++s) {
// position(n, s) += displacement(n, s);
// }
// }
finalize();
if(prank == 0)
std::cout << "OK: test_cohesive_extrinsic_IG_TG was passed!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_insertion_along_physical_surfaces.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_insertion_along_physical_surfaces.cc
index 74d52adbf..b37321c1b 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_insertion_along_physical_surfaces.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_insertion_along_physical_surfaces.cc
@@ -1,118 +1,118 @@
/**
* @file test_cohesive_insertion_along_physical_surfaces.cc
* @author Fabian Barras <fabian.barras@epfl.ch>
* @date Fri Aug 7 09:07:44 2015
*
* @brief Test parallel intrinsic insertion of cohesive elements along physical surfaces
*
* @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 <limits>
#include <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_io_msh.hh"
#include "mesh_utils.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "material.hh"
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize("input_file.dat", argc, argv);
Math::setTolerance(1e-15);
const UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if(prank==0){
mesh.read("3d_spherical_inclusion.msh");
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition);
mesh.createGroupsFromMeshData<std::string>("physical_names");
model.initFull(SolidMechanicsModelCohesiveOptions(_static));
std::vector<std::string> surfaces_name = {"interface", "coh1", "coh2", "coh3", "coh4", "coh5"};
UInt nb_surf = surfaces_name.size();
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
std::string ghost_str;
if(*gt == 1) ghost_str = "ghost";
else ghost_str = "not ghost";
Mesh::type_iterator it = mesh.firstType(spatial_dimension, *gt, _ek_cohesive);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, *gt, _ek_cohesive);
for(; it != end; ++it) {
Array<UInt> & material_id = mesh.getMeshFacets().getData<UInt>("physical_names")(mesh.getFacetType(*it), *gt);
for (UInt i = 0; i < nb_surf; ++i) {
UInt expected_insertion = 0;
for(UInt m = 0; m<material_id.getSize();++m) {
if(material_id(m)==model.SolidMechanicsModel::getMaterialIndex(surfaces_name[i])) ++expected_insertion;
}
UInt inserted_elements;
inserted_elements = model.getMaterial(surfaces_name[i]).getElementFilter()(*it,*gt).getSize();
if (expected_insertion != inserted_elements) {
std::cerr << std::endl << "!!! Mismatch in insertion of surface named "
<< surfaces_name[i] << " in proc n° " << prank
<< " --> " << inserted_elements << " inserted elements of type " << ghost_str
<< " out of "
<< expected_insertion << std::endl;
return EXIT_FAILURE;
}
}
}
}
model.assembleStiffnessMatrix();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_intrinsic_implicit_insertion.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_intrinsic_implicit_insertion.cc
index d6643a5a1..ad60ef2ef 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_intrinsic_implicit_insertion.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_insertion/test_cohesive_parallel_intrinsic_implicit_insertion.cc
@@ -1,270 +1,270 @@
/**
* @file test_cohesive_parallel_intrinsic_implicit_insertion.cc
* @author Fabian Barras <fabian.barras@epfl.ch>
* @date Fri Aug 5 17:05:59 2016
*
* @brief Verifying the proper insertion and synchronization of intrinsic cohesive elements
*
* @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 <limits>
#include <fstream>
#include <iostream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_io_msh.hh"
#include "mesh_utils.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "material.hh"
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
std::ofstream output;
/* -------------------------------------------------------------------------- */
void printMeshContent(Mesh & mesh) {
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
comm.barrier();
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first = mesh.firstType(_all_dimensions, *gt, _ek_not_defined);
Mesh::type_iterator last = mesh.lastType(_all_dimensions, *gt, _ek_not_defined);
for(; first != last; ++first) {
UInt nb_element = mesh.getNbElement(*first,*gt);
output << std::endl
<< "Element type: " << *first << ", " << *gt << ": "
<< nb_element << " in the mesh of processor " << prank << std::endl;
Array<UInt> & conn = mesh.getConnectivity(*first,*gt);
for (UInt i = 0; i < conn.getSize(); ++i) {
output << "Element no " << i << " ";
for (UInt j = 0; j < conn.getNbComponent(); ++j) {
output << conn(i,j) << " ";
}
output << std::endl;
}
}
}
}
/* -------------------------------------------------------------------------- */
void printNodeList(Mesh & mesh) {
Array<double> & nodes = mesh.getNodes();
output << "Number of nodes: " << mesh.getNbNodes()<< std::endl;
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
output<<"Node # " << i
<< ", x-coord: "
<< nodes(i,0)
<< ", y-coord: "
<< nodes(i,1)
<< ", of type: " << mesh.getNodeType(i) << std::endl;
}
output << std::endl;
}
/* -------------------------------------------------------------------------- */
void getGlobalIDs(Mesh & mesh) {
const Array<UInt> & glob_id = mesh.getGlobalNodesIds();
if(&glob_id) {
output << "Global nodes ID: " << std::endl;
for (UInt i = 0; i < glob_id.getSize(); ++i) {
output << i << " " << glob_id(i) << std::endl;
}
}
output << std::endl;
}
/* -------------------------------------------------------------------------- */
void printSynchroinfo(Mesh & mesh, const DistributedSynchronizer & synch) {
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
Int psize = comm.getNbProc();
if(comm.getNbProc()==1)
return;
for (Int p = 0; p < psize; ++p) {
if (p==prank)
continue;
output << "From processor " << prank << " to processor " << p << std::endl;
const Array<Element> & sele = *(synch.getSendElement()+p);
output << " Sending element(s): " << std::endl;
for (UInt i = 0; i < sele.getSize(); ++i) {
output << sele(i) << std::endl;
}
const Array<Element> & rele = *(synch.getReceiveElement()+p);
output <<" Receiving element(s): " << std::endl;
for (UInt i = 0; i < rele.getSize(); ++i) {
output << rele(i) << std::endl;
}
}
output << std::endl;
}
/* -------------------------------------------------------------------------- */
void printDOF(SolidMechanicsModelCohesive & model) {
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
if(comm.getNbProc()==1)
return;
Int prank = comm.whoAmI();
const DOFSynchronizer & dof = model.getDOFSynchronizer();
output << "Number of global dofs " << dof.getNbGlobalDOFs() << " for processor "<< prank << std::endl;
const Array<UInt> & dof_global_ids = dof.getDOFGlobalIDs();
for (UInt i = 0; i < dof_global_ids.getSize(); ++i) {
output << "Local dof " << i << ", global id: " << dof_global_ids(i) << std::endl;
}
output << std::endl;
}
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[]) {
std::string input_file = "input_file_iii.dat";
std::string mesh_file = "2d_basic_interface.msh";
std::string dir = "output_dir/";
initialize(input_file, argc, argv);
debug::setDebugLevel(dbl0);
const UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
std::stringstream filename;
filename << dir.c_str() << "output_from_proc_" << prank << "_out_of_" << psize << ".out";
output.open(filename.str());
if(prank==0){
mesh.read(mesh_file);
partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
const ElementTypeMapArray<UInt> & partitions = partition->getPartitions();
output << "The root processor read the mesh." << std::endl
<< "Only GMSH physical objects are created in the mesh." <<std::endl;
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator first = mesh.firstType(_all_dimensions, *gt);
Mesh::type_iterator last = mesh.lastType(_all_dimensions, *gt);
for(; first != last; ++first) {
output << "Element type: " << *first << " ghost type: " << *gt << std::endl;
UInt nb_element = mesh.getNbElement(*first,*gt);
output << nb_element << " to partitionate between " << psize << " processsors" << std::endl;
Array<UInt> part = partitions(*first, *gt);
for (UInt i = 0; i < part.getSize(); ++i) {
output << i << " " << part(i) << std::endl;
}
}
}
output << "Nodes are also read and set with type -1 (normal node)" << std::endl;
printNodeList(mesh);
}
SolidMechanicsModelCohesive model(mesh);
output << "Before initParallel(), non-root processors have empty Mesh object" << std::endl;
printMeshContent(mesh);
model.initParallel(partition);
output << "After initParallel(), Mesh object on each processor is a local partionated mesh containing ghost elements" << std::endl;
printMeshContent(mesh);
output << "Nodes are also partionated and new node types are defined:" << std::endl;
printNodeList(mesh);
output << "-3: pure ghost node -> not a local node" << std::endl
<< "-2: master node -> node shared with other processor(s) -> local and global node" <<std::endl
<< ">0: slave node -> -> node shared with other processor(s) -> only local node (its id is the rank of the processor owning the master node)" <<std::endl;
output << "Each local node has a corresponding global id used during assembly: " <<std::endl;
getGlobalIDs(mesh);
Mesh & mesh_facets = mesh.getMeshFacets();
output << "Within cohesive element model, initParallel() creates a second Mesh object usually called mesh_facet" << std::endl
<< "This Mesh object contains all sub-dimensional elements where potential cohesive element can be inserted" << std::endl;
printMeshContent(mesh_facets);
const DistributedSynchronizer & synch_model = model.getSynchronizer();
output << "The distributed synchronizer of solid mechanics model is used to synchronize fields with ghost element:" << std::endl;
printSynchroinfo(mesh, synch_model);
mesh.createGroupsFromMeshData<std::string>("physical_names");
model.initFull(SolidMechanicsModelCohesiveOptions(_static));
output << "In case of insertion along physical objects, cohesive elements are created during initFull()" << std::endl;
output << "Elements list after insertion" << std::endl;
printMeshContent(mesh);
output << "Node list after insertion: (Total number of nodes " << mesh.getNbNodes()<< ")"<< std::endl;
printNodeList(mesh);
output << "Node global ids after insertion: (Total number of nodes " << mesh.getNbGlobalNodes()<< ")"<< std::endl;
getGlobalIDs(mesh);
const DistributedSynchronizer & coh_synch_model = *(model.getCohesiveSynchronizer());
output << "Solid mechanics model cohesive has its own distributed synchronizer to handle ghost cohesive element:" << std::endl;
printSynchroinfo(mesh, coh_synch_model);
output << "A synchronizer dedicated to degrees of freedom (DOFs) is used by the solver to build matrices in parallel:"
<< std::endl
<< "This DOFSynchronizer is built based on nodes global id " << std::endl;
printDOF(model);
output.close();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic.cc
index 9bd19c8b7..f4d854bf0 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic.cc
@@ -1,160 +1,160 @@
/**
* @file test_cohesive_parallel_intrinsic.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief parallel test for intrinsic cohesive elements
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char *argv[]) {
initialize("material.dat", argc, argv);
const UInt max_steps = 350;
UInt spatial_dimension = 2;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
akantu::MeshPartition * partition = NULL;
if(prank == 0) {
// Read the mesh
mesh.read("mesh.msh");
// /// insert cohesive elements
// CohesiveElementInserter inserter(mesh);
// inserter.setLimit('x', -0.26, -0.24);
// inserter.insertIntrinsicElements();
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
// debug::setDebugLevel(dblDump);
partition->partitionate(psize);
// debug::setDebugLevel(dblWarning);
}
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition);
model.initFull();
model.limitInsertion(_x, -0.26, -0.24);
model.insertIntrinsicElements();
debug::setDebugLevel(dblDump);
std::cout << mesh << std::endl;
debug::setDebugLevel(dblWarning);
Real time_step = model.getStableTimeStep()*0.8;
model.setTimeStep(time_step);
// std::cout << "Time step: " << time_step << std::endl;
model.assembleMassLumped();
Array<Real> & position = mesh.getNodes();
Array<Real> & velocity = model.getVelocity();
Array<bool> & boundary = model.getBlockedDOFs();
// Array<Real> & displacement = model.getDisplacement();
// const Array<Real> & residual = model.getResidual();
UInt nb_nodes = mesh.getNbNodes();
Real epsilon = std::numeric_limits<Real>::epsilon();
for (UInt n = 0; n < nb_nodes; ++n) {
if (std::abs(position(n, 0) - 1.) < epsilon)
boundary(n, 0) = true;
}
model.synchronizeBoundaries();
model.updateResidual();
model.setBaseName("intrinsic_parallel");
model.addDumpFieldVector("displacement");
model.addDumpField("velocity" );
model.addDumpField("acceleration");
model.addDumpField("residual" );
model.addDumpField("stress");
model.addDumpField("strain");
model.addDumpField("partitions");
model.addDumpField("force");
model.dump();
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_parallel_intrinsic");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.dump("cohesive elements");
/// initial conditions
Real loading_rate = .2;
for (UInt n = 0; n < nb_nodes; ++n) {
velocity(n, 0) = loading_rate * position(n, 0);
}
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.solveStep();
if(s % 20 == 0) {
model.dump();
model.dump("cohesive elements");
if(prank == 0) std::cout << "passing step " << s << "/" << max_steps << std::endl;
}
// // update displacement
// for (UInt n = 0; n < nb_nodes; ++n) {
// if (position(n, 1) + displacement(n, 1) > 0) {
// displacement(n, 0) -= 0.01;
// }
// }
// Real Ed = dynamic_cast<MaterialCohesive&> (model.getMaterial(1)).getDissipatedEnergy();
// Real Er = dynamic_cast<MaterialCohesive&> (model.getMaterial(1)).getReversibleEnergy();
// edis << s << " "
// << Ed << std::endl;
// erev << s << " "
// << Er << std::endl;
}
// edis.close();
// erev.close();
Real Ed = model.getEnergy("dissipated");
Real Edt = 2 * sqrt(2);
if(prank == 0) {
std::cout << Ed << " " << Edt << std::endl;
if (std::abs((Ed - Edt) / Edt) > 0.01 || std::isnan(Ed)) {
std::cout << "The dissipated energy is incorrect" << std::endl;
return EXIT_FAILURE;
}
}
finalize();
if(prank == 0) std::cout << "OK: Test passed!" << std::endl;
return EXIT_SUCCESS;
}
diff --git a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc
index f6607255d..983104b34 100644
--- a/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc
+++ b/test/test_model/test_solid_mechanics_model/test_cohesive/test_parallel_cohesive/test_cohesive_parallel_intrinsic/test_cohesive_parallel_intrinsic_tetrahedron.cc
@@ -1,704 +1,704 @@
/**
* @file test_cohesive_parallel_intrinsic_tetrahedron.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief Test for 3D intrinsic cohesive elements simulation in parallel
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
#include "solid_mechanics_model_cohesive.hh"
#include "dumper_paraview.hh"
#include "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
void updateDisplacement(SolidMechanicsModelCohesive & model,
const ElementTypeMapArray<UInt> & elements,
Vector<Real> & increment);
bool checkTractions(SolidMechanicsModelCohesive & model,
Vector<Real> & opening,
Vector<Real> & theoretical_traction,
Matrix<Real> & rotation);
void findNodesToCheck(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements,
Array<UInt> & nodes_to_check,
Int psize);
bool checkEquilibrium(const Mesh & mesh,
const Array<Real> & residual);
bool checkResidual(const Array<Real> & residual,
const Vector<Real> & traction,
const Array<UInt> & nodes_to_check,
const Matrix<Real> & rotation);
void findElementsToDisplace(const Mesh & mesh,
ElementTypeMapArray<UInt> & elements);
int main(int argc, char *argv[]) {
initialize("material_tetrahedron.dat", argc, argv);
const UInt spatial_dimension = 3;
const UInt max_steps = 60;
const Real increment_constant = 0.01;
ElementType type = _tetrahedron_10;
Math::setTolerance(1.e-10);
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
UInt nb_nodes_to_check_serial = 0;
UInt total_nb_nodes = 0;
UInt nb_elements_check_serial = 0;
akantu::MeshPartition * partition = NULL;
if(prank == 0) {
// Read the mesh
mesh.read("tetrahedron.msh");
/// count nodes with zero position
const Array<Real> & position = mesh.getNodes();
for (UInt n = 0; n < position.getSize(); ++n) {
if (std::abs(position(n, 0) - 0.) < 1e-6)
++nb_nodes_to_check_serial;
}
// /// insert cohesive elements
// CohesiveElementInserter inserter(mesh);
// inserter.setLimit(0, -0.01, 0.01);
// inserter.insertIntrinsicElements();
/// find nodes to check in serial
ElementTypeMapArray<UInt> elements_serial("elements_serial", "");
findElementsToDisplace(mesh, elements_serial);
nb_elements_check_serial = elements_serial(type).getSize();
total_nb_nodes = mesh.getNbNodes() + nb_nodes_to_check_serial;
/// partition the mesh
partition = new MeshPartitionScotch(mesh, spatial_dimension);
debug::setDebugLevel(dblDump);
partition->partitionate(psize);
debug::setDebugLevel(dblInfo);
}
comm.broadcast(&nb_nodes_to_check_serial, 1, 0);
comm.broadcast(&nb_elements_check_serial, 1, 0);
SolidMechanicsModelCohesive model(mesh);
model.initParallel(partition);
model.initFull();
model.limitInsertion(_x, -0.01, 0.01);
model.insertIntrinsicElements();
{
comm.broadcast(&total_nb_nodes, 1, 0);
Array<Int> nb_local_nodes(psize);
nb_local_nodes.clear();
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (mesh.isLocalOrMasterNode(n)) ++nb_local_nodes(prank);
}
comm.allGather(nb_local_nodes.storage(), 1);
UInt total_nb_nodes_parallel = std::accumulate(nb_local_nodes.begin(),
nb_local_nodes.end(), 0);
Array<UInt> global_nodes_list(total_nb_nodes_parallel);
UInt first_global_node = std::accumulate(nb_local_nodes.begin(),
nb_local_nodes.begin() + prank, 0);
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
if (mesh.isLocalOrMasterNode(n)) {
global_nodes_list(first_global_node) = mesh.getNodeGlobalId(n);
++first_global_node;
}
}
comm.allGatherV(global_nodes_list.storage(), nb_local_nodes.storage());
if (prank == 0)
std::cout << "Maximum node index: "
<< *(std::max_element(global_nodes_list.begin(),
global_nodes_list.end())) << std::endl;
Array<UInt> repeated_nodes;
repeated_nodes.resize(0);
for (UInt n = 0; n < total_nb_nodes_parallel; ++n) {
UInt appearances = std::count(global_nodes_list.begin() + n,
global_nodes_list.end(),
global_nodes_list(n));
if (appearances > 1) {
std::cout << "Node " << global_nodes_list(n)
<< " appears " << appearances << " times" << std::endl;
std::cout << " in position: " << n;
repeated_nodes.push_back(global_nodes_list(n));
UInt * node_position = global_nodes_list.storage() + n;
for (UInt i = 1; i < appearances; ++i) {
node_position = std::find(node_position + 1,
global_nodes_list.storage()
+ total_nb_nodes_parallel,
global_nodes_list(n));
UInt current_index = node_position - global_nodes_list.storage();
std::cout << ", " << current_index;
}
std::cout << std::endl << std::endl;
}
}
for (UInt n = 0; n < mesh.getNbNodes(); ++n) {
UInt global_node = mesh.getNodeGlobalId(n);
if (std::find(repeated_nodes.begin(), repeated_nodes.end(), global_node)
!= repeated_nodes.end()) {
std::cout << "Repeated global node " << global_node
<< " corresponds to local node " << n << std::endl;
}
}
if (total_nb_nodes != total_nb_nodes_parallel) {
if (prank == 0) {
std::cout << "Error: total number of nodes is wrong in parallel" << std::endl;
std::cout << "Serial: " << total_nb_nodes
<< " Parallel: " << total_nb_nodes_parallel << std::endl;
}
finalize();
return EXIT_FAILURE;
}
}
model.updateResidual();
model.setBaseName("intrinsic_parallel_tetrahedron");
model.addDumpFieldVector("displacement");
model.addDumpField("residual");
model.addDumpField("partitions");
model.dump();
model.setBaseNameToDumper("cohesive elements",
"cohesive_elements_parallel_tetrahedron");
model.addDumpFieldVectorToDumper("cohesive elements", "displacement");
model.dump("cohesive elements");
/// find elements to displace
ElementTypeMapArray<UInt> elements("elements", "");
findElementsToDisplace(mesh, elements);
UInt nb_elements_check = elements(type).getSize();
comm.allReduce(&nb_elements_check, 1, _so_sum);
if (nb_elements_check != nb_elements_check_serial) {
if (prank == 0) {
std::cout << "Error: number of elements to check is wrong" << std::endl;
std::cout << "Serial: " << nb_elements_check_serial
<< " Parallel: " << nb_elements_check << std::endl;
}
finalize();
return EXIT_FAILURE;
}
/// find nodes to check
Array<UInt> nodes_to_check;
findNodesToCheck(mesh, elements, nodes_to_check, psize);
Vector<Int> nodes_to_check_size(psize);
nodes_to_check_size(prank) = nodes_to_check.getSize();
comm.allGather(nodes_to_check_size.storage(), 1);
UInt nodes_to_check_global_size = std::accumulate(nodes_to_check_size.storage(),
nodes_to_check_size.storage()
+ psize, 0);
if (nodes_to_check_global_size != nb_nodes_to_check_serial) {
if (prank == 0) {
std::cout << "Error: number of nodes to check is wrong in parallel" << std::endl;
std::cout << "Serial: " << nb_nodes_to_check_serial
<< " Parallel: " << nodes_to_check_global_size << std::endl;
}
finalize();
return EXIT_FAILURE;
}
/// rotate mesh
Real angle = 1.;
Matrix<Real> rotation(spatial_dimension, spatial_dimension);
rotation.clear();
rotation(0, 0) = std::cos(angle);
rotation(0, 1) = std::sin(angle) * -1.;
rotation(1, 0) = std::sin(angle);
rotation(1, 1) = std::cos(angle);
rotation(2, 2) = 1.;
Vector<Real> increment_tmp(spatial_dimension);
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
increment_tmp(dim) = (dim + 1) * increment_constant;
}
Vector<Real> increment(spatial_dimension);
increment.mul<false>(rotation, increment_tmp);
Array<Real> & position = mesh.getNodes();
Array<Real> position_tmp(position);
Array<Real>::iterator<Vector<Real> > position_it = position.begin(spatial_dimension);
Array<Real>::iterator<Vector<Real> > position_end = position.end(spatial_dimension);
Array<Real>::iterator<Vector<Real> > position_tmp_it
= position_tmp.begin(spatial_dimension);
for (; position_it != position_end; ++position_it, ++position_tmp_it)
position_it->mul<false>(rotation, *position_tmp_it);
model.dump();
model.dump("cohesive elements");
updateDisplacement(model, elements, increment);
Real theoretical_Ed = 0;
Vector<Real> opening(spatial_dimension);
Vector<Real> traction(spatial_dimension);
Vector<Real> opening_old(spatial_dimension);
Vector<Real> traction_old(spatial_dimension);
opening.clear();
traction.clear();
opening_old.clear();
traction_old.clear();
Vector<Real> Dt(spatial_dimension);
Vector<Real> Do(spatial_dimension);
const Array<Real> & residual = model.getResidual();
/// Main loop
for (UInt s = 1; s <= max_steps; ++s) {
model.updateResidual();
opening += increment_tmp;
if (checkTractions(model, opening, traction, rotation) ||
checkEquilibrium(mesh, residual) ||
checkResidual(residual, traction, nodes_to_check, rotation)) {
finalize();
return EXIT_FAILURE;
}
/// compute energy
Do = opening;
Do -= opening_old;
Dt = traction_old;
Dt += traction;
theoretical_Ed += .5 * Do.dot(Dt);
opening_old = opening;
traction_old = traction;
updateDisplacement(model, elements, increment);
if(s % 10 == 0) {
if (prank == 0)
std::cout << "passing step " << s << "/" << max_steps << std::endl;
model.dump();
model.dump("cohesive elements");
}
}
model.dump();
model.dump("cohesive elements");
Real Ed = model.getEnergy("dissipated");
theoretical_Ed *= 4.;
if (prank == 0)
std::cout << "Dissipated energy: " << Ed
<< ", theoretical value: " << theoretical_Ed << std::endl;
if (!Math::are_float_equal(Ed, theoretical_Ed) || std::isnan(Ed)) {
if (prank == 0)
std::cout << "Error: the dissipated energy is incorrect" << std::endl;
finalize();
return EXIT_FAILURE;
}
finalize();
if(prank == 0) std::cout << "OK: Test passed!" << std::endl;
return EXIT_SUCCESS;
}
/* -------------------------------------------------------------------------- */
void updateDisplacement(SolidMechanicsModelCohesive & model,
const ElementTypeMapArray<UInt> & elements,
Vector<Real> & increment) {
UInt spatial_dimension = model.getSpatialDimension();
Mesh & mesh = model.getFEEngine().getMesh();
UInt nb_nodes = mesh.getNbNodes();
Array<Real> & displacement = model.getDisplacement();
Array<bool> update(nb_nodes);
update.clear();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end();
++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, ghost_type);
for (; it != last; ++it) {
ElementType type = *it;
const Array<UInt> & elem = elements(type, ghost_type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
UInt nb_nodes_per_element = connectivity.getNbComponent();
for (UInt el = 0; el < elem.getSize(); ++el) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity(elem(el), n);
if (!update(node)) {
Vector<Real> node_disp(displacement.storage() + node * spatial_dimension,
spatial_dimension);
node_disp += increment;
update(node) = true;
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
bool checkTractions(SolidMechanicsModelCohesive & model,
Vector<Real> & opening,
Vector<Real> & theoretical_traction,
Matrix<Real> & rotation) {
UInt spatial_dimension = model.getSpatialDimension();
const Mesh & mesh = model.getMesh();
const MaterialCohesive & mat_cohesive
= dynamic_cast < const MaterialCohesive & > (model.getMaterial(1));
Real sigma_c = mat_cohesive.getParam< RandomInternalField<Real, FacetInternalField> >("sigma_c");
const Real beta = mat_cohesive.getParam<Real>("beta");
const Real G_cI = mat_cohesive.getParam<Real>("G_c");
// Real G_cII = mat_cohesive.getParam<Real>("G_cII");
const Real delta_0 = mat_cohesive.getParam<Real>("delta_0");
const Real kappa = mat_cohesive.getParam<Real>("kappa");
Real delta_c = 2 * G_cI / sigma_c;
sigma_c *= delta_c / (delta_c - delta_0);
Vector<Real> normal_opening(spatial_dimension);
normal_opening.clear();
normal_opening(0) = opening(0);
Real normal_opening_norm = normal_opening.norm();
Vector<Real> tangential_opening(spatial_dimension);
tangential_opening.clear();
for (UInt dim = 1; dim < spatial_dimension; ++dim)
tangential_opening(dim) = opening(dim);
Real tangential_opening_norm = tangential_opening.norm();
Real beta2_kappa2 = beta * beta/kappa/kappa;
Real beta2_kappa = beta * beta/kappa;
Real delta = std::sqrt(tangential_opening_norm * tangential_opening_norm
* beta2_kappa2 +
normal_opening_norm * normal_opening_norm);
delta = std::max(delta, delta_0);
Real theoretical_damage = std::min(delta / delta_c, 1.);
if (Math::are_float_equal(theoretical_damage, 1.))
theoretical_traction.clear();
else {
theoretical_traction = tangential_opening;
theoretical_traction *= beta2_kappa;
theoretical_traction += normal_opening;
theoretical_traction *= sigma_c / delta * (1. - theoretical_damage);
}
Vector<Real> theoretical_traction_rotated(spatial_dimension);
theoretical_traction_rotated.mul<false>(rotation, theoretical_traction);
// adjust damage
theoretical_damage = std::max((delta - delta_0) / (delta_c - delta_0), 0.);
theoretical_damage = std::min(theoretical_damage, 1.);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end();
++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it
= mesh.firstType(spatial_dimension, ghost_type, _ek_cohesive);
Mesh::type_iterator last
= mesh.lastType(spatial_dimension, ghost_type, _ek_cohesive);
for (; it != last; ++it) {
ElementType type = *it;
const Array<Real> & traction = mat_cohesive.getTraction(type, ghost_type);
const Array<Real> & damage = mat_cohesive.getDamage(type, ghost_type);
UInt nb_quad_per_el
= model.getFEEngine("CohesiveFEEngine").getNbIntegrationPoints(type);
UInt nb_element = model.getMesh().getNbElement(type, ghost_type);
UInt tot_nb_quad = nb_element * nb_quad_per_el;
for (UInt q = 0; q < tot_nb_quad; ++q) {
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
if (!Math::are_float_equal(std::abs(theoretical_traction_rotated(dim)),
std::abs(traction(q, dim)))) {
std::cout << "Error: tractions are incorrect" << std::endl;
return 1;
}
}
if (ghost_type == _not_ghost)
if (!Math::are_float_equal(theoretical_damage, damage(q))) {
std::cout << "Error: damage is incorrect" << std::endl;
return 1;
}
}
}
}
return 0;
}
/* -------------------------------------------------------------------------- */
void findNodesToCheck(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements,
Array<UInt> & nodes_to_check,
Int psize) {
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
nodes_to_check.resize(0);
Array<UInt> global_nodes_to_check;
UInt spatial_dimension = mesh.getSpatialDimension();
const Array<Real> & position = mesh.getNodes();
UInt nb_nodes = position.getSize();
Array<bool> checked_nodes(nb_nodes);
checked_nodes.clear();
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator last = mesh.lastType(spatial_dimension);
for (; it != last; ++it) {
ElementType type = *it;
const Array<UInt> & elem = elements(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
UInt nb_nodes_per_elem = connectivity.getNbComponent();
for (UInt el = 0; el < elem.getSize(); ++el) {
UInt element = elem(el);
Vector<UInt> conn_el(connectivity.storage() + nb_nodes_per_elem * element,
nb_nodes_per_elem);
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = conn_el(n);
if (std::abs(position(node, 0) - 0.) < 1.e-6
&& !checked_nodes(node)) {
checked_nodes(node) = true;
nodes_to_check.push_back(node);
global_nodes_to_check.push_back(mesh.getNodeGlobalId(node));
}
}
}
}
std::vector<CommunicationRequest *> requests;
for (Int p = prank + 1; p < psize; ++p) {
requests.push_back(comm.asyncSend(global_nodes_to_check.storage(),
global_nodes_to_check.getSize(),
p, prank));
}
Array<UInt> recv_nodes;
for (Int p = 0; p < prank; ++p) {
CommunicationStatus status;
comm.probe<UInt>(p, p, status);
UInt recv_nodes_size = recv_nodes.getSize();
recv_nodes.resize(recv_nodes_size + status.getSize());
comm.receive(recv_nodes.storage() + recv_nodes_size, status.getSize(), p, p);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
for (UInt i = 0; i < recv_nodes.getSize(); ++i) {
Array<UInt>::iterator<UInt> node_position
= std::find(global_nodes_to_check.begin(),
global_nodes_to_check.end(),
recv_nodes(i));
if (node_position != global_nodes_to_check.end()) {
UInt index = node_position - global_nodes_to_check.begin();
nodes_to_check.erase(index);
global_nodes_to_check.erase(index);
}
}
}
/* -------------------------------------------------------------------------- */
bool checkEquilibrium(const Mesh & mesh,
const Array<Real> & residual) {
UInt spatial_dimension = residual.getNbComponent();
Vector<Real> residual_sum(spatial_dimension);
residual_sum.clear();
Array<Real>::const_iterator<Vector<Real> > res_it
= residual.begin(spatial_dimension);
for (UInt n = 0; n < residual.getSize(); ++n, ++res_it) {
if (mesh.isLocalOrMasterNode(n))
residual_sum += *res_it;
}
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
comm.allReduce(residual_sum.storage(), spatial_dimension, _so_sum);
for (UInt s = 0; s < spatial_dimension; ++s) {
if (!Math::are_float_equal(residual_sum(s), 0.)) {
if (comm.whoAmI() == 0)
std::cout << "Error: system is not in equilibrium!" << std::endl;
return 1;
}
}
return 0;
}
/* -------------------------------------------------------------------------- */
bool checkResidual(const Array<Real> & residual,
const Vector<Real> & traction,
const Array<UInt> & nodes_to_check,
const Matrix<Real> & rotation) {
UInt spatial_dimension = residual.getNbComponent();
Vector<Real> total_force(spatial_dimension);
total_force.clear();
for (UInt n = 0; n < nodes_to_check.getSize(); ++n) {
UInt node = nodes_to_check(n);
Vector<Real> res(residual.storage() + node * spatial_dimension,
spatial_dimension);
total_force += res;
}
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
comm.allReduce(total_force.storage(), spatial_dimension, _so_sum);
Vector<Real> theoretical_total_force(spatial_dimension);
theoretical_total_force.mul<false>(rotation, traction);
theoretical_total_force *= -1 * 2 * 2;
for (UInt s = 0; s < spatial_dimension; ++s) {
if (!Math::are_float_equal(total_force(s), theoretical_total_force(s))) {
if (comm.whoAmI() == 0)
std::cout << "Error: total force isn't correct!" << std::endl;
return 1;
}
}
return 0;
}
/* -------------------------------------------------------------------------- */
void findElementsToDisplace(const Mesh & mesh,
ElementTypeMapArray<UInt> & elements) {
UInt spatial_dimension = mesh.getSpatialDimension();
mesh.initElementTypeMapArray(elements, 1, spatial_dimension);
Vector<Real> bary(spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end();
++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, ghost_type);
for (; it != last; ++it) {
ElementType type = *it;
Array<UInt> & elem = elements(type, ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
for (UInt el = 0; el < nb_element; ++el) {
mesh.getBarycenter(el, type, bary.storage(), ghost_type);
if (bary(0) > 0.0001) elem.push_back(el);
}
}
}
}
diff --git a/test/test_solver/test_petsc_matrix_apply_boundary.cc b/test/test_solver/test_petsc_matrix_apply_boundary.cc
index 57b7eeb7b..c89eebdf2 100644
--- a/test/test_solver/test_petsc_matrix_apply_boundary.cc
+++ b/test/test_solver/test_petsc_matrix_apply_boundary.cc
@@ -1,144 +1,144 @@
/**
* @file test_petsc_matrix_apply_boundary.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Mon Oct 13 2014
* @date last modification: Wed Oct 28 2015
*
* @brief test the applyBoundary method of the PETScMatrix class
*
* @section LICENSE
*
* Copyright (©) 2015 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 <cstdlib>
/* -------------------------------------------------------------------------- */
-#include "static_communicator.hh"
+#include "communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "element_synchronizer.hh"
#include "petsc_matrix.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.hh"
#include "mesh_partition_scotch.hh"
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const ElementType element_type = _triangle_3;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 2;
- StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
+ const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
mesh.read("triangle.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
FEEngine *fem = new FEEngineTemplate<IntegratorGauss,ShapeLagrange,_ek_regular>(mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// fill the matrix with
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K(nb_global_nodes * spatial_dimension, _symmetric);
K.buildProfile(mesh, dof_synchronizer, spatial_dimension);
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1);
Array<Real> K_e = Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it = K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end = K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for(; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K, spatial_dimension, element_type, ghost_type);
// create petsc matrix
PETScMatrix petsc_matrix(nb_global_nodes * spatial_dimension, _symmetric);
petsc_matrix.buildProfile(mesh, dof_synchronizer, spatial_dimension);
// add stiffness matrix to petsc matrix
petsc_matrix.add(K, 1);
// create boundary array: block all dofs
UInt nb_nodes = mesh.getNbNodes();
Array<bool> boundary = Array<bool>(nb_nodes, spatial_dimension, true);
// apply boundary
petsc_matrix.applyBoundary(boundary);
// test if all entries except the diagonal ones have been zeroed
Real test_passed = 0;
for (UInt i = 0; i < nb_nodes * spatial_dimension; ++i) {
if (dof_synchronizer.isLocalOrMasterDOF(i)) {
for (UInt j = 0; j < nb_nodes * spatial_dimension; ++j) {
if (dof_synchronizer.isLocalOrMasterDOF(j)) {
if (i == j)
test_passed += petsc_matrix(i, j) - 1;
else
test_passed += petsc_matrix(i, j) - 0;
}
}
}
}
if (std::abs(test_passed) > Math::getTolerance()) {
finalize();
return EXIT_FAILURE;
}
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_petsc_matrix_diagonal.cc b/test/test_solver/test_petsc_matrix_diagonal.cc
index c0cb48b96..145105038 100644
--- a/test/test_solver/test_petsc_matrix_diagonal.cc
+++ b/test/test_solver/test_petsc_matrix_diagonal.cc
@@ -1,151 +1,151 @@
/**
* @file test_petsc_matrix_diagonal.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Mon Oct 13 2014
* @date last modification: Fri Jan 15 2016
*
* @brief test the connectivity is correctly represented in the PETScMatrix
*
* @section LICENSE
*
* Copyright (©) 2015 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 <iostream>
/* -------------------------------------------------------------------------- */
-#include "static_communicator.hh"
+#include "communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "element_synchronizer.hh"
#include "petsc_matrix.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.hh"
#include "dumper_paraview.hh"
#include "mesh_partition_scotch.hh"
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const ElementType element_type = _triangle_3;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 2;
- StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
+ const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
mesh.read("triangle.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
// DumperParaview mesh_dumper("mesh_dumper");
// mesh_dumper.registerMesh(mesh, spatial_dimension, _not_ghost);
// mesh_dumper.dump();
/// initialize the FEEngine and the dof_synchronizer
FEEngine *fem = new FEEngineTemplate<IntegratorGauss,ShapeLagrange,_ek_regular>(mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// construct an Akantu sparse matrix, build the profile and fill the matrix for the given mesh
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K_akantu(nb_global_nodes * spatial_dimension, _unsymmetric);
K_akantu.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// use as elemental matrices a matrix with values equal to 1 every where
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1.);
Array<Real> K_e = Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it = K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end = K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for(; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K_akantu, spatial_dimension, element_type, ghost_type);
/// construct a PETSc matrix
PETScMatrix K_petsc(nb_global_nodes * spatial_dimension, _unsymmetric);
/// build the profile of the PETSc matrix for the mesh of this example
K_petsc.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// add an Akantu sparse matrix to a PETSc sparse matrix
K_petsc.add(K_akantu, 1);
/// check to how many elements each node is connected
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem, spatial_dimension);
/// test the diagonal of the PETSc matrix: the diagonal entries
/// of the PETSc matrix correspond to the number of elements
/// connected to the node of the dof. Note: for an Akantu matrix this is only true for the serial case
Real error = 0.;
/// loop over all diagonal values of the matrix
for (UInt i = 0; i < mesh.getNbNodes(); ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
UInt dof = i * spatial_dimension + j;
/// for PETSc matrix only DOFs on the processor and be accessed
if (dof_synchronizer.isLocalOrMasterDOF(dof)) {
UInt global_dof = dof_synchronizer.getDOFGlobalID(dof);
std::cout << "Number of elements connected: " << node_to_elem.getNbCols(i) << std::endl;
std::cout << "K_petsc(" << global_dof << "," << global_dof << ")=" << K_petsc(dof,dof) << std::endl;
error += std::abs(K_petsc(dof, dof) - node_to_elem.getNbCols(i));
}
}
}
if(error > Math::getTolerance() ) {
std::cout << "error in the stiffness matrix!!!" << std::endl;
finalize();
return EXIT_FAILURE;
}
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_petsc_matrix_profile.cc b/test/test_solver/test_petsc_matrix_profile.cc
index 35439d340..391f22855 100644
--- a/test/test_solver/test_petsc_matrix_profile.cc
+++ b/test/test_solver/test_petsc_matrix_profile.cc
@@ -1,134 +1,134 @@
/**
* @file test_petsc_matrix_profile.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Mon Oct 13 2014
* @date last modification: Tue Apr 28 2015
*
* @brief test the profile generation of the PETScMatrix class
*
* @section LICENSE
*
* Copyright (©) 2015 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 <cstdlib>
#include <fstream>
/* -------------------------------------------------------------------------- */
-#include "static_communicator.hh"
+#include "communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "element_synchronizer.hh"
#include "petsc_matrix.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.hh"
/// #include "dumper_paraview.hh"
#include "mesh_partition_scotch.hh"
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const ElementType element_type = _triangle_3;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 2;
- StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
+ const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
mesh.read("square.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
// dump mesh in paraview
// DumperParaview mesh_dumper("mesh_dumper");
// mesh_dumper.registerMesh(mesh, spatial_dimension, _not_ghost);
// mesh_dumper.dump();
/// initialize the FEEngine and the dof_synchronizer
FEEngine *fem = new FEEngineTemplate<IntegratorGauss,ShapeLagrange,_ek_regular>(mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// construct an Akantu sparse matrix, build the profile and fill the matrix for the given mesh
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K_akantu(nb_global_nodes * spatial_dimension, _unsymmetric);
K_akantu.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// use as elemental matrices a matrix with values equal to 1 every where
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1.);
Array<Real> K_e = Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it = K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end = K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for(; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K_akantu, spatial_dimension, element_type, ghost_type);
/// construct a PETSc matrix
PETScMatrix K_petsc(nb_global_nodes * spatial_dimension, _unsymmetric);
/// build the profile of the PETSc matrix for the mesh of this example
K_petsc.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// add an Akantu sparse matrix to a PETSc sparse matrix
K_petsc.add(K_akantu, 1);
/// save the profile
K_petsc.saveMatrix("profile.txt");
/// print the matrix to screen
std::ifstream profile;
profile.open("profile.txt");
std::string current_line;
while(getline(profile, current_line))
std::cout << current_line << std::endl;
profile.close();
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_petsc_matrix_profile_parallel.cc b/test/test_solver/test_petsc_matrix_profile_parallel.cc
index 5d750d5d1..b638a3c23 100644
--- a/test/test_solver/test_petsc_matrix_profile_parallel.cc
+++ b/test/test_solver/test_petsc_matrix_profile_parallel.cc
@@ -1,135 +1,135 @@
/**
* @file test_petsc_matrix_profile_parallel.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Mon Oct 13 2014
* @date last modification: Tue Apr 28 2015
*
* @brief test the profile generation of the PETScMatrix class in parallel
*
* @section LICENSE
*
* Copyright (©) 2015 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 <cstdlib>
#include <fstream>
/* -------------------------------------------------------------------------- */
-#include "static_communicator.hh"
+#include "communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "element_synchronizer.hh"
#include "petsc_matrix.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.hh"
/// #include "dumper_paraview.hh"
#include "mesh_partition_scotch.hh"
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const ElementType element_type = _triangle_3;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 2;
- StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
+ const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
mesh.read("square.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
// dump mesh in paraview
// DumperParaview mesh_dumper("mesh_dumper");
// mesh_dumper.registerMesh(mesh, spatial_dimension, _not_ghost);
// mesh_dumper.dump();
/// initialize the FEEngine and the dof_synchronizer
FEEngine *fem = new FEEngineTemplate<IntegratorGauss,ShapeLagrange,_ek_regular>(mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// construct an Akantu sparse matrix, build the profile and fill the matrix for the given mesh
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K_akantu(nb_global_nodes * spatial_dimension, _unsymmetric);
K_akantu.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// use as elemental matrices a matrix with values equal to 1 every where
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 1.);
Array<Real> K_e = Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it = K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end = K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for(; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K_akantu, spatial_dimension, element_type, ghost_type);
/// construct a PETSc matrix
PETScMatrix K_petsc(nb_global_nodes * spatial_dimension, _unsymmetric);
/// build the profile of the PETSc matrix for the mesh of this example
K_petsc.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// add an Akantu sparse matrix to a PETSc sparse matrix
K_petsc.add(K_akantu, 1);
/// save the profile
K_petsc.saveMatrix("profile_parallel.txt");
/// print the matrix to screen
if(prank == 0) {
std::ifstream profile;
profile.open("profile_parallel.txt");
std::string current_line;
while(getline(profile, current_line))
std::cout << current_line << std::endl;
profile.close();
}
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_solver_petsc.cc b/test/test_solver/test_solver_petsc.cc
index cddc54227..4c754b6cc 100644
--- a/test/test_solver/test_solver_petsc.cc
+++ b/test/test_solver/test_solver_petsc.cc
@@ -1,165 +1,165 @@
/**
* @file test_solver_petsc.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Mon Oct 13 2014
* @date last modification: Wed Oct 28 2015
*
* @brief test the PETSc solver interface
*
* @section LICENSE
*
* Copyright (©) 2015 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 <cstdlib>
/* -------------------------------------------------------------------------- */
-#include "static_communicator.hh"
+#include "communicator.hh"
#include "aka_common.hh"
#include "aka_csr.hh"
#include "mesh.hh"
#include "mesh_io.hh"
#include "mesh_utils.hh"
#include "element_synchronizer.hh"
#include "petsc_matrix.hh"
#include "solver_petsc.hh"
#include "fe_engine.hh"
#include "dof_synchronizer.hh"
#include "mesh_partition_scotch.hh"
using namespace akantu;
int main(int argc, char *argv[]) {
initialize(argc, argv);
const ElementType element_type = _segment_2;
const GhostType ghost_type = _not_ghost;
UInt spatial_dimension = 1;
- StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
+ const auto & comm = akantu::Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
/// read the mesh and partition it
Mesh mesh(spatial_dimension);
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
ElementSynchronizer * communicator = NULL;
if(prank == 0) {
/// creation mesh
mesh.read("1D_bar.msh");
MeshPartitionScotch * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
FEEngine *fem = new FEEngineTemplate<IntegratorGauss,ShapeLagrange,_ek_regular>(mesh, spatial_dimension, "my_fem");
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
UInt nb_global_nodes = mesh.getNbGlobalNodes();
dof_synchronizer.initGlobalDOFEquationNumbers();
// fill the matrix with
UInt nb_element = mesh.getNbElement(element_type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(element_type);
UInt nb_dofs_per_element = spatial_dimension * nb_nodes_per_element;
SparseMatrix K(nb_global_nodes * spatial_dimension, _symmetric);
K.buildProfile(mesh, dof_synchronizer, spatial_dimension);
Matrix<Real> element_input(nb_dofs_per_element, nb_dofs_per_element, 0);
for (UInt i = 0; i < nb_dofs_per_element; ++i) {
for (UInt j = 0; j < nb_dofs_per_element; ++j) {
element_input(i, j) = ((i == j) ? 1 : -1);
}
}
Array<Real> K_e = Array<Real>(nb_element, nb_dofs_per_element * nb_dofs_per_element, "K_e");
Array<Real>::matrix_iterator K_e_it = K_e.begin(nb_dofs_per_element, nb_dofs_per_element);
Array<Real>::matrix_iterator K_e_end = K_e.end(nb_dofs_per_element, nb_dofs_per_element);
for(; K_e_it != K_e_end; ++K_e_it)
*K_e_it = element_input;
// assemble the test matrix
fem->assembleMatrix(K_e, K, spatial_dimension, element_type, ghost_type);
// apply boundary: block first node
const Array<Real> & position = mesh.getNodes();
UInt nb_nodes = mesh.getNbNodes();
Array<bool> boundary = Array<bool>(nb_nodes, spatial_dimension, false);
for (UInt i = 0; i < nb_nodes; ++i) {
if (std::abs(position(i, 0)) < Math::getTolerance() )
boundary(i, 0) = true;
}
K.applyBoundary(boundary);
/// create the PETSc matrix for the solve step
PETScMatrix petsc_matrix(nb_global_nodes * spatial_dimension, _symmetric);
petsc_matrix.buildProfile(mesh, dof_synchronizer, spatial_dimension);
/// copy the stiffness matrix into the petsc matrix
petsc_matrix.add(K, 1);
// initialize internal forces: they are zero because imposed displacement is zero
Array<Real> internal_forces(nb_nodes, spatial_dimension, 0.);
// compute residual: apply nodal force on last node
Array<Real> residual(nb_nodes, spatial_dimension, 0.);
for (UInt i = 0; i < nb_nodes; ++i) {
if (std::abs(position(i, 0) - 10) < Math::getTolerance() )
residual(i, 0) += 2;
}
residual -= internal_forces;
/// initialize solver and solution
Array<Real> solution(nb_nodes, spatial_dimension, 0.);
SolverPETSc solver(petsc_matrix);
solver.initialize();
solver.setOperators();
solver.setRHS(residual);
solver.solve(solution);
/// verify solution
Math::setTolerance(1e-11);
for (UInt i = 0; i < nb_nodes; ++i) {
if (!dof_synchronizer.isPureGhostDOF(i) && !Math::are_float_equal(2 * position(i, 0), solution(i, 0))) {
std::cout << "The solution is not correct!!!!" << std::endl;
finalize();
return EXIT_FAILURE;
}
}
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_sparse_matrix_product.cc b/test/test_solver/test_sparse_matrix_product.cc
index e08961cc2..ce24921de 100644
--- a/test/test_solver/test_sparse_matrix_product.cc
+++ b/test/test_solver/test_sparse_matrix_product.cc
@@ -1,115 +1,115 @@
/**
* @file test_sparse_matrix_product.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
* @date last modification: Sun Oct 19 2014
*
* @brief test the matrix vector product in parallel
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 <iostream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_partition_scotch.hh"
#include "element_synchronizer.hh"
#include "sparse_matrix.hh"
#include "dof_synchronizer.hh"
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[])
{
initialize(argc, argv);
const UInt spatial_dimension = 2;
const UInt nb_dof = 2;
- StaticCommunicator & comm = akantu::StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
Mesh mesh(spatial_dimension);
mesh.read("bar.msh");
mesh.distribute();
UInt nb_nodes = mesh.getNbNodes();
DOFManagerDefault dof_manager(mesh, "test_dof_manager");
Array<Real> test_synchronize(nb_nodes, nb_dof, "Test vector");
dof_manager.registerDOFs("test_synchronize", test_synchronize, _dst_nodal);
if (prank == 0) std::cout << "Creating a SparseMatrix" << std::endl;
auto & A = dof_manager.getNewMatrix("A", _symmetric);
Array<Real> dof_vector(nb_nodes, nb_dof, "vector");
if (prank == 0) std::cout << "Filling the matrix" << std::endl;
for (UInt i = 0; i < nb_nodes*nb_dof; ++i) {
if(dof_manager.isLocalOrMasterDOF(i))
A.add(i, i, 2.);
}
std::stringstream str; str << "Matrix_" << prank << ".mtx";
A.saveMatrix(str.str());
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt d = 0; d < nb_dof; ++d) {
dof_vector(n, d) = 1.;
}
}
if (prank == 0) std::cout << "Computing x = A * x" << std::endl;
dof_vector *= A;
auto & sync = dynamic_cast<DOFManagerDefault &>(dof_manager)
.getSynchronizer();
if (prank == 0) std::cout << "Gathering the results on proc 0" << std::endl;
if(psize > 1) {
if(prank == 0) {
Array<Real> gathered;
sync.gather(dof_vector, gathered);
debug::setDebugLevel(dblTest);
std::cout << gathered << std::endl;
debug::setDebugLevel(dblWarning);
} else {
sync.gather(dof_vector);
}
} else {
debug::setDebugLevel(dblTest);
std::cout << dof_vector << std::endl;
debug::setDebugLevel(dblWarning);
}
finalize();
return 0;
}
diff --git a/test/test_solver/test_sparse_matrix_profile_parallel.cc b/test/test_solver/test_sparse_matrix_profile_parallel.cc
index 4ea513a55..67682f43b 100644
--- a/test/test_solver/test_sparse_matrix_profile_parallel.cc
+++ b/test/test_solver/test_sparse_matrix_profile_parallel.cc
@@ -1,114 +1,114 @@
/**
* @file test_sparse_matrix_profile_parallel.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 12 2010
* @date last modification: Sun Oct 19 2014
*
* @brief test the sparse matrix class in parallel
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "mesh.hh"
#include "mesh_io_msh.hh"
#include "mesh_partition_scotch.hh"
#include "communicator.hh"
#include "sparse_matrix.hh"
#include "solver_mumps.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[])
{
akantu::initialize(argc, argv);
int dim = 2;
//#ifdef AKANTU_USE_IOHELPER
//akantu::ElementType type = akantu::_triangle_6;
//#endif //AKANTU_USE_IOHELPER
akantu::Mesh mesh(dim);
// akantu::debug::setDebugLevel(akantu::dblDump);
- akantu::StaticCommunicator * comm = akantu::StaticCommunicator::getStaticCommunicator();
+ akantu::StaticCommunicator * comm = akantu::Communicator::getStaticCommunicator();
akantu::Int psize = comm->getNbProc();
akantu::Int prank = comm->whoAmI();
akantu::UInt n = 0;
/* ------------------------------------------------------------------------ */
/* Parallel initialization */
/* ------------------------------------------------------------------------ */
akantu::Communicator * communicator;
if(prank == 0) {
akantu::MeshIOMSH mesh_io;
mesh_io.read("triangle.msh", mesh);
akantu::MeshPartition * partition =
new akantu::MeshPartitionScotch(mesh, dim);
// partition->reorder();
mesh_io.write("triangle_reorder.msh", mesh);
n = mesh.getNbNodes();
partition->partitionate(psize);
communicator = akantu::Communicator::createCommunicatorDistributeMesh(mesh, partition);
delete partition;
} else {
communicator = akantu::Communicator::createCommunicatorDistributeMesh(mesh, NULL);
}
std::cout << "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA " << mesh.getNbGlobalNodes() << std::endl;
akantu::SparseMatrix sparse_matrix(mesh, akantu::_symmetric, 2, "mesh");
sparse_matrix.buildProfile();
akantu::Solver * solver = new akantu::SolverMumps(sparse_matrix);
if(prank == 0) {
for(akantu::UInt i = 0; i < n; ++i) {
solver->getRHS().storage()[i] = 1.;
}
}
akantu::debug::setDebugLevel(akantu::dblDump);
solver->initialize();
std::stringstream sstr; sstr << "profile_" << prank << ".mtx";
sparse_matrix.saveProfile(sstr.str());
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_solver/test_sparse_solver_mumps.cc b/test/test_solver/test_sparse_solver_mumps.cc
index b8ff41186..b3ba6aaf8 100644
--- a/test/test_solver/test_sparse_solver_mumps.cc
+++ b/test/test_solver/test_sparse_solver_mumps.cc
@@ -1,159 +1,158 @@
/**
* @file test_sparse_matrix_product.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
* @date last modification: Sun Oct 19 2014
*
* @brief test the matrix vector product in parallel
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "dof_synchronizer.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
#include "mesh_partition_scotch.hh"
#include "sparse_matrix_aij.hh"
#include "sparse_solver_mumps.hh"
#include "terms_to_assemble.hh"
/* -------------------------------------------------------------------------- */
#include <iostream>
/* -------------------------------------------------------------------------- */
using namespace akantu;
/* -------------------------------------------------------------------------- */
void genMesh(Mesh & mesh, UInt nb_nodes);
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 1;
const UInt nb_global_dof = 11;
- StaticCommunicator & comm =
- akantu::StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
// Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
Mesh mesh(spatial_dimension);
if (prank == 0) {
genMesh(mesh, nb_global_dof);
RandomGenerator<UInt>::seed(1496137735);
} else {
RandomGenerator<UInt>::seed(2992275470);
}
mesh.distribute();
UInt node = 0;
for (auto pos : mesh.getNodes()) {
std::cout << prank << " " << node << " pos: " << pos << " ["
<< mesh.getNodeGlobalId(node) << "] " << mesh.getNodeType(node)
<< std::endl;
++node;
}
UInt nb_nodes = mesh.getNbNodes();
DOFManagerDefault dof_manager(mesh, "test_dof_manager");
Array<Real> x(nb_nodes);
dof_manager.registerDOFs("x", x, _dst_nodal);
const auto & local_equation_number = dof_manager.getEquationsNumbers("x");
auto & A = dof_manager.getNewMatrix("A", _symmetric);
Array<Real> b(nb_nodes);
TermsToAssemble terms;
for (UInt i = 0; i < nb_nodes; ++i) {
if (dof_manager.isLocalOrMasterDOF(i)) {
auto li = local_equation_number(i);
auto gi = dof_manager.localToGlobalEquationNumber(li);
terms(i, i) = 1. / (1. + gi);
}
}
dof_manager.assemblePreassembledMatrix("x", "x", "A", terms);
std::stringstream str;
str << "Matrix_" << prank << ".mtx";
A.saveMatrix(str.str());
for (UInt n = 0; n < nb_nodes; ++n) {
b(n) = 1.;
}
SparseSolverMumps solver(dof_manager, "A");
solver.solve(x, b);
auto & sync =
dynamic_cast<DOFManagerDefault &>(dof_manager).getSynchronizer();
if (prank == 0) {
Array<Real> x_gathered(dof_manager.getSystemSize());
sync.gather(x, x_gathered);
debug::setDebugLevel(dblTest);
std::cout << x_gathered << std::endl;
debug::setDebugLevel(dblWarning);
UInt d = 1.;
for (auto x : x_gathered) {
if (std::abs(x - d) / d > 1e-15)
AKANTU_EXCEPTION("Error in the solution: " << x << " != " << d << " ["
<< (std::abs(x - d) / d)
<< "].");
++d;
}
} else {
sync.gather(x);
}
finalize();
return 0;
}
/* -------------------------------------------------------------------------- */
void genMesh(Mesh & mesh, UInt nb_nodes) {
MeshAccessor mesh_accessor(mesh);
Array<Real> & nodes = mesh_accessor.getNodes();
Array<UInt> & conn = mesh_accessor.getConnectivity(_segment_2);
nodes.resize(nb_nodes);
for (UInt n = 0; n < nb_nodes; ++n) {
nodes(n, _x) = n * (1. / (nb_nodes - 1));
}
conn.resize(nb_nodes - 1);
for (UInt n = 0; n < nb_nodes - 1; ++n) {
conn(n, 0) = n;
conn(n, 1) = n + 1;
}
}
diff --git a/test/test_synchronizer/test_data_distribution.cc b/test/test_synchronizer/test_data_distribution.cc
index b5f970ae0..59ba6be9b 100644
--- a/test/test_synchronizer/test_data_distribution.cc
+++ b/test/test_synchronizer/test_data_distribution.cc
@@ -1,173 +1,173 @@
/**
* @file test_data_distribution.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Sep 05 2014
* @date last modification: Sun Oct 19 2014
*
* @brief Test the mesh distribution on creation of a distributed synchonizer
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 "aka_iterators.hh"
#include "aka_random_generator.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "mesh_iterators.hh"
#include "mesh_partition_mesh_data.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
initialize(argc, argv);
const UInt spatial_dimension = 3;
Mesh mesh_group_after(spatial_dimension, "after");
Mesh mesh_group_before(spatial_dimension, "before");
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
if (prank == 0) {
mesh_group_before.read("data_split.msh");
mesh_group_after.read("data_split.msh");
mesh_group_before.registerData<UInt>("global_id");
mesh_group_after.registerData<UInt>("global_id");
for (const auto & type : mesh_group_after.elementTypes(_all_dimensions)) {
auto & gidb = mesh_group_before.getDataPointer<UInt>("global_id", type);
auto & gida = mesh_group_after.getDataPointer<UInt>("global_id", type);
for (auto && data : zip(arange(gida.size()), gida, gidb)) {
std::get<1>(data) = std::get<0>(data);
std::get<2>(data) = std::get<0>(data);
}
}
}
RandomGenerator<UInt>::seed(1);
mesh_group_before.distribute();
RandomGenerator<UInt>::seed(1);
mesh_group_after.distribute();
if (prank == 0)
std::cout << mesh_group_after;
for (const auto & agrp : ElementGroupsIterable(mesh_group_after)) {
const ElementGroup & bgrp =
mesh_group_before.getElementGroup(agrp.getName());
for (auto && ghost_type : ghost_types) {
for (const auto & type : bgrp.elementTypes(_all_dimensions, ghost_type)) {
Array<UInt> & gidb = mesh_group_before.getDataPointer<UInt>(
"global_id", type, ghost_type);
Array<UInt> & gida = mesh_group_after.getDataPointer<UInt>(
"global_id", type, ghost_type);
Array<UInt> bgelem(bgrp.getElements(type, ghost_type));
Array<UInt> agelem(agrp.getElements(type, ghost_type));
std::transform(agelem.begin(), agelem.end(), agelem.begin(),
[&gida](auto & i) { return gida(i); });
std::transform(bgelem.begin(), bgelem.end(), bgelem.begin(),
[&gidb](auto & i) { return gidb(i); });
std::sort(bgelem.begin(), bgelem.end());
std::sort(agelem.begin(), agelem.end());
if (not std::equal(bgelem.begin(), bgelem.end(), agelem.begin())) {
std::cerr << "The filters array for the group " << agrp.getName()
<< " and for the element type " << type << ", "
<< ghost_type << " do not match" << std::endl;
debug::setDebugLevel(dblTest);
std::cerr << bgelem << std::endl;
std::cerr << agelem << std::endl;
debug::debugger.exit(EXIT_FAILURE);
}
}
}
}
for (const auto & agrp : NodeGroupsIterable(mesh_group_after)) {
const NodeGroup & bgrp = mesh_group_before.getNodeGroup(agrp.getName());
const Array<UInt> & gidb = mesh_group_before.getGlobalNodesIds();
const Array<UInt> & gida = mesh_group_after.getGlobalNodesIds();
Array<UInt> bgnode(0, 1);
Array<UInt> agnode(0, 1);
for (auto && pair : zip(bgrp, agrp)) {
UInt a,b;
std::tie(b, a) = pair;
if (psize > 1) {
if (mesh_group_before.isLocalOrMasterNode(b))
bgnode.push_back(gidb(b));
if (mesh_group_after.isLocalOrMasterNode(a))
agnode.push_back(gida(a));
}
}
std::sort(bgnode.begin(), bgnode.end());
std::sort(agnode.begin(), agnode.end());
if (!std::equal(bgnode.begin(), bgnode.end(), agnode.begin())) {
std::cerr << "The filters array for the group " << agrp.getName() << " do not match"
<< std::endl;
debug::setDebugLevel(dblTest);
std::cerr << bgnode << std::endl;
std::cerr << agnode << std::endl;
debug::debugger.exit(EXIT_FAILURE);
}
}
mesh_group_after.getElementGroup("inside").setBaseName("after_inside");
mesh_group_after.getElementGroup("inside").dump();
mesh_group_after.getElementGroup("outside").setBaseName("after_outside");
mesh_group_after.getElementGroup("outside").dump();
mesh_group_after.getElementGroup("volume").setBaseName("after_volume");
mesh_group_after.getElementGroup("volume").dump();
mesh_group_before.getElementGroup("inside").setBaseName("before_inside");
mesh_group_before.getElementGroup("inside").dump();
mesh_group_before.getElementGroup("outside").setBaseName("before_outside");
mesh_group_before.getElementGroup("outside").dump();
mesh_group_before.getElementGroup("volume").setBaseName("before_volume");
mesh_group_before.getElementGroup("volume").dump();
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_synchronizer/test_dof_synchronizer.cc b/test/test_synchronizer/test_dof_synchronizer.cc
index 70fcb3c34..aab3c5d66 100644
--- a/test/test_synchronizer/test_dof_synchronizer.cc
+++ b/test/test_synchronizer/test_dof_synchronizer.cc
@@ -1,149 +1,149 @@
/**
* @file test_dof_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 17 2011
* @date last modification: Sun Oct 19 2014
*
* @brief Test the functionality of the DOFSynchronizer class
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "dof_synchronizer.hh"
#include "element_synchronizer.hh"
#include "mesh_io.hh"
#include "mesh_partition_scotch.hh"
-#include "static_communicator.hh"
+#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "io_helper.hh"
#endif // AKANTU_USE_IOHELPER
/* -------------------------------------------------------------------------- */
using namespace akantu;
int main(int argc, char * argv[]) {
const UInt spatial_dimension = 2;
initialize(argc, argv);
- StaticCommunicator & comm =
- akantu::StaticCommunicator::getStaticCommunicator();
+ const auto & comm =
+ akantu::Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
Mesh mesh(spatial_dimension);
if (prank == 0)
mesh.read("bar.msh");
mesh.distribute();
DOFManagerDefault dof_manager(mesh, "test_dof_manager");
UInt nb_nodes = mesh.getNbNodes();
/* ------------------------------------------------------------------------ */
/* test the synchronization */
/* ------------------------------------------------------------------------ */
Array<Real> test_synchronize(nb_nodes, spatial_dimension, "Test vector");
dof_manager.registerDOFs("test_synchronize", test_synchronize, _dst_nodal);
auto & equation_number =
dof_manager.getLocalEquationNumbers("test_synchronize");
DOFSynchronizer & dof_synchronizer = dof_manager.getSynchronizer();
std::cout << "Synchronizing a dof vector" << std::endl;
Array<Int> local_data_array(dof_manager.getLocalSystemSize(), 2);
auto it_data = local_data_array.begin(2);
for (UInt local_dof = 0; local_dof < dof_manager.getLocalSystemSize();
++local_dof) {
UInt equ_number = equation_number(local_dof);
Vector<Int> val;
if (dof_manager.isLocalOrMasterDOF(equ_number)) {
UInt global_dof = dof_manager.localToGlobalEquationNumber(local_dof);
val = {0, 1};
val += global_dof * 2;
} else {
val = {-1, -1};
}
Vector<Int> data = it_data[local_dof];
data = val;
}
dof_synchronizer.synchronize(local_data_array);
auto test_data = [&]() -> void {
auto it_data = local_data_array.begin(2);
for (UInt local_dof = 0; local_dof < dof_manager.getLocalSystemSize();
++local_dof) {
UInt equ_number = equation_number(local_dof);
Vector<Int> exp_val;
UInt global_dof = dof_manager.localToGlobalEquationNumber(local_dof);
if (dof_manager.isLocalOrMasterDOF(equ_number) ||
dof_manager.isSlaveDOF(equ_number)) {
exp_val = {0, 1};
exp_val += global_dof * 2;
} else {
exp_val = {-1, -1};
}
Vector<Int> val = it_data[local_dof];
if (exp_val != val) {
std::cerr << "Failed !" << prank << " DOF: " << global_dof << " - l"
<< local_dof << " value:" << val << " expected: " << exp_val
<< std::endl;
exit(1);
}
}
};
test_data();
if (prank == 0) {
Array<Int> test_gathered(dof_manager.getSystemSize(), 2);
dof_synchronizer.gather(local_data_array, test_gathered);
local_data_array.set(-1);
dof_synchronizer.scatter(local_data_array, test_gathered);
} else {
dof_synchronizer.gather(local_data_array);
local_data_array.set(-1);
dof_synchronizer.scatter(local_data_array);
}
test_data();
finalize();
return 0;
}
diff --git a/test/test_synchronizer/test_dof_synchronizer_communication.cc b/test/test_synchronizer/test_dof_synchronizer_communication.cc
index 295b2e1c9..dd6245ff9 100644
--- a/test/test_synchronizer/test_dof_synchronizer_communication.cc
+++ b/test/test_synchronizer/test_dof_synchronizer_communication.cc
@@ -1,102 +1,102 @@
/**
* @file test_dof_synchronizer_communication.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Tue Dec 09 2014
*
* @brief test to synchronize global equation numbers
*
* @section LICENSE
*
* Copyright (©) 2015 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 "aka_common.hh"
#include "element_synchronizer.hh"
#include "dof_synchronizer.hh"
#include "synchronizer_registry.hh"
#include "mesh.hh"
#include "mesh_partition_scotch.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
# include "dumper_paraview.hh"
#endif //AKANTU_USE_IOHELPER
#include "test_dof_data_accessor.hh"
using namespace akantu;
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[])
{
initialize(argc, argv);
UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
bool wait=true;
if(argc >1) {
if(prank == 0)
while(wait);
}
ElementSynchronizer * communicator = NULL;
if(prank == 0) {
mesh.read("cube.msh");
MeshPartition * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
communicator = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
/* -------------------------------------------------------------------------- */
/* test the communications of the dof synchronizer */
/* -------------------------------------------------------------------------- */
std::cout << "Initializing the synchronizer" << std::endl;
DOFSynchronizer dof_synchronizer(mesh, spatial_dimension);
dof_synchronizer.initGlobalDOFEquationNumbers();
AKANTU_DEBUG_INFO("Creating TestDOFAccessor");
TestDOFAccessor test_dof_accessor(dof_synchronizer.getGlobalDOFEquationNumbers());
SynchronizerRegistry synch_registry(test_dof_accessor);
synch_registry.registerSynchronizer(dof_synchronizer,_gst_test);
AKANTU_DEBUG_INFO("Synchronizing tag");
synch_registry.synchronize(_gst_test);
delete communicator;
finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_synchronizer/test_facet_synchronizer.cc b/test/test_synchronizer/test_facet_synchronizer.cc
index d3b2c8d36..ca7acdf31 100644
--- a/test/test_synchronizer/test_facet_synchronizer.cc
+++ b/test/test_synchronizer/test_facet_synchronizer.cc
@@ -1,100 +1,61 @@
/**
* @file test_facet_synchronizer.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
*
* @brief Facet synchronizer test
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
*/
/* -------------------------------------------------------------------------- */
-
-#include "test_data_accessor.hh"
#include "facet_synchronizer.hh"
#include "mesh_utils.hh"
#include "synchronizer_registry.hh"
+#include "test_data_accessor.hh"
#include <iostream>
-
/* -------------------------------------------------------------------------- */
using namespace akantu;
-int main(int argc, char *argv[]) {
+int main(int argc, char * argv[]) {
akantu::initialize(argc, argv);
UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
- Int psize = comm.getNbProc();
+ const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
- DistributedSynchronizer * dist = NULL;
/// partition the mesh
- if(prank == 0) {
+ if (prank == 0) {
mesh.read("facet.msh");
- MeshPartition * partition = new MeshPartitionScotch(mesh, spatial_dimension);
- partition->partitionate(psize);
- dist = DistributedSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
- delete partition;
- } else {
- dist = DistributedSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
- /// create facets
- Mesh mesh_facets(mesh.initMeshFacets("mesh_facets"));
- MeshUtils::buildAllFacets(mesh, mesh_facets, 0, dist);
-
- /// compute barycenter for each facet
- ElementTypeMapArray<Real> barycenters("barycenters", "", 0);
- mesh_facets.initElementTypeMapArray(barycenters,
- spatial_dimension,
- spatial_dimension - 1);
+ mesh.distribute();
- for (ghost_type_t::iterator gt = ghost_type_t::begin();
- gt != ghost_type_t::end(); ++gt) {
- GhostType ghost_type = *gt;
- Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1,
- ghost_type);
- Mesh::type_iterator last_type = mesh_facets.lastType(spatial_dimension - 1,
- ghost_type);
+ auto & synchronizer = mesh.getElementSynchronizer();
- for(; it != last_type; ++it) {
- UInt nb_element = mesh_facets.getNbElement(*it, ghost_type);
- Array<Real> & barycenter = barycenters(*it, ghost_type);
- barycenter.resize(nb_element);
-
- Array<Real>::iterator< Vector<Real> > bary_it
- = barycenter.begin(spatial_dimension);
-
- for (UInt elem = 0; elem < nb_element; ++elem, ++bary_it)
- mesh_facets.getBarycenter(elem, *it, bary_it->storage(), ghost_type);
- }
- }
+ /// create facets
+ Mesh & mesh_facets = mesh.initMeshFacets("mesh_facets");
/// setup facet communications
- FacetSynchronizer * facet_synchronizer =
- FacetSynchronizer::createFacetSynchronizer(*dist, mesh_facets);
-
- AKANTU_DEBUG_INFO("Creating TestAccessor");
- TestAccessor test_accessor(mesh, barycenters);
- SynchronizerRegistry synch_registry(test_accessor);
+ auto & facet_synchronizer = mesh_facets.getElementSynchronizer();
- synch_registry.registerSynchronizer(*facet_synchronizer, _gst_test);
+ // AKANTU_DEBUG_INFO("Creating TestAccessor");
+ // TestAccessor test_accessor(mesh);
+ // SynchronizerRegistry synch_registry(test_accessor);
- /// synchronize facets and check results
- AKANTU_DEBUG_INFO("Synchronizing tag");
- synch_registry.synchronize(_gst_test);
+ // synch_registry.registerSynchronizer(facet_synchronizer, _gst_test);
- delete facet_synchronizer;
- delete dist;
- akantu::finalize();
+ // /// synchronize facets and check results
+ // AKANTU_DEBUG_INFO("Synchronizing tag");
+ // synch_registry.synchronize(_gst_test);
- return EXIT_SUCCESS;
+ return 0;
}
diff --git a/test/test_synchronizer/test_grid_synchronizer.cc b/test/test_synchronizer/test_grid_synchronizer.cc
index 71b601229..90e97ddcc 100644
--- a/test/test_synchronizer/test_grid_synchronizer.cc
+++ b/test/test_synchronizer/test_grid_synchronizer.cc
@@ -1,299 +1,299 @@
/**
* @file test_grid_synchronizer.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Fri Feb 27 2015
*
* @brief test the GridSynchronizer object
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "aka_grid_dynamic.hh"
#include "mesh.hh"
#include "grid_synchronizer.hh"
#include "mesh_partition.hh"
#include "synchronizer_registry.hh"
#include "test_data_accessor.hh"
#ifdef AKANTU_USE_IOHELPER
# include "io_helper.hh"
#endif //AKANTU_USE_IOHELPER
using namespace akantu;
const UInt spatial_dimension = 2;
typedef std::map<std::pair<Element, Element>, Real> pair_list;
#include "test_grid_tools.hh"
static void updatePairList(const ElementTypeMapArray<Real> & barycenter,
const SpatialGrid<Element> & grid,
Real radius,
pair_list & neighbors,
neighbors_map_t<spatial_dimension>::type & neighbors_map) {
AKANTU_DEBUG_IN();
GhostType ghost_type = _not_ghost;
Element e;
e.ghost_type = ghost_type;
// generate the pair of neighbor depending of the cell_list
ElementTypeMapArray<Real>::type_iterator it = barycenter.firstType(_all_dimensions, ghost_type);
ElementTypeMapArray<Real>::type_iterator last_type = barycenter.lastType(0, ghost_type);
for(; it != last_type; ++it) {
// loop over quad points
e.type = *it;
e.element = 0;
const Array<Real> & barycenter_vect = barycenter(*it, ghost_type);
UInt sp = barycenter_vect.getNbComponent();
Array<Real>::const_iterator< Vector<Real> > bary =
barycenter_vect.begin(sp);
Array<Real>::const_iterator< Vector<Real> > bary_end =
barycenter_vect.end(sp);
for(;bary != bary_end; ++bary, e.element++) {
#if !defined(AKANTU_NDEBUG)
Point<spatial_dimension> pt1(*bary);
#endif
SpatialGrid<Element>::CellID cell_id = grid.getCellID(*bary);
SpatialGrid<Element>::neighbor_cells_iterator first_neigh_cell =
grid.beginNeighborCells(cell_id);
SpatialGrid<Element>::neighbor_cells_iterator last_neigh_cell =
grid.endNeighborCells(cell_id);
// loop over neighbors cells of the one containing the current element
for (; first_neigh_cell != last_neigh_cell; ++first_neigh_cell) {
SpatialGrid<Element>::Cell::const_iterator first_neigh_el =
grid.beginCell(*first_neigh_cell);
SpatialGrid<Element>::Cell::const_iterator last_neigh_el =
grid.endCell(*first_neigh_cell);
// loop over the quadrature point in the current cell of the cell list
for (;first_neigh_el != last_neigh_el; ++first_neigh_el){
const Element & elem = *first_neigh_el;
Array<Real>::const_iterator< Vector<Real> > neigh_it =
barycenter(elem.type, elem.ghost_type).begin(sp);
const Vector<Real> & neigh_bary = neigh_it[elem.element];
Real distance = bary->distance(neigh_bary);
if(distance <= radius) {
#if !defined(AKANTU_NDEBUG)
Point<spatial_dimension> pt2(neigh_bary);
neighbors_map[pt1].push_back(pt2);
#endif
std::pair<Element, Element> pair = std::make_pair(e, elem);
pair_list::iterator p = neighbors.find(pair);
if(p != neighbors.end()) {
AKANTU_DEBUG_ERROR("Pair already registered [" << e << " " << elem << "] -> " << p->second << " " << distance);
} else {
neighbors[pair] = distance;
}
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char *argv[]) {
akantu::initialize(argc, argv);
Real radius = 0.001;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
ElementSynchronizer * dist = NULL;
if(prank == 0) {
mesh.read("bar.msh");
MeshPartition * partition = new MeshPartitionScotch(mesh, spatial_dimension);
partition->partitionate(psize);
dist = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, partition);
delete partition;
} else {
dist = ElementSynchronizer::createDistributedSynchronizerMesh(mesh, NULL);
}
mesh.computeBoundingBox();
const Vector<Real> & lower_bounds = mesh.getLowerBounds();
const Vector<Real> & upper_bounds = mesh.getUpperBounds();
Vector<Real> center = 0.5 * (upper_bounds + lower_bounds);
Vector<Real> spacing(spatial_dimension);
for (UInt i = 0; i < spatial_dimension; ++i) {
spacing[i] = radius * 1.2;
}
SpatialGrid<Element> grid(spatial_dimension, spacing, center);
GhostType ghost_type = _not_ghost;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, ghost_type);
ElementTypeMapArray<Real> barycenters("", "");
mesh.initElementTypeMapArray(barycenters, spatial_dimension, spatial_dimension);
Element e;
e.ghost_type = ghost_type;
for(; it != last_type; ++it) {
UInt nb_element = mesh.getNbElement(*it, ghost_type);
e.type = *it;
Array<Real> & barycenter = barycenters(*it, ghost_type);
barycenter.resize(nb_element);
Array<Real>::iterator< Vector<Real> > bary_it = barycenter.begin(spatial_dimension);
for (UInt elem = 0; elem < nb_element; ++elem) {
mesh.getBarycenter(elem, *it, bary_it->storage(), ghost_type);
e.element = elem;
grid.insert(e, *bary_it);
++bary_it;
}
}
std::stringstream sstr; sstr << "mesh_" << prank << ".msh";
mesh.write(sstr.str());
Mesh grid_mesh(spatial_dimension, "grid_mesh", 0);
std::stringstream sstr_grid; sstr_grid << "grid_mesh_" << prank << ".msh";
grid.saveAsMesh(grid_mesh);
grid_mesh.write(sstr_grid.str());
std::cout << "Pouet 1" << std::endl;
AKANTU_DEBUG_INFO("Creating TestAccessor");
TestAccessor test_accessor(mesh, barycenters);
SynchronizerRegistry synch_registry(test_accessor);
GridSynchronizer * grid_communicator = GridSynchronizer::createGridSynchronizer(mesh, grid);
std::cout << "Pouet 2" << std::endl;
ghost_type = _ghost;
it = mesh.firstType(spatial_dimension, ghost_type);
last_type = mesh.lastType(spatial_dimension, ghost_type);
e.ghost_type = ghost_type;
for(; it != last_type; ++it) {
UInt nb_element = mesh.getNbElement(*it, ghost_type);
e.type = *it;
Array<Real> & barycenter = barycenters(*it, ghost_type);
barycenter.resize(nb_element);
Array<Real>::iterator< Vector<Real> > bary_it = barycenter.begin(spatial_dimension);
for (UInt elem = 0; elem < nb_element; ++elem) {
mesh.getBarycenter(elem, *it, bary_it->storage(), ghost_type);
e.element = elem;
grid.insert(e, *bary_it);
++bary_it;
}
}
Mesh grid_mesh_ghost(spatial_dimension, "grid_mesh_ghost", 0);
std::stringstream sstr_gridg; sstr_gridg << "grid_mesh_ghost_" << prank << ".msh";
grid.saveAsMesh(grid_mesh_ghost);
grid_mesh_ghost.write(sstr_gridg.str());
std::cout << "Pouet 3" << std::endl;
neighbors_map_t<spatial_dimension>::type neighbors_map;
pair_list neighbors;
updatePairList(barycenters, grid, radius, neighbors, neighbors_map);
pair_list::iterator nit = neighbors.begin();
pair_list::iterator nend = neighbors.end();
std::stringstream sstrp; sstrp << "pairs_" << prank;
std::ofstream fout(sstrp.str().c_str());
for(;nit != nend; ++nit) {
fout << "[" << nit->first.first << "," << nit->first.second << "] -> "
<< nit->second << std::endl;
}
std::string file = "neighbors_ref";
std::stringstream sstrf; sstrf << file << "_" << psize << "_" << prank;
file = sstrf.str();
std::ofstream nout;
nout.open(file.c_str());
neighbors_map_t<spatial_dimension>::type::iterator it_n = neighbors_map.begin();
neighbors_map_t<spatial_dimension>::type::iterator end_n = neighbors_map.end();
for(;it_n != end_n; ++it_n) {
std::sort(it_n->second.begin(), it_n->second.end());
std::vector< Point<spatial_dimension> >::iterator it_v = it_n->second.begin();
std::vector< Point<spatial_dimension> >::iterator end_v = it_n->second.end();
nout << "####" << std::endl;
nout << it_n->second.size() << std::endl;
nout << it_n->first << std::endl;
nout << "#" << std::endl;
for(;it_v != end_v; ++it_v) {
nout << *it_v << std::endl;
}
}
fout.close();
synch_registry.registerSynchronizer(*dist, _gst_smm_mass);
synch_registry.registerSynchronizer(*grid_communicator, _gst_test);
AKANTU_DEBUG_INFO("Synchronizing tag on Dist");
synch_registry.synchronize(_gst_smm_mass);
AKANTU_DEBUG_INFO("Synchronizing tag on Grid");
synch_registry.synchronize(_gst_test);
delete grid_communicator;
delete dist;
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_synchronizer/test_grid_synchronizer_check_neighbors.cc b/test/test_synchronizer/test_grid_synchronizer_check_neighbors.cc
index a9ee15a17..e5b3eeff6 100644
--- a/test/test_synchronizer/test_grid_synchronizer_check_neighbors.cc
+++ b/test/test_synchronizer/test_grid_synchronizer_check_neighbors.cc
@@ -1,122 +1,122 @@
/**
* @file test_grid_synchronizer_check_neighbors.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Mar 11 2013
* @date last modification: Fri Feb 27 2015
*
* @brief Test the generation of neighbors list based on a akaentu::Grid
*
* @section LICENSE
*
* Copyright (©) 2014, 2015 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 <fstream>
#include <iostream>
#include <string>
#include "aka_common.hh"
-#include "static_communicator.hh"
+#include "communicator.hh"
using namespace akantu;
const UInt spatial_dimension = 3;
#include "test_grid_tools.hh"
void readNeighbors(std::ifstream & nin,
neighbors_map_t<spatial_dimension>::type & neighbors_map_read) {
std::string line;
while (std::getline(nin, line)) {
std::getline(nin, line);
std::istringstream iss(line);
UInt nb_neig;
iss >> nb_neig;
std::getline(nin, line);
Point<spatial_dimension> pt;
pt.read(line);
std::getline(nin, line);
for (UInt i = 0; i < nb_neig; ++i) {
std::getline(nin, line);
Point<spatial_dimension> ne;
ne.read(line);
neighbors_map_read[pt].push_back(ne);
}
}
}
int main(int argc, char *argv[]) {
initialize(argc, argv);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int psize = comm.getNbProc();
Int prank = comm.whoAmI();
std::string file_ref = "neighbors_ref_1_0";
std::string file = "neighbors_ref";
std::stringstream sstr; sstr << file << "_" << psize << "_" << prank;
file = sstr.str();
std::ifstream nin;
neighbors_map_t<spatial_dimension>::type neighbors_map_read;
nin.open(file_ref.c_str());
readNeighbors(nin, neighbors_map_read);
nin.close();
neighbors_map_t<spatial_dimension>::type neighbors_map;
nin.open(file.c_str());
readNeighbors(nin, neighbors_map);
nin.close();
neighbors_map_t<spatial_dimension>::type::iterator it_n = neighbors_map.begin();
neighbors_map_t<spatial_dimension>::type::iterator end_n = neighbors_map.end();
for(;it_n != end_n; ++it_n) {
std::sort(it_n->second.begin(), it_n->second.end());
std::vector< Point<spatial_dimension> >::iterator it_v = it_n->second.begin();
std::vector< Point<spatial_dimension> >::iterator end_v = it_n->second.end();
neighbors_map_t<spatial_dimension>::type::iterator it_nr = neighbors_map_read.find(it_n->first);
if(it_nr == neighbors_map_read.end())
AKANTU_DEBUG_ERROR("Argh what is this point that is not present in the ref file " << it_n->first);
std::vector< Point<spatial_dimension> >::iterator it_vr = it_nr->second.begin();
std::vector< Point<spatial_dimension> >::iterator end_vr = it_nr->second.end();
for(;it_v != end_v && it_vr != end_vr; ++it_v, ++it_vr) {
if(*it_vr != *it_v) AKANTU_DEBUG_ERROR("Neighbors does not match " << *it_v << " != " << *it_vr
<< " neighbor of " << it_n->first);
}
if(it_v == end_v && it_vr != end_vr) {
AKANTU_DEBUG_ERROR("Some neighbors of " << it_n->first << " are missing!");
}
if(it_v != end_v && it_vr == end_vr)
AKANTU_DEBUG_ERROR("Some neighbors of " << it_n->first << " are in excess!");
}
akantu::finalize();
return EXIT_SUCCESS;
}
diff --git a/test/test_synchronizer/test_node_synchronizer.cc b/test/test_synchronizer/test_node_synchronizer.cc
index 94452ce1c..f0c4986fa 100644
--- a/test/test_synchronizer/test_node_synchronizer.cc
+++ b/test/test_synchronizer/test_node_synchronizer.cc
@@ -1,130 +1,130 @@
/**
* @file test_node_synchronizer.cc
*
* @author Nicolas Richart
*
* @date creation Tue Apr 04 2017
*
* @brief test the default node synchronizer present in the mesh
*
* @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 "data_accessor.hh"
#include "mesh.hh"
#include "node_synchronizer.hh"
-#include "static_communicator.hh"
+#include "communicator.hh"
/* -------------------------------------------------------------------------- */
#include <limits>
/* -------------------------------------------------------------------------- */
using namespace akantu;
class DataAccessorTest : public DataAccessor<UInt> {
public:
explicit DataAccessorTest(Array<int> & data) : data(data) {}
UInt getNbData(const Array<UInt> & nodes,
const SynchronizationTag &) const {
return nodes.size() * sizeof(int);
}
void packData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag &) const {
for (auto node : nodes) {
buffer << data(node);
}
}
void unpackData(CommunicationBuffer & buffer, const Array<UInt> & nodes,
const SynchronizationTag &) {
for (auto node : nodes) {
buffer >> data(node);
}
}
protected:
Array<int> & data;
};
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
if (prank == 0)
mesh.read("cube.msh");
mesh.distribute();
UInt nb_nodes = mesh.getNbNodes();
Array<int> node_data(nb_nodes);
constexpr int max_int = std::numeric_limits<int>::max();
for (UInt n = 0; n < nb_nodes; ++n) {
UInt gn = mesh.getNodeGlobalId(n);
if (mesh.isMasterNode(n))
node_data(n) = gn;
else if (mesh.isLocalNode(n))
node_data(n) = -gn;
else if (mesh.isSlaveNode(n))
node_data(n) = max_int;
else
node_data(n) = -max_int;
}
DataAccessorTest data_accessor(node_data);
auto & node_synchronizer = mesh.getNodeSynchronizer();
node_synchronizer.synchronize(data_accessor, _gst_test);
for (UInt n = 0; n < nb_nodes; ++n) {
int gn = mesh.getNodeGlobalId(n);
if(!((mesh.isMasterNode(n) && node_data(n) == gn) ||
(mesh.isLocalNode(n) && node_data(n) == -gn) ||
(mesh.isSlaveNode(n) && node_data(n) == gn) ||
(mesh.isPureGhostNode(n) && node_data(n) == -max_int)
)
)
{
debug::setDebugLevel(dblTest);
std::cout << "prank : " << prank << " (node " << gn << "[" << n << "]) - "
<< "( isMaster: " << mesh.isMasterNode(n) << " && " << node_data(n) << " == " << gn << ") "
<< "( isLocal: " << mesh.isLocalNode(n) << " && " << node_data(n) << " == " << - gn << ") "
<< "( isSlave: " << mesh.isSlaveNode(n) << " && " << node_data(n) << " == " << gn << ") "
<< "( isPureGhost: " << mesh.isPureGhostNode(n) << " && " << node_data(n) << " == " << -max_int << ") "
<< std::endl;
debug::setDebugLevel(dblDebug);
return -1;
}
}
finalize();
return 0;
}
diff --git a/test/test_synchronizer/test_synchronizer_communication.cc b/test/test_synchronizer/test_synchronizer_communication.cc
index 18aab7d4d..aab198caa 100644
--- a/test/test_synchronizer/test_synchronizer_communication.cc
+++ b/test/test_synchronizer/test_synchronizer_communication.cc
@@ -1,160 +1,160 @@
/**
* @file test_synchronizer_communication.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 01 2010
* @date last modification: Sun Oct 19 2014
*
* @brief test to synchronize barycenters
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014, 2015 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 "aka_common.hh"
#include "aka_random_generator.hh"
#include "element_synchronizer.hh"
#include "mesh.hh"
#include "mesh_partition_scotch.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
//#define DUMP
#if defined(AKANTU_USE_IOHELPER) && defined(DUMP)
#include "dumper_paraview.hh"
#endif // AKANTU_USE_IOHELPER
#include "test_data_accessor.hh"
using namespace akantu;
/* -------------------------------------------------------------------------- */
/* Main */
/* -------------------------------------------------------------------------- */
int main(int argc, char * argv[]) {
initialize(argc, argv);
UInt spatial_dimension = 3;
Mesh mesh(spatial_dimension);
- StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
+ const auto & comm = Communicator::getStaticCommunicator();
Int prank = comm.whoAmI();
bool wait = true;
if (argc > 1) {
if (prank == 0)
while (wait)
;
}
if (prank == 0)
mesh.read("cube.msh");
mesh.distribute();
/// compute barycenter for each facet
ElementTypeMapArray<Real> barycenters("barycenters", "", 0);
barycenters.initialize(mesh, _nb_component = spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, ghost_type);
for (; it != last_type; ++it) {
UInt nb_element = mesh.getNbElement(*it, ghost_type);
Array<Real> & barycenter = barycenters(*it, ghost_type);
barycenter.resize(nb_element);
Array<Real>::iterator<Vector<Real>> bary_it =
barycenter.begin(spatial_dimension);
for (UInt elem = 0; elem < nb_element; ++elem, ++bary_it)
mesh.getBarycenter(elem, *it, bary_it->storage(), ghost_type);
}
}
AKANTU_DEBUG_INFO("Creating TestAccessor");
TestAccessor test_accessor(mesh, barycenters);
SynchronizerRegistry synch_registry;
synch_registry.registerDataAccessor(test_accessor);
synch_registry.registerSynchronizer(mesh.getElementSynchronizer(), _gst_test);
AKANTU_DEBUG_INFO("Synchronizing tag");
synch_registry.synchronize(_gst_test);
// Checking the tags in MeshData (not a very good test because they're all
// identical,
// but still...)
Mesh::type_iterator it = mesh.firstType(_all_dimensions);
Mesh::type_iterator last_type = mesh.lastType(_all_dimensions);
for (; it != last_type; ++it) {
Array<UInt> & tags = mesh.getData<UInt>("tag_0", *it);
Array<UInt>::const_vector_iterator tags_it = tags.begin(1);
Array<UInt>::const_vector_iterator tags_end = tags.end(1);
AKANTU_DEBUG_ASSERT(
mesh.getNbElement(*it) == tags.size(),
"The number of tags does not match the number of elements on rank "
<< prank << ".");
std::cout << std::dec << " I am rank " << prank
<< " and here's my MeshData dump for types " << *it
<< " (it should contain " << mesh.getNbElement(*it)
<< " elements and it has " << tags.size()
<< "!) :" << std::endl;
std::cout << std::hex;
debug::setDebugLevel(dblTest);
for (; tags_it != tags_end; ++tags_it) {
std::cout << tags_it->operator()(0) << " ";
}
debug::setDebugLevel(dblInfo);
std::cout << std::endl;
}
#if defined(AKANTU_USE_IOHELPER) && defined(DUMP)
DumperParaview dumper("test-scotch-partition");
dumper.registerMesh(mesh, spatial_dimension, _not_ghost);
dumper.registerField("partitions",
new DumperIOHelper::ElementPartitionField<>(mesh,
spatial_dimension, _not_ghost));
dumper.dump();
DumperParaview dumper_ghost("test-scotch-partition-ghost");
dumper_ghost.registerMesh(mesh, spatial_dimension, _ghost);
dumper_ghost.registerField("partitions",
new DumperIOHelper::ElementPartitionField<>(mesh,
spatial_dimension, _ghost));
dumper_ghost.dump();
#endif //AKANTU_USE_IOHELPER
finalize();
return EXIT_SUCCESS;
}
diff --git a/third-party/iohelper/src/paraview_helper.tcc b/third-party/iohelper/src/paraview_helper.tcc
index b016755c0..6afdb9259 100644
--- a/third-party/iohelper/src/paraview_helper.tcc
+++ b/third-party/iohelper/src/paraview_helper.tcc
@@ -1,308 +1,309 @@
#include <cassert>
#if defined(__INTEL_COMPILER)
#pragma warning ( push )
/// remark #981: operands are evaluated in unspecified order
#pragma warning ( disable : 981 )
#endif //defined(__INTEL_COMPILER)
inline std::string ParaviewHelper::dataTypeToStr(DataType data_type) {
std::string str;
switch(data_type) {
case _bool : str = "UInt8" ; break;
case _uint : str = "UInt32" ; break;
case _int : str = "Int32" ; break;
case _float : str = "Float32"; break;
case _double : str = "Float64"; break;
case _uint64 : str = "UInt64" ; break;
case _int64 : str = "Int64" ; break;
}
return str;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::visitField(T & visited){
this->position_flag = false;
switch (current_stage){
case _s_writeFieldProperty: writeFieldProperty(visited); break;
- case _s_writePosition: this->position_flag = true;
+ case _s_writePosition: this->position_flag = true; /* FALLTHRU */
+ // [[fallthrough]] un-comment when compiler gets it
case _s_writeField: writeField(visited); break;
case _s_writeConnectivity: writeConnectivity(visited); break;
case _s_writeElemType: writeElemType(visited); break;
case _s_buildOffsets: writeOffsets(visited); break;
default:
std::stringstream sstr;
sstr << "the stage " << current_stage << " is not a known paraviewhelper stage";
IOHELPER_THROW(sstr.str(),
IOHelperException::_et_unknown_visitor_stage);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writeFieldProperty(T & data){
if (data.isHomogeneous() == false)
IOHELPER_THROW(std::string("try to write field property of a non homogeneous field"),
IOHelperException::_et_non_homogeneous_data);
UInt dim = data.getDim();
std::string name = data.getName();
PDataArray(name, dim, dataTypeToStr(data.getDataType()));
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writeField(T & data){
typename T::iterator it = data.begin();
typename T::iterator end = data.end();
compteur = 0;
UInt dim;
if(data.isHomogeneous()) {
dim = data.getDim();
if(position_flag)
dim = 3;
for (; it != end; ++it)
pushData((*it), dim);
}
else {
for (; it != end; ++it)
pushData((*it));
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writeConnectivity(T & data) {
typename T::iterator it = data.begin();
typename T::iterator end = data.end();
for (; it != end; ++it) {
ElemType type = (ElemType) it.element_type();
//typename T::iterator::type & n = *it;
UInt dim = (*it).size();
assert(nb_node_per_elem[type] == dim);
UInt * reorder = this->write_reorder[type];
for (UInt i = 0; i < dim; ++i) {
this->pushDatum((*it)[reorder[i]], dim);
}
}
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writeElemType(T & data){
typename T::iterator it = data.begin();
typename T::iterator end = data.end();
for (; it != end; ++it) {
ElemType type = (ElemType) it.element_type();
this->pushDatum(this->paraview_code_type[type], 1);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writeOffsets(T & data){
typename T::iterator it = data.begin();
typename T::iterator end = data.end();
UInt count = 0;
for (; it != end; ++it) {
count += (*it).size();
pushDatum(count);
}
}
/* -------------------------------------------------------------------------- */
template <template<typename T> class Cont, typename T>
inline void ParaviewHelper::pushData(const Cont<T> & n, UInt dim){
for (UInt i = 0; i < n.size(); ++i) {
pushDatum<T>(n[i], dim);
}
for (UInt i = n.size(); i < dim; ++i) { T t = T(); this->pushDatum<T>(t, dim); }
}
/* -------------------------------------------------------------------------- */
template <template<typename T> class Cont, typename T>
inline void ParaviewHelper::pushData(const Cont<T> & n) {
for (UInt i = 0; i < n.size(); ++i) {
pushDatum<T>(n[i], n.size());
}
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::setMode(int mode){
bflag = BASE64 & mode;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::writePVTU(T & per_node_data, T & per_elem_data,
const std::vector<std::string> & vtus){
current_stage = _s_writeFieldProperty;
file << "<VTKFile type=\"PUnstructuredGrid\" version=\"0.1\" " << std::endl;
file << "byte_order=\"LittleEndian\">" << std::endl;
file << " <PUnstructuredGrid GhostLevel=\"0\">" << std::endl;
file << " <PPoints>" << std::endl;
file << " <PDataArray type=\"Float64\" NumberOfComponents=\"3\" format=\"";
if (bflag == BASE64) file << "binary";
else file << "ascii";
file << "\" />" << std::endl;
file << " </PPoints>" << std::endl;
file << " <PPointData>" << std::endl;
typename T::iterator itNodeField = per_node_data.begin();
typename T::iterator endNodeField = per_node_data.end();
for ( ; itNodeField != endNodeField ; ++itNodeField)
if ((*itNodeField).first != "positions")
(*itNodeField).second->accept(*this);
file << " </PPointData>" << std::endl;
file << " <PCellData>" << std::endl;
typename T::iterator itElemField = per_elem_data.begin();
typename T::iterator endElemField = per_elem_data.end();
for (; itElemField != endElemField ; ++itElemField) {
std::string name = (*itElemField).first;
if (name == "connectivities" ||
name == "element_type") continue;
(*itElemField).second->accept(*this);
}
file << " </PCellData>" << std::endl;
for (UInt l = 0 ; l < vtus.size() ; ++l)
file << " <Piece Source=\"" << vtus[l] << "\" />" << std::endl;
file << " </PUnstructuredGrid>" << std::endl;
file << "</VTKFile>" << std::endl;
file.close();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParaviewHelper::pushDataFields(T & per_node_data, T & per_elem_data){
startPointDataList();
{
typename T::iterator itNodeField = per_node_data.begin();
typename T::iterator endNodeField = per_node_data.end();
for ( ; itNodeField != endNodeField ; ++itNodeField) {
std::string name = (*itNodeField).first;
if (name == "positions") continue;
FieldInterface & f = *(*itNodeField).second;
startData(f.getName(), f.getDim(), dataTypeToStr(f.getDataType()));
pushField(f);
endData();
}
}
endPointDataList();
startCellDataList();
{
typename T::iterator itElemField = per_elem_data.begin();
typename T::iterator endElemField = per_elem_data.end();
for ( ; itElemField != endElemField ; ++itElemField) {
std::string name = (*itElemField).first;
if (name == "connectivities" ||
name == "element_type") continue;
FieldInterface & f = *(*itElemField).second;
startData(f.getName(),f.getDim(), dataTypeToStr(f.getDataType()));
pushField(f);
endData();
}
}
endCellDataList();
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParaviewHelper::pushDatum(const T & n,
__attribute__((unused)) UInt size){
if (bflag == BASE64)
b64.push<T>(n);
else{
if (compteur == 0)
file << " ";
++compteur;
file << n << " ";
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void ParaviewHelper::pushDatum<double>(const double & n,
UInt size){
if (bflag == BASE64)
b64.push<double>(n);
else {
if (compteur % size == 0)
file << " ";
file << std::setw(22);
file << std::setprecision(15);
file << std::scientific;
file << n;
file << " ";
++compteur;
if (compteur % size == 0)
file << std::endl;
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void ParaviewHelper::pushDatum<ElemType>(const ElemType & type,
__attribute__((unused)) UInt size){
UInt n = this->paraview_code_type[type];
pushDatum<UInt>(n);
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::pushPosition(FieldInterface & f){
current_stage = _s_writePosition;
f.accept(*this);
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::pushField(FieldInterface & f){
current_stage = _s_writeField;
f.accept(*this);
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::pushConnectivity(FieldInterface & f) {
current_stage = _s_writeConnectivity;
f.accept(*this);
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::pushElemType(FieldInterface & f) {
current_stage = _s_writeElemType;
f.accept(*this);
}
/* -------------------------------------------------------------------------- */
inline void ParaviewHelper::buildOffsets(FieldInterface & f){
current_stage = _s_buildOffsets;
f.accept(*this);
}
/* -------------------------------------------------------------------------- */
#if defined(__INTEL_COMPILER)
#pragma warning ( pop )
#endif //defined(__INTEL_COMPILER)