diff --git a/src/common/aka_array.cc b/src/common/aka_array.cc
index 31bf3f4fb..08e70d815 100644
--- a/src/common/aka_array.cc
+++ b/src/common/aka_array.cc
@@ -1,123 +1,123 @@
/**
* @file aka_array.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Aug 18 2015
*
* @brief Implementation of akantu::Array
*
* @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 <memory>
#include <utility>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_array.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* Functions ArrayBase */
/* -------------------------------------------------------------------------- */
ArrayBase::ArrayBase(ID id)
: id(std::move(id)), allocated_size(0), size(0), nb_component(1),
size_of_type(0) {}
/* -------------------------------------------------------------------------- */
ArrayBase::~ArrayBase() = default;
/* -------------------------------------------------------------------------- */
void ArrayBase::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "ArrayBase [" << std::endl;
stream << space << " + size : " << size << std::endl;
stream << space << " + nb component : " << nb_component << std::endl;
stream << space << " + allocated size : " << allocated_size << std::endl;
Real mem_size = (allocated_size * nb_component * size_of_type) / 1024.;
stream << space << " + size of type : " << size_of_type << "B"
<< std::endl;
stream << space << " + memory allocated : " << mem_size << "kB" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
template <> Int Array<Real>::find(const Real & elem) const {
AKANTU_DEBUG_IN();
UInt i = 0;
Real epsilon = std::numeric_limits<Real>::epsilon();
for (; (i < size) && (fabs(values[i] - elem) <= epsilon); ++i)
;
AKANTU_DEBUG_OUT();
return (i == size) ? -1 : (Int)i;
}
/* -------------------------------------------------------------------------- */
template <>
Array<ElementType> & Array<ElementType>::operator*=(__attribute__((unused))
const ElementType & alpha) {
AKANTU_DEBUG_TO_IMPLEMENT();
return *this;
}
template <>
Array<ElementType> & Array<ElementType>::
operator-=(__attribute__((unused)) const Array<ElementType> & vect) {
AKANTU_DEBUG_TO_IMPLEMENT();
return *this;
}
template <>
Array<ElementType> & Array<ElementType>::
operator+=(__attribute__((unused)) const Array<ElementType> & vect) {
AKANTU_DEBUG_TO_IMPLEMENT();
return *this;
}
template <>
Array<char> & Array<char>::operator*=(__attribute__((unused))
const char & alpha) {
AKANTU_DEBUG_TO_IMPLEMENT();
return *this;
}
template <>
Array<char> & Array<char>::operator-=(__attribute__((unused))
const Array<char> & vect) {
AKANTU_DEBUG_TO_IMPLEMENT();
return *this;
}
template <>
Array<char> & Array<char>::operator+=(__attribute__((unused))
const Array<char> & vect) {
AKANTU_DEBUG_TO_IMPLEMENT();
return *this;
}
-__END_AKANTU__
+} // akantu
diff --git a/src/common/aka_blas_lapack.hh b/src/common/aka_blas_lapack.hh
index 951944ec0..725fbcd0e 100644
--- a/src/common/aka_blas_lapack.hh
+++ b/src/common/aka_blas_lapack.hh
@@ -1,343 +1,343 @@
/**
* @file aka_blas_lapack.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Mar 06 2013
* @date last modification: Mon Jan 18 2016
*
* @brief Interface of the Fortran BLAS/LAPACK libraries
*
* @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_AKA_BLAS_LAPACK_HH__
#define __AKANTU_AKA_BLAS_LAPACK_HH__
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_BLAS
#include "aka_fortran_mangling.hh"
extern "C" {
/* ------------------------------------------------------------------------ */
/* Double precision */
/* ------------------------------------------------------------------------ */
// LEVEL 1
double AKA_FC_GLOBAL(ddot, DDOT)(int *, double *, int *, double *, int *);
void AKA_FC_GLOBAL(daxpy, DAXPY)(int *, double *, double *, int *, double *,
int *);
// LEVEL 2
void AKA_FC_GLOBAL(dgemv, DGEMV)(char *, int *, int *, double *, double *,
int *, double *, int *, double *, double *,
int *);
// LEVEL 3
void AKA_FC_GLOBAL(dgemm, DGEMM)(char *, char *, int *, int *, int *, double *,
double *, int *, double *, int *, double *,
double *, int *);
/* ------------------------------------------------------------------------ */
/* Simple precision */
/* ------------------------------------------------------------------------ */
// LEVEL 1
float AKA_FC_GLOBAL(sdot, SDOT)(int *, float *, int *, float *, int *);
void AKA_FC_GLOBAL(saxpy, SAXPY)(int *, float *, float *, int *, float *,
int *);
// LEVEL 2
void AKA_FC_GLOBAL(sgemv, SGEMV)(char *, int *, int *, float *, float *, int *,
float *, int *, float *, float *, int *);
// LEVEL 3
void AKA_FC_GLOBAL(sgemm, SGEMM)(char *, char *, int *, int *, int *, float *,
float *, int *, float *, int *, float *,
float *, int *);
}
#endif
-__BEGIN_AKANTU__
+namespace akantu {
#define AKANTU_WARNING_IGNORE_UNUSED_PARAMETER
#include "aka_warning.hh"
/// Wrapper around the S/DDOT BLAS function that returns the dot product of two
/// vectors
template <typename T>
inline T aka_dot(int * n, T * x, int * incx, T * y, int * incy) {
AKANTU_DEBUG_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DAXPY BLAS function that computes \f$y := \alpha x +
/// y\f$
template <typename T>
inline void aka_axpy(int * n, T * alpha, T * x, int * incx, T * y, int * incy) {
AKANTU_DEBUG_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DGEMV BLAS function that computes matrix-vector product
/// \f$y := \alpha A^{(T)}x + \beta y \f$
template <typename T>
inline void aka_gemv(char * trans, int * m, int * n, T * alpha, T * a,
int * lda, T * x, int * incx, T * beta, T * y,
int * incy) {
AKANTU_DEBUG_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
/// Wrapper around the S/DGEMM BLAS function that computes the product of two
/// matrices \f$C := \alpha A^{(T)} B^{(T)} + \beta C \f$
template <typename T>
inline void aka_gemm(char * transa, char * transb, int * m, int * n, int * k,
T * alpha, T * a, int * lda, T * b, int * ldb, T * beta,
T * c, int * ldc) {
AKANTU_DEBUG_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"BLAS in the compilation options!");
}
#if defined(AKANTU_USE_BLAS)
template <>
inline double aka_dot<double>(int * n, double * x, int * incx, double * y,
int * incy) {
return AKA_FC_GLOBAL(ddot, DDOT)(n, x, incx, y, incy);
}
template <>
inline void aka_axpy(int * n, double * alpha, double * x, int * incx,
double * y, int * incy) {
return AKA_FC_GLOBAL(daxpy, DAXPY)(n, alpha, x, incx, y, incy);
}
template <>
inline void aka_gemv<double>(char * trans, int * m, int * n, double * alpha,
double * a, int * lda, double * x, int * incx,
double * beta, double * y, int * incy) {
return AKA_FC_GLOBAL(dgemv, DGEMV)(trans, m, n, alpha, a, lda, x, incx, beta,
y, incy);
}
template <>
inline void aka_gemm<double>(char * transa, char * transb, int * m, int * n,
int * k, double * alpha, double * a, int * lda,
double * b, int * ldb, double * beta, double * c,
int * ldc) {
AKA_FC_GLOBAL(dgemm, DGEMM)
(transa, transb, m, n, k, alpha, a, lda, b, ldb, beta, c, ldc);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <>
inline float aka_dot<float>(int * n, float * x, int * incx, float * y,
int * incy) {
return AKA_FC_GLOBAL(sdot, SDOT)(n, x, incx, y, incy);
}
template <>
inline void aka_axpy(int * n, float * alpha, float * x, int * incx, float * y,
int * incy) {
return AKA_FC_GLOBAL(daxpy, DAXPY)(n, alpha, x, incx, y, incy);
}
template <>
inline void aka_gemv<float>(char * trans, int * m, int * n, float * alpha,
float * a, int * lda, float * x, int * incx,
float * beta, float * y, int * incy) {
AKA_FC_GLOBAL(sgemv, SGEMV)
(trans, m, n, alpha, a, lda, x, incx, beta, y, incy);
}
template <>
inline void aka_gemm<float>(char * transa, char * transb, int * m, int * n,
int * k, float * alpha, float * a, int * lda,
float * b, int * ldb, float * beta, float * c,
int * ldc) {
AKA_FC_GLOBAL(sgemm, SGEMM)
(transa, transb, m, n, k, alpha, a, lda, b, ldb, beta, c, ldc);
}
#endif
-__END_AKANTU__
+} // akantu
#ifdef AKANTU_USE_LAPACK
#include "aka_fortran_mangling.hh"
extern "C" {
/* ------------------------------------------------------------------------ */
/* Double general matrix */
/* ------------------------------------------------------------------------ */
/// compute the eigenvalues/vectors
void AKA_FC_GLOBAL(dgeev, DGEEV)(char * jobvl, char * jobvr, int * n,
double * a, int * lda, double * wr,
double * wi, double * vl, int * ldvl,
double * vr, int * ldvr, double * work,
int * lwork, int * info);
/// LU decomposition of a general matrix
void AKA_FC_GLOBAL(dgetrf, DGETRF)(int * m, int * n, double * a, int * lda,
int * ipiv, int * info);
/// generate inverse of a matrix given its LU decomposition
void AKA_FC_GLOBAL(dgetri, DGETRI)(int * n, double * a, int * lda, int * ipiv,
double * work, int * lwork, int * info);
/// solving A x = b using a LU factorization
void AKA_FC_GLOBAL(dgetrs, DGETRS)(char * trans, int * n, int * nrhs,
double * A, int * lda, int * ipiv,
double * b, int * ldb, int * info);
/* ------------------------------------------------------------------------ */
/* Simple general matrix */
/* ------------------------------------------------------------------------ */
/// compute the eigenvalues/vectors
void AKA_FC_GLOBAL(sgeev, SGEEV)(char * jobvl, char * jobvr, int * n, float * a,
int * lda, float * wr, float * wi, float * vl,
int * ldvl, float * vr, int * ldvr,
float * work, int * lwork, int * info);
/// LU decomposition of a general matrix
void AKA_FC_GLOBAL(sgetrf, SGETRF)(int * m, int * n, float * a, int * lda,
int * ipiv, int * info);
/// generate inverse of a matrix given its LU decomposition
void AKA_FC_GLOBAL(sgetri, SGETRI)(int * n, float * a, int * lda, int * ipiv,
float * work, int * lwork, int * info);
/// solving A x = b using a LU factorization
void AKA_FC_GLOBAL(sgetrs, SGETRS)(char * trans, int * n, int * nrhs, float * A,
int * lda, int * ipiv, float * b, int * ldb,
int * info);
}
#endif // AKANTU_USE_LAPACK
-__BEGIN_AKANTU__
+namespace akantu {
/// Wrapper around the S/DGEEV BLAS function that computes the eigenvalues and
/// eigenvectors of a matrix
template <typename T>
inline void aka_geev(char * jobvl, char * jobvr, int * n, T * a, int * lda,
T * wr, T * wi, T * vl, int * ldvl, T * vr, int * ldvr,
T * work, int * lwork, int * info) {
AKANTU_DEBUG_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRF BLAS function that computes the LU decomposition
/// of a matrix
template <typename T>
inline void aka_getrf(int * m, int * n, T * a, int * lda, int * ipiv,
int * info) {
AKANTU_DEBUG_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRI BLAS function that computes the inverse of a
/// matrix given its LU decomposition
template <typename T>
inline void aka_getri(int * n, T * a, int * lda, int * ipiv, T * work,
int * lwork, int * info) {
AKANTU_DEBUG_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
/// Wrapper around the S/DGETRS BLAS function that solves \f$A^{(T)}x = b\f$
/// using LU decomposition
template <typename T>
inline void aka_getrs(char * trans, int * n, int * nrhs, T * A, int * lda,
int * ipiv, T * b, int * ldb, int * info) {
AKANTU_DEBUG_ERROR(debug::demangle(typeid(T).name())
<< "is not a type recognized, or you didn't activated "
"LAPACK in the compilation options!");
}
#include "aka_warning_restore.hh"
#ifdef AKANTU_USE_LAPACK
template <>
inline void aka_geev<double>(char * jobvl, char * jobvr, int * n, double * a,
int * lda, double * wr, double * wi, double * vl,
int * ldvl, double * vr, int * ldvr, double * work,
int * lwork, int * info) {
AKA_FC_GLOBAL(dgeev, DGEEV)
(jobvl, jobvr, n, a, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
}
template <>
inline void aka_getrf<double>(int * m, int * n, double * a, int * lda,
int * ipiv, int * info) {
AKA_FC_GLOBAL(dgetrf, DGETRF)(m, n, a, lda, ipiv, info);
}
template <>
inline void aka_getri<double>(int * n, double * a, int * lda, int * ipiv,
double * work, int * lwork, int * info) {
AKA_FC_GLOBAL(dgetri, DGETRI)(n, a, lda, ipiv, work, lwork, info);
}
template <>
inline void aka_getrs<double>(char * trans, int * n, int * nrhs, double * A,
int * lda, int * ipiv, double * b, int * ldb,
int * info) {
AKA_FC_GLOBAL(dgetrs, DGETRS)(trans, n, nrhs, A, lda, ipiv, b, ldb, info);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <>
inline void aka_geev<float>(char * jobvl, char * jobvr, int * n, float * a,
int * lda, float * wr, float * wi, float * vl,
int * ldvl, float * vr, int * ldvr, float * work,
int * lwork, int * info) {
AKA_FC_GLOBAL(sgeev, SGEEV)
(jobvl, jobvr, n, a, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
}
template <>
inline void aka_getrf<float>(int * m, int * n, float * a, int * lda, int * ipiv,
int * info) {
AKA_FC_GLOBAL(sgetrf, SGETRF)(m, n, a, lda, ipiv, info);
}
template <>
inline void aka_getri<float>(int * n, float * a, int * lda, int * ipiv,
float * work, int * lwork, int * info) {
AKA_FC_GLOBAL(sgetri, SGETRI)(n, a, lda, ipiv, work, lwork, info);
}
template <>
inline void aka_getrs<float>(char * trans, int * n, int * nrhs, float * A,
int * lda, int * ipiv, float * b, int * ldb,
int * info) {
AKA_FC_GLOBAL(sgetrs, SGETRS)(trans, n, nrhs, A, lda, ipiv, b, ldb, info);
}
#endif
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_AKA_BLAS_LAPACK_HH__ */
diff --git a/src/common/aka_circular_array.hh b/src/common/aka_circular_array.hh
index af005df7c..34ed0fb1b 100644
--- a/src/common/aka_circular_array.hh
+++ b/src/common/aka_circular_array.hh
@@ -1,140 +1,140 @@
/**
* @file aka_circular_array.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief class of circular array
*
* @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_AKA_CIRCULAR_ARRAY_HH__
#define __AKANTU_AKA_CIRCULAR_ARRAY_HH__
/* -------------------------------------------------------------------------- */
#include <typeinfo>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
template<class T>
class CircularArray : protected Array<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef typename Array<T>::value_type value_type;
typedef typename Array<T>::reference reference;
typedef typename Array<T>::pointer_type pointer_type;
typedef typename Array<T>::const_reference const_reference;
/// Allocation of a new array with a default value
CircularArray(UInt size, UInt nb_component = 1,
const_reference value = value_type(), const ID & id = "") :
Array<T>(size, nb_component, value, id),
start_position(0),
end_position(size-1) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
virtual ~CircularArray() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
advance start and end position by one:
the first element is now at the end of the array
**/
inline void makeStep();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
private:
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
inline reference operator()(UInt i, UInt j = 0);
inline const_reference operator()(UInt i, UInt j = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
UInt getSize() const{ return this->size; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// indice of first element in this circular array
UInt start_position;
/// indice of last element in this circular array
UInt end_position;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "aka_circular_array_inline_impl.cc"
#endif
/// standard output stream operator
template <typename T>
inline std::ostream & operator <<(std::ostream & stream, const CircularArray<T> & _this)
{
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_AKA_CIRCULAR_ARRAY_HH__ */
diff --git a/src/common/aka_common.cc b/src/common/aka_common.cc
index 51708f754..dd5955a94 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 "static_communicator.hh"
#include "aka_random_generator.hh"
#include "parser.hh"
#include "cppargparse.hh"
#include "communication_tag.hh"
/* -------------------------------------------------------------------------- */
#include <ctime>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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();
StaticCommunicator & comm =
StaticCommunicator::getStaticCommunicator(argc, argv);
Tag::setMaxTag(comm.getMaxTag());
debug::debugger.setParallelContext(comm.whoAmI(), comm.getNbProc());
debug::initSignalHandler();
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 *= (comm.whoAmI() + 1);
#if not defined(_WIN32)
Rand48Generator<Real>::seed(seed);
#endif
RandGenerator<Real>::seed(seed);
int dbl_level = static_argparser["aka_debug_level"];
debug::setDebugLevel(DebugLevel(dbl_level));
AKANTU_DEBUG_INFO("Random seed set to " << seed);
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);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/common/aka_common.hh b/src/common/aka_common.hh
index e4a818674..306b774a0 100644
--- a/src/common/aka_common.hh
+++ b/src/common/aka_common.hh
@@ -1,447 +1,447 @@
/**
* @file aka_common.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jun 14 2010
* @date last modification: Thu Jan 21 2016
*
* @brief common type descriptions for akantu
*
* @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
*
* All common things to be included in the projects files
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COMMON_HH__
#define __AKANTU_COMMON_HH__
/* -------------------------------------------------------------------------- */
#include <list>
#include <limits>
#include <type_traits>
#if __cplusplus < 201402L
namespace std {
template< bool B, class T = void >
using enable_if_t = typename enable_if<B,T>::type;
}
#endif
/* -------------------------------------------------------------------------- */
-#define __BEGIN_AKANTU__ namespace akantu {
-#define __END_AKANTU__ }
+#define namespace akantu { namespace akantu {
+#define } // akantu }
/* -------------------------------------------------------------------------- */
#define __BEGIN_AKANTU_DUMPER__ namespace dumper {
#define __END_AKANTU_DUMPER__ }
/* -------------------------------------------------------------------------- */
#if defined(WIN32)
#define __attribute__(x)
#endif
/* -------------------------------------------------------------------------- */
#include "aka_config.hh"
#include "aka_error.hh"
#include "aka_safe_enum.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* Common types */
/* -------------------------------------------------------------------------- */
using ID = std::string;
#ifdef AKANTU_NDEBUG
static const Real REAL_INIT_VALUE = Real(0.);
#else
static const Real REAL_INIT_VALUE = std::numeric_limits<Real>::quiet_NaN();
#endif
/* -------------------------------------------------------------------------- */
/* Memory types */
/* -------------------------------------------------------------------------- */
using MemoryID = UInt;
using Surface = std::string;
typedef std::pair<Surface, Surface> SurfacePair;
using SurfacePairList = std::list<SurfacePair>;
/* -------------------------------------------------------------------------- */
extern const UInt _all_dimensions;
/* -------------------------------------------------------------------------- */
/* Mesh/FEM/Model types */
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#include "aka_element_classes_info.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/// small help to use names for directions
enum SpacialDirection { _x = 0, _y = 1, _z = 2 };
/// enum MeshIOType type of mesh reader/writer
enum MeshIOType {
_miot_auto, ///< Auto guess of the reader to use based on the extension
_miot_gmsh, ///< Gmsh files
_miot_gmsh_struct, ///< Gsmh reader with reintpretation of elements has
/// structures elements
_miot_diana, ///< TNO Diana mesh format
_miot_abaqus ///< Abaqus mesh format
};
/// enum AnalysisMethod type of solving method used to solve the equation of
/// motion
enum AnalysisMethod {
_static = 0,
_implicit_dynamic = 1,
_explicit_lumped_mass = 2,
_explicit_lumped_capacity = 2,
_explicit_consistent_mass = 3
};
/// enum DOFSupportType defines which kind of dof that can exists
enum DOFSupportType { _dst_nodal, _dst_generic };
/// Type of non linear resolution available in akantu
enum NonLinearSolverType {
_nls_linear, ///< No non linear convergence loop
_nls_newton_raphson, ///< Regular Newton-Raphson
_nls_newton_raphson_modified, ///< Newton-Raphson with initial tangent
_nls_lumped, ///< Case of lumped mass or equivalent matrix
_nls_auto ///< This will take a default value that make sense in case of
/// model::getNewSolver
};
/// Define the node/dof type
enum NodeType : Int {
_nt_pure_gost = -3,
_nt_master = -2,
_nt_normal = -1
};
/// Type of time stepping solver
enum TimeStepSolverType {
_tsst_static, ///< Static solution
_tsst_dynamic, ///< Dynamic solver
_tsst_dynamic_lumped, ///< Dynamic solver with lumped mass
};
/// Type of integration scheme
enum IntegrationSchemeType {
_ist_pseudo_time, ///< Pseudo Time
_ist_forward_euler, ///< GeneralizedTrapezoidal(0)
_ist_trapezoidal_rule_1, ///< GeneralizedTrapezoidal(1/2)
_ist_backward_euler, ///< GeneralizedTrapezoidal(1)
_ist_central_difference, ///< NewmarkBeta(0, 1/2)
_ist_fox_goodwin, ///< NewmarkBeta(1/6, 1/2)
_ist_trapezoidal_rule_2, ///< NewmarkBeta(1/2, 1/2)
_ist_linear_acceleration, ///< NewmarkBeta(1/3, 1/2)
_ist_newmark_beta, ///< generic NewmarkBeta with user defined
/// alpha and beta
_ist_generalized_trapezoidal ///< generic GeneralizedTrapezoidal with user
/// defined alpha
};
/// enum SolveConvergenceCriteria different convergence criteria
enum SolveConvergenceCriteria {
_scc_residual, ///< Use residual to test the convergence
_scc_solution, ///< Use solution to test the convergence
_scc_residual_mass_wgh ///< Use residual weighted by inv. nodal mass to testb
};
/// enum CohesiveMethod type of insertion of cohesive elements
enum CohesiveMethod { _intrinsic, _extrinsic };
/// @enum SparseMatrixType type of sparse matrix used
enum MatrixType { _unsymmetric, _symmetric };
/* -------------------------------------------------------------------------- */
/* Ghosts handling */
/* -------------------------------------------------------------------------- */
using SynchronizerID = ID;
/// @enum CommunicatorType type of communication method to use
enum CommunicatorType { _communicator_mpi, _communicator_dummy };
/// @enum SynchronizationTag type of synchronizations
enum SynchronizationTag {
//--- Generic tags ---
_gst_whatever,
_gst_update,
_gst_size,
//--- SolidMechanicsModel tags ---
_gst_smm_mass, ///< synchronization of the SolidMechanicsModel.mass
_gst_smm_for_gradu, ///< synchronization of the
/// SolidMechanicsModel.displacement
_gst_smm_boundary, ///< synchronization of the boundary, forces, velocities
/// and displacement
_gst_smm_uv, ///< synchronization of the nodal velocities and displacement
_gst_smm_res, ///< synchronization of the nodal residual
_gst_smm_init_mat, ///< synchronization of the data to initialize materials
_gst_smm_stress, ///< synchronization of the stresses to compute the internal
/// forces
_gst_smmc_facets, ///< synchronization of facet data to setup facet synch
_gst_smmc_facets_conn, ///< synchronization of facet global connectivity
_gst_smmc_facets_stress, ///< synchronization of facets' stress to setup facet
/// synch
_gst_smmc_damage, ///< synchronization of damage
// --- GlobalIdsUpdater tags ---
_gst_giu_global_conn, ///< synchronization of global connectivities
// --- CohesiveElementInserter tags ---
_gst_ce_groups, ///< synchronization of cohesive element insertion depending
/// on facet groups
// --- GroupManager tags ---
_gst_gm_clusters, ///< synchronization of clusters
// --- HeatTransfer tags ---
_gst_htm_capacity, ///< synchronization of the nodal heat capacity
_gst_htm_temperature, ///< synchronization of the nodal temperature
_gst_htm_gradient_temperature, ///< synchronization of the element gradient
/// temperature
// --- LevelSet tags ---
_gst_htm_phi, ///< synchronization of the nodal level set value phi
_gst_htm_gradient_phi, ///< synchronization of the element gradient phi
//--- Material non local ---
_gst_mnl_for_average, ///< synchronization of data to average in non local
/// material
_gst_mnl_weight, ///< synchronization of data for the weight computations
// --- NeighborhoodSynchronization tags ---
_gst_nh_criterion,
// --- General tags ---
_gst_test, ///< Test tag
_gst_user_1, ///< tag for user simulations
_gst_user_2, ///< tag for user simulations
_gst_material_id, ///< synchronization of the material ids
_gst_for_dump, ///< everything that needs to be synch before dump
// --- Contact & Friction ---
_gst_cf_nodal, ///< synchronization of disp, velo, and current position
_gst_cf_incr, ///< synchronization of increment
// --- Solver tags ---
_gst_solver_solution ///< synchronization of the solution obained with the
/// PETSc solver
};
/// standard output stream operator for SynchronizationTag
inline std::ostream & operator<<(std::ostream & stream,
SynchronizationTag type);
/// @enum GhostType type of ghost
enum GhostType {
_not_ghost,
_ghost,
_casper // not used but a real cute ghost
};
/* -------------------------------------------------------------------------- */
struct GhostType_def {
using type = GhostType;
static const type _begin_ = _not_ghost;
static const type _end_ = _casper;
};
using ghost_type_t = safe_enum<GhostType_def>;
extern ghost_type_t ghost_types;
/// standard output stream operator for GhostType
inline std::ostream & operator<<(std::ostream & stream, GhostType type);
/// @enum SynchronizerOperation reduce operation that the synchronizer can
/// perform
enum SynchronizerOperation {
_so_sum,
_so_min,
_so_max,
_so_prod,
_so_land,
_so_band,
_so_lor,
_so_bor,
_so_lxor,
_so_bxor,
_so_min_loc,
_so_max_loc,
_so_null
};
/* -------------------------------------------------------------------------- */
/* Global defines */
/* -------------------------------------------------------------------------- */
#define AKANTU_MIN_ALLOCATION 2000
#define AKANTU_INDENT " "
#define AKANTU_INCLUDE_INLINE_IMPL
/* -------------------------------------------------------------------------- */
template <class T> struct is_scalar {
enum { value = false };
};
#define AKANTU_SPECIFY_IS_SCALAR(type) \
template <> struct is_scalar<type> { \
enum { value = true }; \
}
AKANTU_SPECIFY_IS_SCALAR(Real);
AKANTU_SPECIFY_IS_SCALAR(UInt);
AKANTU_SPECIFY_IS_SCALAR(Int);
AKANTU_SPECIFY_IS_SCALAR(bool);
template <typename T1, typename T2> struct is_same {
enum { value = false }; // is_same represents a bool.
};
template <typename T> struct is_same<T, T> {
enum { value = true };
};
/* -------------------------------------------------------------------------- */
#define AKANTU_SET_MACRO(name, variable, type) \
inline void set##name(type variable) { this->variable = variable; }
#define AKANTU_GET_MACRO(name, variable, type) \
inline type get##name() const { return variable; }
#define AKANTU_GET_MACRO_NOT_CONST(name, variable, type) \
inline type get##name() { return variable; }
#define AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, support, con) \
inline con Array<type> & get##name( \
const support & el_type, const GhostType & ghost_type = _not_ghost) \
con { \
return variable(el_type, ghost_type); \
}
#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, )
#define AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, ElementType, const)
#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, )
#define AKANTU_GET_MACRO_BY_GEOMETRIE_TYPE_CONST(name, variable, type) \
AKANTU_GET_MACRO_BY_SUPPORT_TYPE(name, variable, type, GeometricalType, const)
/* -------------------------------------------------------------------------- */
/// initialize the static part of akantu
void initialize(int & argc, char **& argv);
/// initialize the static part of akantu and read the global input_file
void initialize(const std::string & input_file, int & argc, char **& argv);
/* -------------------------------------------------------------------------- */
/// finilize correctly akantu and clean the memory
void finalize();
/* -------------------------------------------------------------------------- */
/// Read an new input file
void readInputFile(const std::string & input_file);
/* -------------------------------------------------------------------------- */
/*
* For intel compiler annoying remark
*/
// #if defined(__INTEL_COMPILER)
// /// remark #981: operands are evaluated in unspecified order
// #pragma warning(disable : 981)
// /// remark #383: value copied to temporary, reference to temporary used
// #pragma warning(disable : 383)
// #endif // defined(__INTEL_COMPILER)
/* -------------------------------------------------------------------------- */
/* string manipulation */
/* -------------------------------------------------------------------------- */
inline std::string to_lower(const std::string & str);
/* -------------------------------------------------------------------------- */
inline std::string trim(const std::string & to_trim);
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/// give a string representation of the a human readable size in bit
template <typename T> std::string printMemorySize(UInt size);
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#include "aka_fwd.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/// get access to the internal argument parser
cppargparse::ArgumentParser & getStaticArgumentParser();
/// get access to the internal input file parser
Parser & getStaticParser();
/// get access to the user part of the internal input file parser
const ParserSection & getUserParser();
-__END_AKANTU__
+} // akantu
#include "aka_common_inline_impl.cc"
/* -------------------------------------------------------------------------- */
#if AKANTU_INTEGER_SIZE == 4
#define AKANTU_HASH_COMBINE_MAGIC_NUMBER 0x9e3779b9
#elif AKANTU_INTEGER_SIZE == 8
#define AKANTU_HASH_COMBINE_MAGIC_NUMBER 0x9e3779b97f4a7c13LL
#endif
namespace std {
/**
* Hashing function for pairs based on hash_combine from boost The magic number
* is coming from the golden number @f[\phi = \frac{1 + \sqrt5}{2}@f]
* @f[\frac{2^32}{\phi} = 0x9e3779b9@f]
* http://stackoverflow.com/questions/4948780/magic-number-in-boosthash-combine
* http://burtleburtle.net/bob/hash/doobs.html
*/
template <typename a, typename b> struct hash<std::pair<a, b> > {
public:
hash() : ah(), bh() {}
size_t operator()(const std::pair<a, b> & p) const {
size_t seed = ah(p.first);
return bh(p.second) + AKANTU_HASH_COMBINE_MAGIC_NUMBER + (seed << 6) +
(seed >> 2);
}
private:
const hash<a> ah;
const hash<b> bh;
};
} //std
#endif /* __AKANTU_COMMON_HH__ */
diff --git a/src/common/aka_common_inline_impl.cc b/src/common/aka_common_inline_impl.cc
index 23509586e..820bb02c1 100644
--- a/src/common/aka_common_inline_impl.cc
+++ b/src/common/aka_common_inline_impl.cc
@@ -1,456 +1,456 @@
/**
* @file aka_common_inline_impl.cc
*
* @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 15 2015
*
* @brief inline implementations of common akantu type descriptions
*
* @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
*
* All common things to be included in the projects files
*
*/
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <cctype>
#include <iomanip>
#include <iostream>
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_COMMON_INLINE_IMPL_CC__
#define __AKANTU_AKA_COMMON_INLINE_IMPL_CC__
namespace akantu {
/* -------------------------------------------------------------------------- */
/// standard output stream operator for GhostType
inline std::ostream & operator<<(std::ostream & stream, GhostType type) {
switch (type) {
case _not_ghost:
stream << "not_ghost";
break;
case _ghost:
stream << "ghost";
break;
case _casper:
stream << "Casper the friendly ghost";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for TimeStepSolverType
inline std::ostream & operator<<(std::ostream & stream,
const TimeStepSolverType & type) {
switch (type) {
case _tsst_static:
stream << "static";
break;
case _tsst_dynamic:
stream << "dynamic";
break;
case _tsst_dynamic_lumped:
stream << "dynamic_lumped";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard input stream operator for TimeStepSolverType
inline std::istream & operator>>(std::istream & stream,
TimeStepSolverType & type) {
std::string str;
stream >> str;
if (str == "static")
type = _tsst_static;
else if (str == "dynamic")
type = _tsst_dynamic;
else if (str == "dynamic_lumped")
type = _tsst_dynamic_lumped;
else {
AKANTU_DEBUG_ERROR("The type "
<< str << " is not a recognized TimeStepSolverType");
stream.setstate(std::ios::failbit);
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for NonLinearSolverType
inline std::ostream & operator<<(std::ostream & stream,
const NonLinearSolverType & type) {
switch (type) {
case _nls_linear:
stream << "linear";
break;
case _nls_newton_raphson:
stream << "newton_raphson";
break;
case _nls_newton_raphson_modified:
stream << "newton_raphson_modified";
break;
case _nls_lumped:
stream << "lumped";
break;
case _nls_auto:
stream << "auto";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard input stream operator for NonLinearSolverType
inline std::istream & operator>>(std::istream & stream,
NonLinearSolverType & type) {
std::string str;
stream >> str;
if (str == "linear")
type = _nls_linear;
else if (str == "newton_raphson")
type = _nls_newton_raphson;
else if (str == "newton_raphson_modified")
type = _nls_newton_raphson_modified;
else if (str == "lumped")
type = _nls_lumped;
else if (str == "auto")
type = _nls_auto;
else
type = _nls_auto;
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for IntegrationSchemeType
inline std::ostream & operator<<(std::ostream & stream,
const IntegrationSchemeType & type) {
switch (type) {
case _ist_pseudo_time:
stream << "pseudo_time";
break;
case _ist_forward_euler:
stream << "forward_euler";
break;
case _ist_trapezoidal_rule_1:
stream << "trapezoidal_rule_1";
break;
case _ist_backward_euler:
stream << "backward_euler";
break;
case _ist_central_difference:
stream << "central_difference";
break;
case _ist_fox_goodwin:
stream << "fox_goodwin";
break;
case _ist_trapezoidal_rule_2:
stream << "trapezoidal_rule_2";
break;
case _ist_linear_acceleration:
stream << "linear_acceleration";
break;
case _ist_newmark_beta:
stream << "newmark_beta";
break;
case _ist_generalized_trapezoidal:
stream << "generalized_trapezoidal";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard input stream operator for IntegrationSchemeType
inline std::istream & operator>>(std::istream & stream,
IntegrationSchemeType & type) {
std::string str;
stream >> str;
if (str == "pseudo_time")
type = _ist_pseudo_time;
else if (str == "forward_euler")
type = _ist_forward_euler;
else if (str == "trapezoidal_rule_1")
type = _ist_trapezoidal_rule_1;
else if (str == "backward_euler")
type = _ist_backward_euler;
else if (str == "central_difference")
type = _ist_central_difference;
else if (str == "fox_goodwin")
type = _ist_fox_goodwin;
else if (str == "trapezoidal_rule_2")
type = _ist_trapezoidal_rule_2;
else if (str == "linear_acceleration")
type = _ist_linear_acceleration;
else if (str == "newmark_beta")
type = _ist_newmark_beta;
else if (str == "generalized_trapezoidal")
type = _ist_generalized_trapezoidal;
else {
AKANTU_DEBUG_ERROR("The type "
<< str << " is not a recognized IntegrationSchemeType");
stream.setstate(std::ios::failbit);
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for SynchronizationTag
inline std::ostream & operator<<(std::ostream & stream,
SynchronizationTag type) {
switch (type) {
case _gst_whatever:
stream << "_gst_whatever";
break;
case _gst_update:
stream << "_gst_update";
break;
case _gst_size:
stream << "_gst_size";
break;
case _gst_smm_mass:
stream << "_gst_smm_mass";
break;
case _gst_smm_for_gradu:
stream << "_gst_smm_for_gradu";
break;
case _gst_smm_boundary:
stream << "_gst_smm_boundary";
break;
case _gst_smm_uv:
stream << "_gst_smm_uv";
break;
case _gst_smm_res:
stream << "_gst_smm_res";
break;
case _gst_smm_init_mat:
stream << "_gst_smm_init_mat";
break;
case _gst_smm_stress:
stream << "_gst_smm_stress";
break;
case _gst_smmc_facets:
stream << "_gst_smmc_facets";
break;
case _gst_smmc_facets_conn:
stream << "_gst_smmc_facets_conn";
break;
case _gst_smmc_facets_stress:
stream << "_gst_smmc_facets_stress";
break;
case _gst_smmc_damage:
stream << "_gst_smmc_damage";
break;
case _gst_giu_global_conn:
stream << "_gst_giu_global_conn";
break;
case _gst_ce_groups:
stream << "_gst_ce_groups";
break;
case _gst_gm_clusters:
stream << "_gst_gm_clusters";
break;
case _gst_htm_capacity:
stream << "_gst_htm_capacity";
break;
case _gst_htm_temperature:
stream << "_gst_htm_temperature";
break;
case _gst_htm_gradient_temperature:
stream << "_gst_htm_gradient_temperature";
break;
case _gst_htm_phi:
stream << "_gst_htm_phi";
break;
case _gst_htm_gradient_phi:
stream << "_gst_htm_gradient_phi";
break;
case _gst_mnl_for_average:
stream << "_gst_mnl_for_average";
break;
case _gst_mnl_weight:
stream << "_gst_mnl_weight";
break;
case _gst_nh_criterion:
stream << "_gst_nh_criterion";
break;
case _gst_test:
stream << "_gst_test";
break;
case _gst_user_1:
stream << "_gst_user_1";
break;
case _gst_user_2:
stream << "_gst_user_2";
break;
case _gst_material_id:
stream << "_gst_material_id";
break;
case _gst_for_dump:
stream << "_gst_for_dump";
break;
case _gst_cf_nodal:
stream << "_gst_cf_nodal";
break;
case _gst_cf_incr:
stream << "_gst_cf_incr";
break;
case _gst_solver_solution:
stream << "_gst_solver_solution";
break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for SolveConvergenceCriteria
inline std::ostream & operator<<(std::ostream & stream,
const SolveConvergenceCriteria & criteria) {
switch (criteria) {
case _scc_residual:
stream << "_scc_residual";
break;
case _scc_solution:
stream << "_scc_solution";
break;
case _scc_residual_mass_wgh:
stream << "_scc_residual_mass_wgh";
break;
}
return stream;
}
inline std::istream & operator>>(std::istream & stream,
SolveConvergenceCriteria & criteria) {
std::string str;
stream >> str;
if (str == "residual")
criteria = _scc_residual;
else if (str == "solution")
criteria = _scc_solution;
else if (str == "residual_mass_wgh")
criteria = _scc_residual_mass_wgh;
else {
stream.setstate(std::ios::failbit);
}
return stream;
}
/* -------------------------------------------------------------------------- */
inline std::string to_lower(const std::string & str) {
std::string lstr = str;
std::transform(lstr.begin(), lstr.end(), lstr.begin(), (int (*)(int))tolower);
return lstr;
}
/* -------------------------------------------------------------------------- */
inline std::string trim(const std::string & to_trim) {
std::string trimed = to_trim;
// left trim
trimed.erase(trimed.begin(),
std::find_if(trimed.begin(), trimed.end(),
std::not1(std::ptr_fun<int, int>(isspace))));
// right trim
trimed.erase(std::find_if(trimed.rbegin(), trimed.rend(),
std::not1(std::ptr_fun<int, int>(isspace)))
.base(),
trimed.end());
return trimed;
}
-__END_AKANTU__
+} // akantu
#include <cmath>
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> std::string printMemorySize(UInt size) {
Real real_size = size * sizeof(T);
UInt mult = 0;
if (real_size != 0)
mult = (std::log(real_size) / std::log(2)) / 10;
std::stringstream sstr;
real_size /= Real(1 << (10 * mult));
sstr << std::setprecision(2) << std::fixed << real_size;
std::string size_prefix;
switch (mult) {
case 0:
sstr << "";
break;
case 1:
sstr << "Ki";
break;
case 2:
sstr << "Mi";
break;
case 3:
sstr << "Gi";
break; // I started on this type of machines
// (32bit computers) (Nicolas)
case 4:
sstr << "Ti";
break;
case 5:
sstr << "Pi";
break;
case 6:
sstr << "Ei";
break; // theoritical limit of RAM of the current
// computers in 2014 (64bit computers) (Nicolas)
case 7:
sstr << "Zi";
break;
case 8:
sstr << "Yi";
break;
default:
AKANTU_DEBUG_ERROR(
"The programmer in 2014 didn't thought so far (even wikipedia does not "
"go further)."
<< " You have at least 1024 times more than a yobibit of RAM!!!"
<< " Just add the prefix corresponding in this switch case.");
}
sstr << "Byte";
return sstr.str();
}
} // akantu
#endif /* __AKANTU_AKA_COMMON_INLINE_IMPL_CC__ */
diff --git a/src/common/aka_csr.hh b/src/common/aka_csr.hh
index 464e5ec2f..9e2d72a0b 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__
-__BEGIN_AKANTU__
+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.getSize() - 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){};
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;
// }
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_AKA_CSR_HH__ */
diff --git a/src/common/aka_element_classes_info.hh.in b/src/common/aka_element_classes_info.hh.in
index e71f120fc..8f7511918 100644
--- a/src/common/aka_element_classes_info.hh.in
+++ b/src/common/aka_element_classes_info.hh.in
@@ -1,199 +1,199 @@
/**
* @file aka_element_classes_info.hh.in
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Jul 19 2015
* @date last modification: Fri Oct 16 2015
*
* @brief Declaration of the enums for the element classes
*
* @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 <boost/preprocessor.hpp>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* Element Types */
/* -------------------------------------------------------------------------- */
/// @enum ElementType type of elements
enum ElementType {
_not_defined,
@AKANTU_ELEMENT_TYPES_ENUM@
_max_element_type
};
@AKANTU_ELEMENT_TYPES_BOOST_SEQ@
@AKANTU_ALL_ELEMENT_BOOST_SEQ@
/* -------------------------------------------------------------------------- */
/* Element Kinds */
/* -------------------------------------------------------------------------- */
@AKANTU_ELEMENT_KINDS_BOOST_SEQ@
@AKANTU_ELEMENT_KIND_BOOST_SEQ@
#ifndef SWIG
enum ElementKind {
BOOST_PP_SEQ_ENUM(AKANTU_ELEMENT_KIND),
_ek_not_defined
};
/* -------------------------------------------------------------------------- */
struct ElementKind_def {
using type = ElementKind;
static const type _begin_ = BOOST_PP_SEQ_HEAD(AKANTU_ELEMENT_KIND);
static const type _end_ = _ek_not_defined;
};
using element_kind_t = safe_enum<ElementKind_def> ;
#else
enum ElementKind;
#endif
/* -------------------------------------------------------------------------- */
/// @enum GeometricalType type of element potentially contained in a Mesh
enum GeometricalType {
@AKANTU_GEOMETRICAL_TYPES_ENUM@
_gt_not_defined
};
/* -------------------------------------------------------------------------- */
/* Interpolation Types */
/* -------------------------------------------------------------------------- */
@AKANTU_INTERPOLATION_TYPES_BOOST_SEQ@
#ifndef SWIG
/// @enum InterpolationType type of elements
enum InterpolationType {
BOOST_PP_SEQ_ENUM(AKANTU_INTERPOLATION_TYPES),
_itp_not_defined
};
#else
enum InterpolationType;
#endif
/* -------------------------------------------------------------------------- */
/* Some sub types less probable to change */
/* -------------------------------------------------------------------------- */
/// @enum GeometricalShapeType types of shapes to define the contains
/// function in the element classes
enum GeometricalShapeType {
@AKANTU_GEOMETRICAL_SHAPES_ENUM@
_gst_not_defined
};
/* -------------------------------------------------------------------------- */
/// @enum GaussIntegrationType classes of types using common
/// description of the gauss point position and weights
enum GaussIntegrationType {
@AKANTU_GAUSS_INTEGRATION_TYPES_ENUM@
_git_not_defined
};
/* -------------------------------------------------------------------------- */
/// @enum InterpolationKind the family of interpolation types
enum InterpolationKind {
@AKANTU_INTERPOLATION_KIND_ENUM@
_itk_not_defined
};
/* -------------------------------------------------------------------------- */
// BOOST PART: TOUCH ONLY IF YOU KNOW WHAT YOU ARE DOING
#define AKANTU_BOOST_CASE_MACRO(r,macro,_type) \
case _type : { macro(_type); break; }
#define AKANTU_BOOST_LIST_SWITCH(macro1, list1, var) \
do { \
switch(var) { \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, macro1, list1) \
default: { \
AKANTU_DEBUG_ERROR("Type (" << var << ") not handled by this function"); \
} \
} \
} while(0)
#define AKANTU_BOOST_ELEMENT_SWITCH(macro1, list1) \
AKANTU_BOOST_LIST_SWITCH(macro1, list1, type)
#define AKANTU_BOOST_ALL_ELEMENT_SWITCH(macro) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_BOOST_LIST_MACRO(r, macro, type) \
macro(type)
#define AKANTU_BOOST_APPLY_ON_LIST(macro, list) \
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_LIST_MACRO, macro, list)
#define AKANTU_BOOST_ALL_ELEMENT_LIST(macro) \
AKANTU_BOOST_APPLY_ON_LIST(macro, \
AKANTU_ALL_ELEMENT_TYPE)
#define AKANTU_GET_ELEMENT_LIST(kind) \
AKANTU##kind##_ELEMENT_TYPE
#define AKANTU_BOOST_KIND_ELEMENT_SWITCH(macro, kind) \
AKANTU_BOOST_ELEMENT_SWITCH(macro, \
AKANTU_GET_ELEMENT_LIST(kind))
// BOOST_PP_SEQ_TO_LIST does not exists in Boost < 1.49
#define AKANTU_GENERATE_KIND_LIST(seq) \
BOOST_PP_TUPLE_TO_LIST(BOOST_PP_SEQ_SIZE(seq), \
BOOST_PP_SEQ_TO_TUPLE(seq))
#define AKANTU_ELEMENT_KIND_BOOST_LIST AKANTU_GENERATE_KIND_LIST(AKANTU_ELEMENT_KIND)
#define AKANTU_BOOST_ALL_KIND_LIST(macro, list) \
BOOST_PP_LIST_FOR_EACH(AKANTU_BOOST_LIST_MACRO, macro, list)
#define AKANTU_BOOST_ALL_KIND(macro) \
AKANTU_BOOST_ALL_KIND_LIST(macro, AKANTU_ELEMENT_KIND_BOOST_LIST)
#define AKANTU_BOOST_ALL_KIND_SWITCH(macro) \
AKANTU_BOOST_LIST_SWITCH(macro, \
AKANTU_ELEMENT_KIND, \
kind)
@AKANTU_ELEMENT_KINDS_BOOST_MACROS@
// /// define kept for compatibility reasons (they are most probably not needed
// /// anymore) \todo check if they can be removed
// #define AKANTU_REGULAR_ELEMENT_TYPE AKANTU_ek_regular_ELEMENT_TYPE
// #define AKANTU_COHESIVE_ELEMENT_TYPE AKANTU_ek_cohesive_ELEMENT_TYPE
// #define AKANTU_STRUCTURAL_ELEMENT_TYPE AKANTU_ek_structural_ELEMENT_TYPE
// #define AKANTU_IGFEM_ELEMENT_TYPE AKANTU_ek_igfem_ELEMENT_TYPE
/* -------------------------------------------------------------------------- */
/* Lists of interests for FEEngineTemplate functions */
/* -------------------------------------------------------------------------- */
@AKANTU_FE_ENGINE_LISTS@
-__END_AKANTU__
+} // akantu
#include "aka_element_classes_info_inline_impl.cc"
diff --git a/src/common/aka_element_classes_info_inline_impl.cc b/src/common/aka_element_classes_info_inline_impl.cc
index e9d7877ec..39320f2fd 100644
--- a/src/common/aka_element_classes_info_inline_impl.cc
+++ b/src/common/aka_element_classes_info_inline_impl.cc
@@ -1,96 +1,96 @@
/**
* @file aka_element_classes_info_inline_impl.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Jun 18 2015
* @date last modification: Sun Jul 19 2015
*
* @brief Implementation of the streaming fonction for the element classes enums
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
#define STRINGIFY(type) \
stream << BOOST_PP_STRINGIZE(type)
/* -------------------------------------------------------------------------- */
//! standard output stream operator for ElementType
inline std::ostream & operator <<(std::ostream & stream, ElementType type) {
switch(type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, \
STRINGIFY, \
AKANTU_ALL_ELEMENT_TYPE)
case _not_defined: stream << "_not_defined"; break;
case _max_element_type: stream << "_max_element_type"; break;
}
return stream;
}
/* -------------------------------------------------------------------------- */
//! standard input stream operator for ElementType
inline std::istream & operator >>(std::istream & stream, ElementType & type) {
#define IF_SEQUENCE(_type) \
else if (tmp == BOOST_PP_STRINGIZE(_type)) type = _type;
std::string tmp;
stream >> tmp;
if (1 == 2) {}
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_LIST_MACRO, \
IF_SEQUENCE, \
AKANTU_ALL_ELEMENT_TYPE)
else AKANTU_EXCEPTION("unknown element type: '" << tmp << "'");
#undef IF_SEQUENCE
return stream;
}
/* -------------------------------------------------------------------------- */
//! standard output stream operator for ElementType
inline std::ostream & operator <<(std::ostream & stream, ElementKind kind ) {
AKANTU_BOOST_ALL_KIND_SWITCH(STRINGIFY);
return stream;
}
/* -------------------------------------------------------------------------- */
/// standard output stream operator for InterpolationType
inline std::ostream & operator <<(std::ostream & stream, InterpolationType type)
{
switch(type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_BOOST_CASE_MACRO, \
STRINGIFY, \
AKANTU_INTERPOLATION_TYPES)
case _itp_not_defined : stream << "_itp_not_defined" ; break;
}
return stream;
}
#undef STRINGIFY
-__END_AKANTU__
+} // akantu
diff --git a/src/common/aka_event_handler_manager.hh b/src/common/aka_event_handler_manager.hh
index 0d47d5c80..ae60d0671 100644
--- a/src/common/aka_event_handler_manager.hh
+++ b/src/common/aka_event_handler_manager.hh
@@ -1,129 +1,129 @@
/**
* @file aka_event_handler_manager.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Dec 16 2015
*
* @brief Base of Event Handler 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_AKA_EVENT_HANDLER_MANAGER_HH__
#define __AKANTU_AKA_EVENT_HANDLER_MANAGER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#include <list>
#include <algorithm>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
template <class EventHandler> class EventHandlerManager {
private:
typedef std::pair<UInt, EventHandler *> priority_value;
typedef std::list<priority_value> priority_list;
struct KeyComp {
bool operator()(const priority_value & a, const priority_value & b) const {
return (a.first < b.first);
}
bool operator()(const priority_value & a, UInt b) const {
return (a.first < b);
}
};
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
virtual ~EventHandlerManager(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register a new EventHandler to the Manager. The register object
/// will then be informed about the events the manager observes.
void registerEventHandler(EventHandler & event_handler, UInt priority = 100) {
typename priority_list::iterator it =
this->searchEventHandler(event_handler);
if (it != this->event_handlers.end()) {
AKANTU_EXCEPTION("This event handler was already registered");
}
typename priority_list::iterator pos =
std::lower_bound(this->event_handlers.begin(),
this->event_handlers.end(), priority, KeyComp());
this->event_handlers.insert(pos, std::make_pair(priority, &event_handler));
}
/// unregister a EventHandler object. This object will not be
/// notified anymore about the events this manager observes.
void unregisterEventHandler(EventHandler & event_handler) {
typename priority_list::iterator it =
this->searchEventHandler(event_handler);
if (it == this->event_handlers.end()) {
AKANTU_EXCEPTION("This event handler is not registered");
}
this->event_handlers.erase(it);
}
/// Notify all the registered EventHandlers about the event that just occured.
template <class Event> void sendEvent(const Event & event) {
typename priority_list::iterator it = event_handlers.begin();
typename priority_list::iterator end = event_handlers.end();
for (; it != end; ++it)
it->second->sendEvent(event);
}
private:
typename priority_list::iterator searchEventHandler(EventHandler & handler) {
typename priority_list::iterator it = this->event_handlers.begin();
typename priority_list::iterator end = this->event_handlers.end();
for (; it != end && it->second != &handler; ++it)
;
return it;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// list of the event handlers
priority_list event_handlers;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_AKA_EVENT_HANDLER_MANAGER_HH__ */
diff --git a/src/common/aka_grid_dynamic.hh b/src/common/aka_grid_dynamic.hh
index c1758cf2f..b69b5700d 100644
--- a/src/common/aka_grid_dynamic.hh
+++ b/src/common/aka_grid_dynamic.hh
@@ -1,507 +1,507 @@
/**
* @file aka_grid_dynamic.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Sat Sep 26 2015
*
* @brief Grid that is auto balanced
*
* @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_array.hh"
#include "aka_types.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_AKA_GRID_DYNAMIC_HH__
#define __AKANTU_AKA_GRID_DYNAMIC_HH__
-__BEGIN_AKANTU__
+namespace akantu {
class Mesh;
template<typename T>
class SpatialGrid {
public:
SpatialGrid(UInt dimension) : dimension(dimension),
spacing(dimension),
center(dimension),
lower(dimension),
upper(dimension),
empty_cell() {}
SpatialGrid(UInt dimension,
const Vector<Real> & spacing,
const Vector<Real> & center) : dimension(dimension),
spacing(spacing),
center(center),
lower(dimension),
upper(dimension),
empty_cell() {
for (UInt i = 0; i < dimension; ++i) {
lower(i) = std::numeric_limits<Real>::max();
upper(i) = - std::numeric_limits<Real>::max();
}
}
virtual ~SpatialGrid() {};
class neighbor_cells_iterator;
class cells_iterator;
class CellID {
public:
CellID() : ids() {}
CellID(UInt dimention) : ids(dimention) {}
void setID(UInt dir, Int id) { ids(dir) = id; }
Int getID(UInt dir) const { return ids(dir); }
bool operator<(const CellID & id) const {
return std::lexicographical_compare(ids.storage(), ids.storage() + ids.size(),
id.ids.storage(), id.ids.storage() + id.ids.size());
}
bool operator==(const CellID & id) const {
return std::equal(ids.storage(), ids.storage() + ids.size(),
id.ids.storage());
}
bool operator!=(const CellID & id) const {
return !(operator==(id));
}
private:
friend class neighbor_cells_iterator;
friend class cells_iterator;
Vector<Int> ids;
};
/* -------------------------------------------------------------------------- */
class Cell {
public:
typedef typename std::vector<T>::iterator iterator;
typedef typename std::vector<T>::const_iterator const_iterator;
Cell() : id(), data() { }
Cell(const CellID &cell_id) : id(cell_id), data() { }
bool operator==(const Cell & cell) const { return id == cell.id; }
bool operator!=(const Cell & cell) const { return id != cell.id; }
Cell & add(const T & d) { data.push_back(d); return *this; }
iterator begin() { return data.begin(); }
const_iterator begin() const { return data.begin(); }
iterator end() { return data.end(); }
const_iterator end() const { return data.end(); }
// #if not defined(AKANTU_NDEBUG)
// Cell & add(const T & d, const Vector<Real> & pos) {
// data.push_back(d); positions.push_back(pos); return *this;
// }
// typedef typename std::vector< Vector<Real> >::const_iterator position_iterator;
// position_iterator begin_pos() const { return positions.begin(); }
// position_iterator end_pos() const { return positions.end(); }
// #endif
private:
CellID id;
std::vector<T> data;
// #if not defined(AKANTU_NDEBUG)
// std::vector< Vector<Real> > positions;
// #endif
};
private:
typedef std::map<CellID, Cell> cells_container;
public:
const Cell & getCell(const CellID & cell_id) const {
typename cells_container::const_iterator it = cells.find(cell_id);
if(it != cells.end()) return it->second;
else return empty_cell;
}
typename Cell::iterator beginCell(const CellID & cell_id) {
typename cells_container::iterator it = cells.find(cell_id);
if(it != cells.end()) return it->second.begin();
else return empty_cell.begin();
}
typename Cell::iterator endCell(const CellID & cell_id) {
typename cells_container::iterator it = cells.find(cell_id);
if(it != cells.end()) return it->second.end();
else return empty_cell.end();
}
typename Cell::const_iterator beginCell(const CellID & cell_id) const {
typename cells_container::const_iterator it = cells.find(cell_id);
if(it != cells.end()) return it->second.begin();
else return empty_cell.begin();
}
typename Cell::const_iterator endCell(const CellID & cell_id) const {
typename cells_container::const_iterator it = cells.find(cell_id);
if(it != cells.end()) return it->second.end();
else return empty_cell.end();
}
class neighbor_cells_iterator : private std::iterator<std::forward_iterator_tag, UInt> {
public:
neighbor_cells_iterator(const CellID & cell_id, bool end) :
cell_id(cell_id),
position(cell_id.ids.size(), end ? 1 : -1) {
this->updateIt();
if(end) this->it++;
}
neighbor_cells_iterator& operator++() {
UInt i = 0;
for (; i < position.size() && position(i) == 1; ++i);
if(i == position.size()) ++it;
else {
for (UInt j = 0; j < i; ++j) position(j) = -1;
position(i)++;
updateIt();
}
return *this;
}
neighbor_cells_iterator operator++(int) { neighbor_cells_iterator tmp(*this); operator++(); return tmp; };
bool operator==(const neighbor_cells_iterator& rhs) const { return cell_id == rhs.cell_id && it == rhs.it; };
bool operator!=(const neighbor_cells_iterator& rhs) const { return ! operator==(rhs); };
CellID operator*() const {
CellID cur_cell_id(cell_id);
cur_cell_id.ids += position;
return cur_cell_id;
};
private:
void updateIt() {
it = 0;
for (UInt i = 0; i < position.size(); ++i) it = it * 3 + (position(i) + 1);
}
private:
/// central cell id
const CellID & cell_id;
// number representing the current neighbor in base 3;
UInt it;
Vector<Int> position;
};
class cells_iterator : private std::iterator<std::forward_iterator_tag, CellID> {
public:
cells_iterator(typename std::map<CellID, Cell>::const_iterator it) :
it(it) { }
cells_iterator & operator++() {
this->it++;
return *this;
}
cells_iterator operator++(int) {cells_iterator tmp(*this); operator++(); return tmp; };
bool operator==(const cells_iterator& rhs) const { return it == rhs.it; };
bool operator!=(const cells_iterator& rhs) const { return ! operator==(rhs); };
CellID operator*() const {
CellID cur_cell_id(this->it->first);
return cur_cell_id;
};
private:
/// map iterator
typename std::map<CellID, Cell>::const_iterator it;
};
public:
template<class vector_type>
Cell & insert(const T & d, const vector_type & position) {
CellID cell_id = getCellID(position);
typename cells_container::iterator it = cells.find(cell_id);
if(it == cells.end()) {
Cell cell(cell_id);
// #if defined(AKANTU_NDEBUG)
Cell & tmp = (cells[cell_id] = cell).add(d);
// #else
// Cell & tmp = (cells[cell_id] = cell).add(d, position);
// #endif
for (UInt i = 0; i < dimension; ++i) {
Real posl = center(i) + cell_id.getID(i) * spacing(i);
Real posu = posl + spacing(i);
if(posl < lower(i)) lower(i) = posl;
if(posu > upper(i)) upper(i) = posu;
}
return tmp;
} else {
// #if defined(AKANTU_NDEBUG)
return it->second.add(d);
// #else
// return it->second.add(d, position);
// #endif
}
}
inline neighbor_cells_iterator beginNeighborCells(const CellID & cell_id) const {
return neighbor_cells_iterator(cell_id, false);
}
inline neighbor_cells_iterator endNeighborCells(const CellID & cell_id) const {
return neighbor_cells_iterator(cell_id, true);
}
inline cells_iterator beginCells() const {
typename std::map<CellID, Cell>::const_iterator begin = this->cells.begin();
return cells_iterator(begin);
}
inline cells_iterator endCells() const {
typename std::map<CellID, Cell>::const_iterator end = this->cells.end();
return cells_iterator(end);
}
template<class vector_type>
CellID getCellID(const vector_type & position) const {
CellID cell_id(dimension);
for (UInt i = 0; i < dimension; ++i) {
cell_id.setID(i, getCellID(position(i), i));
}
return cell_id;
}
void printself(std::ostream & stream, int indent = 0) 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(5);
stream << space << "SpatialGrid<" << debug::demangle(typeid(T).name()) << "> [" << std::endl;
stream << space << " + dimension : " << this->dimension << std::endl;
stream << space << " + lower bounds : {";
for (UInt i = 0; i < lower.size(); ++i) { if(i != 0) stream << ", "; stream << lower(i); };
stream << "}" << std::endl;
stream << space << " + upper bounds : {";
for (UInt i = 0; i < upper.size(); ++i) { if(i != 0) stream << ", "; stream << upper(i); };
stream << "}" << std::endl;
stream << space << " + spacing : {";
for (UInt i = 0; i < spacing.size(); ++i) { if(i != 0) stream << ", "; stream << spacing(i); };
stream << "}" << std::endl;
stream << space << " + center : {";
for (UInt i = 0; i < center.size(); ++i) { if(i != 0) stream << ", "; stream << center(i); };
stream << "}" << std::endl;
stream << space << " + nb_cells : " << this->cells.size() << "/";
Vector<Real> dist(this->dimension);
dist = upper;
dist -= lower;
for (UInt i = 0; i < this->dimension; ++i) {
dist(i) /= spacing(i);
}
UInt nb_cells = std::ceil(dist(0));
for (UInt i = 1; i < this->dimension; ++i) {
nb_cells *= std::ceil(dist(i));
}
stream << nb_cells << std::endl;
stream << space << "]" << std::endl;
stream.precision(prec);
stream.flags(ff);
}
void saveAsMesh(Mesh & mesh) const;
private:
/* -------------------------------------------------------------------------- */
inline UInt getCellID(Real position, UInt direction) const {
AKANTU_DEBUG_ASSERT(direction < center.size(), "The direction asked ("
<< direction << ") is out of range " << center.size());
Real dist_center = position - center(direction);
Int id = std::floor(dist_center / spacing(direction));
//if(dist_center < 0) id--;
return id;
}
friend class GridSynchronizer;
public:
AKANTU_GET_MACRO(LowerBounds, lower, const Vector<Real> &);
AKANTU_GET_MACRO(UpperBounds, upper, const Vector<Real> &);
AKANTU_GET_MACRO(Spacing, spacing, const Vector<Real> &);
protected:
UInt dimension;
cells_container cells;
Vector<Real> spacing;
Vector<Real> center;
Vector<Real> lower;
Vector<Real> upper;
Cell empty_cell;
};
/// standard output stream operator
template<typename T>
inline std::ostream & operator <<(std::ostream & stream, const SpatialGrid<T> & _this)
{
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#include "mesh.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<typename T>
void SpatialGrid<T>::saveAsMesh(Mesh & mesh) const {
Array<Real> & nodes = const_cast<Array<Real> &>(mesh.getNodes());
ElementType type;
switch(dimension) {
case 1: type = _segment_2; break;
case 2: type = _quadrangle_4; break;
case 3: type = _hexahedron_8; break;
}
mesh.addConnectivityType(type);
Array<UInt> & connectivity = const_cast<Array<UInt> &>(mesh.getConnectivity(type));
Array<UInt> & uint_data = *mesh.getDataPointer<UInt>("tag_1", type);
typename cells_container::const_iterator it = cells.begin();
typename cells_container::const_iterator end = cells.end();
Vector<Real> pos(dimension);
UInt global_id = 0;
for (;it != end; ++it, ++global_id) {
UInt cur_node = nodes.getSize();
UInt cur_elem = connectivity.getSize();
const CellID & cell_id = it->first;
for (UInt i = 0; i < dimension; ++i) pos(i) = center(i) + cell_id.getID(i) * spacing(i);
nodes.push_back(pos);
for (UInt i = 0; i < dimension; ++i) pos(i) += spacing(i);
nodes.push_back(pos);
connectivity.push_back(cur_node);
switch(dimension) {
case 1:
connectivity(cur_elem, 1) = cur_node + 1;
break;
case 2:
pos(0) -= spacing(0); nodes.push_back(pos);
pos(0) += spacing(0); pos(1) -= spacing(1); nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 3;
connectivity(cur_elem, 2) = cur_node + 1;
connectivity(cur_elem, 3) = cur_node + 2;
break;
case 3:
pos(1) -= spacing(1); pos(2) -= spacing(2); nodes.push_back(pos);
pos(1) += spacing(1); nodes.push_back(pos);
pos(0) -= spacing(0); nodes.push_back(pos);
pos(1) -= spacing(1); pos(2) += spacing(2); nodes.push_back(pos);
pos(0) += spacing(0); nodes.push_back(pos);
pos(0) -= spacing(0); pos(1) += spacing(1); nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 2;
connectivity(cur_elem, 2) = cur_node + 3;
connectivity(cur_elem, 3) = cur_node + 4;
connectivity(cur_elem, 4) = cur_node + 5;
connectivity(cur_elem, 5) = cur_node + 6;
connectivity(cur_elem, 6) = cur_node + 1;
connectivity(cur_elem, 7) = cur_node + 7;
break;
}
uint_data.push_back(global_id);
}
// #if not defined(AKANTU_NDEBUG)
// mesh.addConnectivityType(_point_1);
// Array<UInt> & connectivity_pos = const_cast<Array<UInt> &>(mesh.getConnectivity(_point_1));
// Array<UInt> & uint_data_pos = *mesh.getDataPointer<UInt>( "tag_1", _point_1);
// Array<UInt> & uint_data_pos_ghost = *mesh.getDataPointer<UInt>("tag_0", _point_1);
// it = cells.begin();
// global_id = 0;
// for (;it != end; ++it, ++global_id) {
// typename Cell::position_iterator cell_it = it->second.begin_pos();
// typename Cell::const_iterator cell_it_cont = it->second.begin();
// typename Cell::position_iterator cell_end = it->second.end_pos();
// for (;cell_it != cell_end; ++cell_it, ++cell_it_cont) {
// nodes.push_back(*cell_it);
// connectivity_pos.push_back(nodes.getSize()-1);
// uint_data_pos.push_back(global_id);
// uint_data_pos_ghost.push_back(cell_it_cont->ghost_type==_ghost);
// }
// }
// #endif
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_AKA_GRID_DYNAMIC_HH__ */
diff --git a/src/common/aka_math.cc b/src/common/aka_math.cc
index 3129d10ca..ae03ed59a 100644
--- a/src/common/aka_math.cc
+++ b/src/common/aka_math.cc
@@ -1,251 +1,251 @@
/**
* @file aka_math.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@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 Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Fri May 15 2015
*
* @brief Implementation of the math toolbox
*
* @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_math.hh"
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
void Math::matrix_vector(UInt m, UInt n, const Array<Real> & A,
const Array<Real> & x, Array<Real> & y, Real alpha) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(A.getSize() == x.getSize(),
"The vector A(" << A.getID() << ") and the vector x("
<< x.getID()
<< ") must have the same size");
AKANTU_DEBUG_ASSERT(A.getNbComponent() == m * n,
"The vector A(" << A.getID()
<< ") has the good number of component.");
AKANTU_DEBUG_ASSERT(
x.getNbComponent() == n,
"The vector x(" << x.getID() << ") do not the good number of component.");
AKANTU_DEBUG_ASSERT(
y.getNbComponent() == n,
"The vector y(" << y.getID() << ") do not the good number of component.");
UInt nb_element = A.getSize();
UInt offset_A = A.getNbComponent();
UInt offset_x = x.getNbComponent();
y.resize(nb_element);
Real * A_val = A.storage();
Real * x_val = x.storage();
Real * y_val = y.storage();
for (UInt el = 0; el < nb_element; ++el) {
matrix_vector(m, n, A_val, x_val, y_val, alpha);
A_val += offset_A;
x_val += offset_x;
y_val += offset_x;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Math::matrix_matrix(UInt m, UInt n, UInt k, const Array<Real> & A,
const Array<Real> & B, Array<Real> & C, Real alpha) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(A.getSize() == B.getSize(),
"The vector A(" << A.getID() << ") and the vector B("
<< B.getID()
<< ") must have the same size");
AKANTU_DEBUG_ASSERT(A.getNbComponent() == m * k,
"The vector A(" << A.getID()
<< ") has the good number of component.");
AKANTU_DEBUG_ASSERT(
B.getNbComponent() == k * n,
"The vector B(" << B.getID() << ") do not the good number of component.");
AKANTU_DEBUG_ASSERT(
C.getNbComponent() == m * n,
"The vector C(" << C.getID() << ") do not the good number of component.");
UInt nb_element = A.getSize();
UInt offset_A = A.getNbComponent();
UInt offset_B = B.getNbComponent();
UInt offset_C = C.getNbComponent();
C.resize(nb_element);
Real * A_val = A.storage();
Real * B_val = B.storage();
Real * C_val = C.storage();
for (UInt el = 0; el < nb_element; ++el) {
matrix_matrix(m, n, k, A_val, B_val, C_val, alpha);
A_val += offset_A;
B_val += offset_B;
C_val += offset_C;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Math::matrix_matrixt(UInt m, UInt n, UInt k, const Array<Real> & A,
const Array<Real> & B, Array<Real> & C, Real alpha) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(A.getSize() == B.getSize(),
"The vector A(" << A.getID() << ") and the vector B("
<< B.getID()
<< ") must have the same size");
AKANTU_DEBUG_ASSERT(A.getNbComponent() == m * k,
"The vector A(" << A.getID()
<< ") has the good number of component.");
AKANTU_DEBUG_ASSERT(
B.getNbComponent() == k * n,
"The vector B(" << B.getID() << ") do not the good number of component.");
AKANTU_DEBUG_ASSERT(
C.getNbComponent() == m * n,
"The vector C(" << C.getID() << ") do not the good number of component.");
UInt nb_element = A.getSize();
UInt offset_A = A.getNbComponent();
UInt offset_B = B.getNbComponent();
UInt offset_C = C.getNbComponent();
C.resize(nb_element);
Real * A_val = A.storage();
Real * B_val = B.storage();
Real * C_val = C.storage();
for (UInt el = 0; el < nb_element; ++el) {
matrix_matrixt(m, n, k, A_val, B_val, C_val, alpha);
A_val += offset_A;
B_val += offset_B;
C_val += offset_C;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Math::compute_tangents(const Array<Real> & normals,
Array<Real> & tangents) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = normals.getNbComponent();
UInt tangent_components = spatial_dimension * (spatial_dimension - 1);
AKANTU_DEBUG_ASSERT(
tangent_components == tangents.getNbComponent(),
"Cannot compute the tangents, the storage array for tangents"
<< " does not have the good amount of components.");
UInt nb_normals = normals.getSize();
tangents.resize(nb_normals);
Real * normal_it = normals.storage();
Real * tangent_it = tangents.storage();
/// compute first tangent
for (UInt q = 0; q < nb_normals; ++q) {
/// if normal is orthogonal to xy plane, arbitrarly define tangent
if (Math::are_float_equal(Math::norm2(normal_it), 0))
tangent_it[0] = 1;
else
Math::normal2(normal_it, tangent_it);
normal_it += spatial_dimension;
tangent_it += tangent_components;
}
/// compute second tangent (3D case)
if (spatial_dimension == 3) {
normal_it = normals.storage();
tangent_it = tangents.storage();
for (UInt q = 0; q < nb_normals; ++q) {
Math::normal3(normal_it, tangent_it, tangent_it + spatial_dimension);
normal_it += spatial_dimension;
tangent_it += tangent_components;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real Math::reduce(Array<Real> & array) {
UInt nb_values = array.getSize();
if (nb_values == 0)
return 0.;
UInt nb_values_to_sum = nb_values >> 1;
std::sort(array.begin(), array.end());
// as long as the half is not empty
while (nb_values_to_sum) {
UInt remaining = (nb_values - 2 * nb_values_to_sum);
if (remaining)
array(nb_values - 2) += array(nb_values - 1);
// sum to consecutive values and store the sum in the first half
for (UInt i = 0; i < nb_values_to_sum; ++i) {
array(i) = array(2 * i) + array(2 * i + 1);
}
nb_values = nb_values_to_sum;
nb_values_to_sum >>= 1;
}
return array(0);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/common/aka_math.hh b/src/common/aka_math.hh
index 44389f462..18409e62b 100644
--- a/src/common/aka_math.hh
+++ b/src/common/aka_math.hh
@@ -1,291 +1,291 @@
/**
* @file aka_math.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Fri May 15 2015
*
* @brief mathematical operations
*
* @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_AKA_MATH_H__
#define __AKANTU_AKA_MATH_H__
/* -------------------------------------------------------------------------- */
#include <utility>
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, bool is_scal> class Array;
class Math {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Matrix algebra */
/* ------------------------------------------------------------------------ */
/// @f$ y = A*x @f$
static void matrix_vector(UInt m, UInt n, const Array<Real, true> & A,
const Array<Real, true> & x, Array<Real, true> & y,
Real alpha = 1.);
/// @f$ y = A*x @f$
static inline void matrix_vector(UInt m, UInt n, Real * A, Real * x, Real * y,
Real alpha = 1.);
/// @f$ y = A^t*x @f$
static inline void matrixt_vector(UInt m, UInt n, Real * A, Real * x,
Real * y, Real alpha = 1.);
/// @f$ C = A*B @f$
static void matrix_matrix(UInt m, UInt n, UInt k, const Array<Real, true> & A,
const Array<Real, true> & B, Array<Real, true> & C,
Real alpha = 1.);
/// @f$ C = A*B^t @f$
static void matrix_matrixt(UInt m, UInt n, UInt k,
const Array<Real, true> & A,
const Array<Real, true> & B, Array<Real, true> & C,
Real alpha = 1.);
/// @f$ C = A*B @f$
static inline void matrix_matrix(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
/// @f$ C = A^t*B @f$
static inline void matrixt_matrix(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
/// @f$ C = A*B^t @f$
static inline void matrix_matrixt(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
/// @f$ C = A^t*B^t @f$
static inline void matrixt_matrixt(UInt m, UInt n, UInt k, Real * A, Real * B,
Real * C, Real alpha = 1.);
template <bool tr_A, bool tr_B>
static inline void matMul(UInt m, UInt n, UInt k, Real alpha, Real * A,
Real * B, Real beta, Real * C);
template <bool tr_A>
static inline void matVectMul(UInt m, UInt n, Real alpha, Real * A, Real * x,
Real beta, Real * y);
static inline void aXplusY(UInt n, Real alpha, Real * x, Real * y);
static inline void matrix33_eigenvalues(Real * A, Real * Adiag);
static inline void matrix22_eigenvalues(Real * A, Real * Adiag);
template <UInt dim> static inline void eigenvalues(Real * A, Real * d);
/// solve @f$ A x = \Lambda x @f$ and return d and V such as @f$ A V[i:] =
/// d[i] V[i:]@f$
template <typename T>
static void matrixEig(UInt n, T * A, T * d, T * V = nullptr);
/// determinent of a 2x2 matrix
static inline Real det2(const Real * mat);
/// determinent of a 3x3 matrix
static inline Real det3(const Real * mat);
/// determinent of a nxn matrix
template <UInt n> static inline Real det(const Real * mat);
/// determinent of a nxn matrix
template <typename T> static inline T det(UInt n, const T * mat);
/// inverse a nxn matrix
template <UInt n> static inline void inv(const Real * mat, Real * inv);
/// inverse a nxn matrix
template <typename T> static inline void inv(UInt n, const T * mat, T * inv);
/// inverse a 3x3 matrix
static inline void inv3(const Real * mat, Real * inv);
/// inverse a 2x2 matrix
static inline void inv2(const Real * mat, Real * inv);
/// solve A x = b using a LU factorization
template <typename T>
static inline void solve(UInt n, const T * A, T * x, const T * b);
/// return the double dot product between 2 tensors in 2d
static inline Real matrixDoubleDot22(Real * A, Real * B);
/// return the double dot product between 2 tensors in 3d
static inline Real matrixDoubleDot33(Real * A, Real * B);
/// extension of the double dot product to two 2nd order tensor in dimension n
static inline Real matrixDoubleDot(UInt n, Real * A, Real * B);
/* ------------------------------------------------------------------------ */
/* Array algebra */
/* ------------------------------------------------------------------------ */
/// vector cross product
static inline void vectorProduct3(const Real * v1, const Real * v2,
Real * res);
/// normalize a vector
static inline void normalize2(Real * v);
/// normalize a vector
static inline void normalize3(Real * v);
/// return norm of a 2-vector
static inline Real norm2(const Real * v);
/// return norm of a 3-vector
static inline Real norm3(const Real * v);
/// return norm of a vector
static inline Real norm(UInt n, const Real * v);
/// return the dot product between 2 vectors in 2d
static inline Real vectorDot2(const Real * v1, const Real * v2);
/// return the dot product between 2 vectors in 3d
static inline Real vectorDot3(const Real * v1, const Real * v2);
/// return the dot product between 2 vectors
static inline Real vectorDot(Real * v1, Real * v2, UInt n);
/* ------------------------------------------------------------------------ */
/* Geometry */
/* ------------------------------------------------------------------------ */
/// compute normal a normal to a vector
static inline void normal2(const Real * v1, Real * res);
/// compute normal a normal to a vector
static inline void normal3(const Real * v1, const Real * v2, Real * res);
/// compute the tangents to an array of normal vectors
static void compute_tangents(const Array<Real> & normals,
Array<Real> & tangents);
/// distance in 2D between x and y
static inline Real distance_2d(const Real * x, const Real * y);
/// distance in 3D between x and y
static inline Real distance_3d(const Real * x, const Real * y);
/// radius of the in-circle of a triangle
static inline Real triangle_inradius(const Real * coord1, const Real * coord2,
const Real * coord3);
/// radius of the in-circle of a tetrahedron
static inline Real tetrahedron_inradius(const Real * coord1,
const Real * coord2,
const Real * coord3,
const Real * coord4);
/// volume of a tetrahedron
static inline Real tetrahedron_volume(const Real * coord1,
const Real * coord2,
const Real * coord3,
const Real * coord4);
/// compute the barycenter of n points
static inline void barycenter(const Real * coord, UInt nb_points,
UInt spatial_dimension, Real * barycenter);
/// vector between x and y
static inline void vector_2d(const Real * x, const Real * y, Real * vec);
/// vector pointing from x to y in 3 spatial dimension
static inline void vector_3d(const Real * x, const Real * y, Real * vec);
/// test if two scalar are equal within a given tolerance
static inline bool are_float_equal(Real x, Real y);
/// test if two vectors are equal within a given tolerance
static inline bool are_vector_equal(UInt n, Real * x, Real * y);
#ifdef isnan
#error \
"You probably included <math.h> which is incompatible with aka_math please use\
<cmath> or add a \"#undef isnan\" before akantu includes"
#endif
/// test if a real is a NaN
static inline bool isnan(Real x);
/// test if the line x and y intersects each other
static inline bool intersects(Real x_min, Real x_max, Real y_min, Real y_max);
/// test if a is in the range [x_min, x_max]
static inline bool is_in_range(Real a, Real x_min, Real x_max);
static inline Real getTolerance() { return tolerance; };
static inline void setTolerance(Real tol) { tolerance = tol; };
template <UInt p, typename T> static inline T pow(T x);
/// reduce all the values of an array, the summation is done in place and the
/// array is modified
static Real reduce(Array<Real> & array);
class NewtonRaphson {
public:
NewtonRaphson(Real tolerance, Real max_iteration)
: tolerance(tolerance), max_iteration(max_iteration) {}
template <class Functor> Real solve(const Functor & funct, Real x_0);
private:
Real tolerance;
Real max_iteration;
};
struct NewtonRaphsonFunctor {
NewtonRaphsonFunctor(std::string name) : name(std::move(name)) {}
virtual Real f(Real x) const = 0;
virtual Real f_prime(Real x) const = 0;
std::string name;
};
private:
/// tolerance for functions that need one
static Real tolerance;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "aka_math_tmpl.hh"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_AKA_MATH_H__ */
diff --git a/src/common/aka_math_tmpl.hh b/src/common/aka_math_tmpl.hh
index 18f64791e..ebf148bfb 100644
--- a/src/common/aka_math_tmpl.hh
+++ b/src/common/aka_math_tmpl.hh
@@ -1,786 +1,786 @@
/**
* @file aka_math_tmpl.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Mathilde Radiguet <mathilde.radiguet@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Leonardo Snozzi <leonardo.snozzi@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Aug 04 2010
* @date last modification: Wed Oct 21 2015
*
* @brief Implementation of the inline functions of the math toolkit
*
* @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/>.
*
*/
-__END_AKANTU__
+} // akantu
#include <cmath>
#include <cstring>
#include <typeinfo>
#include "aka_blas_lapack.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
inline void Math::matrix_vector(UInt im, UInt in, Real * A, Real * x, Real * y,
Real alpha) {
#ifdef AKANTU_USE_BLAS
/// y = alpha*op(A)*x + beta*y
char tran_A = 'N';
int incx = 1;
int incy = 1;
double beta = 0.;
int m = im;
int n = in;
aka_gemv(&tran_A, &m, &n, &alpha, A, &m, x, &incx, &beta, y, &incy);
#else
memset(y, 0, im * sizeof(Real));
for (UInt i = 0; i < im; ++i) {
for (UInt j = 0; j < in; ++j) {
y[i] += A[i + j * im] * x[j];
}
y[i] *= alpha;
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::matrixt_vector(UInt im, UInt in, Real * A, Real * x, Real * y,
Real alpha) {
#ifdef AKANTU_USE_BLAS
/// y = alpha*op(A)*x + beta*y
char tran_A = 'T';
int incx = 1;
int incy = 1;
double beta = 0.;
int m = im;
int n = in;
aka_gemv(&tran_A, &m, &n, &alpha, A, &m, x, &incx, &beta, y, &incy);
#else
memset(y, 0, in * sizeof(Real));
for (UInt i = 0; i < im; ++i) {
for (UInt j = 0; j < in; ++j) {
y[j] += A[j * im + i] * x[i];
}
y[i] *= alpha;
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::matrix_matrix(UInt im, UInt in, UInt ik, Real * A, Real * B,
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'N';
char trans_b = 'N';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &m, B, &k, &beta, C, &m);
#else
memset(C, 0, im * in * sizeof(Real));
for (UInt j = 0; j < in; ++j) {
UInt _jb = j * ik;
UInt _jc = j * im;
for (UInt i = 0; i < im; ++i) {
for (UInt l = 0; l < ik; ++l) {
UInt _la = l * im;
C[i + _jc] += A[i + _la] * B[l + _jb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::matrixt_matrix(UInt im, UInt in, UInt ik, Real * A, Real * B,
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'T';
char trans_b = 'N';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &k, B, &k, &beta, C, &m);
#else
memset(C, 0, im * in * sizeof(Real));
for (UInt j = 0; j < in; ++j) {
UInt _jc = j * im;
UInt _jb = j * ik;
for (UInt i = 0; i < im; ++i) {
UInt _ia = i * ik;
for (UInt l = 0; l < ik; ++l) {
C[i + _jc] += A[l + _ia] * B[l + _jb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::matrix_matrixt(UInt im, UInt in, UInt ik, Real * A, Real * B,
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'N';
char trans_b = 'T';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &m, B, &n, &beta, C, &m);
#else
memset(C, 0, im * in * sizeof(Real));
for (UInt j = 0; j < in; ++j) {
UInt _jc = j * im;
for (UInt i = 0; i < im; ++i) {
for (UInt l = 0; l < ik; ++l) {
UInt _la = l * im;
UInt _lb = l * in;
C[i + _jc] += A[i + _la] * B[j + _lb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::matrixt_matrixt(UInt im, UInt in, UInt ik, Real * A, Real * B,
Real * C, Real alpha) {
#ifdef AKANTU_USE_BLAS
/// C := alpha*op(A)*op(B) + beta*C
char trans_a = 'T';
char trans_b = 'T';
double beta = 0.;
int m = im, n = in, k = ik;
aka_gemm(&trans_a, &trans_b, &m, &n, &k, &alpha, A, &k, B, &n, &beta, C, &m);
#else
memset(C, 0, im * in * sizeof(Real));
for (UInt j = 0; j < in; ++j) {
UInt _jc = j * im;
for (UInt i = 0; i < im; ++i) {
UInt _ia = i * ik;
for (UInt l = 0; l < ik; ++l) {
UInt _lb = l * in;
C[i + _jc] += A[l + _ia] * B[j + _lb];
}
C[i + _jc] *= alpha;
}
}
#endif
}
/* -------------------------------------------------------------------------- */
inline void Math::aXplusY(UInt n, Real alpha, Real * x, Real * y) {
#ifdef AKANTU_USE_BLAS
/// y := alpha x + y
int incx = 1, incy = 1;
aka_axpy(&n, &alpha, x, &incx, y, &incy);
#else
for (UInt i = 0; i < n; ++i)
*(y++) += alpha * *(x++);
#endif
}
/* -------------------------------------------------------------------------- */
inline Real Math::vectorDot(Real * v1, Real * v2, UInt in) {
#ifdef AKANTU_USE_BLAS
/// d := v1 . v2
int incx = 1, incy = 1, n = in;
Real d = aka_dot(&n, v1, &incx, v2, &incy);
#else
Real d = 0;
for (UInt i = 0; i < in; ++i) {
d += v1[i] * v2[i];
}
#endif
return d;
}
/* -------------------------------------------------------------------------- */
template <bool tr_A, bool tr_B>
inline void Math::matMul(UInt m, UInt n, UInt k, Real alpha, Real * A, Real * B,
__attribute__((unused)) Real beta, Real * C) {
if (tr_A) {
if (tr_B)
matrixt_matrixt(m, n, k, A, B, C, alpha);
else
matrixt_matrix(m, n, k, A, B, C, alpha);
} else {
if (tr_B)
matrix_matrixt(m, n, k, A, B, C, alpha);
else
matrix_matrix(m, n, k, A, B, C, alpha);
}
}
/* -------------------------------------------------------------------------- */
template <bool tr_A>
inline void Math::matVectMul(UInt m, UInt n, Real alpha, Real * A, Real * x,
__attribute__((unused)) Real beta, Real * y) {
if (tr_A) {
matrixt_vector(m, n, A, x, y, alpha);
} else {
matrix_vector(m, n, A, x, y, alpha);
}
}
/* -------------------------------------------------------------------------- */
template <typename T> inline void Math::matrixEig(UInt n, T * A, T * d, T * V) {
// Matrix A is row major, so the lapack function in fortran will process
// A^t. Asking for the left eigenvectors of A^t will give the transposed right
// eigenvectors of A so in the C++ code the right eigenvectors.
char jobvl;
if (V != nullptr)
jobvl = 'V'; // compute left eigenvectors
else
jobvl = 'N'; // compute left eigenvectors
char jobvr('N'); // compute right eigenvectors
auto * di = new T[n]; // imaginary part of the eigenvalues
int info;
int N = n;
T wkopt;
int lwork = -1;
// query and allocate the optimal workspace
aka_geev<T>(&jobvl, &jobvr, &N, A, &N, d, di, V, &N, nullptr, &N, &wkopt,
&lwork, &info);
lwork = int(wkopt);
auto * work = new T[lwork];
// solve the eigenproblem
aka_geev<T>(&jobvl, &jobvr, &N, A, &N, d, di, V, &N, nullptr, &N, work,
&lwork, &info);
AKANTU_DEBUG_ASSERT(
info == 0,
"Problem computing eigenvalues/vectors. DGEEV exited with the value "
<< info);
delete[] work;
delete[] di; // I hope for you that there was no complex eigenvalues !!!
}
/* -------------------------------------------------------------------------- */
inline void Math::matrix22_eigenvalues(Real * A, Real * Adiag) {
/// d = determinant of Matrix A
Real d = det2(A);
/// b = trace of Matrix A
Real b = A[0] + A[3];
Real c = sqrt(b * b - 4 * d);
Adiag[0] = .5 * (b + c);
Adiag[1] = .5 * (b - c);
}
/* -------------------------------------------------------------------------- */
inline void Math::matrix33_eigenvalues(Real * A, Real * Adiag) {
matrixEig(3, A, Adiag);
}
/* -------------------------------------------------------------------------- */
template <UInt dim> inline void Math::eigenvalues(Real * A, Real * d) {
if (dim == 1) {
d[0] = A[0];
} else if (dim == 2) {
matrix22_eigenvalues(A, d);
}
// else if(dim == 3) { matrix33_eigenvalues(A, d); }
else
matrixEig(dim, A, d);
}
/* -------------------------------------------------------------------------- */
inline Real Math::det2(const Real * mat) {
return mat[0] * mat[3] - mat[1] * mat[2];
}
/* -------------------------------------------------------------------------- */
inline Real Math::det3(const Real * mat) {
return mat[0] * (mat[4] * mat[8] - mat[7] * mat[5]) -
mat[3] * (mat[1] * mat[8] - mat[7] * mat[2]) +
mat[6] * (mat[1] * mat[5] - mat[4] * mat[2]);
}
/* -------------------------------------------------------------------------- */
template <UInt n> inline Real Math::det(const Real * mat) {
if (n == 1)
return *mat;
else if (n == 2)
return det2(mat);
else if (n == 3)
return det3(mat);
else
return det(n, mat);
}
/* -------------------------------------------------------------------------- */
template <typename T> inline T Math::det(UInt n, const T * A) {
int N = n;
int info;
auto * ipiv = new int[N + 1];
auto * LU = new T[N * N];
std::copy(A, A + N * N, LU);
// LU factorization of A
aka_getrf(&N, &N, LU, &N, ipiv, &info);
if (info > 0) {
AKANTU_DEBUG_ERROR("Singular matrix - cannot factorize it (info: " << info
<< " )");
}
// det(A) = det(L) * det(U) = 1 * det(U) = product_i U_{ii}
T det = 1.;
for (int i = 0; i < N; ++i)
det *= (2 * (ipiv[i] == i) - 1) * LU[i * n + i];
delete[] ipiv;
delete[] LU;
return det;
}
/* -------------------------------------------------------------------------- */
inline void Math::normal2(const Real * vec, Real * normal) {
normal[0] = vec[1];
normal[1] = -vec[0];
Math::normalize2(normal);
}
/* -------------------------------------------------------------------------- */
inline void Math::normal3(const Real * vec1, const Real * vec2, Real * normal) {
Math::vectorProduct3(vec1, vec2, normal);
Math::normalize3(normal);
}
/* -------------------------------------------------------------------------- */
inline void Math::normalize2(Real * vec) {
Real norm = Math::norm2(vec);
vec[0] /= norm;
vec[1] /= norm;
}
/* -------------------------------------------------------------------------- */
inline void Math::normalize3(Real * vec) {
Real norm = Math::norm3(vec);
vec[0] /= norm;
vec[1] /= norm;
vec[2] /= norm;
}
/* -------------------------------------------------------------------------- */
inline Real Math::norm2(const Real * vec) {
return sqrt(vec[0] * vec[0] + vec[1] * vec[1]);
}
/* -------------------------------------------------------------------------- */
inline Real Math::norm3(const Real * vec) {
return sqrt(vec[0] * vec[0] + vec[1] * vec[1] + vec[2] * vec[2]);
}
/* -------------------------------------------------------------------------- */
inline Real Math::norm(UInt n, const Real * vec) {
Real norm = 0.;
for (UInt i = 0; i < n; ++i) {
norm += vec[i] * vec[i];
}
return sqrt(norm);
}
/* -------------------------------------------------------------------------- */
inline void Math::inv2(const Real * mat, Real * inv) {
Real det_mat = det2(mat);
inv[0] = mat[3] / det_mat;
inv[1] = -mat[1] / det_mat;
inv[2] = -mat[2] / det_mat;
inv[3] = mat[0] / det_mat;
}
/* -------------------------------------------------------------------------- */
inline void Math::inv3(const Real * mat, Real * inv) {
Real det_mat = det3(mat);
inv[0] = (mat[4] * mat[8] - mat[7] * mat[5]) / det_mat;
inv[1] = (mat[2] * mat[7] - mat[8] * mat[1]) / det_mat;
inv[2] = (mat[1] * mat[5] - mat[4] * mat[2]) / det_mat;
inv[3] = (mat[5] * mat[6] - mat[8] * mat[3]) / det_mat;
inv[4] = (mat[0] * mat[8] - mat[6] * mat[2]) / det_mat;
inv[5] = (mat[2] * mat[3] - mat[5] * mat[0]) / det_mat;
inv[6] = (mat[3] * mat[7] - mat[6] * mat[4]) / det_mat;
inv[7] = (mat[1] * mat[6] - mat[7] * mat[0]) / det_mat;
inv[8] = (mat[0] * mat[4] - mat[3] * mat[1]) / det_mat;
}
/* -------------------------------------------------------------------------- */
template <UInt n> inline void Math::inv(const Real * A, Real * Ainv) {
if (n == 1)
*Ainv = 1. / *A;
else if (n == 2)
inv2(A, Ainv);
else if (n == 3)
inv3(A, Ainv);
else
inv(n, A, Ainv);
}
/* -------------------------------------------------------------------------- */
template <typename T> inline void Math::inv(UInt n, const T * A, T * invA) {
int N = n;
int info;
auto * ipiv = new int[N + 1];
int lwork = N * N;
auto * work = new T[lwork];
std::copy(A, A + n * n, invA);
aka_getrf(&N, &N, invA, &N, ipiv, &info);
if (info > 0) {
AKANTU_DEBUG_ERROR("Singular matrix - cannot factorize it (info: " << info
<< " )");
}
aka_getri(&N, invA, &N, ipiv, work, &lwork, &info);
if (info != 0) {
AKANTU_DEBUG_ERROR("Cannot invert the matrix (info: " << info << " )");
}
delete[] ipiv;
delete[] work;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Math::solve(UInt n, const T * A, T * x, const T * b) {
int N = n;
int info;
auto * ipiv = new int[N];
auto * lu_A = new T[N * N];
std::copy(A, A + N * N, lu_A);
aka_getrf(&N, &N, lu_A, &N, ipiv, &info);
if (info > 0) {
AKANTU_DEBUG_ERROR("Singular matrix - cannot factorize it (info: " << info
<< " )");
exit(EXIT_FAILURE);
}
char trans = 'N';
int nrhs = 1;
std::copy(b, b + N, x);
aka_getrs(&trans, &N, &nrhs, lu_A, &N, ipiv, x, &N, &info);
if (info != 0) {
AKANTU_DEBUG_ERROR("Cannot solve the system (info: " << info << " )");
exit(EXIT_FAILURE);
}
delete[] ipiv;
delete[] lu_A;
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
inline Real Math::matrixDoubleDot22(Real * A, Real * B) {
Real d;
d = A[0] * B[0] + A[1] * B[1] + A[2] * B[2] + A[3] * B[3];
return d;
}
/* -------------------------------------------------------------------------- */
inline Real Math::matrixDoubleDot33(Real * A, Real * B) {
Real d;
d = A[0] * B[0] + A[1] * B[1] + A[2] * B[2] + A[3] * B[3] + A[4] * B[4] +
A[5] * B[5] + A[6] * B[6] + A[7] * B[7] + A[8] * B[8];
return d;
}
/* -------------------------------------------------------------------------- */
inline Real Math::matrixDoubleDot(UInt n, Real * A, Real * B) {
Real d = 0.;
for (UInt i = 0; i < n; ++i) {
for (UInt j = 0; j < n; ++j) {
d += A[i * n + j] * B[i * n + j];
}
}
return d;
}
/* -------------------------------------------------------------------------- */
inline void Math::vectorProduct3(const Real * v1, const Real * v2, Real * res) {
res[0] = v1[1] * v2[2] - v1[2] * v2[1];
res[1] = v1[2] * v2[0] - v1[0] * v2[2];
res[2] = v1[0] * v2[1] - v1[1] * v2[0];
}
/* -------------------------------------------------------------------------- */
inline Real Math::vectorDot2(const Real * v1, const Real * v2) {
return (v1[0] * v2[0] + v1[1] * v2[1]);
}
/* -------------------------------------------------------------------------- */
inline Real Math::vectorDot3(const Real * v1, const Real * v2) {
return (v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2]);
}
/* -------------------------------------------------------------------------- */
inline Real Math::distance_2d(const Real * x, const Real * y) {
return sqrt((y[0] - x[0]) * (y[0] - x[0]) + (y[1] - x[1]) * (y[1] - x[1]));
}
/* -------------------------------------------------------------------------- */
inline Real Math::triangle_inradius(const Real * coord1, const Real * coord2,
const Real * coord3) {
/**
* @f{eqnarray*}{
* r &=& A / s \\
* A &=& 1/4 * \sqrt{(a + b + c) * (a - b + c) * (a + b - c) (-a + b + c)} \\
* s &=& \frac{a + b + c}{2}
* @f}
*/
Real a, b, c;
a = distance_2d(coord1, coord2);
b = distance_2d(coord2, coord3);
c = distance_2d(coord1, coord3);
Real s;
s = (a + b + c) * 0.5;
return sqrt((s - a) * (s - b) * (s - c) / s);
}
/* -------------------------------------------------------------------------- */
inline Real Math::distance_3d(const Real * x, const Real * y) {
return sqrt((y[0] - x[0]) * (y[0] - x[0]) + (y[1] - x[1]) * (y[1] - x[1]) +
(y[2] - x[2]) * (y[2] - x[2]));
}
/* -------------------------------------------------------------------------- */
inline Real Math::tetrahedron_volume(const Real * coord1, const Real * coord2,
const Real * coord3, const Real * coord4) {
Real xx[9], vol;
xx[0] = coord2[0];
xx[1] = coord2[1];
xx[2] = coord2[2];
xx[3] = coord3[0];
xx[4] = coord3[1];
xx[5] = coord3[2];
xx[6] = coord4[0];
xx[7] = coord4[1];
xx[8] = coord4[2];
vol = det3(xx);
xx[0] = coord1[0];
xx[1] = coord1[1];
xx[2] = coord1[2];
xx[3] = coord3[0];
xx[4] = coord3[1];
xx[5] = coord3[2];
xx[6] = coord4[0];
xx[7] = coord4[1];
xx[8] = coord4[2];
vol -= det3(xx);
xx[0] = coord1[0];
xx[1] = coord1[1];
xx[2] = coord1[2];
xx[3] = coord2[0];
xx[4] = coord2[1];
xx[5] = coord2[2];
xx[6] = coord4[0];
xx[7] = coord4[1];
xx[8] = coord4[2];
vol += det3(xx);
xx[0] = coord1[0];
xx[1] = coord1[1];
xx[2] = coord1[2];
xx[3] = coord2[0];
xx[4] = coord2[1];
xx[5] = coord2[2];
xx[6] = coord3[0];
xx[7] = coord3[1];
xx[8] = coord3[2];
vol -= det3(xx);
vol /= 6;
return vol;
}
/* -------------------------------------------------------------------------- */
inline Real Math::tetrahedron_inradius(const Real * coord1, const Real * coord2,
const Real * coord3,
const Real * coord4) {
Real l12, l13, l14, l23, l24, l34;
l12 = distance_3d(coord1, coord2);
l13 = distance_3d(coord1, coord3);
l14 = distance_3d(coord1, coord4);
l23 = distance_3d(coord2, coord3);
l24 = distance_3d(coord2, coord4);
l34 = distance_3d(coord3, coord4);
Real s1, s2, s3, s4;
s1 = (l12 + l23 + l13) * 0.5;
s1 = sqrt(s1 * (s1 - l12) * (s1 - l23) * (s1 - l13));
s2 = (l12 + l24 + l14) * 0.5;
s2 = sqrt(s2 * (s2 - l12) * (s2 - l24) * (s2 - l14));
s3 = (l23 + l34 + l24) * 0.5;
s3 = sqrt(s3 * (s3 - l23) * (s3 - l34) * (s3 - l24));
s4 = (l13 + l34 + l14) * 0.5;
s4 = sqrt(s4 * (s4 - l13) * (s4 - l34) * (s4 - l14));
Real volume = Math::tetrahedron_volume(coord1, coord2, coord3, coord4);
return 3 * volume / (s1 + s2 + s3 + s4);
}
/* -------------------------------------------------------------------------- */
inline void Math::barycenter(const Real * coord, UInt nb_points,
UInt spatial_dimension, Real * barycenter) {
memset(barycenter, 0, spatial_dimension * sizeof(Real));
for (UInt n = 0; n < nb_points; ++n) {
UInt offset = n * spatial_dimension;
for (UInt i = 0; i < spatial_dimension; ++i) {
barycenter[i] += coord[offset + i] / (Real)nb_points;
}
}
}
/* -------------------------------------------------------------------------- */
inline void Math::vector_2d(const Real * x, const Real * y, Real * res) {
res[0] = y[0] - x[0];
res[1] = y[1] - x[1];
}
/* -------------------------------------------------------------------------- */
inline void Math::vector_3d(const Real * x, const Real * y, Real * res) {
res[0] = y[0] - x[0];
res[1] = y[1] - x[1];
res[2] = y[2] - x[2];
}
/* -------------------------------------------------------------------------- */
/// Combined absolute and relative tolerance test proposed in
/// Real-time collision detection by C. Ericson (2004)
inline bool Math::are_float_equal(const Real x, const Real y) {
Real abs_max = std::max(std::abs(x), std::abs(y));
abs_max = std::max(abs_max, Real(1.));
return std::abs(x - y) <= (tolerance * abs_max);
}
/* -------------------------------------------------------------------------- */
inline bool Math::isnan(Real x) {
#if defined(__INTEL_COMPILER)
#pragma warning(push)
#pragma warning(disable : 1572)
#endif // defined(__INTEL_COMPILER)
// x = x return false means x = quiet_NaN
return !(x == x);
#if defined(__INTEL_COMPILER)
#pragma warning(pop)
#endif // defined(__INTEL_COMPILER)
}
/* -------------------------------------------------------------------------- */
inline bool Math::are_vector_equal(UInt n, Real * x, Real * y) {
bool test = true;
for (UInt i = 0; i < n; ++i) {
test &= are_float_equal(x[i], y[i]);
}
return test;
}
/* -------------------------------------------------------------------------- */
inline bool Math::intersects(Real x_min, Real x_max, Real y_min, Real y_max) {
return !((x_max <= y_min) || (x_min >= y_max));
}
/* -------------------------------------------------------------------------- */
inline bool Math::is_in_range(Real a, Real x_min, Real x_max) {
return ((a >= x_min) && (a <= x_max));
}
/* -------------------------------------------------------------------------- */
template <UInt p, typename T> inline T Math::pow(T x) {
return (pow<p - 1, T>(x) * x);
}
template <> inline UInt Math::pow<0, UInt>(__attribute__((unused)) UInt x) {
return (1);
}
template <> inline Real Math::pow<0, Real>(__attribute__((unused)) Real x) {
return (1.);
}
/* -------------------------------------------------------------------------- */
template <class Functor>
Real Math::NewtonRaphson::solve(const Functor & funct, Real x_0) {
Real x = x_0;
Real f_x = funct.f(x);
UInt iter = 0;
while (std::abs(f_x) > this->tolerance && iter < this->max_iteration) {
x -= f_x / funct.f_prime(x);
f_x = funct.f(x);
iter++;
}
AKANTU_DEBUG_ASSERT(iter < this->max_iteration,
"Newton Raphson ("
<< funct.name << ") solve did not converge in "
<< this->max_iteration << " iterations (tolerance: "
<< this->tolerance << ")");
return x;
}
diff --git a/src/common/aka_memory.cc b/src/common/aka_memory.cc
index 7db2e7a1b..748167122 100644
--- a/src/common/aka_memory.cc
+++ b/src/common/aka_memory.cc
@@ -1,64 +1,64 @@
/**
* @file aka_memory.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief static memory wrapper
*
* @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 "aka_static_memory.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
Memory::Memory(ID id, MemoryID memory_id) : static_memory(StaticMemory::getStaticMemory()),
id(id),
memory_id(memory_id) {
}
/* -------------------------------------------------------------------------- */
Memory::~Memory() {
if(StaticMemory::isInstantiated()) {
std::list<ID>::iterator it;
for (it = handeld_vectors_id.begin(); it != handeld_vectors_id.end(); ++it) {
AKANTU_DEBUG(dblAccessory, "Deleting the vector " << *it);
static_memory.sfree(memory_id, *it);
}
static_memory.destroy();
}
handeld_vectors_id.clear();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/common/aka_memory.hh b/src/common/aka_memory.hh
index ede733233..04d942c02 100644
--- a/src/common/aka_memory.hh
+++ b/src/common/aka_memory.hh
@@ -1,115 +1,115 @@
/**
* @file aka_memory.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief wrapper for the static_memory, all object which wants
* to access the static_memory as to inherit from the class memory
*
* @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_MEMORY_HH__
#define __AKANTU_MEMORY_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_static_memory.hh"
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <list>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
protected:
Memory(ID id, MemoryID memory_id = 0);
virtual ~Memory();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// malloc
template <class T>
inline Array<T> & alloc(const ID & name, UInt size, UInt nb_component);
/// malloc
template <class T>
inline Array<T> & alloc(const ID & name, UInt size, UInt nb_component,
const T & init_value);
/* ------------------------------------------------------------------------ */
/// free an array
inline void dealloc(ID name);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
template <typename T> inline Array<T> & getArray(const ID & name);
template <typename T> inline const Array<T> & getArray(const ID & name) const;
public:
AKANTU_GET_MACRO(MemoryID, memory_id, const MemoryID &);
AKANTU_GET_MACRO(ID, id, const ID &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the static memory instance
StaticMemory & static_memory;
/// list of allocated vectors id
std::list<ID> handeld_vectors_id;
protected:
ID id;
/// the id registred in the static memory
MemoryID memory_id;
};
/* -------------------------------------------------------------------------- */
/* Inline functions */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_INCLUDE_INLINE_IMPL)
#include "aka_memory_inline_impl.cc"
#endif
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MEMORY_HH__ */
diff --git a/src/common/aka_random_generator.hh b/src/common/aka_random_generator.hh
index 8b756c20f..de6913d7a 100644
--- a/src/common/aka_random_generator.hh
+++ b/src/common/aka_random_generator.hh
@@ -1,376 +1,376 @@
/**
* @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 "aka_common.hh"
#ifndef __AKANTU_AKA_RANDOM_GENERATOR_HH__
#define __AKANTU_AKA_RANDOM_GENERATOR_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* List of available distributions */
/* -------------------------------------------------------------------------- */
#define AKANTU_RANDOM_DISTRIBUTION_TYPES \
((uniform, UniformDistribution))((weibull, WeibullDistribution))
#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
};
/* -------------------------------------------------------------------------- */
/* Distribution */
/* -------------------------------------------------------------------------- */
/// Empty base to be able to store a distribution
template <typename T> class RandomDistributionBase {
public:
virtual ~RandomDistributionBase() {}
virtual void printself(std::ostream & stream, int indent = 0) const = 0;
};
/* -------------------------------------------------------------------------- */
/* Uniform distribution */
/* -------------------------------------------------------------------------- */
template <typename T>
class UniformDistribution : public RandomDistributionBase<T> {
public:
UniformDistribution(T min = T(0.), T max = T(1.)) : min(min), max(max){};
/* ------------------------------------------------------------------------ */
template <template <class> class RandomGenerator>
T operator()(RandomGenerator<T> & generator) {
T x = generator() / (RandomGenerator<T>::max() - RandomGenerator<T>::min());
return (x * (max - min) + min);
}
virtual void setParams(std::string value) {
std::stringstream sstr(value);
sstr >> min;
sstr >> max;
}
/// function to print the contain of the class
virtual void printself(std::ostream & stream,
__attribute__((unused)) int indent = 0) const {
stream << "Uniform [ min=" << min << ", max=" << max << " ]";
};
/* ------------------------------------------------------------------------ */
private:
T min;
T max;
};
/* -------------------------------------------------------------------------- */
/* Weibull distribution */
/* -------------------------------------------------------------------------- */
template <typename T>
class WeibullDistribution : public RandomDistributionBase<T> {
public:
WeibullDistribution(T scale, T shape) : m(shape), lambda(scale){};
/* ------------------------------------------------------------------------ */
template <template <class> class RandomGenerator>
T operator()(RandomGenerator<T> & generator) {
T x = generator() / (RandomGenerator<T>::max() - RandomGenerator<T>::min());
T e = T(1) / m;
return lambda * std::pow(-std::log(1. - x), e);
}
virtual void setParams(std::string value) {
std::stringstream sstr(value);
sstr >> m;
sstr >> lambda;
}
/// function to print the contain of the class
virtual void printself(std::ostream & stream,
__attribute__((unused)) int indent = 0) const {
stream << "Weibull [ shape=" << m << ", scale=" << lambda << "]";
}
/* ------------------------------------------------------------------------ */
private:
/// shape parameter or Weibull modulus
T m;
/// scale parameter
T lambda;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* Generator */
/* -------------------------------------------------------------------------- */
#if not defined(_WIN32)
template <typename T> class Rand48Generator {
/* ------------------------------------------------------------------------ */
public:
inline T operator()();
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
public:
static void seed(long int s);
static long int seed();
static constexpr T min();
static constexpr T max();
/* ------------------------------------------------------------------------ */
private:
static long int _seed;
};
/* -------------------------------------------------------------------------- */
template <typename T> inline T Rand48Generator<T>::operator()() {
AKANTU_DEBUG_TO_IMPLEMENT();
}
template <> inline double Rand48Generator<double>::operator()() {
return drand48();
}
template <typename T>
void Rand48Generator<T>::printself(std::ostream & stream,
__attribute__((unused)) int indent) const {
stream << "Rand48Generator [seed=" << seed << "]";
}
template <typename T> void Rand48Generator<T>::seed(long int s) {
_seed = s;
srand48(_seed);
}
template <typename T> long int Rand48Generator<T>::seed() { return _seed; }
template <typename T> constexpr T Rand48Generator<T>::min() { return 0.; }
template <typename T> constexpr T Rand48Generator<T>::max() { return 1.; }
#endif
/* -------------------------------------------------------------------------- */
template <typename T> class RandGenerator {
/* ------------------------------------------------------------------------ */
public:
inline T operator()() { return rand(); }
/// function to print the contain of the class
virtual void printself(std::ostream & stream,
__attribute__((unused)) int indent = 0) const {
stream << "RandGenerator [seed=" << _seed << "]";
}
/* ------------------------------------------------------------------------ */
public:
static void seed(long int s) {
_seed = s;
srand(_seed);
}
static long int seed() { return _seed; }
static constexpr T min() { return 0.; }
static constexpr T max() { return RAND_MAX; }
/* ------------------------------------------------------------------------ */
private:
static long int _seed;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#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, template <typename> 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)> { \
enum { \
value = AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
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
/* -------------------------------------------------------------------------- */
/* RandomParameter */
/* -------------------------------------------------------------------------- */
template <typename T> class RandomParameter {
public:
explicit RandomParameter(T base_value)
: base_value(base_value), type(_rdt_not_defined), distribution(NULL) {}
template <template <typename> class Distribution>
RandomParameter(T base_value, const Distribution<T> & distribution)
: base_value(base_value),
type((RandomDistributionType)
RandomDistributionTypeHelper<T, Distribution>::value),
distribution(new Distribution<T>(distribution)) {}
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_NEW(r, data, elem) \
else if (type == AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem))) { \
typedef BOOST_PP_TUPLE_ELEM(2, 1, elem)<T> Dist; \
distribution = new Dist(*static_cast<Dist *>(other.distribution)); \
}
RandomParameter(const RandomParameter & other)
: base_value(other.base_value), type(other.type) {
if (type == _rdt_not_defined)
distribution = NULL;
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_NEW, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
}
inline void setBaseValue(const T & value) { this->base_value = value; }
inline T getBaseValue() const { return this->base_value; }
RandomParameter & operator=(const RandomParameter & other) {
if (this != &other) {
base_value = other.base_value;
type = other.type;
delete distribution;
if (type == _rdt_not_defined)
distribution = NULL;
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_NEW, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
}
return *this;
}
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_NEW
/* ------------------------------------------------------------------------ */
#define AKANTU_RANDOM_DISTRIBUTION_TYPE_SET(r, data, elem) \
else if (type == AKANTU_RANDOM_DISTRIBUTION_TYPES_PREFIX( \
BOOST_PP_TUPLE_ELEM(2, 0, elem))) { \
this->set<BOOST_PP_TUPLE_ELEM(2, 1, elem), Generator>(it, end); \
}
template <template <typename> class Generator, class iterator>
void setValues(iterator it, iterator end) {
if (type == _rdt_not_defined) {
for (; it != end; ++it)
*it = this->base_value;
}
BOOST_PP_SEQ_FOR_EACH(AKANTU_RANDOM_DISTRIBUTION_TYPE_SET, _,
AKANTU_RANDOM_DISTRIBUTION_TYPES)
}
#undef AKANTU_RANDOM_DISTRIBUTION_TYPE_SET
virtual void printself(std::ostream & stream,
__attribute__((unused)) int indent = 0) const {
stream << base_value;
if (type != _rdt_not_defined)
stream << " " << *distribution;
}
private:
template <template <typename> class Distribution,
template <typename> class Generator, class iterator>
void set(iterator it, iterator end) {
typedef Distribution<T> Dist;
Dist & dist = *(static_cast<Dist *>(this->distribution));
Generator<T> gen;
for (; it != end; ++it)
*it = this->base_value + dist(gen);
}
private:
/// Value with no random variations
T base_value;
/// Random distribution type
RandomDistributionType type;
/// Random distribution to use
RandomDistributionBase<T> * distribution;
};
/* -------------------------------------------------------------------------- */
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
RandomDistributionBase<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;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_AKA_RANDOM_GENERATOR_HH__ */
diff --git a/src/common/aka_static_memory.cc b/src/common/aka_static_memory.cc
index 7a7a48ce5..7d8709f47 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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
bool StaticMemory::is_instantiated = false;
StaticMemory * StaticMemory::single_static_memory = NULL;
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;
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);
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/common/aka_static_memory.hh b/src/common/aka_static_memory.hh
index 912e30d93..43e4a4415 100644
--- a/src/common/aka_static_memory.hh
+++ b/src/common/aka_static_memory.hh
@@ -1,157 +1,157 @@
/**
* @file aka_static_memory.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @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/>.
*
* @section DESCRIPTION
*
* The class handling the memory, allocation/reallocation/desallocation
* The objects can register their array and ask for allocation or realocation
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STATIC_MEMORY_HH__
#define __AKANTU_STATIC_MEMORY_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_array.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
typedef std::map<ID, ArrayBase *> ArrayMap;
typedef std::map<MemoryID, ArrayMap> MemoryMap;
/**
* @class StaticMemory
* @brief Class for memory management common to all objects (this class as to
* be accessed by an interface class memory)
*/
class StaticMemory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
private:
/// Default constructor
StaticMemory(){};
public:
virtual ~StaticMemory();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the global instance of the StaticMemory
static StaticMemory & getStaticMemory();
static bool isInstantiated() { return is_instantiated; };
/// remove a reference on the static memory
void destroy();
/// access to an Array
inline const ArrayBase & getArray(const MemoryID & memory_id,
const ID & name) const;
/// get all vectors of a memory
inline const ArrayMap & getMemory(const MemoryID & memory_id) const;
/* ------------------------------------------------------------------------ */
/* Class Methods */
/* ------------------------------------------------------------------------ */
public:
/**
* Allocation of an array of type
*
* @param memory_id the id of the memory accessing to the static memory
* @param name name of the array (for example connectivity)
* @param size number of size (for example number of nodes)
* @param nb_component number of component (for example spatial dimension)
* @param type the type code of the array to be allocated
*
* @return pointer to an array of size nb_tupes * nb_component * sizeof(T)
*/
template <typename T>
Array<T> & smalloc(const MemoryID & memory_id, const ID & name, UInt size,
UInt nb_component);
template <typename T>
Array<T> & smalloc(const MemoryID & memory_id, const ID & name, UInt size,
UInt nb_component, const T & init_value);
/**
* free the memory associated to the array name
*
* @param memory_id the id of the memory accessing to the static memory
* @param name the name of an existing array
*/
void sfree(const MemoryID & memory_id, const ID & name);
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// is the static memory instantiated
static bool is_instantiated;
/// unique instance of the StaticMemory
static StaticMemory * single_static_memory;
/// map of all allocated arrays, indexed by their names
MemoryMap memories;
/// number of references on the static memory
static UInt nb_reference;
};
#include "aka_static_memory_tmpl.hh"
#include "aka_static_memory_inline_impl.cc"
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const StaticMemory & _this) {
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_STATIC_MEMORY_HH__ */
diff --git a/src/common/aka_typelist.hh b/src/common/aka_typelist.hh
index 8fa5a6444..d4d5d22df 100644
--- a/src/common/aka_typelist.hh
+++ b/src/common/aka_typelist.hh
@@ -1,184 +1,184 @@
/**
* @file aka_typelist.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Sun Oct 19 2014
*
* @brief Objects that support the visitor design pattern
*
* @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_TYPELIST_HH__
#define __AKANTU_TYPELIST_HH__
#include "aka_common.hh"
-__BEGIN_AKANTU__
+namespace akantu {
struct Empty_type {};
class Null_type {};
template <class T, class U>
struct Typelist {
typedef T Head;
typedef U Tail;
};
template <
typename T1 = Null_type, typename T2 = Null_type, typename T3 = Null_type,
typename T4 = Null_type, typename T5 = Null_type, typename T6 = Null_type,
typename T7 = Null_type, typename T8 = Null_type, typename T9 = Null_type,
typename T10 = Null_type, typename T11 = Null_type, typename T12 = Null_type,
typename T13 = Null_type, typename T14 = Null_type, typename T15 = Null_type,
typename T16 = Null_type, typename T17 = Null_type, typename T18 = Null_type,
typename T19 = Null_type, typename T20 = Null_type
>
struct MakeTypelist
{
private:
typedef typename MakeTypelist
<
T2 , T3 , T4 ,
T5 , T6 , T7 ,
T8 , T9 , T10,
T11, T12, T13,
T14, T15, T16,
T17, T18, T19, T20
>
::Result TailResult;
public:
typedef Typelist<T1, TailResult> Result;
};
template<>
struct MakeTypelist<> {
typedef Null_type Result;
};
////////////////////////////////////////////////////////////////////////////////
// class template Length
// Computes the length of a typelist
// Invocation (TList is a typelist):
// Length<TList>::value
// returns a compile-time constant containing the length of TList, not counting
// the end terminator (which by convention is Null_type)
////////////////////////////////////////////////////////////////////////////////
template <class TList> struct Length;
template <> struct Length<Null_type>
{
enum { value = 0 };
};
template <class T, class U>
struct Length< Typelist<T, U> >
{
enum { value = 1 + Length<U>::value };
};
////////////////////////////////////////////////////////////////////////////////
// class template TypeAt
// Finds the type at a given index in a typelist
// Invocation (TList is a typelist and index is a compile-time integral
// constant):
// TypeAt<TList, index>::Result
// returns the type in position 'index' in TList
// If you pass an out-of-bounds index, the result is a compile-time error
////////////////////////////////////////////////////////////////////////////////
template <class TList, unsigned int index> struct TypeAt;
template <class Head, class Tail>
struct TypeAt<Typelist<Head, Tail>, 0>
{
typedef Head Result;
};
template <class Head, class Tail, unsigned int i>
struct TypeAt<Typelist<Head, Tail>, i>
{
typedef typename TypeAt<Tail, i - 1>::Result Result;
};
////////////////////////////////////////////////////////////////////////////////
// class template Erase
// Erases the first occurence, if any, of a type in a typelist
// Invocation (TList is a typelist and T is a type):
// Erase<TList, T>::Result
// returns a typelist that is TList without the first occurence of T
////////////////////////////////////////////////////////////////////////////////
template <class TList, class T> struct Erase;
template <class T> // Specialization 1
struct Erase<Null_type, T>
{
typedef Null_type Result;
};
template <class T, class Tail> // Specialization 2
struct Erase<Typelist<T, Tail>, T>
{
typedef Tail Result;
};
template <class Head, class Tail, class T> // Specialization 3
struct Erase<Typelist<Head, Tail>, T>
{
typedef Typelist<Head,
typename Erase<Tail, T>::Result>
Result;
};
template <class TList, class T> struct IndexOf;
template <class T>
struct IndexOf<Null_type, T>
{
enum { value = -1 };
};
template <class T, class Tail>
struct IndexOf<Typelist<T, Tail>, T>
{
enum { value = 0 };
};
template <class Head, class Tail, class T>
struct IndexOf<Typelist<Head, Tail>, T>
{
private:
enum { temp = IndexOf<Tail, T>::value };
public:
enum { value = (temp == -1 ? -1 : 1 + temp) };
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_TYPELIST_HH__ */
diff --git a/src/common/aka_types.hh b/src/common/aka_types.hh
index 0e467af92..fd25e8b19 100644
--- a/src/common/aka_types.hh
+++ b/src/common/aka_types.hh
@@ -1,1236 +1,1236 @@
/**
* @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__
-__BEGIN_AKANTU__
+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:
using value_type = 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) {
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;
this->values = new T[this->_size];
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 RetType & src) {
if (this != &src) {
if (this->wrapped) {
// 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:
friend class Array<T>;
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};
};
// template <typename T, UInt ndim, class RetType>
// inline TensorProxy<T, ndim, RetType>::TensorProxy(
// const TensorStorage<T, ndim, RetType> & other) {
// this->values = other.storage();
// for (UInt i = 0; i < ndim; ++i)
// this->n[i] = other.size(i);
// }
/* -------------------------------------------------------------------------- */
/* 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 VectorProxy<T> & 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) {
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;
/* ------------------------------------------------------------------------ */
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)
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>
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;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_AKA_TYPES_HH__ */
diff --git a/src/common/aka_visitor.hh b/src/common/aka_visitor.hh
index cd72e500d..3c3bcd800 100644
--- a/src/common/aka_visitor.hh
+++ b/src/common/aka_visitor.hh
@@ -1,175 +1,175 @@
/**
* @file aka_visitor.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Sun Oct 19 2014
*
* @brief Objects that support the visitor design pattern
*
* @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_VISITOR_HH__
#define __AKANTU_VISITOR_HH__
#include "aka_typelist.hh"
-__BEGIN_AKANTU__
+namespace akantu {
///////////////////////////////////////////////////////////////////////////
// visitor class template, adapted from the Andrei Alexandrescu's
// "Modern C++ Design"
enum Visit_type { Mutable, Immutable };
template <class T, typename R = void, Visit_type = Mutable>
class StrictVisitor;
template <class T, typename R>
class StrictVisitor<T, R, Mutable>
{
public:
typedef R ReturnType;
typedef T ParamType;
virtual ~StrictVisitor() {}
virtual ReturnType Visit(ParamType&) = 0;
};
template <class T, typename R>
class StrictVisitor<T, R, Immutable>
{
public:
typedef R ReturnType;
typedef const T ParamType;
virtual ~StrictVisitor() {}
virtual ReturnType Visit(ParamType&) = 0;
};
/// class template StrictVisitor (specialization)
template <class Head, class Tail, typename R>
class StrictVisitor<Typelist<Head, Tail>, R, Mutable>
: public StrictVisitor<Head, R, Mutable>, public StrictVisitor<Tail, R, Mutable>
{
public:
typedef R ReturnType;
typedef Head ParamType;
// using StrictVisitor<Head, R>::Visit;
// using StrictVisitor<Tail, R>::Visit;
};
template <class Head, typename R>
class StrictVisitor<Typelist<Head, Null_type>, R, Mutable> : public StrictVisitor<Head, R, Mutable>
{
public:
typedef R ReturnType;
typedef Head ParamType;
using StrictVisitor<Head, R, Mutable>::Visit;
};
template <class Head, class Tail, typename R>
class StrictVisitor<Typelist<Head, Tail>, R, Immutable>
: public StrictVisitor<Head, R, Immutable>, public StrictVisitor<Tail, R, Immutable>
{
public:
typedef R ReturnType;
typedef Head ParamType;
// using StrictVisitor<Head, R>::Visit;
// using StrictVisitor<Tail, R>::Visit;
};
template <class Head, typename R>
class StrictVisitor<Typelist<Head, Null_type>, R, Immutable> : public StrictVisitor<Head, R, Immutable>
{
public:
typedef R ReturnType;
typedef Head ParamType;
using StrictVisitor<Head, R, Immutable>::Visit;
};
////////////////////////////////////////////////////////////////////////////////
// class template NonStrictVisitor
// Implements non-strict visitation (you can implement only part of the Visit
// functions)
//
template <class R>
struct DefaultFunctor {
template <class T>
R operator()(T&) { return R(); }
};
template <class T, typename R = void, Visit_type V = Mutable, class F = DefaultFunctor<R> > class BaseVisitorImpl;
template <class Head, class Tail, typename R, Visit_type V, class F>
class BaseVisitorImpl<Typelist<Head, Tail>, R, V, F>
: public StrictVisitor<Head, R, V>, public BaseVisitorImpl<Tail, R, V, F> {
public:
typedef typename StrictVisitor<Head, R, V>::ParamType ParamType;
virtual R Visit(ParamType& h)
{ return F()(h); }
};
template <class Head, typename R, Visit_type V, class F >
class BaseVisitorImpl<Typelist<Head, Null_type>, R, V, F> : public StrictVisitor<Head, R, V>
{
public:
typedef typename StrictVisitor<Head, R, V>::ParamType ParamType;
virtual R Visit(ParamType& h)
{ return F()(h); }
};
/// Visitor
template <class R>
struct Strict {};
template <typename R, class TList, Visit_type V = Mutable, template <class> class FunctorPolicy = DefaultFunctor>
class Visitor : public BaseVisitorImpl<TList, R, V, FunctorPolicy<R> > {
public:
typedef R ReturnType;
template <class Visited>
ReturnType GenericVisit(Visited& host) {
StrictVisitor<Visited, ReturnType, V>& subObj = *this;
return subObj.Visit(host);
}
};
template <typename R, class TList, Visit_type V>
class Visitor<R, TList, V, Strict> : public StrictVisitor<TList, R, V> {
public:
typedef R ReturnType;
template <class Visited>
ReturnType GenericVisit(Visited& host) {
StrictVisitor<Visited, ReturnType, V>& subObj = *this;
return subObj.Visit(host);
}
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_VISITOR_HH__ */
diff --git a/src/common/aka_voigthelper.cc b/src/common/aka_voigthelper.cc
index 415141ba7..32111160c 100644
--- a/src/common/aka_voigthelper.cc
+++ b/src/common/aka_voigthelper.cc
@@ -1,68 +1,68 @@
/**
* @file aka_voigthelper.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Dec 20 2013
* @date last modification: Sun Oct 19 2014
*
* @brief Voigt indices
*
* @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_voigthelper.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* clang-format off */
template <> const UInt VoigtHelper<1>::mat[][1] = {{0}};
template <> const UInt VoigtHelper<2>::mat[][2] = {{0, 2},
{3, 1}};
template <> const UInt VoigtHelper<3>::mat[][3] = {{0, 5, 4},
{8, 1, 3},
{7, 6, 2}};
template <> const UInt VoigtHelper<1>::vec[][2] = {{0, 0}};
template <> const UInt VoigtHelper<2>::vec[][2] = {{0, 0},
{1, 1},
{0, 1},
{1, 0}};
template <> const UInt VoigtHelper<3>::vec[][2] = {{0, 0},
{1, 1},
{2, 2},
{1, 2},
{0, 2},
{0, 1},
{2, 1},
{2, 0},
{1, 0}};
template <> const Real VoigtHelper<1>::factors[] = {1.};
template <> const Real VoigtHelper<2>::factors[] = {1., 1., 2.};
template <> const Real VoigtHelper<3>::factors[] = {1., 1., 1.,
2., 2., 2.};
/* clang-format on */
-__END_AKANTU__
+} // akantu
diff --git a/src/common/aka_voigthelper.hh b/src/common/aka_voigthelper.hh
index 2e85f67e8..9f5ec37b0 100644
--- a/src/common/aka_voigthelper.hh
+++ b/src/common/aka_voigthelper.hh
@@ -1,77 +1,77 @@
/**
* @file aka_voigthelper.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Till Junge <till.junge@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Dec 20 2013
* @date last modification: Fri Jan 22 2016
*
* @brief Helper file for Voigt notation
*
* @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 __AKA_VOIGTHELPER_HH__
#define __AKA_VOIGTHELPER_HH__
#include "aka_common.hh"
#include "aka_types.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim> class VoigtHelper {
public:
/// transfer the B matrix to a Voigt notation B matrix
inline static void transferBMatrixToSymVoigtBMatrix(
const Matrix<Real> & B, Matrix<Real> & Bvoigt, UInt nb_nodes_per_element);
/// transfer the BNL matrix to a Voigt notation B matrix (See Bathe et al.
/// IJNME vol 9, 1975)
inline static void transferBMatrixToBNL(const Matrix<Real> & B,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element);
/// transfer the BL2 matrix to a Voigt notation B matrix (See Bathe et al.
/// IJNME vol 9, 1975)
inline static void transferBMatrixToBL2(const Matrix<Real> & B,
const Matrix<Real> & grad_u,
Matrix<Real> & Bvoigt,
UInt nb_nodes_per_element);
public:
const static UInt size;
// matrix of vector index I as function of tensor indices i,j
const static UInt mat[dim][dim];
// array of matrix indices ij as function of vector index I
const static UInt vec[dim * dim][2];
// factors to multiply the strain by for voigt notation
const static Real factors[((dim * (dim - 1)) / 2 + dim)];
};
-__END_AKANTU__
+} // akantu
#include "aka_voigthelper_tmpl.hh"
#endif
diff --git a/src/fe_engine/cohesive_element.cc b/src/fe_engine/cohesive_element.cc
index 8265aecf5..580aad513 100644
--- a/src/fe_engine/cohesive_element.cc
+++ b/src/fe_engine/cohesive_element.cc
@@ -1,150 +1,150 @@
/**
* @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 "cohesive_element.hh"
-__BEGIN_AKANTU__
+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_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_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_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;
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/cohesive_element.hh b/src/fe_engine/cohesive_element.hh
index f5a188c3e..968604ffd 100644
--- a/src/fe_engine/cohesive_element.hh
+++ b/src/fe_engine/cohesive_element.hh
@@ -1,91 +1,91 @@
/**
* @file cohesive_element.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 Jun 18 2010
* @date last modification: Thu Oct 22 2015
*
* @brief Generates the cohesive element structres (defined in
* element_class.hh)
*
* @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 "element_class.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_ELEMENT_HH__
#define __AKANTU_COHESIVE_ELEMENT_HH__
-__BEGIN_AKANTU__
+namespace akantu {
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_2d_4, _gt_cohesive_2d_4,
_itp_lagrange_segment_2, _ek_cohesive, 2,
_git_segment, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_2d_6, _gt_cohesive_2d_6,
_itp_lagrange_segment_3, _ek_cohesive, 2,
_git_segment, 3);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_1d_2, _gt_cohesive_1d_2,
_itp_lagrange_point_1, _ek_cohesive, 1,
_git_point, 1);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_6, _gt_cohesive_3d_6,
_itp_lagrange_triangle_3, _ek_cohesive, 3,
_git_triangle, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_12, _gt_cohesive_3d_12,
_itp_lagrange_triangle_6, _ek_cohesive, 3,
_git_triangle, 3);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_8, _gt_cohesive_3d_8,
_itp_lagrange_quadrangle_4, _ek_cohesive,
3, _git_segment, 2);
AKANTU_DEFINE_ELEMENT_CLASS_PROPERTY(_cohesive_3d_16, _gt_cohesive_3d_16,
_itp_serendip_quadrangle_8, _ek_cohesive,
3, _git_segment, 3);
template <ElementType> struct CohesiveFacetProperty {
static const ElementType cohesive_type = _not_defined;
};
#define AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(ftype, ctype) \
template <> struct CohesiveFacetProperty<ftype> { \
static const ElementType cohesive_type = ctype; \
}
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_point_1, _cohesive_1d_2);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_segment_2, _cohesive_2d_4);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_segment_3, _cohesive_2d_6);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_triangle_3, _cohesive_3d_6);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_triangle_6, _cohesive_3d_12);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_quadrangle_4, _cohesive_3d_8);
AKANTU_DEFINE_COHESIVE_FACET_PROPERTY(_quadrangle_8, _cohesive_3d_16);
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_COHESIVE_ELEMENT_HH__ */
diff --git a/src/fe_engine/element.hh b/src/fe_engine/element.hh
index a2e35603e..3541a12e7 100644
--- a/src/fe_engine/element.hh
+++ b/src/fe_engine/element.hh
@@ -1,127 +1,127 @@
/**
* @file element.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Sat Jul 11 2015
*
* @brief Element helper 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_ELEMENT_HH__
#define __AKANTU_ELEMENT_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* Element */
/* -------------------------------------------------------------------------- */
class Element;
extern const Element ElementNull;
class Element {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit Element(ElementType type = _not_defined, UInt element = 0,
GhostType ghost_type = _not_ghost, ElementKind kind = _ek_regular) :
type(type), element(element),
ghost_type(ghost_type), kind(kind) {};
Element(const Element & element) {
this->type = element.type;
this->element = element.element;
this->ghost_type = element.ghost_type;
this->kind = element.kind;
}
virtual ~Element() {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline bool operator==(const Element & elem) const {
return ((element == elem.element)
&& (type == elem.type)
&& (ghost_type == elem.ghost_type)
&& (kind == elem.kind));
}
inline bool operator!=(const Element & elem) const {
return ((element != elem.element)
|| (type != elem.type)
|| (ghost_type != elem.ghost_type)
|| (kind != elem.kind));
}
bool operator<(const Element& rhs) const {
bool res = (rhs == ElementNull) || ((this->kind < rhs.kind) ||
((this->kind == rhs.kind) &&
((this->ghost_type < rhs.ghost_type) ||
((this->ghost_type == rhs.ghost_type) &&
((this->type < rhs.type) ||
((this->type == rhs.type) &&
(this->element < rhs.element)))))));
return res;
}
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
const ElementType & getType(){return type;}
const UInt & getIndex(){return element;};
const GhostType & getGhostType(){return ghost_type;}
const ElementKind & getElementKind(){return kind;}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
ElementType type;
UInt element;
GhostType ghost_type;
ElementKind kind;
};
struct CompElementLess {
bool operator() (const Element& lhs, const Element& rhs) const {
return lhs < rhs;
}
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_ELEMENT_HH__ */
diff --git a/src/fe_engine/element_class.cc b/src/fe_engine/element_class.cc
index 379148d0f..688de3b4a 100644
--- a/src/fe_engine/element_class.cc
+++ b/src/fe_engine/element_class.cc
@@ -1,86 +1,86 @@
/**
* @file element_class.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Peter Spijker <peter.spijker@epfl.ch>
*
* @date creation: Tue Jul 20 2010
* @date last modification: Thu Jul 16 2015
*
* @brief Common part of element_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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
using std::sqrt;
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_not_defined>::p1_type = _not_defined;
template<> ElementType ElementClass<_not_defined>::facet_type[] = {_not_defined};
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_point_1>::p1_type = _point_1;
template<> ElementType ElementClass<_point_1>::facet_type[] = {_point_1};
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_segment_2>::p1_type = _segment_2;
template<> ElementType ElementClass<_segment_2>::facet_type[] = {_point_1};
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_segment_3>::p1_type = _segment_2;
template<> ElementType ElementClass<_segment_3>::facet_type[] = {_point_1};
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_triangle_3>::p1_type = _triangle_3;
template<> ElementType ElementClass<_triangle_3>::facet_type[] = {_segment_2};
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_triangle_6>::p1_type = _triangle_3;
template<> ElementType ElementClass<_triangle_6>::facet_type[] = {_segment_3};
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_tetrahedron_4>::p1_type = _tetrahedron_4;
template<> ElementType ElementClass<_tetrahedron_4>::facet_type[]= {_triangle_3};
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_tetrahedron_10>::p1_type = _tetrahedron_4;
template<> ElementType ElementClass<_tetrahedron_10>::facet_type[] = {_triangle_6};
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_quadrangle_4>::p1_type = _quadrangle_4;
template<> ElementType ElementClass<_quadrangle_4>::facet_type[] = {_segment_2};
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_quadrangle_8>::p1_type = _quadrangle_4;
template<> ElementType ElementClass<_quadrangle_8>::facet_type[] = { _segment_3 };
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_hexahedron_8>::p1_type = _hexahedron_8;
template<> ElementType ElementClass<_hexahedron_8>::facet_type[] = { _quadrangle_4 };
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_hexahedron_20>::p1_type = _hexahedron_8;
template<> ElementType ElementClass<_hexahedron_20>::facet_type[] = { _quadrangle_8 };
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_pentahedron_6>::p1_type = _pentahedron_6;
template<> ElementType ElementClass<_pentahedron_6>::facet_type[] = { _triangle_3, _quadrangle_4 };
/* -------------------------------------------------------------------------- */
template<> ElementType ElementClass<_pentahedron_15>::p1_type = _pentahedron_6;
template<> ElementType ElementClass<_pentahedron_15>::facet_type[] = { _triangle_6, _quadrangle_8 };
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/element_class.hh b/src/fe_engine/element_class.hh
index 154908799..e8eac82ac 100644
--- a/src/fe_engine/element_class.hh
+++ b/src/fe_engine/element_class.hh
@@ -1,398 +1,398 @@
/**
* @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__
-__BEGIN_AKANTU__
+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; \
}
/* -------------------------------------------------------------------------- */
/// 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[];
/// 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 InterpolationPorperty structure
template <InterpolationType interpolation_type> struct InterpolationPorperty {
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 InterpolationPorperty structures for different
/// interpolation types
#define AKANTU_DEFINE_INTERPOLATION_TYPE_PROPERTY(itp_type, itp_kind, \
nb_nodes, ndim) \
template <> struct InterpolationPorperty<itp_type> { \
static const InterpolationKind kind = itp_kind; \
static const UInt nb_nodes_per_element = nb_nodes; \
static const UInt natural_space_dimension = ndim; \
}
#include "interpolation_element_tmpl.hh"
/* -------------------------------------------------------------------------- */
/// 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 =
InterpolationPorperty<interpolation_type>::kind>
class InterpolationElement {
public:
typedef InterpolationPorperty<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(__attribute__((unused))
const vector_type & natural_coord,
__attribute__((unused)) vector_type & N) {
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(__attribute__((unused))
const vector_type & natural_coord,
__attribute__((unused)) matrix_type & dnds) {
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(__attribute__((unused))
const Matrix<Real> & J,
__attribute__((unused))
Real & jacobians) {
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,
InterpolationPorperty<interpolation_type>::nb_nodes_per_element, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
ShapeDerivativesSize,
(InterpolationPorperty<interpolation_type>::nb_nodes_per_element *
InterpolationPorperty<interpolation_type>::natural_space_dimension),
UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NaturalSpaceDimension,
InterpolationPorperty<interpolation_type>::natural_space_dimension, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NbNodesPerInterpolationElement,
InterpolationPorperty<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-8);
/// 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-8);
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;
};
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#include "element_class_tmpl.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
#include "element_class_point_1_inline_impl.cc"
#include "element_class_segment_2_inline_impl.cc"
#include "element_class_segment_3_inline_impl.cc"
#include "element_class_triangle_3_inline_impl.cc"
#include "element_class_triangle_6_inline_impl.cc"
#include "element_class_tetrahedron_4_inline_impl.cc"
#include "element_class_tetrahedron_10_inline_impl.cc"
#include "element_class_quadrangle_4_inline_impl.cc"
#include "element_class_quadrangle_8_inline_impl.cc"
#include "element_class_hexahedron_8_inline_impl.cc"
#include "element_class_hexahedron_20_inline_impl.cc"
#include "element_class_pentahedron_6_inline_impl.cc"
#include "element_class_pentahedron_15_inline_impl.cc"
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "element_class_structural.hh"
#endif
#if defined(AKANTU_IGFEM)
#include "element_class_igfem.hh"
#endif
#endif /* __AKANTU_ELEMENT_CLASS_HH__ */
diff --git a/src/fe_engine/element_class_structural.hh b/src/fe_engine/element_class_structural.hh
index 7f5c81720..4ef4c017c 100644
--- a/src/fe_engine/element_class_structural.hh
+++ b/src/fe_engine/element_class_structural.hh
@@ -1,260 +1,260 @@
/**
* @file element_class_structural.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Thu Oct 22 2015
*
* @brief Specialization of the element classes for structural elements
*
* @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/>.
*
*/
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type>
class InterpolationElement<interpolation_type, _itk_structural> {
public:
typedef InterpolationPorperty<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,
const Matrix<Real> & real_nodal_coord,
UInt n = 0) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np = N(p);
computeShapes(natural_coord(p), Np, real_nodal_coord, n);
}
}
/// compute the shape values for a given point in natural coordinates
static inline void computeShapes(const Vector<Real> & natural_coord,
Vector<Real> & N,
const Matrix<Real> & real_nodal_coord,
UInt n = 0);
/**
* 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,
const Matrix<Real> & real_nodal_coord,
UInt n = 0) {
for (UInt i = 0; i < natural_coord.cols(); ++i) {
Matrix<Real> dnds_t = dnds(i);
computeDNDS(natural_coord(i), dnds_t, real_nodal_coord, n);
}
}
/**
* 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
*/
static inline void computeDNDS(const Vector<Real> & natural_coord,
Matrix<Real> & dnds,
const Matrix<Real> & real_nodal_coord,
UInt n = 0);
public:
static AKANTU_GET_MACRO_NOT_CONST(NbShapeFunctions, nb_shape_functions, UInt);
static AKANTU_GET_MACRO_NOT_CONST(NbShapeDerivatives, nb_shape_derivatives,
UInt);
static AKANTU_GET_MACRO_NOT_CONST(
ShapeSize, interpolation_property::nb_nodes_per_element, UInt);
static AKANTU_GET_MACRO_NOT_CONST(
ShapeDerivativesSize, (interpolation_property::nb_nodes_per_element *
interpolation_property::natural_space_dimension),
UInt);
static AKANTU_GET_MACRO_NOT_CONST(
NaturalSpaceDimension, interpolation_property::natural_space_dimension,
UInt);
protected:
/// nb shape functions
static const UInt nb_shape_functions;
static const UInt nb_shape_derivatives;
};
/// Macro to generate the element class structures for different structural
/// element types
/* -------------------------------------------------------------------------- */
#define AKANTU_DEFINE_STRUCTURAL_ELEMENT_CLASS_PROPERTY( \
elem_type, geom_type, interp_type, parent_el_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 ElementType parent_element_type = parent_el_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; \
}
/* -------------------------------------------------------------------------- */
/* ElementClass for structural elements */
/* -------------------------------------------------------------------------- */
template <ElementType element_type>
class ElementClass<element_type, _ek_structural>
: 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 ElementClass<ElementClassProperty<element_type>::parent_element_type>
parent_element;
public:
/// compute shape derivatives (input is dxds) for a set of points
static inline void
computeShapeDerivatives(const Matrix<Real> & natural_coord,
Tensor3<Real> & shape_deriv,
const Matrix<Real> & real_nodal_coord, UInt n = 0) {
UInt nb_points = natural_coord.cols();
if (element_type == _kirchhoff_shell) {
/// TO BE CONTINUED and moved in a _tmpl.hh
UInt spatial_dimension = real_nodal_coord.cols();
UInt nb_nodes = real_nodal_coord.rows();
const UInt projected_dim = natural_coord.rows();
Matrix<Real> rotation_matrix(real_nodal_coord);
Matrix<Real> rotated_nodal_coord(real_nodal_coord);
Matrix<Real> projected_nodal_coord(natural_coord);
/* --------------------------------------------------------------------------
*/
/* --------------------------------------------------------------------------
*/
Matrix<Real> Pe(real_nodal_coord);
Matrix<Real> Pg(real_nodal_coord);
Matrix<Real> inv_Pg(real_nodal_coord);
/// compute matrix Pe
Pe.eye();
/// compute matrix Pg
Vector<Real> Pg_col_1(spatial_dimension);
Pg_col_1(0) = real_nodal_coord(0, 1) - real_nodal_coord(0, 0);
Pg_col_1(1) = real_nodal_coord(1, 1) - real_nodal_coord(1, 0);
Pg_col_1(2) = real_nodal_coord(2, 1) - real_nodal_coord(2, 0);
Vector<Real> Pg_col_2(spatial_dimension);
Pg_col_2(0) = real_nodal_coord(0, 2) - real_nodal_coord(0, 0);
Pg_col_2(1) = real_nodal_coord(1, 2) - real_nodal_coord(1, 0);
Pg_col_2(2) = real_nodal_coord(2, 2) - real_nodal_coord(2, 0);
Vector<Real> Pg_col_3(spatial_dimension);
Pg_col_3.crossProduct(Pg_col_1, Pg_col_2);
for (UInt i = 0; i < nb_points; ++i) {
Pg(i, 0) = Pg_col_1(i);
Pg(i, 1) = Pg_col_2(i);
Pg(i, 2) = Pg_col_3(i);
}
/// compute inverse of Pg
inv_Pg.inverse(Pg);
/// compute rotation matrix
// rotation_matrix=Pe*inv_Pg;
rotation_matrix.eye();
/* --------------------------------------------------------------------------
*/
/* --------------------------------------------------------------------------
*/
rotated_nodal_coord.mul<false, false>(rotation_matrix, real_nodal_coord);
for (UInt i = 0; i < projected_dim; ++i) {
for (UInt j = 0; j < nb_points; ++j) {
projected_nodal_coord(i, j) = rotated_nodal_coord(i, j);
}
}
Tensor3<Real> dnds(projected_dim, nb_nodes, natural_coord.cols());
Tensor3<Real> J(projected_dim, projected_dim, natural_coord.cols());
parent_element::computeDNDS(natural_coord, dnds);
parent_element::computeJMat(dnds, projected_nodal_coord, J);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> shape_deriv_p = shape_deriv(p);
interpolation_element::computeDNDS(natural_coord(p), shape_deriv_p,
projected_nodal_coord, n);
Matrix<Real> dNdS = shape_deriv_p;
Matrix<Real> inv_J(projected_dim, projected_dim);
inv_J.inverse(J(p));
shape_deriv_p.mul<false, false>(inv_J, dNdS);
}
} else {
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> shape_deriv_p = shape_deriv(p);
interpolation_element::computeDNDS(natural_coord(p), shape_deriv_p,
real_nodal_coord, n);
}
}
}
/// compute jacobian (or integration variable change factor) for a given point
static inline void computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & nodal_coords,
Vector<Real> & jacobians) {
parent_element::computeJacobian(natural_coords, nodal_coords, jacobians);
}
public:
static AKANTU_GET_MACRO_NOT_CONST(Kind, _ek_structural, ElementKind);
static AKANTU_GET_MACRO_NOT_CONST(P1ElementType, _not_defined, ElementType);
static AKANTU_GET_MACRO_NOT_CONST(FacetType, _not_defined, ElementType);
static ElementType getFacetType(__attribute__((unused)) UInt t = 0) {
return _not_defined;
}
static AKANTU_GET_MACRO_NOT_CONST(
SpatialDimension, ElementClassProperty<element_type>::spatial_dimension,
UInt);
static ElementType * getFacetTypeInternal() { return NULL; }
};
#include "element_classes/element_class_bernoulli_beam_inline_impl.cc"
#include "element_classes/element_class_kirchhoff_shell_inline_impl.cc"
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/element_class_tmpl.hh b/src/fe_engine/element_class_tmpl.hh
index 6827f7be8..e6bdc6db1 100644
--- a/src/fe_engine/element_class_tmpl.hh
+++ b/src/fe_engine/element_class_tmpl.hh
@@ -1,510 +1,510 @@
/**
* @file element_class_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Thu Oct 22 2015
*
* @brief Implementation of the inline templated function of the element class
* descriptions
*
* @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 "gauss_integration_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include <type_traits>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* GeometricalElement */
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline const MatrixProxy<UInt>
GeometricalElement<geometrical_type,
shape>::getFacetLocalConnectivityPerElement(UInt t) {
return MatrixProxy<UInt>(facet_connectivity[t], nb_facets[t],
nb_nodes_per_facet[t]);
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline UInt
GeometricalElement<geometrical_type, shape>::getNbFacetsPerElement() {
UInt total_nb_facets = 0;
for (UInt n = 0; n < nb_facet_types; ++n) {
total_nb_facets += nb_facets[n];
}
return total_nb_facets;
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
inline UInt
GeometricalElement<geometrical_type, shape>::getNbFacetsPerElement(UInt t) {
return nb_facets[t];
}
/* -------------------------------------------------------------------------- */
template <GeometricalType geometrical_type, GeometricalShapeType shape>
template <class vector_type>
inline bool GeometricalElement<geometrical_type, shape>::contains(
const vector_type & coords) {
return GeometricalShapeContains<shape>::contains(coords);
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_point>::contains(const vector_type & coords) {
return (coords(0) < std::numeric_limits<Real>::epsilon());
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_square>::contains(const vector_type & coords) {
bool in = true;
for (UInt i = 0; i < coords.size() && in; ++i)
in &= ((coords(i) >= -(1. + std::numeric_limits<Real>::epsilon())) &&
(coords(i) <= (1. + std::numeric_limits<Real>::epsilon())));
return in;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_triangle>::contains(const vector_type & coords) {
bool in = true;
Real sum = 0;
for (UInt i = 0; (i < coords.size()) && in; ++i) {
in &= ((coords(i) >= -(Math::getTolerance())) &&
(coords(i) <= (1. + Math::getTolerance())));
sum += coords(i);
}
if (in)
return (in && (sum <= (1. + Math::getTolerance())));
return in;
}
/* -------------------------------------------------------------------------- */
template <>
template <class vector_type>
inline bool
GeometricalShapeContains<_gst_prism>::contains(const vector_type & coords) {
bool in = ((coords(0) >= -1.) && (coords(0) <= 1.)); // x in segment [-1, 1]
// y and z in triangle
in &= ((coords(1) >= 0) && (coords(1) <= 1.));
in &= ((coords(2) >= 0) && (coords(2) <= 1.));
Real sum = coords(1) + coords(2);
return (in && (sum <= 1));
}
/* -------------------------------------------------------------------------- */
/* InterpolationElement */
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::computeShapes(
const Matrix<Real> & natural_coord, Matrix<Real> & N) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np(N(p));
Vector<Real> ncoord_p(natural_coord(p));
computeShapes(ncoord_p, Np);
}
}
/* -------------------------------------------------------------------------- */
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::computeDNDS(
const Matrix<Real> & natural_coord, Tensor3<Real> & dnds) {
UInt nb_points = natural_coord.cols();
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> dnds_p(dnds(p));
Vector<Real> ncoord_p(natural_coord(p));
computeDNDS(ncoord_p, dnds_p);
}
}
/* -------------------------------------------------------------------------- */
/**
* interpolate on a point a field for which values are given on the
* node of the element using the shape functions at this interpolation point
*
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param shapes value of shape functions at the interpolation point
* @param interpolated interpolated value of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::interpolate(
const Matrix<Real> & nodal_values, const Vector<Real> & shapes,
Vector<Real> & interpolated) {
Matrix<Real> interpm(interpolated.storage(), nodal_values.rows(), 1);
Matrix<Real> shapesm(
shapes.storage(),
InterpolationPorperty<interpolation_type>::nb_nodes_per_element, 1);
interpm.mul<false, false>(nodal_values, shapesm);
}
/* -------------------------------------------------------------------------- */
/**
* interpolate on several points a field for which values are given on the
* node of the element using the shape functions at the interpolation point
*
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param shapes value of shape functions at the interpolation point
* @param interpolated interpolated values of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void InterpolationElement<interpolation_type, kind>::interpolate(
const Matrix<Real> & nodal_values, const Matrix<Real> & shapes,
Matrix<Real> & interpolated) {
UInt nb_points = shapes.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> Np(shapes(p));
Vector<Real> interpolated_p(interpolated(p));
interpolate(nodal_values, Np, interpolated_p);
}
}
/* -------------------------------------------------------------------------- */
/**
* interpolate the field on a point given in natural coordinates the field which
* values are given on the node of the element
*
* @param natural_coords natural coordinates of point where to interpolate \xi
* @param nodal_values values of the function per node @f$ f_{ij} = f_{n_i j}
*@f$ so it should be a matrix of size nb_nodes_per_element @f$\times@f$
*nb_degree_of_freedom
* @param interpolated interpolated value of f @f$ f_j(\xi) = \sum_i f_{n_i j}
*N_i @f$
*/
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void
InterpolationElement<interpolation_type, kind>::interpolateOnNaturalCoordinates(
const Vector<Real> & natural_coords, const Matrix<Real> & nodal_values,
Vector<Real> & interpolated) {
Vector<Real> shapes(
InterpolationPorperty<interpolation_type>::nb_nodes_per_element);
computeShapes(natural_coords, shapes);
interpolate(nodal_values, shapes, interpolated);
}
/* -------------------------------------------------------------------------- */
/// @f$ gradient_{ij} = \frac{\partial f_j}{\partial s_i} = \sum_k
/// \frac{\partial N_k}{\partial s_i}f_{j n_k} @f$
template <InterpolationType interpolation_type, InterpolationKind kind>
inline void
InterpolationElement<interpolation_type, kind>::gradientOnNaturalCoordinates(
const Vector<Real> & natural_coords, const Matrix<Real> & f,
Matrix<Real> & gradient) {
Matrix<Real> dnds(
InterpolationPorperty<interpolation_type>::natural_space_dimension,
InterpolationPorperty<interpolation_type>::nb_nodes_per_element);
computeDNDS(natural_coords, dnds);
gradient.mul<false, true>(f, dnds);
}
/* -------------------------------------------------------------------------- */
/* ElementClass */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJMat(const Tensor3<Real> & dnds,
const Matrix<Real> & node_coords,
Tensor3<Real> & J) {
UInt nb_points = dnds.size(2);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> J_p(J(p));
Matrix<Real> dnds_p(dnds(p));
computeJMat(dnds_p, node_coords, J_p);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJMat(const Matrix<Real> & dnds,
const Matrix<Real> & node_coords,
Matrix<Real> & J) {
/// @f$ J = dxds = dnds * x @f$
J.mul<false, true>(dnds, node_coords);
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJacobian(const Matrix<Real> & natural_coords,
const Matrix<Real> & node_coords,
Vector<Real> & jacobians) {
UInt nb_points = natural_coords.cols();
Matrix<Real> dnds(interpolation_property::natural_space_dimension,
interpolation_property::nb_nodes_per_element);
Matrix<Real> J(natural_coords.rows(), node_coords.rows());
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> ncoord_p(natural_coords(p));
interpolation_element::computeDNDS(ncoord_p, dnds);
computeJMat(dnds, node_coords, J);
computeJacobian(J, jacobians(p));
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeJacobian(const Tensor3<Real> & J,
Vector<Real> & jacobians) {
UInt nb_points = J.size(2);
for (UInt p = 0; p < nb_points; ++p) {
computeJacobian(J(p), jacobians(p));
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::computeJacobian(const Matrix<Real> & J,
Real & jacobians) {
if (J.rows() == J.cols()) {
jacobians = Math::det<element_property::spatial_dimension>(J.storage());
} else {
interpolation_element::computeSpecialJacobian(J, jacobians);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeShapeDerivatives(const Tensor3<Real> & J,
const Tensor3<Real> & dnds,
Tensor3<Real> & shape_deriv) {
UInt nb_points = J.size(2);
for (UInt p = 0; p < nb_points; ++p) {
Matrix<Real> shape_deriv_p(shape_deriv(p));
computeShapeDerivatives(J(p), dnds(p), shape_deriv_p);
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void
ElementClass<type, kind>::computeShapeDerivatives(const Matrix<Real> & J,
const Matrix<Real> & dnds,
Matrix<Real> & shape_deriv) {
Matrix<Real> inv_J(J.rows(), J.cols());
Math::inv<element_property::spatial_dimension>(J.storage(), inv_J.storage());
shape_deriv.mul<false, false>(inv_J, dnds);
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::computeNormalsOnNaturalCoordinates(
const Matrix<Real> & coord, Matrix<Real> & f, Matrix<Real> & normals) {
UInt dimension = normals.rows();
UInt nb_points = coord.cols();
AKANTU_DEBUG_ASSERT((dimension - 1) ==
interpolation_property::natural_space_dimension,
"cannot extract a normal because of dimension mismatch "
<< dimension - 1 << " "
<< interpolation_property::natural_space_dimension);
Matrix<Real> J(dimension, interpolation_property::natural_space_dimension);
for (UInt p = 0; p < nb_points; ++p) {
interpolation_element::gradientOnNaturalCoordinates(coord(p), f, J);
if (dimension == 2) {
Math::normal2(J.storage(), normals(p).storage());
}
if (dimension == 3) {
Math::normal3(J(0).storage(), J(1).storage(), normals(p).storage());
}
}
}
/* ------------------------------------------------------------------------- */
/**
* In the non linear cases we need to iterate to find the natural coordinates
*@f$\xi@f$
* provided real coordinates @f$x@f$.
*
* We want to solve: @f$ x- \phi(\xi) = 0@f$ with @f$\phi(\xi) = \sum_I N_I(\xi)
*x_I@f$
* the mapping function which uses the nodal coordinates @f$x_I@f$.
*
* To that end we use the Newton method and the following series:
*
* @f$ \frac{\partial \phi(x_k)}{\partial \xi} \left( \xi_{k+1} - \xi_k \right)
*= x - \phi(x_k)@f$
*
* When we consider elements embedded in a dimension higher than them (2D
*triangle in a 3D space for example)
* @f$ J = \frac{\partial \phi(\xi_k)}{\partial \xi}@f$ is of dimension
*@f$dim_{space} \times dim_{elem}@f$ which
* is not invertible in most cases. Rather we can solve the problem:
*
* @f$ J^T J \left( \xi_{k+1} - \xi_k \right) = J^T \left( x - \phi(\xi_k)
*\right) @f$
*
* So that
*
* @f$ d\xi = \xi_{k+1} - \xi_k = (J^T J)^{-1} J^T \left( x - \phi(\xi_k)
*\right) @f$
*
* So that if the series converges we have:
*
* @f$ 0 = J^T \left( \phi(\xi_\infty) - x \right) @f$
*
* And we see that this is ill-posed only if @f$ J^T x = 0@f$ which means that
*the vector provided
* is normal to any tangent which means it is outside of the element itself.
*
* @param real_coords: the real coordinates the natural coordinates are sought
*for
* @param node_coords: the coordinates of the nodes forming the element
* @param natural_coords: output->the sought natural coordinates
* @param spatial_dimension: spatial dimension of the problem
*
**/
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::inverseMap(
const Vector<Real> & real_coords, const Matrix<Real> & node_coords,
Vector<Real> & natural_coords, Real tolerance) {
UInt spatial_dimension = real_coords.size();
UInt dimension = natural_coords.size();
// matrix copy of the real_coords
Matrix<Real> mreal_coords(real_coords.storage(), spatial_dimension, 1);
// initial guess
// Matrix<Real> natural_guess(natural_coords.storage(), dimension, 1);
natural_coords.clear();
// real space coordinates provided by initial guess
Matrix<Real> physical_guess(dimension, 1);
// objective function f = real_coords - physical_guess
Matrix<Real> f(dimension, 1);
// dnds computed on the natural_guess
// Matrix<Real> dnds(interpolation_element::nb_nodes_per_element,
// spatial_dimension);
// J Jacobian matrix computed on the natural_guess
Matrix<Real> J(spatial_dimension, dimension);
// G = J^t * J
Matrix<Real> G(spatial_dimension, spatial_dimension);
// Ginv = G^{-1}
Matrix<Real> Ginv(spatial_dimension, spatial_dimension);
// J = Ginv * J^t
Matrix<Real> F(spatial_dimension, dimension);
// dxi = \xi_{k+1} - \xi in the iterative process
Matrix<Real> dxi(spatial_dimension, 1);
/* --------------------------- */
/* init before iteration loop */
/* --------------------------- */
// do interpolation
Vector<Real> physical_guess_v(physical_guess.storage(), dimension);
interpolation_element::interpolateOnNaturalCoordinates(
natural_coords, node_coords, physical_guess_v);
// compute initial objective function value f = real_coords - physical_guess
f = mreal_coords;
f -= physical_guess;
// compute initial error
Real inverse_map_error = f.norm<L_2>();
/* --------------------------- */
/* iteration loop */
/* --------------------------- */
while (tolerance < inverse_map_error) {
// compute J^t
interpolation_element::gradientOnNaturalCoordinates(natural_coords,
node_coords, J);
// compute G
G.mul<true, false>(J, J);
// inverse G
Ginv.inverse(G);
// compute F
F.mul<false, true>(Ginv, J);
// compute increment
dxi.mul<false, false>(F, f);
// update our guess
natural_coords += Vector<Real>(dxi(0));
// interpolate
interpolation_element::interpolateOnNaturalCoordinates(
natural_coords, node_coords, physical_guess_v);
// compute error
f = mreal_coords;
f -= physical_guess;
inverse_map_error = f.norm<L_2>();
}
// memcpy(natural_coords.storage(), natural_guess.storage(), sizeof(Real) *
// natural_coords.size());
}
/* -------------------------------------------------------------------------- */
template <ElementType type, ElementKind kind>
inline void ElementClass<type, kind>::inverseMap(
const Matrix<Real> & real_coords, const Matrix<Real> & node_coords,
Matrix<Real> & natural_coords, Real tolerance) {
UInt nb_points = real_coords.cols();
for (UInt p = 0; p < nb_points; ++p) {
Vector<Real> X(real_coords(p));
Vector<Real> ncoord_p(natural_coords(p));
inverseMap(X, node_coords, ncoord_p, tolerance);
}
}
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/fe_engine.cc b/src/fe_engine/fe_engine.cc
index 0b0ca4afa..88ee79e4d 100644
--- a/src/fe_engine/fe_engine.cc
+++ b/src/fe_engine/fe_engine.cc
@@ -1,85 +1,85 @@
/**
* @file fe_engine.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 20 2010
* @date last modification: Fri Dec 11 2015
*
* @brief Implementation of the FEEngine 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 "fe_engine.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
FEEngine::FEEngine(Mesh & mesh, UInt element_dimension, ID id,
MemoryID memory_id)
: Memory(id, memory_id), mesh(mesh),
normals_on_integration_points("normals_on_quad_points", id, memory_id) {
AKANTU_DEBUG_IN();
this->element_dimension = (element_dimension != _all_dimensions)
? element_dimension
: mesh.getSpatialDimension();
init();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FEEngine::init() {}
/* -------------------------------------------------------------------------- */
FEEngine::~FEEngine() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FEEngine::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "FEEngine [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + element dimension : " << element_dimension
<< std::endl;
stream << space << " + mesh [" << std::endl;
mesh.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/fe_engine.hh b/src/fe_engine/fe_engine.hh
index 046eab625..4908b104e 100644
--- a/src/fe_engine/fe_engine.hh
+++ b/src/fe_engine/fe_engine.hh
@@ -1,385 +1,385 @@
/**
* @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"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Mesh;
class Integrator;
class ShapeFunctions;
class DOFManager;
class Element;
}
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* The generic FEEngine class derived in a FEEngineTemplate class
* containing the
* shape functions and the integration method
*/
class FEEngine : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FEEngine(Mesh & mesh, UInt spatial_dimension = _all_dimensions, ID id = "fem",
MemoryID memory_id = 0);
virtual ~FEEngine();
/* ------------------------------------------------------------------------ */
/* 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;
/// 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;
/// 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();
}
/// assemble a field as a lumped matrix (ex. rho in lumped mass)
virtual void assembleFieldLumped(__attribute__((unused))
const Array<Real> & field,
__attribute__((unused)) const ID & lumped,
__attribute__((unused)) const ID & dof_id,
__attribute__((unused))
DOFManager & dof_manager,
__attribute__((unused)) ElementType type,
__attribute__((unused))
const GhostType & ghost_type) const {
AKANTU_DEBUG_TO_IMPLEMENT();
};
/// assemble a field as a matrix (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 & matrix,
__attribute__((unused)) ElementType type,
__attribute__((unused))
const GhostType & ghost_type) 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();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// 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;
}
-__END_AKANTU__
+} // 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_inline_impl.cc b/src/fe_engine/fe_engine_inline_impl.cc
index 6d33519a5..b70246dc9 100644
--- a/src/fe_engine/fe_engine_inline_impl.cc
+++ b/src/fe_engine/fe_engine_inline_impl.cc
@@ -1,207 +1,207 @@
/**
* @file fe_engine_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jul 20 2010
* @date last modification: Sat Sep 05 2015
*
* @brief Implementation of the inline functions of the FEEngine 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 "fe_engine.hh"
#include "mesh.hh"
#include "element_class.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_FE_ENGINE_INLINE_IMPL_CC__
#define __AKANTU_FE_ENGINE_INLINE_IMPL_CC__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
inline Real FEEngine::getElementInradius(const Matrix<Real> & coord,
const ElementType & type) {
AKANTU_DEBUG_IN();
Real inradius = 0;
#define GET_INRADIUS(type) inradius = ElementClass<type>::getInradius(coord);
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_INRADIUS);
#undef GET_INRADIUS
AKANTU_DEBUG_OUT();
return inradius;
}
/* -------------------------------------------------------------------------- */
inline InterpolationType
FEEngine::getInterpolationType(const ElementType & type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = _itp_not_defined;
#define GET_ITP(type) itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_ITP);
#undef GET_ITP
AKANTU_DEBUG_OUT();
return itp_type;
}
/* -------------------------------------------------------------------------- */
/// @todo rewrite this function in order to get the cohesive element
/// type directly from the facet
#if defined(AKANTU_COHESIVE_ELEMENT)
inline ElementType FEEngine::getCohesiveElementType(const ElementType & type) {
AKANTU_DEBUG_IN();
ElementType ctype;
#define GET_COHESIVE_TYPE(type) \
ctype = CohesiveFacetProperty<type>::cohesive_type;
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_COHESIVE_TYPE);
#undef GET_COHESIVE_TYPE
AKANTU_DEBUG_OUT();
return ctype;
}
#else
inline ElementType
FEEngine::getCohesiveElementType(__attribute__((unused))
const ElementType & type_facet) {
return _not_defined;
}
#endif
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_IGFEM)
-__END_AKANTU__
+} // akantu
#include "igfem_helper.hh"
-__BEGIN_AKANTU__
+namespace akantu {
inline Vector<ElementType>
FEEngine::getIGFEMElementTypes(const ElementType & type) {
#define GET_IGFEM_ELEMENT_TYPES(type) \
return IGFEMHelper::getIGFEMElementTypes<type>();
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(GET_IGFEM_ELEMENT_TYPES);
#undef GET_IGFEM_ELEMENT_TYPES
}
#endif
/* -------------------------------------------------------------------------- */
template <typename T>
void FEEngine::extractNodalToElementField(const Mesh & mesh,
const Array<T> & nodal_f,
Array<T> & elemental_f,
const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_degree_of_freedom = nodal_f.getNbComponent();
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt * conn_val = mesh.getConnectivity(type, ghost_type).storage();
if (filter_elements != empty_filter) {
nb_element = filter_elements.getSize();
}
elemental_f.resize(nb_element);
T * nodal_f_val = nodal_f.storage();
T * f_val = elemental_f.storage();
UInt * el_conn;
for (UInt el = 0; el < nb_element; ++el) {
if (filter_elements != empty_filter)
el_conn = conn_val + filter_elements(el) * nb_nodes_per_element;
else
el_conn = conn_val + el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = *(el_conn + n);
std::copy(nodal_f_val + node * nb_degree_of_freedom,
nodal_f_val + (node + 1) * nb_degree_of_freedom, f_val);
f_val += nb_degree_of_freedom;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void FEEngine::filterElementalData(const Mesh & mesh, const Array<T> & elem_f,
Array<T> & filtered_f,
const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (nb_element == 0) {
filtered_f.resize(0);
return;
}
UInt nb_degree_of_freedom = elem_f.getNbComponent();
UInt nb_data_per_element = elem_f.getSize() / nb_element;
if (filter_elements != empty_filter) {
nb_element = filter_elements.getSize();
}
filtered_f.resize(nb_element * nb_data_per_element);
T * elem_f_val = elem_f.storage();
T * f_val = filtered_f.storage();
UInt el_offset;
for (UInt el = 0; el < nb_element; ++el) {
if (filter_elements != empty_filter)
el_offset = filter_elements(el);
else
el_offset = el;
std::copy(elem_f_val +
el_offset * nb_data_per_element * nb_degree_of_freedom,
elem_f_val +
(el_offset + 1) * nb_data_per_element * nb_degree_of_freedom,
f_val);
f_val += nb_degree_of_freedom * nb_data_per_element;
}
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_FE_ENGINE_INLINE_IMPL_CC__ */
diff --git a/src/fe_engine/fe_engine_template.hh b/src/fe_engine/fe_engine_template.hh
index e87f95d9e..b5891f36f 100644
--- a/src/fe_engine/fe_engine_template.hh
+++ b/src/fe_engine/fe_engine_template.hh
@@ -1,368 +1,368 @@
/**
* @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;
}
-__BEGIN_AKANTU__
+namespace akantu {
template <ElementKind> struct AssembleLumpedTemplateHelper;
template <ElementKind> struct AssembleFieldMatrixHelper;
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();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// pre-compute all the shape functions, their derivatives and the jacobians
void initShapeFunctions(const GhostType & ghost_type = _not_ghost);
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;
/// 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;
/// 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;
/// 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;
/// 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;
/// get the number of integration points
UInt getNbIntegrationPoints(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/// get shapes precomputed
const Array<Real> & getShapes(const ElementType & type,
const GhostType & ghost_type = _not_ghost,
UInt id = 0) const;
/// get the derivatives of shapes
const Array<Real> &
getShapesDerivatives(const ElementType & type,
const GhostType & ghost_type = _not_ghost,
UInt id = 0) const;
/// get integration points
const inline Matrix<Real> &
getIntegrationPoints(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* 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;
/// 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;
/// 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;
/// 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;
/// 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;
/// 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;
/// 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;
/// 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;
/// 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;
/// 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;
/* ------------------------------------------------------------------------ */
/* Other methods */
/* ------------------------------------------------------------------------ */
/// pre-compute normals on integration points
void
computeNormalsOnIntegrationPoints(const GhostType & ghost_type = _not_ghost);
void
computeNormalsOnIntegrationPoints(const Array<Real> & field,
const GhostType & ghost_type = _not_ghost);
void computeNormalsOnIntegrationPoints(
const Array<Real> & field, Array<Real> & normal, const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
template <ElementType type>
void computeNormalsOnIntegrationPoints(const Array<Real> & field,
Array<Real> & normal,
const GhostType & ghost_type) const;
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// assemble a field as a lumped matrix (ex. rho in lumped mass)
void assembleFieldLumped(const Array<Real> & field, const ID & lumped,
const ID & dof_id, DOFManager & dof_manager,
ElementType type,
const GhostType & ghost_type = _not_ghost) const;
/// assemble a field as a matrix (ex. rho to mass matrix)
template <class Functor>
void assembleFieldMatrix(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 AssembleLumpedTemplateHelper<kind>;
friend struct AssembleFieldMatrixHelper<kind>;
friend struct AssembleFieldMatrixStructHelper<kind, void>;
/// templated function to compute the scaling to assemble a lumped matrix
template <ElementType type>
void assembleLumpedTemplate(const Array<Real> & field, const ID & lumped,
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 & lumped,
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 & lumped, 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(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
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the shape class (probably useless: see getShapeFunction)
const ShapeFunctions & getShapeFunctionsInterface() const {
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 { return integrator; };
/// get the integrator class
const Integ & getIntegrator() const { return integrator; };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
Integ integrator;
Shape shape_functions;
};
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "fe_engine_template_tmpl.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_cohesive.cc b/src/fe_engine/fe_engine_template_cohesive.cc
index 2d3fce764..eb2ad7c71 100644
--- a/src/fe_engine/fe_engine_template_cohesive.cc
+++ b/src/fe_engine/fe_engine_template_cohesive.cc
@@ -1,174 +1,174 @@
/**
* @file fe_engine_template_cohesive.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Oct 31 2012
* @date last modification: Thu Oct 15 2015
*
* @brief Specialization of the FEEngineTemplate for cohesive element
*
* @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 "fe_engine_template.hh"
#include "shape_cohesive.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* compatibility functions */
/* -------------------------------------------------------------------------- */
template <>
Real FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
integrate(const Array<Real> & f, const ElementType & type,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
#ifndef AKANTU_NDEBUG
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements != empty_filter)
nb_element = filter_elements.getSize();
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.getSize() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID()
<< ") has not the good size.");
AKANTU_DEBUG_ASSERT(f.getNbComponent() == 1,
"The vector f("
<< f.getID()
<< ") has not the good number of component.");
#endif
Real integral = 0.;
#define INTEGRATE(type) \
integral = integrator.integrate<type>(f, ghost_type, filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INTEGRATE);
#undef INTEGRATE
AKANTU_DEBUG_OUT();
return integral;
}
/* -------------------------------------------------------------------------- */
template <>
void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
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 {
#ifndef AKANTU_NDEBUG
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (filter_elements == filter_elements)
nb_element = filter_elements.getSize();
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.getSize() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.getSize()
<< ") 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.");
AKANTU_DEBUG_ASSERT(intf.getSize() == nb_element,
"The vector intf(" << intf.getID()
<< ") has not the good size.");
#endif
#define INTEGRATE(type) \
integrator.integrate<type>(f, intf, nb_degree_of_freedom, ghost_type, \
filter_elements);
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(INTEGRATE);
#undef INTEGRATE
}
/* -------------------------------------------------------------------------- */
template <>
void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
gradientOnIntegrationPoints(const Array<Real> &, Array<Real> &, const UInt,
const ElementType &, const GhostType &,
const Array<UInt> &) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
template <>
void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive,
DefaultIntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints<_cohesive_1d_2>(
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 1D cohesive elements!");
const ElementType type = _cohesive_1d_2;
const ElementType facet_type = Mesh::getFacetType(type);
UInt nb_element = mesh.getConnectivity(type, ghost_type).getSize();
normal.resize(nb_element);
Array<Element> & facets =
mesh.getMeshFacets().getSubelementToElement(type, ghost_type);
Array<std::vector<Element> > & segments =
mesh.getMeshFacets().getElementToSubelement(facet_type, ghost_type);
Real values[2];
for (UInt elem = 0; elem < nb_element; ++elem) {
for (UInt p = 0; p < 2; ++p) {
Element f = facets(elem, p);
Element seg = segments(f.element)[0];
mesh.getBarycenter(seg.element, seg.type, &(values[p]), seg.ghost_type);
}
Real difference = values[0] - values[1];
AKANTU_DEBUG_ASSERT(difference != 0.,
"Error in normal computation for cohesive elements");
normal(elem) = difference / std::abs(difference);
}
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/fe_engine_template_tmpl.hh b/src/fe_engine/fe_engine_template_tmpl.hh
index 11813e4a7..b134a3d4f 100644
--- a/src/fe_engine/fe_engine_template_tmpl.hh
+++ b/src/fe_engine/fe_engine_template_tmpl.hh
@@ -1,1671 +1,1671 @@
/**
* @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"
-__BEGIN_AKANTU__
+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
*/
template <ElementKind kind> struct GradientOnIntegrationPointsHelper {
template <class S>
static void call(__attribute__((unused)) const S & shape_functions,
__attribute__((unused)) Mesh & mesh,
__attribute__((unused)) const Array<Real> & u,
__attribute__((unused)) Array<Real> & nablauq,
__attribute__((unused)) const UInt nb_degree_of_freedom,
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) const GhostType & ghost_type,
__attribute__((unused))
const Array<UInt> & filter_elements) {
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
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.getSize();
UInt nb_points =
shape_functions.getIntegrationPoints(type, ghost_type).cols();
#ifndef AKANTU_NDEBUG
UInt element_dimension = mesh.getSpatialDimension(type);
AKANTU_DEBUG_ASSERT(u.getSize() == 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.getSize() == nb_element * nb_points,
// "The vector nablauq(" << nablauq.getID()
// << ") has not the good size.");
#endif
nablauq.resize(nb_element * nb_points);
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();
Mesh::type_iterator it = mesh.firstType(element_dimension, ghost_type, kind);
Mesh::type_iterator end = mesh.lastType(element_dimension, ghost_type, kind);
for (; it != end; ++it) {
ElementType type = *it;
integrator.initIntegrator(nodes, type, ghost_type);
const Matrix<Real> & 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
*/
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
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.getSize();
#ifndef AKANTU_NDEBUG
UInt nb_quadrature_points = getNbIntegrationPoints(type);
AKANTU_DEBUG_ASSERT(f.getSize() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.getSize()
<< ") 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);
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
*/
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
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.getSize();
UInt nb_quadrature_points = getNbIntegrationPoints(type, ghost_type);
AKANTU_DEBUG_ASSERT(f.getSize() == nb_element * nb_quadrature_points,
"The vector f("
<< f.getID() << ") has not the good size. ("
<< f.getSize()
<< "!=" << 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 = 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
*/
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
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 = 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
*/
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
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.getSize();
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.getSize() == nb_element * nb_quadrature_points,
"The vector f(" << f.getID() << " size " << f.getSize()
<< ") 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);
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
*/
template <ElementKind kind> struct InterpolateOnIntegrationPointsHelper {
template <class S>
static void call(__attribute__((unused)) const S & shape_functions,
__attribute__((unused)) const Array<Real> & u,
__attribute__((unused)) Array<Real> & uq,
__attribute__((unused)) const UInt nb_degree_of_freedom,
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) const GhostType & ghost_type,
__attribute__((unused))
const Array<UInt> & filter_elements) {
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
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.getSize();
#ifndef AKANTU_NDEBUG
AKANTU_DEBUG_ASSERT(u.getSize() == 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);
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;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
ElementTypeMapArray<Real>::type_iterator it =
uq.firstType(_all_dimensions, ghost_type, kind);
ElementTypeMapArray<Real>::type_iterator last =
uq.lastType(_all_dimensions, ghost_type, kind);
for (; it != last; ++it) {
ElementType type = *it;
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->getSize();
} 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());
mesh.initElementTypeMapArray(quadrature_points_coordinates, spatial_dimension,
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
*/
template <ElementKind kind> struct InterpolateHelper {
template <class S>
static void call(__attribute__((unused)) const S & shape_functions,
__attribute__((unused)) const Vector<Real> & real_coords,
__attribute__((unused)) UInt elem,
__attribute__((unused)) const Matrix<Real> & nodal_values,
__attribute__((unused)) Vector<Real> & interpolated,
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) const GhostType & ghost_type) {
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
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();
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
Mesh::type_iterator it = mesh.firstType(element_dimension, ghost_type, kind);
Mesh::type_iterator end = mesh.lastType(element_dimension, ghost_type, kind);
for (; it != end; ++it) {
ElementType type = *it;
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
it = mesh.firstType(element_dimension, ghost_type, kind);
for (; it != end; ++it) {
Array<Real> & normals_on_quad =
normals_on_integration_points(*it, ghost_type);
computeNormalsOnIntegrationPoints(field, normals_on_quad, *it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
template <ElementKind kind> struct ComputeNormalsOnIntegrationPoints {
template <template <ElementKind, class> class I,
template <ElementKind> class S, ElementKind k, class IOF>
static void call(__attribute__((unused))
const FEEngineTemplate<I, S, k, IOF> & fem,
__attribute__((unused)) const Array<Real> & field,
__attribute__((unused)) Array<Real> & normal,
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) const GhostType & ghost_type) {
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
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 {
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();
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).getSize();
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();
}
/* -------------------------------------------------------------------------- */
/* Matrix lumping functions */
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
template <ElementKind kind> struct AssembleLumpedTemplateHelper {};
#define ASSEMBLE_LUMPED(type) \
fem.template assembleLumpedTemplate<type>(field_1, lumped, dof_id, \
dof_manager, ghost_type)
#define AKANTU_SPECIALIZE_ASSEMBLE_HELPER(kind) \
template <> struct AssembleLumpedTemplateHelper<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_1, const ID & lumped, \
const ID & dof_id, DOFManager & dof_manager, \
ElementType type, const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_LUMPED, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_ASSEMBLE_HELPER)
#undef AKANTU_SPECIALIZE_ASSEMBLE_HELPER
#undef ASSEMBLE_LUMPED
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IOF>
void FEEngineTemplate<I, S, kind, IOF>::assembleFieldLumped(
const Array<Real> & field, const ID & lumped, const ID & dof_id,
DOFManager & dof_manager, ElementType type,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
AssembleLumpedTemplateHelper<kind>::call(*this, field, lumped, dof_id,
dof_manager, type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
template <ElementKind kind> struct AssembleFieldMatrixHelper {};
#define ASSEMBLE_MATRIX(type) \
fem.template assembleFieldMatrix<Functor, type>( \
field_funct, matrix_id, dof_id, dof_manager, ghost_type)
#define AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER(kind) \
template <> struct AssembleFieldMatrixHelper<kind> { \
template <template <ElementKind, class> class I, \
template <ElementKind> class S, ElementKind k, class IOF, \
class Functor> \
static void call(const FEEngineTemplate<I, S, k, IOF> & fem, \
Functor field_funct, const ID & matrix_id, \
const ID & dof_id, DOFManager & dof_manager, \
ElementType type, const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_MATRIX, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER)
#undef AKANTU_SPECIALIZE_ASSEMBLE_FIELD_MATRIX_HELPER
#undef ASSEMBLE_MATRIX
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IOF>
template <class Functor>
void FEEngineTemplate<I, S, kind, IOF>::assembleFieldMatrix(
Functor field_funct, const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager, ElementType type,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
AssembleFieldMatrixHelper<kind>::template call(
*this, field_funct, matrix_id, dof_id, dof_manager, type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
assembleLumpedTemplate(const Array<Real> & field, const ID & lumped,
const ID & dof_id, DOFManager & dof_manager,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
this->template assembleLumpedRowSum<type>(field, lumped, dof_id, dof_manager,
ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j dV =
* \int \rho \varphi_i dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
assembleLumpedRowSum(const Array<Real> & field, const ID & lumped,
const ID & dof_id, DOFManager & dof_manager,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt shapes_size = ElementClass<type>::getShapeSize();
UInt nb_degree_of_freedom = field.getNbComponent();
Array<Real> * field_times_shapes =
new Array<Real>(0, shapes_size * nb_degree_of_freedom);
shape_functions.template fieldTimesShapes<type>(field, *field_times_shapes,
ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<Real> * int_field_times_shapes = new Array<Real>(
nb_element, shapes_size * nb_degree_of_freedom, "inte_rho_x_shapes");
integrator.template integrate<type>(
*field_times_shapes, *int_field_times_shapes,
nb_degree_of_freedom * shapes_size, ghost_type, empty_filter);
delete field_times_shapes;
dof_manager.assembleElementalArrayToLumpedMatrix(
dof_id, *int_field_times_shapes, lumped, type, ghost_type);
delete int_field_times_shapes;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = c * M_{ii} = \int_{V_e} \rho dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::
assembleLumpedDiagonalScaling(const Array<Real> & field, const ID & lumped,
const ID & dof_id, DOFManager & dof_manager,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
const ElementType & type_p1 = ElementClass<type>::getP1ElementType();
UInt nb_nodes_per_element_p1 = Mesh::getNbNodesPerElement(type_p1);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points =
integrator.template getIntegrationPoints<type>(ghost_type).cols();
UInt nb_degree_of_freedom = field.getNbComponent();
UInt nb_element = field.getSize() / nb_quadrature_points;
Vector<Real> nodal_factor(nb_nodes_per_element);
#define ASSIGN_WEIGHT_TO_NODES(corner, mid) \
{ \
for (UInt n = 0; n < nb_nodes_per_element_p1; n++) \
nodal_factor(n) = corner; \
for (UInt n = nb_nodes_per_element_p1; n < nb_nodes_per_element; n++) \
nodal_factor(n) = mid; \
}
if (type == _triangle_6)
ASSIGN_WEIGHT_TO_NODES(1. / 12., 1. / 4.);
if (type == _tetrahedron_10)
ASSIGN_WEIGHT_TO_NODES(1. / 32., 7. / 48.);
if (type == _quadrangle_8)
ASSIGN_WEIGHT_TO_NODES(
3. / 76.,
16. / 76.); /** coeff. derived by scaling
* the diagonal terms of the corresponding
* consistent mass computed with 3x3 gauss points;
* coeff. are (1./36., 8./36.) for 2x2 gauss points */
if (type == _hexahedron_20)
ASSIGN_WEIGHT_TO_NODES(
7. / 248.,
16. / 248.); /** coeff. derived by scaling
* the diagonal terms of the corresponding
* consistent mass computed with 3x3x3 gauss points;
* coeff. are (1./40.,
* 1./15.) for 2x2x2 gauss points */
if (type == _pentahedron_15) {
// coefficients derived by scaling the diagonal terms of the corresponding
// consistent mass computed with 8 gauss points;
for (UInt n = 0; n < nb_nodes_per_element_p1; n++)
nodal_factor(n) = 51. / 2358.;
Real mid_triangle = 192. / 2358.;
Real mid_quadrangle = 300. / 2358.;
nodal_factor(6) = mid_triangle;
nodal_factor(7) = mid_triangle;
nodal_factor(8) = mid_triangle;
nodal_factor(9) = mid_quadrangle;
nodal_factor(10) = mid_quadrangle;
nodal_factor(11) = mid_quadrangle;
nodal_factor(12) = mid_triangle;
nodal_factor(13) = mid_triangle;
nodal_factor(14) = mid_triangle;
}
if (nb_element == 0) {
AKANTU_DEBUG_OUT();
return;
}
#undef ASSIGN_WEIGHT_TO_NODES
/// compute @f$ \int \rho dV = \rho V @f$ for each element
Array<Real> * int_field =
new Array<Real>(field.getSize(), nb_degree_of_freedom, "inte_rho_x");
integrator.template integrate<type>(field, *int_field, nb_degree_of_freedom,
ghost_type, empty_filter);
/// distribute the mass of the element to the nodes
Array<Real> * lumped_per_node = new Array<Real>(
nb_element, nb_degree_of_freedom * nb_nodes_per_element, "mass_per_node");
Array<Real>::const_vector_iterator int_field_it =
int_field->begin(nb_degree_of_freedom);
Array<Real>::matrix_iterator lumped_per_node_it =
lumped_per_node->begin(nb_degree_of_freedom, nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
Vector<Real> l = (*lumped_per_node_it)(n);
l = *int_field_it;
l *= nodal_factor(n);
}
++int_field_it;
++lumped_per_node_it;
}
delete int_field;
dof_manager.assembleElementalArrayToLumpedMatrix(dof_id, *lumped_per_node,
lumped, type, ghost_type);
delete lumped_per_node;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* @f$ \tilde{M}_{i} = \sum_j M_{ij} = \sum_j \int \rho \varphi_i \varphi_j dV =
* \int \rho \varphi_i dV @f$
*/
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <class Functor, ElementType type>
void FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
Functor field_funct, const ID & matrix_id, const ID & dof_id,
DOFManager & dof_manager, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt shapes_size = ElementClass<type>::getShapeSize();
UInt nb_degree_of_freedom = dof_manager.getDOFs(dof_id).getNbComponent();
UInt lmat_size = nb_degree_of_freedom * shapes_size;
UInt nb_element = mesh.getNbElement(type, ghost_type);
// \int N * N so degree 2 * degree of N
const UInt polynomial_degree =
2 * ElementClassProperty<type>::polynomial_degree;
Matrix<Real> integration_points =
integrator.template getIntegrationPoints<type, polynomial_degree>();
UInt nb_integration_points = integration_points.cols();
UInt vect_size = nb_integration_points * nb_element;
Array<Real> shapes(0, shapes_size);
shape_functions.template computeShapesOnIntegrationPoints<type>(
mesh.getNodes(), integration_points, shapes, ghost_type);
Array<Real> integration_points_pos(vect_size, mesh.getSpatialDimension());
shape_functions.template interpolateOnIntegrationPoints<type>(
mesh.getNodes(), integration_points_pos, mesh.getSpatialDimension(),
shapes, ghost_type, empty_filter);
Array<Real> * modified_shapes =
new Array<Real>(vect_size, lmat_size * nb_degree_of_freedom);
modified_shapes->clear();
Array<Real> * local_mat = new Array<Real>(vect_size, lmat_size * lmat_size);
Array<Real>::matrix_iterator mshapes_it =
modified_shapes->begin(nb_degree_of_freedom, lmat_size);
Array<Real>::const_vector_iterator shapes_it = shapes.begin(shapes_size);
for (UInt q = 0; q < vect_size; ++q, ++mshapes_it, ++shapes_it) {
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
for (UInt s = 0; s < shapes_size; ++s) {
(*mshapes_it)(d, s * nb_degree_of_freedom + d) = (*shapes_it)(s);
}
}
}
Array<Real> field(vect_size, nb_degree_of_freedom);
Array<Real>::matrix_iterator field_c_it = field.begin_reinterpret(
nb_degree_of_freedom, nb_integration_points, nb_element);
Array<Real>::const_matrix_iterator pos_it =
integration_points_pos.begin_reinterpret(
mesh.getSpatialDimension(), nb_integration_points, nb_element);
Element el;
el.type = type, el.ghost_type = ghost_type;
for (el.element = 0; el.element < nb_element;
++el.element, ++field_c_it, ++pos_it) {
field_funct(*field_c_it, el, *pos_it);
}
mshapes_it = modified_shapes->begin(nb_degree_of_freedom, lmat_size);
Array<Real>::matrix_iterator lmat = local_mat->begin(lmat_size, lmat_size);
Array<Real>::const_vector_iterator field_it =
field.begin_reinterpret(nb_degree_of_freedom, field.getSize());
for (UInt q = 0; q < vect_size; ++q, ++lmat, ++mshapes_it, ++field_it) {
const Vector<Real> & rho = *field_it;
const Matrix<Real> & N = *mshapes_it;
Matrix<Real> & mat = *lmat;
Matrix<Real> Nt = N.transpose();
for (UInt d = 0; d < Nt.cols(); ++d) {
Nt(d) *= rho(d);
}
mat.mul<false, false>(Nt, N);
}
delete modified_shapes;
Array<Real> * int_field_times_shapes =
new Array<Real>(nb_element, lmat_size * lmat_size, "inte_rho_x_shapes");
this->integrator.template integrate<type, polynomial_degree>(
*local_mat, *int_field_times_shapes, lmat_size * lmat_size, ghost_type);
delete local_mat;
dof_manager.assembleElementalMatricesToMatrix(
matrix_id, dof_id, *int_field_times_shapes, type, ghost_type);
delete int_field_times_shapes;
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(__attribute__((unused)) const S & shape_functions,
__attribute__((unused)) const Vector<Real> & real_coords,
__attribute__((unused)) UInt element,
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) Vector<Real> & natural_coords,
__attribute__((unused)) 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
*/
template <ElementKind kind> struct ContainsHelper {
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)) const GhostType & ghost_type) {
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
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 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
*/
template <ElementKind kind> struct ComputeShapesHelper {
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)) Vector<Real> & shapes,
__attribute__((unused)) const GhostType & ghost_type) {
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
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();
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
*/
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
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();
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
*/
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
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 GetNbIntegrationPointsHelper<kind>::call(integrator, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
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
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 GetShapesHelper<kind>::call(shape_functions, type, ghost_type);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
template <ElementKind kind> struct GetShapesDerivativesHelper {
template <template <ElementKind> class S, ElementKind k>
static const Array<Real> &
call(__attribute__((unused)) const S<k> & shape_functions,
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) const GhostType & ghost_type,
__attribute__((unused)) UInt id) {
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
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 GetShapesDerivativesHelper<kind>::call(shape_functions, type,
ghost_type, id);
}
/* -------------------------------------------------------------------------- */
/**
* Helper class to be able to write a partial specialization on the element kind
*/
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
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 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;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#include "integrator_gauss.hh"
#include "shape_lagrange.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
template <>
inline void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular>::
assembleLumpedTemplate<_triangle_6>(const Array<Real> & field,
const ID & lumped, const ID & dof_id,
DOFManager & dof_manager,
const GhostType & ghost_type) const {
assembleLumpedDiagonalScaling<_triangle_6>(field, lumped, dof_id, dof_manager,
ghost_type);
}
/* -------------------------------------------------------------------------- */
template <>
template <>
inline void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular,
DefaultIntegrationOrderFunctor>::
assembleLumpedTemplate<_tetrahedron_10>(
const Array<Real> & field, const ID & lumped, const ID & dof_id,
DOFManager & dof_manager, const GhostType & ghost_type) const {
assembleLumpedDiagonalScaling<_tetrahedron_10>(field, lumped, dof_id,
dof_manager, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <>
template <>
inline void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular>::
assembleLumpedTemplate<_quadrangle_8>(const Array<Real> & field,
const ID & lumped, const ID & dof_id,
DOFManager & dof_manager,
const GhostType & ghost_type) const {
assembleLumpedDiagonalScaling<_quadrangle_8>(field, lumped, dof_id,
dof_manager, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <>
template <>
inline void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular>::
assembleLumpedTemplate<_hexahedron_20>(const Array<Real> & field,
const ID & lumped, const ID & dof_id,
DOFManager & dof_manager,
const GhostType & ghost_type) const {
assembleLumpedDiagonalScaling<_hexahedron_20>(field, lumped, dof_id,
dof_manager, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <>
template <>
inline void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular,
DefaultIntegrationOrderFunctor>::
assembleLumpedTemplate<_pentahedron_15>(
const Array<Real> & field, const ID & lumped, const ID & dof_id,
DOFManager & dof_manager, const GhostType & ghost_type) const {
assembleLumpedDiagonalScaling<_pentahedron_15>(field, lumped, dof_id,
dof_manager, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <>
template <>
inline void FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular,
DefaultIntegrationOrderFunctor>::
computeNormalsOnIntegrationPoints<_point_1>(
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).getSize();
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();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/fe_engine_template_tmpl_struct.hh b/src/fe_engine/fe_engine_template_tmpl_struct.hh
index 2d21759a3..3f1396218 100644
--- a/src/fe_engine/fe_engine_template_tmpl_struct.hh
+++ b/src/fe_engine/fe_engine_template_tmpl_struct.hh
@@ -1,246 +1,246 @@
/**
* @file fe_engine_template_tmpl_struct.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 07 2014
* @date last modification: Thu Oct 15 2015
*
* @brief Template implementation of FEEngineTemplate for Structural Element
* Kinds
*
* @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 "shape_linked.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <>
inline const Array<Real> &
FEEngineTemplate<IntegratorGauss, ShapeLinked, _ek_structural,
DefaultIntegrationOrderFunctor>::
getShapesDerivatives(const ElementType & type, const GhostType & ghost_type,
UInt id) const {
AKANTU_DEBUG_IN();
const Array<Real> * ret = NULL;
#define GET_SHAPES(type) \
ret = &(shape_functions.getShapesDerivatives(type, ghost_type, id));
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(GET_SHAPES);
#undef GET_SHAPES
AKANTU_DEBUG_OUT();
return *ret;
}
/* -------------------------------------------------------------------------- */
template <>
inline const Array<Real> & FEEngineTemplate<
IntegratorGauss, ShapeLinked, _ek_structural,
DefaultIntegrationOrderFunctor>::getShapes(const ElementType & type,
const GhostType & ghost_type,
UInt id) const {
AKANTU_DEBUG_IN();
const Array<Real> * ret = NULL;
#define GET_SHAPES(type) \
ret = &(shape_functions.getShapes(type, ghost_type, id));
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(GET_SHAPES);
#undef GET_SHAPES
AKANTU_DEBUG_OUT();
return *ret;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, typename = void>
struct AssembleFieldMatrixStructHelper {};
template <ElementKind kind>
struct AssembleFieldMatrixStructHelper<
kind, typename std::enable_if<kind == _ek_structural>::type> {
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_1, UInt nb_degree_of_freedom,
SparseMatrix & M, Array<Real> * n,
ElementTypeMapArray<Real> & rotation_mat,
const ElementType & type, const GhostType & ghost_type) {
#define ASSEMBLE_MATRIX(type) \
fem.template assembleFieldMatrix<type>(field_1, nb_degree_of_freedom, M, n, \
rotation_mat, ghost_type)
AKANTU_BOOST_KIND_ELEMENT_SWITCH(ASSEMBLE_MATRIX, _ek_structural);
#undef ASSEMBLE_MATRIX
}
};
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::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) const {
AKANTU_DEBUG_IN();
AssembleFieldMatrixStructHelper<kind>::template call(
*this, field_1, nb_degree_of_freedom, M, n, rotation_mat, type,
ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::computeShapesMatrix(
const ElementType &, UInt, UInt, Array<Real> *,
__attribute__((unused)) UInt, UInt, UInt, const bool,
const GhostType &) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
inline void FEEngineTemplate<IntegratorGauss, ShapeLinked, _ek_structural,
DefaultIntegrationOrderFunctor>::
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, // true +, false -
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type);
UInt nb_quadrature_points = getNbIntegrationPoints(type);
UInt nt_n_field_size = nb_degree_of_freedom * nb_nodes_per_element;
UInt n_size = n->getNbComponent() / nt_n_field_size;
Array<Real>::const_vector_iterator shape =
getShapes(type, ghost_type, id).begin(nb_nodes_per_element);
Array<Real>::matrix_iterator N_it = n->begin(n_size, nt_n_field_size);
int c;
if (sign == true) {
c = 1;
} else {
c = -1;
}
UInt line = degree_interpolated;
UInt coll = degree_to_interpolate;
for (UInt e = 0; e < nb_element; ++e) {
for (UInt q = 0; q < nb_quadrature_points; ++q, ++N_it, ++shape) {
const Vector<Real> & shapes = *shape;
Matrix<Real> & N = *N_it;
N(line, coll) = shapes(0) * c;
N(line, coll + nb_degree_of_freedom) = shapes(1) * c;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
template <ElementType type>
inline void FEEngineTemplate<IntegratorGauss, ShapeLinked, _ek_structural,
DefaultIntegrationOrderFunctor>::
assembleFieldMatrix(const Array<Real> & field_1, UInt nb_degree_of_freedom,
SparseMatrix & M, Array<Real> * n,
ElementTypeMapArray<Real> & rotation_mat,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt nb_quadrature_points = getNbIntegrationPoints(type);
UInt nt_n_field_size = nb_degree_of_freedom * nb_nodes_per_element;
UInt n_size = n->getNbComponent() / nt_n_field_size;
Array<Real> * nt_n_field = new Array<Real>(
nb_element * nb_quadrature_points, // nt_n_size * nt_n_size, nb_elem *
// nb_quad_points?
nt_n_field_size * nt_n_field_size, "NT*N*field");
Array<Real> * nt = new Array<Real>(nb_element * nb_quadrature_points,
n_size * nt_n_field_size, "N*T");
Array<Real> t = rotation_mat(type);
nt_n_field->clear();
nt->clear();
Array<Real>::matrix_iterator N = n->begin(n_size, nt_n_field_size);
Array<Real>::matrix_iterator Nt_N_field =
nt_n_field->begin(nt_n_field_size, nt_n_field_size);
Array<Real>::matrix_iterator T =
rotation_mat(type).begin(nt_n_field_size, nt_n_field_size);
Array<Real>::matrix_iterator NT = nt->begin(n_size, nt_n_field_size);
Real * field_val = field_1.storage();
for (UInt e = 0; e < nb_element; ++e, ++T) {
for (UInt q = 0; q < nb_quadrature_points;
++q, ++N, ++NT, ++Nt_N_field, /*++T,*/ ++field_val) {
NT->mul<false, false>(*N, *T);
Nt_N_field->mul<true, false>(*NT, *NT, *field_val);
}
}
Array<Real> * int_nt_n_field = new Array<Real>(
nb_element, nt_n_field_size * nt_n_field_size, "NT*N*field");
int_nt_n_field->clear();
integrate(*nt_n_field, *int_nt_n_field, nt_n_field_size * nt_n_field_size,
type);
// integrate(*nt_n_field, *int_nt_n_field, nb_degree_of_freedom, type);
assembleMatrix(*int_nt_n_field, M, nb_degree_of_freedom, type);
delete nt;
delete nt_n_field;
delete int_nt_n_field;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <template <ElementKind, class> class I, template <ElementKind> class S,
ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void
FEEngineTemplate<I, S, kind, IntegrationOrderFunctor>::assembleFieldMatrix(
const Array<Real> & field_1, UInt nb_degree_of_freedom, SparseMatrix & M,
Array<Real> * n, ElementTypeMapArray<Real> & rotation_mat,
const GhostType & ghost_type) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/gauss_integration.cc b/src/fe_engine/gauss_integration.cc
index e9bc85558..d4f4d8caf 100644
--- a/src/fe_engine/gauss_integration.cc
+++ b/src/fe_engine/gauss_integration.cc
@@ -1,238 +1,238 @@
/**
* @file integration_element.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Thu Nov 05 2015
*
* @brief Definition of the integration constants, some of the value are taken
* from r3.01.01 doc from Code Aster
*
* @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 "element_class.hh"
using std::sqrt;
-__BEGIN_AKANTU__
+namespace akantu {
/* clang-format off */
/* -------------------------------------------------------------------------- */
/* Points */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_point, 1>::quad_positions[] = {0};
template<> Real GaussIntegrationTypeData<_git_point, 1>::quad_weights[] = {1.};
/* -------------------------------------------------------------------------- */
/* Segments */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 1>::quad_positions[] = {0.};
template<> Real GaussIntegrationTypeData<_git_segment, 1>::quad_weights[] = {2.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 2>::quad_positions[] = {-1./sqrt(3.), 1./sqrt(3.)};
template<> Real GaussIntegrationTypeData<_git_segment, 2>::quad_weights[] = {1., 1.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 3>::quad_positions[] = {-sqrt(3./5.), 0., sqrt(3./5.)};
template<> Real GaussIntegrationTypeData<_git_segment, 3>::quad_weights[] = {5./9., 8./9., 5./9.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_segment, 4>::quad_positions[] = {-sqrt((3. + 2.*sqrt(6./5.))/7.),
-sqrt((3. - 2.*sqrt(6./5.))/7.),
sqrt((3. - 2.*sqrt(6./5.))/7.),
sqrt((3. + 2.*sqrt(6./5.))/7.)};
template<> Real GaussIntegrationTypeData<_git_segment, 4>::quad_weights[] = {(18. - sqrt(30.))/36.,
(18. + sqrt(30.))/36.,
(18. + sqrt(30.))/36.,
(18. - sqrt(30.))/36.};
/* -------------------------------------------------------------------------- */
/* Triangles */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_triangle, 1>::quad_positions[] = {1./3., 1./3.};
template<> Real GaussIntegrationTypeData<_git_triangle, 1>::quad_weights[] = {1./2.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_triangle, 3>::quad_positions[] = {1./6., 1./6.,
2./3., 1./6.,
1./6., 2./3.};
template<> Real GaussIntegrationTypeData<_git_triangle, 3>::quad_weights[] = {1./6., 1./6., 1./6.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_triangle, 4>::quad_positions[] = {1./5., 1./5.,
3./5., 1./5.,
1./5., 3./5.,
1./3., 1./3.};
template<> Real GaussIntegrationTypeData<_git_triangle, 4>::quad_weights[] = {25./(24.*4.), 25./(24.*4.), 25./(24.*4.), -27/(24.*4.)};
/* -------------------------------------------------------------------------- */
/// Found those one in the TrigGaussRuleInfo from mathematica and matched them to the code aster values
/// http://www.colorado.edu/engineering/CAS/courses.d/AFEM.d/AFEM.AppI.d/AFEM.AppI.pdf
static const Real tri_6_a = (8. - std::sqrt(10.) + std::sqrt(38.-44.*std::sqrt(2./5.)))/18.;
static const Real tri_6_b = (8. - std::sqrt(10.) - std::sqrt(38.-44.*std::sqrt(2./5.)))/18.;
static const Real tri_6_w1 = (620. - std::sqrt(213125. - 53320.*std::sqrt(10.)))/7440.;
static const Real tri_6_w2 = (620. + std::sqrt(213125. - 53320.*std::sqrt(10.)))/7440.;
template<> Real GaussIntegrationTypeData<_git_triangle, 6>::quad_positions[] = {tri_6_b, tri_6_b,
1. - 2. * tri_6_b, tri_6_b,
tri_6_b, 1. - 2. * tri_6_b,
tri_6_a, 1. - 2. * tri_6_a,
tri_6_a, tri_6_a,
1. - 2. * tri_6_a, tri_6_a};
template<> Real GaussIntegrationTypeData<_git_triangle, 6>::quad_weights[] = {tri_6_w1, tri_6_w1, tri_6_w1,
tri_6_w2, tri_6_w2, tri_6_w2};
/* -------------------------------------------------------------------------- */
static const Real tri_7_a = (6. + std::sqrt(15.)) / 21.;
static const Real tri_7_b = (6. - std::sqrt(15.)) / 21.;
static const Real tri_7_w1 = (155. + std::sqrt(15.))/2400.;
static const Real tri_7_w2 = (155. - std::sqrt(15.))/2400.;
template<> Real GaussIntegrationTypeData<_git_triangle, 7>::quad_positions[] = { 1./3., 1./3.,
tri_7_a, tri_7_a,
1. - 2.*tri_7_a, tri_7_a,
tri_7_a, 1. - 2.*tri_7_a,
tri_7_b, tri_7_b,
1. - 2.*tri_7_b, tri_7_b,
tri_7_b, 1. - 2.*tri_7_b};
template<> Real GaussIntegrationTypeData<_git_triangle, 7>::quad_weights[] = {9./80.,
tri_7_w1, tri_7_w1, tri_7_w1,
tri_7_w2, tri_7_w2, tri_7_w2};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* Tetrahedrons */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 1>::quad_positions[] = {1./4., 1./4., 1./4.};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 1>::quad_weights[] = {1./6.};
/* -------------------------------------------------------------------------- */
static const Real tet_4_a = (5. - std::sqrt(5.))/20.;
static const Real tet_4_b = (5. + 3.*std::sqrt(5.))/20.;
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 4>::quad_positions[] = {tet_4_a, tet_4_a, tet_4_a,
tet_4_b, tet_4_a, tet_4_a,
tet_4_a, tet_4_b, tet_4_a,
tet_4_a, tet_4_a, tet_4_b};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 4>::quad_weights[] = {1./24., 1./24., 1./24., 1./24.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 5>::quad_positions[] = {1./4., 1./4., 1./4.,
1./6., 1./6., 1./6.,
1./6., 1./6., 1./2.,
1./6., 1./2., 1./6.,
1./2., 1./6., 1./6.,};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 5>::quad_weights[] = {-2./15., 3./40.,
3./40., 3./40.,
3./40.};
/* -------------------------------------------------------------------------- */
static const Real tet_15_a = (7. + std::sqrt(15.))/34.;
static const Real tet_15_b = (13. - 3. * std::sqrt(15.))/34.;
static const Real tet_15_c = (7. - std::sqrt(15.))/34.;
static const Real tet_15_d = (13. + 3. * std::sqrt(15.))/34.;
static const Real tet_15_e = (5. - std::sqrt(15.))/20.;
static const Real tet_15_f = (5. + std::sqrt(15.))/20.;
static const Real tet_15_w1 = (2665. - 14. * std::sqrt(15.))/226800.;
static const Real tet_15_w2 = (2665. + 14. * std::sqrt(15.))/226800.;
static const Real tet_15_w3 = 5./567.;
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 15>::quad_positions[] = {1./4., 1./4., 1./4.,
tet_15_a, tet_15_a, tet_15_a,
tet_15_a, tet_15_a, tet_15_b,
tet_15_a, tet_15_b, tet_15_a,
tet_15_b, tet_15_a, tet_15_a,
tet_15_c, tet_15_c, tet_15_c,
tet_15_c, tet_15_c, tet_15_d,
tet_15_c, tet_15_d, tet_15_c,
tet_15_d, tet_15_c, tet_15_c,
tet_15_e, tet_15_e, tet_15_f,
tet_15_e, tet_15_f, tet_15_e,
tet_15_f, tet_15_e, tet_15_e,
tet_15_e, tet_15_f, tet_15_f,
tet_15_f, tet_15_e, tet_15_f,
tet_15_f, tet_15_f, tet_15_e};
template<> Real GaussIntegrationTypeData<_git_tetrahedron, 15>::quad_weights[] = {8./405.,
tet_15_w1, tet_15_w1, tet_15_w1, tet_15_w1,
tet_15_w2, tet_15_w2, tet_15_w2, tet_15_w2,
tet_15_w3, tet_15_w3, tet_15_w3, tet_15_w3, tet_15_w3, tet_15_w3};
/* -------------------------------------------------------------------------- */
/* Pentahedrons */
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_pentahedron, 6>::quad_positions[] = {-1./sqrt(3.), 0.5, 0.5,
-1./sqrt(3.), 0. , 0.5,
-1./sqrt(3.), 0.5, 0.,
1./sqrt(3.), 0.5, 0.5,
1./sqrt(3.), 0. , 0.5,
1./sqrt(3.), 0.5 ,0.};
template<> Real GaussIntegrationTypeData<_git_pentahedron, 6>::quad_weights[] = {1./6., 1./6., 1./6.,
1./6., 1./6., 1./6.};
/* -------------------------------------------------------------------------- */
template<> Real GaussIntegrationTypeData<_git_pentahedron, 8>::quad_positions[] = {-sqrt(3.)/3., 1./3., 1./3.,
-sqrt(3.)/3., 0.6, 0.2,
-sqrt(3.)/3., 0.2, 0.6,
-sqrt(3.)/3., 0.2, 0.2,
sqrt(3.)/3., 1./3., 1./3.,
sqrt(3.)/3., 0.6, 0.2,
sqrt(3.)/3., 0.2, 0.6,
sqrt(3.)/3., 0.2, 0.2};
template<> Real GaussIntegrationTypeData<_git_pentahedron, 8>::quad_weights[] = {-27./96., 25./96., 25./96., 25./96.,
-27./96., 25./96., 25./96., 25./96.};
/* -------------------------------------------------------------------------- */
static const Real pent_21_x = std::sqrt(3./5.);
static const Real pent_21_a = (6. + std::sqrt(15.)) / 21.;
static const Real pent_21_b = (6. - std::sqrt(15.)) / 21.;
static const Real pent_21_w1_1 = 5./9.;
static const Real pent_21_w2_1 = 8./9.;
static const Real pent_21_w1_2 = (155. + std::sqrt(15.))/2400.;
static const Real pent_21_w2_2 = (155. - std::sqrt(15.))/2400.;
template<> Real GaussIntegrationTypeData<_git_pentahedron, 21>::quad_positions[] = {- pent_21_x, 1./3., 1./3.,
- pent_21_x, pent_21_a, pent_21_a,
- pent_21_x, 1. - 2.*pent_21_a, pent_21_a,
- pent_21_x, pent_21_a, 1. - 2.*pent_21_a,
- pent_21_x, pent_21_b, pent_21_b,
- pent_21_x, 1. - 2.*pent_21_b, pent_21_b,
- pent_21_x, pent_21_b, 1. - 2.*pent_21_b,
0., 1./3., 1./3.,
0., pent_21_a, pent_21_a,
0., 1. - 2.*pent_21_a, pent_21_a,
0., pent_21_a, 1. - 2.*pent_21_a,
0., pent_21_b, pent_21_b,
0., 1. - 2.*pent_21_b, pent_21_b,
0., pent_21_b, 1. - 2.*pent_21_b,
pent_21_x, 1./3., 1./3.,
pent_21_x, pent_21_a, pent_21_a,
pent_21_x, 1. - 2.*pent_21_a, pent_21_a,
pent_21_x, pent_21_a, 1. - 2.*pent_21_a,
pent_21_x, pent_21_b, pent_21_b,
pent_21_x, 1. - 2.*pent_21_b, pent_21_b,
pent_21_x, pent_21_b, 1. - 2.*pent_21_b};
template<> Real GaussIntegrationTypeData<_git_pentahedron, 21>::quad_weights[] = {pent_21_w1_1 * 9. / 80.,
pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2,
pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2,
pent_21_w2_1 * 9. / 80.,
pent_21_w1_2*pent_21_w1_2, pent_21_w1_2*pent_21_w1_2, pent_21_w1_2*pent_21_w1_2,
pent_21_w1_2*pent_21_w2_2, pent_21_w1_2*pent_21_w2_2, pent_21_w1_2*pent_21_w2_2,
pent_21_w1_1 * 9. / 80.,
pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2, pent_21_w1_1*pent_21_w1_2,
pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2, pent_21_w1_1*pent_21_w2_2};
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/gauss_integration_tmpl.hh b/src/fe_engine/gauss_integration_tmpl.hh
index 5498895f1..01b1aa7b3 100644
--- a/src/fe_engine/gauss_integration_tmpl.hh
+++ b/src/fe_engine/gauss_integration_tmpl.hh
@@ -1,271 +1,271 @@
/**
* @file gauss_integration_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue May 10 10:48:21 2016
*
* @brief implementation of the gauss integration helpers
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GAUSS_INTEGRATION_TMPL_HH__
#define __AKANTU_GAUSS_INTEGRATION_TMPL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* GaussIntegrationElement */
/* -------------------------------------------------------------------------- */
namespace _aka_gauss_helpers {
template <GaussIntegrationType type, UInt n> struct GaussIntegrationNbPoints {
};
template <UInt n> struct GaussIntegrationNbPoints<_git_not_defined, n> {
static const UInt nb_points = 0;
};
template <UInt n> struct GaussIntegrationNbPoints<_git_point, n> {
static const UInt nb_points = 1;
};
template <UInt n> struct GaussIntegrationNbPoints<_git_segment, n> {
static const UInt nb_points = (n + 1) / 2 + ((n + 1) % 2 ? 1 : 0);
};
#define DECLARE_GAUSS_NB_POINTS(type, order, points) \
template <> struct GaussIntegrationNbPoints<type, order> { \
static const UInt nb_points = points; \
}
#define DECLARE_GAUSS_NB_POINTS_PENT(type, order, xo, yo) \
template <> struct GaussIntegrationNbPoints<type, order> { \
static const UInt x_order = xo; \
static const UInt yz_order = yo; \
static const UInt nb_points = 1; \
}
DECLARE_GAUSS_NB_POINTS(_git_triangle, 1, 1);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 2, 3);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 3, 4);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 4, 6);
DECLARE_GAUSS_NB_POINTS(_git_triangle, 5, 7);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 1, 1);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 2, 4);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 3, 5);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 4, 15);
DECLARE_GAUSS_NB_POINTS(_git_tetrahedron, 5, 15);
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 1, 3,
2); // order 3 in x, order 2 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 2, 3,
2); // order 3 in x, order 2 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 3, 3,
3); // order 3 in x, order 3 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 4, 5,
5); // order 5 in x, order 5 in y and z
DECLARE_GAUSS_NB_POINTS_PENT(_git_pentahedron, 5, 5,
5); // order 5 in x, order 5 in y and z
template <GaussIntegrationType type, UInt n, UInt on = n,
bool end_recurse = false>
struct GaussIntegrationNbPointsHelper {
static const UInt pnp = GaussIntegrationNbPoints<type, n>::nb_points;
static const UInt order = n;
static const UInt nb_points = pnp;
};
template <GaussIntegrationType type, UInt n, UInt on>
struct GaussIntegrationNbPointsHelper<type, n, on, true> {
static const UInt nb_points = 0;
};
/* ------------------------------------------------------------------------ */
/* Generic helper */
/* ------------------------------------------------------------------------ */
template <GaussIntegrationType type, UInt dimension, UInt n>
struct GaussIntegrationTypeDataHelper {
typedef GaussIntegrationNbPoints<type, n> git_np;
typedef GaussIntegrationTypeData<type, git_np::nb_points> git_data;
static UInt getNbQuadraturePoints() { return git_np::nb_points; }
static const Matrix<Real> getQuadraturePoints() {
return Matrix<Real>(git_data::quad_positions, dimension, git_np::nb_points);
}
static const Vector<Real> getWeights() {
return Vector<Real>(git_data::quad_weights, git_np::nb_points);
}
};
/* ------------------------------------------------------------------------ */
/* helper for _segment _quadrangle _hexahedron */
/* ------------------------------------------------------------------------ */
template <UInt dimension, UInt dp>
struct GaussIntegrationTypeDataHelper<_git_segment, dimension, dp> {
typedef GaussIntegrationNbPoints<_git_segment, dp> git_np;
typedef GaussIntegrationTypeData<_git_segment, git_np::nb_points> git_data;
static UInt getNbQuadraturePoints() {
return Math::pow<dimension>(git_np::nb_points);
}
static const Matrix<Real> getQuadraturePoints() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad = git_np::nb_points;
Matrix<Real> quads(dimension, tot_nquad);
Vector<Real> pos(git_data::quad_positions, nquad);
UInt offset = 1;
for (UInt d = 0; d < dimension; ++d) {
for (UInt n = 0, q = 0; n < tot_nquad; ++n, q += offset) {
UInt rq = q % tot_nquad + q / tot_nquad;
quads(d, rq) = pos(n % nquad);
}
offset *= nquad;
}
return quads;
}
static const Vector<Real> getWeights() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad = git_np::nb_points;
Vector<Real> quads_weights(tot_nquad, 1.);
Vector<Real> weights(git_data::quad_weights, nquad);
UInt offset = 1;
for (UInt d = 0; d < dimension; ++d) {
for (UInt n = 0, q = 0; n < tot_nquad; ++n, q += offset) {
UInt rq = q % tot_nquad + q / tot_nquad;
quads_weights(rq) *= weights(n % nquad);
}
offset *= nquad;
}
return quads_weights;
}
};
/* ------------------------------------------------------------------------ */
/* helper for _pentahedron */
/* ------------------------------------------------------------------------ */
template <UInt dimension, UInt dp>
struct GaussIntegrationTypeDataHelper<_git_pentahedron, dimension, dp> {
typedef GaussIntegrationNbPoints<_git_pentahedron, dp> git_info;
typedef GaussIntegrationNbPoints<_git_segment, git_info::x_order> git_np_seg;
typedef GaussIntegrationNbPoints<_git_triangle, git_info::yz_order> git_np_tri;
typedef GaussIntegrationTypeData<_git_segment, git_np_seg::nb_points>
git_data_seg;
typedef GaussIntegrationTypeData<_git_triangle, git_np_tri::nb_points>
git_data_tri;
static UInt getNbQuadraturePoints() {
return git_np_seg::nb_points * git_np_tri::nb_points;
}
static const Matrix<Real> getQuadraturePoints() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad_seg = git_np_seg::nb_points;
UInt nquad_tri = git_np_tri::nb_points;
Matrix<Real> quads(dimension, tot_nquad);
Matrix<Real> pos_seg_w(git_data_seg::quad_positions, 1, nquad_seg);
Matrix<Real> pos_tri_w(git_data_tri::quad_positions, 2, nquad_tri);
for (UInt ns = 0, q = 0; ns < nquad_seg; ++ns) {
Vector<Real> pos_seg = pos_seg_w(ns);
for (UInt nt = 0; nt < nquad_tri; ++nt, ++q) {
Vector<Real> pos_tri = pos_tri_w(nt);
Vector<Real> quad = quads(q);
quad(_x) = pos_seg(_x);
quad(_y) = pos_tri(_x);
quad(_z) = pos_tri(_y);
}
}
return quads;
}
static const Vector<Real> getWeights() {
UInt tot_nquad = getNbQuadraturePoints();
UInt nquad_seg = git_np_seg::nb_points;
UInt nquad_tri = git_np_tri::nb_points;
Vector<Real> quads_weights(tot_nquad);
Vector<Real> weight_seg(git_data_seg::quad_weights, nquad_seg);
Vector<Real> weight_tri(git_data_tri::quad_weights, nquad_tri);
for (UInt ns = 0, q = 0; ns < nquad_seg; ++ns) {
for (UInt nt = 0; nt < nquad_tri; ++nt, ++q) {
quads_weights(q) = weight_seg(ns) * weight_tri(nt);
}
}
return quads_weights;
}
};
}
template <ElementType element_type, UInt n>
const Matrix<Real>
GaussIntegrationElement<element_type, n>::getQuadraturePoints() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
typedef InterpolationPorperty<itp_type> interpolation_property;
typedef _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n> data_helper;
Matrix<Real> tmp(data_helper::getQuadraturePoints());
return tmp;
}
/* -------------------------------------------------------------------------- */
template <ElementType element_type, UInt n>
const Vector<Real> GaussIntegrationElement<element_type, n>::getWeights() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
typedef InterpolationPorperty<itp_type> interpolation_property;
typedef _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n> data_helper;
Vector<Real> tmp(data_helper::getWeights());
return tmp;
}
/* -------------------------------------------------------------------------- */
template <ElementType element_type, UInt n>
UInt GaussIntegrationElement<element_type, n>::getNbQuadraturePoints() {
const InterpolationType itp_type =
ElementClassProperty<element_type>::interpolation_type;
typedef InterpolationPorperty<itp_type> interpolation_property;
typedef _aka_gauss_helpers::GaussIntegrationTypeDataHelper<
ElementClassProperty<element_type>::gauss_integration_type,
interpolation_property::natural_space_dimension, n> data_helper;
return data_helper::getNbQuadraturePoints();
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_GAUSS_INTEGRATION_TMPL_HH__ */
diff --git a/src/fe_engine/geometrical_element.cc b/src/fe_engine/geometrical_element.cc
index 35abaefc4..ce39baa40 100644
--- a/src/fe_engine/geometrical_element.cc
+++ b/src/fe_engine/geometrical_element.cc
@@ -1,209 +1,209 @@
/**
* @file geometrical_element.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Thomas Menouillard <tmenouillard@stucky.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Thu Jan 21 2016
*
* @brief Specialization of the geometrical types
*
* @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 "element_class.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* clang-format off */
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_not_defined>::spatial_dimension = 0;
template<> UInt GeometricalElement<_gt_not_defined>::nb_nodes_per_element = 0;
template<> UInt GeometricalElement<_gt_not_defined>::nb_facets[] = { 0 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_point>::spatial_dimension = 0;
template<> UInt GeometricalElement<_gt_point>::nb_nodes_per_element = 1;
template<> UInt GeometricalElement<_gt_point>::nb_facets[] = { 1 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_segment_2>::spatial_dimension = 1;
template<> UInt GeometricalElement<_gt_segment_2>::nb_nodes_per_element = 2;
template<> UInt GeometricalElement<_gt_segment_2>::nb_facets[] = { 2 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_segment_3>::spatial_dimension = 1;
template<> UInt GeometricalElement<_gt_segment_3>::nb_nodes_per_element = 3;
template<> UInt GeometricalElement<_gt_segment_3>::nb_facets[] = { 2 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_triangle_3>::spatial_dimension = 2;
template<> UInt GeometricalElement<_gt_triangle_3>::nb_nodes_per_element = 3;
template<> UInt GeometricalElement<_gt_triangle_3>::nb_facets[] = { 3 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_triangle_6>::spatial_dimension = 2;
template<> UInt GeometricalElement<_gt_triangle_6>::nb_nodes_per_element = 6;
template<> UInt GeometricalElement<_gt_triangle_6>::nb_facets[] = { 3 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_tetrahedron_4>::spatial_dimension = 3;
template<> UInt GeometricalElement<_gt_tetrahedron_4>::nb_nodes_per_element = 4;
template<> UInt GeometricalElement<_gt_tetrahedron_4>::nb_facets[] = { 4 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_tetrahedron_10>::spatial_dimension = 3;
template<> UInt GeometricalElement<_gt_tetrahedron_10>::nb_nodes_per_element = 10;
template<> UInt GeometricalElement<_gt_tetrahedron_10>::nb_facets[] = { 4 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_quadrangle_4>::spatial_dimension = 2;
template<> UInt GeometricalElement<_gt_quadrangle_4>::nb_nodes_per_element = 4;
template<> UInt GeometricalElement<_gt_quadrangle_4>::nb_facets[] = { 4 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_quadrangle_8>::spatial_dimension = 2;
template<> UInt GeometricalElement<_gt_quadrangle_8>::nb_nodes_per_element = 8;
template<> UInt GeometricalElement<_gt_quadrangle_8>::nb_facets[] = { 4 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_hexahedron_8>::spatial_dimension = 3;
template<> UInt GeometricalElement<_gt_hexahedron_8>::nb_nodes_per_element = 8;
template<> UInt GeometricalElement<_gt_hexahedron_8>::nb_facets[] = { 6 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_hexahedron_20>::spatial_dimension = 3;
template<> UInt GeometricalElement<_gt_hexahedron_20>::nb_nodes_per_element = 20;
template<> UInt GeometricalElement<_gt_hexahedron_20>::nb_facets[] = { 6 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_pentahedron_6>::spatial_dimension = 3;
template<> UInt GeometricalElement<_gt_pentahedron_6>::nb_nodes_per_element = 6;
template<> UInt GeometricalElement<_gt_pentahedron_6>::nb_facets[] = { 2, 3 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_pentahedron_15>::spatial_dimension = 3;
template<> UInt GeometricalElement<_gt_pentahedron_15>::nb_nodes_per_element = 15;
template<> UInt GeometricalElement<_gt_pentahedron_15>::nb_facets[] = { 2, 3 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_not_defined>::nb_nodes_per_facet[] = { 0 };
template<> UInt GeometricalElement<_gt_point>::nb_nodes_per_facet[] = { 1 };
template<> UInt GeometricalElement<_gt_segment_2>::nb_nodes_per_facet[] = { 1 };
template<> UInt GeometricalElement<_gt_segment_3>::nb_nodes_per_facet[] = { 1 };
template<> UInt GeometricalElement<_gt_triangle_3>::nb_nodes_per_facet[] = { 2 };
template<> UInt GeometricalElement<_gt_triangle_6>::nb_nodes_per_facet[] = { 3 };
template<> UInt GeometricalElement<_gt_tetrahedron_4>::nb_nodes_per_facet[] = { 3 };
template<> UInt GeometricalElement<_gt_tetrahedron_10>::nb_nodes_per_facet[] = { 6 };
template<> UInt GeometricalElement<_gt_quadrangle_4>::nb_nodes_per_facet[] = { 2 };
template<> UInt GeometricalElement<_gt_quadrangle_8>::nb_nodes_per_facet[] = { 3 };
template<> UInt GeometricalElement<_gt_hexahedron_8>::nb_nodes_per_facet[] = { 4 };
template<> UInt GeometricalElement<_gt_hexahedron_20>::nb_nodes_per_facet[] = { 8 };
template<> UInt GeometricalElement<_gt_pentahedron_6>::nb_nodes_per_facet[] = { 3, 4 };
template<> UInt GeometricalElement<_gt_pentahedron_15>::nb_nodes_per_facet[] = { 6, 8 };
/* -------------------------------------------------------------------------- */
template<> UInt GeometricalElement<_gt_not_defined>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_point>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_segment_2>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_segment_3>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_triangle_3>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_triangle_6>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_tetrahedron_4>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_tetrahedron_10>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_quadrangle_4>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_quadrangle_8>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_hexahedron_8>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_hexahedron_20>::nb_facet_types = 1;
template<> UInt GeometricalElement<_gt_pentahedron_6>::nb_facet_types = 2;
template<> UInt GeometricalElement<_gt_pentahedron_15>::nb_facet_types = 2;
/* !!! stored as a matrix nb_facets X nb_nodes_per_facet in COL MAJOR */
/* -------------------------------------------------------------------------- */
/* f1|f2|f3|f4|f5|f6 */
template<> UInt GeometricalElement<_gt_not_defined>::facet_connectivity_vect[] = {0};
template<> UInt GeometricalElement<_gt_point>::facet_connectivity_vect[] = {0};
template<> UInt GeometricalElement<_gt_segment_2>::facet_connectivity_vect[] = {0, 1};
template<> UInt GeometricalElement<_gt_segment_3>::facet_connectivity_vect[] = {0, 1};
template<> UInt GeometricalElement<_gt_triangle_3>::facet_connectivity_vect[] = {0, 1, 2,
1, 2, 0};
template<> UInt GeometricalElement<_gt_triangle_6>::facet_connectivity_vect[] = {0, 1, 2,
1, 2, 0,
3, 4, 5};
template<> UInt GeometricalElement<_gt_tetrahedron_4>::facet_connectivity_vect[] = {0, 1, 2, 0,
2, 2, 0, 1,
1, 3, 3, 3};
template<> UInt GeometricalElement<_gt_tetrahedron_10>::facet_connectivity_vect[] = {0, 1, 2, 0,
2, 2, 0, 1,
1, 3, 3, 3,
6, 5, 6, 4,
5, 9, 7, 8,
4, 8, 9, 7};
template<> UInt GeometricalElement<_gt_quadrangle_4>::facet_connectivity_vect[] = {0, 1, 2, 3,
1, 2, 3, 0};
template<> UInt GeometricalElement<_gt_quadrangle_8>::facet_connectivity_vect[] = {0, 1, 2, 3,
1, 2, 3, 0,
4, 5, 6, 7};
template<> UInt GeometricalElement<_gt_hexahedron_8>::facet_connectivity_vect[] = {0, 0, 1, 2, 3, 4,
3, 1, 2, 3, 0, 5,
2, 5, 6, 7, 4, 6,
1, 4, 5, 6, 7, 7};
template<> UInt GeometricalElement<_gt_hexahedron_20>::facet_connectivity_vect[] = {0, 1, 2, 3, 0, 4,
1, 2, 3, 0, 3, 5,
5, 6, 7, 4, 2, 6,
4, 5, 6, 7, 1, 7,
8, 9, 10, 11, 11, 16,
13, 14, 15, 12, 10, 17,
16, 17, 18, 19, 9, 18,
12, 13, 14, 15, 8, 19};
template<> UInt GeometricalElement<_gt_pentahedron_6>::facet_connectivity_vect[] = {// first type
0, 3,
2, 4,
1, 5,
// second type
0, 0, 1,
1, 3, 2,
4, 5, 5,
3, 2, 4};
template<> UInt GeometricalElement<_gt_pentahedron_15>::facet_connectivity_vect[] = {// first type
0, 3,
2, 4,
1, 5,
8, 12,
7, 13,
6, 14,
// second type
0, 0, 1,
1, 3, 2,
4, 5, 5,
3, 2, 4,
6, 9, 7,
10, 14, 11,
12, 11, 13,
9, 8, 10};
template<> UInt * GeometricalElement<_gt_not_defined>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_point>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_segment_2>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_segment_3>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_triangle_3>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_triangle_6>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_tetrahedron_4>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_tetrahedron_10>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_quadrangle_4>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_quadrangle_8>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_hexahedron_8>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_hexahedron_20>::facet_connectivity[] = { &facet_connectivity_vect[0] };
template<> UInt * GeometricalElement<_gt_pentahedron_6>::facet_connectivity[] = { &facet_connectivity_vect[0], &facet_connectivity_vect[2*3] };
template<> UInt * GeometricalElement<_gt_pentahedron_15>::facet_connectivity[] = { &facet_connectivity_vect[0], &facet_connectivity_vect[2*6] };
/* clang-format on */
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/integration_point.hh b/src/fe_engine/integration_point.hh
index 58d3fbab9..fe0e493db 100644
--- a/src/fe_engine/integration_point.hh
+++ b/src/fe_engine/integration_point.hh
@@ -1,169 +1,169 @@
/**
* @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
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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((Real *)NULL, 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((Real *)NULL, 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((Real *)NULL, 0) {
this->position.shallowCopy(position);
};
IntegrationPoint(const IntegrationPoint & quad)
: Element(quad), num_point(quad.num_point), global_num(quad.global_num),
position((Real *)NULL, 0) {
position.shallowCopy(quad.position);
};
/* ------------------------------------------------------------------------ */
/* 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 != quad.element) || (type != quad.type) ||
(ghost_type != quad.ghost_type) || (kind != quad.kind) ||
(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 [";
Element::printself(stream, 0);
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;
}
-__END_AKANTU__
+} // akantu
#endif /* AKANTU_QUADRATURE_POINT_H */
diff --git a/src/fe_engine/integrator.hh b/src/fe_engine/integrator.hh
index 1f787abdf..7e22cfc4a 100644
--- a/src/fe_engine/integrator.hh
+++ b/src/fe_engine/integrator.hh
@@ -1,129 +1,129 @@
/**
* @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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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(){};
/* ------------------------------------------------------------------------ */
/* 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;
};
/* ------------------------------------------------------------------------ */
/* 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);
};
/* ------------------------------------------------------------------------ */
/* 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;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_INTEGRATOR_HH__ */
diff --git a/src/fe_engine/integrator_gauss.hh b/src/fe_engine/integrator_gauss.hh
index 0c810bb12..92e04f32a 100644
--- a/src/fe_engine/integrator_gauss.hh
+++ b/src/fe_engine/integrator_gauss.hh
@@ -1,182 +1,182 @@
/**
* @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/>.
*
*/
#ifndef __AKANTU_INTEGRATOR_GAUSS_HH__
#define __AKANTU_INTEGRATOR_GAUSS_HH__
/* -------------------------------------------------------------------------- */
#include "integrator.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
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(){};
/* ------------------------------------------------------------------------ */
/* 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$)
template <ElementType type>
void integrateOnIntegrationPoints(const Array<Real> & in_f,
Array<Real> & intf,
UInt nb_degree_of_freedom,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const;
/// return a matrix with quadrature points natural coordinates
template <ElementType type>
const Matrix<Real> & getIntegrationPoints(const GhostType & ghost_type) const;
/// return number of quadrature points
template <ElementType type>
UInt getNbIntegrationPoints(const GhostType & ghost_type) const;
template <ElementType type, UInt n> Matrix<Real> getIntegrationPoints() const;
template <ElementType type, UInt n>
Vector<Real> getIntegrationWeights() const;
protected:
template <ElementType type>
void computeJacobiansOnIntegrationPoints(const Array<Real> & nodes,
const Matrix<Real> & quad_points,
Array<Real> & jacobians,
const GhostType & ghost_type) const;
/// precompute jacobians on elements of type "type"
template <ElementType type>
void precomputeJacobiansOnQuadraturePoints(const Array<Real> & nodes,
const GhostType & ghost_type);
// multiply the jacobians by the integration weights and stores the results in
// jacobians
template <ElementType type, UInt polynomial_degree>
void multiplyJacobiansByWeights(Array<Real> & jacobians) const;
/// compute the vector of quadrature points natural coordinates
template <ElementType type>
void computeQuadraturePoints(const GhostType & ghost_type);
/// check that the jacobians are not negative
template <ElementType type>
void checkJacobians(const GhostType & ghost_type) const;
/// internal integrate partially around a quadrature point (@f$ 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;
/* ------------------------------------------------------------------------ */
/* 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;
};
-__END_AKANTU__
+} // akantu
#include "integrator_gauss_inline_impl.cc"
#endif /* __AKANTU_INTEGRATOR_GAUSS_HH__ */
diff --git a/src/fe_engine/integrator_gauss_inline_impl.cc b/src/fe_engine/integrator_gauss_inline_impl.cc
index f2c578e29..387836053 100644
--- a/src/fe_engine/integrator_gauss_inline_impl.cc
+++ b/src/fe_engine/integrator_gauss_inline_impl.cc
@@ -1,561 +1,561 @@
/**
* @file integrator_gauss_inline_impl.cc
*
* @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 19 2015
*
* @brief inline function of gauss integrator
*
* @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 "fe_engine.hh"
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#endif
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::integrateOnElement(
const Array<Real> & f, Real * intf, UInt nb_degree_of_freedom,
const UInt elem, const GhostType & ghost_type) const {
Array<Real> & jac_loc = jacobians(type, ghost_type);
UInt nb_quadrature_points = ElementClass<type>::getNbQuadraturePoints();
AKANTU_DEBUG_ASSERT(f.getNbComponent() == nb_degree_of_freedom,
"The vector f do not have the good number of component.");
Real * f_val = f.storage() + elem * f.getNbComponent();
Real * jac_val = jac_loc.storage() + elem * nb_quadrature_points;
integrate(f_val, jac_val, intf, nb_degree_of_freedom, nb_quadrature_points);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Vector<Real> & in_f, UInt index, const GhostType & ghost_type) const {
const Array<Real> & jac_loc = jacobians(type, ghost_type);
UInt nb_quadrature_points =
GaussIntegrationElement<type>::getNbQuadraturePoints();
AKANTU_DEBUG_ASSERT(in_f.size() == nb_quadrature_points,
"The vector f do not have nb_quadrature_points entries.");
Real * jac_val = jac_loc.storage() + index * nb_quadrature_points;
Real intf;
integrate(in_f.storage(), jac_val, &intf, 1, nb_quadrature_points);
return intf;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
Real * f, Real * jac, Real * inte, UInt nb_degree_of_freedom,
UInt nb_quadrature_points) const {
memset(inte, 0, nb_degree_of_freedom * sizeof(Real));
Real * cjac = jac;
for (UInt q = 0; q < nb_quadrature_points; ++q) {
for (UInt dof = 0; dof < nb_degree_of_freedom; ++dof) {
inte[dof] += *f * *cjac;
++f;
}
++cjac;
}
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline const Matrix<Real> &
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationPoints(
const GhostType & ghost_type) const {
AKANTU_DEBUG_ASSERT(
quadrature_points.exists(type, ghost_type),
"Quadrature points for type "
<< quadrature_points.printType(type, ghost_type)
<< " have not been initialized."
<< " Did you use 'computeQuadraturePoints' function ?");
return quadrature_points(type, ghost_type);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline UInt
IntegratorGauss<kind, IntegrationOrderFunctor>::getNbIntegrationPoints(
const GhostType & ghost_type) const {
AKANTU_DEBUG_ASSERT(
quadrature_points.exists(type, ghost_type),
"Quadrature points for type "
<< quadrature_points.printType(type, ghost_type)
<< " have not been initialized."
<< " Did you use 'computeQuadraturePoints' function ?");
return quadrature_points(type, ghost_type).cols();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
inline Matrix<Real>
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationPoints() const {
return GaussIntegrationElement<type,
polynomial_degree>::getQuadraturePoints();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
inline Vector<Real>
IntegratorGauss<kind, IntegrationOrderFunctor>::getIntegrationWeights() const {
return GaussIntegrationElement<type, polynomial_degree>::getWeights();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void
IntegratorGauss<kind, IntegrationOrderFunctor>::computeQuadraturePoints(
const GhostType & ghost_type) {
Matrix<Real> & quads = quadrature_points(type, ghost_type);
const UInt polynomial_degree =
IntegrationOrderFunctor::template getOrder<type>();
quads =
GaussIntegrationElement<type, polynomial_degree>::getQuadraturePoints();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobianOnQuadPointsByElement(const Matrix<Real> & node_coords,
const Matrix<Real> & quad,
Vector<Real> & jacobians) const {
// jacobian
ElementClass<type>::computeJacobian(quad, node_coords, jacobians);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
IntegratorGauss<kind, IntegrationOrderFunctor>::IntegratorGauss(
const Mesh & mesh, const ID & id, const MemoryID & memory_id)
: Integrator(mesh, id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::checkJacobians(
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->quadrature_points(type, ghost_type).cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).getSize();
Real * jacobians_val = jacobians(type, ghost_type).storage();
for (UInt i = 0; i < nb_element * nb_quadrature_points;
++i, ++jacobians_val) {
if (*jacobians_val < 0)
AKANTU_DEBUG_ERROR(
"Negative jacobian computed,"
<< " possible problem in the element node ordering (Quadrature Point "
<< i % nb_quadrature_points << ":" << i / nb_quadrature_points << ":"
<< type << ":" << ghost_type << ")");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(const Array<Real> & nodes,
const Matrix<Real> & quad_points,
Array<Real> & jacobians,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = quad_points.cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
Array<Real>::vector_iterator jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
Array<Real>::const_matrix_iterator x_it =
x_el.begin(spatial_dimension, nb_nodes_per_element);
// Matrix<Real> local_coord(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem, ++jacobians_it, ++x_it) {
const Matrix<Real> & x = *x_it;
Vector<Real> & J = *jacobians_it;
computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
template <>
template <ElementType type>
void IntegratorGauss<_ek_cohesive, DefaultIntegrationOrderFunctor>::
computeJacobiansOnIntegrationPoints(const Array<Real> & nodes,
const Matrix<Real> & quad_points,
Array<Real> & jacobians,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points = quad_points.cols();
UInt nb_element = mesh.getNbElement(type, ghost_type);
jacobians.resize(nb_element * nb_quadrature_points);
Array<Real>::vector_iterator jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
Vector<Real> weights = GaussIntegrationElement<type>::getWeights();
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
Array<Real>::const_matrix_iterator x_it =
x_el.begin(spatial_dimension, nb_nodes_per_element);
UInt nb_nodes_per_subelement = nb_nodes_per_element / 2;
Matrix<Real> x(spatial_dimension, nb_nodes_per_subelement);
for (UInt elem = 0; elem < nb_element; ++elem, ++jacobians_it, ++x_it) {
for (UInt s = 0; s < spatial_dimension; ++s)
for (UInt n = 0; n < nb_nodes_per_subelement; ++n)
x(s, n) =
((*x_it)(s, n) + (*x_it)(s, n + nb_nodes_per_subelement)) * .5;
Vector<Real> & J = *jacobians_it;
if (type == _cohesive_1d_2)
J(0) = 1;
else
computeJacobianOnQuadPointsByElement<type>(x, quad_points, J);
}
AKANTU_DEBUG_OUT();
}
#endif
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
precomputeJacobiansOnQuadraturePoints(const Array<Real> & nodes,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & jacobians_tmp =
jacobians.alloc(0, 1, type, ghost_type);
this->computeJacobiansOnIntegrationPoints<type>(
nodes, quadrature_points(type, ghost_type), jacobians_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
void IntegratorGauss<kind, IntegrationOrderFunctor>::multiplyJacobiansByWeights(
Array<Real> & jacobians) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points =
GaussIntegrationElement<type, polynomial_degree>::getNbQuadraturePoints();
UInt nb_element = jacobians.getSize() / nb_quadrature_points;
Vector<Real> weights =
GaussIntegrationElement<type, polynomial_degree>::getWeights();
Array<Real>::vector_iterator jacobians_it =
jacobians.begin_reinterpret(nb_quadrature_points, nb_element);
Array<Real>::vector_iterator jacobians_end =
jacobians.end_reinterpret(nb_quadrature_points, nb_element);
for (; jacobians_it != jacobians_end; ++jacobians_it) {
Vector<Real> & J = *jacobians_it;
J *= weights;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
const Array<Real> & jacobians, UInt nb_element) const {
AKANTU_DEBUG_IN();
intf.resize(nb_element);
if(nb_element == 0) return;
UInt nb_points = jacobians.getSize() / nb_element;
Array<Real>::const_matrix_iterator J_it;
Array<Real>::matrix_iterator inte_it;
Array<Real>::const_matrix_iterator f_it;
f_it = in_f.begin_reinterpret(nb_degree_of_freedom, nb_points, nb_element);
inte_it = intf.begin_reinterpret(nb_degree_of_freedom, 1, nb_element);
J_it = jacobians.begin_reinterpret(nb_points, 1, nb_element);
for (UInt el = 0; el < nb_element; ++el, ++J_it, ++f_it, ++inte_it) {
const Matrix<Real> & f = *f_it;
const Matrix<Real> & J = *J_it;
Matrix<Real> & inte_f = *inte_it;
inte_f.mul<false, false>(f, J);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
const GhostType & ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
const Array<Real> & jac_loc = jacobians(type, ghost_type);
if (filter_elements != empty_filter) {
UInt nb_element = filter_elements.getSize();
Array<Real> * filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
FEEngine::filterElementalData(mesh, jac_loc, *filtered_J, type, ghost_type,
filter_elements);
this->integrate(in_f, intf, nb_degree_of_freedom, *filtered_J, nb_element);
delete filtered_J;
} else {
UInt nb_element = mesh.getNbElement(type, ghost_type);
this->integrate(in_f, intf, nb_degree_of_freedom, jac_loc, nb_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
void IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, Array<Real> & intf, UInt nb_degree_of_freedom,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
Matrix<Real> quads = this->getIntegrationPoints<type, polynomial_degree>();
Array<Real> jacobians;
this->computeJacobiansOnIntegrationPoints<type>(mesh.getNodes(), quads,
jacobians, ghost_type);
this->multiplyJacobiansByWeights<type, polynomial_degree>(jacobians);
this->integrate(in_f, intf, nb_degree_of_freedom, jacobians,
mesh.getNbElement(type, ghost_type));
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type, UInt polynomial_degree>
Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
Array<Real> intfv(0, 1);
integrate<type, polynomial_degree>(in_f, intfv, 1, ghost_type);
Real res = Math::reduce(intfv);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
Real IntegratorGauss<kind, IntegrationOrderFunctor>::integrate(
const Array<Real> & in_f, const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
Array<Real> intfv(0, 1);
integrate<type>(in_f, intfv, 1, ghost_type, filter_elements);
Real res = Math::reduce(intfv);
AKANTU_DEBUG_OUT();
return res;
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom,
const Array<Real> & jacobians,
UInt nb_element) const {
AKANTU_DEBUG_IN();
UInt nb_points = jacobians.getSize() / nb_element;
Array<Real>::const_scalar_iterator J_it;
Array<Real>::vector_iterator inte_it;
Array<Real>::const_vector_iterator f_it;
intf.resize(nb_element * nb_points);
J_it = jacobians.begin();
f_it = in_f.begin(nb_degree_of_freedom);
inte_it = intf.begin(nb_degree_of_freedom);
for (UInt el = 0; el < nb_element; ++el, ++J_it, ++f_it, ++inte_it) {
const Real & J = *J_it;
const Vector<Real> & f = *f_it;
Vector<Real> & inte_f = *inte_it;
inte_f = f;
inte_f *= J;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
void IntegratorGauss<kind, IntegrationOrderFunctor>::
integrateOnIntegrationPoints(const Array<Real> & in_f, Array<Real> & intf,
UInt nb_degree_of_freedom,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(jacobians.exists(type, ghost_type),
"No jacobians for the type "
<< jacobians.printType(type, ghost_type));
const Array<Real> & jac_loc = this->jacobians(type, ghost_type);
if (filter_elements != empty_filter) {
UInt nb_element = filter_elements.getSize();
Array<Real> * filtered_J = new Array<Real>(0, jac_loc.getNbComponent());
FEEngine::filterElementalData(mesh, jac_loc, *filtered_J, type, ghost_type,
filter_elements);
this->integrateOnIntegrationPoints(in_f, intf, nb_degree_of_freedom,
*filtered_J, nb_element);
} else {
UInt nb_element = mesh.getNbElement(type, ghost_type);
this->integrateOnIntegrationPoints(in_f, intf, nb_degree_of_freedom,
jac_loc, nb_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind, class IntegrationOrderFunctor>
template <ElementType type>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::initIntegrator(
const Array<Real> & nodes, const GhostType & ghost_type) {
computeQuadraturePoints<type>(ghost_type);
precomputeJacobiansOnQuadraturePoints<type>(nodes, ghost_type);
checkJacobians<type>(ghost_type);
constexpr UInt polynomial_degree =
IntegrationOrderFunctor::template getOrder<type>();
multiplyJacobiansByWeights<type, polynomial_degree>(
this->jacobians(type, ghost_type));
}
template <ElementKind kind> struct GaussIntegratorInitHelper {};
#define INIT_INTEGRATOR(type) \
_int.template initIntegrator<type>(nodes, ghost_type)
#define AKANTU_GAUSS_INTERGRATOR_INIT_HELPER(kind) \
template <> struct GaussIntegratorInitHelper<kind> { \
template <ElementKind k, class IOF> \
static void call(IntegratorGauss<k, IOF> & _int, \
const Array<Real> & nodes, const ElementType & type, \
const GhostType & ghost_type) { \
AKANTU_BOOST_KIND_ELEMENT_SWITCH(INIT_INTEGRATOR, kind); \
} \
};
AKANTU_BOOST_ALL_KIND(AKANTU_GAUSS_INTERGRATOR_INIT_HELPER)
#undef AKANTU_GAUSS_INTERGRATOR_INIT_HELPER
#undef INIT_INTEGRATOR
template <ElementKind kind, class IntegrationOrderFunctor>
inline void IntegratorGauss<kind, IntegrationOrderFunctor>::initIntegrator(
const Array<Real> & nodes, const ElementType & type,
const GhostType & ghost_type) {
GaussIntegratorInitHelper<kind>::call(*this, nodes, type, ghost_type);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/interpolation_element.cc b/src/fe_engine/interpolation_element.cc
index b4291d578..cf5b90ed8 100644
--- a/src/fe_engine/interpolation_element.cc
+++ b/src/fe_engine/interpolation_element.cc
@@ -1,48 +1,48 @@
/**
* @file interpolation_element.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Sun Oct 19 2014
*
* @brief Common part of element_classes
*
* @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 "element_class.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* Structural elements */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_STRUCTURAL_MECHANICS)
template<> const UInt InterpolationElement<_itp_bernoulli_beam>::nb_shape_functions = 5;
template<> const UInt InterpolationElement<_itp_kirchhoff_shell>::nb_shape_functions = 9;
template<> const UInt InterpolationElement<_itp_bernoulli_beam>::nb_shape_derivatives = 3;
template<> const UInt InterpolationElement<_itp_kirchhoff_shell>::nb_shape_derivatives = 7;
#endif
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/shape_cohesive.hh b/src/fe_engine/shape_cohesive.hh
index e6beca1bc..c2c5e4332 100644
--- a/src/fe_engine/shape_cohesive.hh
+++ b/src/fe_engine/shape_cohesive.hh
@@ -1,201 +1,201 @@
/**
* @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_functions.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SHAPE_COHESIVE_HH__
#define __AKANTU_SHAPE_COHESIVE_HH__
-__BEGIN_AKANTU__
+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 ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, const ID & id = "shape_cohesive",
const MemoryID & memory_id = 0);
virtual ~ShapeLagrange() {}
/* ------------------------------------------------------------------------ */
/* 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;
/// 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();
}
/* ------------------------------------------------------------------------ */
/* 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;
};
-// __END_AKANTU__
+// } // akantu
// #include "shape_lagrange.hh"
-// __BEGIN_AKANTU__
+// namespace akantu {
// template<>
// class ShapeLagrange<_ek_cohesive> : public ShapeCohesive<
// ShapeLagrange<_ek_regular> > {
// public:
// ShapeLagrange(const Mesh & mesh,
// const ID & id = "shape_cohesive",
// const MemoryID & memory_id = 0) :
// ShapeCohesive< ShapeLagrange<_ek_regular> >(mesh, id, memory_id) { }
// virtual ~ShapeLagrange() { };
// };
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "shape_cohesive_inline_impl.cc"
/// standard output stream operator
template <class ShapeFunction>
inline std::ostream & operator<<(std::ostream & stream,
const ShapeCohesive<ShapeFunction> & _this) {
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_SHAPE_COHESIVE_HH__ */
diff --git a/src/fe_engine/shape_functions.hh b/src/fe_engine/shape_functions.hh
index e4a1d1d3b..64a33e3d0 100644
--- a/src/fe_engine/shape_functions.hh
+++ b/src/fe_engine/shape_functions.hh
@@ -1,189 +1,189 @@
/**
* @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__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
class ShapeFunctions : protected Memory {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeFunctions(const Mesh & mesh, const ID & id = "shape",
const MemoryID & memory_id = 0)
: Memory(id, memory_id), mesh(mesh){};
virtual ~ShapeFunctions(){};
/* ------------------------------------------------------------------------ */
/* 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)
inline 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
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;
protected:
/// interpolate nodal values stored by element on the integration points
template <ElementType type>
void interpolateElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & uq, 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, 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, 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;
/* ------------------------------------------------------------------------ */
/* 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);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// associated mesh
const Mesh & mesh;
/// shape functions for all elements
ElementTypeMap<Matrix<Real> > integration_points;
};
#if defined(AKANTU_INCLUDE_INLINE_IMPL)
#include "shape_functions_inline_impl.cc"
#endif
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ShapeFunctions & _this) {
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_SHAPE_FUNCTIONS_HH__ */
diff --git a/src/fe_engine/shape_functions_inline_impl.cc b/src/fe_engine/shape_functions_inline_impl.cc
index 51bae3df1..c09c2d643 100644
--- a/src/fe_engine/shape_functions_inline_impl.cc
+++ b/src/fe_engine/shape_functions_inline_impl.cc
@@ -1,609 +1,609 @@
/**
* @file shape_functions_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Oct 27 2010
* @date last modification: Thu Oct 15 2015
*
* @brief ShapeFunctions inline 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/>.
*
*/
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#include "fe_engine.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt ShapeFunctions::getShapeSize(const ElementType & type) {
AKANTU_DEBUG_IN();
UInt shape_size = 0;
#define GET_SHAPE_SIZE(type) shape_size = ElementClass<type>::getShapeSize()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SHAPE_SIZE); // ,
#undef GET_SHAPE_SIZE
AKANTU_DEBUG_OUT();
return shape_size;
}
/* -------------------------------------------------------------------------- */
inline UInt ShapeFunctions::getShapeDerivativesSize(const ElementType & type) {
AKANTU_DEBUG_IN();
UInt shape_derivatives_size = 0;
#define GET_SHAPE_DERIVATIVES_SIZE(type) \
shape_derivatives_size = ElementClass<type>::getShapeDerivativesSize()
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_SHAPE_DERIVATIVES_SIZE); // ,
#undef GET_SHAPE_DERIVATIVES_SIZE
AKANTU_DEBUG_OUT();
return shape_derivatives_size;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeFunctions::setIntegrationPointsByType(const Matrix<Real> & points,
const GhostType & ghost_type) {
integration_points(type, ghost_type).shallowCopy(points);
}
/* -------------------------------------------------------------------------- */
inline void
ShapeFunctions::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 {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator it, last;
if (element_filter) {
it = element_filter->firstType(spatial_dimension, ghost_type);
last = element_filter->lastType(spatial_dimension, ghost_type);
} else {
it = mesh.firstType(spatial_dimension, ghost_type);
last = mesh.lastType(spatial_dimension, ghost_type);
}
for (; it != last; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (nb_element == 0)
continue;
const Array<UInt> * elem_filter;
if (element_filter)
elem_filter = &((*element_filter)(type, ghost_type));
else
elem_filter = &(empty_filter);
#define AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS(type) \
initElementalFieldInterpolationFromIntegrationPoints<type>( \
interpolation_points_coordinates(type, ghost_type), \
interpolation_points_coordinates_matrices, \
quad_points_coordinates_inv_matrices, \
quadrature_points_coordinates(type, ghost_type), ghost_type, \
*elem_filter)
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(
AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS);
#undef AKANTU_INIT_ELEMENTAL_FIELD_INTERPOLATION_FROM_C_POINTS
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void
ShapeFunctions::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, GhostType & ghost_type,
const Array<UInt> & element_filter) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
UInt nb_element_filter;
if (element_filter == empty_filter)
nb_element_filter = nb_element;
else
nb_element_filter = element_filter.getSize();
UInt nb_quad_per_element =
GaussIntegrationElement<type>::getNbQuadraturePoints();
UInt nb_interpolation_points_per_elem =
interpolation_points_coordinates.getSize() / nb_element;
AKANTU_DEBUG_ASSERT(interpolation_points_coordinates.getSize() % nb_element ==
0,
"Number of interpolation points should be a multiple of "
"total number of elements");
if (!quad_points_coordinates_inv_matrices.exists(type, ghost_type))
quad_points_coordinates_inv_matrices.alloc(
nb_element_filter, nb_quad_per_element * nb_quad_per_element, type,
ghost_type);
else
quad_points_coordinates_inv_matrices(type, ghost_type)
.resize(nb_element_filter);
if (!interpolation_points_coordinates_matrices.exists(type, ghost_type))
interpolation_points_coordinates_matrices.alloc(
nb_element_filter,
nb_interpolation_points_per_elem * nb_quad_per_element, type,
ghost_type);
else
interpolation_points_coordinates_matrices(type, ghost_type)
.resize(nb_element_filter);
Array<Real> & quad_inv_mat =
quad_points_coordinates_inv_matrices(type, ghost_type);
Array<Real> & interp_points_mat =
interpolation_points_coordinates_matrices(type, ghost_type);
Matrix<Real> quad_coord_matrix(nb_quad_per_element, nb_quad_per_element);
Array<Real>::const_matrix_iterator quad_coords_it =
quadrature_points_coordinates.begin_reinterpret(
spatial_dimension, nb_quad_per_element, nb_element_filter);
Array<Real>::const_matrix_iterator points_coords_begin =
interpolation_points_coordinates.begin_reinterpret(
spatial_dimension, nb_interpolation_points_per_elem, nb_element);
Array<Real>::matrix_iterator inv_quad_coord_it =
quad_inv_mat.begin(nb_quad_per_element, nb_quad_per_element);
Array<Real>::matrix_iterator int_points_mat_it = interp_points_mat.begin(
nb_interpolation_points_per_elem, nb_quad_per_element);
/// loop over the elements of the current material and element type
for (UInt el = 0; el < nb_element_filter;
++el, ++inv_quad_coord_it, ++int_points_mat_it, ++quad_coords_it) {
/// matrix containing the quadrature points coordinates
const Matrix<Real> & quad_coords = *quad_coords_it;
/// matrix to store the matrix inversion result
Matrix<Real> & inv_quad_coord_matrix = *inv_quad_coord_it;
/// insert the quad coordinates in a matrix compatible with the
/// interpolation
buildElementalFieldInterpolationMatrix<type>(quad_coords,
quad_coord_matrix);
/// invert the interpolation matrix
inv_quad_coord_matrix.inverse(quad_coord_matrix);
/// matrix containing the interpolation points coordinates
const Matrix<Real> & points_coords =
points_coords_begin[element_filter(el)];
/// matrix to store the interpolation points coordinates
/// compatible with these functions
Matrix<Real> & inv_points_coord_matrix = *int_points_mat_it;
/// insert the quad coordinates in a matrix compatible with the
/// interpolation
buildElementalFieldInterpolationMatrix<type>(points_coords,
inv_points_coord_matrix);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void
ShapeFunctions::buildInterpolationMatrix(const Matrix<Real> & coordinates,
Matrix<Real> & coordMatrix,
UInt integration_order) const {
switch (integration_order) {
case 1: {
for (UInt i = 0; i < coordinates.cols(); ++i)
coordMatrix(i, 0) = 1;
break;
}
case 2: {
UInt nb_quadrature_points = coordMatrix.cols();
for (UInt i = 0; i < coordinates.cols(); ++i) {
coordMatrix(i, 0) = 1;
for (UInt j = 1; j < nb_quadrature_points; ++j)
coordMatrix(i, j) = coordinates(j - 1, i);
}
break;
}
default: {
AKANTU_DEBUG_TO_IMPLEMENT();
break;
}
}
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix(
__attribute__((unused)) const Matrix<Real> & coordinates,
__attribute__((unused)) Matrix<Real> & coordMatrix,
__attribute__((unused)) UInt integration_order) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_segment_2>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_segment_3>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_triangle_3>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeFunctions::buildElementalFieldInterpolationMatrix<_triangle_6>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_tetrahedron_4>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_tetrahedron_10>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
buildInterpolationMatrix(coordinates, coordMatrix, integration_order);
}
/**
* @todo Write a more efficient interpolation for quadrangles by
* dropping unnecessary quadrature points
*
*/
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_quadrangle_4>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
if (integration_order !=
ElementClassProperty<_quadrangle_4>::polynomial_degree) {
AKANTU_DEBUG_TO_IMPLEMENT();
} else {
for (UInt i = 0; i < coordinates.cols(); ++i) {
Real x = coordinates(0, i);
Real y = coordinates(1, i);
coordMatrix(i, 0) = 1;
coordMatrix(i, 1) = x;
coordMatrix(i, 2) = y;
coordMatrix(i, 3) = x * y;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ShapeFunctions::buildElementalFieldInterpolationMatrix<_quadrangle_8>(
const Matrix<Real> & coordinates, Matrix<Real> & coordMatrix,
UInt integration_order) const {
if (integration_order !=
ElementClassProperty<_quadrangle_8>::polynomial_degree) {
AKANTU_DEBUG_TO_IMPLEMENT();
} else {
for (UInt i = 0; i < coordinates.cols(); ++i) {
UInt j = 0;
Real x = coordinates(0, i);
Real y = coordinates(1, i);
for (UInt e = 0; e <= 2; ++e) {
for (UInt n = 0; n <= 2; ++n) {
coordMatrix(i, j) = std::pow(x, e) * std::pow(y, n);
++j;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void ShapeFunctions::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 {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->mesh.getSpatialDimension();
Mesh::type_iterator it, last;
if (element_filter) {
it = element_filter->firstType(spatial_dimension, ghost_type);
last = element_filter->lastType(spatial_dimension, ghost_type);
} else {
it = mesh.firstType(spatial_dimension, ghost_type);
last = mesh.lastType(spatial_dimension, ghost_type);
}
for (; it != last; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type, ghost_type);
if (nb_element == 0)
continue;
const Array<UInt> * elem_filter;
if (element_filter)
elem_filter = &((*element_filter)(type, ghost_type));
else
elem_filter = &(empty_filter);
#define AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS(type) \
interpolateElementalFieldFromIntegrationPoints<type>( \
field(type, ghost_type), \
interpolation_points_coordinates_matrices(type, ghost_type), \
quad_points_coordinates_inv_matrices(type, ghost_type), result, \
ghost_type, *elem_filter)
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(
AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS);
#undef AKANTU_INTERPOLATE_ELEMENTAL_FIELD_FROM_C_POINTS
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::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 {
AKANTU_DEBUG_IN();
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
UInt nb_quad_per_element =
GaussIntegrationElement<type>::getNbQuadraturePoints();
UInt nb_interpolation_points_per_elem =
interpolation_points_coordinates_matrices.getNbComponent() /
nb_quad_per_element;
if (!result.exists(type, ghost_type))
result.alloc(nb_element * nb_interpolation_points_per_elem,
field.getNbComponent(), type, ghost_type);
if (element_filter != empty_filter)
nb_element = element_filter.getSize();
Matrix<Real> coefficients(nb_quad_per_element, field.getNbComponent());
Array<Real> & result_vec = result(type, ghost_type);
Array<Real>::const_matrix_iterator field_it = field.begin_reinterpret(
field.getNbComponent(), nb_quad_per_element, nb_element);
Array<Real>::const_matrix_iterator interpolation_points_coordinates_it =
interpolation_points_coordinates_matrices.begin(
nb_interpolation_points_per_elem, nb_quad_per_element);
Array<Real>::matrix_iterator result_begin = result_vec.begin_reinterpret(
field.getNbComponent(), nb_interpolation_points_per_elem,
result_vec.getSize() / nb_interpolation_points_per_elem);
Array<Real>::const_matrix_iterator inv_quad_coord_it =
quad_points_coordinates_inv_matrices.begin(nb_quad_per_element,
nb_quad_per_element);
/// loop over the elements of the current filter and element type
for (UInt el = 0; el < nb_element; ++el, ++field_it, ++inv_quad_coord_it,
++interpolation_points_coordinates_it) {
/**
* matrix containing the inversion of the quadrature points'
* coordinates
*/
const Matrix<Real> & inv_quad_coord_matrix = *inv_quad_coord_it;
/**
* multiply it by the field values over quadrature points to get
* the interpolation coefficients
*/
coefficients.mul<false, true>(inv_quad_coord_matrix, *field_it);
/// matrix containing the points' coordinates
const Matrix<Real> & coord = *interpolation_points_coordinates_it;
/// multiply the coordinates matrix by the coefficients matrix and store the
/// result
Matrix<Real> res(result_begin[element_filter(el)]);
res.mul<true, true>(coefficients, coord);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
inline void ShapeFunctions::interpolateElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & uq, GhostType ghost_type,
const Array<Real> & shapes, const Array<UInt> & filter_elements) const {
UInt nb_element;
UInt nb_nodes_per_element = ElementClass<type>::getShapeSize();
UInt nb_points = shapes.getSize() / mesh.getNbElement(type, ghost_type);
UInt nb_degree_of_freedom = u_el.getNbComponent() / nb_nodes_per_element;
Array<Real>::const_matrix_iterator N_it;
Array<Real>::const_matrix_iterator u_it;
Array<Real>::matrix_iterator inter_u_it;
Array<Real> * filtered_N = NULL;
if (filter_elements != empty_filter) {
nb_element = filter_elements.getSize();
filtered_N = new Array<Real>(0, shapes.getNbComponent());
FEEngine::filterElementalData(mesh, shapes, *filtered_N, type, ghost_type,
filter_elements);
N_it = filtered_N->begin_reinterpret(nb_nodes_per_element, nb_points,
nb_element);
} else {
nb_element = mesh.getNbElement(type, ghost_type);
N_it =
shapes.begin_reinterpret(nb_nodes_per_element, nb_points, nb_element);
}
uq.resize(nb_element * nb_points);
u_it = u_el.begin(nb_degree_of_freedom, nb_nodes_per_element);
inter_u_it =
uq.begin_reinterpret(nb_degree_of_freedom, nb_points, nb_element);
for (UInt el = 0; el < nb_element; ++el, ++N_it, ++u_it, ++inter_u_it) {
const Matrix<Real> & u = *u_it;
const Matrix<Real> & N = *N_it;
Matrix<Real> & inter_u = *inter_u_it;
inter_u.mul<false, false>(u, N);
}
delete filtered_N;
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
void ShapeFunctions::gradientElementalFieldOnIntegrationPoints(
const Array<Real> & u_el, Array<Real> & out_nablauq, GhostType ghost_type,
const Array<Real> & shapes_derivatives,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_points = integration_points(type, ghost_type).cols();
UInt element_dimension = ElementClass<type>::getNaturalSpaceDimension();
UInt nb_degree_of_freedom = u_el.getNbComponent() / nb_nodes_per_element;
Array<Real>::const_matrix_iterator B_it;
Array<Real>::const_matrix_iterator u_it;
Array<Real>::matrix_iterator nabla_u_it;
UInt nb_element;
Array<Real> * filtered_B = NULL;
if (filter_elements != empty_filter) {
nb_element = filter_elements.getSize();
filtered_B = new Array<Real>(0, shapes_derivatives.getNbComponent());
FEEngine::filterElementalData(mesh, shapes_derivatives, *filtered_B, type,
ghost_type, filter_elements);
B_it = filtered_B->begin(element_dimension, nb_nodes_per_element);
} else {
B_it = shapes_derivatives.begin(element_dimension, nb_nodes_per_element);
nb_element = mesh.getNbElement(type, ghost_type);
}
out_nablauq.resize(nb_element * nb_points);
u_it = u_el.begin(nb_degree_of_freedom, nb_nodes_per_element);
nabla_u_it = out_nablauq.begin(nb_degree_of_freedom, element_dimension);
for (UInt el = 0; el < nb_element; ++el, ++u_it) {
const Matrix<Real> & u = *u_it;
for (UInt q = 0; q < nb_points; ++q, ++B_it, ++nabla_u_it) {
const Matrix<Real> & B = *B_it;
Matrix<Real> & nabla_u = *nabla_u_it;
nabla_u.mul<false, true>(u, B);
}
}
delete filtered_B;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
diff --git a/src/fe_engine/shape_lagrange.hh b/src/fe_engine/shape_lagrange.hh
index 2a75648fd..c8a074bd3 100644
--- a/src/fe_engine/shape_lagrange.hh
+++ b/src/fe_engine/shape_lagrange.hh
@@ -1,185 +1,185 @@
/**
* @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/>.
*
*/
#ifndef __AKANTU_SHAPE_LAGRANGE_HH__
#define __AKANTU_SHAPE_LAGRANGE_HH__
#include "shape_functions.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <class Shape> class ShapeCohesive;
class ShapeIGFEM;
template <ElementKind kind> class ShapeLagrange : public ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ShapeLagrange(const Mesh & mesh, const ID & id = "shape_lagrange",
const MemoryID & memory_id = 0);
virtual ~ShapeLagrange(){};
/* ------------------------------------------------------------------------ */
/* 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 for given interpolation points
template <ElementType type>
void computeShapesOnIntegrationPoints(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
Array<Real> & shapes, const GhostType & ghost_type) 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;
/// 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;
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) 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;
/* ------------------------------------------------------------------------ */
/* 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;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "shape_lagrange_inline_impl.cc"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_SHAPE_LAGRANGE_HH__ */
diff --git a/src/fe_engine/shape_lagrange_inline_impl.cc b/src/fe_engine/shape_lagrange_inline_impl.cc
index 27a13d4f8..a2812bd96 100644
--- a/src/fe_engine/shape_lagrange_inline_impl.cc
+++ b/src/fe_engine/shape_lagrange_inline_impl.cc
@@ -1,466 +1,466 @@
/**
* @file shape_lagrange_inline_impl.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Oct 27 2010
* @date last modification: Thu Oct 15 2015
*
* @brief ShapeLagrange inline 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/>.
*
*/
-__END_AKANTU__
+} // akantu
#include "fe_engine.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
inline const Array<Real> &
ShapeLagrange<kind>::getShapes(const ElementType & el_type,
const GhostType & ghost_type) const {
return shapes(FEEngine::getInterpolationType(el_type), ghost_type);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
inline const Array<Real> &
ShapeLagrange<kind>::getShapesDerivatives(const ElementType & el_type,
const GhostType & ghost_type) const {
return shapes_derivatives(FEEngine::getInterpolationType(el_type),
ghost_type);
}
/* -------------------------------------------------------------------------- */
#define INIT_SHAPE_FUNCTIONS(type) \
setIntegrationPointsByType<type>(integration_points, ghost_type); \
precomputeShapesOnIntegrationPoints<type>(nodes, ghost_type); \
if (ElementClass<type>::getNaturalSpaceDimension() == \
mesh.getSpatialDimension() || \
kind != _ek_regular) \
precomputeShapeDerivativesOnIntegrationPoints<type>(nodes, ghost_type);
template <ElementKind kind>
inline void ShapeLagrange<kind>::initShapeFunctions(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
const ElementType & type, const GhostType & ghost_type) {
AKANTU_BOOST_REGULAR_ELEMENT_SWITCH(INIT_SHAPE_FUNCTIONS);
}
#if defined(AKANTU_STRUCTURAL_MECHANICS)
/* -------------------------------------------------------------------------- */
template <>
inline void ShapeLagrange<_ek_structural>::initShapeFunctions(
__attribute__((unused)) const Array<Real> & nodes,
__attribute__((unused)) const Matrix<Real> & integration_points,
__attribute__((unused)) const ElementType & type,
__attribute__((unused)) const GhostType & ghost_type) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
#endif
#undef INIT_SHAPE_FUNCTIONS
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
inline void ShapeLagrange<kind>::computeShapeDerivativesOnCPointsByElement(
const Matrix<Real> & node_coords, const Matrix<Real> & natural_coords,
Tensor3<Real> & shapesd) const {
AKANTU_DEBUG_IN();
// compute dnds
Tensor3<Real> dnds(node_coords.rows(), node_coords.cols(),
natural_coords.cols());
ElementClass<type>::computeDNDS(natural_coords, dnds);
// compute dxds
Tensor3<Real> J(node_coords.rows(), natural_coords.rows(),
natural_coords.cols());
ElementClass<type>::computeJMat(dnds, node_coords, J);
// compute shape derivatives
ElementClass<type>::computeShapeDerivatives(J, dnds, shapesd);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::inverseMap(const Vector<Real> & real_coords,
UInt elem, Vector<Real> & natural_coords,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(mesh.getNodes(), nodes_coord.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
ElementClass<type>::inverseMap(real_coords, nodes_coord, natural_coords);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
bool ShapeLagrange<kind>::contains(const Vector<Real> & real_coords, UInt elem,
const GhostType & ghost_type) const {
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> natural_coords(spatial_dimension);
inverseMap<type>(real_coords, elem, natural_coords, ghost_type);
return ElementClass<type>::contains(natural_coords);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolate(const Vector<Real> & real_coords,
UInt elem,
const Matrix<Real> & nodal_values,
Vector<Real> & interpolated,
const GhostType & ghost_type) const {
UInt nb_shapes = ElementClass<type>::getShapeSize();
Vector<Real> shapes(nb_shapes);
computeShapes<type>(real_coords, elem, shapes, ghost_type);
ElementClass<type>::interpolate(nodal_values, shapes, interpolated);
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapes(const Vector<Real> & real_coords,
UInt elem, Vector<Real> & shapes,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> natural_coords(spatial_dimension);
inverseMap<type>(real_coords, elem, natural_coords, ghost_type);
ElementClass<type>::computeShapes(natural_coords, shapes);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapeDerivatives(
const Matrix<Real> & real_coords, UInt elem, Tensor3<Real> & shapesd,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_points = real_coords.cols();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
AKANTU_DEBUG_ASSERT(mesh.getSpatialDimension() == shapesd.size(0) &&
nb_nodes_per_element == shapesd.size(1),
"Shape size doesn't match");
AKANTU_DEBUG_ASSERT(nb_points == shapesd.size(2),
"Number of points doesn't match shapes size");
Matrix<Real> natural_coords(spatial_dimension, nb_points);
// Creates the matrix of natural coordinates
for (UInt i = 0; i < nb_points; i++) {
Vector<Real> real_point = real_coords(i);
Vector<Real> natural_point = natural_coords(i);
inverseMap<type>(real_point, elem, natural_point, ghost_type);
}
UInt * elem_val = mesh.getConnectivity(type, ghost_type).storage();
Matrix<Real> nodes_coord(spatial_dimension, nb_nodes_per_element);
mesh.extractNodalValuesFromElement(mesh.getNodes(), nodes_coord.storage(),
elem_val + elem * nb_nodes_per_element,
nb_nodes_per_element, spatial_dimension);
computeShapeDerivativesOnCPointsByElement<type>(nodes_coord, natural_coords,
shapesd);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
ShapeLagrange<kind>::ShapeLagrange(const Mesh & mesh, const ID & id,
const MemoryID & memory_id)
: ShapeFunctions(mesh, id, memory_id),
shapes("shapes_generic", id, memory_id),
shapes_derivatives("shapes_derivatives_generic", id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapesOnIntegrationPoints(
__attribute__((unused)) const Array<Real> & nodes,
const Matrix<Real> & integration_points, Array<Real> & shapes,
const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).getSize();
shapes.resize(nb_element * nb_points);
#if !defined(AKANTU_NDEBUG)
UInt size_of_shapes = ElementClass<type>::getShapeSize();
AKANTU_DEBUG_ASSERT(shapes.getNbComponent() == size_of_shapes,
"The shapes array does not have the correct "
<< "number of component");
#endif
Array<Real>::matrix_iterator shapes_it = shapes.begin_reinterpret(
ElementClass<type>::getNbNodesPerInterpolationElement(), nb_points,
nb_element);
for (UInt elem = 0; elem < nb_element; ++elem, ++shapes_it) {
Matrix<Real> & N = *shapes_it;
ElementClass<type>::computeShapes(integration_points, N);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::precomputeShapesOnIntegrationPoints(
const Array<Real> & nodes, const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
UInt size_of_shapes = ElementClass<type>::getShapeSize();
Array<Real> & shapes_tmp =
shapes.alloc(0,
size_of_shapes, itp_type, ghost_type);
this->computeShapesOnIntegrationPoints<type>(nodes, natural_coords,
shapes_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::computeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const Matrix<Real> & integration_points,
Array<Real> & shape_derivatives, const GhostType & ghost_type) const {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
UInt nb_points = integration_points.cols();
UInt nb_element = mesh.getConnectivity(type, ghost_type).getSize();
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
AKANTU_DEBUG_ASSERT(shape_derivatives.getNbComponent() == size_of_shapesd,
"The shapes_derivatives array does not have the correct "
<< "number of component");
shape_derivatives.resize(nb_element * nb_points);
Array<Real> x_el(0, spatial_dimension * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, nodes, x_el, type, ghost_type);
Real * shapesd_val = shape_derivatives.storage();
Array<Real>::matrix_iterator x_it =
x_el.begin(spatial_dimension, nb_nodes_per_element);
for (UInt elem = 0; elem < nb_element; ++elem, ++x_it) {
Matrix<Real> & X = *x_it;
Tensor3<Real> B(shapesd_val, spatial_dimension, nb_nodes_per_element,
nb_points);
computeShapeDerivativesOnCPointsByElement<type>(X, integration_points, B);
shapesd_val += size_of_shapesd * nb_points;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::precomputeShapeDerivativesOnIntegrationPoints(
const Array<Real> & nodes, const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
Matrix<Real> & natural_coords = integration_points(type, ghost_type);
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
UInt size_of_shapesd = ElementClass<type>::getShapeDerivativesSize();
Array<Real> & shapes_derivatives_tmp =
shapes_derivatives.alloc(0,
size_of_shapesd, itp_type, ghost_type);
this->computeShapeDerivativesOnIntegrationPoints<type>(
nodes, natural_coords, shapes_derivatives_tmp, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
const Array<Real> & shapes, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
this->interpolateElementalFieldOnIntegrationPoints<type>(
u_el, out_uq, ghost_type, shapes, filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::interpolateOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_uq, UInt nb_degree_of_freedom,
GhostType ghost_type, const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(shapes.exists(itp_type, ghost_type),
"No shapes for the type "
<< shapes.printType(itp_type, ghost_type));
this->interpolateOnIntegrationPoints<type>(in_u, out_uq, nb_degree_of_freedom,
shapes(itp_type, ghost_type),
ghost_type, filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::gradientOnIntegrationPoints(
const Array<Real> & in_u, Array<Real> & out_nablauq,
UInt nb_degree_of_freedom, GhostType ghost_type,
const Array<UInt> & filter_elements) const {
AKANTU_DEBUG_IN();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
AKANTU_DEBUG_ASSERT(
shapes_derivatives.exists(itp_type, ghost_type),
"No shapes derivatives for the type "
<< shapes_derivatives.printType(itp_type, ghost_type));
UInt nb_nodes_per_element =
ElementClass<type>::getNbNodesPerInterpolationElement();
Array<Real> u_el(0, nb_degree_of_freedom * nb_nodes_per_element);
FEEngine::extractNodalToElementField(mesh, in_u, u_el, type, ghost_type,
filter_elements);
this->gradientElementalFieldOnIntegrationPoints<type>(
u_el, out_nablauq, ghost_type, shapes_derivatives(itp_type, ghost_type),
filter_elements);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
template <ElementType type>
void ShapeLagrange<kind>::fieldTimesShapes(const Array<Real> & field,
Array<Real> & field_times_shapes,
GhostType ghost_type) const {
AKANTU_DEBUG_IN();
field_times_shapes.resize(field.getSize());
UInt size_of_shapes = ElementClass<type>::getShapeSize();
InterpolationType itp_type = ElementClassProperty<type>::interpolation_type;
UInt nb_degree_of_freedom = field.getNbComponent();
const Array<Real> & shape = shapes(itp_type, ghost_type);
Array<Real>::const_matrix_iterator field_it =
field.begin(nb_degree_of_freedom, 1);
Array<Real>::const_matrix_iterator shapes_it = shape.begin(1, size_of_shapes);
Array<Real>::matrix_iterator it =
field_times_shapes.begin(nb_degree_of_freedom, size_of_shapes);
Array<Real>::matrix_iterator end =
field_times_shapes.end(nb_degree_of_freedom, size_of_shapes);
for (; it != end; ++it, ++field_it, ++shapes_it) {
it->mul<false, false>(*field_it, *shapes_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <ElementKind kind>
void ShapeLagrange<kind>::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Shapes Lagrange [" << std::endl;
ShapeFunctions::printself(stream, indent + 1);
shapes.printself(stream, indent + 1);
shapes_derivatives.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
diff --git a/src/fe_engine/shape_linked.cc b/src/fe_engine/shape_linked.cc
index eb5f8eaa1..86392fec7 100644
--- a/src/fe_engine/shape_linked.cc
+++ b/src/fe_engine/shape_linked.cc
@@ -1,82 +1,82 @@
/**
* @file shape_linked.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Sun Oct 19 2014
*
* @brief ShapeLinked 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_memory.hh"
#include "mesh.hh"
#include "shape_linked.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
#if defined(AKANTU_STRUCTURAL_MECHANICS)
/* -------------------------------------------------------------------------- */
template <>
ShapeLinked<_ek_structural>::ShapeLinked(Mesh & mesh, const ID & id, const MemoryID & memory_id) :
ShapeFunctions(mesh, id, memory_id)
{
}
/* -------------------------------------------------------------------------- */
template <>
ShapeLinked<_ek_structural>::~ShapeLinked() {
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
// delete all the shapes id
ElementTypeMapMultiReal::type_iterator s_type_it =
shapes.firstType(_all_dimensions, ghost_type, _ek_structural);
ElementTypeMapMultiReal::type_iterator s_type_end =
shapes.lastType (_all_dimensions, ghost_type, _ek_structural);
for(; s_type_it != s_type_end; ++s_type_it) {
delete [] shapes(*s_type_it, ghost_type);
}
// delete all the shapes derivatives id
ElementTypeMapMultiReal::type_iterator sd_type_it =
shapes_derivatives.firstType(_all_dimensions, ghost_type, _ek_structural);
ElementTypeMapMultiReal::type_iterator sd_type_end =
shapes_derivatives.lastType (_all_dimensions, ghost_type, _ek_structural);
for(; sd_type_it != sd_type_end; ++sd_type_it) {
delete [] shapes_derivatives(*sd_type_it, ghost_type);
}
}
}
#endif
-__END_AKANTU__
+} // akantu
diff --git a/src/fe_engine/shape_linked.hh b/src/fe_engine/shape_linked.hh
index 48dc59731..1e0c6eae5 100644
--- a/src/fe_engine/shape_linked.hh
+++ b/src/fe_engine/shape_linked.hh
@@ -1,161 +1,161 @@
/**
* @file shape_linked.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Feb 15 2011
* @date last modification: Thu Oct 22 2015
*
* @brief shape class for element with different set of shapes functions
*
* @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_functions.hh"
#ifndef __AKANTU_SHAPE_LINKED_HH__
#define __AKANTU_SHAPE_LINKED_HH__
-__BEGIN_AKANTU__
+namespace akantu {
template <ElementKind kind>
class ShapeLinked : public ShapeFunctions {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef ElementTypeMap<Array<Real> **> ElementTypeMapMultiReal;
ShapeLinked(Mesh & mesh, const ID & id = "shape_linked", const MemoryID & memory_id = 0);
virtual ~ShapeLinked();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialization function for structural elements
inline void initShapeFunctions(const Array<Real> & nodes,
const Matrix<Real> & integration_points,
const ElementType & type,
const GhostType & ghost_type);
/// 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 shapes 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,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter,
bool accumulate = false,
UInt id_shape = 0,
UInt num_degre_of_freedom_to_interpolate = 0,
UInt num_degre_of_freedom_interpolated = 0) 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,
const GhostType & ghost_type = _not_ghost,
const Array<UInt> & filter_elements = empty_filter,
bool accumulate = false,
UInt id_shape = 0,
UInt num_degre_of_freedom_to_interpolate = 0,
UInt num_degre_of_freedom_interpolated = 0) 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)) const GhostType & ghost_type) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
private:
/// extract the nodal field value to fill an elemental field
template <ElementType type>
void extractNodalToElementField(const Array<Real> & nodal_f,
Array<Real> & elemental_f,
UInt num_degre_of_freedom_to_extract,
const GhostType & ghost_type,
const Array<UInt> & filter_elements) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get a the shapes vector
inline const Array<Real> & getShapes(const ElementType & type,
const GhostType & ghost_type,
UInt id = 0) const;
/// get a the shapes derivatives vector
inline const Array<Real> & getShapesDerivatives(const ElementType & type,
const GhostType & ghost_type,
UInt id = 0) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// shape functions for all elements
ElementTypeMapMultiReal shapes;
/// shape derivatives for all elements
ElementTypeMapMultiReal shapes_derivatives;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "shape_linked_inline_impl.cc"
#endif
/// standard output stream operator
// inline std::ostream & operator <<(std::ostream & stream, const ShapeLinked & _this)
// {
// _this.printself(stream);
// return stream;
// }
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_SHAPE_LINKED_HH__ */
diff --git a/src/geometry/aabb_primitives/aabb_primitive.cc b/src/geometry/aabb_primitives/aabb_primitive.cc
index 3a511c8bc..3470de999 100644
--- a/src/geometry/aabb_primitives/aabb_primitive.cc
+++ b/src/geometry/aabb_primitives/aabb_primitive.cc
@@ -1,49 +1,49 @@
/**
* @file aabb_primitive.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Thu Jan 14 2016
*
* @brief Macro classe (primitive) for AABB CGAL algos
*
* @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 "aabb_primitive.hh"
-__BEGIN_AKANTU__
+namespace akantu {
Triangle_primitive::Point Triangle_primitive::reference_point() const {
return primitive.vertex(0);
}
Line_arc_primitive::Point Line_arc_primitive::reference_point() const {
Real x = to_double(primitive.source().x());
Real y = to_double(primitive.source().y());
Real z = to_double(primitive.source().z());
return Spherical::Point_3(x, y, z);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/geometry/aabb_primitives/aabb_primitive.hh b/src/geometry/aabb_primitives/aabb_primitive.hh
index aadefaf24..4a9a9f506 100644
--- a/src/geometry/aabb_primitives/aabb_primitive.hh
+++ b/src/geometry/aabb_primitives/aabb_primitive.hh
@@ -1,90 +1,90 @@
/**
* @file aabb_primitive.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Mar 13 2015
* @date last modification: Thu Jan 14 2016
*
* @brief Macro classe (primitive) for AABB CGAL algos
*
* @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_AABB_PRIMITIVE_HH__
#define __AKANTU_AABB_PRIMITIVE_HH__
#include "aka_common.hh"
#include "line_arc.hh"
#include "triangle.hh"
#include "tetrahedron.hh"
#include "mesh_geom_common.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/**
* This macro defines a class that is used in the CGAL AABB tree algorithm.
* All the `typedef`s and methods are required by the AABB module.
*
* The member variables are
* - the id of the element associated to the primitive
* - the geometric primitive of the element
*
* @param name the name of the primitive type
* @param kernel the name of the kernel used
*/
#define AKANTU_AABB_CLASS(name, kernel) \
class name##_primitive { \
typedef std::list< name<kernel> >::iterator Iterator; \
\
public: \
typedef UInt Id; \
typedef kernel::Point_3 Point; \
typedef kernel::name##_3 Datum; \
\
public: \
name##_primitive() : meshId(0), primitive() {} \
name##_primitive(Iterator it) : meshId(it->id()), primitive(*it) {} \
\
public: \
const Datum & datum() const { return primitive; } \
Point reference_point() const; \
const Id & id() const { return meshId; } \
\
protected: \
Id meshId; \
name<kernel> primitive; \
\
}
// If the primitive is supported by CGAL::intersection() then the
// implementation process is really easy with this macro
AKANTU_AABB_CLASS(Triangle, Cartesian);
AKANTU_AABB_CLASS(Line_arc, Spherical);
#undef AKANTU_AABB_CLASS
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_AABB_PRIMITIVE_HH__
diff --git a/src/geometry/aabb_primitives/line_arc.hh b/src/geometry/aabb_primitives/line_arc.hh
index 71bcd5d09..409cc91d8 100644
--- a/src/geometry/aabb_primitives/line_arc.hh
+++ b/src/geometry/aabb_primitives/line_arc.hh
@@ -1,78 +1,78 @@
/**
* @file line_arc.hh
*
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Thu Jan 14 2016
*
* @brief Segment classe (geometry) for AABB CGAL algos
*
* @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_LINE_ARC_HH__
#define __AKANTU_LINE_ARC_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Triangle_3 primitive
template<typename K>
class Line_arc : public CGAL::Line_arc_3<K> {
public:
/// Default constructor
Line_arc() :
CGAL::Line_arc_3<K>(), mesh_id(0), seg_id(0) {}
/// Copy constructor
Line_arc(const Line_arc & other) :
CGAL::Line_arc_3<K>(other), mesh_id(other.mesh_id), seg_id(other.seg_id) {}
/// Construct from 3 points
// "CGAL-4.5/doc_html/Circular_kernel_3/classCGAL_1_1Line__arc__3.html"
Line_arc(const CGAL::Line_3<K> & l, const CGAL::Circular_arc_point_3<K> & a,
const CGAL::Circular_arc_point_3<K> & b):
CGAL::Line_arc_3<K>(l, a, b), mesh_id(0), seg_id(0) {}
public:
UInt id() const { return mesh_id; }
UInt segId() const { return seg_id; }
void setId(UInt newId) { mesh_id = newId; }
void setSegId(UInt newId) { seg_id = newId; }
protected:
/// Id of the element represented by the primitive
UInt mesh_id;
/// Id of the segment represented by the primitive
UInt seg_id;
};
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_LINE_ARC_HH__
diff --git a/src/geometry/aabb_primitives/tetrahedron.hh b/src/geometry/aabb_primitives/tetrahedron.hh
index cc309ba07..daf0d4145 100644
--- a/src/geometry/aabb_primitives/tetrahedron.hh
+++ b/src/geometry/aabb_primitives/tetrahedron.hh
@@ -1,74 +1,74 @@
/**
* @file tetrahedron.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Feb 27 2015
* @date last modification: Thu Jan 14 2016
*
* @brief Tetrahedron classe (geometry) for AABB CGAL algos
*
* @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_TETRAHEDRON_HH__
#define __AKANTU_TETRAHEDRON_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Tetrahedron_3 primitive
template<typename K>
class Tetrahedron : public CGAL::Tetrahedron_3<K> {
public:
/// Default constructor
Tetrahedron() :
CGAL::Tetrahedron_3<K>(), meshId(0) {}
/// Copy constructor
Tetrahedron(const Tetrahedron & other) :
CGAL::Tetrahedron_3<K>(other), meshId(other.meshId) {}
/// Construct from 4 points
Tetrahedron(const CGAL::Point_3<K> & a,
const CGAL::Point_3<K> & b,
const CGAL::Point_3<K> & c,
const CGAL::Point_3<K> & d) :
CGAL::Tetrahedron_3<K>(a, b, c, d), meshId(0) {}
public:
UInt id() const { return meshId; }
void setId(UInt newId) { meshId = newId; }
protected:
/// Id of the element represented by the primitive
UInt meshId;
};
-__END_AKANTU__
+} // akantu
#endif
diff --git a/src/geometry/aabb_primitives/triangle.hh b/src/geometry/aabb_primitives/triangle.hh
index 9243e73d0..d25912af9 100644
--- a/src/geometry/aabb_primitives/triangle.hh
+++ b/src/geometry/aabb_primitives/triangle.hh
@@ -1,71 +1,71 @@
/**
* @file triangle.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Thu Jan 14 2016
*
* @brief Triangle classe (geometry) for AABB CGAL algos
*
* @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_TRIANGLE_HH__
#define __AKANTU_TRIANGLE_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/// Class used for substitution of CGAL::Triangle_3 primitive
template<typename K>
class Triangle : public CGAL::Triangle_3<K> {
public:
/// Default constructor
Triangle() :
CGAL::Triangle_3<K>(), meshId(0) {}
/// Copy constructor
Triangle(const Triangle & other) :
CGAL::Triangle_3<K>(other), meshId(other.meshId) {}
/// Construct from 3 points
Triangle(const CGAL::Point_3<K> & a, const CGAL::Point_3<K> & b, const CGAL::Point_3<K> & c):
CGAL::Triangle_3<K>(a, b, c), meshId(0) {}
public:
UInt id() const { return meshId; }
void setId(UInt newId) { meshId = newId; }
protected:
/// Id of the element represented by the primitive
UInt meshId;
};
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_TRIANGLE_HH__
diff --git a/src/geometry/geom_helper_functions.hh b/src/geometry/geom_helper_functions.hh
index fbe6bbaca..14e933bf3 100644
--- a/src/geometry/geom_helper_functions.hh
+++ b/src/geometry/geom_helper_functions.hh
@@ -1,104 +1,104 @@
/**
* @file geom_helper_functions.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Thu Jan 14 2016
*
* @brief Helper functions for the computational geometry algorithms
*
* @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_GEOM_HELPER_FUNCTIONS_HH__
#define _AKANTU_GEOM_HELPER_FUNCTIONS_HH__
#include "aka_common.hh"
#include "aka_math.hh"
#include "tree_type_helper.hh"
#include "mesh_geom_common.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/// Fuzzy compare of two points
template <class Point>
inline bool comparePoints(const Point & a, const Point & b) {
return Math::are_float_equal(a.x(), b.x()) &&
Math::are_float_equal(a.y(), b.y()) &&
Math::are_float_equal(a.z(), b.z());
}
template <>
inline bool comparePoints(const Spherical::Circular_arc_point_3 & a,
const Spherical::Circular_arc_point_3 & b) {
return Math::are_float_equal(CGAL::to_double(a.x()), CGAL::to_double(b.x())) &&
Math::are_float_equal(CGAL::to_double(a.y()), CGAL::to_double(b.y())) &&
Math::are_float_equal(CGAL::to_double(a.z()), CGAL::to_double(b.z()));
}
/// Fuzzy compare of two segments
template <class K>
inline bool compareSegments(const CGAL::Segment_3<K> & a, const CGAL::Segment_3<K> & b) {
return (comparePoints(a.source(), b.source()) && comparePoints(a.target(), b.target())) ||
(comparePoints(a.source(), b.target()) && comparePoints(a.target(), b.source()));
}
typedef Cartesian K;
/// Compare segment pairs
inline bool compareSegmentPairs(const std::pair<K::Segment_3, UInt> & a, const std::pair<K::Segment_3, UInt> & b) {
return compareSegments(a.first, b.first);
}
/// Pair ordering operator based on first member
struct segmentPairsLess {
inline bool operator()(const std::pair<K::Segment_3, UInt> & a, const std::pair<K::Segment_3, UInt> & b) {
return CGAL::compare_lexicographically(a.first.min(), b.first.min()) || CGAL::compare_lexicographically(a.first.max(), b.first.max());
}
};
/* -------------------------------------------------------------------------- */
/* Predicates */
/* -------------------------------------------------------------------------- */
/// Predicate used to determine if two segments are equal
class IsSameSegment {
public:
IsSameSegment(const K::Segment_3 & segment):
segment(segment)
{}
bool operator()(const std::pair<K::Segment_3, UInt> & test_pair) {
return compareSegments(segment, test_pair.first);
}
protected:
const K::Segment_3 segment;
};
-__END_AKANTU__
+} // akantu
#endif // _AKANTU_GEOM_HELPER_FUNCTIONS_HH__
diff --git a/src/geometry/mesh_abstract_intersector.hh b/src/geometry/mesh_abstract_intersector.hh
index b69beb764..6c1222924 100644
--- a/src/geometry/mesh_abstract_intersector.hh
+++ b/src/geometry/mesh_abstract_intersector.hh
@@ -1,108 +1,108 @@
/**
* @file mesh_abstract_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Thu Jan 14 2016
*
* @brief Abstract class for intersection computations
*
* @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_MESH_ABSTRACT_INTERSECTOR_HH__
#define __AKANTU_MESH_ABSTRACT_INTERSECTOR_HH__
#include "aka_common.hh"
#include "mesh_geom_abstract.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/**
* @brief Class used to perform intersections on a mesh and construct output data
*/
template<class Query>
class MeshAbstractIntersector : public MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshAbstractIntersector(Mesh & mesh);
/// Destructor
virtual ~MeshAbstractIntersector();
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the new_node_per_elem array
AKANTU_GET_MACRO(NewNodePerElem, *new_node_per_elem, const Array<UInt> &);
/// get the intersection_points array
AKANTU_GET_MACRO(IntersectionPoints, intersection_points, const Array<Real> *);
/// get the nb_seg_by_el UInt
AKANTU_GET_MACRO(NbSegByEl, nb_seg_by_el, UInt);
/**
* @brief Compute the intersection with a query object
*
* This function needs to be implemented for every subclass. It computes the intersections
* with the tree of primitives and creates the data for the user.
*
* @param query the CGAL primitive of the query object
*/
virtual void computeIntersectionQuery(const Query & query) = 0;
/// Compute intersection points between the mesh primitives (segments) and a query (surface in 3D or a curve in 2D), double intersection points for the same primitives are not considered. A maximum intersection node per element is set : 2 in 2D and 4 in 3D
virtual void computeMeshQueryIntersectionPoint(const Query & query, UInt nb_old_nodes) = 0;
/// Compute intersection between the mesh and a list of queries
virtual void computeIntersectionQueryList(const std::list<Query> & query_list);
/// Compute intersection points between the mesh and a list of queries
virtual void computeMeshQueryListIntersectionPoint(const std::list<Query> & query_list,
UInt nb_old_nodes);
/// Compute whatever result is needed from the user (should be move to the appropriate specific classe for genericity)
virtual void buildResultFromQueryList(const std::list<Query> & query_list) = 0;
protected:
/// new node per element (column 0: number of new nodes, then odd is the intersection node number and even the ID of the intersected segment)
Array<UInt> * new_node_per_elem;
/// intersection output: new intersection points (computeMeshQueryListIntersectionPoint)
Array<Real> * intersection_points;
/// number of segment in a considered element of the templated type of element specialized intersector
const UInt nb_seg_by_el;
};
-__END_AKANTU__
+} // akantu
#include "mesh_abstract_intersector_tmpl.hh"
#endif // __AKANTU_MESH_ABSTRACT_INTERSECTOR_HH__
diff --git a/src/geometry/mesh_abstract_intersector_tmpl.hh b/src/geometry/mesh_abstract_intersector_tmpl.hh
index 9782cee04..6d4b4d75f 100644
--- a/src/geometry/mesh_abstract_intersector_tmpl.hh
+++ b/src/geometry/mesh_abstract_intersector_tmpl.hh
@@ -1,89 +1,89 @@
/**
* @file mesh_abstract_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Thu Jan 14 2016
*
* @brief General class for intersection computations
*
* @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_MESH_ABSTRACT_INTERSECTOR_TMPL_HH__
#define __AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH__
#include "aka_common.hh"
#include "mesh_abstract_intersector.hh"
-__BEGIN_AKANTU__
+namespace akantu {
template<class Query>
MeshAbstractIntersector<Query>::MeshAbstractIntersector(Mesh & mesh):
MeshGeomAbstract(mesh),
new_node_per_elem(NULL),
intersection_points(NULL),
nb_seg_by_el(0)
{}
template<class Query>
MeshAbstractIntersector<Query>::~MeshAbstractIntersector()
{}
template<class Query>
void MeshAbstractIntersector<Query>::computeIntersectionQueryList(
const std::list<Query> & query_list) {
AKANTU_DEBUG_IN();
typename std::list<Query>::const_iterator
query_it = query_list.begin(),
query_end = query_list.end();
for (; query_it != query_end ; ++query_it) {
computeIntersectionQuery(*query_it);
}
AKANTU_DEBUG_OUT();
}
template<class Query>
void MeshAbstractIntersector<Query>::computeMeshQueryListIntersectionPoint(
const std::list<Query> & query_list, UInt nb_old_nodes) {
AKANTU_DEBUG_IN();
typename std::list<Query>::const_iterator
query_it = query_list.begin(),
query_end = query_list.end();
for (; query_it != query_end ; ++query_it) {
computeMeshQueryIntersectionPoint(*query_it, nb_old_nodes);
}
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_MESH_ABSTRACT_INTERSECTOR_TMPL_HH__
diff --git a/src/geometry/mesh_geom_abstract.hh b/src/geometry/mesh_geom_abstract.hh
index 9ab8ff286..a3b2f39b0 100644
--- a/src/geometry/mesh_geom_abstract.hh
+++ b/src/geometry/mesh_geom_abstract.hh
@@ -1,65 +1,65 @@
/**
* @file mesh_geom_abstract.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Thu Jan 14 2016
*
* @brief Class for constructing the CGAL primitives of a mesh
*
* @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_GEOM_ABSTRACT_HH__
#define __AKANTU_MESH_GEOM_ABSTRACT_HH__
#include "aka_common.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/// Abstract class for mesh geometry operations
class MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshGeomAbstract(Mesh & mesh) : mesh(mesh) {};
/// Destructor
virtual ~MeshGeomAbstract() {};
public:
/// Construct geometric data for computational geometry algorithms
virtual void constructData(GhostType ghost_type = _not_ghost) = 0;
protected:
/// Mesh used to construct the primitives
Mesh & mesh;
};
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_MESH_GEOM_ABSTRACT_HH__
diff --git a/src/geometry/mesh_geom_common.hh b/src/geometry/mesh_geom_common.hh
index c326329bc..72289b9c9 100644
--- a/src/geometry/mesh_geom_common.hh
+++ b/src/geometry/mesh_geom_common.hh
@@ -1,58 +1,58 @@
/**
* @file mesh_geom_common.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Thu Jan 14 2016
*
* @brief Common file for MeshGeom module
*
* @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_GEOM_COMMON_HH__
#define __AKANTU_MESH_GEOM_COMMON_HH__
#include "aka_common.hh"
#include <CGAL/MP_Float.h>
#include <CGAL/Quotient.h>
#include <CGAL/Cartesian.h>
#include <CGAL/Simple_cartesian.h>
#include <CGAL/Spherical_kernel_3.h>
#include <CGAL/Algebraic_kernel_for_spheres_2_3.h>
#include <CGAL/Lazy_exact_nt.h>
-__BEGIN_AKANTU__
+namespace akantu {
typedef CGAL::Simple_cartesian<Real> Cartesian;
typedef CGAL::Quotient<CGAL::MP_Float> NT;
typedef CGAL::Spherical_kernel_3<CGAL::Simple_cartesian<NT>, CGAL::Algebraic_kernel_for_spheres_2_3<NT> > Spherical;
//typedef CGAL::Lazy_exact_nt<CGAL::Quotient<CGAL::MP_Float> > NT;
//typedef CGAL::Spherical_kernel_3<CGAL::Simple_cartesian<NT>, CGAL::Algebraic_kernel_for_spheres_2_3<NT> > Spherical;
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_MESH_GEOM_COMMON_HH__
diff --git a/src/geometry/mesh_geom_factory.hh b/src/geometry/mesh_geom_factory.hh
index 74c464368..651e447f0 100644
--- a/src/geometry/mesh_geom_factory.hh
+++ b/src/geometry/mesh_geom_factory.hh
@@ -1,108 +1,108 @@
/**
* @file mesh_geom_factory.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 27 2015
* @date last modification: Thu Jan 14 2016
*
* @brief Class for constructing the CGAL primitives of a mesh
*
* @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_MESH_GEOM_FACTORY_HH__
#define __AKANTU_MESH_GEOM_FACTORY_HH__
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_geom_abstract.hh"
#include "tree_type_helper.hh"
#include "geom_helper_functions.hh"
#include <algorithm>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/**
* @brief Class used to construct AABB tree for intersection computations
*
* This class constructs a CGAL AABB tree of one type of element in a mesh
* for fast intersection computations.
*/
template<UInt dim, ElementType el_type, class Primitive, class Kernel>
class MeshGeomFactory : public MeshGeomAbstract {
public:
/// Construct from mesh
explicit MeshGeomFactory(Mesh & mesh);
/// Desctructor
virtual ~MeshGeomFactory();
public:
/// Construct AABB tree for fast intersection computing
virtual void constructData(GhostType ghost_type = _not_ghost);
/**
* @brief Construct a primitive and add it to a list of primitives
*
* This function needs to be specialized for every type that is wished to be supported.
* @param node_coordinates coordinates of the nodes making up the element
* @param id element number
* @param list the primitive list (not used inside MeshGeomFactory)
*/
inline void addPrimitive(
const Matrix<Real> & node_coordinates,
UInt id,
typename TreeTypeHelper<Primitive, Kernel>::container_type & list
);
inline void addPrimitive(
const Matrix<Real> & node_coordinates,
UInt id
);
/// Getter for the AABB tree
const typename TreeTypeHelper<Primitive, Kernel>::tree & getTree() const { return *data_tree; }
/// Getter for primitive list
const typename TreeTypeHelper<Primitive, Kernel>::container_type & getPrimitiveList() const
{ return primitive_list; }
protected:
/// AABB data tree
typename TreeTypeHelper<Primitive, Kernel>::tree * data_tree;
/// Primitive list
typename TreeTypeHelper<Primitive, Kernel>::container_type primitive_list;
};
-__END_AKANTU__
+} // akantu
#include "mesh_geom_factory_tmpl.hh"
#endif // __AKANTU_MESH_GEOM_FACTORY_HH__
diff --git a/src/geometry/mesh_geom_factory_tmpl.hh b/src/geometry/mesh_geom_factory_tmpl.hh
index 9f2450e3b..dfd7f01e3 100644
--- a/src/geometry/mesh_geom_factory_tmpl.hh
+++ b/src/geometry/mesh_geom_factory_tmpl.hh
@@ -1,259 +1,259 @@
/**
* @file mesh_geom_factory_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 27 2015
* @date last modification: Thu Jan 14 2016
*
* @brief Class for constructing the CGAL primitives of a mesh
*
* @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_MESH_GEOM_FACTORY_TMPL_HH__
#define __AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "mesh_geom_factory.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
template<UInt dim, ElementType type, class Primitive, class Kernel>
MeshGeomFactory<dim, type, Primitive, Kernel>::MeshGeomFactory(Mesh & mesh) :
MeshGeomAbstract(mesh),
data_tree(NULL),
primitive_list()
{}
template<UInt dim, ElementType type, class Primitive, class Kernel>
MeshGeomFactory<dim, type, Primitive, Kernel>::~MeshGeomFactory() {
delete data_tree;
}
/**
* This function loops over the elements of `type` in the mesh and creates the
* AABB tree of geometrical primitves (`data_tree`).
*/
template<UInt dim, ElementType type, class Primitive, class Kernel>
void MeshGeomFactory<dim, type, Primitive, Kernel>::constructData(GhostType ghost_type) {
AKANTU_DEBUG_IN();
primitive_list.clear();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, ghost_type);
const Array<Real> & nodes = mesh.getNodes();
UInt el_index = 0;
Array<UInt>::const_vector_iterator it = connectivity.begin(nb_nodes_per_element);
Array<UInt>::const_vector_iterator end = connectivity.end(nb_nodes_per_element);
Matrix<Real> node_coordinates(dim, nb_nodes_per_element);
// This loop builds the list of primitives
for (; it != end ; ++it, ++el_index) {
const Vector<UInt> & el_connectivity = *it;
for (UInt i = 0 ; i < nb_nodes_per_element ; i++)
for (UInt j = 0 ; j < dim ; j++)
node_coordinates(j, i) = nodes(el_connectivity(i), j);
// the unique elemental id assigned to the primitive is the
// linearized element index over ghost type
addPrimitive(node_coordinates, el_index);
}
delete data_tree;
// This condition allows the use of the mesh geom module
// even if types are not compatible with AABB tree algorithm
if (TreeTypeHelper<Primitive, Kernel>::is_valid)
data_tree = new typename TreeTypeHelper<Primitive, Kernel>::tree(primitive_list.begin(), primitive_list.end());
AKANTU_DEBUG_OUT();
}
template<UInt dim, ElementType type, class Primitive, class Kernel>
void MeshGeomFactory<dim, type, Primitive, Kernel>::addPrimitive(const Matrix<Real> & node_coordinates,
UInt id) {
this->addPrimitive(node_coordinates, id, this->primitive_list);
}
// (2D, _triangle_3) decomposed into Triangle<Cartesian>
template<>
inline void MeshGeomFactory<2, _triangle_3, Triangle<Cartesian>, Cartesian>::addPrimitive(
const Matrix<Real> & node_coordinates,
UInt id,
TreeTypeHelper<Triangle<Cartesian>, Cartesian>::container_type & list) {
TreeTypeHelper<Triangle<Cartesian>, Cartesian>::point_type
a(node_coordinates(0, 0), node_coordinates(1, 0), 0.),
b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
Triangle<Cartesian> t(a, b, c);
t.setId(id);
list.push_back(t);
}
// (2D, _triangle_6) decomposed into Triangle<Cartesian>
template<>
inline void MeshGeomFactory<2, _triangle_6, Triangle<Cartesian>, Cartesian>::addPrimitive(
const Matrix<Real> & node_coordinates,
UInt id,
TreeTypeHelper<Triangle<Cartesian>, Cartesian>::container_type & list) {
TreeTypeHelper<Triangle<Cartesian>, Cartesian>::point_type
a(node_coordinates(0, 0), node_coordinates(1, 0), 0.),
b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
Triangle<Cartesian> t(a, b, c);
t.setId(id);
list.push_back(t);
}
// (2D, _triangle_3) decomposed into Line_arc<Spherical>
template<>
inline void MeshGeomFactory<2, _triangle_3, Line_arc<Spherical>, Spherical>::addPrimitive(
const Matrix<Real> & node_coordinates,
UInt id,
TreeTypeHelper<Line_arc<Spherical>, Spherical>::container_type & list) {
TreeTypeHelper<Line_arc<Spherical>, Spherical>::point_type
a(node_coordinates(0, 0), node_coordinates(1, 0), 0.),
b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
/*std::cout << "elem " << id << " node 1 : x_node=" << node_coordinates(0, 0)
<< ", x_arc_node=" << a.x() << ", y_node=" << node_coordinates(1, 0)
<< ", y_arc_node=" << a.y() << std::endl ;
std::cout << "elem " << id << " node 2 : x_node=" << node_coordinates(0, 1)
<< ", x_arc_node=" << b.x() << ", y_node=" << node_coordinates(1, 1)
<< ", y_arc_node=" << b.y() << std::endl ;
std::cout << "elem " << id << " node 2 : x_node=" << node_coordinates(0, 2)
<< ", x_arc_node=" << c.x() << ", y_node=" << node_coordinates(1, 2)
<< ", y_arc_node=" << c.y() << std::endl ;*/
CGAL::Line_3<Spherical> l1(a, b), l2(b, c), l3(c, a);
Line_arc<Spherical> s1(l1,a, b), s2(l2, b, c), s3(l3, c, a);
s1.setId(id); s1.setSegId(0);
s2.setId(id); s2.setSegId(1);
s3.setId(id); s3.setSegId(2);
list.push_back(s1);
list.push_back(s2);
list.push_back(s3);
}
#if defined(AKANTU_IGFEM)
// (2D, _igfem_triangle_4) decomposed into Line_arc<Spherical>
template<>
inline void MeshGeomFactory<2, _igfem_triangle_4, Line_arc<Spherical>, Spherical>::addPrimitive(
const Matrix<Real> & node_coordinates,
UInt id,
TreeTypeHelper<Line_arc<Spherical>, Spherical>::container_type & list) {
TreeTypeHelper<Line_arc<Spherical>, Spherical>::point_type
a(node_coordinates(0, 0), node_coordinates(1, 0), 0.),
b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
CGAL::Line_3<Spherical> l1(a, b), l2(b, c), l3(c, a);
Line_arc<Spherical> s1(l1,a, b), s2(l2, b, c), s3(l3, c, a);
s1.setId(id); s1.setSegId(0);
s2.setId(id); s2.setSegId(1);
s3.setId(id); s3.setSegId(2);
list.push_back(s1);
list.push_back(s2);
list.push_back(s3);
}
// (2D, _igfem_triangle_4) decomposed into Line_arc<Spherical>
template<>
inline void MeshGeomFactory<2, _igfem_triangle_5, Line_arc<Spherical>, Spherical>::addPrimitive(
const Matrix<Real> & node_coordinates,
UInt id,
TreeTypeHelper<Line_arc<Spherical>, Spherical>::container_type & list) {
TreeTypeHelper<Line_arc<Spherical>, Spherical>::point_type
a(node_coordinates(0, 0), node_coordinates(1, 0), 0.),
b(node_coordinates(0, 1), node_coordinates(1, 1), 0.),
c(node_coordinates(0, 2), node_coordinates(1, 2), 0.);
CGAL::Line_3<Spherical> l1(a, b), l2(b, c), l3(c, a);
Line_arc<Spherical> s1(l1,a, b), s2(l2, b, c), s3(l3, c, a);
s1.setId(id); s1.setSegId(0);
s2.setId(id); s2.setSegId(1);
s3.setId(id); s3.setSegId(2);
list.push_back(s1);
list.push_back(s2);
list.push_back(s3);
}
#endif
// (3D, _tetrahedron_4) decomposed into Triangle<Cartesian>
template<>
inline void MeshGeomFactory<3, _tetrahedron_4, Triangle<Cartesian>, Cartesian>::addPrimitive(
const Matrix<Real> & node_coordinates,
UInt id,
TreeTypeHelper<Triangle<Cartesian>, Cartesian>::container_type & list) {
TreeTypeHelper<Triangle<Cartesian>, Cartesian>::point_type
a(node_coordinates(0, 0), node_coordinates(1, 0), node_coordinates(2, 0)),
b(node_coordinates(0, 1), node_coordinates(1, 1), node_coordinates(2, 1)),
c(node_coordinates(0, 2), node_coordinates(1, 2), node_coordinates(2, 2)),
d(node_coordinates(0, 3), node_coordinates(1, 3), node_coordinates(2, 3));
Triangle<Cartesian>
t1(a, b, c),
t2(b, c, d),
t3(c, d, a),
t4(d, a, b);
t1.setId(id);
t2.setId(id);
t3.setId(id);
t4.setId(id);
list.push_back(t1);
list.push_back(t2);
list.push_back(t3);
list.push_back(t4);
}
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_MESH_GEOM_FACTORY_TMPL_HH__
diff --git a/src/geometry/mesh_geom_intersector.hh b/src/geometry/mesh_geom_intersector.hh
index 230d77249..ae1d3a633 100644
--- a/src/geometry/mesh_geom_intersector.hh
+++ b/src/geometry/mesh_geom_intersector.hh
@@ -1,72 +1,72 @@
/**
* @file mesh_geom_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Thu Jan 14 2016
*
* @brief General class for intersection computations
*
* @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_MESH_GEOM_INTERSECTOR_HH__
#define __AKANTU_MESH_GEOM_INTERSECTOR_HH__
#include "aka_common.hh"
#include "mesh_abstract_intersector.hh"
#include "mesh_geom_factory.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/**
* @brief Class used to perform intersections on a mesh and construct output data
*/
template<UInt dim, ElementType type, class Primitive, class Query, class Kernel>
class MeshGeomIntersector : public MeshAbstractIntersector<Query> {
public:
/// Construct from mesh
explicit MeshGeomIntersector(Mesh & mesh);
/// Destructor
virtual ~MeshGeomIntersector();
public:
/// Construct the primitive tree object
virtual void constructData(GhostType ghost_type = _not_ghost);
protected:
/// Factory object containing the primitive tree
MeshGeomFactory<dim, type, Primitive, Kernel> factory;
};
-__END_AKANTU__
+} // akantu
#include "mesh_geom_intersector_tmpl.hh"
#endif // __AKANTU_MESH_GEOM_INTERSECTOR_HH__
diff --git a/src/geometry/mesh_geom_intersector_tmpl.hh b/src/geometry/mesh_geom_intersector_tmpl.hh
index ec2454717..a1a5582b2 100644
--- a/src/geometry/mesh_geom_intersector_tmpl.hh
+++ b/src/geometry/mesh_geom_intersector_tmpl.hh
@@ -1,62 +1,62 @@
/**
* @file mesh_geom_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Thu Jan 14 2016
*
* @brief General class for intersection computations
*
* @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_MESH_GEOM_INTERSECTOR_TMPL_HH__
#define __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
template<UInt dim, ElementType type, class Primitive, class Query, class Kernel>
MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::MeshGeomIntersector(Mesh & mesh) :
MeshAbstractIntersector<Query>(mesh),
factory(mesh)
{}
template<UInt dim, ElementType type, class Primitive, class Query, class Kernel>
MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::~MeshGeomIntersector()
{}
template<UInt dim, ElementType type, class Primitive, class Query, class Kernel>
void MeshGeomIntersector<dim, type, Primitive, Query, Kernel>::constructData(GhostType ghost_type) {
this->intersection_points->resize(0);
factory.constructData(ghost_type);
}
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_MESH_GEOM_INTERSECTOR_TMPL_HH__
diff --git a/src/geometry/mesh_segment_intersector.hh b/src/geometry/mesh_segment_intersector.hh
index 940a8105a..8ef17445d 100644
--- a/src/geometry/mesh_segment_intersector.hh
+++ b/src/geometry/mesh_segment_intersector.hh
@@ -1,103 +1,103 @@
/**
* @file mesh_segment_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Thu Jan 14 2016
*
* @brief Computation of mesh intersection with segments
*
* @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_MESH_SEGMENT_INTERSECTOR_HH__
#define __AKANTU_MESH_SEGMENT_INTERSECTOR_HH__
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
#include "mesh_geom_common.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/// Here, we know what kernel we have to use
typedef Cartesian K;
template<UInt dim, ElementType type>
class MeshSegmentIntersector : public MeshGeomIntersector<dim, type, Triangle<K>, K::Segment_3, K> {
/// Parent class type
typedef MeshGeomIntersector<dim, type, Triangle<K>, K::Segment_3, K> parent_type;
/// Result of intersection function type
typedef typename IntersectionTypeHelper<TreeTypeHelper< Triangle<K>, K>, K::Segment_3>::intersection_type result_type;
/// Pair of segments and element id
typedef std::pair<K::Segment_3, UInt> pair_type;
public:
/// Construct from mesh
explicit MeshSegmentIntersector(Mesh & mesh, Mesh & result_mesh);
/// Destructor
virtual ~MeshSegmentIntersector();
public:
/**
* @brief Computes the intersection of the mesh with a segment
*
* @param query the segment to compute the intersections with the mesh
*/
virtual void computeIntersectionQuery(const K::Segment_3 & query);
/// Compute intersection points between the mesh and a query
virtual void computeMeshQueryIntersectionPoint(const K::Segment_3 & query, UInt nb_old_nodes);
/// Compute the embedded mesh
virtual void buildResultFromQueryList(const std::list<K::Segment_3> & query_list);
void setPhysicalName(const std::string & other)
{ current_physical_name = other; }
protected:
/// Compute segments from intersection list
void computeSegments(const std::list<result_type> & intersections,
std::set<pair_type, segmentPairsLess> & segments,
const K::Segment_3 & query);
protected:
/// Result mesh
Mesh & result_mesh;
/// Physical name of the current batch of queries
std::string current_physical_name;
};
-__END_AKANTU__
+} // akantu
#include "mesh_segment_intersector_tmpl.hh"
#endif // __AKANTU_MESH_SEGMENT_INTERSECTOR_HH__
diff --git a/src/geometry/mesh_segment_intersector_tmpl.hh b/src/geometry/mesh_segment_intersector_tmpl.hh
index 37fe10631..897bfcfb8 100644
--- a/src/geometry/mesh_segment_intersector_tmpl.hh
+++ b/src/geometry/mesh_segment_intersector_tmpl.hh
@@ -1,270 +1,270 @@
/**
* @file mesh_segment_intersector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 29 2015
* @date last modification: Thu Jan 14 2016
*
* @brief Computation of mesh intersection with segments
*
* @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_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
#define __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "tree_type_helper.hh"
-__BEGIN_AKANTU__
+namespace akantu {
template<UInt dim, ElementType type>
MeshSegmentIntersector<dim, type>::MeshSegmentIntersector(Mesh & mesh, Mesh & result_mesh):
parent_type(mesh),
result_mesh(result_mesh),
current_physical_name()
{
this->intersection_points = new Array<Real>(0,dim);
this->constructData();
}
template<UInt dim, ElementType type>
MeshSegmentIntersector<dim, type>::~MeshSegmentIntersector()
{}
template<UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::computeIntersectionQuery(const K::Segment_3 & query) {
AKANTU_DEBUG_IN();
result_mesh.addConnectivityType(_segment_2, _not_ghost);
result_mesh.addConnectivityType(_segment_2, _ghost);
std::list<result_type> result_list;
std::set<std::pair<K::Segment_3, UInt>, segmentPairsLess> segment_set;
this->factory.getTree().all_intersections(query, std::back_inserter(result_list));
this->computeSegments(result_list, segment_set, query);
// Arrays for storing nodes and connectivity
Array<Real> & nodes = result_mesh.getNodes();
Array<UInt> & connectivity = result_mesh.getConnectivity(_segment_2);
// Arrays for storing associated element and physical name
bool valid_elemental_data = true;
Array<Element> * associated_element = NULL;
Array<std::string> * associated_physical_name = NULL;
try {
associated_element = &result_mesh.getData<Element>("associated_element", _segment_2);
associated_physical_name = &result_mesh.getData<std::string>("physical_names", _segment_2);
} catch (debug::Exception & e) {
valid_elemental_data = false;
}
std::set<pair_type, segmentPairsLess>::iterator
it = segment_set.begin(),
end = segment_set.end();
// Loop over the segment pairs
for (; it != end ; ++it) {
if (!it->first.is_degenerate()) {
Vector<UInt> segment_connectivity(2);
segment_connectivity(0) = result_mesh.getNbNodes();
segment_connectivity(1) = result_mesh.getNbNodes() + 1;
connectivity.push_back(segment_connectivity);
// Copy nodes
Vector<Real> source(dim), target(dim);
for (UInt j = 0 ; j < dim ; j++) {
source(j) = it->first.source()[j];
target(j) = it->first.target()[j];
}
nodes.push_back(source);
nodes.push_back(target);
// Copy associated element info
if (valid_elemental_data) {
associated_element->push_back(Element(type, it->second));
associated_physical_name->push_back(current_physical_name);
}
}
}
AKANTU_DEBUG_OUT();
}
template<UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>:: computeMeshQueryIntersectionPoint(const K::Segment_3 & query,
UInt nb_old_nodes) {
AKANTU_DEBUG_ERROR("The method: computeMeshQueryIntersectionPoint has not been implemented in class MeshSegmentIntersector!");
}
template<UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::buildResultFromQueryList(const std::list<K::Segment_3> & query_list) {
AKANTU_DEBUG_IN();
this->computeIntersectionQueryList(query_list);
AKANTU_DEBUG_OUT();
}
template<UInt dim, ElementType type>
void MeshSegmentIntersector<dim, type>::computeSegments(const std::list<result_type> & intersections,
std::set<pair_type, segmentPairsLess> & segments,
const K::Segment_3 & query) {
AKANTU_DEBUG_IN();
/*
* Number of intersections = 0 means
*
* - query is completely outside mesh
* - query is completely inside primitive
*
* We try to determine the case and still construct the segment list
*/
if (intersections.size() == 0) {
// We look at all the primitives intersected by two rays
// If there is one primitive in common, then query is inside
// that primitive
K::Ray_3 ray1(query.source(), query.target());
K::Ray_3 ray2(query.target(), query.source());
std::set<UInt> ray1_results, ray2_results;
this->factory.getTree().all_intersected_primitives(ray1, std::inserter(ray1_results, ray1_results.begin()));
this->factory.getTree().all_intersected_primitives(ray2, std::inserter(ray2_results, ray2_results.begin()));
bool inside_primitive = false;
UInt primitive_id = 0;
std::set<UInt>::iterator
ray2_it = ray2_results.begin(),
ray2_end = ray2_results.end();
// Test if first list contains an element of second list
for (; ray2_it != ray2_end && !inside_primitive ; ++ray2_it) {
if (ray1_results.find(*ray2_it) != ray1_results.end()) {
inside_primitive = true;
primitive_id = *ray2_it;
}
}
if (inside_primitive) {
segments.insert(std::make_pair(query, primitive_id));
}
}
else {
typename std::list<result_type>::const_iterator
it = intersections.begin(),
end = intersections.end();
for(; it != end ; ++it) {
UInt el = (*it)->second;
// Result of intersection is a segment
if (const K::Segment_3 * segment = boost::get<K::Segment_3>(&((*it)->first))) {
// Check if the segment was alread created
segments.insert(std::make_pair(*segment, el));
}
// Result of intersection is a point
else if (const K::Point_3 * point = boost::get<K::Point_3>(&((*it)->first))) {
// We only want to treat points differently if we're in 3D with Tetra4 elements
// This should be optimized by compilator
if (dim == 3 && type == _tetrahedron_4) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
TreeTypeHelper<Triangle<K>, K>::container_type facets;
const Array<Real> & nodes = this->mesh.getNodes();
Array<UInt>::const_vector_iterator
connectivity_vec = this->mesh.getConnectivity(type).begin(nb_nodes_per_element);
const Vector<UInt> & el_connectivity = connectivity_vec[el];
Matrix<Real> node_coordinates(dim, nb_nodes_per_element);
for (UInt i = 0 ; i < nb_nodes_per_element ; i++)
for (UInt j = 0 ; j < dim ; j++)
node_coordinates(j, i) = nodes(el_connectivity(i), j);
this->factory.addPrimitive(node_coordinates, el, facets);
// Local tree
TreeTypeHelper<Triangle<K>, K>::tree * local_tree =
new TreeTypeHelper<Triangle<K>, K>::tree(facets.begin(), facets.end());
// Compute local intersections (with current element)
std::list<result_type> local_intersections;
local_tree->all_intersections(query, std::back_inserter(local_intersections));
bool out_point_found = false;
typename std::list<result_type>::const_iterator
local_it = local_intersections.begin(),
local_end = local_intersections.end();
for (; local_it != local_end ; ++local_it) {
if (const K::Point_3 * local_point = boost::get<K::Point_3>(&((*local_it)->first))) {
if (!comparePoints(*point, *local_point)) {
K::Segment_3 seg(*point, *local_point);
segments.insert(std::make_pair(seg, el));
out_point_found = true;
}
}
}
if (!out_point_found) {
TreeTypeHelper<Triangle<K>, K>::point_type
a(node_coordinates(0, 0), node_coordinates(1, 0), node_coordinates(2, 0)),
b(node_coordinates(0, 1), node_coordinates(1, 1), node_coordinates(2, 1)),
c(node_coordinates(0, 2), node_coordinates(1, 2), node_coordinates(2, 2)),
d(node_coordinates(0, 3), node_coordinates(1, 3), node_coordinates(2, 3));
K::Tetrahedron_3 tetra(a, b, c, d);
const K::Point_3 * inside_point = NULL;
if (tetra.has_on_bounded_side(query.source()) && !tetra.has_on_boundary(query.source()))
inside_point = &query.source();
else if (tetra.has_on_bounded_side(query.target()) && !tetra.has_on_boundary(query.target()))
inside_point = &query.target();
if (inside_point) {
K::Segment_3 seg(*inside_point, *point);
segments.insert(std::make_pair(seg, el));
}
}
delete local_tree;
}
}
}
}
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_MESH_SEGMENT_INTERSECTOR_TMPL_HH__
diff --git a/src/geometry/mesh_sphere_intersector.hh b/src/geometry/mesh_sphere_intersector.hh
index cc0b5335d..63bcea07b 100644
--- a/src/geometry/mesh_sphere_intersector.hh
+++ b/src/geometry/mesh_sphere_intersector.hh
@@ -1,105 +1,105 @@
/**
* @file mesh_sphere_intersector.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jun 23 2015
* @date last modification: Thu Jan 14 2016
*
* @brief Computation of mesh intersection with sphere(s)
*
* @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_MESH_SPHERE_INTERSECTOR_HH__
#define __AKANTU_MESH_SPHERE_INTERSECTOR_HH__
#include "aka_common.hh"
#include "mesh_geom_intersector.hh"
#include "mesh_geom_common.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/// Here, we know what kernel we have to use
typedef Spherical SK;
template<UInt dim, ElementType type>
class MeshSphereIntersector : public MeshGeomIntersector<dim, type, Line_arc<SK>, SK::Sphere_3, SK> {
/// Parent class type
typedef MeshGeomIntersector<dim, type, Line_arc<SK>, SK::Sphere_3, SK> parent_type;
/// Result of intersection function type
typedef typename IntersectionTypeHelper<TreeTypeHelper< Triangle<K>, K>, K::Segment_3>::intersection_type result_type;
/// Pair of intersection points and element id
typedef std::pair<SK::Circular_arc_point_3, UInt> pair_type;
public:
/// Construct from mesh
explicit MeshSphereIntersector(Mesh & mesh);
/// Destructor
virtual ~MeshSphereIntersector();
public:
/// Construct the primitive tree object
virtual void constructData(GhostType ghost_type = _not_ghost);
/**
* @brief Computes the intersection of the mesh with a sphere
*
* @param query (sphere) to compute the intersections with the mesh
*/
virtual void computeIntersectionQuery(const SK::Sphere_3 & query){
AKANTU_DEBUG_ERROR("This function is not implemented for spheres (It was to generic and has been replaced by computeMeshQueryIntersectionPoint");
}
/// Compute intersection points between the mesh primitives (segments) and a query (surface in 3D or a curve in 2D), double intersection points for the same primitives are not considered. A maximum is set to the number of intersection nodes per element: 2 in 2D and 4 in 3D
virtual void computeMeshQueryIntersectionPoint(const SK::Sphere_3 & query, UInt nb_old_nodes);
/// Build the IGFEM mesh
virtual void buildResultFromQueryList(const std::list<SK::Sphere_3> & query){
AKANTU_DEBUG_ERROR("This function is no longer implemented to split geometrical operations and dedicated result construction");
}
/// Set the tolerance
void setToleranceIntersectionOnNode(UInt tol) {
this->tol_intersection_on_node = tol;
}
protected:
/// tolerance for which the intersection is considered on the mesh node (relative to the segment lenght)
Real tol_intersection_on_node;
};
-__END_AKANTU__
+} // akantu
#include "mesh_sphere_intersector_tmpl.hh"
#endif // __AKANTU_MESH_SPHERE_INTERSECTOR_HH__
diff --git a/src/geometry/mesh_sphere_intersector_tmpl.hh b/src/geometry/mesh_sphere_intersector_tmpl.hh
index 44a5120e0..07b2745fe 100644
--- a/src/geometry/mesh_sphere_intersector_tmpl.hh
+++ b/src/geometry/mesh_sphere_intersector_tmpl.hh
@@ -1,196 +1,196 @@
/**
* @file mesh_sphere_intersector_tmpl.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jun 23 2015
* @date last modification: Thu Jan 14 2016
*
* @brief Computation of mesh intersection with spheres
*
* @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_MESH_SPHERE_INTERSECTOR_TMPL_HH__
#define __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "tree_type_helper.hh"
#include "mesh_sphere_intersector.hh"
#include "static_communicator.hh"
-__BEGIN_AKANTU__
+namespace akantu {
template<UInt dim, ElementType type>
MeshSphereIntersector<dim, type>::MeshSphereIntersector(Mesh & mesh):
parent_type(mesh),
tol_intersection_on_node(1e-10)
{
#if defined(AKANTU_IGFEM)
if( (type == _triangle_3) || (type == _igfem_triangle_4) || (type == _igfem_triangle_5) ){
const_cast<UInt &>(this->nb_seg_by_el) = 3;
} else {
AKANTU_DEBUG_ERROR("Not ready for mesh type " << type);
}
#else
if( (type != _triangle_3) )
AKANTU_DEBUG_ERROR("Not ready for mesh type " << type);
#endif
// initialize the intersection pointsss array with the spatial dimension
this->intersection_points = new Array<Real>(0,dim);
// A maximum is set to the number of intersection nodes per element to limit the size of new_node_per_elem: 2 in 2D and 4 in 3D
this->new_node_per_elem = new Array<UInt>(0, 1 + 4 * (dim-1));
}
template<UInt dim, ElementType type>
MeshSphereIntersector<dim, type>::~MeshSphereIntersector() {
delete this->new_node_per_elem;
delete this->intersection_points;
}
template<UInt dim, ElementType type>
void MeshSphereIntersector<dim, type>::constructData(GhostType ghost_type) {
this->new_node_per_elem->resize(this->mesh.getNbElement(type, ghost_type));
this->new_node_per_elem->clear();
MeshGeomIntersector<dim, type, Line_arc<SK>, SK::Sphere_3, SK>::constructData(ghost_type);
}
template<UInt dim, ElementType type>
void MeshSphereIntersector<dim, type>:: computeMeshQueryIntersectionPoint(const SK::Sphere_3 & query,
UInt nb_old_nodes) {
/// function to replace computeIntersectionQuery in a more generic geometry module version
// The newNodeEvent is not send from this method who only compute the intersection points
AKANTU_DEBUG_IN();
Array<Real> & nodes = this->mesh.getNodes();
UInt nb_node = nodes.getSize() + this->intersection_points->getSize();
// Tolerance for proximity checks should be defined by user
Real global_tolerance = Math::getTolerance();
Math::setTolerance(tol_intersection_on_node);
typedef boost::variant<pair_type> sk_inter_res;
TreeTypeHelper<Line_arc<Spherical>, Spherical>::const_iterator
it = this->factory.getPrimitiveList().begin(),
end= this->factory.getPrimitiveList().end();
for (; it != end ; ++it) { // loop on the primitives (segments)
std::list<sk_inter_res> s_results;
CGAL::intersection(*it, query, std::back_inserter(s_results));
if (s_results.size() == 1) { // just one point
if (pair_type * pair = boost::get<pair_type>(&s_results.front())) {
if (pair->second == 1) { // not a point tangent to the sphere
// the intersection point written as a vector
Vector<Real> new_node(dim, 0.0);
Cartesian::Point_3 point(CGAL::to_double(pair->first.x()),
CGAL::to_double(pair->first.y()),
CGAL::to_double(pair->first.z()));
for (UInt i = 0 ; i < dim ; i++) {
new_node(i) = point[i];
}
/// boolean to decide wheter intersection point is on a standard node of the mesh or not
bool is_on_mesh = false;
/// boolean to decide if this intersection point has been already computed for a neighbor element
bool is_new = true;
/// check if intersection point has already been computed
UInt n = nb_old_nodes;
// check if we already compute this intersection and add it as a node for a neighboor element of another type
Array<Real>::vector_iterator existing_node = nodes.begin(dim);
for (; n < nodes.getSize() ; ++n) {// loop on the nodes from nb_old_nodes
if (Math::are_vector_equal(dim, new_node.storage(), existing_node[n].storage())) {
is_new = false;
break;
}
}
if(is_new){
Array<Real>::vector_iterator intersection_points_it = this->intersection_points->begin(dim);
Array<Real>::vector_iterator intersection_points_end = this->intersection_points->end(dim);
for (; intersection_points_it != intersection_points_end ; ++intersection_points_it, ++n) {
if (Math::are_vector_equal(dim, new_node.storage(), intersection_points_it->storage())) {
is_new = false;
break;
}
}
}
// get the initial and final points of the primitive (segment) and write them as vectors
Cartesian::Point_3 source_cgal(CGAL::to_double(it->source().x()),
CGAL::to_double(it->source().y()),
CGAL::to_double(it->source().z()));
Cartesian::Point_3 target_cgal(CGAL::to_double(it->target().x()),
CGAL::to_double(it->target().y()),
CGAL::to_double(it->target().z()));
Vector<Real> source(dim), target(dim);
for (UInt i = 0 ; i < dim ; i++) {
source(i) = source_cgal[i];
target(i) = target_cgal[i];
}
// Check if we are close from a node of the primitive (segment)
if (Math::are_vector_equal(dim, source.storage(), new_node.storage()) ||
Math::are_vector_equal(dim, target.storage(), new_node.storage())) {
is_on_mesh = true;
is_new = false;
}
if (is_new) {// if the intersection point is a new one add it to the list
this->intersection_points->push_back(new_node);
nb_node++;
}
// deduce the element id
UInt element_id = it->id();
// fill the new_node_per_elem array
if (!is_on_mesh) { // if the node is not on a mesh node
UInt & nb_new_nodes_per_el = (*this->new_node_per_elem)(element_id, 0);
nb_new_nodes_per_el += 1;
AKANTU_DEBUG_ASSERT(2 * nb_new_nodes_per_el < this->new_node_per_elem->getNbComponent(),
"You might have to interface crossing the same material");
(*this->new_node_per_elem)(element_id, (2 * nb_new_nodes_per_el) - 1) = n;
(*this->new_node_per_elem)(element_id, 2 * nb_new_nodes_per_el) = it->segId();
}
}
}
}
}
Math::setTolerance(global_tolerance);
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_MESH_SPHERE_INTERSECTOR_TMPL_HH__
diff --git a/src/geometry/tree_type_helper.hh b/src/geometry/tree_type_helper.hh
index 3e6646664..853bc63ff 100644
--- a/src/geometry/tree_type_helper.hh
+++ b/src/geometry/tree_type_helper.hh
@@ -1,111 +1,111 @@
/**
* @file tree_type_helper.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Thu Jan 14 2016
*
* @brief Converts element types of a mesh to CGAL primitive types
*
* @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_TREE_TYPE_HELPER_HH__
#define __AKANTU_TREE_TYPE_HELPER_HH__
#include "aka_common.hh"
#include "line_arc.hh"
#include "triangle.hh"
#include "tetrahedron.hh"
#include "aabb_primitive.hh"
#include "mesh_geom_common.hh"
#include <CGAL/AABB_traits.h>
#include <CGAL/AABB_tree.h>
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/// Replacement class for algorithm that can't use the AABB tree types
template<typename iterator>
struct VoidTree {
VoidTree(const iterator & begin, const iterator & end) {}
};
/// Helper class used to ease the use of CGAL AABB tree algorithm
template<class Primitive, class Kernel>
struct TreeTypeHelper {
static const bool is_valid = false;
typedef Primitive primitive_type;
typedef typename std::list<primitive_type> container_type;
typedef typename container_type::iterator iterator;
typedef typename container_type::const_iterator const_iterator;
typedef typename CGAL::Point_3<Kernel> point_type;
typedef VoidTree<iterator> tree;
};
/// Helper class used to ease the use of intersections
template<class TTHelper, class Query>
struct IntersectionTypeHelper;
/**
* Macro used to specialize TreeTypeHelper
* @param my_primitive associated primitive type
* @param my_query query_type
* @param my_kernel kernel type
*/
#define TREE_TYPE_HELPER_MACRO(my_primitive, my_query, my_kernel) \
template<> \
struct TreeTypeHelper<my_primitive<my_kernel>, my_kernel> { \
static const bool is_valid = true; \
typedef my_primitive<my_kernel> primitive_type; \
typedef my_primitive##_primitive aabb_primitive_type; \
typedef CGAL::Point_3<my_kernel> point_type; \
\
typedef std::list<primitive_type> container_type; \
typedef container_type::iterator iterator; \
typedef CGAL::AABB_traits<my_kernel, aabb_primitive_type> aabb_traits_type; \
typedef CGAL::AABB_tree<aabb_traits_type> tree; \
typedef tree::Primitive_id id_type; \
}; \
\
template<> \
struct IntersectionTypeHelper<TreeTypeHelper<my_primitive<my_kernel>, my_kernel>, my_query> { \
typedef boost::optional< \
TreeTypeHelper<my_primitive<my_kernel>, my_kernel>::tree::Intersection_and_primitive_id<my_query>::Type \
> intersection_type; \
}
TREE_TYPE_HELPER_MACRO(Triangle, Cartesian::Segment_3, Cartesian);
//TREE_TYPE_HELPER_MACRO(Line_arc, Spherical::Sphere_3, Spherical);
#undef TREE_TYPE_HELPER_MACRO
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_TREE_TYPE_HELPER_HH__
diff --git a/src/io/dumper/dumpable.cc b/src/io/dumper/dumpable.cc
index fceb2baee..c7a27ef22 100644
--- a/src/io/dumper/dumpable.cc
+++ b/src/io/dumper/dumpable.cc
@@ -1,285 +1,285 @@
/**
* @file dumpable.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Jan 21 2016
*
* @brief Implementation of the dumpable 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 "dumpable.hh"
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include <io_helper.hh>
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
Dumpable::Dumpable() : default_dumper("") {}
/* -------------------------------------------------------------------------- */
Dumpable::~Dumpable() {
DumperMap::iterator it = dumpers.begin();
DumperMap::iterator end = dumpers.end();
for (; it != end; ++it) {
delete it->second;
}
}
/* -------------------------------------------------------------------------- */
void Dumpable::registerExternalDumper(DumperIOHelper & dumper,
const std::string & dumper_name,
const bool is_default) {
this->dumpers[dumper_name] = &dumper;
if (is_default)
this->default_dumper = dumper_name;
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpMesh(const Mesh & mesh, UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & element_kind) {
this->addDumpMeshToDumper(this->default_dumper, mesh, spatial_dimension,
ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpMeshToDumper(const std::string & dumper_name,
const Mesh & mesh, UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & element_kind) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerMesh(mesh, spatial_dimension, ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFilteredMesh(
const Mesh & mesh, const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
const GhostType & ghost_type, const ElementKind & element_kind) {
this->addDumpFilteredMeshToDumper(this->default_dumper, mesh, elements_filter,
nodes_filter, spatial_dimension, ghost_type,
element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFilteredMeshToDumper(
const std::string & dumper_name, const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter, UInt spatial_dimension,
const GhostType & ghost_type, const ElementKind & element_kind) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerFilteredMesh(mesh, elements_filter, nodes_filter,
spatial_dimension, ghost_type, element_kind);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpField(const std::string & field_id) {
this->addDumpFieldToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldToDumper(__attribute__((unused))
const std::string & dumper_name,
__attribute__((unused))
const std::string & field_id) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldExternal(const std::string & field_id,
dumper::Field * field) {
this->addDumpFieldExternalToDumper(this->default_dumper, field_id, field);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field);
}
/* -------------------------------------------------------------------------- */
void Dumpable::removeDumpField(const std::string & field_id) {
this->removeDumpFieldFromDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.unRegisterField(field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldVector(const std::string & field_id) {
this->addDumpFieldVectorToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldVectorToDumper(__attribute__((unused))
const std::string & dumper_name,
__attribute__((unused))
const std::string & field_id) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldTensor(const std::string & field_id) {
this->addDumpFieldTensorToDumper(this->default_dumper, field_id);
}
/* -------------------------------------------------------------------------- */
void Dumpable::addDumpFieldTensorToDumper(__attribute__((unused))
const std::string & dumper_name,
__attribute__((unused))
const std::string & field_id) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/* -------------------------------------------------------------------------- */
void Dumpable::setDirectory(const std::string & directory) {
this->setDirectoryToDumper(this->default_dumper, directory);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setDirectory(directory);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setBaseName(const std::string & basename) {
this->setBaseNameToDumper(this->default_dumper, basename);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setBaseName(basename);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTimeStepToDumper(Real time_step) {
this->setTimeStepToDumper(this->default_dumper, time_step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTimeStepToDumper(const std::string & dumper_name,
Real time_step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.setTimeStep(time_step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTextModeToDumper(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.getDumper().setMode(iohelper::TEXT);
}
/* -------------------------------------------------------------------------- */
void Dumpable::setTextModeToDumper() {
DumperIOHelper & dumper = this->getDumper(this->default_dumper);
dumper.getDumper().setMode(iohelper::TEXT);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump();
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump() { this->dump(this->default_dumper); }
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name, UInt step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump(step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(UInt step) { this->dump(this->default_dumper, step); }
/* -------------------------------------------------------------------------- */
void Dumpable::dump(const std::string & dumper_name, Real time, UInt step) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.dump(time, step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::dump(Real time, UInt step) {
this->dump(this->default_dumper, time, step);
}
/* -------------------------------------------------------------------------- */
void Dumpable::internalAddDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field);
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Dumpable::getDumper() {
return this->getDumper(this->default_dumper);
}
/* -------------------------------------------------------------------------- */
DumperIOHelper & Dumpable::getDumper(const std::string & dumper_name) {
DumperMap::iterator it = this->dumpers.find(dumper_name);
DumperMap::iterator end = this->dumpers.end();
if (it == end)
AKANTU_EXCEPTION("Dumper " << dumper_name
<< "has not been registered, yet.");
return *(it->second);
}
/* -------------------------------------------------------------------------- */
std::string Dumpable::getDefaultDumperName() const {
return this->default_dumper;
}
-__END_AKANTU__
+} // akantu
#endif
diff --git a/src/io/dumper/dumpable_dummy.hh b/src/io/dumper/dumpable_dummy.hh
index d955275af..7973056b1 100644
--- a/src/io/dumper/dumpable_dummy.hh
+++ b/src/io/dumper/dumpable_dummy.hh
@@ -1,252 +1,252 @@
/**
* @file dumpable_dummy.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 Oct 26 2012
* @date last modification: Fri Aug 21 2015
*
* @brief Interface for object who wants to dump themselves
*
* @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_DUMPABLE_DUMMY_HH__
#define __AKANTU_DUMPABLE_DUMMY_HH__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wunused"
namespace dumper {
class Field;
}
class DumperIOHelper;
class Mesh;
/* -------------------------------------------------------------------------- */
class Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Dumpable() {};
virtual ~Dumpable() { };
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template<class T>
inline void registerDumper(const std::string & dumper_name,
const std::string & file_name = "",
const bool is_default = false) { }
void registerExternalDumper(DumperIOHelper * dumper,
const std::string & dumper_name,
const bool is_default = false) { }
void addDumpMesh(const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {
}
void addDumpMeshToDumper(const std::string & dumper_name,
const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {
}
void addDumpFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {
}
void addDumpFilteredMeshToDumper(const std::string & dumper_name,
const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {
}
virtual void addDumpField(const std::string & field_id){
AKANTU_DEBUG_TO_IMPLEMENT();
}
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id){
AKANTU_DEBUG_TO_IMPLEMENT();
}
virtual void addDumpFieldExternal(const std::string & field_id,
dumper::Field * field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
virtual void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
template<typename T>
void addDumpFieldExternal(const std::string & field_id,
const Array<T> & field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
template<typename T>
void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
template<typename T>
void addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
template<typename T>
void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void removeDumpField(const std::string & field_id) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void setDirectory(const std::string & directory) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void setBaseName(const std::string & basename) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void setTextModeToDumper(const std::string & dumper_name){
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void setTextModeToDumper(){
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void dump() {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void dump(UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name,
UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void dump(Real current_time,
UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
void dump(const std::string & dumper_name,
Real current_time,
UInt step) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
protected:
void internalAddDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field) {
AKANTU_DEBUG_WARNING("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
protected:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper & getDumper() {
AKANTU_DEBUG_ERROR("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
DumperIOHelper & getDumper(const std::string & dumper_name){
AKANTU_DEBUG_ERROR("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
template<class T>
T & getDumper(const std::string & dumper_name) {
AKANTU_DEBUG_ERROR("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
std::string getDefaultDumperName() {
AKANTU_DEBUG_ERROR("No dumper activated at compilation, turn on AKANTU_USE_IOHELPER in cmake.");
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
#pragma GCC diagnostic pop
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPABLE_DUMMY_HH__ */
diff --git a/src/io/dumper/dumpable_inline_impl.hh b/src/io/dumper/dumpable_inline_impl.hh
index 24e641d36..5406cccbc 100644
--- a/src/io/dumper/dumpable_inline_impl.hh
+++ b/src/io/dumper/dumpable_inline_impl.hh
@@ -1,134 +1,134 @@
/**
* @file dumpable_inline_impl.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: Wed Nov 13 2013
* @date last modification: Thu Jan 21 2016
*
* @brief Implementation of the Dumpable 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_DUMPABLE_INLINE_IMPL_HH__
#define __AKANTU_DUMPABLE_INLINE_IMPL_HH__
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
#include "dumper_elemental_field.hh"
#include "dumper_nodal_field.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <class T>
inline void Dumpable::registerDumper(const std::string & dumper_name,
const std::string & file_name,
const bool is_default) {
if (this->dumpers.find(dumper_name) != this->dumpers.end()) {
AKANTU_DEBUG_INFO("Dumper " + dumper_name + "is already registered.");
}
std::string name = file_name;
if (name == "")
name = dumper_name;
this->dumpers[dumper_name] = new T(name);
if (is_default)
this->default_dumper = dumper_name;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternal(const std::string & field_id,
const Array<T> & field) {
this->addDumpFieldExternalToDumper<T>(this->default_dumper, field_id, field);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void
Dumpable::addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field) {
dumper::Field * field_cont = new dumper::NodalField<T>(field);
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field_cont);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & element_kind) {
this->addDumpFieldExternalToDumper(this->default_dumper, field_id, field,
spatial_dimension, ghost_type,
element_kind);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Dumpable::addDumpFieldExternalToDumper(
const std::string & dumper_name, const std::string & field_id,
const ElementTypeMapArray<T> & field, UInt spatial_dimension,
const GhostType & ghost_type, const ElementKind & element_kind) {
dumper::Field * field_cont;
#if defined(AKANTU_IGFEM)
if (element_kind == _ek_igfem) {
field_cont = new dumper::IGFEMElementalField<T>(field, spatial_dimension,
ghost_type, element_kind);
} else
#endif
field_cont = new dumper::ElementalField<T>(field, spatial_dimension,
ghost_type, element_kind);
DumperIOHelper & dumper = this->getDumper(dumper_name);
dumper.registerField(field_id, field_cont);
}
/* -------------------------------------------------------------------------- */
template <class T>
inline T & Dumpable::getDumper(const std::string & dumper_name) {
DumperIOHelper & dumper = this->getDumper(dumper_name);
try {
T & templated_dumper = dynamic_cast<T &>(dumper);
return templated_dumper;
} catch (...) {
AKANTU_EXCEPTION("Dumper " << dumper_name << " is not of type: "
<< debug::demangle(typeid(T).name()));
}
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif
#endif /* __AKANTU_DUMPABLE_INLINE_IMPL_HH__ */
diff --git a/src/io/dumper/dumpable_iohelper.hh b/src/io/dumper/dumpable_iohelper.hh
index 3d7330154..db0a8ee8c 100644
--- a/src/io/dumper/dumpable_iohelper.hh
+++ b/src/io/dumper/dumpable_iohelper.hh
@@ -1,195 +1,195 @@
/**
* @file dumpable_iohelper.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: Tue Jan 06 2015
* @date last modification: Thu Nov 19 2015
*
* @brief Interface for object who wants to dump themselves
*
* @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_DUMPABLE_IOHELPER_HH__
#define __AKANTU_DUMPABLE_IOHELPER_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
#include <set>
-__BEGIN_AKANTU__
+namespace akantu {
class Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Dumpable();
virtual ~Dumpable();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create a new dumper (of templated type T) and register it under
/// dumper_name. file_name is used for construction of T. is default states if
/// this dumper is the default dumper.
template<class T>
inline void registerDumper(const std::string & dumper_name,
const std::string & file_name = "",
const bool is_default = false);
/// register an externally created dumper
void registerExternalDumper(DumperIOHelper & dumper,
const std::string & dumper_name,
const bool is_default = false);
/// register a mesh to the default dumper
void addDumpMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// register a mesh to the default identified by its name
void addDumpMeshToDumper(const std::string & dumper_name,
const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// register a filtered mesh as the default dumper
void addDumpFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// register a filtered mesh and provides a name
void addDumpFilteredMeshToDumper(const std::string & dumper_name,
const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// to implement
virtual void addDumpField(const std::string & field_id);
/// to implement
virtual void addDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id);
/// add a field
virtual void addDumpFieldExternal(const std::string & field_id,
dumper::Field * field);
virtual void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field);
template<typename T>
inline void addDumpFieldExternal(const std::string & field_id,
const Array<T> & field);
template<typename T>
inline void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const Array<T> & field);
template<typename T>
inline void addDumpFieldExternal(const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
template<typename T>
inline void addDumpFieldExternalToDumper(const std::string & dumper_name,
const std::string & field_id,
const ElementTypeMapArray<T> & field,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
void removeDumpField(const std::string & field_id);
void removeDumpFieldFromDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldVector(const std::string & field_id);
virtual void addDumpFieldVectorToDumper(const std::string & dumper_name,
const std::string & field_id);
virtual void addDumpFieldTensor(const std::string & field_id);
virtual void addDumpFieldTensorToDumper(const std::string & dumper_name,
const std::string & field_id);
void setDirectory(const std::string & directory);
void setDirectoryToDumper(const std::string & dumper_name,
const std::string & directory);
void setBaseName(const std::string & basename);
void setBaseNameToDumper(const std::string & dumper_name,
const std::string & basename);
void setTimeStepToDumper(Real time_step);
void setTimeStepToDumper(const std::string & dumper_name,
Real time_step);
void setTextModeToDumper(const std::string & dumper_name);
void setTextModeToDumper();
virtual void dump();
virtual void dump(UInt step);
virtual void dump(Real time, UInt step);
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);
public:
void internalAddDumpFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
dumper::Field * field);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper & getDumper();
DumperIOHelper & getDumper(const std::string & dumper_name);
template<class T> T & getDumper(const std::string & dumper_name);
std::string getDefaultDumperName() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
typedef std::map<std::string, DumperIOHelper *> DumperMap;
typedef std::set<std::string> DumperSet;
DumperMap dumpers;
std::string default_dumper;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPABLE_IOHELPER_HH__ */
diff --git a/src/io/dumper/dumper_compute.hh b/src/io/dumper/dumper_compute.hh
index b97c989dc..a55f37291 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>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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(){};
};
/* -------------------------------------------------------------------------- */
template <typename input_type, typename return_type>
class ComputeFunctor : public ComputeFunctorOutput<return_type> {
public:
ComputeFunctor(){};
virtual ~ComputeFunctor(){};
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() {
delete &(this->sub_field);
delete &(this->func);
}
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) {
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; };
iohelper::DataType getDataType() {
return iohelper::getDataType<data_type>();
}
/// get the number of components of the hosted field
virtual ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) {
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);
/// for connection to a FieldCompute
virtual ComputeFunctorInterface * connect(HomogenizerProxy & proxy);
/* ------------------------------------------------------------------------ */
/* 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;
}
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;
}
/* ------------------------------------------------------------------------ */
/* 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__
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPER_COMPUTE_HH__ */
diff --git a/src/io/dumper/dumper_element_iterator.hh b/src/io/dumper/dumper_element_iterator.hh
index d28dd853f..5daeff6b3 100644
--- a/src/io/dumper/dumper_element_iterator.hh
+++ b/src/io/dumper/dumper_element_iterator.hh
@@ -1,193 +1,193 @@
/**
* @file dumper_element_iterator.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Fri May 15 2015
*
* @brief Iterators 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_ELEMENT_ITERATOR_HH__
#define __AKANTU_DUMPER_ELEMENT_ITERATOR_HH__
/* -------------------------------------------------------------------------- */
#include "element.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template<class types, template <class> class final_iterator>
class element_iterator {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
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 final_iterator<types> iterator;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
element_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)
: field(field),
tit(t_it),
tit_end(t_it_end),
array_it(array_it),
array_it_end(array_it_end),
ghost_type(ghost_type) {
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
bool operator!=(const iterator & it) const {
return (ghost_type != it.ghost_type)
|| (tit != it.tit || (array_it != it.array_it));
}
iterator & operator++() {
++array_it;
while(array_it == array_it_end && tit != tit_end) {
++tit;
if(tit != tit_end) {
const array_type & vect = field(*tit, ghost_type);
UInt _nb_data_per_elem = getNbDataPerElem(*tit);
UInt nb_component = vect.getNbComponent();
UInt size = (vect.getSize() * nb_component) / _nb_data_per_elem;
array_it = vect.begin_reinterpret(_nb_data_per_elem,size);
array_it_end = vect.end_reinterpret (_nb_data_per_elem,size);
}
}
return *(static_cast<iterator *>(this));
};
ElementType getType() { return *tit; }
UInt element_type() { return getIOHelperType(*tit); }
Element getCurrentElement(){
return Element(*tit,array_it.getCurrentIndex());
}
UInt getNbDataPerElem(const ElementType & type) const {
if (!nb_data_per_elem.exists(type, ghost_type))
return field(type,ghost_type).getNbComponent();
return nb_data_per_elem(type,ghost_type);
}
void setNbDataPerElem(const ElementTypeMap<UInt> & nb_data){
this->nb_data_per_elem = nb_data;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the field to iterate on
const field_type & field;
/// field iterator
typename field_type::type_iterator tit;
/// field iterator end
typename field_type::type_iterator tit_end;
/// array iterator
array_iterator array_it;
/// internal iterator end
array_iterator array_it_end;
/// ghost type identification
const GhostType ghost_type;
/// number of data per element
ElementTypeMap<UInt> nb_data_per_elem;
};
/* -------------------------------------------------------------------------- */
template<typename types>
class elemental_field_iterator
: public element_iterator<types, elemental_field_iterator> {
public:
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
typedef element_iterator<types, ::akantu::dumper::elemental_field_iterator> parent;
typedef typename types::it_type it_type;
typedef typename types::return_type return_type;
typedef typename types::field_type field_type;
typedef typename types::array_iterator array_iterator;
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
elemental_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) { }
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
return_type operator*(){
return *this->array_it;
}
private:
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_DUMPER_ELEMENT_ITERATOR_HH__ */
diff --git a/src/io/dumper/dumper_element_partition.hh b/src/io/dumper/dumper_element_partition.hh
index a4eb05d66..21296b317 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/>.
*
*/
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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 = StaticCommunicator::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; }
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // akantu
diff --git a/src/io/dumper/dumper_elemental_field.hh b/src/io/dumper/dumper_elemental_field.hh
index cec891358..452c277d3 100644
--- a/src/io/dumper/dumper_elemental_field.hh
+++ b/src/io/dumper/dumper_elemental_field.hh
@@ -1,80 +1,80 @@
/**
* @file dumper_elemental_field.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Aug 17 2015
*
* @brief description of elemental 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_ELEMENTAL_FIELD_HH__
#define __AKANTU_DUMPER_ELEMENTAL_FIELD_HH__
/* -------------------------------------------------------------------------- */
#include "static_communicator.hh"
#include "dumper_field.hh"
#include "dumper_generic_elemental_field.hh"
#ifdef AKANTU_IGFEM
# include "dumper_igfem_elemental_field.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template<typename T, template <class> class ret = Vector,bool filtered = false>
class ElementalField
: public GenericElementalField<SingleType<T,ret,filtered>,
elemental_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef SingleType<T,ret,filtered> types;
typedef typename types::field_type field_type;
typedef elemental_field_iterator<types> iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementalField(const field_type & field,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) :
GenericElementalField<types,elemental_field_iterator>(field,
spatial_dimension,
ghost_type,
element_kind) { }
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPER_ELEMENTAL_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_field.hh b/src/io/dumper/dumper_field.hh
index b36fcfae8..7c7170e3f 100644
--- a/src/io/dumper/dumper_field.hh
+++ b/src/io/dumper/dumper_field.hh
@@ -1,137 +1,137 @@
/**
* @file dumper_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 Common interface for 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_FIELD_HH__
#define __AKANTU_DUMPER_FIELD_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
class FieldComputeProxy;
class FieldComputeBaseInterface;
class ComputeFunctorInterface;
class HomogenizerProxy;
/* -------------------------------------------------------------------------- */
/// Field interface
class Field {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
Field() : homogeneous(false) {}
virtual ~Field(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
#ifdef AKANTU_USE_IOHELPER
/// register this to the provided dumper
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) = 0;
#endif
/// set the number of data per item (used for elements fields at the moment)
virtual void setNbData(__attribute__((unused)) UInt nb_data) {
AKANTU_DEBUG_TO_IMPLEMENT();
};
/// set the number of data per elem (used for elements fields at the moment)
virtual void setNbDataPerElem(__attribute__((unused))
const ElementTypeMap<UInt> & nb_data) {
AKANTU_DEBUG_TO_IMPLEMENT();
};
/// set the number of data per elem (used for elements fields at the moment)
virtual void setNbDataPerElem(__attribute__((unused)) UInt nb_data) {
AKANTU_DEBUG_TO_IMPLEMENT();
};
/// get the number of components of the hosted field
virtual ElementTypeMap<UInt>
getNbComponents(__attribute__((unused)) UInt dim = _all_dimensions,
__attribute__((unused)) GhostType ghost_type = _not_ghost,
__attribute__((unused)) ElementKind kind = _ek_not_defined) {
throw;
};
/// for connection to a FieldCompute
inline virtual Field * connect(__attribute__((unused))
FieldComputeProxy & proxy) {
throw;
};
/// for connection to a FieldCompute
inline virtual ComputeFunctorInterface * connect(__attribute__((unused))
HomogenizerProxy & proxy) {
throw;
};
/// check if the same quantity of data for all element types
virtual void checkHomogeneity() = 0;
/// return the dumper name
std::string getGroupName() { return group_name; };
/// return the id of the field
std::string getID() { return field_id; };
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// return the flag to know if the field is homogeneous/contiguous
virtual bool isHomogeneous() { return homogeneous; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the flag to know if it is homogeneous
bool homogeneous;
/// the name of the group it was associated to
std::string group_name;
/// the name of the dumper it was associated to
std::string field_id;
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPER_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_filtered_connectivity.hh b/src/io/dumper/dumper_filtered_connectivity.hh
index 9f4f313e7..ebc21227e 100644
--- a/src/io/dumper/dumper_filtered_connectivity.hh
+++ b/src/io/dumper/dumper_filtered_connectivity.hh
@@ -1,151 +1,151 @@
/**
* @file dumper_filtered_connectivity.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Mon Aug 17 2015
*
* @brief FilteredConnectivities 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/>.
*
*/
#include "dumper_generic_elemental_field.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <class types>
class filtered_connectivity_field_iterator
: public element_iterator<types, filtered_connectivity_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef element_iterator<types, dumper::filtered_connectivity_field_iterator> parent;
typedef typename types::return_type return_type;
typedef typename types::field_type field_type;
typedef typename types::array_iterator array_iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
filtered_connectivity_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) { }
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
return_type operator*(){
const Vector<UInt> & old_connect = *this->array_it;
Vector<UInt> new_connect(old_connect.size());
Array<UInt>::const_iterator<UInt> nodes_begin = nodal_filter->begin();
Array<UInt>::const_iterator<UInt> nodes_end = nodal_filter->end();
for(UInt i(0); i<old_connect.size(); ++i) {
Array<UInt>::const_iterator<UInt> new_id =
std::find(nodes_begin, nodes_end, old_connect(i));
if(new_id == nodes_end) AKANTU_EXCEPTION("Node not found in the filter!");
new_connect(i) = new_id - nodes_begin;
}
return new_connect;
}
void setNodalFilter(const Array<UInt> & new_nodal_filter) {
nodal_filter = &new_nodal_filter;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Array<UInt> * nodal_filter;
};
/* -------------------------------------------------------------------------- */
class FilteredConnectivityField :
public GenericElementalField<SingleType<UInt,Vector,true>,
filtered_connectivity_field_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef SingleType<UInt,Vector,true> types;
typedef filtered_connectivity_field_iterator<types> iterator;
typedef types::field_type field_type;
typedef GenericElementalField<types,filtered_connectivity_field_iterator> parent;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FilteredConnectivityField(const field_type & field,
const Array<UInt> & nodal_filter,
UInt spatial_dimension = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind element_kind = _ek_not_defined) :
parent(field, spatial_dimension, ghost_type, element_kind),
nodal_filter(nodal_filter) { }
~FilteredConnectivityField() {
// since the field is created in registerFilteredMesh it is destroyed here
delete const_cast<field_type *>(&this->field);
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
iterator begin() {
iterator it = parent::begin();
it.setNodalFilter(nodal_filter);
return it;
}
iterator end() {
iterator it = parent::end();
it.setNodalFilter(nodal_filter);
return it;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Array<UInt> & nodal_filter;
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
diff --git a/src/io/dumper/dumper_generic_elemental_field.hh b/src/io/dumper/dumper_generic_elemental_field.hh
index e722fc882..da45b65e4 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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) {
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();
public:
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) {
dumper.addElemDataField(id, *this);
};
/// for connection to a FieldCompute
inline virtual Field * connect(FieldComputeProxy & proxy) {
return proxy.connectToField(this);
}
/// for connection to a Homogenizer
inline virtual ComputeFunctorInterface * connect(HomogenizerProxy & proxy) {
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).getSize() == 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.getSize() * 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.getSize() * 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) {
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__ __END_AKANTU__
+__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 67308ee7a..ad50139dd 100644
--- a/src/io/dumper/dumper_homogenizing_field.hh
+++ b/src/io/dumper/dumper_homogenizing_field.hh
@@ -1,217 +1,217 @@
/**
* @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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <typename type>
inline type typeConverter(const type & input,
__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) {
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) {
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; };
/* ------------------------------------------------------------------------ */
/* 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> >(
__attribute__((unused)) ElementTypeMap<UInt> & nb_components) {
throw;
return NULL;
}
/* -------------------------------------------------------------------------- */
/// 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__
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPER_HOMOGENIZING_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_internal_material_field.hh b/src/io/dumper/dumper_internal_material_field.hh
index 84c68f24f..72e25e5d2 100644
--- a/src/io/dumper/dumper_internal_material_field.hh
+++ b/src/io/dumper/dumper_internal_material_field.hh
@@ -1,78 +1,78 @@
/**
* @file dumper_internal_material_field.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 Sep 17 2015
*
* @brief description of material internal field
*
* @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_INTERNAL_MATERIAL_FIELD_HH__
#define __AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_quadrature_point_iterator.hh"
#ifdef AKANTU_IGFEM
# include "dumper_igfem_material_internal_field.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template<typename T, bool filtered = false>
class InternalMaterialField
: public GenericElementalField<SingleType<T,Vector,filtered>,
quadrature_point_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef SingleType<T,Vector,filtered> types;
typedef GenericElementalField<types,quadrature_point_iterator> parent;
typedef typename types::field_type field_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
InternalMaterialField(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){}
};
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPER_INTERNAL_MATERIAL_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_iohelper.cc b/src/io/dumper/dumper_iohelper.cc
index 542e7f91e..124f17255 100644
--- a/src/io/dumper/dumper_iohelper.cc
+++ b/src/io/dumper/dumper_iohelper.cc
@@ -1,302 +1,302 @@
/**
* @file dumper_iohelper.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>
*
* @date creation: Fri Oct 26 2012
* @date last modification: Thu Sep 17 2015
*
* @brief implementation of DumperIOHelper
*
* @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 <io_helper.hh>
#include "dumper_iohelper.hh"
#include "dumper_elemental_field.hh"
#include "dumper_nodal_field.hh"
#include "dumper_filtered_connectivity.hh"
#include "dumper_variable.hh"
#include "mesh.hh"
#if defined(AKANTU_IGFEM)
#include "dumper_igfem_connectivity.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
DumperIOHelper::DumperIOHelper() : count(0), time_activated(false) {}
/* -------------------------------------------------------------------------- */
DumperIOHelper::~DumperIOHelper() {
for (Fields::iterator it = fields.begin(); it != fields.end(); ++it) {
delete it->second;
}
delete dumper;
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setParallelContext(bool is_parallel) {
UInt whoami = StaticCommunicator::getStaticCommunicator().whoAmI();
UInt nb_proc = StaticCommunicator::getStaticCommunicator().getNbProc();
if(is_parallel)
dumper->setParallelContext(whoami, nb_proc);
else
dumper->setParallelContext(0, 1);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setDirectory(const std::string & directory) {
this->directory = directory;
dumper->setPrefix(directory);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setBaseName(const std::string & basename) {
filename = basename;
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::setTimeStep(Real time_step) {
if(!time_activated)
this->dumper->activateTimeDescFiles(time_step);
else
this->dumper->setTimeStep(time_step);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump() {
try {
dumper->dump(filename, count);
} catch (iohelper::IOHelperException & e) {
AKANTU_DEBUG_ERROR("I was not able to dump your data with a Dumper: " << e.what());
}
++count;
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump(UInt step) {
this->count = step;
this->dump();
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::dump(Real current_time, UInt step) {
this->dumper->setCurrentTime(current_time);
this->dump(step);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerMesh(const Mesh & mesh,
UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & element_kind) {
#if defined(AKANTU_IGFEM)
if (element_kind == _ek_igfem) {
registerField("connectivities",
new dumper::IGFEMConnectivityField(mesh.getConnectivities(),
spatial_dimension,
ghost_type));
} else
#endif
registerField("connectivities",
new dumper::ElementalField<UInt>(mesh.getConnectivities(),
spatial_dimension,
ghost_type,
element_kind));
registerField("positions",
new dumper::NodalField<Real>(mesh.getNodes()));
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension,
const GhostType & ghost_type,
const ElementKind & element_kind) {
ElementTypeMapArrayFilter<UInt> * f_connectivities =
new ElementTypeMapArrayFilter<UInt>(mesh.getConnectivities(), elements_filter);
this->registerField("connectivities",
new dumper::FilteredConnectivityField(*f_connectivities,
nodes_filter,
spatial_dimension,
ghost_type,
element_kind));
this->registerField("positions",new dumper::NodalField<Real,true>(
mesh.getNodes(),
0,
0,
&nodes_filter));
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerField(const std::string & field_id,
dumper::Field * field) {
Fields::iterator it = fields.find(field_id);
if(it != fields.end()) {
AKANTU_DEBUG_WARNING("The field " << field_id
<< " is already registered in this Dumper. Field ignored.");
return;
}
fields[field_id] = field;
field->registerToDumper(field_id, *dumper);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::unRegisterField(const std::string & field_id) {
Fields::iterator it = fields.find(field_id);
if(it == fields.end()) {
AKANTU_DEBUG_WARNING("The field " << field_id
<< " is not registered in this Dumper. Nothing to do.");
return;
}
delete it->second;
fields.erase(it);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::registerVariable(const std::string & variable_id,
dumper::VariableBase * variable) {
Variables::iterator it = variables.find(variable_id);
if(it != variables.end()) {
AKANTU_DEBUG_WARNING("The Variable " << variable_id
<< " is already registered in this Dumper. Variable ignored.");
return;
}
variables[variable_id] = variable;
variable->registerToDumper(variable_id, *dumper);
}
/* -------------------------------------------------------------------------- */
void DumperIOHelper::unRegisterVariable(const std::string & variable_id) {
Variables::iterator it = variables.find(variable_id);
if(it == variables.end()) {
AKANTU_DEBUG_WARNING("The variable " << variable_id
<< " is not registered in this Dumper. Nothing to do.");
return;
}
delete it->second;
variables.erase(it);
}
/* -------------------------------------------------------------------------- */
template <ElementType type>
iohelper::ElemType getIOHelperType() {
AKANTU_DEBUG_TO_IMPLEMENT();
return iohelper::MAX_ELEM_TYPE;
}
template <>
iohelper::ElemType getIOHelperType<_point_1>() { return iohelper::POINT_SET; }
template <>
iohelper::ElemType getIOHelperType<_segment_2>() { return iohelper::LINE1; }
template <>
iohelper::ElemType getIOHelperType<_segment_3>() { return iohelper::LINE2; }
template <>
iohelper::ElemType getIOHelperType<_triangle_3>() { return iohelper::TRIANGLE1; }
template <>
iohelper::ElemType getIOHelperType<_triangle_6>() { return iohelper::TRIANGLE2; }
template <>
iohelper::ElemType getIOHelperType<_quadrangle_4>() { return iohelper::QUAD1; }
template <>
iohelper::ElemType getIOHelperType<_quadrangle_8>() { return iohelper::QUAD2; }
template <>
iohelper::ElemType getIOHelperType<_tetrahedron_4>() { return iohelper::TETRA1; }
template <>
iohelper::ElemType getIOHelperType<_tetrahedron_10>() { return iohelper::TETRA2; }
template <>
iohelper::ElemType getIOHelperType<_hexahedron_8>() { return iohelper::HEX1; }
template <>
iohelper::ElemType getIOHelperType<_hexahedron_20>() { return iohelper::HEX2; }
template <>
iohelper::ElemType getIOHelperType<_pentahedron_6>() { return iohelper::PRISM1; }
template <>
iohelper::ElemType getIOHelperType<_pentahedron_15>() { return iohelper::PRISM2; }
#if defined(AKANTU_COHESIVE_ELEMENT)
template <>
iohelper::ElemType getIOHelperType<_cohesive_2d_4>() { return iohelper::COH2D4; }
template <>
iohelper::ElemType getIOHelperType<_cohesive_2d_6>() { return iohelper::COH2D6; }
template <>
iohelper::ElemType getIOHelperType<_cohesive_3d_6>() { return iohelper::COH3D6; }
template <>
iohelper::ElemType getIOHelperType<_cohesive_3d_12>() { return iohelper::COH3D12; }
template <>
iohelper::ElemType getIOHelperType<_cohesive_3d_8>() { return iohelper::COH3D8; }
//template <>
//iohelper::ElemType getIOHelperType<_cohesive_3d_16>() { return iohelper::COH3D16; }
#endif
#if defined(AKANTU_STRUCTURAL_MECHANICS)
template <>
iohelper::ElemType getIOHelperType<_bernoulli_beam_2>() { return iohelper::BEAM2; }
template <>
iohelper::ElemType getIOHelperType<_bernoulli_beam_3>() { return iohelper::BEAM3; }
#endif
/* -------------------------------------------------------------------------- */
UInt getIOHelperType(ElementType type) {
UInt ioh_type = iohelper::MAX_ELEM_TYPE;
#define GET_IOHELPER_TYPE(type) \
ioh_type = getIOHelperType<type>();
AKANTU_BOOST_ALL_ELEMENT_SWITCH(GET_IOHELPER_TYPE);
#undef GET_IOHELPER_TYPE
return ioh_type;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
namespace iohelper {
template<>
DataType getDataType<akantu::NodeType>() { return _int; }
}
diff --git a/src/io/dumper/dumper_iohelper.hh b/src/io/dumper/dumper_iohelper.hh
index 0c75b299e..6ff00d584 100644
--- a/src/io/dumper/dumper_iohelper.hh
+++ b/src/io/dumper/dumper_iohelper.hh
@@ -1,158 +1,158 @@
/**
* @file dumper_iohelper.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>
*
* @date creation: Fri Oct 26 2012
* @date last modification: Tue Jan 19 2016
*
* @brief Define the akantu dumper interface for IOhelper dumpers
*
* @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"
#include "aka_array.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DUMPER_IOHELPER_HH__
#define __AKANTU_DUMPER_IOHELPER_HH__
/* -------------------------------------------------------------------------- */
namespace iohelper {
class Dumper;
}
-__BEGIN_AKANTU__
+namespace akantu {
UInt getIOHelperType(ElementType type);
namespace dumper {
class Field;
class VariableBase;
}
class Mesh;
class DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperIOHelper();
virtual ~DumperIOHelper();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register a given Mesh for the current dumper
virtual void registerMesh(const Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// register a filtered Mesh (provided filter lists) for the current dumper
virtual void
registerFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
/// register a Field object identified by name and provided by pointer
void registerField(const std::string & field_id, dumper::Field * field);
/// remove the Field identified by name from managed fields
void unRegisterField(const std::string & field_id);
/// register a VariableBase object identified by name and provided by pointer
void registerVariable(const std::string & variable_id,
dumper::VariableBase * variable);
/// remove a VariableBase identified by name from managed fields
void unRegisterVariable(const std::string & variable_id);
/// request dump: this calls IOHelper dump routine
virtual void dump();
/// request dump: this first set the current step and then calls IOHelper dump
/// routine
virtual void dump(UInt step);
/// request dump: this first set the current step and current time and then
/// calls IOHelper dump routine
virtual void dump(Real current_time, UInt step);
/// set the parallel context for IOHeper
virtual void setParallelContext(bool is_parallel);
/// set the directory where to generate the dumped files
virtual void setDirectory(const std::string & directory);
/// set the base name (needed by most IOHelper dumpers)
virtual void setBaseName(const std::string & basename);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// direct access to the iohelper::Dumper object
AKANTU_GET_MACRO(Dumper, *dumper, iohelper::Dumper &)
/// set the timestep of the iohelper::Dumper
void setTimeStep(Real time_step);
public:
/* ------------------------------------------------------------------------ */
/* Variable wrapper */
template <typename T, bool is_scal = is_scalar<T>::value> class Variable;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// internal iohelper::Dumper
iohelper::Dumper * dumper;
typedef std::map<std::string, dumper::Field *> Fields;
typedef std::map<std::string, dumper::VariableBase *> Variables;
/// list of registered fields to dump
Fields fields;
Variables variables;
/// dump counter
UInt count;
/// directory name
std::string directory;
/// filename prefix
std::string filename;
/// is time tracking activated in the dumper
bool time_activated;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPER_IOHELPER_HH__ */
diff --git a/src/io/dumper/dumper_material_padders.hh b/src/io/dumper/dumper_material_padders.hh
index cb9c3546a..bb49ff18e 100644
--- a/src/io/dumper/dumper_material_padders.hh
+++ b/src/io/dumper/dumper_material_padders.hh
@@ -1,297 +1,297 @@
/**
* @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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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.getIndex();
UInt material_id = material_index(global_index.getType())(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.getType();
}
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) {
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 getNbComponent(__attribute__((unused)) 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) {
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 getNbComponent(__attribute__((unused)) 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) {
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 getNbComponent(__attribute__((unused)) 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) {
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 getNbComponent(__attribute__((unused)) 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) {
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 getNbComponent(__attribute__((unused)) UInt old_nb_comp) {
return this->getDim();
};
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // 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 86ce33f9d..ead527197 100644
--- a/src/io/dumper/dumper_nodal_field.hh
+++ b/src/io/dumper/dumper_nodal_field.hh
@@ -1,240 +1,240 @@
/**
* @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>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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) :
internal_it(vect), offset(offset), n(n), stride(stride) {}
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!");
if(n == 0) { this->n = field.getNbComponent() - stride; }
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) {
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.getSize(),
field.getNbComponent(), n, stride);
}
bool isHomogeneous() { return true; }
void checkHomogeneity() { 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.getSize(); }
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 {
return filter != it.filter;
}
iterator & operator++() {
++filter;
return *this;
}
Vector<T> operator* () {
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->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) {
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->getSize());
}
bool isHomogeneous() {
return true;
}
void checkHomogeneity() { 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->getSize();
}
iohelper::DataType getDataType() {
return iohelper::getDataType<T>();
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
const Container & field;
UInt n, stride;
const Filter * filter;
UInt padding;
};
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_DUMPER_NODAL_FIELD_HH__ */
diff --git a/src/io/dumper/dumper_padding_helper.hh b/src/io/dumper/dumper_padding_helper.hh
index 7c99fed0e..f36ea33c3 100644
--- a/src/io/dumper/dumper_padding_helper.hh
+++ b/src/io/dumper/dumper_padding_helper.hh
@@ -1,147 +1,147 @@
/**
* @file dumper_padding_helper.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Sun Oct 19 2014
*
* @brief Padding helper for field iterators
*
* @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_PADDING_HELPER_HH__
#define __AKANTU_DUMPER_PADDING_HELPER_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_compute.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
class PadderInterface {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PadderInterface(){
padding_m = 0;
padding_n = 0;
}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void setPadding(UInt m, UInt n = 0){
padding_m = m;
padding_n = n;
}
virtual UInt getPaddedDim(UInt nb_data) {
return nb_data;
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
/// padding informations
UInt padding_n, padding_m;
};
/* -------------------------------------------------------------------------- */
template<class input_type, class output_type>
class PadderGeneric :
public ComputeFunctor<input_type, output_type > , public PadderInterface {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PadderGeneric() : PadderInterface(){}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
inline output_type pad(const input_type & in,__attribute__((unused)) UInt nb_data) {
return in; // trick due to the fact that IOHelper padds the vectors (avoid a copy of data)
}
};
/* -------------------------------------------------------------------------- */
template<class T>
class PadderGeneric<Vector<T>, Matrix<T> > :
public ComputeFunctor<Vector<T>, Matrix<T> > , public PadderInterface {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
inline Matrix<T> pad(const Vector<T> & _in,
UInt nrows, UInt ncols,
UInt nb_data) {
Matrix<T> in(_in.storage(), nrows, ncols);
if(padding_m <= nrows && padding_n*nb_data <= ncols)
return in;
else {
Matrix<T> ret(padding_m, padding_n * nb_data);
UInt nb_cols_per_data = in.cols() / nb_data;
for (UInt d = 0; d < nb_data; ++d)
for (UInt i = 0; i < in.rows(); ++i)
for (UInt j = 0; j < nb_cols_per_data; ++j)
ret(i, j + d * padding_n) = in(i, j + d * nb_cols_per_data);
return ret;
}
}
};
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
__END_AKANTU_DUMPER__
#endif /* __AKANTU_DUMPER_PADDING_HELPER_HH__ */
diff --git a/src/io/dumper/dumper_paraview.cc b/src/io/dumper/dumper_paraview.cc
index 5801c0e84..51bb948ef 100644
--- a/src/io/dumper/dumper_paraview.cc
+++ b/src/io/dumper/dumper_paraview.cc
@@ -1,67 +1,67 @@
/**
* @file dumper_paraview.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 26 2010
* @date last modification: Sun Oct 19 2014
*
* @brief implementations of DumperParaview
*
* @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 <io_helper.hh>
#include "dumper_paraview.hh"
#include "static_communicator.hh"
#include <fstream>
-__BEGIN_AKANTU__
+namespace akantu {
DumperParaview::DumperParaview(const std::string & filename,
const std::string & directory,
bool parallel) : DumperIOHelper() {
iohelper::DumperParaview * dumper_para = new iohelper::DumperParaview();
dumper = dumper_para;
setBaseName(filename);
this->setParallelContext(parallel);
dumper_para->setMode(iohelper::BASE64);
dumper_para->setPrefix(directory);
dumper_para->init();
}
/* -------------------------------------------------------------------------- */
DumperParaview::~DumperParaview() {
}
/* -------------------------------------------------------------------------- */
void DumperParaview::setBaseName(const std::string & basename) {
DumperIOHelper::setBaseName(basename);
static_cast<iohelper::DumperParaview*>(dumper)->setVTUSubDirectory(filename + "-VTU");
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/dumper/dumper_paraview.hh b/src/io/dumper/dumper_paraview.hh
index 81812ea5f..448fd2ee3 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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class DumperParaview : public DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperParaview(const std::string & filename,
const std::string & directory = "./paraview",
bool parallel = true);
virtual ~DumperParaview();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
// void dump();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
void setBaseName(const std::string & basename);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPER_PARAVIEW_HH__ */
diff --git a/src/io/dumper/dumper_quadrature_point_iterator.hh b/src/io/dumper/dumper_quadrature_point_iterator.hh
index 7c740aa4e..2bd3f6699 100644
--- a/src/io/dumper/dumper_quadrature_point_iterator.hh
+++ b/src/io/dumper/dumper_quadrature_point_iterator.hh
@@ -1,77 +1,77 @@
/**
* @file dumper_quadrature_point_iterator.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Thu Sep 17 2015
*
* @brief Description of quadrature point iterator
*
* @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_QUADRATURE_POINT_ITERATOR_HH__
#define __AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH__
/* -------------------------------------------------------------------------- */
#include "dumper_elemental_field.hh"
-__BEGIN_AKANTU__
+namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template<typename types>
class quadrature_point_iterator
: public element_iterator<types, quadrature_point_iterator> {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef element_iterator<types, dumper::quadrature_point_iterator> parent;
typedef typename types::data_type data_type;
typedef typename types::return_type return_type;
typedef typename types::field_type field_type;
typedef typename types::array_iterator array_iterator;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
quadrature_point_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) { }
return_type operator*() {
return *this->array_it;
}
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPER_QUADRATURE_POINT_ITERATOR_HH__ */
diff --git a/src/io/dumper/dumper_text.cc b/src/io/dumper/dumper_text.cc
index df3ae7a48..a06258cc5 100644
--- a/src/io/dumper/dumper_text.cc
+++ b/src/io/dumper/dumper_text.cc
@@ -1,113 +1,113 @@
/**
* @file dumper_text.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief implementation of text dumper
*
* @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 <io_helper.hh>
#include "dumper_text.hh"
#include "dumper_nodal_field.hh"
#include "mesh.hh"
#include "static_communicator.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
DumperText::DumperText(const std::string & basename,
iohelper::TextDumpMode mode, bool parallel)
: DumperIOHelper() {
AKANTU_DEBUG_IN();
iohelper::DumperText * dumper_text = new iohelper::DumperText(mode);
this->dumper = dumper_text;
this->setBaseName(basename);
this->setParallelContext(parallel);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DumperText::registerMesh(const Mesh & mesh,
__attribute__((unused)) UInt spatial_dimension,
__attribute__((unused))
const GhostType & ghost_type,
__attribute__((unused))
const ElementKind & element_kind) {
registerField("position", new dumper::NodalField<Real>(mesh.getNodes()));
// in parallel we need node type
UInt nb_proc = StaticCommunicator::getStaticCommunicator().getNbProc();
if (nb_proc > 1) {
registerField("nodes_type",
new dumper::NodalField<NodeType>(mesh.getNodesType()));
}
}
/* -------------------------------------------------------------------------- */
void DumperText::registerFilteredMesh(
const Mesh & mesh,
__attribute__((unused)) const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
__attribute__((unused)) UInt spatial_dimension,
__attribute__((unused)) const GhostType & ghost_type,
__attribute__((unused)) const ElementKind & element_kind) {
registerField("position", new dumper::NodalField<Real, true>(
mesh.getNodes(), 0, 0, &nodes_filter));
// in parallel we need node type
UInt nb_proc = StaticCommunicator::getStaticCommunicator().getNbProc();
if (nb_proc > 1) {
registerField("nodes_type", new dumper::NodalField<NodeType, true>(
mesh.getNodesType(), 0, 0, &nodes_filter));
}
}
/* -------------------------------------------------------------------------- */
void DumperText::setBaseName(const std::string & basename) {
AKANTU_DEBUG_IN();
DumperIOHelper::setBaseName(basename);
static_cast<iohelper::DumperText *>(this->dumper)
->setDataSubDirectory(this->filename + "-DataFiles");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void DumperText::setPrecision(UInt prec) {
AKANTU_DEBUG_IN();
static_cast<iohelper::DumperText *>(this->dumper)->setPrecision(prec);
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/dumper/dumper_text.hh b/src/io/dumper/dumper_text.hh
index cd698f947..8a367d021 100644
--- a/src/io/dumper/dumper_text.hh
+++ b/src/io/dumper/dumper_text.hh
@@ -1,88 +1,88 @@
/**
* @file dumper_text.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief to dump into a text 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 "dumper_iohelper.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DUMPER_TEXT_HH__
#define __AKANTU_DUMPER_TEXT_HH__
/* -------------------------------------------------------------------------- */
#include <io_helper.hh>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class DumperText : public DumperIOHelper {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DumperText(const std::string & basename = "dumper_text",
iohelper::TextDumpMode mode = iohelper::_tdm_space,
bool parallel = true);
virtual ~DumperText() {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void registerMesh(const Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
virtual void registerFilteredMesh(const Mesh & mesh,
const ElementTypeMapArray<UInt> & elements_filter,
const Array<UInt> & nodes_filter,
UInt spatial_dimension = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & element_kind = _ek_not_defined);
virtual void setBaseName(const std::string & basename);
private:
void registerNodeTypeField();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
void setPrecision(UInt prec);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPER_TEXT_HH__ */
diff --git a/src/io/dumper/dumper_type_traits.hh b/src/io/dumper/dumper_type_traits.hh
index be7ce42ce..d9b1b33ad 100644
--- a/src/io/dumper/dumper_type_traits.hh
+++ b/src/io/dumper/dumper_type_traits.hh
@@ -1,99 +1,99 @@
/**
* @file dumper_type_traits.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Mon Sep 21 2015
*
* @brief Type traits for field 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/>.
*
*/
#ifndef __AKANTU_DUMPER_TYPE_TRAITS_HH__
#define __AKANTU_DUMPER_TYPE_TRAITS_HH__
/* -------------------------------------------------------------------------- */
#include "element_type_map.hh"
#include "element_type_map_filter.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
template <class data, class ret, class field>
struct TypeTraits {
//! the stored data (real, int, uint, ...)
typedef data data_type;
//! the type returned by the operator *
typedef ret return_type;
//! the field type (ElementTypeMap or ElementTypeMapFilter)
typedef field field_type;
//! the type over which we iterate
typedef typename field_type::type it_type;
//! the type of array (Array<T> or ArrayFilter<T>)
typedef typename field_type::array_type array_type;
//! the iterator over the array
typedef typename array_type::const_vector_iterator array_iterator;
};
/* -------------------------------------------------------------------------- */
// specialization for the case in which input and output types are the same
template <class T, template <class> class ret, bool filtered>
struct SingleType
: public TypeTraits<T,ret<T>,ElementTypeMapArray<T> >{
};
/* -------------------------------------------------------------------------- */
// same as before but for filtered data
template <class T, template <class> class ret>
struct SingleType<T,ret,true> :
public TypeTraits<T,ret<T>, ElementTypeMapArrayFilter<T> >{
};
/* -------------------------------------------------------------------------- */
// specialization for the case in which input and output types are different
template <class it_type, class data_type, template <class> class ret,
bool filtered>
struct DualType
: public TypeTraits<data_type,ret<data_type>, ElementTypeMapArray<it_type> >{
};
/* -------------------------------------------------------------------------- */
// same as before but for filtered data
template <class it_type, class data_type,template <class> class ret>
struct DualType<it_type,data_type,ret,true> :
public TypeTraits<data_type,ret<data_type>, ElementTypeMapArrayFilter<it_type> >{
};
/* -------------------------------------------------------------------------- */
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_DUMPER_TYPE_TRAITS_HH__ */
diff --git a/src/io/dumper/dumper_variable.hh b/src/io/dumper/dumper_variable.hh
index 0bdda9da1..498ea37c9 100644
--- a/src/io/dumper/dumper_variable.hh
+++ b/src/io/dumper/dumper_variable.hh
@@ -1,118 +1,118 @@
/**
* @file dumper_variable.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Tue Jun 04 2013
* @date last modification: Sun Oct 19 2014
*
* @brief template of variable
*
* @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_IOHELPER_TMPL_VARIABLE_HH__
#define __AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
__BEGIN_AKANTU_DUMPER__
/* -------------------------------------------------------------------------- */
/// Variable interface
class VariableBase {
public:
VariableBase() {};
virtual ~VariableBase() {};
virtual void registerToDumper(const std::string & id, iohelper::Dumper & dumper) = 0;
};
/* -------------------------------------------------------------------------- */
template<typename T, bool is_scal = is_scalar<T>::value >
class Variable : public VariableBase {
public:
Variable(const T & t) : vari(t) {}
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) {
dumper.addVariable(id, *this);
}
const T & operator[](UInt i) const {
return vari[i];
}
UInt getDim() { return vari.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const T & vari;
};
/* -------------------------------------------------------------------------- */
template<typename T>
class Variable<Vector<T>, false> : public VariableBase {
public:
Variable(const Vector<T> & t) : vari(t) {}
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) {
dumper.addVariable(id, *this);
}
const T & operator[](UInt i) const {
return vari[i];
}
UInt getDim() { return vari.size(); }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const Vector<T> & vari;
};
/* -------------------------------------------------------------------------- */
template<typename T>
class Variable<T, true> : public VariableBase {
public:
Variable(const T & t) : vari(t) {}
virtual void registerToDumper(const std::string & id,
iohelper::Dumper & dumper) {
dumper.addVariable(id, *this);
}
const T & operator[](__attribute__((unused)) UInt i) const {
return vari;
}
UInt getDim() { return 1; }
iohelper::DataType getDataType() { return iohelper::getDataType<T>(); }
protected:
const T & vari;
};
__END_AKANTU_DUMPER__
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DUMPER_IOHELPER_TMPL_VARIABLE_HH__ */
diff --git a/src/io/mesh_io.cc b/src/io/mesh_io.cc
index 9235a8d3b..e4ed84cca 100644
--- a/src/io/mesh_io.cc
+++ b/src/io/mesh_io.cc
@@ -1,156 +1,156 @@
/**
* @file mesh_io.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Jun 01 2015
*
* @brief common part for all mesh io 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIO::MeshIO() {
canReadSurface = false;
canReadExtendedData = false;
}
/* -------------------------------------------------------------------------- */
MeshIO::~MeshIO() {}
/* -------------------------------------------------------------------------- */
MeshIO * MeshIO::getMeshIO(const std::string & filename,
const MeshIOType & type) {
MeshIOType t = type;
if (type == _miot_auto) {
std::string::size_type idx = filename.rfind('.');
std::string ext;
if (idx != std::string::npos) {
ext = filename.substr(idx + 1);
}
if (ext == "msh") {
t = _miot_gmsh;
} else if (ext == "diana") {
t = _miot_diana;
} else if (ext == "inp") {
t = _miot_abaqus;
} else
AKANTU_EXCEPTION("Cannot guess the type of file of "
<< filename << " (ext " << ext << "). "
<< "Please provide the MeshIOType to the read function");
}
switch (t) {
case _miot_gmsh:
return new MeshIOMSH();
#if defined(AKANTU_STRUCTURAL_MECHANICS)
case _miot_gmsh_struct:
return new MeshIOMSHStruct();
#endif
case _miot_diana:
return new MeshIODiana();
case _miot_abaqus:
return new MeshIOAbaqus();
default:
return NULL;
}
}
/* -------------------------------------------------------------------------- */
void MeshIO::read(const std::string & filename, Mesh & mesh,
const MeshIOType & type) {
MeshIO * mesh_io = getMeshIO(filename, type);
mesh_io->read(filename, mesh);
delete mesh_io;
}
/* -------------------------------------------------------------------------- */
void MeshIO::write(const std::string & filename, Mesh & mesh,
const MeshIOType & type) {
MeshIO * mesh_io = getMeshIO(filename, type);
mesh_io->write(filename, mesh);
delete mesh_io;
}
/* -------------------------------------------------------------------------- */
void MeshIO::constructPhysicalNames(const std::string & tag_name, Mesh & mesh) {
if (!phys_name_map.empty()) {
for (Mesh::type_iterator type_it = mesh.firstType();
type_it != mesh.lastType(); ++type_it) {
Array<std::string> * name_vec =
mesh.getDataPointer<std::string>("physical_names", *type_it);
const Array<UInt> & tags_vec = mesh.getData<UInt>(tag_name, *type_it);
for (UInt i(0); i < tags_vec.getSize(); i++) {
std::map<UInt, std::string>::const_iterator map_it =
phys_name_map.find(tags_vec(i));
if (map_it == phys_name_map.end()) {
std::stringstream sstm;
sstm << tags_vec(i);
name_vec->operator()(i) = sstm.str();
} else {
name_vec->operator()(i) = map_it->second;
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void MeshIO::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
if (phys_name_map.size()) {
stream << space << "Physical map:" << std::endl;
std::map<UInt, std::string>::const_iterator it = phys_name_map.begin();
std::map<UInt, std::string>::const_iterator end = phys_name_map.end();
for (; it != end; ++it) {
stream << space << it->first << ": " << it->second << std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/io/mesh_io.hh b/src/io/mesh_io.hh
index 2184bc2b0..680d7d418 100644
--- a/src/io/mesh_io.hh
+++ b/src/io/mesh_io.hh
@@ -1,118 +1,118 @@
/**
* @file mesh_io.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Jun 01 2015
*
* @brief interface of a mesh io class, reader and writer
*
* @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_HH__
#define __AKANTU_MESH_IO_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIO();
virtual ~MeshIO();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void read(const std::string & filename, Mesh & mesh, const MeshIOType & type);
void write(const std::string & filename, Mesh & mesh,
const MeshIOType & type);
/// read a mesh from the file
virtual void read(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) Mesh & mesh) {}
/// write a mesh to a file
virtual void write(__attribute__((unused)) const std::string & filename,
__attribute__((unused)) const Mesh & mesh) {}
/// function to request the manual construction of the physical names maps
virtual void constructPhysicalNames(const std::string & tag_name,
Mesh & mesh);
/// method to permit to be printed to a generic stream
virtual void printself(std::ostream & stream, int indent = 0) const;
/// static contruction of a meshio object
static MeshIO * getMeshIO(const std::string & filename,
const MeshIOType & type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
std::map<UInt, std::string> & getPhysicalNameMap() { return phys_name_map; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
bool canReadSurface;
bool canReadExtendedData;
/// correspondance between a tag and physical names (if applicable)
std::map<UInt, std::string> phys_name_map;
};
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream, const MeshIO & _this) {
_this.printself(stream);
return stream;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#include "mesh_io_msh.hh"
#include "mesh_io_diana.hh"
#include "mesh_io_abaqus.hh"
#if defined(AKANTU_STRUCTURAL_MECHANICS)
#include "mesh_io_msh_struct.hh"
#endif
#endif /* __AKANTU_MESH_IO_HH__ */
diff --git a/src/io/mesh_io/mesh_io_abaqus.cc b/src/io/mesh_io/mesh_io_abaqus.cc
index f5b8105d8..2caf717c8 100644
--- a/src/io/mesh_io/mesh_io_abaqus.cc
+++ b/src/io/mesh_io/mesh_io_abaqus.cc
@@ -1,483 +1,483 @@
/**
* @file mesh_io_abaqus.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jan 04 2013
* @date last modification: Fri Dec 11 2015
*
* @brief read a mesh from an abaqus input 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/>.
*
*/
/* -------------------------------------------------------------------------- */
// std library header files
#include <fstream>
// akantu header files
#include "mesh_io_abaqus.hh"
#include "mesh.hh"
#include "mesh_utils.hh"
#include "element_group.hh"
#include "node_group.hh"
#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__))
# define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
# if GCC_VERSION > 40600
# pragma GCC diagnostic push
# endif
# pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include <boost/config/warning_disable.hpp>
#include <boost/spirit/include/qi.hpp>
#include <boost/spirit/include/phoenix.hpp>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
MeshIOAbaqus::MeshIOAbaqus() {}
/* -------------------------------------------------------------------------- */
MeshIOAbaqus::~MeshIOAbaqus() {}
/* -------------------------------------------------------------------------- */
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace ascii = boost::spirit::ascii;
namespace lbs = boost::spirit::qi::labels;
namespace phx = boost::phoenix;
/* -------------------------------------------------------------------------- */
void element_read(Mesh & mesh, const ElementType & type, UInt id, const std::vector<Int> & conn,
const std::map<UInt, UInt> & nodes_mapping,
std::map<UInt, Element> & elements_mapping) {
Vector<UInt> tmp_conn(Mesh::getNbNodesPerElement(type));
AKANTU_DEBUG_ASSERT(conn.size() == tmp_conn.size(),
"The nodes in the Abaqus file have too many coordinates"
<< " for the mesh you try to fill.");
mesh.addConnectivityType(type);
Array<UInt> & connectivity = mesh.getConnectivity(type);
UInt i = 0;
for (std::vector<Int>::const_iterator it = conn.begin(); it != conn.end(); ++it) {
std::map<UInt, UInt>::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;
}
Element el(type, connectivity.getSize());
elements_mapping[id] = el;
connectivity.push_back(tmp_conn);
}
void node_read(Mesh & mesh, UInt id, const std::vector<Real> & pos,
std::map<UInt, UInt> & nodes_mapping) {
Vector<Real> tmp_pos(mesh.getSpatialDimension());
UInt i = 0;
for (std::vector<Real>::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);
}
/* ------------------------------------------------------------------------ */
void add_element_to_group(ElementGroup * el_grp, UInt element,
const std::map<UInt, Element> & elements_mapping) {
std::map<UInt, Element>::const_iterator eit = elements_mapping.find(element);
AKANTU_DEBUG_ASSERT(eit != elements_mapping.end(),
"There is an unknown element ("
<< element << ") in the in the ELSET "
<< el_grp->getName() << ".");
el_grp->add(eit->second, true, false);
}
ElementGroup * element_group_create(Mesh & mesh, const ID & name) {
Mesh::element_group_iterator eg_it = mesh.element_group_find(name);
if (eg_it != mesh.element_group_end()) {
return eg_it->second;
} else {
return &mesh.createElementGroup(name, _all_dimensions);
}
}
NodeGroup * node_group_create(Mesh & mesh, const ID & name) {
Mesh::node_group_iterator ng_it = mesh.node_group_find(name);
if (ng_it != mesh.node_group_end()) {
return ng_it->second;
} else {
return &mesh.createNodeGroup(name, mesh.getSpatialDimension());
}
}
void add_node_to_group(NodeGroup * node_grp, UInt node,
const std::map<UInt, UInt> & nodes_mapping) {
std::map<UInt, UInt>::const_iterator nit = nodes_mapping.find(node);
AKANTU_DEBUG_ASSERT(nit != nodes_mapping.end(),
"There is an unknown node in the in the NSET "
<< node_grp->getName() << ".");
node_grp->add(nit->second, false);
}
void optimize_group(NodeGroup * grp) { grp->optimize(); }
void optimize_element_group(ElementGroup * grp) { grp->optimize(); }
/* -------------------------------------------------------------------------- */
template <class Iterator> struct AbaqusSkipper : qi::grammar<Iterator> {
AbaqusSkipper() : AbaqusSkipper::base_type(skip, "abaqus_skipper") {
/* clang-format off */
skip
= (ascii::space - spirit::eol)
| "**" >> *(qi::char_ - spirit::eol) >> spirit::eol
;
/* clang-format on */
}
qi::rule<Iterator> skip;
};
/* -------------------------------------------------------------------------- */
template <class Iterator, typename Skipper = AbaqusSkipper<Iterator> >
struct AbaqusMeshGrammar : qi::grammar<Iterator, void(), Skipper> {
public:
AbaqusMeshGrammar(Mesh & mesh)
: AbaqusMeshGrammar::base_type(start, "abaqus_mesh_reader"), mesh(mesh) {
/* clang-format off */
start
= *(
(qi::char_('*')
> ( (qi::no_case[ qi::lit("node output") ] > any_section)
| (qi::no_case[ qi::lit("element output") ] > any_section)
| (qi::no_case[ qi::lit("node") ] > nodes)
| (qi::no_case[ qi::lit("element") ] > elements)
| (qi::no_case[ qi::lit("heading") ] > header)
| (qi::no_case[ qi::lit("elset") ] > elements_set)
| (qi::no_case[ qi::lit("nset") ] > nodes_set)
| (qi::no_case[ qi::lit("material") ] > material)
| (keyword > any_section)
)
)
| spirit::eol
)
;
header
= spirit::eol
> *any_line
;
nodes
= *(qi::char_(',') >> option)
>> spirit::eol
>> *( (qi::int_
> node_position) [ phx::bind(&node_read,
phx::ref(mesh),
lbs::_1,
lbs::_2,
phx::ref(abaqus_nodes_to_akantu)) ]
>> spirit::eol
)
;
elements
= (
( qi::char_(',') >> qi::no_case[qi::lit("type")] >> '='
>> abaqus_element_type [ lbs::_a = lbs::_1 ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> *( (qi::int_
> connectivity) [ phx::bind(&element_read,
phx::ref(mesh),
lbs::_a,
lbs::_1,
lbs::_2,
phx::cref(abaqus_nodes_to_akantu),
phx::ref(abaqus_elements_to_akantu)) ]
>> spirit::eol
)
;
elements_set
= (
(
( qi::char_(',') >> qi::no_case[ qi::lit("elset") ] >> '='
>> value [ lbs::_a = phx::bind<ElementGroup *>(&element_group_create,
phx::ref(mesh),
lbs::_1) ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> qi::skip
(qi::char_(',') | qi::space)
[ +(qi::int_ [ phx::bind(&add_element_to_group,
lbs::_a,
lbs::_1,
phx::cref(abaqus_elements_to_akantu)
)
]
)
]
) [ phx::bind(&optimize_element_group, lbs::_a) ]
;
nodes_set
= (
(
( qi::char_(',')
>> qi::no_case[ qi::lit("nset") ] >> '='
>> value [ lbs::_a = phx::bind<NodeGroup *>(&node_group_create, phx::ref(mesh), lbs::_1) ]
)
^ *(qi::char_(',') >> option)
)
>> spirit::eol
>> qi::skip
(qi::char_(',') | qi::space)
[ +(qi::int_ [ phx::bind(&add_node_to_group,
lbs::_a,
lbs::_1,
phx::cref(abaqus_nodes_to_akantu)
)
]
)
]
) [ phx::bind(&optimize_group, lbs::_a) ]
;
material
= (
( qi::char_(',') >> qi::no_case[ qi::lit("name") ] >> '='
>> value [ phx::push_back(phx::ref(material_names), lbs::_1) ]
)
^ *(qi::char_(',') >> option)
) >> spirit::eol;
;
node_position
= +(qi::char_(',') > real [ phx::push_back(lbs::_val, lbs::_1) ])
;
connectivity
= +(qi::char_(',') > qi::int_ [ phx::push_back(lbs::_val, lbs::_1) ])
;
any_section
= *(qi::char_(',') >> option) > spirit::eol
> *any_line
;
any_line
= *(qi::char_ - spirit::eol - qi::char_('*')) >> spirit::eol
;
keyword
= qi::lexeme[ +(qi::char_ - (qi::char_('*') | spirit::eol)) ]
;
option
= key > -( '=' >> value );
key
= qi::char_("a-zA-Z_") >> *(qi::char_("a-zA-Z_0-9") | qi::char_('-'))
;
value
= key.alias()
;
BOOST_SPIRIT_DEBUG_NODE(start);
abaqus_element_type.add
#if defined(AKANTU_STRUCTURAL_MECHANICS)
("BE21" , _bernoulli_beam_2)
("BE31" , _bernoulli_beam_3)
#endif
("T3D2" , _segment_2) // Gmsh generates this elements
("T3D3" , _segment_3) // Gmsh generates this elements
("CPE3" , _triangle_3)
("CPS3" , _triangle_3)
("DC2D3" , _triangle_3)
("CPE6" , _triangle_6)
("CPS6" , _triangle_6)
("DC2D6" , _triangle_6)
("CPE4" , _quadrangle_4)
("CPS4" , _quadrangle_4)
("DC2D4" , _quadrangle_4)
("CPE8" , _quadrangle_8)
("CPS8" , _quadrangle_8)
("DC2D8" , _quadrangle_8)
("C3D4" , _tetrahedron_4)
("DC3D4" , _tetrahedron_4)
("C3D8" , _hexahedron_8)
("C3D8R" , _hexahedron_8)
("DC3D8" , _hexahedron_8)
("C3D10" , _tetrahedron_10)
("DC3D10", _tetrahedron_10);
#if !defined(AKANTU_NDEBUG) && defined(AKANTU_CORE_CXX_11)
qi::on_error<qi::fail>(start, error_handler(lbs::_4, lbs::_3, lbs::_2));
#endif
start .name("abaqus-start-rule");
connectivity .name("abaqus-connectivity");
node_position .name("abaqus-nodes-position");
nodes .name("abaqus-nodes");
any_section .name("abaqus-any_section");
header .name("abaqus-header");
material .name("abaqus-material");
elements .name("abaqus-elements");
elements_set .name("abaqus-elements-set");
nodes_set .name("abaqus-nodes-set");
key .name("abaqus-key");
value .name("abaqus-value");
option .name("abaqus-option");
keyword .name("abaqus-keyword");
any_line .name("abaqus-any-line");
abaqus_element_type.name("abaqus-element-type");
/* clang-format on */
}
public:
AKANTU_GET_MACRO(MaterialNames, material_names,
const std::vector<std::string> &);
/* ------------------------------------------------------------------------ */
/* Rules */
/* ------------------------------------------------------------------------ */
private:
qi::rule<Iterator, void(), Skipper> start;
qi::rule<Iterator, std::vector<int>(), Skipper> connectivity;
qi::rule<Iterator, std::vector<Real>(), Skipper> node_position;
qi::rule<Iterator, void(), Skipper> nodes, any_section, header, material;
qi::rule<Iterator, void(), qi::locals<ElementType>, Skipper> elements;
qi::rule<Iterator, void(), qi::locals<ElementGroup *>, Skipper> elements_set;
qi::rule<Iterator, void(), qi::locals<NodeGroup *>, Skipper> nodes_set;
qi::rule<Iterator, std::string(), Skipper> key, value, option, keyword,
any_line;
qi::real_parser<Real, qi::real_policies<Real> > real;
qi::symbols<char, ElementType> abaqus_element_type;
/* ------------------------------------------------------------------------ */
/* Mambers */
/* ------------------------------------------------------------------------ */
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> abaqus_nodes_to_akantu;
/// correspondance between the element number in the abaqus file and the
/// Element in the akantu mesh
std::map<UInt, Element> abaqus_elements_to_akantu;
/// list of the material names
std::vector<std::string> material_names;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
void MeshIOAbaqus::read(const std::string & filename, Mesh & mesh) {
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
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 AbaqusSkipper<iterator_t> skipper;
typedef AbaqusMeshGrammar<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);
std::vector<std::string>::const_iterator mnit = g.getMaterialNames().begin();
std::vector<std::string>::const_iterator mnend = g.getMaterialNames().end();
MeshAccessor mesh_accessor(mesh);
for (; mnit != mnend; ++mnit) {
Mesh::element_group_iterator eg_it = mesh.element_group_find(*mnit);
ElementGroup & eg = *eg_it->second;
if (eg_it != mesh.element_group_end()) {
ElementGroup::type_iterator tit = eg.firstType();
ElementGroup::type_iterator tend = eg.lastType();
for (; tit != tend; ++tit) {
Array<std::string> & abaqus_material =
mesh_accessor.getData<std::string>("abaqus_material", *tit);
ElementGroup::const_element_iterator eit = eg.element_begin(*tit);
ElementGroup::const_element_iterator eend = eg.element_end(*tit);
for (; eit != eend; ++eit) {
abaqus_material(*eit) = *mnit;
}
}
}
}
mesh_accessor.setNbGlobalNodes(mesh.getNodes().getSize());
MeshUtils::fillElementToSubElementsData(mesh);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/mesh_io/mesh_io_abaqus.hh b/src/io/mesh_io/mesh_io_abaqus.hh
index 9500115fc..877d87efc 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__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
class MeshIOAbaqus : public MeshIO {
public:
MeshIOAbaqus();
virtual ~MeshIOAbaqus();
/// read a mesh from the file
virtual void read(const std::string & filename, Mesh & mesh);
/// 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;
};
-__END_AKANTU__
+} // 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 e94065209..2014b6b92 100644
--- a/src/io/mesh_io/mesh_io_diana.cc
+++ b/src/io/mesh_io/mesh_io_diana.cc
@@ -1,587 +1,587 @@
/**
* @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 "mesh_io_diana.hh"
#include "mesh_utils.hh"
#include "element_group.hh"
/* -------------------------------------------------------------------------- */
#include <string.h>
/* -------------------------------------------------------------------------- */
#include <stdio.h>
-__BEGIN_AKANTU__
+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->getSize(); ++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->getSize(); ++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;
UInt node_per_element = 0;
Element elem;
UInt * read_order = NULL;
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->getSize() - 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.getSize(); ++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;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/io/mesh_io/mesh_io_diana.hh b/src/io/mesh_io/mesh_io_diana.hh
index 737c4de68..7ddcbed5c 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>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class MeshIODiana : public MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIODiana();
virtual ~MeshIODiana();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
virtual void read(const std::string & filename, Mesh & mesh);
/// write a mesh to a file
virtual void write(const std::string & filename, const Mesh & mesh);
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;
};
-__END_AKANTU__
+} // 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 cd58e9614..44990b5b2 100644
--- a/src/io/mesh_io/mesh_io_msh.cc
+++ b/src/io/mesh_io/mesh_io_msh.cc
@@ -1,981 +1,981 @@
/**
* @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>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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.getSize());
// 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().getSize());
// 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;
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.getSize() << std::endl;
outfile << std::uppercase;
for (UInt i = 0; i < nodes.getSize(); ++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;
;
Mesh::type_iterator it =
mesh.firstType(_all_dimensions, _not_ghost, _ek_not_defined);
Mesh::type_iterator end =
mesh.lastType(_all_dimensions, _not_ghost, _ek_not_defined);
Int nb_elements = 0;
for (; it != end; ++it) {
const Array<UInt> & connectivity = mesh.getConnectivity(*it, _not_ghost);
nb_elements += connectivity.getSize();
}
outfile << nb_elements << std::endl;
UInt element_idx = 1;
for (it = mesh.firstType(_all_dimensions, _not_ghost, _ek_not_defined);
it != end; ++it) {
ElementType type = *it;
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
UInt * tag[2] = {NULL, NULL};
try {
const Array<UInt> & data_tag_0 =
mesh.getData<UInt>("tag_0", type, _not_ghost);
tag[0] = data_tag_0.storage();
} catch (...) {
tag[0] = NULL;
}
try {
const Array<UInt> & data_tag_1 =
mesh.getData<UInt>("tag_1", type, _not_ghost);
tag[1] = data_tag_1.storage();
} catch (...) {
tag[1] = NULL;
}
for (UInt i = 0; i < connectivity.getSize(); ++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();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/io/mesh_io/mesh_io_msh.hh b/src/io/mesh_io/mesh_io_msh.hh
index f36eed4e4..143bd095e 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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class MeshIOMSH : public MeshIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIOMSH();
virtual ~MeshIOMSH();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a mesh from the file
virtual void read(const std::string & filename, Mesh & mesh);
/// write a mesh to a file
virtual void write(const std::string & filename, const Mesh & mesh);
/* ------------------------------------------------------------------------ */
/* 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;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MESH_IO_MSH_HH__ */
diff --git a/src/io/mesh_io/mesh_io_msh_struct.cc b/src/io/mesh_io/mesh_io_msh_struct.cc
index b774895c3..05d02f96c 100644
--- a/src/io/mesh_io/mesh_io_msh_struct.cc
+++ b/src/io/mesh_io/mesh_io_msh_struct.cc
@@ -1,80 +1,80 @@
/**
* @file mesh_io_msh_struct.cc
*
* @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 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "mesh_io.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
MeshIOMSHStruct::MeshIOMSHStruct() : MeshIOMSH() {
canReadSurface = true;
canReadExtendedData = true;
_msh_to_akantu_element_types.clear();
_msh_to_akantu_element_types[_msh_not_defined ] = _not_defined;
_msh_to_akantu_element_types[_msh_segment_2 ] = _bernoulli_beam_2;
_msh_to_akantu_element_types[_msh_triangle_3 ] = _kirchhoff_shell;
_akantu_to_msh_element_types.clear();
_akantu_to_msh_element_types[_not_defined ] = _msh_not_defined;
_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;
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;
_read_order[it->first] = tmp;
}
}
/* -------------------------------------------------------------------------- */
void MeshIOMSHStruct::read(const std::string & filename, Mesh & mesh) {
if(mesh.getSpatialDimension() == 2) {
_msh_to_akantu_element_types[_msh_segment_2 ] = _bernoulli_beam_2;
} else if (mesh.getSpatialDimension() == 3) {
_msh_to_akantu_element_types[_msh_segment_2 ] = _bernoulli_beam_3;
AKANTU_DEBUG_WARNING("The MeshIOMSHStruct is reading bernoulli beam 3D be sure to provide the missing normals");
}
MeshIOMSH::read(filename, mesh);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/mesh_io/mesh_io_msh_struct.hh b/src/io/mesh_io/mesh_io_msh_struct.hh
index 698b8e73e..2a30df9a5 100644
--- a/src/io/mesh_io/mesh_io_msh_struct.hh
+++ b/src/io/mesh_io/mesh_io_msh_struct.hh
@@ -1,56 +1,56 @@
/**
* @file mesh_io_msh_struct.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @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_STRUCT_HH__
#define __AKANTU_MESH_IO_MSH_STRUCT_HH__
-__BEGIN_AKANTU__
+namespace akantu {
class MeshIOMSHStruct : public MeshIOMSH {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshIOMSHStruct();
/// read a mesh from the file
virtual void read(const std::string & filename, Mesh & mesh);
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MESH_IO_MSH_STRUCT_HH__ */
diff --git a/src/io/model_io.cc b/src/io/model_io.cc
index 12a2e72d2..edfd6c372 100644
--- a/src/io/model_io.cc
+++ b/src/io/model_io.cc
@@ -1,50 +1,50 @@
/**
* @file model_io.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Sun Oct 19 2014
*
* @brief Reader for models (this is deprecated)
*
* @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 "model_io.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
ModelIO::ModelIO() {
}
/* -------------------------------------------------------------------------- */
ModelIO::~ModelIO() {
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/io/model_io.hh b/src/io/model_io.hh
index 42892f73e..f008df2c5 100644
--- a/src/io/model_io.hh
+++ b/src/io/model_io.hh
@@ -1,82 +1,82 @@
/**
* @file model_io.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief Reader for models (this is deprecated)
*
* @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_MODEL_IO_HH__
#define __AKANTU_MODEL_IO_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class ModelIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ModelIO();
virtual ~ModelIO();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a model from file
virtual void read(const std::string & filename, Model & model) = 0;
/// write a mesh to a file
virtual void write(const std::string & filename, const Model & model) = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MODEL_IO_HH__ */
diff --git a/src/io/model_io/model_io_ibarras.cc b/src/io/model_io/model_io_ibarras.cc
index 62a8eaf24..e30831808 100644
--- a/src/io/model_io/model_io_ibarras.cc
+++ b/src/io/model_io/model_io_ibarras.cc
@@ -1,313 +1,313 @@
/**
* @file model_io_ibarras.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Fri Jan 22 2016
*
* @brief Mesh Reader specially created for Wood's Tower analysis performed by
* the Institute I-Barras
*
* @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 "model_io_ibarras.hh"
#include "static_communicator.hh"
#include "aka_math.hh"
#include "static_communicator.hh"
#include "sparse_matrix.hh"
#include "solver.hh"
#include "integration_scheme_2nd_order.hh"
/* -------------------------------------------------------------------------- */
#include <string.h>
/* -------------------------------------------------------------------------- */
#include <stdio.h>
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* Methods Implentations */
/* -------------------------------------------------------------------------- */
void ModelIOIBarras::read(const std::string & filename, Model & mod) {
if (!dynamic_cast<StructuralMechanicsModel *>(&mod)) {
AKANTU_DEBUG_ERROR("");
}
StructuralMechanicsModel & model =
static_cast<StructuralMechanicsModel &>(mod);
Mesh * mesh = new Mesh(3);
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt current_line = 0;
if (!infile.good()) {
AKANTU_DEBUG_ERROR("Cannot open file " << filename);
}
// Get Nodes Position
std::getline(infile, line);
current_line++;
std::stringstream sstr(line);
UInt nb_nodes;
sstr >> nb_nodes;
const UInt spatial_dimension = 3;
Real coord[spatial_dimension];
Real * temp_nodes = new Real[nb_nodes * spatial_dimension];
UInt * connect_to_akantu = new UInt[nb_nodes];
std::fill_n(connect_to_akantu, 0, nb_nodes);
std::fill_n(temp_nodes, 0., nb_nodes * spatial_dimension);
for (UInt i = 0; i < nb_nodes; ++i) {
UInt offset = i * spatial_dimension;
std::getline(infile, line);
std::stringstream sstr_node(line);
sstr_node >> coord[0] >> coord[1] >> coord[2];
current_line++;
/// read the coordinates of structural nodes and help nodes
for (UInt j = 0; j < spatial_dimension; ++j)
temp_nodes[offset + j] = coord[j];
}
// Get Connectivities
std::getline(infile, line);
current_line++;
std::stringstream sstr_elem(line);
UInt nb_elements;
sstr_elem >> nb_elements;
mesh->addConnectivityType(_bernoulli_beam_3);
Array<UInt> & connectivity =
const_cast<Array<UInt> &>(mesh->getConnectivity(_bernoulli_beam_3));
connectivity.resize(nb_elements);
UInt nonodes[2];
UInt nb_struct_nodes = 1;
for (UInt i = 0; i < nb_elements; ++i) {
std::getline(infile, line);
std::stringstream sstr_element(line);
sstr_element >> nonodes[0] >> nonodes[1];
current_line++;
/// read the connectivities
for (UInt j = 0; j < 2; ++j) {
if (connect_to_akantu[nonodes[j] - 1] == 0) {
connect_to_akantu[nonodes[j] - 1] = nb_struct_nodes;
++nb_struct_nodes;
}
connectivity(i, j) = connect_to_akantu[nonodes[j] - 1] - 1;
}
}
nb_struct_nodes -= 1;
/// read the coordinates of structural nodes
Array<Real> & nodes = const_cast<Array<Real> &>(mesh->getNodes());
nodes.resize(nb_struct_nodes);
for (UInt k = 0; k < nb_nodes; ++k) {
if (connect_to_akantu[k] != 0) {
for (UInt j = 0; j < spatial_dimension; ++j)
nodes(connect_to_akantu[k] - 1, j) =
temp_nodes[k * spatial_dimension + j];
}
}
// MeshPartitionScotch partition(*mesh, spatial_dimension);
// partition.reorder();
/// Apply Boundaries
model.registerFEEngineObject<StructuralMechanicsModel::MyFEEngineType>(
"StructuralMechanicsModel", *mesh, spatial_dimension);
model.initModel();
model.initArrays();
Array<bool> & blocked_dofs = model.getBlockedDOFs();
std::getline(infile, line);
std::stringstream sstr_nb_boundaries(line);
UInt nb_boundaries;
sstr_nb_boundaries >> nb_boundaries;
current_line++;
for (UInt i = 0; i < nb_boundaries; ++i) {
std::getline(infile, line);
std::stringstream sstr_boundary(line);
UInt boundnary_node;
sstr_boundary >> boundnary_node;
current_line++;
for (UInt j = 0; j < spatial_dimension; ++j)
blocked_dofs(connect_to_akantu[boundnary_node - 1] - 1, j) = true;
}
/// Define Materials
std::getline(infile, line);
std::stringstream sstr_nb_materials(line);
UInt nb_materials;
sstr_nb_materials >> nb_materials;
current_line++;
for (UInt i = 0; i < nb_materials; ++i) {
std::getline(infile, line);
std::stringstream sstr_material(line);
Real material[6];
sstr_material >> material[0] >> material[1] >> material[2] >> material[3] >>
material[4] >> material[5];
current_line++;
StructuralMaterial mat;
mat.E = material[0];
mat.GJ = material[1] * material[2];
mat.Iy = material[3];
mat.Iz = material[4];
mat.A = material[5];
model.addMaterial(mat);
}
/// Apply normals and Material TO IMPLEMENT
UInt property[2];
Array<UInt> & element_material = model.getElementMaterial(_bernoulli_beam_3);
mesh->initNormals();
Array<Real> & normals =
const_cast<Array<Real> &>(mesh->getNormals(_bernoulli_beam_3));
normals.resize(nb_elements);
for (UInt i = 0; i < nb_elements; ++i) {
std::getline(infile, line);
std::stringstream sstr_properties(line);
sstr_properties >> property[0] >> property[1];
current_line++;
/// Assign material
element_material(i) = property[0] - 1;
/// Compute normals
Real x[3];
Real v[3];
Real w[3];
Real n[3];
if (property[1] == 0) {
for (UInt j = 0; j < spatial_dimension; ++j) {
x[j] = nodes(connectivity(i, 1), j) - nodes(connectivity(i, 0), j);
}
n[0] = x[1];
n[1] = -x[0];
n[2] = 0.;
}
else {
for (UInt j = 0; j < spatial_dimension; ++j) {
x[j] = nodes(connectivity(i, 1), j) - nodes(connectivity(i, 0), j);
v[j] = nodes(connectivity(i, 1), j) -
temp_nodes[(property[1] - 1) * spatial_dimension + j];
Math::vectorProduct3(x, v, w);
Math::vectorProduct3(x, w, n);
}
}
Math::normalize3(n);
for (UInt j = 0; j < spatial_dimension; ++j) {
normals(i, j) = n[j];
}
}
model.computeRotationMatrix(_bernoulli_beam_3);
infile.close();
}
/* -------------------------------------------------------------------------- */
void ModelIOIBarras::assign_sets(const std::string & filename,
StructuralMechanicsModel & model) {
std::ifstream infile;
infile.open(filename.c_str());
std::string line;
UInt current_line = 0;
if (!infile.good()) {
AKANTU_DEBUG_ERROR("Cannot open file " << filename);
}
// Define Sets of Beams
Array<UInt> & set_ID = model.getSet_ID(_bernoulli_beam_3);
set_ID.clear();
std::getline(infile, line);
std::stringstream sstr_nb_sets(line);
UInt nb_sets;
sstr_nb_sets >> nb_sets;
current_line++;
UInt no_element[2];
for (UInt i = 0; i < nb_sets; ++i) {
std::getline(infile, line);
std::stringstream sstr_set(line);
sstr_set >> no_element[0];
no_element[1] = no_element[0];
sstr_set >> no_element[1];
while (no_element[0] != 0) {
for (UInt j = no_element[0] - 1; j < no_element[1]; ++j) {
set_ID(j) = i + 1;
}
std::getline(infile, line);
std::stringstream sstr_sets(line);
sstr_sets >> no_element[0];
no_element[1] = no_element[0];
sstr_sets >> no_element[1];
}
}
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/model_io/model_io_ibarras.hh b/src/io/model_io/model_io_ibarras.hh
index 03535edf2..b86399428 100644
--- a/src/io/model_io/model_io_ibarras.hh
+++ b/src/io/model_io/model_io_ibarras.hh
@@ -1,65 +1,65 @@
/**
* @file model_io_ibarras.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief ModelIO implementation for IBarras input 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_MODEL_IO_IBARRAS_HH__
#define __AKANTU_MODEL_IO_IBARRAS_HH__
/* -------------------------------------------------------------------------- */
#include "model_io.hh"
#include "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class ModelIOIBarras : public ModelIO {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ModelIOIBarras(){};
virtual ~ModelIOIBarras(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// read a model from the file
virtual void read(const std::string & filename, Model & model);
/// assign sets of member to an already constructed model
virtual void assign_sets(const std::string & filename,
StructuralMechanicsModel & model);
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MODEL_IO_IBARRAS_HH__ */
diff --git a/src/io/parser/input_file_parser.hh b/src/io/parser/input_file_parser.hh
index 8a4bbe997..3494dae39 100644
--- a/src/io/parser/input_file_parser.hh
+++ b/src/io/parser/input_file_parser.hh
@@ -1,263 +1,263 @@
/**
* @file input_file_parser.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Tue May 19 2015
*
* @brief Grammar definition for the input files
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
// Boost
/* -------------------------------------------------------------------------- */
#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_operator.hpp>
#include <boost/spirit/include/phoenix_bind.hpp>
#include <boost/variant/recursive_variant.hpp>
#ifndef __AKANTU_INPUT_FILE_PARSER_HH__
#define __AKANTU_INPUT_FILE_PARSER_HH__
namespace spirit = boost::spirit;
namespace qi = boost::spirit::qi;
namespace lbs = boost::spirit::qi::labels;
namespace ascii = boost::spirit::ascii;
namespace phx = boost::phoenix;
-__BEGIN_AKANTU__
+namespace akantu {
namespace parser {
struct error_handler_ {
template <typename, typename, typename, typename> struct result {
typedef void type;
};
template <typename Iterator>
void operator()(qi::info const & what, Iterator err_pos,
__attribute__((unused)) Iterator first,
__attribute__((unused)) Iterator last) const {
spirit::classic::file_position pos = err_pos.get_position();
AKANTU_EXCEPTION("Parse error [ "
<< "Expecting " << what << " instead of \"" << *err_pos
<< "\" ]"
<< " in file " << pos.file << " line " << pos.line
<< " column " << pos.column << std::endl
<< "'" << err_pos.get_currentline() << "'" << std::endl
<< std::setw(pos.column) << " "
<< "^- here");
}
private:
};
static ParserSection &
create_subsection(const SectionType & type, const std::string & name,
const boost::optional<std::string> & option,
ParserSection & sect) {
std::string opt = "";
if (option)
opt = *option;
ParserSection sect_tmp(name, type, opt, sect);
return sect.addSubSection(sect_tmp);
}
template <typename Iter>
static bool create_parameter(boost::iterator_range<Iter> & rng,
std::string & value, ParserSection & sect) {
try {
std::string name(rng.begin(), rng.end());
name = trim(name);
spirit::classic::file_position pos = rng.begin().get_position();
ParserParameter param_tmp(name, value, sect);
param_tmp.setDebugInfo(pos.file, pos.line, pos.column);
sect.addParameter(param_tmp);
} catch (debug::Exception & e) {
return false;
}
return true;
}
static std::string concatenate(const std::string & t1, const std::string & t2) {
return (t1 + t2);
}
/* ---------------------------------------------------------------------- */
/* Grammars definitions */
/* ---------------------------------------------------------------------- */
template <class Iterator>
struct InputFileGrammar
: qi::grammar<Iterator, void(), typename Skipper<Iterator>::type> {
InputFileGrammar(ParserSection * sect)
: InputFileGrammar::base_type(start, "input_file_grammar"),
parent_section(sect) {
/* clang-format off */
start
= mini_section(parent_section)
;
mini_section
= *(
entry (lbs::_r1)
| section(lbs::_r1)
)
;
entry
= (
qi::raw[key]
>> '='
> value
) [ lbs::_pass = phx::bind(&create_parameter<Iterator>,
lbs::_1,
lbs::_2,
*lbs::_r1) ]
;
section
= (
qi::no_case[section_type]
> qi::lexeme
[
section_name
> -section_option
]
) [ lbs::_a = &phx::bind(&create_subsection,
lbs::_1,
phx::at_c<0>(lbs::_2),
phx::at_c<1>(lbs::_2),
*lbs::_r1) ]
> '['
> mini_section(lbs::_a)
> ']'
;
section_name
= qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")
;
section_option
= (+ascii::space >> section_name) [ lbs::_val = lbs::_2 ]
;
key
= qi::char_("a-zA-Z_") >> *qi::char_("a-zA-Z_0-9")
;
value
= (
mono_line_value [ lbs::_a = phx::bind(&concatenate, lbs::_a, lbs::_1) ]
> *(
'\\' > mono_line_value [ lbs::_a = phx::bind(&concatenate, lbs::_a, lbs::_1) ]
)
) [ lbs::_val = lbs::_a ]
;
mono_line_value
= qi::lexeme
[
+(qi::char_ - (qi::char_('=') | spirit::eol | '#' | ';' | '\\'))
]
;
skipper
= ascii::space
| "#" >> *(qi::char_ - spirit::eol)
;
/* clang-format on */
#define AKANTU_SECTION_TYPE_ADD(r, data, elem) \
(BOOST_PP_STRINGIZE(elem), AKANTU_SECTION_TYPES_PREFIX(elem))
section_type.add BOOST_PP_SEQ_FOR_EACH(AKANTU_SECTION_TYPE_ADD, _,
AKANTU_SECTION_TYPES);
#undef AKANTU_SECTION_TYPE_ADD
#if !defined(AKANTU_NDEBUG) && defined(AKANTU_CORE_CXX_11)
phx::function<error_handler_> const error_handler = error_handler_();
qi::on_error<qi::fail>(start,
error_handler(lbs::_4, lbs::_3, lbs::_1, lbs::_2));
#endif
section.name("section");
section_name.name("section-name");
section_option.name("section-option");
mini_section.name("section-content");
entry.name("parameter");
key.name("parameter-name");
value.name("parameter-value");
section_type.name("section-types-list");
mono_line_value.name("mono-line-value");
#if !defined AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDebug)) {
// qi::debug(section);
qi::debug(section_name);
qi::debug(section_option);
// qi::debug(mini_section);
// qi::debug(entry);
qi::debug(key);
qi::debug(value);
qi::debug(mono_line_value);
}
#endif
}
const std::string & getErrorMessage() const { return error_message; };
typedef typename Skipper<Iterator>::type skipper_type;
skipper_type skipper;
private:
std::string error_message;
qi::rule<Iterator, void(ParserSection *), skipper_type> mini_section;
qi::rule<Iterator, void(ParserSection *), qi::locals<ParserSection *>,
skipper_type> section;
qi::rule<Iterator, void(), skipper_type> start;
qi::rule<Iterator, std::string()> section_name;
qi::rule<Iterator, std::string()> section_option;
qi::rule<Iterator, void(ParserSection *), skipper_type> entry;
qi::rule<Iterator, std::string(), skipper_type> key;
qi::rule<Iterator, std::string(), qi::locals<std::string>, skipper_type>
value;
qi::rule<Iterator, std::string(), skipper_type> mono_line_value;
qi::symbols<char, SectionType> section_type;
ParserSection * parent_section;
};
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_INPUT_FILE_PARSER_HH__ */
diff --git a/src/io/parser/parameter_registry.cc b/src/io/parser/parameter_registry.cc
index ac1db11e8..264ef1822 100644
--- a/src/io/parser/parameter_registry.cc
+++ b/src/io/parser/parameter_registry.cc
@@ -1,152 +1,152 @@
/**
* @file parameter_registry.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Nov 19 2015
*
* @brief Parameter Registry and derived classes implementation
*
* @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 "parameter_registry.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
Parameter::Parameter() : name(""), description(""), param_type(_pat_internal) {}
/* -------------------------------------------------------------------------- */
Parameter::Parameter(std::string name, std::string description,
ParameterAccessType param_type)
: name(name), description(description), param_type(param_type) {}
/* -------------------------------------------------------------------------- */
bool Parameter::isWritable() const { return param_type & _pat_writable; }
/* -------------------------------------------------------------------------- */
bool Parameter::isReadable() const { return param_type & _pat_readable; }
/* -------------------------------------------------------------------------- */
bool Parameter::isInternal() const { return param_type & _pat_internal; }
/* -------------------------------------------------------------------------- */
bool Parameter::isParsable() const { return param_type & _pat_parsable; }
/* -------------------------------------------------------------------------- */
void Parameter::setAccessType(ParameterAccessType ptype) {
this->param_type = ptype;
}
/* -------------------------------------------------------------------------- */
void Parameter::printself(std::ostream & stream) const {
stream << " ";
if (isInternal())
stream << "iii";
else {
if (isReadable())
stream << "r";
else
stream << "-";
if (isWritable())
stream << "w";
else
stream << "-";
if (isParsable())
stream << "p";
else
stream << "-";
}
stream << " ";
std::stringstream sstr;
sstr << name;
UInt width = std::max(int(10 - sstr.str().length()), 0);
sstr.width(width);
if (description != "") {
sstr << " [" << description << "]";
}
stream << sstr.str();
width = std::max(int(50 - sstr.str().length()), 0);
stream.width(width);
stream << " : ";
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
ParameterRegistry::ParameterRegistry() : consisder_sub(true) {
}
/* -------------------------------------------------------------------------- */
ParameterRegistry::~ParameterRegistry() {
std::map<std::string, Parameter *>::iterator it, end;
for (it = params.begin(); it != params.end(); ++it) {
delete it->second;
it->second = NULL;
}
this->params.clear();
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
Parameters::const_iterator it;
for (it = params.begin(); it != params.end(); ++it) {
stream << space;
it->second->printself(stream);
}
SubRegisteries::const_iterator sub_it;
for (sub_it = sub_registries.begin(); sub_it != sub_registries.end(); ++sub_it) {
stream << space << "Registry [" << std::endl;
sub_it->second->printself(stream, indent + 1);
stream << space << "]";
}
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::registerSubRegistry(const ID & id,
ParameterRegistry & registry) {
sub_registries[id] = ®istry;
}
/* -------------------------------------------------------------------------- */
void ParameterRegistry::setParameterAccessType(const std::string & name,
ParameterAccessType ptype) {
Parameters::iterator it = params.find(name);
if (it == params.end())
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name));
Parameter & param = *(it->second);
param.setAccessType(ptype);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/parser/parameter_registry.hh b/src/io/parser/parameter_registry.hh
index b74fc48fb..8bc290a48 100644
--- a/src/io/parser/parameter_registry.hh
+++ b/src/io/parser/parameter_registry.hh
@@ -1,195 +1,195 @@
/**
* @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;
}
-__BEGIN_AKANTU__
+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(){};
/* ------------------------------------------------------------------------ */
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;
template <typename T> inline operator T() const;
/* ------------------------------------------------------------------------ */
virtual void printself(std::ostream & stream) const;
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();
private:
/// Name of parameter
std::string name;
/// 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);
T & getTyped();
const T & getTyped() const;
virtual void printself(std::ostream & stream) const;
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;
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;
};
-__END_AKANTU__
+} // akantu
#include "parameter_registry_tmpl.hh"
#endif /* __AKANTU_PARAMETER_REGISTRY_HH__ */
diff --git a/src/io/parser/parameter_registry_tmpl.hh b/src/io/parser/parameter_registry_tmpl.hh
index ab806ed0b..8c7d07b08 100644
--- a/src/io/parser/parameter_registry_tmpl.hh
+++ b/src/io/parser/parameter_registry_tmpl.hh
@@ -1,301 +1,301 @@
/**
* @file parameter_registry_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 09 2012
* @date last modification: Fri Mar 27 2015
*
* @brief implementation of the templated part of ParameterRegistry class and
* the derivated ones
*
* @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 "parser.hh"
/* -------------------------------------------------------------------------- */
#include <string>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
namespace debug {
class ParameterException : public Exception {
public:
ParameterException(const std::string & name, const std::string & message)
: Exception(message), name(name) {}
const std::string & name;
};
class ParameterUnexistingException : public ParameterException {
public:
ParameterUnexistingException(const std::string & name)
: ParameterException(name, "Parameter " + name +
" does not exists in this scope") {}
};
class ParameterAccessRightException : public ParameterException {
public:
ParameterAccessRightException(const std::string & name,
const std::string & perm)
: ParameterException(name, "Parameter " + name + " is not " + perm) {}
};
class ParameterWrongTypeException : public ParameterException {
public:
ParameterWrongTypeException(const std::string name, const std::string & type)
: ParameterException(name,
"Parameter " + name + " is not of type " + type) {}
};
}
/* -------------------------------------------------------------------------- */
template <typename T>
const ParameterTyped<T> & Parameter::getParameterTyped() const {
try {
const ParameterTyped<T> & tmp =
dynamic_cast<const ParameterTyped<T> &>(*this);
return tmp;
} catch (std::bad_cast &) {
AKANTU_CUSTOM_EXCEPTION(debug::ParameterWrongTypeException(
name, debug::demangle(typeid(T).name())));
}
}
/* -------------------------------------------------------------------------- */
template <typename T> ParameterTyped<T> & Parameter::getParameterTyped() {
try {
ParameterTyped<T> & tmp = dynamic_cast<ParameterTyped<T> &>(*this);
return tmp;
} catch (...) {
AKANTU_CUSTOM_EXCEPTION(debug::ParameterWrongTypeException(
name, debug::demangle(typeid(T).name())));
}
}
/* ------------------------------------------------------------------------ */
template <typename T, typename V> void Parameter::set(const V & value) {
if (!(isWritable()))
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "writable"));
ParameterTyped<T> & typed_param = getParameterTyped<T>();
typed_param.setTyped(value);
}
/* ------------------------------------------------------------------------ */
inline void Parameter::setAuto(__attribute__((unused))
const ParserParameter & value) {
if (!(isParsable()))
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "parsable"));
}
/* -------------------------------------------------------------------------- */
template <typename T> const T & Parameter::get() const {
if (!(isReadable()))
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "readable"));
const ParameterTyped<T> & typed_param = getParameterTyped<T>();
return typed_param.getTyped();
}
/* -------------------------------------------------------------------------- */
template <typename T> T & Parameter::get() {
ParameterTyped<T> & typed_param = getParameterTyped<T>();
if (!(isReadable()) || !(this->isWritable()))
AKANTU_CUSTOM_EXCEPTION(
debug::ParameterAccessRightException(name, "accessible"));
return typed_param.getTyped();
}
/* -------------------------------------------------------------------------- */
template <typename T> inline Parameter::operator T() const {
return this->get<T>();
}
/* -------------------------------------------------------------------------- */
template <typename T>
ParameterTyped<T>::ParameterTyped(std::string name, std::string description,
ParameterAccessType param_type, T & param)
: Parameter(name, description, param_type), param(param) {}
/* -------------------------------------------------------------------------- */
template <typename T>
template <typename V>
void ParameterTyped<T>::setTyped(const V & value) {
param = value;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParameterTyped<T>::setAuto(const ParserParameter & value) {
Parameter::setAuto(value);
param = static_cast<T>(value);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<std::string>::setAuto(const ParserParameter & value) {
Parameter::setAuto(value);
param = value.getValue();
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<Vector<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Vector<Real> tmp = in_param;
for (UInt i = 0; i < param.size(); ++i) {
param(i) = tmp(i);
}
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParameterTyped<Matrix<Real>>::setAuto(const ParserParameter & in_param) {
Parameter::setAuto(in_param);
Matrix<Real> tmp = in_param;
for (UInt i = 0; i < param.rows(); ++i) {
for (UInt j = 0; j < param.cols(); ++j) {
param(i, j) = tmp(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename T> const T & ParameterTyped<T>::getTyped() const {
return param;
}
/* -------------------------------------------------------------------------- */
template <typename T> T & ParameterTyped<T>::getTyped() { return param; }
/* -------------------------------------------------------------------------- */
template <typename T>
inline void ParameterTyped<T>::printself(std::ostream & stream) const {
Parameter::printself(stream);
stream << param << std::endl;
}
/* -------------------------------------------------------------------------- */
template <>
inline void ParameterTyped<bool>::printself(std::ostream & stream) const {
Parameter::printself(stream);
stream << std::boolalpha << param << std::endl;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParameterRegistry::registerParam(std::string name, T & variable,
ParameterAccessType type,
const std::string description) {
std::map<std::string, Parameter *>::iterator it = params.find(name);
if (it != params.end())
AKANTU_CUSTOM_EXCEPTION(debug::ParameterException(
name, "Parameter named " + name + " already registered."));
ParameterTyped<T> * param =
new ParameterTyped<T>(name, description, type, variable);
params[name] = param;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParameterRegistry::registerParam(std::string name, T & variable,
const T & default_value,
ParameterAccessType type,
const std::string description) {
variable = default_value;
registerParam(name, variable, type, description);
}
/* -------------------------------------------------------------------------- */
template <typename T, typename V>
void ParameterRegistry::setMixed(const std::string & name, const V & value) {
std::map<std::string, Parameter *>::iterator it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (SubRegisteries::iterator it = sub_registries.begin();
it != sub_registries.end(); ++it) {
it->second->setMixed<T>(name, value);
}
} else {
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name));
}
} else {
Parameter & param = *(it->second);
param.set<T>(value);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void ParameterRegistry::set(const std::string & name, const T & value) {
this->template setMixed<T>(name, value);
}
/* -------------------------------------------------------------------------- */
template <typename T> T & ParameterRegistry::get(const std::string & name) {
Parameters::iterator it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (SubRegisteries::iterator it = sub_registries.begin();
it != sub_registries.end(); ++it) {
try {
return it->second->get<T>(name);
} catch (...) {
}
}
}
// nothing was found not even in sub registries
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name));
}
Parameter & param = *(it->second);
return param.get<T>();
}
/* -------------------------------------------------------------------------- */
const Parameter & ParameterRegistry::get(const std::string & name) const {
Parameters::const_iterator it = params.find(name);
if (it == params.end()) {
if (consisder_sub) {
for (SubRegisteries::const_iterator it = sub_registries.begin();
it != sub_registries.end(); ++it) {
try {
return it->second->get(name);
} catch (...) {
}
}
}
// nothing was found not even in sub registries
AKANTU_CUSTOM_EXCEPTION(debug::ParameterUnexistingException(name));
}
Parameter & param = *(it->second);
return param;
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/parser/parsable.cc b/src/io/parser/parsable.cc
index 511f03d81..12021b1d6 100644
--- a/src/io/parser/parsable.cc
+++ b/src/io/parser/parsable.cc
@@ -1,111 +1,111 @@
/**
* @file parsable.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Nov 19 2015
*
* @brief Parsable implementation
*
* @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 "parsable.hh"
#include "aka_random_generator.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
Parsable::Parsable(const SectionType & section_type, const ID & id)
: section_type(section_type), pid(id) {
this->consisder_sub = false;
}
/* -------------------------------------------------------------------------- */
Parsable::~Parsable() {}
/* -------------------------------------------------------------------------- */
void Parsable::registerSubSection(const SectionType & type,
const std::string & name,
Parsable & sub_section) {
SubSectionKey key(type, name);
sub_sections[key] = &sub_section;
this->registerSubRegistry(name, sub_section);
}
/* -------------------------------------------------------------------------- */
void Parsable::parseParam(const ParserParameter & in_param) {
std::map<std::string, Parameter *>::iterator it =
params.find(in_param.getName());
if (it == params.end()) {
if (Parser::isPermissive()) {
AKANTU_DEBUG_WARNING("No parameter named " << in_param.getName()
<< " registered in " << pid
<< ".");
return;
} else
AKANTU_EXCEPTION("No parameter named " << in_param.getName()
<< " registered in " << pid
<< ".");
}
Parameter & param = *(it->second);
param.setAuto(in_param);
}
/* -------------------------------------------------------------------------- */
void Parsable::parseSection(const ParserSection & section) {
if (section_type != section.getType())
AKANTU_EXCEPTION("The object "
<< pid << " is meant to parse section of type "
<< section_type << ", so it cannot parse section of type "
<< section.getType());
std::pair<Parser::const_parameter_iterator, Parser::const_parameter_iterator>
params = section.getParameters();
Parser::const_parameter_iterator it = params.first;
for (; it != params.second; ++it) {
parseParam(*it);
}
Parser::const_section_iterator sit = section.getSubSections().first;
for (; sit != section.getSubSections().second; ++sit) {
parseSubSection(*sit);
}
}
/* -------------------------------------------------------------------------- */
void Parsable::parseSubSection(const ParserSection & section) {
SubSectionKey key(section.getType(), section.getName());
SubSections::iterator it = sub_sections.find(key);
if (it != sub_sections.end()) {
it->second->parseSection(section);
} else if (!Parser::isPermissive()) {
AKANTU_EXCEPTION("No parsable defined for sub sections of type <"
<< key.first << "," << key.second << "> in " << pid);
} else
AKANTU_DEBUG_WARNING("No parsable defined for sub sections of type <"
<< key.first << "," << key.second << "> in " << pid);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/parser/parsable.hh b/src/io/parser/parsable.hh
index 0c4bf071c..16dfab955 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__
-__BEGIN_AKANTU__
+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();
/// 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;
};
-__END_AKANTU__
+} // akantu
#include "parsable_tmpl.hh"
#endif /* __AKANTU_PARSABLE_HH__ */
diff --git a/src/io/parser/parsable_tmpl.hh b/src/io/parser/parsable_tmpl.hh
index a79d9a3be..8012ed900 100644
--- a/src/io/parser/parsable_tmpl.hh
+++ b/src/io/parser/parsable_tmpl.hh
@@ -1,38 +1,38 @@
/**
* @file parsable_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 09 2012
* @date last modification: Fri Mar 27 2015
*
* @brief implementation of the templated part of ParsableParam Parsable and
* ParsableParamTyped
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
-__END_AKANTU__
+} // akantu
diff --git a/src/io/parser/parser.cc b/src/io/parser/parser.cc
index e166b1b53..53c8eba19 100644
--- a/src/io/parser/parser.cc
+++ b/src/io/parser/parser.cc
@@ -1,98 +1,98 @@
/**
* @file parser.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Wed Jan 13 2016
*
* @brief implementation of the 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/>.
*
*/
/* -------------------------------------------------------------------------- */
// STL
#include <fstream>
#include <iomanip>
#include <map>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "parser.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
ParserSection::~ParserSection() { this->clean(); }
/* -------------------------------------------------------------------------- */
ParserParameter & ParserSection::addParameter(const ParserParameter & param) {
if (parameters.find(param.getName()) != parameters.end())
AKANTU_EXCEPTION("The parameter \"" + param.getName() +
"\" is already defined in this section");
return (parameters.insert(std::pair<std::string, ParserParameter>(
param.getName(), param)).first->second);
}
/* -------------------------------------------------------------------------- */
ParserSection & ParserSection::addSubSection(const ParserSection & section) {
return ((sub_sections_by_type.insert(std::pair<SectionType, ParserSection>(
section.getType(), section)))->second);
}
/* -------------------------------------------------------------------------- */
std::string Parser::getLastParsedFile() const { return last_parsed_file; }
/* -------------------------------------------------------------------------- */
void ParserSection::printself(std::ostream & stream,
unsigned int indent) const {
std::string space;
std::string ind = AKANTU_INDENT;
for (unsigned int i = 0; i < indent; i++, space += ind)
;
stream << space << "Section(" << this->type << ") " << this->name
<< (option != "" ? (" " + option) : "") << " [" << std::endl;
if (!this->parameters.empty()) {
stream << space << ind << "Parameters [" << std::endl;
Parameters::const_iterator pit = this->parameters.begin();
for (; pit != this->parameters.end(); ++pit) {
stream << space << ind << " + ";
pit->second.printself(stream);
stream << std::endl;
}
stream << space << ind << "]" << std::endl;
}
if (!this->sub_sections_by_type.empty()) {
stream << space << ind << "Subsections [" << std::endl;
SubSections::const_iterator sit = this->sub_sections_by_type.begin();
for (; sit != this->sub_sections_by_type.end(); ++sit)
sit->second.printself(stream, indent + 2);
stream << std::endl;
stream << space << ind << "]" << std::endl;
}
stream << space << "]" << std::endl;
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/parser/parser.hh b/src/io/parser/parser.hh
index a00c9d868..e1118b5ad 100644
--- a/src/io/parser/parser.hh
+++ b/src/io/parser/parser.hh
@@ -1,497 +1,497 @@
/**
* @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__
-__BEGIN_AKANTU__
+namespace akantu {
#define AKANTU_SECTION_TYPES \
(global)(material)(model)(mesh)(heat)(contact)(friction)( \
embedded_interface)(rules)(non_local)(user)(solver)(neighborhood)( \
time_step_solver)(non_linear_solver)(model_solver)(integration_scheme)( \
not_defined)
#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()),
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) {}
ParserSection(const std::string & name, SectionType type)
: parent_section(NULL), 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;
}
-__END_AKANTU__
+} // akantu
#include "parser_tmpl.hh"
#endif /* __AKANTU_PARSER_HH__ */
diff --git a/src/io/parser/parser_grammar_tmpl.hh b/src/io/parser/parser_grammar_tmpl.hh
index fd2aefc0c..fc04f6418 100644
--- a/src/io/parser/parser_grammar_tmpl.hh
+++ b/src/io/parser/parser_grammar_tmpl.hh
@@ -1,81 +1,81 @@
/**
* @file parser_grammar_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 11 2015
*
* @brief implementation of the templated part of ParsableParam Parsable and
* ParsableParamTyped
*
* @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 <boost/config/warning_disable.hpp>
#include <boost/spirit/include/qi.hpp>
#include <boost/spirit/include/support_multi_pass.hpp>
#include <boost/spirit/include/classic_position_iterator.hpp>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_PARSER_GRAMMAR_TMPL_HH
#define AKANTU_PARSER_GRAMMAR_TMPL_HH
-__BEGIN_AKANTU__
+namespace akantu {
namespace qi = boost::spirit::qi;
/* -------------------------------------------------------------------------- */
template <class T, class Grammar>
T Parser::parseType(const std::string & value, Grammar & grammar) {
using boost::spirit::ascii::space;
std::string::const_iterator b = value.begin();
std::string::const_iterator e = value.end();
T resultat = T();
bool res = false;
try {
res = qi::phrase_parse(b, e, grammar, space, resultat);
} catch(debug::Exception & ex) {
AKANTU_EXCEPTION("Could not parse '" << value << "' as a "
<< debug::demangle(typeid(T).name()) << ", an unknown error append '"
<< ex.what());
}
if(!res || (b != e)) {
AKANTU_EXCEPTION("Could not parse '" << value << "' as a "
<< debug::demangle(typeid(T).name()) << ", an unknown error append '"
<< std::string(value.begin(), b) << "<HERE>" << std::string(b, e) << "'");
}
return resultat;
}
namespace parser {
template<class Iterator>
struct Skipper {
typedef qi::rule<Iterator, void()> type;
};
}
-__END_AKANTU__
+} // akantu
#endif //AKANTU_PARSER_GRAMMAR_TMPL_HH
diff --git a/src/io/parser/parser_input_files.cc b/src/io/parser/parser_input_files.cc
index 3d6ebe1ef..c777bef21 100644
--- a/src/io/parser/parser_input_files.cc
+++ b/src/io/parser/parser_input_files.cc
@@ -1,117 +1,117 @@
/**
* @file parser_input_files.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 11 2015
* @date last modification: Wed Jan 13 2016
*
* @brief implementation of the parser
*
* @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/>.
*
*/
#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__))
# define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
# if GCC_VERSION > 40600
# pragma GCC diagnostic push
# endif
# pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "input_file_parser.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
void Parser::parse(const std::string & filename) {
this->clean();
std::ifstream input(filename.c_str());
if (!input.good()) {
AKANTU_EXCEPTION("Could not open file " << filename << "!");
}
input.unsetf(std::ios::skipws);
// wrap istream into iterator
spirit::istream_iterator fwd_begin(input);
spirit::istream_iterator fwd_end;
// wrap forward iterator with position iterator, to record the position
typedef spirit::classic::position_iterator2<spirit::istream_iterator>
pos_iterator_type;
pos_iterator_type position_begin(fwd_begin, fwd_end, filename);
pos_iterator_type position_end;
// parse
parser::InputFileGrammar<pos_iterator_type> ag(this);
bool result = qi::phrase_parse(position_begin, position_end, ag, ag.skipper);
if (!result || position_begin != position_end) {
spirit::classic::file_position pos = position_begin.get_position();
AKANTU_EXCEPTION("Parse error [ "
<< ag.getErrorMessage() << " ]"
<< " in file " << filename << " line " << pos.line
<< " column " << pos.column << std::endl
<< "'" << position_begin.get_currentline() << "'"
<< std::endl
<< std::setw(pos.column) << " "
<< "^- here");
}
try {
bool permissive = getParameter("permissive_parser", _ppsc_current_scope);
permissive_parser = permissive;
AKANTU_DEBUG_INFO("Parser switched permissive mode to "
<< std::boolalpha << permissive_parser);
} catch (debug::Exception & e) {
}
last_parsed_file = filename;
input.close();
}
-__END_AKANTU__
+} // akantu
#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(__GNUG__)
# if GCC_VERSION > 40600
# pragma GCC diagnostic pop
# else
# pragma GCC diagnostic warning "-Wunused-local-typedefs"
# endif
#endif
diff --git a/src/io/parser/parser_random.cc b/src/io/parser/parser_random.cc
index c17d43714..1afe8d60b 100644
--- a/src/io/parser/parser_random.cc
+++ b/src/io/parser/parser_random.cc
@@ -1,69 +1,69 @@
/**
* @file parser_random.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Mon Dec 07 2015
*
* @brief implementation of the 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/>.
*
*/
#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__))
# define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
# if GCC_VERSION > 40600
# pragma GCC diagnostic push
# endif
# pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "algebraic_parser.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
RandomParameter<Real> Parser::parseRandomParameter(const std::string & value, const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::RandomGeneratorGrammar<std::string::const_iterator, space_type> grammar(section);
grammar.name("random_grammar");
parser::ParsableRandomGenerator rg = Parser::parseType<parser::ParsableRandomGenerator>(value, grammar);
Vector<Real> params = rg.parameters;
switch(rg.type) {
case _rdt_not_defined: return RandomParameter<Real>(rg.base);
case _rdt_uniform: return RandomParameter<Real>(rg.base, UniformDistribution<Real>(params(0), params(1)));
case _rdt_weibull: return RandomParameter<Real>(rg.base, WeibullDistribution<Real>(params(0), params(1)));
default:
AKANTU_EXCEPTION("This is an unknown random distribution in the parser");
}
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/io/parser/parser_real.cc b/src/io/parser/parser_real.cc
index accd1ff36..c232530fd 100644
--- a/src/io/parser/parser_real.cc
+++ b/src/io/parser/parser_real.cc
@@ -1,59 +1,59 @@
/**
* @file parser_real.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Nov 11 2015
*
* @brief implementation of the 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/>.
*
*/
#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__))
# define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
# if GCC_VERSION > 40600
# pragma GCC diagnostic push
# endif
# pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "algebraic_parser.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
Real Parser::parseReal(const std::string & value, const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::AlgebraicGrammar<std::string::const_iterator, space_type> grammar(section);
grammar.name("algebraic_grammar");
return Parser::parseType<Real>(value, grammar);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/parser/parser_tmpl.hh b/src/io/parser/parser_tmpl.hh
index 336ffef75..7463032be 100644
--- a/src/io/parser/parser_tmpl.hh
+++ b/src/io/parser/parser_tmpl.hh
@@ -1,106 +1,106 @@
/**
* @file parser_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Wed Apr 22 2015
*
* @brief Implementation of the parser templated methods
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T>
inline ParserParameter::operator T() const {
T t;
std::stringstream sstr(value);
sstr >> t;
if(sstr.bad())
AKANTU_EXCEPTION("No known conversion of a ParserParameter \""
<< name << "\" to the type "
<< typeid(T).name());
return t;
}
/* -------------------------------------------------------------------------- */
template<>
inline ParserParameter::operator const char *() const {
return value.c_str();
}
/* -------------------------------------------------------------------------- */
template<>
inline ParserParameter::operator Real() const {
return Parser::parseReal(value, *parent_section);
}
/* --------------------------------------------------------- ----------------- */
template<>
inline ParserParameter::operator bool() const {
bool b;
std::stringstream sstr(value);
sstr >> std::boolalpha >> b;
if(sstr.fail()) {
sstr.clear();
sstr >> std::noboolalpha >> b;
}
return b;
}
/* --------------------------------------------------------- ----------------- */
template<>
inline ParserParameter::operator Vector<Real>() const {
return Parser::parseVector(value, *parent_section);
}
/* --------------------------------------------------------- ----------------- */
template<>
inline ParserParameter::operator Vector<UInt>() const {
Vector<Real> tmp = Parser::parseVector(value, *parent_section);
Vector<UInt> tmp_uint(tmp.size());
for (UInt i=0; i<tmp.size(); ++i) {
tmp_uint(i) = UInt(tmp(i));
}
return tmp_uint;
}
/* --------------------------------------------------------- ----------------- */
template<>
inline ParserParameter::operator Matrix<Real>() const {
return Parser::parseMatrix(value, *parent_section);
}
/* -------------------------------------------------------------------------- */
template<>
inline ParserParameter::operator RandomParameter<Real>() const {
return Parser::parseRandomParameter(value, *parent_section);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/io/parser/parser_types.cc b/src/io/parser/parser_types.cc
index a30bcf903..ff6565216 100644
--- a/src/io/parser/parser_types.cc
+++ b/src/io/parser/parser_types.cc
@@ -1,69 +1,69 @@
/**
* @file parser_types.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Nov 11 2015
*
* @brief implementation of the 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/>.
*
*/
#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__))
# define GCC_VERSION (__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
# if GCC_VERSION > 40600
# pragma GCC diagnostic push
# endif
# pragma GCC diagnostic ignored "-Wunused-local-typedefs"
#endif
/* -------------------------------------------------------------------------- */
#include "parser.hh"
#include "parser_grammar_tmpl.hh"
/* -------------------------------------------------------------------------- */
#include "algebraic_parser.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
Vector<Real> Parser::parseVector(const std::string & value, const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::VectorGrammar<std::string::const_iterator, space_type> grammar(section);
grammar.name("vector_grammar");
return Parser::parseType<parser::parsable_vector>(value, grammar);
}
/* -------------------------------------------------------------------------- */
Matrix<Real> Parser::parseMatrix(const std::string & value, const ParserSection & section) {
using boost::spirit::ascii::space_type;
parser::MatrixGrammar<std::string::const_iterator, space_type> grammar(section);
grammar.name("matrix_grammar");
return Parser::parseType<parser::parsable_matrix>(value, grammar);
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh/element_group.cc b/src/mesh/element_group.cc
index 24bf91037..591a66141 100644
--- a/src/mesh/element_group.cc
+++ b/src/mesh/element_group.cc
@@ -1,201 +1,201 @@
/**
* @file element_group.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Tue Aug 18 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 <sstream>
#include <algorithm>
#include <iterator>
#include "mesh.hh"
#include "group_manager.hh"
#include "group_manager_inline_impl.cc"
#include "dumpable.hh"
#include "dumpable_inline_impl.hh"
#include "aka_csr.hh"
#include "mesh_utils.hh"
#include "element_group.hh"
#if defined(AKANTU_USE_IOHELPER)
# include "dumper_paraview.hh"
#endif
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
ElementGroup::ElementGroup(const std::string & group_name,
const Mesh & mesh,
NodeGroup & node_group,
UInt dimension,
const std::string & id,
const MemoryID & mem_id) :
Memory(id, mem_id),
mesh(mesh),
name(group_name),
elements("elements", id, mem_id),
node_group(node_group),
dimension(dimension) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_USE_IOHELPER)
this->registerDumper<DumperParaview>("paraview_" + group_name, group_name, true);
this->addDumpFilteredMesh(mesh, elements, node_group.getNodes(), dimension);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::empty() {
elements.free();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::append(const ElementGroup & other_group) {
AKANTU_DEBUG_IN();
node_group.append(other_group.node_group);
/// loop on all element types in all dimensions
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
type_iterator it = other_group.firstType(_all_dimensions,
ghost_type,
_ek_not_defined);
type_iterator last = other_group.lastType(_all_dimensions,
ghost_type,
_ek_not_defined);
for (; it != last; ++it) {
ElementType type = *it;
const Array<UInt> & other_elem_list = other_group.elements(type, ghost_type);
UInt nb_other_elem = other_elem_list.getSize();
Array<UInt> * elem_list;
UInt nb_elem = 0;
/// create current type if doesn't exists, otherwise get information
if (elements.exists(type, ghost_type)) {
elem_list = &elements(type, ghost_type);
nb_elem = elem_list->getSize();
}
else {
elem_list = &(elements.alloc(0, 1, type, ghost_type));
}
/// append new elements to current list
elem_list->resize(nb_elem + nb_other_elem);
std::copy(other_elem_list.begin(),
other_elem_list.end(),
elem_list->begin() + nb_elem);
/// remove duplicates
std::sort(elem_list->begin(), elem_list->end());
Array<UInt>::iterator<> end = std::unique(elem_list->begin(), elem_list->end());
elem_list->resize(end - elem_list->begin());
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
stream << space << "ElementGroup [" << std::endl;
stream << space << " + name: " << name << std::endl;
stream << space << " + dimension: " << dimension << std::endl;
elements.printself(stream, indent + 1);
node_group.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void ElementGroup::optimize() {
// increasing the locality of data when iterating on the element of a group
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
ElementList::type_iterator it = elements.firstType(_all_dimensions, ghost_type);
ElementList::type_iterator last = elements.lastType(_all_dimensions, ghost_type);
for (; it != last; ++it) {
Array<UInt> & els = elements(*it, ghost_type);
std::sort(els.begin(), els.end());
Array<UInt>::iterator<> end = std::unique(els.begin(), els.end());
els.resize(end - els.begin());
}
}
node_group.optimize();
}
/* -------------------------------------------------------------------------- */
void ElementGroup::fillFromNodeGroup() {
CSR<Element> node_to_elem;
MeshUtils::buildNode2Elements(this->mesh, node_to_elem, this->dimension);
std::set<Element> seen;
Array<UInt>::const_iterator<> itn = this->node_group.begin();
Array<UInt>::const_iterator<> endn = this->node_group.end();
for (;itn != endn; ++itn) {
CSR<Element>::iterator ite = node_to_elem.begin(*itn);
CSR<Element>::iterator ende = node_to_elem.end(*itn);
for (;ite != ende; ++ite) {
const Element & elem = *ite;
if(this->dimension != _all_dimensions && this->dimension != Mesh::getSpatialDimension(elem.type)) continue;
if(seen.find(elem) != seen.end()) continue;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(elem.type);
Array<UInt>::const_iterator< Vector<UInt> > conn_it =
this->mesh.getConnectivity(elem.type, elem.ghost_type).begin(nb_nodes_per_element);
const Vector<UInt> & conn = conn_it[elem.element];
UInt count = 0;
for (UInt n = 0; n < conn.size(); ++n) {
count += (this->node_group.getNodes().find(conn(n)) != -1 ? 1 : 0);
}
if(count == nb_nodes_per_element) this->add(elem);
seen.insert(elem);
}
}
this->optimize();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh/element_group.hh b/src/mesh/element_group.hh
index 895b9e745..be5a6ab5c 100644
--- a/src/mesh/element_group.hh
+++ b/src/mesh/element_group.hh
@@ -1,188 +1,188 @@
/**
* @file element_group.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Tue Aug 18 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 "aka_common.hh"
#include "aka_memory.hh"
#include "dumpable.hh"
#include "element_type_map.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_GROUP_HH__
#define __AKANTU_ELEMENT_GROUP_HH__
namespace akantu {
class Mesh;
class Element;
} // akantu
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
class ElementGroup : private Memory, public Dumpable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementGroup(const std::string & name, const Mesh & mesh,
NodeGroup & node_group, UInt dimension = _all_dimensions,
const std::string & id = "element_group",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Type definitions */
/* ------------------------------------------------------------------------ */
public:
typedef ElementTypeMapArray<UInt> ElementList;
typedef Array<UInt> NodeList;
/* ------------------------------------------------------------------------ */
/* Node iterator */
/* ------------------------------------------------------------------------ */
typedef NodeGroup::const_node_iterator const_node_iterator;
inline const_node_iterator node_begin() const;
inline const_node_iterator node_end() const;
/* ------------------------------------------------------------------------ */
/* Element iterator */
/* ------------------------------------------------------------------------ */
typedef ElementList::type_iterator type_iterator;
inline type_iterator firstType(UInt dim = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & kind = _ek_regular) const;
inline type_iterator lastType(UInt dim = _all_dimensions,
const GhostType & ghost_type = _not_ghost,
const ElementKind & kind = _ek_regular) const;
typedef Array<UInt>::const_iterator<UInt> const_element_iterator;
inline const_element_iterator
element_begin(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
inline const_element_iterator
element_end(const ElementType & type,
const GhostType & ghost_type = _not_ghost) const;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// empty the element group
void empty();
/// append another group to this group
/// BE CAREFUL: it doesn't conserve the element order
void append(const ElementGroup & other_group);
/// add an element to the group. By default the it does not add the nodes to
/// the group
inline void add(const Element & el, bool add_nodes = false,
bool check_for_duplicate = true);
/// \todo fix the default for add_nodes : make it coherent with the other
/// method
inline void add(const ElementType & type, UInt element,
const GhostType & ghost_type = _not_ghost,
bool add_nodes = true, bool check_for_duplicate = true);
inline void addNode(UInt node_id, bool check_for_duplicate = true);
inline void removeNode(UInt node_id);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// fill the elements based on the underlying node group.
virtual void fillFromNodeGroup();
// sort and remove duplicated values
void optimize();
private:
inline void addElement(const ElementType & elem_type, UInt elem_id,
const GhostType & ghost_type);
friend class GroupManager;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Elements, elements, UInt);
AKANTU_GET_MACRO(Elements, elements, const ElementTypeMapArray<UInt> &);
AKANTU_GET_MACRO(Nodes, node_group.getNodes(), const Array<UInt> &);
AKANTU_GET_MACRO(NodeGroup, node_group, const NodeGroup &);
AKANTU_GET_MACRO_NOT_CONST(NodeGroup, node_group, NodeGroup &);
AKANTU_GET_MACRO(Dimension, dimension, UInt);
AKANTU_GET_MACRO(Name, name, std::string);
inline UInt getNbNodes() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// Mesh to which this group belongs
const Mesh & mesh;
/// name of the group
std::string name;
/// list of elements composing the group
ElementList elements;
/// sub list of nodes which are composing the elements
NodeGroup & node_group;
/// group dimension
UInt dimension;
/// empty arry for the iterator to work when an element type not present
Array<UInt> empty_elements;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const ElementGroup & _this) {
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#include "element.hh"
#include "element_group_inline_impl.cc"
#endif /* __AKANTU_ELEMENT_GROUP_HH__ */
diff --git a/src/mesh/element_group_inline_impl.cc b/src/mesh/element_group_inline_impl.cc
index d6047bf81..ba16ea036 100644
--- a/src/mesh/element_group_inline_impl.cc
+++ b/src/mesh/element_group_inline_impl.cc
@@ -1,137 +1,137 @@
/**
* @file element_group_inline_impl.cc
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Tue Aug 18 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 "mesh.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
inline void ElementGroup::add(const Element & el, bool add_nodes,
bool check_for_duplicate) {
this->add(el.type,el.element,el.ghost_type,add_nodes,check_for_duplicate);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::add(const ElementType & type, UInt element,
const GhostType & ghost_type,bool add_nodes,
bool check_for_duplicate) {
addElement(type, element, ghost_type);
if(add_nodes) {
Array<UInt>::const_vector_iterator it =
mesh.getConnectivity(type, ghost_type).begin(mesh.getNbNodesPerElement(type)) + element;
const Vector<UInt> & conn = *it;
for (UInt i = 0; i < conn.size(); ++i) addNode(conn[i], check_for_duplicate);
}
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::addNode(UInt node_id, bool check_for_duplicate) {
node_group.add(node_id, check_for_duplicate);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::removeNode(UInt node_id) {
node_group.remove(node_id);
}
/* -------------------------------------------------------------------------- */
inline void ElementGroup::addElement(const ElementType & elem_type,
UInt elem_id,
const GhostType & ghost_type) {
if(!(elements.exists(elem_type, ghost_type))) {
elements.alloc(0, 1, elem_type, ghost_type);
}
elements(elem_type, ghost_type).push_back(elem_id);
this->dimension = UInt(std::max(Int(this->dimension), Int(mesh.getSpatialDimension(elem_type))));
}
/* -------------------------------------------------------------------------- */
inline UInt ElementGroup::getNbNodes() const {
return node_group.getSize();
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::const_node_iterator ElementGroup::node_begin() const {
return node_group.begin();
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::const_node_iterator ElementGroup::node_end() const {
return node_group.end();
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::type_iterator ElementGroup::firstType(UInt dim,
const GhostType & ghost_type,
const ElementKind & kind) const {
return elements.firstType(dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::type_iterator ElementGroup::lastType(UInt dim,
const GhostType & ghost_type,
const ElementKind & kind) const {
return elements.lastType(dim, ghost_type, kind);
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::const_element_iterator ElementGroup::element_begin(const ElementType & type,
const GhostType & ghost_type) const {
if(elements.exists(type, ghost_type)) {
return elements(type, ghost_type).begin();
} else {
return empty_elements.begin();
}
}
/* -------------------------------------------------------------------------- */
inline ElementGroup::const_element_iterator ElementGroup::element_end(const ElementType & type,
const GhostType & ghost_type) const {
if(elements.exists(type, ghost_type)) {
return elements(type, ghost_type).end();
} else {
return empty_elements.end();
}
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh/element_type_map.hh b/src/mesh/element_type_map.hh
index 348d1940f..f005c409a 100644
--- a/src/mesh/element_type_map.hh
+++ b/src/mesh/element_type_map.hh
@@ -1,368 +1,368 @@
/**
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_TYPE_MAP_HH__
#define __AKANTU_ELEMENT_TYPE_MAP_HH__
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_memory.hh"
-__BEGIN_AKANTU__
+namespace akantu {
template <class Stored, typename SupportType = ElementType>
class ElementTypeMap;
/* -------------------------------------------------------------------------- */
/* ElementTypeMapBase */
/* -------------------------------------------------------------------------- */
/// Common non templated base class for the ElementTypeMap class
class ElementTypeMapBase {
public:
virtual ~ElementTypeMapBase(){};
};
/* -------------------------------------------------------------------------- */
/* ElementTypeMap */
/* -------------------------------------------------------------------------- */
template <class Stored, typename SupportType>
class ElementTypeMap : public ElementTypeMapBase {
public:
ElementTypeMap();
~ElementTypeMap();
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:
typedef const SupportType value_type;
typedef const SupportType * pointer;
typedef const SupportType & reference;
protected:
typedef typename ElementTypeMap<Stored>::DataMap::const_iterator
DataMapIterator;
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 = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular)
: container(std::cref(container)), dim(dim), ghost_type(ghost_type), kind(kind) {}
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;
};
/// method to create the helper class to use in range for constructs
ElementTypesIteratorHelper elementTypes(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_regular) const;
/*! 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:
typedef T type;
typedef Array<T> array_type;
protected:
typedef ElementTypeMap<Array<T> *, SupportType> parent;
typedef typename parent::DataMap DataMap;
private:
private:
/// standard assigment (copy) operator
void operator=(const ElementTypeMap<T, SupportType> &){};
public:
typedef typename parent::type_iterator type_iterator;
/*! 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;
/* 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;
/*! 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;
type_iterator tit = this->firstType(dim, ghost_type, kind);
type_iterator end = this->lastType(dim, ghost_type, kind);
while (tit != end) {
UInt nb_comp = (*this)(*tit, ghost_type).getNbComponent();
nb_components(*tit, ghost_type) = nb_comp;
++tit;
}
return nb_components;
}
/* --------------------------------------------------------------------------
*/
/* Accesssors */
/* --------------------------------------------------------------------------
*/
public:
/// get the name of the internal field
AKANTU_GET_MACRO(Name, name, ID);
private:
ElementTypeMapArray operator=(__attribute__((unused))
const ElementTypeMapArray & other){};
/// name of the elment type map: e.g. connectivity, grad_u
ID name;
};
/// to store data Array<Real> by element type
typedef ElementTypeMapArray<Real> ElementTypeMapReal;
/// to store data Array<Int> by element type
typedef ElementTypeMapArray<Int> ElementTypeMapInt;
/// to store data Array<UInt> by element type
typedef ElementTypeMapArray<UInt, ElementType> ElementTypeMapUInt;
/// Map of data of type UInt stored in a mesh
typedef std::map<std::string, Array<UInt> *> UIntDataMap;
typedef ElementTypeMap<UIntDataMap, ElementType> ElementTypeMapUIntDataMap;
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_ELEMENT_TYPE_MAP_HH__ */
diff --git a/src/mesh/element_type_map_filter.hh b/src/mesh/element_type_map_filter.hh
index 32011621b..99b94ae06 100644
--- a/src/mesh/element_type_map_filter.hh
+++ b/src/mesh/element_type_map_filter.hh
@@ -1,335 +1,335 @@
/**
* @file element_type_map_filter.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Sep 02 2014
* @date last modification: Fri Dec 18 2015
*
* @brief Filtered version based on a an akantu::ElementGroup of a
* akantu::ElementTypeMap
*
* @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_BY_ELEMENT_TYPE_FILTER_HH__
#define __AKANTU_BY_ELEMENT_TYPE_FILTER_HH__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* ArrayFilter */
/* -------------------------------------------------------------------------- */
template <typename T> class ArrayFilter {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
/// standard iterator
template <typename R = T> class iterator {
inline bool operator!=(__attribute__((unused)) iterator<R> & other) { throw; };
inline bool operator==(__attribute__((unused)) iterator<R> & other) { throw; };
inline iterator<R> & operator++() { throw; };
inline T operator*() {
throw;
return T();
};
};
/// const iterator
template <template <class S> class original_iterator, typename Shape,
typename filter_iterator>
class const_iterator {
public:
UInt getCurrentIndex() {
return (*this->filter_it * this->nb_item_per_elem +
this->sub_element_counter);
}
inline const_iterator(){};
inline const_iterator(const original_iterator<Shape> & origin_it,
const filter_iterator & filter_it,
UInt nb_item_per_elem)
: origin_it(origin_it), filter_it(filter_it),
nb_item_per_elem(nb_item_per_elem), sub_element_counter(0){};
inline bool operator!=(const_iterator & other) const {
return !((*this) == other);
}
inline bool operator==(const_iterator & other) const {
return (this->origin_it == other.origin_it &&
this->filter_it == other.filter_it &&
this->sub_element_counter == other.sub_element_counter);
}
inline bool operator!=(const const_iterator & other) const {
return !((*this) == other);
}
inline bool operator==(const const_iterator & other) const {
return (this->origin_it == other.origin_it &&
this->filter_it == other.filter_it &&
this->sub_element_counter == other.sub_element_counter);
}
inline const_iterator & operator++() {
++sub_element_counter;
if (sub_element_counter == nb_item_per_elem) {
sub_element_counter = 0;
++filter_it;
}
return *this;
};
inline Shape operator*() {
return origin_it[nb_item_per_elem * (*filter_it) + sub_element_counter];
};
private:
original_iterator<Shape> origin_it;
filter_iterator filter_it;
/// the number of item per element
UInt nb_item_per_elem;
/// counter for every sub element group
UInt sub_element_counter;
};
typedef iterator<Vector<T> > vector_iterator;
typedef Array<T> array_type;
typedef const_iterator<array_type::template const_iterator, Vector<T>,
Array<UInt>::const_iterator<UInt> >
const_vector_iterator;
typedef typename array_type::value_type value_type;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ArrayFilter(const Array<T> & array, const Array<UInt> & filter,
UInt nb_item_per_elem)
: array(array), filter(filter), nb_item_per_elem(nb_item_per_elem){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
const_vector_iterator begin_reinterpret(UInt n, UInt new_size) const {
AKANTU_DEBUG_ASSERT(
n * new_size == this->getNbComponent() * this->getSize(),
"The new values for size ("
<< new_size << ") and nb_component (" << n
<< ") are not compatible with the one of this array("
<< this->getSize() << "," << this->getNbComponent() << ")");
UInt new_full_array_size =
this->array.getSize() * array.getNbComponent() / n;
UInt new_nb_item_per_elem = this->nb_item_per_elem;
if (new_size != 0 && n != 0)
new_nb_item_per_elem = this->array.getNbComponent() *
this->filter.getSize() * this->nb_item_per_elem /
(n * new_size);
return const_vector_iterator(
this->array.begin_reinterpret(n, new_full_array_size),
this->filter.begin(), new_nb_item_per_elem);
};
const_vector_iterator end_reinterpret(UInt n, UInt new_size) const {
AKANTU_DEBUG_ASSERT(
n * new_size == this->getNbComponent() * this->getSize(),
"The new values for size ("
<< new_size << ") and nb_component (" << n
<< ") are not compatible with the one of this array("
<< this->getSize() << "," << this->getNbComponent() << ")");
UInt new_full_array_size =
this->array.getSize() * this->array.getNbComponent() / n;
UInt new_nb_item_per_elem = this->nb_item_per_elem;
if (new_size != 0 && n != 0)
new_nb_item_per_elem = this->array.getNbComponent() *
this->filter.getSize() * this->nb_item_per_elem /
(n * new_size);
return const_vector_iterator(
this->array.begin_reinterpret(n, new_full_array_size),
this->filter.end(), new_nb_item_per_elem);
};
vector_iterator begin_reinterpret(UInt, UInt) { throw; };
vector_iterator end_reinterpret(UInt, UInt) { throw; };
/// return the size of the filtered array which is the filter size
UInt getSize() const {
return this->filter.getSize() * this->nb_item_per_elem;
};
/// the number of components of the filtered array
UInt getNbComponent() const { return this->array.getNbComponent(); };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// reference to array of data
const Array<T> & array;
/// reference to the filter used to select elements
const Array<UInt> & filter;
/// the number of item per element
UInt nb_item_per_elem;
};
/* -------------------------------------------------------------------------- */
/* ElementTypeMapFilter */
/* -------------------------------------------------------------------------- */
template <class T, typename SupportType = ElementType>
class ElementTypeMapArrayFilter {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
public:
typedef T type;
typedef ArrayFilter<T> array_type;
typedef typename array_type::value_type value_type;
typedef typename ElementTypeMapArray<UInt, SupportType>::type_iterator
type_iterator;
// class type_iterator{
// public:
// typedef typename ElementTypeMapArray<T,SupportType>::type_iterator
// type_it;
// public:
// type_iterator(){};
// // type_iterator(const type_iterator & it){original_it =
// it.original_it;};
// type_iterator(const type_it & it){original_it = it;};
// inline ElementType & operator*(){throw;};
// inline ElementType & operator*() const{throw;};
// inline type_iterator & operator++(){throw;return *this;};
// type_iterator operator++(int){throw; return *this;};
// inline bool operator==(const type_iterator & other) const{throw;return
// false;};
// inline bool operator!=(const type_iterator & other) const{throw;return
// false;};
// // type_iterator & operator=(const type_iterator & other){throw;return
// *this;};
// type_it original_it;
// };
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ElementTypeMapArrayFilter(
const ElementTypeMapArray<T, SupportType> & array,
const ElementTypeMapArray<UInt, SupportType> & filter,
const ElementTypeMap<UInt, SupportType> & nb_data_per_elem)
: array(array), filter(filter), nb_data_per_elem(nb_data_per_elem) {}
ElementTypeMapArrayFilter(
const ElementTypeMapArray<T, SupportType> & array,
const ElementTypeMapArray<UInt, SupportType> & filter)
: array(array), filter(filter) {}
~ElementTypeMapArrayFilter() {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
inline const ArrayFilter<T>
operator()(const SupportType & type,
const GhostType & ghost_type = _not_ghost) const {
if (filter.exists(type, ghost_type)) {
if (nb_data_per_elem.exists(type, ghost_type))
return ArrayFilter<T>(array(type, ghost_type), filter(type, ghost_type),
nb_data_per_elem(type, ghost_type) /
array(type, ghost_type).getNbComponent());
else
return ArrayFilter<T>(array(type, ghost_type), filter(type, ghost_type),
1);
} else {
return ArrayFilter<T>(empty_array, empty_filter, 1);
}
};
inline type_iterator firstType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
return filter.firstType(dim, ghost_type, kind);
};
inline type_iterator lastType(UInt dim = _all_dimensions,
GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
return filter.lastType(dim, ghost_type, kind);
};
ElementTypeMap<UInt>
getNbComponents(UInt dim = _all_dimensions, GhostType ghost_type = _not_ghost,
ElementKind kind = _ek_not_defined) const {
return this->array.getNbComponents(dim, ghost_type, kind);
};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
std::string getID() {
return std::string("filtered:" + this->array().getID());
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
const ElementTypeMapArray<T, SupportType> & array;
const ElementTypeMapArray<UInt, SupportType> & filter;
ElementTypeMap<UInt> nb_data_per_elem;
/// Empty array to be able to return consistent filtered arrays
Array<T> empty_array;
Array<UInt> empty_filter;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_BY_ELEMENT_TYPE_FILTER_HH__ */
diff --git a/src/mesh/group_manager.cc b/src/mesh/group_manager.cc
index 5e2fa9a07..536964d94 100644
--- a/src/mesh/group_manager.cc
+++ b/src/mesh/group_manager.cc
@@ -1,1028 +1,1028 @@
/**
* @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 "mesh.hh"
#include "mesh_utils.hh"
#include "data_accessor.hh"
#include "element_synchronizer.hh"
#include "element_group.hh"
#include "node_group.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iterator>
#include <list>
#include <numeric>
#include <queue>
#include <sstream>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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() {
ElementGroups::iterator eit = element_groups.begin();
ElementGroups::iterator eend = element_groups.end();
for (; eit != eend; ++eit)
delete (eit->second);
NodeGroups::iterator nit = node_groups.begin();
NodeGroups::iterator 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();
NodeGroups::iterator 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);
ElementGroups::iterator 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();
ElementGroups::iterator eit = element_groups.find(group_name);
ElementGroups::iterator 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();
ElementGroups::iterator eit = element_groups.begin();
ElementGroups::iterator 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;
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> {
typedef std::set<std::pair<UInt, UInt> > DistantIDs;
public:
ClusterSynchronizer(GroupManager & group_manager, UInt element_dimension,
std::string cluster_name_prefix,
ElementTypeMapArray<UInt> & element_to_fragment,
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() {
StaticCommunicator & comm = StaticCommunicator::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.computeBufferSize(*this, _gst_gm_clusters);
element_synchronizer.asynchronousSynchronize(*this, _gst_gm_clusters);
element_synchronizer.waitEndSynchronize(*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);
DistantIDs::iterator ids_it = distant_ids.begin();
DistantIDs::iterator ids_end = distant_ids.end();
for (; ids_it != ids_end; ++ids_it, ++local_pair_index) {
total_pairs(local_pair_index, 0) = ids_it->first;
total_pairs(local_pair_index, 1) = ids_it->second;
}
/// 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.getSize() != 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.getSize() * 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;
GroupManager::element_group_iterator 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 {
if (tag == _gst_gm_clusters)
return elements.getSize() * sizeof(UInt);
return 0;
}
inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
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) {
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;
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");
}
/* -------------------------------------------------------------------------- */
//// \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,
ElementSynchronizer * element_synchronizer, Mesh * mesh_facets) {
AKANTU_DEBUG_IN();
UInt nb_proc = StaticCommunicator::getStaticCommunicator().getNbProc();
std::string tmp_cluster_name_prefix = cluster_name_prefix;
ElementTypeMapArray<UInt> * element_to_fragment = NULL;
if (nb_proc > 1 && element_synchronizer) {
element_to_fragment =
new ElementTypeMapArray<UInt>("element_to_fragment", id, memory_id);
mesh.initElementTypeMapArray(*element_to_fragment, 1, element_dimension,
false, _ek_not_defined, true);
tmp_cluster_name_prefix = "tmp_" + tmp_cluster_name_prefix;
}
/// Get facets
bool mesh_facets_created = false;
if (!mesh_facets && element_dimension > 0) {
mesh_facets = new Mesh(mesh.getSpatialDimension(), mesh.getNodes().getID(),
"mesh_facets_for_clusters");
mesh_facets->defineMeshParent(mesh);
MeshUtils::buildAllFacets(mesh, *mesh_facets, element_dimension,
element_dimension - 1);
}
ElementTypeMapArray<bool> seen_elements("seen_elements", id, memory_id);
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;
el.kind = Mesh::getKind(*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.getSize(); ++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 && element_synchronizer)
(*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 && element_synchronizer) {
ClusterSynchronizer cluster_synchronizer(
*this, element_dimension, cluster_name_prefix, *element_to_fragment,
*element_synchronizer, nb_cluster);
nb_cluster = cluster_synchronizer.synchronize();
delete element_to_fragment;
}
if (mesh_facets_created)
delete mesh_facets;
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.getSize() == nb_element,
"Not the same number of elements ("
<< *type_it << ":" << *gt
<< ") in the map from MeshData ("
<< dataset.getSize() << ") " << 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.getSize() == 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();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
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.getSize())
<< " from proc " << p);
CommunicationBuffer recv_buffer(status.getSize());
comm.receive(recv_buffer, p, p);
this->checkAndAddGroups(recv_buffer);
}
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
UInt buffer_size = comm_buffer.getSize();
comm.broadcast(buffer_size, 0);
AKANTU_DEBUG_INFO("Initiating broadcast with "
<< printMemorySize<char>(comm_buffer.getSize()));
comm.broadcast(comm_buffer, 0);
} else {
DynamicCommunicationBuffer comm_buffer;
this->fillBufferWithGroupNames(comm_buffer);
AKANTU_DEBUG_INFO("Sending " << printMemorySize<char>(comm_buffer.getSize())
<< " 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.getSize()));
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);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh/group_manager.hh b/src/mesh/group_manager.hh
index 8537c8b00..1147edbfa 100644
--- a/src/mesh/group_manager.hh
+++ b/src/mesh/group_manager.hh
@@ -1,296 +1,296 @@
/**
* @file group_manager.hh
*
* @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 Nov 16 2015
*
* @brief Stores information relevent to the notion of element and nodes
*groups.
*
* @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_GROUP_MANAGER_HH__
#define __AKANTU_GROUP_MANAGER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "element_type_map.hh"
/* -------------------------------------------------------------------------- */
#include <set>
/* -------------------------------------------------------------------------- */
namespace akantu {
class ElementGroup;
class NodeGroup;
class Mesh;
class Element;
class ElementSynchronizer;
template <bool> class CommunicationBufferTemplated;
namespace dumper {
class Field;
}
}
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
class GroupManager {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
typedef std::map<std::string, ElementGroup *> ElementGroups;
typedef std::map<std::string, NodeGroup *> NodeGroups;
public:
typedef std::set<ElementType> GroupManagerTypeSet;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GroupManager(const Mesh & mesh, const ID & id = "group_manager",
const MemoryID & memory_id = 0);
virtual ~GroupManager();
/* ------------------------------------------------------------------------ */
/* Groups iterators */
/* ------------------------------------------------------------------------ */
public:
typedef NodeGroups::iterator node_group_iterator;
typedef ElementGroups::iterator element_group_iterator;
typedef NodeGroups::const_iterator const_node_group_iterator;
typedef ElementGroups::const_iterator const_element_group_iterator;
#ifndef SWIG
#define AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(group_type, function, \
param_in, param_out) \
inline BOOST_PP_CAT(BOOST_PP_CAT(const_, group_type), _iterator) \
BOOST_PP_CAT(BOOST_PP_CAT(group_type, _), function)(param_in) const { \
return BOOST_PP_CAT(group_type, s).function(param_out); \
}; \
\
inline BOOST_PP_CAT(group_type, _iterator) \
BOOST_PP_CAT(BOOST_PP_CAT(group_type, _), function)(param_in) { \
return BOOST_PP_CAT(group_type, s).function(param_out); \
}
#define AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(group_type, function) \
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION( \
group_type, function, BOOST_PP_EMPTY(), BOOST_PP_EMPTY())
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(node_group, begin);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(node_group, end);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(element_group, begin);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION_NP(element_group, end);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(element_group, find,
const std::string & name, name);
AKANTU_GROUP_MANAGER_DEFINE_ITERATOR_FUNCTION(node_group, find,
const std::string & name, name);
#endif
/* ------------------------------------------------------------------------ */
/* Clustering filter */
/* ------------------------------------------------------------------------ */
public:
class ClusteringFilter {
public:
virtual bool operator()(const Element &) const { return true; }
};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create an empty node group
NodeGroup & createNodeGroup(const std::string & group_name,
bool replace_group = false);
/// create a node group from another node group but filtered
template <typename T>
NodeGroup & createFilteredNodeGroup(const std::string & group_name,
const NodeGroup & node_group, T & filter);
/// destroy a node group
void destroyNodeGroup(const std::string & group_name);
/// create an element group and the associated node group
ElementGroup & createElementGroup(const std::string & group_name,
UInt dimension = _all_dimensions,
bool replace_group = false);
/// create an element group from another element group but filtered
template <typename T>
ElementGroup &
createFilteredElementGroup(const std::string & group_name, UInt dimension,
const NodeGroup & node_group, T & filter);
/// destroy an element group and the associated node group
void destroyElementGroup(const std::string & group_name,
bool destroy_node_group = false);
/// destroy all element groups and the associated node groups
void destroyAllElementGroups(bool destroy_node_groups = false);
/// create a element group using an existing node group
ElementGroup & createElementGroup(const std::string & group_name,
UInt dimension, NodeGroup & node_group);
/// create groups based on values stored in a given mesh data
template <typename T>
void createGroupsFromMeshData(const std::string & dataset_name);
/// create boundaries group by a clustering algorithm \todo extend to parallel
UInt createBoundaryGroupFromGeometry();
/// create element clusters for a given dimension
UInt createClusters(UInt element_dimension,
std::string cluster_name_prefix = "cluster",
const ClusteringFilter & filter = ClusteringFilter(),
ElementSynchronizer * element_synchronizer = NULL,
Mesh * mesh_facets = NULL);
/// Create an ElementGroup based on a NodeGroup
void createElementGroupFromNodeGroup(const std::string & name,
const std::string & node_group,
UInt dimension = _all_dimensions);
virtual void printself(std::ostream & stream, int indent = 0) const;
/// this function insure that the group names are present on all processors
/// /!\ it is a SMP call
void synchronizeGroupNames();
/// register an elemental field to the given group name (overloading for
/// ElementalPartionField)
#ifndef SWIG
template <typename T, template <bool> class dump_type>
inline dumper::Field * createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem = ElementTypeMap<UInt>());
/// register an elemental field to the given group name (overloading for
/// ElementalField)
template <typename T, template <class> class ret_type,
template <class, template <class> class, bool> class dump_type>
inline dumper::Field * createElementalField(
const ElementTypeMapArray<T> & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem = ElementTypeMap<UInt>());
/// register an elemental field to the given group name (overloading for
/// MaterialInternalField)
template <typename T,
/// type of InternalMaterialField
template <typename, bool filtered> class dump_type>
inline dumper::Field *
createElementalField(const ElementTypeMapArray<T> & field,
const std::string & group_name, UInt spatial_dimension,
const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem);
template <typename type, bool flag, template <class, bool> class ftype>
inline dumper::Field * createNodalField(const ftype<type, flag> * field,
const std::string & group_name,
UInt padding_size = 0);
template <typename type, bool flag, template <class, bool> class ftype>
inline dumper::Field *
createStridedNodalField(const ftype<type, flag> * field,
const std::string & group_name, UInt size,
UInt stride, UInt padding_size);
protected:
/// fill a buffer with all the group names
void fillBufferWithGroupNames(
CommunicationBufferTemplated<false> & comm_buffer) const;
/// take a buffer and create the missing groups localy
void checkAndAddGroups(CommunicationBufferTemplated<true> & buffer);
/// register an elemental field to the given group name
template <class dump_type, typename field_type>
inline dumper::Field *
createElementalField(const field_type & field, const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem);
/// register an elemental field to the given group name
template <class dump_type, typename field_type>
inline dumper::Field *
createElementalFilteredField(const field_type & field,
const std::string & group_name,
UInt spatial_dimension, const ElementKind & kind,
ElementTypeMap<UInt> nb_data_per_elem);
#endif
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
const ElementGroup & getElementGroup(const std::string & name) const;
const NodeGroup & getNodeGroup(const std::string & name) const;
ElementGroup & getElementGroup(const std::string & name);
NodeGroup & getNodeGroup(const std::string & name);
UInt getNbElementGroups(UInt dimension = _all_dimensions) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// id to create element and node groups
ID id;
/// memory_id to create element and node groups
MemoryID memory_id;
/// list of the node groups managed
NodeGroups node_groups;
/// list of the element groups managed
ElementGroups element_groups;
/// Mesh to which the element belongs
const Mesh & mesh;
};
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const GroupManager & _this) {
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_GROUP_MANAGER_HH__ */
diff --git a/src/mesh/group_manager_inline_impl.cc b/src/mesh/group_manager_inline_impl.cc
index c6d3b6dce..d6ebfbbf2 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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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 (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 (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 (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 (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 (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 (group_name == "all") {
typedef typename dumper::NodalField<type, false> DumpType;
DumpType * dumper = new DumpType(*field, 0, 0, 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, 0, 0, nodal_filter);
dumper->setPadding(padding_size);
return dumper;
}
return NULL;
}
/* -------------------------------------------------------------------------- */
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;
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;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif
diff --git a/src/mesh/mesh_accessor.hh b/src/mesh/mesh_accessor.hh
index 5c4bdef09..abf01fe45 100644
--- a/src/mesh/mesh_accessor.hh
+++ b/src/mesh/mesh_accessor.hh
@@ -1,129 +1,129 @@
/**
* @file mesh_accessor.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Jun 30 2015
*
* @brief this class allow to access some private member of mesh it is used for
* IO for examples
*
* @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 "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MESH_ACCESSOR_HH__
#define __AKANTU_MESH_ACCESSOR_HH__
namespace akantu {
class NodeSynchronizer;
class ElementSynchronizer;
} // akantu
-__BEGIN_AKANTU__
+namespace akantu {
class MeshAccessor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MeshAccessor(Mesh & mesh) : _mesh(mesh){};
virtual ~MeshAccessor(){};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the global number of nodes
inline UInt getNbGlobalNodes() const { return this->_mesh.nb_global_nodes; };
/// set the global number of nodes
inline void setNbGlobalNodes(UInt nb_global_nodes) {
this->_mesh.nb_global_nodes = nb_global_nodes;
};
/// set the mesh as being distributed
inline void setDistributed() { this->_mesh.is_distributed = true; }
/// get a pointer to the nodes_global_ids Array<UInt> and create it if
/// necessary
inline Array<UInt> & getNodesGlobalIds() {
return *(this->_mesh.getNodesGlobalIdsPointer());
}
/// get a pointer to the nodes_type Array<Int> and create it if necessary
inline Array<NodeType> & getNodesType() {
return *(this->_mesh.getNodesTypePointer());
}
/// get a pointer to the coordinates Array
inline Array<Real> & getNodes() { return *(this->_mesh.getNodesPointer()); }
/// get a pointer to the connectivity Array for the given type and create it
/// if necessary
inline Array<UInt> &
getConnectivity(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return *(this->_mesh.getConnectivityPointer(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> > &
getElementToSubelement(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return *(this->_mesh.getElementToSubelementPointer(type, ghost_type));
}
/// get a pointer to the subelement_to_element Array for the given type and
/// create it if necessary
inline Array<Element> &
getSubelementToElement(const ElementType & type,
const GhostType & ghost_type = _not_ghost) {
return *(this->_mesh.getSubelementToElementPointer(type, ghost_type));
}
template <typename T>
inline Array<T> &
getData(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) {
return *(this->_mesh.getDataPointer<T>(data_name, el_type, ghost_type,
nb_component, size_to_nb_element,
resize_with_parent));
}
MeshData & getMeshData() { return this->_mesh.getMeshData(); }
/// get the node synchonizer
NodeSynchronizer & getNodeSynchronizer();
/// get the element synchonizer
ElementSynchronizer & getElementSynchronizer();
private:
Mesh & _mesh;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MESH_ACCESSOR_HH__ */
diff --git a/src/mesh/mesh_data.cc b/src/mesh/mesh_data.cc
index 6c49bc088..f669598df 100644
--- a/src/mesh/mesh_data.cc
+++ b/src/mesh/mesh_data.cc
@@ -1,49 +1,49 @@
/**
* @file mesh_data.cc
*
* @author Dana Christen <dana.christen@gmail.com>
*
* @date creation: Fri Apr 13 2012
* @date last modification: Sun Oct 19 2014
*
* @brief Stores generic data loaded from the mesh 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.hh"
#include "mesh_data.hh"
-__BEGIN_AKANTU__
+namespace akantu {
MeshData::MeshData(const ID & _id, const ID & parent_id, const MemoryID & mem_id)
: Memory(parent_id + ":" + _id, mem_id) {
}
MeshData::~MeshData() {
ElementalDataMap::iterator it, end;
for(it = elemental_data.begin(); it != elemental_data.end(); ++it) {
delete it->second;
}
}
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh/mesh_data.hh b/src/mesh/mesh_data.hh
index 2a240f464..c2b943cc8 100644
--- a/src/mesh/mesh_data.hh
+++ b/src/mesh/mesh_data.hh
@@ -1,145 +1,145 @@
/**
* @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 "element_type_map.hh"
#include "aka_memory.hh"
#include <map>
#include <string>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* Methods and accessors */
/* ------------------------------------------------------------------------ */
public:
/// Register new elemental data (and alloc data) with check if the name is new
template<typename T>
void registerElementalData(const std::string & name);
inline void registerElementalData(const std::string & name, TypeCode type);
/// Get an existing elemental data array
template<typename T>
const Array<T> & getElementalDataArray(const std::string & data_name,
const ElementType & el_type,
const GhostType & ghost_type = _not_ghost) const;
template<typename T>
Array<T> & getElementalDataArray(const std::string & 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 std::string & 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 std::string name) const;
template<typename T>
inline UInt getNbComponentTemplated(const std::string, const ElementType & el_type, const GhostType & ghost_type) const;
inline UInt getNbComponent(const std::string 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 std::string & name) const;
template<typename T>
ElementTypeMapArray<T> & getElementalData(const std::string & name);
private:
/// Register new elemental data (add alloc data)
template<typename T>
ElementTypeMapArray<T> * allocElementalData(const std::string & 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;
};
#include "mesh_data_tmpl.hh"
#undef AKANTU_MESH_DATA_TUPLE_FIRST_ELEM
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MESH_DATA_HH__ */
diff --git a/src/mesh/mesh_data_tmpl.hh b/src/mesh/mesh_data_tmpl.hh
index 27343db0f..17fb098ac 100644
--- a/src/mesh/mesh_data_tmpl.hh
+++ b/src/mesh/mesh_data_tmpl.hh
@@ -1,218 +1,218 @@
/**
* @file mesh_data_tmpl.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/>.
*
*/
-__END_AKANTU__
+} // akantu
#include <iostream>
#define MESH_DATA_GET_TYPE(r, data, type) \
template<> \
inline MeshDataTypeCode MeshData::getTypeCode<BOOST_PP_TUPLE_ELEM(2, 1, type)>() const { \
return BOOST_PP_TUPLE_ELEM(2, 0, type); \
}
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
// get the type of the data stored in elemental_data
template<typename T>
inline MeshDataTypeCode MeshData::getTypeCode() const {
AKANTU_DEBUG_ERROR("Type " << debug::demangle(typeid(T).name()) << "not implemented by MeshData.");
}
/* -------------------------------------------------------------------------- */
BOOST_PP_SEQ_FOR_EACH(MESH_DATA_GET_TYPE, void, AKANTU_MESH_DATA_TYPES)
#undef MESH_DATA_GET_TYPE
inline MeshDataTypeCode MeshData::getTypeCode(const std::string name) const {
TypeCodeMap::const_iterator it = typecode_map.find(name);
if(it == typecode_map.end()) AKANTU_EXCEPTION("No dataset named " << name << " found.");
return it->second;
}
/* -------------------------------------------------------------------------- */
// Register new elemental data templated (and alloc data) with check if the name is new
template<typename T>
void MeshData::registerElementalData(const std::string & name) {
ElementalDataMap::iterator it = elemental_data.find(name);
if(it == elemental_data.end()) {
allocElementalData<T>(name);
} else{
AKANTU_DEBUG_INFO("Data named " << name << " already registered.");
}
}
/* -------------------------------------------------------------------------- */
// Register new elemental data of a given MeshDataTypeCode with check if the name is new
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem) : { registerElementalData<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(name); break; }
inline void MeshData::registerElementalData(const std::string & name, MeshDataTypeCode type) {
switch(type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, name, AKANTU_MESH_DATA_TYPES)
default : AKANTU_DEBUG_ERROR("Type " << type << "not implemented by MeshData.");
}
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
/// Register new elemental data (and alloc data)
template<typename T>
ElementTypeMapArray<T> * MeshData::allocElementalData(const std::string & name) {
ElementTypeMapArray<T> * dataset = new ElementTypeMapArray<T>(name, id, memory_id);
elemental_data[name] = dataset;
typecode_map[name] = getTypeCode<T>();
return dataset;
}
/* -------------------------------------------------------------------------- */
template<typename T>
const ElementTypeMapArray<T> & MeshData::getElementalData(const std::string & name) const {
ElementalDataMap::const_iterator it = elemental_data.find(name);
if(it == elemental_data.end()) AKANTU_EXCEPTION("No dataset named " << name << " found.");
return dynamic_cast<const ElementTypeMapArray<T> &>(*(it->second));
}
/* -------------------------------------------------------------------------- */
// Get an existing elemental data
template<typename T>
ElementTypeMapArray<T> & MeshData::getElementalData(const std::string & name) {
ElementalDataMap::iterator it = elemental_data.find(name);
if(it == elemental_data.end()) AKANTU_EXCEPTION("No dataset named " << name << " found.");
return dynamic_cast<ElementTypeMapArray<T> &>(*(it->second));
}
/* -------------------------------------------------------------------------- */
// Get an existing elemental data array for an element type
template<typename T>
const Array<T> & MeshData::getElementalDataArray(const std::string & name,
const ElementType & elem_type,
const GhostType & ghost_type) const {
ElementalDataMap::const_iterator it = elemental_data.find(name);
if(it == elemental_data.end()) {
AKANTU_EXCEPTION("Data named " << name << " not registered for type: " << elem_type << " - ghost_type:" << ghost_type << "!");
}
return dynamic_cast<const ElementTypeMapArray<T> &>(*(it->second))(elem_type, ghost_type);
}
template<typename T>
Array<T> & MeshData::getElementalDataArray(const std::string & name,
const ElementType & elem_type,
const GhostType & ghost_type) {
ElementalDataMap::iterator it = elemental_data.find(name);
if(it == elemental_data.end()) {
AKANTU_EXCEPTION("Data named " << name << " not registered for type: " << elem_type << " - ghost_type:" << ghost_type << "!");
}
return dynamic_cast<ElementTypeMapArray<T> &>(*(it->second))(elem_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
// Get an elemental data array, if it does not exist: allocate it
template<typename T>
Array<T> & MeshData::getElementalDataArrayAlloc(const std::string & name,
const ElementType & elem_type,
const GhostType & ghost_type,
UInt nb_component) {
ElementalDataMap::iterator it = elemental_data.find(name);
ElementTypeMapArray<T> * dataset;
if(it == elemental_data.end()) {
dataset = allocElementalData<T>(name);
} else {
dataset = dynamic_cast<ElementTypeMapArray<T> *>(it->second);
}
AKANTU_DEBUG_ASSERT(getTypeCode<T>() == typecode_map.find(name)->second, "Function getElementalDataArrayAlloc called with the wrong type!");
if(!(dataset->exists(elem_type, ghost_type))) {
dataset->alloc(0, nb_component, elem_type, ghost_type);
}
return (*dataset)(elem_type, ghost_type);
}
/* -------------------------------------------------------------------------- */
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem) : { \
nb_comp = getNbComponentTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(name, el_type, ghost_type); \
break; \
} \
inline UInt MeshData::getNbComponent(const std::string name, const ElementType & el_type, const GhostType & ghost_type) const {
TypeCodeMap::const_iterator it = typecode_map.find(name);
UInt nb_comp(0);
if(it == typecode_map.end()) {
AKANTU_EXCEPTION("Could not determine the type held in dataset " << name << " for type: " << el_type << " - ghost_type:" << ghost_type << ".");
}
MeshDataTypeCode type = it->second;
switch(type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, name, AKANTU_MESH_DATA_TYPES)
default : AKANTU_DEBUG_ERROR("Could not call the correct instance of getNbComponentTemplated."); break;
}
return nb_comp;
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
template<typename T>
inline UInt MeshData::getNbComponentTemplated(const std::string name, const ElementType & el_type, const GhostType & ghost_type) const {
return getElementalDataArray<T>(name, el_type, ghost_type).getNbComponent();
}
/* -------------------------------------------------------------------------- */
// get the names of the data stored in elemental_data
#define AKANTU_MESH_DATA_CASE_MACRO(r, name, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem) : { \
ElementTypeMapArray<BOOST_PP_TUPLE_ELEM(2, 1, elem)> * dataset; \
dataset = dynamic_cast< ElementTypeMapArray<BOOST_PP_TUPLE_ELEM(2, 1, elem)> * >(it->second); \
exists = dataset->exists(el_type, ghost_type); \
break; \
} \
inline void MeshData::getTagNames(StringVector & tags, const ElementType & el_type, const GhostType & ghost_type) const {
tags.clear();
bool exists(false);
ElementalDataMap::const_iterator it = elemental_data.begin();
ElementalDataMap::const_iterator it_end = elemental_data.end();
for(; it != it_end; ++it) {
MeshDataTypeCode type = getTypeCode(it->first);
switch(type) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_MESH_DATA_CASE_MACRO, , AKANTU_MESH_DATA_TYPES)
default : AKANTU_DEBUG_ERROR("Could not determine the proper type to (dynamic-)cast."); break;
}
if(exists) {
tags.push_back(it->first);
}
}
}
#undef AKANTU_MESH_DATA_CASE_MACRO
/* -------------------------------------------------------------------------- */
diff --git a/src/mesh/mesh_events.hh b/src/mesh/mesh_events.hh
index 2a3fd8855..bb0cb2539 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__
-__BEGIN_AKANTU__
+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(){};
};
/// akantu::MeshEvent related to nodes removed from the mesh
class RemovedNodesEvent : public MeshEvent<UInt> {
public:
virtual ~RemovedNodesEvent(){};
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(){};
};
/// akantu::MeshEvent related to elements removed from the mesh
class RemovedElementsEvent : public MeshEvent<Element> {
public:
virtual ~RemovedElementsEvent(){};
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(){};
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;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MESH_EVENTS_HH__ */
diff --git a/src/mesh/mesh_filter.hh b/src/mesh/mesh_filter.hh
index fcd25618d..9b812fbe4 100644
--- a/src/mesh/mesh_filter.hh
+++ b/src/mesh/mesh_filter.hh
@@ -1,75 +1,75 @@
/**
* @file mesh_filter.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Dec 18 2015
*
* @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_FILTER_HH__
#define __AKANTU_MESH_FILTER_HH__
/* -------------------------------------------------------------------------- */
#include "element.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* Filter Functors */
/* -------------------------------------------------------------------------- */
/// struct for the possible filter functors
struct FilterFunctor {
enum Type { _node_filter_functor, _element_filter_functor };
};
/// class (functor) for the node filter
class NodeFilterFunctor : public FilterFunctor {
public:
bool operator()(__attribute__((unused)) UInt node) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
public:
static const Type type = _node_filter_functor;
};
/// class (functor) for the element filter
class ElementFilterFunctor : public FilterFunctor {
public:
bool operator()(__attribute__((unused)) const Element & element) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
public:
static const Type type = _element_filter_functor;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MESH_FILTER_HH__ */
diff --git a/src/mesh/mesh_inline_impl.cc b/src/mesh/mesh_inline_impl.cc
index 506027a8e..3e74a8532 100644
--- a/src/mesh/mesh_inline_impl.cc
+++ b/src/mesh/mesh_inline_impl.cc
@@ -1,630 +1,630 @@
/**
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_COHESIVE_ELEMENT)
#include "cohesive_element.hh"
#endif
#ifndef __AKANTU_MESH_INLINE_IMPL_CC__
#define __AKANTU_MESH_INLINE_IMPL_CC__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
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<RemovedElementsEvent>(RemovedElementsEvent & event) {
this->connectivities.onElementsRemoved(event.getNewNumbering());
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <>
inline void Mesh::sendEvent<RemovedNodesEvent>(RemovedNodesEvent & event) {
if (created_nodes)
this->removeNodesFromArray(*nodes, event.getNewNumbering());
if (nodes_global_ids)
this->removeNodesFromArray(*nodes_global_ids, event.getNewNumbering());
if (nodes_type.getSize() != 0)
this->removeNodesFromArray(nodes_type, event.getNewNumbering());
EventHandlerManager<MeshEventHandler>::sendEvent(event);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Mesh::removeNodesFromArray(Array<T> & vect,
const Array<UInt> & new_numbering) {
Array<T> tmp(vect.getSize(), vect.getNbComponent());
UInt nb_component = vect.getNbComponent();
UInt new_nb_nodes = 0;
for (UInt i = 0; i < new_numbering.getSize(); ++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 UInt Mesh::elementToLinearized(const Element & elem) const {
AKANTU_DEBUG_ASSERT(elem.type < _max_element_type &&
elem.element < types_offsets.storage()[elem.type + 1],
"The element " << elem << "does not exists in the mesh "
<< getID());
return types_offsets.storage()[elem.type] + elem.element;
}
/* -------------------------------------------------------------------------- */
inline Element Mesh::linearizedToElement(UInt linearized_element) const {
UInt t;
for (t = _not_defined;
t != _max_element_type && linearized_element >= types_offsets(t); ++t)
;
AKANTU_DEBUG_ASSERT(linearized_element < types_offsets(t),
"The linearized element "
<< linearized_element
<< "does not exists in the mesh " << getID());
--t;
ElementType type = ElementType(t);
return Element(type, linearized_element - types_offsets.storage()[t],
_not_ghost, getKind(type));
}
/* -------------------------------------------------------------------------- */
inline void Mesh::updateTypesOffsets(const GhostType & ghost_type) {
Array<UInt> * types_offsets_ptr = &this->types_offsets;
if (ghost_type == _ghost)
types_offsets_ptr = &this->ghost_types_offsets;
Array<UInt> & types_offsets = *types_offsets_ptr;
types_offsets.clear();
for (auto type : elementTypes(_all_dimensions, ghost_type, _ek_not_defined))
types_offsets(type) = connectivities(type, ghost_type).getSize();
for (UInt t = _not_defined + 1; t < _max_element_type; ++t)
types_offsets(t) += types_offsets(t - 1);
for (UInt t = _max_element_type; t > _not_defined; --t)
types_offsets(t) = types_offsets(t - 1);
types_offsets(0) = 0;
}
/* -------------------------------------------------------------------------- */
inline const Mesh::ConnectivityTypeList &
Mesh::getConnectivityTypeList(const GhostType & ghost_type) const {
if (ghost_type == _not_ghost)
return type_set;
else
return ghost_type_set;
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> * Mesh::getNodesGlobalIdsPointer() {
AKANTU_DEBUG_IN();
if (nodes_global_ids == NULL) {
std::stringstream sstr;
sstr << getID() << ":nodes_global_ids";
nodes_global_ids = &(alloc<UInt>(sstr.str(), nodes->getSize(), 1));
for (UInt i = 0; i < nodes->getSize(); ++i) {
(*nodes_global_ids)(i) = i;
}
}
AKANTU_DEBUG_OUT();
return nodes_global_ids;
}
/* -------------------------------------------------------------------------- */
inline Array<NodeType> * Mesh::getNodesTypePointer() {
AKANTU_DEBUG_IN();
if (nodes_type.getSize() == 0) {
nodes_type.resize(nodes->getSize());
nodes_type.set(_nt_normal);
}
AKANTU_DEBUG_OUT();
return &nodes_type;
}
/* -------------------------------------------------------------------------- */
inline Array<UInt> *
Mesh::getConnectivityPointer(const ElementType & type,
const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> * tmp;
if (!connectivities.exists(type, ghost_type)) {
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
tmp = &(connectivities.alloc(0, nb_nodes_per_element, type, ghost_type));
AKANTU_DEBUG_INFO("The connectivity vector for the type " << type
<< " created");
if (ghost_type == _not_ghost)
type_set.insert(type);
else
ghost_type_set.insert(type);
updateTypesOffsets(ghost_type);
} else {
tmp = &connectivities(type, ghost_type);
}
AKANTU_DEBUG_OUT();
return tmp;
}
/* -------------------------------------------------------------------------- */
inline Array<std::vector<Element>> *
Mesh::getElementToSubelementPointer(const ElementType & type,
const GhostType & ghost_type) {
Array<std::vector<Element>> * tmp = getDataPointer<std::vector<Element>>(
"element_to_subelement", type, ghost_type, 1, true);
return tmp;
}
/* -------------------------------------------------------------------------- */
inline Array<Element> *
Mesh::getSubelementToElementPointer(const ElementType & type,
const GhostType & ghost_type) {
Array<Element> * tmp = getDataPointer<Element>(
"subelement_to_element", type, ghost_type, getNbFacetsPerElement(type),
true, is_mesh_facets);
return tmp;
}
/* -------------------------------------------------------------------------- */
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 std::string & 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 const Array<T> & Mesh::getData(const std::string & 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 std::string & 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 std::string & data_name) const {
return mesh_data.getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> & Mesh::getData(const std::string & data_name) {
return mesh_data.getElementalData<T>(data_name);
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMapArray<T> &
Mesh::registerData(const std::string & 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.getSize();
} 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.getSize() ? (nodes_type(n) == _nt_pure_gost) : false;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalOrMasterNode(UInt n) const {
return nodes_type.getSize()
? (nodes_type(n) == _nt_master) || (nodes_type(n) == _nt_normal)
: true;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isLocalNode(UInt n) const {
return nodes_type.getSize() ? nodes_type(n) == _nt_normal : true;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isMasterNode(UInt n) const {
return nodes_type.getSize() ? nodes_type(n) == _nt_master : false;
}
/* -------------------------------------------------------------------------- */
inline bool Mesh::isSlaveNode(UInt n) const {
return nodes_type.getSize() ? nodes_type(n) >= 0 : false;
}
/* -------------------------------------------------------------------------- */
inline NodeType Mesh::getNodeType(UInt local_id) const {
return nodes_type.getSize() ? 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.");
return nodes_global_ids->find(global_id);
}
/* -------------------------------------------------------------------------- */
inline UInt Mesh::getNbGlobalNodes() const {
return nodes_global_ids ? nb_global_nodes : nodes->getSize();
}
/* -------------------------------------------------------------------------- */
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;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MESH_INLINE_IMPL_CC__ */
diff --git a/src/mesh/node_group.cc b/src/mesh/node_group.cc
index 5bb93cec5..df513dd9e 100644
--- a/src/mesh/node_group.cc
+++ b/src/mesh/node_group.cc
@@ -1,111 +1,111 @@
/**
* @file node_group.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief Implementation of the node group
*
* @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 "node_group.hh"
#include "dumpable.hh"
#include "dumpable_inline_impl.hh"
#include "mesh.hh"
#if defined(AKANTU_USE_IOHELPER)
# include "dumper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NodeGroup::NodeGroup(const std::string & name,
const Mesh & mesh,
const std::string & id,
const MemoryID & memory_id) :
Memory(id, memory_id),
name(name),
node_group(alloc<UInt>(std::string(this->id + ":nodes"), 0, 1))//,
// mesh(mesh)
{
#if defined(AKANTU_USE_IOHELPER)
this->registerDumper<DumperParaview>("paraview_" + name, name, true);
this->getDumper().registerField("positions",new dumper::NodalField<Real,true>(
mesh.getNodes(),
0,
0,
&this->getNodes()));
#endif
}
/* -------------------------------------------------------------------------- */
NodeGroup::~NodeGroup() {}
/* -------------------------------------------------------------------------- */
void NodeGroup::empty() {
node_group.resize(0);
}
/* -------------------------------------------------------------------------- */
void NodeGroup::optimize() {
std::sort(node_group.begin(), node_group.end());
Array<UInt>::iterator<> end = std::unique(node_group.begin(), node_group.end());
node_group.resize(end - node_group.begin());
}
/* -------------------------------------------------------------------------- */
void NodeGroup::append(const NodeGroup & other_group) {
AKANTU_DEBUG_IN();
UInt nb_nodes = node_group.getSize();
/// append new nodes to current list
node_group.resize(nb_nodes + other_group.node_group.getSize());
std::copy(other_group.node_group.begin(),
other_group.node_group.end(),
node_group.begin() + nb_nodes);
optimize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeGroup::printself(std::ostream & stream, int indent) const {
std::string space;
for(Int i = 0; i < indent; i++, space += AKANTU_INDENT);
stream << space << "NodeGroup [" << std::endl;
stream << space << " + name: " << name << std::endl;
node_group.printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh/node_group.hh b/src/mesh/node_group.hh
index c783039e7..a1602815a 100644
--- a/src/mesh/node_group.hh
+++ b/src/mesh/node_group.hh
@@ -1,137 +1,137 @@
/**
* @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__
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* 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);
/// 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 getSize() 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;
}
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "node_group_inline_impl.cc"
#endif /* __AKANTU_NODE_GROUP_HH__ */
diff --git a/src/mesh/node_group_inline_impl.cc b/src/mesh/node_group_inline_impl.cc
index e3e0fe046..5a4a22330 100644
--- a/src/mesh/node_group_inline_impl.cc
+++ b/src/mesh/node_group_inline_impl.cc
@@ -1,102 +1,102 @@
/**
* @file node_group_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief Node group inline function definitions
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::begin() const {
return node_group.begin();
}
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::end() const {
return node_group.end();
}
/* -------------------------------------------------------------------------- */
inline NodeGroup::const_node_iterator NodeGroup::add(UInt node, bool check_for_duplicate) {
if(check_for_duplicate) {
const_node_iterator it = std::find(begin(), end(), node);
if(it == node_group.end()) {
node_group.push_back(node);
return (node_group.end() - 1);
}
return it;
} else {
node_group.push_back(node);
return (node_group.end() - 1);
}
}
/* -------------------------------------------------------------------------- */
inline void NodeGroup::remove(UInt node) {
Array<UInt>::iterator<> it = this->node_group.begin();
Array<UInt>::iterator<> end = this->node_group.end();
AKANTU_DEBUG_ASSERT(it != end, "The node group is empty!!");
for (; it != node_group.end(); ++it) {
if (*it == node) {
it = node_group.erase(it);
}
}
AKANTU_DEBUG_ASSERT(it != end, "The node was not found!");
}
/* -------------------------------------------------------------------------- */
inline UInt NodeGroup::getSize() const {
return node_group.getSize();
}
/* -------------------------------------------------------------------------- */
struct FilterFunctor;
template <typename T>
void NodeGroup::applyNodeFilter(T & filter) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(T::type == FilterFunctor::_node_filter_functor,
"NodeFilter can only apply node filter functor");
Array<UInt>::iterator<> it = this->node_group.begin();
for (; it != node_group.end(); ++it) {
/// filter == true -> keep node
if (!filter(*it)) {
it = node_group.erase(it);
}
}
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh_utils/cohesive_element_inserter.cc b/src/mesh_utils/cohesive_element_inserter.cc
index 7678abca9..c069c2639 100644
--- a/src/mesh_utils/cohesive_element_inserter.cc
+++ b/src/mesh_utils/cohesive_element_inserter.cc
@@ -1,438 +1,438 @@
/**
* @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 <algorithm>
#include <limits>
#include "cohesive_element_inserter.hh"
#include "element_group.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
CohesiveElementInserter::CohesiveElementInserter(Mesh & mesh,
bool is_extrinsic,
ElementSynchronizer * synchronizer,
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, synchronizer);
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
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) {
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.getSize();
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 (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) {
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);
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"));
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.element_begin
(type_facet, ghost_type));
el_it!= group.element_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) {
NewNodesEvent node_event;
node_event.getList().extendComponentsInterlaced(2, 1);
NewElementsEvent element_event;
UInt nb_new_elements = MeshUtils::insertCohesiveElements(mesh,
mesh_facets,
insertion_facets,
node_event.getList(),
element_event.getList(),
only_double_facets);
UInt nb_new_nodes = node_event.getList().getSize();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (mesh.getNodesType().getSize()) {
/// 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
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
comm.allReduce(&nb_new_elements, 1, _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.getNodesType().getSize()) {
/// 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.getSize();
for (UInt f = 0; f < ins_facets.getSize(); ++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;
}
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh_utils/cohesive_element_inserter.hh b/src/mesh_utils/cohesive_element_inserter.hh
index d64517497..5f343b633 100644
--- a/src/mesh_utils/cohesive_element_inserter.hh
+++ b/src/mesh_utils/cohesive_element_inserter.hh
@@ -1,209 +1,209 @@
/**
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
#define __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__
/* -------------------------------------------------------------------------- */
#include <numeric>
#include "data_accessor.hh"
#include "mesh_utils.hh"
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
# include "global_ids_updater.hh"
# include "facet_synchronizer.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class CohesiveElementInserter : public DataAccessor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
CohesiveElementInserter(Mesh & mesh,
bool is_extrinsic = false,
ElementSynchronizer * synchronizer = NULL,
const ID & id = "cohesive_element_inserter");
virtual ~CohesiveElementInserter();
/* ------------------------------------------------------------------------ */
/* 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();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
/// 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 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);
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;
#endif
/* ------------------------------------------------------------------------ */
/* 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;
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
/// facet synchronizer
FacetSynchronizer * facet_synchronizer;
/// global connectivity ids updater
GlobalIdsUpdater * global_ids_updater;
#endif
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
# include "cohesive_element_inserter_inline_impl.cc"
#endif
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const CohesiveElementInserter & _this)
{
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_COHESIVE_ELEMENT_INSERTER_HH__ */
diff --git a/src/mesh_utils/global_ids_updater.cc b/src/mesh_utils/global_ids_updater.cc
index a87489d75..92e86dd74 100644
--- a/src/mesh_utils/global_ids_updater.cc
+++ b/src/mesh_utils/global_ids_updater.cc
@@ -1,59 +1,59 @@
/**
* @file global_ids_updater.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Apr 13 2012
* @date last modification: Fri Oct 02 2015
*
* @brief Functions of the GlobalIdsUpdater
*
* @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 "global_ids_updater.hh"
#include "mesh_utils.hh"
#include "element_synchronizer.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
UInt GlobalIdsUpdater::updateGlobalIDs(UInt old_nb_nodes) {
UInt total_nb_new_nodes = this->updateGlobalIDsLocally(old_nb_nodes);
this->synchronizeGlobalIDs();
return total_nb_new_nodes;
}
UInt GlobalIdsUpdater::updateGlobalIDsLocally(UInt old_nb_nodes) {
UInt total_nb_new_nodes = MeshUtils::updateLocalMasterGlobalConnectivity(mesh, old_nb_nodes);
return total_nb_new_nodes;
}
void GlobalIdsUpdater::synchronizeGlobalIDs() {
this->synchronizer->computeBufferSize(*this, _gst_giu_global_conn);
this->synchronizer->asynchronousSynchronize(*this, _gst_giu_global_conn);
this->synchronizer->waitEndSynchronize(*this, _gst_giu_global_conn);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh_utils/global_ids_updater_inline_impl.cc b/src/mesh_utils/global_ids_updater_inline_impl.cc
index 73132a490..4976cc9e0 100644
--- a/src/mesh_utils/global_ids_updater_inline_impl.cc
+++ b/src/mesh_utils/global_ids_updater_inline_impl.cc
@@ -1,132 +1,132 @@
/**
* @file global_ids_updater_inline_impl.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Oct 02 2015
* @date last modification: Sun Oct 04 2015
*
* @brief Implementation of the inline functions of GlobalIdsUpdater
*
* @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 "global_ids_updater.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_CC__
#define __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_CC__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt GlobalIdsUpdater::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
UInt size = 0;
if (elements.getSize() == 0)
return size;
if (tag == _gst_giu_global_conn)
size += Mesh::getNbNodesPerElementList(elements) * sizeof(UInt);
return size;
}
/* -------------------------------------------------------------------------- */
inline void GlobalIdsUpdater::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_giu_global_conn)
packUnpackGlobalConnectivity<true>(buffer, elements);
}
/* -------------------------------------------------------------------------- */
inline void GlobalIdsUpdater::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == _gst_giu_global_conn)
packUnpackGlobalConnectivity<false>(buffer, elements);
}
/* -------------------------------------------------------------------------- */
template <bool pack_mode>
inline void GlobalIdsUpdater::packUnpackGlobalConnectivity(
CommunicationBuffer & buffer, const Array<Element> & elements) const {
AKANTU_DEBUG_IN();
ElementType current_element_type = _not_defined;
GhostType current_ghost_type = _casper;
Array<UInt>::const_vector_iterator conn_begin;
UInt nb_nodes_per_elem = 0;
UInt index;
Array<UInt> & global_nodes_ids = mesh.getGlobalNodesIds();
Array<Element>::const_scalar_iterator it = elements.begin();
Array<Element>::const_scalar_iterator 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;
const Array<UInt> & connectivity =
mesh.getConnectivity(current_element_type, current_ghost_type);
nb_nodes_per_elem = connectivity.getNbComponent();
conn_begin = connectivity.begin(nb_nodes_per_elem);
}
/// get element connectivity
const Vector<UInt> current_conn = conn_begin[el.element];
/// loop on all connectivity nodes
for (UInt n = 0; n < nb_nodes_per_elem; ++n) {
UInt node = current_conn(n);
if (pack_mode) {
/// if node is local or master pack its global id, otherwise
/// dummy data
if (mesh.isLocalOrMasterNode(node))
index = global_nodes_ids(node);
else
index = UInt(-1);
buffer << index;
} else {
buffer >> index;
/// update slave nodes' index
if (index != UInt(-1) && mesh.isSlaveNode(node))
global_nodes_ids(node) = index;
}
}
}
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_GLOBAL_IDS_UPDATER_INLINE_IMPL_CC__ */
diff --git a/src/mesh_utils/mesh_partition.cc b/src/mesh_utils/mesh_partition.cc
index 27e60375a..648214182 100644
--- a/src/mesh_utils/mesh_partition.cc
+++ b/src/mesh_utils/mesh_partition.cc
@@ -1,441 +1,441 @@
/**
* @file mesh_partition.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 17 2010
* @date last modification: Fri Jan 22 2016
*
* @brief implementation of common part of all partitioner
*
* @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_partition.hh"
#include "mesh_utils.hh"
#include "aka_types.hh"
/* -------------------------------------------------------------------------- */
#include <unordered_map>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
MeshPartition::MeshPartition(const Mesh & mesh, UInt spatial_dimension,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), mesh(mesh), spatial_dimension(spatial_dimension),
partitions("partition", id, memory_id),
ghost_partitions("ghost_partition", id, memory_id),
ghost_partitions_offset("ghost_partition_offset", id, memory_id),
saved_connectivity("saved_connectivity", id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MeshPartition::~MeshPartition() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* TODO this function should most probably be rewritten in a more modern way
* conversion in c++ of the GENDUALMETIS (mesh.c) function wrote by George in
* Metis (University of Minnesota)
*/
void MeshPartition::buildDualGraph(Array<Int> & dxadj, Array<Int> & dadjncy,
Array<Int> & edge_loads,
const EdgeLoadFunctor & edge_load_func) {
AKANTU_DEBUG_IN();
// tweak mesh;
const Mesh::ConnectivityTypeList & type_list = mesh.getConnectivityTypeList();
UInt nb_types = type_list.size();
UInt nb_good_types = 0;
Vector<UInt> nb_nodes_per_element_p1(nb_types);
Vector<UInt> magic_number(nb_types);
// UInt * conn_val[nb_types];
Vector<UInt> nb_element(nb_types);
Array<UInt> ** conn = new Array<UInt> *[nb_types];
Array<Element> lin_to_element;
Element elem;
elem.ghost_type = _not_ghost;
const_cast<Mesh &>(mesh).updateTypesOffsets(_not_ghost);
const_cast<Mesh &>(mesh).updateTypesOffsets(_ghost);
Mesh::ConnectivityTypeList::const_iterator it;
for (it = type_list.begin(); it != type_list.end(); ++it) {
ElementType type = *it;
if (Mesh::getSpatialDimension(type) != mesh.getSpatialDimension())
continue;
elem.type = type;
ElementType type_p1 = Mesh::getP1ElementType(type);
nb_nodes_per_element_p1[nb_good_types] =
Mesh::getNbNodesPerElement(type_p1);
nb_element[nb_good_types] =
mesh.getConnectivity(type, _not_ghost).getSize();
magic_number[nb_good_types] =
Mesh::getNbNodesPerElement(Mesh::getFacetType(type_p1));
conn[nb_good_types] =
&const_cast<Array<UInt> &>(mesh.getConnectivity(type, _not_ghost));
for (UInt i = 0; i < nb_element[nb_good_types]; ++i) {
elem.element = i;
lin_to_element.push_back(elem);
}
nb_good_types++;
}
CSR<UInt> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem);
UInt nb_total_element = 0;
UInt nb_total_node_element = 0;
for (UInt t = 0; t < nb_good_types; ++t) {
nb_total_element += nb_element[t];
nb_total_node_element += nb_element[t] * nb_nodes_per_element_p1[t];
}
dxadj.resize(nb_total_element + 1);
/// initialize the dxadj array
for (UInt t = 0, linerized_el = 0; t < nb_good_types; ++t)
for (UInt el = 0; el < nb_element[t]; ++el, ++linerized_el)
dxadj(linerized_el) = nb_nodes_per_element_p1[t];
/// convert the dxadj_val array in a csr one
for (UInt i = 1; i < nb_total_element; ++i)
dxadj(i) += dxadj(i - 1);
for (UInt i = nb_total_element; i > 0; --i)
dxadj(i) = dxadj(i - 1);
dxadj(0) = 0;
dadjncy.resize(2 * dxadj(nb_total_element));
edge_loads.resize(2 * dxadj(nb_total_element));
/// weight map to determine adjacency
std::unordered_map<UInt, UInt> weight_map;
for (UInt t = 0, linerized_el = 0; t < nb_good_types; ++t) {
for (UInt el = 0; el < nb_element[t]; ++el, ++linerized_el) {
/// fill the weight map
for (UInt n = 0; n < nb_nodes_per_element_p1[t]; ++n) {
UInt node = (*conn[t])(el, n);
CSR<UInt>::iterator k;
for (k = node_to_elem.rbegin(node); k != node_to_elem.rend(node); --k) {
UInt current_el = *k;
if (current_el <= linerized_el)
break;
auto it_w = weight_map.find(current_el);
if (it_w == weight_map.end()) {
weight_map[current_el] = 1;
} else {
it_w->second++;
}
}
}
/// each element with a weight of the size of a facet are adjacent
for (auto it_w = weight_map.begin(); it_w != weight_map.end(); ++it_w) {
if (it_w->second == magic_number[t]) {
UInt adjacent_el = it_w->first;
#if defined(AKANTU_COHESIVE_ELEMENT)
/// Patch in order to prevent neighboring cohesive elements
/// from detecting each other
ElementKind linearized_el_kind =
mesh.linearizedToElement(linerized_el).kind;
ElementKind adjacent_el_kind =
mesh.linearizedToElement(adjacent_el).kind;
if (linearized_el_kind == adjacent_el_kind &&
linearized_el_kind == _ek_cohesive)
continue;
#endif
UInt index_adj = dxadj(adjacent_el)++;
UInt index_lin = dxadj(linerized_el)++;
dadjncy(index_lin) = adjacent_el;
dadjncy(index_adj) = linerized_el;
}
}
weight_map.clear();
}
}
Int k_start = 0;
for (UInt t = 0, linerized_el = 0, j = 0; t < nb_good_types; ++t)
for (UInt el = 0; el < nb_element[t]; ++el, ++linerized_el) {
for (Int k = k_start; k < dxadj(linerized_el); ++k, ++j)
dadjncy(j) = dadjncy(k);
dxadj(linerized_el) = j;
k_start += nb_nodes_per_element_p1[t];
}
for (UInt i = nb_total_element; i > 0; --i)
dxadj(i) = dxadj(i - 1);
dxadj(0) = 0;
UInt adj = 0;
for (UInt i = 0; i < nb_total_element; ++i) {
UInt nb_adj = dxadj(i + 1) - dxadj(i);
for (UInt j = 0; j < nb_adj; ++j, ++adj) {
Int el_adj_id = dadjncy(dxadj(i) + j);
Element el = lin_to_element(i);
Element el_adj = lin_to_element(el_adj_id);
Int load = edge_load_func(el, el_adj);
edge_loads(adj) = load;
}
}
delete [] conn;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::fillPartitionInformation(
const Mesh & mesh, const Int * linearized_partitions) {
AKANTU_DEBUG_IN();
CSR<UInt> node_to_elem;
MeshUtils::buildNode2Elements(mesh, node_to_elem);
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, _not_ghost, _ek_not_defined);
Mesh::type_iterator end =
mesh.lastType(spatial_dimension, _not_ghost, _ek_not_defined);
UInt linearized_el = 0;
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
partitions.alloc(nb_element, 1, type, _not_ghost);
CSR<UInt> & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
ghost_part_csr.resizeRows(nb_element);
ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
ghost_partitions.alloc(0, 1, type, _ghost);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
UInt part = linearized_partitions[linearized_el];
partitions(type, _not_ghost)(el) = part;
std::list<UInt> list_adj_part;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity.storage()[el * nb_nodes_per_element + n];
CSR<UInt>::iterator ne;
for (ne = node_to_elem.begin(node); ne != node_to_elem.end(node);
++ne) {
UInt adj_el = *ne;
UInt adj_part = linearized_partitions[adj_el];
if (part != adj_part) {
list_adj_part.push_back(adj_part);
}
}
}
list_adj_part.sort();
list_adj_part.unique();
for (std::list<UInt>::iterator adj_it = list_adj_part.begin();
adj_it != list_adj_part.end(); ++adj_it) {
ghost_part_csr.getRows().push_back(*adj_it);
ghost_part_csr.rowOffset(el)++;
ghost_partitions(type, _ghost).push_back(*adj_it);
ghost_partitions_offset(type, _ghost)(el)++;
}
}
ghost_part_csr.countToCSR();
/// convert the ghost_partitions_offset array in an offset array
Array<UInt> & ghost_partitions_offset_ptr =
ghost_partitions_offset(type, _ghost);
for (UInt i = 1; i < nb_element; ++i)
ghost_partitions_offset_ptr(i) += ghost_partitions_offset_ptr(i - 1);
for (UInt i = nb_element; i > 0; --i)
ghost_partitions_offset_ptr(i) = ghost_partitions_offset_ptr(i - 1);
ghost_partitions_offset_ptr(0) = 0;
}
// All Facets
for (Int sp = spatial_dimension - 1; sp >= 0; --sp) {
Mesh::type_iterator fit = mesh.firstType(sp, _not_ghost, _ek_not_defined);
Mesh::type_iterator fend = mesh.lastType(sp, _not_ghost, _ek_not_defined);
for (; fit != fend; ++fit) {
ElementType type = *fit;
UInt nb_element = mesh.getNbElement(type);
partitions.alloc(nb_element, 1, type, _not_ghost);
AKANTU_DEBUG_INFO("Allocating partitions for " << type);
CSR<UInt> & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
ghost_part_csr.resizeRows(nb_element);
ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
ghost_partitions.alloc(0, 1, type, _ghost);
AKANTU_DEBUG_INFO("Allocating ghost_partitions for " << type);
const Array<std::vector<Element> > & elem_to_subelem =
mesh.getElementToSubelement(type, _not_ghost);
for (UInt i(0); i < mesh.getNbElement(type, _not_ghost);
++i) { // Facet loop
const std::vector<Element> & adjacent_elems = elem_to_subelem(i);
if (!adjacent_elems.empty()) {
Element min_elem;
UInt min_part(std::numeric_limits<UInt>::max());
std::set<UInt> adjacent_parts;
for (UInt j(0); j < adjacent_elems.size(); ++j) {
UInt adjacent_elem_id = adjacent_elems[j].element;
UInt adjacent_elem_part =
partitions(adjacent_elems[j].type,
adjacent_elems[j].ghost_type)(adjacent_elem_id);
if (adjacent_elem_part < min_part) {
min_part = adjacent_elem_part;
min_elem = adjacent_elems[j];
}
adjacent_parts.insert(adjacent_elem_part);
}
partitions(type, _not_ghost)(i) = min_part;
CSR<UInt>::iterator git =
ghost_partitions_csr(min_elem.type, _not_ghost)
.begin(min_elem.element);
CSR<UInt>::iterator gend =
ghost_partitions_csr(min_elem.type, _not_ghost)
.end(min_elem.element);
for (; git != gend; ++git) {
adjacent_parts.insert(*git);
}
adjacent_parts.erase(min_part);
std::set<UInt>::const_iterator pit = adjacent_parts.begin();
std::set<UInt>::const_iterator pend = adjacent_parts.end();
for (; pit != pend; ++pit) {
ghost_part_csr.getRows().push_back(*pit);
ghost_part_csr.rowOffset(i)++;
ghost_partitions(type, _ghost).push_back(*pit);
}
ghost_partitions_offset(type, _ghost)(i + 1) =
ghost_partitions_offset(type, _ghost)(i + 1) +
adjacent_elems.size();
} else {
partitions(type, _not_ghost)(i) = 0;
}
}
ghost_part_csr.countToCSR();
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::tweakConnectivity(const Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
if (pairs.getSize() == 0)
return;
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, _not_ghost, _ek_not_defined);
Mesh::type_iterator end =
mesh.lastType(spatial_dimension, _not_ghost, _ek_not_defined);
for (; it != end; ++it) {
ElementType type = *it;
Array<UInt> & conn =
const_cast<Array<UInt> &>(mesh.getConnectivity(type, _not_ghost));
UInt nb_nodes_per_element = conn.getNbComponent();
UInt nb_element = conn.getSize();
Array<UInt> & saved_conn = saved_connectivity.alloc(
nb_element, nb_nodes_per_element, type, _not_ghost);
saved_conn.copy(conn);
for (UInt i = 0; i < pairs.getSize(); ++i) {
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
if (pairs(i, 1) == conn(el, n))
conn(el, n) = pairs(i, 0);
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartition::restoreConnectivity() {
AKANTU_DEBUG_IN();
ElementTypeMapArray<UInt>::type_iterator it = saved_connectivity.firstType(
spatial_dimension, _not_ghost, _ek_not_defined);
ElementTypeMapArray<UInt>::type_iterator end = saved_connectivity.lastType(
spatial_dimension, _not_ghost, _ek_not_defined);
for (; it != end; ++it) {
ElementType type = *it;
Array<UInt> & conn =
const_cast<Array<UInt> &>(mesh.getConnectivity(type, _not_ghost));
Array<UInt> & saved_conn = saved_connectivity(type, _not_ghost);
conn.copy(saved_conn);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh_utils/mesh_partition.hh b/src/mesh_utils/mesh_partition.hh
index 600f73ee4..849530369 100644
--- a/src/mesh_utils/mesh_partition.hh
+++ b/src/mesh_utils/mesh_partition.hh
@@ -1,150 +1,150 @@
/**
* @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_memory.hh"
#include "aka_csr.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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();
class EdgeLoadFunctor {
public:
virtual Int operator()(__attribute__((unused)) const Element & el1,
__attribute__((unused)) const Element & el2) const = 0;
};
class ConstEdgeLoadFunctor : public EdgeLoadFunctor {
public:
virtual inline Int operator()(__attribute__((unused)) const Element & el1,
__attribute__((unused)) const Element & el2) const {
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:
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;
};
-__END_AKANTU__
+} // 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.cc b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
index 5665b17fa..1088437c9 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
+++ b/src/mesh_utils/mesh_partition/mesh_partition_mesh_data.cc
@@ -1,141 +1,141 @@
/**
* @file mesh_partition_mesh_data.cc
*
* @author Dana Christen <dana.christen@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Wed Nov 11 2015
*
* @brief implementation of the MeshPartitionMeshData 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/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "mesh_partition_mesh_data.hh"
#if !defined(AKANTU_NDEBUG)
#include <set>
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
MeshPartitionMeshData::MeshPartitionMeshData(const Mesh & mesh,
UInt spatial_dimension,
const ID & id,
const MemoryID & memory_id)
: MeshPartition(mesh, spatial_dimension, id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MeshPartitionMeshData::MeshPartitionMeshData(
const Mesh & mesh, const ElementTypeMapArray<UInt> & mapping,
UInt spatial_dimension, const ID & id, const MemoryID & memory_id)
: MeshPartition(mesh, spatial_dimension, id, memory_id),
partition_mapping(&mapping) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::partitionate(UInt nb_part,
__attribute__((unused))
const EdgeLoadFunctor & edge_load_func,
const Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
tweakConnectivity(pairs);
nb_partitions = nb_part;
GhostType ghost_type = _not_ghost;
UInt spatial_dimension = mesh.getSpatialDimension();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_not_defined);
Mesh::type_iterator end =
mesh.lastType(spatial_dimension, ghost_type, _ek_not_defined);
UInt linearized_el = 0;
UInt nb_elements = mesh.getNbElement(mesh.getSpatialDimension(), ghost_type);
Int * partition_list = new Int[nb_elements];
#if !defined(AKANTU_NDEBUG)
std::set<UInt> partitions;
#endif
for (; it != end; ++it) {
ElementType type = *it;
const Array<UInt> & partition_array =
(*partition_mapping)(type, ghost_type);
Array<UInt>::const_iterator<Vector<UInt> > p_it = partition_array.begin(1);
Array<UInt>::const_iterator<Vector<UInt> > p_end = partition_array.end(1);
AKANTU_DEBUG_ASSERT(UInt(p_end - p_it) ==
mesh.getNbElement(type, ghost_type),
"The partition mapping does not have the right number "
<< "of entries for type " << type
<< " and ghost type " << ghost_type << "."
<< " Tags=" << p_end - p_it
<< " Mesh=" << mesh.getNbElement(type, ghost_type));
for (; p_it != p_end; ++p_it, ++linearized_el) {
partition_list[linearized_el] = (*p_it)(0);
#if !defined(AKANTU_NDEBUG)
partitions.insert((*p_it)(0));
#endif
}
}
#if !defined(AKANTU_NDEBUG)
AKANTU_DEBUG_ASSERT(partitions.size() == nb_part,
"The number of real partitions does not match with the "
"number of asked partitions");
#endif
fillPartitionInformation(mesh, partition_list);
delete[] partition_list;
restoreConnectivity();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::reorder() { AKANTU_DEBUG_TO_IMPLEMENT(); }
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::setPartitionMapping(
const ElementTypeMapArray<UInt> & mapping) {
partition_mapping = &mapping;
}
/* -------------------------------------------------------------------------- */
void MeshPartitionMeshData::setPartitionMappingFromMeshData(
const std::string & data_name) {
partition_mapping = &(mesh.getData<UInt>(data_name));
}
-__END_AKANTU__
+} // akantu
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 aab69b9e5..bfb340547 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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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:
virtual void partitionate(UInt nb_part,
const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
const Array<UInt> & pairs = Array<UInt>());
virtual void reorder();
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 */
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MESH_PARTITION_MESH_DATA_HH__ */
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc b/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
index eb6195dd8..7ba52fd3c 100644
--- a/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
+++ b/src/mesh_utils/mesh_partition/mesh_partition_scotch.cc
@@ -1,478 +1,478 @@
/**
* @file mesh_partition_scotch.cc
*
* @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 Jan 22 2016
*
* @brief implementation of the MeshPartitionScotch 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 <cstdio>
#include <fstream>
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "mesh_partition_scotch.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
#if !defined(AKANTU_USE_PTSCOTCH)
#ifndef AKANTU_SCOTCH_NO_EXTERN
extern "C" {
#endif // AKANTU_SCOTCH_NO_EXTERN
#include <scotch.h>
#ifndef AKANTU_SCOTCH_NO_EXTERN
}
#endif // AKANTU_SCOTCH_NO_EXTERN
#else // AKANTU_USE_PTSCOTCH
#include <ptscotch.h>
#endif // AKANTU_USE_PTSCOTCH
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
MeshPartitionScotch::MeshPartitionScotch(const Mesh & mesh,
UInt spatial_dimension, const ID & id,
const MemoryID & memory_id)
: MeshPartition(mesh, spatial_dimension, id, memory_id) {
AKANTU_DEBUG_IN();
// check if the akantu types and Scotch one are consistent
#if __cplusplus > 199711L
static_assert(sizeof(Int) == sizeof(SCOTCH_Num),
"The integer type of Akantu does not match the one from Scotch");
#else
AKANTU_DEBUG_ASSERT(
sizeof(Int) == sizeof(SCOTCH_Num),
"The integer type of Akantu does not match the one from Scotch");
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
static SCOTCH_Mesh * createMesh(const Mesh & mesh) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_nodes = mesh.getNbNodes();
UInt total_nb_element = 0;
UInt nb_edge = 0;
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator end = mesh.lastType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
total_nb_element += nb_element;
nb_edge += nb_element * nb_nodes_per_element;
}
SCOTCH_Num vnodbas = 0;
SCOTCH_Num vnodnbr = nb_nodes;
SCOTCH_Num velmbas = vnodnbr;
SCOTCH_Num velmnbr = total_nb_element;
SCOTCH_Num * verttab = new SCOTCH_Num[vnodnbr + velmnbr + 1];
SCOTCH_Num * vendtab = verttab + 1;
SCOTCH_Num * velotab = NULL;
SCOTCH_Num * vnlotab = NULL;
SCOTCH_Num * vlbltab = NULL;
memset(verttab, 0, (vnodnbr + velmnbr + 1) * sizeof(SCOTCH_Num));
it = mesh.firstType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
if (Mesh::getSpatialDimension(type) != spatial_dimension)
continue;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
/// count number of occurrence of each node
for (UInt el = 0; el < nb_element; ++el) {
UInt * conn_val = connectivity.storage() + el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
verttab[*(conn_val++)]++;
}
}
}
/// convert the occurrence array in a csr one
for (UInt i = 1; i < nb_nodes; ++i)
verttab[i] += verttab[i - 1];
for (UInt i = nb_nodes; i > 0; --i)
verttab[i] = verttab[i - 1];
verttab[0] = 0;
/// rearrange element to get the node-element list
SCOTCH_Num edgenbr = verttab[vnodnbr] + nb_edge;
SCOTCH_Num * edgetab = new SCOTCH_Num[edgenbr];
UInt linearized_el = 0;
it = mesh.firstType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
UInt * conn_val = connectivity.storage() + el * nb_nodes_per_element;
for (UInt n = 0; n < nb_nodes_per_element; ++n)
edgetab[verttab[*(conn_val++)]++] = linearized_el + velmbas;
}
}
for (UInt i = nb_nodes; i > 0; --i)
verttab[i] = verttab[i - 1];
verttab[0] = 0;
SCOTCH_Num * verttab_tmp = verttab + vnodnbr + 1;
SCOTCH_Num * edgetab_tmp = edgetab + verttab[vnodnbr];
it = mesh.firstType(spatial_dimension);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el) {
*verttab_tmp = *(verttab_tmp - 1) + nb_nodes_per_element;
verttab_tmp++;
UInt * conn = connectivity.storage() + el * nb_nodes_per_element;
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
*(edgetab_tmp++) = *(conn++) + vnodbas;
}
}
}
SCOTCH_Mesh * meshptr = new SCOTCH_Mesh;
SCOTCH_meshInit(meshptr);
SCOTCH_meshBuild(meshptr, velmbas, vnodbas, velmnbr, vnodnbr, verttab,
vendtab, velotab, vnlotab, vlbltab, edgenbr, edgetab);
/// Check the mesh
AKANTU_DEBUG_ASSERT(SCOTCH_meshCheck(meshptr) == 0,
"Scotch mesh is not consistent");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save initial graph
FILE * fmesh = fopen("ScotchMesh.msh", "w");
SCOTCH_meshSave(meshptr, fmesh);
fclose(fmesh);
/// write geometry file
std::ofstream fgeominit;
fgeominit.open("ScotchMesh.xyz");
fgeominit << spatial_dimension << std::endl
<< nb_nodes << std::endl;
const Array<Real> & nodes = mesh.getNodes();
Real * nodes_val = nodes.storage();
for (UInt i = 0; i < nb_nodes; ++i) {
fgeominit << i << " ";
for (UInt s = 0; s < spatial_dimension; ++s)
fgeominit << *(nodes_val++) << " ";
fgeominit << std::endl;
;
}
fgeominit.close();
}
#endif
AKANTU_DEBUG_OUT();
return meshptr;
}
/* -------------------------------------------------------------------------- */
static void destroyMesh(SCOTCH_Mesh * meshptr) {
AKANTU_DEBUG_IN();
SCOTCH_Num velmbas, vnodbas, vnodnbr, velmnbr, *verttab, *vendtab, *velotab,
*vnlotab, *vlbltab, edgenbr, *edgetab, degrptr;
SCOTCH_meshData(meshptr, &velmbas, &vnodbas, &velmnbr, &vnodnbr, &verttab,
&vendtab, &velotab, &vnlotab, &vlbltab, &edgenbr, &edgetab,
°rptr);
delete[] verttab;
delete[] edgetab;
SCOTCH_meshExit(meshptr);
delete meshptr;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionScotch::partitionate(UInt nb_part,
const EdgeLoadFunctor & edge_load_func,
const Array<UInt> & pairs) {
AKANTU_DEBUG_IN();
nb_partitions = nb_part;
tweakConnectivity(pairs);
AKANTU_DEBUG_INFO("Partitioning the mesh " << mesh.getID() << " in "
<< nb_part << " parts.");
Array<Int> dxadj;
Array<Int> dadjncy;
Array<Int> edge_loads;
buildDualGraph(dxadj, dadjncy, edge_loads, edge_load_func);
/// variables that will hold our structures in scotch format
SCOTCH_Graph scotch_graph;
SCOTCH_Strat scotch_strat;
/// description number and arrays for struct mesh for scotch
SCOTCH_Num baseval = 0; // base numbering for element and
// nodes (0 -> C , 1 -> fortran)
SCOTCH_Num vertnbr = dxadj.getSize() - 1; // number of vertexes
SCOTCH_Num * parttab; // array of partitions
SCOTCH_Num edgenbr = dxadj(vertnbr); // twice the number of "edges"
//(an "edge" bounds two nodes)
SCOTCH_Num * verttab = dxadj.storage(); // array of start indices in edgetab
SCOTCH_Num * vendtab = NULL; // array of after-last indices in edgetab
SCOTCH_Num * velotab = NULL; // integer load associated with
// every vertex ( optional )
SCOTCH_Num * edlotab = edge_loads.storage(); // integer load associated with
// every edge ( optional )
SCOTCH_Num * edgetab = dadjncy.storage(); // adjacency array of every vertex
SCOTCH_Num * vlbltab = NULL; // vertex label array (optional)
/// Allocate space for Scotch arrays
parttab = new SCOTCH_Num[vertnbr];
/// Initialize the strategy structure
SCOTCH_stratInit(&scotch_strat);
/// Initialize the graph structure
SCOTCH_graphInit(&scotch_graph);
/// Build the graph from the adjacency arrays
SCOTCH_graphBuild(&scotch_graph, baseval, vertnbr, verttab, vendtab, velotab,
vlbltab, edgenbr, edgetab, edlotab);
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save initial graph
FILE * fgraphinit = fopen("GraphIniFile.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraphinit);
fclose(fgraphinit);
/// write geometry file
std::ofstream fgeominit;
fgeominit.open("GeomIniFile.xyz");
fgeominit << spatial_dimension << std::endl
<< vertnbr << std::endl;
const Array<Real> & nodes = mesh.getNodes();
Mesh::type_iterator f_it =
mesh.firstType(spatial_dimension, _not_ghost, _ek_not_defined);
Mesh::type_iterator f_end =
mesh.lastType(spatial_dimension, _not_ghost, _ek_not_defined);
Array<Real>::const_vector_iterator nodes_it =
nodes.begin(spatial_dimension);
UInt out_linerized_el = 0;
for (; f_it != f_end; ++f_it) {
ElementType type = *f_it;
UInt nb_element = mesh.getNbElement(*f_it);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type);
Vector<Real> mid(spatial_dimension);
for (UInt el = 0; el < nb_element; ++el) {
mid.set(0.);
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt node = connectivity.storage()[nb_nodes_per_element * el + n];
mid += Vector<Real>(nodes_it[node]);
}
mid /= nb_nodes_per_element;
fgeominit << out_linerized_el++ << " ";
for (UInt s = 0; s < spatial_dimension; ++s)
fgeominit << mid[s] << " ";
fgeominit << std::endl;
;
}
}
fgeominit.close();
}
#endif
/// Check the graph
AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
"Graph to partition is not consistent");
/// Partition the mesh
SCOTCH_graphPart(&scotch_graph, nb_part, &scotch_strat, parttab);
/// Check the graph
AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
"Partitioned graph is not consistent");
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
/// save the partitioned graph
FILE * fgraph = fopen("GraphFile.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraph);
fclose(fgraph);
/// save the partition map
std::ofstream fmap;
fmap.open("MapFile.map");
fmap << vertnbr << std::endl;
for (Int i = 0; i < vertnbr; i++)
fmap << i << " " << parttab[i] << std::endl;
fmap.close();
}
#endif
/// free the scotch data structures
SCOTCH_stratExit(&scotch_strat);
SCOTCH_graphFree(&scotch_graph);
SCOTCH_graphExit(&scotch_graph);
fillPartitionInformation(mesh, parttab);
delete[] parttab;
restoreConnectivity();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshPartitionScotch::reorder() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Reordering the mesh " << mesh.getID());
SCOTCH_Mesh * scotch_mesh = createMesh(mesh);
UInt nb_nodes = mesh.getNbNodes();
SCOTCH_Strat scotch_strat;
// SCOTCH_Ordering scotch_order;
SCOTCH_Num * permtab = new SCOTCH_Num[nb_nodes];
SCOTCH_Num * peritab = NULL;
SCOTCH_Num cblknbr = 0;
SCOTCH_Num * rangtab = NULL;
SCOTCH_Num * treetab = NULL;
/// Initialize the strategy structure
SCOTCH_stratInit(&scotch_strat);
SCOTCH_Graph scotch_graph;
SCOTCH_graphInit(&scotch_graph);
SCOTCH_meshGraph(scotch_mesh, &scotch_graph);
#ifndef AKANTU_NDEBUG
if (AKANTU_DEBUG_TEST(dblDump)) {
FILE * fgraphinit = fopen("ScotchMesh.grf", "w");
SCOTCH_graphSave(&scotch_graph, fgraphinit);
fclose(fgraphinit);
}
#endif
/// Check the graph
// AKANTU_DEBUG_ASSERT(SCOTCH_graphCheck(&scotch_graph) == 0,
// "Mesh to Graph is not consistent");
SCOTCH_graphOrder(&scotch_graph, &scotch_strat, permtab, peritab, &cblknbr,
rangtab, treetab);
SCOTCH_graphExit(&scotch_graph);
SCOTCH_stratExit(&scotch_strat);
destroyMesh(scotch_mesh);
/// Renumbering
UInt spatial_dimension = mesh.getSpatialDimension();
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
Mesh::type_iterator it = mesh.firstType(_all_dimensions, gt);
Mesh::type_iterator end = mesh.lastType(_all_dimensions, gt);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type, gt);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const Array<UInt> & connectivity = mesh.getConnectivity(type, gt);
UInt * conn = connectivity.storage();
for (UInt el = 0; el < nb_element * nb_nodes_per_element; ++el, ++conn) {
*conn = permtab[*conn];
}
}
}
/// \todo think of a in-place way to do it
Real * new_coordinates = new Real[spatial_dimension * nb_nodes];
Real * old_coordinates = mesh.getNodes().storage();
for (UInt i = 0; i < nb_nodes; ++i) {
memcpy(new_coordinates + permtab[i] * spatial_dimension,
old_coordinates + i * spatial_dimension,
spatial_dimension * sizeof(Real));
}
memcpy(old_coordinates, new_coordinates,
nb_nodes * spatial_dimension * sizeof(Real));
delete[] new_coordinates;
delete[] permtab;
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh b/src/mesh_utils/mesh_partition/mesh_partition_scotch.hh
index 56fd76021..81eb819b3 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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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:
virtual void partitionate(UInt nb_part,
const EdgeLoadFunctor & edge_load_func = ConstEdgeLoadFunctor(),
const Array<UInt> & pairs = Array<UInt>());
virtual void reorder();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MESH_PARTITION_SCOTCH_HH__ */
diff --git a/src/mesh_utils/mesh_utils.cc b/src/mesh_utils/mesh_utils.cc
index ff5862672..6bda16b0e 100644
--- a/src/mesh_utils/mesh_utils.cc
+++ b/src/mesh_utils/mesh_utils.cc
@@ -1,2369 +1,2369 @@
/**
* @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>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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;
e.kind = Mesh::getKind(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).getSize();
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).getSize();
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");
const ElementTypeMapArray<UInt> * prank_to_element = nullptr;
if (mesh.isDistributed()) {
prank_to_element = &(mesh.getElementSynchronizer().getPrankToElement());
}
/// generate facets
buildFacetsDimension(mesh, mesh_facets, false, from_dimension,
prank_to_element);
/// 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, prank_to_element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildFacetsDimension(
const Mesh & mesh, Mesh & mesh_facets, bool boundary_only, UInt dimension,
const ElementTypeMapArray<UInt> * prank_to_element) {
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 (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
Mesh::type_iterator first = mesh.firstType(dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(dimension, ghost_type);
for (; first != last; ++first) {
ElementType type = *first;
mesh_accessor.getSubelementToElement(type, ghost_type);
Vector<ElementType> facet_types = mesh.getAllFacetTypes(type);
for (UInt ft = 0; ft < facet_types.size(); ++ft) {
ElementType facet_type = facet_types(ft);
mesh_accessor.getElementToSubelement(facet_type, ghost_type);
mesh_accessor.getConnectivity(facet_type, ghost_type);
}
}
}
Element current_element;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType ghost_type = *gt;
GhostType facet_ghost_type = ghost_type;
current_element.ghost_type = ghost_type;
Mesh::type_iterator first = mesh.firstType(dimension, ghost_type);
Mesh::type_iterator last = mesh.lastType(dimension, ghost_type);
for (; first != last; ++first) {
ElementType type = *first;
Vector<ElementType> facet_types = mesh.getAllFacetTypes(type);
current_element.type = type;
for (UInt ft = 0; ft < facet_types.size(); ++ft) {
ElementType facet_type = facet_types(ft);
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<std::vector<Element>> * element_to_subelement =
&mesh_facets.getElementToSubelement(facet_type, ghost_type);
Array<UInt> * connectivity_facets =
&mesh_facets.getConnectivity(facet_type, ghost_type);
UInt nb_facet_per_element = mesh.getNbFacetsPerElement(type, ft);
const Array<UInt> & element_connectivity =
mesh.getConnectivity(type, ghost_type);
const Matrix<UInt> facet_local_connectivity =
mesh.getFacetLocalConnectivity(type, ft);
UInt 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
CSR<Element>::iterator first_node_elements =
node_to_elem.begin(facet(0));
CSR<Element>::iterator first_node_elements_end =
node_to_elem.end(facet(0));
UInt local_el = 0;
for (; first_node_elements != first_node_elements_end;
++first_node_elements, ++local_el) {
for (UInt n = 1; n < nb_nodes_per_facet; ++n) {
CSR<Element>::iterator node_elements_begin =
node_to_elem.begin(facet(n));
CSR<Element>::iterator 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 (counter(el_f) == nb_nodes_per_facet - 1) {
++nb_element_connected_to_facet;
minimum_el = std::min(minimum_el, real_el);
connected_elements.push_back(real_el);
}
}
if (minimum_el == current_element) {
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) {
if (!boundary_only ||
(boundary_only && nb_element_connected_to_facet == 1)) {
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);
/// boundary facet
if (nb_element_connected_to_facet == 1)
elements.push_back(ElementNull);
/// internal facet
else if (nb_element_connected_to_facet == 2) {
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] == 1) {
if (prank_to_element) {
UInt prank[2];
for (UInt el = 0; el < 2; ++el) {
UInt current_el = connected_elements[el].element;
ElementType current_type =
connected_elements[el].type;
GhostType current_gt =
connected_elements[el].ghost_type;
const Array<UInt> & prank_to_el =
(*prank_to_element)(current_type, current_gt);
prank[el] = prank_to_el(current_el);
}
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);
}
}
}
/// facet of facet
else {
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->getSize() - 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) {
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) {
if (subelement_to_element(loc_el.element, f_in).type ==
_not_defined) {
subelement_to_element(loc_el.element, f_in).type =
facet_type;
subelement_to_element(loc_el.element, f_in).element =
current_facet;
subelement_to_element(loc_el.element, f_in)
.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.getSize(); ++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);
std::map<UInt, UInt>::iterator it = renumbering_map.begin();
std::map<UInt, UInt>::iterator end = renumbering_map.end();
old_nodes_numbers.resize(renumbering_map.size());
for (; it != end; ++it) {
old_nodes_numbers(it->second) = it->first;
}
renumbering_map.clear();
MeshAccessor mesh_accessor(mesh);
/// copy the renumbered connectivity to the right place
Array<UInt> & 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));
Array<UInt> & ghost_conn = mesh_accessor.getConnectivity(type, _ghost);
ghost_conn.resize(nb_ghost_element);
memcpy(ghost_conn.storage(), local_connectivities.storage() +
nb_local_element * nb_nodes_per_element,
nb_ghost_element * nb_nodes_per_element * sizeof(UInt));
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.getSize());
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.getSize(); ++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.getSize();
UInt new_nb_nodes = old_nb_nodes + old_nodes.size();
UInt old_nb_doubled_nodes = doubled_nodes.getSize();
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.getSize();
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<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.getSize();
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;
for (UInt f = 0; f < f_insertion.getSize(); ++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.getSize() - 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.getSize();
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;
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;
UInt old_nb_facet = subfacet_to_facet.getSize() - 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;
/// 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;
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.getSize();
if (nb_facet_to_double == 0)
continue;
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
Array<Element> * facet_to_coh_element =
mesh_facets.getSubelementToElementPointer(type_cohesive, gt_facet);
Array<UInt> & conn_facet =
mesh_facets.getConnectivity(type_facet, gt_facet);
Array<UInt> * conn_cohesive =
mesh.getConnectivityPointer(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->getSize();
UInt new_nb_cohesive_elements =
conn_cohesive->getSize() + nb_facet_to_double;
UInt old_nb_facet = element_to_facet.getSize() - 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.getSize();
new_elements.resize(new_elements_old_size + nb_facet_to_double);
Element c_element(type_cohesive, 0, gt_facet, _ek_cohesive);
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.getSize();
UInt old_nb_facet = element_to_facet.getSize() - nb_facet_to_double;
UInt new_nb_facet = element_to_facet.getSize();
UInt old_nb_nodes = position.getSize();
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.getSize();
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.getSize();
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;
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.getSize();
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.getSize();
/// update subfacet_to_facet vector
ElementType type_facet = _not_defined;
GhostType gt_facet = _casper;
Array<Element> * subfacet_to_facet = NULL;
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;
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.getSize();
Array<std::vector<Element>> & facet_to_subfacet =
mesh_facets.getElementToSubelement(type_subfacet, gt_subfacet);
Array<std::vector<Element>> * facet_to_subfacet_double = NULL;
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.getSize();
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.getSize();
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.getSize();
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.getSize();
/// 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;
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());
mesh_facets.initElementTypeMapArray(global_connectivity_tmp, 1,
spatial_dimension - 1, gt_facet, true,
_ek_regular, true);
mesh_facets.getGlobalConnectivity(global_connectivity_tmp,
spatial_dimension - 1, gt_facet);
Mesh::type_iterator it =
mesh_facets.firstType(spatial_dimension - 1, gt_facet);
Mesh::type_iterator end =
mesh_facets.lastType(spatial_dimension - 1, gt_facet);
/// loop on every facet
for (; it != end; ++it) {
ElementType type_facet = *it;
Array<UInt> & connectivity =
mesh_facets.getConnectivity(type_facet, gt_facet);
const Array<UInt> & g_connectivity =
global_connectivity(type_facet, gt_facet);
Array<std::vector<Element>> & el_to_f =
mesh_facets.getElementToSubelement(type_facet, gt_facet);
Array<Element> & 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.getSize();
UInt nb_nodes_per_P1_facet =
Mesh::getNbNodesPerElement(Mesh::getP1ElementType(type_facet));
Array<UInt> & global_conn_tmp =
global_connectivity_tmp(type_facet, gt_facet);
Array<UInt>::iterator<Vector<UInt>> conn_it =
connectivity.begin(nb_nodes_per_facet);
Array<UInt>::iterator<Vector<UInt>> gconn_tmp_it =
global_conn_tmp.begin(nb_nodes_per_facet);
Array<UInt>::const_iterator<Vector<UInt>> conn_glob_it =
g_connectivity.begin(nb_nodes_per_facet);
Array<Element>::iterator<Vector<Element>> 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());
mesh.initElementTypeMapArray(barycenters, spatial_dimension, _all_dimensions);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
Mesh::type_iterator it = mesh.firstType(_all_dimensions, *gt);
Mesh::type_iterator end = mesh.lastType(_all_dimensions, *gt);
for (; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it, *gt);
Array<Real> & barycenters_arr = barycenters(*it, *gt);
barycenters_arr.resize(nb_element);
Array<Real>::vector_iterator bary =
barycenters_arr.begin(spatial_dimension);
Array<Real>::vector_iterator bary_end =
barycenters_arr.end(spatial_dimension);
for (UInt el = 0; bary != bary_end; ++bary, ++el) {
mesh.getBarycenter(el, *it, bary->storage(), *gt);
}
}
}
MeshAccessor mesh_accessor(mesh);
for (Int sp(spatial_dimension); sp >= 1; --sp) {
if (mesh.getNbElement(sp) == 0)
continue;
for (ghost_type_t::iterator git = ghost_type_t::begin();
git != ghost_type_t::end(); ++git) {
Mesh::type_iterator tit = mesh.firstType(sp, *git);
Mesh::type_iterator tend = mesh.lastType(sp, *git);
for (; tit != tend; ++tit) {
mesh_accessor.getSubelementToElement(*tit, *git)
.resize(mesh.getNbElement(*tit, *git));
mesh_accessor.getSubelementToElement(*tit, *git).clear();
}
tit = mesh.firstType(sp - 1, *git);
tend = mesh.lastType(sp - 1, *git);
for (; tit != tend; ++tit) {
mesh_accessor.getElementToSubelement(*tit, *git)
.resize(mesh.getNbElement(*tit, *git));
mesh.getElementToSubelement(*tit, *git).clear();
}
}
CSR<Element> nodes_to_elements;
buildNode2Elements(mesh, nodes_to_elements, sp);
Element facet_element;
for (ghost_type_t::iterator git = ghost_type_t::begin();
git != ghost_type_t::end(); ++git) {
Mesh::type_iterator tit = mesh.firstType(sp - 1, *git);
Mesh::type_iterator tend = mesh.lastType(sp - 1, *git);
facet_element.ghost_type = *git;
for (; tit != tend; ++tit) {
facet_element.type = *tit;
Array<std::vector<Element>> & element_to_subelement =
mesh.getElementToSubelement(*tit, *git);
const Array<UInt> & connectivity = mesh.getConnectivity(*tit, *git);
Array<UInt>::const_iterator<Vector<UInt>> fit =
connectivity.begin(mesh.getNbNodesPerElement(*tit));
Array<UInt>::const_iterator<Vector<UInt>> fend =
connectivity.end(mesh.getNbNodesPerElement(*tit));
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(*tit));
for (UInt n(0); n < nb_nodes_per_facet; ++n) {
CSR<Element>::iterator eit = nodes_to_elements.begin(facet(n));
CSR<Element>::iterator eend = nodes_to_elements.end(facet(n));
for (; eit != eend; ++eit) {
Element & elem = *eit;
std::map<Element, UInt>::iterator 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;
std::map<Element, UInt>::iterator cit = element_seen_counter.begin();
std::map<Element, UInt>::iterator cend = element_seen_counter.end();
for (; cit != cend; ++cit) {
if (cit->second == nb_nodes_per_facet)
connected_elements.push_back(cit->first);
}
std::vector<Element>::iterator ceit = connected_elements.begin();
std::vector<Element>::iterator 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;
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 Element * opposing_el = NULL;
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;
}
/* -------------------------------------------------------------------------- */
void MeshUtils::buildSegmentToNodeType(const Mesh & mesh, Mesh & mesh_facets) {
buildAllFacets(mesh, mesh_facets, 1);
UInt spatial_dimension = mesh.getSpatialDimension();
const ElementTypeMapArray<UInt> & element_to_rank =
mesh.getElementSynchronizer().getPrankToElement();
Int local_rank = StaticCommunicator::getStaticCommunicator().whoAmI();
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(1, ghost_type);
Mesh::type_iterator end = mesh_facets.lastType(1, ghost_type);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_segments = mesh_facets.getNbElement(type, ghost_type);
// allocate the data
Array<Int> & segment_to_nodetype = *(mesh_facets.getDataPointer<Int>(
"segment_to_nodetype", type, ghost_type));
std::set<Element> connected_elements;
const Array<std::vector<Element>> & segment_to_2Delement =
mesh_facets.getElementToSubelement(type, ghost_type);
// loop over segments
for (UInt s = 0; s < nb_segments; ++s) {
// determine the elements connected to the segment
connected_elements.clear();
const std::vector<Element> & twoD_elements = segment_to_2Delement(s);
if (spatial_dimension == 2) {
// if 2D just take the elements connected to the segments
connected_elements.insert(twoD_elements.begin(), twoD_elements.end());
} else if (spatial_dimension == 3) {
// if 3D a second loop is needed to get to the 3D elements
std::vector<Element>::const_iterator facet = twoD_elements.begin();
for (; facet != twoD_elements.end(); ++facet) {
const std::vector<Element> & threeD_elements =
mesh_facets.getElementToSubelement(
facet->type, facet->ghost_type)(facet->element);
connected_elements.insert(threeD_elements.begin(),
threeD_elements.end());
}
}
// get the minimum processor rank associated to the connected
// elements and verify if ghost and not ghost elements are
// found
Int minimum_rank = std::numeric_limits<Int>::max();
// two booleans saying if not ghost and ghost elements are found in the
// loop
bool ghost_found[2];
ghost_found[0] = false;
ghost_found[1] = false;
std::set<Element>::iterator connected_elements_it =
connected_elements.begin();
for (; connected_elements_it != connected_elements.end();
++connected_elements_it) {
if (*connected_elements_it == ElementNull)
continue;
ghost_found[connected_elements_it->ghost_type] = true;
const Array<UInt> & el_to_rank_array = element_to_rank(
connected_elements_it->type, connected_elements_it->ghost_type);
minimum_rank =
std::min(minimum_rank,
Int(el_to_rank_array(connected_elements_it->element)));
}
// if no ghost elements are found the segment is local
if (!ghost_found[1])
segment_to_nodetype(s) = -1;
// if no not ghost elements are found the segment is pure ghost
else if (!ghost_found[0])
segment_to_nodetype(s) = -3;
// if the minimum rank is equal to the local rank, the segment is master
else if (local_rank == minimum_rank)
segment_to_nodetype(s) = -2;
// if the minimum rank is less than the local rank, the segment is slave
else if (local_rank > minimum_rank)
segment_to_nodetype(s) = minimum_rank;
else
AKANTU_DEBUG_ERROR("The local rank cannot be smaller than the "
"minimum rank if both ghost and not ghost "
"elements are found");
}
}
}
}
/* -------------------------------------------------------------------------- */
UInt MeshUtils::updateLocalMasterGlobalConnectivity(Mesh & mesh,
UInt local_nb_new_nodes) {
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
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;
}
/* -------------------------------------------------------------------------- */
// Deactivating -Wunused-parameter
#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__))
#define GCC_VERSION \
(__GNUC__ * 10000 + __GNUC_MINOR__ * 100 + __GNUC_PATCHLEVEL__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic push
#endif
#pragma GCC diagnostic ignored "-Wunused-parameter"
#endif
/* -------------------------------------------------------------------------- */
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;
#if defined(AKANTU_COHESIVE_ELEMENT)
const Array<Element> * cohesive_facets = NULL;
#endif
UInt nb_nodes_per_element = 0;
UInt * n_update = NULL;
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,
"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();
}
// Reactivating -Wunused-parameter
#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(__GNUG__)
#if GCC_VERSION > 40600
#pragma GCC diagnostic pop
#else
#pragma GCC diagnostic warning "-Wunused-parameter"
#endif
#endif
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
// LocalWords: ElementType
diff --git a/src/mesh_utils/mesh_utils.hh b/src/mesh_utils/mesh_utils.hh
index 329ed0586..2c79aaa1a 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__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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,
const ElementTypeMapArray<UInt> * prank_to_element = nullptr);
/// 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);
/// 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"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MESH_UTILS_HH__ */
diff --git a/src/mesh_utils/mesh_utils_pbc.cc b/src/mesh_utils/mesh_utils_pbc.cc
index ea00ebf40..bc11d7891 100644
--- a/src/mesh_utils/mesh_utils_pbc.cc
+++ b/src/mesh_utils/mesh_utils_pbc.cc
@@ -1,298 +1,298 @@
/**
* @file mesh_utils_pbc.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
*
* @date creation: Wed Feb 09 2011
* @date last modification: Tue Sep 15 2015
*
* @brief periodic boundary condition connectivity tweak
*
* @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 <map>
/* -------------------------------------------------------------------------- */
#include "element_group.hh"
#include "mesh_accessor.hh"
#include "mesh_utils.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/// class that sorts a set of nodes of same coordinates in 'dir' direction
class CoordinatesComparison {
public:
CoordinatesComparison(const UInt dimension, const UInt dir_1, const UInt dir_2,
Real normalization, Real tolerance, const Array<Real> & coords)
: dim(dimension), dir_1(dir_1), dir_2(dir_2), normalization(normalization),
tolerance(tolerance), coords_it(coords.begin(dim)) {}
// answers the question whether n2 is larger or equal to n1
bool operator()(const UInt n1, const UInt n2) {
Vector<Real> coords_n1 = coords_it[n1];
Vector<Real> coords_n2 = coords_it[n2];
return this->operator()(coords_n1, coords_n2);
}
bool operator()(const Vector<Real> & coords_n1, const Vector<Real> & coords_n2) {
Real diff = coords_n1(dir_1) - coords_n2(dir_1);;
if (dim == 2 || std::abs(diff) / normalization > tolerance)
return diff > 0. ? false : true;
else if (dim > 2) {
diff = coords_n1(dir_2) - coords_n2(dir_2);;
return diff > 0 ? false : true;
}
return true;
}
private:
UInt dim;
UInt dir_1;
UInt dir_2;
Real normalization;
Real tolerance;
const Array<Real>::const_vector_iterator coords_it;
};
/* -------------------------------------------------------------------------- */
void MeshUtils::computePBCMap(const Mesh & mesh, const UInt dir,
std::map<UInt, UInt> & pbc_pair) {
Array<UInt> selected_left;
Array<UInt> selected_right;
const UInt dim = mesh.getSpatialDimension();
Array<Real>::const_vector_iterator it = mesh.getNodes().begin(dim);
Array<Real>::const_vector_iterator end = mesh.getNodes().end(dim);
if (dim <= dir)
return;
const Vector<Real> & lower_bounds = mesh.getLowerBounds();
const Vector<Real> & upper_bounds = mesh.getUpperBounds();
AKANTU_DEBUG_INFO("min " << lower_bounds(dir));
AKANTU_DEBUG_INFO("max " << upper_bounds(dir));
for (UInt node = 0; it != end; ++it, ++node) {
const Vector<Real> & coords = *it;
AKANTU_DEBUG_TRACE("treating " << coords(dir));
if (Math::are_float_equal(coords(dir), lower_bounds(dir))) {
AKANTU_DEBUG_TRACE("pushing node " << node << " on the left side");
selected_left.push_back(node);
} else if (Math::are_float_equal(coords(dir), upper_bounds(dir))) {
selected_right.push_back(node);
AKANTU_DEBUG_TRACE("pushing node " << node << " on the right side");
}
}
AKANTU_DEBUG_INFO(
"found " << selected_left.getSize() << " and " << selected_right.getSize()
<< " nodes at each boundary for direction " << dir);
// match pairs
MeshUtils::matchPBCPairs(mesh, dir, selected_left, selected_right, pbc_pair);
}
/* -------------------------------------------------------------------------- */
void MeshUtils::computePBCMap(const Mesh & mesh,
const SurfacePair & surface_pair,
std::map<UInt, UInt> & pbc_pair) {
Array<UInt> selected_first;
Array<UInt> selected_second;
// find nodes on surfaces
const ElementGroup & first_surf = mesh.getElementGroup(surface_pair.first);
const ElementGroup & second_surf = mesh.getElementGroup(surface_pair.second);
// if this surface pair is not on this proc
if (first_surf.getNbNodes() == 0 || second_surf.getNbNodes() == 0) {
AKANTU_DEBUG_WARNING("computePBCMap has at least one surface without any "
"nodes. I will ignore it.");
return;
}
// copy nodes from element group
selected_first.copy(first_surf.getNodeGroup().getNodes());
selected_second.copy(second_surf.getNodeGroup().getNodes());
// coordinates
const Array<Real> & coords = mesh.getNodes();
const UInt dim = mesh.getSpatialDimension();
// variables to find min and max of surfaces
Real first_max[3], first_min[3];
Real second_max[3], second_min[3];
for (UInt i = 0; i < dim; ++i) {
first_min[i] = std::numeric_limits<Real>::max();
second_min[i] = std::numeric_limits<Real>::max();
first_max[i] = -std::numeric_limits<Real>::max();
second_max[i] = -std::numeric_limits<Real>::max();
}
// find min and max of surface nodes
for (Array<UInt>::scalar_iterator it = selected_first.begin();
it != selected_first.end(); ++it) {
for (UInt i = 0; i < dim; ++i) {
if (first_min[i] > coords(*it, i))
first_min[i] = coords(*it, i);
if (first_max[i] < coords(*it, i))
first_max[i] = coords(*it, i);
}
}
for (Array<UInt>::scalar_iterator it = selected_second.begin();
it != selected_second.end(); ++it) {
for (UInt i = 0; i < dim; ++i) {
if (second_min[i] > coords(*it, i))
second_min[i] = coords(*it, i);
if (second_max[i] < coords(*it, i))
second_max[i] = coords(*it, i);
}
}
// find direction of pbc
Int first_dir = -1;
#ifndef AKANTU_NDEBUG
Int second_dir = -2;
#endif
for (UInt i = 0; i < dim; ++i) {
if (Math::are_float_equal(first_min[i], first_max[i])) {
first_dir = i;
}
#ifndef AKANTU_NDEBUG
if (Math::are_float_equal(second_min[i], second_max[i])) {
second_dir = i;
}
#endif
}
AKANTU_DEBUG_ASSERT(first_dir == second_dir,
"Surface pair has not same direction. Surface "
<< surface_pair.first << " dir=" << first_dir
<< " ; Surface " << surface_pair.second
<< " dir=" << second_dir);
UInt dir = first_dir;
// match pairs
if (first_min[dir] < second_min[dir])
MeshUtils::matchPBCPairs(mesh, dir, selected_first, selected_second,
pbc_pair);
else
MeshUtils::matchPBCPairs(mesh, dir, selected_second, selected_first,
pbc_pair);
}
/* -------------------------------------------------------------------------- */
void MeshUtils::matchPBCPairs(const Mesh & mesh, const UInt dir,
Array<UInt> & selected_left,
Array<UInt> & selected_right,
std::map<UInt, UInt> & pbc_pair) {
// tolerance is that large because most meshers generate points coordinates
// with single precision only (it is the case of GMSH for instance)
Real tolerance = 1e-7;
const UInt dim = mesh.getSpatialDimension();
Real normalization = mesh.getUpperBounds()(dir) - mesh.getLowerBounds()(dir);
AKANTU_DEBUG_ASSERT(std::abs(normalization) > Math::getTolerance(),
"In matchPBCPairs: The normalization is zero. "
<< "Did you compute the bounding box of the mesh?");
UInt odir_1 = UInt(-1), odir_2 = UInt(-1);
if (dim == 3) {
if (dir == _x) {
odir_1 = _y;
odir_2 = _z;
} else if (dir == _y) {
odir_1 = _x;
odir_2 = _z;
} else if (dir == _z) {
odir_1 = _x;
odir_2 = _y;
}
} else if (dim == 2) {
if (dir == _x) {
odir_1 = _y;
} else if (dir == _y) {
odir_1 = _x;
}
}
CoordinatesComparison compare_nodes(dim, odir_1, odir_2, normalization,
tolerance, mesh.getNodes());
std::sort(selected_left.begin(), selected_left.end(), compare_nodes);
std::sort(selected_right.begin(), selected_right.end(), compare_nodes);
Array<UInt>::scalar_iterator it_left = selected_left.begin();
Array<UInt>::scalar_iterator end_left = selected_left.end();
Array<UInt>::scalar_iterator it_right = selected_right.begin();
Array<UInt>::scalar_iterator end_right = selected_right.end();
Array<Real>::const_vector_iterator nit = mesh.getNodes().begin(dim);
while ((it_left != end_left) && (it_right != end_right)) {
UInt i1 = *it_left;
UInt i2 = *it_right;
Vector<Real> coords1 = nit[i1];
Vector<Real> coords2 = nit[i2];
AKANTU_DEBUG_TRACE("do I pair? " << i1 << "(" << coords1 << ") with" << i2
<< "(" << coords2 << ") in direction "
<< dir);
Real dx = 0.0;
Real dy = 0.0;
if (dim >= 2)
dx = coords1(odir_1) - coords2(odir_1);
if (dim == 3)
dy = coords1(odir_2) - coords2(odir_2);
if (std::abs(dx * dx + dy * dy) / normalization < tolerance) {
// then i match these pairs
if (pbc_pair.count(i2)) {
i2 = pbc_pair[i2];
}
pbc_pair[i1] = i2;
AKANTU_DEBUG_TRACE("pairing "
<< i1 << "(" << coords1
<< ") with" << i2 << "(" << coords2
<< ") in direction " << dir);
++it_left;
++it_right;
} else if (compare_nodes(coords1, coords2)) {
++it_left;
} else {
++it_right;
}
}
AKANTU_DEBUG_INFO("found " << pbc_pair.size() << " pairs for direction "
<< dir);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/boundary_condition.hh b/src/model/boundary_condition.hh
index 26543509c..ed18419b2 100644
--- a/src/model/boundary_condition.hh
+++ b/src/model/boundary_condition.hh
@@ -1,106 +1,106 @@
/**
* @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"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
template <class ModelType>
class BoundaryCondition {
/* ------------------------------------------------------------------------ */
/* Typedefs */
/* ------------------------------------------------------------------------ */
private:
/* ------------------------------------------------------------------------ */
/* Constructors / Destructors / Initializers */
/* ------------------------------------------------------------------------ */
public:
BoundaryCondition() : model(NULL), primal(NULL), dual(NULL), primal_increment(NULL) {}
///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;
};
-__END_AKANTU__
+} // 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 92aee20bc..cbc7358d8 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__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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() {}
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const;
protected:
Matrix<Real> bc_data;
};
/* ---------------------------------------------------------------------- */
class FromSameDim : public NeumannFunctor {
public:
explicit FromSameDim(const Vector<Real> & vec) : bc_data(vec) {}
virtual ~FromSameDim() {}
public:
inline void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual, const Vector<Real> & coord,
const Vector<Real> & normals) const;
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;
};
} // end namespace Neumann
} // end namespace BC
-__END_AKANTU__
+} // akantu
#include "boundary_condition_functor_inline_impl.cc"
#endif /* __AKANTU_BOUNDARY_CONDITION_FUNCTOR_HH__ */
diff --git a/src/model/boundary_condition_functor_inline_impl.cc b/src/model/boundary_condition_functor_inline_impl.cc
index 712363225..fd76c9510 100644
--- a/src/model/boundary_condition_functor_inline_impl.cc
+++ b/src/model/boundary_condition_functor_inline_impl.cc
@@ -1,139 +1,139 @@
/**
* @file boundary_condition_functor_inline_impl.cc
*
* @author Dana Christen <dana.christen@gmail.com>
*
* @date creation: Fri May 03 2013
* @date last modification: Thu Oct 15 2015
*
* @brief implementation of the BC::Functors
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#define DIRICHLET_SANITY_CHECK \
AKANTU_DEBUG_ASSERT( \
coord.size() <= flags.size(), \
"The coordinates and flags vectors given to the boundary" \
<< " condition functor have different sizes!"); \
AKANTU_DEBUG_ASSERT( \
primal.size() <= coord.size(), \
"The primal vector and coordinates vector given" \
<< " to the boundary condition functor have different sizes!");
#define NEUMANN_SANITY_CHECK \
AKANTU_DEBUG_ASSERT( \
coord.size() <= normals.size(), \
"The coordinates and normals vectors given to the" \
<< " boundary condition functor have different sizes!"); \
AKANTU_DEBUG_ASSERT( \
dual.size() <= coord.size(), \
"The dual vector and coordinates vector given to" \
<< " the boundary condition functor have different sizes!");
-__BEGIN_AKANTU__
+namespace akantu {
namespace BC {
namespace Dirichlet {
/* ------------------------------------------------------------------------ */
inline void FlagOnly::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags, __attribute__((unused))
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
}
/* ------------------------------------------------------------------------ */
inline void FreeBoundary::
operator()(__attribute__((unused)) UInt node, Vector<bool> & flags,
__attribute__((unused)) Vector<Real> & primal,
__attribute__((unused)) const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = false;
}
/* ------------------------------------------------------------------------ */
inline void FixedValue::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
primal(this->axis) = value;
}
/* ------------------------------------------------------------------------ */
inline void IncrementValue::operator()(__attribute__((unused)) UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
__attribute__((unused))
const Vector<Real> & coord) const {
DIRICHLET_SANITY_CHECK;
flags(this->axis) = true;
primal(this->axis) += value;
}
} // end namespace Dirichlet
/* -------------------------------------------------------------------------- */
/* Neumann */
/* -------------------------------------------------------------------------- */
namespace Neumann {
/* ------------------------------------------------------------------------ */
inline void FreeBoundary::
operator()(__attribute__((unused)) const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused)) const Vector<Real> & coord,
__attribute__((unused)) const Vector<Real> & normals) const {
for (UInt i(0); i < dual.size(); ++i) {
dual(i) = 0.0;
}
}
/* ------------------------------------------------------------------------ */
inline void FromHigherDim::operator()(__attribute__((unused))
const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused))
const Vector<Real> & coord,
const Vector<Real> & normals) const {
dual.mul<false>(this->bc_data, normals);
}
/* ------------------------------------------------------------------------ */
inline void FromSameDim::
operator()(__attribute__((unused)) const IntegrationPoint & quad_point,
Vector<Real> & dual,
__attribute__((unused)) const Vector<Real> & coord,
__attribute__((unused)) const Vector<Real> & normals) const {
dual = this->bc_data;
}
} // end namespace Neumann
} // end namespace BC
-__END_AKANTU__
+} // akantu
diff --git a/src/model/boundary_condition_python_functor.cc b/src/model/boundary_condition_python_functor.cc
index cae69819a..fbaf982cd 100644
--- a/src/model/boundary_condition_python_functor.cc
+++ b/src/model/boundary_condition_python_functor.cc
@@ -1,66 +1,66 @@
/**
* @file boundary_condition_python_functor.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Wed Aug 31 2011
* @date last modification: Fri Nov 13 2015
*
* @brief Interface for BC::Functor written in python
*
* @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_python_functor.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
namespace BC {
void PythonFunctorDirichlet::operator ()(UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const{
this->callFunctor<void>("operator",node,flags,primal,coord);
}
void PythonFunctorNeumann::operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual,
const Vector<Real> & coord,
const Vector<Real> & normals) const{
this->callFunctor<void>("operator",quad_point,dual,coord,normals);
}
}//end namespace BC
-__END_AKANTU__
+} // akantu
diff --git a/src/model/boundary_condition_python_functor.hh b/src/model/boundary_condition_python_functor.hh
index ff93856d5..50549bd2b 100644
--- a/src/model/boundary_condition_python_functor.hh
+++ b/src/model/boundary_condition_python_functor.hh
@@ -1,116 +1,116 @@
/**
* @file boundary_condition_python_functor.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Fri Nov 13 2015
*
* @brief interface for BC::Functor writen in python
*
* @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 "boundary_condition_functor.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_BOUNDARY_CONDITION_PYTHON_FUNCTOR_HH__
#define __AKANTU_BOUNDARY_CONDITION_PYTHON_FUNCTOR_HH__
/* -------------------------------------------------------------------------- */
#include "boundary_condition_functor.hh"
#include "python_functor.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
namespace BC {
class PythonFunctorDirichlet : public PythonFunctor, public Functor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PythonFunctorDirichlet(PyObject * obj) : PythonFunctor(obj) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void operator()(UInt node,
Vector<bool> & flags,
Vector<Real> & primal,
const Vector<Real> & coord) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
static const Type type = _dirichlet;
};
/* -------------------------------------------------------------------------- */
class PythonFunctorNeumann : public PythonFunctor, public Functor{
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PythonFunctorNeumann(PyObject * obj) : PythonFunctor(obj) {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void operator()(const IntegrationPoint & quad_point,
Vector<Real> & dual,
const Vector<Real> & coord,
const Vector<Real> & normals) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
public:
static const Type type = _neumann;
};
}//end namespace BC
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_BOUNDARY_CONDITION_PYTHON_FUNCTOR_HH__ */
diff --git a/src/model/boundary_condition_tmpl.hh b/src/model/boundary_condition_tmpl.hh
index 299e35fe5..4957dd61e 100644
--- a/src/model/boundary_condition_tmpl.hh
+++ b/src/model/boundary_condition_tmpl.hh
@@ -1,270 +1,270 @@
/**
* @file boundary_condition_tmpl.hh
*
* @author Dana Christen <dana.christen@gmail.com>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri May 03 2013
* @date last modification: Fri Oct 16 2015
*
* @brief implementation of the applyBC
*
* @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 "element_group.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename ModelType>
void BoundaryCondition<ModelType>::initBC(ModelType & model,
Array<Real> & primal,
Array<Real> & dual) {
this->model = &model;
this->primal = &primal;
this->dual = &dual;
if (this->model->getSpatialDimension() > 1)
this->model->initFEEngineBoundary();
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
void BoundaryCondition<ModelType>::initBC(ModelType & model,
Array<Real> & primal,
Array<Real> & primal_increment,
Array<Real> & dual) {
this->initBC(model, primal, dual);
this->primal_increment = &primal_increment;
}
/* -------------------------------------------------------------------------- */
/* Partial specialization for DIRICHLET functors */
template <typename ModelType>
template <typename FunctorType>
struct BoundaryCondition<ModelType>::TemplateFunctionWrapper<
FunctorType, BC::Functor::_dirichlet> {
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance) {
ModelType & model = bc_instance.getModel();
Array<Real> & primal = bc_instance.getPrimal();
const Array<Real> & coords = model.getMesh().getNodes();
Array<bool> & boundary_flags = model.getBlockedDOFs();
UInt dim = model.getMesh().getSpatialDimension();
Array<Real>::vector_iterator primal_iter =
primal.begin(primal.getNbComponent());
Array<Real>::const_vector_iterator coords_iter = coords.begin(dim);
Array<bool>::vector_iterator flags_iter =
boundary_flags.begin(boundary_flags.getNbComponent());
for (ElementGroup::const_node_iterator nodes_it(group.node_begin());
nodes_it != group.node_end(); ++nodes_it) {
UInt n = *nodes_it;
Vector<bool> flag(flags_iter[n]);
Vector<Real> primal(primal_iter[n]);
Vector<Real> coords(coords_iter[n]);
func(n, flag, primal, coords);
}
}
};
/* -------------------------------------------------------------------------- */
/* Partial specialization for NEUMANN functors */
template <typename ModelType>
template <typename FunctorType>
struct BoundaryCondition<ModelType>::TemplateFunctionWrapper<
FunctorType, BC::Functor::_neumann> {
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance) {
UInt dim = bc_instance.getModel().getSpatialDimension();
switch (dim) {
case 1: {
AKANTU_DEBUG_TO_IMPLEMENT();
break;
}
case 2:
case 3: {
applyBC(func, group, bc_instance, _not_ghost);
applyBC(func, group, bc_instance, _ghost);
break;
}
}
}
static inline void applyBC(const FunctorType & func,
const ElementGroup & group,
BoundaryCondition<ModelType> & bc_instance,
GhostType ghost_type) {
ModelType & model = bc_instance.getModel();
Array<Real> & dual = bc_instance.getDual();
const Mesh & mesh = model.getMesh();
const Array<Real> & nodes_coords = mesh.getNodes();
const FEEngine & fem_boundary = model.getFEEngineBoundary();
UInt dim = model.getSpatialDimension();
UInt nb_degree_of_freedom = dual.getNbComponent();
IntegrationPoint quad_point;
quad_point.ghost_type = ghost_type;
ElementGroup::type_iterator type_it = group.firstType(dim - 1, ghost_type);
ElementGroup::type_iterator type_end = group.lastType(dim - 1, ghost_type);
// Loop over the boundary element types
for (; type_it != type_end; ++type_it) {
const Array<UInt> & element_ids = group.getElements(*type_it, ghost_type);
Array<UInt>::const_scalar_iterator elem_iter = element_ids.begin();
Array<UInt>::const_scalar_iterator elem_iter_end = element_ids.end();
UInt nb_quad_points =
fem_boundary.getNbIntegrationPoints(*type_it, ghost_type);
UInt nb_elements = element_ids.getSize();
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(*type_it);
Array<Real> * dual_before_integ = new Array<Real>(
nb_elements * nb_quad_points, nb_degree_of_freedom, 0.);
Array<Real> * quad_coords =
new Array<Real>(nb_elements * nb_quad_points, dim);
const Array<Real> & normals_on_quad =
fem_boundary.getNormalsOnIntegrationPoints(*type_it, ghost_type);
fem_boundary.interpolateOnIntegrationPoints(
nodes_coords, *quad_coords, dim, *type_it, ghost_type, element_ids);
Array<Real>::const_vector_iterator normals_begin =
normals_on_quad.begin(dim);
Array<Real>::const_vector_iterator normals_iter;
Array<Real>::const_vector_iterator quad_coords_iter =
quad_coords->begin(dim);
Array<Real>::vector_iterator dual_iter =
dual_before_integ->begin(nb_degree_of_freedom);
quad_point.type = *type_it;
for (; elem_iter != elem_iter_end; ++elem_iter) {
UInt el = *elem_iter;
quad_point.element = el;
normals_iter = normals_begin + el * nb_quad_points;
for (UInt q(0); q < nb_quad_points; ++q) {
quad_point.num_point = q;
func(quad_point, *dual_iter, *quad_coords_iter, *normals_iter);
++dual_iter;
++quad_coords_iter;
++normals_iter;
}
}
delete quad_coords;
/* -------------------------------------------------------------------- */
// Initialization of iterators
Array<Real>::matrix_iterator dual_iter_mat =
dual_before_integ->begin(nb_degree_of_freedom, 1);
elem_iter = element_ids.begin();
Array<Real>::const_matrix_iterator shapes_iter_begin =
fem_boundary.getShapes(*type_it, ghost_type)
.begin(1, nb_nodes_per_element);
Array<Real> * dual_by_shapes =
new Array<Real>(nb_elements * nb_quad_points,
nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::matrix_iterator dual_by_shapes_iter =
dual_by_shapes->begin(nb_degree_of_freedom, nb_nodes_per_element);
Array<Real>::const_matrix_iterator shapes_iter;
/* -------------------------------------------------------------------- */
// Loop computing dual x shapes
for (; elem_iter != elem_iter_end; ++elem_iter) {
shapes_iter = shapes_iter_begin + *elem_iter * nb_quad_points;
for (UInt q(0); q < nb_quad_points;
++q, ++dual_iter_mat, ++dual_by_shapes_iter, ++shapes_iter) {
dual_by_shapes_iter->mul<false, false>(*dual_iter_mat, *shapes_iter);
}
}
delete dual_before_integ;
Array<Real> * dual_by_shapes_integ = new Array<Real>(
nb_elements, nb_degree_of_freedom * nb_nodes_per_element);
fem_boundary.integrate(*dual_by_shapes, *dual_by_shapes_integ,
nb_degree_of_freedom * nb_nodes_per_element,
*type_it, ghost_type, element_ids);
delete dual_by_shapes;
// assemble the result into force vector
model.getDOFManager().assembleElementalArrayLocalArray(
*dual_by_shapes_integ, dual, *type_it, ghost_type, 1., element_ids);
delete dual_by_shapes_integ;
}
}
};
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void BoundaryCondition<ModelType>::applyBC(const FunctorType & func) {
GroupManager::const_element_group_iterator bit =
model->getMesh().getGroupManager().element_group_begin();
GroupManager::const_element_group_iterator bend =
model->getMesh().getGroupManager().element_group_end();
for (; bit != bend; ++bit)
applyBC(func, *bit);
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void
BoundaryCondition<ModelType>::applyBC(const FunctorType & func,
const std::string & group_name) {
try {
const ElementGroup & element_group =
model->getMesh().getElementGroup(group_name);
applyBC(func, element_group);
} catch (akantu::debug::Exception e) {
AKANTU_EXCEPTION("Error applying a boundary condition onto \""
<< group_name << "\"! [" << e.what() << "]");
}
}
/* -------------------------------------------------------------------------- */
template <typename ModelType>
template <typename FunctorType>
inline void
BoundaryCondition<ModelType>::applyBC(const FunctorType & func,
const ElementGroup & element_group) {
#if !defined(AKANTU_NDEBUG)
if (element_group.getDimension() != model->getSpatialDimension() - 1)
AKANTU_DEBUG_WARNING("The group "
<< element_group.getName()
<< " does not contain only boundaries elements");
#endif
TemplateFunctionWrapper<FunctorType>::applyBC(func, element_group, *this);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/common/neighborhood_base.cc b/src/model/common/neighborhood_base.cc
index fd1852828..7f8858b9b 100644
--- a/src/model/common/neighborhood_base.cc
+++ b/src/model/common/neighborhood_base.cc
@@ -1,314 +1,314 @@
/**
* @file neighborhood_base.cc
*
* @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 Implementation of generic neighborhood base
*
* @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 "grid_synchronizer.hh"
#include "model.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NeighborhoodBase::NeighborhoodBase(Model & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), model(model), neighborhood_radius(0.),
spatial_grid(NULL), is_creating_grid(false), grid_synchronizer(NULL),
quad_coordinates(quad_coordinates),
spatial_dimension(this->model.getMesh().getSpatialDimension()) {
AKANTU_DEBUG_IN();
this->registerDataAccessor(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NeighborhoodBase::~NeighborhoodBase() {
AKANTU_DEBUG_IN();
delete spatial_grid;
delete grid_synchronizer;
AKANTU_DEBUG_OUT();
}
// /* --------------------------------------------------------------------------
// */
// void NeighborhoodBase::createSynchronizerRegistry(DataAccessor *
// data_accessor){
// this->synch_registry = new SynchronizerRegistry(*data_accessor);
// }
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::initNeighborhood() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Creating the grid");
this->createGrid();
AKANTU_DEBUG_OUT();
}
/* ------------------------------------------------------------------------- */
void NeighborhoodBase::createGrid() {
AKANTU_DEBUG_IN();
const Real safety_factor = 1.2; // for the cell grid spacing
Mesh & mesh = this->model.getMesh();
mesh.computeBoundingBox();
const Vector<Real> & lower_bounds = mesh.getLocalLowerBounds();
const Vector<Real> & upper_bounds = mesh.getLocalUpperBounds();
Vector<Real> center = 0.5 * (upper_bounds + lower_bounds);
Vector<Real> spacing(spatial_dimension,
this->neighborhood_radius * safety_factor);
spatial_grid =
new SpatialGrid<IntegrationPoint>(spatial_dimension, spacing, center);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::updatePairList() {
AKANTU_DEBUG_IN();
//// loop over all quads -> all cells
SpatialGrid<IntegrationPoint>::cells_iterator cell_it =
spatial_grid->beginCells();
SpatialGrid<IntegrationPoint>::cells_iterator cell_end =
spatial_grid->endCells();
Vector<Real> q1_coords(spatial_dimension);
Vector<Real> q2_coords(spatial_dimension);
IntegrationPoint q1;
IntegrationPoint q2;
UInt counter = 0;
for (; cell_it != cell_end; ++cell_it) {
AKANTU_DEBUG_INFO("Looping on next cell");
SpatialGrid<IntegrationPoint>::Cell::iterator first_quad =
spatial_grid->beginCell(*cell_it);
SpatialGrid<IntegrationPoint>::Cell::iterator last_quad =
spatial_grid->endCell(*cell_it);
for (; first_quad != last_quad; ++first_quad, ++counter) {
q1 = *first_quad;
if (q1.ghost_type == _ghost)
break;
Array<Real>::const_vector_iterator coords_type_1_it =
this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
q1_coords = coords_type_1_it[q1.global_num];
AKANTU_DEBUG_INFO("Current quadrature point in this cell: " << q1);
SpatialGrid<IntegrationPoint>::CellID cell_id =
spatial_grid->getCellID(q1_coords);
/// loop over all the neighbouring cells of the current quad
SpatialGrid<IntegrationPoint>::neighbor_cells_iterator first_neigh_cell =
spatial_grid->beginNeighborCells(cell_id);
SpatialGrid<IntegrationPoint>::neighbor_cells_iterator last_neigh_cell =
spatial_grid->endNeighborCells(cell_id);
for (; first_neigh_cell != last_neigh_cell; ++first_neigh_cell) {
SpatialGrid<IntegrationPoint>::Cell::iterator first_neigh_quad =
spatial_grid->beginCell(*first_neigh_cell);
SpatialGrid<IntegrationPoint>::Cell::iterator last_neigh_quad =
spatial_grid->endCell(*first_neigh_cell);
// loop over the quadrature point in the current neighboring cell
for (; first_neigh_quad != last_neigh_quad; ++first_neigh_quad) {
q2 = *first_neigh_quad;
Array<Real>::const_vector_iterator coords_type_2_it =
this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
q2_coords = coords_type_2_it[q2.global_num];
Real distance = q1_coords.distance(q2_coords);
if (distance <= this->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));
}
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::savePairs(const std::string & filename) const {
std::ofstream pout;
std::stringstream sstr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
pout.open(sstr.str().c_str());
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType)gt;
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
for (; first_pair != last_pair; ++first_pair) {
const IntegrationPoint & q1 = first_pair->first;
const IntegrationPoint & q2 = first_pair->second;
pout << q1 << " " << q2 << " " << std::endl;
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::saveNeighborCoords(const std::string & filename) const {
/// this function is not optimazed and only used for tests on small meshes
/// @todo maybe optimize this function for better performance?
Vector<Real> q1_coords(spatial_dimension);
Vector<Real> q2_coords(spatial_dimension);
IntegrationPoint q1;
IntegrationPoint q2;
std::ofstream pout;
std::stringstream sstr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int prank = comm.whoAmI();
sstr << filename << "." << prank;
pout.open(sstr.str().c_str());
/// loop over all the quads and write the position of their neighbors
SpatialGrid<IntegrationPoint>::cells_iterator cell_it =
spatial_grid->beginCells();
SpatialGrid<IntegrationPoint>::cells_iterator cell_end =
spatial_grid->endCells();
for (; cell_it != cell_end; ++cell_it) {
SpatialGrid<IntegrationPoint>::Cell::iterator first_quad =
spatial_grid->beginCell(*cell_it);
SpatialGrid<IntegrationPoint>::Cell::iterator last_quad =
spatial_grid->endCell(*cell_it);
for (; first_quad != last_quad; ++first_quad) {
q1 = *first_quad;
Array<Real>::const_vector_iterator coords_type_1_it =
this->quad_coordinates(q1.type, q1.ghost_type)
.begin(spatial_dimension);
q1_coords = coords_type_1_it[q1.global_num];
pout << "#neighbors for quad " << q1.global_num << std::endl;
pout << q1_coords << std::endl;
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType)gt;
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
for (; first_pair != last_pair; ++first_pair) {
if (q1 == first_pair->first && first_pair->second != q1) {
q2 = first_pair->second;
Array<Real>::const_vector_iterator coords_type_2_it =
this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
q2_coords = coords_type_2_it[q2.global_num];
pout << q2_coords << std::endl;
}
if (q1 == first_pair->second && first_pair->first != q1) {
q2 = first_pair->first;
Array<Real>::const_vector_iterator coords_type_2_it =
this->quad_coordinates(q2.type, q2.ghost_type)
.begin(spatial_dimension);
q2_coords = coords_type_2_it[q2.global_num];
pout << q2_coords << std::endl;
}
}
}
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodBase::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
AKANTU_DEBUG_IN();
FEEngine & fem = this->model.getFEEngine();
UInt nb_quad = 0;
// Change the pairs in new global numbering
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType)gt;
PairList::iterator first_pair = pair_list[ghost_type2].begin();
PairList::iterator last_pair = pair_list[ghost_type2].end();
for (; first_pair != last_pair; ++first_pair) {
IntegrationPoint & q1 = first_pair->first;
if (new_numbering.exists(q1.type, q1.ghost_type)) {
UInt q1_new_el = new_numbering(q1.type, q1.ghost_type)(q1.element);
AKANTU_DEBUG_ASSERT(q1_new_el != UInt(-1), "A local quadrature_point "
"as been removed instead of "
"just being renumbered");
q1.element = q1_new_el;
nb_quad = fem.getNbIntegrationPoints(q1.type, q1.ghost_type);
q1.global_num = nb_quad * q1.element + q1.num_point;
}
IntegrationPoint & q2 = first_pair->second;
if (new_numbering.exists(q2.type, q2.ghost_type)) {
UInt q2_new_el = new_numbering(q2.type, q2.ghost_type)(q2.element);
AKANTU_DEBUG_ASSERT(q2_new_el != UInt(-1), "A local quadrature_point "
"as been removed instead of "
"just being renumbered");
q2.element = q2_new_el;
nb_quad = fem.getNbIntegrationPoints(q2.type, q2.ghost_type);
q2.global_num = nb_quad * q2.element + q2.num_point;
}
}
}
this->grid_synchronizer->onElementsRemoved(element_list, new_numbering,
event);
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/common/neighborhood_base.hh b/src/model/common/neighborhood_base.hh
index dbbaa4a39..7b4546880 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;
} // akantu
-__BEGIN_AKANTU__
+namespace akantu {
class NeighborhoodBase : public 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();
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 insertQuad(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;
/// 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
SpatialGrid<IntegrationPoint> * spatial_grid;
bool is_creating_grid;
/// the grid synchronizer for parallel computations
GridSynchronizer * grid_synchronizer;
/// the quadrature point positions
const ElementTypeMapArray<Real> & quad_coordinates;
/// the spatial dimension of the problem
const UInt spatial_dimension;
};
-__END_AKANTU__
+} // akantu
#include "neighborhood_base_inline_impl.cc"
#endif /* __AKANTU_NEIGHBORHOOD_BASE_HH__ */
diff --git a/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc b/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
index 76f66985e..7e7a03bc5 100644
--- a/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
+++ b/src/model/common/neighborhoods_criterion_evaluation/neighborhood_max_criterion.cc
@@ -1,312 +1,312 @@
/**
* @file neighborhood_max_criterion.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Thu Oct 15 2015
* @date last modification: Tue Nov 24 2015
*
* @brief Implementation of class NeighborhoodMaxCriterion
*
* @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_max_criterion.hh"
#include "grid_synchronizer.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NeighborhoodMaxCriterion::NeighborhoodMaxCriterion(
Model & model,
const ElementTypeMapReal & quad_coordinates, const ID & criterion_id,
const ID & id, const MemoryID & memory_id)
: NeighborhoodBase(model, quad_coordinates, id, memory_id),
Parsable(_st_non_local, id), is_highest("is_highest", id, memory_id),
criterion(criterion_id, id, memory_id) {
AKANTU_DEBUG_IN();
this->registerParam("radius", neighborhood_radius, 100.,
_pat_parsable | _pat_readable, "Non local radius");
Mesh & mesh = this->model.getMesh();
/// allocate the element type map arrays for _not_ghosts: One entry per quad
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);
for (; it != last_type; ++it) {
UInt new_size = this->quad_coordinates(*it, ghost_type).getSize();
this->is_highest.alloc(new_size, 1, *it, ghost_type, true);
this->criterion.alloc(new_size, 1, *it, ghost_type, true);
}
/// criterion needs allocation also for ghost
ghost_type = _ghost;
it = mesh.firstType(spatial_dimension, ghost_type);
last_type = mesh.lastType(spatial_dimension, ghost_type);
for (; it != last_type; ++it) {
UInt new_size = this->quad_coordinates(*it, ghost_type).getSize();
this->criterion.alloc(new_size, 1, *it, ghost_type, true);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NeighborhoodMaxCriterion::~NeighborhoodMaxCriterion() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::initNeighborhood() {
AKANTU_DEBUG_IN();
/// parse the input parameter
const Parser & parser = getStaticParser();
const ParserSection & section_neighborhood =
*(parser.getSubSections(_st_neighborhood).first);
this->parseSection(section_neighborhood);
AKANTU_DEBUG_INFO("Creating the grid");
this->createGrid();
/// insert the non-ghost quads into the grid
this->insertAllQuads(_not_ghost);
/// store the number of current ghost elements for each type in the mesh
ElementTypeMap<UInt> nb_ghost_protected;
Mesh & mesh = this->model.getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _ghost);
for (; it != last_type; ++it)
nb_ghost_protected(mesh.getNbElement(*it, _ghost), *it, _ghost);
/// create the grid synchronizer
this->createGridSynchronizer();
/// insert the ghost quads into the grid
this->insertAllQuads(_ghost);
/// create the pair lists
this->updatePairList();
/// remove the unneccessary ghosts
this->cleanupExtraGhostElements(nb_ghost_protected);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::createGridSynchronizer() {
this->is_creating_grid = true;
std::set<SynchronizationTag> tags;
tags.insert(_gst_nh_criterion);
std::stringstream sstr;
sstr << getID() << ":grid_synchronizer";
this->grid_synchronizer = GridSynchronizer::createGridSynchronizer(
this->model.getMesh(), *spatial_grid, sstr.str(), this, tags, 0,
false);
this->is_creating_grid = false;
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::insertAllQuads(const GhostType & ghost_type) {
IntegrationPoint q;
q.ghost_type = ghost_type;
Mesh & mesh = this->model.getMesh();
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);
UInt nb_quad =
this->model.getFEEngine().getNbIntegrationPoints(*it, ghost_type);
const Array<Real> & quads = this->quad_coordinates(*it, ghost_type);
q.type = *it;
Array<Real>::const_vector_iterator quad = quads.begin(spatial_dimension);
for (UInt e = 0; e < nb_element; ++e) {
q.element = e;
for (UInt nq = 0; nq < nb_quad; ++nq) {
q.num_point = nq;
q.global_num = q.element * nb_quad + nq;
spatial_grid->insert(q, *quad);
++quad;
}
}
}
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::findMaxQuads(
std::vector<IntegrationPoint> & max_quads) {
AKANTU_DEBUG_IN();
/// clear the element type maps
this->is_highest.clear();
this->criterion.clear();
/// update the values of the criterion
this->model.updateDataForNonLocalCriterion(criterion);
/// start the exchange the value of the criterion on the ghost elements
this->model.asynchronousSynchronize(_gst_nh_criterion);
/// compare to not-ghost neighbors
checkNeighbors(_not_ghost);
/// finish the exchange
this->model.waitEndSynchronize(_gst_nh_criterion);
/// compare to ghost neighbors
checkNeighbors(_ghost);
/// extract the quads with highest criterion in their neighborhood
IntegrationPoint quad;
quad.ghost_type = _not_ghost;
Mesh & mesh = this->model.getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _not_ghost);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _not_ghost);
for (; it != last_type; ++it) {
quad.type = *it;
Array<bool>::const_scalar_iterator is_highest_it =
is_highest(*it, _not_ghost).begin();
Array<bool>::const_scalar_iterator is_highest_end =
is_highest(*it, _not_ghost).end();
UInt nb_quadrature_points =
this->model.getFEEngine().getNbIntegrationPoints(*it, _not_ghost);
UInt q = 0;
/// loop over is_highest for the current element type
for (; is_highest_it != is_highest_end; ++is_highest_it, ++q) {
if (*is_highest_it) {
/// gauss point has the highest stress in his neighbourhood
quad.element = q / nb_quadrature_points;
quad.global_num = q;
quad.num_point = q % nb_quadrature_points;
max_quads.push_back(quad);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::checkNeighbors(const GhostType & ghost_type2) {
AKANTU_DEBUG_IN();
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
// Compute the weights
for (; first_pair != last_pair; ++first_pair) {
const IntegrationPoint & lq1 = first_pair->first;
const IntegrationPoint & lq2 = first_pair->second;
Array<bool> & has_highest_eq_stress_1 =
is_highest(lq1.type, lq1.ghost_type);
const Array<Real> & criterion_1 = this->criterion(lq1.type, lq1.ghost_type);
const Array<Real> & criterion_2 = this->criterion(lq2.type, lq2.ghost_type);
if (criterion_1(lq1.global_num) < criterion_2(lq2.global_num))
has_highest_eq_stress_1(lq1.global_num) = false;
else if (ghost_type2 != _ghost) {
Array<bool> & has_highest_eq_stress_2 =
is_highest(lq2.type, lq2.ghost_type);
has_highest_eq_stress_2(lq2.global_num) = false;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NeighborhoodMaxCriterion::cleanupExtraGhostElements(
const ElementTypeMap<UInt> & nb_ghost_protected) {
Mesh & mesh = this->model.getMesh();
/// create remove elements event
RemovedElementsEvent remove_elem(mesh);
/// create set of ghosts to keep
std::set<Element> relevant_ghost_elements;
PairList::const_iterator first_pair = pair_list[_ghost].begin();
PairList::const_iterator last_pair = pair_list[_ghost].end();
for (; first_pair != last_pair; ++first_pair) {
const IntegrationPoint & q2 = first_pair->second;
relevant_ghost_elements.insert(q2);
}
Array<Element> ghosts_to_erase(0);
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _ghost);
Element element;
element.ghost_type = _ghost;
std::set<Element>::const_iterator end = relevant_ghost_elements.end();
for (; it != last_type; ++it) {
element.type = *it;
UInt nb_ghost_elem = mesh.getNbElement(*it, _ghost);
UInt nb_ghost_elem_protected = 0;
try {
nb_ghost_elem_protected = nb_ghost_protected(*it, _ghost);
} catch (...) {
}
if (!remove_elem.getNewNumbering().exists(*it, _ghost))
remove_elem.getNewNumbering().alloc(nb_ghost_elem, 1, *it, _ghost);
else
remove_elem.getNewNumbering(*it, _ghost).resize(nb_ghost_elem);
Array<UInt> & new_numbering = remove_elem.getNewNumbering(*it, _ghost);
for (UInt g = 0; g < nb_ghost_elem; ++g) {
element.element = g;
if (element.element >= nb_ghost_elem_protected &&
relevant_ghost_elements.find(element) == end) {
ghosts_to_erase.push_back(element);
new_numbering(element.element) = UInt(-1);
}
}
/// renumber remaining ghosts
UInt ng = 0;
for (UInt g = 0; g < nb_ghost_elem; ++g) {
if (new_numbering(g) != UInt(-1)) {
new_numbering(g) = ng;
++ng;
}
}
}
mesh.sendEvent(remove_elem);
this->onElementsRemoved(ghosts_to_erase, remove_elem.getNewNumbering(),
remove_elem);
}
-__END_AKANTU__
+} // akantu
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 59744a10f..3ea9e3e94 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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the neighborhood
virtual void initNeighborhood();
/// create grid synchronizer and exchange ghost cells
virtual void createGridSynchronizer();
/// 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;
};
-__END_AKANTU__
+} // akantu
#include "neighborhood_max_criterion_inline_impl.cc"
#endif /* __AKANTU_NEIGHBORHOOD_MAX_CRITERION_BASE_HH__ */
diff --git a/src/model/common/non_local_toolbox/non_local_manager.cc b/src/model/common/non_local_toolbox/non_local_manager.cc
index 966e80009..763ff7843 100644
--- a/src/model/common/non_local_toolbox/non_local_manager.cc
+++ b/src/model/common/non_local_toolbox/non_local_manager.cc
@@ -1,700 +1,700 @@
/**
* @file non_local_manager.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Apr 13 2012
* @date last modification: Wed Dec 16 2015
*
* @brief Implementation of non-local manager
*
* @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 "non_local_manager.hh"
#include "base_weight_function.hh"
#include "material_non_local.hh"
#include "non_local_neighborhood.hh"
/* -------------------------------------------------------------------------- */
#include <numeric>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NonLocalManager::NonLocalManager(SolidMechanicsModel & model, const ID & id,
const MemoryID & memory_id)
: Memory(id, memory_id), Parsable(_st_neighborhoods, id), model(model),
quad_positions("quad_positions", id, memory_id),
volumes("volumes", id, memory_id),
spatial_dimension(this->model.getSpatialDimension()),
compute_stress_calls(0), dummy_registry(NULL), dummy_grid(NULL) {
Mesh & mesh = this->model.getMesh();
mesh.registerEventHandler(*this);
/// initialize the element type map array
/// it will be resized to nb_quad * nb_element during the computation of
/// coords
mesh.initElementTypeMapArray(quad_positions, spatial_dimension,
spatial_dimension, false, _ek_regular, true);
this->initElementTypeMap(1, volumes, this->model.getFEEngine());
/// parse the neighborhood information from the input file
const Parser & parser = getStaticParser();
/// iterate over all the non-local sections and store them in a map
std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
weight_sect = parser.getSubSections(_st_non_local);
Parser::const_section_iterator it = weight_sect.first;
for (; it != weight_sect.second; ++it) {
const ParserSection & section = *it;
ID name = section.getName();
this->weight_function_types[name] = section;
}
this->dummy_registry = new SynchronizerRegistry(this->dummy_accessor);
}
/* -------------------------------------------------------------------------- */
NonLocalManager::~NonLocalManager() {
/// delete neighborhoods
NeighborhoodMap::iterator it;
for (it = neighborhoods.begin(); it != neighborhoods.end(); ++it) {
if (it->second)
delete it->second;
}
/// delete non-local variables
std::map<ID, NonLocalVariable *>::iterator it_variables;
for (it_variables = non_local_variables.begin();
it_variables != non_local_variables.end(); ++it_variables) {
if (it_variables->second)
delete it_variables->second;
}
std::map<ID, ElementTypeMapReal *>::iterator it_internals;
for (it_internals = weight_function_internals.begin();
it_internals != weight_function_internals.end(); ++it_internals) {
if (it_internals->second)
delete it_internals->second;
}
std::map<ID, GridSynchronizer *>::iterator grid_synch_it;
for (grid_synch_it = dummy_synchronizers.begin();
grid_synch_it != dummy_synchronizers.end(); ++grid_synch_it) {
if (grid_synch_it->second)
delete grid_synch_it->second;
}
/// delete all objects related to the dummy synchronizers
delete dummy_registry;
delete dummy_grid;
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::setJacobians(const FEEngine & fe_engine,
const ElementKind & kind) {
Mesh & mesh = this->model.getMesh();
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt, kind);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, gt, kind);
for (; it != last_type; ++it) {
jacobians(*it, gt) =
&fe_engine.getIntegratorInterface().getJacobians(*it, gt);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::createNeighborhood(const ID & weight_func,
const ID & neighborhood_id) {
AKANTU_DEBUG_IN();
const ParserSection & section = this->weight_function_types[weight_func];
const ID weight_func_type = section.getOption();
/// create new neighborhood for given ID
std::stringstream sstr;
sstr << id << ":neighborhood:" << neighborhood_id;
if (weight_func_type == "base_wf")
neighborhoods[neighborhood_id] =
new NonLocalNeighborhood<BaseWeightFunction>(
*this, this->quad_positions, sstr.str());
else if (weight_func_type == "remove_wf")
neighborhoods[neighborhood_id] =
new NonLocalNeighborhood<RemoveDamagedWeightFunction>(
*this, this->quad_positions, sstr.str());
else if (weight_func_type == "stress_wf")
neighborhoods[neighborhood_id] =
new NonLocalNeighborhood<StressBasedWeightFunction>(
*this, this->quad_positions, sstr.str());
else if (weight_func_type == "damage_wf")
neighborhoods[neighborhood_id] =
new NonLocalNeighborhood<DamagedWeightFunction>(
*this, this->quad_positions, sstr.str());
else
AKANTU_EXCEPTION("error in weight function type provided in material file");
neighborhoods[neighborhood_id]->parseSection(section);
neighborhoods[neighborhood_id]->initNeighborhood();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::createNeighborhoodSynchronizers() {
/// exchange all the neighborhood IDs, so that every proc knows how many
/// neighborhoods exist globally
/// First: Compute locally the maximum ID size
UInt max_id_size = 0;
UInt current_size = 0;
NeighborhoodMap::const_iterator it;
for (it = neighborhoods.begin(); it != neighborhoods.end(); ++it) {
current_size = it->first.size();
if (current_size > max_id_size)
max_id_size = current_size;
}
/// get the global maximum ID size on each proc
StaticCommunicator & static_communicator =
akantu::StaticCommunicator::getStaticCommunicator();
static_communicator.allReduce(&max_id_size, 1, _so_max);
/// get the rank for this proc and the total nb proc
UInt prank = static_communicator.whoAmI();
UInt psize = static_communicator.getNbProc();
/// exchange the number of neighborhoods on each proc
Array<Int> nb_neighborhoods_per_proc(psize);
nb_neighborhoods_per_proc(prank) = neighborhoods.size();
static_communicator.allGather(nb_neighborhoods_per_proc.storage(), 1);
/// compute the total number of neighborhoods
UInt nb_neighborhoods_global = std::accumulate(
nb_neighborhoods_per_proc.begin(), nb_neighborhoods_per_proc.end(), 0);
/// allocate an array of chars to store the names of all neighborhoods
Array<char> buffer(nb_neighborhoods_global, max_id_size);
/// starting index on this proc
UInt starting_index =
std::accumulate(nb_neighborhoods_per_proc.begin(),
nb_neighborhoods_per_proc.begin() + prank, 0);
it = neighborhoods.begin();
/// store the names of local neighborhoods in the buffer
for (UInt i = 0; i < neighborhoods.size(); ++i, ++it) {
UInt c = 0;
for (; c < it->first.size(); ++c)
buffer(i + starting_index, c) = it->first[c];
for (; c < max_id_size; ++c)
buffer(i + starting_index, c) = char(0);
}
/// store the nb of data to send in the all gather
Array<Int> buffer_size(nb_neighborhoods_per_proc);
buffer_size *= max_id_size;
/// exchange the names of all the neighborhoods with all procs
static_communicator.allGatherV(buffer.storage(), buffer_size.storage());
for (UInt i = 0; i < nb_neighborhoods_global; ++i) {
std::stringstream neighborhood_id;
for (UInt c = 0; c < max_id_size; ++c) {
if (buffer(i, c) == char(0))
break;
neighborhood_id << buffer(i, c);
}
global_neighborhoods.insert(neighborhood_id.str());
}
/// this proc does not know all the neighborhoods -> create dummy
/// grid so that this proc can participate in the all gather for
/// detecting the overlap of neighborhoods this proc doesn't know
Vector<Real> grid_center(this->spatial_dimension);
for (UInt s = 0; s < this->spatial_dimension; ++s)
grid_center(s) = std::numeric_limits<Real>::max();
dummy_grid =
new SpatialGrid<IntegrationPoint>(spatial_dimension, 0., grid_center);
std::set<SynchronizationTag> tags;
tags.insert(_gst_mnl_for_average);
tags.insert(_gst_mnl_weight);
std::set<ID>::const_iterator global_neighborhoods_it =
global_neighborhoods.begin();
for (; global_neighborhoods_it != global_neighborhoods.end();
++global_neighborhoods_it) {
it = neighborhoods.find(*global_neighborhoods_it);
if (it != neighborhoods.end()) {
it->second->createGridSynchronizer();
} else {
ID neighborhood_name = *global_neighborhoods_it;
std::stringstream sstr;
sstr << getID() << ":" << neighborhood_name << ":grid_synchronizer";
dummy_synchronizers[neighborhood_name] =
GridSynchronizer::createGridSynchronizer(
this->model.getMesh(), *dummy_grid, sstr.str(), dummy_registry,
tags, 0, false);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::flattenInternal(ElementTypeMapReal & internal_flat,
const GhostType & ghost_type,
const ElementKind & kind) {
const ID field_name = internal_flat.getName();
for (UInt m = 0; m < this->non_local_materials.size(); ++m) {
Material & material = *(this->non_local_materials[m]);
if (material.isInternal<Real>(field_name, kind))
material.flattenInternal(field_name, internal_flat, ghost_type, kind);
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::averageInternals(const GhostType & ghost_type) {
/// update the weights of the weight function
if (ghost_type == _not_ghost)
this->computeWeights();
/// loop over all neighborhoods and compute the non-local variables
NeighborhoodMap::iterator neighborhood_it = neighborhoods.begin();
NeighborhoodMap::iterator neighborhood_end = neighborhoods.end();
for (; neighborhood_it != neighborhood_end; ++neighborhood_it) {
/// loop over all the non-local variables of the given neighborhood
std::map<ID, NonLocalVariable *>::iterator non_local_variable_it =
non_local_variables.begin();
std::map<ID, NonLocalVariable *>::iterator non_local_variable_end =
non_local_variables.end();
for (; non_local_variable_it != non_local_variable_end;
++non_local_variable_it) {
NonLocalVariable * non_local_var = non_local_variable_it->second;
neighborhood_it->second->weightedAverageOnNeighbours(
non_local_var->local, non_local_var->non_local,
non_local_var->nb_component, ghost_type);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::init() {
/// store the number of current ghost elements for each type in the mesh
ElementTypeMap<UInt> nb_ghost_protected;
Mesh & mesh = this->model.getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _ghost);
for (; it != last_type; ++it)
nb_ghost_protected(mesh.getNbElement(*it, _ghost), *it, _ghost);
/// exchange the missing ghosts for the non-local neighborhoods
this->createNeighborhoodSynchronizers();
/// insert the ghost quadrature points of the non-local materials into the
/// non-local neighborhoods
for (UInt m = 0; m < this->non_local_materials.size(); ++m) {
switch (spatial_dimension) {
case 1:
dynamic_cast<MaterialNonLocal<1> &>(*(this->non_local_materials[m]))
.insertQuadsInNeighborhoods(_ghost);
break;
case 2:
dynamic_cast<MaterialNonLocal<2> &>(*(this->non_local_materials[m]))
.insertQuadsInNeighborhoods(_ghost);
break;
case 3:
dynamic_cast<MaterialNonLocal<3> &>(*(this->non_local_materials[m]))
.insertQuadsInNeighborhoods(_ghost);
break;
}
}
FEEngine & fee = this->model.getFEEngine();
this->updatePairLists();
/// cleanup the unneccessary ghost elements
this->cleanupExtraGhostElements(nb_ghost_protected);
this->setJacobians(fee, _ek_regular);
this->initNonLocalVariables();
this->computeWeights();
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::initNonLocalVariables() {
/// loop over all the non-local variables
std::map<ID, NonLocalVariable *>::iterator non_local_variable_it =
non_local_variables.begin();
std::map<ID, NonLocalVariable *>::iterator non_local_variable_end =
non_local_variables.end();
for (; non_local_variable_it != non_local_variable_end;
++non_local_variable_it) {
NonLocalVariable & variable = *(non_local_variable_it->second);
this->initElementTypeMap(variable.nb_component, variable.non_local,
this->model.getFEEngine());
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::initElementTypeMap(UInt nb_component,
ElementTypeMapReal & element_map,
const FEEngine & fee,
const ElementKind el_kind) {
Mesh & mesh = this->model.getMesh();
/// need to resize the arrays
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt, el_kind);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, gt, el_kind);
for (; it != end; ++it) {
ElementType el_type = *it;
UInt nb_element = mesh.getNbElement(*it, gt);
UInt nb_quads = fee.getNbIntegrationPoints(*it, gt);
if (!element_map.exists(el_type, gt)) {
element_map.alloc(nb_element * nb_quads, nb_component, el_type, gt);
}
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::distributeInternals(ElementKind kind) {
/// loop over all the non-local variables and copy back their values into the
/// materials
std::map<ID, NonLocalVariable *>::iterator non_local_variable_it =
non_local_variables.begin();
std::map<ID, NonLocalVariable *>::iterator non_local_variable_end =
non_local_variables.end();
for (; non_local_variable_it != non_local_variable_end;
++non_local_variable_it) {
NonLocalVariable * non_local_var = non_local_variable_it->second;
const ID field_name = non_local_var->non_local.getName();
/// loop over all the materials
for (UInt m = 0; m < this->non_local_materials.size(); ++m) {
if (this->non_local_materials[m]->isInternal<Real>(field_name, kind))
switch (spatial_dimension) {
case 1:
dynamic_cast<MaterialNonLocal<1> &>(*(this->non_local_materials[m]))
.updateNonLocalInternals(non_local_var->non_local, field_name,
non_local_var->nb_component);
break;
case 2:
dynamic_cast<MaterialNonLocal<2> &>(*(this->non_local_materials[m]))
.updateNonLocalInternals(non_local_var->non_local, field_name,
non_local_var->nb_component);
break;
case 3:
dynamic_cast<MaterialNonLocal<3> &>(*(this->non_local_materials[m]))
.updateNonLocalInternals(non_local_var->non_local, field_name,
non_local_var->nb_component);
break;
}
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::computeAllNonLocalStresses() {
/// update the flattened version of the internals
std::map<ID, NonLocalVariable *>::iterator non_local_variable_it =
non_local_variables.begin();
std::map<ID, NonLocalVariable *>::iterator non_local_variable_end =
non_local_variables.end();
for (; non_local_variable_it != non_local_variable_end;
++non_local_variable_it) {
non_local_variable_it->second->local.clear();
non_local_variable_it->second->non_local.clear();
for (UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType)gt;
this->flattenInternal(non_local_variable_it->second->local, ghost_type,
_ek_regular);
}
}
this->volumes.clear();
/// loop over all the neighborhoods and compute intiate the
/// exchange of the non-local_variables
// std::set<ID>::const_iterator global_neighborhood_it =
// global_neighborhoods.begin();
// NeighborhoodMap::iterator it;
// for(; global_neighborhood_it != global_neighborhoods.end();
// ++global_neighborhood_it) {
// it = neighborhoods.find(*global_neighborhood_it);
// if (it != neighborhoods.end())
// it->second->getSynchronizerRegistry().asynchronousSynchronize(_gst_mnl_for_average);
// else
// dummy_synchronizers[*global_neighborhood_it]->asynchronousSynchronize(dummy_accessor,
// _gst_mnl_for_average);
// }
NeighborhoodMap::iterator neighborhood_it = neighborhoods.begin();
// NeighborhoodMap::iterator neighborhood_end = neighborhoods.end();
for (; neighborhood_it != neighborhoods.end(); ++neighborhood_it) {
neighborhood_it->second->getSynchronizerRegistry().asynchronousSynchronize(
_gst_mnl_for_average);
}
this->averageInternals(_not_ghost);
AKANTU_DEBUG_INFO("Wait distant non local stresses");
/// loop over all the neighborhoods and block until all non-local
/// variables have been exchanged
// global_neighborhood_it = global_neighborhoods.begin();
// for(; global_neighborhood_it != global_neighborhoods.end();
// ++global_neighborhood_it) {
// it = neighborhoods.find(*global_neighborhood_it);
// if (it != neighborhoods.end())
// it->second->getSynchronizerRegistry().waitEndSynchronize(_gst_mnl_for_average);
// else
// dummy_synchronizers[*global_neighborhood_it]->waitEndSynchronize(dummy_accessor,
// _gst_mnl_for_average);
// }
neighborhood_it = neighborhoods.begin();
for (; neighborhood_it != neighborhoods.end(); ++neighborhood_it) {
neighborhood_it->second->getSynchronizerRegistry().waitEndSynchronize(
_gst_mnl_for_average);
}
this->averageInternals(_ghost);
/// copy the results in the materials
this->distributeInternals(_ek_regular);
/// loop over all the materials and update the weights
for (UInt m = 0; m < this->non_local_materials.size(); ++m) {
switch (spatial_dimension) {
case 1:
dynamic_cast<MaterialNonLocal<1> &>(*(this->non_local_materials[m]))
.computeNonLocalStresses(_not_ghost);
break;
case 2:
dynamic_cast<MaterialNonLocal<2> &>(*(this->non_local_materials[m]))
.computeNonLocalStresses(_not_ghost);
break;
case 3:
dynamic_cast<MaterialNonLocal<3> &>(*(this->non_local_materials[m]))
.computeNonLocalStresses(_not_ghost);
break;
}
}
++this->compute_stress_calls;
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::cleanupExtraGhostElements(
ElementTypeMap<UInt> & nb_ghost_protected) {
typedef std::set<Element> ElementSet;
ElementSet relevant_ghost_elements;
ElementSet to_keep_per_neighborhood;
/// loop over all the neighborhoods and get their protected ghosts
NeighborhoodMap::iterator neighborhood_it = neighborhoods.begin();
NeighborhoodMap::iterator neighborhood_end = neighborhoods.end();
for (; neighborhood_it != neighborhood_end; ++neighborhood_it) {
neighborhood_it->second->cleanupExtraGhostElements(
to_keep_per_neighborhood);
ElementSet::const_iterator it = to_keep_per_neighborhood.begin();
for (; it != to_keep_per_neighborhood.end(); ++it)
relevant_ghost_elements.insert(*it);
to_keep_per_neighborhood.clear();
}
/// remove all unneccessary ghosts from the mesh
/// Create list of element to remove and new numbering for element to keep
Mesh & mesh = this->model.getMesh();
ElementSet ghost_to_erase;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _ghost);
RemovedElementsEvent remove_elem(mesh);
Element element;
element.ghost_type = _ghost;
for (; it != last_type; ++it) {
element.type = *it;
UInt nb_ghost_elem = mesh.getNbElement(*it, _ghost);
UInt nb_ghost_elem_protected = 0;
try {
nb_ghost_elem_protected = nb_ghost_protected(*it, _ghost);
} catch (...) {
}
if (!remove_elem.getNewNumbering().exists(*it, _ghost))
remove_elem.getNewNumbering().alloc(nb_ghost_elem, 1, *it, _ghost);
else
remove_elem.getNewNumbering(*it, _ghost).resize(nb_ghost_elem);
Array<UInt> & new_numbering = remove_elem.getNewNumbering(*it, _ghost);
for (UInt g = 0; g < nb_ghost_elem; ++g) {
element.element = g;
if (element.element >= nb_ghost_elem_protected &&
relevant_ghost_elements.find(element) ==
relevant_ghost_elements.end()) {
remove_elem.getList().push_back(element);
new_numbering(element.element) = UInt(-1);
}
}
/// renumber remaining ghosts
UInt ng = 0;
for (UInt g = 0; g < nb_ghost_elem; ++g) {
if (new_numbering(g) != UInt(-1)) {
new_numbering(g) = ng;
++ng;
}
}
}
it = mesh.firstType(spatial_dimension, _not_ghost);
last_type = mesh.lastType(spatial_dimension, _not_ghost);
for (; it != last_type; ++it) {
UInt nb_elem = mesh.getNbElement(*it, _not_ghost);
if (!remove_elem.getNewNumbering().exists(*it, _not_ghost))
remove_elem.getNewNumbering().alloc(nb_elem, 1, *it, _not_ghost);
Array<UInt> & new_numbering = remove_elem.getNewNumbering(*it, _not_ghost);
for (UInt e = 0; e < nb_elem; ++e) {
new_numbering(e) = e;
}
}
mesh.sendEvent(remove_elem);
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::onElementsRemoved(
const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const RemovedElementsEvent & event) {
FEEngine & fee = this->model.getFEEngine();
this->removeIntegrationPointsFromMap(event.getNewNumbering(),
spatial_dimension, quad_positions, fee,
_ek_regular);
this->removeIntegrationPointsFromMap(event.getNewNumbering(), 1, volumes, fee,
_ek_regular);
/// loop over all the neighborhoods and call onElementsRemoved
std::set<ID>::const_iterator global_neighborhood_it =
global_neighborhoods.begin();
NeighborhoodMap::iterator it;
for (; global_neighborhood_it != global_neighborhoods.end();
++global_neighborhood_it) {
it = neighborhoods.find(*global_neighborhood_it);
if (it != neighborhoods.end())
it->second->onElementsRemoved(element_list, new_numbering, event);
else
dummy_synchronizers[*global_neighborhood_it]->onElementsRemoved(
element_list, new_numbering, event);
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::onElementsAdded(__attribute__((unused))
const Array<Element> & element_list,
__attribute__((unused))
const NewElementsEvent & event) {
this->resizeElementTypeMap(1, volumes, model.getFEEngine());
this->resizeElementTypeMap(spatial_dimension, quad_positions,
model.getFEEngine());
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::resizeElementTypeMap(UInt nb_component,
ElementTypeMapReal & element_map,
const FEEngine & fee,
const ElementKind el_kind) {
Mesh & mesh = this->model.getMesh();
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt, el_kind);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, gt, el_kind);
for (; it != end; ++it) {
UInt nb_element = mesh.getNbElement(*it, gt);
UInt nb_quads = fee.getNbIntegrationPoints(*it, gt);
if (!element_map.exists(*it, gt))
element_map.alloc(nb_element * nb_quads, nb_component, *it, gt);
else
element_map(*it, gt).resize(nb_element * nb_quads);
}
}
}
/* -------------------------------------------------------------------------- */
void NonLocalManager::removeIntegrationPointsFromMap(
const ElementTypeMapArray<UInt> & new_numbering, UInt nb_component,
ElementTypeMapReal & element_map, const FEEngine & fee,
const ElementKind el_kind) {
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
ElementTypeMapArray<UInt>::type_iterator it =
new_numbering.firstType(_all_dimensions, gt, el_kind);
ElementTypeMapArray<UInt>::type_iterator end =
new_numbering.lastType(_all_dimensions, gt, el_kind);
for (; it != end; ++it) {
ElementType type = *it;
if (element_map.exists(type, gt)) {
const Array<UInt> & renumbering = new_numbering(type, gt);
Array<Real> & vect = element_map(type, gt);
UInt nb_quad_per_elem = fee.getNbIntegrationPoints(type, gt);
Array<Real> tmp(renumbering.getSize() * nb_quad_per_elem, nb_component);
AKANTU_DEBUG_ASSERT(
tmp.getSize() == vect.getSize(),
"Something strange append some mater was created from nowhere!!");
AKANTU_DEBUG_ASSERT(
tmp.getSize() == vect.getSize(),
"Something strange append some mater was created or disappeared in "
<< vect.getID() << "(" << vect.getSize()
<< "!=" << tmp.getSize() << ") "
"!!");
UInt new_size = 0;
for (UInt i = 0; i < renumbering.getSize(); ++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(Real));
++new_size;
}
}
tmp.resize(new_size * nb_quad_per_elem);
vect.copy(tmp);
}
}
}
}
-__END_AKANTU__
+} // akantu
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 299b6204b..e86c19905 100644
--- a/src/model/common/non_local_toolbox/non_local_manager.hh
+++ b/src/model/common/non_local_toolbox/non_local_manager.hh
@@ -1,289 +1,289 @@
/**
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_MANAGER_HH__
#define __AKANTU_NON_LOCAL_MANAGER_HH__
/* -------------------------------------------------------------------------- */
#include "aka_memory.hh"
#include "solid_mechanics_model.hh"
#include "non_local_neighborhood_base.hh"
#include "mesh_events.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class NonLocalManager : public Memory,
public Parsable,
public MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalManager(SolidMechanicsModel & model,
const ID & id,
const MemoryID & memory_id);
virtual ~NonLocalManager();
typedef std::map<ID, NonLocalNeighborhoodBase *> NeighborhoodMap;
typedef std::pair<ID, ID> KeyCOO;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ----------------------------------------------------------------------- */
public:
/// initialize the non-local manager: compute pair lists and weights for all
/// neighborhoods
virtual void init();
/// insert new quadrature point in the grid
inline void insertQuad(const IntegrationPoint & quad,
const Vector<Real> & coords, const ID & neighborhood);
/// register non-local neighborhood
inline void registerNeighborhood(const ID & neighborhood,
const ID & weight_func_id);
/// associate a non-local variable to a neighborhood
void nonLocalVariableToNeighborhood(const ID & id, const ID & neighborhood);
/// return the fem object associated with a provided name
inline NonLocalNeighborhoodBase & getNeighborhood(const ID & name) const;
/// create the grid synchronizers for each neighborhood
void createNeighborhoodSynchronizers();
/// compute the weights in each neighborhood for non-local averaging
inline void computeWeights();
/// compute the weights in each neighborhood for non-local averaging
inline void updatePairLists();
/// register a new non-local material
inline void registerNonLocalMaterial(Material & new_mat);
/// register a non-local variable
inline void registerNonLocalVariable(const ID & variable_name,
const ID & nl_variable_name,
UInt nb_component);
/// average the non-local variables
void averageInternals(const GhostType & ghost_type = _not_ghost);
/// average the internals and compute the non-local stresses
virtual void computeAllNonLocalStresses();
/// register a new internal needed for the weight computations
inline ElementTypeMapReal &
registerWeightFunctionInternal(const ID & field_name);
/// update the flattened version of the weight function internals
inline void updateWeightFunctionInternals();
/// get Nb data for synchronization in parallel
inline UInt getNbDataForElements(const Array<Element> & elements,
const ID & id) const;
/// pack data for synchronization in parallel
inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag, const ID & id) const;
/// unpack data for synchronization in parallel
inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag, const ID & id) const;
protected:
/// create a new neighborhood for a given domain ID
void createNeighborhood(const ID & weight_func, const ID & neighborhood);
/// flatten the material internal fields needed for the non-local computations
void flattenInternal(ElementTypeMapReal & internal_flat,
const GhostType & ghost_type, const ElementKind & kind);
/// 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();
/// copy the results of the averaging in the materials
void distributeInternals(ElementKind kind);
/// cleanup unneccessary ghosts
void cleanupExtraGhostElements(ElementTypeMap<UInt> & nb_ghost_protected);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
virtual void onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
virtual void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event);
virtual void onElementsChanged(__attribute__((unused)) const Array<Element> & old_elements_list,
__attribute__((unused)) const Array<Element> & new_elements_list,
__attribute__((unused)) const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const ChangedElementsEvent & event) {};
virtual void onNodesAdded(__attribute__((unused)) const Array<UInt> & nodes_list,
__attribute__((unused)) const NewNodesEvent & event) {};
virtual void onNodesRemoved(__attribute__((unused)) const Array<UInt> & nodes_list,
__attribute__((unused)) const Array<UInt> & new_numbering,
__attribute__((unused)) const RemovedNodesEvent & event) {};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
AKANTU_GET_MACRO(Model, model, const SolidMechanicsModel &);
AKANTU_GET_MACRO_NOT_CONST(Volumes, volumes, ElementTypeMapReal &)
AKANTU_GET_MACRO(NbStressCalls, compute_stress_calls, UInt);
inline const Array<Real> & getJacobians(const ElementType & type,
const GhostType & ghost_type) {
return *jacobians(type, ghost_type);
}
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the non-local neighborhoods present
NeighborhoodMap neighborhoods;
/// list of all the non-local materials in the model
std::vector<Material *> 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, NonLocalVariable *> non_local_variables;
/// reference to the model
SolidMechanicsModel & model;
/// jacobians for all the elements in the mesh
ElementTypeMap<const Array<Real> *> jacobians;
/// store the position of the quadrature points
ElementTypeMapReal quad_positions;
/// store the volume of each quadrature point for the non-local weight
/// normalization
ElementTypeMapReal volumes;
/// the spatial dimension
const UInt spatial_dimension;
/// 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, 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
SynchronizerRegistry * dummy_registry;
/// map of dummy synchronizers
std::map<ID, GridSynchronizer *> dummy_synchronizers;
/// dummy spatial grid
SpatialGrid<IntegrationPoint> * dummy_grid;
/// create a set of all neighborhoods present in the simulation
std::set<ID> global_neighborhoods;
class DummyDataAccessor : public DataAccessor {
public:
virtual inline UInt getNbDataForElements(__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) SynchronizationTag tag) const { return 0; };
virtual inline void packElementData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & element,
__attribute__((unused)) SynchronizationTag tag) const {};
virtual inline void unpackElementData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & element,
__attribute__((unused)) SynchronizationTag tag) {};
};
DummyDataAccessor dummy_accessor;
};
-__END_AKANTU__
+} // 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_manager_inline_impl.cc b/src/model/common/non_local_toolbox/non_local_manager_inline_impl.cc
index 1bb8c95dd..ea8412cc1 100644
--- a/src/model/common/non_local_toolbox/non_local_manager_inline_impl.cc
+++ b/src/model/common/non_local_toolbox/non_local_manager_inline_impl.cc
@@ -1,248 +1,248 @@
/**
* @file non_local_manager_inline_impl.cc
*
* @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 inline implementation of non-local manager functions
*
* @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 "grid_synchronizer.hh"
#include "synchronizer_registry.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_CC__
#define __AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_CC__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::insertQuad(const IntegrationPoint & quad,
const Vector<Real> & coords,
const ID & neighborhood) {
AKANTU_DEBUG_ASSERT(neighborhoods[neighborhood] != NULL,
"The neighborhood " << neighborhood
<< "has not been created");
neighborhoods[neighborhood]->insertQuad(quad, coords);
}
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::registerNeighborhood(const ID & neighborhood,
const ID & weight_func_id) {
/// check if neighborhood has already been created
NeighborhoodMap::const_iterator it = neighborhoods.find(neighborhood);
if (it == neighborhoods.end()) {
this->createNeighborhood(weight_func_id, neighborhood);
}
}
/* -------------------------------------------------------------------------- */
inline NonLocalNeighborhoodBase &
NonLocalManager::getNeighborhood(const ID & name) const {
AKANTU_DEBUG_IN();
NeighborhoodMap::const_iterator it = neighborhoods.find(name);
AKANTU_DEBUG_ASSERT(it != neighborhoods.end(),
"The neighborhood " << name << " is not registered");
AKANTU_DEBUG_OUT();
return *(it->second);
}
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::computeWeights() {
AKANTU_DEBUG_IN();
this->updateWeightFunctionInternals();
this->volumes.clear();
// NeighborhoodMap::iterator it = neighborhoods.begin();
// NeighborhoodMap::iterator end = neighborhoods.end();
// for (; it != end; ++it)
// it->second->updateWeights();
/// loop over all the neighborhoods and call onElementsRemoved
std::set<ID>::const_iterator global_neighborhood_it =
global_neighborhoods.begin();
NeighborhoodMap::iterator it;
for (; global_neighborhood_it != global_neighborhoods.end();
++global_neighborhood_it) {
it = neighborhoods.find(*global_neighborhood_it);
if (it != neighborhoods.end())
it->second->updateWeights();
else {
dummy_synchronizers[*global_neighborhood_it]->asynchronousSynchronize(
dummy_accessor, _gst_mnl_weight);
dummy_synchronizers[*global_neighborhood_it]->waitEndSynchronize(
dummy_accessor, _gst_mnl_weight);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::updatePairLists() {
AKANTU_DEBUG_IN();
/// compute the position of the quadrature points
this->model.getFEEngine().computeIntegrationPointsCoordinates(quad_positions);
NeighborhoodMap::iterator it = neighborhoods.begin();
NeighborhoodMap::iterator end = neighborhoods.end();
for (; it != end; ++it)
it->second->updatePairList();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::registerNonLocalVariable(
const ID & variable_name, const ID & nl_variable_name, UInt nb_component) {
AKANTU_DEBUG_IN();
std::map<ID, NonLocalVariable *>::iterator non_local_variable_it =
non_local_variables.find(variable_name);
if (non_local_variable_it == non_local_variables.end())
non_local_variables[nl_variable_name] = new NonLocalVariable(
variable_name, nl_variable_name, this->id, nb_component);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::registerNonLocalMaterial(Material & new_mat) {
non_local_materials.push_back(&new_mat);
}
/* -------------------------------------------------------------------------- */
inline ElementTypeMapReal &
NonLocalManager::registerWeightFunctionInternal(const ID & field_name) {
AKANTU_DEBUG_IN();
std::map<ID, ElementTypeMapReal *>::const_iterator it =
this->weight_function_internals.find(field_name);
if (it == weight_function_internals.end()) {
weight_function_internals[field_name] = new ElementTypeMapReal(field_name, id, memory_id);
}
return *(weight_function_internals[field_name]);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::updateWeightFunctionInternals() {
std::map<ID, ElementTypeMapReal *>::const_iterator it =
this->weight_function_internals.begin();
std::map<ID, ElementTypeMapReal *>::const_iterator end =
this->weight_function_internals.end();
for (; it != end; ++it) {
it->second->clear();
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType ghost_type = (GhostType)g;
this->flattenInternal(*(it->second), ghost_type, _ek_regular);
}
}
}
/* -------------------------------------------------------------------------- */
inline void
NonLocalManager::nonLocalVariableToNeighborhood(const ID & variable_name,
const ID & neighborhood) {
NeighborhoodMap::const_iterator it = neighborhoods.find(neighborhood);
AKANTU_DEBUG_ASSERT(it != neighborhoods.end(), "The neighborhood "
<< neighborhood
<< " is not registered");
it->second->registerNonLocalVariable(variable_name);
}
/* -------------------------------------------------------------------------- */
inline UInt
NonLocalManager::getNbDataForElements(const Array<Element> & elements,
const ID & id) const {
UInt size = 0;
UInt nb_quadrature_points = this->getModel().getNbIntegrationPoints(elements);
std::map<ID, NonLocalVariable *>::const_iterator it =
non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
size += it->second->nb_component * sizeof(Real) * nb_quadrature_points;
return size;
}
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
__attribute__((unused))
SynchronizationTag tag,
const ID & id) const {
std::map<ID, NonLocalVariable *>::const_iterator it =
non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
DataAccessor::packElementalDataHelper<Real>(
it->second->local, buffer, elements, true, this->model.getFEEngine());
}
/* -------------------------------------------------------------------------- */
inline void NonLocalManager::unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
__attribute__((unused))
SynchronizationTag tag,
const ID & id) const {
std::map<ID, NonLocalVariable *>::const_iterator it =
non_local_variables.find(id);
AKANTU_DEBUG_ASSERT(it != non_local_variables.end(),
"The non-local variable " << id << " is not registered");
DataAccessor::unpackElementalDataHelper<Real>(
it->second->local, buffer, elements, true, this->model.getFEEngine());
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_NON_LOCAL_MANAGER_INLINE_IMPL_CC__ */
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 401b24f97..cbd6e7437 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood.hh
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood.hh
@@ -1,136 +1,136 @@
/**
* @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 TestWeightFunction;
}
-__BEGIN_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();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// compute the weights for non-local averaging
void computeWeights();
/// save the pair of weights in a file
void saveWeights(const std::string & filename) const;
/// 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;
/// update the weights based on the weight function
void updateWeights();
/// register a new non-local variable in the neighborhood
virtual void registerNonLocalVariable(const ID & id);
protected:
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);
/* -------------------------------------------------------------------------- */
/* Accessor */
/* -------------------------------------------------------------------------- */
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
Array<Real> * pair_weight[2];
/// weight function
WeightFunction * weight_function;
};
-__END_AKANTU__
+} // 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.cc b/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
index ec6d58a8d..0413c8735 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_base.cc
@@ -1,113 +1,113 @@
/**
* @file non_local_neighborhood_base.cc
*
* @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 Implementation of non-local neighborhood base
*
* @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_neighborhood_base.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NonLocalNeighborhoodBase::NonLocalNeighborhoodBase(const SolidMechanicsModel & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id,
const MemoryID & memory_id) :
NeighborhoodBase(model, quad_coordinates, id, memory_id),
Parsable(_st_non_local, id) {
AKANTU_DEBUG_IN();
this->registerParam("radius" , neighborhood_radius , 100.,
_pat_parsable | _pat_readable , "Non local radius");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
NonLocalNeighborhoodBase::~NonLocalNeighborhoodBase() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::createGridSynchronizer() {
this->is_creating_grid = true;
std::set<SynchronizationTag> tags;
tags.insert(_gst_mnl_for_average);
tags.insert(_gst_mnl_weight);
std::stringstream sstr; sstr << getID() << ":grid_synchronizer";
this->grid_synchronizer = GridSynchronizer::createGridSynchronizer(this->model.getMesh(),
*spatial_grid,
sstr.str(),
synch_registry,
tags, 0, false);
this->is_creating_grid = false;
}
/* -------------------------------------------------------------------------- */
void NonLocalNeighborhoodBase::cleanupExtraGhostElements(std::set<Element> & relevant_ghost_elements) {
PairList::const_iterator first_pair = pair_list[_ghost].begin();
PairList::const_iterator last_pair = pair_list[_ghost].end();
for(;first_pair != last_pair; ++first_pair) {
const IntegrationPoint & q2 = first_pair->second;
relevant_ghost_elements.insert(q2);
}
Array<Element> ghosts_to_erase(0);
Mesh & mesh = this->model.getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _ghost);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, _ghost);
Element element;
element.ghost_type = _ghost;
std::set<Element>::const_iterator end = relevant_ghost_elements.end();
for(; it != last_type; ++it) {
element.type = *it;
UInt nb_ghost_elem = mesh.getNbElement(*it, _ghost);
for (UInt g = 0; g < nb_ghost_elem; ++g) {
element.element = g;
if (relevant_ghost_elements.find(element) == end) {
ghosts_to_erase.push_back(element);
}
}
}
/// remove the unneccessary ghosts from the synchronizer
this->grid_synchronizer->removeElements(ghosts_to_erase);
}
-__END_AKANTU__
+} // akantu
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 c00a8b6a8..3edb674e1 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
@@ -1,127 +1,127 @@
/**
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__
#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__
/* -------------------------------------------------------------------------- */
#include "neighborhood_base.hh"
#include "parsable.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class NonLocalNeighborhoodBase : public NeighborhoodBase, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
NonLocalNeighborhoodBase(const SolidMechanicsModel & model,
const ElementTypeMapReal & quad_coordinates,
const ID & id = "non_local_neighborhood",
const MemoryID & memory_id = 0);
virtual ~NonLocalNeighborhoodBase();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create grid synchronizer and exchange ghost cells
virtual void createGridSynchronizer();
/// 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(
__attribute__((unused)) const ElementTypeMapReal & to_accumulate,
__attribute__((unused)) ElementTypeMapReal & accumulated,
__attribute__((unused)) UInt nb_degree_of_freedom,
__attribute__((unused)) const GhostType & ghost_type2) const {};
/// update the weights for the non-local averaging
virtual void updateWeights(){};
/// register a new non-local variable in the neighborhood
virtual void registerNonLocalVariable(__attribute__((unused))
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:
virtual inline UInt getNbDataForElements(__attribute__((unused))
const Array<Element> & elements,
__attribute__((unused))
SynchronizationTag tag) const {
return 0;
};
virtual inline void
packElementData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) SynchronizationTag tag) const {};
virtual inline void
unpackElementData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) SynchronizationTag tag){};
/* --------------------------------------------------------------------------
*/
/* 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;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_BASE_HH__ */
diff --git a/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc b/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc
index 636c2bcea..ac85c64a0 100644
--- a/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc
+++ b/src/model/common/non_local_toolbox/non_local_neighborhood_inline_impl.cc
@@ -1,95 +1,95 @@
/**
* @file non_local_neighborhood_inline_impl.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 06 2015
* @date last modification: Wed Nov 25 2015
*
* @brief Implementation of inline functions of non-local neighborhood 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_CC__
#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_CC__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<class WeightFunction>
inline UInt NonLocalNeighborhood<WeightFunction>::getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const {
UInt size = 0;
if(tag == _gst_mnl_for_average) {
std::set<ID>::const_iterator it = non_local_variables.begin();
std::set<ID>::const_iterator end = non_local_variables.end();
for(;it != end; ++it) {
size += this->non_local_manager->getNbDataForElements(elements, *it);
}
}
size += this->weight_function->getNbDataForElements(elements, tag);
return size;
}
/* -------------------------------------------------------------------------- */
template<class WeightFunction>
inline void NonLocalNeighborhood<WeightFunction>::packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
if(tag == _gst_mnl_for_average) {
std::set<ID>::const_iterator it = non_local_variables.begin();
std::set<ID>::const_iterator end = non_local_variables.end();
for(;it != end; ++it) {
this->non_local_manager->packElementData(buffer, elements, tag, *it);
}
}
this->weight_function->packElementData(buffer, elements, tag);
}
/* -------------------------------------------------------------------------- */
template<class WeightFunction>
inline void NonLocalNeighborhood<WeightFunction>::unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
if(tag == _gst_mnl_for_average) {
std::set<ID>::const_iterator it = non_local_variables.begin();
std::set<ID>::const_iterator end = non_local_variables.end();
for(;it != end; ++it) {
this->non_local_manager->unpackElementData(buffer, elements, tag, *it);
}
}
this->weight_function->unpackElementData(buffer, elements, tag);
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_INLINE_IMPL_CC__ */
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 39af89d5d..9d12110d0 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
@@ -1,286 +1,286 @@
/**
* @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"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH__
#define __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
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();
for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType) gt;
pair_weight[ghost_type] = NULL;
}
this->weight_function = new WeightFunction(this->getNonLocalManager());
this->registerSubSection(_st_weight_function, "weight_parameter", *weight_function);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<class WeightFunction>
NonLocalNeighborhood<WeightFunction>::~NonLocalNeighborhood() {
AKANTU_DEBUG_IN();
for(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType) gt;
delete pair_weight[ghost_type];
}
delete weight_function;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
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(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type = (GhostType) gt;
/// allocate the array to store the weight, if it doesn't exist already
if(!(pair_weight[ghost_type])) {
std::string ghost_id = "";
if (ghost_type == _ghost) ghost_id = ":ghost";
std::stringstream sstr; sstr << this->id <<":pair_weight:" << ghost_id;
pair_weight[ghost_type] = new Array<Real>(0, nb_weights_per_pair, sstr.str());
}
/// 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(UInt gt = _not_ghost; gt <= _ghost; ++gt) {
GhostType ghost_type2 = (GhostType) gt;
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
Array<Real>::vector_iterator weight_it = pair_weight[ghost_type2]->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;
Array<Real> & quad_volumes_1 = quadrature_points_volumes(q1.type, q1.ghost_type);
Array<Real> & quad_volumes_2 = quadrature_points_volumes(q2.type, q2.ghost_type);
Real q1_volume = quad_volumes_1(q1.global_num);
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;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
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.getSize(); ++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 {
AKANTU_DEBUG_IN();
std::set<ID>::iterator it = non_local_variables.find(accumulated.getName());
///do averaging only for variables registered in the neighborhood
if (it != non_local_variables.end()) {
PairList::const_iterator first_pair = pair_list[ghost_type2].begin();
PairList::const_iterator last_pair = pair_list[ghost_type2].end();
Array<Real>::vector_iterator weight_it = pair_weight[ghost_type2]->begin(2);
// 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;
const Array<Real> & to_acc_1 = to_accumulate(q1.type, q1.ghost_type);
Array<Real> & acc_1 = accumulated(q1.type, q1.ghost_type);
const Array<Real> & to_acc_2 = to_accumulate(q2.type, q2.ghost_type);
Array<Real> & acc_2 = accumulated(q2.type, q2.ghost_type);
for(UInt d = 0; d < nb_degree_of_freedom; ++d) {
acc_1(q1.global_num, d) += weight(0) * to_acc_2(q2.global_num, d);
}
if(ghost_type2 != _ghost) {
for(UInt d = 0; d < nb_degree_of_freedom; ++d) {
acc_2(q2.global_num, d) += weight(1) * to_acc_1(q1.global_num, d);
}
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
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)) {
this->synch_registry->asynchronousSynchronize(_gst_mnl_weight);
this->synch_registry->waitEndSynchronize(_gst_mnl_weight);
this->computeWeights();
}
}
/* -------------------------------------------------------------------------- */
template<class WeightFunction>
void NonLocalNeighborhood<WeightFunction>::registerNonLocalVariable(const ID & id) {
this->non_local_variables.insert(id);
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_NON_LOCAL_NEIGHBORHOOD_TMPL__ */
diff --git a/src/model/dof_manager_default_inline_impl.cc b/src/model/dof_manager_default_inline_impl.cc
index b26b77f4c..c3ef864b2 100644
--- a/src/model/dof_manager_default_inline_impl.cc
+++ b/src/model/dof_manager_default_inline_impl.cc
@@ -1,105 +1,105 @@
/**
* @file dof_manager_default_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Aug 12 10:57:47 2015
*
* @brief Implementation of the DOFManagerDefault inline functions
*
* @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"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_CC__
#define __AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_CC__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
inline bool DOFManagerDefault::isLocalOrMasterDOF(UInt dof_num) {
Int dof_type = this->dofs_type(dof_num);
return (dof_type == Int(_nt_normal)) || (dof_type == Int(_nt_master));
}
/* -------------------------------------------------------------------------- */
inline bool DOFManagerDefault::isSlaveDOF(UInt dof_num) {
Int dof_type = this->dofs_type(dof_num);
return (dof_type >= 0);
}
/* -------------------------------------------------------------------------- */
inline const Array<UInt> &
DOFManagerDefault::getLocalEquationNumbers(const ID & dof_id) const {
return this->getDOFData(dof_id).local_equation_number;
}
inline const Array<UInt> &
DOFManagerDefault::getDOFsAssociatedNodes(const ID & dof_id) const {
const DOFDataDefault & dof_data =
this->getDOFDataTyped<DOFDataDefault>(dof_id);
return dof_data.associated_nodes;
}
/* -------------------------------------------------------------------------- */
inline void DOFManagerDefault::extractElementEquationNumber(
const Array<UInt> & equation_numbers, const Vector<UInt> & connectivity,
UInt nb_degree_of_freedom, Vector<UInt> & element_equation_number) {
for (UInt i = 0, ld = 0; i < connectivity.size(); ++i) {
UInt n = connectivity(i);
for (UInt d = 0; d < nb_degree_of_freedom; ++d, ++ld) {
element_equation_number(ld) =
equation_numbers(n * nb_degree_of_freedom + d);
}
}
}
/* -------------------------------------------------------------------------- */
inline UInt DOFManagerDefault::localToGlobalEquationNumber(UInt local) const {
return this->global_equation_number(local);
}
/* -------------------------------------------------------------------------- */
inline bool DOFManagerDefault::hasGlobalEquationNumber(UInt global) const {
auto it = this->global_to_local_mapping.find(global);
return (it != this->global_to_local_mapping.end());
}
/* -------------------------------------------------------------------------- */
inline UInt DOFManagerDefault::globalToLocalEquationNumber(UInt global) const {
auto it = this->global_to_local_mapping.find(global);
AKANTU_DEBUG_ASSERT(it != this->global_to_local_mapping.end(),
"This global equation number "
<< global << " does not exists in " << this->id);
return it->second;
}
/* -------------------------------------------------------------------------- */
inline Int DOFManagerDefault::getDOFType(UInt local_id) const {
return this->dofs_type(local_id);
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DOF_MANAGER_DEFAULT_INLINE_IMPL_CC_ */
diff --git a/src/model/dof_manager_petsc.cc b/src/model/dof_manager_petsc.cc
index 14f47fdb6..b34b3d7b5 100644
--- a/src/model/dof_manager_petsc.cc
+++ b/src/model/dof_manager_petsc.cc
@@ -1,396 +1,396 @@
/**
* @file dof_manager_petsc.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Oct 5 21:19:58 2015
*
* @brief DOFManaterPETSc is the PETSc implementation of the 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_petsc.hh"
#include "cppargparse.hh"
#if defined(AKANTU_USE_MPI)
#include "static_communicator.hh"
#include "mpi_type_wrapper.hh"
#endif
/* -------------------------------------------------------------------------- */
#include <petscsys.h>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
#if not defined(PETSC_CLANGUAGE_CXX)
/// small hack to use the c binding of petsc when the cxx binding does notation
/// exists
int aka_PETScError(int ierr) {
CHKERRQ(ierr);
return 0;
}
#endif
UInt DOFManagerPETSc::petsc_dof_manager_instances = 0;
/// Error handler to make PETSc errors caught by Akantu
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
static PetscErrorCode PETScErrorHandler(MPI_Comm, int line, const char * dir,
const char * file,
PetscErrorCode number,
PetscErrorType type,
const char * message, void *) {
AKANTU_DEBUG_ERROR("An error occured in PETSc in file \""
<< file << ":" << line << "\" - PetscErrorCode " << number
<< " - \"" << message << "\"");
}
#else
static PetscErrorCode PETScErrorHandler(MPI_Comm, int line, const char * func,
const char * dir, const char * file,
PetscErrorCode number,
PetscErrorType type,
const char * message, void *) {
AKANTU_DEBUG_ERROR("An error occured in PETSc in file \""
<< file << ":" << line << "\" - PetscErrorCode " << number
<< " - \"" << message << "\"");
}
#endif
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::DOFManagerPETSc(const ID & id,
const MemoryID & memory_id)
: DOFManager(id, memory_id) {
// check if the akantu types and PETSc one are consistant
#if __cplusplus > 199711L
static_assert(sizeof(Int) == sizeof(PetscInt),
"The integer type of Akantu does not match the one from PETSc");
static_assert(sizeof(Real) == sizeof(PetscReal),
"The integer type of Akantu does not match the one from PETSc");
#else
AKANTU_DEBUG_ASSERT(
sizeof(Int) == sizeof(PetscInt),
"The integer type of Akantu does not match the one from PETSc");
AKANTU_DEBUG_ASSERT(
sizeof(Real) == sizeof(PetscReal),
"The integer type of Akantu does not match the one from PETSc");
#endif
if (this->petsc_dof_manager_instances == 0) {
#if defined(AKANTU_USE_MPI)
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
const StaticCommunicatorMPI & mpi_st_comm =
dynamic_cast<const StaticCommunicatorMPI &>(
comm.getRealStaticCommunicator());
this->mpi_communicator = mpi_st_comm.getMPITypeWrapper().getMPICommunicator();
#else
this->mpi_communicator = PETSC_COMM_SELF;
#endif
cppargparse::ArgumentParser & argparser = getStaticArgumentParser();
int & argc = argparser.getArgC();
char **& argv = argparser.getArgV();
PetscErrorCode petsc_error = PetscInitialize(&argc, &argv, NULL, NULL);
if (petsc_error != 0) {
AKANTU_DEBUG_ERROR(
"An error occured while initializing Petsc (PetscErrorCode "
<< petsc_error << ")");
}
PetscPushErrorHandler(PETScErrorHandler, NULL);
this->petsc_dof_manager_instances++;
}
VecCreate(PETSC_COMM_WORLD, &this->residual);
VecCreate(PETSC_COMM_WORLD, &this->solution);
}
/* -------------------------------------------------------------------------- */
DOFManagerPETSc::~DOFManagerPETSc() {
PetscErrorCode ierr;
ierr = VecDestroy(&(this->residual));
CHKERRXX(ierr);
ierr = VecDestroy(&(this->solution));
CHKERRXX(ierr);
this->petsc_dof_manager_instances--;
if (this->petsc_dof_manager_instances == 0) {
PetscFinalize();
}
}
/* -------------------------------------------------------------------------- */
void DOFManagerPETSc::registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
DOFSupportType & support_type) {
DOFManager::registerDOFs(dof_id, dofs_array, support_type);
PetscErrorCode ierr;
PetscInt current_size;
ierr = VecGetSize(this->residual, ¤t_size);
CHKERRXX(ierr);
if (current_size == 0) { // first time vector is set
PetscInt local_size = this->pure_local_system_size;
ierr = VecSetSizes(this->residual, local_size, PETSC_DECIDE);
CHKERRXX(ierr);
ierr = VecSetFromOptions(this->residual);
CHKERRXX(ierr);
#ifndef AKANTU_NDEBUG
PetscInt global_size;
ierr = VecGetSize(this->residual, &global_size);
CHKERRXX(ierr);
AKANTU_DEBUG_ASSERT(this->system_size == UInt(global_size),
"The local value of the system size does not match the "
"one determined by PETSc");
#endif
PetscInt start_dof, end_dof;
VecGetOwnershipRange(this->residual, &start_dof, &end_dof);
PetscInt * global_indices = new PetscInt[local_size];
global_indices[0] = start_dof;
for (PetscInt d = 0; d < local_size; d++)
global_indices[d + 1] = global_indices[d] + 1;
// To be change if we switch to a block definition
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
ISLocalToGlobalMappingCreate(this->communicator, 1, local_size,
global_indices, PETSC_COPY_VALUES,
&this->is_ltog);
#else
ISLocalToGlobalMappingCreate(this->communicator, local_size, global_indices,
PETSC_COPY_VALUES, &this->is_ltog);
#endif
VecSetLocalToGlobalMapping(this->residual, this->is_ltog);
delete[] global_indices;
ierr = VecDuplicate(this->residual, &this->solution);
CHKERRXX(ierr);
} else { // this is an update of the object already created
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// set the solution to zero
// ierr = VecZeroEntries(this->solution);
// CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
/**
* This function creates the non-zero pattern of the PETSc matrix. In
* PETSc the parallel matrix is partitioned across processors such
* that the first m0 rows belong to process 0, the next m1 rows belong
* to process 1, the next m2 rows belong to process 2 etc.. where
* m0,m1,m2,.. are the input parameter 'm'. i.e each processor stores
* values corresponding to [m x N] submatrix
* (http://www.mcs.anl.gov/petsc/).
* @param mesh mesh discretizing the domain we want to analyze
* @param dof_synchronizer dof synchronizer that maps the local
* dofs to the global dofs and the equation numbers, i.e., the
* position at which the dof is assembled in the matrix
*/
// void SparseMatrixPETSc::buildProfile(const Mesh & mesh,
// const DOFSynchronizer &
// dof_synchronizer,
// UInt nb_degree_of_freedom) {
// AKANTU_DEBUG_IN();
// // clearProfile();
// this->dof_synchronizer = &const_cast<DOFSynchronizer &>(dof_synchronizer);
// this->setSize();
// PetscErrorCode ierr;
// /// resize arrays to store the number of nonzeros in each row
// this->d_nnz.resize(this->local_size);
// this->o_nnz.resize(this->local_size);
// /// set arrays to zero everywhere
// this->d_nnz.set(0);
// this->o_nnz.set(0);
// // if(irn_jcn_to_k) delete irn_jcn_to_k;
// // irn_jcn_to_k = new std::map<std::pair<UInt, UInt>, UInt>;
// coordinate_list_map::iterator irn_jcn_k_it;
// Int * eq_nb_val = dof_synchronizer.getGlobalDOFEquationNumbers().storage();
// UInt nb_global_dofs = dof_synchronizer.getNbGlobalDOFs();
// Array<Int> index_pair(2);
// /// Loop over all the ghost types
// for (ghost_type_t::iterator gt = ghost_type_t::begin();
// gt != ghost_type_t::end(); ++gt) {
// const GhostType & ghost_type = *gt;
// Mesh::type_iterator it =
// mesh.firstType(mesh.getSpatialDimension(), ghost_type,
// _ek_not_defined);
// Mesh::type_iterator end =
// mesh.lastType(mesh.getSpatialDimension(), ghost_type,
// _ek_not_defined);
// for (; it != end; ++it) {
// UInt nb_element = mesh.getNbElement(*it, ghost_type);
// UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
// UInt size_mat = nb_nodes_per_element * nb_degree_of_freedom;
// UInt * conn_val = mesh.getConnectivity(*it, ghost_type).storage();
// Int * local_eq_nb_val =
// new Int[nb_degree_of_freedom * nb_nodes_per_element];
// for (UInt e = 0; e < nb_element; ++e) {
// Int * tmp_local_eq_nb_val = local_eq_nb_val;
// for (UInt i = 0; i < nb_nodes_per_element; ++i) {
// UInt n = conn_val[i];
// for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
// /**
// * !!!!!!Careful!!!!!! This is a ugly fix. @todo this is a
// * very ugly fix, because the offset for the global
// * equation number, where the dof will be assembled, is
// * hardcoded. In the future a class dof manager has to be
// * added to Akantu to handle the mapping between the dofs
// * and the equation numbers
// *
// */
// *tmp_local_eq_nb_val++ =
// eq_nb_val[n * nb_degree_of_freedom + d] -
// (dof_synchronizer.isPureGhostDOF(n * nb_degree_of_freedom +
// d)
// ? nb_global_dofs
// : 0);
// }
// }
// for (UInt i = 0; i < size_mat; ++i) {
// Int c_irn = local_eq_nb_val[i];
// UInt j_start = 0;
// for (UInt j = j_start; j < size_mat; ++j) {
// Int c_jcn = local_eq_nb_val[j];
// index_pair(0) = c_irn;
// index_pair(1) = c_jcn;
// AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, 2,
// index_pair.storage());
// if (index_pair(0) >= first_global_index &&
// index_pair(0) < first_global_index + this->local_size) {
// KeyCOO irn_jcn = keyPETSc(c_irn, c_jcn);
// irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
// if (irn_jcn_k_it == irn_jcn_k.end()) {
// irn_jcn_k[irn_jcn] = nb_non_zero;
// // check if node is slave node
// if (index_pair(1) >= first_global_index &&
// index_pair(1) < first_global_index + this->local_size)
// this->d_nnz(index_pair(0) - first_global_index) += 1;
// else
// this->o_nnz(index_pair(0) - first_global_index) += 1;
// nb_non_zero++;
// }
// }
// }
// }
// conn_val += nb_nodes_per_element;
// }
// delete[] local_eq_nb_val;
// }
// }
// // /// for pbc @todo correct it for parallel
// // if(StaticCommunicator::getStaticCommunicator().getNbProc() == 1) {
// // for (UInt i = 0; i < size; ++i) {
// // KeyCOO irn_jcn = key(i, i);
// // irn_jcn_k_it = irn_jcn_k.find(irn_jcn);
// // if(irn_jcn_k_it == irn_jcn_k.end()) {
// // irn_jcn_k[irn_jcn] = nb_non_zero;
// // irn.push_back(i + 1);
// // jcn.push_back(i + 1);
// // nb_non_zero++;
// // }
// // }
// // }
// // std::string mat_type;
// // mat_type.resize(20, 'a');
// // std::cout << "MatType: " << mat_type << std::endl;
// // const char * mat_type_ptr = mat_type.c_str();
// MatType type;
// MatGetType(this->petsc_matrix_wrapper->mat, &type);
// /// std::cout << "the matrix type is: " << type << std::endl;
// /**
// * PETSc will use only one of the following preallocation commands
// * depending on the matrix type and ignore the rest. Note that for
// * the block matrix format a block size of 1 is used. This might
// * result in bad performance. @todo For better results implement
// * buildProfile() with larger block size.
// *
// */
// /// build profile:
// if (strcmp(type, MATSEQAIJ) == 0) {
// ierr = MatSeqAIJSetPreallocation(this->petsc_matrix_wrapper->mat, 0,
// d_nnz.storage());
// CHKERRXX(ierr);
// } else if ((strcmp(type, MATMPIAIJ) == 0)) {
// ierr = MatMPIAIJSetPreallocation(this->petsc_matrix_wrapper->mat, 0,
// d_nnz.storage(), 0, o_nnz.storage());
// CHKERRXX(ierr);
// } else {
// AKANTU_DEBUG_ERROR("The type " << type
// << " of PETSc matrix is not handled by"
// << " akantu in the preallocation step");
// }
// // ierr = MatSeqSBAIJSetPreallocation(this->petsc_matrix_wrapper->mat, 1,
// // 0, d_nnz.storage()); CHKERRXX(ierr);
// if (this->sparse_matrix_type == _symmetric) {
// /// set flag for symmetry to enable ICC/Cholesky preconditioner
// ierr = MatSetOption(this->petsc_matrix_wrapper->mat, MAT_SYMMETRIC,
// PETSC_TRUE);
// CHKERRXX(ierr);
// /// set flag for symmetric positive definite
// ierr = MatSetOption(this->petsc_matrix_wrapper->mat, MAT_SPD,
// PETSC_TRUE);
// CHKERRXX(ierr);
// }
// /// once the profile has been build ignore any new nonzero locations
// ierr = MatSetOption(this->petsc_matrix_wrapper->mat,
// MAT_NEW_NONZERO_LOCATIONS, PETSC_TRUE);
// CHKERRXX(ierr);
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/dof_manager_petsc.hh b/src/model/dof_manager_petsc.hh
index e9e01bba1..0a8140a14 100644
--- a/src/model/dof_manager_petsc.hh
+++ b/src/model/dof_manager_petsc.hh
@@ -1,172 +1,172 @@
/**
* @file dof_manager_petsc.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 11 14:06:18 2015
*
* @brief PETSc 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 <petscvec.h>
#include <petscis.h>
/* -------------------------------------------------------------------------- */
#if not defined(PETSC_CLANGUAGE_CXX)
extern int aka_PETScError(int ierr);
#define CHKERRXX(x) \
do { \
int error = aka_PETScError(x); \
if (error != 0) { \
AKANTU_EXCEPTION("Error in PETSC"); \
} \
} while (0)
#endif
#ifndef __AKANTU_DOF_MANAGER_PETSC_HH__
#define __AKANTU_DOF_MANAGER_PETSC_HH__
-__BEGIN_AKANTU__
+namespace akantu {
class SparseMatrixPETSc;
class DOFManagerPETSc : public DOFManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
DOFManagerPETSc(const ID & id = "dof_manager_petsc",
const MemoryID & memory_id = 0);
DOFManagerPETSc(Mesh & mesh, const ID & id = "dof_manager_petsc",
const MemoryID & memory_id = 0);
virtual ~DOFManagerPETSc();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register an array of degree of freedom
void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
DOFSupportType & support_type);
/// 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.);
/**
* 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 assembleElementalArrayResidual(
const ID & dof_id, const Array<Real> & array_to_assemble,
const ElementType & type, const GhostType & ghost_type,
Real scale_factor = 1.);
/**
* 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, const MatrixType & elemental_matrix_type,
const Array<UInt> & filter_elements);
protected:
/// Get the part of the solution corresponding to the dof_id
virtual void getSolutionPerDOFs(const ID & dof_id, Array<Real> & solution_array);
private:
/// Add a symmetric matrices to a symmetric sparse matrix
inline 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)
inline 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
inline void addElementalMatrixToUnsymmetric(
SparseMatrixAIJ & matrix, const Matrix<Real> & element_mat,
const Vector<UInt> & equation_numbers, UInt max_size);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get an instance of a new SparseMatrix
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type);
/// 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);
/// Get the reference of an existing matrix
SparseMatrixPETSc & getMatrix(const ID & matrix_id);
/// Get the solution array
AKANTU_GET_MACRO_NOT_CONST(GlobalSolution, this->solution, Vec &);
/// Get the residual array
AKANTU_GET_MACRO_NOT_CONST(Residual, this->residual, Vec &);
/// Get the blocked dofs array
// AKANTU_GET_MACRO(BlockedDOFs, blocked_dofs, const Array<bool> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
typedef std::map<ID, SparseMatrixPETSc *> PETScMatrixMap;
/// list of matrices registered to the dof manager
PETScMatrixMap petsc_matrices;
/// PETSc version of the solution
Vec solution;
/// PETSc version of the residual
Vec residual;
/// PETSc local to global mapping of dofs
ISLocalToGlobalMapping is_ltog;
/// Communicator associated to PETSc
MPI_Comm mpi_communicator;
/// Static handler for petsc to know if it was initialized or not
static UInt petsc_dof_manager_instances;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_DOF_MANAGER_PETSC_HH__ */
diff --git a/src/model/heat_transfer/heat_transfer_model.cc b/src/model/heat_transfer/heat_transfer_model.cc
index 548b671ac..e77a516fd 100644
--- a/src/model/heat_transfer/heat_transfer_model.cc
+++ b/src/model/heat_transfer/heat_transfer_model.cc
@@ -1,1282 +1,1282 @@
/**
* @file heat_transfer_model.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Rui Wang <rui.wang@epfl.ch>
*
* @date creation: Sun May 01 2011
* @date last modification: Mon Nov 30 2015
*
* @brief Implementation of HeatTransferModel 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 "heat_transfer_model.hh"
#include "group_manager_inline_impl.cc"
#include "dumpable_inline_impl.hh"
#include "aka_math.hh"
#include "aka_common.hh"
#include "fe_engine_template.hh"
#include "mesh.hh"
#include "static_communicator.hh"
#include "parser.hh"
#include "generalized_trapezoidal.hh"
#ifdef AKANTU_USE_MUMPS
#include "solver_mumps.hh"
#endif
#ifdef AKANTU_USE_IOHELPER
#include "dumper_paraview.hh"
#include "dumper_elemental_field.hh"
#include "dumper_element_partition.hh"
#include "dumper_internal_material_field.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
const HeatTransferModelOptions
default_heat_transfer_model_options(_explicit_lumped_capacity);
/* -------------------------------------------------------------------------- */
HeatTransferModel::HeatTransferModel(Mesh & mesh, UInt dim, const ID & id,
const MemoryID & memory_id)
: Model(mesh, dim, id, memory_id), Parsable(_st_heat, id), integrator(NULL),
conductivity_matrix(NULL), capacity_matrix(NULL), jacobian_matrix(NULL),
temperature_gradient("temperature_gradient", id),
temperature_on_qpoints("temperature_on_qpoints", id),
conductivity_on_qpoints("conductivity_on_qpoints", id),
k_gradt_on_qpoints("k_gradt_on_qpoints", id),
int_bt_k_gT("int_bt_k_gT", id), bt_k_gT("bt_k_gT", id),
conductivity(spatial_dimension, spatial_dimension),
thermal_energy("thermal_energy", id), solver(NULL), pbc_synch(NULL) {
AKANTU_DEBUG_IN();
createSynchronizerRegistry(this);
std::stringstream sstr;
sstr << id << ":fem";
registerFEEngineObject<MyFEEngineType>(sstr.str(), mesh, spatial_dimension);
this->temperature = NULL;
this->residual = NULL;
this->blocked_dofs = NULL;
#ifdef AKANTU_USE_IOHELPER
this->mesh.registerDumper<DumperParaview>("paraview_all", id, true);
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_regular);
#endif
this->registerParam("conductivity", conductivity, _pat_parsmod);
this->registerParam("conductivity_variation", conductivity_variation, 0.,
_pat_parsmod);
this->registerParam("temperature_reference", T_ref, 0., _pat_parsmod);
this->registerParam("capacity", capacity, _pat_parsmod);
this->registerParam("density", density, _pat_parsmod);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initModel() {
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initParallel(MeshPartition * partition,
DataAccessor * data_accessor) {
AKANTU_DEBUG_IN();
if (data_accessor == NULL)
data_accessor = this;
Synchronizer & synch_parallel = createParallelSynch(partition, data_accessor);
synch_registry->registerSynchronizer(synch_parallel, _gst_htm_capacity);
synch_registry->registerSynchronizer(synch_parallel, _gst_htm_temperature);
synch_registry->registerSynchronizer(synch_parallel,
_gst_htm_gradient_temperature);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initPBC() {
AKANTU_DEBUG_IN();
Model::initPBC();
pbc_synch = new PBCSynchronizer(pbc_pair);
synch_registry->registerSynchronizer(*pbc_synch, _gst_htm_capacity);
synch_registry->registerSynchronizer(*pbc_synch, _gst_htm_temperature);
changeLocalEquationNumberForPBC(pbc_pair, 1);
// as long as there are ones on the diagonal of the matrix, we can put
// boudandary true for slaves
std::map<UInt, UInt>::iterator it = pbc_pair.begin();
std::map<UInt, UInt>::iterator end = pbc_pair.end();
while (it != end) {
(*blocked_dofs)((*it).first, 0) = true;
++it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initArrays() {
AKANTU_DEBUG_IN();
UInt nb_nodes = getFEEngine().getMesh().getNbNodes();
std::stringstream sstr_temp;
sstr_temp << Model::id << ":temperature";
std::stringstream sstr_temp_rate;
sstr_temp_rate << Model::id << ":temperature_rate";
std::stringstream sstr_inc;
sstr_inc << Model::id << ":increment";
std::stringstream sstr_ext_flx;
sstr_ext_flx << Model::id << ":external_flux";
std::stringstream sstr_residual;
sstr_residual << Model::id << ":residual";
std::stringstream sstr_lump;
sstr_lump << Model::id << ":lumped";
std::stringstream sstr_boun;
sstr_boun << Model::id << ":blocked_dofs";
temperature = &(alloc<Real>(sstr_temp.str(), nb_nodes, 1, REAL_INIT_VALUE));
temperature_rate =
&(alloc<Real>(sstr_temp_rate.str(), nb_nodes, 1, REAL_INIT_VALUE));
increment = &(alloc<Real>(sstr_inc.str(), nb_nodes, 1, REAL_INIT_VALUE));
external_heat_rate =
&(alloc<Real>(sstr_ext_flx.str(), nb_nodes, 1, REAL_INIT_VALUE));
residual = &(alloc<Real>(sstr_residual.str(), nb_nodes, 1, REAL_INIT_VALUE));
capacity_lumped =
&(alloc<Real>(sstr_lump.str(), nb_nodes, 1, REAL_INIT_VALUE));
blocked_dofs = &(alloc<bool>(sstr_boun.str(), nb_nodes, 1, false));
Mesh::ConnectivityTypeList::const_iterator it;
/* --------------------------------------------------------------------------
*/
// byelementtype vectors
getFEEngine().getMesh().initElementTypeMapArray(temperature_on_qpoints, 1,
spatial_dimension);
getFEEngine().getMesh().initElementTypeMapArray(
temperature_gradient, spatial_dimension, spatial_dimension);
getFEEngine().getMesh().initElementTypeMapArray(
conductivity_on_qpoints, spatial_dimension * spatial_dimension,
spatial_dimension);
getFEEngine().getMesh().initElementTypeMapArray(
k_gradt_on_qpoints, spatial_dimension, spatial_dimension);
getFEEngine().getMesh().initElementTypeMapArray(bt_k_gT, 1, spatial_dimension,
true);
getFEEngine().getMesh().initElementTypeMapArray(int_bt_k_gT, 1,
spatial_dimension, true);
getFEEngine().getMesh().initElementTypeMapArray(thermal_energy, 1,
spatial_dimension);
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
const Mesh::ConnectivityTypeList & type_list =
getFEEngine().getMesh().getConnectivityTypeList(gt);
for (it = type_list.begin(); it != type_list.end(); ++it) {
if (Mesh::getSpatialDimension(*it) != spatial_dimension)
continue;
UInt nb_element = getFEEngine().getMesh().getNbElement(*it, gt);
UInt nb_quad_points =
this->getFEEngine().getNbIntegrationPoints(*it, gt) * nb_element;
temperature_on_qpoints(*it, gt).resize(nb_quad_points);
temperature_on_qpoints(*it, gt).clear();
temperature_gradient(*it, gt).resize(nb_quad_points);
temperature_gradient(*it, gt).clear();
conductivity_on_qpoints(*it, gt).resize(nb_quad_points);
conductivity_on_qpoints(*it, gt).clear();
k_gradt_on_qpoints(*it, gt).resize(nb_quad_points);
k_gradt_on_qpoints(*it, gt).clear();
bt_k_gT(*it, gt).resize(nb_quad_points);
bt_k_gT(*it, gt).clear();
int_bt_k_gT(*it, gt).resize(nb_element);
int_bt_k_gT(*it, gt).clear();
thermal_energy(*it, gt).resize(nb_element);
thermal_energy(*it, gt).clear();
}
}
/* --------------------------------------------------------------------------
*/
dof_synchronizer = new DOFSynchronizer(getFEEngine().getMesh(), 1);
dof_synchronizer->initLocalDOFEquationNumbers();
dof_synchronizer->initGlobalDOFEquationNumbers();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initSolver(__attribute__((unused))
SolverOptions & options) {
#if !defined(AKANTU_USE_MUMPS) // or other solver in the future \todo add
// AKANTU_HAS_SOLVER in CMake
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#else
UInt nb_global_nodes = mesh.getNbGlobalNodes();
delete jacobian_matrix;
std::stringstream sstr;
sstr << Memory::id << ":jacobian_matrix";
jacobian_matrix =
new SparseMatrix(nb_global_nodes, _symmetric, sstr.str(), memory_id);
jacobian_matrix->buildProfile(mesh, *dof_synchronizer, 1);
delete conductivity_matrix;
std::stringstream sstr_sti;
sstr_sti << Memory::id << ":conductivity_matrix";
conductivity_matrix =
new SparseMatrix(*jacobian_matrix, sstr_sti.str(), memory_id);
#ifdef AKANTU_USE_MUMPS
std::stringstream sstr_solv;
sstr_solv << Memory::id << ":solver";
solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
dof_synchronizer->initScatterGatherCommunicationScheme();
#else
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#endif // AKANTU_USE_MUMPS
if (solver)
solver->initialize(options);
#endif // AKANTU_HAS_SOLVER
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initImplicit(bool dynamic,
SolverOptions & solver_options) {
AKANTU_DEBUG_IN();
method = dynamic ? _implicit_dynamic : _static;
initSolver(solver_options);
if (method == _implicit_dynamic) {
if (integrator)
delete integrator;
integrator = new TrapezoidalRule1();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
HeatTransferModel::~HeatTransferModel() {
AKANTU_DEBUG_IN();
if (integrator)
delete integrator;
if (conductivity_matrix)
delete conductivity_matrix;
if (capacity_matrix)
delete capacity_matrix;
if (jacobian_matrix)
delete jacobian_matrix;
if (solver)
delete solver;
delete pbc_synch;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacityLumped(const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
FEEngine & fem = getFEEngine();
const Mesh::ConnectivityTypeList & type_list =
fem.getMesh().getConnectivityTypeList(ghost_type);
Mesh::ConnectivityTypeList::const_iterator it;
for (it = type_list.begin(); it != type_list.end(); ++it) {
if (Mesh::getSpatialDimension(*it) != spatial_dimension)
continue;
UInt nb_element = getFEEngine().getMesh().getNbElement(*it, ghost_type);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(*it, ghost_type);
Array<Real> rho_1(nb_element * nb_quadrature_points, 1, capacity * density);
fem.assembleFieldLumped(rho_1, 1, *capacity_lumped,
dof_synchronizer->getLocalDOFEquationNumbers(), *it,
ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacityLumped() {
AKANTU_DEBUG_IN();
capacity_lumped->clear();
assembleCapacityLumped(_not_ghost);
assembleCapacityLumped(_ghost);
getSynchronizerRegistry().synchronize(_gst_htm_capacity);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::updateResidual(
__attribute__((unused)) bool compute_conductivity) {
AKANTU_DEBUG_IN();
/// @f$ r = q_{ext} - q_{int} - C \dot T @f$
// start synchronization
synch_registry->asynchronousSynchronize(_gst_htm_temperature);
// finalize communications
synch_registry->waitEndSynchronize(_gst_htm_temperature);
// clear the array
/// first @f$ r = q_{ext} @f$
// residual->clear();
residual->copy(*external_heat_rate);
/// then @f$ r -= q_{int} @f$
// update the not ghost ones
updateResidual(_not_ghost);
// update for the received ghosts
updateResidual(_ghost);
/* if (method == _explicit_lumped_capacity) {
this->solveExplicitLumped();
}*/
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleConductivityMatrix(bool compute_conductivity) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix.");
conductivity_matrix->clear();
switch (mesh.getSpatialDimension()) {
case 1:
this->assembleConductivityMatrix<1>(_not_ghost, compute_conductivity);
break;
case 2:
this->assembleConductivityMatrix<2>(_not_ghost, compute_conductivity);
break;
case 3:
this->assembleConductivityMatrix<3>(_not_ghost, compute_conductivity);
break;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void HeatTransferModel::assembleConductivityMatrix(const GhostType & ghost_type,
bool compute_conductivity) {
AKANTU_DEBUG_IN();
Mesh & mesh = this->getFEEngine().getMesh();
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) {
this->assembleConductivityMatrix<dim>(*it, ghost_type,
compute_conductivity);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
template <UInt dim>
void HeatTransferModel::assembleConductivityMatrix(const ElementType & type,
const GhostType & ghost_type,
bool compute_conductivity) {
AKANTU_DEBUG_IN();
SparseMatrix & K = *conductivity_matrix;
const Array<Real> & shapes_derivatives =
this->getFEEngine().getShapesDerivatives(type, ghost_type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(type, ghost_type);
/// compute @f$\mathbf{B}^t * \mathbf{D} * \mathbf{B}@f$
UInt bt_d_b_size = 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> Bt_D(nb_nodes_per_element, dim);
Array<Real>::const_iterator<Matrix<Real> > shapes_derivatives_it =
shapes_derivatives.begin(dim, nb_nodes_per_element);
Array<Real>::iterator<Matrix<Real> > Bt_D_B_it =
bt_d_b->begin(bt_d_b_size, bt_d_b_size);
if (compute_conductivity)
this->computeConductivityOnQuadPoints(ghost_type);
Array<Real>::iterator<Matrix<Real> > D_it =
conductivity_on_qpoints(type, ghost_type).begin(dim, dim);
Array<Real>::iterator<Matrix<Real> > D_end =
conductivity_on_qpoints(type, ghost_type).end(dim, dim);
for (; D_it != D_end; ++D_it, ++Bt_D_B_it, ++shapes_derivatives_it) {
Matrix<Real> & D = *D_it;
const Matrix<Real> & B = *shapes_derivatives_it;
Matrix<Real> & Bt_D_B = *Bt_D_B_it;
Bt_D.mul<true, false>(B, D);
Bt_D_B.mul<false, false>(Bt_D, B);
}
/// 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");
this->getFEEngine().integrate(*bt_d_b, *K_e, bt_d_b_size * bt_d_b_size, type,
ghost_type);
delete bt_d_b;
this->getFEEngine().assembleMatrix(*K_e, K, 1, type, ghost_type);
delete K_e;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::updateResidualInternal() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Update the residual");
// f = q_ext - q_int - Mddot = q - Mddot;
if (method != _static) {
// f -= Mddot
if (capacity_matrix) {
// if full mass_matrix
Array<Real> * Mddot = new Array<Real>(*temperature_rate, true, "Mddot");
*Mddot *= *capacity_matrix;
*residual -= *Mddot;
delete Mddot;
} else if (capacity_lumped) {
// else lumped mass
UInt nb_nodes = temperature_rate->getSize();
UInt nb_degree_of_freedom = temperature_rate->getNbComponent();
Real * capacity_val = capacity_lumped->storage();
Real * temp_rate_val = temperature_rate->storage();
Real * res_val = residual->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
if (!(*blocked_dofs_val)) {
*res_val -= *temp_rate_val ** capacity_val;
}
blocked_dofs_val++;
res_val++;
capacity_val++;
temp_rate_val++;
}
} else {
AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::solveStatic() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Solving Ku = f");
AKANTU_DEBUG_ASSERT(conductivity_matrix != NULL,
"You should first initialize the implicit solver and "
"assemble the stiffness matrix");
UInt nb_nodes = temperature->getSize();
UInt nb_degree_of_freedom = temperature->getNbComponent() * nb_nodes;
jacobian_matrix->copyContent(*conductivity_matrix);
jacobian_matrix->applyBoundary(*blocked_dofs);
increment->clear();
solver->setRHS(*residual);
solver->factorize();
solver->solve(*increment);
Real * increment_val = increment->storage();
Real * temperature_val = temperature->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt j = 0; j < nb_degree_of_freedom;
++j, ++temperature_val, ++increment_val, ++blocked_dofs_val) {
if (!(*blocked_dofs_val)) {
*temperature_val += *increment_val;
} else {
*increment_val = 0.0;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::computeConductivityOnQuadPoints(
const GhostType & ghost_type) {
const Mesh::ConnectivityTypeList & type_list =
this->getFEEngine().getMesh().getConnectivityTypeList(ghost_type);
Mesh::ConnectivityTypeList::const_iterator it;
for (it = type_list.begin(); it != type_list.end(); ++it) {
if (Mesh::getSpatialDimension(*it) != spatial_dimension)
continue;
Array<Real> & temperature_interpolated =
temperature_on_qpoints(*it, ghost_type);
// compute the temperature on quadrature points
this->getFEEngine().interpolateOnIntegrationPoints(
*temperature, temperature_interpolated, 1, *it, ghost_type);
Array<Real>::matrix_iterator C_it =
conductivity_on_qpoints(*it, ghost_type)
.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator C_end =
conductivity_on_qpoints(*it, ghost_type)
.end(spatial_dimension, spatial_dimension);
Array<Real>::iterator<Real> T_it = temperature_interpolated.begin();
for (; C_it != C_end; ++C_it, ++T_it) {
Matrix<Real> & C = *C_it;
Real & T = *T_it;
C = conductivity;
Matrix<Real> variation(spatial_dimension, spatial_dimension,
conductivity_variation * (T - T_ref));
C += conductivity_variation;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::computeKgradT(const GhostType & ghost_type,
bool compute_conductivity) {
if (compute_conductivity)
computeConductivityOnQuadPoints(ghost_type);
const Mesh::ConnectivityTypeList & type_list =
this->getFEEngine().getMesh().getConnectivityTypeList(ghost_type);
Mesh::ConnectivityTypeList::const_iterator it;
for (it = type_list.begin(); it != type_list.end(); ++it) {
const ElementType & type = *it;
if (Mesh::getSpatialDimension(*it) != spatial_dimension)
continue;
Array<Real> & gradient = temperature_gradient(*it, ghost_type);
this->getFEEngine().gradientOnIntegrationPoints(*temperature, gradient, 1,
*it, ghost_type);
Array<Real>::matrix_iterator C_it =
conductivity_on_qpoints(*it, ghost_type)
.begin(spatial_dimension, spatial_dimension);
Array<Real>::vector_iterator BT_it = gradient.begin(spatial_dimension);
Array<Real>::vector_iterator k_BT_it =
k_gradt_on_qpoints(type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator k_BT_end =
k_gradt_on_qpoints(type, ghost_type).end(spatial_dimension);
for (; k_BT_it != k_BT_end; ++k_BT_it, ++BT_it, ++C_it) {
Vector<Real> & k_BT = *k_BT_it;
Vector<Real> & BT = *BT_it;
Matrix<Real> & C = *C_it;
k_BT.mul<false>(C, BT);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::updateResidual(const GhostType & ghost_type,
bool compute_conductivity) {
AKANTU_DEBUG_IN();
const Mesh::ConnectivityTypeList & type_list =
this->getFEEngine().getMesh().getConnectivityTypeList(ghost_type);
Mesh::ConnectivityTypeList::const_iterator it;
for (it = type_list.begin(); it != type_list.end(); ++it) {
if (Mesh::getSpatialDimension(*it) != spatial_dimension)
continue;
Array<Real> & shapes_derivatives = const_cast<Array<Real> &>(
getFEEngine().getShapesDerivatives(*it, ghost_type));
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
// compute k \grad T
computeKgradT(ghost_type, compute_conductivity);
Array<Real>::vector_iterator k_BT_it =
k_gradt_on_qpoints(*it, ghost_type).begin(spatial_dimension);
Array<Real>::matrix_iterator B_it =
shapes_derivatives.begin(spatial_dimension, nb_nodes_per_element);
Array<Real>::vector_iterator Bt_k_BT_it =
bt_k_gT(*it, ghost_type).begin(nb_nodes_per_element);
Array<Real>::vector_iterator Bt_k_BT_end =
bt_k_gT(*it, ghost_type).end(nb_nodes_per_element);
for (; Bt_k_BT_it != Bt_k_BT_end; ++Bt_k_BT_it, ++B_it, ++k_BT_it) {
Vector<Real> & k_BT = *k_BT_it;
Vector<Real> & Bt_k_BT = *Bt_k_BT_it;
Matrix<Real> & B = *B_it;
Bt_k_BT.mul<true>(B, k_BT);
}
this->getFEEngine().integrate(bt_k_gT(*it, ghost_type),
int_bt_k_gT(*it, ghost_type),
nb_nodes_per_element, *it, ghost_type);
this->getFEEngine().assembleArray(
int_bt_k_gT(*it, ghost_type), *residual,
dof_synchronizer->getLocalDOFEquationNumbers(), 1, *it, ghost_type,
empty_filter, -1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::solveExplicitLumped() {
AKANTU_DEBUG_IN();
/// finally @f$ r -= C \dot T @f$
// lumped C
UInt nb_nodes = temperature_rate->getSize();
UInt nb_degree_of_freedom = temperature_rate->getNbComponent();
Real * capacity_val = capacity_lumped->storage();
Real * temp_rate_val = temperature_rate->storage();
Real * res_val = residual->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
if (!(*blocked_dofs_val)) {
*res_val -= *capacity_val ** temp_rate_val;
}
blocked_dofs_val++;
res_val++;
capacity_val++;
temp_rate_val++;
}
#ifndef AKANTU_NDEBUG
getSynchronizerRegistry().synchronize(akantu::_gst_htm_gradient_temperature);
#endif
capacity_val = capacity_lumped->storage();
res_val = residual->storage();
blocked_dofs_val = blocked_dofs->storage();
Real * inc = increment->storage();
for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
if (!(*blocked_dofs_val)) {
*inc = (*res_val / *capacity_val);
}
res_val++;
blocked_dofs_val++;
inc++;
capacity_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::explicitPred() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(integrator, "integrator was not instanciated");
integrator->integrationSchemePred(time_step, *temperature, *temperature_rate,
*blocked_dofs);
UInt nb_nodes = temperature->getSize();
UInt nb_degree_of_freedom = temperature->getNbComponent();
Real * temp = temperature->storage();
for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n, ++temp)
if (*temp < 0.)
*temp = 0.;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::explicitCorr() {
AKANTU_DEBUG_IN();
integrator->integrationSchemeCorrTempRate(
time_step, *temperature, *temperature_rate, *blocked_dofs, *increment);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::implicitPred() {
AKANTU_DEBUG_IN();
if (method == _implicit_dynamic)
integrator->integrationSchemePred(time_step, *temperature,
*temperature_rate, *blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::implicitCorr() {
AKANTU_DEBUG_IN();
if (method == _implicit_dynamic) {
integrator->integrationSchemeCorrTemp(
time_step, *temperature, *temperature_rate, *blocked_dofs, *increment);
} else {
UInt nb_nodes = temperature->getSize();
UInt nb_degree_of_freedom = temperature->getNbComponent() * nb_nodes;
Real * incr_val = increment->storage();
Real * temp_val = temperature->storage();
bool * boun_val = blocked_dofs->storage();
for (UInt j = 0; j < nb_degree_of_freedom;
++j, ++temp_val, ++incr_val, ++boun_val) {
*incr_val *= (1. - *boun_val);
*temp_val += *incr_val;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getStableTimeStep() {
AKANTU_DEBUG_IN();
Real el_size;
Real min_el_size = std::numeric_limits<Real>::max();
Real conductivitymax = conductivity(0, 0);
// get the biggest parameter from k11 until k33//
for (UInt i = 0; i < spatial_dimension; i++)
for (UInt j = 0; j < spatial_dimension; j++)
conductivitymax = std::max(conductivity(i, j), conductivitymax);
const Mesh::ConnectivityTypeList & type_list =
getFEEngine().getMesh().getConnectivityTypeList();
Mesh::ConnectivityTypeList::const_iterator it;
for (it = type_list.begin(); it != type_list.end(); ++it) {
if (getFEEngine().getMesh().getSpatialDimension(*it) != spatial_dimension)
continue;
UInt nb_nodes_per_element =
getFEEngine().getMesh().getNbNodesPerElement(*it);
Array<Real> coord(0, nb_nodes_per_element * spatial_dimension);
FEEngine::extractNodalToElementField(getFEEngine().getMesh(),
getFEEngine().getMesh().getNodes(),
coord, *it, _not_ghost);
Array<Real>::matrix_iterator el_coord =
coord.begin(spatial_dimension, nb_nodes_per_element);
UInt nb_element = getFEEngine().getMesh().getNbElement(*it);
for (UInt el = 0; el < nb_element; ++el, ++el_coord) {
el_size = getFEEngine().getElementInradius(*el_coord, *it);
min_el_size = std::min(min_el_size, el_size);
}
AKANTU_DEBUG_INFO("The minimum element size : "
<< min_el_size
<< " and the max conductivity is : " << conductivitymax);
}
Real min_dt =
2 * min_el_size * min_el_size * density * capacity / conductivitymax;
StaticCommunicator::getStaticCommunicator().allReduce(&min_dt, 1, _so_min);
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::readMaterials() {
std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
sub_sect = this->parser->getSubSections(_st_heat);
Parser::const_section_iterator it = sub_sect.first;
const ParserSection & section = *it;
this->parseSection(section);
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initFull(const ModelOptions & options) {
Model::initFull(options);
readMaterials();
const HeatTransferModelOptions & my_options =
dynamic_cast<const HeatTransferModelOptions &>(options);
method = my_options.analysis_method;
// initialize the vectors
initArrays();
temperature->clear();
temperature_rate->clear();
external_heat_rate->clear();
// initialize pbc
if (pbc_pair.size() != 0)
initPBC();
if (method == _explicit_lumped_capacity) {
integrator = new ForwardEuler();
}
if (method == _implicit_dynamic) {
initImplicit(true);
}
if (method == _static) {
initImplicit(false);
}
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacity() {
AKANTU_DEBUG_IN();
if (!capacity_matrix) {
std::stringstream sstr;
sstr << id << ":capacity_matrix";
capacity_matrix = new SparseMatrix(*jacobian_matrix, sstr.str(), memory_id);
}
assembleCapacity(_not_ghost);
// assembleMass(_ghost);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
class ComputeRhoFunctor {
public:
ComputeRhoFunctor(const HeatTransferModel & model) : model(model){};
void operator()(Matrix<Real> & rho, const Element &,
const Matrix<Real> &) const {
rho.set(model.getCapacity());
}
private:
const HeatTransferModel & model;
};
/* -------------------------------------------------------------------------- */
void HeatTransferModel::assembleCapacity(GhostType ghost_type) {
AKANTU_DEBUG_IN();
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctor rho_functor(*this);
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;
fem.assembleFieldMatrix(rho_functor, 1, *capacity_matrix, type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::computeRho(Array<Real> & rho, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
FEEngine & fem = this->getFEEngine();
UInt nb_element = fem.getMesh().getNbElement(type, ghost_type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type, ghost_type);
rho.resize(nb_element * nb_quadrature_points);
Real * rho_1_val = rho.storage();
/// compute @f$ rho @f$ for each nodes of each element
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < nb_quadrature_points; ++n) {
*rho_1_val++ = this->capacity;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
bool HeatTransferModel::testConvergence<_scc_increment>(Real tolerance,
Real & error) {
AKANTU_DEBUG_IN();
UInt nb_nodes = temperature->getSize();
UInt nb_degree_of_freedom = temperature->getNbComponent();
error = 0;
Real norm[2] = {0., 0.};
Real * increment_val = increment->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
Real * temperature_val = temperature->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
if (!(*blocked_dofs_val) && is_local_node) {
norm[0] += *increment_val * *increment_val;
norm[1] += *temperature_val * *temperature_val;
}
blocked_dofs_val++;
increment_val++;
temperature_val++;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(norm, 2, _so_sum);
norm[0] = sqrt(norm[0]);
norm[1] = sqrt(norm[1]);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm[0]),
"Something goes wrong in the solve phase");
if (norm[1] < Math::getTolerance()) {
error = norm[0];
AKANTU_DEBUG_OUT();
// cout<<"Error 1: "<<error<<endl;
return error < tolerance;
}
AKANTU_DEBUG_OUT();
if (norm[1] > Math::getTolerance())
error = norm[0] / norm[1];
else
error = norm[0]; // In case the total displacement is zero!
// cout<<"Error 2: "<<error<<endl;
return (error < tolerance);
}
/* -------------------------------------------------------------------------- */
void HeatTransferModel::initFEEngineBoundary(bool create_surface) {
if (create_surface)
MeshUtils::buildFacets(getFEEngine().getMesh());
FEEngine & fem_boundary = getFEEngineBoundary();
fem_boundary.initShapeFunctions();
fem_boundary.computeNormalsOnIntegrationPoints();
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::computeThermalEnergyByNode() {
AKANTU_DEBUG_IN();
Real ethermal = 0.;
Array<Real>::vector_iterator heat_rate_it =
residual->begin(residual->getNbComponent());
Array<Real>::vector_iterator heat_rate_end =
residual->end(residual->getNbComponent());
UInt n = 0;
for (; heat_rate_it != heat_rate_end; ++heat_rate_it, ++n) {
Real heat = 0;
bool is_local_node = mesh.isLocalOrMasterNode(n);
bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
bool count_node = is_local_node && is_not_pbc_slave_node;
Vector<Real> & heat_rate = *heat_rate_it;
for (UInt i = 0; i < heat_rate.size(); ++i) {
if (count_node)
heat += heat_rate[i] * time_step;
}
ethermal += heat;
}
StaticCommunicator::getStaticCommunicator().allReduce(ðermal, 1, _so_sum);
AKANTU_DEBUG_OUT();
return ethermal;
}
/* -------------------------------------------------------------------------- */
template <class iterator>
void HeatTransferModel::getThermalEnergy(
iterator Eth, Array<Real>::const_iterator<Real> T_it,
Array<Real>::const_iterator<Real> T_end) const {
for (; T_it != T_end; ++T_it, ++Eth) {
*Eth = capacity * density ** T_it;
}
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getThermalEnergy(const ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
Vector<Real> Eth_on_quarature_points(nb_quadrature_points);
Array<Real>::iterator<Real> T_it = this->temperature_on_qpoints(type).begin();
T_it += index * nb_quadrature_points;
Array<Real>::iterator<Real> T_end = T_it + nb_quadrature_points;
getThermalEnergy(Eth_on_quarature_points.storage(), T_it, T_end);
return getFEEngine().integrate(Eth_on_quarature_points, type, index);
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getThermalEnergy() {
Real Eth = 0;
Mesh & mesh = getFEEngine().getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension);
for (; it != last_type; ++it) {
UInt nb_element = getFEEngine().getMesh().getNbElement(*it, _not_ghost);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(*it, _not_ghost);
Array<Real> Eth_per_quad(nb_element * nb_quadrature_points, 1);
Array<Real>::iterator<Real> T_it =
this->temperature_on_qpoints(*it).begin();
Array<Real>::iterator<Real> T_end = this->temperature_on_qpoints(*it).end();
getThermalEnergy(Eth_per_quad.begin(), T_it, T_end);
Eth += getFEEngine().integrate(Eth_per_quad, *it);
}
return Eth;
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getEnergy(const std::string & id) {
AKANTU_DEBUG_IN();
Real energy = 0;
if (id == "thermal")
energy = getThermalEnergy();
// reduction sum over all processors
StaticCommunicator::getStaticCommunicator().allReduce(&energy, 1, _so_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real HeatTransferModel::getEnergy(const std::string & id,
const ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
Real energy = 0.;
if (id == "thermal")
energy = getThermalEnergy(type, index);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
dumper::Field * HeatTransferModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs;
dumper::Field * field = NULL;
field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field * HeatTransferModel::createNodalFieldReal(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<Real> *> real_nodal_fields;
real_nodal_fields["temperature"] = temperature;
real_nodal_fields["temperature_rate"] = temperature_rate;
real_nodal_fields["external_heat_rate"] = external_heat_rate;
real_nodal_fields["residual"] = residual;
real_nodal_fields["capacity_lumped"] = capacity_lumped;
real_nodal_fields["increment"] = increment;
dumper::Field * field =
mesh.createNodalField(real_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field * HeatTransferModel::createElementalField(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag,
__attribute__((unused)) const UInt & spatial_dimension,
const ElementKind & element_kind) {
dumper::Field * field = NULL;
if (field_name == "partitions")
field = mesh.createElementalField<UInt, dumper::ElementPartitionField>(
mesh.getConnectivities(), group_name, this->spatial_dimension,
element_kind);
else if (field_name == "temperature_gradient") {
ElementTypeMap<UInt> nb_data_per_elem =
this->mesh.getNbDataPerElem(temperature_gradient, element_kind);
field = mesh.createElementalField<Real, dumper::InternalMaterialField>(
temperature_gradient, group_name, this->spatial_dimension, element_kind,
nb_data_per_elem);
} else if (field_name == "conductivity") {
ElementTypeMap<UInt> nb_data_per_elem =
this->mesh.getNbDataPerElem(conductivity_on_qpoints, element_kind);
field = mesh.createElementalField<Real, dumper::InternalMaterialField>(
conductivity_on_qpoints, group_name, this->spatial_dimension,
element_kind, nb_data_per_elem);
}
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* -------------------------------------------------------------------------- */
dumper::Field * HeatTransferModel::createElementalField(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag,
__attribute__((unused)) const ElementKind & element_kind) {
return NULL;
}
/* -------------------------------------------------------------------------- */
dumper::Field * HeatTransferModel::createNodalFieldBool(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return NULL;
}
/* -------------------------------------------------------------------------- */
dumper::Field * HeatTransferModel::createNodalFieldReal(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return NULL;
}
#endif
-__END_AKANTU__
+} // akantu
diff --git a/src/model/heat_transfer/heat_transfer_model.hh b/src/model/heat_transfer/heat_transfer_model.hh
index c32e85634..0826bebb4 100644
--- a/src/model/heat_transfer/heat_transfer_model.hh
+++ b/src/model/heat_transfer/heat_transfer_model.hh
@@ -1,456 +1,456 @@
/**
* @file heat_transfer_model.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Srinivasa Babu Ramisetti <srinivasa.ramisetti@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Rui Wang <rui.wang@epfl.ch>
*
* @date creation: Sun May 01 2011
* @date last modification: Tue Dec 08 2015
*
* @brief Model of Heat Transfer
*
* @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_HEAT_TRANSFER_MODEL_HH__
#define __AKANTU_HEAT_TRANSFER_MODEL_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_types.hh"
#include "aka_voigthelper.hh"
#include "aka_memory.hh"
#include "model.hh"
#include "integrator_gauss.hh"
#include "shape_lagrange.hh"
#include "dumpable.hh"
#include "parsable.hh"
#include "solver.hh"
#include "generalized_trapezoidal.hh"
namespace akantu {
class IntegrationScheme1stOrder;
}
-__BEGIN_AKANTU__
+namespace akantu {
struct HeatTransferModelOptions : public ModelOptions {
HeatTransferModelOptions(AnalysisMethod analysis_method = _explicit_lumped_capacity ) : analysis_method(analysis_method) {}
AnalysisMethod analysis_method;
};
extern const HeatTransferModelOptions default_heat_transfer_model_options;
class HeatTransferModel : public Model, public DataAccessor, public Parsable {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef FEEngineTemplate<IntegratorGauss,ShapeLagrange> MyFEEngineType;
HeatTransferModel(Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "heat_transfer_model",
const MemoryID & memory_id = 0);
virtual ~HeatTransferModel() ;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// generic function to initialize everything ready for explicit dynamics
void initFull(const ModelOptions & options = default_heat_transfer_model_options);
/// initialize the fem object of the boundary
void initFEEngineBoundary(bool create_surface = true);
/// read one material file to instantiate all the materials
void readMaterials();
/// allocate all vectors
void initArrays();
/// register the tags associated with the parallel synchronizer
void initParallel(MeshPartition * partition, DataAccessor * data_accessor=NULL);
/// initialize the model
void initModel();
/// init PBC synchronizer
void initPBC();
/// initialize the solver and the jacobian_matrix (called by initImplicit)
void initSolver(SolverOptions & solver_options);
/// initialize the stuff for the implicit solver
void initImplicit(bool dynamic, SolverOptions & solver_options = _solver_no_options);
/// function to print the contain of the class
virtual void printself(__attribute__ ((unused)) std::ostream & stream,
__attribute__ ((unused)) int indent = 0) const {};
/* ------------------------------------------------------------------------ */
/* Methods for explicit */
/* ------------------------------------------------------------------------ */
public:
/// compute and get the stable time step
Real getStableTimeStep();
/// compute the heat flux
void updateResidual(bool compute_conductivity = false);
/// calculate the lumped capacity vector for heat transfer problem
void assembleCapacityLumped();
/// update the temperature from the temperature rate
void explicitPred();
/// update the temperature rate from the increment
void explicitCorr();
/// implicit time integration predictor
void implicitPred();
/// implicit time integration corrector
void implicitCorr();
/// solve the system in temperature rate @f$C\delta \dot T = q_{n+1} - C \dot T_{n}@f$
/// this function needs to be run for dynamics
void solveExplicitLumped();
// /// initialize the heat flux
// void initializeResidual(Array<Real> &temp);
// /// initialize temperature
// void initializeTemperature(Array<Real> &temp);
/* ------------------------------------------------------------------------ */
/* Methods for implicit */
/* ------------------------------------------------------------------------ */
public:
/**
* solve Kt = q
**/
void solveStatic();
/// test if the system is converged
template <SolveConvergenceCriteria criteria>
bool testConvergence(Real tolerance, Real & error);
/**
* solve a step (predictor + convergence loop + corrector) using the
* the given convergence method (see akantu::SolveConvergenceMethod)
* and the given convergence criteria (see
* akantu::SolveConvergenceCriteria)
**/
template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
bool solveStep(Real tolerance, UInt max_iteration = 100);
template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
bool solveStep(Real tolerance,
Real & error,
UInt max_iteration = 100,
bool do_not_factorize = false);
/// assemble the conductivity matrix
void assembleConductivityMatrix(bool compute_conductivity = true);
/// assemble the conductivity matrix
void assembleCapacity();
/// assemble the conductivity matrix
void assembleCapacity(GhostType ghost_type);
/// compute the capacity on quadrature points
void computeRho(Array<Real> & rho, ElementType type,
GhostType ghost_type);
protected:
/// compute A and solve @f[ A\delta u = f_ext - f_int @f]
template <GeneralizedTrapezoidal::IntegrationSchemeCorrectorType type>
void solve(Array<Real> &increment, Real block_val = 1.,
bool need_factorize = true, bool has_profile_changed = false);
/// computation of the residual for the convergence loop
void updateResidualInternal();
private:
/// compute the heat flux on ghost types
void updateResidual(const GhostType & ghost_type, bool compute_conductivity = false);
/// calculate the lumped capacity vector for heat transfer problem (w ghosttype)
void assembleCapacityLumped(const GhostType & ghost_type);
/// assemble the conductivity matrix (w/ ghost type)
template <UInt dim>
void assembleConductivityMatrix(const GhostType & ghost_type,
bool compute_conductivity = true);
/// assemble the conductivity matrix
template <UInt dim>
void assembleConductivityMatrix(const ElementType & type,
const GhostType & ghost_type,
bool compute_conductivity = true);
/// compute the conductivity tensor for each quadrature point in an array
void computeConductivityOnQuadPoints(const GhostType & ghost_type);
/// compute vector k \grad T for each quadrature point
void computeKgradT(const GhostType & ghost_type,bool compute_conductivity);
/// compute the thermal energy
Real computeThermalEnergyByNode();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
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);
inline UInt getNbDataToPack(SynchronizationTag tag) const;
inline UInt getNbDataToUnpack(SynchronizationTag tag) const;
inline void packData(CommunicationBuffer & buffer,
const UInt index,
SynchronizationTag tag) const;
inline void unpackData(CommunicationBuffer & buffer,
const UInt index,
SynchronizationTag tag);
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
virtual dumper::Field * createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
virtual dumper::Field * createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
virtual dumper::Field * createElementalField(const std::string & field_name,
const std::string & group_name,
bool padding_flag,
const UInt & spatial_dimension,
const ElementKind & kind);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
inline FEEngine & getFEEngineBoundary(const std::string & name = "");
AKANTU_GET_MACRO(Density, density, Real);
AKANTU_GET_MACRO(Capacity, capacity, Real);
/// get the dimension of the system space
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the current value of the time step
AKANTU_GET_MACRO(TimeStep, time_step, Real);
/// set the value of the time step
AKANTU_SET_MACRO(TimeStep, time_step, Real);
/// get the assembled heat flux
AKANTU_GET_MACRO(Residual, *residual, Array<Real>&);
/// get the lumped capacity
AKANTU_GET_MACRO(CapacityLumped, *capacity_lumped, Array<Real>&);
/// get the boundary vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<bool>&);
/// get conductivity matrix
AKANTU_GET_MACRO(ConductivityMatrix, *conductivity_matrix, const SparseMatrix&);
/// get the external heat rate vector
AKANTU_GET_MACRO(ExternalHeatRate, *external_heat_rate, Array<Real>&);
/// get the temperature gradient
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(TemperatureGradient, temperature_gradient, Real);
/// get the conductivity on q points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(ConductivityOnQpoints, conductivity_on_qpoints, Real);
/// get the conductivity on q points
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(TemperatureOnQpoints, temperature_on_qpoints, Real);
/// internal variables
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(KGradtOnQpoints, k_gradt_on_qpoints, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(IntBtKgT, int_bt_k_gT, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(BtKgT, bt_k_gT, Real);
/// get the temperature
AKANTU_GET_MACRO(Temperature, *temperature, Array<Real> &);
/// get the temperature derivative
AKANTU_GET_MACRO(TemperatureRate, *temperature_rate, Array<Real> &);
/// get the equation number Array<Int>
AKANTU_GET_MACRO(EquationNumber, *equation_number, const Array<Int> &);
/// get the energy denominated by thermal
Real getEnergy(const std::string & energy_id, const ElementType & type, UInt index);
/// get the energy denominated by thermal
Real getEnergy(const std::string & energy_id);
/// get the thermal energy for a given element
Real getThermalEnergy(const ElementType & type, UInt index);
/// get the thermal energy for a given element
Real getThermalEnergy();
protected:
/* ----------------------------------------------------------------------- */
template<class iterator>
void getThermalEnergy(iterator Eth,
Array<Real>::const_iterator<Real> T_it,
Array<Real>::const_iterator<Real> T_end) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// number of iterations
UInt n_iter;
IntegrationScheme1stOrder * integrator;
/// time step
Real time_step;
/// temperatures array
Array<Real> * temperature;
/// temperatures derivatives array
Array<Real> * temperature_rate;
/// increment array (@f$\delta \dot T@f$ or @f$\delta T@f$)
Array<Real> * increment;
/// conductivity matrix
SparseMatrix * conductivity_matrix;
/// capacity matrix
SparseMatrix *capacity_matrix;
/// jacobian matrix
SparseMatrix * jacobian_matrix;
/// the density
Real density;
/// the speed of the changing temperature
ElementTypeMapArray<Real> temperature_gradient;
/// temperature field on quadrature points
ElementTypeMapArray<Real> temperature_on_qpoints;
/// conductivity tensor on quadrature points
ElementTypeMapArray<Real> conductivity_on_qpoints;
/// vector k \grad T on quad points
ElementTypeMapArray<Real> k_gradt_on_qpoints;
/// vector \int \grad N k \grad T
ElementTypeMapArray<Real> int_bt_k_gT;
/// vector \grad N k \grad T
ElementTypeMapArray<Real> bt_k_gT;
/// external flux vector
Array<Real> * external_heat_rate;
/// residuals array
Array<Real> * residual;
/// position of a dof in the K matrix
Array<Int> * equation_number;
//lumped vector
Array<Real> * capacity_lumped;
/// boundary vector
Array<bool> * blocked_dofs;
//realtime
Real time;
///capacity
Real capacity;
//conductivity matrix
Matrix<Real> conductivity;
//linear variation of the conductivity (for temperature dependent conductivity)
Real conductivity_variation;
// reference temperature for the interpretation of temperature variation
Real T_ref;
//the biggest parameter of conductivity matrix
Real conductivitymax;
/// thermal energy by element
ElementTypeMapArray<Real> thermal_energy;
/// Solver
Solver * solver;
/// analysis method
AnalysisMethod method;
/// pointer to the pbc synchronizer
PBCSynchronizer * pbc_synch;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "heat_transfer_model_inline_impl.cc"
#endif
/// standard output stream operator
inline std::ostream & operator <<(std::ostream & stream, const HeatTransferModel & _this)
{
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_HEAT_TRANSFER_MODEL_HH__ */
diff --git a/src/model/integration_scheme/generalized_trapezoidal.cc b/src/model/integration_scheme/generalized_trapezoidal.cc
index cef1e7214..5ef035f12 100644
--- a/src/model/integration_scheme/generalized_trapezoidal.cc
+++ b/src/model/integration_scheme/generalized_trapezoidal.cc
@@ -1,192 +1,192 @@
/**
* @file generalized_trapezoidal.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 04 2011
* @date last modification: Thu Jun 05 2014
*
* @brief implementation of inline functions
*
* @section LICENSE
*
* Copyright (©) 2010-2012, 2014 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "generalized_trapezoidal.hh"
#include "mesh.hh"
#include "aka_array.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
GeneralizedTrapezoidal::GeneralizedTrapezoidal(DOFManager & dof_manager,
const ID & dof_id, Real alpha)
: IntegrationScheme1stOrder(dof_manager, dof_id), alpha(alpha) {
this->registerParam("alpha", this->alpha, alpha, _pat_parsmod, "The alpha parameter");
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::predictor(Real delta_t, Array<Real> & u,
Array<Real> & u_dot,
const Array<bool> & blocked_dofs) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.getSize();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt d = 0; d < nb_degree_of_freedom; d++) {
if (!(*blocked_dofs_val)) {
*u_val += (1. - alpha) * delta_t * *u_dot_val;
}
u_val++;
u_dot_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
switch (type) {
case _temperature:
this->allCorrector<_temperature>(delta_t, u, u_dot, blocked_dofs, delta);
break;
case _temperature_rate:
this->allCorrector<_temperature_rate>(delta_t, u, u_dot, blocked_dofs,
delta);
break;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real GeneralizedTrapezoidal::getTemperatureCoefficient(
const SolutionType & type, Real delta_t) const {
switch (type) {
case _temperature:
return 1.;
case _temperature_rate:
return alpha * delta_t;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real GeneralizedTrapezoidal::getTemperatureRateCoefficient(
const SolutionType & type, Real delta_t) const {
switch (type) {
case _temperature:
return 1. / (alpha * delta_t);
case _temperature_rate:
return 1.;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
template <IntegrationScheme::SolutionType type>
void GeneralizedTrapezoidal::allCorrector(Real delta_t, Array<Real> & u,
Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.getSize();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real e = getTemperatureCoefficient(type, delta_t);
Real d = getTemperatureRateCoefficient(type, delta_t);
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * delta_val = delta.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt dof = 0; dof < nb_degree_of_freedom; dof++) {
if (!(*blocked_dofs_val)) {
*u_val += e ** delta_val;
*u_dot_val += d ** delta_val;
}
u_val++;
u_dot_val++;
delta_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void GeneralizedTrapezoidal::assembleJacobian(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & M = this->dof_manager.getMatrix("M");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
bool does_j_need_update = false;
does_j_need_update |= M.getRelease() != m_release;
does_j_need_update |= K.getRelease() != k_release;
if (!does_j_need_update) {
AKANTU_DEBUG_OUT();
return;
}
J.clear();
Real c = this->getTemperatureRateCoefficient(type, delta_t);
Real e = this->getTemperatureCoefficient(type, delta_t);
J.add(M, e);
J.add(K, c);
m_release = M.getRelease();
k_release = K.getRelease();
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/integration_scheme/generalized_trapezoidal.hh b/src/model/integration_scheme/generalized_trapezoidal.hh
index 7a2256941..d2e2d4f83 100644
--- a/src/model/integration_scheme/generalized_trapezoidal.hh
+++ b/src/model/integration_scheme/generalized_trapezoidal.hh
@@ -1,166 +1,166 @@
/**
* @file generalized_trapezoidal.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Jul 04 2011
* @date last modification: Fri Oct 23 2015
*
* @brief Generalized Trapezoidal Method. 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_GENERALIZED_TRAPEZOIDAL_HH__
#define __AKANTU_GENERALIZED_TRAPEZOIDAL_HH__
#include "integration_scheme_1st_order.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/**
* The two differentiate equation (thermal and kinematic) are :
* @f{eqnarray*}{
* C\dot{u}_{n+1} + Ku_{n+1} = q_{n+1}\\
* u_{n+1} = u_{n} + (1-\alpha) \Delta t \dot{u}_{n} + \alpha \Delta t
*\dot{u}_{n+1}
* @f}
*
* To solve it :
* Predictor :
* @f{eqnarray*}{
* u^0_{n+1} &=& u_{n} + (1-\alpha) \Delta t v_{n} \\
* \dot{u}^0_{n+1} &=& \dot{u}_{n}
* @f}
*
* Solve :
* @f[ (a C + b K^i_{n+1}) w = q_{n+1} - f^i_{n+1} - C \dot{u}^i_{n+1} @f]
*
* Corrector :
* @f{eqnarray*}{
* \dot{u}^{i+1}_{n+1} &=& \dot{u}^{i}_{n+1} + a w \\
* u^{i+1}_{n+1} &=& u^{i}_{n+1} + b w
* @f}
*
* a and b depends on the resolution method : temperature (u) or temperature
*rate (@f$\dot{u}@f$)
*
* For temperature : @f$ w = \delta u, a = 1 / (\alpha \Delta t) , b = 1 @f$ @n
* For temperature rate : @f$ w = \delta \dot{u}, a = 1, b = \alpha \Delta t @f$
*/
class GeneralizedTrapezoidal : public IntegrationScheme1stOrder {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
GeneralizedTrapezoidal(DOFManager & dof_manager, const ID & dof_id,
Real alpha = 0);
virtual ~GeneralizedTrapezoidal(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs) const;
virtual void corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const;
virtual void assembleJacobian(const SolutionType & type, Real time_step);
public:
/// the coeffichent @f{b@f} in the description
Real getTemperatureCoefficient(const SolutionType & type, Real delta_t) const;
/// the coeffichent @f{a@f} in the description
Real getTemperatureRateCoefficient(const SolutionType & type,
Real delta_t) const;
private:
template <SolutionType type>
void allCorrector(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & blocked_dofs,
const Array<Real> & delta) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(Alpha, alpha, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the @f$\alpha@f$ parameter
Real alpha;
/// last release of M matrix
UInt m_release;
/// last release of K matrix
UInt k_release;
};
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/**
* Forward Euler (explicit) -> condition on delta_t
*/
class ForwardEuler : public GeneralizedTrapezoidal {
public:
ForwardEuler(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, 0.){};
};
/**
* Trapezoidal rule (implicit), midpoint rule or Crank-Nicolson
*/
class TrapezoidalRule1 : public GeneralizedTrapezoidal {
public:
TrapezoidalRule1(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, .5){};
};
/**
* Backward Euler (implicit)
*/
class BackwardEuler : public GeneralizedTrapezoidal {
public:
BackwardEuler(DOFManager & dof_manager, const ID & dof_id)
: GeneralizedTrapezoidal(dof_manager, dof_id, 1.){};
};
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_GENERALIZED_TRAPEZOIDAL_HH__ */
diff --git a/src/model/integration_scheme/integration_scheme.cc b/src/model/integration_scheme/integration_scheme.cc
index 1e92fdaed..82c60d006 100644
--- a/src/model/integration_scheme/integration_scheme.cc
+++ b/src/model/integration_scheme/integration_scheme.cc
@@ -1,92 +1,92 @@
/**
* @file integration_scheme.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Oct 23 15:33:36 2015
*
* @brief Common interface to all interface 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 "integration_scheme.hh"
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
IntegrationScheme::IntegrationScheme(DOFManager & dof_manager,
const ID & dof_id, UInt order)
: Parsable(_st_integration_scheme, dof_id),
dof_manager(dof_manager), dof_id(dof_id), order(order) {}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
// /// standard output stream operator for SolutionType
// std::ostream & operator<<(std::ostream & stream,
// const IntegrationScheme::SolutionType & type) {
// switch (type) {
// case IntegrationScheme::_displacement:
// stream << "displacement";
// break;
// case IntegrationScheme::_temperature:
// stream << "temperature";
// break;
// case IntegrationScheme::_velocity:
// stream << "velocity";
// break;
// case IntegrationScheme::_temperature_rate:
// stream << "temperature_rate";
// break;
// case IntegrationScheme::_acceleration:
// stream << "acceleration";
// break;
// }
// return stream;
// }
/* -------------------------------------------------------------------------- */
/// standard input stream operator for SolutionType
std::istream & operator>>(std::istream & stream,
IntegrationScheme::SolutionType & type) {
std::string str;
stream >> str;
if (str == "displacement")
type = IntegrationScheme::_displacement;
else if (str == "temperature")
type = IntegrationScheme::_temperature;
else if (str == "velocity")
type = IntegrationScheme::_velocity;
else if (str == "temperature_rate")
type = IntegrationScheme::_temperature_rate;
else if (str == "acceleration")
type = IntegrationScheme::_acceleration;
else {
stream.setstate(std::ios::failbit);
}
return stream;
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/integration_scheme/integration_scheme.hh b/src/model/integration_scheme/integration_scheme.hh
index 3a8d9c454..6a11db54f 100644
--- a/src/model/integration_scheme/integration_scheme.hh
+++ b/src/model/integration_scheme/integration_scheme.hh
@@ -1,107 +1,107 @@
/**
* @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;
}
-__BEGIN_AKANTU__
+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() {}
/* ------------------------------------------------------------------------ */
/* 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;
/* ------------------------------------------------------------------------ */
/* 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);
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_INTEGRATION_SCHEME_HH__ */
diff --git a/src/model/integration_scheme/integration_scheme_1st_order.cc b/src/model/integration_scheme/integration_scheme_1st_order.cc
index 99c607d45..bfdce85eb 100644
--- a/src/model/integration_scheme/integration_scheme_1st_order.cc
+++ b/src/model/integration_scheme/integration_scheme_1st_order.cc
@@ -1,88 +1,88 @@
/**
* @file integration_scheme_1st_order.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Oct 23 12:31:32 2015
*
* @brief Implementation of the common functions for 1st order time
*integrations
*
* @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_1st_order.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::predictor(Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->predictor(delta_t, u, u_dot, blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::corrector(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
const Array<Real> & solution = this->dof_manager.getSolution(this->dof_id);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->corrector(type, delta_t, u, u_dot, blocked_dofs, solution);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme1stOrder::assembleResidual(bool is_lumped) {
AKANTU_DEBUG_IN();
const Array<Real> & first_derivative =
dof_manager.getDOFsDerivatives(this->dof_id, 1);
if (!is_lumped) {
this->dof_manager.assembleMatMulVectToResidual(this->dof_id, "C",
first_derivative, -1);
} else {
this->dof_manager.assembleLumpedMatMulVectToResidual(this->dof_id, "C",
first_derivative, -1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/integration_scheme/integration_scheme_1st_order.hh b/src/model/integration_scheme/integration_scheme_1st_order.hh
index af70e2a4e..7f73dc8b9 100644
--- a/src/model/integration_scheme/integration_scheme_1st_order.hh
+++ b/src/model/integration_scheme/integration_scheme_1st_order.hh
@@ -1,93 +1,93 @@
/**
* @file integration_scheme_1st_order.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Oct 23 2015
*
* @brief Interface of the time integrator of first 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_common.hh"
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH__
#define __AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH__
-__BEGIN_AKANTU__
+namespace akantu {
class IntegrationScheme1stOrder : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
IntegrationScheme1stOrder(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 1){};
virtual ~IntegrationScheme1stOrder(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// generic interface of a predictor
virtual void predictor(Real delta_t);
/// generic interface of a corrector
virtual void corrector(const SolutionType & type, Real delta_t);
/// assemble the residual
virtual void assembleResidual(bool is_lumped);
protected:
/// generic interface of a predictor of 1st order
virtual void predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & boundary) const = 0;
/// generic interface of a corrector of 1st order
virtual void corrector(const SolutionType & type, Real delta_t,
Array<Real> & u, Array<Real> & u_dot,
const Array<bool> & boundary,
const Array<Real> & delta) const = 0;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
protected:
virtual Real getTemperatureCoefficient(const SolutionType & type,
Real delta_t) const = 0;
virtual Real getTemperatureRateCoefficient(const SolutionType & type,
Real delta_t) const = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
-__END_AKANTU__
+} // akantu
#include "generalized_trapezoidal.hh"
#endif /* __AKANTU_INTEGRATION_SCHEME_1ST_ORDER_HH__ */
diff --git a/src/model/integration_scheme/integration_scheme_2nd_order.cc b/src/model/integration_scheme/integration_scheme_2nd_order.cc
index 190e5b3b5..6af699f99 100644
--- a/src/model/integration_scheme/integration_scheme_2nd_order.cc
+++ b/src/model/integration_scheme/integration_scheme_2nd_order.cc
@@ -1,100 +1,100 @@
/**
* @file integration_scheme_2nd_order.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Oct 20 10:41:12 2015
*
* @brief Implementation of the common part of 2nd order 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 "integration_scheme_2nd_order.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
void IntegrationScheme2ndOrder::predictor(Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
Array<Real> & u_dot_dot =
this->dof_manager.getDOFsDerivatives(this->dof_id, 2);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->predictor(delta_t, u, u_dot, u_dot_dot, blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme2ndOrder::corrector(const SolutionType & type,
Real delta_t) {
AKANTU_DEBUG_IN();
Array<Real> & u = this->dof_manager.getDOFs(this->dof_id);
Array<Real> & u_dot = this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
Array<Real> & u_dot_dot =
this->dof_manager.getDOFsDerivatives(this->dof_id, 2);
const Array<Real> & solution = this->dof_manager.getSolution(this->dof_id);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
this->corrector(type, delta_t, u, u_dot, u_dot_dot, blocked_dofs, solution);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void IntegrationScheme2ndOrder::assembleResidual(bool is_lumped) {
AKANTU_DEBUG_IN();
if (this->dof_manager.hasMatrix("C")) {
const Array<Real> & first_derivative =
this->dof_manager.getDOFsDerivatives(this->dof_id, 1);
this->dof_manager.assembleMatMulVectToResidual(this->dof_id, "C",
first_derivative, -1);
}
const Array<Real> & second_derivative =
this->dof_manager.getDOFsDerivatives(this->dof_id, 2);
if (!is_lumped) {
this->dof_manager.assembleMatMulVectToResidual(this->dof_id, "M",
second_derivative, -1);
} else {
this->dof_manager.assembleLumpedMatMulVectToResidual(this->dof_id, "M",
second_derivative, -1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/integration_scheme/integration_scheme_2nd_order.hh b/src/model/integration_scheme/integration_scheme_2nd_order.hh
index ba2e9b62b..9ae6b095e 100644
--- a/src/model/integration_scheme/integration_scheme_2nd_order.hh
+++ b/src/model/integration_scheme/integration_scheme_2nd_order.hh
@@ -1,104 +1,104 @@
/**
* @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;
}
-__BEGIN_AKANTU__
+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(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// generic interface of a predictor
virtual void predictor(Real delta_t);
/// generic interface of a corrector
virtual void corrector(const SolutionType & type, Real delta_t);
virtual void assembleResidual(bool is_lumped);
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:
};
-__END_AKANTU__
+} // akantu
#include "newmark-beta.hh"
#endif /* __AKANTU_INTEGRATION_SCHEME_2ND_ORDER_HH__ */
diff --git a/src/model/integration_scheme/newmark-beta.cc b/src/model/integration_scheme/newmark-beta.cc
index 9527dfc6c..44ba3091a 100644
--- a/src/model/integration_scheme/newmark-beta.cc
+++ b/src/model/integration_scheme/newmark-beta.cc
@@ -1,260 +1,260 @@
/**
* @file newmark-beta.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Oct 05 2010
* @date last modification: Thu Jun 05 2014
*
* @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 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 "newmark-beta.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NewmarkBeta::NewmarkBeta(DOFManager & dof_manager, const ID & dof_id,
Real alpha, Real beta)
: IntegrationScheme2ndOrder(dof_manager, dof_id), beta(beta), alpha(alpha),
k(0.), h(0.), m_release(0), k_release(0), c_release(0) {
this->registerParam("alpha", this->alpha, alpha, _pat_parsmod,
"The alpha parameter");
this->registerParam("beta", this->beta, beta, _pat_parsmod,
"The beta parameter");
}
/* -------------------------------------------------------------------------- */
/*
* @f$ \tilde{u_{n+1}} = u_{n} + \Delta t \dot{u}_n + \frac{\Delta t^2}{2}
* \ddot{u}_n @f$
* @f$ \tilde{\dot{u}_{n+1}} = \dot{u}_{n} + \Delta t \ddot{u}_{n} @f$
* @f$ \tilde{\ddot{u}_{n}} = \ddot{u}_{n} @f$
*/
void NewmarkBeta::predictor(Real delta_t, Array<Real> & u, Array<Real> & u_dot,
Array<Real> & u_dot_dot,
const Array<bool> & blocked_dofs) const {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.getSize();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * u_dot_dot_val = u_dot_dot.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt d = 0; d < nb_degree_of_freedom; d++) {
if (!(*blocked_dofs_val)) {
Real dt_a_n = delta_t * *u_dot_dot_val;
*u_val += (1 - k * alpha) * delta_t * *u_dot_val +
(.5 - h * alpha * beta) * delta_t * dt_a_n;
*u_dot_val = (1 - k) * *u_dot_val + (1 - h * beta) * dt_a_n;
*u_dot_dot_val = (1 - h) * *u_dot_dot_val;
}
u_val++;
u_dot_val++;
u_dot_dot_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NewmarkBeta::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 {
AKANTU_DEBUG_IN();
switch (type) {
case _acceleration: {
this->allCorrector<_acceleration>(delta_t, u, u_dot, u_dot_dot,
blocked_dofs, delta);
break;
}
case _velocity: {
this->allCorrector<_velocity>(delta_t, u, u_dot, u_dot_dot, blocked_dofs,
delta);
break;
}
case _displacement: {
this->allCorrector<_displacement>(delta_t, u, u_dot, u_dot_dot,
blocked_dofs, delta);
break;
}
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return 1.;
case _velocity:
return 1. / (beta * delta_t);
case _displacement:
return 1. / (alpha * beta * delta_t * delta_t);
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getVelocityCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return beta * delta_t;
case _velocity:
return 1.;
case _displacement:
return 1. / (alpha * delta_t);
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
Real NewmarkBeta::getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const {
switch (type) {
case _acceleration:
return alpha * beta * delta_t * delta_t;
case _velocity:
return alpha * delta_t;
case _displacement:
return 1.;
default:
AKANTU_EXCEPTION("The corrector type : "
<< type
<< " is not supported by this type of integration scheme");
}
}
/* -------------------------------------------------------------------------- */
template <IntegrationScheme::SolutionType type>
void NewmarkBeta::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 {
AKANTU_DEBUG_IN();
UInt nb_nodes = u.getSize();
UInt nb_degree_of_freedom = u.getNbComponent() * nb_nodes;
Real c = getAccelerationCoefficient(type, delta_t);
Real d = getVelocityCoefficient(type, delta_t);
Real e = getDisplacementCoefficient(type, delta_t);
Real * u_val = u.storage();
Real * u_dot_val = u_dot.storage();
Real * u_dot_dot_val = u_dot_dot.storage();
Real * delta_val = delta.storage();
bool * blocked_dofs_val = blocked_dofs.storage();
for (UInt dof = 0; dof < nb_degree_of_freedom; dof++) {
if (!(*blocked_dofs_val)) {
*u_val += e * *delta_val;
*u_dot_val += d * *delta_val;
*u_dot_dot_val += c * *delta_val;
}
u_val++;
u_dot_val++;
u_dot_dot_val++;
delta_val++;
blocked_dofs_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NewmarkBeta::assembleJacobian(const SolutionType & type, Real delta_t) {
AKANTU_DEBUG_IN();
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & M = this->dof_manager.getMatrix("M");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
bool does_j_need_update = false;
does_j_need_update |= M.getRelease() != m_release;
does_j_need_update |= K.getRelease() != k_release;
if (this->dof_manager.hasMatrix("C")) {
const SparseMatrix & C = this->dof_manager.getMatrix("C");
does_j_need_update |= C.getRelease() != c_release;
}
if (!does_j_need_update) {
AKANTU_DEBUG_OUT();
return;
}
J.clear();
Real c = this->getAccelerationCoefficient(type, delta_t);
Real e = this->getDisplacementCoefficient(type, delta_t);
if (!(e == 0.)) { // in explicit this coefficient is exactly 0.
J.add(K, e);
}
J.add(M, c);
m_release = M.getRelease();
k_release = K.getRelease();
if (this->dof_manager.hasMatrix("C")) {
Real d = this->getVelocityCoefficient(type, delta_t);
const SparseMatrix & C = this->dof_manager.getMatrix("C");
J.add(C, d);
c_release = C.getRelease();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/integration_scheme/newmark-beta.hh b/src/model/integration_scheme/newmark-beta.hh
index 6272757e4..ac976a2ed 100644
--- a/src/model/integration_scheme/newmark-beta.hh
+++ b/src/model/integration_scheme/newmark-beta.hh
@@ -1,195 +1,195 @@
/**
* @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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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.);
~NewmarkBeta(){};
/* ------------------------------------------------------------------------ */
/* 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;
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;
void assembleJacobian(const SolutionType & type, Real delta_t);
public:
Real getAccelerationCoefficient(const SolutionType & type,
Real delta_t) const;
Real getVelocityCoefficient(const SolutionType & type, Real delta_t) const;
Real getDisplacementCoefficient(const SolutionType & type,
Real delta_t) const;
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.){};
};
//#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.){};
};
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_NEWMARK_BETA_HH__ */
diff --git a/src/model/integration_scheme/pseudo_time.cc b/src/model/integration_scheme/pseudo_time.cc
index 2acfd2ad2..c19ff6ffe 100644
--- a/src/model/integration_scheme/pseudo_time.cc
+++ b/src/model/integration_scheme/pseudo_time.cc
@@ -1,85 +1,85 @@
/**
* @file pseudo_time.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Feb 17 09:49:10 2016
*
* @brief Implementation of a really simple integration scheme
*
* @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 "pseudo_time.hh"
#include "dof_manager.hh"
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
PseudoTime::PseudoTime(DOFManager & dof_manager, const ID & dof_id)
: IntegrationScheme(dof_manager, dof_id, 0), k_release(0) {}
/* -------------------------------------------------------------------------- */
void PseudoTime::predictor(Real) {}
/* -------------------------------------------------------------------------- */
void PseudoTime::corrector(const SolutionType &, Real) {
Array<Real> & us = this->dof_manager.getDOFs(this->dof_id);
const Array<Real> & deltas = this->dof_manager.getSolution(this->dof_id);
const Array<bool> & blocked_dofs =
this->dof_manager.getBlockedDOFs(this->dof_id);
UInt nb_degree_of_freedom = deltas.getSize();
auto u_it = us.begin_reinterpret(nb_degree_of_freedom);
auto bld_it = blocked_dofs.begin_reinterpret(nb_degree_of_freedom);
for (const auto & delta : deltas) {
const auto & bld = *bld_it;
auto & u = *u_it;
if (! bld) u += delta;
++u_it;
++bld_it;
}
}
/* -------------------------------------------------------------------------- */
void PseudoTime::assembleJacobian(const SolutionType &, Real) {
SparseMatrix & J = this->dof_manager.getMatrix("J");
const SparseMatrix & K = this->dof_manager.getMatrix("K");
if (K.getRelease() == k_release)
return;
J.clear();
J.add(K);
k_release = K.getRelease();
}
/* -------------------------------------------------------------------------- */
void PseudoTime::assembleResidual(bool) {}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/integration_scheme/pseudo_time.hh b/src/model/integration_scheme/pseudo_time.hh
index 9be2d22d3..cfd37f8aa 100644
--- a/src/model/integration_scheme/pseudo_time.hh
+++ b/src/model/integration_scheme/pseudo_time.hh
@@ -1,70 +1,70 @@
/**
* @file pseudo_time.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Feb 17 09:46:05 2016
*
* @brief Pseudo time integration scheme
*
* @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"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_PSEUDO_TIME_HH__
#define __AKANTU_PSEUDO_TIME_HH__
-__BEGIN_AKANTU__
+namespace akantu {
class PseudoTime : public IntegrationScheme {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
PseudoTime(DOFManager & dof_manager, const ID & dof_id);
virtual ~PseudoTime() {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// generic interface of a predictor
virtual void predictor(Real delta_t);
/// generic interface of a corrector
virtual void corrector(const SolutionType & type, Real delta_t);
/// assemble the jacobian matrix
virtual void assembleJacobian(const SolutionType & type, Real delta_t);
/// assemble the residual
virtual void assembleResidual(bool is_lumped);
protected:
/// last release of K matrix
UInt k_release;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_PSEUDO_TIME_HH__ */
diff --git a/src/model/model.cc b/src/model/model.cc
index a439f3dfb..abf830ba8 100644
--- a/src/model/model.cc
+++ b/src/model/model.cc
@@ -1,342 +1,342 @@
/**
* @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 "element_group.hh"
#include "synchronizer_registry.hh"
#include "data_accessor.hh"
#include "static_communicator.hh"
#include "element_synchronizer.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Model::~Model() {
AKANTU_DEBUG_IN();
FEEngineMap::iterator it;
for (it = fems.begin(); it != fems.end(); ++it) {
if (it->second)
delete it->second;
}
for (it = fems_boundary.begin(); it != fems_boundary.end(); ++it) {
if (it->second)
delete it->second;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void Model::setParser(Parser & parser) { this->parser = &parser; }
/* -------------------------------------------------------------------------- */
void Model::initFull(__attribute__((unused)) const ModelOptions & options) {
AKANTU_DEBUG_IN();
initModel();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
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;
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(); }
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/model_solver.cc b/src/model/model_solver.cc
index 4199f603f..6fafb2844 100644
--- a/src/model/model_solver.cc
+++ b/src/model/model_solver.cc
@@ -1,673 +1,673 @@
/**
* @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 "non_linear_solver.hh"
#include "time_step_solver.hh"
#include "mesh.hh"
#if defined(AKANTU_USE_MPI)
#include "mpi_type_wrapper.hh"
#endif
#include "dof_manager_default.hh"
#if defined(AKANTU_USE_PETSC)
#include "dof_manager_petsc.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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),
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;
Parser::const_section_iterator it;
for (it = sub_sect.first; it != sub_sect.second && section == NULL; ++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;
}
}
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;
}
/* -------------------------------------------------------------------------- */
// void ModelSolver::setIntegrationScheme(
// const ID & solver_id, const ID & dof_id,
// const IntegrationSchemeType & integration_scheme_type) {}
/* -------------------------------------------------------------------------- */
// /* --------------------------------------------------------------------------
// */
// template <NewmarkBeta::IntegrationSchemeCorrectorType type>
// void SolidMechanicsModel::solve(Array<Real> &increment, Real block_val,
// bool need_factorize, bool
// has_profile_changed) {
// if(has_profile_changed) {
// this->initJacobianMatrix();
// need_factorize = true;
// }
// updateResidualInternal(); //doesn't do anything for static
// if(need_factorize) {
// Real c = 0.,d = 0.,e = 0.;
// if(method == _static) {
// AKANTU_DEBUG_INFO("Solving K inc = r");
// e = 1.;
// } else {
// AKANTU_DEBUG_INFO("Solving (c M + d C + e K) inc = r");
// NewmarkBeta * nmb_int = dynamic_cast<NewmarkBeta *>(integrator);
// c = nmb_int->getAccelerationCoefficient<type>(time_step);
// d = nmb_int->getVelocityCoefficient<type>(time_step);
// e = nmb_int->getDisplacementCoefficient<type>(time_step);
// }
// jacobian_matrix->clear();
// // J = c M + d C + e K
// if(stiffness_matrix)
// jacobian_matrix->add(*stiffness_matrix, e);
// if(mass_matrix)
// jacobian_matrix->add(*mass_matrix, c);
// #if !defined(AKANTU_NDEBUG)
// if(mass_matrix && AKANTU_DEBUG_TEST(dblDump))
// mass_matrix->saveMatrix("M.mtx");
// #endif
// if(velocity_damping_matrix)
// jacobian_matrix->add(*velocity_damping_matrix, d);
// jacobian_matrix->applyBoundary(*blocked_dofs, block_val);
// #if !defined(AKANTU_NDEBUG)
// if(AKANTU_DEBUG_TEST(dblDump))
// jacobian_matrix->saveMatrix("J.mtx");
// #endif
// solver->factorize();
// }
// // if (rhs.getSize() != 0)
// // solver->setRHS(rhs);
// // else
// solver->setOperators();
// solver->setRHS(*residual);
// // solve @f[ J \delta w = r @f]
// solver->solve(increment);
// UInt nb_nodes = displacement-> getSize();
// UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;
// bool * blocked_dofs_val = blocked_dofs->storage();
// Real * increment_val = increment.storage();
// for (UInt j = 0; j < nb_degree_of_freedom;
// ++j,++increment_val, ++blocked_dofs_val) {
// if ((*blocked_dofs_val))
// *increment_val = 0.0;
// }
// }
// /* --------------------------------------------------------------------------
// */
// template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
// bool SolidMechanicsModel::solveStatic(Real tolerance, UInt max_iteration,
// bool do_not_factorize) {
// AKANTU_DEBUG_INFO("Solving Ku = f");
// AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
// "You should first initialize the implicit solver and
// assemble the stiffness matrix by calling
// initImplicit");
// AnalysisMethod analysis_method=method;
// Real error = 0.;
// method=_static;
// bool converged = this->template solveStep<cmethod, criteria>(tolerance,
// error, max_iteration, do_not_factorize);
// method=analysis_method;
// return converged;
// }
// /* --------------------------------------------------------------------------
// */
// template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
// bool SolidMechanicsModel::solveStep(Real tolerance,
// UInt max_iteration) {
// Real error = 0.;
// return this->template solveStep<cmethod,criteria>(tolerance,
// error,
// max_iteration);
// }
// /* --------------------------------------------------------------------------
// */
// template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
// bool SolidMechanicsModel::solveStep(Real tolerance, Real & error, UInt
// max_iteration,
// bool do_not_factorize) {
// EventManager::sendEvent(SolidMechanicsModelEvent::BeforeSolveStepEvent(method));
// this->implicitPred();
// this->updateResidual();
// AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
// "You should first initialize the implicit solver and
// assemble the stiffness matrix");
// bool need_factorize = !do_not_factorize;
// if (method==_implicit_dynamic) {
// AKANTU_DEBUG_ASSERT(mass_matrix != NULL,
// "You should first initialize the implicit solver and
// assemble the mass matrix");
// }
// switch (cmethod) {
// case _scm_newton_raphson_tangent:
// case _scm_newton_raphson_tangent_not_computed:
// break;
// case _scm_newton_raphson_tangent_modified:
// this->assembleStiffnessMatrix();
// break;
// default:
// AKANTU_DEBUG_ERROR("The resolution method " << cmethod << " has not been
// implemented!");
// }
// this->n_iter = 0;
// bool converged = false;
// error = 0.;
// if(criteria == _scc_residual) {
// converged = this->testConvergence<criteria> (tolerance, error);
// if(converged) return converged;
// }
// do {
// if (cmethod == _scm_newton_raphson_tangent)
// this->assembleStiffnessMatrix();
// solve<NewmarkBeta::_displacement_corrector> (*increment, 1.,
// need_factorize);
// this->implicitCorr();
// if(criteria == _scc_residual) this->updateResidual();
// converged = this->testConvergence<criteria> (tolerance, error);
// if(criteria == _scc_increment && !converged) this->updateResidual();
// //this->dump();
// this->n_iter++;
// AKANTU_DEBUG_INFO("[" << criteria << "] Convergence iteration "
// << std::setw(std::log10(max_iteration)) << this->n_iter
// << ": error " << error << (converged ? " < " : " > ")
// << tolerance);
// switch (cmethod) {
// case _scm_newton_raphson_tangent:
// need_factorize = true;
// break;
// case _scm_newton_raphson_tangent_not_computed:
// case _scm_newton_raphson_tangent_modified:
// need_factorize = false;
// break;
// default:
// AKANTU_DEBUG_ERROR("The resolution method " << cmethod << " has not
// been implemented!");
// }
// } while (!converged && this->n_iter < max_iteration);
// // this makes sure that you have correct strains and stresses after the
// solveStep function (e.g., for dumping)
// if(criteria == _scc_increment) this->updateResidual();
// if (converged) {
// EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));
// } else if(this->n_iter == max_iteration) {
// AKANTU_DEBUG_WARNING("[" << criteria << "] Convergence not reached after
// "
// << std::setw(std::log10(max_iteration)) <<
// this->n_iter <<
// " iteration" << (this->n_iter == 1 ? "" : "s") <<
// "!" << std::endl);
// }
// return converged;
// }
// void SolidMechanicsModel::updateResidualInternal() {
// AKANTU_DEBUG_IN();
// AKANTU_DEBUG_INFO("Update the residual");
// // f = f_ext - f_int - Ma - Cv = r - Ma - Cv;
// if(method != _static) {
// // f -= Ma
// if(mass_matrix) {
// // if full mass_matrix
// Array<Real> * Ma = new Array<Real>(*acceleration, true, "Ma");
// *Ma *= *mass_matrix;
// /// \todo check unit conversion for implicit dynamics
// // *Ma /= f_m2a
// *residual -= *Ma;
// delete Ma;
// } else if (mass) {
// // else lumped mass
// UInt nb_nodes = acceleration->getSize();
// UInt nb_degree_of_freedom = acceleration->getNbComponent();
// Real * mass_val = mass->storage();
// Real * accel_val = acceleration->storage();
// Real * res_val = residual->storage();
// bool * blocked_dofs_val = blocked_dofs->storage();
// for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
// if(!(*blocked_dofs_val)) {
// *res_val -= *accel_val * *mass_val /f_m2a;
// }
// blocked_dofs_val++;
// res_val++;
// mass_val++;
// accel_val++;
// }
// } else {
// AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
// }
// // f -= Cv
// if(velocity_damping_matrix) {
// Array<Real> * Cv = new Array<Real>(*velocity);
// *Cv *= *velocity_damping_matrix;
// *residual -= *Cv;
// delete Cv;
// }
// }
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */
// void SolidMechanicsModel::solveLumped(Array<Real> & x,
// const Array<Real> & A,
// const Array<Real> & b,
// const Array<bool> & blocked_dofs,
// Real alpha) {
// Real * A_val = A.storage();
// Real * b_val = b.storage();
// Real * x_val = x.storage();
// bool * blocked_dofs_val = blocked_dofs.storage();
// UInt nb_degrees_of_freedom = x.getSize() * x.getNbComponent();
// for (UInt n = 0; n < nb_degrees_of_freedom; ++n) {
// if(!(*blocked_dofs_val)) {
// *x_val = alpha * (*b_val / *A_val);
// }
// x_val++;
// A_val++;
// b_val++;
// blocked_dofs_val++;
// }
// }
/* -------------------------------------------------------------------------- */
// void TimeStepSolverDefault::updateAcceleration() {
// AKANTU_DEBUG_IN();
// updateResidualInternal();
// if (method == _explicit_lumped_mass) {
// /* residual = residual_{n+1} - M * acceleration_n therefore
// solution = increment acceleration not acceleration */
// solveLumped(*increment_acceleration, *mass, *residual, *blocked_dofs,
// f_m2a);
// } else if (method == _explicit_consistent_mass) {
// solve<NewmarkBeta::_acceleration_corrector>(*increment_acceleration);
// }
// AKANTU_DEBUG_OUT();
// }
-__END_AKANTU__
+} // akantu
diff --git a/src/model/model_solver.hh b/src/model/model_solver.hh
index 1bbcf8629..27dd227f5 100644
--- a/src/model/model_solver.hh
+++ b/src/model/model_solver.hh
@@ -1,191 +1,191 @@
/**
* @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;
}
-__BEGIN_AKANTU__
+namespace akantu {
class ModelSolver : public Parsable,
public SolverCallback,
public SynchronizerRegistry {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
ModelSolver(Mesh & mesh, const ID & id, UInt memory_id);
virtual ~ModelSolver();
/// 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
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
virtual void predictor();
/// Corrector interface for the callback
virtual void corrector();
/// AssembleResidual interface for the callback
virtual void assembleResidual() = 0;
/// AssembleJacobian interface for the callback
virtual void assembleJacobian() = 0;
/* ------------------------------------------------------------------------ */
/* 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;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MODEL_SOLVER_HH__ */
diff --git a/src/model/model_solver_tmpl.hh b/src/model/model_solver_tmpl.hh
index c351fcc17..3294541e2 100644
--- a/src/model/model_solver_tmpl.hh
+++ b/src/model/model_solver_tmpl.hh
@@ -1,54 +1,54 @@
/**
* @file model_solver_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Apr 29 17:16:33 2016
*
* @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 "time_step_solver.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MODEL_SOLVER_TMPL_HH__
#define __AKANTU_MODEL_SOLVER_TMPL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
template<typename T>
void ModelSolver::set(const ID & param, const T & value, const ID & solver_id) {
TimeStepSolver & solver = this->getSolver(solver_id);
solver.setParam(param, value);
}
inline Parameter ModelSolver::get(const ID & param, const ID & solver_id) {
TimeStepSolver & solver = this->getSolver(solver_id);
return solver.getParam(param);
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MODEL_SOLVER_TMPL_HH__ */
diff --git a/src/model/non_linear_solver.cc b/src/model/non_linear_solver.cc
index 3dd79dedb..a970e4210 100644
--- a/src/model/non_linear_solver.cc
+++ b/src/model/non_linear_solver.cc
@@ -1,66 +1,66 @@
/**
* @file non_linear_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Oct 13 15:34:43 2015
*
* @brief Implementation of the base class NonLinearSolver
*
* @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 "solver_callback.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolver::NonLinearSolver(
DOFManager & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: Memory(id, memory_id), Parsable(_st_non_linear_solver, id),
_dof_manager(dof_manager),
non_linear_solver_type(non_linear_solver_type) {
this->registerParam("type", this->non_linear_solver_type, _pat_parsable,
"Non linear solver type");
}
/* -------------------------------------------------------------------------- */
NonLinearSolver::~NonLinearSolver() {}
/* -------------------------------------------------------------------------- */
void NonLinearSolver::checkIfTypeIsSupported() {
if (this->supported_type.find(this->non_linear_solver_type) ==
this->supported_type.end()) {
AKANTU_EXCEPTION("The resolution method "
<< this->non_linear_solver_type
<< " is not implemented in the non linear solver "
<< this->id << "!");
}
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/non_linear_solver.hh b/src/model/non_linear_solver.hh
index 616fa6a52..750e0536d 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;
}
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* 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;
};
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_HH__ */
diff --git a/src/model/non_linear_solver_callback.hh b/src/model/non_linear_solver_callback.hh
index c9a393af6..9c1950aa4 100644
--- a/src/model/non_linear_solver_callback.hh
+++ b/src/model/non_linear_solver_callback.hh
@@ -1,61 +1,61 @@
/**
* @file non_linear_solver_callback.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Sep 28 18:48:21 2015
*
* @brief Interface to implement for the non linear solver to work
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_NON_LINEAR_SOLVER_CALLBACK_HH__
#define __AKANTU_NON_LINEAR_SOLVER_CALLBACK_HH__
-__BEGIN_AKANTU__
+namespace akantu {
class NonLinearSolverCallback {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// callback to assemble the Jacobian Matrix
virtual void assembleJacobian() { AKANTU_DEBUG_TO_IMPLEMENT(); }
/// callback to assemble the residual (rhs)
virtual void assembleResidual() { AKANTU_DEBUG_TO_IMPLEMENT(); }
/* ------------------------------------------------------------------------ */
/* Dynamic simulations part */
/* ------------------------------------------------------------------------ */
/// callback for the predictor (in case of dynamic simulation)
virtual void predictor() { AKANTU_DEBUG_TO_IMPLEMENT(); }
/// callback for the corrector (in case of dynamic simulation)
virtual void corrector() { AKANTU_DEBUG_TO_IMPLEMENT(); }
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_CALLBACK_HH__ */
diff --git a/src/model/non_linear_solver_linear.cc b/src/model/non_linear_solver_linear.cc
index 8b518193c..fd10e5b2f 100644
--- a/src/model/non_linear_solver_linear.cc
+++ b/src/model/non_linear_solver_linear.cc
@@ -1,71 +1,71 @@
/**
* @file non_linear_solver_linear.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 25 00:57:00 2015
*
* @brief Implementation of the default NonLinearSolver
*
* @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_linear.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverLinear::NonLinearSolverLinear(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id, memory_id),
dof_manager(dof_manager),
solver(dof_manager, "J", id + ":sparse_solver", memory_id) {
this->supported_type.insert(_nls_linear);
this->checkIfTypeIsSupported();
}
/* -------------------------------------------------------------------------- */
NonLinearSolverLinear::~NonLinearSolverLinear() {}
/* ------------------------------------------------------------------------ */
void NonLinearSolverLinear::solve(SolverCallback & solver_callback) {
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
solver_callback.assembleResidual();
solver_callback.assembleJacobian();
this->solver.solve();
solver_callback.corrector();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/non_linear_solver_linear.hh b/src/model/non_linear_solver_linear.hh
index 09f8b2915..c52b5a693 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;
}
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* 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);
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;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_LINEAR_HH__ */
diff --git a/src/model/non_linear_solver_lumped.cc b/src/model/non_linear_solver_lumped.cc
index 7fc359883..5b3a89f80 100644
--- a/src/model/non_linear_solver_lumped.cc
+++ b/src/model/non_linear_solver_lumped.cc
@@ -1,103 +1,103 @@
/**
* @file non_linear_solver_lumped.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 25 00:57:00 2015
*
* @brief Implementation of the default NonLinearSolver
*
* @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_lumped.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverLumped::NonLinearSolverLumped(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id, memory_id),
dof_manager(dof_manager) {
this->supported_type.insert(_nls_lumped);
this->checkIfTypeIsSupported();
this->registerParam("b_a2x", this->alpha, 1., _pat_parsmod,
"Conversion coefficient between x and A^{-1} b");
}
/* -------------------------------------------------------------------------- */
NonLinearSolverLumped::~NonLinearSolverLumped() {}
/* ------------------------------------------------------------------------ */
void NonLinearSolverLumped::solve(SolverCallback & solver_callback) {
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
const Array<Real> & A = this->dof_manager.getLumpedMatrix("M");
Array<Real> & x = this->dof_manager.getGlobalSolution();
const Array<Real> & b = this->dof_manager.getResidual();
x.resize(b.getSize());
this->dof_manager.updateGlobalBlockedDofs();
const Array<bool> & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
solver_callback.assembleResidual();
// alpha is the conversion factor from from force/mass to acceleration needed
// in model coupled with atomistic \todo find a way to define alpha per dof
// type
this->solveLumped(A, x, b, blocked_dofs, alpha);
this->dof_manager.splitSolutionPerDOFs();
solver_callback.corrector();
}
/* -------------------------------------------------------------------------- */
void NonLinearSolverLumped::solveLumped(const Array<Real> & A, Array<Real> & x,
const Array<Real> & b,
const Array<bool> & blocked_dofs,
Real alpha) {
Array<Real>::const_scalar_iterator A_it = A.begin();
Array<Real>::scalar_iterator x_it = x.begin();
Array<Real>::scalar_iterator x_end = x.end();
Array<Real>::const_scalar_iterator b_it = b.begin();
Array<bool>::const_scalar_iterator blocked_it = blocked_dofs.begin();
for (; x_it != x_end; ++x_it, ++b_it, ++A_it, ++blocked_it) {
if (!(*blocked_it)) {
*x_it = alpha *(*b_it / *A_it);
}
}
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/non_linear_solver_lumped.hh b/src/model/non_linear_solver_lumped.hh
index 03ec67c44..834791c3c 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;
}
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* 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);
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;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_NON_LINEAR_SOLVER_LUMPED_HH__ */
diff --git a/src/model/non_linear_solver_newton_raphson.cc b/src/model/non_linear_solver_newton_raphson.cc
index 59a5d6c1f..c2fb7ba4a 100644
--- a/src/model/non_linear_solver_newton_raphson.cc
+++ b/src/model/non_linear_solver_newton_raphson.cc
@@ -1,186 +1,186 @@
/**
* @file non_linear_solver_newton_raphson.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 25 00:57:00 2015
*
* @brief Implementation of the default NonLinearSolver
*
* @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_newton_raphson.hh"
#include "dof_manager_default.hh"
#include "solver_callback.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NonLinearSolverNewtonRaphson::NonLinearSolverNewtonRaphson(
DOFManagerDefault & dof_manager,
const NonLinearSolverType & non_linear_solver_type, const ID & id,
UInt memory_id)
: NonLinearSolver(dof_manager, non_linear_solver_type, id, memory_id),
dof_manager(dof_manager),
solver(dof_manager, "J", id + ":sparse_solver", memory_id), n_iter(0),
error(0.), converged(false) {
this->supported_type.insert(_nls_newton_raphson_modified);
this->supported_type.insert(_nls_newton_raphson);
this->supported_type.insert(_nls_linear);
this->checkIfTypeIsSupported();
this->registerParam("threshold", convergence_criteria, 1e-10, _pat_parsmod,
"Threshold to consider results as converged");
this->registerParam("convergence_type", convergence_criteria_type,
_scc_solution, _pat_parsmod,
"Type of convergence criteria");
this->registerParam("max_iterations", max_iterations, 10, _pat_parsmod,
"Max number of iterations");
this->registerParam("error", error, _pat_readable, "Last reached error");
this->registerParam("nb_iterations", n_iter, _pat_readable,
"Last reached number of iterations");
this->registerParam("converged", converged, _pat_readable,
"Did last solve converged");
this->registerParam("force_linear_recompute", force_linear_recompute, true,
_pat_modifiable,
"Force reassembly of the jacobian matrix");
}
/* -------------------------------------------------------------------------- */
NonLinearSolverNewtonRaphson::~NonLinearSolverNewtonRaphson() {}
/* ------------------------------------------------------------------------ */
void NonLinearSolverNewtonRaphson::solve(SolverCallback & solver_callback) {
this->dof_manager.updateGlobalBlockedDofs();
solver_callback.predictor();
solver_callback.assembleResidual();
if (this->non_linear_solver_type == _nls_newton_raphson_modified ||
(this->non_linear_solver_type == _nls_linear &&
this->force_linear_recompute)) {
solver_callback.assembleJacobian();
this->force_linear_recompute = false;
}
this->n_iter = 0;
this->converged = false;
if (this->convergence_criteria_type == _scc_residual) {
this->converged = this->testConvergence(this->dof_manager.getResidual());
if (this->converged)
return;
}
do {
if (this->non_linear_solver_type == _nls_newton_raphson)
solver_callback.assembleJacobian();
this->solver.solve();
solver_callback.corrector();
// EventManager::sendEvent(NonLinearSolver::AfterSparseSolve(method));
if (this->convergence_criteria_type == _scc_residual) {
solver_callback.assembleResidual();
this->converged = this->testConvergence(this->dof_manager.getResidual());
} else {
this->converged =
this->testConvergence(this->dof_manager.getGlobalSolution());
}
if (this->convergence_criteria_type == _scc_solution && !this->converged)
solver_callback.assembleResidual();
// this->dump();
this->n_iter++;
AKANTU_DEBUG_INFO(
"[" << this->convergence_criteria_type << "] Convergence iteration "
<< std::setw(std::log10(this->max_iterations)) << this->n_iter
<< ": error " << this->error << (this->converged ? " < " : " > ")
<< this->convergence_criteria);
} while (!this->converged && this->n_iter < this->max_iterations);
// this makes sure that you have correct strains and stresses after the
// solveStep function (e.g., for dumping)
if (this->convergence_criteria_type == _scc_solution)
solver_callback.assembleResidual();
if (this->converged) {
// EventManager::sendEvent(
// SolidMechanicsModelEvent::AfterNonLinearSolverSolves(method));
} else if (this->n_iter == this->max_iterations) {
AKANTU_CUSTOM_EXCEPTION(debug::NLSNotConvergedException(
this->convergence_criteria, this->n_iter, this->error));
AKANTU_DEBUG_WARNING("[" << this->convergence_criteria_type
<< "] Convergence not reached after "
<< std::setw(std::log10(this->max_iterations))
<< this->n_iter << " iteration"
<< (this->n_iter == 1 ? "" : "s") << "!");
}
return;
}
/* -------------------------------------------------------------------------- */
bool NonLinearSolverNewtonRaphson::testConvergence(const Array<Real> & array) {
AKANTU_DEBUG_IN();
const Array<bool> & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
UInt nb_degree_of_freedoms = array.getSize();
auto arr_it = array.begin();
auto bld_it = blocked_dofs.begin();
Real norm = 0.;
for (UInt n = 0; n < nb_degree_of_freedoms; ++n, ++arr_it, ++bld_it) {
bool is_local_node = this->dof_manager.isLocalOrMasterDOF(n);
if ((! *bld_it) && is_local_node) {
norm += *arr_it * *arr_it;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(norm, _so_sum);
norm = std::sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm),
"Something went wrong in the solve phase");
this->error = norm;
return (error < this->convergence_criteria);
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/non_linear_solver_newton_raphson.hh b/src/model/non_linear_solver_newton_raphson.hh
index 7faf40241..1b07a299d 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;
}
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* 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);
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;
};
-__END_AKANTU__
+} // 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 7dc88bfd3..01f28e949 100644
--- a/src/model/solid_mechanics/material.cc
+++ b/src/model/solid_mechanics/material.cc
@@ -1,1628 +1,1628 @@
/**
* @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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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
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();
mesh.initElementTypeMapArray(element_filter, 1, spatial_dimension, false,
_ek_regular);
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Material::~Material() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
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.getSize();
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 (auto type : element_filter.elementTypes(spatial_dimension, ghost_type)) {
Array<UInt> & elem_filter = element_filter(type, ghost_type);
if (elem_filter.getSize() == 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.getSize()) {
const Array<Real> & shapes_derivatives = fem->getShapesDerivatives(type,
ghost_type);
Array<Real> & gradu_vect = gradu(type, ghost_type);
UInt nb_element = elem_filter.getSize();
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.getSize();
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.getSize();
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.getSize() == 0)
continue;
UInt size_of_shapes_derivatives = shapes_derivatives.getNbComponent();
UInt nb_element = elem_filter.getSize();
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.getSize();
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.getSize();
UInt nb_element_full =
this->model->getMesh().getNbElement(type, ghost_type);
UInt nb_interpolation_points_per_elem =
by_elem_res.getSize() / 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;
GhostType current_ghost_type = _casper;
Array<Real> * result_vec = NULL;
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.getSize(), 1, type,
ghost_type);
Array<UInt> & mat_renumbering =
material_local_new_numbering(type, ghost_type);
UInt nb_element = elem_filter.getSize();
element.kind = (*el_begin).kind;
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.getSize());
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).getSize()) {
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.getSize(), 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;
el.type = type;
el.ghost_type = gt;
el.kind = Mesh::getKind(type);
for (UInt i = 0; i < elem_filter.getSize(); ++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.getSize());
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::onBeginningSolveStep(__attribute__((unused))
const AnalysisMethod & method) {
this->savePreviousState();
}
/* -------------------------------------------------------------------------- */
void Material::onEndSolveStep(__attribute__((unused))
const AnalysisMethod & method) {
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->updateEnergies(*it, _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).getSize();
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) {
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) {
ElementType type = *it;
if (!element_filter(type, ghost_type).getSize())
continue;
Array<Real>::matrix_iterator eigen_it =
this->eigengradu(type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator eigen_end =
this->eigengradu(type, ghost_type)
.end(spatial_dimension, spatial_dimension);
for (; eigen_it != eigen_end; ++eigen_it) {
Matrix<Real> & current_eigengradu = *eigen_it;
current_eigengradu = prescribed_eigen_grad_u;
}
}
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/material.hh b/src/model/solid_mechanics/material.hh
index dd3307b59..5d5fea53d 100644
--- a/src/model/solid_mechanics/material.hh
+++ b/src/model/solid_mechanics/material.hh
@@ -1,664 +1,664 @@
/**
* @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_common.hh"
#include "aka_memory.hh"
#include "aka_voigthelper.hh"
#include "parser.hh"
#include "parsable.hh"
#include "data_accessor.hh"
#include "integration_point.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;
}
-__BEGIN_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();
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);
/// 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;
/**
* 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(__attribute__((unused)) ElementType el_type,
__attribute__((unused))
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;
virtual inline void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const;
virtual inline void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag);
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(__attribute__((unused))
const Array<UInt> & nodes_list,
__attribute__((unused))
const NewNodesEvent & event){};
virtual void
onNodesRemoved(__attribute__((unused)) const Array<UInt> & nodes_list,
__attribute__((unused)) const Array<UInt> & new_numbering,
__attribute__((unused)) const RemovedNodesEvent & event){};
virtual void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event);
virtual void
onElementsRemoved(const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event);
virtual void onElementsChanged(
__attribute__((unused)) const Array<Element> & old_elements_list,
__attribute__((unused)) const Array<Element> & new_elements_list,
__attribute__((unused)) const ElementTypeMapArray<UInt> & new_numbering,
__attribute__((unused)) const ChangedElementsEvent & event){};
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
virtual void onBeginningSolveStep(const AnalysisMethod & method);
virtual void onEndSolveStep(const AnalysisMethod & method);
virtual void onDamageIteration();
virtual void onDamageUpdate();
virtual void onDump();
/* ------------------------------------------------------------------------ */
/* 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;
}
-__END_AKANTU__
+} // 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).getSize()); \
\
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).getSize()); \
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).getSize()); \
\
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 }
/* -------------------------------------------------------------------------- */
#define INSTANTIATE_MATERIAL(mat_name) \
template class mat_name<1>; \
template class mat_name<2>; \
template class mat_name<3>
#endif /* __AKANTU_MATERIAL_HH__ */
// LocalWords: ElementNull
diff --git a/src/model/solid_mechanics/material_inline_impl.cc b/src/model/solid_mechanics/material_inline_impl.cc
index d09480d68..fbd6f1946 100644
--- a/src/model/solid_mechanics/material_inline_impl.cc
+++ b/src/model/solid_mechanics/material_inline_impl.cc
@@ -1,461 +1,461 @@
/**
* @file material_inline_impl.cc
*
* @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: Wed Nov 25 2015
*
* @brief Implementation of the inline functions of the class material
*
* @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 "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_INLINE_IMPL_CC__
#define __AKANTU_MATERIAL_INLINE_IMPL_CC__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
inline UInt Material::addElement(const ElementType & type, UInt element,
const GhostType & ghost_type) {
Array<UInt> & el_filter = this->element_filter(type, ghost_type);
el_filter.push_back(element);
return el_filter.getSize() - 1;
}
/* -------------------------------------------------------------------------- */
inline UInt Material::getTangentStiffnessVoigtSize(UInt dim) const {
return (dim * (dim - 1) / 2 + dim);
}
/* -------------------------------------------------------------------------- */
inline UInt Material::getCauchyStressMatrixSize(UInt dim) const {
return (dim * dim);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToF(const Matrix<Real> & grad_u, Matrix<Real> & F) {
AKANTU_DEBUG_ASSERT(F.size() >= grad_u.size() && grad_u.size() == dim * dim,
"The dimension of the tensor F should be greater or "
"equal to the dimension of the tensor grad_u.");
F.eye();
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
F(i, j) += grad_u(i, j);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::computeCauchyStressOnQuad(const Matrix<Real> & F,
const Matrix<Real> & piola,
Matrix<Real> & sigma,
const Real & C33) const {
Real J = F.det() * sqrt(C33);
Matrix<Real> F_S(dim, dim);
F_S.mul<false, false>(F, piola);
Real constant = J ? 1. / J : 0;
sigma.mul<false, true>(F_S, F, constant);
}
/* -------------------------------------------------------------------------- */
inline void Material::rightCauchy(const Matrix<Real> & F, Matrix<Real> & C) {
C.mul<true, false>(F, F);
}
/* -------------------------------------------------------------------------- */
inline void Material::leftCauchy(const Matrix<Real> & F, Matrix<Real> & B) {
B.mul<false, true>(F, F);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToEpsilon(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon) {
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
epsilon(i, j) = 0.5 * (grad_u(i, j) + grad_u(j, i));
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::gradUToGreenStrain(const Matrix<Real> & grad_u,
Matrix<Real> & epsilon) {
epsilon.mul<true, false>(grad_u, grad_u, .5);
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
epsilon(i, j) += 0.5 * (grad_u(i, j) + grad_u(j, i));
}
/* -------------------------------------------------------------------------- */
inline Real Material::stressToVonMises(const Matrix<Real> & stress) {
// compute deviatoric stress
UInt dim = stress.cols();
Matrix<Real> deviatoric_stress =
Matrix<Real>::eye(dim, -1. * stress.trace() / 3.);
for (UInt i = 0; i < dim; ++i)
for (UInt j = 0; j < dim; ++j)
deviatoric_stress(i, j) += stress(i, j);
// return Von Mises stress
return std::sqrt(3. * deviatoric_stress.doubleDot(deviatoric_stress) / 2.);
}
/* ---------------------------------------------------------------------------*/
template <UInt dim>
inline void Material::setCauchyStressArray(const Matrix<Real> & S_t,
Matrix<Real> & sigma_voight) {
AKANTU_DEBUG_IN();
sigma_voight.clear();
// see Finite ekement formulations for large deformation dynamic analysis,
// Bathe et al. IJNME vol 9, 1975, page 364 ^t\tau
/*
* 1d: [ s11 ]'
* 2d: [ s11 s22 s12 ]'
* 3d: [ s11 s22 s33 s23 s13 s12 ]
*/
for (UInt i = 0; i < dim; ++i) // diagonal terms
sigma_voight(i, 0) = S_t(i, i);
for (UInt i = 1; i < dim; ++i) // term s12 in 2D and terms s23 s13 in 3D
sigma_voight(dim + i - 1, 0) = S_t(dim - i - 1, dim - 1);
for (UInt i = 2; i < dim; ++i) // term s13 in 3D
sigma_voight(dim + i, 0) = S_t(0, 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
inline void Material::setCauchyStressMatrix(const Matrix<Real> & S_t,
Matrix<Real> & sigma) {
AKANTU_DEBUG_IN();
sigma.clear();
/// see Finite ekement formulations for large deformation dynamic analysis,
/// Bathe et al. IJNME vol 9, 1975, page 364 ^t\tau
for (UInt i = 0; i < dim; ++i) {
for (UInt m = 0; m < dim; ++m) {
for (UInt n = 0; n < dim; ++n) {
sigma(i * dim + m, i * dim + n) = S_t(m, n);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline Element
Material::convertToLocalElement(const Element & global_element) const {
UInt ge = global_element.element;
#ifndef AKANTU_NDEBUG
UInt model_mat_index = this->model->getMaterialByElement(
global_element.type, global_element.ghost_type)(ge);
UInt mat_index = this->model->getMaterialIndex(this->name);
AKANTU_DEBUG_ASSERT(model_mat_index == mat_index,
"Conversion of a global element in a local element for "
"the wrong material "
<< this->name << std::endl);
#endif
UInt le = this->model->getMaterialLocalNumbering(
global_element.type, global_element.ghost_type)(ge);
Element tmp_quad(global_element.type, le, global_element.ghost_type,
global_element.kind);
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline Element
Material::convertToGlobalElement(const Element & local_element) const {
UInt le = local_element.element;
UInt ge =
this->element_filter(local_element.type, local_element.ghost_type)(le);
Element tmp_quad(local_element.type, ge, local_element.ghost_type,
local_element.kind);
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline IntegrationPoint
Material::convertToLocalPoint(const IntegrationPoint & global_point) const {
const FEEngine & fem = this->model->getFEEngine();
UInt nb_quad = fem.getNbIntegrationPoints(global_point.type);
Element el =
this->convertToLocalElement(static_cast<const Element &>(global_point));
IntegrationPoint tmp_quad(el, global_point.num_point, nb_quad);
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline IntegrationPoint
Material::convertToGlobalPoint(const IntegrationPoint & local_point) const {
const FEEngine & fem = this->model->getFEEngine();
UInt nb_quad = fem.getNbIntegrationPoints(local_point.type);
Element el =
this->convertToGlobalElement(static_cast<const Element &>(local_point));
IntegrationPoint tmp_quad(el, local_point.num_point, nb_quad);
return tmp_quad;
}
/* -------------------------------------------------------------------------- */
inline UInt Material::getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_smm_stress) {
return (this->isFiniteDeformation() ? 3 : 1) * spatial_dimension *
spatial_dimension * sizeof(Real) *
this->getModel().getNbIntegrationPoints(elements);
}
return 0;
}
/* -------------------------------------------------------------------------- */
inline void Material::packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const {
if (tag == _gst_smm_stress) {
if (this->isFiniteDeformation()) {
packElementDataHelper(piola_kirchhoff_2, buffer, elements);
packElementDataHelper(gradu, buffer, elements);
}
packElementDataHelper(stress, buffer, elements);
}
}
/* -------------------------------------------------------------------------- */
inline void Material::unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) {
if (tag == _gst_smm_stress) {
if (this->isFiniteDeformation()) {
unpackElementDataHelper(piola_kirchhoff_2, buffer, elements);
unpackElementDataHelper(gradu, buffer, elements);
}
unpackElementDataHelper(stress, buffer, elements);
}
}
/* -------------------------------------------------------------------------- */
inline const Parameter & Material::getParam(const ID & param) const {
try {
return get(param);
} catch (...) {
AKANTU_EXCEPTION("No parameter " << param << " in the material "
<< getID());
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::setParam(const ID & param, T value) {
try {
set<T>(param, value);
} catch (...) {
AKANTU_EXCEPTION("No parameter " << param << " in the material "
<< getID());
}
updateInternalParameters();
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::packElementDataHelper(
const ElementTypeMapArray<T> & data_to_pack, CommunicationBuffer & buffer,
const Array<Element> & elements, const ID & fem_id) const {
DataAccessor::packElementalDataHelper<T>(data_to_pack, buffer, elements, true,
model->getFEEngine(fem_id));
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline void Material::unpackElementDataHelper(
ElementTypeMapArray<T> & data_to_unpack, CommunicationBuffer & buffer,
const Array<Element> & elements, const ID & fem_id) {
DataAccessor::unpackElementalDataHelper<T>(data_to_unpack, buffer, elements,
true, model->getFEEngine(fem_id));
}
/* -------------------------------------------------------------------------- */
template <>
inline void Material::registerInternal<Real>(InternalField<Real> & vect) {
internal_vectors_real[vect.getID()] = &vect;
}
template <>
inline void Material::registerInternal<UInt>(InternalField<UInt> & vect) {
internal_vectors_uint[vect.getID()] = &vect;
}
template <>
inline void Material::registerInternal<bool>(InternalField<bool> & vect) {
internal_vectors_bool[vect.getID()] = &vect;
}
/* -------------------------------------------------------------------------- */
template <>
inline void Material::unregisterInternal<Real>(InternalField<Real> & vect) {
internal_vectors_real.erase(vect.getID());
}
template <>
inline void Material::unregisterInternal<UInt>(InternalField<UInt> & vect) {
internal_vectors_uint.erase(vect.getID());
}
template <>
inline void Material::unregisterInternal<bool>(InternalField<bool> & vect) {
internal_vectors_bool.erase(vect.getID());
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline bool Material::isInternal(__attribute__((unused)) const ID & id,
__attribute__((unused)) const ElementKind & element_kind) const {
AKANTU_DEBUG_TO_IMPLEMENT();
}
template <>
inline bool Material::isInternal<Real>(const ID & id,
const ElementKind & element_kind) const {
std::map<ID, InternalField<Real> *>::const_iterator internal_array =
internal_vectors_real.find(this->getID() + ":" + id);
if (internal_array == internal_vectors_real.end() ||
internal_array->second->getElementKind() != element_kind)
return false;
return true;
}
/* -------------------------------------------------------------------------- */
template <typename T>
inline ElementTypeMap<UInt>
Material::getInternalDataPerElem(const ID & field_id,
const ElementKind & element_kind) const {
if (!this->template isInternal<T>(field_id, element_kind))
AKANTU_EXCEPTION("Cannot find internal field " << id << " in material "
<< this->name);
const InternalField<T> & internal_field =
this->template getInternal<T>(field_id);
const FEEngine & fe_engine = internal_field.getFEEngine();
UInt nb_data_per_quad = internal_field.getNbComponent();
ElementTypeMap<UInt> res;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
typedef typename InternalField<T>::type_iterator type_iterator;
type_iterator tit = internal_field.firstType(*gt);
type_iterator tend = internal_field.lastType(*gt);
for (; tit != tend; ++tit) {
UInt nb_quadrature_points = fe_engine.getNbIntegrationPoints(*tit, *gt);
res(*tit, *gt) = nb_data_per_quad * nb_quadrature_points;
}
}
return res;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void Material::flattenInternal(const std::string & field_id,
ElementTypeMapArray<T> & internal_flat,
const GhostType ghost_type,
ElementKind element_kind) const {
if (!this->template isInternal<T>(field_id, element_kind))
AKANTU_EXCEPTION("Cannot find internal field " << id << " in material "
<< this->name);
const InternalField<T> & internal_field =
this->template getInternal<T>(field_id);
const FEEngine & fe_engine = internal_field.getFEEngine();
const Mesh & mesh = fe_engine.getMesh();
typedef typename InternalField<T>::filter_type_iterator type_iterator;
type_iterator tit = internal_field.filterFirstType(ghost_type);
type_iterator tend = internal_field.filterLastType(ghost_type);
for (; tit != tend; ++tit) {
ElementType type = *tit;
const Array<Real> & src_vect = internal_field(type, ghost_type);
const Array<UInt> & filter = internal_field.getFilter(type, ghost_type);
// total number of elements in the corresponding mesh
UInt nb_element_dst = mesh.getNbElement(type, ghost_type);
// number of element in the internal field
UInt nb_element_src = filter.getSize();
// number of quadrature points per elem
UInt nb_quad_per_elem = fe_engine.getNbIntegrationPoints(type);
// number of data per quadrature point
UInt nb_data_per_quad = internal_field.getNbComponent();
if (!internal_flat.exists(type, ghost_type)) {
internal_flat.alloc(nb_element_dst * nb_quad_per_elem, nb_data_per_quad,
type, ghost_type);
}
if (nb_element_src == 0)
continue;
// number of data per element
UInt nb_data = nb_quad_per_elem * nb_data_per_quad;
Array<Real> & dst_vect = internal_flat(type, ghost_type);
dst_vect.resize(nb_element_dst * nb_quad_per_elem);
Array<UInt>::const_scalar_iterator it = filter.begin();
Array<UInt>::const_scalar_iterator end = filter.end();
Array<Real>::const_vector_iterator it_src =
src_vect.begin_reinterpret(nb_data, nb_element_src);
Array<Real>::vector_iterator it_dst =
dst_vect.begin_reinterpret(nb_data, nb_element_dst);
for (; it != end; ++it, ++it_src) {
it_dst[*it] = *it_src;
}
}
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_INLINE_IMPL_CC__ */
diff --git a/src/model/solid_mechanics/material_selector.hh b/src/model/solid_mechanics/material_selector.hh
index 9f55a061f..603a250b9 100644
--- a/src/model/solid_mechanics/material_selector.hh
+++ b/src/model/solid_mechanics/material_selector.hh
@@ -1,147 +1,147 @@
/**
* @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__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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:
DefaultMaterialSelector(const ElementTypeMapArray<UInt> & material_index)
: material_index(material_index) {}
UInt operator()(const Element & element) {
try {
DebugLevel dbl = debug::getDebugLevel();
debug::setDebugLevel(dblError);
const Array<UInt> & mat_indexes =
material_index(element.type, element.ghost_type);
UInt mat = this->fallback_value;
if (element.element < mat_indexes.getSize())
mat = mat_indexes(element.element);
debug::setDebugLevel(dbl);
return mat;
} catch (...) {
return MaterialSelector::operator()(element);
}
}
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) {
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);
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_SELECTOR_HH__ */
diff --git a/src/model/solid_mechanics/material_selector_tmpl.hh b/src/model/solid_mechanics/material_selector_tmpl.hh
index adf4bda9a..71083761f 100644
--- a/src/model/solid_mechanics/material_selector_tmpl.hh
+++ b/src/model/solid_mechanics/material_selector_tmpl.hh
@@ -1,70 +1,70 @@
/**
* @file material_selector_tmpl.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Fri May 01 2015
*
* @brief Implementation of the template MaterialSelector
*
* @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_MATERIAL_SELECTOR_TMPL_HH__
#define __AKANTU_MATERIAL_SELECTOR_TMPL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<typename T>
MeshDataMaterialSelector<T>::MeshDataMaterialSelector(const std::string & name,
const SolidMechanicsModel & model,
UInt first_index):
ElementDataMaterialSelector<T>(model.getMesh().getData<T>(name), model, first_index)
{}
/* -------------------------------------------------------------------------- */
template<>
inline UInt ElementDataMaterialSelector<std::string>::operator() (const Element & element) {
try {
std::string material_name = this->elementData(element);
return model.getMaterialIndex(material_name);
} catch (...) {
return MaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
template<>
inline UInt ElementDataMaterialSelector<UInt>::operator() (const Element & element) {
try {
return this->elementData(element) - first_index;
} catch (...) {
return MaterialSelector::operator()(element);
}
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_SELECTOR_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/internal_field.hh b/src/model/solid_mechanics/materials/internal_field.hh
index ef2c3ecc2..25cd18f86 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__
-__BEGIN_AKANTU__
+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();
/// 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;
/// 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,
"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,
"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,
"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,
"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); }
/// 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;
}
-__END_AKANTU__
+} // 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 074fdf1e7..156bd55e7 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__
-__BEGIN_AKANTU__
+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) {}
/* -------------------------------------------------------------------------- */
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) {}
/* -------------------------------------------------------------------------- */
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) {}
/* -------------------------------------------------------------------------- */
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) {
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).getSize();
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;
if (this->exists(*it, *gt)) {
vect = &(this->operator()(*it, *gt));
old_size = vect->getSize();
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.getSize() * 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).getSize();
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,
"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.getSize())
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.getSize() * nb_quad_per_elem, nb_component);
AKANTU_DEBUG_ASSERT(
tmp.getSize() == vect.getSize(),
"Something strange append some mater was created from nowhere!!");
AKANTU_DEBUG_ASSERT(
tmp.getSize() == vect.getSize(),
"Something strange append some mater was created or disappeared in "
<< vect.getID() << "(" << vect.getSize()
<< "!=" << tmp.getSize() << ") "
"!!");
UInt new_size = 0;
for (UInt i = 0; i < renumbering.getSize(); ++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;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_INTERNAL_FIELD_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/cohesive_internal_field.hh b/src/model/solid_mechanics/materials/material_cohesive/cohesive_internal_field.hh
index b8835bf54..241604669 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/cohesive_internal_field.hh
+++ b/src/model/solid_mechanics/materials/material_cohesive/cohesive_internal_field.hh
@@ -1,70 +1,70 @@
/**
* @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__
-__BEGIN_AKANTU__
+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();
/// initialize the field to a given number of component
void initialize(UInt nb_component);
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();
/// initialize the field to a given number of component
void initialize(UInt nb_component);
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_COHESIVE_INTERNAL_FIELD_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/cohesive_internal_field_tmpl.hh b/src/model/solid_mechanics/materials/material_cohesive/cohesive_internal_field_tmpl.hh
index 85c8c5090..a8e3aef34 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/cohesive_internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_cohesive/cohesive_internal_field_tmpl.hh
@@ -1,94 +1,94 @@
/**
* @file cohesive_internal_field_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Nov 13 2013
* @date last modification: Thu Jan 21 2016
*
* @brief implementation of the cohesive internal 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_COHESIVE_INTERNAL_FIELD_TMPL_HH__
#define __AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
template <typename T>
CohesiveInternalField<T>::CohesiveInternalField(const ID & id,
Material & material)
: InternalField<T>(
id, material, material.getModel().getFEEngine("CohesiveFEEngine"),
dynamic_cast<MaterialCohesive &>(material).getElementFilter()) {
this->element_kind = _ek_cohesive;
}
template <typename T> CohesiveInternalField<T>::~CohesiveInternalField() {}
template <typename T>
void CohesiveInternalField<T>::initialize(UInt nb_component) {
this->internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <typename T>
FacetInternalField<T>::FacetInternalField(const ID & id, Material & material)
: InternalField<T>(
id, material, material.getModel().getFEEngine("FacetsFEEngine"),
dynamic_cast<MaterialCohesive &>(material).getFacetFilter()) {
this->spatial_dimension -= 1;
this->element_kind = _ek_regular;
}
template <typename T> FacetInternalField<T>::~FacetInternalField() {}
template <typename T>
void FacetInternalField<T>::initialize(UInt nb_component) {
this->internalInitialize(nb_component);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParsableParamTyped<RandomInternalField<Real, FacetInternalField> >::parseParam(
const ParserParameter & in_param) {
ParsableParam::parseParam(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
/* -------------------------------------------------------------------------- */
template <>
inline void
ParsableParamTyped<RandomInternalField<Real, CohesiveInternalField> >::
parseParam(const ParserParameter & in_param) {
ParsableParam::parseParam(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_COHESIVE_INTERNAL_FIELD_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_bilinear.cc b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_bilinear.cc
index eb91a47ec..27d48cc8d 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_bilinear.cc
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_bilinear.cc
@@ -1,211 +1,211 @@
/**
* @file material_cohesive_bilinear.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
* @date last modification: Thu Oct 15 2015
*
* @brief Bilinear cohesive constitutive law
*
* @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_cohesive_bilinear.hh"
#include "solid_mechanics_model_cohesive.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialCohesiveBilinear<spatial_dimension>::MaterialCohesiveBilinear(SolidMechanicsModel & model, const ID & id) :
MaterialCohesiveLinear<spatial_dimension>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("delta_0", delta_0, Real(0.),
_pat_parsable | _pat_readable,
"Elastic limit displacement");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
this->sigma_c_eff.setRandomDistribution(this->sigma_c.getRandomParameter());
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
this->delta_max .setDefaultValue(delta_0);
this->insertion_stress.setDefaultValue(0);
this->delta_max .reset();
this->insertion_stress.reset();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::onElementsAdded(element_list, event);
bool scale_traction = false;
// don't scale sigma_c if volume_s hasn't been specified by the user
if (!Math::are_float_equal(this->volume_s, 0.)) scale_traction = true;
Array<Element>::const_scalar_iterator el_it = element_list.begin();
Array<Element>::const_scalar_iterator el_end = element_list.end();
for (; el_it != el_end; ++el_it) {
// filter not ghost cohesive elements
if (el_it->ghost_type != _not_ghost || el_it->kind != _ek_cohesive) continue;
UInt index = el_it->element;
ElementType type = el_it->type;
UInt nb_element = this->model->getMesh().getNbElement(type);
UInt nb_quad_per_element = this->fem_cohesive->getNbIntegrationPoints(type);
Array<Real>::vector_iterator sigma_c_begin
= this->sigma_c_eff(type).begin_reinterpret(nb_quad_per_element, nb_element);
Vector<Real> sigma_c_vec = sigma_c_begin[index];
Array<Real>::vector_iterator delta_c_begin
= this->delta_c_eff(type).begin_reinterpret(nb_quad_per_element, nb_element);
Vector<Real> delta_c_vec = delta_c_begin[index];
if (scale_traction) scaleTraction(*el_it, sigma_c_vec);
/**
* Recompute sigma_c as
* @f$ {\sigma_c}_\textup{new} =
* \frac{{\sigma_c}_\textup{old} \delta_c} {\delta_c - \delta_0} @f$
*/
for (UInt q = 0; q < nb_quad_per_element; ++q) {
delta_c_vec(q) = 2 * this->G_c / sigma_c_vec(q);
if (delta_c_vec(q) - delta_0 < Math::getTolerance())
AKANTU_DEBUG_ERROR("delta_0 = " << delta_0 <<
" must be lower than delta_c = " << delta_c_vec(q)
<< ", modify your material file");
sigma_c_vec(q) *= delta_c_vec(q) / (delta_c_vec(q) - delta_0);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::scaleTraction(const Element & el,
Vector<Real> & sigma_c_vec) {
AKANTU_DEBUG_IN();
Real base_sigma_c = this->sigma_c_eff;
const Mesh & mesh_facets = this->model->getMeshFacets();
const FEEngine & fe_engine = this->model->getFEEngine();
Array<Element>::const_vector_iterator coh_element_to_facet_begin
= mesh_facets.getSubelementToElement(el.type).begin(2);
const Vector<Element> & coh_element_to_facet
= coh_element_to_facet_begin[el.element];
// compute bounding volume
Real volume = 0;
// loop over facets
for (UInt f = 0; f < 2; ++f) {
const Element & facet = coh_element_to_facet(f);
const Array< std::vector<Element> > & facet_to_element
= mesh_facets.getElementToSubelement(facet.type, facet.ghost_type);
const std::vector<Element> & element_list = facet_to_element(facet.element);
std::vector<Element>::const_iterator elem = element_list.begin();
std::vector<Element>::const_iterator elem_end = element_list.end();
// loop over elements connected to each facet
for (; elem != elem_end; ++elem) {
// skip cohesive elements and dummy elements
if (*elem == ElementNull || elem->kind == _ek_cohesive) continue;
// unit vector for integration in order to obtain the volume
UInt nb_quadrature_points = fe_engine.getNbIntegrationPoints(elem->type);
Vector<Real> unit_vector(nb_quadrature_points, 1);
volume += fe_engine.integrate(unit_vector, elem->type,
elem->element, elem->ghost_type);
}
}
// scale sigma_c
sigma_c_vec -= base_sigma_c;
sigma_c_vec *= std::pow(this->volume_s / volume, 1. / this->m_s);
sigma_c_vec += base_sigma_c;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveBilinear<spatial_dimension>::computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::computeTraction(normal,
el_type,
ghost_type);
// adjust damage
Array<Real>::scalar_iterator delta_c_it
= this->delta_c_eff(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_max_it
= this->delta_max(el_type, ghost_type).begin();
Array<Real>::scalar_iterator damage_it
= this->damage(el_type, ghost_type).begin();
Array<Real>::scalar_iterator damage_end
= this->damage(el_type, ghost_type).end();
for (; damage_it != damage_end; ++damage_it, ++delta_max_it, ++delta_c_it) {
*damage_it = std::max((*delta_max_it - delta_0) / (*delta_c_it - delta_0), Real(0.));
*damage_it = std::min(*damage_it, Real(1.));
}
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialCohesiveBilinear);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_bilinear.hh b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_bilinear.hh
index 17e11e33c..241d81e97 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_bilinear.hh
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_bilinear.hh
@@ -1,113 +1,113 @@
/**
* @file material_cohesive_bilinear.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief Bilinear cohesive constitutive law
*
* @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_cohesive_linear.hh"
#ifndef __AKANTU_MATERIAL_COHESIVE_BILINEAR_HH__
#define __AKANTU_MATERIAL_COHESIVE_BILINEAR_HH__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Cohesive material bilinear
*
* parameters in the material files :
* - delta_0 : elastic limit displacement (default: 0)
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default: 0)
* - G_cI : fracture energy for mode I (default: 0)
* - G_cII : fracture energy for mode II (default: 0)
* - penalty : stiffness in compression to prevent penetration
*/
template<UInt spatial_dimension>
class MaterialCohesiveBilinear : public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveBilinear(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
virtual void initMaterial();
/// set material parameters for new elements
virtual void onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event);
protected:
/// constitutive law
void computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/**
* Scale traction sigma_c according to the volume of the
* two elements surrounding an element
*/
void scaleTraction(const Element & el, Vector<Real> & sigma_c_vec);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// elastic limit displacement
Real delta_0;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "material_cohesive_elastic_inline_impl.cc"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_COHESIVE_BILINEAR_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_exponential.cc b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_exponential.cc
index 69749adec..c1af5b1bf 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_exponential.cc
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_exponential.cc
@@ -1,365 +1,365 @@
/**
* @file material_cohesive_exponential.cc
*
* @author Seyedeh Mohadeseh Taheri Mousavi <mohadeseh.taherimousavi@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Mon Jul 09 2012
* @date last modification: Tue Aug 04 2015
*
* @brief Exponential irreversible cohesive law of mixed mode loading
*
* @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_cohesive_exponential.hh"
#include "solid_mechanics_model.hh"
#include "sparse_matrix.hh"
#include "dof_synchronizer.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialCohesiveExponential<spatial_dimension>::MaterialCohesiveExponential(SolidMechanicsModel & model,
const ID & id) :
MaterialCohesive(model,id) {
AKANTU_DEBUG_IN();
this->registerParam("beta", beta, Real(0.),
_pat_parsable,
"Beta parameter");
this->registerParam("exponential_penalty", exp_penalty, true,
_pat_parsable,
"Is contact penalty following the exponential law?");
this->registerParam("contact_tangent", contact_tangent, Real(1.0),
_pat_parsable,
"Ratio of contact tangent over the initial exponential tangent");
// this->initInternalArray(delta_max, 1, _ek_cohesive);
use_previous_delta_max=true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesive::initMaterial();
if ((exp_penalty) && (contact_tangent != 1)){
contact_tangent = 1;
AKANTU_DEBUG_WARNING("The parsed paramter <contact_tangent> is forced to 1.0 when the contact penalty follows the exponential law");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
Array<Real>::vector_iterator traction_it =
tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator opening_it =
opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::const_vector_iterator normal_it =
normal.begin(spatial_dimension);
Array<Real>::vector_iterator traction_end =
tractions(el_type, ghost_type).end(spatial_dimension);
Array<Real>::iterator<Real> delta_max_it =
delta_max(el_type, ghost_type).begin();
Array<Real>::iterator<Real> delta_max_prev_it =
delta_max.previous(el_type, ghost_type).begin();
/// compute scalars
Real beta2 = beta * beta;
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++normal_it, ++delta_max_it, ++delta_max_prev_it) {
/// compute normal and tangential opening vectors
Real normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening(spatial_dimension);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening(spatial_dimension);
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \beta^2 \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta = tangential_opening_norm;
delta *= delta * beta2;
delta += normal_opening_norm * normal_opening_norm;
delta = sqrt(delta);
if ((normal_opening_norm < 0) && (std::abs(normal_opening_norm) > Math::getTolerance())) {
Vector<Real> op_n(*normal_it);
op_n *= normal_opening_norm;
Vector<Real> delta_s(*opening_it);
delta_s -= op_n;
delta = tangential_opening_norm * beta;
computeCoupledTraction(*traction_it, *normal_it, delta, delta_s,
*delta_max_it, *delta_max_prev_it);
computeCompressiveTraction(*traction_it, *normal_it, normal_opening_norm,
*opening_it);
}
else computeCoupledTraction(*traction_it, *normal_it, delta, *opening_it,
*delta_max_it, *delta_max_prev_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCoupledTraction(Vector<Real> & tract,
const Vector<Real> & normal,
Real delta,
const Vector<Real> & opening,
Real & delta_max_new,
Real delta_max) {
AKANTU_DEBUG_IN();
/// full damage case
if (std::abs(delta) < Math::getTolerance()) {
/// set traction to zero
tract.clear();
} else { /// element not fully damaged
/**
* Compute traction loading @f$ \mathbf{T} =
* e \sigma_c \frac{\delta}{\delta_c} e^{-\delta/ \delta_c}@f$
*/
/**
* Compute traction unloading @f$ \mathbf{T} =
* \frac{t_{max}}{\delta_{max}} \delta @f$
*/
Real beta2 = beta * beta;
Real normal_open_norm = opening.dot(normal);
Vector<Real> op_n_n(spatial_dimension);
op_n_n = normal;
op_n_n *= (1 - beta2);
op_n_n *= normal_open_norm;
tract = beta2 * opening;
tract += op_n_n;
delta_max_new = std::max(delta_max, delta);
tract *= exp(1) * sigma_c * exp(-delta_max_new / delta_c) / delta_c;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCompressiveTraction(Vector<Real> & tract,
const Vector<Real> & normal,
Real delta_n,
__attribute__((unused)) const Vector<Real> & opening) {
Vector<Real> temp_tract(normal);
if(exp_penalty) {
temp_tract *= delta_n * exp(1) * sigma_c * exp(-delta_n / delta_c) / delta_c;
}
else {
Real initial_tg = contact_tangent * exp(1) * sigma_c * delta_n / delta_c;
temp_tract *= initial_tg;
}
tract += temp_tract;
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real>::matrix_iterator tangent_it =
tangent_matrix.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator tangent_end =
tangent_matrix.end(spatial_dimension, spatial_dimension);
Array<Real>::const_vector_iterator normal_it =
normal.begin(spatial_dimension);
Array<Real>::vector_iterator opening_it =
opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::iterator<Real>delta_max_it =
delta_max.previous(el_type, ghost_type).begin();
Real beta2 = beta * beta;
/**
* compute tangent matrix @f$ \frac{\partial \mathbf{t}}
* {\partial \delta} = \hat{\mathbf{t}} \otimes
* \frac{\partial (t/\delta)}{\partial \delta}
* \frac{\hat{\mathbf{t}}}{\delta}+ \frac{t}{\delta} [ \beta^2 \mathbf{I} +
* (1-\beta^2) (\mathbf{n} \otimes \mathbf{n})] @f$
**/
/**
* In which @f$
* \frac{\partial(t/ \delta)}{\partial \delta} =
* \left\{\begin{array} {l l}
* -e \frac{\sigma_c}{\delta_c^2 }e^{-\delta / \delta_c} & \quad if
* \delta \geq \delta_{max} \\
* 0 & \quad if \delta < \delta_{max}, \delta_n > 0
* \end{array}\right. @f$
**/
for (; tangent_it != tangent_end; ++tangent_it, ++normal_it,
++opening_it, ++ delta_max_it) {
Real normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening(spatial_dimension);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening(spatial_dimension);
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
Real delta = tangential_opening_norm;
delta *= delta * beta2;
delta += normal_opening_norm * normal_opening_norm;
delta = sqrt(delta);
if ((normal_opening_norm < 0) && (std::abs(normal_opening_norm) > Math::getTolerance())) {
Vector<Real> op_n(*normal_it);
op_n *= normal_opening_norm;
Vector<Real> delta_s(*opening_it);
delta_s -= op_n;
delta = tangential_opening_norm * beta;
computeCoupledTangent(*tangent_it, *normal_it, delta, delta_s, *delta_max_it);
computeCompressivePenalty(*tangent_it, *normal_it, normal_opening_norm);
}
else computeCoupledTangent(*tangent_it, *normal_it, delta, *opening_it, *delta_max_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCoupledTangent(Matrix<Real> & tangent,
const Vector<Real> & normal,
Real delta,
const Vector<Real> & opening,
Real delta_max_new) {
AKANTU_DEBUG_IN();
Real beta2 = beta * beta;
Matrix<Real> J(spatial_dimension,spatial_dimension);
J.eye(beta2);
if(std::abs(delta) < Math::getTolerance()){
delta = Math::getTolerance();
}
Real opening_normal;
opening_normal = opening.dot(normal);
Vector<Real>delta_e(normal);
delta_e *= opening_normal;
delta_e *= (1 - beta2);
delta_e += (beta2 * opening);
Real exponent = exp(1 - delta / delta_c) * sigma_c / delta_c;
Matrix<Real> first_term(spatial_dimension, spatial_dimension);
first_term.outerProduct(normal, normal);
first_term *= (1 - beta2);
first_term += J;
Matrix<Real>second_term(spatial_dimension, spatial_dimension);
second_term.outerProduct(delta_e,delta_e);
second_term /= delta;
second_term /= delta_c;
Matrix<Real>diff(first_term);
diff -= second_term;
tangent = diff;
tangent *= exponent;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveExponential<spatial_dimension>::computeCompressivePenalty(Matrix<Real> & tangent,
const Vector<Real> & normal,
Real delta_n) {
if (!exp_penalty) delta_n=0;
Matrix<Real> n_outer_n(spatial_dimension,spatial_dimension);
n_outer_n.outerProduct(normal,normal);
Real normal_tg = contact_tangent * exp(1) * sigma_c * exp(-delta_n / delta_c) * (1 - delta_n / delta_c) / delta_c;
n_outer_n *= normal_tg;
tangent += n_outer_n;
}
INSTANTIATE_MATERIAL(MaterialCohesiveExponential);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_exponential.hh b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_exponential.hh
index 11de18644..a5a83b6e6 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_exponential.hh
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_exponential.hh
@@ -1,128 +1,128 @@
/**
* @file material_cohesive_exponential.hh
*
* @author Fabian Barras <fabian.barras@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: Fri Feb 06 2015
*
* @brief Exponential irreversible cohesive law of mixed mode loading
*
* @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_cohesive.hh"
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH__
#define __AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Cohesive material Exponential damage
*
* parameters in the material files :
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default: 0)
* - delta_c : critical opening (default: 0)
*/
template<UInt spatial_dimension>
class MaterialCohesiveExponential : public MaterialCohesive {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveExponential(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// Initialization
void initMaterial();
/// constitutive law
void computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/// compute the tangent stiffness matrix for an element type
void computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type = _not_ghost);
private:
void computeCoupledTraction(Vector<Real> & tract, const Vector<Real> & normal,
Real delta, const Vector<Real> & opening,
Real & delta_max_new, Real delta_max);
void computeCompressiveTraction(Vector<Real> & tract, const Vector<Real> & normal,
Real delta_n, const Vector<Real> & opening);
void computeCoupledTangent(Matrix<Real> & tangent,
const Vector<Real> & normal, Real delta,
const Vector<Real> & opening, Real delta_max_new);
void computeCompressivePenalty(Matrix<Real> & tangent, const Vector<Real> & normal,
Real delta_n);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// beta parameter
Real beta;
/// contact penalty = initial slope ?
bool exp_penalty;
/// Ratio of contact tangent over the initial exponential tangent
Real contact_tangent;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
// #include "material_cohesive_exponential_inline_impl.cc"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_COHESIVE_EXPONENTIAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.cc b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.cc
index fb0f01b3e..0472fae90 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.cc
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.cc
@@ -1,701 +1,701 @@
/**
* @file material_cohesive_linear.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Feb 22 2012
* @date last modification: Thu Jan 14 2016
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic 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 <algorithm>
#include <numeric>
/* -------------------------------------------------------------------------- */
#include "dof_synchronizer.hh"
#include "material_cohesive_linear.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "sparse_matrix.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinear<spatial_dimension>::MaterialCohesiveLinear(
SolidMechanicsModel & model, const ID & id)
: MaterialCohesive(model, id), sigma_c_eff("sigma_c_eff", *this),
delta_c_eff("delta_c_eff", *this),
insertion_stress("insertion_stress", *this),
opening_prec("opening_prec", *this),
reduction_penalty("reduction_penalty", *this) {
AKANTU_DEBUG_IN();
this->registerParam("beta", beta, Real(0.), _pat_parsable | _pat_readable,
"Beta parameter");
this->registerParam("G_c", G_c, Real(0.), _pat_parsable | _pat_readable,
"Mode I fracture energy");
this->registerParam("penalty", penalty, Real(0.),
_pat_parsable | _pat_readable, "Penalty coefficient");
this->registerParam("volume_s", volume_s, Real(0.),
_pat_parsable | _pat_readable,
"Reference volume for sigma_c scaling");
this->registerParam("m_s", m_s, Real(1.), _pat_parsable | _pat_readable,
"Weibull exponent for sigma_c scaling");
this->registerParam("kappa", kappa, Real(1.), _pat_parsable | _pat_readable,
"Kappa parameter");
this->registerParam(
"contact_after_breaking", contact_after_breaking, false,
_pat_parsable | _pat_readable,
"Activation of contact when the elements are fully damaged");
this->registerParam("max_quad_stress_insertion", max_quad_stress_insertion,
false, _pat_parsable | _pat_readable,
"Insertion of cohesive element when stress is high "
"enough just on one quadrature point");
this->registerParam("recompute", recompute, false,
_pat_parsable | _pat_modifiable, "recompute solution");
this->use_previous_delta_max = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesive::initMaterial();
/// compute scalars
beta2_kappa2 = beta * beta / kappa / kappa;
beta2_kappa = beta * beta / kappa;
if (Math::are_float_equal(beta, 0))
beta2_inv = 0;
else
beta2_inv = 1. / beta / beta;
sigma_c_eff.initialize(1);
delta_c_eff.initialize(1);
insertion_stress.initialize(spatial_dimension);
opening_prec.initialize(spatial_dimension);
reduction_penalty.initialize(1);
if (!Math::are_float_equal(delta_c, 0.))
delta_c_eff.setDefaultValue(delta_c);
else
delta_c_eff.setDefaultValue(2 * G_c / sigma_c);
if (model->getIsExtrinsic())
scaleInsertionTraction();
opening_prec.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::scaleInsertionTraction() {
AKANTU_DEBUG_IN();
// do nothing if volume_s hasn't been specified by the user
if (Math::are_float_equal(volume_s, 0.))
return;
const Mesh & mesh_facets = model->getMeshFacets();
const FEEngine & fe_engine = model->getFEEngine();
const FEEngine & fe_engine_facet = model->getFEEngine("FacetsFEEngine");
// loop over facet type
Mesh::type_iterator first = mesh_facets.firstType(spatial_dimension - 1);
Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1);
Real base_sigma_c = sigma_c;
for (; first != last; ++first) {
ElementType type_facet = *first;
const Array<std::vector<Element> > & facet_to_element =
mesh_facets.getElementToSubelement(type_facet);
UInt nb_facet = facet_to_element.getSize();
UInt nb_quad_per_facet = fe_engine_facet.getNbIntegrationPoints(type_facet);
// iterator to modify sigma_c for all the quadrature points of a facet
Array<Real>::vector_iterator sigma_c_iterator =
sigma_c(type_facet).begin_reinterpret(nb_quad_per_facet, nb_facet);
for (UInt f = 0; f < nb_facet; ++f, ++sigma_c_iterator) {
const std::vector<Element> & element_list = facet_to_element(f);
// compute bounding volume
Real volume = 0;
std::vector<Element>::const_iterator elem = element_list.begin();
std::vector<Element>::const_iterator elem_end = element_list.end();
for (; elem != elem_end; ++elem) {
if (*elem == ElementNull)
continue;
// unit vector for integration in order to obtain the volume
UInt nb_quadrature_points =
fe_engine.getNbIntegrationPoints(elem->type);
Vector<Real> unit_vector(nb_quadrature_points, 1);
volume += fe_engine.integrate(unit_vector, elem->type, elem->element,
elem->ghost_type);
}
// scale sigma_c
*sigma_c_iterator -= base_sigma_c;
*sigma_c_iterator *= std::pow(volume_s / volume, 1. / m_s);
*sigma_c_iterator += base_sigma_c;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::checkInsertion(
bool check_only) {
AKANTU_DEBUG_IN();
const Mesh & mesh_facets = model->getMeshFacets();
CohesiveElementInserter & inserter = model->getElementInserter();
Real tolerance = Math::getTolerance();
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1);
Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1);
for (; it != last; ++it) {
ElementType type_facet = *it;
ElementType type_cohesive = FEEngine::getCohesiveElementType(type_facet);
const Array<bool> & facets_check = inserter.getCheckFacets(type_facet);
Array<bool> & f_insertion = inserter.getInsertionFacets(type_facet);
Array<UInt> & f_filter = facet_filter(type_facet);
Array<Real> & sig_c_eff = sigma_c_eff(type_cohesive);
Array<Real> & del_c = delta_c_eff(type_cohesive);
Array<Real> & ins_stress = insertion_stress(type_cohesive);
Array<Real> & trac_old = tractions_old(type_cohesive);
Array<Real> & open_prec = opening_prec(type_cohesive);
Array<bool> & red_penalty = reduction_penalty(type_cohesive);
const Array<Real> & f_stress = model->getStressOnFacets(type_facet);
const Array<Real> & sigma_lim = sigma_c(type_facet);
Real max_ratio = 0.;
UInt index_f = 0;
UInt index_filter = 0;
UInt nn = 0;
UInt nb_quad_facet =
model->getFEEngine("FacetsFEEngine").getNbIntegrationPoints(type_facet);
UInt nb_quad_cohesive = model->getFEEngine("CohesiveFEEngine")
.getNbIntegrationPoints(type_cohesive);
AKANTU_DEBUG_ASSERT(nb_quad_cohesive == nb_quad_facet,
"The cohesive element and the corresponding facet do "
"not have the same numbers of integration points");
UInt nb_facet = f_filter.getSize();
// if (nb_facet == 0) continue;
Array<Real>::const_iterator<Real> sigma_lim_it = sigma_lim.begin();
Matrix<Real> stress_tmp(spatial_dimension, spatial_dimension);
Matrix<Real> normal_traction(spatial_dimension, nb_quad_facet);
Vector<Real> stress_check(nb_quad_facet);
UInt sp2 = spatial_dimension * spatial_dimension;
const Array<Real> & tangents = model->getTangents(type_facet);
const Array<Real> & normals =
model->getFEEngine("FacetsFEEngine")
.getNormalsOnIntegrationPoints(type_facet);
Array<Real>::const_vector_iterator normal_begin =
normals.begin(spatial_dimension);
Array<Real>::const_vector_iterator tangent_begin =
tangents.begin(tangents.getNbComponent());
Array<Real>::const_matrix_iterator facet_stress_begin =
f_stress.begin(spatial_dimension, spatial_dimension * 2);
std::vector<Real> new_sigmas;
std::vector<Vector<Real> > new_normal_traction;
std::vector<Real> new_delta_c;
// loop over each facet belonging to this material
for (UInt f = 0; f < nb_facet; ++f, ++sigma_lim_it) {
UInt facet = f_filter(f);
// skip facets where check shouldn't be realized
if (!facets_check(facet))
continue;
// compute the effective norm on each quadrature point of the facet
for (UInt q = 0; q < nb_quad_facet; ++q) {
UInt current_quad = facet * nb_quad_facet + q;
const Vector<Real> & normal = normal_begin[current_quad];
const Vector<Real> & tangent = tangent_begin[current_quad];
const Matrix<Real> & facet_stress_it = facet_stress_begin[current_quad];
// compute average stress on the current quadrature point
Matrix<Real> stress_1(facet_stress_it.storage(), spatial_dimension,
spatial_dimension);
Matrix<Real> stress_2(facet_stress_it.storage() + sp2,
spatial_dimension, spatial_dimension);
stress_tmp.copy(stress_1);
stress_tmp += stress_2;
stress_tmp /= 2.;
Vector<Real> normal_traction_vec(normal_traction(q));
// compute normal and effective stress
stress_check(q) = computeEffectiveNorm(stress_tmp, normal, tangent,
normal_traction_vec);
}
// verify if the effective stress overcomes the threshold
Real final_stress = stress_check.mean();
if (max_quad_stress_insertion)
final_stress = *std::max_element(
stress_check.storage(), stress_check.storage() + nb_quad_facet);
if (final_stress > (*sigma_lim_it - tolerance)) {
if (model->isExplicit()) {
f_insertion(facet) = true;
if (!check_only) {
// store the new cohesive material parameters for each quadrature
// point
for (UInt q = 0; q < nb_quad_facet; ++q) {
Real new_sigma = stress_check(q);
Vector<Real> normal_traction_vec(normal_traction(q));
if (spatial_dimension != 3)
normal_traction_vec *= -1.;
new_sigmas.push_back(new_sigma);
new_normal_traction.push_back(normal_traction_vec);
Real new_delta;
// set delta_c in function of G_c or a given delta_c value
if (Math::are_float_equal(delta_c, 0.))
new_delta = 2 * G_c / new_sigma;
else
new_delta = (*sigma_lim_it) / new_sigma * delta_c;
new_delta_c.push_back(new_delta);
}
}
} else {
Real ratio = final_stress / (*sigma_lim_it);
if (ratio > max_ratio) {
++nn;
max_ratio = ratio;
index_f = f;
index_filter = f_filter(f);
}
}
}
}
/// Insertion of only 1 cohesive element in case of implicit approach. The
/// one subjected to the highest stress.
if (!model->isExplicit()) {
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Array<Real> abs_max(comm.getNbProc());
abs_max(comm.whoAmI()) = max_ratio;
comm.allGather(abs_max.storage(), 1);
Array<Real>::scalar_iterator it =
std::max_element(abs_max.begin(), abs_max.end());
Int pos = it - abs_max.begin();
if (pos != comm.whoAmI()) {
AKANTU_DEBUG_OUT();
return;
}
if (nn) {
f_insertion(index_filter) = true;
if (!check_only) {
// Array<Real>::iterator<Matrix<Real> > normal_traction_it =
// normal_traction.begin_reinterpret(nb_quad_facet,
// spatial_dimension, nb_facet);
Array<Real>::const_iterator<Real> sigma_lim_it = sigma_lim.begin();
for (UInt q = 0; q < nb_quad_cohesive; ++q) {
Real new_sigma = (sigma_lim_it[index_f]);
Vector<Real> normal_traction_vec(spatial_dimension, 0.0);
new_sigmas.push_back(new_sigma);
new_normal_traction.push_back(normal_traction_vec);
Real new_delta;
// set delta_c in function of G_c or a given delta_c value
if (!Math::are_float_equal(delta_c, 0.))
new_delta = delta_c;
else
new_delta = 2 * G_c / (new_sigma);
new_delta_c.push_back(new_delta);
}
}
}
}
// update material data for the new elements
UInt old_nb_quad_points = sig_c_eff.getSize();
UInt new_nb_quad_points = new_sigmas.size();
sig_c_eff.resize(old_nb_quad_points + new_nb_quad_points);
ins_stress.resize(old_nb_quad_points + new_nb_quad_points);
trac_old.resize(old_nb_quad_points + new_nb_quad_points);
del_c.resize(old_nb_quad_points + new_nb_quad_points);
open_prec.resize(old_nb_quad_points + new_nb_quad_points);
red_penalty.resize(old_nb_quad_points + new_nb_quad_points);
for (UInt q = 0; q < new_nb_quad_points; ++q) {
sig_c_eff(old_nb_quad_points + q) = new_sigmas[q];
del_c(old_nb_quad_points + q) = new_delta_c[q];
red_penalty(old_nb_quad_points + q) = false;
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
ins_stress(old_nb_quad_points + q, dim) = new_normal_traction[q](dim);
trac_old(old_nb_quad_points + q, dim) = new_normal_traction[q](dim);
open_prec(old_nb_quad_points + q, dim) = 0.;
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::computeTraction(
const Array<Real> & normal, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
Array<Real>::vector_iterator traction_it =
tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator opening_it =
opening(el_type, ghost_type).begin(spatial_dimension);
/// opening_prec is the opening of the previous step in the
/// Newton-Raphson loop
Array<Real>::vector_iterator opening_prec_it =
opening_prec(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator contact_traction_it =
contact_tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator contact_opening_it =
contact_opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::const_vector_iterator normal_it =
normal.begin(spatial_dimension);
Array<Real>::vector_iterator traction_end =
tractions(el_type, ghost_type).end(spatial_dimension);
Array<Real>::scalar_iterator sigma_c_it =
sigma_c_eff(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_max_it =
delta_max(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_max_prev_it =
delta_max.previous(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_c_it =
delta_c_eff(el_type, ghost_type).begin();
Array<Real>::scalar_iterator damage_it = damage(el_type, ghost_type).begin();
Array<Real>::vector_iterator insertion_stress_it =
insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Array<bool>::scalar_iterator reduction_penalty_it =
reduction_penalty(el_type, ghost_type).begin();
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
if (!this->model->isExplicit())
this->delta_max(el_type, ghost_type)
.copy(this->delta_max.previous(el_type, ghost_type));
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++opening_prec_it, ++normal_it,
++sigma_c_it, ++delta_max_it, ++delta_c_it, ++damage_it,
++contact_traction_it, ++insertion_stress_it, ++contact_opening_it,
++delta_max_prev_it, ++reduction_penalty_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
Real current_penalty = 0.;
this->computeTractionOnQuad(
*traction_it, *delta_max_it, *delta_max_prev_it, *delta_c_it,
*insertion_stress_it, *sigma_c_it, *opening_it, *opening_prec_it,
*normal_it, normal_opening, tangential_opening, normal_opening_norm,
tangential_opening_norm, *damage_it, penetration, *reduction_penalty_it,
current_penalty, *contact_traction_it, *contact_opening_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::checkDeltaMax(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/**
* This function set a predefined value to the parameter
* delta_max_prev of the elements that have been inserted in the
* last loading step for which convergence has not been
* reached. This is done before reducing the loading and re-doing
* the step. Otherwise, the updating of delta_max_prev would be
* done with reference to the non-convergent solution. In this
* function also other variables related to the contact and
* friction behavior are correctly set.
*/
Mesh & mesh = fem_cohesive->getMesh();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_cohesive);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, ghost_type, _ek_cohesive);
/**
* the variable "recompute" is set to true to activate the
* procedure that reduce the penalty parameter for
* compression. This procedure is set true only during the phase of
* load_reduction, that has to be set in the maiin file. The
* penalty parameter will be reduced only for the elements having
* reduction_penalty = true.
*/
recompute = true;
for (; it != last_type; ++it) {
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
if (nb_element == 0)
continue;
ElementType el_type = *it;
/// define iterators
Array<Real>::scalar_iterator delta_max_it =
delta_max(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_max_end =
delta_max(el_type, ghost_type).end();
Array<Real>::scalar_iterator delta_max_prev_it =
delta_max.previous(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_c_it =
delta_c_eff(el_type, ghost_type).begin();
Array<Real>::vector_iterator opening_prec_it =
opening_prec(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator opening_prec_prev_it =
opening_prec.previous(el_type, ghost_type).begin(spatial_dimension);
/// loop on each quadrature point
for (; delta_max_it != delta_max_end; ++delta_max_it, ++delta_max_prev_it,
++delta_c_it, ++opening_prec_it,
++opening_prec_prev_it) {
if (*delta_max_prev_it == 0)
/// elements inserted in the last incremental step, that did
/// not converge
*delta_max_it = *delta_c_it / 1000;
else
/// elements introduced in previous incremental steps, for
/// which a correct value of delta_max_prev already exists
*delta_max_it = *delta_max_prev_it;
/// in case convergence is not reached, set opening_prec to the
/// value referred to the previous incremental step
*opening_prec_it = *opening_prec_prev_it;
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::resetVariables(
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/**
* This function set the variables "recompute" and
* "reduction_penalty" to false. It is called by solveStepCohesive
* when convergence is reached. Such variables, in fact, have to be
* false at the beginning of a new incremental step.
*/
Mesh & mesh = fem_cohesive->getMesh();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_cohesive);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, ghost_type, _ek_cohesive);
recompute = false;
for (; it != last_type; ++it) {
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
if (nb_element == 0)
continue;
ElementType el_type = *it;
Array<bool>::scalar_iterator reduction_penalty_it =
reduction_penalty(el_type, ghost_type).begin();
Array<bool>::scalar_iterator reduction_penalty_end =
reduction_penalty(el_type, ghost_type).end();
/// loop on each quadrature point
for (; reduction_penalty_it != reduction_penalty_end;
++reduction_penalty_it) {
*reduction_penalty_it = false;
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinear<spatial_dimension>::computeTangentTraction(
const ElementType & el_type, Array<Real> & tangent_matrix,
const Array<Real> & normal, GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
Array<Real>::matrix_iterator tangent_it =
tangent_matrix.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator tangent_end =
tangent_matrix.end(spatial_dimension, spatial_dimension);
Array<Real>::const_vector_iterator normal_it =
normal.begin(spatial_dimension);
Array<Real>::vector_iterator opening_it =
opening(el_type, ghost_type).begin(spatial_dimension);
/// NB: delta_max_it points on delta_max_previous, i.e. the
/// delta_max related to the solution of the previous incremental
/// step
Array<Real>::scalar_iterator delta_max_it =
delta_max.previous(el_type, ghost_type).begin();
Array<Real>::scalar_iterator sigma_c_it =
sigma_c_eff(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_c_it =
delta_c_eff(el_type, ghost_type).begin();
Array<Real>::scalar_iterator damage_it = damage(el_type, ghost_type).begin();
Array<Real>::vector_iterator contact_opening_it =
contact_opening(el_type, ghost_type).begin(spatial_dimension);
Array<bool>::scalar_iterator reduction_penalty_it =
reduction_penalty(el_type, ghost_type).begin();
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end; ++tangent_it, ++normal_it, ++opening_it,
++delta_max_it, ++sigma_c_it, ++delta_c_it,
++damage_it, ++contact_opening_it,
++reduction_penalty_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
Real current_penalty = 0.;
this->computeTangentTractionOnQuad(
*tangent_it, *delta_max_it, *delta_c_it, *sigma_c_it, *opening_it,
*normal_it, normal_opening, tangential_opening, normal_opening_norm,
tangential_opening_norm, *damage_it, penetration, *reduction_penalty_it,
current_penalty, *contact_opening_it);
// check if the tangential stiffness matrix is symmetric
// for (UInt h = 0; h < spatial_dimension; ++h){
// for (UInt l = h; l < spatial_dimension; ++l){
// if (l > h){
// Real k_ls = (*tangent_it)[spatial_dimension*h+l];
// Real k_us = (*tangent_it)[spatial_dimension*l+h];
// // std::cout << "k_ls = " << k_ls << std::endl;
// // std::cout << "k_us = " << k_us << std::endl;
// if (std::abs(k_ls) > 1e-13 && std::abs(k_us) > 1e-13){
// Real error = std::abs((k_ls - k_us) / k_us);
// if (error > 1e-10){
// std::cout << "non symmetric cohesive matrix" << std::endl;
// // std::cout << "error " << error << std::endl;
// }
// }
// }
// }
// }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialCohesiveLinear);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.hh b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.hh
index e9bfe93e2..012ba1084 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.hh
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear.hh
@@ -1,216 +1,216 @@
/**
* @file material_cohesive_linear.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Jan 14 2016
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic 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 "material_cohesive.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Cohesive material linear damage for extrinsic case
*
* parameters in the material files :
* - sigma_c : critical stress sigma_c (default: 0)
* - beta : weighting parameter for sliding and normal opening (default: 0)
* - G_cI : fracture energy for mode I (default: 0)
* - G_cII : fracture energy for mode II (default: 0)
* - penalty : stiffness in compression to prevent penetration
*/
template<UInt spatial_dimension>
class MaterialCohesiveLinear : public MaterialCohesive {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveLinear(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
virtual void initMaterial();
/// check stress for cohesive elements' insertion
virtual void checkInsertion(bool check_only = false);
/// compute effective stress norm for insertion check
Real computeEffectiveNorm(const Matrix<Real> & stress,
const Vector<Real> & normal,
const Vector<Real> & tangent,
Vector<Real> & normal_stress) const;
protected:
/// constitutive law
virtual void computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/// check delta_max for cohesive elements in case of no convergence
/// in the solveStep (only for extrinsic-implicit)
virtual void checkDeltaMax(GhostType ghost_type = _not_ghost);
/// reset variables when convergence is reached (only for
/// extrinsic-implicit)
void resetVariables(GhostType ghost_type = _not_ghost);
/// compute tangent stiffness matrix
virtual void computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type);
/**
* Scale insertion traction sigma_c according to the volume of the
* two elements surrounding a facet
*
* see the article: F. Zhou and J. F. Molinari "Dynamic crack
* propagation with cohesive elements: a methodology to address mesh
* dependency" International Journal for Numerical Methods in
* Engineering (2004)
*/
void scaleInsertionTraction();
/// compute the traction for a given quadrature point
inline void computeTractionOnQuad(Vector<Real> & traction, Real & delta_max,
const Real & delta_max_prev, const Real & delta_c,
const Vector<Real> & insertion_stress, const Real & sigma_c,
Vector<Real> & opening, Vector<Real> & opening_prec, const Vector<Real> & normal,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, bool & reduction_penalty, Real & current_penalty,
Vector<Real> & contact_traction, Vector<Real> & contact_opening);
inline void computeTangentTractionOnQuad(Matrix<Real> & tangent,
Real & delta_max, const Real & delta_c,
const Real & sigma_c,
Vector<Real> & opening, const Vector<Real> & normal,
Vector<Real> & normal_opening, Vector<Real> & tangential_opening,
Real & normal_opening_norm, Real & tangential_opening_norm, Real & damage,
bool & penetration, bool & reduction_penalty, Real & current_penalty,
Vector<Real> & contact_opening);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get sigma_c_eff
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(InsertionTraction, sigma_c_eff, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// beta parameter
Real beta;
/// beta square inverse to compute effective norm
Real beta2_inv;
/// mode I fracture energy
Real G_c;
/// kappa parameter
Real kappa;
/// constitutive law scalar to compute delta
Real beta2_kappa2;
/// constitutive law scalar to compute traction
Real beta2_kappa;
/// penalty coefficient
Real penalty;
/// reference volume used to scale sigma_c
Real volume_s;
/// weibull exponent used to scale sigma_c
Real m_s;
/// variable defining if we are recomputing the last loading step
/// after load_reduction
bool recompute;
/// critical effective stress
RandomInternalField<Real, CohesiveInternalField> sigma_c_eff;
/// effective critical displacement (each element can have a
/// different value)
CohesiveInternalField<Real> delta_c_eff;
/// stress at insertion
CohesiveInternalField<Real> insertion_stress;
/// delta of the previous step
CohesiveInternalField<Real> opening_prec;
/**
* variable that defines if the penalty parameter for compression
* has to be decreased for problems of convergence in the solution
* loops
*/
CohesiveInternalField<bool> reduction_penalty;
/// variable saying if there should be penalty contact also after
/// breaking the cohesive elements
bool contact_after_breaking;
/// insertion of cohesive element when stress is high enough just on
/// one quadrature point
bool max_quad_stress_insertion;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#include "material_cohesive_linear_inline_impl.cc"
#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_fatigue.cc b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_fatigue.cc
index d467c7b81..27b8ac4b5 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_fatigue.cc
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_fatigue.cc
@@ -1,296 +1,296 @@
/**
* @file material_cohesive_linear_fatigue.cc
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Feb 20 2015
* @date last modification: Tue Jan 12 2016
*
* @brief See material_cohesive_linear_fatigue.hh for information
*
* @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_cohesive_linear_fatigue.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialCohesiveLinearFatigue<spatial_dimension>
::MaterialCohesiveLinearFatigue(SolidMechanicsModel & model,
const ID & id) :
MaterialCohesiveLinear<spatial_dimension>(model, id),
delta_prec("delta_prec", *this),
K_plus("K_plus", *this),
K_minus("K_minus", *this),
T_1d("T_1d", *this),
switches("switches", *this),
delta_dot_prec("delta_dot_prec", *this),
normal_regime("normal_regime", *this) {
this->registerParam("delta_f", delta_f, Real(-1.) ,
_pat_parsable | _pat_readable,
"delta_f");
this->registerParam("progressive_delta_f", progressive_delta_f, false,
_pat_parsable | _pat_readable,
"Whether or not delta_f is equal to delta_max");
this->registerParam("count_switches", count_switches, false,
_pat_parsable | _pat_readable,
"Count the opening/closing switches per element");
this->registerParam("fatigue_ratio", fatigue_ratio, Real(1.),
_pat_parsable | _pat_readable,
"What portion of the cohesive law is subjected to fatigue");
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialCohesiveLinearFatigue<spatial_dimension>::initMaterial() {
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
// check that delta_f has a proper value or assign a defaul value
if (delta_f < 0) delta_f = this->delta_c_eff;
else if (delta_f < this->delta_c_eff)
AKANTU_DEBUG_ERROR("Delta_f must be greater or equal to delta_c");
delta_prec.initialize(1);
K_plus.initialize(1);
K_minus.initialize(1);
T_1d.initialize(1);
normal_regime.initialize(1);
if (count_switches) {
switches.initialize(1);
delta_dot_prec.initialize(1);
}
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinearFatigue<spatial_dimension>
::computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
Array<Real>::vector_iterator traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator opening_it =
this->opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::const_vector_iterator normal_it = normal.begin(spatial_dimension);
Array<Real>::vector_iterator traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
const Array<Real> & sigma_c_array = this->sigma_c_eff(el_type, ghost_type);
Array<Real> & delta_max_array = this->delta_max(el_type, ghost_type);
const Array<Real> & delta_c_array = this->delta_c_eff(el_type, ghost_type);
Array<Real> & damage_array = this->damage(el_type, ghost_type);
Array<Real>::vector_iterator insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Array<Real> & delta_prec_array = delta_prec(el_type, ghost_type);
Array<Real> & K_plus_array = K_plus(el_type, ghost_type);
Array<Real> & K_minus_array = K_minus(el_type, ghost_type);
Array<Real> & T_1d_array = T_1d(el_type, ghost_type);
Array<bool> & normal_regime_array = normal_regime(el_type, ghost_type);
Array<UInt> * switches_array = NULL;
Array<Real> * delta_dot_prec_array = NULL;
if (count_switches) {
switches_array = &switches(el_type, ghost_type);
delta_dot_prec_array = &delta_dot_prec(el_type, ghost_type);
}
Real * memory_space = new Real[2*spatial_dimension];
Vector<Real> normal_opening(memory_space, spatial_dimension);
Vector<Real> tangential_opening(memory_space + spatial_dimension,
spatial_dimension);
Real tolerance = Math::getTolerance();
/// loop on each quadrature point
for (UInt q = 0; traction_it != traction_end;
++traction_it, ++opening_it, ++normal_it,
++contact_traction_it, ++insertion_stress_it, ++contact_opening_it, ++q) {
/// compute normal and tangential opening vectors
Real normal_opening_norm = opening_it->dot(*normal_it);
normal_opening = (*normal_it);
normal_opening *= normal_opening_norm;
tangential_opening = *opening_it;
tangential_opening -= normal_opening;
Real tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \frac{\beta^2}{\kappa^2} \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta = tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
bool penetration = normal_opening_norm < -tolerance;
if (this->contact_after_breaking == false && Math::are_float_equal(damage_array(q), 1.))
penetration = false;
if (penetration) {
/// use penalty coefficient in case of penetration
*contact_traction_it = normal_opening;
*contact_traction_it *= this->penalty;
*contact_opening_it = normal_opening;
/// don't consider penetration contribution for delta
*opening_it = tangential_opening;
normal_opening.clear();
}
else {
delta += normal_opening_norm * normal_opening_norm;
contact_traction_it->clear();
contact_opening_it->clear();
}
delta = std::sqrt(delta);
/**
* Compute traction @f$ \mathbf{T} = \left(
* \frac{\beta^2}{\kappa} \Delta_t \mathbf{t} + \Delta_n
* \mathbf{n} \right) \frac{\sigma_c}{\delta} \left( 1-
* \frac{\delta}{\delta_c} \right)@f$
*/
// update maximum displacement and damage
delta_max_array(q) = std::max(delta, delta_max_array(q));
damage_array(q) = std::min(delta_max_array(q) / delta_c_array(q), Real(1.));
Real delta_dot = delta - delta_prec_array(q);
// count switches if asked
if (count_switches) {
if ( (delta_dot > 0. && (*delta_dot_prec_array)(q) <= 0.) ||
(delta_dot < 0. && (*delta_dot_prec_array)(q) >= 0.) )
++((*switches_array)(q));
(*delta_dot_prec_array)(q) = delta_dot;
}
// set delta_f equal to delta_max if desired
if (progressive_delta_f) delta_f = delta_max_array(q);
// broken element case
if (Math::are_float_equal(damage_array(q), 1.))
traction_it->clear();
// just inserted element case
else if (Math::are_float_equal(damage_array(q), 0.)) {
if (penetration)
traction_it->clear();
else
*traction_it = *insertion_stress_it;
// initialize the 1d traction to sigma_c
T_1d_array(q) = sigma_c_array(q);
}
// normal case
else {
// if element is closed then there are zero tractions
if (delta <= tolerance)
traction_it->clear();
// otherwise compute new tractions if the new delta is different
// than the previous one
else if (std::abs(delta_dot) > tolerance) {
// loading case
if (delta_dot > 0.) {
if (!normal_regime_array(q)) {
// equation (4) of the article
K_plus_array(q) *= 1. - delta_dot / delta_f;
// equivalent to equation (2) of the article
T_1d_array(q) += K_plus_array(q) * delta_dot;
// in case of reloading, traction must not exceed that of the
// envelop of the cohesive law
Real max_traction = sigma_c_array(q) * (1 - delta / delta_c_array(q));
bool max_traction_exceeded = T_1d_array(q) > max_traction;
if (max_traction_exceeded) T_1d_array(q) = max_traction;
// switch to standard linear cohesive law
if (delta_max_array(q) > fatigue_ratio * delta_c_array(q)) {
// reset delta_max to avoid big jumps in the traction
delta_max_array(q) = sigma_c_array(q) / (T_1d_array(q) / delta + sigma_c_array(q) / delta_c_array(q));
damage_array(q) = std::min(delta_max_array(q) / delta_c_array(q), Real(1.));
K_minus_array(q) = sigma_c_array(q) / delta_max_array(q) * (1. - damage_array(q));
normal_regime_array(q) = true;
} else {
// equation (3) of the article
K_minus_array(q) = T_1d_array(q) / delta;
// if the traction is following the cohesive envelop, then
// K_plus has to be reset
if (max_traction_exceeded) K_plus_array(q) = K_minus_array(q);
}
} else {
// compute stiffness according to the standard law
K_minus_array(q) = sigma_c_array(q) / delta_max_array(q) * (1. - damage_array(q));
}
}
// unloading case
else if (!normal_regime_array(q)) {
// equation (4) of the article
K_plus_array(q) += (K_plus_array(q) - K_minus_array(q)) * delta_dot / delta_f;
// equivalent to equation (2) of the article
T_1d_array(q) = K_minus_array(q) * delta;
}
// applying the actual stiffness
*traction_it = tangential_opening;
*traction_it *= this->beta2_kappa;
*traction_it += normal_opening;
*traction_it *= K_minus_array(q);
}
}
// update precendent delta
delta_prec_array(q) = delta;
}
delete [] memory_space;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialCohesiveLinearFatigue);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_fatigue.hh b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_fatigue.hh
index dedda9b19..b90cc640c 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_fatigue.hh
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_fatigue.hh
@@ -1,136 +1,136 @@
/**
* @file material_cohesive_linear_fatigue.hh
*
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Jun 25 2015
*
* @brief Linear irreversible cohesive law with dissipative
* unloading-reloading cycles
*
* @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_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Linear irreversible cohesive law with dissipative
* unloading-reloading cycles
*
* This law uses two different stiffnesses during unloading and
* reloading. The implementation is based on the article entitled "A
* cohesive model for fatigue crack growth" by Nguyen, Repetto, Ortiz
* and Radovitzky (2001). This law is identical to the
* MaterialCohesiveLinear one except for the unloading-reloading
* phase.
*
* input parameter:
*
* - delta_f : it must be greater than delta_c and it is inversely
* proportional to the dissipation in the unloading-reloading
* cycles (default: delta_c)
*/
template <UInt spatial_dimension>
class MaterialCohesiveLinearFatigue : public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialCohesiveLinearFatigue(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
virtual void initMaterial();
protected:
/// constitutive law
virtual void computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get the switches
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Switches, switches, UInt);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// delta_f parameter
Real delta_f;
/// variable saying if delta_f is equal to delta_max for each
/// element when the traction is computed
bool progressive_delta_f;
/// count the opening/closing switches per element
bool count_switches;
/// delta of the previous step
CohesiveInternalField<Real> delta_prec;
/// stiffness for reloading
CohesiveInternalField<Real> K_plus;
/// stiffness for unloading
CohesiveInternalField<Real> K_minus;
/// 1D traction in the cohesive law
CohesiveInternalField<Real> T_1d;
/// Number of opening/closing switches
CohesiveInternalField<UInt> switches;
/// delta increment of the previous time step
CohesiveInternalField<Real> delta_dot_prec;
/// has the element passed to normal regime (not in fatigue anymore)
CohesiveInternalField<bool> normal_regime;
/// ratio indicating until what point fatigue is applied in the cohesive law
Real fatigue_ratio;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_FATIGUE_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_friction.cc b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_friction.cc
index 94e88ed3a..4892833f3 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_friction.cc
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_friction.cc
@@ -1,401 +1,401 @@
/**
* @file material_cohesive_linear_friction.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Tue Jan 12 2016
* @date last modification: Thu Jan 14 2016
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic 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 "material_cohesive_linear_friction.hh"
#include "solid_mechanics_model_cohesive.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialCohesiveLinearFriction<spatial_dimension>::MaterialCohesiveLinearFriction(SolidMechanicsModel & model,
const ID & id) :
MaterialParent(model,id),
residual_sliding("residual_sliding", *this),
friction_force("friction_force", *this) {
AKANTU_DEBUG_IN();
this->registerParam("mu", mu_max, Real(0.),
_pat_parsable | _pat_readable,
"Maximum value of the friction coefficient");
this->registerParam("penalty_for_friction", friction_penalty, Real(0.),
_pat_parsable | _pat_readable,
"Penalty parameter for the friction behavior");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialParent::initMaterial();
friction_force.initialize(spatial_dimension);
residual_sliding.initialize(1);
residual_sliding.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::computeTraction(__attribute__((unused)) const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
residual_sliding.resize();
friction_force.resize();
/// define iterators
Array<Real>::vector_iterator traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
Array<Real>::vector_iterator opening_it =
this->opening(el_type, ghost_type).begin(spatial_dimension);
/// opening_prec is the opening at the end of the previous step in
/// the Newton-Raphson loop
Array<Real>::vector_iterator opening_prec_it =
this->opening_prec(el_type, ghost_type).begin(spatial_dimension);
/// opening_prec_prev is the opening (opening + penetration)
/// referred to the convergence of the previous incremental step
Array<Real>::vector_iterator opening_prec_prev_it =
this->opening_prec.previous(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::const_iterator< Vector<Real> > normal_it =
this->normal.begin(spatial_dimension);
Array<Real>::iterator<Real>sigma_c_it =
this->sigma_c_eff(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_max_it =
this->delta_max(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_max_prev_it =
this->delta_max.previous(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_c_it =
this->delta_c_eff(el_type, ghost_type).begin();
Array<Real>::iterator<Real>damage_it =
this->damage(el_type, ghost_type).begin();
Array<Real>::vector_iterator insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::iterator<Real>res_sliding_it =
this->residual_sliding(el_type, ghost_type).begin();
Array<Real>::iterator<Real>res_sliding_prev_it =
this->residual_sliding.previous(el_type, ghost_type).begin();
Array<Real>::vector_iterator friction_force_it =
this->friction_force(el_type, ghost_type).begin(spatial_dimension);
Array<bool>::iterator<bool> reduction_penalty_it =
this->reduction_penalty(el_type, ghost_type).begin();
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
if (! this->model->isExplicit())
this->delta_max(el_type, ghost_type).copy(this->delta_max.previous(el_type, ghost_type));
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++opening_prec_prev_it, ++opening_prec_it,
++normal_it, ++sigma_c_it, ++delta_max_it, ++delta_c_it, ++damage_it,
++contact_traction_it, ++insertion_stress_it, ++contact_opening_it,
++delta_max_prev_it, ++res_sliding_it, ++res_sliding_prev_it,
++friction_force_it, ++reduction_penalty_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
Real current_penalty = 0.;
this->computeTractionOnQuad(*traction_it,
*delta_max_it,
*delta_max_prev_it,
*delta_c_it,
*insertion_stress_it,
*sigma_c_it,
*opening_it,
*opening_prec_it,
*normal_it,
normal_opening,
tangential_opening,
normal_opening_norm,
tangential_opening_norm,
*damage_it,
penetration,
*reduction_penalty_it,
current_penalty,
*contact_traction_it,
*contact_opening_it);
if (penetration) {
/// the friction coefficient mu increases with the damage. It
/// equals the maximum value when damage = 1.
// Real damage = std::min(*delta_max_prev_it / *delta_c_it, Real(1.));
Real mu = mu_max; // * damage;
/// the definition of tau_max refers to the opening
/// (penetration) of the previous incremental step
Real normal_opening_prev_norm = std::min(opening_prec_prev_it->dot(*normal_it), Real(0.));
// Vector<Real> normal_opening_prev = (*normal_it);
// normal_opening_prev *= normal_opening_prev_norm;
Real tau_max = mu * current_penalty * (std::abs(normal_opening_prev_norm));
Real delta_sliding_norm = std::abs(tangential_opening_norm - *res_sliding_prev_it);
/// tau is the norm of the friction force, acting tangentially to the surface
Real tau = std::min(friction_penalty * delta_sliding_norm, tau_max);
if ((tangential_opening_norm - *res_sliding_prev_it) < 0.0)
tau = -tau;
/// from tau get the x and y components of friction, to be added in the force vector
Vector<Real> tangent_unit_vector(spatial_dimension);
tangent_unit_vector = tangential_opening / tangential_opening_norm;
*friction_force_it = tau * tangent_unit_vector;
/// update residual_sliding
*res_sliding_it = tangential_opening_norm - (std::abs(tau) / friction_penalty);
} else {
friction_force_it->clear();
}
*traction_it += *friction_force_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::checkDeltaMax(GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialParent::checkDeltaMax();
Mesh & mesh = this->fem_cohesive->getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension,
ghost_type, _ek_cohesive);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension,
ghost_type, _ek_cohesive);
for(; it != last_type; ++it) {
Array<UInt> & elem_filter = this->element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
if (nb_element == 0) continue;
ElementType el_type = *it;
/// define iterators
Array<Real>::iterator<Real>delta_max_it =
this->delta_max(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_max_end =
this->delta_max(el_type, ghost_type).end();
Array<Real>::iterator<Real>res_sliding_it =
this->residual_sliding(el_type, ghost_type).begin();
Array<Real>::iterator<Real>res_sliding_prev_it =
this->residual_sliding.previous(el_type, ghost_type).begin();
/// loop on each quadrature point
for (; delta_max_it != delta_max_end;
++delta_max_it, ++res_sliding_it, ++res_sliding_prev_it) {
/**
* in case convergence is not reached, set "residual_sliding"
* for the friction behaviour to the value referred to the
* previous incremental step
*/
*res_sliding_it = *res_sliding_prev_it;
}
}
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinearFriction<spatial_dimension>::computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
__attribute__((unused)) const Array<Real> & normal,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
Array<Real>::matrix_iterator tangent_it =
tangent_matrix.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator tangent_end =
tangent_matrix.end(spatial_dimension, spatial_dimension);
Array<Real>::const_vector_iterator normal_it =
this->normal.begin(spatial_dimension);
Array<Real>::vector_iterator opening_it =
this->opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator opening_prec_prev_it =
this->opening_prec.previous(el_type, ghost_type).begin(spatial_dimension);
/**
* NB: delta_max_it points on delta_max_previous, i.e. the
* delta_max related to the solution of the previous incremental
* step
*/
Array<Real>::iterator<Real>delta_max_it =
this->delta_max.previous(el_type, ghost_type).begin();
Array<Real>::iterator<Real>sigma_c_it =
this->sigma_c_eff(el_type, ghost_type).begin();
Array<Real>::iterator<Real>delta_c_it =
this->delta_c_eff(el_type, ghost_type).begin();
Array<Real>::iterator<Real>damage_it =
this->damage(el_type, ghost_type).begin();
Array<Real>::iterator< Vector<Real> > contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::iterator<Real>res_sliding_prev_it =
this->residual_sliding.previous(el_type, ghost_type).begin();
Array<bool>::iterator<bool> reduction_penalty_it =
this->reduction_penalty(el_type, ghost_type).begin();
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end;
++tangent_it, ++normal_it, ++opening_it, ++opening_prec_prev_it,
++delta_max_it, ++sigma_c_it, ++delta_c_it, ++damage_it,
++contact_opening_it, ++res_sliding_prev_it, ++reduction_penalty_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
Real current_penalty = 0.;
this->computeTangentTractionOnQuad(*tangent_it,
*delta_max_it,
*delta_c_it,
*sigma_c_it,
*opening_it,
*normal_it,
normal_opening,
tangential_opening,
normal_opening_norm,
tangential_opening_norm,
*damage_it,
penetration,
*reduction_penalty_it,
current_penalty,
*contact_opening_it);
if (penetration) {
// Real damage = std::min(*delta_max_it / *delta_c_it, Real(1.));
Real mu = mu_max; // * damage;
Real normal_opening_prev_norm = std::min(opening_prec_prev_it->dot(*normal_it), Real(0.));
// Vector<Real> normal_opening_prev = (*normal_it);
// normal_opening_prev *= normal_opening_prev_norm;
Real tau_max = mu * current_penalty * (std::abs(normal_opening_prev_norm));
Real delta_sliding_norm = std::abs(tangential_opening_norm - *res_sliding_prev_it);
// tau is the norm of the friction force, acting tangentially to the surface
Real tau = std::min(friction_penalty * delta_sliding_norm, tau_max);
if (tau < tau_max && tau_max > Math::getTolerance()){
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye(1.);
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(*normal_it, *normal_it);
Matrix<Real> nn(n_outer_n);
I -= nn;
*tangent_it += I * friction_penalty;
}
}
// check if the tangential stiffness matrix is symmetric
// for (UInt h = 0; h < spatial_dimension; ++h){
// for (UInt l = h; l < spatial_dimension; ++l){
// if (l > h){
// Real k_ls = (*tangent_it)[spatial_dimension*h+l];
// Real k_us = (*tangent_it)[spatial_dimension*l+h];
// // std::cout << "k_ls = " << k_ls << std::endl;
// // std::cout << "k_us = " << k_us << std::endl;
// if (std::abs(k_ls) > 1e-13 && std::abs(k_us) > 1e-13){
// Real error = std::abs((k_ls - k_us) / k_us);
// if (error > 1e-10){
// std::cout << "non symmetric cohesive matrix" << std::endl;
// // std::cout << "error " << error << std::endl;
// }
// }
// }
// }
// }
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialCohesiveLinearFriction);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_friction.hh b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_friction.hh
index 841913221..687d72b89 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_friction.hh
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_friction.hh
@@ -1,112 +1,112 @@
/**
* @file material_cohesive_linear_friction.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Jan 12 2016
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic 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 "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Cohesive material linear with friction force
*
* parameters in the material files :
* - mu : friction coefficient
* - penalty_for_friction : Penalty parameter for the friction behavior
*/
template<UInt spatial_dimension>
class MaterialCohesiveLinearFriction : public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
typedef MaterialCohesiveLinear<spatial_dimension> MaterialParent;
public:
MaterialCohesiveLinearFriction(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
virtual void initMaterial();
protected:
/// constitutive law
virtual void computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/// check delta_max for cohesive elements in case of no convergence
/// in the solveStep (only for extrinsic-implicit)
virtual void checkDeltaMax(GhostType ghost_type = _not_ghost);
/// compute tangent stiffness matrix
virtual void computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// maximum value of the friction coefficient
Real mu_max;
/// penalty parameter for the friction law
Real friction_penalty;
/// history parameter for the friction law
CohesiveInternalField<Real> residual_sliding;
/// friction force
CohesiveInternalField<Real> friction_force;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_FRICTION_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_inline_impl.cc b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_inline_impl.cc
index 0b1847bc2..3ad8dc6d9 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_inline_impl.cc
@@ -1,315 +1,315 @@
/**
* @file material_cohesive_linear_inline_impl.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Wed Apr 22 2015
* @date last modification: Thu Jan 14 2016
*
* @brief Inline functions of the MaterialCohesiveLinear
*
* @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_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_CC__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_CC__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt dim>
inline Real MaterialCohesiveLinear<dim>::computeEffectiveNorm(const Matrix<Real> & stress,
const Vector<Real> & normal,
const Vector<Real> & tangent,
Vector<Real> & normal_traction) const {
normal_traction.mul<false>(stress, normal);
Real normal_contrib = normal_traction.dot(normal);
/// in 3D tangential components must be summed
Real tangent_contrib = 0;
if (dim == 2) {
Real tangent_contrib_tmp = normal_traction.dot(tangent);
tangent_contrib += tangent_contrib_tmp * tangent_contrib_tmp;
}
else if (dim == 3) {
for (UInt s = 0; s < dim - 1; ++s) {
const Vector<Real> tangent_v(tangent.storage() + s * dim, dim);
Real tangent_contrib_tmp = normal_traction.dot(tangent_v);
tangent_contrib += tangent_contrib_tmp * tangent_contrib_tmp;
}
}
tangent_contrib = std::sqrt(tangent_contrib);
normal_contrib = std::max(Real(0.), normal_contrib);
return std::sqrt(normal_contrib * normal_contrib + tangent_contrib * tangent_contrib * beta2_inv);
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
inline void MaterialCohesiveLinear<dim>::computeTractionOnQuad(
Vector<Real> & traction,
Real & delta_max,
__attribute__((unused)) const Real & delta_max_prev,
const Real & delta_c,
const Vector<Real> & insertion_stress,
const Real & sigma_c,
Vector<Real> & opening,
Vector<Real> & opening_prec,
const Vector<Real> & normal,
Vector<Real> & normal_opening,
Vector<Real> & tangential_opening,
Real & normal_opening_norm,
Real & tangential_opening_norm,
Real & damage,
bool & penetration,
bool & reduction_penalty,
Real & current_penalty,
Vector<Real> & contact_traction,
Vector<Real> & contact_opening) {
/// compute normal and tangential opening vectors
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
tangential_opening = opening;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
/**
* compute effective opening displacement
* @f$ \delta = \sqrt{
* \frac{\beta^2}{\kappa^2} \Delta_t^2 + \Delta_n^2 } @f$
*/
Real delta = tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
if (this->contact_after_breaking == false && Math::are_float_equal(damage, 1.))
penetration = false;
/**
* if during the convergence loop a cohesive element continues to
* jumps from penetration to opening, and convergence is not
* reached, its penalty parameter will be reduced in the
* recomputation of the same incremental step. recompute is set
* equal to true when convergence is not reached in the
* solveStepCohesive function and the execution of the program
* goes back to the main file where the variable load_reduction
* is set equal to true.
*/
Real normal_opening_prec_norm = opening_prec.dot(normal);
opening_prec = opening;
if (!this->model->isExplicit() && !this->recompute)
if ((normal_opening_prec_norm * normal_opening_norm) < 0.0) {
reduction_penalty = true;
}
if (penetration) {
if (this->recompute && reduction_penalty){
/// the penalty parameter is locally reduced
current_penalty = this->penalty / 100.;
}
else
current_penalty = this->penalty;
/// use penalty coefficient in case of penetration
contact_traction = normal_opening;
contact_traction *= current_penalty;
contact_opening = normal_opening;
/// don't consider penetration contribution for delta
opening = tangential_opening;
normal_opening.clear();
}
else {
delta += normal_opening_norm * normal_opening_norm;
contact_traction.clear();
contact_opening.clear();
}
delta = std::sqrt(delta);
/// update maximum displacement and damage
delta_max = std::max(delta_max, delta);
damage = std::min(delta_max / delta_c, Real(1.));
/**
* Compute traction @f$ \mathbf{T} = \left(
* \frac{\beta^2}{\kappa} \Delta_t \mathbf{t} + \Delta_n
* \mathbf{n} \right) \frac{\sigma_c}{\delta} \left( 1-
* \frac{\delta}{\delta_c} \right)@f$
*/
if (Math::are_float_equal(damage, 1.))
traction.clear();
else if (Math::are_float_equal(damage, 0.)) {
if (penetration)
traction.clear();
else
traction = insertion_stress;
}
else {
traction = tangential_opening;
traction *= this->beta2_kappa;
traction += normal_opening;
AKANTU_DEBUG_ASSERT(delta_max != 0.,
"Division by zero, tolerance might be too low");
traction *= sigma_c / delta_max * (1. - damage);
}
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
inline void MaterialCohesiveLinear<dim>::computeTangentTractionOnQuad(
Matrix<Real> & tangent,
Real & delta_max,
const Real & delta_c,
const Real & sigma_c,
Vector<Real> & opening,
const Vector<Real> & normal,
Vector<Real> & normal_opening,
Vector<Real> & tangential_opening,
Real & normal_opening_norm,
Real & tangential_opening_norm,
Real & damage,
bool & penetration,
bool & reduction_penalty,
Real & current_penalty,
Vector<Real> & contact_opening) {
/**
* During the update of the residual the interpenetrations are
* stored in the array "contact_opening", therefore, in the case
* of penetration, in the array "opening" there are only the
* tangential components.
*/
opening += contact_opening;
/// compute normal and tangential opening vectors
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
tangential_opening = opening;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
Real delta = tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
if (this->contact_after_breaking == false && Math::are_float_equal(damage, 1.))
penetration = false;
Real derivative = 0; // derivative = d(t/delta)/ddelta
Real t = 0;
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(normal, normal);
if (penetration){
if (this->recompute && reduction_penalty)
current_penalty = this->penalty / 100.;
else
current_penalty = this->penalty;
/// stiffness in compression given by the penalty parameter
tangent += n_outer_n;
tangent *= current_penalty;
opening = tangential_opening;
normal_opening_norm = opening.dot(normal);
normal_opening = normal;
normal_opening *= normal_opening_norm;
}
else{
delta += normal_opening_norm * normal_opening_norm;
}
delta = std::sqrt(delta);
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
if (delta < Math::getTolerance())
delta = delta_c / 1000.;
if (delta >= delta_max){
if (delta <= delta_c){
derivative = -sigma_c / (delta * delta);
t = sigma_c * (1 - delta / delta_c);
} else {
derivative = 0.;
t = 0.;
}
} else if (delta < delta_max){
Real tmax = sigma_c * (1 - delta_max / delta_c);
t = tmax / delta_max * delta;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye(this->beta2_kappa);
Matrix<Real> nn(n_outer_n);
nn *= (1. - this->beta2_kappa);
nn += I;
nn *= t/delta;
Vector<Real> t_tilde(normal_opening);
t_tilde *= (1. - this->beta2_kappa2);
Vector<Real> mm(opening);
mm *= this->beta2_kappa2;
t_tilde += mm;
Vector<Real> t_hat(normal_opening);
t_hat += this->beta2_kappa * tangential_opening;
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(t_hat, t_tilde);
prov *= derivative/delta;
prov += nn;
Matrix<Real> prov_t = prov.transpose();
tangent += prov_t;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
#endif //__AKANTU_MATERIAL_COHESIVE_LINEAR_INLINE_IMPL_CC__
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_uncoupled.cc b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_uncoupled.cc
index a8641f161..053303060 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_uncoupled.cc
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_uncoupled.cc
@@ -1,599 +1,599 @@
/**
* @file material_cohesive_linear_uncoupled.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Wed Feb 22 2012
* @date last modification: Thu Jan 14 2016
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic 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 <algorithm>
#include <numeric>
/* -------------------------------------------------------------------------- */
#include "material_cohesive_linear_uncoupled.hh"
#include "solid_mechanics_model_cohesive.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialCohesiveLinearUncoupled<spatial_dimension>
::MaterialCohesiveLinearUncoupled(SolidMechanicsModel & model,
const ID & id) :
MaterialCohesiveLinear<spatial_dimension>(model,id),
delta_n_max("delta_n_max", *this),
delta_t_max("delta_t_max", *this),
damage_n("damage_n", *this),
damage_t("damage_t", *this){
AKANTU_DEBUG_IN();
this->registerParam("roughness", R, Real(1.),
_pat_parsable | _pat_readable,
"Roughness to define coupling between mode II and mode I");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialCohesiveLinear<spatial_dimension>::initMaterial();
delta_n_max.initialize(1);
delta_t_max.initialize(1);
damage_n.initialize(1);
damage_t.initialize(1);
delta_n_max.initializeHistory();
delta_t_max.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
delta_n_max.resize();
delta_t_max.resize();
damage_n.resize();
damage_t.resize();
/// define iterators
Array<Real>::vector_iterator traction_it =
this->tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator traction_end =
this->tractions(el_type, ghost_type).end(spatial_dimension);
Array<Real>::vector_iterator opening_it =
this->opening(el_type, ghost_type).begin(spatial_dimension);
/// opening_prec is the opening of the previous step in the
/// Newton-Raphson loop
Array<Real>::vector_iterator opening_prec_it =
this->opening_prec(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator contact_traction_it =
this->contact_tractions(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::const_vector_iterator normal_it =
this->normal.begin(spatial_dimension);
Array<Real>::scalar_iterator sigma_c_it =
this->sigma_c_eff(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_n_max_it =
delta_n_max(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_t_max_it =
delta_t_max(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_c_it =
this->delta_c_eff(el_type, ghost_type).begin();
Array<Real>::scalar_iterator damage_n_it =
damage_n(el_type, ghost_type).begin();
Array<Real>::scalar_iterator damage_t_it =
damage_t(el_type, ghost_type).begin();
Array<Real>::vector_iterator insertion_stress_it =
this->insertion_stress(el_type, ghost_type).begin(spatial_dimension);
Array<bool>::scalar_iterator reduction_penalty_it =
this->reduction_penalty(el_type, ghost_type).begin();
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
if (!this->model->isExplicit()){
this->delta_n_max(el_type, ghost_type).copy(this->delta_n_max.previous(el_type, ghost_type));
this->delta_t_max(el_type, ghost_type).copy(this->delta_t_max.previous(el_type, ghost_type));
}
/// loop on each quadrature point
for (; traction_it != traction_end;
++traction_it, ++opening_it, ++opening_prec_it,
++contact_traction_it, ++contact_opening_it, ++normal_it,
++sigma_c_it, ++delta_n_max_it, ++delta_t_max_it,
++delta_c_it, ++damage_n_it, ++damage_t_it,
++insertion_stress_it, ++reduction_penalty_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
Real current_penalty = 0.;
Real delta_c2_R2 = *delta_c_it * (*delta_c_it) / R / R;
/// compute normal and tangential opening vectors
normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening = *normal_it;
normal_opening *= normal_opening_norm;
// std::cout<< "normal_opening_norm = " << normal_opening_norm <<std::endl;
Vector<Real> tangential_opening = *opening_it;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
/// compute effective opening displacement
Real delta_n = tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
Real delta_t = tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
if (this->contact_after_breaking == false && Math::are_float_equal(*damage_n_it, 1.))
penetration = false;
/**
* If during the convergence loop a cohesive element continues to
* jumps from penetration to opening, and convergence is not
* reached, its penalty parameter will be reduced in the
* recomputation of the same incremental step. Recompute is set
* equal to true when convergence is not reached in the
* solveStepCohesive function and the execution of the program
* goes back to the main file where the variable load_reduction
* is set equal to true.
*/
Real normal_opening_prec_norm = opening_prec_it->dot(*normal_it);
// Vector<Real> normal_opening_prec = *normal_it;
// normal_opening_prec *= normal_opening_prec_norm;
if (!this->model->isExplicit()) // && !this->recompute)
if ((normal_opening_prec_norm * normal_opening_norm) < 0.0)
*reduction_penalty_it = true;
*opening_prec_it = *opening_it;
if (penetration) {
if (this->recompute && *reduction_penalty_it){
/// the penalty parameter is locally reduced
current_penalty = this->penalty / 100.;
}
else
current_penalty = this->penalty;
/// use penalty coefficient in case of penetration
*contact_traction_it = normal_opening;
*contact_traction_it *= current_penalty;
*contact_opening_it = normal_opening;
/// don't consider penetration contribution for delta
*opening_it = tangential_opening;
normal_opening.clear();
}
else {
delta_n += normal_opening_norm * normal_opening_norm;
delta_t += normal_opening_norm * normal_opening_norm * delta_c2_R2;
contact_traction_it->clear();
contact_opening_it->clear();
}
delta_n = std::sqrt(delta_n);
delta_t = std::sqrt(delta_t);
/// update maximum displacement and damage
*delta_n_max_it = std::max(*delta_n_max_it, delta_n);
*damage_n_it = std::min(*delta_n_max_it / *delta_c_it, Real(1.));
*delta_t_max_it = std::max(*delta_t_max_it, delta_t);
*damage_t_it = std::min(*delta_t_max_it / *delta_c_it, Real(1.));
Vector<Real> normal_traction(spatial_dimension);
Vector<Real> shear_traction(spatial_dimension);
/// NORMAL TRACTIONS
if (Math::are_float_equal(*damage_n_it, 1.))
normal_traction.clear();
else if (Math::are_float_equal(*damage_n_it, 0.)) {
if (penetration)
normal_traction.clear();
else
normal_traction = *insertion_stress_it;
}
else {
// the following formulation holds both in loading and in
// unloading-reloading
normal_traction = normal_opening;
AKANTU_DEBUG_ASSERT(*delta_n_max_it != 0.,
"Division by zero, tolerance might be too low");
normal_traction *= *sigma_c_it / (*delta_n_max_it) * (1. - *damage_n_it);
}
/// SHEAR TRACTIONS
if (Math::are_float_equal(*damage_t_it, 1.))
shear_traction.clear();
else if (Math::are_float_equal(*damage_t_it, 0.)) {
shear_traction.clear();
}
else {
shear_traction = tangential_opening;
AKANTU_DEBUG_ASSERT(*delta_t_max_it != 0.,
"Division by zero, tolerance might be too low");
shear_traction *= this->beta2_kappa;
shear_traction *= *sigma_c_it / (*delta_t_max_it) * (1. - *damage_t_it);
}
*traction_it = normal_traction;
*traction_it += shear_traction;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::checkDeltaMax(GhostType ghost_type) {
AKANTU_DEBUG_IN();
/**
* This function set a predefined value to the parameter
* delta_max_prev of the elements that have been inserted in the
* last loading step for which convergence has not been
* reached. This is done before reducing the loading and re-doing
* the step. Otherwise, the updating of delta_max_prev would be
* done with reference to the non-convergent solution. In this
* function also other variables related to the contact and
* friction behavior are correctly set.
*/
Mesh & mesh = this->fem_cohesive->getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension,
ghost_type, _ek_cohesive);
Mesh::type_iterator last_type = mesh.lastType(spatial_dimension,
ghost_type, _ek_cohesive);
/**
* the variable "recompute" is set to true to activate the
* procedure that reduces the penalty parameter for
* compression. This procedure is available only during the phase of
* load_reduction, that has to be set in the main file. The
* penalty parameter will be reduced only for the elements having
* reduction_penalty = true.
*/
this->recompute = true;
for(; it != last_type; ++it) {
Array<UInt> & elem_filter = this->element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
if (nb_element == 0) continue;
ElementType el_type = *it;
// std::cout << "element type: " << el_type << std::endl;
/// define iterators
Array<Real>::scalar_iterator delta_n_max_it =
delta_n_max(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_n_max_end =
delta_n_max(el_type, ghost_type).end();
Array<Real>::scalar_iterator delta_n_max_prev_it =
delta_n_max.previous(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_t_max_it =
delta_t_max(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_t_max_prev_it =
delta_t_max.previous(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_c_it =
this-> delta_c_eff(el_type, ghost_type).begin();
Array<Real>::vector_iterator opening_prec_it =
this->opening_prec(el_type, ghost_type).begin(spatial_dimension);
Array<Real>::vector_iterator opening_prec_prev_it =
this->opening_prec.previous(el_type, ghost_type).begin(spatial_dimension);
Int it = 0;
/// loop on each quadrature point
for (; delta_n_max_it != delta_n_max_end;
++delta_n_max_it, ++delta_t_max_it, ++delta_c_it,
++delta_n_max_prev_it, ++delta_t_max_prev_it,
++opening_prec_it, ++opening_prec_prev_it) {
++it;
if (*delta_n_max_prev_it == 0){
/// elements inserted in the last incremental step, that did
/// not converge
*delta_n_max_it = *delta_c_it / 1000.;
}
else
/// elements introduced in previous incremental steps, for
/// which a correct value of delta_max_prev already exists
*delta_n_max_it = *delta_n_max_prev_it;
if (*delta_t_max_prev_it == 0){
*delta_t_max_it = *delta_c_it * this->kappa / this->beta / 1000.;
}
else
*delta_t_max_it = *delta_t_max_prev_it;
/// in case convergence is not reached, set opening_prec to the
/// value referred to the previous incremental step
*opening_prec_it = *opening_prec_prev_it;
}
}
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialCohesiveLinearUncoupled<spatial_dimension>::computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
/// define iterators
Array<Real>::matrix_iterator tangent_it =
tangent_matrix.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator tangent_end =
tangent_matrix.end(spatial_dimension, spatial_dimension);
Array<Real>::const_vector_iterator normal_it =
this->normal.begin(spatial_dimension);
Array<Real>::vector_iterator opening_it =
this->opening(el_type, ghost_type).begin(spatial_dimension);
/// NB: delta_max_it points on delta_max_previous, i.e. the
/// delta_max related to the solution of the previous incremental
/// step
Array<Real>::scalar_iterator delta_n_max_it =
delta_n_max.previous(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_t_max_it =
delta_t_max.previous(el_type, ghost_type).begin();
Array<Real>::scalar_iterator sigma_c_it =
this->sigma_c_eff(el_type, ghost_type).begin();
Array<Real>::scalar_iterator delta_c_it =
this->delta_c_eff(el_type, ghost_type).begin();
Array<Real>::scalar_iterator damage_n_it =
damage_n(el_type, ghost_type).begin();
Array<Real>::vector_iterator contact_opening_it =
this->contact_opening(el_type, ghost_type).begin(spatial_dimension);
Array<bool>::scalar_iterator reduction_penalty_it =
this->reduction_penalty(el_type, ghost_type).begin();
Vector<Real> normal_opening(spatial_dimension);
Vector<Real> tangential_opening(spatial_dimension);
for (; tangent_it != tangent_end;
++tangent_it, ++normal_it, ++opening_it, ++sigma_c_it,
++delta_c_it, ++delta_n_max_it, ++delta_t_max_it, ++damage_n_it,
++contact_opening_it, ++reduction_penalty_it) {
Real normal_opening_norm, tangential_opening_norm;
bool penetration;
Real current_penalty = 0.;
Real delta_c2_R2 = *delta_c_it * (*delta_c_it) / R / R;
/**
* During the update of the residual the interpenetrations are
* stored in the array "contact_opening", therefore, in the case
* of penetration, in the array "opening" there are only the
* tangential components.
*/
*opening_it += *contact_opening_it;
/// compute normal and tangential opening vectors
normal_opening_norm = opening_it->dot(*normal_it);
Vector<Real> normal_opening = *normal_it;
normal_opening *= normal_opening_norm;
Vector<Real> tangential_opening = *opening_it;
tangential_opening -= normal_opening;
tangential_opening_norm = tangential_opening.norm();
Real delta_n = tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
Real delta_t = tangential_opening_norm * tangential_opening_norm * this->beta2_kappa2;
penetration = normal_opening_norm < 0.0;
if (this->contact_after_breaking == false && Math::are_float_equal(*damage_n_it, 1.))
penetration = false;
Real derivative = 0; // derivative = d(t/delta)/ddelta
Real T = 0;
/// TANGENT STIFFNESS FOR NORMAL TRACTIONS
Matrix<Real> n_outer_n(spatial_dimension, spatial_dimension);
n_outer_n.outerProduct(*normal_it, *normal_it);
if (penetration){
if (this->recompute && *reduction_penalty_it)
current_penalty = this->penalty / 100.;
else
current_penalty = this->penalty;
/// stiffness in compression given by the penalty parameter
*tangent_it = n_outer_n;
*tangent_it *= current_penalty;
*opening_it = tangential_opening;
normal_opening.clear();
}
else{
delta_n += normal_opening_norm * normal_opening_norm;
delta_n = std::sqrt(delta_n);
delta_t += normal_opening_norm * normal_opening_norm * delta_c2_R2;
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
if (delta_n < Math::getTolerance())
delta_n = *delta_c_it / 1000.;
// loading
if (delta_n >= *delta_n_max_it){
if (delta_n <= *delta_c_it){
derivative = - (*sigma_c_it) / (delta_n * delta_n);
T = *sigma_c_it * (1 - delta_n / *delta_c_it);
} else {
derivative = 0.;
T = 0.;
}
// unloading-reloading
} else if (delta_n < *delta_n_max_it){
Real T_max = *sigma_c_it * (1 - *delta_n_max_it / *delta_c_it);
derivative = 0.;
T = T_max / *delta_n_max_it * delta_n;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> nn(n_outer_n);
nn *= T / delta_n;
Vector<Real> Delta_tilde(normal_opening);
Delta_tilde *= (1. - this->beta2_kappa2);
Vector<Real> mm(*opening_it);
mm *= this->beta2_kappa2;
Delta_tilde += mm;
Vector<Real> Delta_hat(normal_opening);
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(Delta_hat, Delta_tilde);
prov *= derivative / delta_n;
prov += nn;
Matrix<Real> prov_t = prov.transpose();
*tangent_it = prov_t;
}
derivative = 0.;
T = 0.;
/// TANGENT STIFFNESS FOR SHEAR TRACTIONS
delta_t = std::sqrt(delta_t);
/**
* Delta has to be different from 0 to have finite values of
* tangential stiffness. At the element insertion, delta =
* 0. Therefore, a fictictious value is defined, for the
* evaluation of the first value of K.
*/
if (delta_t < Math::getTolerance())
delta_t = *delta_c_it / 1000.;
// loading
if (delta_t >= *delta_t_max_it){
if (delta_t <= *delta_c_it){
derivative = - (*sigma_c_it) / (delta_t * delta_t);
T = *sigma_c_it * (1 - delta_t / *delta_c_it);
} else {
derivative = 0.;
T = 0.;
}
// unloading-reloading
} else if (delta_t < *delta_t_max_it){
Real T_max = *sigma_c_it * (1 - *delta_t_max_it / *delta_c_it);
derivative = 0.;
T = T_max / *delta_t_max_it * delta_t;
}
/// computation of the derivative of the constitutive law (dT/ddelta)
Matrix<Real> I(spatial_dimension, spatial_dimension);
I.eye();
Matrix<Real> nn(n_outer_n);
I -= nn;
I *= T / delta_t;
Vector<Real> Delta_tilde(normal_opening);
Delta_tilde *= (delta_c2_R2 - this->beta2_kappa2);
Vector<Real> mm(*opening_it);
mm *= this->beta2_kappa2;
Delta_tilde += mm;
Vector<Real> Delta_hat(tangential_opening);
Delta_hat *= this->beta2_kappa;
Matrix<Real> prov(spatial_dimension, spatial_dimension);
prov.outerProduct(Delta_hat, Delta_tilde);
prov *= derivative / delta_t;
prov += I;
Matrix<Real> prov_t = prov.transpose();
*tangent_it += prov_t;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialCohesiveLinearUncoupled);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_uncoupled.hh b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_uncoupled.hh
index 393d151ab..1c5b2dfbe 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_uncoupled.hh
+++ b/src/model/solid_mechanics/materials/material_cohesive/constitutive_laws/material_cohesive_linear_uncoupled.hh
@@ -1,115 +1,115 @@
/**
* @file material_cohesive_linear.hh
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Jan 14 2016
*
* @brief Linear irreversible cohesive law of mixed mode loading with
* random stress definition for extrinsic 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 "material_cohesive_linear.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH__
#define __AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH__
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Cohesive material linear with two different laws for mode I and
* mode II, for extrinsic case
*
* parameters in the material files :
* - roughness : define the interaction between mode I and mode II (default: 0)
*/
template<UInt spatial_dimension>
class MaterialCohesiveLinearUncoupled : public MaterialCohesiveLinear<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
// typedef MaterialCohesiveLinear<spatial_dimension> MaterialParent;
public:
MaterialCohesiveLinearUncoupled(SolidMechanicsModel & model, const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material parameters
virtual void initMaterial();
protected:
/// constitutive law
virtual void computeTraction(const Array<Real> & normal,
ElementType el_type,
GhostType ghost_type = _not_ghost);
/// check delta_max for cohesive elements in case of no convergence
/// in the solveStep (only for extrinsic-implicit)
virtual void checkDeltaMax(GhostType ghost_type = _not_ghost);
/// compute tangent stiffness matrix
virtual void computeTangentTraction(const ElementType & el_type,
Array<Real> & tangent_matrix,
const Array<Real> & normal,
GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// parameter to tune the interaction between mode II and mode I
Real R;
/// maximum normal displacement
CohesiveInternalField<Real> delta_n_max;
/// maximum tangential displacement
CohesiveInternalField<Real> delta_t_max;
/// damage associated to normal tractions
CohesiveInternalField<Real> damage_n;
/// damage associated to shear tractions
CohesiveInternalField<Real> damage_t;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_COHESIVE_LINEAR_UNCOUPLED_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_cohesive/material_cohesive.cc b/src/model/solid_mechanics/materials/material_cohesive/material_cohesive.cc
index e4bf64f71..d32efadc0 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/material_cohesive.cc
+++ b/src/model/solid_mechanics/materials/material_cohesive/material_cohesive.cc
@@ -1,616 +1,616 @@
/**
* @file material_cohesive.cc
*
* @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: Wed Feb 22 2012
* @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_cohesive.hh"
#include "aka_random_generator.hh"
#include "dof_synchronizer.hh"
#include "shape_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "sparse_matrix.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
MaterialCohesive::MaterialCohesive(SolidMechanicsModel & model, const ID & id)
: Material(model, id),
facet_filter("facet_filter", id, this->getMemoryID()),
fem_cohesive(&(
model.getFEEngineClass<MyFEEngineCohesiveType>("CohesiveFEEngine"))),
reversible_energy("reversible_energy", *this),
total_energy("total_energy", *this), opening("opening", *this),
opening_old("opening (old)", *this), tractions("tractions", *this),
tractions_old("tractions (old)", *this),
contact_tractions("contact_tractions", *this),
contact_opening("contact_opening", *this), delta_max("delta max", *this),
use_previous_delta_max(false), use_previous_opening(false),
damage("damage", *this), sigma_c("sigma_c", *this),
normal(0, spatial_dimension, "normal") {
AKANTU_DEBUG_IN();
this->model = dynamic_cast<SolidMechanicsModelCohesive *>(&model);
this->registerParam("sigma_c", sigma_c, _pat_parsable | _pat_readable,
"Critical stress");
this->registerParam("delta_c", delta_c, Real(0.),
_pat_parsable | _pat_readable, "Critical displacement");
this->model->getMesh().initElementTypeMapArray(
this->element_filter, 1, spatial_dimension, false, _ek_cohesive);
if (this->model->getIsExtrinsic())
this->model->getMeshFacets().initElementTypeMapArray(facet_filter, 1,
spatial_dimension - 1);
this->reversible_energy.initialize(1);
this->total_energy.initialize(1);
this->tractions_old.initialize(spatial_dimension);
this->tractions.initialize(spatial_dimension);
this->opening_old.initialize(spatial_dimension);
this->contact_tractions.initialize(spatial_dimension);
this->contact_opening.initialize(spatial_dimension);
this->opening.initialize(spatial_dimension);
this->delta_max.initialize(1);
this->damage.initialize(1);
if (this->model->getIsExtrinsic())
this->sigma_c.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
MaterialCohesive::~MaterialCohesive() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
if (this->use_previous_delta_max)
this->delta_max.initializeHistory();
if (this->use_previous_opening)
this->opening.initializeHistory();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_material_cohesive,
"Cohesive Tractions", tractions);
#endif
Array<Real> & residual = const_cast<Array<Real> &>(model->getInternalForce());
Mesh & mesh = fem_cohesive->getMesh();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_cohesive);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, ghost_type, _ek_cohesive);
for (; it != last_type; ++it) {
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
if (nb_element == 0)
continue;
const Array<Real> & shapes = fem_cohesive->getShapes(*it, ghost_type);
Array<Real> & traction = tractions(*it, ghost_type);
Array<Real> & contact_traction = contact_tractions(*it, ghost_type);
UInt size_of_shapes = shapes.getNbComponent();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
UInt nb_quadrature_points =
fem_cohesive->getNbIntegrationPoints(*it, ghost_type);
/// compute @f$t_i N_a@f$
Array<Real> * traction_cpy = new Array<Real>(
nb_element * nb_quadrature_points, spatial_dimension * size_of_shapes);
Array<Real>::iterator<Matrix<Real> > traction_it =
traction.begin(spatial_dimension, 1);
Array<Real>::iterator<Matrix<Real> > contact_traction_it =
contact_traction.begin(spatial_dimension, 1);
Array<Real>::const_iterator<Matrix<Real> > shapes_filtered_begin =
shapes.begin(1, size_of_shapes);
Array<Real>::iterator<Matrix<Real> > traction_cpy_it =
traction_cpy->begin(spatial_dimension, size_of_shapes);
Matrix<Real> traction_tmp(spatial_dimension, 1);
for (UInt el = 0; el < nb_element; ++el) {
UInt current_quad = elem_filter(el) * nb_quadrature_points;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++traction_it,
++contact_traction_it, ++current_quad, ++traction_cpy_it) {
const Matrix<Real> & shapes_filtered =
shapes_filtered_begin[current_quad];
traction_tmp.copy(*traction_it);
traction_tmp += *contact_traction_it;
traction_cpy_it->mul<false, false>(traction_tmp, shapes_filtered);
}
}
/**
* compute @f$\int t \cdot N\, dS@f$ by @f$ \sum_q \mathbf{N}^t
* \mathbf{t}_q \overline w_q J_q@f$
*/
Array<Real> * int_t_N = new Array<Real>(
nb_element, spatial_dimension * size_of_shapes, "int_t_N");
fem_cohesive->integrate(*traction_cpy, *int_t_N,
spatial_dimension * size_of_shapes, *it, ghost_type,
elem_filter);
delete traction_cpy;
int_t_N->extendComponentsInterlaced(2, int_t_N->getNbComponent());
Real * int_t_N_val = int_t_N->storage();
for (UInt el = 0; el < nb_element; ++el) {
for (UInt n = 0; n < size_of_shapes * spatial_dimension; ++n)
int_t_N_val[n] *= -1.;
int_t_N_val += nb_nodes_per_element * spatial_dimension;
}
/// assemble
model->getFEEngineBoundary().assembleArray(
*int_t_N, residual,
model->getDOFSynchronizer().getLocalDOFEquationNumbers(),
residual.getNbComponent(), *it, ghost_type, elem_filter, 1);
delete int_t_N;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::assembleStiffnessMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
SparseMatrix & K = const_cast<SparseMatrix &>(model->getStiffnessMatrix());
Mesh & mesh = fem_cohesive->getMesh();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_cohesive);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, ghost_type, _ek_cohesive);
for (; it != last_type; ++it) {
UInt nb_quadrature_points =
fem_cohesive->getNbIntegrationPoints(*it, ghost_type);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(*it);
const Array<Real> & shapes = fem_cohesive->getShapes(*it, ghost_type);
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
if (!nb_element)
continue;
UInt size_of_shapes = shapes.getNbComponent();
Array<Real> * shapes_filtered = new Array<Real>(
nb_element * nb_quadrature_points, size_of_shapes, "filtered shapes");
Real * shapes_val = shapes.storage();
Real * shapes_filtered_val = shapes_filtered->storage();
UInt * elem_filter_val = elem_filter.storage();
for (UInt el = 0; el < nb_element; ++el) {
shapes_val = shapes.storage() +
elem_filter_val[el] * size_of_shapes * nb_quadrature_points;
memcpy(shapes_filtered_val, shapes_val,
size_of_shapes * nb_quadrature_points * sizeof(Real));
shapes_filtered_val += size_of_shapes * nb_quadrature_points;
}
/**
* compute A matrix @f$ \mathbf{A} = \left[\begin{array}{c c c c c c c c c c
*c c}
* 1 & 0 & 0 & 0 & 0 & 0 & -1 & 0 & 0 & 0 & 0 & 0 \\
* 0 & 1 & 0 & 0 & 0 & 0 & 0 & -1 & 0 & 0 & 0 & 0 \\
* 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & -1 & 0 & 0 & 0 \\
* 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & -1 & 0 & 0 \\
* 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & -1 & 0 \\
* 0 & 0 & 0 & 0 & 0 & 1 & 0 & 0 & 0 & 0 & 0 & -1
* \end{array} \right]@f$
**/
// UInt size_of_A =
// spatial_dimension*size_of_shapes*spatial_dimension*nb_nodes_per_element;
// Real * A = new Real[size_of_A];
// memset(A, 0, size_of_A*sizeof(Real));
Matrix<Real> A(spatial_dimension * size_of_shapes,
spatial_dimension * nb_nodes_per_element);
for (UInt i = 0; i < spatial_dimension * size_of_shapes; ++i) {
A(i, i) = 1;
A(i, i + spatial_dimension * size_of_shapes) = -1;
}
// compute traction. This call is not necessary for the linear
// cohesive law that, currently, is the only one used for the
// extrinsic approach.
// if (!model->getIsExtrinsic()){
// computeTraction(ghost_type);
//}
/// get the tangent matrix @f$\frac{\partial{(t/\delta)}}{\partial{\delta}}
/// @f$
Array<Real> * tangent_stiffness_matrix = new Array<Real>(
nb_element * nb_quadrature_points,
spatial_dimension * spatial_dimension, "tangent_stiffness_matrix");
// Array<Real> * normal = new Array<Real>(nb_element *
// nb_quadrature_points, spatial_dimension, "normal");
normal.resize(nb_quadrature_points);
model->updateCurrentPosition();
computeNormal(model->getCurrentPosition(), normal, *it, ghost_type);
/// compute openings @f$\mathbf{\delta}@f$
// computeOpening(model->getDisplacement(), opening(*it, ghost_type), *it,
// ghost_type);
tangent_stiffness_matrix->clear();
computeTangentTraction(*it, *tangent_stiffness_matrix, normal, ghost_type);
// delete normal;
UInt size_at_nt_d_n_a = spatial_dimension * nb_nodes_per_element *
spatial_dimension * nb_nodes_per_element;
Array<Real> * at_nt_d_n_a = new Array<Real>(
nb_element * nb_quadrature_points, size_at_nt_d_n_a, "A^t*N^t*D*N*A");
Array<Real>::iterator<Vector<Real> > shapes_filt_it =
shapes_filtered->begin(size_of_shapes);
Array<Real>::matrix_iterator D_it =
tangent_stiffness_matrix->begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator At_Nt_D_N_A_it =
at_nt_d_n_a->begin(spatial_dimension * nb_nodes_per_element,
spatial_dimension * nb_nodes_per_element);
Array<Real>::matrix_iterator At_Nt_D_N_A_end =
at_nt_d_n_a->end(spatial_dimension * nb_nodes_per_element,
spatial_dimension * nb_nodes_per_element);
Matrix<Real> N(spatial_dimension, spatial_dimension * size_of_shapes);
Matrix<Real> N_A(spatial_dimension,
spatial_dimension * nb_nodes_per_element);
Matrix<Real> D_N_A(spatial_dimension,
spatial_dimension * nb_nodes_per_element);
for (; At_Nt_D_N_A_it != At_Nt_D_N_A_end;
++At_Nt_D_N_A_it, ++D_it, ++shapes_filt_it) {
N.clear();
/**
* store the shapes in voigt notations matrix @f$\mathbf{N} =
* \begin{array}{cccccc} N_0(\xi) & 0 & N_1(\xi) &0 & N_2(\xi) & 0 \\
* 0 & * N_0(\xi)& 0 &N_1(\xi)& 0 & N_2(\xi) \end{array} @f$
**/
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt n = 0; n < size_of_shapes; ++n)
N(i, i + spatial_dimension * n) = (*shapes_filt_it)(n);
/**
* compute stiffness matrix @f$ \mathbf{K} = \delta \mathbf{U}^T
* \int_{\Gamma_c} {\mathbf{P}^t \frac{\partial{\mathbf{t}}}
*{\partial{\delta}}
* \mathbf{P} d\Gamma \Delta \mathbf{U}} @f$
**/
N_A.mul<false, false>(N, A);
D_N_A.mul<false, false>(*D_it, N_A);
(*At_Nt_D_N_A_it).mul<true, false>(D_N_A, N_A);
}
delete tangent_stiffness_matrix;
delete shapes_filtered;
Array<Real> * K_e = new Array<Real>(nb_element, size_at_nt_d_n_a, "K_e");
fem_cohesive->integrate(*at_nt_d_n_a, *K_e, size_at_nt_d_n_a, *it,
ghost_type, elem_filter);
delete at_nt_d_n_a;
model->getFEEngine().assembleMatrix(*K_e, K, spatial_dimension, *it,
ghost_type, elem_filter);
delete K_e;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- *
* Compute traction from displacements
*
* @param[in] ghost_type compute the residual for _ghost or _not_ghost element
*/
void MaterialCohesive::computeTraction(GhostType ghost_type) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_material_cohesive,
"Cohesive Openings", opening);
#endif
Mesh & mesh = fem_cohesive->getMesh();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, ghost_type, _ek_cohesive);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, ghost_type, _ek_cohesive);
for (; it != last_type; ++it) {
Array<UInt> & elem_filter = element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
if (nb_element == 0)
continue;
UInt nb_quadrature_points =
nb_element * fem_cohesive->getNbIntegrationPoints(*it, ghost_type);
normal.resize(nb_quadrature_points);
/// compute normals @f$\mathbf{n}@f$
model->updateCurrentPosition();
computeNormal(model->getCurrentPosition(), normal, *it, ghost_type);
/// compute openings @f$\mathbf{\delta}@f$
computeOpening(model->getDisplacement(), opening(*it, ghost_type), *it,
ghost_type);
/// compute traction @f$\mathbf{t}@f$
computeTraction(normal, *it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::computeNormal(const Array<Real> & position,
Array<Real> & normal, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (type == _cohesive_1d_2)
fem_cohesive->computeNormalsOnIntegrationPoints(position, normal, type,
ghost_type);
else {
#define COMPUTE_NORMAL(type) \
fem_cohesive->getShapeFunctions() \
.computeNormalsOnIntegrationPoints<type, CohesiveReduceFunctionMean>( \
position, normal, ghost_type, element_filter(type, ghost_type));
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(COMPUTE_NORMAL);
#undef COMPUTE_NORMAL
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::computeOpening(const Array<Real> & displacement,
Array<Real> & opening, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
#define COMPUTE_OPENING(type) \
fem_cohesive->getShapeFunctions() \
.interpolateOnIntegrationPoints<type, CohesiveReduceFunctionOpening>( \
displacement, opening, spatial_dimension, ghost_type, \
element_filter(type, ghost_type));
AKANTU_BOOST_COHESIVE_ELEMENT_SWITCH(COMPUTE_OPENING);
#undef COMPUTE_OPENING
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialCohesive::computeEnergies() {
AKANTU_DEBUG_IN();
Mesh & mesh = fem_cohesive->getMesh();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, _not_ghost, _ek_cohesive);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, _not_ghost, _ek_cohesive);
Real * memory_space = new Real[2 * spatial_dimension];
Vector<Real> b(memory_space, spatial_dimension);
Vector<Real> h(memory_space + spatial_dimension, spatial_dimension);
for (; it != last_type; ++it) {
Array<Real>::iterator<Real> erev =
reversible_energy(*it, _not_ghost).begin();
Array<Real>::iterator<Real> etot = total_energy(*it, _not_ghost).begin();
Array<Real>::vector_iterator traction_it =
tractions(*it, _not_ghost).begin(spatial_dimension);
Array<Real>::vector_iterator traction_old_it =
tractions_old(*it, _not_ghost).begin(spatial_dimension);
Array<Real>::vector_iterator opening_it =
opening(*it, _not_ghost).begin(spatial_dimension);
Array<Real>::vector_iterator opening_old_it =
opening_old(*it, _not_ghost).begin(spatial_dimension);
Array<Real>::vector_iterator traction_end =
tractions(*it, _not_ghost).end(spatial_dimension);
/// loop on each quadrature point
for (; traction_it != traction_end; ++traction_it, ++traction_old_it,
++opening_it, ++opening_old_it, ++erev,
++etot) {
/// trapezoidal integration
b = *opening_it;
b -= *opening_old_it;
h = *traction_old_it;
h += *traction_it;
*etot += .5 * b.dot(h);
*erev = .5 * traction_it->dot(*opening_it);
}
}
delete[] memory_space;
/// update old values
it = mesh.firstType(spatial_dimension, _not_ghost, _ek_cohesive);
GhostType ghost_type = _not_ghost;
for (; it != last_type; ++it) {
tractions_old(*it, ghost_type).copy(tractions(*it, ghost_type));
opening_old(*it, ghost_type).copy(opening(*it, ghost_type));
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getReversibleEnergy() {
AKANTU_DEBUG_IN();
Real erev = 0.;
/// integrate reversible energy for each type of elements
Mesh & mesh = fem_cohesive->getMesh();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, _not_ghost, _ek_cohesive);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, _not_ghost, _ek_cohesive);
for (; it != last_type; ++it) {
erev +=
fem_cohesive->integrate(reversible_energy(*it, _not_ghost), *it,
_not_ghost, element_filter(*it, _not_ghost));
}
AKANTU_DEBUG_OUT();
return erev;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getDissipatedEnergy() {
AKANTU_DEBUG_IN();
Real edis = 0.;
/// integrate dissipated energy for each type of elements
Mesh & mesh = fem_cohesive->getMesh();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, _not_ghost, _ek_cohesive);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, _not_ghost, _ek_cohesive);
for (; it != last_type; ++it) {
Array<Real> dissipated_energy(total_energy(*it, _not_ghost));
dissipated_energy -= reversible_energy(*it, _not_ghost);
edis += fem_cohesive->integrate(dissipated_energy, *it, _not_ghost,
element_filter(*it, _not_ghost));
}
AKANTU_DEBUG_OUT();
return edis;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getContactEnergy() {
AKANTU_DEBUG_IN();
Real econ = 0.;
/// integrate contact energy for each type of elements
Mesh & mesh = fem_cohesive->getMesh();
Mesh::type_iterator it =
mesh.firstType(spatial_dimension, _not_ghost, _ek_cohesive);
Mesh::type_iterator last_type =
mesh.lastType(spatial_dimension, _not_ghost, _ek_cohesive);
for (; it != last_type; ++it) {
Array<UInt> & el_filter = element_filter(*it, _not_ghost);
UInt nb_quad_per_el = fem_cohesive->getNbIntegrationPoints(*it, _not_ghost);
UInt nb_quad_points = el_filter.getSize() * nb_quad_per_el;
Array<Real> contact_energy(nb_quad_points);
Array<Real>::vector_iterator contact_traction_it =
contact_tractions(*it, _not_ghost).begin(spatial_dimension);
Array<Real>::vector_iterator contact_opening_it =
contact_opening(*it, _not_ghost).begin(spatial_dimension);
/// loop on each quadrature point
for (UInt el = 0; el < nb_quad_points;
++contact_traction_it, ++contact_opening_it, ++el) {
contact_energy(el) = .5 * contact_traction_it->dot(*contact_opening_it);
}
econ += fem_cohesive->integrate(contact_energy, *it, _not_ghost, el_filter);
}
AKANTU_DEBUG_OUT();
return econ;
}
/* -------------------------------------------------------------------------- */
Real MaterialCohesive::getEnergy(std::string type) {
AKANTU_DEBUG_IN();
if (type == "reversible")
return getReversibleEnergy();
else if (type == "dissipated")
return getDissipatedEnergy();
else if (type == "cohesive contact")
return getContactEnergy();
AKANTU_DEBUG_OUT();
return 0.;
}
/* -------------------------------------------------------------------------- */
- __END_AKANTU__
+ } // akantu
diff --git a/src/model/solid_mechanics/materials/material_cohesive/material_cohesive.hh b/src/model/solid_mechanics/materials/material_cohesive/material_cohesive.hh
index eb963b128..981ec2cd5 100644
--- a/src/model/solid_mechanics/materials/material_cohesive/material_cohesive.hh
+++ b/src/model/solid_mechanics/materials/material_cohesive/material_cohesive.hh
@@ -1,266 +1,266 @@
/**
* @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 "aka_common.hh"
#include "material.hh"
#include "fe_engine_template.hh"
#include "aka_common.hh"
#include "cohesive_internal_field.hh"
#include "cohesive_element_inserter.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_COHESIVE_HH__
#define __AKANTU_MATERIAL_COHESIVE_HH__
/* -------------------------------------------------------------------------- */
namespace akantu {
class SolidMechanicsModelCohesive;
}
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
virtual void initMaterial();
/// compute tractions (including normals and openings)
void computeTraction(GhostType ghost_type = _not_ghost);
/// assemble residual
void assembleInternalForces(GhostType ghost_type = _not_ghost);
/// 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) {
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) {
AKANTU_DEBUG_TO_IMPLEMENT();
}
/// reset variables when convergence is reached (only for
/// extrinsic-implicit)
virtual void resetVariables(__attribute__((unused))
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){};
/// compute the stresses
virtual void computeAllStresses(__attribute__((unused))
GhostType ghost_type = _not_ghost){};
// 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) {
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);
/// 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);
/// return the energy (identified by id) for the provided element
virtual Real getEnergy(std::string energy_id, ElementType type, UInt index) {
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
MyFEEngineCohesiveType * 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"
-__END_AKANTU__
+} // akantu
#include "cohesive_internal_field_tmpl.hh"
#endif /* __AKANTU_MATERIAL_COHESIVE_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage.hh b/src/model/solid_mechanics/materials/material_damage/material_damage.hh
index aace57a4c..3671ba428 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage.hh
@@ -1,113 +1,113 @@
/**
* @file material_damage.hh
*
* @author Marion Estelle Chambart <marion.chambart@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: Sat Jul 11 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_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_DAMAGE_HH__
#define __AKANTU_MATERIAL_DAMAGE_HH__
-__BEGIN_AKANTU__
+namespace akantu {
template <UInt spatial_dimension,
template <UInt> class Parent = MaterialElastic>
class MaterialDamage : public Parent<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialDamage(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialDamage(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void initMaterial();
/// compute the tangent stiffness matrix for an element type
virtual void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost);
virtual bool hasStiffnessMatrixChanged() { return true; }
protected:
/// update the dissipated energy, must be called after the stress have been
/// computed
virtual void updateEnergies(ElementType el_type, GhostType ghost_type);
/// compute the tangent stiffness matrix for a given quadrature point
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent, Real & dam);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy for the time step
Real getDissipatedEnergy() const;
virtual Real getEnergy(std::string type);
virtual Real getEnergy(std::string energy_id, ElementType type, UInt index) {
return Parent<spatial_dimension>::getEnergy(energy_id, type, index);
};
AKANTU_GET_MACRO_NOT_CONST(Damage, damage, ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO(Damage, damage, const ElementTypeMapArray<Real> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Damage, damage, Real)
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// damage internal variable
InternalField<Real> damage;
/// dissipated energy
InternalField<Real> dissipated_energy;
/// contain the current value of @f$ \int_0^{\epsilon}\sigma(\omega)d\omega
/// @f$ the dissipated energy
InternalField<Real> int_sigma;
};
-__END_AKANTU__
+} // akantu
#include "material_damage_tmpl.hh"
#endif /* __AKANTU_MATERIAL_DAMAGE_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
index cc2a92e95..500ad4bb2 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage_non_local.hh
@@ -1,108 +1,108 @@
/**
* @file material_damage_non_local.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Aug 23 2012
* @date last modification: Wed Oct 21 2015
*
* @brief interface for non local damage material
*
* @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_non_local.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH__
#define __AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
template <UInt spatial_dimension, class MaterialDamageLocal>
class MaterialDamageNonLocal : public MaterialDamageLocal,
public MaterialNonLocal<spatial_dimension> {
public:
typedef MaterialNonLocal<spatial_dimension> MaterialNonLocalParent;
typedef MaterialDamageLocal MaterialDamageParent;
MaterialDamageNonLocal(SolidMechanicsModel & model, const ID & id)
: Material(model, id), MaterialDamageParent(model, id),
MaterialNonLocalParent(model, id){};
/* ------------------------------------------------------------------------ */
virtual void initMaterial() {
MaterialDamageParent::initMaterial();
MaterialNonLocalParent::initMaterial();
}
protected:
/* --------------------------------------------------------------------------
*/
virtual void computeNonLocalStress(ElementType type,
GhostType ghost_type = _not_ghost) = 0;
/* ------------------------------------------------------------------------ */
void computeNonLocalStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = this->model->getFEEngine().getMesh().firstType(
spatial_dimension, ghost_type);
Mesh::type_iterator last_type =
this->model->getFEEngine().getMesh().lastType(spatial_dimension,
ghost_type);
for (; it != last_type; ++it) {
Array<UInt> & elem_filter = this->element_filter(*it, ghost_type);
if (elem_filter.getSize() == 0)
continue;
computeNonLocalStress(*it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
public:
/* ------------------------------------------------------------------------ */
virtual inline UInt getNbDataForElements(const Array<Element> & elements,
SynchronizationTag tag) const {
return MaterialNonLocalParent::getNbDataForElements(elements, tag) +
MaterialDamageParent::getNbDataForElements(elements, tag);
}
virtual inline void packElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) const {
MaterialNonLocalParent::packElementData(buffer, elements, tag);
MaterialDamageParent::packElementData(buffer, elements, tag);
}
virtual inline void unpackElementData(CommunicationBuffer & buffer,
const Array<Element> & elements,
SynchronizationTag tag) {
MaterialNonLocalParent::unpackElementData(buffer, elements, tag);
MaterialDamageParent::unpackElementData(buffer, elements, tag);
}
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_DAMAGE_NON_LOCAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh b/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
index 54e0dc2a6..dc58b0d33 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_damage_tmpl.hh
@@ -1,173 +1,173 @@
/**
* @file material_damage_tmpl.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@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: Tue Aug 18 2015
*
* @brief Specialization of the material class for the damage material
*
* @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_damage.hh"
#include "solid_mechanics_model.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template<UInt> class Parent>
MaterialDamage<spatial_dimension, Parent>::MaterialDamage(SolidMechanicsModel & model,
const ID & id) :
Material(model, id), Parent<spatial_dimension>(model, id),
damage("damage", *this),
dissipated_energy("damage dissipated energy", *this),
int_sigma("integral of sigma", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = false;
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->damage .initialize(1);
this->dissipated_energy.initialize(1);
this->int_sigma .initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template<UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::initMaterial() {
AKANTU_DEBUG_IN();
Parent<spatial_dimension>::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Compute the dissipated energy in each element by a trapezoidal approximation
* of
* @f$ Ed = \int_0^{\epsilon}\sigma(\omega)d\omega - \frac{1}{2}\sigma:\epsilon@f$
*/
template<UInt spatial_dimension, template<UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::updateEnergies(ElementType el_type, GhostType ghost_type) {
Parent<spatial_dimension>::updateEnergies(el_type, ghost_type);
this->computePotentialEnergy(el_type, ghost_type);
Array<Real>::matrix_iterator epsilon_p =
this->gradu.previous(el_type, ghost_type).begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator sigma_p =
this->stress.previous(el_type, ghost_type).begin(spatial_dimension, spatial_dimension);
Array<Real>::const_scalar_iterator epot = this->potential_energy(el_type, ghost_type).begin();
Array<Real>::scalar_iterator ints = this->int_sigma(el_type, ghost_type).begin();
Array<Real>::scalar_iterator ed = this->dissipated_energy(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> delta_gradu_it(*gradu_it);
delta_gradu_it -= *epsilon_p;
Matrix<Real> sigma_h(sigma);
sigma_h += *sigma_p;
Real dint = .5 * sigma_h.doubleDot(delta_gradu_it);
*ints += dint;
*ed = *ints - *epot;
++epsilon_p;
++sigma_p;
++epot;
++ints;
++ed;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template<UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent<spatial_dimension>::computeTangentModuli(el_type, tangent_matrix, ghost_type);
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, *dam);
++dam;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template<UInt> class Parent>
void MaterialDamage<spatial_dimension, Parent>::computeTangentModuliOnQuad(Matrix<Real> & tangent,
Real & dam) {
tangent *= (1-dam);
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template<UInt> class Parent>
Real MaterialDamage<spatial_dimension, Parent>::getDissipatedEnergy() const {
AKANTU_DEBUG_IN();
Real de = 0.;
const Mesh & mesh = this->model->getFEEngine().getMesh();
/// integrate the dissipated energy for each type of elements
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _not_ghost);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, _not_ghost);
for(; it != end; ++it) {
de += this->model->getFEEngine().integrate(dissipated_energy(*it, _not_ghost), *it,
_not_ghost, this->element_filter(*it, _not_ghost));
}
AKANTU_DEBUG_OUT();
return de;
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension, template<UInt> class Parent>
Real MaterialDamage<spatial_dimension, Parent>::getEnergy(std::string type) {
if(type == "dissipated") return getDissipatedEnergy();
else return Parent<spatial_dimension>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo.cc b/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
index 4088340ff..349e29fe5 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo.cc
@@ -1,106 +1,106 @@
/**
* @file material_marigo.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 08 2015
*
* @brief Specialization of the material class for the marigo material
*
* @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_marigo.hh"
#include "solid_mechanics_model.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialMarigo<spatial_dimension>::MaterialMarigo(SolidMechanicsModel & model,
const ID & id) :
Material(model, id),
MaterialDamage<spatial_dimension>(model, id),
Yd("Yd", *this), damage_in_y(false), yc_limit(false) {
AKANTU_DEBUG_IN();
this->registerParam("Sd", Sd, Real(5000.), _pat_parsable | _pat_modifiable);
this->registerParam("epsilon_c", epsilon_c, Real(0.), _pat_parsable, "Critical strain");
this->registerParam("Yc limit", yc_limit, false, _pat_internal, "As the material a critical Y");
this->registerParam("damage_in_y", damage_in_y, false, _pat_parsable, "Use threshold (1-D)Y");
this->registerParam("Yd", Yd, _pat_parsable, "Damaging energy threshold");
this->Yd.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialDamage<spatial_dimension>::initMaterial();
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::updateInternalParameters() {
MaterialDamage<spatial_dimension>::updateInternalParameters();
Yc = .5 * epsilon_c * this->E * epsilon_c;
if(std::abs(epsilon_c) > std::numeric_limits<Real>::epsilon()) yc_limit = true;
else yc_limit = false;
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialMarigo<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real>::scalar_iterator dam = this->damage(el_type, ghost_type).begin();
Array<Real>::scalar_iterator Yd_q = this->Yd(el_type, ghost_type) .begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Real Y = 0.;
computeStressOnQuad(grad_u, sigma, *dam, Y, *Yd_q);
++dam;
++Yd_q;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
INSTANTIATE_MATERIAL(MaterialMarigo);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo.hh b/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
index 667662940..450eb7354 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo.hh
@@ -1,124 +1,124 @@
/**
* @file material_marigo.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief Marigo damage law
*
* @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"
#include "material_damage.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_MARIGO_HH__
#define __AKANTU_MATERIAL_MARIGO_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Material marigo
*
* parameters in the material files :
* - Yd : (default: 50)
* - Sd : (default: 5000)
* - Ydrandomness : (default:0)
*/
template <UInt spatial_dimension>
class MaterialMarigo : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialMarigo(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialMarigo(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
virtual void updateInternalParameters();
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u, Matrix<Real> & sigma,
Real & dam, Real & Y, Real & Ydq);
inline void computeDamageAndStressOnQuad(Matrix<Real> & sigma, Real & dam,
Real & Y, Real & Ydq);
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
inline virtual UInt getNbData(const Array<Element> & elements,
const SynchronizationTag & tag) const;
inline virtual void packData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag) const;
inline virtual void unpackData(CommunicationBuffer & buffer,
const Array<Element> & elements,
const SynchronizationTag & tag);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// resistance to damage
RandomInternalField<Real> Yd;
/// damage threshold
Real Sd;
/// critical epsilon when the material is considered as broken
Real epsilon_c;
Real Yc;
bool damage_in_y;
bool yc_limit;
};
-__END_AKANTU__
+} // akantu
#include "material_marigo_inline_impl.cc"
#endif /* __AKANTU_MATERIAL_MARIGO_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
index f9c23eb9b..26fba660d 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local.hh
@@ -1,99 +1,99 @@
/**
* @file material_marigo_non_local.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 15 2015
*
* @brief Marigo non-local 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_common.hh"
#include "material_damage_non_local.hh"
#include "material_marigo.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH__
#define __AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* Material Marigo
*
* parameters in the material files :
*/
template<UInt spatial_dimension>
class MaterialMarigoNonLocal : public MaterialDamageNonLocal<spatial_dimension, MaterialMarigo<spatial_dimension> > {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef MaterialDamageNonLocal<spatial_dimension, MaterialMarigo<spatial_dimension> > MaterialMarigoNonLocalParent;
MaterialMarigoNonLocal(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialMarigoNonLocal() {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
protected:
/// constitutive law
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
void computeNonLocalStress(ElementType type, GhostType ghost_type = _not_ghost);
private:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Y, Y, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
InternalField<Real> Y;
InternalField<Real> Ynl;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_marigo_non_local_inline_impl.cc"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_MARIGO_NON_LOCAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local_inline_impl.cc b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local_inline_impl.cc
index 1a0284831..317478899 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_marigo_non_local_inline_impl.cc
@@ -1,105 +1,105 @@
/**
* @file material_marigo_non_local_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 15 2015
*
* @brief Marigo non-local inline function 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/>.
*
*/
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#include <string>
#endif
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialMarigoNonLocal<spatial_dimension>::MaterialMarigoNonLocal(SolidMechanicsModel & model, const ID & id) :
Material(model, id),
MaterialMarigoNonLocalParent(model, id),
Y("Y", *this), Ynl("Y non local", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = true;
this->Y.initialize(1);
this->Ynl.initialize(1);
this->model->getNonLocalManager().registerNonLocalVariable(this->Y.getName(), Ynl.getName(), 1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialMarigoNonLocal<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialMarigoNonLocalParent::initMaterial();
this->model->getNonLocalManager().nonLocalVariableToNeighborhood(Ynl.getName(), this->name);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialMarigoNonLocal<spatial_dimension>::computeStress(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * dam = this->damage(el_type, ghost_type).storage();
Real * Yt = this->Y(el_type, ghost_type).storage();
Real * Ydq = this->Yd(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
MaterialMarigo<spatial_dimension>::computeStressOnQuad(grad_u, sigma,
*dam, *Yt, *Ydq);
++dam;
++Yt;
++Ydq;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialMarigoNonLocal<spatial_dimension>::computeNonLocalStress(ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * dam = this->damage(type, ghost_type).storage();
Real * Ydq = this->Yd(type, ghost_type).storage();
Real * Ynlt = this->Ynl(type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(type, ghost_type);
this->computeDamageAndStressOnQuad(sigma, *dam, *Ynlt, *Ydq);
++dam;
++Ynlt;
++Ydq;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars.cc b/src/model/solid_mechanics/materials/material_damage/material_mazars.cc
index 0929b493e..46baaa4f8 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars.cc
@@ -1,84 +1,84 @@
/**
* @file material_mazars.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Aug 18 2015
*
* @brief Specialization of the material class for the damage material
*
* @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_mazars.hh"
#include "solid_mechanics_model.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialMazars<spatial_dimension>::MaterialMazars(SolidMechanicsModel & model,
const ID & id) :
Material(model, id),
MaterialDamage<spatial_dimension>(model, id),
K0("K0", *this),
damage_in_compute_stress(true) {
AKANTU_DEBUG_IN();
this->registerParam("K0" , K0 , _pat_parsable, "K0");
this->registerParam("At" , At , Real(0.8 ), _pat_parsable, "At");
this->registerParam("Ac" , Ac , Real(1.4 ), _pat_parsable, "Ac");
this->registerParam("Bc" , Bc , Real(1900. ), _pat_parsable, "Bc");
this->registerParam("Bt" , Bt , Real(12000.), _pat_parsable, "Bt");
this->registerParam("beta", beta, Real(1.06 ), _pat_parsable, "beta");
this->K0.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialMazars<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * dam = this->damage(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Real Ehat = 0;
computeStressOnQuad(grad_u, sigma, *dam, Ehat);
++dam;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialMazars);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars.hh b/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
index fe9da5555..3359bac63 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars.hh
@@ -1,129 +1,129 @@
/**
* @file material_mazars.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief Material Following the Mazars law for damage evolution
*
* @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_damage.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_MAZARS_HH__
#define __AKANTU_MATERIAL_MAZARS_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Material Mazars
*
* parameters in the material files :
* - rho : density (default: 0)
* - E : Young's modulus (default: 0)
* - nu : Poisson's ratio (default: 1/2)
* - K0 : Damage threshold
* - At : Parameter damage traction 1
* - Bt : Parameter damage traction 2
* - Ac : Parameter damage compression 1
* - Bc : Parameter damage compression 2
* - beta : Parameter for shear
*/
template<UInt spatial_dimension>
class MaterialMazars : public MaterialDamage<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialMazars(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialMazars() {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
protected:
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma,
Real & damage,
Real & Ehat);
inline void computeDamageAndStressOnQuad(const Matrix<Real> & grad_u,
Matrix<Real> & sigma,
Real & damage,
Real & Ehat);
inline void computeDamageOnQuad(const Real & epsilon_equ,
const Matrix<Real> & sigma,
const Vector<Real> & epsilon_princ,
Real & dam);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// damage threshold
RandomInternalField<Real> K0;
///parameter damage traction 1
Real At ;
///parameter damage traction 2
Real Bt ;
///parameter damage compression 1
Real Ac ;
///parameter damage compression 2
Real Bc ;
///parameter for shear
Real beta ;
/// specify the variable to average false = ehat, true = damage (only valid for non local version)
bool damage_in_compute_stress;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_mazars_inline_impl.cc"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_MAZARS_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
index 496c58e4f..911e6d4fd 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.cc
@@ -1,148 +1,148 @@
/**
* @file material_mazars_non_local.cc
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 15 2015
*
* @brief Specialization of the material class for the non-local mazars
* material
*
* @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_mazars_non_local.hh"
#include "solid_mechanics_model.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialMazarsNonLocal<spatial_dimension>::MaterialMazarsNonLocal(
SolidMechanicsModel & model, const ID & id)
: Material(model, id), MaterialMazars<spatial_dimension>(model, id),
MaterialNonLocalParent(model, id), Ehat("epsilon_equ", *this) {
AKANTU_DEBUG_IN();
this->is_non_local = true;
this->Ehat.initialize(1);
this->registerParam("average_on_damage", this->damage_in_compute_stress,
false, _pat_parsable | _pat_modifiable,
"Is D the non local variable");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
MaterialMazars<spatial_dimension>::initMaterial();
MaterialNonLocalParent::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * damage = this->damage(el_type, ghost_type).storage();
Real * epsilon_equ = this->Ehat(el_type, ghost_type).storage();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
MaterialMazars<spatial_dimension>::computeStressOnQuad(grad_u, sigma, *damage,
*epsilon_equ);
++damage;
++epsilon_equ;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::computeNonLocalStresses(
__attribute__((unused)) GhostType ghost_type) {
AKANTU_DEBUG_IN();
InternalField<Real> nl_var("Non local variable", *this);
nl_var.initialize(1);
// if(this->damage_in_compute_stress)
// this->weightedAvergageOnNeighbours(this->damage, nl_var, 1);
// else
// this->weightedAvergageOnNeighbours(this->Ehat, nl_var, 1);
// Mesh::type_iterator it =
// this->model->getFEEngine().getMesh().firstType(spatial_dimension,
// ghost_type);
// Mesh::type_iterator last_type =
// this->model->getFEEngine().getMesh().lastType(spatial_dimension,
// ghost_type);
// for(; it != last_type; ++it) {
// this->computeNonLocalStress(nl_var(*it, ghost_type), *it, ghost_type);
// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<spatial_dimension>::computeNonLocalStress(
Array<Real> & non_loc_var, ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real * damage;
Real * epsilon_equ;
if (this->damage_in_compute_stress) {
damage = non_loc_var.storage();
epsilon_equ = this->Ehat(el_type, ghost_type).storage();
} else {
damage = this->damage(el_type, ghost_type).storage();
epsilon_equ = non_loc_var.storage();
}
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computeDamageAndStressOnQuad(grad_u, sigma, *damage, *epsilon_equ);
++damage;
++epsilon_equ;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialMazarsNonLocal<
spatial_dimension>::nonLocalVariableToNeighborhood() {}
INSTANTIATE_MATERIAL(MaterialMazarsNonLocal);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
index 1b2be905a..9e2539ef4 100644
--- a/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_damage/material_mazars_non_local.hh
@@ -1,103 +1,103 @@
/**
* @file material_mazars_non_local.hh
*
* @author Marion Estelle Chambart <marion.chambart@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 08 2015
*
* @brief Mazars non-local 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_common.hh"
#include "material_mazars.hh"
#include "material_non_local.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH__
#define __AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Material Mazars Non local
*
* parameters in the material files :
*/
template<UInt spatial_dimension>
class MaterialMazarsNonLocal : public MaterialMazars<spatial_dimension>,
public MaterialNonLocal<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef MaterialNonLocal<spatial_dimension> MaterialNonLocalParent;
MaterialMazarsNonLocal(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialMazarsNonLocal() {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void initMaterial();
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
/// constitutive law
void computeNonLocalStresses(GhostType ghost_type = _not_ghost);
void computeNonLocalStress(Array<Real> & Ehatnl,
ElementType el_type,
GhostType ghost_type = _not_ghost);
protected:
/// associate the non-local variables of the material to their neighborhoods
virtual void nonLocalVariableToNeighborhood();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// the ehat per quadrature points to perform the averaging
InternalField<Real> Ehat;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
//#include "material_mazars_non_local_inline_impl.cc"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_MAZARS_NON_LOCAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_elastic.cc b/src/model/solid_mechanics/materials/material_elastic.cc
index 9d6979933..6cbacc296 100644
--- a/src/model/solid_mechanics/materials/material_elastic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic.cc
@@ -1,255 +1,255 @@
/**
* @file material_elastic.cc
*
* @author Lucas Frerot <lucas.frerot@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: Fri Jun 18 2010
* @date last modification: Thu Oct 15 2015
*
* @brief Specialization of the material class for the elastic material
*
* @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_elastic.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElastic<dim>::MaterialElastic(SolidMechanicsModel & model,
const ID & id)
: Material(model, id), Parent(model, id), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElastic<dim>::MaterialElastic(SolidMechanicsModel & model,
__attribute__((unused)) UInt a_dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id)
: Material(model, dim, mesh, fe_engine, id),
Parent(model, dim, mesh, fe_engine, id), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::initialize() {
this->registerParam("lambda", lambda, _pat_readable,
"First Lamé coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lamé coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::initMaterial() {
AKANTU_DEBUG_IN();
Parent::initMaterial();
if (dim == 1)
this->nu = 0.;
this->updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElastic<dim>::updateInternalParameters() {
MaterialThermal<dim>::updateInternalParameters();
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - 2 * this->nu));
this->mu = this->E / (2 * (1 + this->nu));
this->kpa = this->lambda + 2. / 3. * this->mu;
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <> void MaterialElastic<2>::updateInternalParameters() {
MaterialThermal<2>::updateInternalParameters();
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - 2 * this->nu));
this->mu = this->E / (2 * (1 + this->nu));
if (this->plane_stress)
this->lambda = this->nu * this->E / ((1 + this->nu) * (1 - this->nu));
this->kpa = this->lambda + 2. / 3. * this->mu;
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElastic<spatial_dimension>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Parent::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator sigma_th_it =
this->sigma_th(el_type, ghost_type).begin();
if (!this->finite_deformation) {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
const Real & sigma_th = *sigma_th_it;
this->computeStressOnQuad(grad_u, sigma, sigma_th);
++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
/// finite gradus
Matrix<Real> E(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
/// compute E
this->template gradUToGreenStrain<spatial_dimension>(grad_u, E);
const Real & sigma_th = *sigma_th_it;
/// compute second Piola-Kirchhoff stress tensor
this->computeStressOnQuad(E, sigma, sigma_th);
++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElastic<spatial_dimension>::computeTangentModuli(
const ElementType & el_type, Array<Real> & tangent_matrix, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
this->computeTangentModuliOnQuad(tangent);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialElastic<spatial_dimension>::getPushWaveSpeed(
const Element &) const {
return sqrt((lambda + 2 * mu) / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialElastic<spatial_dimension>::getShearWaveSpeed(
const Element &) const {
return sqrt(mu / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElastic<spatial_dimension>::computePotentialEnergy(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialThermal<spatial_dimension>::computePotentialEnergy(el_type,
ghost_type);
if (ghost_type != _not_ghost)
return;
auto epot = this->potential_energy(el_type, ghost_type).begin();
if (!this->finite_deformation) {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->computePotentialEnergyOnQuad(grad_u, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
Matrix<Real> E(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
this->template gradUToGreenStrain<spatial_dimension>(grad_u, E);
this->computePotentialEnergyOnQuad(E, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialElastic<spatial_dimension>::computePotentialEnergyByElement(
ElementType type, UInt index, Vector<Real> & epot_on_quad_points) {
auto gradu_it = this->gradu(type).begin(spatial_dimension, spatial_dimension);
auto gradu_end =
this->gradu(type).begin(spatial_dimension, spatial_dimension);
auto stress_it =
this->stress(type).begin(spatial_dimension, spatial_dimension);
if (this->finite_deformation)
stress_it = this->piola_kirchhoff_2(type).begin(spatial_dimension,
spatial_dimension);
UInt nb_quadrature_points =
this->model->getFEEngine().getNbIntegrationPoints(type);
gradu_it += index * nb_quadrature_points;
gradu_end += (index + 1) * nb_quadrature_points;
stress_it += index * nb_quadrature_points;
Real * epot_quad = epot_on_quad_points.storage();
Matrix<Real> grad_u(spatial_dimension, spatial_dimension);
for (; gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
if (this->finite_deformation)
this->template gradUToGreenStrain<spatial_dimension>(*gradu_it, grad_u);
else
grad_u.copy(*gradu_it);
this->computePotentialEnergyOnQuad(grad_u, *stress_it, *epot_quad);
}
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialElastic);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
index 617bb1e6b..7274d8521 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.cc
@@ -1,313 +1,313 @@
/**
* @file material_elastic_linear_anisotropic.cc
*
* @author Till Junge <till.junge@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Sep 25 2013
* @date last modification: Thu Oct 15 2015
*
* @brief Anisotropic elastic 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/>.
*
*/
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "material_elastic_linear_anisotropic.hh"
#include "solid_mechanics_model.hh"
#include <algorithm>
#include <sstream>
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElasticLinearAnisotropic<dim>::MaterialElasticLinearAnisotropic(
SolidMechanicsModel & model, const ID & id, bool symmetric)
: Material(model, id), rot_mat(dim, dim), Cprime(dim * dim, dim * dim),
C(voigt_h::size, voigt_h::size), eigC(voigt_h::size),
symmetric(symmetric), alpha(0), was_stiffness_assembled(false) {
AKANTU_DEBUG_IN();
this->dir_vecs.push_back(new Vector<Real>(dim));
(*this->dir_vecs.back())[0] = 1.;
this->registerParam("n1", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of main material axis");
this->dir_vecs.push_back(new Vector<Real>(dim));
(*this->dir_vecs.back())[1] = 1.;
this->registerParam("n2", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of secondary material axis");
if (dim > 2) {
this->dir_vecs.push_back(new Vector<Real>(dim));
(*this->dir_vecs.back())[2] = 1.;
this->registerParam("n3", *(this->dir_vecs.back()), _pat_parsmod,
"Direction of tertiary material axis");
}
for (UInt i = 0; i < voigt_h::size; ++i) {
UInt start = 0;
if (this->symmetric) {
start = i;
}
for (UInt j = start; j < voigt_h::size; ++j) {
std::stringstream param("C");
param << "C" << i + 1 << j + 1;
this->registerParam(param.str(), this->Cprime(i, j), Real(0.),
_pat_parsmod, "Coefficient " + param.str());
}
}
this->registerParam("alpha", this->alpha, _pat_parsmod,
"Proportion of viscous stress");
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialElasticLinearAnisotropic<dim>::~MaterialElasticLinearAnisotropic() {
for (UInt i = 0; i < dim; ++i) {
delete this->dir_vecs[i];
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialElasticLinearAnisotropic<dim>::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::updateInternalParameters() {
Material::updateInternalParameters();
if (this->symmetric) {
for (UInt i = 0; i < voigt_h::size; ++i) {
for (UInt j = i + 1; j < voigt_h::size; ++j) {
this->Cprime(j, i) = this->Cprime(i, j);
}
}
}
this->rotateCprime();
this->C.eig(this->eigC);
this->was_stiffness_assembled = false;
}
/* -------------------------------------------------------------------------- */
template <UInt Dim> void MaterialElasticLinearAnisotropic<Dim>::rotateCprime() {
// start by filling the empty parts fo Cprime
UInt diff = Dim * Dim - voigt_h::size;
for (UInt i = voigt_h::size; i < Dim * Dim; ++i) {
for (UInt j = 0; j < Dim * Dim; ++j) {
this->Cprime(i, j) = this->Cprime(i - diff, j);
}
}
for (UInt i = 0; i < Dim * Dim; ++i) {
for (UInt j = voigt_h::size; j < Dim * Dim; ++j) {
this->Cprime(i, j) = this->Cprime(i, j - diff);
}
}
// construction of rotator tensor
// normalise rotation matrix
for (UInt j = 0; j < Dim; ++j) {
Vector<Real> rot_vec = this->rot_mat(j);
rot_vec = *this->dir_vecs[j];
rot_vec.normalize();
}
// make sure the vectors form a right-handed base
Vector<Real> test_axis(3);
Vector<Real> v1(3), v2(3), v3(3);
if (Dim == 2) {
for (UInt i = 0; i < Dim; ++i) {
v1[i] = this->rot_mat(0, i);
v2[i] = this->rot_mat(1, i);
v3[i] = 0.;
}
v3[2] = 1.;
v1[2] = 0.;
v2[2] = 0.;
} else if (Dim == 3) {
v1 = this->rot_mat(0);
v2 = this->rot_mat(1);
v3 = this->rot_mat(2);
}
test_axis.crossProduct(v1, v2);
test_axis -= v3;
if (test_axis.norm() > 8 * std::numeric_limits<Real>::epsilon()) {
AKANTU_DEBUG_ERROR("The axis vectors do not form a right-handed coordinate "
<< "system. I. e., ||n1 x n2 - n3|| should be zero, but "
<< "it is " << test_axis.norm() << ".");
}
// create the rotator and the reverse rotator
Matrix<Real> rotator(Dim * Dim, Dim * Dim);
Matrix<Real> revrotor(Dim * Dim, Dim * Dim);
for (UInt i = 0; i < Dim; ++i) {
for (UInt j = 0; j < Dim; ++j) {
for (UInt k = 0; k < Dim; ++k) {
for (UInt l = 0; l < Dim; ++l) {
UInt I = voigt_h::mat[i][j];
UInt J = voigt_h::mat[k][l];
rotator(I, J) = this->rot_mat(k, i) * this->rot_mat(l, j);
revrotor(I, J) = this->rot_mat(i, k) * this->rot_mat(j, l);
}
}
}
}
// create the full rotated matrix
Matrix<Real> Cfull(Dim * Dim, Dim * Dim);
Cfull = rotator * Cprime * revrotor;
for (UInt i = 0; i < voigt_h::size; ++i) {
for (UInt j = 0; j < voigt_h::size; ++j) {
this->C(i, j) = Cfull(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computeStress(
ElementType el_type, GhostType ghost_type) {
// Wikipedia convention:
// 2*eps_ij (i!=j) = voigt_eps_I
// http://en.wikipedia.org/wiki/Voigt_notation
AKANTU_DEBUG_IN();
Array<Real>::iterator<Matrix<Real>> gradu_it =
this->gradu(el_type, ghost_type).begin(dim, dim);
Array<Real>::iterator<Matrix<Real>> gradu_end =
this->gradu(el_type, ghost_type).end(dim, dim);
UInt nb_quad_pts = gradu_end - gradu_it;
// create array for strains and stresses of all dof of all gauss points
// for efficient computation of stress
Matrix<Real> voigt_strains(voigt_h::size, nb_quad_pts);
Matrix<Real> voigt_stresses(voigt_h::size, nb_quad_pts);
// copy strains
Matrix<Real> strain(dim, dim);
for (UInt q = 0; gradu_it != gradu_end; ++gradu_it, ++q) {
Matrix<Real> & grad_u = *gradu_it;
for (UInt I = 0; I < voigt_h::size; ++I) {
Real voigt_factor = voigt_h::factors[I];
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_strains(I, q) = voigt_factor * (grad_u(i, j) + grad_u(j, i)) / 2.;
}
}
// compute the strain rate proportional part if needed
// bool viscous = this->alpha == 0.; // only works if default value
bool viscous = false;
if (viscous) {
Array<Real> strain_rate(0, dim * dim, "strain_rate");
Array<Real> & velocity = this->model->getVelocity();
const Array<UInt> & elem_filter = this->element_filter(el_type, ghost_type);
this->model->getFEEngine().gradientOnIntegrationPoints(
velocity, strain_rate, dim, el_type, ghost_type, elem_filter);
Array<Real>::matrix_iterator gradu_dot_it = strain_rate.begin(dim, dim);
Array<Real>::matrix_iterator gradu_dot_end = strain_rate.end(dim, dim);
Matrix<Real> strain_dot(dim, dim);
for (UInt q = 0; gradu_dot_it != gradu_dot_end; ++gradu_dot_it, ++q) {
Matrix<Real> & grad_u_dot = *gradu_dot_it;
for (UInt I = 0; I < voigt_h::size; ++I) {
Real voigt_factor = voigt_h::factors[I];
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
voigt_strains(I, q) = this->alpha * voigt_factor *
(grad_u_dot(i, j) + grad_u_dot(j, i)) / 2.;
}
}
}
// compute stresses
voigt_stresses = this->C * voigt_strains;
// copy stresses back
Array<Real>::iterator<Matrix<Real>> stress_it =
this->stress(el_type, ghost_type).begin(dim, dim);
Array<Real>::iterator<Matrix<Real>> stress_end =
this->stress(el_type, ghost_type).end(dim, dim);
for (UInt q = 0; stress_it != stress_end; ++stress_it, ++q) {
Matrix<Real> & stress = *stress_it;
for (UInt I = 0; I < voigt_h::size; ++I) {
UInt i = voigt_h::vec[I][0];
UInt j = voigt_h::vec[I][1];
stress(i, j) = stress(j, i) = voigt_stresses(I, q);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialElasticLinearAnisotropic<dim>::computeTangentModuli(
const ElementType & el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
tangent.copy(this->C);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
Real MaterialElasticLinearAnisotropic<dim>::getCelerity(
__attribute__((unused)) const Element & element) const {
return std::sqrt(this->eigC(0) / rho);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialElasticLinearAnisotropic);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
index 2b1b854ac..24f87cef8 100644
--- a/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_linear_anisotropic.hh
@@ -1,128 +1,128 @@
/**
* @file material_elastic_linear_anisotropic.hh
*
* @author Till Junge <till.junge@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Aug 18 2015
*
* @brief Orthotropic elastic material
*
* @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"
#include "material_elastic.hh"
#include <vector>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH__
#define __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/**
* General linear anisotropic elastic material
* The only constraint on the elastic tensor is that it can be represented
* as a symmetric 6x6 matrix (3D) or 3x3 (2D).
*
* parameters in the material files :
* - rho : density (default: 0)
* - C_ij : entry on the stiffness
*/
template <UInt Dim>
class MaterialElasticLinearAnisotropic : public virtual Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialElasticLinearAnisotropic(SolidMechanicsModel & model,
const ID & id = "", bool symmetric = true);
~MaterialElasticLinearAnisotropic();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void initMaterial();
/// constitutive law for all element of a type
virtual void computeStress(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost);
virtual void updateInternalParameters();
virtual bool hasStiffnessMatrixChanged() {
return (! was_stiffness_assembled);
}
protected:
// compute C from Cprime
void rotateCprime();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// compute max wave celerity
virtual Real getCelerity(const Element & element) const;
AKANTU_GET_MACRO(VoigtStiffness, C, Matrix<Real>);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
typedef VoigtHelper<Dim> voigt_h;
/// direction matrix and vectors
std::vector<Vector<Real> *> dir_vecs;
Matrix<Real> rot_mat;
/// Elastic stiffness tensor in material frame and full vectorised notation
Matrix<Real> Cprime;
/// Elastic stiffness tensor in voigt notation
Matrix<Real> C;
/// eigenvalues of stiffness tensor
Vector<Real> eigC;
bool symmetric;
/// viscous proportion
Real alpha;
/// defines if the stiffness was computed
bool was_stiffness_assembled;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_ELASTIC_LINEAR_ANISOTROPIC_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc b/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
index 5a1158eda..f5c0d8588 100644
--- a/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
+++ b/src/model/solid_mechanics/materials/material_elastic_orthotropic.cc
@@ -1,213 +1,213 @@
/**
* @file material_elastic_orthotropic.cc
*
* @author Till Junge <till.junge@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 Oct 15 2015
*
* @brief Orthotropic elastic material
*
* @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_elastic_orthotropic.hh"
#include "solid_mechanics_model.hh"
#include <algorithm>
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt Dim>
MaterialElasticOrthotropic<Dim>::MaterialElasticOrthotropic(SolidMechanicsModel & model,
const ID & id) :
Material(model, id),
MaterialElasticLinearAnisotropic<Dim>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("E1", E1 , Real(0.), _pat_parsmod, "Young's modulus (n1)");
this->registerParam("E2", E2 , Real(0.), _pat_parsmod, "Young's modulus (n2)");
this->registerParam("nu12", nu12, Real(0.), _pat_parsmod, "Poisson's ratio (12)");
this->registerParam("G12", G12 , Real(0.), _pat_parsmod, "Shear modulus (12)");
if (Dim > 2) {
this->registerParam("E3" , E3 , Real(0.), _pat_parsmod, "Young's modulus (n3)");
this->registerParam("nu13", nu13, Real(0.), _pat_parsmod, "Poisson's ratio (13)");
this->registerParam("nu23", nu23, Real(0.), _pat_parsmod, "Poisson's ratio (23)");
this->registerParam("G13" , G13 , Real(0.), _pat_parsmod, "Shear modulus (13)");
this->registerParam("G23" , G23 , Real(0.), _pat_parsmod, "Shear modulus (23)");
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt Dim>
MaterialElasticOrthotropic<Dim>::~MaterialElasticOrthotropic() {
}
/* -------------------------------------------------------------------------- */
template<UInt Dim>
void MaterialElasticOrthotropic<Dim>::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
inline Real vector_norm(Vector<Real> & vec) {
Real norm = 0;
for (UInt i = 0 ; i < vec.size() ; ++i) {
norm += vec(i)*vec(i);
}
return std::sqrt(norm);
}
/* -------------------------------------------------------------------------- */
template<UInt Dim>
void MaterialElasticOrthotropic<Dim>::updateInternalParameters() {
/* 1) construction of temporary material frame stiffness tensor------------ */
// http://solidmechanics.org/Text/Chapter3_2/Chapter3_2.php#Sect3_2_13
Real nu21 = nu12 * E2 / E1;
Real nu31 = nu13 * E3 / E1;
Real nu32 = nu23 * E3 / E2;
// Full (i.e. dim^2 by dim^2) stiffness tensor in material frame
if (Dim == 1) {
AKANTU_DEBUG_ERROR("Dimensions 1 not implemented: makes no sense to have orthotropy for 1D");
}
Real Gamma;
if (Dim == 3)
Gamma = 1/(1 - nu12 * nu21 - nu23 * nu32 - nu31 * nu13 - 2 * nu21 * nu32 * nu13);
if (Dim == 2)
Gamma = 1/(1 - nu12 * nu21);
// Lamé's first parameters
this->Cprime(0, 0) = E1 * (1 - nu23 * nu32) * Gamma;
this->Cprime(1, 1) = E2 * (1 - nu13 * nu31) * Gamma;
if (Dim == 3)
this->Cprime(2, 2) = E3 * (1 - nu12 * nu21) * Gamma;
// normalised poisson's ratio's
this->Cprime(1, 0) = this->Cprime(0, 1) = E1 * (nu21 + nu31 * nu23) * Gamma;
if (Dim == 3) {
this->Cprime(2, 0) = this->Cprime(0, 2) = E1 * (nu31 + nu21 * nu32) * Gamma;
this->Cprime(2, 1) = this->Cprime(1, 2) = E2 * (nu32 + nu12 * nu31) * Gamma;
}
// Lamé's second parameters (shear moduli)
if (Dim == 3) {
this->Cprime(3, 3) = G23;
this->Cprime(4, 4) = G13;
this->Cprime(5, 5) = G12;
}
else
this->Cprime(2, 2) = G12;
/* 1) rotation of C into the global frame */
this->rotateCprime();
this->C.eig(this->eigC);
}
/* -------------------------------------------------------------------------- */
template<UInt dim>
inline void MaterialElasticOrthotropic<dim>::computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & sigma,
Real & epot) {
epot = .5 * sigma.doubleDot(grad_u);
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialElasticOrthotropic<spatial_dimension>::computePotentialEnergy(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Material::computePotentialEnergy(el_type, ghost_type);
AKANTU_DEBUG_ASSERT(!this->finite_deformation,"finite deformation not possible in material orthotropic (TO BE IMPLEMENTED)");
if(ghost_type != _not_ghost) return;
Array<Real>::scalar_iterator epot = this->potential_energy(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computePotentialEnergyOnQuad(grad_u, sigma, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialElasticOrthotropic<spatial_dimension>::computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points) {
AKANTU_DEBUG_ASSERT(!this->finite_deformation,"finite deformation not possible in material orthotropic (TO BE IMPLEMENTED)");
Array<Real>::matrix_iterator gradu_it =
this->gradu(type).begin(spatial_dimension,
spatial_dimension);
Array<Real>::matrix_iterator gradu_end =
this->gradu(type).begin(spatial_dimension,
spatial_dimension);
Array<Real>::matrix_iterator stress_it =
this->stress(type).begin(spatial_dimension,
spatial_dimension);
UInt nb_quadrature_points = this->model->getFEEngine().getNbIntegrationPoints(type);
gradu_it += index*nb_quadrature_points;
gradu_end += (index+1)*nb_quadrature_points;
stress_it += index*nb_quadrature_points;
Real * epot_quad = epot_on_quad_points.storage();
Matrix<Real> grad_u(spatial_dimension, spatial_dimension);
for(;gradu_it != gradu_end; ++gradu_it, ++stress_it, ++epot_quad) {
grad_u.copy(*gradu_it);
computePotentialEnergyOnQuad(grad_u, *stress_it, *epot_quad);
}
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialElasticOrthotropic);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh b/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
index 53922cd66..e0a6a4c1d 100644
--- a/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
+++ b/src/model/solid_mechanics/materials/material_elastic_orthotropic.hh
@@ -1,149 +1,149 @@
/**
* @file material_elastic_orthotropic.hh
*
* @author Till Junge <till.junge@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief Orthotropic elastic material
*
* @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_elastic_linear_anisotropic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH__
#define __AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Orthotropic elastic material
*
* parameters in the material files :
* - n1 : direction of x-axis in material base, normalisation not necessary (default: {1, 0, 0})
* - n2 : direction of y-axis in material base, normalisation not necessary (default: {0, 1, 0})
* - n3 : direction of z-axis in material base, normalisation not necessary (default: {0, 0, 1})
* - rho : density (default: 0)
* - E1 : Young's modulus along n1 (default: 0)
* - E2 : Young's modulus along n2 (default: 0)
* - E3 : Young's modulus along n3 (default: 0)
* - nu12 : Poisson's ratio along 12 (default: 0)
* - nu13 : Poisson's ratio along 13 (default: 0)
* - nu23 : Poisson's ratio along 23 (default: 0)
* - G12 : Shear modulus along 12 (default: 0)
* - G13 : Shear modulus along 13 (default: 0)
* - G23 : Shear modulus along 23 (default: 0)
*/
template<UInt Dim>
class MaterialElasticOrthotropic :
public MaterialElasticLinearAnisotropic<Dim> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialElasticOrthotropic(SolidMechanicsModel & model, const ID & id = "");
~MaterialElasticOrthotropic();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void initMaterial();
virtual void updateInternalParameters();
/// compute the elastic potential energy
virtual void computePotentialEnergy(ElementType el_type,
GhostType ghost_type = _not_ghost);
virtual void computePotentialEnergyByElement(ElementType type, UInt index,
Vector<Real> & epot_on_quad_points);
protected:
inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & sigma,
Real & epot);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(E1, E1, Real);
AKANTU_GET_MACRO(E2, E2, Real);
AKANTU_GET_MACRO(E3, E3, Real);
AKANTU_GET_MACRO(Nu12, nu12, Real);
AKANTU_GET_MACRO(Nu13, nu13, Real);
AKANTU_GET_MACRO(Nu23, nu23, Real);
AKANTU_GET_MACRO(G12, G12, Real);
AKANTU_GET_MACRO(G13, G13, Real);
AKANTU_GET_MACRO(G23, G23, Real);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the n1 young modulus
Real E1;
/// the n2 young modulus
Real E2;
/// the n3 young modulus
Real E3;
/// 12 Poisson coefficient
Real nu12;
/// 13 Poisson coefficient
Real nu13;
/// 23 Poisson coefficient
Real nu23;
/// 12 shear modulus
Real G12;
/// 13 shear modulus
Real G13;
/// 23 shear modulus
Real G23;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_ELASTIC_ORTHOTROPIC_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_embedded/embedded_internal_field.hh b/src/model/solid_mechanics/materials/material_embedded/embedded_internal_field.hh
index b40e84454..2d139f5b7 100644
--- a/src/model/solid_mechanics/materials/material_embedded/embedded_internal_field.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/embedded_internal_field.hh
@@ -1,83 +1,83 @@
/**
* @file embedded_internal_field.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Jun 30 2015
*
* @brief Embedded 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 "internal_field.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_EMBEDDED_INTERNAL_FIELD_HH__
#define __AKANTU_EMBEDDED_INTERNAL_FIELD_HH__
-__BEGIN_AKANTU__
+namespace akantu {
class Material;
class FEEngine;
/// This class is used for MaterialReinforcement internal fields
template<typename T>
class EmbeddedInternalField : public InternalField<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/// Constructor
EmbeddedInternalField(const ID & id, Material & material):
InternalField<T>(id,
material,
material.getModel().getFEEngine("EmbeddedInterfaceFEEngine"),
material.getElementFilter()) {
this->spatial_dimension = 1;
}
/// Copy constructor
EmbeddedInternalField(const ID & id, const EmbeddedInternalField & other):
InternalField<T>(id, other) {
this->spatial_dimension = 1;
}
void operator=(const EmbeddedInternalField & other) {
InternalField<T>::operator=(other);
this->spatial_dimension = 1;
}
};
/// Method used to initialise the embedded internal fields from material file
template<>
inline void ParsableParamTyped< EmbeddedInternalField<Real> >::parseParam(const ParserParameter & in_param) {
ParsableParam::parseParam(in_param);
Real r = in_param;
param.setDefaultValue(r);
}
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_EMBEDDED_INTERNAL_FIELD_HH__
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.cc b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.cc
index 96f790fa6..304c97685 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.cc
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.cc
@@ -1,784 +1,784 @@
/**
* @file material_reinforcement.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Mar 25 2015
* @date last modification: Tue Dec 08 2015
*
* @brief Reinforcement material
*
* @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 "aka_voigthelper.hh"
#include "material_reinforcement.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialReinforcement<dim>::MaterialReinforcement(SolidMechanicsModel & model,
UInt spatial_dimension,
const Mesh & mesh,
FEEngine & fe_engine,
const ID & id)
: Material(model, dim, mesh, fe_engine,
id), // /!\ dim, not spatial_dimension !
model(NULL),
stress_embedded("stress_embedded", *this, 1, fe_engine,
this->element_filter),
gradu_embedded("gradu_embedded", *this, 1, fe_engine,
this->element_filter),
directing_cosines("directing_cosines", *this, 1, fe_engine,
this->element_filter),
pre_stress("pre_stress", *this, 1, fe_engine, this->element_filter),
area(1.0), shape_derivatives() {
AKANTU_DEBUG_IN();
this->initialize(model);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialReinforcement<dim>::initialize(SolidMechanicsModel & a_model) {
AKANTU_DEBUG_IN();
this->model = dynamic_cast<EmbeddedInterfaceModel *>(&a_model);
AKANTU_DEBUG_ASSERT(this->model != NULL,
"MaterialReinforcement needs an EmbeddedInterfaceModel");
this->registerParam("area", area, _pat_parsable | _pat_modifiable,
"Reinforcement cross-sectional area");
this->registerParam("pre_stress", pre_stress, _pat_parsable | _pat_modifiable,
"Uniform pre-stress");
this->unregisterInternal(this->stress);
// Fool the AvgHomogenizingFunctor
// stress.initialize(dim * dim);
// Reallocate the element filter
this->element_filter.free();
this->model->getInterfaceMesh().initElementTypeMapArray(this->element_filter,
1, 1, false, _ek_regular);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> MaterialReinforcement<dim>::~MaterialReinforcement() {
AKANTU_DEBUG_IN();
ElementTypeMap<ElementTypeMapArray<Real> *>::type_iterator
it = shape_derivatives.firstType(),
end = shape_derivatives.lastType();
for (; it != end; ++it) {
delete shape_derivatives(*it, _not_ghost);
delete shape_derivatives(*it, _ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialReinforcement<dim>::initMaterial() {
Material::initMaterial();
stress_embedded.initialize(dim * dim);
gradu_embedded.initialize(dim * dim);
pre_stress.initialize(1);
/// We initialise the stuff that is not going to change during the simulation
this->allocBackgroundShapeDerivatives();
this->initBackgroundShapeDerivatives();
this->initDirectingCosines();
}
/* -------------------------------------------------------------------------- */
/**
* Background shape derivatives need to be stored per background element
* types but also per embedded element type, which is why they are stored
* in an ElementTypeMap<ElementTypeMapArray<Real> *>. The outer ElementTypeMap
* refers to the embedded types, and the inner refers to the background types.
*/
template <UInt dim>
void MaterialReinforcement<dim>::allocBackgroundShapeDerivatives() {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = model->getInterfaceMesh();
Mesh & mesh = model->getMesh();
ghost_type_t::iterator int_ghost_it = ghost_type_t::begin();
// Loop over interface ghosts
for (; int_ghost_it != ghost_type_t::end(); ++int_ghost_it) {
Mesh::type_iterator interface_type_it =
interface_mesh.firstType(1, *int_ghost_it);
Mesh::type_iterator interface_type_end =
interface_mesh.lastType(1, *int_ghost_it);
// Loop over interface types
for (; interface_type_it != interface_type_end; ++interface_type_it) {
Mesh::type_iterator background_type_it =
mesh.firstType(dim, *int_ghost_it);
Mesh::type_iterator background_type_end =
mesh.lastType(dim, *int_ghost_it);
// Loop over background types
for (; background_type_it != background_type_end ; ++background_type_it) {
const ElementType & int_type = *interface_type_it;
const ElementType & back_type = *background_type_it;
const GhostType & int_ghost = *int_ghost_it;
std::string shaped_id = "embedded_shape_derivatives";
if (int_ghost == _ghost) shaped_id += ":ghost";
ElementTypeMapArray<Real> * shaped_etma = new ElementTypeMapArray<Real>(shaped_id, this->name);
UInt nb_points = Mesh::getNbNodesPerElement(back_type);
UInt nb_quad_points = model->getFEEngine("EmbeddedInterfaceFEEngine").getNbIntegrationPoints(int_type);
UInt nb_elements = element_filter(int_type, int_ghost).getSize();
// Alloc the background ElementTypeMapArray
shaped_etma->alloc(nb_elements * nb_quad_points,
dim * nb_points,
back_type);
// Insert the background ElementTypeMapArray in the interface
// ElementTypeMap
shape_derivatives(shaped_etma, int_type, int_ghost);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialReinforcement<dim>::initBackgroundShapeDerivatives() {
AKANTU_DEBUG_IN();
Mesh & mesh = model->getMesh();
Mesh::type_iterator type_it = mesh.firstType(dim, _not_ghost);
Mesh::type_iterator type_end = mesh.lastType(dim, _not_ghost);
for (; type_it != type_end; ++type_it) {
computeBackgroundShapeDerivatives(*type_it, _not_ghost);
// computeBackgroundShapeDerivatives(*type_it, _ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim> void MaterialReinforcement<dim>::initDirectingCosines() {
AKANTU_DEBUG_IN();
Mesh & mesh = model->getInterfaceMesh();
Mesh::type_iterator type_it = mesh.firstType(1, _not_ghost);
Mesh::type_iterator type_end = mesh.lastType(1, _not_ghost);
const UInt voigt_size = getTangentStiffnessVoigtSize(dim);
directing_cosines.initialize(voigt_size * voigt_size);
for (; type_it != type_end; ++type_it) {
computeDirectingCosines(*type_it, _not_ghost);
// computeDirectingCosines(*type_it, _ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialReinforcement<dim>::assembleStiffnessMatrix(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = model->getInterfaceMesh();
Mesh::type_iterator type_it = interface_mesh.firstType(1, _not_ghost);
Mesh::type_iterator type_end = interface_mesh.lastType(1, _not_ghost);
for (; type_it != type_end; ++type_it) {
assembleStiffnessMatrix(*type_it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialReinforcement<dim>::assembleInternalForces(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = model->getInterfaceMesh();
Mesh::type_iterator type_it = interface_mesh.firstType(1, _not_ghost);
Mesh::type_iterator type_end = interface_mesh.lastType(1, _not_ghost);
for (; type_it != type_end; ++type_it) {
this->assembleInternalForces(*type_it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialReinforcement<dim>::computeGradU(const ElementType & type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<UInt> & elem_filter = element_filter(type, ghost_type);
UInt nb_element = elem_filter.getSize();
UInt nb_quad_points = model->getFEEngine("EmbeddedInterfaceFEEngine")
.getNbIntegrationPoints(type);
Array<Real> & gradu_vec = gradu_embedded(type, ghost_type);
Mesh::type_iterator back_it = model->getMesh().firstType(dim, ghost_type);
Mesh::type_iterator back_end = model->getMesh().lastType(dim, ghost_type);
for (; back_it != back_end; ++back_it) {
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(*back_it);
Array<Real> & shapesd =
shape_derivatives(type, ghost_type)->operator()(*back_it, ghost_type);
Array<UInt> * background_filter =
new Array<UInt>(nb_element, 1, "background_filter");
filterInterfaceBackgroundElements(*background_filter, *back_it, type,
ghost_type);
Array<Real> * disp_per_element = new Array<Real>(0, dim * nodes_per_background_e, "disp_elem");
FEEngine::extractNodalToElementField(model->getMesh(),
model->getDisplacement(),
*disp_per_element,
*back_it, ghost_type, *background_filter);
Array<Real>::matrix_iterator disp_it =
disp_per_element->begin(dim, nodes_per_background_e);
Array<Real>::matrix_iterator disp_end =
disp_per_element->end(dim, nodes_per_background_e);
Array<Real>::matrix_iterator shapes_it =
shapesd.begin(dim, nodes_per_background_e);
Array<Real>::matrix_iterator grad_u_it = gradu_vec.begin(dim, dim);
for (; disp_it != disp_end; ++disp_it) {
for (UInt i = 0; i < nb_quad_points; i++, ++shapes_it, ++grad_u_it) {
Matrix<Real> & B = *shapes_it;
Matrix<Real> & du = *grad_u_it;
Matrix<Real> & u = *disp_it;
du.mul<false, true>(u, B);
}
}
delete background_filter;
delete disp_per_element;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialReinforcement<dim>::computeAllStresses(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = model->getInterfaceMesh().firstType();
Mesh::type_iterator last_type = model->getInterfaceMesh().lastType();
for (; it != last_type; ++it) {
computeGradU(*it, ghost_type);
computeStress(*it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialReinforcement<dim>::assembleInternalForces(
const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & mesh = model->getMesh();
Mesh::type_iterator type_it = mesh.firstType(dim, ghost_type);
Mesh::type_iterator type_end = mesh.lastType(dim, ghost_type);
for (; type_it != type_end; ++type_it) {
assembleInternalForcesInterface(type, *type_it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Computes and assemble the residual. Residual in reinforcement is computed as
* :
* \f[
* \vec{r} = A_s \int_S{\mathbf{B}^T\mathbf{C}^T \vec{\sigma_s}\,\mathrm{d}s}
* \f]
*/
template <UInt dim>
void MaterialReinforcement<dim>::assembleInternalForcesInterface(
const ElementType & interface_type, const ElementType & background_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt voigt_size = getTangentStiffnessVoigtSize(dim);
Array<Real> & residual = const_cast<Array<Real> &>(model->getResidual());
FEEngine & interface_engine = model->getFEEngine("EmbeddedInterfaceFEEngine");
FEEngine & background_engine = model->getFEEngine();
Array<UInt> & elem_filter = element_filter(interface_type, ghost_type);
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(background_type);
UInt nb_quadrature_points =
interface_engine.getNbIntegrationPoints(interface_type, ghost_type);
UInt nb_element = elem_filter.getSize();
UInt back_dof = dim * nodes_per_background_e;
Array<Real> & shapesd = shape_derivatives(interface_type, ghost_type)
->
operator()(background_type, ghost_type);
Array<Real> * integrant = new Array<Real>(nb_quadrature_points * nb_element,
back_dof,
"integrant");
Array<Real>::vector_iterator integrant_it = integrant->begin(back_dof);
Array<Real>::vector_iterator integrant_end = integrant->end(back_dof);
Array<Real>::matrix_iterator B_it =
shapesd.begin(dim, nodes_per_background_e);
Array<Real>::matrix_iterator C_it =
directing_cosines(interface_type, ghost_type)
.begin(voigt_size, voigt_size);
Array<Real>::matrix_iterator sigma_it =
stress_embedded(interface_type, ghost_type).begin(dim, dim);
Vector<Real> sigma(voigt_size);
Matrix<Real> Bvoigt(voigt_size, back_dof);
Vector<Real> Ct_sigma(voigt_size);
for (; integrant_it != integrant_end ; ++integrant_it,
++B_it,
++C_it,
++sigma_it) {
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(*B_it, Bvoigt, nodes_per_background_e);
Matrix<Real> & C = *C_it;
Vector<Real> & BtCt_sigma = *integrant_it;
stressTensorToVoigtVector(*sigma_it, sigma);
Ct_sigma.mul<true>(C, sigma);
BtCt_sigma.mul<true>(Bvoigt, Ct_sigma);
BtCt_sigma *= area;
}
Array<Real> * residual_interface =
new Array<Real>(nb_element, back_dof, "residual_interface");
interface_engine.integrate(*integrant, *residual_interface, back_dof,
interface_type, ghost_type, elem_filter);
delete integrant;
Array<UInt> * background_filter =
new Array<UInt>(nb_element, 1, "background_filter");
filterInterfaceBackgroundElements(*background_filter, background_type,
interface_type, ghost_type);
background_engine.assembleArray(
*residual_interface, residual,
model->getDOFSynchronizer().getLocalDOFEquationNumbers(), dim,
background_type, ghost_type, *background_filter, -1.0);
delete residual_interface;
delete background_filter;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialReinforcement<dim>::filterInterfaceBackgroundElements(
Array<UInt> & filter, const ElementType & type,
const ElementType & interface_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
filter.resize(0);
filter.clear();
Array<Element> & elements =
model->getInterfaceAssociatedElements(interface_type, ghost_type);
Array<UInt> & elem_filter = element_filter(interface_type, ghost_type);
Array<UInt>::scalar_iterator filter_it = elem_filter.begin(),
filter_end = elem_filter.end();
for (; filter_it != filter_end; ++filter_it) {
Element & elem = elements(*filter_it);
if (elem.type == type)
filter.push_back(elem.element);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialReinforcement<dim>::computeDirectingCosines(
const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = this->model->getInterfaceMesh();
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
const UInt steel_dof = dim * nb_nodes_per_element;
const UInt voigt_size = getTangentStiffnessVoigtSize(dim);
const UInt nb_quad_points = model->getFEEngine("EmbeddedInterfaceFEEngine")
.getNbIntegrationPoints(type, ghost_type);
Array<Real> node_coordinates(this->element_filter(type, ghost_type).getSize(),
steel_dof);
this->model->getFEEngine().template extractNodalToElementField<Real>(interface_mesh,
interface_mesh.getNodes(),
node_coordinates,
type,
ghost_type,
this->element_filter(type, ghost_type));
Array<Real>::matrix_iterator directing_cosines_it =
directing_cosines(type, ghost_type).begin(voigt_size, voigt_size);
Array<Real>::matrix_iterator node_coordinates_it =
node_coordinates.begin(dim, nb_nodes_per_element);
Array<Real>::matrix_iterator node_coordinates_end =
node_coordinates.end(dim, nb_nodes_per_element);
for (; node_coordinates_it != node_coordinates_end; ++node_coordinates_it) {
for (UInt i = 0; i < nb_quad_points; i++, ++directing_cosines_it) {
Matrix<Real> & nodes = *node_coordinates_it;
Matrix<Real> & cosines = *directing_cosines_it;
computeDirectingCosinesOnQuad(nodes, cosines);
}
}
// Mauro: the directing_cosines internal is defined on the quadrature points of each element
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialReinforcement<dim>::assembleStiffnessMatrix(
const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & mesh = model->getMesh();
Mesh::type_iterator type_it = mesh.firstType(dim, ghost_type);
Mesh::type_iterator type_end = mesh.lastType(dim, ghost_type);
for (; type_it != type_end; ++type_it) {
assembleStiffnessMatrixInterface(type, *type_it, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Computes the reinforcement stiffness matrix (Gomes & Awruch, 2001)
* \f[
* \mathbf{K}_e = \sum_{i=1}^R{A_i\int_{S_i}{\mathbf{B}^T
* \mathbf{C}_i^T \mathbf{D}_{s, i} \mathbf{C}_i \mathbf{B}\,\mathrm{d}s}}
* \f]
*/
template <UInt dim>
void MaterialReinforcement<dim>::assembleStiffnessMatrixInterface(
const ElementType & interface_type, const ElementType & background_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt voigt_size = getTangentStiffnessVoigtSize(dim);
SparseMatrix & K = const_cast<SparseMatrix &>(model->getStiffnessMatrix());
FEEngine & background_engine = model->getFEEngine();
FEEngine & interface_engine = model->getFEEngine("EmbeddedInterfaceFEEngine");
Array<UInt> & elem_filter = element_filter(interface_type, ghost_type);
Array<Real> & grad_u = gradu_embedded(interface_type, ghost_type);
UInt nb_element = elem_filter.getSize();
UInt nodes_per_background_e = Mesh::getNbNodesPerElement(background_type);
UInt nb_quadrature_points =
interface_engine.getNbIntegrationPoints(interface_type, ghost_type);
UInt back_dof = dim * nodes_per_background_e;
UInt integrant_size = back_dof;
grad_u.resize(nb_quadrature_points * nb_element);
Array<Real> * tangent_moduli = new Array<Real>(
nb_element * nb_quadrature_points, 1, "interface_tangent_moduli");
tangent_moduli->clear();
computeTangentModuli(interface_type, *tangent_moduli, ghost_type);
Array<Real> & shapesd = shape_derivatives(interface_type, ghost_type)
->
operator()(background_type, ghost_type);
Array<Real> * integrant = new Array<Real>(nb_element * nb_quadrature_points,
integrant_size * integrant_size,
"B^t*C^t*D*C*B");
integrant->clear();
/// Temporary matrices for integrant product
Matrix<Real> Bvoigt(voigt_size, back_dof);
Matrix<Real> DC(voigt_size, voigt_size);
Matrix<Real> DCB(voigt_size, back_dof);
Matrix<Real> CtDCB(voigt_size, back_dof);
Array<Real>::scalar_iterator D_it = tangent_moduli->begin();
Array<Real>::scalar_iterator D_end = tangent_moduli->end();
Array<Real>::matrix_iterator C_it =
directing_cosines(interface_type, ghost_type)
.begin(voigt_size, voigt_size);
Array<Real>::matrix_iterator B_it =
shapesd.begin(dim, nodes_per_background_e);
Array<Real>::matrix_iterator integrant_it =
integrant->begin(integrant_size, integrant_size);
for (; D_it != D_end; ++D_it, ++C_it, ++B_it, ++integrant_it) {
Real & D = *D_it;
Matrix<Real> & C = *C_it;
Matrix<Real> & B = *B_it;
Matrix<Real> & BtCtDCB = *integrant_it;
VoigtHelper<dim>::transferBMatrixToSymVoigtBMatrix(B, Bvoigt,
nodes_per_background_e);
DC.clear();
DC(0, 0) = D * area;
DC *= C;
DCB.mul<false, false>(DC, Bvoigt);
CtDCB.mul<true, false>(C, DCB);
BtCtDCB.mul<true, false>(Bvoigt, CtDCB);
}
delete tangent_moduli;
Array<Real> * K_interface = new Array<Real>(
nb_element, integrant_size * integrant_size, "K_interface");
interface_engine.integrate(*integrant, *K_interface,
integrant_size * integrant_size, interface_type,
ghost_type, elem_filter);
delete integrant;
// Mauro: Here K_interface contains the local stiffness matrices,
// directing_cosines contains the information about the orientation
// of the reinforcements, any rotation of the local stiffness matrix
// can be done here
Array<UInt> * background_filter = new Array<UInt>(nb_element, 1, "background_filter");
filterInterfaceBackgroundElements(*background_filter, background_type,
interface_type, ghost_type);
background_engine.assembleMatrix(*K_interface, K, dim, background_type,
ghost_type, *background_filter);
delete K_interface;
delete background_filter;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// In this function, type and ghost_type refer to background elements
template <UInt dim>
void MaterialReinforcement<dim>::computeBackgroundShapeDerivatives(
const ElementType & type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Mesh & interface_mesh = model->getInterfaceMesh();
FEEngine & engine = model->getFEEngine();
FEEngine & interface_engine = model->getFEEngine("EmbeddedInterfaceFEEngine");
Mesh::type_iterator interface_type = interface_mesh.firstType();
Mesh::type_iterator interface_last = interface_mesh.lastType();
for (; interface_type != interface_last; ++interface_type) {
Array<UInt> & filter = element_filter(*interface_type, ghost_type);
const UInt nb_elements = filter.getSize();
const UInt nb_nodes = Mesh::getNbNodesPerElement(type);
const UInt nb_quad_per_element =
interface_engine.getNbIntegrationPoints(*interface_type);
Array<Real> quad_pos(nb_quad_per_element * nb_elements, dim,
"interface_quad_points");
quad_pos.resize(nb_quad_per_element * nb_elements);
interface_engine.interpolateOnIntegrationPoints(
interface_mesh.getNodes(), quad_pos, dim, *interface_type, ghost_type,
filter);
Array<Real> & background_shapesd =
shape_derivatives(*interface_type, ghost_type)
->
operator()(type, ghost_type);
background_shapesd.clear();
Array<UInt> * background_elements = new Array<UInt>(
nb_elements, 1, "computeBackgroundShapeDerivatives:background_filter");
filterInterfaceBackgroundElements(*background_elements, type,
*interface_type, ghost_type);
Array<UInt>::scalar_iterator back_it = background_elements->begin(),
back_end = background_elements->end();
Array<Real>::matrix_iterator shapesd_it =
background_shapesd.begin(dim, nb_nodes);
Array<Real>::vector_iterator quad_pos_it = quad_pos.begin(dim);
for (; back_it != back_end; ++back_it) {
for (UInt i = 0; i < nb_quad_per_element;
i++, ++shapesd_it, ++quad_pos_it)
engine.computeShapeDerivatives(*quad_pos_it, *back_it, type,
*shapesd_it, ghost_type);
}
delete background_elements;
}
AKANTU_DEBUG_OUT();
}
template <UInt dim> Real MaterialReinforcement<dim>::getEnergy(std::string id) {
AKANTU_DEBUG_IN();
if (id == "potential") {
Real epot = 0.;
computePotentialEnergyByElements();
Mesh::type_iterator it = element_filter.firstType(spatial_dimension),
end = element_filter.lastType(spatial_dimension);
for (; it != end; ++it) {
FEEngine & interface_engine =
model->getFEEngine("EmbeddedInterfaceFEEngine");
epot += interface_engine.integrate(potential_energy(*it, _not_ghost), *it,
_not_ghost,
element_filter(*it, _not_ghost));
epot *= area;
}
return epot;
}
AKANTU_DEBUG_OUT();
return 0;
}
// /* --------------------------------------------------------------------------
// */
// template<UInt dim>
// ElementTypeMap<UInt> MaterialReinforcement<dim>::getInternalDataPerElem(const
// ID & field_name,
// const
// ElementKind
// &
// kind,
// const
// ID &
// fe_engine_id)
// const
// {
// return Material::getInternalDataPerElem(field_name, kind,
// "EmbeddedInterfaceFEEngine");
// }
// /* --------------------------------------------------------------------------
// */
// // Author is Guillaume Anciaux, see material.cc
// template<UInt dim>
// void MaterialReinforcement<dim>::flattenInternal(const std::string &
// field_id,
// ElementTypeMapArray<Real> &
// internal_flat,
// const GhostType ghost_type,
// ElementKind element_kind)
// const {
// AKANTU_DEBUG_IN();
// if (field_id == "stress_embedded" || field_id == "inelastic_strain") {
// Material::flattenInternalIntern(field_id,
// internal_flat,
// 1,
// ghost_type,
// _ek_not_defined,
// &(this->element_filter),
// &(this->model->getInterfaceMesh()));
// }
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialReinforcement);
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
index ef6a4c8b1..fd8c6b52e 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement.hh
@@ -1,200 +1,200 @@
/**
* @file material_reinforcement.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Mar 13 2015
* @date last modification: Tue Nov 24 2015
*
* @brief Reinforcement material
*
* @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_MATERIAL_REINFORCEMENT_HH__
#define __AKANTU_MATERIAL_REINFORCEMENT_HH__
#include "aka_common.hh"
#include "material.hh"
#include "embedded_interface_model.hh"
#include "embedded_internal_field.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/**
* @brief Material used to represent embedded reinforcements
*
* This class is used for computing the reinforcement stiffness matrix
* along with the reinforcement residual. Room is made for constitutive law,
* but actual use of contitutive laws is made in MaterialReinforcementTemplate.
*
* Be careful with the dimensions in this class :
* - this->spatial_dimension is always 1
* - the template parameter dim is the dimension of the problem
*/
template <UInt dim> class MaterialReinforcement : virtual public Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/// Constructor
MaterialReinforcement(SolidMechanicsModel & model, UInt spatial_dimension,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "");
/// Destructor
virtual ~MaterialReinforcement();
protected:
void initialize(SolidMechanicsModel & a_model);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Init the material
virtual void initMaterial();
/// Init the background shape derivatives
void initBackgroundShapeDerivatives();
/// Init the cosine matrices
void initDirectingCosines();
/// Assemble stiffness matrix
virtual void assembleStiffnessMatrix(GhostType ghost_type);
/// Update the residual
virtual void updateResidual(GhostType ghost_type = _not_ghost);
/// Assembled the residual
virtual void assembleResidual(GhostType ghost_type);
/// Compute all the stresses !
virtual void computeAllStresses(GhostType ghost_type);
/// Compute the stiffness parameter for elements of a type
virtual void computeTangentModuli(const ElementType & type,
Array<Real> & tangent,
GhostType ghost_type) = 0;
/// Compute energy
virtual Real getEnergy(std::string id);
// virtual ElementTypeMap<UInt> getInternalDataPerElem(const ID & field_name,
// const ElementKind &
// kind,
// const ID &
// fe_engine_id) const;
// /// Reimplementation of Material's function to accomodate for interface
// mesh
// virtual void flattenInternal(const std::string & field_id,
// ElementTypeMapArray<Real> & internal_flat,
// const GhostType ghost_type = _not_ghost,
// ElementKind element_kind = _ek_not_defined)
// const;
/* ------------------------------------------------------------------------ */
/* Protected methods */
/* ------------------------------------------------------------------------ */
protected:
/// Allocate the background shape derivatives
void allocBackgroundShapeDerivatives();
/// Compute the directing cosines matrix for one element type
void computeDirectingCosines(const ElementType & type, GhostType ghost_type);
/// Compute the directing cosines matrix on quadrature points.
inline void computeDirectingCosinesOnQuad(const Matrix<Real> & nodes,
Matrix<Real> & cosines);
/// Assemble the stiffness matrix for an element type (typically _segment_2)
void assembleStiffnessMatrix(const ElementType & type, GhostType ghost_type);
/// Assemble the stiffness matrix for background & interface types
void assembleStiffnessMatrixInterface(const ElementType & interface_type,
const ElementType & background_type,
GhostType ghost_type);
/// Compute the background shape derivatives for a type
void computeBackgroundShapeDerivatives(const ElementType & type,
GhostType ghost_type);
/// Filter elements crossed by interface of a type
void filterInterfaceBackgroundElements(Array<UInt> & filter,
const ElementType & type,
const ElementType & interface_type,
GhostType ghost_type);
/// Assemble the residual of one type of element (typically _segment_2)
void assembleInternalForces(const ElementType & type, GhostType ghost_type);
/// Assemble the residual for a pair of elements
void assembleInternalForcesInterface(const ElementType & interface_type,
const ElementType & background_type,
GhostType ghost_type);
// TODO figure out why voigt size is 4 in 2D
inline void stressTensorToVoigtVector(const Matrix<Real> & tensor,
Vector<Real> & vector);
inline void strainTensorToVoigtVector(const Matrix<Real> & tensor,
Vector<Real> & vector);
/// Compute gradu on the interface quadrature points
virtual void computeGradU(const ElementType & type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Embedded model
EmbeddedInterfaceModel * model;
/// Stress in the reinforcement
InternalField<Real> stress_embedded;
/// Gradu of concrete on reinforcement
InternalField<Real> gradu_embedded;
/// C matrix on quad
InternalField<Real> directing_cosines;
/// Prestress on quad
InternalField<Real> pre_stress;
/// Cross-sectional area
Real area;
/// Background mesh shape derivatives
ElementTypeMap<ElementTypeMapArray<Real> *> shape_derivatives;
};
#include "material_reinforcement_inline_impl.cc"
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_MATERIAL_REINFORCEMENT_HH__
diff --git a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template.hh b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template.hh
index 2a6e23721..3c489e38a 100644
--- a/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template.hh
+++ b/src/model/solid_mechanics/materials/material_embedded/material_reinforcement_template.hh
@@ -1,109 +1,109 @@
/**
* @file material_reinforcement_template.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Wed Mar 25 2015
* @date last modification: Mon Jun 01 2015
*
* @brief Reinforcement material templated with constitutive law
*
* @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_MATERIAL_REINFORCEMENT_TEMPLATE_HH__
#define __AKANTU_MATERIAL_REINFORCEMENT_TEMPLATE_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material_reinforcement.hh"
#include "material_elastic.hh"
#include "material_linear_isotropic_hardening.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/**
* @brief Implementation of MaterialReinforcement with 1D constitutive law
* @see MaterialReinforcement, MaterialElastic
*
* This class is a reinforcement featuring a constitutive law.
* <strong>Be careful !</strong> Because of multiple inheritance, this class
* forms a diamond.
*/
template<UInt dim, class ConstLaw = MaterialElastic<1> >
class MaterialReinforcementTemplate : public MaterialReinforcement<dim>,
public ConstLaw {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/// Constructor
MaterialReinforcementTemplate(SolidMechanicsModel & a_model, const ID & id = "");
/// Destructor
virtual ~MaterialReinforcementTemplate();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Initialises the material
void initMaterial();
/// Compute the stiffness parameter for elements of a type
virtual void computeTangentModuli(const ElementType & type,
Array<Real> & tangent,
GhostType ghost_type);
/// Computes stress used by constitutive law
virtual void computeStress(ElementType type, GhostType ghost_type);
/// Computes gradu to be used by the constitutive law
virtual void computeGradU(const ElementType & type, GhostType ghost_type);
/// Compute the potential energy of the reinforcement
virtual void computePotentialEnergy(ElementType type, GhostType ghost_type = _not_ghost);
/// Get energy in reinforcement (currently limited to potential)
virtual Real getEnergy(std::string id);
protected:
/**
* @brief Compute interface gradu from bulk gradu
* \f[
* \varepsilon_s = C \varepsilon_c
* \f]
*/
inline void computeInterfaceGradUOnQuad(const Matrix<Real> & full_gradu,
Real & gradu,
const Matrix<Real> & C);
};
#include "material_reinforcement_template_tmpl.hh"
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_MATERIAL_REINFORCEMENT_TEMPLATE_HH__
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
index a55a8e331..23bedea4a 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.cc
@@ -1,292 +1,292 @@
/**
* @file material_neohookean.cc
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Mon Apr 08 2013
* @date last modification: Tue Aug 04 2015
*
* @brief Specialization of the material class for finite deformation
* neo-hookean 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_neohookean.hh"
#include "solid_mechanics_model.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialNeohookean<spatial_dimension>::MaterialNeohookean(
SolidMechanicsModel & model, const ID & id)
: PlaneStressToolbox<spatial_dimension>(model, id) {
AKANTU_DEBUG_IN();
this->registerParam("E", E, Real(0.), _pat_parsable | _pat_modifiable,
"Young's modulus");
this->registerParam("nu", nu, Real(0.5), _pat_parsable | _pat_modifiable,
"Poisson's ratio");
this->registerParam("lambda", lambda, _pat_readable,
"First Lamé coefficient");
this->registerParam("mu", mu, _pat_readable, "Second Lamé coefficient");
this->registerParam("kapa", kpa, _pat_readable, "Bulk coefficient");
this->finite_deformation = true;
this->initialize_third_axis_deformation = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
PlaneStressToolbox<spatial_dimension>::initMaterial();
if (spatial_dimension == 1)
nu = 0.;
this->updateInternalParameters();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <> void MaterialNeohookean<2>::initMaterial() {
AKANTU_DEBUG_IN();
PlaneStressToolbox<2>::initMaterial();
this->updateInternalParameters();
if (this->plane_stress)
this->third_axis_deformation.setDefaultValue(1.);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::updateInternalParameters() {
lambda = nu * E / ((1 + nu) * (1 - 2 * nu));
mu = E / (2 * (1 + nu));
kpa = lambda + 2. / 3. * mu;
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeCauchyStressPlaneStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
PlaneStressToolbox<dim>::computeCauchyStressPlaneStress(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeCauchyStressPlaneStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real>::matrix_iterator gradu_it =
this->gradu(el_type, ghost_type).begin(2, 2);
Array<Real>::matrix_iterator gradu_end =
this->gradu(el_type, ghost_type).end(2, 2);
Array<Real>::matrix_iterator piola_it =
this->piola_kirchhoff_2(el_type, ghost_type).begin(2, 2);
Array<Real>::matrix_iterator stress_it =
this->stress(el_type, ghost_type).begin(2, 2);
Array<Real>::const_scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
Matrix<Real> F_tensor(2, 2);
for (; gradu_it != gradu_end; ++gradu_it, ++piola_it, ++stress_it, ++c33_it) {
Matrix<Real> & grad_u = *gradu_it;
Matrix<Real> & piola = *piola_it;
Matrix<Real> & sigma = *stress_it;
gradUToF<2>(grad_u, F_tensor);
computeCauchyStressOnQuad<2>(F_tensor, piola, sigma, *c33_it);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeStress(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
PlaneStressToolbox<2>::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma, *c33_it);
++c33_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
} else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeStressOnQuad(grad_u, sigma);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNeohookean<dim>::computeThirdAxisDeformation(
__attribute__((unused)) ElementType el_type,
__attribute__((unused)) GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeThirdAxisDeformation(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_ASSERT(this->plane_stress, "The third component of the strain "
"can only be computed for 2D "
"problems in Plane Stress!!");
Array<Real>::scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computeThirdAxisDeformationOnQuad(grad_u, *c33_it);
++c33_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::computePotentialEnergy(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Material::computePotentialEnergy(el_type, ghost_type);
if (ghost_type != _not_ghost)
return;
Array<Real>::scalar_iterator epot =
this->potential_energy(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
computePotentialEnergyOnQuad(grad_u, *epot);
++epot;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialNeohookean<spatial_dimension>::computeTangentModuli(
__attribute__((unused)) const ElementType & el_type,
Array<Real> & tangent_matrix,
__attribute__((unused)) GhostType ghost_type) {
AKANTU_DEBUG_IN();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void MaterialNeohookean<2>::computeTangentModuli(__attribute__((unused))
const ElementType & el_type,
Array<Real> & tangent_matrix,
__attribute__((unused))
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if (this->plane_stress) {
PlaneStressToolbox<2>::computeStress(el_type, ghost_type);
Array<Real>::const_scalar_iterator c33_it =
this->third_axis_deformation(el_type, ghost_type).begin();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u, *c33_it);
++c33_it;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
} else {
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u);
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialNeohookean<spatial_dimension>::getPushWaveSpeed(
__attribute__((unused)) const Element & element) const {
return sqrt((this->lambda + 2 * this->mu) / this->rho);
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
Real MaterialNeohookean<spatial_dimension>::getShearWaveSpeed(
__attribute__((unused)) const Element & element) const {
return sqrt(this->mu / this->rho);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialNeohookean);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
index a95a6998c..a0bcbd715 100644
--- a/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
+++ b/src/model/solid_mechanics/materials/material_finite_deformation/material_neohookean.hh
@@ -1,171 +1,171 @@
/**
* @file material_neohookean.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 08 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.hh"
#include "plane_stress_toolbox.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_NEOHOOKEAN_HH__
#define __AKANTU_MATERIAL_NEOHOOKEAN_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Material elastic isotropic
*
* parameters in the material files :
* - rho : density (default: 0)
* - 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 MaterialNeohookean : public virtual PlaneStressToolbox<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialNeohookean(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialNeohookean() {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
virtual void initMaterial();
/// constitutive law for all element of a type
virtual void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
/// Computation of the cauchy stress for plane strain materials
virtual void computeCauchyStressPlaneStress(ElementType el_type, GhostType ghost_type = _not_ghost);
/// Non linear computation of the third direction strain in 2D plane stress case
virtual void computeThirdAxisDeformation(ElementType el_type, GhostType ghost_type = _not_ghost);
/// compute the elastic potential energy
virtual void computePotentialEnergy(ElementType el_type,
GhostType ghost_type = _not_ghost);
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost);
/// compute the p-wave speed in the material
virtual Real getPushWaveSpeed(const Element & element) const;
/// compute the s-wave speed in the material
virtual Real getShearWaveSpeed(const Element & element) const;
protected:
/// constitutive law for a given quadrature point
inline void computePiolaKirchhoffOnQuad(const Matrix<Real> &E,
Matrix<Real> &S);
/// constitutive law for a given quadrature point (first piola)
inline void computeFirstPiolaKirchhoffOnQuad(const Matrix<Real> &grad_u,
const Matrix<Real> &S,
Matrix<Real> &P);
/// constitutive law for a given quadrature point
inline void computeDeltaStressOnQuad(const Matrix<Real> & grad_u, const Matrix<Real> & grad_delta_u,
Matrix<Real> & delta_S);
/// constitutive law for a given quadrature point
inline void computeStressOnQuad(Matrix<Real> & grad_u,
Matrix<Real> & S,
const Real & C33 = 1.0 );
/// constitutive law for a given quadrature point
inline void computeThirdAxisDeformationOnQuad(Matrix<Real> & grad_u, Real & c33_value);
/// constitutive law for a given quadrature point
//inline void updateStressOnQuad(const Matrix<Real> & sigma,
// Matrix<Real> & cauchy_sigma);
/// compute the potential energy for a quadrature point
inline void computePotentialEnergyOnQuad(const Matrix<Real> & grad_u,
Real & epot);
/// compute the tangent stiffness matrix for an element
void computeTangentModuliOnQuad(Matrix<Real> & tangent,
Matrix<Real> & grad_u,
const Real & C33 = 1.0 );
/// recompute the lame coefficient if E or nu changes
virtual void updateInternalParameters();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// the young modulus
Real E;
/// Poisson coefficient
Real nu;
/// First Lamé coefficient
Real lambda;
/// Second Lamé coefficient (shear modulus)
Real mu;
/// Bulk modulus
Real kpa;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_neohookean_inline_impl.cc"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_NEOHOOKEAN_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_non_local.cc b/src/model/solid_mechanics/materials/material_non_local.cc
index 24d8d434d..2ef2aa5f6 100644
--- a/src/model/solid_mechanics/materials/material_non_local.cc
+++ b/src/model/solid_mechanics/materials/material_non_local.cc
@@ -1,168 +1,168 @@
/**
* @file material_non_local.cc
*
* @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: Tue Dec 08 2015
*
* @brief Implementation of material non-local
*
* @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_non_local.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialNonLocal<dim>::MaterialNonLocal(SolidMechanicsModel & model,
const ID & id)
: Material(model, id) {
AKANTU_DEBUG_IN();
NonLocalManager & manager = this->model->getNonLocalManager();
manager.registerNonLocalMaterial(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialNonLocal<dim>::~MaterialNonLocal() {}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNonLocal<dim>::initMaterial() {
this->registerNeighborhood();
this->insertQuadsInNeighborhoods(_not_ghost);
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNonLocal<dim>::insertQuadsInNeighborhoods(
GhostType ghost_type) {
NonLocalManager & manager = this->model->getNonLocalManager();
InternalField<Real> quadrature_points_coordinates(
"quadrature_points_coordinates_tmp_nl", *this);
quadrature_points_coordinates.initialize(dim);
/// intialize quadrature point object
IntegrationPoint q;
q.ghost_type = ghost_type;
q.kind = _ek_regular;
Mesh::type_iterator it = this->element_filter.firstType(
dim, ghost_type, _ek_regular);
Mesh::type_iterator last_type =
this->element_filter.lastType(dim, ghost_type, _ek_regular);
for (; it != last_type; ++it) {
q.type = *it;
const Array<UInt> & elem_filter = this->element_filter(*it, ghost_type);
UInt nb_element = elem_filter.getSize();
if (nb_element) {
UInt nb_quad = this->fem->getNbIntegrationPoints(*it, ghost_type);
UInt nb_tot_quad = nb_quad * nb_element;
Array<Real> & quads = quadrature_points_coordinates(*it, ghost_type);
quads.resize(nb_tot_quad);
this->model->getFEEngine().computeIntegrationPointsCoordinates(
quads, *it, ghost_type, elem_filter);
Array<Real>::const_vector_iterator quad = quads.begin(dim);
UInt * elem = elem_filter.storage();
for (UInt e = 0; e < nb_element; ++e) {
q.element = *elem;
for (UInt nq = 0; nq < nb_quad; ++nq) {
q.num_point = nq;
q.global_num = q.element * nb_quad + nq;
manager.insertQuad(q, *quad, this->name);
++quad;
}
++elem;
}
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNonLocal<dim>::updateNonLocalInternals(
ElementTypeMapReal & non_local_flattened, const ID & field_id,
const UInt nb_component) {
for (ghost_type_t::iterator g = ghost_type_t::begin();
g != ghost_type_t::end(); ++g) {
GhostType ghost_type = *g;
/// loop over all types in the material
typedef ElementTypeMapArray<UInt>::type_iterator iterator;
iterator it = this->element_filter.firstType(dim, ghost_type,
_ek_regular);
iterator last_type = this->element_filter.lastType(dim,
ghost_type, _ek_regular);
for (; it != last_type; ++it) {
ElementType el_type = *it;
Array<Real> & internal =
this->getInternal<Real>(field_id)(el_type, ghost_type);
Array<Real>::vector_iterator internal_it = internal.begin(nb_component);
Array<Real> & internal_flat = non_local_flattened(el_type, ghost_type);
Array<Real>::const_vector_iterator internal_flat_it =
internal_flat.begin(nb_component);
/// loop all elements for the given type
const Array<UInt> & filter = this->element_filter(el_type, ghost_type);
UInt nb_elements = filter.getSize();
UInt nb_quads =
this->getFEEngine().getNbIntegrationPoints(el_type, ghost_type);
for (UInt e = 0; e < nb_elements; ++e) {
UInt global_el = filter(e);
for (UInt q = 0; q < nb_quads; ++q, ++internal_it) {
UInt global_quad = global_el * nb_quads + q;
*internal_it = internal_flat_it[global_quad];
}
}
}
}
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNonLocal<dim>::updateResidual(__attribute__((unused))
GhostType ghost_type) {
AKANTU_EXCEPTION("this method has not been implemented");
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialNonLocal<dim>::registerNeighborhood() {
this->model->getNonLocalManager().registerNeighborhood(this->name,
this->name);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialNonLocal);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_non_local.hh b/src/model/solid_mechanics/materials/material_non_local.hh
index bee5198f4..e5ce642f8 100644
--- a/src/model/solid_mechanics/materials/material_non_local.hh
+++ b/src/model/solid_mechanics/materials/material_non_local.hh
@@ -1,86 +1,86 @@
/**
* @file material_non_local.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 Material class that handle the non locality of a law for example
* damage.
*
* @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"
#include "fe_engine.hh"
#include "non_local_manager.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_NON_LOCAL_HH__
#define __AKANTU_MATERIAL_NON_LOCAL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim> class MaterialNonLocal : public virtual Material {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialNonLocal(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialNonLocal();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
virtual void initMaterial();
virtual void updateResidual(GhostType ghost_type);
/// insert the quadrature points in the neighborhoods of the non-local manager
virtual void insertQuadsInNeighborhoods(GhostType ghost_type = _not_ghost);
/// update the values in the non-local internal fields
void updateNonLocalInternals(ElementTypeMapReal & non_local_flattened,
const ID & field_id, const UInt nb_component);
/// constitutive law
virtual void computeNonLocalStresses(GhostType ghost_type = _not_ghost) = 0;
/// register the neighborhoods for the material
virtual void registerNeighborhood();
protected:
virtual inline void onElementsAdded(const Array<Element> &,
const NewElementsEvent &) {
}
protected:
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_NON_LOCAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_non_local_inline_impl.cc b/src/model/solid_mechanics/materials/material_non_local_inline_impl.cc
index 893ff9745..de5e4a295 100644
--- a/src/model/solid_mechanics/materials/material_non_local_inline_impl.cc
+++ b/src/model/solid_mechanics/materials/material_non_local_inline_impl.cc
@@ -1,36 +1,36 @@
/**
* @file material_non_local_inline_impl.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Wed Aug 31 2011
* @date last modification: Thu Oct 08 2015
*
* @brief Non-local inline 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/>.
*
*/
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
-__BEGIN_AKANTU__
+namespace akantu {
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
index 6757554d1..9bae61a24 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.cc
@@ -1,203 +1,203 @@
/**
* @file material_linear_isotropic_hardening.cc
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
* @date last modification: Tue Aug 18 2015
*
* @brief Specialization of the material class for isotropic finite deformation
* linear hardening plasticity
*
* @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_linear_isotropic_hardening.hh"
#include "solid_mechanics_model.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <UInt dim>
MaterialLinearIsotropicHardening<dim>::MaterialLinearIsotropicHardening(
SolidMechanicsModel & model, const ID & id)
: Material(model, id), MaterialPlastic<dim>(model, id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
MaterialLinearIsotropicHardening<spatial_dimension>::
MaterialLinearIsotropicHardening(SolidMechanicsModel & model, UInt dim,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id)
:
Material(model, dim, mesh, fe_engine, id),
MaterialPlastic<spatial_dimension>(model, dim, mesh, fe_engine, id) {}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialLinearIsotropicHardening<spatial_dimension>::computeStress(
ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialThermal<spatial_dimension>::computeStress(el_type, ghost_type);
// infinitesimal and finite deformation
auto sigma_th_it = this->sigma_th(el_type, ghost_type).begin();
auto previous_sigma_th_it =
this->sigma_th.previous(el_type, ghost_type).begin();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto inelastic_strain_it = this->inelastic_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto iso_hardening_it = this->iso_hardening(el_type, ghost_type).begin();
auto previous_iso_hardening_it =
this->iso_hardening.previous(el_type, ghost_type).begin();
//
// Finite Deformations
//
if (this->finite_deformation) {
auto previous_piola_kirchhoff_2_it =
this->piola_kirchhoff_2.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto green_strain_it = this->green_strain(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_piola_kirchhoff_2_it;
auto & green_strain = *green_strain_it;
this->template gradUToGreenStrain<spatial_dimension>(grad_u, green_strain);
Matrix<Real> previous_green_strain(spatial_dimension, spatial_dimension);
this->template gradUToGreenStrain<spatial_dimension>(previous_grad_u,
previous_green_strain);
Matrix<Real> F_tensor(spatial_dimension, spatial_dimension);
this->template gradUToF<spatial_dimension>(grad_u, F_tensor);
computeStressOnQuad(green_strain, previous_green_strain, sigma,
previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *iso_hardening_it,
*previous_iso_hardening_it, *sigma_th_it,
*previous_sigma_th_it, F_tensor);
++sigma_th_it;
++inelastic_strain_it;
++iso_hardening_it;
++previous_sigma_th_it;
//++previous_stress_it;
++previous_gradu_it;
++green_strain_it;
++previous_inelastic_strain_it;
++previous_iso_hardening_it;
++previous_piola_kirchhoff_2_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
// Infinitesimal deformations
else {
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
auto & inelastic_strain_tensor = *inelastic_strain_it;
auto & previous_inelastic_strain_tensor = *previous_inelastic_strain_it;
auto & previous_grad_u = *previous_gradu_it;
auto & previous_sigma = *previous_stress_it;
computeStressOnQuad(
grad_u, previous_grad_u, sigma, previous_sigma, inelastic_strain_tensor,
previous_inelastic_strain_tensor, *iso_hardening_it,
*previous_iso_hardening_it, *sigma_th_it, *previous_sigma_th_it);
++sigma_th_it;
++inelastic_strain_it;
++iso_hardening_it;
++previous_sigma_th_it;
++previous_stress_it;
++previous_gradu_it;
++previous_inelastic_strain_it;
++previous_iso_hardening_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt spatial_dimension>
void MaterialLinearIsotropicHardening<spatial_dimension>::computeTangentModuli(
const ElementType & el_type, Array<Real> & tangent_matrix,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
auto previous_gradu_it = this->gradu.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto previous_stress_it = this->stress.previous(el_type, ghost_type)
.begin(spatial_dimension, spatial_dimension);
auto iso_hardening = this->iso_hardening(el_type, ghost_type).begin();
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_BEGIN(tangent_matrix);
computeTangentModuliOnQuad(tangent, grad_u, *previous_gradu_it, sigma_tensor,
*previous_stress_it, *iso_hardening);
++previous_gradu_it;
++previous_stress_it;
++iso_hardening;
MATERIAL_TANGENT_QUADRATURE_POINT_LOOP_END;
this->was_stiffness_assembled = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialLinearIsotropicHardening);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
index 06fe1da02..2ebbf5280 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_linear_isotropic_hardening.hh
@@ -1,121 +1,121 @@
/**
* @file material_linear_isotropic_hardening.hh
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Benjamin Paccaud <benjamin.paccaud@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: Mon Jun 01 2015
*
* @brief Specialization of the material class for isotropic finite deformation linear hardening plasticity
*
* @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_voigthelper.hh"
#include "material_plastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH__
#define __AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Material plastic with a linear evolution of the yielding stress
*/
template <UInt spatial_dimension>
class MaterialLinearIsotropicHardening : public MaterialPlastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialLinearIsotropicHardening(SolidMechanicsModel & model, const ID & id = "");
MaterialLinearIsotropicHardening(SolidMechanicsModel & model,
UInt dim,
const Mesh & mesh,
FEEngine & fe_engine,
const ID & id = "");
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// constitutive law for all element of a type
virtual void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
/// compute the tangent stiffness matrix for an element type
void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost);
protected:
/// Infinitesimal deformations
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma,
Matrix<Real> & inelas_strain,
const Matrix<Real> & previous_inelas_strain,
Real & iso_hardening,
const Real & previous_iso_hardening,
const Real & sigma_th,
const Real & previous_sigma_th);
/// Finite deformations
inline void computeStressOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma,
Matrix<Real> & inelas_strain,
const Matrix<Real> & previous_inelas_strain,
Real & iso_hardening,
const Real & previous_iso_hardening,
const Real & sigma_th,
const Real & previous_sigma_th,
const Matrix<Real> & F_tensor);
inline void computeTangentModuliOnQuad(Matrix<Real> & tangent,
const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
const Matrix<Real> & sigma_tensor,
const Matrix<Real> & previous_sigma_tensor,
const Real & iso_hardening) const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material_linear_isotropic_hardening_inline_impl.cc"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_LINEAR_ISOTROPIC_HARDENING_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc b/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
index bdcb5c66d..06bf3b8e9 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
+++ b/src/model/solid_mechanics/materials/material_plastic/material_plastic.cc
@@ -1,203 +1,203 @@
/**
* @file material_plastic.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Apr 07 2014
* @date last modification: Tue Aug 18 2015
*
* @brief Implemantation of the akantu::MaterialPlastic 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "material_plastic.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialPlastic<spatial_dimension>::MaterialPlastic(SolidMechanicsModel & model, const ID & id) :
Material(model, id),
MaterialElastic<spatial_dimension>(model, id),
iso_hardening("iso_hardening", *this),
inelastic_strain("inelastic_strain", *this),
plastic_energy("plastic_energy", *this),
d_plastic_energy("d_plastic_energy", *this) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
template<UInt spatial_dimension>
MaterialPlastic<spatial_dimension>::MaterialPlastic(SolidMechanicsModel & model,
UInt dim,
const Mesh & mesh,
FEEngine & fe_engine,
const ID & id) :
Material(model, dim, mesh, fe_engine, id),
MaterialElastic<spatial_dimension>(model, dim, mesh, fe_engine, id),
iso_hardening ("iso_hardening" , *this, dim, fe_engine, this->element_filter),
inelastic_strain("inelastic_strain", *this, dim, fe_engine, this->element_filter),
plastic_energy ("plastic_energy" , *this, dim, fe_engine, this->element_filter),
d_plastic_energy("d_plastic_energy", *this, dim, fe_engine, this->element_filter) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::initialize() {
this->registerParam( "h", h, Real(0.), _pat_parsable | _pat_modifiable, "Hardening modulus");
this->registerParam("sigma_y", sigma_y, Real(0.), _pat_parsable | _pat_modifiable, "Yield stress");
this->iso_hardening.initialize(1);
this->iso_hardening.initializeHistory();
this->plastic_energy.initialize(1);
this->d_plastic_energy.initialize(1);
this->use_previous_stress = true;
this->use_previous_gradu = true;
this->use_previous_stress_thermal = true;
this->inelastic_strain.initialize(spatial_dimension * spatial_dimension);
this->inelastic_strain.initializeHistory();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
Real MaterialPlastic<spatial_dimension>::getEnergy(std::string type) {
if (type == "plastic") return getPlasticEnergy();
else return MaterialElastic<spatial_dimension>::getEnergy(type);
return 0.;
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
Real MaterialPlastic<spatial_dimension>::getPlasticEnergy() {
AKANTU_DEBUG_IN();
Real penergy = 0.;
const Mesh & mesh = this->model->getFEEngine().getMesh();
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _not_ghost);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, _not_ghost);
for(; it != end; ++it) {
penergy += this->model->getFEEngine().integrate(plastic_energy(*it, _not_ghost),
*it, _not_ghost,
this->element_filter(*it, _not_ghost));
}
AKANTU_DEBUG_OUT();
return penergy;
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::computePotentialEnergy(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
if(ghost_type != _not_ghost) return;
Array<Real>::scalar_iterator epot = this->potential_energy(el_type, ghost_type).begin();
Array<Real>::const_iterator< Matrix<Real> > inelastic_strain_it
= this->inelastic_strain(el_type, ghost_type).begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> elastic_strain(spatial_dimension, spatial_dimension);
elastic_strain.copy(grad_u);
elastic_strain -= *inelastic_strain_it;
MaterialElastic<spatial_dimension>::computePotentialEnergyOnQuad(elastic_strain, sigma, *epot);
++epot;
++inelastic_strain_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialPlastic<spatial_dimension>::updateEnergies(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
MaterialElastic<spatial_dimension>::updateEnergies(el_type, ghost_type);
Array<Real>::iterator<> pe_it =
this->plastic_energy(el_type, ghost_type).begin();
Array<Real>::iterator<> wp_it =
this->d_plastic_energy(el_type, ghost_type).begin();
Array<Real>::iterator< Matrix<Real> > inelastic_strain_it =
this->inelastic_strain(el_type, ghost_type).begin(spatial_dimension, spatial_dimension);
Array<Real>::iterator< Matrix<Real> > previous_inelastic_strain_it =
this->inelastic_strain.previous(el_type, ghost_type).begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator previous_sigma =
this->stress.previous(el_type, ghost_type).begin(spatial_dimension, spatial_dimension);
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> delta_strain_it(*inelastic_strain_it);
delta_strain_it -= *previous_inelastic_strain_it;
Matrix<Real> sigma_h(sigma);
sigma_h += *previous_sigma;
*wp_it = .5 * sigma_h.doubleDot(delta_strain_it);
*pe_it += *wp_it;
++pe_it;
++wp_it;
++inelastic_strain_it;
++previous_inelastic_strain_it;
++previous_sigma;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialPlastic);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh b/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
index 8ca083a3e..7830851f9 100644
--- a/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
+++ b/src/model/solid_mechanics/materials/material_plastic/material_plastic.hh
@@ -1,142 +1,142 @@
/**
* @file material_plastic.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 08 2015
*
* @brief Common interface for plastic 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 "material_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_PLASTIC_HH__
#define __AKANTU_MATERIAL_PLASTIC_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Parent class for the plastic constitutive laws
* parameters in the material files :
* - h : Hardening parameter (default: 0)
* - sigmay : Yield stress
*/
template<UInt dim>
class MaterialPlastic : public MaterialElastic<dim> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialPlastic(SolidMechanicsModel & model, const ID & id = "");
MaterialPlastic(SolidMechanicsModel & model,
UInt a_dim,
const Mesh & mesh,
FEEngine & fe_engine,
const ID & id = "");
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get the energy specifying the type for the time step
Real getEnergy(std::string type) override;
/// Compute the plastic energy
virtual void updateEnergies(ElementType el_type, GhostType ghost_type = _not_ghost);
/// Compute the true potential energy
void computePotentialEnergy(ElementType el_type, GhostType ghost_type) override;
protected:
/// compute the stress and inelastic strain for the quadrature point
inline void computeStressAndInelasticStrainOnQuad(const Matrix<Real> & grad_u,
const Matrix<Real> & previous_grad_u,
Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma,
Matrix<Real> & inelas_strain,
const Matrix<Real> & previous_inelas_strain,
const Matrix<Real> & delta_inelastic_strain) const;
inline void computeStressAndInelasticStrainOnQuad(const Matrix<Real> & delta_grad_u,
Matrix<Real> & sigma,
const Matrix<Real> & previous_sigma,
Matrix<Real> & inelas_strain,
const Matrix<Real> & previous_inelas_strain,
const Matrix<Real> & delta_inelastic_strain) const;
/// get the plastic energy for the time step
Real getPlasticEnergy();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Yield stresss
Real sigma_y;
/// hardening modulus
Real h;
/// isotropic hardening, r
InternalField<Real> iso_hardening;
/// inelastic strain arrays ordered by element types (inelastic deformation)
InternalField<Real> inelastic_strain;
/// Plastic energy
InternalField<Real> plastic_energy;
/// @todo : add a coefficient beta that will multiply the plastic energy increment
/// to compute the energy converted to heat
/// Plastic energy increment
InternalField<Real> d_plastic_energy;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#include "material_plastic_inline_impl.cc"
#endif /* __AKANTU_MATERIAL_PLASTIC_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_python/material_python.cc b/src/model/solid_mechanics/materials/material_python/material_python.cc
index 273890d16..4abed2e0e 100644
--- a/src/model/solid_mechanics/materials/material_python/material_python.cc
+++ b/src/model/solid_mechanics/materials/material_python/material_python.cc
@@ -1,212 +1,212 @@
/**
* @file material_python.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Nov 13 2015
* @date last modification: Fri Nov 13 2015
*
* @brief Material python implementation
*
* @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_python.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
MaterialPython::MaterialPython(SolidMechanicsModel & model, PyObject * obj,
const ID & id)
:
Material(model, id),
PythonFunctor(obj) {
AKANTU_DEBUG_IN();
this->registerInternals();
std::vector<std::string> param_names =
this->callFunctor<std::vector<std::string> >("registerParam");
for (UInt i = 0; i < param_names.size(); ++i) {
std::stringstream sstr;
sstr << "PythonParameter" << i;
this->registerParam(param_names[i], local_params[param_names[i]], 0.,
_pat_parsable, sstr.str());
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialPython::registerInternals() {
std::vector<std::string> internal_names =
this->callFunctor<std::vector<std::string> >("registerInternals");
std::vector<UInt> internal_sizes;
try {
internal_sizes =
this->callFunctor<std::vector<UInt> >("registerInternalSizes");
} catch (...) {
internal_sizes.assign(internal_names.size(), 1);
}
for (UInt i = 0; i < internal_names.size(); ++i) {
std::stringstream sstr;
sstr << "PythonInternal" << i;
this->internals[internal_names[i]] =
new InternalField<Real>(internal_names[i], *this);
AKANTU_DEBUG_INFO("alloc internal " << internal_names[i] << " "
<< this->internals[internal_names[i]]);
this->internals[internal_names[i]]->initialize(internal_sizes[i]);
}
// making an internal with the quadrature points coordinates
this->internals["quad_coordinates"] = new InternalField<Real>("quad_coordinates", *this);
auto && coords = *this->internals["quad_coordinates"];
coords.initialize(this->getSpatialDimension());
}
/* -------------------------------------------------------------------------- */
void MaterialPython::initMaterial() {
AKANTU_DEBUG_IN();
Material::initMaterial();
auto && coords = *this->internals["quad_coordinates"];
this->model->getFEEngine().computeIntegrationPointsCoordinates(coords,
&this->element_filter);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void MaterialPython::computeStress(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
std::map<std::string, Array<Real> *> internal_arrays;
for (auto & i : this->internals) {
auto & array = (*i.second)(el_type, ghost_type);
auto & name = i.first;
internal_arrays[name] = &array;
}
auto params = local_params;
params["rho"] = this->rho;
this->callFunctor<void>("computeStress", this->gradu(el_type, ghost_type),
this->stress(el_type, ghost_type), internal_arrays,
params);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename it_type>
void MaterialPython::computeStress(Matrix<Real> & grad_u, Matrix<Real> & sigma,
std::vector<it_type> & internal_iterators) {
std::vector<Real> inputs;
for (auto & i : internal_iterators) {
inputs.push_back(*i);
}
for (UInt i = 0; i < inputs.size(); ++i) {
*internal_iterators[i] = inputs[i];
}
}
/* -------------------------------------------------------------------------- */
// void MaterialPython::computeStress(ElementType el_type, GhostType ghost_type)
// {
// AKANTU_DEBUG_IN();
// typedef Array<Real>::iterator<Real> it_type;
// std::vector<it_type> its;
// for (auto & i : this->internals) {
// its.push_back((*i)(el_type, ghost_type).begin());
// }
// MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
// computeStress(grad_u, sigma, its);
// for (auto & b : its)
// ++b;
// MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */
// template <typename it_type>
// void MaterialPython::computeStress(Matrix<Real> & grad_u, Matrix<Real> &
// sigma,
// std::vector<it_type> & internal_iterators)
// {
// std::vector<Real> inputs;
// for (auto & i : internal_iterators) {
// inputs.push_back(*i);
// }
// this->callFunctor<void>("computeStress", grad_u, sigma, inputs);
// for (UInt i = 0; i < inputs.size(); ++i) {
// *internal_iterators[i] = inputs[i];
// }
// }
/* -------------------------------------------------------------------------- */
void MaterialPython::computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type) {
std::map<std::string, Array<Real> *> internal_arrays;
for (auto & i : this->internals) {
auto & array = (*i.second)(el_type, ghost_type);
auto & name = i.first;
internal_arrays[name] = &array;
}
auto params = local_params;
params["rho"] = this->rho;
this->callFunctor<void>("computeTangentModuli",
this->gradu(el_type, ghost_type), tangent_matrix,
internal_arrays, params);
}
/* -------------------------------------------------------------------------- */
Real MaterialPython::getPushWaveSpeed(__attribute__((unused))
const Element & element) const {
auto params = local_params;
params["rho"] = this->rho;
return this->callFunctor<Real>("getPushWaveSpeed", params);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_python/material_python.hh b/src/model/solid_mechanics/materials/material_python/material_python.hh
index d8de6de6b..52f8d3ff8 100644
--- a/src/model/solid_mechanics/materials/material_python/material_python.hh
+++ b/src/model/solid_mechanics/materials/material_python/material_python.hh
@@ -1,123 +1,123 @@
/**
* @file material_python.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Fri Nov 13 2015
* @date last modification: Fri Nov 13 2015
*
* @brief Python material
*
* @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/>.
*
*/
/**
* @file material_python.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_PYTHON_HH__
#define __AKANTU_MATERIAL_PYTHON_HH__
/* -------------------------------------------------------------------------- */
#include "python_functor.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class MaterialPython : public Material, PythonFunctor {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialPython(SolidMechanicsModel & model, PyObject * obj, const ID & id = "");
virtual ~MaterialPython() {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void registerInternals();
virtual void initMaterial();
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
/// constitutive law for a given quad point
template <typename it_type>
void computeStress(Matrix<Real> & grad_u,
Matrix<Real> & sigma,
std::vector<it_type> & internal_iterators);
/// compute the tangent stiffness matrix for an element type
virtual void computeTangentModuli(const ElementType & el_type,
Array<Real> & tangent_matrix,
GhostType ghost_type = _not_ghost);
/// compute the push wave speed of the material
Real getPushWaveSpeed(const Element & element) const;
protected:
/// update the dissipated energy, must be called after the stress have been computed
//virtual void updateEnergies(ElementType el_type, GhostType ghost_type){};
/// compute the tangent stiffness matrix for a given quadrature point
//inline void computeTangentModuliOnQuad(Matrix<Real> & tangent, Real & dam){};
/* ------------------------------------------------------------------------ */
/* DataAccessor inherited members */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
//virtual Real getEnergy(std::string type){};
//virtual Real getEnergy(std::string energy_id, ElementType type, UInt index){};
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
std::map<std::string, Real> local_params;
std::map<std::string, InternalField<Real> *> internals;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_PYTHON_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_thermal.cc b/src/model/solid_mechanics/materials/material_thermal.cc
index 6c54c86c7..f0491b3a0 100644
--- a/src/model/solid_mechanics/materials/material_thermal.cc
+++ b/src/model/solid_mechanics/materials/material_thermal.cc
@@ -1,123 +1,123 @@
/**
* @file material_thermal.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Aug 04 2015
*
* @brief Specialization of the material class for the thermal material
*
* @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_thermal.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialThermal<spatial_dimension>::MaterialThermal(SolidMechanicsModel & model, const ID & id) :
Material(model, id),
delta_T("delta_T", *this),
sigma_th("sigma_th", *this),
use_previous_stress_thermal(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialThermal<spatial_dimension>::MaterialThermal(SolidMechanicsModel & model,
UInt dim,
const Mesh & mesh,
FEEngine & fe_engine,
const ID & id) :
Material(model, dim, mesh, fe_engine, id),
delta_T("delta_T", *this, dim, fe_engine, this->element_filter),
sigma_th("sigma_th", *this, dim, fe_engine, this->element_filter),
use_previous_stress_thermal(false) {
AKANTU_DEBUG_IN();
this->initialize();
AKANTU_DEBUG_OUT();
}
template<UInt spatial_dimension>
void MaterialThermal<spatial_dimension>::initialize() {
this->registerParam("E" , E , Real(0. ) , _pat_parsable | _pat_modifiable, "Young's modulus" );
this->registerParam("nu" , nu , Real(0.5) , _pat_parsable | _pat_modifiable, "Poisson's ratio" );
this->registerParam("alpha" , alpha , Real(0. ) , _pat_parsable | _pat_modifiable, "Thermal expansion coefficient");
this->registerParam("delta_T", delta_T, _pat_parsable | _pat_modifiable, "Uniform temperature field");
delta_T.initialize(1);
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialThermal<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
sigma_th.initialize(1);
if(use_previous_stress_thermal) {
sigma_th.initializeHistory();
}
Material::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <UInt dim>
void MaterialThermal<dim>::computeStress(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real>::iterator<> delta_t_it = this->delta_T(el_type, ghost_type).begin();
Array<Real>::iterator<> sigma_th_it = this->sigma_th(el_type, ghost_type).begin();
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
/// TODO : implement with the matrix alpha
if (dim == 1) {
*sigma_th_it = - this->E * this->alpha * *delta_t_it;
}
else {
*sigma_th_it = - this->E/(1.-2.*this->nu) * this->alpha * *delta_t_it;
}
++delta_t_it;
++sigma_th_it;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialThermal);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_thermal.hh b/src/model/solid_mechanics/materials/material_thermal.hh
index e4e3abd75..17c5a6e7e 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__
-__BEGIN_AKANTU__
+namespace akantu {
template<UInt spatial_dimension>
class MaterialThermal : public virtual 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() {};
protected:
void initialize();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
virtual void initMaterial();
/// constitutive law for all element of a type
virtual void computeStress(ElementType el_type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* 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;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_THERMAL_HH__ */
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
index a36d25944..ed5461e1e 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.cc
@@ -1,299 +1,299 @@
/**
* @file material_standard_linear_solid_deviatoric.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Vladislav Yastrebov <vladislav.yastrebov@epfl.ch>
*
* @date creation: Wed May 04 2011
* @date last modification: Thu Oct 15 2015
*
* @brief Material Visco-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 "material_standard_linear_solid_deviatoric.hh"
#include "solid_mechanics_model.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
MaterialStandardLinearSolidDeviatoric<spatial_dimension>::MaterialStandardLinearSolidDeviatoric(SolidMechanicsModel & model, const ID & id) :
Material(model, id), MaterialElastic<spatial_dimension>(model, id),
stress_dev("stress_dev", *this),
history_integral("history_integral", *this),
dissipated_energy("dissipated_energy", *this) {
AKANTU_DEBUG_IN();
this->registerParam("Eta", eta, Real(1.), _pat_parsable | _pat_modifiable, "Viscosity");
this->registerParam("Ev", Ev, Real(1.), _pat_parsable | _pat_modifiable, "Stiffness of the viscous element");
this->registerParam("Einf", E_inf, Real(1.), _pat_readable, "Stiffness of the elastic element");
UInt stress_size = spatial_dimension * spatial_dimension;
this->stress_dev .initialize(stress_size);
this->history_integral .initialize(stress_size);
this->dissipated_energy.initialize(1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialStandardLinearSolidDeviatoric<spatial_dimension>::initMaterial() {
AKANTU_DEBUG_IN();
updateInternalParameters();
MaterialElastic<spatial_dimension>::initMaterial();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialStandardLinearSolidDeviatoric<spatial_dimension>::updateInternalParameters() {
MaterialElastic<spatial_dimension>::updateInternalParameters();
E_inf = this->E - this->Ev;
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialStandardLinearSolidDeviatoric<spatial_dimension>::setToSteadyState(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d = stress_dev_vect.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator history_int = history_int_vect.begin(spatial_dimension, spatial_dimension);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
/// Compute the first invariant of strain
Real Theta = grad_u.trace();
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j) {
dev_s(i, j) = 2 * this->mu * (.5 * (grad_u(i,j) + grad_u(j,i)) - 1./3. * Theta *(i == j));
h(i, j) = 0.;
}
/// Save the deviator of stress
++stress_d;
++history_int;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialStandardLinearSolidDeviatoric<spatial_dimension>::computeStress(ElementType el_type, GhostType ghost_type) {
AKANTU_DEBUG_IN();
Real tau = 0.;
// if(std::abs(Ev) > std::numeric_limits<Real>::epsilon())
tau = eta / Ev;
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d = stress_dev_vect.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator history_int = history_int_vect.begin(spatial_dimension, spatial_dimension);
Matrix<Real> s(spatial_dimension, spatial_dimension);
Real dt = this->model->getTimeStep();
Real exp_dt_tau = exp( -dt/tau );
Real exp_dt_tau_2 = exp( -.5*dt/tau );
Matrix<Real> epsilon_d(spatial_dimension, spatial_dimension);
Matrix<Real> epsilon_v(spatial_dimension, spatial_dimension);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
s.clear();
sigma.clear();
/// Compute the first invariant of strain
Real gamma_inf = E_inf / this->E;
Real gamma_v = Ev / this->E;
this->template gradUToEpsilon<spatial_dimension>(grad_u, epsilon_d);
Real Theta = epsilon_d.trace();
epsilon_v.eye(Theta / Real(3.));
epsilon_d -= epsilon_v;
Matrix<Real> U_rond_prim(spatial_dimension, spatial_dimension);
U_rond_prim.eye(gamma_inf * this->kpa * Theta);
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j) {
s(i, j) = 2 * this->mu * epsilon_d(i, j);
h(i, j) = exp_dt_tau * h(i, j) + exp_dt_tau_2 * (s(i, j) - dev_s(i, j));
dev_s(i, j) = s(i, j);
sigma(i, j) = U_rond_prim(i,j) + gamma_inf * s(i, j) + gamma_v * h(i, j);
}
/// Save the deviator of stress
++stress_d;
++history_int;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
this->updateDissipatedEnergy(el_type, ghost_type);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
void MaterialStandardLinearSolidDeviatoric<spatial_dimension>::updateDissipatedEnergy(ElementType el_type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
// if(ghost_type == _ghost) return 0.;
Real tau = 0.;
tau = eta / Ev;
Real * dis_energy = dissipated_energy(el_type, ghost_type).storage();
Array<Real> & stress_dev_vect = stress_dev(el_type, ghost_type);
Array<Real> & history_int_vect = history_integral(el_type, ghost_type);
Array<Real>::matrix_iterator stress_d = stress_dev_vect.begin(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator history_int = history_int_vect.begin(spatial_dimension, spatial_dimension);
Matrix<Real> q(spatial_dimension, spatial_dimension);
Matrix<Real> q_rate(spatial_dimension, spatial_dimension);
Matrix<Real> epsilon_d(spatial_dimension, spatial_dimension);
Matrix<Real> epsilon_v(spatial_dimension, spatial_dimension);
Real dt = this->model->getTimeStep();
Real gamma_v = Ev / this->E;
Real alpha = 1. / (2. * this->mu * gamma_v);
/// Loop on all quadrature points
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_BEGIN(el_type, ghost_type);
Matrix<Real> & dev_s = *stress_d;
Matrix<Real> & h = *history_int;
/// Compute the first invariant of strain
this->template gradUToEpsilon<spatial_dimension>(grad_u, epsilon_d);
Real Theta = epsilon_d.trace();
epsilon_v.eye(Theta / Real(3.));
epsilon_d -= epsilon_v;
q.copy(dev_s);
q -= h;
q *= gamma_v;
q_rate.copy(dev_s);
q_rate *= gamma_v;
q_rate -= q;
q_rate /= tau;
for (UInt i = 0; i < spatial_dimension; ++i)
for (UInt j = 0; j < spatial_dimension; ++j)
*dis_energy += (epsilon_d(i, j) - alpha * q(i, j)) * q_rate(i, j) * dt;
/// Save the deviator of stress
++stress_d;
++history_int;
++dis_energy;
MATERIAL_STRESS_QUADRATURE_POINT_LOOP_END;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
Real MaterialStandardLinearSolidDeviatoric<spatial_dimension>::getDissipatedEnergy() const {
AKANTU_DEBUG_IN();
Real de = 0.;
const Mesh & mesh = this->model->getFEEngine().getMesh();
/// integrate the dissipated energy for each type of elements
Mesh::type_iterator it = mesh.firstType(spatial_dimension, _not_ghost);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, _not_ghost);
for(; it != end; ++it) {
de += this->model->getFEEngine().integrate(dissipated_energy(*it, _not_ghost), *it,
_not_ghost, this->element_filter(*it, _not_ghost));
}
AKANTU_DEBUG_OUT();
return de;
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
Real MaterialStandardLinearSolidDeviatoric<spatial_dimension>::getDissipatedEnergy(ElementType type, UInt index) const {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = this->model->getFEEngine().getNbIntegrationPoints(type);
Array<Real>::const_vector_iterator it = this->dissipated_energy(type, _not_ghost).begin(nb_quadrature_points);
UInt gindex = (this->element_filter(type, _not_ghost))(index);
AKANTU_DEBUG_OUT();
return this->model->getFEEngine().integrate(it[index], type, gindex);
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
Real MaterialStandardLinearSolidDeviatoric<spatial_dimension>::getEnergy(std::string type) {
if(type == "dissipated") return getDissipatedEnergy();
else if(type == "dissipated_sls_deviatoric") return getDissipatedEnergy();
else return MaterialElastic<spatial_dimension>::getEnergy(type);
}
/* -------------------------------------------------------------------------- */
template<UInt spatial_dimension>
Real MaterialStandardLinearSolidDeviatoric<spatial_dimension>::getEnergy(std::string energy_id, ElementType type, UInt index) {
if(energy_id == "dissipated") return getDissipatedEnergy(type, index);
else if(energy_id == "dissipated_sls_deviatoric") return getDissipatedEnergy(type, index);
else return MaterialElastic<spatial_dimension>::getEnergy(energy_id, type, index);
}
/* -------------------------------------------------------------------------- */
INSTANTIATE_MATERIAL(MaterialStandardLinearSolidDeviatoric);
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
index 54eb0b7c1..9d4e4cc5d 100644
--- a/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
+++ b/src/model/solid_mechanics/materials/material_viscoelastic/material_standard_linear_solid_deviatoric.hh
@@ -1,137 +1,137 @@
/**
* @file material_standard_linear_solid_deviatoric.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Vladislav Yastrebov <vladislav.yastrebov@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Thu Oct 08 2015
*
* @brief Material Visco-elastic, based on Standard Solid rheological model, see
* [] J.C. Simo, T.J.R. Hughes, "Computational Inelasticity", Springer (1998),
* see Sections 10.2 and 10.3
*
* @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_elastic.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH__
#define __AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/**
* Material standard linear solid deviatoric
*
*
* @verbatim
E_\inf
------|\/\/\|------
| |
---| |---
| |
----|\/\/\|--[|----
E_v \eta
@endverbatim
*
* keyword : sls_deviatoric
*
* parameters in the material files :
* - E : Initial Young's modulus @f$ E = E_i + E_v @f$
* - eta : viscosity
* - Ev : stiffness of the viscous element
*/
template<UInt spatial_dimension>
class MaterialStandardLinearSolidDeviatoric : public MaterialElastic<spatial_dimension> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
MaterialStandardLinearSolidDeviatoric(SolidMechanicsModel & model, const ID & id = "");
virtual ~MaterialStandardLinearSolidDeviatoric() {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize the material computed parameter
void initMaterial();
/// update the internal parameters (for modifiable parameters)
virtual void updateInternalParameters();
/// set material to steady state
void setToSteadyState(ElementType el_type, GhostType ghost_type = _not_ghost);
/// constitutive law for all element of a type
void computeStress(ElementType el_type, GhostType ghost_type = _not_ghost);
protected:
/// update the dissipated energy, is called after the stress have been computed
void updateDissipatedEnergy(ElementType el_type, GhostType ghost_type);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// give the dissipated energy for the time step
Real getDissipatedEnergy() const;
Real getDissipatedEnergy(ElementType type, UInt index) const;
/// get the energy using an energy type string for the time step
virtual Real getEnergy(std::string type);
virtual Real getEnergy(std::string energy_id, ElementType type, UInt index);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// viscosity, viscous elastic modulus
Real eta, Ev, E_inf;
/// history of deviatoric stress
InternalField<Real> stress_dev;
/// Internal variable: history integral
InternalField<Real> history_integral;
/// Dissipated energy
InternalField<Real> dissipated_energy;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MATERIAL_STANDARD_LINEAR_SOLID_DEVIATORIC_HH__ */
diff --git a/src/model/solid_mechanics/materials/plane_stress_toolbox.hh b/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
index 852158597..7f2b702e1 100644
--- a/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
+++ b/src/model/solid_mechanics/materials/plane_stress_toolbox.hh
@@ -1,101 +1,101 @@
/**
* @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__
-__BEGIN_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 = "")
: Material(model, id), ParentMaterial(model, id) {}
PlaneStressToolbox(SolidMechanicsModel & model, UInt spatial_dimension,
const Mesh & mesh, FEEngine & fe_engine,
const ID & id = "")
: Material(model, spatial_dimension, mesh, fe_engine, id),
ParentMaterial(model, spatial_dimension, mesh, fe_engine, id) {}
virtual ~PlaneStressToolbox() {}
protected:
void initialize();
public:
virtual void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) {
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)
-__END_AKANTU__
+} // 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 6fc33053b..a16c33ffb 100644
--- a/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
+++ b/src/model/solid_mechanics/materials/plane_stress_toolbox_tmpl.hh
@@ -1,174 +1,174 @@
/**
* @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__
-__BEGIN_AKANTU__
+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() {}
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() {
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) {
ParentMaterial::computeStress(el_type, ghost_type);
if (this->plane_stress)
computeThirdAxisDeformation(el_type, ghost_type);
}
/* ------------------------------------------------------------------------ */
virtual void computeThirdAxisDeformation(__attribute__((unused))
ElementType el_type,
__attribute__((unused))
GhostType ghost_type) {}
/// Computation of Cauchy stress tensor in the case of finite deformation
virtual void computeAllCauchyStresses(GhostType ghost_type = _not_ghost) {
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->model->getFEEngine().getMesh().firstType(2, ghost_type);
Mesh::type_iterator last_type =
this->model->getFEEngine().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)
: Material(model, 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)
: Material(model, dim, mesh, fe_engine, 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");
}
-__END_AKANTU__
+} // 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 595725b9a..dcca9ecb8 100644
--- a/src/model/solid_mechanics/materials/random_internal_field.hh
+++ b/src/model/solid_mechanics/materials/random_internal_field.hh
@@ -1,109 +1,109 @@
/**
* @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__
-__BEGIN_AKANTU__
+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 = RandGenerator>
class RandomInternalField : public BaseField<T> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
RandomInternalField(const ID & id, Material & material);
virtual ~RandomInternalField();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
RandomInternalField operator=(__attribute__((unused)) const RandomInternalField & other) {};
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);
/// set the field to a given value
void setDefaultValue(const T & value);
/// 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;
protected:
virtual void setArrayValues(T * begin, T * end);
/* ------------------------------------------------------------------------ */
/* 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;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_RANDOM_INTERNAL_FIELD_HH__ */
diff --git a/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh b/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
index 9cc50c67d..19c15c18d 100644
--- a/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
+++ b/src/model/solid_mechanics/materials/random_internal_field_tmpl.hh
@@ -1,125 +1,125 @@
/**
* @file random_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 Random internal material parameter implementation
*
* @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 "internal_field_tmpl.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH__
#define __AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
RandomInternalField<T, BaseField, Generator>::RandomInternalField(
const ID & id, Material & material)
: BaseField<T>(id, material), random_parameter(T()) {}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
RandomInternalField<T, BaseField, Generator>::~RandomInternalField() {}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::initialize(
UInt nb_component) {
this->internalInitialize(nb_component);
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setDefaultValue(
const T & value) {
random_parameter.setBaseValue(value);
this->reset();
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setRandomDistribution(
const RandomParameter<T> & param) {
random_parameter = param;
this->reset();
}
/* ------------------------------------------------------------------------ */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::printself(
std::ostream & stream, int indent) const {
stream << "RandomInternalField [ ";
random_parameter.printself(stream);
stream << " ]";
#if !defined(AKANTU_NDEBUG)
if (AKANTU_DEBUG_TEST(dblDump)) {
stream << std::endl;
InternalField<T>::printself(stream, indent);
}
#endif
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
void RandomInternalField<T, BaseField, Generator>::setArrayValues(T * begin,
T * end) {
random_parameter.template setValues<Generator>(begin, end);
}
/* -------------------------------------------------------------------------- */
template <typename T, template <typename> class BaseField,
template <typename> class Generator>
inline RandomInternalField<T, BaseField, Generator>::operator Real() const {
return random_parameter.getBaseValue();
}
/* -------------------------------------------------------------------------- */
template <>
inline void ParameterTyped<RandomInternalField<Real> >::setAuto(
const ParserParameter & in_param) {
Parameter::setAuto(in_param);
RandomParameter<Real> r = in_param;
param.setRandomDistribution(r);
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_RANDOM_INTERNAL_FIELD_TMPL_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/base_weight_function.hh b/src/model/solid_mechanics/materials/weight_functions/base_weight_function.hh
index a47b5c7d2..26cfe18a2 100644
--- a/src/model/solid_mechanics/materials/weight_functions/base_weight_function.hh
+++ b/src/model/solid_mechanics/materials/weight_functions/base_weight_function.hh
@@ -1,183 +1,183 @@
/**
* @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 "aka_common.hh"
#include "aka_types.hh"
#include "parsable.hh"
#include <cmath>
#if defined(AKANTU_DEBUG_TOOLS)
#include "aka_debug_tools.hh"
#include <string>
#endif
#include "non_local_manager.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
#include "material_damage.hh"
#ifndef __AKANTU_BASE_WEIGHT_FUNCTION_HH__
#define __AKANTU_BASE_WEIGHT_FUNCTION_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* Normal weight function */
/* -------------------------------------------------------------------------- */
class BaseWeightFunction : public Parsable {
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().getSpatialDimension()) {
this->registerParam("update_rate" , update_rate, 1U ,
_pat_parsmod, "Update frequency");
}
virtual ~BaseWeightFunction() {}
/* -------------------------------------------------------------------------- */
/* 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 __attribute__((unused)) IntegrationPoint & q1,
const __attribute__((unused)) IntegrationPoint & q2);
/// print function
void printself(std::ostream & stream, int indent = 0) const {
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 */
/* ------------------------------------------------------------------------ */
virtual UInt getNbDataForElements(__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) SynchronizationTag tag) const {
return 0;
}
virtual inline void packElementData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) SynchronizationTag tag) const {}
virtual inline void unpackElementData(__attribute__((unused)) CommunicationBuffer & buffer,
__attribute__((unused)) const Array<Element> & elements,
__attribute__((unused)) SynchronizationTag tag) {}
/* ------------------------------------------------------------------------ */
/* 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;
}
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "base_weight_function_inline_impl.cc"
#endif
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
/* Include all other weight function types */
/* -------------------------------------------------------------------------- */
# 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 /* __AKANTU_BASE_WEIGHT_FUNCTION_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 d0e3473c2..ad13d065b 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
@@ -1,83 +1,83 @@
/**
* @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__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* Damage weight function */
/* -------------------------------------------------------------------------- */
class DamagedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
DamagedWeightFunction(NonLocalManager & manager) : BaseWeightFunction(manager, "damaged"),
damage(NULL) {
this->init();
}
/* -------------------------------------------------------------------------- */
/* Base Weight Function inherited methods */
/* -------------------------------------------------------------------------- */
/// set the pointers of internals to the right flattend version
virtual void init();
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
-__END_AKANTU__
+} // 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 f969ba02c..a42c54d75 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
@@ -1,99 +1,99 @@
/**
* @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__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/* Remove damaged weight function */
/* -------------------------------------------------------------------------- */
class RemoveDamagedWeightFunction : public BaseWeightFunction {
public:
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
RemoveDamagedWeightFunction(NonLocalManager & manager) : BaseWeightFunction(manager, "remove_damaged"),
damage(NULL){
this->registerParam("damage_limit", this->damage_limit, 1., _pat_parsable, "Damage Threshold");
this->init();
}
/* -------------------------------------------------------------------------- */
/* Base Weight Function inherited methods */
/* -------------------------------------------------------------------------- */
virtual inline void init();
inline Real operator()(Real r,
const __attribute__((unused)) IntegrationPoint & q1,
const IntegrationPoint & q2);
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
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);
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;
};
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "remove_damaged_weight_function_inline_impl.cc"
#endif
-__END_AKANTU__
+} // akantu
#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 a959aa1ab..dca670cba 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 +1,82 @@
/**
* @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__
-__BEGIN_AKANTU__
+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) {
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();
/* ------------------------------------------------------------------------ */
/* 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
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_REMOVE_DAMAGED_WITH_DAMAGE_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc
index d1fe4c526..c3e111249 100644
--- a/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc
+++ b/src/model/solid_mechanics/materials/weight_functions/stress_based_weight_function.cc
@@ -1,117 +1,117 @@
/**
* @file stress_based_weight_function.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Aug 24 2015
* @date last modification: Wed Oct 07 2015
*
* @brief implementation of the stres based weight function classes
*
* @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 "stress_based_weight_function.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
StressBasedWeightFunction::StressBasedWeightFunction(NonLocalManager & manager) :
BaseWeightFunction(manager, "stress_based")
// stress_diag("stress_diag", material), selected_stress_diag(NULL),
// stress_base("stress_base", material), selected_stress_base(NULL),
// characteristic_size("lc", material), selected_characteristic_size(NULL)
{
// this->registerParam("ft", this->ft, 0., _pat_parsable, "Tensile strength");
// stress_diag.initialize(spatial_dimension);
// stress_base.initialize(spatial_dimension * spatial_dimension);
// characteristic_size.initialize(1);
}
/* -------------------------------------------------------------------------- */
/// During intialization the characteristic sizes for all quadrature
/// points are computed
void StressBasedWeightFunction::init() {
// const Mesh & mesh = this->material.getModel().getFEEngine().getMesh();
// for (UInt g = _not_ghost; g <= _ghost; ++g) {
// GhostType gt = GhostType(g);
// Mesh::type_iterator it = mesh.firstType(spatial_dimension, gt);
// Mesh::type_iterator last_type = mesh.lastType(spatial_dimension, gt);
// for(; it != last_type; ++it) {
// UInt nb_quadrature_points =
// this->material.getModel().getFEEngine().getNbQuadraturePoints(*it, gt);
// const Array<UInt> & element_filter = this->material.getElementFilter(*it, gt);
// UInt nb_element = element_filter.getSize();
// Array<Real> ones(nb_element*nb_quadrature_points, 1, 1.);
// Array<Real> & lc = characteristic_size(*it, gt);
// this->material.getModel().getFEEngine().integrateOnQuadraturePoints(ones,
// lc,
// 1,
// *it,
// gt,
// element_filter);
// for (UInt q = 0; q < nb_quadrature_points * nb_element; q++) {
// lc(q) = pow(lc(q), 1./ Real(spatial_dimension));
// }
// }
// }
}
/* -------------------------------------------------------------------------- */
/// computation of principals stresses and principal directions
void StressBasedWeightFunction::updatePrincipalStress(__attribute__((unused)) GhostType ghost_type) {
// AKANTU_DEBUG_IN();
// const Mesh & mesh = this->material.getModel().getFEEngine().getMesh();
// 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) {
// Array<Real>::const_matrix_iterator sigma =
// this->material.getStress(*it, ghost_type).begin(spatial_dimension, spatial_dimension);
// Array<Real>::vector_iterator eigenvalues =
// stress_diag(*it, ghost_type).begin(spatial_dimension);
// Array<Real>::vector_iterator eigenvalues_end =
// stress_diag(*it, ghost_type).end(spatial_dimension);
// Array<Real>::matrix_iterator eigenvector =
// stress_base(*it, ghost_type).begin(spatial_dimension, spatial_dimension);
// #ifndef __trick__
// Array<Real>::iterator<Real> cl = characteristic_size(*it, ghost_type).begin();
// #endif
// UInt q = 0;
// for(;eigenvalues != eigenvalues_end; ++sigma, ++eigenvalues, ++eigenvector, ++cl, ++q) {
// sigma->eig(*eigenvalues, *eigenvector);
// *eigenvalues /= ft;
// #ifndef __trick__
// // specify a lower bound for principal stress based on the size of the element
// for (UInt i = 0; i < spatial_dimension; ++i) {
// (*eigenvalues)(i) = std::max(*cl / this->R, (*eigenvalues)(i));
// }
// #endif
// }
// }
// AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
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 56593df10..fd3e0744e 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__
-__BEGIN_AKANTU__
+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();
virtual inline void updateInternals();
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
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_STRESS_BASED_WEIGHT_FUNCTION_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model.cc b/src/model/solid_mechanics/solid_mechanics_model.cc
index ef421541b..76bbbe5ff 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model.cc
@@ -1,1511 +1,1511 @@
/**
* @file solid_mechanics_model.cc
*
* @author Ramin Aghababaei <ramin.aghababaei@epfl.ch>
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Clement Roux <clement.roux@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue Jul 27 2010
* @date last modification: Tue Jan 19 2016
*
* @brief Implementation of the SolidMechanicsModel 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 "solid_mechanics_model.hh"
#include "aka_math.hh"
#include "element_group.hh"
#include "element_synchronizer.hh"
#include "group_manager_inline_impl.cc"
#include "static_communicator.hh"
#include "synchronizer_registry.hh"
#include "sparse_matrix.hh"
#include "dumpable_inline_impl.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_element_partition.hh"
#include "dumper_elemental_field.hh"
#include "dumper_field.hh"
#include "dumper_homogenizing_field.hh"
#include "dumper_internal_material_field.hh"
#include "dumper_iohelper.hh"
#include "dumper_material_padders.hh"
#include "dumper_paraview.hh"
#endif
#ifdef AKANTU_DAMAGE_NON_LOCAL
#include "non_local_manager.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* A solid mechanics model need a mesh and a dimension to be created. the model
* by it self can not do a lot, the good init functions should be called in
* order to configure the model depending on what we want to do.
*
* @param mesh mesh representing the model we want to simulate
* @param dim spatial dimension of the problem, if dim = 0 (default value) the
* dimension of the problem is assumed to be the on of the mesh
* @param id an id to identify the model
*/
SolidMechanicsModel::SolidMechanicsModel(Mesh & mesh, UInt dim, const ID & id,
const MemoryID & memory_id)
: Model(mesh, dim, id, memory_id), BoundaryCondition<SolidMechanicsModel>(),
f_m2a(1.0), displacement(NULL), previous_displacement(NULL),
displacement_increment(NULL), mass(NULL), velocity(NULL),
acceleration(NULL), external_force(NULL), internal_force(NULL),
blocked_dofs(NULL), current_position(NULL), mass_matrix(NULL),
velocity_damping_matrix(NULL), stiffness_matrix(NULL),
jacobian_matrix(NULL), material_index("material index", id, memory_id),
material_local_numbering("material local numbering", id, memory_id),
material_selector(new DefaultMaterialSelector(material_index)),
is_default_material_selector(true), increment_flag(false),
are_materials_instantiated(false),
non_local_manager(NULL) { //, pbc_synch(NULL) {
AKANTU_DEBUG_IN();
this->registerFEEngineObject<MyFEEngineType>("SolidMechanicsFEEngine", mesh,
spatial_dimension);
this->mesh.registerEventHandler(*this);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("paraview_all", id, true);
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_regular);
#endif
this->initDOFManager();
this->registerDataAccessor(*this);
if (this->mesh.isDistributed()) {
auto & synchronizer = this->mesh.getElementSynchronizer();
this->registerSynchronizer(synchronizer, _gst_material_id);
this->registerSynchronizer(synchronizer, _gst_smm_mass);
this->registerSynchronizer(synchronizer, _gst_smm_stress);
this->registerSynchronizer(synchronizer, _gst_smm_boundary);
this->registerSynchronizer(synchronizer, _gst_for_dump);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModel::~SolidMechanicsModel() {
AKANTU_DEBUG_IN();
if (is_default_material_selector) {
delete material_selector;
material_selector = NULL;
}
for (auto & internal : this->registered_internals) {
delete internal.second;
}
#ifdef AKANTU_DAMAGE_NON_LOCAL
delete non_local_manager;
non_local_manager = NULL;
#endif
// delete pbc_synch;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::setTimeStep(Real time_step, const ID & solver_id) {
Model::setTimeStep(time_step, solver_id);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper().setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
/* Initialization */
/* -------------------------------------------------------------------------- */
/**
* This function groups many of the initialization in on function. For most of
* basics case the function should be enough. The functions initialize the
* model, the internal vectors, set them to 0, and depending on the parameters
* it also initialize the explicit or implicit solver.
*
* @param material_file the file containing the materials to use
* @param method the analysis method wanted. See the akantu::AnalysisMethod for
* the different possibilities
*/
void SolidMechanicsModel::initFull(const ModelOptions & options) {
Model::initFull(options);
const SolidMechanicsModelOptions & smm_options =
dynamic_cast<const SolidMechanicsModelOptions &>(options);
this->method = smm_options.analysis_method;
// initialize the vectors
this->initArrays();
if (!this->hasDefaultSolver())
this->initNewSolver(this->method);
// initialize pbc
if (this->pbc_pair.size() != 0)
this->initPBC();
#ifdef AKANTU_DAMAGE_NON_LOCAL
/// create the non-local manager object for non-local damage computations
std::stringstream nl_manager_name;
nl_manager_name << "NLManager" << this->id;
this->non_local_manager =
new NonLocalManager(*this, nl_manager_name.str(), this->memory_id);
#endif
// initialize the materials
if (this->parser->getLastParsedFile() != "") {
this->instantiateMaterials();
}
if (!smm_options.no_init_materials) {
this->initMaterials();
}
// if (increment_flag)
this->initBC(*this, *displacement, *displacement_increment, *external_force);
// else
// this->initBC(*this, *displacement, *external_force);
}
/* -------------------------------------------------------------------------- */
TimeStepSolverType SolidMechanicsModel::getDefaultSolverType() const {
return _tsst_dynamic_lumped;
}
/* -------------------------------------------------------------------------- */
ModelSolverOptions SolidMechanicsModel::getDefaultSolverOptions(
const TimeStepSolverType & type) const {
ModelSolverOptions options;
switch (type) {
case _tsst_dynamic_lumped: {
options.non_linear_solver_type = _nls_lumped;
options.integration_scheme_type["displacement"] = _ist_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
break;
}
case _tsst_static: {
options.non_linear_solver_type = _nls_newton_raphson;
options.integration_scheme_type["displacement"] = _ist_pseudo_time;
options.solution_type["displacement"] = IntegrationScheme::_not_defined;
break;
}
case _tsst_dynamic: {
if (this->method == _explicit_consistent_mass) {
options.non_linear_solver_type = _nls_newton_raphson;
options.integration_scheme_type["displacement"] = _ist_central_difference;
options.solution_type["displacement"] = IntegrationScheme::_acceleration;
} else {
options.non_linear_solver_type = _nls_newton_raphson;
options.integration_scheme_type["displacement"] = _ist_trapezoidal_rule_2;
options.solution_type["displacement"] = IntegrationScheme::_displacement;
}
break;
}
}
return options;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initNewSolver(const AnalysisMethod & method) {
ID solver_name;
TimeStepSolverType tss_type;
this->method = method;
switch (this->method) {
case _explicit_lumped_mass: {
solver_name = "explicit_lumped";
tss_type = _tsst_dynamic_lumped;
break;
}
case _explicit_consistent_mass: {
solver_name = "explicit";
tss_type = _tsst_dynamic;
break;
}
case _static: {
solver_name = "static";
tss_type = _tsst_static;
break;
}
case _implicit_dynamic: {
solver_name = "implicit";
tss_type = _tsst_dynamic;
break;
}
}
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->setDefaultSolver(solver_name);
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void SolidMechanicsModel::allocNodalField(Array<T> *& array,
__attribute__((unused))
UInt nb_component,
const ID & name) {
if (array == NULL) {
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_disp;
sstr_disp << id << ":" << name;
array = &(alloc<T>(sstr_disp.str(), nb_nodes, spatial_dimension, T()));
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initSolver(
TimeStepSolverType time_step_solver_type,
__attribute__((unused)) NonLinearSolverType non_linear_solver_type) {
DOFManager & dof_manager = this->getDOFManager();
/* ------------------------------------------------------------------------ */
// for alloc type of solvers
this->allocNodalField(this->displacement, spatial_dimension, "displacement");
this->allocNodalField(this->previous_displacement, spatial_dimension,
"previous_displacement");
this->allocNodalField(this->displacement_increment, spatial_dimension,
"displacement_increment");
this->allocNodalField(this->internal_force, spatial_dimension,
"internal_force");
this->allocNodalField(this->external_force, spatial_dimension,
"external_force");
this->allocNodalField(this->blocked_dofs, spatial_dimension, "blocked_dofs");
this->allocNodalField(this->current_position, spatial_dimension,
"current_position");
/* ------------------------------------------------------------------------ */
if (!dof_manager.hasDOFs("displacement")) {
dof_manager.registerDOFs("displacement", *this->displacement, _dst_nodal);
dof_manager.registerBlockedDOFs("displacement", *this->blocked_dofs);
dof_manager.registerDOFsIncrement("displacement",
*this->displacement_increment);
dof_manager.registerDOFsPrevious("displacement",
*this->previous_displacement);
}
/* ------------------------------------------------------------------------ */
// for dynamic
if (time_step_solver_type == _tsst_dynamic ||
time_step_solver_type == _tsst_dynamic_lumped) {
this->allocNodalField(this->velocity, spatial_dimension, "velocity");
this->allocNodalField(this->acceleration, spatial_dimension,
"acceleration");
if (!dof_manager.hasDOFsDerivatives("displacement", 1)) {
dof_manager.registerDOFsDerivative("displacement", 1, *this->velocity);
dof_manager.registerDOFsDerivative("displacement", 2,
*this->acceleration);
}
}
if (time_step_solver_type == _tsst_dynamic ||
time_step_solver_type == _tsst_static) {
if (!dof_manager.hasMatrix("K")) {
dof_manager.getNewMatrix("K", _symmetric);
}
if (!dof_manager.hasMatrix("J")) {
dof_manager.getNewMatrix("J", "K");
}
}
}
/* -------------------------------------------------------------------------- */
// void SolidMechanicsModel::initParallel(MeshPartition & partition,
// DataAccessor<Element> * data_accessor)
// {
// AKANTU_DEBUG_IN();
// if (data_accessor == NULL)
// data_accessor = this;
// synch_parallel = &createParallelSynch(partition, *data_accessor);
// synch_registry->registerSynchronizer(*synch_parallel, _gst_material_id);
// synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_mass);
// synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_stress);
// synch_registry->registerSynchronizer(*synch_parallel, _gst_smm_boundary);
// synch_registry->registerSynchronizer(*synch_parallel, _gst_for_dump);
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initFEEngineBoundary() {
FEEngine & fem_boundary = getFEEngineBoundary();
fem_boundary.initShapeFunctions(_not_ghost);
fem_boundary.initShapeFunctions(_ghost);
fem_boundary.computeNormalsOnIntegrationPoints(_not_ghost);
fem_boundary.computeNormalsOnIntegrationPoints(_ghost);
}
/* -------------------------------------------------------------------------- */
// void SolidMechanicsModel::initArraysPreviousDisplacment() {
// AKANTU_DEBUG_IN();
// this->setIncrementFlagOn();
// if (not this->previous_displacement) {
// this->allocNodalField(this->previous_displacement, spatial_dimension,
// "previous_displacement");
// this->getDOFManager().registerDOFsPrevious("displacement",
// *this->previous_displacement);
// }
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
/**
* Allocate all the needed vectors. By default their are not necessarily set to
* 0
*/
void SolidMechanicsModel::initArrays() {
AKANTU_DEBUG_IN();
for (auto ghost_type : ghost_types) {
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
this->material_index.alloc(nb_element, 1, type, ghost_type);
this->material_local_numbering.alloc(nb_element, 1, type, ghost_type);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the model,basically it pre-compute the shapes, shapes derivatives
* and jacobian
*
*/
void SolidMechanicsModel::initModel() {
/// \todo add the current position as a parameter to initShapeFunctions for
/// large deformation
getFEEngine().initShapeFunctions(_not_ghost);
getFEEngine().initShapeFunctions(_ghost);
}
/* -------------------------------------------------------------------------- */
// void SolidMechanicsModel::initPBC() {
// Model::initPBC();
// registerPBCSynchronizer();
// // as long as there are ones on the diagonal of the matrix, we can put
// // boudandary true for slaves
// std::map<UInt, UInt>::iterator it = pbc_pair.begin();
// std::map<UInt, UInt>::iterator end = pbc_pair.end();
// UInt dim = mesh.getSpatialDimension();
// while (it != end) {
// for (UInt i = 0; i < dim; ++i)
// (*blocked_dofs)((*it).first, i) = true;
// ++it;
// }
// }
// /* --------------------------------------------------------------------------
// */
// void SolidMechanicsModel::registerPBCSynchronizer() {
// pbc_synch = new PBCSynchronizer(pbc_pair);
// synch_registry->registerSynchronizer(*pbc_synch, _gst_smm_uv);
// synch_registry->registerSynchronizer(*pbc_synch, _gst_smm_mass);
// synch_registry->registerSynchronizer(*pbc_synch, _gst_smm_res);
// synch_registry->registerSynchronizer(*pbc_synch, _gst_for_dump);
// // changeLocalEquationNumberForPBC(pbc_pair, mesh.getSpatialDimension());
// }
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleResidual() {
AKANTU_DEBUG_IN();
/* ------------------------------------------------------------------------ */
// computes the internal forces
this->assembleInternalForces();
/* ------------------------------------------------------------------------ */
this->getDOFManager().assembleToResidual("displacement",
*this->external_force, 1);
this->getDOFManager().assembleToResidual("displacement",
*this->internal_force, -1);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleJacobian() {
this->assembleStiffnessMatrix();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::predictor() {}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::corrector() {}
/* -------------------------------------------------------------------------- */
/**
* This function computes the internal forces as F_{int} = \int_{\Omega} N
* \sigma d\Omega@f$
*/
void SolidMechanicsModel::assembleInternalForces() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the internal forces");
this->internal_force->clear();
// compute the stresses of local elements
AKANTU_DEBUG_INFO("Compute local stresses");
for (auto & material : materials) {
material->computeAllStresses(_not_ghost);
}
#ifdef AKANTU_DAMAGE_NON_LOCAL
/* ------------------------------------------------------------------------ */
/* Computation of the non local part */
this->non_local_manager->computeAllNonLocalStresses();
#endif
// communicate the stresses
AKANTU_DEBUG_INFO("Send data for residual assembly");
this->asynchronousSynchronize(_gst_smm_stress);
// assemble the forces due to local stresses
AKANTU_DEBUG_INFO("Assemble residual for local elements");
for (auto & material : materials) {
material->assembleInternalForces(_not_ghost);
}
// finalize communications
AKANTU_DEBUG_INFO("Wait distant stresses");
this->waitEndSynchronize(_gst_smm_stress);
// assemble the stresses due to ghost elements
AKANTU_DEBUG_INFO("Assemble residual for ghost elements");
for (auto & material : materials) {
material->assembleInternalForces(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Assemble the new stiffness matrix.");
// Check if materials need to recompute the matrix
bool need_to_reassemble = false;
for (auto & material : materials) {
need_to_reassemble |= material->hasStiffnessMatrixChanged();
}
if (need_to_reassemble) {
this->getDOFManager().getMatrix("K").clear();
// call compute stiffness matrix on each local elements
for (auto & material : materials) {
material->assembleStiffnessMatrix(_not_ghost);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateCurrentPosition() {
AKANTU_DEBUG_IN();
this->current_position->copy(this->mesh.getNodes());
auto cpos_it = this->current_position->begin(spatial_dimension);
auto cpos_end = this->current_position->end(spatial_dimension);
auto disp_it = this->displacement->begin(spatial_dimension);
for (; cpos_it != cpos_end; ++cpos_it, ++disp_it) {
*cpos_it += *disp_it;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
// void SolidMechanicsModel::initializeUpdateResidualData() {
// AKANTU_DEBUG_IN();
// UInt nb_nodes = mesh.getNbNodes();
// internal_force->resize(nb_nodes);
// /// copy the forces in residual for boundary conditions
// this->getDOFManager().assembleToResidual("displacement",
// *this->external_force);
// // start synchronization
// this->asynchronousSynchronize(_gst_smm_uv);
// this->waitEndSynchronize(_gst_smm_uv);
// this->updateCurrentPosition();
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
/* Explicit scheme */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
// void SolidMechanicsModel::computeStresses() {
// if (isExplicit()) {
// // start synchronization
// this->asynchronousSynchronize(_gst_smm_uv);
// this->waitEndSynchronize(_gst_smm_uv);
// // compute stresses on all local elements for each materials
// std::vector<Material *>::iterator mat_it;
// for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
// Material & mat = **mat_it;
// mat.computeAllStresses(_not_ghost);
// }
// #ifdef AKANTU_DAMAGE_NON_LOCAL
// /* Computation of the non local part */
// this->non_local_manager->computeAllNonLocalStresses();
// #endif
// } else {
// std::vector<Material *>::iterator mat_it;
// for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
// Material & mat = **mat_it;
// mat.computeAllStressesFromTangentModuli(_not_ghost);
// }
// }
// }
/* -------------------------------------------------------------------------- */
/* Implicit scheme */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
// /**
// * Initialize the solver and create the sparse matrices needed.
// *
// */
// void SolidMechanicsModel::initSolver(__attribute__((unused))
// SolverOptions & options) {
// UInt nb_global_nodes = mesh.getNbGlobalNodes();
// jacobian_matrix = &(this->getDOFManager().getNewMatrix("jacobian",
// _symmetric));
// // jacobian_matrix->buildProfile(mesh, *dof_synchronizer,
// spatial_dimension);
// if (!isExplicit()) {
// delete stiffness_matrix;
// std::stringstream sstr_sti;
// sstr_sti << id << ":stiffness_matrix";
// stiffness_matrix = &(this->getDOFManager().getNewMatrix("stiffness",
// _symmetric));
// }
// if (solver) solver->initialize(options);
// }
// /* --------------------------------------------------------------------------
// */
// void SolidMechanicsModel::initJacobianMatrix() {
// // @todo make it more flexible: this is an ugly patch to treat the case of
// non
// // fix profile of the K matrix
// delete jacobian_matrix;
// jacobian_matrix = &(this->getDOFManager().getNewMatrix("jacobian",
// "stiffness"));
// std::stringstream sstr_solv; sstr_solv << id << ":solver";
// delete solver;
// solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
// if(solver)
// solver->initialize(_solver_no_options);
// }
/* -------------------------------------------------------------------------- */
/**
* Initialize the implicit solver, either for dynamic or static cases,
*
* @param dynamic
*/
// void SolidMechanicsModel::initImplicit(bool dynamic) {
// AKANTU_DEBUG_IN();
// method = dynamic ? _implicit_dynamic : _static;
// if (!increment)
// setIncrementFlagOn();
// initSolver();
// // if(method == _implicit_dynamic) {
// // if(integrator) delete integrator;
// // integrator = new TrapezoidalRule2();
// // }
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
// SparseMatrix & SolidMechanicsModel::initVelocityDampingMatrix() {
// return this->getDOFManager().getNewMatrix("velocity_damping", "jacobian");
// }
// /* --------------------------------------------------------------------------
// */
// void SolidMechanicsModel::implicitPred() {
// AKANTU_DEBUG_IN();
// if(previous_displacement) previous_displacement->copy(*displacement);
// if(method == _implicit_dynamic)
// integrator->integrationSchemePred(time_step,
// *displacement,
// *velocity,
// *acceleration,
// *blocked_dofs);
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */
// void SolidMechanicsModel::implicitCorr() {
// AKANTU_DEBUG_IN();
// if(method == _implicit_dynamic) {
// integrator->integrationSchemeCorrDispl(time_step,
// *displacement,
// *velocity,
// *acceleration,
// *blocked_dofs,
// *increment);
// } else {
// UInt nb_nodes = displacement->getSize();
// UInt nb_degree_of_freedom = displacement->getNbComponent() * nb_nodes;
// Real * incr_val = increment->storage();
// Real * disp_val = displacement->storage();
// bool * boun_val = blocked_dofs->storage();
// for (UInt j = 0; j < nb_degree_of_freedom; ++j, ++disp_val, ++incr_val,
// ++boun_val){
// *incr_val *= (1. - *boun_val);
// *disp_val += *incr_val;
// }
// }
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
// void SolidMechanicsModel::updateIncrement() {
// AKANTU_DEBUG_IN();
// auto incr_it = this->displacement_increment->begin(spatial_dimension);
// auto incr_end = this->displacement_increment->end(spatial_dimension);
// auto disp_it = this->displacement->begin(spatial_dimension);
// auto prev_disp_it = this->previous_displacement->begin(spatial_dimension);
// for (; incr_it != incr_end; ++incr_it) {
// *incr_it = *disp_it;
// *incr_it -= *prev_disp_it;
// }
// AKANTU_DEBUG_OUT();
// }
// /* --------------------------------------------------------------------------
// */ void SolidMechanicsModel::updatePreviousDisplacement() {
// AKANTU_DEBUG_IN();
// AKANTU_DEBUG_ASSERT(
// previous_displacement,
// "The previous displacement has to be initialized."
// << " Are you working with Finite or Ineslactic deformations?");
// previous_displacement->copy(*displacement);
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::updateDataForNonLocalCriterion(
ElementTypeMapReal & criterion) {
const ID field_name = criterion.getName();
for (auto & material : materials) {
if (!material->isInternal<Real>(field_name, _ek_regular))
continue;
for (auto ghost_type : ghost_types) {
material->flattenInternal(field_name, criterion, ghost_type,
_ek_regular);
}
}
}
/* -------------------------------------------------------------------------- */
/* Information */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
// void SolidMechanicsModel::synchronizeBoundaries() {
// AKANTU_DEBUG_IN();
// this->synchronize(_gst_smm_boundary);
// AKANTU_DEBUG_OUT();
// }
// /* -------------------------------------------------------------------------- */
// void SolidMechanicsModel::synchronizeResidual() {
// AKANTU_DEBUG_IN();
// this->synchronize(_gst_smm_res);
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
// void SolidMechanicsModel::setIncrementFlagOn() {
// AKANTU_DEBUG_IN();
// if (!displacement_increment) {
// this->allocNodalField(displacement_increment, spatial_dimension,
// "displacement_increment");
// this->getDOFManager().registerDOFsIncrement("displacement",
// *this->displacement_increment);
// }
// increment_flag = true;
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep() {
AKANTU_DEBUG_IN();
Real min_dt = getStableTimeStep(_not_ghost);
/// reduction min over all processors
StaticCommunicator::getStaticCommunicator().allReduce(min_dt, _so_min);
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getStableTimeStep(const GhostType & ghost_type) {
AKANTU_DEBUG_IN();
Real min_dt = std::numeric_limits<Real>::max();
this->updateCurrentPosition();
Element elem;
elem.ghost_type = ghost_type;
elem.kind = _ek_regular;
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_regular)) {
elem.type = type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type);
auto mat_indexes = material_index(type, ghost_type).begin();
auto mat_loc_num = material_local_numbering(type, ghost_type).begin();
Array<Real> X(0, nb_nodes_per_element * spatial_dimension);
FEEngine::extractNodalToElementField(mesh, *current_position, X, type,
_not_ghost);
auto X_el = X.begin(spatial_dimension, nb_nodes_per_element);
for (UInt el = 0; el < nb_element;
++el, ++X_el, ++mat_indexes, ++mat_loc_num) {
elem.element = *mat_loc_num;
Real el_h = getFEEngine().getElementInradius(*X_el, type);
Real el_c = this->materials[*mat_indexes]->getCelerity(elem);
Real el_dt = el_h / el_c;
min_dt = std::min(min_dt, el_dt);
}
}
AKANTU_DEBUG_OUT();
return min_dt;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy() {
AKANTU_DEBUG_IN();
Real ekin = 0.;
UInt nb_nodes = mesh.getNbNodes();
if (this->getDOFManager().hasLumpedMatrix("M")) {
auto m_it = this->mass->begin(spatial_dimension);
auto m_end = this->mass->end(spatial_dimension);
auto v_it = this->velocity->begin(spatial_dimension);
for (UInt n = 0; m_it != m_end; ++n, ++m_it, ++v_it) {
const Vector<Real> & v = *v_it;
const Vector<Real> & m = *m_it;
Real mv2 = 0;
bool is_local_node = mesh.isLocalOrMasterNode(n);
// bool is_not_pbc_slave_node = !isPBCSlaveNode(n);
bool count_node = is_local_node; // && is_not_pbc_slave_node;
if (count_node) {
for (UInt i = 0; i < spatial_dimension; ++i) {
if (m(i) > std::numeric_limits<Real>::epsilon())
mv2 += v(i) * v(i) * m(i);
}
}
ekin += mv2;
}
} else if (this->getDOFManager().hasMatrix("M")) {
Array<Real> Mv(nb_nodes, spatial_dimension);
this->getDOFManager().getMatrix("M").matVecMul(*this->velocity, Mv);
Array<Real>::const_vector_iterator mv_it = Mv.begin(spatial_dimension);
Array<Real>::const_vector_iterator mv_end = Mv.end(spatial_dimension);
Array<Real>::const_vector_iterator v_it =
this->velocity->begin(spatial_dimension);
for (; mv_it != mv_end; ++mv_it, ++v_it) {
ekin += v_it->dot(*mv_it);
}
} else {
AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
}
StaticCommunicator::getStaticCommunicator().allReduce(ekin, _so_sum);
AKANTU_DEBUG_OUT();
return ekin * .5;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getKineticEnergy(const ElementType & type,
UInt index) {
AKANTU_DEBUG_IN();
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
Array<Real> vel_on_quad(nb_quadrature_points, spatial_dimension);
Array<UInt> filter_element(1, 1, index);
getFEEngine().interpolateOnIntegrationPoints(*velocity, vel_on_quad,
spatial_dimension, type,
_not_ghost, filter_element);
Array<Real>::vector_iterator vit = vel_on_quad.begin(spatial_dimension);
Array<Real>::vector_iterator vend = vel_on_quad.end(spatial_dimension);
Vector<Real> rho_v2(nb_quadrature_points);
Real rho = materials[material_index(type)(index)]->getRho();
for (UInt q = 0; vit != vend; ++vit, ++q) {
rho_v2(q) = rho * vit->dot(*vit);
}
AKANTU_DEBUG_OUT();
return .5 * getFEEngine().integrate(rho_v2, type, index);
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getExternalWork() {
AKANTU_DEBUG_IN();
auto incr_or_velo_it = this->velocity->begin(spatial_dimension);
if (this->method == _static) {
incr_or_velo_it = this->displacement_increment->begin(spatial_dimension);
}
auto ext_force_it = external_force->begin(spatial_dimension);
auto int_force_it = internal_force->begin(spatial_dimension);
auto boun_it = blocked_dofs->begin(spatial_dimension);
Real work = 0.;
UInt nb_nodes = this->mesh.getNbNodes();
for (UInt n = 0; n < nb_nodes;
++n, ++ext_force_it, ++int_force_it, ++boun_it, ++incr_or_velo_it) {
const auto & int_force = *int_force_it;
const auto & ext_force = *ext_force_it;
const auto & boun = *boun_it;
const auto & incr_or_velo = *incr_or_velo_it;
bool is_local_node = this->mesh.isLocalOrMasterNode(n);
// bool is_not_pbc_slave_node = !this->isPBCSlaveNode(n);
bool count_node = is_local_node; // && is_not_pbc_slave_node;
if (count_node) {
for (UInt i = 0; i < this->spatial_dimension; ++i) {
if (boun(i))
work -= int_force(i) * incr_or_velo(i);
else
work += ext_force(i) * incr_or_velo(i);
}
}
}
StaticCommunicator::getStaticCommunicator().allReduce(work, _so_sum);
if (this->method != _static)
work *= this->getTimeStep();
AKANTU_DEBUG_OUT();
return work;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id) {
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy();
} else if (energy_id == "external work") {
return getExternalWork();
}
Real energy = 0.;
for (auto & material : materials)
energy += material->getEnergy(energy_id);
/// reduction sum over all processors
StaticCommunicator::getStaticCommunicator().allReduce(energy, _so_sum);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
Real SolidMechanicsModel::getEnergy(const std::string & energy_id,
const ElementType & type, UInt index) {
AKANTU_DEBUG_IN();
if (energy_id == "kinetic") {
return getKineticEnergy(type, index);
}
UInt mat_index = this->material_index(type, _not_ghost)(index);
UInt mat_loc_num = this->material_local_numbering(type, _not_ghost)(index);
Real energy =
this->materials[mat_index]->getEnergy(energy_id, type, mat_loc_num);
AKANTU_DEBUG_OUT();
return energy;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsAdded(const Array<Element> & element_list,
const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
this->getFEEngine().initShapeFunctions(_not_ghost);
this->getFEEngine().initShapeFunctions(_ghost);
for (auto ghost_type : ghost_types) {
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
UInt nb_element = this->mesh.getNbElement(type, ghost_type);
if (!material_index.exists(type, ghost_type)) {
this->material_index.alloc(nb_element, 1, type, ghost_type);
this->material_local_numbering.alloc(nb_element, 1, type, ghost_type);
} else {
this->material_index(type, ghost_type).resize(nb_element);
this->material_local_numbering(type, ghost_type).resize(nb_element);
}
}
}
ElementTypeMapArray<UInt> filter("new_element_filter", this->getID(),
this->getMemoryID());
for (auto & elem : element_list) {
if (!filter.exists(elem.type, elem.ghost_type))
filter.alloc(0, 1, elem.type, elem.ghost_type);
filter(elem.type, elem.ghost_type).push_back(elem.element);
}
this->assignMaterialToElements(&filter);
for (auto & material : materials)
material->onElementsAdded(element_list, event);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onElementsRemoved(
__attribute__((unused)) const Array<Element> & element_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) {
this->getFEEngine().initShapeFunctions(_not_ghost);
this->getFEEngine().initShapeFunctions(_ghost);
for (auto & material : materials) {
material->onElementsRemoved(element_list, new_numbering, event);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesAdded(const Array<UInt> & nodes_list,
__attribute__((unused))
const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
if (displacement)
displacement->resize(nb_nodes, 0.);
if (mass)
mass->resize(nb_nodes, 0.);
if (velocity)
velocity->resize(nb_nodes, 0.);
if (acceleration)
acceleration->resize(nb_nodes, 0.);
if (external_force)
external_force->resize(nb_nodes, 0.);
if (internal_force)
internal_force->resize(nb_nodes, 0.);
if (blocked_dofs)
blocked_dofs->resize(nb_nodes, 0.);
if (previous_displacement)
previous_displacement->resize(nb_nodes, 0.);
if (displacement_increment)
displacement_increment->resize(nb_nodes, 0.);
for (auto & material : materials) {
material->onNodesAdded(nodes_list, event);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onNodesRemoved(__attribute__((unused))
const Array<UInt> & element_list,
const Array<UInt> & new_numbering,
__attribute__((unused))
const RemovedNodesEvent & event) {
if (displacement)
mesh.removeNodesFromArray(*displacement, new_numbering);
if (mass)
mesh.removeNodesFromArray(*mass, new_numbering);
if (velocity)
mesh.removeNodesFromArray(*velocity, new_numbering);
if (acceleration)
mesh.removeNodesFromArray(*acceleration, new_numbering);
if (internal_force)
mesh.removeNodesFromArray(*internal_force, new_numbering);
if (external_force)
mesh.removeNodesFromArray(*external_force, new_numbering);
if (blocked_dofs)
mesh.removeNodesFromArray(*blocked_dofs, new_numbering);
// if (increment_acceleration)
// mesh.removeNodesFromArray(*increment_acceleration, new_numbering);
if (displacement_increment)
mesh.removeNodesFromArray(*displacement_increment, new_numbering);
if (previous_displacement)
mesh.removeNodesFromArray(*previous_displacement, new_numbering);
// if (method != _explicit_lumped_mass) {
// this->initSolver();
// }
}
/* -------------------------------------------------------------------------- */
bool SolidMechanicsModel::isInternal(const std::string & field_name,
const ElementKind & element_kind) {
/// check if at least one material contains field_id as an internal
for (auto & material : materials) {
bool is_internal = material->isInternal<Real>(field_name, element_kind);
if (is_internal)
return true;
}
return false;
}
/* -------------------------------------------------------------------------- */
ElementTypeMap<UInt>
SolidMechanicsModel::getInternalDataPerElem(const std::string & field_name,
const ElementKind & element_kind) {
if (!(this->isInternal(field_name, element_kind)))
AKANTU_EXCEPTION("unknown internal " << field_name);
for (auto & material : materials) {
if (material->isInternal<Real>(field_name, element_kind))
return material->getInternalDataPerElem<Real>(field_name, element_kind);
}
return ElementTypeMap<UInt>();
}
/* -------------------------------------------------------------------------- */
ElementTypeMapArray<Real> &
SolidMechanicsModel::flattenInternal(const std::string & field_name,
const ElementKind & kind,
const GhostType ghost_type) {
std::pair<std::string, ElementKind> key(field_name, kind);
if (this->registered_internals.count(key) == 0) {
this->registered_internals[key] =
new ElementTypeMapArray<Real>(field_name, this->id, this->memory_id);
}
ElementTypeMapArray<Real> * internal_flat = this->registered_internals[key];
for (auto type : mesh.elementTypes(spatial_dimension, ghost_type, kind)) {
if (internal_flat->exists(type, ghost_type)) {
auto & internal = (*internal_flat)(type, ghost_type);
// internal.clear();
internal.resize(0);
}
}
for (auto & material : materials) {
if (material->isInternal<Real>(field_name, kind))
material->flattenInternal(field_name, *internal_flat, ghost_type, kind);
}
return *internal_flat;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::flattenAllRegisteredInternals(
const ElementKind & kind) {
ElementKind _kind;
ID _id;
for (auto & internal : this->registered_internals) {
std::tie(_id, _kind) = internal.first;
if (kind == _kind)
this->flattenInternal(_id, kind);
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::onDump() {
this->flattenAllRegisteredInternals(_ek_regular);
}
/* -------------------------------------------------------------------------- */
#ifdef AKANTU_USE_IOHELPER
dumper::Field * SolidMechanicsModel::createElementalField(
const std::string & field_name, const std::string & group_name,
bool padding_flag, const UInt & spatial_dimension,
const ElementKind & kind) {
dumper::Field * field = NULL;
if (field_name == "partitions")
field = mesh.createElementalField<UInt, dumper::ElementPartitionField>(
mesh.getConnectivities(), group_name, spatial_dimension, kind);
else if (field_name == "material_index")
field = mesh.createElementalField<UInt, Vector, dumper::ElementalField>(
material_index, group_name, spatial_dimension, kind);
else {
// this copy of field_name is used to compute derivated data such as
// strain and von mises stress that are based on grad_u and stress
std::string field_name_copy(field_name);
if (field_name == "strain" || field_name == "Green strain" ||
field_name == "principal strain" ||
field_name == "principal Green strain")
field_name_copy = "grad_u";
else if (field_name == "Von Mises stress")
field_name_copy = "stress";
bool is_internal = this->isInternal(field_name_copy, kind);
if (is_internal) {
ElementTypeMap<UInt> nb_data_per_elem =
this->getInternalDataPerElem(field_name_copy, kind);
ElementTypeMapArray<Real> & internal_flat =
this->flattenInternal(field_name_copy, kind);
field = mesh.createElementalField<Real, dumper::InternalMaterialField>(
internal_flat, group_name, spatial_dimension, kind, nb_data_per_elem);
if (field_name == "strain") {
dumper::ComputeStrain<false> * foo =
new dumper::ComputeStrain<false>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "Von Mises stress") {
dumper::ComputeVonMisesStress * foo =
new dumper::ComputeVonMisesStress(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "Green strain") {
dumper::ComputeStrain<true> * foo =
new dumper::ComputeStrain<true>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "principal strain") {
dumper::ComputePrincipalStrain<false> * foo =
new dumper::ComputePrincipalStrain<false>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
} else if (field_name == "principal Green strain") {
dumper::ComputePrincipalStrain<true> * foo =
new dumper::ComputePrincipalStrain<true>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
}
// treat the paddings
if (padding_flag) {
if (field_name == "stress") {
if (spatial_dimension == 2) {
dumper::StressPadder<2> * foo = new dumper::StressPadder<2>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
}
} else if (field_name == "strain" || field_name == "Green strain") {
if (spatial_dimension == 2) {
dumper::StrainPadder<2> * foo = new dumper::StrainPadder<2>(*this);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
}
}
}
// homogenize the field
dumper::ComputeFunctorInterface * foo =
dumper::HomogenizerProxy::createHomogenizer(*field);
field = dumper::FieldComputeProxy::createFieldCompute(field, *foo);
}
}
return field;
}
/* --------------------------------------------------------------------------
*/
dumper::Field *
SolidMechanicsModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
std::map<std::string, Array<Real> *> real_nodal_fields;
real_nodal_fields["displacement"] = this->displacement;
real_nodal_fields["mass"] = this->mass;
real_nodal_fields["velocity"] = this->velocity;
real_nodal_fields["acceleration"] = this->acceleration;
real_nodal_fields["external_force"] = this->external_force;
real_nodal_fields["internal_force"] = this->internal_force;
real_nodal_fields["increment"] = this->displacement_increment;
if (field_name == "force") {
AKANTU_EXCEPTION("The 'force' field has been renamed in 'external_force'");
} else if (field_name == "residual") {
AKANTU_EXCEPTION(
"The 'residual' field has been replaced by 'internal_force'");
}
dumper::Field * field = NULL;
if (padding_flag)
field = this->mesh.createNodalField(real_nodal_fields[field_name],
group_name, 3);
else
field =
this->mesh.createNodalField(real_nodal_fields[field_name], group_name);
return field;
}
/* --------------------------------------------------------------------------
*/
dumper::Field * SolidMechanicsModel::createNodalFieldBool(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs;
dumper::Field * field = NULL;
field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
#else
/* --------------------------------------------------------------------------
*/
dumper::Field * SolidMechanicsModel::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;
}
/* --------------------------------------------------------------------------
*/
dumper::Field * SolidMechanicsModel::createNodalFieldReal(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return NULL;
}
/* --------------------------------------------------------------------------
*/
dumper::Field * SolidMechanicsModel::createNodalFieldBool(
__attribute__((unused)) const std::string & field_name,
__attribute__((unused)) const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
return NULL;
}
#endif
/* --------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(const std::string & dumper_name) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name);
}
/* --------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(const std::string & dumper_name, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name, step);
}
/* -------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(const std::string & dumper_name, Real time,
UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(dumper_name, time, step);
}
/* --------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump() {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump();
}
/* --------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(step);
}
/* --------------------------------------------------------------------------
*/
void SolidMechanicsModel::dump(Real time, UInt step) {
this->onDump();
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeDumpEvent());
mesh.dump(time, step);
}
/* --------------------------------------------------------------------------
*/
void SolidMechanicsModel::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "Solid Mechanics Model [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + spatial dimension : " << spatial_dimension
<< std::endl;
stream << space << " + fem [" << std::endl;
getFEEngine().printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + nodals information [" << std::endl;
displacement->printself(stream, indent + 2);
mass->printself(stream, indent + 2);
velocity->printself(stream, indent + 2);
acceleration->printself(stream, indent + 2);
external_force->printself(stream, indent + 2);
internal_force->printself(stream, indent + 2);
blocked_dofs->printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + material information [" << std::endl;
material_index.printself(stream, indent + 2);
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << " + materials [" << std::endl;
for (auto & material : materials) {
material->printself(stream, indent + 1);
}
stream << space << AKANTU_INDENT << "]" << std::endl;
stream << space << "]" << std::endl;
}
/* --------------------------------------------------------------------------
*/
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model.hh b/src/model/solid_mechanics/solid_mechanics_model.hh
index 1f885d1a8..ff11bb0e2 100644
--- a/src/model/solid_mechanics/solid_mechanics_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model.hh
@@ -1,814 +1,814 @@
/**
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_HH__
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "aka_named_argument.hh"
#include "aka_types.hh"
#include "boundary_condition.hh"
#include "data_accessor.hh"
#include "dumpable.hh"
#include "integrator_gauss.hh"
#include "material_selector.hh"
#include "mesh.hh"
#include "model.hh"
#include "shape_lagrange.hh"
#include "solid_mechanics_model_event_handler.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class Material;
class DumperIOHelper;
class NonLocalManager;
} // namespace akantu
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
DECLARE_NAMED_ARGUMENT(analysis_method);
DECLARE_NAMED_ARGUMENT(no_init_materials);
struct SolidMechanicsModelOptions : public ModelOptions {
SolidMechanicsModelOptions(AnalysisMethod analysis_method = _explicit_lumped_mass,
bool no_init_materials = false)
: analysis_method(analysis_method), no_init_materials(no_init_materials) {
}
template <typename... pack>
SolidMechanicsModelOptions(use_named_args_t, pack &&... _pack)
: SolidMechanicsModelOptions(
OPTIONAL_NAMED_ARG(analysis_method, _explicit_lumped_mass),
OPTIONAL_NAMED_ARG(no_init_materials, false)) {}
AnalysisMethod analysis_method;
bool no_init_materials;
};
extern const SolidMechanicsModelOptions default_solid_mechanics_model_options;
class SolidMechanicsModel
: public Model,
public DataAccessor<Element>,
public DataAccessor<UInt>,
public MeshEventHandler,
public BoundaryCondition<SolidMechanicsModel>,
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;
};
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange> MyFEEngineType;
protected:
typedef EventHandlerManager<SolidMechanicsModelEventHandler> EventManager;
public:
SolidMechanicsModel(Mesh & mesh, UInt spatial_dimension = _all_dimensions,
const ID & id = "solid_mechanics_model",
const MemoryID & memory_id = 0);
virtual ~SolidMechanicsModel();
/* ------------------------------------------------------------------------ */
/* 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();
/// register the tags associated with the parallel synchronizer
// virtual void initParallel(MeshPartition * partition,
// DataAccessor<Element> * data_accessor = NULL);
/// allocate all vectors
virtual void initArrays();
/// allocate all vectors
// void initArraysPreviousDisplacment();
/// initialize all internal arrays for materials
virtual void initMaterials();
/// initialize the model
virtual void initModel();
/// init PBC synchronizer
// void initPBC();
/// initialize a new solver and sets it as the default one to use
void initNewSolver(const AnalysisMethod & method);
/// function to print the containt of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
protected:
/// allocate an array if needed
template <typename T>
void allocNodalField(Array<T> *& array, UInt nb_component, const ID & name);
/* ------------------------------------------------------------------------ */
/* PBC */
/* ------------------------------------------------------------------------ */
public:
/// change the equation number for proper assembly when using PBC
// void changeEquationNumberforPBC(std::map <UInt, UInt> & pbc_pair);
/// synchronize Residual for output
// void synchronizeResidual();
protected:
/// register PBC synchronizer
// void registerPBCSynchronizer();
/* ------------------------------------------------------------------------ */
/* 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;
/// callback for the solver, this assembles the stiffness matrix
void assembleJacobian() 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 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;
/* ------------------------------------------------------------------------ */
/* Explicit */
/* ------------------------------------------------------------------------ */
// public:
// /// initialize the stuff for the explicit scheme
// void initExplicit(AnalysisMethod analysis_method =
// _explicit_lumped_mass);
// bool isExplicit() {
// return method == _explicit_lumped_mass ||
// method == _explicit_consistent_mass;
// }
// /// initialize the array needed by updateResidual (residual,
// current_position)
// void initializeUpdateResidualData();
/// update the current position vector
void updateCurrentPosition();
// /// assemble the residual for the explicit scheme
// virtual void updateResidual(bool need_initialize = true);
// /**
// * \brief compute the acceleration from the residual
// * this function is the explicit equivalent to solveDynamic in implicit
// * In the case of lumped mass just divide the residual by the mass
// * In the case of not lumped mass call
// solveDynamic<_acceleration_corrector>
// */
// void updateAcceleration();
/// Update the increment of displacement
// void updateIncrement();
// /// Copy the actuel displacement into previous displacement
// void updatePreviousDisplacement();
// /// Save stress and strain through EventManager
// void saveStressAndStrainBeforeDamage();
// /// Update energies through EventManager
// void updateEnergiesAfterDamage();
// /// Solve the system @f[ A x = \alpha b @f] with A a lumped matrix
// void solveLumped(Array<Real> & x, const Array<Real> & A,
// const Array<Real> & b, const Array<bool> & blocked_dofs,
// Real alpha);
// /// explicit integration predictor
// void explicitPred();
// /// explicit integration corrector
// void explicitCorr();
// public:
// void solveStep();
// /*
// ------------------------------------------------------------------------
// */
// /* Implicit */
// /*
// ------------------------------------------------------------------------
// */
// public:
// /// initialize the solver and the jacobian_matrix (called by
// initImplicit)
// void initSolver();
// /// initialize the stuff for the implicit solver
// void initImplicit(bool dynamic = false);
// /// solve Ma = f to get the initial acceleration
// void initialAcceleration();
// /// assemble the stiffness matrix
// void assembleStiffnessMatrix();
// public:
// /**
// * solve a step (predictor + convergence loop + corrector) using the
// * the given convergence method (see akantu::SolveConvergenceMethod)
// * and the given convergence criteria (see
// * akantu::SolveConvergenceCriteria)
// **/
// template <SolveConvergenceMethod method, SolveConvergenceCriteria
// criteria>
// bool solveStep(Real tolerance, UInt max_iteration = 100);
// template <SolveConvergenceMethod method, SolveConvergenceCriteria
// criteria>
// bool solveStep(Real tolerance, Real & error, UInt max_iteration = 100,
// bool do_not_factorize = false);
// public:
// /**
// * solve Ku = f using the the given convergence method (see
// * akantu::SolveConvergenceMethod) and the given convergence
// * criteria (see akantu::SolveConvergenceCriteria)
// **/
// template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria
// criteria>
// bool solveStatic(Real tolerance, UInt max_iteration,
// bool do_not_factorize = false);
// /// create and return the velocity damping matrix
// SparseMatrix & initVelocityDampingMatrix();
// /// implicit time integration predictor
// void implicitPred();
// /// implicit time integration corrector
// void implicitCorr();
// /// compute the Cauchy stress on user demand.
// void computeCauchyStresses();
// // /// compute A and solve @f[ A\delta u = f_ext - f_int @f]
// // template <NewmarkBeta::IntegrationSchemeCorrectorType type>
// // void solve(Array<Real> &increment, Real block_val = 1.,
// // bool need_factorize = true, bool has_profile_changed =
// false);
// protected:
// /// finish the computation of residual to solve in increment
// void updateResidualInternal();
// /// compute the support reaction and store it in force
// void updateSupportReaction();
// private:
// /// re-initialize the J matrix (to use if the profile of K changed)
// void initJacobianMatrix();
/* ------------------------------------------------------------------------ */
void updateDataForNonLocalCriterion(ElementTypeMapReal & criterion) override;
// public:
/// Update the stresses for the computation of the residual of the Stiffness
/// matrix in the case of finite deformation
// void computeStresses();
/// synchronize the ghost element boundaries values
// void synchronizeBoundaries();
/* ------------------------------------------------------------------------ */
/* Materials (solid_mechanics_model_material.cc) */
/* ------------------------------------------------------------------------ */
public:
/// registers all the custom materials of a given type present in the input
/// file
template <typename M> void registerNewCustomMaterials(const ID & mat_type);
/// register an empty material of a given type
template <typename M>
Material & registerNewEmptyMaterial(const std::string & name);
// /// Use a UIntData in the mesh to specify the material to use per element
// void setMaterialIDsFromIntData(const std::string & data_name);
/// 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
template <typename M>
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);
/// reinitialize dof_synchronizer and solver (either in implicit or
/// explicit) when cohesive elements are inserted
void reinitializeSolver();
/* ------------------------------------------------------------------------ */
/* 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();
/* ------------------------------------------------------------------------ */
/* Data Accessor inherited members */
/* ------------------------------------------------------------------------ */
public:
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;
inline UInt getNbData(const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
inline void packData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) const override;
inline void unpackData(CommunicationBuffer & buffer, const Array<UInt> & dofs,
const SynchronizationTag & tag) override;
protected:
inline void splitElementByMaterial(const Array<Element> & elements,
Array<Element> * elements_per_mat) 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, spatial_dimension, UInt);
/// get the current value of the time step
// AKANTU_GET_MACRO(TimeStep, time_step, Real);
/// set the value of the time step
void setTimeStep(Real time_step, const ID & solver_id = "") override;
/// void setTimeStep(Real time_step);
/// return the of iterations done in the last solveStep
// AKANTU_GET_MACRO(NumberIter, n_iter, UInt);
/// 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
AKANTU_GET_MACRO(CurrentPosition, *current_position, const Array<Real> &);
/// 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 SolidMechnicsModel::incrementAcceleration vector
// AKANTU_GET_MACRO(IncrementAcceleration, *increment_acceleration,
// Array<Real> &);
/// 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);
/**
* @brief set the SolidMechanicsModel::increment_flag to on, the activate the
* update of the SolidMechanicsModel::increment vector
*/
// void setIncrementFlagOn();
// /// get the stiffness matrix
// AKANTU_GET_MACRO(StiffnessMatrix, *stiffness_matrix, SparseMatrix &);
// /// get the global jacobian matrix of the system
// AKANTU_GET_MACRO(GlobalJacobianMatrix, *jacobian_matrix, const SparseMatrix
// &);
// /// get the mass matrix
// AKANTU_GET_MACRO(MassMatrix, *mass_matrix, SparseMatrix &);
// /// get the velocity damping matrix
// AKANTU_GET_MACRO(VelocityDampingMatrix, *velocity_damping_matrix,
// SparseMatrix &);
/// get the FEEngine object to integrate or interpolate on the boundary
inline FEEngine & getFEEngineBoundary(const ID & name = "");
// /// get integrator
// AKANTU_GET_MACRO(Integrator, *integrator, const IntegrationScheme2ndOrder
// &);
// /// get synchronizer
// AKANTU_GET_MACRO(Synchronizer, *synch_parallel, const ElementSynchronizer
// &);
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);
/// Get the type of analysis method used
AKANTU_GET_MACRO(AnalysisMethod, method, AnalysisMethod);
/// get the non-local manager
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:
/// number of iterations
// UInt n_iter;
/// time step
// Real time_step;
/// conversion coefficient form force/mass to acceleration
Real f_m2a;
/// displacements array
Array<Real> * displacement;
/// displacements array at the previous time step (used in finite deformation)
Array<Real> * previous_displacement;
/// increment of displacement
Array<Real> * displacement_increment;
/// lumped mass array
Array<Real> * mass;
/// velocities array
Array<Real> * velocity;
/// accelerations array
Array<Real> * acceleration;
/// accelerations array
// Array<Real> * increment_acceleration;
/// external forces array
Array<Real> * external_force;
/// internal forces array
Array<Real> * internal_force;
/// array specifing if a degree of freedom is blocked or not
Array<bool> * blocked_dofs;
/// array of current position used during update residual
Array<Real> * current_position;
/// mass matrix
SparseMatrix * mass_matrix;
/// velocity damping matrix
SparseMatrix * velocity_damping_matrix;
/// stiffness matrix
SparseMatrix * stiffness_matrix;
/// jacobian matrix @f[A = cM + dD + K@f] with @f[c = \frac{1}{\beta \Delta
/// t^2}, d = \frac{\gamma}{\beta \Delta t} @f]
SparseMatrix * jacobian_matrix;
/// 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;
// /// integration scheme of second order used
// IntegrationScheme2ndOrder *integrator;
/// flag defining if the increment must be computed or not
bool increment_flag;
/// analysis method check the list in akantu::AnalysisMethod
AnalysisMethod method;
/// 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;
/// pointer to non-local manager: For non-local continuum damage computations
NonLocalManager * non_local_manager;
/// pointer to the pbc synchronizer
// PBCSynchronizer * pbc_synch;
};
/* -------------------------------------------------------------------------- */
namespace BC {
namespace Neumann {
typedef FromHigherDim FromStress;
typedef FromSameDim FromTraction;
} // namespace Neumann
} // namespace BC
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "material.hh"
#include "parser.hh"
-__BEGIN_AKANTU__
+namespace akantu {
#include "solid_mechanics_model_inline_impl.cc"
#include "solid_mechanics_model_tmpl.hh"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const SolidMechanicsModel & _this) {
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#include "material_selector_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 11c6bf67a..bb191635c 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
@@ -1,650 +1,650 @@
/**
* @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 "material_cohesive.hh"
#include <numeric>
#include <algorithm>
#include <functional>
-__BEGIN_AKANTU__
+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
mesh.initElementTypeMapArray(quad_coordinates,
spatial_dimension,
spatial_dimension,
_not_ghost);
model.getFEEngine().interpolateOnIntegrationPoints(model.getMesh().getNodes(),
quad_coordinates);
/// store mass density per quadrature point
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 {
if (el.kind == _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.getSize(),
"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
ElementSynchronizer & synchronizer
= const_cast<ElementSynchronizer &>(model.getSynchronizer());
Mesh & 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,
fragment_prefix,
CohesiveElementFilter(model,
damage_limit),
&synchronizer,
&mesh_facets);
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);
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.getSize() * 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);
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.getSize() * 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);
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();
ElementTypeMapArray<UInt>::type_iterator type_it = el_list.firstType(spatial_dimension,
_not_ghost,
_ek_regular);
ElementTypeMapArray<UInt>::type_iterator type_end = el_list.lastType(spatial_dimension,
_not_ghost,
_ek_regular);
/// loop over elements of the fragment
for (; type_it != type_end; ++type_it) {
ElementType type = *type_it;
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.getSize(); ++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();
ElementTypeMapArray<UInt>::type_iterator type_it = el_list.firstType(spatial_dimension,
_not_ghost,
_ek_regular);
ElementTypeMapArray<UInt>::type_iterator type_end = el_list.lastType(spatial_dimension,
_not_ghost,
_ek_regular);
/// loop over elements of the fragment
for (; type_it != type_end; ++type_it) {
ElementType type = *type_it;
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.getSize();
/// generate array to be integrated by filtering fragment's elements
Array<Real> integration_array(elements.getSize() * 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.getSize() / nb_quad_per_element);
Array<Real>::const_vector_iterator density_array_begin
= density_array.begin_reinterpret(nb_quad_per_element,
density_array.getSize() / 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.getSize(), 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
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
comm.allReduce(output.storage(), global_nb_fragment * nb_component, _so_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();
ElementTypeMapArray<UInt>::type_iterator type_it = el_list.firstType(spatial_dimension,
_not_ghost,
_ek_regular);
ElementTypeMapArray<UInt>::type_iterator type_end = el_list.lastType(spatial_dimension,
_not_ghost,
_ek_regular);
/// loop over elements of the fragment
for (; type_it != type_end; ++type_it) {
ElementType type = *type_it;
UInt nb_element = el_list(type).getSize();
nb_elements_per_fragment(*fragment_index_it) += nb_element;
}
}
/// sum values over all processors
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
comm.allReduce(nb_elements_per_fragment.storage(), global_nb_fragment, _so_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.getSize() == 0) return;
typedef typename Array<T>::vector_iterator data_iterator;
Mesh & mesh_not_const = const_cast<Mesh &>(mesh);
UInt spatial_dimension = mesh.getSpatialDimension();
UInt nb_component = data.getNbComponent();
UInt * fragment_index_it = fragment_index.storage();
data_iterator data_begin = data.begin(nb_component);
/// loop over fragments
for(const_element_group_iterator it(element_group_begin());
it != element_group_end(); ++it, ++fragment_index_it) {
const ElementGroup & fragment = *(it->second);
/// loop over cluster types
ElementGroup::type_iterator type_it = fragment.firstType(spatial_dimension);
ElementGroup::type_iterator type_end = fragment.lastType(spatial_dimension);
for(; type_it != type_end; ++type_it) {
ElementType type = *type_it;
/// init mesh data
Array<T> * mesh_data
= mesh_not_const.getDataPointer<T>(name, type, _not_ghost, nb_component);
data_iterator mesh_data_begin = mesh_data->begin(nb_component);
ElementGroup::const_element_iterator el_it = fragment.element_begin(type);
ElementGroup::const_element_iterator el_end = fragment.element_end(type);
/// fill mesh data
if (fragment_index_output) {
for (; el_it != el_end; ++el_it) {
Vector<T> md_tmp(mesh_data_begin[*el_it]);
md_tmp(0) = *fragment_index_it;
}
} else {
for (; el_it != el_end; ++el_it) {
Vector<T> md_tmp(mesh_data_begin[*el_it]);
md_tmp = data_begin[*fragment_index_it];
}
}
}
}
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
index 2c04d8eb2..4cfed97eb 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/fragment_manager.hh
@@ -1,174 +1,174 @@
/**
* @file fragment_manager.hh
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_FRAGMENT_MANAGER_HH__
#define __AKANTU_FRAGMENT_MANAGER_HH__
#include "group_manager.hh"
#include "solid_mechanics_model_cohesive.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
class FragmentManager : public GroupManager {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FragmentManager(SolidMechanicsModelCohesive & model,
bool dump_data = true,
const ID & id = "fragment_manager",
const MemoryID & memory_id = 0);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
private:
/// store mass density per integration point
void storeMassDensityPerIntegrationPoint();
/// integrate an elemental field multiplied by density on global
/// fragments
void integrateFieldOnFragments(ElementTypeMapArray<Real> & field,
Array<Real> & output);
/// compute fragments' mass
void computeMass();
/// create dump data for a single array
template <typename T>
void createDumpDataArray(Array<T> & data,
std::string name,
bool fragment_index_output = false);
public:
/// build fragment list (cohesive elements are considered broken if
/// damage >= damage_limit)
void buildFragments(Real damage_limit = 1.);
/// compute fragments' center of mass
void computeCenterOfMass();
/// compute fragments' velocity
void computeVelocity();
/// computes principal moments of inertia with respect to the center
/// of mass of each fragment
void computeInertiaMoments();
/// compute all fragments' data
void computeAllData();
/// compute number of elements per fragment
void computeNbElementsPerFragment();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get number of fragments
AKANTU_GET_MACRO(NbFragment, global_nb_fragment, UInt);
/// get fragments' mass
AKANTU_GET_MACRO(Mass, mass, const Array<Real> &);
/// get fragments' center of mass
AKANTU_GET_MACRO(CenterOfMass, mass_center, const Array<Real> &);
/// get fragments' velocity
AKANTU_GET_MACRO(Velocity, velocity, const Array<Real> &);
/// get fragments' principal moments of inertia
AKANTU_GET_MACRO(MomentsOfInertia, inertia_moments, const Array<Real> &);
/// get fragments' principal directions
AKANTU_GET_MACRO(PrincipalDirections, principal_directions, const Array<Real> &);
/// get number of elements per fragment
AKANTU_GET_MACRO(NbElementsPerFragment,
nb_elements_per_fragment, const Array<UInt> &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// local_fragment index
Array<UInt> fragment_index;
/// global number of fragments (parallel simulations)
UInt global_nb_fragment;
/// number of fragments
UInt nb_fragment;
/// cohesive solid mechanics model associated
SolidMechanicsModelCohesive & model;
/// fragments' center of mass
Array<Real> mass_center;
/// fragments' mass
Array<Real> mass;
/// fragments' velocity
Array<Real> velocity;
/// fragments' principal moments of inertia with respect to the
/// center of mass
Array<Real> inertia_moments;
/// fragments' principal directions
Array<Real> principal_directions;
/// quadrature points' coordinates
ElementTypeMapArray<Real> quad_coordinates;
/// mass density per quadrature point
ElementTypeMapArray<Real> mass_density;
/// fragment filter
Array<UInt> nb_elements_per_fragment;
/// dump data
bool dump_data;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_FRAGMENT_MANAGER_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
index 2cce818e8..2c8d683bb 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/material_selector_cohesive.cc
@@ -1,97 +1,97 @@
/**
* @file material_selector_cohesive.cc
*
* @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 selector 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_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
DefaultMaterialCohesiveSelector::DefaultMaterialCohesiveSelector(
const SolidMechanicsModelCohesive &model)
: DefaultMaterialSelector(model.getMaterialByElement()),
facet_material(model.getFacetMaterial()), mesh(model.getMesh()) {}
/* -------------------------------------------------------------------------- */
UInt DefaultMaterialCohesiveSelector::operator()(const Element &element) {
if (Mesh::getKind(element.type) == _ek_cohesive) {
try {
const Array<Element> &cohesive_el_to_facet =
mesh.getMeshFacets().getSubelementToElement(element.type,
element.ghost_type);
bool third_dimension = (mesh.getSpatialDimension() == 3);
const Element &facet =
cohesive_el_to_facet(element.element, third_dimension);
if (facet_material.exists(facet.type, facet.ghost_type)) {
return facet_material(facet.type, facet.ghost_type)(facet.element);
} else {
return MaterialSelector::operator()(element);
}
} catch (...) {
return MaterialSelector::operator()(element);
}
} else if (Mesh::getSpatialDimension(element.type) ==
mesh.getSpatialDimension() - 1) {
return facet_material(element.type, element.ghost_type)(element.element);
} else {
return DefaultMaterialSelector::operator()(element);
}
}
/* -------------------------------------------------------------------------- */
MeshDataMaterialCohesiveSelector::MeshDataMaterialCohesiveSelector(
const SolidMechanicsModelCohesive &model)
: MeshDataMaterialSelector<std::string>("physical_names", model),
mesh_facets(model.getMeshFacets()),
material_index(mesh_facets.getData<UInt>("physical_names")) {
third_dimension = (model.getSpatialDimension() == 3);
}
/* -------------------------------------------------------------------------- */
UInt MeshDataMaterialCohesiveSelector::operator()(const Element &element) {
if (element.kind == _ek_cohesive) {
const Array<Element> &cohesive_el_to_facet =
mesh_facets.getSubelementToElement(element.type, element.ghost_type);
const Element &facet =
cohesive_el_to_facet(element.element, third_dimension);
UInt material_id =
material_index(facet.type, facet.ghost_type)(facet.element);
UInt fallback_id = MaterialSelector::operator()(element);
return std::max(material_id,fallback_id);
}
else
return MeshDataMaterialSelector<std::string>::operator()(element);
}
-__END_AKANTU__
+} // 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 8d423a4b9..c2f8b7501 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
@@ -1,76 +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;
}
-__BEGIN_AKANTU__
+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);
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);
protected:
const Mesh &mesh_facets;
const ElementTypeMapArray<UInt> & material_index;
bool third_dimension;
};
#endif /* __AKANTU_MATERIAL_SELECTOR_COHESIVE_HH__ */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
index 0156d06eb..c09dc035c 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.cc
@@ -1,794 +1,794 @@
/**
* @file solid_mechanics_model_cohesive.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Wed Jan 13 2016
*
* @brief Solid mechanics model 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 <algorithm>
#include "shape_cohesive.hh"
#include "solid_mechanics_model_cohesive.hh"
#include "dumpable_inline_impl.hh"
#include "material_cohesive.hh"
#ifdef AKANTU_USE_IOHELPER
#include "dumper_paraview.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
const SolidMechanicsModelCohesiveOptions
default_solid_mechanics_model_cohesive_options(_explicit_lumped_mass, false,
false);
/* -------------------------------------------------------------------------- */
SolidMechanicsModelCohesive::SolidMechanicsModelCohesive(
Mesh & mesh, UInt dim, const ID & id, const MemoryID & memory_id)
: SolidMechanicsModel(mesh, dim, id, memory_id), tangents("tangents", id),
facet_stress("facet_stress", id), facet_material("facet_material", id) {
AKANTU_DEBUG_IN();
inserter = NULL;
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
facet_synchronizer = NULL;
facet_stress_synchronizer = NULL;
cohesive_element_synchronizer = NULL;
global_connectivity = NULL;
#endif
delete material_selector;
material_selector = new DefaultMaterialCohesiveSelector(*this);
this->registerEventHandler(*this);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("cohesive elements", id);
this->mesh.addDumpMeshToDumper("cohesive elements", mesh, spatial_dimension,
_not_ghost, _ek_cohesive);
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SolidMechanicsModelCohesive::~SolidMechanicsModelCohesive() {
AKANTU_DEBUG_IN();
delete inserter;
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
delete cohesive_element_synchronizer;
delete facet_synchronizer;
delete facet_stress_synchronizer;
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::setTimeStep(Real time_step) {
SolidMechanicsModel::setTimeStep(time_step);
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper("cohesive elements").setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initFull(const ModelOptions & options) {
AKANTU_DEBUG_IN();
const SolidMechanicsModelCohesiveOptions & smmc_options =
dynamic_cast<const SolidMechanicsModelCohesiveOptions &>(options);
this->is_extrinsic = smmc_options.extrinsic;
if (!inserter)
inserter = new CohesiveElementInserter(mesh, is_extrinsic, synch_parallel,
id + ":cohesive_element_inserter");
SolidMechanicsModel::initFull(options);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initMaterials() {
AKANTU_DEBUG_IN();
// make sure the material are instantiated
if (!are_materials_instantiated)
instantiateMaterials();
/// find the first cohesive material
UInt cohesive_index = 0;
while (
(dynamic_cast<MaterialCohesive *>(materials[cohesive_index]) == NULL) &&
cohesive_index <= materials.size())
++cohesive_index;
AKANTU_DEBUG_ASSERT(cohesive_index != materials.size(),
"No cohesive materials in the material input file");
material_selector->setFallback(cohesive_index);
// set the facet information in the material in case of dynamic insertion
if (is_extrinsic) {
const Mesh & mesh_facets = inserter->getMeshFacets();
mesh_facets.initElementTypeMapArray(facet_material, 1,
spatial_dimension - 1);
Element element;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
element.ghost_type = *gt;
Mesh::type_iterator first =
mesh_facets.firstType(spatial_dimension - 1, *gt);
Mesh::type_iterator last =
mesh_facets.lastType(spatial_dimension - 1, *gt);
for (; first != last; ++first) {
element.type = *first;
Array<UInt> & f_material = facet_material(*first, *gt);
UInt nb_element = mesh_facets.getNbElement(*first, *gt);
f_material.resize(nb_element);
f_material.set(cohesive_index);
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
UInt mat_index = (*material_selector)(element);
f_material(el) = mat_index;
MaterialCohesive & mat =
dynamic_cast<MaterialCohesive &>(*materials[mat_index]);
mat.addFacet(element);
}
}
}
SolidMechanicsModel::initMaterials();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (facet_synchronizer != NULL)
inserter->initParallel(facet_synchronizer, cohesive_element_synchronizer);
// inserter->initParallel(facet_synchronizer, synch_parallel);
#endif
initAutomaticInsertion();
} else {
// TODO think of something a bit mor consistant than just coding the first
// thing that comes in Fabian's head....
typedef ParserSection::const_section_iterator const_section_iterator;
std::pair<const_section_iterator, const_section_iterator> sub_sections =
this->parser->getSubSections(_st_mesh);
if (sub_sections.first != sub_sections.second) {
std::string cohesive_surfaces =
sub_sections.first->getParameter("cohesive_surfaces");
this->initIntrinsicCohesiveMaterials(cohesive_surfaces);
} else {
this->initIntrinsicCohesiveMaterials(cohesive_index);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initIntrinsicCohesiveMaterials(
std::string cohesive_surfaces) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (facet_synchronizer != NULL)
inserter->initParallel(facet_synchronizer, cohesive_element_synchronizer);
// inserter->initParallel(facet_synchronizer, synch_parallel);
#endif
std::istringstream split(cohesive_surfaces);
std::string physname;
while (std::getline(split, physname, ',')) {
AKANTU_DEBUG_INFO(
"Pre-inserting cohesive elements along facets from physical surface: "
<< physname);
insertElementsFromMeshData(physname);
}
synchronizeInsertionData();
SolidMechanicsModel::initMaterials();
if (is_default_material_selector)
delete material_selector;
material_selector = new MeshDataMaterialCohesiveSelector(*this);
UInt nb_new_elements = inserter->insertElements();
if (nb_new_elements > 0) {
this->reinitializeSolver();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::synchronizeInsertionData() {
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (facet_synchronizer != NULL) {
facet_synchronizer->asynchronousSynchronize(*inserter, _gst_ce_groups);
facet_synchronizer->waitEndSynchronize(*inserter, _gst_ce_groups);
}
#endif
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initIntrinsicCohesiveMaterials(
UInt cohesive_index) {
AKANTU_DEBUG_IN();
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_cohesive);
Mesh::type_iterator last =
mesh.lastType(spatial_dimension, *gt, _ek_cohesive);
for (; first != last; ++first) {
Array<UInt> & mat_indexes = this->material_index(*first, *gt);
Array<UInt> & mat_loc_num = this->material_local_numbering(*first, *gt);
mat_indexes.set(cohesive_index);
mat_loc_num.clear();
}
}
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (facet_synchronizer != NULL)
inserter->initParallel(facet_synchronizer, cohesive_element_synchronizer);
// inserter->initParallel(facet_synchronizer, synch_parallel);
#endif
SolidMechanicsModel::initMaterials();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Initialize the model,basically it pre-compute the shapes, shapes derivatives
* and jacobian
*
*/
void SolidMechanicsModelCohesive::initModel() {
AKANTU_DEBUG_IN();
SolidMechanicsModel::initModel();
registerFEEngineObject<MyFEEngineCohesiveType>("CohesiveFEEngine", mesh,
spatial_dimension);
/// add cohesive type connectivity
ElementType type = _not_defined;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType type_ghost = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, type_ghost);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, type_ghost);
for (; it != last; ++it) {
const Array<UInt> & connectivity = mesh.getConnectivity(*it, type_ghost);
if (connectivity.getSize() != 0) {
type = *it;
ElementType type_facet = Mesh::getFacetType(type);
ElementType type_cohesive =
FEEngine::getCohesiveElementType(type_facet);
mesh.addConnectivityType(type_cohesive, type_ghost);
}
}
}
AKANTU_DEBUG_ASSERT(type != _not_defined, "No elements in the mesh");
getFEEngine("CohesiveFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("CohesiveFEEngine").initShapeFunctions(_ghost);
registerFEEngineObject<MyFEEngineFacetType>("FacetsFEEngine", mesh.getMeshFacets(),
spatial_dimension - 1);
if (is_extrinsic) {
getFEEngine("FacetsFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("FacetsFEEngine").initShapeFunctions(_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::limitInsertion(BC::Axis axis,
Real first_limit,
Real second_limit) {
AKANTU_DEBUG_IN();
inserter->setLimit(axis, first_limit, second_limit);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::insertIntrinsicElements() {
AKANTU_DEBUG_IN();
UInt nb_new_elements = inserter->insertIntrinsicElements();
if (nb_new_elements > 0) {
this->reinitializeSolver();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::insertElementsFromMeshData(
std::string physname) {
AKANTU_DEBUG_IN();
UInt material_index = SolidMechanicsModel::getMaterialIndex(physname);
inserter->insertIntrinsicElements(physname, material_index);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initAutomaticInsertion() {
AKANTU_DEBUG_IN();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (facet_stress_synchronizer != NULL) {
DataAccessor * data_accessor = this;
const ElementTypeMapArray<UInt> & rank_to_element =
synch_parallel->getPrankToElement();
facet_stress_synchronizer->updateFacetStressSynchronizer(
*inserter, rank_to_element, *data_accessor);
}
#endif
inserter->getMeshFacets().initElementTypeMapArray(
facet_stress, 2 * spatial_dimension * spatial_dimension,
spatial_dimension - 1);
resizeFacetStress();
/// compute normals on facets
computeNormals();
initStressInterpolation();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateAutomaticInsertion() {
AKANTU_DEBUG_IN();
inserter->limitCheckFacets();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (facet_stress_synchronizer != NULL) {
DataAccessor * data_accessor = this;
const ElementTypeMapArray<UInt> & rank_to_element =
synch_parallel->getPrankToElement();
facet_stress_synchronizer->updateFacetStressSynchronizer(
*inserter, rank_to_element, *data_accessor);
}
#endif
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::initStressInterpolation() {
Mesh & mesh_facets = inserter->getMeshFacets();
/// compute quadrature points coordinates on facets
Array<Real> & position = mesh.getNodes();
ElementTypeMapArray<Real> quad_facets("quad_facets", id);
mesh_facets.initElementTypeMapArray(quad_facets, spatial_dimension,
spatial_dimension - 1);
getFEEngine("FacetsFEEngine")
.interpolateOnIntegrationPoints(position, quad_facets);
/// compute elements quadrature point positions and build
/// element-facet quadrature points data structure
ElementTypeMapArray<Real> elements_quad_facets("elements_quad_facets", id);
mesh.initElementTypeMapArray(elements_quad_facets, spatial_dimension,
spatial_dimension);
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
GhostType elem_gt = *gt;
Mesh::type_iterator it = mesh.firstType(spatial_dimension, elem_gt);
Mesh::type_iterator last = mesh.lastType(spatial_dimension, elem_gt);
for (; it != last; ++it) {
ElementType type = *it;
UInt nb_element = mesh.getNbElement(type, elem_gt);
if (nb_element == 0)
continue;
/// compute elements' quadrature points and list of facet
/// quadrature points positions by element
Array<Element> & facet_to_element =
mesh_facets.getSubelementToElement(type, elem_gt);
UInt nb_facet_per_elem = facet_to_element.getNbComponent();
Array<Real> & el_q_facet = elements_quad_facets(type, elem_gt);
ElementType facet_type = Mesh::getFacetType(type);
UInt nb_quad_per_facet =
getFEEngine("FacetsFEEngine").getNbIntegrationPoints(facet_type);
el_q_facet.resize(nb_element * nb_facet_per_elem * nb_quad_per_facet);
for (UInt el = 0; el < nb_element; ++el) {
for (UInt f = 0; f < nb_facet_per_elem; ++f) {
Element global_facet_elem = facet_to_element(el, f);
UInt global_facet = global_facet_elem.element;
GhostType facet_gt = global_facet_elem.ghost_type;
const Array<Real> & quad_f = quad_facets(facet_type, facet_gt);
for (UInt q = 0; q < nb_quad_per_facet; ++q) {
for (UInt s = 0; s < spatial_dimension; ++s) {
el_q_facet(el * nb_facet_per_elem * nb_quad_per_facet +
f * nb_quad_per_facet + q,
s) = quad_f(global_facet * nb_quad_per_facet + q, s);
}
}
}
}
}
}
/// loop over non cohesive materials
for (UInt m = 0; m < materials.size(); ++m) {
try {
MaterialCohesive & mat __attribute__((unused)) =
dynamic_cast<MaterialCohesive &>(*materials[m]);
} catch (std::bad_cast &) {
/// initialize the interpolation function
materials[m]->initElementalFieldInterpolation(elements_quad_facets);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::updateResidual(bool need_initialize) {
AKANTU_DEBUG_IN();
if (need_initialize)
initializeUpdateResidualData();
// f -= fint
std::vector<Material *>::iterator mat_it;
for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
try {
MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(**mat_it);
mat.computeTraction(_not_ghost);
} catch (std::bad_cast & bce) {
}
}
SolidMechanicsModel::updateResidual(false);
if (isExplicit()) {
for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
try {
MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(**mat_it);
mat.computeEnergies();
} catch (std::bad_cast & bce) {
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::computeNormals() {
AKANTU_DEBUG_IN();
Mesh & mesh_facets = this->inserter->getMeshFacets();
this->getFEEngine("FacetsFEEngine")
.computeNormalsOnIntegrationPoints(_not_ghost);
/**
* @todo store tangents while computing normals instead of
* recomputing them as follows:
*/
/* ------------------------------------------------------------------------ */
UInt tangent_components = spatial_dimension * (spatial_dimension - 1);
mesh_facets.initElementTypeMapArray(tangents, tangent_components,
spatial_dimension - 1);
Mesh::type_iterator it = mesh_facets.firstType(spatial_dimension - 1);
Mesh::type_iterator last = mesh_facets.lastType(spatial_dimension - 1);
for (; it != last; ++it) {
ElementType facet_type = *it;
const Array<Real> & normals =
this->getFEEngine("FacetsFEEngine")
.getNormalsOnIntegrationPoints(facet_type);
Array<Real> & tangents = this->tangents(facet_type);
Math::compute_tangents(normals, tangents);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::interpolateStress() {
ElementTypeMapArray<Real> by_elem_result("temporary_stress_by_facets", id);
for (UInt m = 0; m < materials.size(); ++m) {
try {
MaterialCohesive & mat __attribute__((unused)) =
dynamic_cast<MaterialCohesive &>(*materials[m]);
} catch (std::bad_cast &) {
/// interpolate stress on facet quadrature points positions
materials[m]->interpolateStressOnFacets(facet_stress, by_elem_result);
}
}
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(
debug::_dm_model_cohesive, "Interpolated stresses before", facet_stress);
#endif
synch_registry->synchronize(_gst_smmc_facets_stress);
#if defined(AKANTU_DEBUG_TOOLS)
debug::element_manager.printData(debug::_dm_model_cohesive,
"Interpolated stresses", facet_stress);
#endif
}
/* -------------------------------------------------------------------------- */
UInt SolidMechanicsModelCohesive::checkCohesiveStress() {
interpolateStress();
for (UInt m = 0; m < materials.size(); ++m) {
try {
MaterialCohesive & mat_cohesive =
dynamic_cast<MaterialCohesive &>(*materials[m]);
/// check which not ghost cohesive elements are to be created
mat_cohesive.checkInsertion();
} catch (std::bad_cast &) {
}
}
/* if(static and extrinsic) {
check max mean stresses
and change inserter.getInsertionFacets(type_facet);
}
*/
/// communicate data among processors
synch_registry->synchronize(_gst_smmc_facets);
/// insert cohesive elements
UInt nb_new_elements = inserter->insertElements();
if (nb_new_elements > 0) {
this->reinitializeSolver();
}
return nb_new_elements;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onElementsAdded(
const Array<Element> & element_list, const NewElementsEvent & event) {
AKANTU_DEBUG_IN();
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
updateCohesiveSynchronizers();
#endif
SolidMechanicsModel::onElementsAdded(element_list, event);
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
if (cohesive_element_synchronizer != NULL)
cohesive_element_synchronizer->computeAllBufferSizes(*this);
#endif
/// update shape functions
getFEEngine("CohesiveFEEngine").initShapeFunctions(_not_ghost);
getFEEngine("CohesiveFEEngine").initShapeFunctions(_ghost);
if (is_extrinsic)
resizeFacetStress();
/// if (method != _explicit_lumped_mass) {
/// this->initSolver();
/// }
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onNodesAdded(
const Array<UInt> & doubled_nodes,
__attribute__((unused)) const NewNodesEvent & event) {
AKANTU_DEBUG_IN();
UInt nb_new_nodes = doubled_nodes.getSize();
Array<UInt> nodes_list(nb_new_nodes);
for (UInt n = 0; n < nb_new_nodes; ++n)
nodes_list(n) = doubled_nodes(n, 1);
SolidMechanicsModel::onNodesAdded(nodes_list, event);
for (UInt n = 0; n < nb_new_nodes; ++n) {
UInt old_node = doubled_nodes(n, 0);
UInt new_node = doubled_nodes(n, 1);
for (UInt dim = 0; dim < spatial_dimension; ++dim) {
(*displacement)(new_node, dim) = (*displacement)(old_node, dim);
(*velocity)(new_node, dim) = (*velocity)(old_node, dim);
(*acceleration)(new_node, dim) = (*acceleration)(old_node, dim);
(*blocked_dofs)(new_node, dim) = (*blocked_dofs)(old_node, dim);
if (current_position)
(*current_position)(new_node, dim) = (*current_position)(old_node, dim);
if (increment_acceleration)
(*increment_acceleration)(new_node, dim) =
(*increment_acceleration)(old_node, dim);
if (increment)
(*increment)(new_node, dim) = (*increment)(old_node, dim);
if (previous_displacement)
(*previous_displacement)(new_node, dim) =
(*previous_displacement)(old_node, dim);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onEndSolveStep(
__attribute__((unused)) const AnalysisMethod & method) {
AKANTU_DEBUG_IN();
/*
* This is required because the Cauchy stress is the stress measure that
* is used to check the insertion of cohesive elements
*/
std::vector<Material *>::iterator mat_it;
for (mat_it = materials.begin(); mat_it != materials.end(); ++mat_it) {
Material & mat = **mat_it;
if (mat.isFiniteDeformation())
mat.computeAllCauchyStresses(_not_ghost);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::printself(std::ostream & stream,
int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "SolidMechanicsModelCohesive [" << std::endl;
SolidMechanicsModel::printself(stream, indent + 1);
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::resizeFacetStress() {
AKANTU_DEBUG_IN();
Mesh & mesh_facets = inserter->getMeshFacets();
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;
UInt nb_facet = mesh_facets.getNbElement(type, ghost_type);
UInt nb_quadrature_points = getFEEngine("FacetsFEEngine")
.getNbIntegrationPoints(type, ghost_type);
UInt new_size = nb_facet * nb_quadrature_points;
facet_stress(type, ghost_type).resize(new_size);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::addDumpGroupFieldToDumper(
const std::string & dumper_name, const std::string & field_id,
const std::string & group_name, const ElementKind & element_kind,
bool padding_flag) {
AKANTU_DEBUG_IN();
UInt spatial_dimension = this->spatial_dimension;
ElementKind _element_kind = element_kind;
if (dumper_name == "cohesive elements") {
_element_kind = _ek_cohesive;
} else if (dumper_name == "facets") {
spatial_dimension = this->spatial_dimension - 1;
}
SolidMechanicsModel::addDumpGroupFieldToDumper(dumper_name, field_id,
group_name, spatial_dimension,
_element_kind, padding_flag);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModelCohesive::onDump() {
this->flattenAllRegisteredInternals(_ek_cohesive);
SolidMechanicsModel::onDump();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
index 5026ad0db..75ef8a48c 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive.hh
@@ -1,287 +1,287 @@
/**
* @file solid_mechanics_model_cohesive.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Tue May 08 2012
* @date last modification: Mon Dec 14 2015
*
* @brief Solid mechanics model 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__
#include "cohesive_element_inserter.hh"
#include "material_selector_cohesive.hh"
#include "solid_mechanics_model.hh"
#include "solid_mechanics_model_event_handler.hh"
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
#include "facet_stress_synchronizer.hh"
#include "facet_synchronizer.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
struct FacetsCohesiveIntegrationOrderFunctor {
template <ElementType type, ElementType cohesive_type =
CohesiveFacetProperty<type>::cohesive_type>
struct _helper {
static constexpr int get() {
return ElementClassProperty<cohesive_type>::polynomial_degree;
}
};
template <ElementType type> struct _helper<type, _not_defined> {
static constexpr int get() {
return ElementClassProperty<type>::polynomial_degree;
}
};
template <ElementType type> static inline constexpr int getOrder() {
return _helper<type>::get();
}
};
/* -------------------------------------------------------------------------- */
struct SolidMechanicsModelCohesiveOptions : public SolidMechanicsModelOptions {
SolidMechanicsModelCohesiveOptions(
AnalysisMethod analysis_method = _explicit_lumped_mass,
bool extrinsic = false, bool no_init_materials = false)
: SolidMechanicsModelOptions(analysis_method, no_init_materials),
extrinsic(extrinsic) {}
bool extrinsic;
};
extern const SolidMechanicsModelCohesiveOptions
default_solid_mechanics_model_cohesive_options;
/* -------------------------------------------------------------------------- */
/* Solid Mechanics Model for Cohesive elements */
/* -------------------------------------------------------------------------- */
class SolidMechanicsModelCohesive : public SolidMechanicsModel,
public SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
class NewCohesiveNodesEvent : public NewNodesEvent {
public:
AKANTU_GET_MACRO_NOT_CONST(OldNodesList, old_nodes, Array<UInt> &);
AKANTU_GET_MACRO(OldNodesList, old_nodes, const Array<UInt> &);
protected:
Array<UInt> old_nodes;
};
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_cohesive>
MyFEEngineCohesiveType;
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular,
FacetsCohesiveIntegrationOrderFunctor>
MyFEEngineFacetType;
SolidMechanicsModelCohesive(Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "solid_mechanics_model_cohesive",
const MemoryID & memory_id = 0);
virtual ~SolidMechanicsModelCohesive();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set the value of the time step
void setTimeStep(Real time_step);
/// assemble the residual for the explicit scheme
virtual void updateResidual(bool need_initialize = true);
/// function to print the contain of the class
virtual void printself(std::ostream & stream, int indent = 0) const;
/// function to perform a stress check on each facet and insert
/// cohesive elements if needed (returns the number of new cohesive
/// elements)
UInt checkCohesiveStress();
/// interpolate stress on facets
void interpolateStress();
/// initialize the cohesive model
void initFull(const ModelOptions & options =
default_solid_mechanics_model_cohesive_options);
/// initialize the model
void initModel();
/// initialize cohesive material
void initMaterials();
/// init facet filters for cohesive materials
void initFacetFilter();
/// limit the cohesive element insertion to a given area
void limitInsertion(BC::Axis axis, Real first_limit, Real second_limit);
/// update automatic insertion after a change in the element inserter
void updateAutomaticInsertion();
/// insert intrinsic cohesive elements
void insertIntrinsicElements();
// synchronize facets physical data before insertion along physical surfaces
void synchronizeInsertionData();
// template <SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
// bool solveStepCohesive(Real tolerance, Real & error, UInt max_iteration = 100,
// bool load_reduction = false,
// Real tol_increase_factor = 1.0,
// bool do_not_factorize = false);
/// initialize stress interpolation
void initStressInterpolation();
private:
/// initialize cohesive material with intrinsic insertion (by default)
void initIntrinsicCohesiveMaterials(UInt cohesive_index);
/// initialize cohesive material with intrinsic insertion (if physical
/// surfaces are precised)
void initIntrinsicCohesiveMaterials(std::string cohesive_surfaces);
/// insert cohesive elements along a given physical surface of the mesh
void insertElementsFromMeshData(std::string physical_name);
/// initialize completely the model for extrinsic elements
void initAutomaticInsertion();
/// compute facets' normals
void computeNormals();
/// resize facet stress
void resizeFacetStress();
/// init facets_check array
void initFacetsCheck();
/* ------------------------------------------------------------------------ */
/* Mesh Event Handler inherited members */
/* ------------------------------------------------------------------------ */
protected:
virtual void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event);
virtual void onElementsAdded(const Array<Element> & nodes_list,
const NewElementsEvent & event);
/* ------------------------------------------------------------------------ */
/* SolidMechanicsModelEventHandler inherited members */
/* ------------------------------------------------------------------------ */
public:
virtual void onEndSolveStep(const AnalysisMethod & method);
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
virtual void onDump();
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);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// get facet mesh
AKANTU_GET_MACRO(MeshFacets, mesh.getMeshFacets(), const Mesh &);
/// get stress on facets vector
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(StressOnFacets, facet_stress, Real);
/// get facet material
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(FacetMaterial, facet_material, UInt);
/// get facet material
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(FacetMaterial, facet_material, UInt);
/// get facet material
AKANTU_GET_MACRO(FacetMaterial, facet_material,
const ElementTypeMapArray<UInt> &);
/// @todo THIS HAS TO BE CHANGED
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Tangents, tangents, Real);
/// get element inserter
AKANTU_GET_MACRO_NOT_CONST(ElementInserter, *inserter,
CohesiveElementInserter &);
/// get is_extrinsic boolean
AKANTU_GET_MACRO(IsExtrinsic, is_extrinsic, bool);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// @todo store tangents when normals are computed:
ElementTypeMapArray<Real> tangents;
/// stress on facets on the two sides by quadrature point
ElementTypeMapArray<Real> facet_stress;
/// material to use if a cohesive element is created on a facet
ElementTypeMapArray<UInt> facet_material;
bool is_extrinsic;
/// cohesive element inserter
CohesiveElementInserter * inserter;
#if defined(AKANTU_PARALLEL_COHESIVE_ELEMENT)
#include "solid_mechanics_model_cohesive_parallel.hh"
#endif
};
/* -------------------------------------------------------------------------- */
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const SolidMechanicsModelCohesive & _this) {
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#include "solid_mechanics_model_cohesive_inline_impl.cc"
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.cc b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.cc
index c9fbee16c..d196dd633 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_cohesive/solid_mechanics_model_cohesive_inline_impl.cc
@@ -1,310 +1,310 @@
/**
* @file solid_mechanics_model_cohesive_inline_impl.cc
*
* @author Mauro Corrado <mauro.corrado@epfl.ch>
* @author Marco Vocialta <marco.vocialta@epfl.ch>
*
* @date creation: Fri Jan 18 2013
* @date last modification: Thu Jan 14 2016
*
* @brief Implementation of inline functions for the Cohesive element model
*
* @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 <algorithm>
#include "material_cohesive.hh"
#ifndef __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_CC__
#define __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_CC__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<SolveConvergenceMethod cmethod, SolveConvergenceCriteria criteria>
bool SolidMechanicsModelCohesive::solveStepCohesive(Real tolerance,
Real & error,
UInt max_iteration,
bool load_reduction,
Real tol_increase_factor,
bool do_not_factorize) {
EventManager::sendEvent(SolidMechanicsModelEvent::BeforeSolveStepEvent(method));
this->implicitPred();
bool insertion_new_element = true;
bool converged = false;
Array<Real> * displacement_tmp = NULL;
Array<Real> * velocity_tmp = NULL;
Array<Real> * acceleration_tmp = NULL;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
Int prank = comm.whoAmI();
/// Loop for the insertion of new cohesive elements
while (insertion_new_element) {
if (is_extrinsic) {
/**
* If in extrinsic the solution of the previous incremental step
* is saved in temporary arrays created for displacements,
* velocities and accelerations. Such arrays are used to find
* the solution with the Newton-Raphson scheme (this is done by
* pointing the pointer "displacement" to displacement_tmp). In
* this way, inside the array "displacement" is kept the
* solution of the previous incremental step, and in
* "displacement_tmp" is saved the current solution.
*/
Array<Real> * tmp_swap;
if(!displacement_tmp) {
displacement_tmp = new Array<Real>(*(this->displacement));
} else {
displacement_tmp->resize(this->displacement->getSize());
displacement_tmp->copy(*(this->displacement));
}
tmp_swap = displacement_tmp;
displacement_tmp = this->displacement;
this->displacement = tmp_swap;
if(!velocity_tmp) {
velocity_tmp = new Array<Real>(*(this->velocity));
} else {
velocity_tmp->resize(this->velocity->getSize());
velocity_tmp->copy(*(this->velocity));
}
tmp_swap = velocity_tmp;
velocity_tmp = this->velocity;
this->velocity = tmp_swap;
if(!acceleration_tmp) {
acceleration_tmp = new Array<Real>(*(this->acceleration));
} else {
acceleration_tmp->resize(this->acceleration->getSize());
acceleration_tmp->copy(*(this->acceleration));
}
tmp_swap = acceleration_tmp;
acceleration_tmp = this->acceleration;
this->acceleration = tmp_swap;
}
this->updateResidual();
AKANTU_DEBUG_ASSERT(stiffness_matrix != NULL,
"You should first initialize the implicit solver and assemble the stiffness matrix");
bool need_factorize = !do_not_factorize;
if (method ==_implicit_dynamic) {
AKANTU_DEBUG_ASSERT(mass_matrix != NULL,
"You should first initialize the implicit solver and assemble the mass matrix");
}
switch (cmethod) {
case _scm_newton_raphson_tangent:
case _scm_newton_raphson_tangent_not_computed:
break;
case _scm_newton_raphson_tangent_modified:
this->assembleStiffnessMatrix();
break;
default:
AKANTU_DEBUG_ERROR("The resolution method " << cmethod << " has not been implemented!");
}
UInt iter = 0;
converged = false;
error = 0.;
if(criteria == _scc_residual) {
converged = this->testConvergence<criteria> (tolerance, error);
if(converged) return converged;
}
/// Loop to solve the nonlinear system
do {
if (cmethod == _scm_newton_raphson_tangent)
this->assembleStiffnessMatrix();
solve<NewmarkBeta::_displacement_corrector> (*increment, 1., need_factorize);
this->implicitCorr();
this->updateResidual();
converged = this->testConvergence<criteria> (tolerance, error);
iter++;
AKANTU_DEBUG_INFO("[" << criteria << "] Convergence iteration "
<< std::setw(std::log10(max_iteration)) << iter
<< ": error " << error << (converged ? " < " : " > ") << tolerance);
switch (cmethod) {
case _scm_newton_raphson_tangent:
need_factorize = true;
break;
case _scm_newton_raphson_tangent_not_computed:
case _scm_newton_raphson_tangent_modified:
need_factorize = false;
break;
default:
AKANTU_DEBUG_ERROR("The resolution method " << cmethod << " has not been implemented!");
}
} while (!converged && iter < max_iteration);
/**
* This is to save the obtained result and proceed with the
* simulation even if the error is higher than the pre-fixed
* tolerance. This is done only after loading reduction
* (load_reduction = true).
*/
// if (load_reduction && (error < tolerance * tol_increase_factor)) converged = true;
if ((error < tolerance * tol_increase_factor)) converged = true;
if (converged) {
} else if(iter == max_iteration) {
if (prank==0){
AKANTU_DEBUG_WARNING("[" << criteria << "] Convergence not reached after "
<< std::setw(std::log10(max_iteration)) << iter <<
" iteration" << (iter == 1 ? "" : "s") << "!" << std::endl);
}
}
if (is_extrinsic) {
/**
* If is extrinsic the pointer "displacement" is moved back to
* the array displacement. In this way, the array displacement is
* correctly resized during the checkCohesiveStress function (in
* case new cohesive elements are added). This is possible
* because the procedure called by checkCohesiveStress does not
* use the displacement field (the correct one is now stored in
* displacement_tmp), but directly the stress field that is
* already computed.
*/
Array<Real> * tmp_swap;
tmp_swap = displacement_tmp;
displacement_tmp = this->displacement;
this->displacement = tmp_swap;
tmp_swap = velocity_tmp;
velocity_tmp = this->velocity;
this->velocity = tmp_swap;
tmp_swap = acceleration_tmp;
acceleration_tmp = this->acceleration;
this->acceleration = tmp_swap;
/// If convergence is reached, call checkCohesiveStress in order
/// to check if cohesive elements have to be introduced
if (converged){
UInt new_cohesive_elements = checkCohesiveStress();
if(new_cohesive_elements == 0){
insertion_new_element = false;
} else {
insertion_new_element = true;
}
}
}
if (!converged && load_reduction)
insertion_new_element = false;
/**
* If convergence is not reached, there is the possibility to
* return back to the main file and reduce the load. Before doing
* this, a pre-fixed value as to be defined for the parameter
* delta_max of the cohesive elements introduced in the current
* incremental step. This is done by calling the function
* checkDeltaMax.
*/
if (!converged) {
insertion_new_element = false;
for (UInt m = 0; m < materials.size(); ++m) {
try {
MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(*materials[m]);
mat.checkDeltaMax(_not_ghost);
} catch(std::bad_cast&) { }
}
}
} //end loop for the insertion of new cohesive elements
/**
* When the solution to the current incremental step is computed (no
* more cohesive elements have to be introduced), call the function
* to compute the energies.
*/
if ((is_extrinsic && converged)) {
for(UInt m = 0; m < materials.size(); ++m) {
try {
MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(*materials[m]);
mat.computeEnergies();
} catch (std::bad_cast & bce) { }
}
EventManager::sendEvent(SolidMechanicsModelEvent::AfterSolveStepEvent(method));
/**
* The function resetVariables is necessary to correctly set a
* variable that permit to decrease locally the penalty parameter
* for compression.
*/
for (UInt m = 0; m < materials.size(); ++m) {
try {
MaterialCohesive & mat = dynamic_cast<MaterialCohesive &>(*materials[m]);
mat.resetVariables(_not_ghost);
} catch(std::bad_cast&) { }
}
/// The correct solution is saved
this->displacement->copy(*displacement_tmp);
this->velocity ->copy(*velocity_tmp);
this->acceleration->copy(*acceleration_tmp);
}
delete displacement_tmp;
delete velocity_tmp;
delete acceleration_tmp;
return insertion_new_element;
}
-__END_AKANTU__
+} // akantu
#if defined (AKANTU_PARALLEL_COHESIVE_ELEMENT)
# include "solid_mechanics_model_cohesive_parallel_inline_impl.cc"
#endif
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_COHESIVE_INLINE_IMPL_CC__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
index be8123014..caed2dda1 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.cc
@@ -1,160 +1,160 @@
/**
* @file embedded_interface_intersector.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri May 01 2015
* @date last modification: Mon Jan 04 2016
*
* @brief Class that loads the interface from mesh and computes intersections
*
* @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 "embedded_interface_intersector.hh"
#include "mesh_segment_intersector.hh"
/// Helper macro for types in the mesh. Creates an intersector and computes intersection queries
#define INTERFACE_INTERSECTOR_CASE(dim, type) do { \
MeshSegmentIntersector<dim, type> intersector(this->mesh, interface_mesh); \
name_to_primitives_it = name_to_primitives_map.begin(); \
for (; name_to_primitives_it != name_to_primitives_end ; ++name_to_primitives_it) { \
intersector.setPhysicalName(name_to_primitives_it->first); \
intersector.buildResultFromQueryList(name_to_primitives_it->second); \
} } while(0)
#define INTERFACE_INTERSECTOR_CASE_2D(type) INTERFACE_INTERSECTOR_CASE(2, type)
#define INTERFACE_INTERSECTOR_CASE_3D(type) INTERFACE_INTERSECTOR_CASE(3, type)
-__BEGIN_AKANTU__
+namespace akantu {
EmbeddedInterfaceIntersector::EmbeddedInterfaceIntersector(Mesh & mesh, const Mesh & primitive_mesh) :
MeshGeomAbstract(mesh),
interface_mesh(mesh.getSpatialDimension(), "interface_mesh"),
primitive_mesh(primitive_mesh)
{
// Initiating mesh connectivity and data
interface_mesh.addConnectivityType(_segment_2, _not_ghost);
interface_mesh.addConnectivityType(_segment_2, _ghost);
interface_mesh.registerData<Element>("associated_element").alloc(0, 1, _segment_2);
interface_mesh.registerData<std::string>("physical_names").alloc(0, 1, _segment_2);
}
EmbeddedInterfaceIntersector::~EmbeddedInterfaceIntersector()
{}
void EmbeddedInterfaceIntersector::constructData(GhostType ghost_type) {
AKANTU_DEBUG_IN();
const UInt dim = this->mesh.getSpatialDimension();
if (dim == 1)
AKANTU_DEBUG_ERROR("No embedded model in 1D. Deactivate intersection initialization");
Array<std::string> * physical_names = NULL;
try {
physical_names = &const_cast<Array<std::string> &>(this->primitive_mesh.getData<std::string>("physical_names", _segment_2));
} catch (debug::Exception & e) {
AKANTU_DEBUG_ERROR("You must define physical names to reinforcements in order to use the embedded model");
throw e;
}
const UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(_segment_2);
Array<UInt>::const_vector_iterator connectivity = primitive_mesh.getConnectivity(_segment_2).begin(nb_nodes_per_element);
Array<std::string>::scalar_iterator
names_it = physical_names->begin(),
names_end = physical_names->end();
std::map<std::string, std::list<K::Segment_3> > name_to_primitives_map;
// Loop over the physical names and register segment lists in name_to_primitives_map
for (; names_it != names_end ; ++names_it) {
UInt element_id = names_it - physical_names->begin();
const Vector<UInt> el_connectivity = connectivity[element_id];
K::Segment_3 segment = this->createSegment(el_connectivity);
name_to_primitives_map[*names_it].push_back(segment);
}
// Loop over the background types of the mesh
Mesh::type_iterator
type_it = this->mesh.firstType(dim, _not_ghost),
type_end = this->mesh.lastType(dim, _not_ghost);
std::map<std::string, std::list<K::Segment_3> >::iterator
name_to_primitives_it,
name_to_primitives_end = name_to_primitives_map.end();
for (; type_it != type_end ; ++type_it) {
// Used in AKANTU_BOOST_ELEMENT_SWITCH
ElementType type = *type_it;
AKANTU_DEBUG_INFO("Computing intersections with background element type " << type);
switch(dim) {
case 1:
break;
case 2:
// Compute intersections for supported 2D elements
AKANTU_BOOST_ELEMENT_SWITCH(INTERFACE_INTERSECTOR_CASE_2D, (_triangle_3) (_triangle_6));
break;
case 3:
// Compute intersections for supported 3D elements
AKANTU_BOOST_ELEMENT_SWITCH(INTERFACE_INTERSECTOR_CASE_3D, (_tetrahedron_4));
break;
}
}
AKANTU_DEBUG_OUT();
}
K::Segment_3 EmbeddedInterfaceIntersector::createSegment(const Vector<UInt> & connectivity) {
AKANTU_DEBUG_IN();
K::Point_3 * source = NULL, * target = NULL;
const Array<Real> & nodes = this->primitive_mesh.getNodes();
if (this->mesh.getSpatialDimension() == 2) {
source = new K::Point_3(nodes(connectivity(0), 0), nodes(connectivity(0), 1), 0.);
target = new K::Point_3(nodes(connectivity(1), 0), nodes(connectivity(1), 1), 0.);
} else if (this->mesh.getSpatialDimension() == 3) {
source = new K::Point_3(nodes(connectivity(0), 0), nodes(connectivity(0), 1), nodes(connectivity(0), 2));
target = new K::Point_3(nodes(connectivity(1), 0), nodes(connectivity(1), 1), nodes(connectivity(1), 2));
}
K::Segment_3 segment(*source, *target);
delete source;
delete target;
AKANTU_DEBUG_OUT();
return segment;
}
-__END_AKANTU__
+} // akantu
#undef INTERFACE_INTERSECTOR_CASE
#undef INTERFACE_INTERSECTOR_CASE_2D
#undef INTERFACE_INTERSECTOR_CASE_3D
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
index d36d382d3..889a63c4e 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_intersector.hh
@@ -1,91 +1,91 @@
/**
* @file embedded_interface_intersector.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri May 01 2015
* @date last modification: Mon Dec 14 2015
*
* @brief Class that loads the interface from mesh and computes intersections
*
* @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_EMBEDDED_INTERFACE_INTERSECTOR_HH__
#define __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
#include "aka_common.hh"
#include "mesh_geom_common.hh"
#include "mesh_geom_abstract.hh"
#include "mesh_segment_intersector.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
typedef Cartesian K;
/**
* @brief Computes the intersections of the reinforcements defined in the primitive mesh
*
* The purpose of this class is to look for reinforcements in the primitive mesh, which
* should be defined by physical groups with the same names as the reinforcement materials
* in the model.
*
* It then constructs the CGAL primitives from the elements of those reinforcements
* and computes the intersections with the background mesh, to create an `interface_mesh`,
* which is in turn used by the EmbeddedInterfaceModel.
*
* @see MeshSegmentIntersector, MeshGeomAbstract
* @see EmbeddedInterfaceModel
*/
class EmbeddedInterfaceIntersector : public MeshGeomAbstract {
public:
/// Construct from mesh and a reinforcement mesh
explicit EmbeddedInterfaceIntersector(Mesh & mesh, const Mesh & primitive_mesh);
/// Destructor
virtual ~EmbeddedInterfaceIntersector();
public:
/// Generate the interface mesh
virtual void constructData(GhostType ghost_type = _not_ghost);
/// Create a segment with an element connectivity
K::Segment_3 createSegment(const Vector<UInt> & connectivity);
/// Getter for interface mesh
AKANTU_GET_MACRO_NOT_CONST(InterfaceMesh, interface_mesh, Mesh &);
protected:
/// Resulting mesh of intersection
Mesh interface_mesh;
/// Mesh used for primitive construction
const Mesh & primitive_mesh;
};
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_EMBEDDED_INTERFACE_INTERSECTOR_HH__
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
index 30d1db3f3..910af71ff 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.cc
@@ -1,210 +1,210 @@
/**
* @file embedded_interface_model.cc
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Mar 13 2015
* @date last modification: Mon Dec 14 2015
*
* @brief Model of Solid Mechanics with embedded interfaces
*
* @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 "embedded_interface_model.hh"
#include "material_reinforcement.hh"
#ifdef AKANTU_USE_IOHELPER
# include "dumper_paraview.hh"
# include "dumpable_inline_impl.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
const EmbeddedInterfaceModelOptions
default_embedded_interface_model_options(_explicit_lumped_mass, false, false);
/* -------------------------------------------------------------------------- */
EmbeddedInterfaceModel::EmbeddedInterfaceModel(Mesh & mesh,
Mesh & primitive_mesh,
UInt spatial_dimension,
const ID & id,
const MemoryID & memory_id) :
SolidMechanicsModel(mesh, spatial_dimension, id, memory_id),
intersector(mesh, primitive_mesh),
interface_mesh(NULL),
primitive_mesh(primitive_mesh),
interface_material_selector(NULL)
{
// This pointer should be deleted by ~SolidMechanicsModel()
MaterialSelector * mat_sel_pointer =
new MeshDataMaterialSelector<std::string>("physical_names", *this);
this->setMaterialSelector(*mat_sel_pointer);
interface_mesh = &(intersector.getInterfaceMesh());
// Create 1D FEEngine on the interface mesh
registerFEEngineObject<MyFEEngineType>("EmbeddedInterfaceFEEngine", *interface_mesh, 1);
}
/* -------------------------------------------------------------------------- */
EmbeddedInterfaceModel::~EmbeddedInterfaceModel() {
delete interface_material_selector;
}
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::initFull(const ModelOptions & options) {
const EmbeddedInterfaceModelOptions & eim_options =
dynamic_cast<const EmbeddedInterfaceModelOptions &>(options);
// We don't want to initiate materials before shape functions are initialized
SolidMechanicsModelOptions dummy_options(eim_options.analysis_method, true);
// Do no initialize interface_mesh if told so
if (!eim_options.no_init_intersections)
intersector.constructData();
// Initialize interface FEEngine
FEEngine & engine = getFEEngine("EmbeddedInterfaceFEEngine");
engine.initShapeFunctions(_not_ghost);
engine.initShapeFunctions(_ghost);
SolidMechanicsModel::initFull(dummy_options);
// This will call SolidMechanicsModel::initMaterials() last
this->initMaterials();
#if defined(AKANTU_USE_IOHELPER)
this->mesh.registerDumper<DumperParaview>("reinforcement", id);
this->mesh.addDumpMeshToDumper("reinforcement", *interface_mesh,
1, _not_ghost, _ek_regular);
#endif
}
/* -------------------------------------------------------------------------- */
// This function is very similar to SolidMechanicsModel's
void EmbeddedInterfaceModel::initMaterials() {
Element element;
delete interface_material_selector;
interface_material_selector =
new InterfaceMeshDataMaterialSelector<std::string>("physical_names", *this);
for (ghost_type_t::iterator gt = ghost_type_t::begin(); gt != ghost_type_t::end(); ++gt) {
element.ghost_type = *gt;
Mesh::type_iterator it = interface_mesh->firstType(1, *gt);
Mesh::type_iterator end = interface_mesh->lastType(1, *gt);
for (; it != end ; ++it) {
UInt nb_element = interface_mesh->getNbElement(*it, *gt);
element.type = *it;
Array<UInt> & mat_indexes = material_index.alloc(nb_element, 1, *it, *gt);
for (UInt el = 0 ; el < nb_element ; el++) {
element.element = el;
UInt mat_index = (*interface_material_selector)(element);
AKANTU_DEBUG_ASSERT(mat_index < materials.size(),
"The material selector returned an index that does not exist");
mat_indexes(element.element) = mat_index;
materials.at(mat_index)->addElement(*it, el, *gt);
}
}
}
SolidMechanicsModel::initMaterials();
}
// /**
// * DO NOT REMOVE - This prevents the material reinforcement to register
// * their number of components. Problems arise with AvgHomogenizingFunctor
// * if the material reinforcement gives its number of components for a
// * field. Since AvgHomogenizingFunctor verifies that all the fields
// * have the same number of components, an exception is raised.
// */
// ElementTypeMap<UInt> EmbeddedInterfaceModel::getInternalDataPerElem(const std::string & field_name,
// const ElementKind & kind) {
// if (!(this->isInternal(field_name,kind))) AKANTU_EXCEPTION("unknown internal " << field_name);
// for (UInt m = 0; m < materials.size() ; ++m) {
// if (materials[m]->isInternal<Real>(field_name, kind)) {
// Material * mat = NULL;
// switch(this->spatial_dimension) {
// case 1:
// mat = dynamic_cast<MaterialReinforcement<1> *>(materials[m]);
// break;
// case 2:
// mat = dynamic_cast<MaterialReinforcement<2> *>(materials[m]);
// break;
// case 3:
// mat = dynamic_cast<MaterialReinforcement<3> *>(materials[m]);
// break;
// }
// if (mat == NULL && field_name != "stress_embedded")
// return materials[m]->getInternalDataPerElem<Real>(field_name,kind);
// else if (mat != NULL && field_name == "stress_embedded")
// return mat->getInternalDataPerElem<Real>(field_name, kind, "EmbeddedInterfaceFEEngine");
// }
// }
// return ElementTypeMap<UInt>();
// }
/* -------------------------------------------------------------------------- */
void EmbeddedInterfaceModel::addDumpGroupFieldToDumper(const std::string & dumper_name,
const std::string & field_id,
const std::string & group_name,
const ElementKind & element_kind,
bool padding_flag) {
#ifdef AKANTU_USE_IOHELPER
dumper::Field * field = NULL;
// If dumper is reinforcement, create a 1D elemental field
if (dumper_name == "reinforcement")
field = this->createElementalField(field_id, group_name, padding_flag, 1, element_kind);
else {
try {
SolidMechanicsModel::addDumpGroupFieldToDumper(dumper_name, field_id, group_name, element_kind, padding_flag);
} catch (...) {}
}
if (field) {
DumperIOHelper & dumper = mesh.getGroupDumper(dumper_name,group_name);
Model::addDumpGroupFieldToDumper(field_id,field,dumper);
}
#endif
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
index 3960c2cf8..39edb360d 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_embedded_interface/embedded_interface_model.hh
@@ -1,167 +1,167 @@
/**
* @file embedded_interface_model.hh
*
* @author Lucas Frerot <lucas.frerot@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Mon Dec 14 2015
*
* @brief Model of Solid Mechanics with embedded interfaces
*
* @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_EMBEDDED_INTERFACE_MODEL_HH__
#define __AKANTU_EMBEDDED_INTERFACE_MODEL_HH__
#include "aka_common.hh"
#include "solid_mechanics_model.hh"
#include "mesh.hh"
#include "embedded_interface_intersector.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/// Options for the EmbeddedInterfaceModel
struct EmbeddedInterfaceModelOptions : SolidMechanicsModelOptions {
/**
* @brief Constructor for EmbeddedInterfaceModelOptions
* @param analysis_method see SolidMeechanicsModelOptions
* @param no_init_intersections ignores the embedded elements
* @param no_init_materials see SolidMeechanicsModelOptions
*/
EmbeddedInterfaceModelOptions(AnalysisMethod analysis_method = _explicit_lumped_mass,
bool no_init_intersections = false,
bool no_init_materials = false):
SolidMechanicsModelOptions(analysis_method, no_init_materials),
no_init_intersections(no_init_intersections)
{}
/// Ignore the reinforcements
bool no_init_intersections;
};
extern const EmbeddedInterfaceModelOptions default_embedded_interface_model_options;
/**
* @brief Solid mechanics model using the embedded model.
*
* This SolidMechanicsModel subclass implements the embedded model,
* a method used to represent 1D elements in a finite elements model
* (eg. reinforcements in concrete).
*
* In addition to the SolidMechanicsModel properties, this model has
* a mesh of the 1D elements embedded in the model, and an instance of the
* EmbeddedInterfaceIntersector class for the computation of the intersections of the
* 1D elements with the background (bulk) mesh.
*
* @see MaterialReinforcement
*/
class EmbeddedInterfaceModel : public SolidMechanicsModel {
/// Same type as SolidMechanicsModel
typedef FEEngineTemplate<IntegratorGauss, ShapeLagrange, _ek_regular> MyFEEngineType;
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
/**
* @brief Constructor
*
* @param mesh main mesh (concrete)
* @param primitive_mesh mesh of the embedded reinforcement
*/
EmbeddedInterfaceModel(Mesh & mesh,
Mesh & primitive_mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "embedded_interface_model",
const MemoryID & memory_id = 0);
/// Destructor
virtual ~EmbeddedInterfaceModel();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// Initialise the model
virtual void initFull(const ModelOptions & options = default_embedded_interface_model_options);
/// Initialise the materials
virtual void initMaterials();
/// Allows filtering of dump fields which need to be dumpes on interface mesh
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 ElementTypeMap<UInt> getInternalDataPerElem(const std::string & field_name,
// const ElementKind & kind);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get interface mesh
AKANTU_GET_MACRO(InterfaceMesh, *interface_mesh, Mesh &);
/// Get associated elements
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(InterfaceAssociatedElements,
interface_mesh->getData<Element>("associated_element"),
Element);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// Intersector object to build the interface mesh
EmbeddedInterfaceIntersector intersector;
/// Interface mesh (weak reference)
Mesh * interface_mesh;
/// Mesh used to create the CGAL primitives for intersections
Mesh & primitive_mesh;
/// Material selector for interface
MaterialSelector * interface_material_selector;
};
/// Material selector based on mesh data for interface elements
template<typename T>
class InterfaceMeshDataMaterialSelector : public ElementDataMaterialSelector<T> {
public:
InterfaceMeshDataMaterialSelector(const std::string & name, const EmbeddedInterfaceModel & model, UInt first_index = 1) :
ElementDataMaterialSelector<T>(model.getInterfaceMesh().getData<T>(name), model, first_index)
{}
};
-__END_AKANTU__
+} // akantu
#endif // __AKANTU_EMBEDDED_INTERFACE_MODEL_HH__
diff --git a/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh b/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
index 4adb04969..a51786740 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
+++ b/src/model/solid_mechanics/solid_mechanics_model_event_handler.hh
@@ -1,127 +1,127 @@
/**
* @file solid_mechanics_model_event_handler.hh
*
* @author Daniel Pino Muñoz <daniel.pinomunoz@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Dec 18 2015
*
* @brief EventHandler implementation for SolidMechanicsEvents
*
* @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_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH__
#define __AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/// akantu::SolidMechanicsModelEvent is the base event for model
namespace SolidMechanicsModelEvent {
struct BeforeSolveStepEvent {
BeforeSolveStepEvent(AnalysisMethod & method) : method(method) {}
AnalysisMethod method;
};
struct AfterSolveStepEvent {
AfterSolveStepEvent(AnalysisMethod & method) : method(method) {}
AnalysisMethod method;
};
struct BeforeDumpEvent {
BeforeDumpEvent() {}
};
struct BeginningOfDamageIterationEvent {
BeginningOfDamageIterationEvent() {}
};
struct AfterDamageEvent {
AfterDamageEvent() {}
};
}
/// akantu::SolidMechanicsModelEvent
class SolidMechanicsModelEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
virtual ~SolidMechanicsModelEventHandler(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
protected:
/// Send what is before the solve step to the beginning of solve step through
/// EventManager
inline void
sendEvent(const SolidMechanicsModelEvent::BeforeSolveStepEvent & event) {
onBeginningSolveStep(event.method);
}
/// Send what is after the solve step to the end of solve step through
/// EventManager
inline void
sendEvent(const SolidMechanicsModelEvent::AfterSolveStepEvent & event) {
onEndSolveStep(event.method);
}
/// Send what is before dump to current dump through EventManager
inline void
sendEvent(__attribute__((unused))
const SolidMechanicsModelEvent::BeforeDumpEvent & event) {
onDump();
}
/// Send what is at the beginning of damage iteration to Damage iteration
/// through EventManager
inline void sendEvent(
__attribute__((unused))
const SolidMechanicsModelEvent::BeginningOfDamageIterationEvent & event) {
onDamageIteration();
}
/// Send what is after damage for the damage update through EventManager
inline void
sendEvent(__attribute__((unused))
const SolidMechanicsModelEvent::AfterDamageEvent & event) {
onDamageUpdate();
}
template <class EventHandler> friend class EventHandlerManager;
/* ------------------------------------------------------------------------ */
/* Interface */
/* ------------------------------------------------------------------------ */
public:
/// function to implement to react on akantu::BeforeSolveStepEvent
virtual void onBeginningSolveStep(__attribute__((unused))
const AnalysisMethod & method) {}
/// function to implement to react on akantu::AfterSolveStepEvent
virtual void onEndSolveStep(__attribute__((unused))
const AnalysisMethod & method) {}
/// function to implement to react on akantu::BeforeDumpEvent
virtual void onDump() {}
/// function to implement to react on akantu::BeginningOfDamageIterationEvent
virtual void onDamageIteration() {}
/// function to implement to react on akantu::AfterDamageEvent
virtual void onDamageUpdate() {}
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_SOLID_MECHANICS_MODEL_EVENT_HANDLER_HH__ */
diff --git a/src/model/solid_mechanics/solid_mechanics_model_mass.cc b/src/model/solid_mechanics/solid_mechanics_model_mass.cc
index e4d42481a..d5038332a 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_mass.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_mass.cc
@@ -1,190 +1,190 @@
/**
* @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 "material.hh"
#include "model_solver.hh"
#include "solid_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMassLumped() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
if (this->mass == NULL) {
std::stringstream sstr_mass;
sstr_mass << id << ":mass";
mass = &(alloc<Real>(sstr_mass.str(), nb_nodes, 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->getSize() * mass->getNbComponent());
auto mass_end =
mass->end_reinterpret(mass->getSize() * 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);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMassLumped(GhostType ghost_type) {
AKANTU_DEBUG_IN();
FEEngine & fem = getFEEngine();
Array<Real> rho(0, spatial_dimension);
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;
computeRho(rho, type, ghost_type);
fem.assembleFieldLumped(rho, "M", "displacement", this->getDOFManager(),
type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assembleMass() {
AKANTU_DEBUG_IN();
if (!this->getDOFManager().hasMatrix("M")) {
this->getDOFManager().getNewMatrix("M", "J");
}
this->getDOFManager().clearMatrix("M");
assembleMass(_not_ghost);
AKANTU_DEBUG_OUT();
}
class ComputeRhoFunctor {
public:
explicit ComputeRhoFunctor(const SolidMechanicsModel & model) : model(model){};
void operator()(Matrix<Real> & rho, const Element & element,
__attribute__((unused)) const Matrix<Real> quad_coords) 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::assembleMass(GhostType ghost_type) {
AKANTU_DEBUG_IN();
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
ComputeRhoFunctor compute_rho(*this);
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;
fem.assembleFieldMatrix(compute_rho, "M", "displacement",
this->getDOFManager(), type, ghost_type);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::computeRho(Array<Real> & rho, ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
FEEngine & fem = this->getFEEngine();
UInt nb_element = fem.getMesh().getNbElement(type, ghost_type);
Array<UInt> & mat_indexes = this->material_index(type, ghost_type);
UInt nb_quadrature_points = fem.getNbIntegrationPoints(type);
rho.resize(nb_element * nb_quadrature_points);
Array<Real>::vector_iterator rho_it = rho.begin(spatial_dimension);
/// compute @f$ rho @f$ for each nodes of each element
for (UInt el = 0; el < nb_element; ++el) {
/// here rho is constant in an element
Real mat_rho = this->materials[mat_indexes(el)]->getParam("rho");
for (UInt n = 0; n < nb_quadrature_points; ++n, ++rho_it) {
(*rho_it).set(mat_rho);
}
}
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solid_mechanics/solid_mechanics_model_material.cc b/src/model/solid_mechanics/solid_mechanics_model_material.cc
index 62cd461f8..a312e323d 100644
--- a/src/model/solid_mechanics/solid_mechanics_model_material.cc
+++ b/src/model/solid_mechanics/solid_mechanics_model_material.cc
@@ -1,333 +1,333 @@
/**
* @file solid_mechanics_model_material.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Nov 26 2010
* @date last modification: Mon Nov 16 2015
*
* @brief instatiation of 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_math.hh"
#include "material_list.hh"
#include "solid_mechanics_model.hh"
#ifdef AKANTU_DAMAGE_NON_LOCAL
#include "non_local_manager.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
#define AKANTU_INTANTIATE_MATERIAL_BY_DIM_NO_TMPL(dim, elem) \
registerNewMaterial<BOOST_PP_ARRAY_ELEM(1, elem) < dim>> (section)
#define AKANTU_INTANTIATE_MATERIAL_BY_DIM_TMPL_EACH(r, data, i, elem) \
BOOST_PP_EXPR_IF(BOOST_PP_NOT_EQUAL(0, i), else) \
if (opt_param == BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 0, elem))) { \
registerNewMaterial<BOOST_PP_ARRAY_ELEM(1, data) < \
BOOST_PP_ARRAY_ELEM(0, data), \
BOOST_PP_SEQ_ENUM(BOOST_PP_TUPLE_ELEM(2, 1, elem))>> \
(section); \
}
#define AKANTU_INTANTIATE_MATERIAL_BY_DIM_TMPL(dim, elem) \
BOOST_PP_SEQ_FOR_EACH_I(AKANTU_INTANTIATE_MATERIAL_BY_DIM_TMPL_EACH, \
(2, (dim, BOOST_PP_ARRAY_ELEM(1, elem))), \
BOOST_PP_ARRAY_ELEM(2, elem)) \
else { \
AKANTU_INTANTIATE_MATERIAL_BY_DIM_NO_TMPL(dim, elem); \
}
#define AKANTU_INTANTIATE_MATERIAL_BY_DIM(dim, elem) \
BOOST_PP_IF(BOOST_PP_EQUAL(3, BOOST_PP_ARRAY_SIZE(elem)), \
AKANTU_INTANTIATE_MATERIAL_BY_DIM_TMPL, \
AKANTU_INTANTIATE_MATERIAL_BY_DIM_NO_TMPL) \
(dim, elem)
#define AKANTU_INTANTIATE_MATERIAL(elem) \
switch (spatial_dimension) { \
case 1: { \
AKANTU_INTANTIATE_MATERIAL_BY_DIM(1, elem); \
break; \
} \
case 2: { \
AKANTU_INTANTIATE_MATERIAL_BY_DIM(2, elem); \
break; \
} \
case 3: { \
AKANTU_INTANTIATE_MATERIAL_BY_DIM(3, elem); \
break; \
} \
}
#define AKANTU_INTANTIATE_MATERIAL_IF(elem) \
if (mat_type == BOOST_PP_STRINGIZE(BOOST_PP_ARRAY_ELEM(0, elem))) { \
AKANTU_INTANTIATE_MATERIAL(elem); \
}
#define AKANTU_INTANTIATE_OTHER_MATERIAL(r, data, elem) \
else AKANTU_INTANTIATE_MATERIAL_IF(elem)
#define AKANTU_INSTANTIATE_MATERIALS() \
do { \
AKANTU_INTANTIATE_MATERIAL_IF(BOOST_PP_SEQ_HEAD(AKANTU_MATERIAL_LIST)) \
BOOST_PP_SEQ_FOR_EACH(AKANTU_INTANTIATE_OTHER_MATERIAL, _, \
BOOST_PP_SEQ_TAIL(AKANTU_MATERIAL_LIST)) \
else { \
if (getStaticParser().isPermissive()) \
AKANTU_DEBUG_INFO("Malformed material file " \
<< ": unknown material type '" << mat_type << "'"); \
else \
AKANTU_DEBUG_WARNING("Malformed material file " \
<< ": unknown material type " << mat_type \
<< ". This is perhaps a user" \
<< " defined material ?"); \
} \
} while (0)
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::instantiateMaterials() {
std::pair<Parser::const_section_iterator, Parser::const_section_iterator>
sub_sect = this->parser->getSubSections(_st_material);
Parser::const_section_iterator it = sub_sect.first;
for (; it != sub_sect.second; ++it) {
const ParserSection & section = *it;
std::string mat_type = section.getName();
std::string opt_param = section.getOption();
AKANTU_INSTANTIATE_MATERIALS();
}
are_materials_instantiated = true;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::assignMaterialToElements(
const ElementTypeMapArray<UInt> * filter) {
Element element;
element.ghost_type = _not_ghost;
auto element_types =
mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined);
if (filter != NULL) {
element_types =
filter->elementTypes(spatial_dimension, _not_ghost, _ek_not_defined);
}
// Fill the element material array from the material selector
for (auto type : element_types) {
UInt nb_element = mesh.getNbElement(type, _not_ghost);
const Array<UInt> * filter_array = NULL;
if (filter != NULL) {
filter_array = &((*filter)(type, _not_ghost));
nb_element = filter_array->getSize();
}
element.type = type;
element.kind = mesh.getKind(element.type);
Array<UInt> & mat_indexes = material_index(type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el) {
if (filter != NULL)
element.element = (*filter_array)(el);
else
element.element = el;
UInt mat_index = (*material_selector)(element);
AKANTU_DEBUG_ASSERT(
mat_index < materials.size(),
"The material selector returned an index that does not exists");
mat_indexes(element.element) = mat_index;
}
}
// synchronize the element material arrays
this->synchronize(_gst_material_id);
/// fill the element filters of the materials using the element_material
/// arrays
for (auto ghost_type : ghost_types) {
element_types =
mesh.elementTypes(spatial_dimension, ghost_type, _ek_not_defined);
if (filter != NULL) {
element_types =
filter->elementTypes(spatial_dimension, ghost_type, _ek_not_defined);
}
for (auto type : element_types) {
UInt nb_element = mesh.getNbElement(type, ghost_type);
const Array<UInt> * filter_array = NULL;
if (filter != NULL) {
filter_array = &((*filter)(type, ghost_type));
nb_element = filter_array->getSize();
}
Array<UInt> & mat_indexes = material_index(type, ghost_type);
Array<UInt> & mat_local_num = material_local_numbering(type, ghost_type);
for (UInt el = 0; el < nb_element; ++el) {
UInt element;
if (filter != NULL)
element = (*filter_array)(el);
else
element = el;
UInt mat_index = mat_indexes(element);
UInt index =
materials[mat_index]->addElement(type, element, ghost_type);
mat_local_num(element) = index;
}
}
}
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::initMaterials() {
AKANTU_DEBUG_ASSERT(materials.size() != 0, "No material to initialize !");
if (!are_materials_instantiated)
instantiateMaterials();
this->assignMaterialToElements();
for (auto & material : materials) {
/// init internals properties
material->initMaterial();
}
this->synchronize(_gst_smm_init_mat);
// initialize mass
switch (method) {
case _explicit_lumped_mass:
assembleMassLumped();
break;
case _explicit_consistent_mass:
case _implicit_dynamic:
assembleMass();
break;
case _static:
break;
default:
AKANTU_EXCEPTION("analysis method not recognised by SolidMechanicsModel");
break;
}
// initialize the previous displacement array if at least on material needs it
// for (auto & material : materials) {
// if (material->isFiniteDeformation() || material->isInelasticDeformation()) {
// initArraysPreviousDisplacment();
// break;
// }
// }
#ifdef AKANTU_DAMAGE_NON_LOCAL
/// initialize the non-local manager for non-local computations
this->non_local_manager->init();
#endif
}
/* -------------------------------------------------------------------------- */
Int SolidMechanicsModel::getInternalIndexFromID(const ID & id) const {
AKANTU_DEBUG_IN();
auto it = materials.begin();
auto end = materials.end();
for (; it != end; ++it)
if ((*it)->getID() == id) {
AKANTU_DEBUG_OUT();
return (it - materials.begin());
}
AKANTU_DEBUG_OUT();
return -1;
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::reassignMaterial() {
AKANTU_DEBUG_IN();
std::vector<Array<Element>> element_to_add(materials.size());
std::vector<Array<Element>> element_to_remove(materials.size());
Element element;
for (auto ghost_type : ghost_types) {
element.ghost_type = ghost_type;
for (auto type :
mesh.elementTypes(spatial_dimension, ghost_type, _ek_not_defined)) {
element.type = type;
element.kind = Mesh::getKind(type);
UInt nb_element = mesh.getNbElement(type, ghost_type);
Array<UInt> & mat_indexes = material_index(type, ghost_type);
for (UInt el = 0; el < nb_element; ++el) {
element.element = el;
UInt old_material = mat_indexes(el);
UInt new_material = (*material_selector)(element);
if (old_material != new_material) {
element_to_add[new_material].push_back(element);
element_to_remove[old_material].push_back(element);
}
}
}
}
UInt mat_index = 0;
for (auto mat_it = materials.begin(); mat_it != materials.end();
++mat_it, ++mat_index) {
(*mat_it)->removeElements(element_to_remove[mat_index]);
(*mat_it)->addElements(element_to_add[mat_index]);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolidMechanicsModel::applyEigenGradU(
const Matrix<Real> & prescribed_eigen_grad_u, const ID & material_name,
const GhostType ghost_type) {
AKANTU_DEBUG_ASSERT(prescribed_eigen_grad_u.size() ==
spatial_dimension * spatial_dimension,
"The prescribed grad_u is not of the good size");
for (auto & material : materials) {
if (material->getName() == material_name)
material->applyEigenGradU(prescribed_eigen_grad_u, ghost_type);
}
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solver_callback.cc b/src/model/solver_callback.cc
index feb2b69f6..321fdbbcf 100644
--- a/src/model/solver_callback.cc
+++ b/src/model/solver_callback.cc
@@ -1,63 +1,63 @@
/**
* @file solver_callback.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Wed Mar 2 12:47:17 2016
*
* @brief Default behavior of solver_callbacks
*
* @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 "solver_callback.hh"
#include "dof_manager.hh"
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
SolverCallback::SolverCallback(DOFManager & dof_manager)
: sc_dof_manager(&dof_manager) {}
/* -------------------------------------------------------------------------- */
SolverCallback::SolverCallback() : sc_dof_manager(NULL) {}
/* -------------------------------------------------------------------------- */
SolverCallback::~SolverCallback() {}
/* -------------------------------------------------------------------------- */
void SolverCallback::setDOFManager(DOFManager & dof_manager) {
this->sc_dof_manager = &dof_manager;
}
/* -------------------------------------------------------------------------- */
void SolverCallback::assembleJacobian() {
this->sc_dof_manager->clearMatrix("J");
}
/* -------------------------------------------------------------------------- */
void SolverCallback::assembleResidual() {
this->sc_dof_manager->clearResidual();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/solver_callback.hh b/src/model/solver_callback.hh
index 702989340..c182a10dd 100644
--- a/src/model/solver_callback.hh
+++ b/src/model/solver_callback.hh
@@ -1,83 +1,83 @@
/**
* @file solver_callback.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Sep 15 22:45:27 2015
*
* @brief Class defining the interface for non_linear_solver callbacks
*
* @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"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLVER_CALLBACK_HH__
#define __AKANTU_SOLVER_CALLBACK_HH__
namespace akantu {
class DOFManager;
}
-__BEGIN_AKANTU__
+namespace akantu {
class SolverCallback {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit SolverCallback(DOFManager & dof_manager);
explicit SolverCallback();
/* ------------------------------------------------------------------------ */
virtual ~SolverCallback();
protected:
void setDOFManager(DOFManager & dof_manager);
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// callback to assemble the Jacobian Matrix
virtual void assembleJacobian();
/// callback to assemble the residual (rhs)
virtual void assembleResidual();
/* ------------------------------------------------------------------------ */
/* Dynamic simulations part */
/* ------------------------------------------------------------------------ */
/// callback for the predictor (in case of dynamic simulation)
virtual void predictor() { AKANTU_DEBUG_TO_IMPLEMENT(); }
/// callback for the corrector (in case of dynamic simulation)
virtual void corrector() { AKANTU_DEBUG_TO_IMPLEMENT(); }
protected:
/// DOFManager prefixed to avoid collision in multiple inheritance cases
DOFManager * sc_dof_manager;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_SOLVER_CALLBACK_HH__ */
diff --git a/src/model/structural_mechanics/structural_mechanics_model.cc b/src/model/structural_mechanics/structural_mechanics_model.cc
index 531b7bdce..52168fe3c 100644
--- a/src/model/structural_mechanics/structural_mechanics_model.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model.cc
@@ -1,1225 +1,1225 @@
/**
* @file structural_mechanics_model.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Thu Oct 15 2015
*
* @brief Model implementation for StucturalMechanics 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 "structural_mechanics_model.hh"
#include "group_manager_inline_impl.cc"
#include "dumpable_inline_impl.hh"
#include "aka_math.hh"
#include "integration_scheme_2nd_order.hh"
#include "static_communicator.hh"
#include "sparse_matrix.hh"
#include "solver.hh"
#ifdef AKANTU_USE_MUMPS
#include "solver_mumps.hh"
#endif
#ifdef AKANTU_USE_IOHELPER
#include "dumper_paraview.hh"
#include "dumper_elemental_field.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
const StructuralMechanicsModelOptions
default_structural_mechanics_model_options(_static);
/* -------------------------------------------------------------------------- */
StructuralMechanicsModel::StructuralMechanicsModel(Mesh & mesh, UInt dim,
const ID & id,
const MemoryID & memory_id)
: Model(mesh, dim, id, memory_id), time_step(NAN), f_m2a(1.0),
stress("stress", id, memory_id),
element_material("element_material", id, memory_id),
set_ID("beam sets", id, memory_id), stiffness_matrix(NULL),
mass_matrix(NULL), velocity_damping_matrix(NULL), jacobian_matrix(NULL),
solver(NULL), rotation_matrix("rotation_matices", id, memory_id),
increment_flag(false), integrator(NULL) {
AKANTU_DEBUG_IN();
registerFEEngineObject<MyFEEngineType>("StructuralMechanicsFEEngine", mesh,
spatial_dimension);
this->displacement_rotation = NULL;
this->mass = NULL;
this->velocity = NULL;
this->acceleration = NULL;
this->force_momentum = NULL;
this->residual = NULL;
this->blocked_dofs = NULL;
this->increment = NULL;
this->previous_displacement = NULL;
if (spatial_dimension == 2)
nb_degree_of_freedom = 3;
else if (spatial_dimension == 3)
nb_degree_of_freedom = 6;
else {
AKANTU_DEBUG_TO_IMPLEMENT();
}
this->mesh.registerDumper<DumperParaview>("paraview_all", id, true);
this->mesh.addDumpMesh(mesh, spatial_dimension, _not_ghost, _ek_structural);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
StructuralMechanicsModel::~StructuralMechanicsModel() {
AKANTU_DEBUG_IN();
delete integrator;
delete solver;
delete stiffness_matrix;
delete jacobian_matrix;
delete mass_matrix;
delete velocity_damping_matrix;
AKANTU_DEBUG_OUT();
}
void StructuralMechanicsModel::setTimeStep(Real time_step) {
this->time_step = time_step;
#if defined(AKANTU_USE_IOHELPER)
this->mesh.getDumper().setTimeStep(time_step);
#endif
}
/* -------------------------------------------------------------------------- */
/* Initialisation */
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initFull(const ModelOptions & options) {
const StructuralMechanicsModelOptions & stmm_options =
dynamic_cast<const StructuralMechanicsModelOptions &>(options);
method = stmm_options.analysis_method;
initModel();
initArrays();
displacement_rotation->clear();
velocity->clear();
acceleration->clear();
force_momentum->clear();
residual->clear();
blocked_dofs->clear();
increment->clear();
Mesh::type_iterator it = getFEEngine().getMesh().firstType(
spatial_dimension, _not_ghost, _ek_structural);
Mesh::type_iterator end = getFEEngine().getMesh().lastType(
spatial_dimension, _not_ghost, _ek_structural);
for (; it != end; ++it) {
computeRotationMatrix(*it);
}
switch (method) {
case _implicit_dynamic:
initImplicit();
break;
case _static:
initSolver();
break;
default:
AKANTU_EXCEPTION(
"analysis method not recognised by StructuralMechanicsModel");
break;
}
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initArrays() {
AKANTU_DEBUG_IN();
UInt nb_nodes = getFEEngine().getMesh().getNbNodes();
std::stringstream sstr_disp;
sstr_disp << id << ":displacement";
std::stringstream sstr_velo;
sstr_velo << id << ":velocity";
std::stringstream sstr_acce;
sstr_acce << id << ":acceleration";
std::stringstream sstr_forc;
sstr_forc << id << ":force";
std::stringstream sstr_resi;
sstr_resi << id << ":residual";
std::stringstream sstr_boun;
sstr_boun << id << ":blocked_dofs";
std::stringstream sstr_incr;
sstr_incr << id << ":increment";
displacement_rotation = &(alloc<Real>(sstr_disp.str(), nb_nodes,
nb_degree_of_freedom, REAL_INIT_VALUE));
velocity = &(alloc<Real>(sstr_velo.str(), nb_nodes, nb_degree_of_freedom,
REAL_INIT_VALUE));
acceleration = &(alloc<Real>(sstr_acce.str(), nb_nodes, nb_degree_of_freedom,
REAL_INIT_VALUE));
force_momentum = &(alloc<Real>(sstr_forc.str(), nb_nodes,
nb_degree_of_freedom, REAL_INIT_VALUE));
residual = &(alloc<Real>(sstr_resi.str(), nb_nodes, nb_degree_of_freedom,
REAL_INIT_VALUE));
blocked_dofs =
&(alloc<bool>(sstr_boun.str(), nb_nodes, nb_degree_of_freedom, false));
increment = &(alloc<Real>(sstr_incr.str(), nb_nodes, nb_degree_of_freedom,
REAL_INIT_VALUE));
Mesh::type_iterator it = getFEEngine().getMesh().firstType(
spatial_dimension, _not_ghost, _ek_structural);
Mesh::type_iterator end = getFEEngine().getMesh().lastType(
spatial_dimension, _not_ghost, _ek_structural);
for (; it != end; ++it) {
UInt nb_element = getFEEngine().getMesh().getNbElement(*it);
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(*it);
element_material.alloc(nb_element, 1, *it, _not_ghost);
set_ID.alloc(nb_element, 1, *it, _not_ghost);
UInt size = getTangentStiffnessVoigtSize(*it);
stress.alloc(nb_element * nb_quadrature_points, size, *it, _not_ghost);
}
dof_synchronizer =
new DOFSynchronizer(getFEEngine().getMesh(), nb_degree_of_freedom);
dof_synchronizer->initLocalDOFEquationNumbers();
dof_synchronizer->initGlobalDOFEquationNumbers();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initModel() {
getFEEngine().initShapeFunctions(_not_ghost);
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initSolver(__attribute__((unused))
SolverOptions & options) {
AKANTU_DEBUG_IN();
const Mesh & mesh = getFEEngine().getMesh();
#if !defined(AKANTU_USE_MUMPS) // or other solver in the future \todo add
// AKANTU_HAS_SOLVER in CMake
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#else
UInt nb_global_node = mesh.getNbGlobalNodes();
std::stringstream sstr;
sstr << id << ":jacobian_matrix";
jacobian_matrix = new SparseMatrix(nb_global_node * nb_degree_of_freedom,
_symmetric, sstr.str(), memory_id);
jacobian_matrix->buildProfile(mesh, *dof_synchronizer, nb_degree_of_freedom);
std::stringstream sstr_sti;
sstr_sti << id << ":stiffness_matrix";
stiffness_matrix =
new SparseMatrix(*jacobian_matrix, sstr_sti.str(), memory_id);
#ifdef AKANTU_USE_MUMPS
std::stringstream sstr_solv;
sstr_solv << id << ":solver";
solver = new SolverMumps(*jacobian_matrix, sstr_solv.str());
dof_synchronizer->initScatterGatherCommunicationScheme();
#else
AKANTU_DEBUG_ERROR("You should at least activate one solver.");
#endif // AKANTU_USE_MUMPS
solver->initialize(options);
#endif // AKANTU_HAS_SOLVER
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::initImplicit(
__attribute__((unused)) bool dynamic, SolverOptions & solver_options) {
AKANTU_DEBUG_IN();
if (!increment)
setIncrementFlagOn();
initSolver(solver_options);
if (integrator)
delete integrator;
integrator = new TrapezoidalRule2();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
UInt StructuralMechanicsModel::getTangentStiffnessVoigtSize(
const ElementType & type) {
UInt size;
#define GET_TANGENT_STIFFNESS_VOIGT_SIZE(type) \
size = getTangentStiffnessVoigtSize<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(GET_TANGENT_STIFFNESS_VOIGT_SIZE);
#undef GET_TANGENT_STIFFNESS_VOIGT_SIZE
return size;
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleStiffnessMatrix() {
AKANTU_DEBUG_IN();
stiffness_matrix->clear();
Mesh::type_iterator it = getFEEngine().getMesh().firstType(
spatial_dimension, _not_ghost, _ek_structural);
Mesh::type_iterator end = getFEEngine().getMesh().lastType(
spatial_dimension, _not_ghost, _ek_structural);
for (; it != end; ++it) {
ElementType type = *it;
#define ASSEMBLE_STIFFNESS_MATRIX(type) assembleStiffnessMatrix<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(ASSEMBLE_STIFFNESS_MATRIX);
#undef ASSEMBLE_STIFFNESS_MATRIX
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeRotationMatrix<_bernoulli_beam_2>(
Array<Real> & rotations) {
ElementType type = _bernoulli_beam_2;
Mesh & mesh = getFEEngine().getMesh();
UInt nb_element = mesh.getNbElement(type);
Array<UInt>::iterator<Vector<UInt> > connec_it =
mesh.getConnectivity(type).begin(2);
Array<Real>::vector_iterator nodes_it =
mesh.getNodes().begin(spatial_dimension);
Array<Real>::matrix_iterator R_it =
rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
for (UInt e = 0; e < nb_element; ++e, ++R_it, ++connec_it) {
Matrix<Real> & R = *R_it;
Vector<UInt> & connec = *connec_it;
Vector<Real> x2;
x2 = nodes_it[connec(1)]; // X2
Vector<Real> x1;
x1 = nodes_it[connec(0)]; // X1
Real le = x1.distance(x2);
Real c = (x2(0) - x1(0)) / le;
Real s = (x2(1) - x1(1)) / le;
/// Definition of the rotation matrix
R(0, 0) = c;
R(0, 1) = s;
R(0, 2) = 0.;
R(1, 0) = -s;
R(1, 1) = c;
R(1, 2) = 0.;
R(2, 0) = 0.;
R(2, 1) = 0.;
R(2, 2) = 1.;
}
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeRotationMatrix<_bernoulli_beam_3>(
Array<Real> & rotations) {
ElementType type = _bernoulli_beam_3;
Mesh & mesh = getFEEngine().getMesh();
UInt nb_element = mesh.getNbElement(type);
Array<Real>::vector_iterator n_it =
mesh.getNormals(type).begin(spatial_dimension);
Array<UInt>::iterator<Vector<UInt> > connec_it =
mesh.getConnectivity(type).begin(2);
Array<Real>::vector_iterator nodes_it =
mesh.getNodes().begin(spatial_dimension);
Matrix<Real> Pe(spatial_dimension, spatial_dimension);
Matrix<Real> Pg(spatial_dimension, spatial_dimension);
Matrix<Real> inv_Pg(spatial_dimension, spatial_dimension);
Vector<Real> x_n(spatial_dimension); // x vect n
Array<Real>::matrix_iterator R_it =
rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
for (UInt e = 0; e < nb_element; ++e, ++n_it, ++connec_it, ++R_it) {
Vector<Real> & n = *n_it;
Matrix<Real> & R = *R_it;
Vector<UInt> & connec = *connec_it;
Vector<Real> x;
x = nodes_it[connec(1)]; // X2
Vector<Real> y;
y = nodes_it[connec(0)]; // X1
Real l = x.distance(y);
x -= y; // X2 - X1
x_n.crossProduct(x, n);
Pe.eye();
Pe(0, 0) *= l;
Pe(1, 1) *= -l;
Pg(0, 0) = x(0);
Pg(0, 1) = x_n(0);
Pg(0, 2) = n(0);
Pg(1, 0) = x(1);
Pg(1, 1) = x_n(1);
Pg(1, 2) = n(1);
Pg(2, 0) = x(2);
Pg(2, 1) = x_n(2);
Pg(2, 2) = n(2);
inv_Pg.inverse(Pg);
Pe *= inv_Pg;
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
R(i, j) = Pe(i, j);
R(i + spatial_dimension, j + spatial_dimension) = Pe(i, j);
}
}
}
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeRotationMatrix<_kirchhoff_shell>(
Array<Real> & rotations) {
ElementType type = _kirchhoff_shell;
Mesh & mesh = getFEEngine().getMesh();
UInt nb_element = mesh.getNbElement(type);
Array<UInt>::iterator<Vector<UInt> > connec_it =
mesh.getConnectivity(type).begin(3);
Array<Real>::vector_iterator nodes_it =
mesh.getNodes().begin(spatial_dimension);
Matrix<Real> Pe(spatial_dimension, spatial_dimension);
Matrix<Real> Pg(spatial_dimension, spatial_dimension);
Matrix<Real> inv_Pg(spatial_dimension, spatial_dimension);
Array<Real>::matrix_iterator R_it =
rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
for (UInt e = 0; e < nb_element; ++e, ++connec_it, ++R_it) {
Pe.eye();
Matrix<Real> & R = *R_it;
Vector<UInt> & connec = *connec_it;
Vector<Real> x2;
x2 = nodes_it[connec(1)]; // X2
Vector<Real> x1;
x1 = nodes_it[connec(0)]; // X1
Vector<Real> x3;
x3 = nodes_it[connec(2)]; // X3
Vector<Real> Pg_col_1 = x2 - x1;
Vector<Real> Pg_col_2 = x3 - x1;
Vector<Real> Pg_col_3(spatial_dimension);
Pg_col_3.crossProduct(Pg_col_1, Pg_col_2);
for (UInt i = 0; i < spatial_dimension; ++i) {
Pg(i, 0) = Pg_col_1(i);
Pg(i, 1) = Pg_col_2(i);
Pg(i, 2) = Pg_col_3(i);
}
inv_Pg.inverse(Pg);
// Pe *= inv_Pg;
Pe.eye();
for (UInt i = 0; i < spatial_dimension; ++i) {
for (UInt j = 0; j < spatial_dimension; ++j) {
R(i, j) = Pe(i, j);
R(i + spatial_dimension, j + spatial_dimension) = Pe(i, j);
}
}
}
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::computeRotationMatrix(const ElementType & type) {
Mesh & mesh = getFEEngine().getMesh();
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type);
if (!rotation_matrix.exists(type)) {
rotation_matrix.alloc(nb_element,
nb_degree_of_freedom * nb_nodes_per_element *
nb_degree_of_freedom * nb_nodes_per_element,
type);
} else {
rotation_matrix(type).resize(nb_element);
}
rotation_matrix(type).clear();
Array<Real> rotations(nb_element,
nb_degree_of_freedom * nb_degree_of_freedom);
rotations.clear();
#define COMPUTE_ROTATION_MATRIX(type) computeRotationMatrix<type>(rotations);
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(COMPUTE_ROTATION_MATRIX);
#undef COMPUTE_ROTATION_MATRIX
Array<Real>::matrix_iterator R_it =
rotations.begin(nb_degree_of_freedom, nb_degree_of_freedom);
Array<Real>::matrix_iterator T_it =
rotation_matrix(type).begin(nb_degree_of_freedom * nb_nodes_per_element,
nb_degree_of_freedom * nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el, ++R_it, ++T_it) {
Matrix<Real> & T = *T_it;
Matrix<Real> & R = *R_it;
T.clear();
for (UInt k = 0; k < nb_nodes_per_element; ++k) {
for (UInt i = 0; i < nb_degree_of_freedom; ++i)
for (UInt j = 0; j < nb_degree_of_freedom; ++j)
T(k * nb_degree_of_freedom + i, k * nb_degree_of_freedom + j) =
R(i, j);
}
}
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::computeStresses() {
AKANTU_DEBUG_IN();
Mesh::type_iterator it = getFEEngine().getMesh().firstType(
spatial_dimension, _not_ghost, _ek_structural);
Mesh::type_iterator end = getFEEngine().getMesh().lastType(
spatial_dimension, _not_ghost, _ek_structural);
for (; it != end; ++it) {
ElementType type = *it;
#define COMPUTE_STRESS_ON_QUAD(type) computeStressOnQuad<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(COMPUTE_STRESS_ON_QUAD);
#undef COMPUTE_STRESS_ON_QUAD
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::updateResidual() {
AKANTU_DEBUG_IN();
residual->copy(*force_momentum);
Array<Real> ku(*displacement_rotation, true);
ku *= *stiffness_matrix;
*residual -= ku;
this->updateResidualInternal();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::implicitPred() {
AKANTU_DEBUG_IN();
if (previous_displacement)
previous_displacement->copy(*displacement_rotation);
if (method == _implicit_dynamic)
integrator->integrationSchemePred(time_step, *displacement_rotation,
*velocity, *acceleration, *blocked_dofs);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::implicitCorr() {
AKANTU_DEBUG_IN();
Real * incr_val = increment->storage();
bool * boun_val = blocked_dofs->storage();
UInt nb_nodes = displacement_rotation->getSize();
for (UInt j = 0; j < nb_nodes * nb_degree_of_freedom;
++j, ++incr_val, ++boun_val) {
*incr_val *= (1. - *boun_val);
}
if (method == _implicit_dynamic) {
integrator->integrationSchemeCorrDispl(time_step, *displacement_rotation,
*velocity, *acceleration,
*blocked_dofs, *increment);
} else {
Real * disp_val = displacement_rotation->storage();
incr_val = increment->storage();
for (UInt j = 0; j < nb_nodes * nb_degree_of_freedom;
++j, ++disp_val, ++incr_val) {
*disp_val += *incr_val;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::updateResidualInternal() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Update the residual");
// f = f_ext - f_int - Ma - Cv = r - Ma - Cv;
if (method != _static) {
// f -= Ma
if (mass_matrix) {
// if full mass_matrix
Array<Real> * Ma = new Array<Real>(*acceleration, true, "Ma");
*Ma *= *mass_matrix;
/// \todo check unit conversion for implicit dynamics
// *Ma /= f_m2a
*residual -= *Ma;
delete Ma;
} else if (mass) {
// else lumped mass
UInt nb_nodes = acceleration->getSize();
UInt nb_degree_of_freedom = acceleration->getNbComponent();
Real * mass_val = mass->storage();
Real * accel_val = acceleration->storage();
Real * res_val = residual->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
if (!(*blocked_dofs_val)) {
*res_val -= *accel_val ** mass_val / f_m2a;
}
blocked_dofs_val++;
res_val++;
mass_val++;
accel_val++;
}
} else {
AKANTU_DEBUG_ERROR("No function called to assemble the mass matrix.");
}
// f -= Cv
if (velocity_damping_matrix) {
Array<Real> * Cv = new Array<Real>(*velocity);
*Cv *= *velocity_damping_matrix;
*residual -= *Cv;
delete Cv;
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::setIncrementFlagOn() {
AKANTU_DEBUG_IN();
if (!increment) {
UInt nb_nodes = mesh.getNbNodes();
std::stringstream sstr_inc;
sstr_inc << id << ":increment";
increment = &(alloc<Real>(sstr_inc.str(), nb_nodes, spatial_dimension, 0.));
}
increment_flag = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::solve() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Solving an implicit step.");
UInt nb_nodes = displacement_rotation->getSize();
/// todo residual = force - Kxr * d_bloq
jacobian_matrix->copyContent(*stiffness_matrix);
jacobian_matrix->applyBoundary(*blocked_dofs);
jacobian_matrix->saveMatrix("Kbound.mtx");
increment->clear();
solver->setRHS(*residual);
solver->factorize();
solver->solve(*increment);
Real * increment_val = increment->storage();
Real * displacement_val = displacement_rotation->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes * nb_degree_of_freedom; ++n) {
if (!(*blocked_dofs_val)) {
*displacement_val += *increment_val;
} else {
*increment_val = 0.0;
}
displacement_val++;
blocked_dofs_val++;
increment_val++;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <>
bool StructuralMechanicsModel::testConvergence<_scc_increment>(Real tolerance,
Real & error) {
AKANTU_DEBUG_IN();
UInt nb_nodes = displacement_rotation->getSize();
UInt nb_degree_of_freedom = displacement_rotation->getNbComponent();
error = 0;
Real norm[2] = {0., 0.};
Real * increment_val = increment->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
Real * displacement_val = displacement_rotation->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
if (!(*blocked_dofs_val)) {
norm[0] += *increment_val * *increment_val;
norm[1] += *displacement_val * *displacement_val;
}
blocked_dofs_val++;
increment_val++;
displacement_val++;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(norm, 2, _so_sum);
norm[0] = sqrt(norm[0]);
norm[1] = sqrt(norm[1]);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm[0]),
"Something went wrong in the solve phase");
AKANTU_DEBUG_OUT();
if (norm[1] > Math::getTolerance())
error = norm[0] / norm[1];
else
error = norm[0]; // In case the total displacement is zero!
return (error < tolerance);
}
/* -------------------------------------------------------------------------- */
template <>
bool StructuralMechanicsModel::testConvergence<_scc_residual>(Real tolerance,
Real & norm) {
AKANTU_DEBUG_IN();
UInt nb_nodes = residual->getSize();
norm = 0;
Real * residual_val = residual->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
if (is_local_node) {
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
if (!(*blocked_dofs_val)) {
norm += *residual_val * *residual_val;
}
blocked_dofs_val++;
residual_val++;
}
} else {
blocked_dofs_val += spatial_dimension;
residual_val += spatial_dimension;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(&norm, 1, _so_sum);
norm = sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm),
"Something goes wrong in the solve phase");
AKANTU_DEBUG_OUT();
return (norm < tolerance);
}
/* -------------------------------------------------------------------------- */
bool StructuralMechanicsModel::testConvergenceIncrement(Real tolerance) {
Real error;
bool tmp = testConvergenceIncrement(tolerance, error);
AKANTU_DEBUG_INFO("Norm of increment : " << error);
return tmp;
}
/* -------------------------------------------------------------------------- */
bool StructuralMechanicsModel::testConvergenceIncrement(Real tolerance,
Real & error) {
AKANTU_DEBUG_IN();
Mesh & mesh = getFEEngine().getMesh();
UInt nb_nodes = displacement_rotation->getSize();
UInt nb_degree_of_freedom = displacement_rotation->getNbComponent();
Real norm = 0;
Real * increment_val = increment->storage();
bool * blocked_dofs_val = blocked_dofs->storage();
for (UInt n = 0; n < nb_nodes; ++n) {
bool is_local_node = mesh.isLocalOrMasterNode(n);
for (UInt d = 0; d < nb_degree_of_freedom; ++d) {
if (!(*blocked_dofs_val) && is_local_node) {
norm += *increment_val * *increment_val;
}
blocked_dofs_val++;
increment_val++;
}
}
StaticCommunicator::getStaticCommunicator().allReduce(&norm, 1, _so_sum);
error = sqrt(norm);
AKANTU_DEBUG_ASSERT(!Math::isnan(norm),
"Something goes wrong in the solve phase");
AKANTU_DEBUG_OUT();
return (error < tolerance);
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<_bernoulli_beam_2>(
Array<Real> & tangent_moduli) {
UInt nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_2);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_bernoulli_beam_2);
UInt tangent_size = 2;
Array<Real>::matrix_iterator D_it =
tangent_moduli.begin(tangent_size, tangent_size);
Array<UInt> & el_mat = element_material(_bernoulli_beam_2, _not_ghost);
for (UInt e = 0; e < nb_element; ++e) {
UInt mat = el_mat(e);
Real E = materials[mat].E;
Real A = materials[mat].A;
Real I = materials[mat].I;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_it) {
Matrix<Real> & D = *D_it;
D(0, 0) = E * A;
D(1, 1) = E * I;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<_bernoulli_beam_3>(
Array<Real> & tangent_moduli) {
UInt nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_3);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_bernoulli_beam_3);
UInt tangent_size = 4;
Array<Real>::matrix_iterator D_it =
tangent_moduli.begin(tangent_size, tangent_size);
for (UInt e = 0; e < nb_element; ++e) {
UInt mat = element_material(_bernoulli_beam_3, _not_ghost)(e);
Real E = materials[mat].E;
Real A = materials[mat].A;
Real Iz = materials[mat].Iz;
Real Iy = materials[mat].Iy;
Real GJ = materials[mat].GJ;
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_it) {
Matrix<Real> & D = *D_it;
D(0, 0) = E * A;
D(1, 1) = E * Iz;
D(2, 2) = E * Iy;
D(3, 3) = GJ;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::computeTangentModuli<_kirchhoff_shell>(
Array<Real> & tangent_moduli) {
UInt nb_element = getFEEngine().getMesh().getNbElement(_kirchhoff_shell);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_kirchhoff_shell);
UInt tangent_size = 6;
Array<Real>::matrix_iterator D_it =
tangent_moduli.begin(tangent_size, tangent_size);
for (UInt e = 0; e < nb_element; ++e) {
UInt mat = element_material(_kirchhoff_shell, _not_ghost)(e);
Real E = materials[mat].E;
Real nu = materials[mat].nu;
Real t = materials[mat].t;
Real HH = E * t / (1 - nu * nu);
Real DD = E * t * t * t / (12 * (1 - nu * nu));
for (UInt q = 0; q < nb_quadrature_points; ++q, ++D_it) {
Matrix<Real> & D = *D_it;
D(0, 0) = HH;
D(0, 1) = HH * nu;
D(1, 0) = HH * nu;
D(1, 1) = HH;
D(2, 2) = HH * (1 - nu) / 2;
D(3, 3) = DD;
D(3, 4) = DD * nu;
D(4, 3) = DD * nu;
D(4, 4) = DD;
D(5, 5) = DD * (1 - nu) / 2;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::transferBMatrixToSymVoigtBMatrix<
_bernoulli_beam_2>(Array<Real> & b, __attribute__((unused)) bool local) {
UInt nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_2);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(_bernoulli_beam_2);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_bernoulli_beam_2);
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
Array<Real>::const_vector_iterator shape_Np =
fem.getShapesDerivatives(_bernoulli_beam_2, _not_ghost, 0)
.begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Mpp =
fem.getShapesDerivatives(_bernoulli_beam_2, _not_ghost, 1)
.begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Lpp =
fem.getShapesDerivatives(_bernoulli_beam_2, _not_ghost, 2)
.begin(nb_nodes_per_element);
UInt tangent_size = getTangentStiffnessVoigtSize<_bernoulli_beam_2>();
UInt bt_d_b_size = nb_nodes_per_element * nb_degree_of_freedom;
b.clear();
Array<Real>::matrix_iterator B_it = b.begin(tangent_size, bt_d_b_size);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt q = 0; q < nb_quadrature_points; ++q) {
Matrix<Real> & B = *B_it;
const Vector<Real> & Np = *shape_Np;
const Vector<Real> & Lpp = *shape_Lpp;
const Vector<Real> & Mpp = *shape_Mpp;
B(0, 0) = Np(0);
B(0, 3) = Np(1);
B(1, 1) = Mpp(0);
B(1, 2) = Lpp(0);
B(1, 4) = Mpp(1);
B(1, 5) = Lpp(1);
++B_it;
++shape_Np;
++shape_Mpp;
++shape_Lpp;
}
// ++R_it;
}
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::transferBMatrixToSymVoigtBMatrix<
_bernoulli_beam_3>(Array<Real> & b, __attribute__((unused)) bool local) {
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
UInt nb_element = getFEEngine().getMesh().getNbElement(_bernoulli_beam_3);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(_bernoulli_beam_3);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_bernoulli_beam_3);
Array<Real>::const_vector_iterator shape_Np =
fem.getShapesDerivatives(_bernoulli_beam_3, _not_ghost, 0)
.begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Mpp =
fem.getShapesDerivatives(_bernoulli_beam_3, _not_ghost, 1)
.begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Lpp =
fem.getShapesDerivatives(_bernoulli_beam_3, _not_ghost, 2)
.begin(nb_nodes_per_element);
UInt tangent_size = getTangentStiffnessVoigtSize<_bernoulli_beam_3>();
UInt bt_d_b_size = nb_nodes_per_element * nb_degree_of_freedom;
b.clear();
Array<Real>::matrix_iterator B_it = b.begin(tangent_size, bt_d_b_size);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt q = 0; q < nb_quadrature_points; ++q) {
Matrix<Real> & B = *B_it;
const Vector<Real> & Np = *shape_Np;
const Vector<Real> & Lpp = *shape_Lpp;
const Vector<Real> & Mpp = *shape_Mpp;
B(0, 0) = Np(0);
B(0, 6) = Np(1);
B(1, 1) = Mpp(0);
B(1, 5) = Lpp(0);
B(1, 7) = Mpp(1);
B(1, 11) = Lpp(1);
B(2, 2) = Mpp(0);
B(2, 4) = -Lpp(0);
B(2, 8) = Mpp(1);
B(2, 10) = -Lpp(1);
B(3, 3) = Np(0);
B(3, 9) = Np(1);
++B_it;
++shape_Np;
++shape_Mpp;
++shape_Lpp;
}
}
}
/* -------------------------------------------------------------------------- */
template <>
void StructuralMechanicsModel::transferBMatrixToSymVoigtBMatrix<
_kirchhoff_shell>(Array<Real> & b, __attribute__((unused)) bool local) {
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
UInt nb_element = getFEEngine().getMesh().getNbElement(_kirchhoff_shell);
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(_kirchhoff_shell);
UInt nb_quadrature_points =
getFEEngine().getNbIntegrationPoints(_kirchhoff_shell);
Array<Real>::const_matrix_iterator shape_Np =
fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 0)
.begin(2, nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Nx1p =
fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 1)
.begin(2, nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Nx2p =
fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 2)
.begin(2, nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Nx3p =
fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 3)
.begin(2, nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Ny1p =
fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 4)
.begin(2, nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Ny2p =
fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 5)
.begin(2, nb_nodes_per_element);
Array<Real>::const_matrix_iterator shape_Ny3p =
fem.getShapesDerivatives(_kirchhoff_shell, _not_ghost, 6)
.begin(2, nb_nodes_per_element);
UInt tangent_size = getTangentStiffnessVoigtSize<_kirchhoff_shell>();
UInt bt_d_b_size = nb_nodes_per_element * nb_degree_of_freedom;
b.clear();
Array<Real>::matrix_iterator B_it = b.begin(tangent_size, bt_d_b_size);
for (UInt e = 0; e < nb_element; ++e) {
for (UInt q = 0; q < nb_quadrature_points; ++q) {
Matrix<Real> & B = *B_it;
const Matrix<Real> & Np = *shape_Np;
const Matrix<Real> & Nx1p = *shape_Nx1p;
const Matrix<Real> & Nx2p = *shape_Nx2p;
const Matrix<Real> & Nx3p = *shape_Nx3p;
const Matrix<Real> & Ny1p = *shape_Ny1p;
const Matrix<Real> & Ny2p = *shape_Ny2p;
const Matrix<Real> & Ny3p = *shape_Ny3p;
B(0, 0) = Np(0, 0);
B(0, 6) = Np(0, 1);
B(0, 12) = Np(0, 2);
B(1, 1) = Np(1, 0);
B(1, 7) = Np(1, 1);
B(1, 13) = Np(1, 2);
B(2, 0) = Np(1, 0);
B(2, 1) = Np(0, 0);
B(2, 6) = Np(1, 1);
B(2, 7) = Np(0, 1);
B(2, 12) = Np(1, 2);
B(2, 13) = Np(0, 2);
B(3, 2) = Nx1p(0, 0);
B(3, 3) = Nx2p(0, 0);
B(3, 4) = Nx3p(0, 0);
B(3, 8) = Nx1p(0, 1);
B(3, 9) = Nx2p(0, 1);
B(3, 10) = Nx3p(0, 1);
B(3, 14) = Nx1p(0, 2);
B(3, 15) = Nx2p(0, 2);
B(3, 16) = Nx3p(0, 2);
B(4, 2) = Ny1p(1, 0);
B(4, 3) = Ny2p(1, 0);
B(4, 4) = Ny3p(1, 0);
B(4, 8) = Ny1p(1, 1);
B(4, 9) = Ny2p(1, 1);
B(4, 10) = Ny3p(1, 1);
B(4, 14) = Ny1p(1, 2);
B(4, 15) = Ny2p(1, 2);
B(4, 16) = Ny3p(1, 2);
B(5, 2) = Nx1p(1, 0) + Ny1p(0, 0);
B(5, 3) = Nx2p(1, 0) + Ny2p(0, 0);
B(5, 4) = Nx3p(1, 0) + Ny3p(0, 0);
B(5, 8) = Nx1p(1, 1) + Ny1p(0, 1);
B(5, 9) = Nx2p(1, 1) + Ny2p(0, 1);
B(5, 10) = Nx3p(1, 1) + Ny3p(0, 1);
B(5, 14) = Nx1p(1, 2) + Ny1p(0, 2);
B(5, 15) = Nx2p(1, 2) + Ny2p(0, 2);
B(5, 16) = Nx3p(1, 2) + Ny3p(0, 2);
++B_it;
++shape_Np;
++shape_Nx1p;
++shape_Nx2p;
++shape_Nx3p;
++shape_Ny1p;
++shape_Ny2p;
++shape_Ny3p;
}
}
}
/* -------------------------------------------------------------------------- */
dumper::Field *
StructuralMechanicsModel::createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
__attribute__((unused)) bool padding_flag) {
std::map<std::string, Array<bool> *> uint_nodal_fields;
uint_nodal_fields["blocked_dofs"] = blocked_dofs;
dumper::Field * field = NULL;
field = mesh.createNodalField(uint_nodal_fields[field_name], group_name);
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field *
StructuralMechanicsModel::createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag) {
UInt n;
if (spatial_dimension == 2) {
n = 2;
} else
n = 3;
dumper::Field * field = NULL;
if (field_name == "displacement") {
field = mesh.createStridedNodalField(displacement_rotation, group_name, n,
0, padding_flag);
}
if (field_name == "rotation") {
field =
mesh.createStridedNodalField(displacement_rotation, group_name,
nb_degree_of_freedom - n, n, padding_flag);
}
if (field_name == "force") {
field = mesh.createStridedNodalField(force_momentum, group_name, n, 0,
padding_flag);
}
if (field_name == "momentum") {
field = mesh.createStridedNodalField(
force_momentum, group_name, nb_degree_of_freedom - n, n, padding_flag);
}
if (field_name == "residual") {
field = mesh.createNodalField(residual, group_name, padding_flag);
}
return field;
}
/* -------------------------------------------------------------------------- */
dumper::Field * StructuralMechanicsModel::createElementalField(
const std::string & field_name, const std::string & group_name,
__attribute__((unused)) bool padding_flag, const ElementKind & kind,
__attribute__((unused)) const std::string & fe_engine_id) {
dumper::Field * field = NULL;
if (field_name == "element_index_by_material")
field = mesh.createElementalField<UInt, Vector, dumper::ElementalField>(
field_name, group_name, this->spatial_dimension, kind);
return field;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/structural_mechanics/structural_mechanics_model.hh b/src/model/structural_mechanics/structural_mechanics_model.hh
index 87a3f298b..f884e79dd 100644
--- a/src/model/structural_mechanics/structural_mechanics_model.hh
+++ b/src/model/structural_mechanics/structural_mechanics_model.hh
@@ -1,392 +1,392 @@
/**
* @file structural_mechanics_model.hh
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Thu Jan 21 2016
*
* @brief Particular implementation of the structural elements in the
* StructuralMechanicsModel
*
* @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_STRUCTURAL_MECHANICS_MODEL_HH__
#define __AKANTU_STRUCTURAL_MECHANICS_MODEL_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "model.hh"
#include "integrator_gauss.hh"
#include "shape_linked.hh"
#include "aka_types.hh"
#include "dumpable.hh"
#include "solver.hh"
#include "integration_scheme_2nd_order.hh"
/* -------------------------------------------------------------------------- */
namespace akantu {
class SparseMatrix;
}
-__BEGIN_AKANTU__
+namespace akantu {
struct StructuralMaterial {
Real E;
Real A;
Real I;
Real Iz;
Real Iy;
Real GJ;
Real rho;
Real t;
Real nu;
};
struct StructuralMechanicsModelOptions : public ModelOptions {
StructuralMechanicsModelOptions(AnalysisMethod analysis_method = _static)
: analysis_method(analysis_method) {}
AnalysisMethod analysis_method;
};
extern const StructuralMechanicsModelOptions
default_structural_mechanics_model_options;
class StructuralMechanicsModel : public Model {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
typedef FEEngineTemplate<IntegratorGauss, ShapeLinked, _ek_structural>
MyFEEngineType;
StructuralMechanicsModel(Mesh & mesh,
UInt spatial_dimension = _all_dimensions,
const ID & id = "structural_mechanics_model",
const MemoryID & memory_id = 0);
virtual ~StructuralMechanicsModel();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// initialize fully the model
void initFull(const ModelOptions & options =
default_structural_mechanics_model_options);
/// initialize the internal vectors
void initArrays();
/// initialize the model
void initModel();
/// initialize the solver
void initSolver(SolverOptions & options = _solver_no_options);
/// initialize the stuff for the implicit solver
void initImplicit(bool dynamic = false,
SolverOptions & solver_options = _solver_no_options);
/// compute the stresses per elements
void computeStresses();
/// assemble the stiffness matrix
void assembleStiffnessMatrix();
/// assemble the mass matrix for consistent mass resolutions
void assembleMass();
/// implicit time integration predictor
void implicitPred();
/// implicit time integration corrector
void implicitCorr();
/// update the residual vector
void updateResidual();
/// solve the system
void solve();
bool testConvergenceIncrement(Real tolerance);
bool testConvergenceIncrement(Real tolerance, Real & error);
void computeRotationMatrix(const ElementType & type);
protected:
UInt getTangentStiffnessVoigtSize(const ElementType & type);
/// compute Rotation Matrices
template <const ElementType type>
void computeRotationMatrix(__attribute__((unused)) Array<Real> & rotations) {}
/// compute A and solve @f[ A\delta u = f_ext - f_int @f]
template <NewmarkBeta::IntegrationSchemeCorrectorType type>
void solve(Array<Real> & increment,
__attribute__((unused)) Real block_val = 1.);
/* ------------------------------------------------------------------------ */
/* Mass (structural_mechanics_model_mass.cc) */
/* ------------------------------------------------------------------------ */
/// assemble the mass matrix for either _ghost or _not_ghost elements
void assembleMass(GhostType ghost_type);
/// computes rho
void computeRho(Array<Real> & rho, ElementType type, GhostType ghost_type);
/// finish the computation of residual to solve in increment
void updateResidualInternal();
/* ------------------------------------------------------------------------ */
private:
template <ElementType type> inline UInt getTangentStiffnessVoigtSize();
template <ElementType type> void assembleStiffnessMatrix();
template <ElementType type> void assembleMass();
template <ElementType type> void computeStressOnQuad();
template <ElementType type>
void computeTangentModuli(Array<Real> & tangent_moduli);
template <ElementType type>
void transferBMatrixToSymVoigtBMatrix(Array<Real> & B, bool local = false);
template <ElementType type>
void transferNMatrixToSymVoigtNMatrix(Array<Real> & N_matrix);
/* ------------------------------------------------------------------------ */
/* Dumpable interface */
/* ------------------------------------------------------------------------ */
public:
virtual dumper::Field * createNodalFieldReal(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
virtual dumper::Field * createNodalFieldBool(const std::string & field_name,
const std::string & group_name,
bool padding_flag);
virtual dumper::Field *
createElementalField(const std::string & field_name,
const std::string & group_name, bool padding_flag,
const ElementKind & kind,
const std::string & fe_engine_id = "");
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// set the value of the time step
void setTimeStep(Real time_step);
/// return the dimension of the system space
AKANTU_GET_MACRO(SpatialDimension, spatial_dimension, UInt);
/// get the StructuralMechanicsModel::displacement vector
AKANTU_GET_MACRO(Displacement, *displacement_rotation, Array<Real> &);
/// get the StructuralMechanicsModel::velocity vector
AKANTU_GET_MACRO(Velocity, *velocity, Array<Real> &);
/// get the StructuralMechanicsModel::acceleration vector, updated
/// by
/// StructuralMechanicsModel::updateAcceleration
AKANTU_GET_MACRO(Acceleration, *acceleration, Array<Real> &);
/// get the StructuralMechanicsModel::force vector (boundary forces)
AKANTU_GET_MACRO(Force, *force_momentum, Array<Real> &);
/// get the StructuralMechanicsModel::residual vector, computed by
/// StructuralMechanicsModel::updateResidual
AKANTU_GET_MACRO(Residual, *residual, const Array<Real> &);
/// get the StructuralMechanicsModel::boundary vector
AKANTU_GET_MACRO(BlockedDOFs, *blocked_dofs, Array<bool> &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(RotationMatrix, rotation_matrix, Real);
AKANTU_GET_MACRO(StiffnessMatrix, *stiffness_matrix, const SparseMatrix &);
AKANTU_GET_MACRO(MassMatrix, *mass_matrix, const SparseMatrix &);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST(Stress, stress, Real);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(ElementMaterial, element_material, UInt);
AKANTU_GET_MACRO_BY_ELEMENT_TYPE(Set_ID, set_ID, UInt);
void addMaterial(StructuralMaterial & material) {
materials.push_back(material);
}
/**
* @brief set the StructuralMechanicsModel::increment_flag to on, the
* activate the
* update of the StructuralMechanicsModel::increment vector
*/
void setIncrementFlagOn();
/* ------------------------------------------------------------------------ */
/* Boundaries (structural_mechanics_model_boundary.cc) */
/* ------------------------------------------------------------------------ */
public:
/// Compute Linear load function set in global axis
template <ElementType type>
void computeForcesByGlobalTractionArray(const Array<Real> & tractions);
/// Compute Linear load function set in local axis
template <ElementType type>
void computeForcesByLocalTractionArray(const Array<Real> & tractions);
/// compute force vector from a function(x,y,momentum) that describe stresses
template <ElementType type>
void computeForcesFromFunction(BoundaryFunction in_function,
BoundaryFunctionType function_type);
/**
* solve a step (predictor + convergence loop + corrector) using the
* the given convergence method (see akantu::SolveConvergenceMethod)
* and the given convergence criteria (see
* akantu::SolveConvergenceCriteria)
**/
template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
bool solveStep(Real tolerance, UInt max_iteration = 100);
template <SolveConvergenceMethod method, SolveConvergenceCriteria criteria>
bool solveStep(Real tolerance, Real & error, UInt max_iteration = 100);
/// test if the system is converged
template <SolveConvergenceCriteria criteria>
bool testConvergence(Real tolerance, Real & error);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// time step
Real time_step;
/// conversion coefficient form force/mass to acceleration
Real f_m2a;
/// displacements array
Array<Real> * displacement_rotation;
/// displacements array at the previous time step (used in finite deformation)
Array<Real> * previous_displacement;
/// velocities array
Array<Real> * velocity;
/// accelerations array
Array<Real> * acceleration;
/// forces array
Array<Real> * force_momentum;
/// lumped mass array
Array<Real> * mass;
/// stress arraz
ElementTypeMapArray<Real> stress;
/// residuals array
Array<Real> * residual;
/// boundaries array
Array<bool> * blocked_dofs;
/// position of a dof in the K matrix
Array<Int> * equation_number;
ElementTypeMapArray<UInt> element_material;
// Define sets of beams
ElementTypeMapArray<UInt> set_ID;
/// local equation_number to global
unordered_map<UInt, UInt>::type local_eq_num_to_global;
/// stiffness matrix
SparseMatrix * stiffness_matrix;
/// mass matrix
SparseMatrix * mass_matrix;
/// velocity damping matrix
SparseMatrix * velocity_damping_matrix;
/// jacobian matrix
SparseMatrix * jacobian_matrix;
/// increment of displacement
Array<Real> * increment;
/// solver for implicit
Solver * solver;
/// number of degre of freedom
UInt nb_degree_of_freedom;
// Rotation matrix
ElementTypeMapArray<Real> rotation_matrix;
/// analysis method check the list in akantu::AnalysisMethod
AnalysisMethod method;
/// flag defining if the increment must be computed or not
bool increment_flag;
/// integration scheme of second order used
IntegrationScheme2ndOrder * integrator;
/* --------------------------------------------------------------------------
*/
std::vector<StructuralMaterial> materials;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "structural_mechanics_model_inline_impl.cc"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const StructuralMechanicsModel & _this) {
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_STRUCTURAL_MECHANICS_MODEL_HH__ */
diff --git a/src/model/structural_mechanics/structural_mechanics_model_boundary.cc b/src/model/structural_mechanics/structural_mechanics_model_boundary.cc
index f26c941b0..3b694b7d3 100644
--- a/src/model/structural_mechanics/structural_mechanics_model_boundary.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model_boundary.cc
@@ -1,222 +1,222 @@
/**
* @file structural_mechanics_model_boundary.cc
*
* @author Fabian Barras <fabian.barras@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
* @author Damien Spielmann <damien.spielmann@epfl.ch>
*
* @date creation: Fri Jul 15 2011
* @date last modification: Sun Oct 19 2014
*
* @brief Implementation of the boundary conditions for StructuralMechanicsModel
*
* @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 "structural_mechanics_model.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::transferNMatrixToSymVoigtNMatrix<_bernoulli_beam_2>(Array<Real> & N_matrix) {
AKANTU_DEBUG_IN();
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
UInt nb_nodes_per_element = getFEEngine().getMesh().getNbNodesPerElement(_bernoulli_beam_2);
Array<Real>::const_vector_iterator shape_N0 = fem.getShapeFunctions().getShapes(_bernoulli_beam_2, _not_ghost, 0).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_M0 = fem.getShapeFunctions().getShapes(_bernoulli_beam_2, _not_ghost, 1).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_L0 = fem.getShapeFunctions().getShapes(_bernoulli_beam_2, _not_ghost, 2).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Mp = fem.getShapeFunctions().getShapes(_bernoulli_beam_2, _not_ghost, 3).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Lp = fem.getShapeFunctions().getShapes(_bernoulli_beam_2, _not_ghost, 4).begin(nb_nodes_per_element);
N_matrix.clear();
Array<Real>::matrix_iterator N_it = N_matrix.begin(nb_degree_of_freedom, nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::matrix_iterator N_end = N_matrix.end(nb_degree_of_freedom, nb_degree_of_freedom * nb_nodes_per_element);
for (;N_it != N_end; ++N_it, ++shape_N0, ++shape_M0, ++shape_L0, ++shape_Mp, ++shape_Lp) {
Matrix<Real> & N = *N_it;
const Vector<Real> & N0 = *shape_N0;
const Vector<Real> & M0 = *shape_M0;
const Vector<Real> & L0 = *shape_L0;
const Vector<Real> & Mp = *shape_Mp;
const Vector<Real> & Lp = *shape_Lp;
N(0,0) = N0(0);
N(0,3) = N0(1);
N(1,1) = M0(0);
N(1,2) = L0(0);
N(1,4) = M0(1);
N(1,5) = L0(1);
N(2,1) = Mp(0);
N(2,2) = Lp(0);
N(2,4) = Mp(1);
N(2,5) = Lp(1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::transferNMatrixToSymVoigtNMatrix<_bernoulli_beam_3>(Array<Real> & N_matrix) {
AKANTU_DEBUG_IN();
ElementType type = _bernoulli_beam_3;
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
UInt nb_nodes_per_element = getFEEngine().getMesh().getNbNodesPerElement(type);
Array<Real>::const_vector_iterator shape_N0 = fem.getShapeFunctions().getShapes(type, _not_ghost, 0).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_M0 = fem.getShapeFunctions().getShapes(type, _not_ghost, 1).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_L0 = fem.getShapeFunctions().getShapes(type, _not_ghost, 2).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Mp = fem.getShapeFunctions().getShapes(type, _not_ghost, 3).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Lp = fem.getShapeFunctions().getShapes(type, _not_ghost, 4).begin(nb_nodes_per_element);
N_matrix.clear();
Array<Real>::matrix_iterator N_it = N_matrix.begin(nb_degree_of_freedom, nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::matrix_iterator N_end = N_matrix.end(nb_degree_of_freedom, nb_degree_of_freedom * nb_nodes_per_element);
for (; N_it != N_end; ++N_it, ++shape_N0, ++shape_M0, ++shape_L0, ++shape_Mp, ++shape_Lp) {
Matrix<Real> & N = *N_it;
const Vector<Real> & N0 = *shape_N0;
const Vector<Real> & M0 = *shape_M0;
const Vector<Real> & L0 = *shape_L0;
const Vector<Real> & Mp = *shape_Mp;
const Vector<Real> & Lp = *shape_Lp;
N(0,0) = N0(0);
N(0,6) = N0(1);
N(1,1) = M0(0);
N(1,5) = L0(0);
N(1,7) = M0(1);
N(1,11) = L0(1);
N(2,2) = M0(0);
N(2,4) = -L0(0);
N(2,8) = M0(1);
N(2,10) = -L0(1);
N(3,3) = N0(0);
N(3,9) = N0(1);
N(4,2) = Mp(0);
N(4,4) = -Lp(0);
N(4,8) = Mp(1);
N(4,10) = -Lp(1);
N(5,1) = Mp(0);
N(5,5) = Lp(0);
N(5,7) = Mp(1);
N(5,11) = Lp(1);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template<>
void StructuralMechanicsModel::transferNMatrixToSymVoigtNMatrix<_kirchhoff_shell>(Array<Real> & N_matrix) {
AKANTU_DEBUG_IN();
ElementType type = _kirchhoff_shell;
MyFEEngineType & fem = getFEEngineClass<MyFEEngineType>();
UInt nb_nodes_per_element = getFEEngine().getMesh().getNbNodesPerElement(type);
Array<Real>::const_vector_iterator shape_N0 = fem.getShapeFunctions().getShapes(type, _not_ghost, 0).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Nw2 = fem.getShapeFunctions().getShapes(type, _not_ghost, 1).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Nw3 = fem.getShapeFunctions().getShapes(type, _not_ghost, 2).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Nx1 = fem.getShapeFunctions().getShapes(type, _not_ghost, 3).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Nx2 = fem.getShapeFunctions().getShapes(type, _not_ghost, 4).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Nx3 = fem.getShapeFunctions().getShapes(type, _not_ghost, 5).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Ny1 = fem.getShapeFunctions().getShapes(type, _not_ghost, 6).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Ny2 = fem.getShapeFunctions().getShapes(type, _not_ghost, 7).begin(nb_nodes_per_element);
Array<Real>::const_vector_iterator shape_Ny3 = fem.getShapeFunctions().getShapes(type, _not_ghost, 8).begin(nb_nodes_per_element);
N_matrix.clear();
Array<Real>::matrix_iterator N_it = N_matrix.begin(nb_degree_of_freedom, nb_degree_of_freedom * nb_nodes_per_element);
Array<Real>::matrix_iterator N_end = N_matrix.end(nb_degree_of_freedom, nb_degree_of_freedom * nb_nodes_per_element);
for (; N_it != N_end; ++N_it, ++shape_N0, ++shape_Nw2, ++shape_Nw3, ++shape_Nx1, ++shape_Nx2, ++shape_Nx3, ++shape_Ny1, ++shape_Ny2, ++shape_Ny3) {
Matrix<Real> & N = *N_it;
const Vector<Real> & N0 = *shape_N0;
const Vector<Real> & Nw2 = *shape_Nw2;
const Vector<Real> & Nw3 = *shape_Nw3;
const Vector<Real> & Nx1 = *shape_Nx1;
const Vector<Real> & Nx2 = *shape_Nx2;
const Vector<Real> & Nx3 = *shape_Nx3;
const Vector<Real> & Ny1 = *shape_Ny1;
const Vector<Real> & Ny2 = *shape_Ny2;
const Vector<Real> & Ny3 = *shape_Ny3;
N(0,0) = N0(0);
N(0,5) = N0(1);
N(0,10) = N0(2);
N(1,1) = N0(0);
N(1,5) = N0(1);
N(1,11) = N0(2);
N(2,2) = N0(0);
N(2,3) = Nw2(0);
N(2,4) = Nw3(0);
N(2,7) = N0(1);
N(2,8) = Nw2(1);
N(2,9) = Nw3(1);
N(2,12) = N0(2);
N(2,13) = Nw2(2);
N(2,14) = Nw3(2);
N(3,2) = Nx1(0);
N(3,3) = Nx2(0);
N(3,4) = Nx3(0);
N(3,7) = Nx1(1);
N(3,8) = Nx2(1);
N(3,9) = Nx3(1);
N(3,12) = Nx1(2);
N(3,13) = Nx2(2);
N(3,14) = Nx3(2);
N(4,2) = Ny1(0);
N(4,3) = Ny2(0);
N(4,4) = Ny3(0);
N(4,7) = Ny1(1);
N(4,8) = Ny2(1);
N(4,9) = Ny3(1);
N(4,12) = Ny1(2);
N(4,13) = Ny2(2);
N(4,14) = Ny3(2);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/model/structural_mechanics/structural_mechanics_model_mass.cc b/src/model/structural_mechanics/structural_mechanics_model_mass.cc
index f9643aabc..d7bbc6811 100644
--- a/src/model/structural_mechanics/structural_mechanics_model_mass.cc
+++ b/src/model/structural_mechanics/structural_mechanics_model_mass.cc
@@ -1,100 +1,100 @@
/**
* @file structural_mechanics_model_mass.cc
*
* @author Sébastien Hartmann <sebastien.hartmann@epfl.ch>
*
* @date creation: Mon Jul 07 2014
* @date last modification: Thu Oct 15 2015
*
* @brief function handling mass computation
*
* @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 "structural_mechanics_model.hh"
#include "material.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleMass(){
AKANTU_DEBUG_IN();
if(!mass_matrix){
std::stringstream sstr; sstr << id << ":mass_matrix";
mass_matrix = new SparseMatrix(*jacobian_matrix, sstr.str(), memory_id);
}
assembleMass(_not_ghost);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::assembleMass(GhostType ghost_type) {
AKANTU_DEBUG_IN();
Array<Real> rho_1(0,1);
mass_matrix->clear();
Mesh::type_iterator it = mesh.firstType(spatial_dimension, ghost_type, _ek_structural);
Mesh::type_iterator end = mesh.lastType(spatial_dimension, ghost_type, _ek_structural);
for(; it != end; ++it){
ElementType type = *it;
#define ASSEMBLE_MASS(type) \
assembleMass<type>();
AKANTU_BOOST_STRUCTURAL_ELEMENT_SWITCH(ASSEMBLE_MASS);
#undef ASSEMBLE_MASS
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void StructuralMechanicsModel::computeRho(Array<Real> & rho,
ElementType type,
GhostType ghost_type) {
AKANTU_DEBUG_IN();
UInt nb_element = getFEEngine().getMesh().getNbElement(type);
UInt nb_quadrature_points = getFEEngine().getNbIntegrationPoints(type);
Array<UInt> & el_mat = element_material(type, ghost_type);
for (UInt e = 0; e < nb_element; ++e){
UInt mat = el_mat(e);
Real rho_el = materials[mat].rho;
for (UInt q = e*nb_quadrature_points; q < e*nb_quadrature_points + nb_quadrature_points; ++q){
rho(q) = rho_el;
}
}
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/model/time_step_solver.hh b/src/model/time_step_solver.hh
index ebb306fbd..03c822aa8 100644
--- a/src/model/time_step_solver.hh
+++ b/src/model/time_step_solver.hh
@@ -1,121 +1,121 @@
/**
* @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;
}
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* 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::predictor()
virtual void predictor();
/// implementation of the SolverCallback::corrector()
virtual void corrector();
/// implementation of the SolverCallback::assembleJacobian()
virtual void assembleJacobian();
/// implementation of the SolverCallback::assembleResidual()
virtual void assembleResidual();
/* ------------------------------------------------------------------------ */
/* 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 &);
/* ------------------------------------------------------------------------ */
/* 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;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_TIME_STEP_SOLVER_HH__ */
diff --git a/src/model/time_step_solvers/time_step_solver.cc b/src/model/time_step_solvers/time_step_solver.cc
index 4df58122a..934d68af2 100644
--- a/src/model/time_step_solvers/time_step_solver.cc
+++ b/src/model/time_step_solvers/time_step_solver.cc
@@ -1,93 +1,93 @@
/**
* @file time_step_solver.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Oct 12 16:56:43 2015
*
* @brief Implementation of common part of TimeStepSolvers
*
* @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 "time_step_solver.hh"
#include "non_linear_solver.hh"
#include "dof_manager.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
TimeStepSolver::TimeStepSolver(DOFManager & dof_manager,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver,
const ID & id, UInt memory_id)
: Memory(id, memory_id), SolverCallback(dof_manager),
_dof_manager(dof_manager), type(type), time_step(0.),
solver_callback(NULL), non_linear_solver(non_linear_solver) {
this->registerSubRegistry("non_linear_solver", non_linear_solver);
}
/* -------------------------------------------------------------------------- */
TimeStepSolver::~TimeStepSolver() {}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::predictor() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != NULL,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->predictor();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::corrector() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != NULL,
"This function cannot be called if the solver_callback is not set");
this->solver_callback->corrector();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleJacobian() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != NULL,
"This function cannot be called if the solver_callback is not set");
// this->_dof_manager.clearMatrix("J");
this->solver_callback->assembleJacobian();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolver::assembleResidual() {
AKANTU_DEBUG_ASSERT(
this->solver_callback != NULL,
"This function cannot be called if the solver_callback is not set");
this->_dof_manager.clearResidual();
this->solver_callback->assembleResidual();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
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 7655c1b8c..327d2fa07 100644
--- a/src/model/time_step_solvers/time_step_solver_default.cc
+++ b/src/model/time_step_solvers/time_step_solver_default.cc
@@ -1,273 +1,273 @@
/**
* @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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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;
}
}
/* -------------------------------------------------------------------------- */
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");
}
IntegrationScheme * integration_scheme = NULL;
if (this->is_mass_lumped) {
switch (type) {
case _ist_forward_euler: {
integration_scheme = new ForwardEuler(dof_manager, dof_id);
break;
}
case _ist_central_difference: {
integration_scheme = new 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 = new PseudoTime(dof_manager, dof_id);
break;
}
case _ist_forward_euler: {
integration_scheme = new ForwardEuler(dof_manager, dof_id);
break;
}
case _ist_trapezoidal_rule_1: {
integration_scheme = new TrapezoidalRule1(dof_manager, dof_id);
break;
}
case _ist_backward_euler: {
integration_scheme = new BackwardEuler(dof_manager, dof_id);
break;
}
case _ist_central_difference: {
integration_scheme = new CentralDifference(dof_manager, dof_id);
break;
}
case _ist_fox_goodwin: {
integration_scheme = new FoxGoodwin(dof_manager, dof_id);
break;
}
case _ist_trapezoidal_rule_2: {
integration_scheme = new TrapezoidalRule2(dof_manager, dof_id);
break;
}
case _ist_linear_acceleration: {
integration_scheme = new LinearAceleration(dof_manager, dof_id);
break;
}
case _ist_generalized_trapezoidal: {
integration_scheme = new GeneralizedTrapezoidal(dof_manager, dof_id);
break;
}
case _ist_newmark_beta:
integration_scheme = new NewmarkBeta(dof_manager, dof_id);
break;
}
}
AKANTU_DEBUG_ASSERT(integration_scheme != nullptr,
"No integration scheme was found for the provided types");
this->integration_schemes[dof_id] = 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() {
DOFsIntegrationSchemesOwner::iterator it =
this->integration_schemes_owner.begin();
DOFsIntegrationSchemesOwner::iterator end =
this->integration_schemes_owner.end();
for (; it != end; ++it) {
delete this->integration_schemes[*it];
}
this->integration_schemes.clear();
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::solveStep(SolverCallback & solver_callback) {
this->solver_callback = &solver_callback;
this->non_linear_solver.solve(*this);
this->solver_callback = NULL;
}
/* -------------------------------------------------------------------------- */
void TimeStepSolverDefault::predictor() {
AKANTU_DEBUG_IN();
TimeStepSolver::predictor();
IntegrationScheme * integration_scheme;
ID dof_id;
for(auto & pair : this->integration_schemes) {
std::tie(dof_id, integration_scheme) = pair;
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();
IntegrationScheme * integration_scheme;
ID dof_id;
for(auto & pair : this->integration_schemes) {
std::tie(dof_id, integration_scheme) = pair;
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::assembleJacobian() {
AKANTU_DEBUG_IN();
TimeStepSolver::assembleJacobian();
IntegrationScheme * integration_scheme;
ID dof_id;
for(auto & pair : this->integration_schemes) {
std::tie(dof_id, integration_scheme) = pair;
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();
TimeStepSolver::assembleResidual();
IntegrationScheme * integration_scheme;
ID dof_id;
for(auto & pair : this->integration_schemes) {
std::tie(dof_id, integration_scheme) = pair;
integration_scheme->assembleResidual(this->is_mass_lumped);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // 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 27ebbec39..5c9e57e83 100644
--- a/src/model/time_step_solvers/time_step_solver_default.hh
+++ b/src/model/time_step_solvers/time_step_solver_default.hh
@@ -1,110 +1,110 @@
/**
* @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 "time_step_solver.hh"
#include "integration_scheme.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__
#define __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__
namespace akantu {
class DOFManagerDefault;
}
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* 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);
virtual bool hasIntegrationScheme(const ID & dof_id) const;
/// implementation of the TimeStepSolver::predictor()
virtual void predictor();
/// implementation of the TimeStepSolver::corrector()
virtual void corrector();
/// implementation of the TimeStepSolver::assembleJacobian()
virtual void assembleJacobian();
/// implementation of the TimeStepSolver::assembleResidual()
virtual void assembleResidual();
/// implementation of the generic TimeStepSolver::solveStep()
virtual void solveStep(SolverCallback & solver_callback);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
typedef std::map<ID, 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;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_TIME_STEP_SOLVER_DEFAULT_HH__ */
diff --git a/src/model/time_step_solvers/time_step_solver_default_explicit.hh b/src/model/time_step_solvers/time_step_solver_default_explicit.hh
index 821bf2f6f..cceb0d50d 100644
--- a/src/model/time_step_solvers/time_step_solver_default_explicit.hh
+++ b/src/model/time_step_solvers/time_step_solver_default_explicit.hh
@@ -1,78 +1,78 @@
/**
* @file time_step_solver_default_explicit.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Aug 24 14:21:44 2015
*
* @brief Default solver for explicit resolution
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH__
#define __AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH__
-__BEGIN_AKANTU__
+namespace akantu {
class TimeStepSolverDefaultExplicit : public TimeStepSolverDefault {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
TimeStepSolverDefaultExplicit();
virtual ~TimeStepSolverDefaultExplicit();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
void solveStep();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "time_step_solver_default_explicit_inline_impl.cc"
/// standard output stream operator
inline std::ostream & operator<<(std::ostream & stream,
const TimeStepSolverDefaultExplicit & _this) {
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_TIME_STEP_SOLVER_DEFAULT_EXPLICIT_HH__ */
diff --git a/src/model/time_step_solvers/time_step_solver_default_solver_callback.hh b/src/model/time_step_solvers/time_step_solver_default_solver_callback.hh
index 96fb125a9..2a4cac0f8 100644
--- a/src/model/time_step_solvers/time_step_solver_default_solver_callback.hh
+++ b/src/model/time_step_solvers/time_step_solver_default_solver_callback.hh
@@ -1,63 +1,63 @@
/**
* @file time_step_solver_default_solver_callback.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Mon Sep 28 18:58:07 2015
*
* @brief Implementation of the NonLinearSolverCallback for 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 "non_linear_solver_callback.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_TIME_STEP_SOLVER_DEFAULT_SOLVER_CALLBACK_HH__
#define __AKANTU_TIME_STEP_SOLVER_DEFAULT_SOLVER_CALLBACK_HH__
-__BEGIN_AKANTU__
+namespace akantu {
class TimeStepSolverCallback : public NonLinearSolverCallback {
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// callback to assemble the Jacobian Matrix
virtual void assembleJacobian();
/// callback to assemble the residual (rhs)
virtual void assembleResidual();
/* ------------------------------------------------------------------------ */
/* Dynamic simulations part */
/* ------------------------------------------------------------------------ */
/// callback for the predictor (in case of dynamic simulation)
virtual void predictor();
/// callback for the corrector (in case of dynamic simulation)
virtual void corrector();
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_TIME_STEP_SOLVER_DEFAULT_SOLVER_CALLBACK_HH__ */
diff --git a/src/python/python_functor.cc b/src/python/python_functor.cc
index edde6ddfe..167ca871b 100644
--- a/src/python/python_functor.cc
+++ b/src/python/python_functor.cc
@@ -1,80 +1,80 @@
/**
* @file python_functor.cc
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Fri Nov 13 2015
*
* @brief Python functor 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 <vector>
#include "python_functor.hh"
#include "aka_common.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
PythonFunctor::PythonFunctor(PyObject * obj):python_obj(obj){
}
/* -------------------------------------------------------------------------- */
PyObject * PythonFunctor::callFunctor(PyObject * functor,
PyObject * args,
PyObject * kwargs) const{
if (!PyCallable_Check(functor))
AKANTU_EXCEPTION("Provided functor is not a function");
PyObject * pValue = PyObject_Call(functor, args,kwargs);
PyObject* exception_type = PyErr_Occurred();
if (exception_type){
PyObject * exception;
PyObject * traceback;
PyErr_Fetch(&exception_type, &exception, &traceback);
PyObject_Print(exception_type, stdout, Py_PRINT_RAW);
PyObject_Print(exception, stdout, Py_PRINT_RAW);
std::stringstream sstr;
sstr << "Exception occured while calling the functor: ";
PyObject * exception_mesg = PyObject_GetAttrString(exception,"message");
if (exception_mesg && PyString_Check(exception_mesg))
sstr << PyString_AsString(exception_mesg);
else
sstr << PyString_AsString(exception);
AKANTU_EXCEPTION(sstr.str());
}
return pValue;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/python/python_functor.hh b/src/python/python_functor.hh
index 0c55677ac..61977c71b 100644
--- a/src/python/python_functor.hh
+++ b/src/python/python_functor.hh
@@ -1,134 +1,134 @@
/**
* @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/>.
*
*/
#ifndef __AKANTU_PYTHON_FUNCTOR_HH__
#define __AKANTU_PYTHON_FUNCTOR_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include <vector>
#include <map>
#include <Python.h>
#include <vector>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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 */
/* ------------------------------------------------------------------------ */
PyObject * python_obj;
};
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include "python_functor_inline_impl.cc"
/* -------------------------------------------------------------------------- */
#endif /* __AKANTU_PYTHON_FUNCTOR_HH__ */
diff --git a/src/python/python_functor_inline_impl.cc b/src/python/python_functor_inline_impl.cc
index 3e5721229..bd9bba712 100644
--- a/src/python/python_functor_inline_impl.cc
+++ b/src/python/python_functor_inline_impl.cc
@@ -1,337 +1,337 @@
/**
* @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/>.
*
*/
#ifndef __AKANTU_PYTHON_FUNCTOR_INLINE_IMPL_CC__
#define __AKANTU_PYTHON_FUNCTOR_INLINE_IMPL_CC__
/* -------------------------------------------------------------------------- */
#include "integration_point.hh"
#include <numpy/arrayobject.h>
#include <typeinfo>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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(__attribute__((unused))
const T & akantu_object) const {
AKANTU_DEBUG_ERROR(
__func__ << " : not implemented yet !" << std::endl
<< debug::demangle(typeid(T).name())
<< "\n*************************************************\n\n\n");
}
/* -------------------------------------------------------------------------- */
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.getSize(), 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");
// if (!PyDict_Check(this->python_obj))
// AKANTU_EXCEPTION("Python object is not a dictionary");
// PyObject * keys = PyDict_Keys(dict);
// PyObject_Print(keys, stdout, Py_PRINT_RAW);
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);
// for (auto a: arg_vector) {
// // if (PyDict_Check(a)){
// // PyObject* values = PyDict_Values(a);
// // UInt sz = PyList_GET_SIZE(values);
// // for (UInt i = 0; i < sz; ++i) {
// // Py_XDECREF(PyList_GetItem(values,i));
// // }
// // }
// // Py_XDECREF(a);
// }
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;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_PYTHON_FUNCTOR_INLINE_IMPL_CC__ */
diff --git a/src/solver/petsc_wrapper.hh b/src/solver/petsc_wrapper.hh
index d562af998..0a36e6a0b 100644
--- a/src/solver/petsc_wrapper.hh
+++ b/src/solver/petsc_wrapper.hh
@@ -1,77 +1,77 @@
/**
* @file petsc_wrapper.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Oct 07 2015
*
* @brief Wrapper of PETSc structures
*
* @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_PETSC_WRAPPER_HH__
#define __AKANTU_PETSC_WRAPPER_HH__
/* -------------------------------------------------------------------------- */
#include <mpi.h>
#include <petscmat.h>
#include <petscvec.h>
#include <petscao.h>
#include <petscis.h>
#include <petscksp.h>
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
struct PETScMatrixWrapper {
Mat mat;
AO ao;
ISLocalToGlobalMapping mapping;
/// MPI communicator for PETSc commands
MPI_Comm communicator;
};
/* -------------------------------------------------------------------------- */
struct PETScSolverWrapper {
KSP ksp;
Vec solution;
Vec rhs;
// MPI communicator for PETSc commands
MPI_Comm communicator;
};
#if not defined(PETSC_CLANGUAGE_CXX)
extern int aka_PETScError(int ierr);
#define CHKERRXX(x) \
do { \
int error = aka_PETScError(x); \
if (error != 0) { AKANTU_EXCEPTION("Error in PETSC"); } \
} while (0)
#endif
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_PETSC_WRAPPER_HH__ */
diff --git a/src/solver/solver_petsc.cc b/src/solver/solver_petsc.cc
index e7ca06be2..2a7c03b30 100644
--- a/src/solver/solver_petsc.cc
+++ b/src/solver/solver_petsc.cc
@@ -1,1107 +1,1107 @@
/**
* @file solver_petsc.cc
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 13 2014
* @date last modification: Tue Jan 19 2016
*
* @brief Solver class implementation for the petsc solver
*
* @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 "solver_petsc.hh"
#include "dof_manager_petsc.hh"
#include "sparse_matrix_petsc.hh"
#include "mpi_type_wrapper.hh"
/* -------------------------------------------------------------------------- */
#include <petscksp.h>
//#include <petscsys.h>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
SolverPETSc::SolverPETSc(DOFManagerPETSc & 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),
matrix(dof_manager.getMatrix(matrix_id)),
is_petsc_data_initialized(false) {
PetscErrorCode ierr;
/// create a solver context
ierr = KSPCreate(PETSC_COMM_WORLD, &this->ksp);
CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
SolverPETSc::~SolverPETSc() {
AKANTU_DEBUG_IN();
this->destroyInternalData();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::destroyInternalData() {
AKANTU_DEBUG_IN();
if (this->is_petsc_data_initialized) {
PetscErrorCode ierr;
ierr = KSPDestroy(&(this->ksp));
CHKERRXX(ierr);
this->is_petsc_data_initialized = false;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::initialize() {
AKANTU_DEBUG_IN();
this->is_petsc_data_initialized = true;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SolverPETSc::solve() {
AKANTU_DEBUG_IN();
Vec & rhs = this->dof_manager.getResidual();
Vec & solution = this->dof_manager.getGlobalSolution();
PetscErrorCode ierr;
ierr = KSPSolve(this->ksp, rhs, solution);
CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
// /* -------------------------------------------------------------------------- */
// void SolverPETSc::solve(Array<Real> & solution) {
// AKANTU_DEBUG_IN();
// this->solution = &solution;
// this->solve();
// PetscErrorCode ierr;
// PETScMatrix * petsc_matrix = static_cast<PETScMatrix *>(this->matrix);
// // ierr = VecGetOwnershipRange(this->petsc_solver_wrapper->solution,
// // solution_begin, solution_end); CHKERRXX(ierr);
// // ierr = VecGetArray(this->petsc_solver_wrapper->solution, PetscScalar
// // **array); CHKERRXX(ierr);
// UInt nb_component = solution.getNbComponent();
// UInt size = solution.getSize();
// for (UInt i = 0; i < size; ++i) {
// for (UInt j = 0; j < nb_component; ++j) {
// UInt i_local = i * nb_component + j;
// if (this->matrix->getDOFSynchronizer().isLocalOrMasterDOF(i_local)) {
// Int i_global =
// this->matrix->getDOFSynchronizer().getDOFGlobalID(i_local);
// ierr = AOApplicationToPetsc(petsc_matrix->getPETScMatrixWrapper()->ao,
// 1, &(i_global));
// CHKERRXX(ierr);
// ierr = VecGetValues(this->petsc_solver_wrapper->solution, 1, &i_global,
// &solution(i, j));
// CHKERRXX(ierr);
// }
// }
// }
// synch_registry->synchronize(_gst_solver_solution);
// AKANTU_DEBUG_OUT();
// }
/* -------------------------------------------------------------------------- */
void SolverPETSc::setOperators() {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
/// set the matrix that defines the linear system and the matrix for
/// preconditioning (here they are the same)
#if PETSC_VERSION_MAJOR >= 3 && PETSC_VERSION_MINOR >= 5
ierr = KSPSetOperators(this->ksp,
this->matrix.getPETScMat(),
this->matrix.getPETScMat());
CHKERRXX(ierr);
#else
ierr = KSPSetOperators(this->ksp,
this->matrix.getPETScMat(),
this->matrix.getPETScMat(),
SAME_NONZERO_PATTERN);
CHKERRXX(ierr);
#endif
/// If this is not called the solution vector is zeroed in the call to
/// KSPSolve().
ierr = KSPSetInitialGuessNonzero(this->ksp, PETSC_TRUE);
KSPSetFromOptions(this->ksp);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
// void finalize_petsc() {
// static bool finalized = false;
// if (!finalized) {
// cout<<"*** INFO *** PETSc is finalizing..."<<endl;
// // finalize PETSc
// PetscErrorCode ierr = PetscFinalize();CHKERRCONTINUE(ierr);
// finalized = true;
// }
// }
// SolverPETSc::sparse_vector_type
// SolverPETSc::operator()(const SolverPETSc::sparse_matrix_type& AA,
// const SolverPETSc::sparse_vector_type& bb) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside PETSc solver: "<<timer<<endl;
// #endif
// #ifdef CPPUTILS_VERBOSE
// out<<" Inside operator()(const sparse_matrix_type&, const
// sparse_vector_type&)... "<<timer<<endl;
// #endif
// assert(AA.rows() == bb.size());
// // KSP ksp; //!< linear solver context
// Vec b; /* RHS */
// PC pc; /* preconditioner context */
// PetscErrorCode ierr;
// PetscInt nlocal;
// PetscInt n = bb.size();
// VecScatter ctx;
// /*
// Create vectors. Note that we form 1 vector from scratch and
// then duplicate as needed. For this simple case let PETSc decide how
// many elements of the vector are stored on each processor. The second
// argument to VecSetSizes() below causes PETSc to decide.
// */
// ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(b,PETSC_DECIDE,n);CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(b);CHKERRCONTINUE(ierr);
// if (!allocated_) {
// ierr = VecDuplicate(b,&x_);CHKERRCONTINUE(ierr);
// } else
// VecZeroEntries(x_);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vectors created... "<<timer<<endl;
// #endif
// /* Set hight-hand-side vector */
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
// bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(b, 1, &row, &it->second, ADD_VALUES);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Right hand side set... "<<timer<<endl;
// #endif
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(b);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(b);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Right-hand-side vector assembled... "<<timer<<endl;
// ierr = VecView(b,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// Vec b_all;
// ierr = VecScatterCreateToAll(b, &ctx, &b_all);CHKERRCONTINUE(ierr);
// ierr =
// VecScatterBegin(ctx,b,b_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// ierr =
// VecScatterEnd(ctx,b,b_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// value_type nrm;
// VecNorm(b_all,NORM_2,&nrm);
// out<<" Norm of right hand side... "<<nrm<<endl;
// #endif
// /* Identify the starting and ending mesh points on each
// processor for the interior part of the mesh. We let PETSc decide
// above. */
// // PetscInt rstart,rend;
// // ierr = VecGetOwnershipRange(x_,&rstart,&rend);CHKERRCONTINUE(ierr);
// ierr = VecGetLocalSize(x_,&nlocal);CHKERRCONTINUE(ierr);
// /*
// Create matrix. When using MatCreate(), the matrix format can
// be specified at runtime.
// Performance tuning note: For problems of substantial size,
// preallocation of matrix memory is crucial for attaining good
// performance. See the matrix chapter of the users manual for details.
// We pass in nlocal as the "local" size of the matrix to force it
// to have the same parallel layout as the vector created above.
// */
// if (!allocated_) {
// ierr = MatCreate(PETSC_COMM_WORLD,&A_);CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(A_,nlocal,nlocal,n,n);CHKERRCONTINUE(ierr);
// ierr = MatSetFromOptions(A_);CHKERRCONTINUE(ierr);
// ierr = MatSetUp(A_);CHKERRCONTINUE(ierr);
// } else {
// // zero-out matrix
// MatZeroEntries(A_);
// }
// /*
// Assemble matrix.
// The linear system is distributed across the processors by
// chunks of contiguous rows, which correspond to contiguous
// sections of the mesh on which the problem is discretized.
// For matrix assembly, each processor contributes entries for
// the part that it owns locally.
// */
// #ifdef CPPUTILS_VERBOSE
// out<<" Zeroed-out sparse matrix entries... "<<timer<<endl;
// #endif
// for (sparse_matrix_type::const_hash_iterator it = AA.map_.begin(); it !=
// AA.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = AA.unhash(it->first);
// PetscInt row = subs.first;
// PetscInt col = subs.second;
// ierr = MatSetValues(A_, 1, &row, 1, &col, &it->second,
// ADD_VALUES);CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Filled sparse matrix... "<<timer<<endl;
// #endif
// /* Assemble the matrix */
// ierr = MatAssemblyBegin(A_,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(A_,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// if (!allocated_) {
// // set after the first MatAssemblyEnd
// // ierr = MatSetOption(A_, MAT_NEW_NONZERO_LOCATIONS,
// PETSC_FALSE);CHKERRCONTINUE(ierr);
// ierr = MatSetOption(A_, MAT_NEW_NONZERO_ALLOCATION_ERR,
// PETSC_FALSE);CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Sparse matrix assembled... "<<timer<<endl;
// // view matrix
// MatView(A_, PETSC_VIEWER_STDOUT_WORLD);
// MatNorm(A_,NORM_FROBENIUS,&nrm);
// out<<" Norm of stiffness matrix... "<<nrm<<endl;
// #endif
// /*
// Set operators. Here the matrix that defines the linear system
// also serves as the preconditioning matrix.
// */
// // ierr =
// KSPSetOperators(ksp,A_,A_,DIFFERENT_NONZERO_PATTERN);CHKERRCONTINUE(ierr);
// ierr =
// KSPSetOperators(ksp_,A_,A_,SAME_NONZERO_PATTERN);CHKERRCONTINUE(ierr);
// //
// // /*
// // Set runtime options, e.g.,
// // -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
// // These options will override those specified above as long as
// // KSPSetFromOptions() is called _after_ any other customization
// // routines.
// // */
// // ierr = KSPSetFromOptions(ksp);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Solving system... "<<timer<<endl;
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Solve the linear system
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// /*
// Solve linear system
// */
// ierr = KSPSolve(ksp_,b,x_);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// /*
// View solver info; we could instead use the option -ksp_view to
// print this info to the screen at the conclusion of KSPSolve().
// */
// ierr = KSPView(ksp_,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// int iter;
// KSPGetIterationNumber(ksp_, &iter);
// out<<" System solved in "<<iter<<" iterations... "<<timer<<endl;
// KSPConvergedReason reason;
// ierr = KSPGetConvergedReason(ksp_,&reason);CHKERRCONTINUE(ierr);
// if (reason < 0)
// out<<"*** WARNING *** PETSc solver diverged with flag ";
// else
// out<<"*** INFO *** PETSc solver converged with flag ";
// if (reason == KSP_CONVERGED_RTOL)
// out<<"KSP_CONVERGED_RTOL"<<endl;
// else if (reason == KSP_CONVERGED_ATOL)
// out<<"KSP_CONVERGED_ATOL"<<endl;
// else if (reason == KSP_CONVERGED_ITS)
// out<<"KSP_CONVERGED_ITS"<<endl;
// else if (reason == KSP_CONVERGED_CG_NEG_CURVE)
// out<<"KSP_CONVERGED_CG_NEG_CURVE"<<endl;
// else if (reason == KSP_CONVERGED_CG_CONSTRAINED)
// out<<"KSP_CONVERGED_CG_CONSTRAINED"<<endl;
// else if (reason == KSP_CONVERGED_STEP_LENGTH)
// out<<"KSP_CONVERGED_STEP_LENGTH"<<endl;
// else if (reason == KSP_CONVERGED_HAPPY_BREAKDOWN)
// out<<"KSP_CONVERGED_HAPPY_BREAKDOWN"<<endl;
// else if (reason == KSP_DIVERGED_NULL)
// out<<"KSP_DIVERGED_NULL"<<endl;
// else if (reason == KSP_DIVERGED_ITS)
// out<<"KSP_DIVERGED_ITS"<<endl;
// else if (reason == KSP_DIVERGED_DTOL)
// out<<"KSP_DIVERGED_DTOL"<<endl;
// else if (reason == KSP_DIVERGED_BREAKDOWN)
// out<<"KSP_DIVERGED_BREAKDOWN"<<endl;
// else if (reason == KSP_DIVERGED_BREAKDOWN_BICG)
// out<<"KSP_DIVERGED_BREAKDOWN_BICG"<<endl;
// else if (reason == KSP_DIVERGED_NONSYMMETRIC)
// out<<"KSP_DIVERGED_NONSYMMETRIC"<<endl;
// else if (reason == KSP_DIVERGED_INDEFINITE_PC)
// out<<"KSP_DIVERGED_INDEFINITE_PC"<<endl;
// else if (reason == KSP_DIVERGED_NAN)
// out<<"KSP_DIVERGED_NAN"<<endl;
// else if (reason == KSP_DIVERGED_INDEFINITE_MAT)
// out<<"KSP_DIVERGED_INDEFINITE_MAT"<<endl;
// else if (reason == KSP_CONVERGED_ITERATING)
// out<<"KSP_CONVERGED_ITERATING"<<endl;
// PetscReal rnorm;
// ierr = KSPGetResidualNorm(ksp_,&rnorm);CHKERRCONTINUE(ierr);
// out<<"PETSc last residual norm computed: "<<rnorm<<endl;
// ierr = VecView(x_,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// VecNorm(x_,NORM_2,&nrm);
// out<<" Norm of solution vector... "<<nrm<<endl;
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Check solution and clean up
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// Vec x_all;
// ierr = VecScatterCreateToAll(x_, &ctx, &x_all);CHKERRCONTINUE(ierr);
// ierr =
// VecScatterBegin(ctx,x_,x_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// ierr =
// VecScatterEnd(ctx,x_,x_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Solution vector scattered... "<<timer<<endl;
// VecNorm(x_all,NORM_2,&nrm);
// out<<" Norm of scattered vector... "<<nrm<<endl;
// // ierr = VecView(x_all,PETSC_VIEWER_STDOUT_WORLD);CHKERRCONTINUE(ierr);
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Get values from solution and store them in the object that will be
// returned
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// sparse_vector_type xx(bb.size());
// /* Set solution vector */
// double zero = 0.;
// double val;
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
// bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecGetValues(x_all, 1, &row, &val);
// if (val != zero)
// xx[row] = val;
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Solution vector copied... "<<timer<<endl;
// // out<<" Norm of copied solution vector... "<<norm(xx,
// Insert_t)<<endl;
// #endif
// /*
// Free work space. All PETSc objects should be destroyed when they
// are no longer needed.
// */
// ierr = VecDestroy(&b);CHKERRCONTINUE(ierr);
// // ierr = KSPDestroy(&ksp);CHKERRCONTINUE(ierr);
// // set allocated flag
// if (!allocated_) {
// allocated_ = true;
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return xx;
// }
// SolverPETSc::sparse_vector_type SolverPETSc::operator()(const
// SolverPETSc::sparse_matrix_type& KKpf, const SolverPETSc::sparse_matrix_type&
// KKpp, const SolverPETSc::sparse_vector_type& UUp) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::operator()(const sparse_matrix&, const
// sparse_matrix&, const sparse_vector&). "<<timer<<endl;
// #endif
// Mat Kpf, Kpp;
// Vec Up, Pf, Pp;
// PetscErrorCode ierr =
// MatCreate(PETSC_COMM_WORLD,&Kpf);CHKERRCONTINUE(ierr);
// ierr = MatCreate(PETSC_COMM_WORLD,&Kpp);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Allocating memory... "<<timer<<endl;
// #endif
// ierr = MatSetFromOptions(Kpf);CHKERRCONTINUE(ierr);
// ierr = MatSetFromOptions(Kpp);CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(Kpf,PETSC_DECIDE,PETSC_DECIDE, KKpf.rows(),
// KKpf.columns());CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(Kpp,PETSC_DECIDE,PETSC_DECIDE, KKpp.rows(),
// KKpp.columns());CHKERRCONTINUE(ierr);
// // get number of non-zeros in both diagonal and non-diagonal portions of
// the matrix
// std::pair<size_t,size_t> Kpf_nz = KKpf.non_zero_off_diagonal();
// std::pair<size_t,size_t> Kpp_nz = KKpp.non_zero_off_diagonal();
// ierr = MatMPIAIJSetPreallocation(Kpf, Kpf_nz.first, PETSC_NULL,
// Kpf_nz.second, PETSC_NULL); CHKERRCONTINUE(ierr);
// ierr = MatMPIAIJSetPreallocation(Kpp, Kpp_nz.first, PETSC_NULL,
// Kpp_nz.second, PETSC_NULL); CHKERRCONTINUE(ierr);
// ierr = MatSeqAIJSetPreallocation(Kpf, Kpf_nz.first, PETSC_NULL);
// CHKERRCONTINUE(ierr);
// ierr = MatSeqAIJSetPreallocation(Kpp, Kpp_nz.first, PETSC_NULL);
// CHKERRCONTINUE(ierr);
// for (sparse_matrix_type::const_hash_iterator it = KKpf.map_.begin(); it !=
// KKpf.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = KKpf.unhash(it->first);
// int row = subs.first;
// int col = subs.second;
// ierr = MatSetValues(Kpf, 1, &row, 1, &col, &it->second,
// ADD_VALUES);CHKERRCONTINUE(ierr);
// }
// for (sparse_matrix_type::const_hash_iterator it = KKpp.map_.begin(); it !=
// KKpp.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = KKpp.unhash(it->first);
// int row = subs.first;
// int col = subs.second;
// ierr = MatSetValues(Kpf, 1, &row, 1, &col, &it->second,
// ADD_VALUES);CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Filled sparse matrices... "<<timer<<endl;
// #endif
// /*
// Assemble matrix, using the 2-step process:
// MatAssemblyBegin(), MatAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = MatAssemblyBegin(Kpf,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyBegin(Kpp,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(Kpf,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(Kpp,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Sparse matrices assembled... "<<timer<<endl;
// #endif
// ierr = VecCreate(PETSC_COMM_WORLD,&Up);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(Up,PETSC_DECIDE, UUp.size());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(Up);CHKERRCONTINUE(ierr);
// ierr = VecCreate(PETSC_COMM_WORLD,&Pf);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(Pf,PETSC_DECIDE, KKpf.rows());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(Pf);CHKERRCONTINUE(ierr);
// ierr = VecDuplicate(Pf,&Pp);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vectors created... "<<timer<<endl;
// #endif
// /* Set hight-hand-side vector */
// for (sparse_vector_type::const_hash_iterator it = UUp.map_.begin(); it !=
// UUp.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(Up, 1, &row, &it->second, ADD_VALUES);
// }
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(Up);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(Up);CHKERRCONTINUE(ierr);
// // add Kpf*Uf
// ierr = MatMult(Kpf, x_, Pf);
// // add Kpp*Up
// ierr = MatMultAdd(Kpp, Up, Pf, Pp);
// #ifdef CPPUTILS_VERBOSE
// out<<" Matrices multiplied... "<<timer<<endl;
// #endif
// VecScatter ctx;
// Vec Pp_all;
// ierr = VecScatterCreateToAll(Pp, &ctx, &Pp_all);CHKERRCONTINUE(ierr);
// ierr =
// VecScatterBegin(ctx,Pp,Pp_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// ierr =
// VecScatterEnd(ctx,Pp,Pp_all,INSERT_VALUES,SCATTER_FORWARD);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector scattered... "<<timer<<endl;
// #endif
// /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
// Get values from solution and store them in the object that will be
// returned
// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
// sparse_vector_type pp(KKpf.rows());
// // get reaction vector
// for (int i=0; i<KKpf.rows(); ++i) {
// PetscScalar v;
// ierr = VecGetValues(Pp_all, 1, &i, &v);
// if (v != PetscScalar())
// pp[i] = v;
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector copied... "<<timer<<endl;
// #endif
// ierr = MatDestroy(&Kpf);CHKERRCONTINUE(ierr);
// ierr = MatDestroy(&Kpp);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Up);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Pf);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Pp);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&Pp_all);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return pp;
// }
// SolverPETSc::sparse_vector_type SolverPETSc::operator()(const
// SolverPETSc::sparse_vector_type& aa, const SolverPETSc::sparse_vector_type&
// bb) {
// assert(aa.size() == bb.size());
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::operator()(const sparse_vector&, const
// sparse_vector&). "<<timer<<endl;
// #endif
// Vec r;
// PetscErrorCode ierr = VecCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(r,PETSC_DECIDE, aa.size());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vectors created... "<<timer<<endl;
// #endif
// // set values
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
// aa.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
// }
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
// bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
// }
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(r);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(r);CHKERRCONTINUE(ierr);
// sparse_vector_type rr(aa.size());
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
// aa.map_.end(); ++it) {
// int row = it->first;
// ierr = VecGetValues(r, 1, &row, &rr[row]);
// }
// for (sparse_vector_type::const_hash_iterator it = bb.map_.begin(); it !=
// bb.map_.end(); ++it) {
// int row = it->first;
// ierr = VecGetValues(r, 1, &row, &rr[row]);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector copied... "<<timer<<endl;
// #endif
// ierr = VecDestroy(&r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return rr;
// }
// SolverPETSc::value_type SolverPETSc::norm(const
// SolverPETSc::sparse_matrix_type& aa, Element_insertion_type flag) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::norm(const sparse_matrix&). "<<timer<<endl;
// #endif
// Mat r;
// PetscErrorCode ierr = MatCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
// ierr = MatSetSizes(r,PETSC_DECIDE,PETSC_DECIDE, aa.rows(),
// aa.columns());CHKERRCONTINUE(ierr);
// ierr = MatSetFromOptions(r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Matrix created... "<<timer<<endl;
// #endif
// // set values
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
// aa.map_.end(); ++it) {
// // get subscripts
// std::pair<size_t,size_t> subs = aa.unhash(it->first);
// int row = subs.first;
// int col = subs.second;
// if (flag == Add_t)
// ierr = MatSetValues(r, 1, &row, 1, &col, &it->second, ADD_VALUES);
// else if (flag == Insert_t)
// ierr = MatSetValues(r, 1, &row, 1, &col, &it->second, INSERT_VALUES);
// CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Matrix filled..."<<timer<<endl;
// #endif
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = MatAssemblyBegin(r,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// ierr = MatAssemblyEnd(r,MAT_FINAL_ASSEMBLY);CHKERRCONTINUE(ierr);
// value_type nrm;
// MatNorm(r,NORM_FROBENIUS,&nrm);
// #ifdef CPPUTILS_VERBOSE
// out<<" Norm computed... "<<timer<<endl;
// #endif
// ierr = MatDestroy(&r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return nrm;
// }
// SolverPETSc::value_type SolverPETSc::norm(const
// SolverPETSc::sparse_vector_type& aa, Element_insertion_type flag) {
// #ifdef CPPUTILS_VERBOSE
// // parallel output stream
// Output_stream out;
// // timer
// cpputils::ctimer timer;
// out<<"Inside SolverPETSc::norm(const sparse_vector&). "<<timer<<endl;
// #endif
// Vec r;
// PetscErrorCode ierr = VecCreate(PETSC_COMM_WORLD,&r);CHKERRCONTINUE(ierr);
// ierr = VecSetSizes(r,PETSC_DECIDE, aa.size());CHKERRCONTINUE(ierr);
// ierr = VecSetFromOptions(r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector created... "<<timer<<endl;
// #endif
// // set values
// for (sparse_vector_type::const_hash_iterator it = aa.map_.begin(); it !=
// aa.map_.end(); ++it) {
// int row = it->first;
// if (flag == Add_t)
// ierr = VecSetValues(r, 1, &row, &it->second, ADD_VALUES);
// else if (flag == Insert_t)
// ierr = VecSetValues(r, 1, &row, &it->second, INSERT_VALUES);
// CHKERRCONTINUE(ierr);
// }
// #ifdef CPPUTILS_VERBOSE
// out<<" Vector filled..."<<timer<<endl;
// #endif
// /*
// Assemble vector, using the 2-step process:
// VecAssemblyBegin(), VecAssemblyEnd()
// Computations can be done while messages are in transition
// by placing code between these two statements.
// */
// ierr = VecAssemblyBegin(r);CHKERRCONTINUE(ierr);
// ierr = VecAssemblyEnd(r);CHKERRCONTINUE(ierr);
// value_type nrm;
// VecNorm(r,NORM_2,&nrm);
// #ifdef CPPUTILS_VERBOSE
// out<<" Norm computed... "<<timer<<endl;
// #endif
// ierr = VecDestroy(&r);CHKERRCONTINUE(ierr);
// #ifdef CPPUTILS_VERBOSE
// out<<" Temporary data structures destroyed... "<<timer<<endl;
// #endif
// return nrm;
// }
// //
// ///*
// -------------------------------------------------------------------------- */
// //SolverMumps::SolverMumps(SparseMatrix & matrix,
// // const ID & id,
// // const MemoryID & memory_id) :
// //Solver(matrix, id, memory_id), is_mumps_data_initialized(false),
// rhs_is_local(true) {
// // AKANTU_DEBUG_IN();
// //
// //#ifdef AKANTU_USE_MPI
// // parallel_method = SolverMumpsOptions::_fully_distributed;
// //#else //AKANTU_USE_MPI
// // parallel_method = SolverMumpsOptions::_master_slave_distributed;
// //#endif //AKANTU_USE_MPI
// //
// // CommunicatorEventHandler & comm_event_handler = *this;
// //
// // communicator.registerEventHandler(comm_event_handler);
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///*
// -------------------------------------------------------------------------- */
// //SolverMumps::~SolverMumps() {
// // AKANTU_DEBUG_IN();
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///*
// -------------------------------------------------------------------------- */
// //void SolverMumps::destroyMumpsData() {
// // AKANTU_DEBUG_IN();
// //
// // if(is_mumps_data_initialized) {
// // mumps_data.job = _smj_destroy; // destroy
// // dmumps_c(&mumps_data);
// // is_mumps_data_initialized = false;
// // }
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///*
// -------------------------------------------------------------------------- */
// //void SolverMumps::onCommunicatorFinalize(const StaticCommunicator & comm) {
// // AKANTU_DEBUG_IN();
// //
// // try{
// // const StaticCommunicatorMPI & comm_mpi =
// // dynamic_cast<const StaticCommunicatorMPI
// &>(comm.getRealStaticCommunicator());
// // if(mumps_data.comm_fortran ==
// MPI_Comm_c2f(comm_mpi.getMPICommunicator()))
// // destroyMumpsData();
// // } catch(...) {}
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///*
// -------------------------------------------------------------------------- */
// //void SolverMumps::initMumpsData(SolverMumpsOptions::ParallelMethod
// parallel_method) {
// // switch(parallel_method) {
// // case SolverMumpsOptions::_fully_distributed:
// // icntl(18) = 3; //fully distributed
// // icntl(28) = 0; //automatic choice
// //
// // mumps_data.nz_loc = matrix->getNbNonZero();
// // mumps_data.irn_loc = matrix->getIRN().values;
// // mumps_data.jcn_loc = matrix->getJCN().values;
// // break;
// // case SolverMumpsOptions::_master_slave_distributed:
// // if(prank == 0) {
// // mumps_data.nz = matrix->getNbNonZero();
// // mumps_data.irn = matrix->getIRN().values;
// // mumps_data.jcn = matrix->getJCN().values;
// // } else {
// // mumps_data.nz = 0;
// // mumps_data.irn = NULL;
// // mumps_data.jcn = NULL;
// //
// // icntl(18) = 0; //centralized
// // icntl(28) = 0; //sequential analysis
// // }
// // break;
// // }
// //}
// //
// ///*
// -------------------------------------------------------------------------- */
// //void SolverMumps::initialize(SolverOptions & options) {
// // AKANTU_DEBUG_IN();
// //
// // mumps_data.par = 1;
// //
// // if(SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions
// *>(&options)) {
// // if(opt->parallel_method ==
// SolverMumpsOptions::_master_slave_distributed) {
// // mumps_data.par = 0;
// // }
// // }
// //
// // mumps_data.sym = 2 * (matrix->getSparseMatrixType() == _symmetric);
// // prank = communicator.whoAmI();
// //#ifdef AKANTU_USE_MPI
// // mumps_data.comm_fortran = MPI_Comm_c2f(dynamic_cast<const
// StaticCommunicatorMPI
// &>(communicator.getRealStaticCommunicator()).getMPICommunicator());
// //#endif
// //
// // if(AKANTU_DEBUG_TEST(dblTrace)) {
// // icntl(1) = 2;
// // icntl(2) = 2;
// // icntl(3) = 2;
// // icntl(4) = 4;
// // }
// //
// // mumps_data.job = _smj_initialize; //initialize
// // dmumps_c(&mumps_data);
// // is_mumps_data_initialized = true;
// //
// // /*
// ------------------------------------------------------------------------ */
// // UInt size = matrix->getSize();
// //
// // if(prank == 0) {
// // std::stringstream sstr_rhs; sstr_rhs << id << ":rhs";
// // rhs = &(alloc<Real>(sstr_rhs.str(), size, 1, REAL_INIT_VALUE));
// // } else {
// // rhs = NULL;
// // }
// //
// // /// No outputs
// // icntl(1) = 0;
// // icntl(2) = 0;
// // icntl(3) = 0;
// // icntl(4) = 0;
// // mumps_data.nz_alloc = 0;
// //
// // if (AKANTU_DEBUG_TEST(dblDump)) icntl(4) = 4;
// //
// // mumps_data.n = size;
// //
// // if(AKANTU_DEBUG_TEST(dblDump)) {
// // strcpy(mumps_data.write_problem, "mumps_matrix.mtx");
// // }
// //
// // /*
// ------------------------------------------------------------------------ */
// // // Default Scaling
// // icntl(8) = 77;
// //
// // icntl(5) = 0; // Assembled matrix
// //
// // SolverMumpsOptions * opt = dynamic_cast<SolverMumpsOptions *>(&options);
// // if(opt)
// // parallel_method = opt->parallel_method;
// //
// // initMumpsData(parallel_method);
// //
// // mumps_data.job = _smj_analyze; //analyze
// // dmumps_c(&mumps_data);
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///*
// -------------------------------------------------------------------------- */
// //void SolverMumps::setRHS(Array<Real> & rhs) {
// // if(prank == 0) {
// // matrix->getDOFSynchronizer().gather(rhs, 0, this->rhs);
// // } else {
// // matrix->getDOFSynchronizer().gather(rhs, 0);
// // }
// //}
// //
// ///*
// -------------------------------------------------------------------------- */
// //void SolverMumps::solve() {
// // AKANTU_DEBUG_IN();
// //
// // if(parallel_method == SolverMumpsOptions::_fully_distributed)
// // mumps_data.a_loc = matrix->getA().values;
// // else
// // if(prank == 0) {
// // mumps_data.a = matrix->getA().values;
// // }
// //
// // if(prank == 0) {
// // mumps_data.rhs = rhs->values;
// // }
// //
// // /// Default centralized dense second member
// // icntl(20) = 0;
// // icntl(21) = 0;
// //
// // mumps_data.job = _smj_factorize_solve; //solve
// // dmumps_c(&mumps_data);
// //
// // AKANTU_DEBUG_ASSERT(info(1) != -10, "Singular matrix");
// // AKANTU_DEBUG_ASSERT(info(1) == 0,
// // "Error in mumps during solve process, check mumps
// user guide INFO(1) ="
// // << info(1));
// //
// // AKANTU_DEBUG_OUT();
// //}
// //
// ///*
// -------------------------------------------------------------------------- */
// //void SolverMumps::solve(Array<Real> & solution) {
// // AKANTU_DEBUG_IN();
// //
// // solve();
// //
// // if(prank == 0) {
// // matrix->getDOFSynchronizer().scatter(solution, 0, this->rhs);
// // } else {
// // matrix->getDOFSynchronizer().scatter(solution, 0);
// // }
// //
// // AKANTU_DEBUG_OUT();
// //}
-__END_AKANTU__
+} // akantu
diff --git a/src/solver/solver_petsc.hh b/src/solver/solver_petsc.hh
index 8394d52e8..a992347cd 100644
--- a/src/solver/solver_petsc.hh
+++ b/src/solver/solver_petsc.hh
@@ -1,182 +1,182 @@
/**
* @file solver_petsc.hh
*
* @author Alejandro M. Aragón <alejandro.aragon@epfl.ch>
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue May 13 2014
* @date last modification: Wed Oct 07 2015
*
* @brief Solver class interface for the petsc solver
*
* @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 "sparse_solver.hh"
/* -------------------------------------------------------------------------- */
#include <petscksp.h>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLVER_PETSC_HH__
#define __AKANTU_SOLVER_PETSC_HH__
namespace akantu {
class SparseMatrixPETSc;
class DOFManagerPETSc;
}
-__BEGIN_AKANTU__
+namespace akantu {
class SolverPETSc : public SparseSolver {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SolverPETSc(DOFManagerPETSc & dof_manager, const ID & matrix_id,
const ID & id = "solver_petsc", const MemoryID & memory_id = 0);
virtual ~SolverPETSc();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// create the solver context and set the matrices
virtual void initialize();
virtual void setOperators();
virtual void setRHS(Array<Real> & rhs);
virtual void solve();
virtual void solve(Array<Real> & solution);
private:
/// clean the petsc data
virtual void destroyInternalData();
private:
/// DOFManager correctly typed
DOFManagerPETSc & dof_manager;
/// PETSc linear solver
KSP ksp;
/// Matrix defining the system of equations
SparseMatrixPETSc & matrix;
/// specify if the petsc_data is initialized or not
bool is_petsc_data_initialized;
};
// SolverPETSc(int argc, char *argv[]) : allocated_(false) {
// /*
// Set linear solver defaults for this problem (optional).
// - By extracting the KSP and PC contexts from the KSP context,
// we can then directly call any KSP and PC routines to set
// various options.
// - The following four statements are optional; all of these
// parameters could alternatively be specified at runtime via
// KSPSetFromOptions();
// */
// // ierr = KSPGetPC(ksp_,&pc);CHKERRCONTINUE(ierr);
// // ierr = PCSetType(pc,PCILU);CHKERRCONTINUE(ierr);
// // ierr = PCSetType(pc,PCJACOBI);CHKERRCONTINUE(ierr);
// ierr =
// KSPSetTolerances(ksp_,1.e-5,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRCONTINUE(ierr);
// }
// //! Overload operator() to solve system of linear equations
// sparse_vector_type operator()(const sparse_matrix_type& AA, const
// sparse_vector_type& bb);
// //! Overload operator() to obtain reaction vector
// sparse_vector_type operator()(const sparse_matrix_type& Kpf, const
// sparse_matrix_type& Kpp, const sparse_vector_type& Up);
// //! Overload operator() to obtain the addition two vectors
// sparse_vector_type operator()(const sparse_vector_type& aa, const
// sparse_vector_type& bb);
// value_type norm(const sparse_matrix_type& aa, Element_insertion_type it =
// Add_t);
// value_type norm(const sparse_vector_type& aa, Element_insertion_type it =
// Add_t);
// // NOTE: the destructor will return an error if it is called after
// MPI_Finalize is
// // called because it uses collect communication to free-up allocated
// memory.
// ~SolverPETSc() {
// static bool exit = false;
// if (!exit) {
// // add finalize PETSc function at exit
// atexit(finalize);
// exit = true;
// }
// if (allocated_) {
// PetscErrorCode ierr = MatDestroy(&A_);CHKERRCONTINUE(ierr);
// ierr = VecDestroy(&x_);CHKERRCONTINUE(ierr);
// ierr = KSPDestroy(&ksp_);CHKERRCONTINUE(ierr);
// }
// }
// /* from the PETSc library, these are the options that can be passed
// to the command line
// Options Database Keys
// -options_table - Calls PetscOptionsView()
// -options_left - Prints unused options that remain in the
// database
// -objects_left - Prints list of all objects that have not
// been freed
// -mpidump - Calls PetscMPIDump()
// -malloc_dump - Calls PetscMallocDump()
// -malloc_info - Prints total memory usage
// -malloc_log - Prints summary of memory usage
// Options Database Keys for Profiling
// -log_summary [filename] - Prints summary of flop and timing
// information to screen.
// If the filename is specified the summary is written to the file. See
// PetscLogView().
// -log_summary_python [filename] - Prints data on of flop and timing usage
// to a file or screen.
// -log_all [filename] - Logs extensive profiling information See
// PetscLogDump().
// -log [filename] - Logs basic profiline information See
// PetscLogDump().
// -log_sync - Log the synchronization in scatters,
// inner products and norms
// -log_mpe [filename] - Creates a logfile viewable by the utility
// Upshot/Nupshot (in MPICH distribution)
// }
// }
// };
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_SOLVER_PETSC_HH__ */
diff --git a/src/solver/sparse_matrix.cc b/src/solver/sparse_matrix.cc
index ee229bde1..c24d5d855 100644
--- a/src/solver/sparse_matrix.cc
+++ b/src/solver/sparse_matrix.cc
@@ -1,80 +1,80 @@
/**
* @file sparse_matrix.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Mon Nov 16 2015
*
* @brief implementation of the SparseMatrix 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 <fstream>
/* -------------------------------------------------------------------------- */
#include "dof_manager.hh"
#include "sparse_matrix.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrix::SparseMatrix(DOFManager & dof_manager,
const MatrixType & matrix_type, const ID & id)
: id(id), _dof_manager(dof_manager), matrix_type(matrix_type),
size(dof_manager.getSystemSize()), nb_non_zero(0) {
AKANTU_DEBUG_IN();
const auto & comm = _dof_manager.getCommunicator();
this->nb_proc = comm.getNbProc();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrix::SparseMatrix(const SparseMatrix & matrix, const ID & id)
: SparseMatrix(matrix._dof_manager, matrix.matrix_type, id) {
nb_non_zero = matrix.nb_non_zero;
}
/* -------------------------------------------------------------------------- */
SparseMatrix::~SparseMatrix() {}
/* -------------------------------------------------------------------------- */
Array<Real> & operator*=(Array<Real> & vect, const SparseMatrix & mat) {
Array<Real> tmp(vect.getSize(), vect.getNbComponent(), 0.);
mat.matVecMul(vect, tmp);
vect.copy(tmp);
return vect;
}
/* -------------------------------------------------------------------------- */
void SparseMatrix::add(const SparseMatrix & B, Real alpha) {
B.addMeTo(*this, alpha);
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/solver/sparse_matrix_aij.cc b/src/solver/sparse_matrix_aij.cc
index 9f8e3f1c7..feb34c5cd 100644
--- a/src/solver/sparse_matrix_aij.cc
+++ b/src/solver/sparse_matrix_aij.cc
@@ -1,225 +1,225 @@
/**
* @file sparse_matrix_aij.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 18 16:31:23 2015
*
* @brief Implementation of the AIJ sparse matrix
*
* @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 "sparse_matrix_aij.hh"
#include "dof_manager_default.hh"
#include "dof_synchronizer.hh"
#include "terms_to_assemble.hh"
/* -------------------------------------------------------------------------- */
#include <fstream>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::SparseMatrixAIJ(DOFManagerDefault & dof_manager,
const MatrixType & matrix_type, const ID & id)
: SparseMatrix(dof_manager, matrix_type, id), dof_manager(dof_manager),
irn(0, 1, id + ":irn"), jcn(0, 1, id + ":jcn"), a(0, 1, id + ":a"),
profile_release(1), value_release(1) {}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::SparseMatrixAIJ(const SparseMatrixAIJ & matrix, const ID & id)
: SparseMatrix(matrix, id), dof_manager(matrix.dof_manager),
irn(matrix.irn, true, id + ":irn"), jcn(matrix.jcn, true, id + ":jcn"),
a(matrix.a, true, id + ":a"), profile_release(1), value_release(1) {}
/* -------------------------------------------------------------------------- */
SparseMatrixAIJ::~SparseMatrixAIJ() {}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::applyBoundary(Real block_val) {
AKANTU_DEBUG_IN();
// clang-format off
const auto & blocked_dofs = this->dof_manager.getGlobalBlockedDOFs();
auto irn_it = irn.begin();
auto jcn_it = jcn.begin();
auto a_it = a.begin();
auto a_end = a.end();
for (;a_it != a_end; ++a_it, ++irn_it, ++jcn_it) {
UInt ni = this->dof_manager.globalToLocalEquationNumber(*irn_it - 1);
UInt nj = this->dof_manager.globalToLocalEquationNumber(*jcn_it - 1);
if (blocked_dofs(ni) || blocked_dofs(nj)) {
*a_it = *irn_it != *jcn_it ? 0.
: this->dof_manager.isLocalOrMasterDOF(ni) ? block_val
: 0.;
}
}
this->value_release++;
// clang-format on
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::saveProfile(const std::string & filename) const {
AKANTU_DEBUG_IN();
std::ofstream outfile;
outfile.open(filename.c_str());
UInt m = this->size;
outfile << "%%MatrixMarket matrix coordinate pattern";
if (this->matrix_type == _symmetric)
outfile << " symmetric";
else
outfile << " general";
outfile << std::endl;
outfile << m << " " << m << " " << this->nb_non_zero << std::endl;
for (UInt i = 0; i < this->nb_non_zero; ++i) {
outfile << this->irn.storage()[i] << " " << this->jcn.storage()[i] << " 1"
<< std::endl;
}
outfile.close();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
// open and set the properties of the stream
std::ofstream outfile;
outfile.open(filename.c_str());
outfile.precision(std::numeric_limits<Real>::digits10);
// write header
outfile << "%%MatrixMarket matrix coordinate real";
if (this->matrix_type == _symmetric)
outfile << " symmetric";
else
outfile << " general";
outfile << std::endl;
outfile << this->size << " " << this->size << " " << this->nb_non_zero
<< std::endl;
// write content
for (UInt i = 0; i < this->nb_non_zero; ++i) {
outfile << this->irn(i) << " " << this->jcn(i) << " " << this->a(i)
<< std::endl;
}
// time to end
outfile.close();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::matVecMul(const Array<Real> & x, Array<Real> & y,
Real alpha, Real beta) const {
AKANTU_DEBUG_IN();
y *= beta;
auto i_it = this->irn.begin();
auto j_it = this->jcn.begin();
auto a_it = this->a.begin();
auto a_end = this->a.end();
auto x_it = x.begin_reinterpret(x.getSize() * x.getNbComponent());
auto y_it = y.begin_reinterpret(x.getSize() * x.getNbComponent());
for (; a_it != a_end; ++i_it, ++j_it, ++a_it) {
Int i = this->dof_manager.globalToLocalEquationNumber(*i_it - 1);
Int j = this->dof_manager.globalToLocalEquationNumber(*j_it - 1);
const Real & A = *a_it;
y_it[i] += alpha * A * x_it[j];
if ((this->matrix_type == _symmetric) && (i != j))
y_it[j] += alpha * A * x_it[i];
}
if (this->dof_manager.hasSynchronizer())
this->dof_manager.getSynchronizer().reduceSynchronize<AddOperation>(y);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::copyContent(const SparseMatrix & matrix) {
AKANTU_DEBUG_IN();
const SparseMatrixAIJ & mat = dynamic_cast<const SparseMatrixAIJ &>(matrix);
AKANTU_DEBUG_ASSERT(nb_non_zero == mat.getNbNonZero(),
"The to matrix don't have the same profiles");
memcpy(a.storage(), mat.getA().storage(), nb_non_zero * sizeof(Real));
this->value_release++;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class MatrixType>
void SparseMatrixAIJ::addMeToTemplated(MatrixType & B, Real alpha) const {
auto i_it = this->irn.begin();
auto j_it = this->jcn.begin();
auto a_it = this->a.begin();
auto a_end = this->a.end();
for (; a_it != a_end; ++a_it, ++i_it, ++j_it) {
const Int & i = *i_it;
const Int & j = *j_it;
const Real & A_ij = *a_it;
B.addToMatrix(i - 1, j - 1, alpha * A_ij);
}
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::addMeTo(SparseMatrix & B, Real alpha) const {
if (SparseMatrixAIJ * B_aij = dynamic_cast<SparseMatrixAIJ *>(&B)) {
this->addMeToTemplated<SparseMatrixAIJ>(*B_aij, alpha);
} else {
// this->addMeToTemplated<SparseMatrix>(*this, alpha);
}
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::mul(Real alpha) {
this->a *= alpha;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
void SparseMatrixAIJ::clear() {
a.set(0.);
this->value_release++;
}
-__END_AKANTU__
+} // akantu
diff --git a/src/solver/sparse_matrix_aij.hh b/src/solver/sparse_matrix_aij.hh
index 5c848bdc8..7821f452d 100644
--- a/src/solver/sparse_matrix_aij.hh
+++ b/src/solver/sparse_matrix_aij.hh
@@ -1,181 +1,181 @@
/**
* @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;
}
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// remove the existing profile
inline void clearProfile();
/// add a non-zero element
virtual inline UInt addToProfile(UInt i, UInt j);
/// set the matrix to 0
virtual void clear();
/// assemble a local matrix in the sparse one
virtual inline void addToMatrix(UInt i, UInt j, Real value);
/// set the size of the matrix
void resize(UInt size) { this->size = size; }
/// modify the matrix to "remove" the blocked dof
virtual void applyBoundary(Real block_val = 1.);
/// save the profil in a file using the MatrixMarket file format
virtual void saveProfile(const std::string & filename) const;
/// save the matrix in a file using the MatrixMarket file format
virtual void saveMatrix(const std::string & filename) const;
/// copy assuming the profile are the same
virtual void copyContent(const SparseMatrix & matrix);
/// multiply the matrix by a scalar
void mul(Real alpha);
/// add matrix *this += B
// virtual void add(const SparseMatrix & matrix, Real alpha);
/// Equivalent of *gemv in blas
virtual void matVecMul(const Array<Real> & x, Array<Real> & y,
Real alpha = 1., Real beta = 0.) const;
/* ------------------------------------------------------------------------ */
/// accessor to A_{ij} - if (i, j) not present it returns 0
inline Real operator()(UInt i, UInt j) const;
/// 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);
protected:
/// This is the revert of add B += \alpha * *this;
virtual void addMeTo(SparseMatrix & B, Real alpha) const;
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);
virtual UInt getRelease() const { 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;
/// Value release
UInt value_release;
/*
* map for (i, j) -> k correspondence
*/
coordinate_list_map irn_jcn_k;
};
-__END_AKANTU__
+} // akantu
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "sparse_matrix_aij_inline_impl.cc"
#endif /* __AKANTU_SPARSE_MATRIX_AIJ_HH__ */
diff --git a/src/solver/sparse_matrix_aij_inline_impl.cc b/src/solver/sparse_matrix_aij_inline_impl.cc
index 17d4ded0d..493f9627d 100644
--- a/src/solver/sparse_matrix_aij_inline_impl.cc
+++ b/src/solver/sparse_matrix_aij_inline_impl.cc
@@ -1,111 +1,111 @@
/**
* @file sparse_matrix_aij_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Tue Aug 18 00:42:45 2015
*
* @brief Implementation of inline functions of SparseMatrixAIJ
*
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_CC__
#define __AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_CC__
-__BEGIN_AKANTU__
+namespace akantu {
inline UInt SparseMatrixAIJ::addToProfile(UInt i, UInt j) {
KeyCOO jcn_irn = this->key(i, j);
coordinate_list_map::iterator it = this->irn_jcn_k.find(jcn_irn);
if (!(it == this->irn_jcn_k.end())) return it->second;
if(i + 1 > this->size) this->size = i + 1;
if(j + 1 > this->size) this->size = j + 1;
this->irn.push_back(i + 1);
this->jcn.push_back(j + 1);
this->a.push_back(0.);
this->irn_jcn_k[jcn_irn] = this->nb_non_zero;
(this->nb_non_zero)++;
this->profile_release++;
this->value_release++;
return (this->nb_non_zero - 1);
}
/* -------------------------------------------------------------------------- */
inline void SparseMatrixAIJ::clearProfile() {
SparseMatrix::clearProfile();
this->irn_jcn_k.clear();
this->irn.resize(0);
this->jcn.resize(0);
this->a.resize(0);
this->size = 0;
this->profile_release++;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
inline void SparseMatrixAIJ::addToMatrix(UInt i, UInt j, Real value) {
UInt idx = this->addToProfile(i, j);
this->a(idx) += value;
this->value_release++;
}
/* -------------------------------------------------------------------------- */
inline Real SparseMatrixAIJ::operator()(UInt i, UInt j) const {
KeyCOO jcn_irn = this->key(i, j);
coordinate_list_map::const_iterator irn_jcn_k_it =
this->irn_jcn_k.find(jcn_irn);
if (irn_jcn_k_it == this->irn_jcn_k.end()) return 0.;
return this->a(irn_jcn_k_it->second);
}
/* -------------------------------------------------------------------------- */
inline Real & SparseMatrixAIJ::operator()(UInt i, UInt j) {
KeyCOO jcn_irn = this->key(i, j);
coordinate_list_map::iterator irn_jcn_k_it = this->irn_jcn_k.find(jcn_irn);
AKANTU_DEBUG_ASSERT(irn_jcn_k_it != this->irn_jcn_k.end(),
"Couple (i,j) = (" << i << "," << j
<< ") does not exist in the profile");
// it may change the profile so it is considered as a change
this->value_release++;
return this->a(irn_jcn_k_it->second);
}
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_SPARSE_MATRIX_AIJ_INLINE_IMPL_CC__ */
diff --git a/src/solver/sparse_matrix_inline_impl.cc b/src/solver/sparse_matrix_inline_impl.cc
index 8bce2e569..1ad017022 100644
--- a/src/solver/sparse_matrix_inline_impl.cc
+++ b/src/solver/sparse_matrix_inline_impl.cc
@@ -1,39 +1,39 @@
/**
* @file sparse_matrix_inline_impl.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Tue Aug 18 2015
*
* @brief implementation of inline methods of the SparseMatrix 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/>.
*
*/
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
inline void SparseMatrix::clearProfile() {
this->nb_non_zero = 0;
}
-__END_AKANTU__
+} // akantu
diff --git a/src/solver/sparse_matrix_petsc.cc b/src/solver/sparse_matrix_petsc.cc
index e6705e7c8..48456c6fb 100644
--- a/src/solver/sparse_matrix_petsc.cc
+++ b/src/solver/sparse_matrix_petsc.cc
@@ -1,404 +1,404 @@
/**
* @file petsc_matrix.cc
* @author Aurelia Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @date Mon Jul 21 17:40:41 2014
*
* @brief Implementation of PETSc matrix class
*
* @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 "sparse_matrix_petsc.hh"
#include "mpi_type_wrapper.hh"
#include "dof_manager_petsc.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#include <cstring>
#include <petscsys.h>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
#if not defined(PETSC_CLANGUAGE_CXX)
int aka_PETScError(int ierr) {
CHKERRQ(ierr);
return 0;
}
#endif
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::SparseMatrixPETSc(DOFManagerPETSc & dof_manager,
const MatrixType & sparse_matrix_type, const ID & id,
const MemoryID & memory_id)
: SparseMatrix(dof_manager, matrix_type, id, memory_id),
dof_manager(dof_manager),
d_nnz(0, 1, "dnnz"),
o_nnz(0, 1, "onnz"), first_global_index(0) {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
// create the PETSc matrix object
ierr = MatCreate(PETSC_COMM_WORLD, &this->mat);
CHKERRXX(ierr);
/**
* Set the matrix type
* @todo PETSc does currently not support a straightforward way to
* apply Dirichlet boundary conditions for MPISBAIJ
* matrices. Therefore always the entire matrix is allocated. It
* would be possible to use MATSBAIJ for sequential matrices in case
* memory becomes critical. Also, block matrices would give a much
* better performance. Modify this in the future!
*/
ierr = MatSetType(this->mat, MATAIJ);
CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseMatrixPETSc::~SparseMatrixPETSc() {
AKANTU_DEBUG_IN();
/// destroy all the PETSc data structures used for this matrix
PetscErrorCode ierr;
ierr = MatDestroy(&this->mat);
CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* With this method each processor computes the dimensions of the
* local matrix, i.e. the part of the global matrix it is storing.
* @param dof_synchronizer dof synchronizer that maps the local
* dofs to the global dofs and the equation numbers, i.e., the
* position at which the dof is assembled in the matrix
*/
void SparseMatrixPETSc::setSize() {
AKANTU_DEBUG_IN();
// PetscErrorCode ierr;
/// find the number of dofs corresponding to master or local nodes
UInt nb_dofs = this->dof_manager.getLocalSystemSize();
// UInt nb_local_master_dofs = 0;
/// create array to store the global equation number of all local and master
/// dofs
Array<Int> local_master_eq_nbs(nb_dofs);
Array<Int>::scalar_iterator it_eq_nb = local_master_eq_nbs.begin();
throw;
/// get the pointer to the global equation number array
// Int * eq_nb_val =
// this->dof_synchronizer->getGlobalDOFEquationNumbers().storage();
// for (UInt i = 0; i < nb_dofs; ++i) {
// if (this->dof_synchronizer->isLocalOrMasterDOF(i)) {
// *it_eq_nb = eq_nb_val[i];
// ++it_eq_nb;
// ++nb_local_master_dofs;
// }
// }
// local_master_eq_nbs.resize(nb_local_master_dofs);
// /// set the local size
// this->local_size = nb_local_master_dofs;
// /// resize PETSc matrix
// #if defined(AKANTU_USE_MPI)
// ierr = MatSetSizes(this->petsc_matrix_wrapper->mat, this->local_size,
// this->local_size, this->size, this->size);
// CHKERRXX(ierr);
// #else
// ierr = MatSetSizes(this->petsc_matrix_wrapper->mat, this->local_size,
// this->local_size);
// CHKERRXX(ierr);
// #endif
// /// create mapping from akantu global numbering to petsc global numbering
// this->createGlobalAkantuToPETScMap(local_master_eq_nbs.storage());
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* This method generates a mapping from the global Akantu equation
* numbering to the global PETSc dof ordering
* @param local_master_eq_nbs_ptr Int pointer to the array of equation
* numbers of all local or master dofs, i.e. the row indices of the
* local matrix
*/
void
SparseMatrixPETSc::createGlobalAkantuToPETScMap(Int * local_master_eq_nbs_ptr) {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt rank = comm.whoAmI();
// initialize vector to store the number of local and master nodes that are
// assigned to each processor
Vector<UInt> master_local_ndofs_per_proc(nb_proc);
/// store the nb of master and local dofs on each processor
master_local_ndofs_per_proc(rank) = this->local_size;
/// exchange the information among all processors
comm.allGather(master_local_ndofs_per_proc.storage(), 1);
/// each processor creates a map for his akantu global dofs to the
/// corresponding petsc global dofs
/// determine the PETSc-index for the first dof on each processor
for (UInt i = 0; i < rank; ++i) {
this->first_global_index += master_local_ndofs_per_proc(i);
}
/// create array for petsc ordering
Array<Int> petsc_dofs(this->local_size);
Array<Int>::scalar_iterator it_petsc_dofs = petsc_dofs.begin();
for (Int i = this->first_global_index;
i < this->first_global_index + this->local_size; ++i, ++it_petsc_dofs) {
*it_petsc_dofs = i;
}
ierr = AOCreateBasic(PETSC_COMM_WORLD,
this->local_size, local_master_eq_nbs_ptr,
petsc_dofs.storage(), &(this->ao));
CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Method to save the nonzero pattern and the values stored at each position
* @param filename name of the file in which the information will be stored
*/
void SparseMatrixPETSc::saveMatrix(const std::string & filename) const {
AKANTU_DEBUG_IN();
PetscErrorCode ierr;
/// create Petsc viewer
PetscViewer viewer;
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,
filename.c_str(), &viewer);
CHKERRXX(ierr);
/// set the format
PetscViewerSetFormat(viewer, PETSC_VIEWER_DEFAULT);
CHKERRXX(ierr);
/// save the matrix
/// @todo Write should be done in serial -> might cause problems
ierr = MatView(this->mat, viewer);
CHKERRXX(ierr);
/// destroy the viewer
ierr = PetscViewerDestroy(&viewer);
CHKERRXX(ierr);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/**
* Method to add an Akantu sparse matrix to the PETSc matrix
* @param matrix Akantu sparse matrix to be added
* @param alpha the factor specifying how many times the matrix should be added
*/
// void SparseMatrixPETSc::add(const SparseMatrix & matrix, Real alpha) {
// PetscErrorCode ierr;
// // AKANTU_DEBUG_ASSERT(nb_non_zero == matrix.getNbNonZero(),
// // "The two matrix don't have the same profiles");
// Real val_to_add = 0;
// Array<Int> index(2);
// for (UInt n = 0; n < matrix.getNbNonZero(); ++n) {
// UInt mat_to_add_offset = matrix.getOffset();
// index(0) = matrix.getIRN()(n) - mat_to_add_offset;
// index(1) = matrix.getJCN()(n) - mat_to_add_offset;
// AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, 2, index.storage());
// if (this->sparse_matrix_type == _symmetric && index(0) > index(1))
// std::swap(index(0), index(1));
// val_to_add = matrix.getA()(n) * alpha;
// /// MatSetValue might be very slow for MATBAIJ, might need to use
// /// MatSetValuesBlocked
// ierr = MatSetValue(this->petsc_matrix_wrapper->mat, index(0), index(1),
// val_to_add, ADD_VALUES);
// CHKERRXX(ierr);
// /// chek if sparse matrix to be added is symmetric. In this case
// /// the value also needs to be added at the transposed location in
// /// the matrix because PETSc is using the full profile, also for symmetric
// /// matrices
// if (matrix.getSparseMatrixType() == _symmetric && index(0) != index(1))
// ierr = MatSetValue(this->petsc_matrix_wrapper->mat, index(1), index(0),
// val_to_add, ADD_VALUES);
// CHKERRXX(ierr);
// }
// this->performAssembly();
// }
/* -------------------------------------------------------------------------- */
/**
* Method to add another PETSc matrix to this PETSc matrix
* @param matrix PETSc matrix to be added
* @param alpha the factor specifying how many times the matrix should be added
*/
void SparseMatrixPETSc::add(const SparseMatrixPETSc & matrix, Real alpha) {
PetscErrorCode ierr;
ierr = MatAXPY(this->mat, alpha,
matrix.mat, SAME_NONZERO_PATTERN);
CHKERRXX(ierr);
this->performAssembly();
}
/* -------------------------------------------------------------------------- */
/**
* MatSetValues() generally caches the values. The matrix is ready to
* use only after MatAssemblyBegin() and MatAssemblyEnd() have been
* called. (http://www.mcs.anl.gov/petsc/)
*/
void SparseMatrixPETSc::performAssembly() {
this->beginAssembly();
this->endAssembly();
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::beginAssembly() {
PetscErrorCode ierr;
ierr = MatAssemblyBegin(this->mat, MAT_FINAL_ASSEMBLY);
CHKERRXX(ierr);
ierr = MatAssemblyEnd(this->mat, MAT_FINAL_ASSEMBLY);
CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
void SparseMatrixPETSc::endAssembly() {
PetscErrorCode ierr;
ierr = MatAssemblyEnd(this->mat, MAT_FINAL_ASSEMBLY);
CHKERRXX(ierr);
}
/* -------------------------------------------------------------------------- */
/// access K(i, j). Works only for dofs on this processor!!!!
Real SparseMatrixPETSc::operator()(UInt i, UInt j) const {
AKANTU_DEBUG_IN();
// AKANTU_DEBUG_ASSERT(this->dof_synchronizer->isLocalOrMasterDOF(i) &&
// this->dof_synchronizer->isLocalOrMasterDOF(j),
// "Operator works only for dofs on this processor");
// Array<Int> index(2, 1);
// index(0) = this->dof_synchronizer->getDOFGlobalID(i);
// index(1) = this->dof_synchronizer->getDOFGlobalID(j);
// AOApplicationToPetsc(this->petsc_matrix_wrapper->ao, 2, index.storage());
// Real value = 0;
// PetscErrorCode ierr;
// /// @todo MatGetValue might be very slow for MATBAIJ, might need to use
// /// MatGetValuesBlocked
// ierr = MatGetValues(this->petsc_matrix_wrapper->mat, 1, &index(0), 1,
// &index(1), &value);
// CHKERRXX(ierr);
// AKANTU_DEBUG_OUT();
// return value;
return 0.;
}
/* -------------------------------------------------------------------------- */
/**
* Apply Dirichlet boundary conditions by zeroing the rows and columns which
* correspond to blocked dofs
* @param boundary array of booleans which are true if the dof at this position
* is blocked
* @param block_val the value in the diagonal entry of blocked rows
*/
void SparseMatrixPETSc::applyBoundary(const Array<bool> & boundary,
Real block_val) {
AKANTU_DEBUG_IN();
// PetscErrorCode ierr;
// /// get the global equation numbers to find the rows that need to be zeroed
// /// for the blocked dofs
// Int * eq_nb_val = dof_synchronizer->getGlobalDOFEquationNumbers().storage();
// /// every processor calls the MatSetZero() only for his local or master dofs.
// /// This assures that not two processors or more try to zero the same row
// UInt nb_component = boundary.getNbComponent();
// UInt size = boundary.getSize();
// Int nb_blocked_local_master_eq_nb = 0;
// Array<Int> blocked_local_master_eq_nb(this->local_size);
// Int * blocked_lm_eq_nb_ptr = blocked_local_master_eq_nb.storage();
// for (UInt i = 0; i < size; ++i) {
// for (UInt j = 0; j < nb_component; ++j) {
// UInt local_dof = i * nb_component + j;
// if (boundary(i, j) == true &&
// this->dof_synchronizer->isLocalOrMasterDOF(local_dof)) {
// Int global_eq_nb = *eq_nb_val;
// *blocked_lm_eq_nb_ptr = global_eq_nb;
// ++nb_blocked_local_master_eq_nb;
// ++blocked_lm_eq_nb_ptr;
// }
// ++eq_nb_val;
// }
// }
// blocked_local_master_eq_nb.resize(nb_blocked_local_master_eq_nb);
// ierr = AOApplicationToPetsc(this->petsc_matrix_wrapper->ao,
// nb_blocked_local_master_eq_nb,
// blocked_local_master_eq_nb.storage());
// CHKERRXX(ierr);
// ierr = MatZeroRowsColumns(
// this->petsc_matrix_wrapper->mat, nb_blocked_local_master_eq_nb,
// blocked_local_master_eq_nb.storage(), block_val, 0, 0);
// CHKERRXX(ierr);
// this->performAssembly();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/// set all entries to zero while keeping the same nonzero pattern
void SparseMatrixPETSc::clear() {
MatZeroEntries(this->mat);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/solver/sparse_matrix_petsc.hh b/src/solver/sparse_matrix_petsc.hh
index 68e20d25b..0fcb07f0d 100644
--- a/src/solver/sparse_matrix_petsc.hh
+++ b/src/solver/sparse_matrix_petsc.hh
@@ -1,142 +1,142 @@
/**
* @file petsc_matrix.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Fri Aug 21 2015
*
* @brief Interface for PETSc matrices
*
* @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_PETSC_MATRIX_HH__
#define __AKANTU_PETSC_MATRIX_HH__
/* -------------------------------------------------------------------------- */
#include "sparse_matrix.hh"
/* -------------------------------------------------------------------------- */
#include <petscmat.h>
#include <petscao.h>
/* -------------------------------------------------------------------------- */
namespace akantu {
class DOFManagerPETSc;
}
-__BEGIN_AKANTU__
+namespace akantu {
class SparseMatrixPETSc : public SparseMatrix {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
SparseMatrixPETSc(DOFManagerPETSc & dof_manager, const MatrixType & matrix_type,
const ID & id = "sparse_matrix",
const MemoryID & memory_id = 0);
SparseMatrixPETSc(const SparseMatrix & matrix,
const ID & id = "sparse_matrix_petsc",
const MemoryID & memory_id = 0);
virtual ~SparseMatrixPETSc();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// set the matrix to 0
virtual void clear();
/// modify the matrix to "remove" the blocked dof
virtual void applyBoundary(const Array<bool> & boundary, Real block_val = 1.);
/// save the matrix in a ASCII file format
virtual void saveMatrix(const std::string & filename) const;
/// add a sparse matrix assuming the profile are the same
virtual void add(const SparseMatrix & matrix, Real alpha);
/// add a petsc matrix assuming the profile are the same
virtual void add(const SparseMatrixPETSc & matrix, Real alpha);
Real operator()(UInt i, UInt j) const;
protected:
typedef std::pair<UInt, UInt> KeyCOO;
inline KeyCOO key(UInt i, UInt j) const { return std::make_pair(i, j); }
private:
virtual void destroyInternalData();
/// set the size of the PETSc matrix
void setSize();
void createGlobalAkantuToPETScMap(Int * local_master_eq_nbs_ptr);
void createLocalAkantuToPETScMap();
/// start to assemble the matrix
void beginAssembly();
/// finishes to assemble the matrix
void endAssembly();
/// perform the assembly stuff from petsc
void performAssembly();
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
AKANTU_GET_MACRO(PETScMat, mat, const Mat &);
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
// DOFManagerPETSc that contains the numbering for petsc
DOFManagerPETSc & dof_manager;
/// store the PETSc matrix
Mat mat;
AO ao;
/// size of the diagonal part of the matrix partition
Int local_size;
/// number of nonzeros in every row of the diagonal part
Array<Int> d_nnz;
/// number of nonzeros in every row of the off-diagonal part
Array<Int> o_nnz;
/// the global index of the first local row
Int first_global_index;
/// bool to indicate if the matrix data has been initialized by calling
/// MatCreate
bool is_petsc_matrix_initialized;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_PETSC_MATRIX_HH__ */
diff --git a/src/solver/sparse_solver.cc b/src/solver/sparse_solver.cc
index 7e0ee92b1..abef9dd92 100644
--- a/src/solver/sparse_solver.cc
+++ b/src/solver/sparse_solver.cc
@@ -1,89 +1,89 @@
/**
* @file solver.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Dec 13 2010
* @date last modification: Tue Jan 19 2016
*
* @brief Solver interface 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 "mesh.hh"
#include "dof_manager.hh"
#include "sparse_solver.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
SparseSolver::SparseSolver(DOFManager & dof_manager, const ID & matrix_id,
const ID & id, const MemoryID & memory_id)
: Memory(id, memory_id), Parsable(_st_solver, id),
_dof_manager(dof_manager), matrix_id(matrix_id), communicator(dof_manager.getCommunicator()) {
AKANTU_DEBUG_IN();
// createSynchronizerRegistry();
// this->synch_registry = new SynchronizerRegistry(*this);
// synch_registry->registerSynchronizer(this->matrix->getDOFSynchronizer(),
// _gst_solver_solution);
// OK this is fishy...
const_cast<StaticCommunicator &>(this->communicator).registerEventHandler(*this);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
SparseSolver::~SparseSolver() {
AKANTU_DEBUG_IN();
this->destroyInternalData();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolver::beforeStaticSolverDestroy() {
AKANTU_DEBUG_IN();
try {
this->destroyInternalData();
} catch (...) {
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolver::createSynchronizerRegistry() {
// this->synch_registry = new SynchronizerRegistry(this);
}
void SparseSolver::onCommunicatorFinalize() {
this->destroyInternalData();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/solver/sparse_solver.hh b/src/solver/sparse_solver.hh
index acd0ad49d..40eee3664 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 "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_SOLVER_HH__
#define __AKANTU_SOLVER_HH__
namespace akantu {
enum SolverParallelMethod {
_not_parallel,
_fully_distributed,
_master_slave_distributed
};
class DOFManager;
}
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* 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();
// 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 StaticCommunicator & communicator;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_SOLVER_HH__ */
diff --git a/src/solver/sparse_solver_mumps.cc b/src/solver/sparse_solver_mumps.cc
index 8fa28517c..54786d40a 100644
--- a/src/solver/sparse_solver_mumps.cc
+++ b/src/solver/sparse_solver_mumps.cc
@@ -1,441 +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_type_wrapper.hh"
#include "static_communicator_mpi.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;
// }
-__BEGIN_AKANTU__
+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), matrix(dof_manager.getMatrix(matrix_id)),
master_rhs_solution(0, 1), is_initialized(false) {
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
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
case _fully_distributed:
#ifdef AKANTU_USE_MPI
const StaticCommunicatorMPI & mpi_st_comm =
dynamic_cast<const StaticCommunicatorMPI &>(
communicator.getRealStaticCommunicator());
MPI_Comm mpi_comm = mpi_st_comm.getMPITypeWrapper().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;
}
this->mumps_data.sym = 2 * (this->matrix.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;
this->last_profile_release = this->matrix.getProfileRelease() - 1;
this->last_value_release = this->matrix.getValueRelease() - 1;
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)
AKANTU_EXCEPTION("You cannot use an un/de-initialized mumps solver");
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::setOutputLevel() {
// Output setup
icntl(1) = 0; // error output
icntl(2) = 0; // dignostics output
icntl(3) = 0; // informations
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");
}
icntl(1) = (dbg_lvl >= dblWarning) ? 6 : 0;
icntl(3) = (dbg_lvl >= dblInfo) ? 6 : 0;
icntl(2) = (dbg_lvl >= dblTrace) ? 6 : 0;
if (dbg_lvl >= dblDump) {
icntl(4) = 4;
} else if (dbg_lvl >= dblTrace) {
icntl(4) = 3;
} else if (dbg_lvl >= dblInfo) {
icntl(4) = 2;
} else if (dbg_lvl >= dblWarning) {
icntl(4) = 1;
}
#endif
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::initMumpsData() {
// 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 = this->matrix.getSize();
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 = matrix.getNbNonZero();
this->mumps_data.irn_loc = matrix.getIRN().storage();
this->mumps_data.jcn_loc = matrix.getJCN().storage();
break;
case _not_parallel:
case _master_slave_distributed:
icntl(18) = 0; // centralized
if (prank == 0) {
this->mumps_data.nz = matrix.getNbNonZero();
this->mumps_data.irn = matrix.getIRN().storage();
this->mumps_data.jcn = matrix.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->analysis();
// icntl(14) = 80;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::analysis() {
AKANTU_DEBUG_IN();
initMumpsData();
this->checkInitialized();
this->mumps_data.job = _smj_analyze; // analyze
dmumps_c(&this->mumps_data);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SparseSolverMumps::factorize() {
AKANTU_DEBUG_IN();
// should be null on slaves
// this->mumps_data.rhs = this->master_rhs_solution.storage();
if (parallel_method == _fully_distributed)
this->mumps_data.a_loc = this->matrix.getA().storage();
else {
if (prank == 0)
this->mumps_data.a = this->matrix.getA().storage();
}
this->checkInitialized();
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->setOutputLevel();
if (this->last_profile_release != this->matrix.getProfileRelease()) {
this->analysis();
this->last_profile_release = this->matrix.getProfileRelease();
}
if (AKANTU_DEBUG_TEST(dblDump)) {
std::stringstream sstr;
sstr << prank << ".mtx";
this->matrix.saveMatrix("solver_mumps" + sstr.str());
}
if (this->last_value_release != this->matrix.getValueRelease()) {
this->factorize();
this->last_value_release = this->matrix.getValueRelease();
}
if (prank == 0) {
this->mumps_data.rhs = this->master_rhs_solution.storage();
}
this->checkInitialized();
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
StaticCommunicator::getStaticCommunicator().allReduce(_info_v, _so_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]);
}
}
-__END_AKANTU__
+} // akantu
diff --git a/src/solver/sparse_solver_mumps.hh b/src/solver/sparse_solver_mumps.hh
index b30b0e8dc..43d412235 100644
--- a/src/solver/sparse_solver_mumps.hh
+++ b/src/solver/sparse_solver_mumps.hh
@@ -1,160 +1,160 @@
/**
* @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;
}
-__BEGIN_AKANTU__
+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();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// build the profile and do the analysis part
virtual void initialize();
/// analysis (symbolic facto + permutations)
virtual void analysis();
/// factorize the matrix
virtual void factorize();
/// 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();
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();
/// 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;
/// AIJ Matrix, usualy the jacobian matrix
SparseMatrixAIJ & matrix;
/// 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;
/// matrix release at last solve
UInt last_value_release;
/// check if the solver data are initialized
bool is_initialized;
/* ------------------------------------------------------------------------ */
/* 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
};
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_SOLVER_MUMPS_HH__ */
diff --git a/src/synchronizer/communication_buffer.hh b/src/synchronizer/communication_buffer.hh
index 1a10d2467..b98bde035 100644
--- a/src/synchronizer/communication_buffer.hh
+++ b/src/synchronizer/communication_buffer.hh
@@ -1,193 +1,193 @@
/**
* @file communication_buffer.hh
*
* @author Guillaume Anciaux <guillaume.anciaux@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Sun Oct 19 2014
*
* @brief Buffer for packing and unpacking data
*
* @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 "element.hh"
#ifndef __AKANTU_COMMUNICATION_BUFFER_HH__
#define __AKANTU_COMMUNICATION_BUFFER_HH__
-__BEGIN_AKANTU__
+namespace akantu {
template<bool is_static = true>
class CommunicationBufferTemplated {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
explicit CommunicationBufferTemplated(UInt size) : buffer(size, 1) {
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
};
CommunicationBufferTemplated() : CommunicationBufferTemplated(0) {}
CommunicationBufferTemplated(const CommunicationBufferTemplated & other) {
buffer = other.buffer;
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
}
CommunicationBufferTemplated & operator=(const CommunicationBufferTemplated & other) {
if (this != &other) {
buffer = other.buffer;
ptr_pack = buffer.storage();
ptr_unpack = buffer.storage();
}
return *this;
}
virtual ~CommunicationBufferTemplated() {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// reset to "empty"
inline void reset();
/// resize the internal buffer
inline void resize(UInt size);
/// clear buffer context
inline void clear();
private:
inline void packResize(UInt size);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
inline char * storage() { return buffer.storage(); };
/* ------------------------------------------------------------------------ */
/* Operators */
/* ------------------------------------------------------------------------ */
public:
/// printing tool
template <typename T> inline std::string extractStream(UInt packet_size);
/// packing data
template<typename T>
inline CommunicationBufferTemplated & operator<< (const T & to_pack);
template<typename T>
inline CommunicationBufferTemplated & operator<< (const Vector<T> & to_pack);
template<typename T>
inline CommunicationBufferTemplated & operator<< (const Matrix<T> & to_pack);
template<typename T>
inline CommunicationBufferTemplated & operator<< (const std::vector<T> & to_pack);
/// unpacking data
template<typename T>
inline CommunicationBufferTemplated & operator>> (T & to_unpack);
template<typename T>
inline CommunicationBufferTemplated & operator>> (Vector<T> & to_unpack);
template<typename T>
inline CommunicationBufferTemplated & operator>> (Matrix<T> & to_unpack);
template<typename T>
inline CommunicationBufferTemplated & operator>> (std::vector<T> & to_unpack);
inline CommunicationBufferTemplated & operator<< (const std::string & to_pack);
inline CommunicationBufferTemplated & operator>> (std::string & to_unpack);
private:
template<typename T>
inline void packIterable (T & to_pack);
template<typename T>
inline void unpackIterable (T & to_pack);
/* ------------------------------------------------------------------------ */
/* Accessor */
/* ------------------------------------------------------------------------ */
public:
template <typename T>
static inline UInt sizeInBuffer(const T & data);
template <typename T>
static inline UInt sizeInBuffer(const Vector<T> & data);
template <typename T>
static inline UInt sizeInBuffer(const Matrix<T> & data);
template <typename T>
static inline UInt sizeInBuffer(const std::vector<T> & data);
static inline UInt sizeInBuffer(const std::string & data);
/// return the size in bytes of the stored values
inline UInt getPackedSize(){ return ptr_pack - buffer.storage(); };
/// return the size in bytes of data left to be unpacked
inline UInt getLeftToUnpack(){ return buffer.getSize() - (ptr_unpack - buffer.storage()); };
/// return the global size allocated
inline UInt getSize(){ return buffer.getSize(); };
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
/// current position for packing
char * ptr_pack;
/// current position for unpacking
char * ptr_unpack;
/// storing buffer
Array<char> buffer;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#if defined (AKANTU_INCLUDE_INLINE_IMPL)
# include "communication_buffer_inline_impl.cc"
#endif
typedef CommunicationBufferTemplated<true> CommunicationBuffer;
typedef CommunicationBufferTemplated<false> DynamicCommunicationBuffer;
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_COMMUNICATION_BUFFER_HH__ */
diff --git a/src/synchronizer/dof_synchronizer.cc b/src/synchronizer/dof_synchronizer.cc
index 2bc478a4c..22a0c9d13 100644
--- a/src/synchronizer/dof_synchronizer.cc
+++ b/src/synchronizer/dof_synchronizer.cc
@@ -1,220 +1,220 @@
/**
* @file dof_synchronizer.cc
*
* @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: Wed Oct 21 2015
*
* @brief DOF synchronizing object 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 "dof_synchronizer.hh"
#include "dof_manager_default.hh"
#include "mesh.hh"
#include "node_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
/**
* A DOFSynchronizer needs a mesh and the number of degrees of freedom
* per node to be created. In the constructor computes the local and global dof
* number for each dof. The member
* proc_informations (std vector) is resized with the number of mpi
* processes. Each entry in the vector is a PerProcInformations object
* that contains the interactions of the current mpi process (prank) with the
* mpi process corresponding to the position of that entry. Every
* ProcInformations object contains one array with the dofs that have
* to be sent to prank and a second one with dofs that willl be received form
* prank.
* This information is needed for the asychronous communications. The
* constructor sets up this information.
*/
DOFSynchronizer::DOFSynchronizer(DOFManagerDefault & dof_manager, const ID & id,
MemoryID memory_id,
const StaticCommunicator & comm)
: SynchronizerImpl<UInt>(id, memory_id, comm), root(0),
dof_manager(dof_manager),
root_dofs(0, 1, "dofs-to-receive-from-master"),
dof_changed(true) {
std::vector<ID> dof_ids = dof_manager.getDOFIDs();
// Transfers nodes to global equation numbers in new schemes
for (ID dof_id : dof_ids) {
registerDOFs(dof_id);
}
this->initScatterGatherCommunicationScheme();
}
/* -------------------------------------------------------------------------- */
DOFSynchronizer::~DOFSynchronizer() {}
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::registerDOFs(const ID & dof_id) {
if (this->nb_proc == 1)
return;
typedef Communications<UInt>::const_scheme_iterator const_scheme_iterator;
const Array<UInt> equation_numbers =
dof_manager.getLocalEquationNumbers(dof_id);
if (dof_manager.getSupportType(dof_id) == _dst_nodal) {
const NodeSynchronizer & node_synchronizer =
dof_manager.getMesh().getNodeSynchronizer();
const Array<UInt> & associated_nodes =
dof_manager.getDOFsAssociatedNodes(dof_id);
const Communications<UInt> & node_communications =
node_synchronizer.getCommunications();
auto transcode_node_to_global_dof_scheme =
[this, &associated_nodes,
&equation_numbers](const_scheme_iterator it, const_scheme_iterator end,
const CommunicationSendRecv & sr) -> void {
for (; it != end; ++it) {
auto & scheme = communications.createScheme(it->first, sr);
const auto & node_scheme = it->second;
for (auto & node : node_scheme) {
auto an_begin = associated_nodes.begin();
auto an_it = an_begin;
auto an_end = associated_nodes.end();
std::vector<UInt> global_dofs_per_node;
while ((an_it = std::find(an_it, an_end, node)) != an_end) {
UInt pos = an_it - an_begin;
UInt local_eq_num = equation_numbers(pos);
UInt global_eq_num =
dof_manager.localToGlobalEquationNumber(local_eq_num);
global_dofs_per_node.push_back(global_eq_num);
++an_it;
}
std::sort(global_dofs_per_node.begin(), global_dofs_per_node.end());
std::transform(global_dofs_per_node.begin(),
global_dofs_per_node.end(),
global_dofs_per_node.begin(), [this](UInt g) -> UInt {
UInt l = dof_manager.globalToLocalEquationNumber(g);
return l;
});
for (auto & leqnum : global_dofs_per_node) {
scheme.push_back(leqnum);
}
}
}
};
auto nss_it = node_communications.begin_send_scheme();
auto nss_end = node_communications.end_send_scheme();
transcode_node_to_global_dof_scheme(nss_it, nss_end, _send);
auto nrs_it = node_communications.begin_recv_scheme();
auto nrs_end = node_communications.end_recv_scheme();
transcode_node_to_global_dof_scheme(nrs_it, nrs_end, _recv);
}
dof_changed = true;
}
/* -------------------------------------------------------------------------- */
void DOFSynchronizer::initScatterGatherCommunicationScheme() {
AKANTU_DEBUG_IN();
if (this->nb_proc == 1) {
dof_changed = false;
AKANTU_DEBUG_OUT();
return;
}
UInt nb_dofs = dof_manager.getLocalSystemSize();
this->root_dofs.clear();
this->master_receive_dofs.clear();
Array<UInt> dofs_to_send;
for (UInt n = 0; n < nb_dofs; ++n) {
if (dof_manager.isLocalOrMasterDOF(n)) {
auto & receive_per_proc = master_receive_dofs[this->root];
UInt global_dof = dof_manager.localToGlobalEquationNumber(n);
root_dofs.push_back(n);
receive_per_proc.push_back(global_dof);
dofs_to_send.push_back(global_dof);
}
}
if (this->rank == UInt(this->root)) {
Array<UInt> nb_dof_per_proc(this->nb_proc);
communicator.gather(dofs_to_send.getSize(), nb_dof_per_proc);
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == UInt(this->root))
continue;
auto & receive_per_proc = master_receive_dofs[p];
receive_per_proc.resize(nb_dof_per_proc(p));
if (nb_dof_per_proc(p) != 0)
requests.push_back(communicator.asyncReceive(
receive_per_proc, p,
Tag::genTag(p, 0, Tag::_GATHER_INITIALIZATION, this->hash_id)));
}
communicator.waitAll(requests);
communicator.freeCommunicationRequest(requests);
} else {
communicator.gather(dofs_to_send.getSize(), this->root);
AKANTU_DEBUG(dblDebug, "I have " << nb_dofs << " dofs ("
<< dofs_to_send.getSize()
<< " to send to master proc");
if (dofs_to_send.getSize() != 0)
communicator.send(dofs_to_send, this->root,
Tag::genTag(this->rank, 0, Tag::_GATHER_INITIALIZATION,
this->hash_id));
}
dof_changed = false;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
bool DOFSynchronizer::hasChanged() {
communicator.allReduce(dof_changed, _so_lor);
return dof_changed;
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/synchronizer/element_info_per_processor.cc b/src/synchronizer/element_info_per_processor.cc
index 49e4e86f4..5bbaffe58 100644
--- a/src/synchronizer/element_info_per_processor.cc
+++ b/src/synchronizer/element_info_per_processor.cc
@@ -1,111 +1,111 @@
/**
* @file element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Mar 11 14:56:42 2016
*
* @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 "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
ElementInfoPerProc::ElementInfoPerProc(ElementSynchronizer & synchronizer,
UInt message_cnt, UInt root,
ElementType type)
: MeshAccessor(synchronizer.getMesh()), synchronizer(synchronizer),
rank(synchronizer.getCommunicator().whoAmI()),
nb_proc(synchronizer.getCommunicator().getNbProc()), root(root),
type(type), message_count(message_cnt), mesh(synchronizer.getMesh()),
comm(synchronizer.getCommunicator()) { }
/* -------------------------------------------------------------------------- */
void ElementInfoPerProc::fillCommunicationScheme(
const Array<UInt> & partition) {
AKANTU_DEBUG_IN();
Element element;
element.type = this->type;
element.kind = Mesh::getKind(this->type);
Communications<Element> & communications =
this->synchronizer.getCommunications();
Array<UInt>::const_scalar_iterator part = partition.begin();
std::map<UInt, Array<Element> > send_array_per_proc;
for (UInt lel = 0; lel < nb_local_element; ++lel) {
UInt nb_send = *part;
++part;
element.element = lel;
element.ghost_type = _not_ghost;
for (UInt p = 0; p < nb_send; ++p, ++part) {
UInt proc = *part;
AKANTU_DEBUG(dblAccessory, "Must send : " << element << " to proc "
<< proc);
send_array_per_proc[proc].push_back(element);
}
}
for (auto & send_schemes : send_array_per_proc) {
if (send_schemes.second.getSize() == 0) continue;
auto & scheme = communications.createSendScheme(send_schemes.first);
scheme.append(send_schemes.second);
}
std::map<UInt, Array<Element> > recv_array_per_proc;
for (UInt gel = 0; gel < nb_ghost_element; ++gel, ++part) {
UInt proc = *part;
element.element = gel;
element.ghost_type = _ghost;
AKANTU_DEBUG(dblAccessory, "Must recv : " << element << " from proc "
<< proc);
recv_array_per_proc[proc].push_back(element);
}
for (auto & recv_schemes : recv_array_per_proc) {
if (recv_schemes.second.getSize() == 0) continue;
auto & scheme = communications.createRecvScheme(recv_schemes.first);
scheme.append(recv_schemes.second);
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/synchronizer/element_info_per_processor.hh b/src/synchronizer/element_info_per_processor.hh
index 7be591ea0..88ce97160 100644
--- a/src/synchronizer/element_info_per_processor.hh
+++ b/src/synchronizer/element_info_per_processor.hh
@@ -1,144 +1,144 @@
/**
* @file element_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 "aka_common.hh"
#include "communication_buffer.hh"
#include "mesh.hh"
#include "mesh_accessor.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH__
#define __AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH__
namespace akantu {
class ElementSynchronizer;
class StaticCommunicator;
class MeshPartition;
}
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class ElementInfoPerProc : protected MeshAccessor {
public:
ElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root, ElementType type);
virtual void synchronizeConnectivities() = 0;
virtual void synchronizePartitions() = 0;
virtual void synchronizeTags() = 0;
virtual void synchronizeGroups() = 0;
protected:
void fillCommunicationScheme(const Array<UInt> & partition);
template <class CommunicationBuffer>
void fillElementGroupsFromBuffer(CommunicationBuffer & buffer);
template <typename T, typename BufferType>
void fillMeshDataTemplated(BufferType & buffer, const std::string & tag_name,
UInt nb_component);
template <typename BufferType>
void fillMeshData(BufferType & buffer, const std::string & tag_name,
const MeshDataTypeCode & type_code, UInt nb_component);
protected:
ElementSynchronizer & synchronizer;
UInt rank;
UInt nb_proc;
UInt root;
ElementType type;
UInt nb_tags;
UInt nb_nodes_per_element;
UInt nb_element;
UInt nb_local_element;
UInt nb_ghost_element;
UInt message_count;
Mesh & mesh;
const StaticCommunicator & comm;
};
/* -------------------------------------------------------------------------- */
class MasterElementInfoPerProc : protected ElementInfoPerProc {
public:
MasterElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root, ElementType type,
const MeshPartition & partition);
void synchronizeConnectivities();
void synchronizePartitions();
void synchronizeTags();
void synchronizeGroups();
protected:
template <typename T>
void fillTagBufferTemplated(DynamicCommunicationBuffer * buffers,
const std::string & tag_name);
void fillTagBuffer(DynamicCommunicationBuffer * buffers,
const std::string & tag_name);
private:
const MeshPartition & partition;
Vector<UInt> all_nb_local_element;
Vector<UInt> all_nb_ghost_element;
Vector<UInt> all_nb_element_to_send;
};
/* -------------------------------------------------------------------------- */
class SlaveElementInfoPerProc : protected ElementInfoPerProc {
public:
SlaveElementInfoPerProc(ElementSynchronizer & synchronizer, UInt message_cnt,
UInt root);
void synchronizeConnectivities();
void synchronizePartitions();
void synchronizeTags();
void synchronizeGroups();
bool needSynchronize();
private:
UInt nb_element_to_receive;
};
-__END_AKANTU__
+} // akantu
#include "element_info_per_processor_tmpl.hh"
#endif /* __AKANTU_ELEMENT_INFO_PER_PROCESSOR_HH__ */
diff --git a/src/synchronizer/element_info_per_processor_tmpl.hh b/src/synchronizer/element_info_per_processor_tmpl.hh
index d47ae74f4..20390c680 100644
--- a/src/synchronizer/element_info_per_processor_tmpl.hh
+++ b/src/synchronizer/element_info_per_processor_tmpl.hh
@@ -1,149 +1,149 @@
/**
* @file element_info_per_processor_tmpl.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Mar 11 15:03:12 2016
*
* @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 "element_group.hh"
#include "element_info_per_processor.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH__
#define __AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH__
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T, typename BufferType>
void ElementInfoPerProc::fillMeshDataTemplated(BufferType & buffer,
const std::string & tag_name,
UInt nb_component) {
AKANTU_DEBUG_ASSERT(this->mesh.getNbElement(this->type) == nb_local_element,
"Did not got enought informations for the tag "
<< tag_name << " and the element type " << this->type
<< ":"
<< "_not_ghost."
<< " Got " << nb_local_element << " values, expected "
<< mesh.getNbElement(this->type));
MeshData & mesh_data = this->getMeshData();
mesh_data.registerElementalData<T>(tag_name);
Array<T> & data = mesh_data.getElementalDataArrayAlloc<T>(
tag_name, this->type, _not_ghost, nb_component);
data.resize(nb_local_element);
/// unpacking the data, element by element
for (UInt i(0); i < nb_local_element; ++i) {
for (UInt j(0); j < nb_component; ++j) {
buffer >> data(i, j);
}
}
AKANTU_DEBUG_ASSERT(mesh.getNbElement(this->type, _ghost) == nb_ghost_element,
"Did not got enought informations for the tag "
<< tag_name << " and the element type " << this->type
<< ":"
<< "_ghost."
<< " Got " << nb_ghost_element << " values, expected "
<< mesh.getNbElement(this->type, _ghost));
Array<T> & data_ghost = mesh_data.getElementalDataArrayAlloc<T>(
tag_name, this->type, _ghost, nb_component);
data_ghost.resize(nb_ghost_element);
/// unpacking the ghost data, element by element
for (UInt j(0); j < nb_ghost_element; ++j) {
for (UInt k(0); k < nb_component; ++k) {
buffer >> data_ghost(j, k);
}
}
}
/* -------------------------------------------------------------------------- */
template <typename BufferType>
void ElementInfoPerProc::fillMeshData(BufferType & buffer,
const std::string & tag_name,
const MeshDataTypeCode & type_code,
UInt nb_component) {
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
fillMeshDataTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(buffer, tag_name, \
nb_component); \
break; \
}
switch (type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_DEBUG_ERROR("Could not determine the type of tag" << tag_name
<< "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
template <class CommunicationBuffer>
void ElementInfoPerProc::fillElementGroupsFromBuffer(
CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
Element el;
el.type = type;
for (ghost_type_t::iterator gt = ghost_type_t::begin();
gt != ghost_type_t::end(); ++gt) {
UInt nb_element = mesh.getNbElement(type, *gt);
el.ghost_type = *gt;
for (UInt e = 0; e < nb_element; ++e) {
el.element = e;
std::vector<std::string> element_to_group;
buffer >> element_to_group;
AKANTU_DEBUG_ASSERT(e < mesh.getNbElement(type, *gt),
"The mesh does not have the element " << e);
std::vector<std::string>::iterator it = element_to_group.begin();
std::vector<std::string>::iterator end = element_to_group.end();
for (; it != end; ++it) {
mesh.getElementGroup(*it).add(el, false, false);
}
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_ELEMENT_INFO_PER_PROCESSOR_TMPL_HH__ */
diff --git a/src/synchronizer/filtered_synchronizer.cc b/src/synchronizer/filtered_synchronizer.cc
index a48038869..e61910d00 100644
--- a/src/synchronizer/filtered_synchronizer.cc
+++ b/src/synchronizer/filtered_synchronizer.cc
@@ -1,174 +1,174 @@
/**
* @file filtered_synchronizer.cc
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Mathilde Radiguet <mathilde.radiguet@epfl.ch>
*
* @date creation: Wed Sep 18 2013
* @date last modification: Sat Jul 11 2015
*
* @brief filtered synchronizer
*
* @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 "filtered_synchronizer.hh"
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
FilteredSynchronizer::FilteredSynchronizer(Mesh & mesh, SynchronizerID id,
MemoryID memory_id)
: ElementSynchronizer(mesh, id, memory_id) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
FilteredSynchronizer * FilteredSynchronizer::createFilteredSynchronizer(
const ElementSynchronizer & d_synchronizer, SynchElementFilter & filter) {
AKANTU_DEBUG_IN();
FilteredSynchronizer & f_synchronizer = *(new FilteredSynchronizer(
d_synchronizer.mesh, d_synchronizer.id + ":filtered",
d_synchronizer.memory_id));
f_synchronizer.setupSynchronizer(d_synchronizer, filter);
AKANTU_DEBUG_OUT();
return &f_synchronizer;
}
/* -------------------------------------------------------------------------- */
void FilteredSynchronizer::setupSynchronizer(
const ElementSynchronizer & d_synchronizer, SynchElementFilter & filter) {
AKANTU_DEBUG_IN();
std::vector<CommunicationRequest> isend_requests;
std::map<UInt, Array<UInt> > keep_element_recv;
auto rs_it = d_synchronizer.communications.begin_recv_scheme();
auto rs_end = d_synchronizer.communications.end_recv_scheme();
// Filter the recv list and communicate it to the sender processor
for (; rs_it != rs_end; ++rs_it) {
const auto & scheme = rs_it->second;
auto & proc = rs_it->first;
Array<UInt> & keep_element = keep_element_recv[proc];
auto & new_scheme = this->communications.createRecvScheme(proc);
UInt el_pos = 0;
for (const auto & element : scheme) {
if (filter(element)) {
new_scheme.push_back(element);
keep_element.push_back(el_pos);
}
++el_pos;
}
keep_element.push_back(-1); // just to be sure to send
// something due to some shitty
// MPI implementation who do not
// know what to do with a 0 size
// send
Tag tag = Tag::genTag(this->rank, 0, RECEIVE_LIST_TAG);
AKANTU_DEBUG_INFO("I have " << keep_element.getSize() - 1
<< " elements to still receive from processor "
<< proc << " (communication tag : " << tag
<< ")");
isend_requests.push_back(communicator.asyncSend(keep_element, proc, tag));
}
auto ss_it = d_synchronizer.communications.begin_send_scheme();
auto ss_end = d_synchronizer.communications.end_send_scheme();
// Receive the element to remove from the sender scheme
for (; ss_it != ss_end; ++ss_it) {
const auto & scheme = rs_it->second;
auto & proc = rs_it->first;
auto & new_scheme = this->communications.createSendScheme(proc);
Tag tag = Tag::genTag(proc, 0, RECEIVE_LIST_TAG);
AKANTU_DEBUG_INFO("Waiting list of elements to keep from processor "
<< proc << " (communication tag : " << tag << ")");
CommunicationStatus status;
communicator.probe<UInt>(proc, tag, status);
Array<UInt> keep_element(status.getSize());
AKANTU_DEBUG_INFO("I have "
<< keep_element.getSize() - 1
<< " elements to keep in my send list to processor "
<< proc << " (communication tag : " << tag << ")");
communicator.receive(keep_element, proc, tag);
for (UInt i = 0; i < keep_element.getSize() - 1; ++i) {
new_scheme.push_back(scheme(keep_element(i)));
}
}
communicator.waitAll(isend_requests);
communicator.freeCommunicationRequest(isend_requests);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void FilteredSynchronizer::updateElementList(
Array<Element> * source_elements, Array<Element> * destination_elements,
SynchElementFilter & filter) {
AKANTU_DEBUG_IN();
// loop over procs
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p == this->rank)
continue;
// access the element for this proc
const Array<Element> & unfiltered_elements = source_elements[p];
Array<Element> & filtered_elements = destination_elements[p];
// iterator to loop over all source elements
Array<Element>::const_iterator<Element> it = unfiltered_elements.begin();
Array<Element>::const_iterator<Element> end = unfiltered_elements.end();
// if filter accepts this element, push it into the destination elements
for (; it != end; ++it) {
const Element & element = *it;
if (filter(element)) {
filtered_elements.push_back(element);
}
}
}
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/synchronizer/filtered_synchronizer.hh b/src/synchronizer/filtered_synchronizer.hh
index 061b72ea9..6bd38e2ac 100644
--- a/src/synchronizer/filtered_synchronizer.hh
+++ b/src/synchronizer/filtered_synchronizer.hh
@@ -1,101 +1,101 @@
/**
* @file filtered_synchronizer.hh
*
* @author David Simon Kammer <david.kammer@epfl.ch>
* @author Mathilde Radiguet <mathilde.radiguet@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Dec 08 2015
*
* @brief synchronizer that filters elements from another 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_FILTERED_SYNCHRONIZER_HH__
#define __AKANTU_FILTERED_SYNCHRONIZER_HH__
/* -------------------------------------------------------------------------- */
#include "element_synchronizer.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
class SynchElementFilter {
public:
virtual bool operator()(const Element &) = 0;
};
/* -------------------------------------------------------------------------- */
class FilteredSynchronizer : public ElementSynchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
FilteredSynchronizer(Mesh & mesh,
SynchronizerID id = "filtered_synchronizer",
MemoryID memory_id = 0);
virtual ~FilteredSynchronizer() {};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// get another synchronizer and filter its elements using a functor
static FilteredSynchronizer *
createFilteredSynchronizer(const ElementSynchronizer & d_synchronizer,
SynchElementFilter & filter);
protected:
/// set up the synchronizer
void setupSynchronizer(const ElementSynchronizer & d_synchronizer,
SynchElementFilter & filter);
/// push source elements into destination elements through the filter
void updateElementList(Array<Element> * source_elements,
Array<Element> * destination_elements,
SynchElementFilter & filter);
protected:
/// Define the receive list tag
enum CommTags {
RECEIVE_LIST_TAG = 0
};
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_FILTERED_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/grid_synchronizer.cc b/src/synchronizer/grid_synchronizer.cc
index 9ed515e30..7f92ca617 100644
--- a/src/synchronizer/grid_synchronizer.cc
+++ b/src/synchronizer/grid_synchronizer.cc
@@ -1,603 +1,603 @@
/**
* @file grid_synchronizer.cc
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Mon Oct 03 2011
* @date last modification: Fri Jan 22 2016
*
* @brief implementation of the grid 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/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "grid_synchronizer.hh"
#include "aka_grid_dynamic.hh"
#include "mesh.hh"
#include "fe_engine.hh"
#include "integration_point.hh"
#include "static_communicator.hh"
#include "mesh_io.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
GridSynchronizer::GridSynchronizer(Mesh & mesh, const ID & id,
MemoryID memory_id,
const bool register_to_event_manager)
: ElementSynchronizer(mesh, id, memory_id, register_to_event_manager) {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <class E>
GridSynchronizer * GridSynchronizer::createGridSynchronizer(
Mesh & mesh, const SpatialGrid<E> & grid, SynchronizerID id,
SynchronizerRegistry * synchronizer_registry,
const std::set<SynchronizationTag> & tags_to_register, MemoryID memory_id,
const bool register_to_event_manager) {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt nb_proc = comm.getNbProc();
UInt my_rank = comm.whoAmI();
GridSynchronizer & communicator =
*(new GridSynchronizer(mesh, id, memory_id, register_to_event_manager));
if (nb_proc == 1)
return &communicator;
UInt spatial_dimension = mesh.getSpatialDimension();
Vector<Real> bounding_boxes(2 * spatial_dimension * nb_proc);
Vector<Real> my_bounding_box(bounding_boxes.storage() +
2 * spatial_dimension * my_rank,
2 * spatial_dimension);
// mesh.getLocalLowerBounds(my_bounding_box);
// mesh.getLocalUpperBounds(my_bounding_box + spatial_dimension);
const Vector<Real> & lower = grid.getLowerBounds();
const Vector<Real> & upper = grid.getUpperBounds();
const Vector<Real> & spacing = grid.getSpacing();
for (UInt i = 0; i < spatial_dimension; ++i) {
my_bounding_box[i] = lower(i) - spacing(i);
my_bounding_box[spatial_dimension + i] = upper(i) + spacing(i);
}
AKANTU_DEBUG_INFO(
"Exchange of bounding box to detect the overlapping regions.");
comm.allGather(bounding_boxes);
bool * intersects_proc = new bool[nb_proc];
std::fill_n(intersects_proc, nb_proc, true);
Int * first_cells = new Int[3 * nb_proc];
Int * last_cells = new Int[3 * nb_proc];
std::fill_n(first_cells, 3 * nb_proc, 0);
std::fill_n(first_cells, 3 * nb_proc, 0);
ElementTypeMapArray<UInt> ** element_per_proc =
new ElementTypeMapArray<UInt> * [nb_proc];
for (UInt p = 0; p < nb_proc; ++p)
element_per_proc[p] = NULL;
// check the overlapping between my box and the one from other processors
for (UInt p = 0; p < nb_proc; ++p) {
if (p == my_rank)
continue;
Real * proc_bounding_box = bounding_boxes.storage() + 2 * spatial_dimension * p;
bool intersects = false;
Int * first_cell_p = first_cells + p * spatial_dimension;
Int * last_cell_p = last_cells + p * spatial_dimension;
for (UInt s = 0; s < spatial_dimension; ++s) {
// check overlapping of grid
intersects = Math::intersects(
my_bounding_box[s], my_bounding_box[spatial_dimension + s],
proc_bounding_box[s], proc_bounding_box[spatial_dimension + s]);
intersects_proc[p] &= intersects;
if (intersects) {
AKANTU_DEBUG_INFO("I intersects with processor "
<< p << " in direction " << s);
// is point 1 of proc p in the dimension s in the range ?
bool point1 =
Math::is_in_range(proc_bounding_box[s], my_bounding_box[s],
my_bounding_box[s + spatial_dimension]);
// is point 2 of proc p in the dimension s in the range ?
bool point2 = Math::is_in_range(
proc_bounding_box[s + spatial_dimension], my_bounding_box[s],
my_bounding_box[s + spatial_dimension]);
Real start = 0.;
Real end = 0.;
if (point1 && !point2) {
/* |-----------| my_bounding_box(i)
* |-----------| proc_bounding_box(i)
* 1 2
*/
start = proc_bounding_box[s];
end = my_bounding_box[s + spatial_dimension];
AKANTU_DEBUG_INFO("Intersection scheme 1 in direction "
<< s << " with processor " << p << " [" << start
<< ", " << end << "]");
} else if (point1 && point2) {
/* |-----------------| my_bounding_box(i)
* |-----------| proc_bounding_box(i)
* 1 2
*/
start = proc_bounding_box[s];
end = proc_bounding_box[s + spatial_dimension];
AKANTU_DEBUG_INFO("Intersection scheme 2 in direction "
<< s << " with processor " << p << " [" << start
<< ", " << end << "]");
} else if (!point1 && point2) {
/* |-----------| my_bounding_box(i)
* |-----------| proc_bounding_box(i)
* 1 2
*/
start = my_bounding_box[s];
end = proc_bounding_box[s + spatial_dimension];
AKANTU_DEBUG_INFO("Intersection scheme 3 in direction "
<< s << " with processor " << p << " [" << start
<< ", " << end << "]");
} else {
/* |-----------| my_bounding_box(i)
* |-----------------| proc_bounding_box(i)
* 1 2
*/
start = my_bounding_box[s];
end = my_bounding_box[s + spatial_dimension];
AKANTU_DEBUG_INFO("Intersection scheme 4 in direction "
<< s << " with processor " << p << " [" << start
<< ", " << end << "]");
}
first_cell_p[s] = grid.getCellID(start, s);
last_cell_p[s] = grid.getCellID(end, s);
}
}
// create the list of cells in the overlapping
typedef typename SpatialGrid<E>::CellID CellID;
std::vector<CellID> * cell_ids = new std::vector<CellID>;
if (intersects_proc[p]) {
AKANTU_DEBUG_INFO("I intersects with processor " << p);
CellID cell_id(spatial_dimension);
// for (UInt i = 0; i < spatial_dimension; ++i) {
// if(first_cell_p[i] != 0) --first_cell_p[i];
// if(last_cell_p[i] != 0) ++last_cell_p[i];
// }
for (Int fd = first_cell_p[0]; fd <= last_cell_p[0]; ++fd) {
cell_id.setID(0, fd);
if (spatial_dimension == 1) {
cell_ids->push_back(cell_id);
} else {
for (Int sd = first_cell_p[1]; sd <= last_cell_p[1]; ++sd) {
cell_id.setID(1, sd);
if (spatial_dimension == 2) {
cell_ids->push_back(cell_id);
} else {
for (Int ld = first_cell_p[2]; ld <= last_cell_p[2]; ++ld) {
cell_id.setID(2, ld);
cell_ids->push_back(cell_id);
}
}
}
}
}
// get the list of elements in the cells of the overlapping
typename std::vector<CellID>::iterator cur_cell_id = cell_ids->begin();
typename std::vector<CellID>::iterator last_cell_id = cell_ids->end();
std::set<Element> * to_send = new std::set<Element>();
for (; cur_cell_id != last_cell_id; ++cur_cell_id) {
typename SpatialGrid<E>::Cell::const_iterator cur_elem =
grid.beginCell(*cur_cell_id);
typename SpatialGrid<E>::Cell::const_iterator last_elem =
grid.endCell(*cur_cell_id);
for (; cur_elem != last_elem; ++cur_elem) {
to_send->insert(*cur_elem);
}
}
AKANTU_DEBUG_INFO("I have prepared " << to_send->size()
<< " elements to send to processor "
<< p);
auto & scheme = communicator.getCommunications().createSendScheme(p);
std::stringstream sstr; sstr << "element_per_proc_" << p;
element_per_proc[p] = new ElementTypeMapArray<UInt>(sstr.str(), id, memory_id);
ElementTypeMapArray<UInt> & elempproc = *(element_per_proc[p]);
typename std::set<Element>::iterator elem = to_send->begin();
typename std::set<Element>::iterator last_elem = to_send->end();
for (; elem != last_elem; ++elem) {
ElementType type = elem->type;
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
// /!\ this part must be slow due to the access in the
// ElementTypeMapArray<UInt>
if (!elempproc.exists(type, _not_ghost))
elempproc.alloc(0, nb_nodes_per_element, type, _not_ghost);
Vector<UInt> global_connect(nb_nodes_per_element);
UInt * local_connect = mesh.getConnectivity(type).storage() +
elem->element * nb_nodes_per_element;
for (UInt i = 0; i < nb_nodes_per_element; ++i) {
global_connect(i) = mesh.getNodeGlobalId(local_connect[i]);
AKANTU_DEBUG_ASSERT(
global_connect(i) < mesh.getNbGlobalNodes(),
"This global node send in the connectivity does not seem correct "
<< global_connect(i) << " corresponding to "
<< local_connect[i] << " from element " << elem->element);
}
elempproc(type).push_back(global_connect);
scheme.push_back(*elem);
}
delete to_send;
}
delete cell_ids;
}
delete[] first_cells;
delete[] last_cells;
AKANTU_DEBUG_INFO("I have finished to compute intersection,"
<< " no it's time to communicate with my neighbors");
/**
* Sending loop, sends the connectivity asynchronously to all concerned proc
*/
std::vector<CommunicationRequest> isend_requests;
UInt * space = new UInt[2*nb_proc*_max_element_type];
UInt offset = 0;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == my_rank)
continue;
if (intersects_proc[p]) {
ElementTypeMapArray<UInt> & elempproc = *(element_per_proc[p]);
ElementTypeMapArray<UInt>::type_iterator it_type =
elempproc.firstType(_all_dimensions, _not_ghost);
ElementTypeMapArray<UInt>::type_iterator last_type =
elempproc.lastType(_all_dimensions, _not_ghost);
UInt count = 0;
for (; it_type != last_type; ++it_type) {
Array<UInt> & conn = elempproc(*it_type, _not_ghost);
Vector<UInt> info(space + offset, 2);
offset += 2;
info[0] = (UInt)*it_type;
info[1] = conn.getSize() * conn.getNbComponent();
AKANTU_DEBUG_INFO("I have " << conn.getSize() << " elements of type "
<< *it_type << " to send to processor " << p
<< " (communication tag : "
<< Tag::genTag(my_rank, count, DATA_TAG)
<< ")");
isend_requests.push_back(
comm.asyncSend(info, p, Tag::genTag(my_rank, count, SIZE_TAG)));
if (info[1] != 0)
isend_requests.push_back(
comm.asyncSend<UInt>(conn, p,
Tag::genTag(my_rank, count, DATA_TAG)));
++count;
}
Vector<UInt> info(space + offset, 2);
offset += 2;
info[0] = (UInt)_not_defined;
info[1] = 0;
isend_requests.push_back(
comm.asyncSend(info, p, Tag::genTag(my_rank, count, SIZE_TAG)));
}
}
/**
* Receives the connectivity and store them in the ghosts elements
*/
Array<UInt> & global_nodes_ids =
const_cast<Array<UInt> &>(mesh.getGlobalNodesIds());
Array<NodeType> & nodes_type =
const_cast<Array<NodeType> &>(const_cast<const Mesh &>(mesh).getNodesType());
std::vector<CommunicationRequest> isend_nodes_requests;
Vector<UInt> nb_nodes_to_recv(nb_proc);
UInt nb_total_nodes_to_recv = 0;
UInt nb_current_nodes = global_nodes_ids.getSize();
NewNodesEvent new_nodes;
NewElementsEvent new_elements;
Array<UInt> * ask_nodes_per_proc = new Array<UInt>[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
nb_nodes_to_recv(p) = 0;
if (p == my_rank)
continue;
auto & scheme = communicator.getCommunications().createRecvScheme(p);
Array<UInt> & ask_nodes = ask_nodes_per_proc[p];
UInt count = 0;
if (intersects_proc[p]) {
ElementType type = _not_defined;
do {
Vector<UInt> info(2);
comm.receive(info, p, Tag::genTag(p, count, SIZE_TAG));
type = (ElementType)info[0];
if (type != _not_defined) {
UInt nb_nodes_per_element = mesh.getNbNodesPerElement(type);
;
UInt nb_element = info[1] / nb_nodes_per_element;
Array<UInt> tmp_conn(nb_element, nb_nodes_per_element);
tmp_conn.clear();
if (info[1] != 0)
comm.receive<UInt>(tmp_conn, p,
Tag::genTag(p, count, DATA_TAG));
AKANTU_DEBUG_INFO("I will receive "
<< nb_element << " elements of type "
<< ElementType(info[0]) << " from processor " << p
<< " (communication tag : "
<< Tag::genTag(p, count, DATA_TAG) << ")");
Array<UInt> & ghost_connectivity =
const_cast<Array<UInt> &>(mesh.getConnectivity(type, _ghost));
UInt nb_ghost_element = ghost_connectivity.getSize();
Element element(type, 0, _ghost);
Vector<UInt> conn(nb_nodes_per_element);
for (UInt el = 0; el < nb_element; ++el) {
UInt nb_node_to_ask_for_elem = 0;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
UInt gn = tmp_conn(el, n);
UInt ln = global_nodes_ids.find(gn);
AKANTU_DEBUG_ASSERT(gn < mesh.getNbGlobalNodes(),
"This global node seems not correct "
<< gn << " from element " << el
<< " node " << n);
if (ln == UInt(-1)) {
global_nodes_ids.push_back(gn);
nodes_type.push_back(_nt_pure_gost); // pure ghost node
ln = nb_current_nodes;
new_nodes.getList().push_back(ln);
++nb_current_nodes;
ask_nodes.push_back(gn);
++nb_node_to_ask_for_elem;
}
conn[n] = ln;
}
// all the nodes are already known locally, the element should
// already exists
UInt c = UInt(-1);
if (nb_node_to_ask_for_elem == 0) {
c = ghost_connectivity.find(conn);
element.element = c;
}
if (c == UInt(-1)) {
element.element = nb_ghost_element;
++nb_ghost_element;
ghost_connectivity.push_back(conn);
new_elements.getList().push_back(element);
}
scheme.push_back(element);
}
}
count++;
} while (type != _not_defined);
AKANTU_DEBUG_INFO("I have "
<< ask_nodes.getSize()
<< " missing nodes for elements coming from processor "
<< p << " (communication tag : "
<< Tag::genTag(my_rank, 0, ASK_NODES_TAG) << ")");
ask_nodes.push_back(UInt(-1));
isend_nodes_requests.push_back(
comm.asyncSend(ask_nodes, p,
Tag::genTag(my_rank, 0, ASK_NODES_TAG)));
nb_nodes_to_recv(p) = ask_nodes.getSize() - 1;
nb_total_nodes_to_recv += nb_nodes_to_recv(p);
}
}
comm.waitAll(isend_requests);
comm.freeCommunicationRequest(isend_requests);
delete [] space;
for (UInt p = 0; p < nb_proc; ++p) {
if (element_per_proc[p])
delete element_per_proc[p];
}
delete[] element_per_proc;
/**
* Sends requested nodes to proc
*/
Array<Real> & nodes = const_cast<Array<Real> &>(mesh.getNodes());
UInt nb_nodes = nodes.getSize();
std::vector<CommunicationRequest> isend_coordinates_requests;
Array<Real> * nodes_to_send_per_proc = new Array<Real>[nb_proc];
for (UInt p = 0; p < nb_proc; ++p) {
if (p == my_rank || !intersects_proc[p])
continue;
Array<UInt> asked_nodes;
CommunicationStatus status;
AKANTU_DEBUG_INFO("Waiting list of nodes to send to processor "
<< p << "(communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
comm.probe<UInt>(p, Tag::genTag(p, 0, ASK_NODES_TAG), status);
UInt nb_nodes_to_send = status.getSize();
asked_nodes.resize(nb_nodes_to_send);
AKANTU_DEBUG_INFO("I have " << nb_nodes_to_send - 1
<< " nodes to send to processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
AKANTU_DEBUG_INFO("Getting list of nodes to send to processor "
<< p << " (communication tag : "
<< Tag::genTag(p, 0, ASK_NODES_TAG) << ")");
comm.receive(asked_nodes, p,
Tag::genTag(p, 0, ASK_NODES_TAG));
nb_nodes_to_send--;
asked_nodes.resize(nb_nodes_to_send);
Array<Real> & nodes_to_send = nodes_to_send_per_proc[p];
nodes_to_send.extendComponentsInterlaced(spatial_dimension, 1);
auto it = nodes.begin(spatial_dimension);
for (UInt n = 0; n < nb_nodes_to_send; ++n) {
UInt ln = global_nodes_ids.find(asked_nodes(n));
AKANTU_DEBUG_ASSERT(ln != UInt(-1), "The node ["
<< asked_nodes(n)
<< "] requested by proc " << p
<< " was not found locally!");
nodes_to_send.push_back(it + ln);
}
if (nb_nodes_to_send != 0) {
AKANTU_DEBUG_INFO("Sending the "
<< nb_nodes_to_send << " nodes to processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, SEND_NODES_TAG) << ")");
isend_coordinates_requests.push_back(comm.asyncSend(
nodes_to_send, p,
Tag::genTag(my_rank, 0, SEND_NODES_TAG)));
}
#if not defined(AKANTU_NDEBUG)
else {
AKANTU_DEBUG_INFO("No nodes to send to processor " << p);
}
#endif
}
comm.waitAll(isend_nodes_requests);
comm.freeCommunicationRequest(isend_nodes_requests);
delete[] ask_nodes_per_proc;
nodes.resize(nb_total_nodes_to_recv + nb_nodes);
for (UInt p = 0; p < nb_proc; ++p) {
if ((p != my_rank) && (nb_nodes_to_recv(p) > 0)) {
AKANTU_DEBUG_INFO("Receiving the "
<< nb_nodes_to_recv(p) << " nodes from processor " << p
<< " (communication tag : "
<< Tag::genTag(p, 0, SEND_NODES_TAG) << ")");
Vector<Real> nodes_to_recv(nodes.storage() + nb_nodes * spatial_dimension,
nb_nodes_to_recv(p) * spatial_dimension);
comm.receive(nodes_to_recv, p,
Tag::genTag(p, 0, SEND_NODES_TAG));
nb_nodes += nb_nodes_to_recv(p);
}
#if not defined(AKANTU_NDEBUG)
else {
if (p != my_rank) {
AKANTU_DEBUG_INFO("No nodes to receive from processor " << p);
}
}
#endif
}
comm.waitAll(isend_coordinates_requests);
comm.freeCommunicationRequest(isend_coordinates_requests);
delete[] nodes_to_send_per_proc;
// Register the tags if any
if (synchronizer_registry) {
std::set<SynchronizationTag>::const_iterator it = tags_to_register.begin();
std::set<SynchronizationTag>::const_iterator end = tags_to_register.end();
for (; it != end; ++it) {
synchronizer_registry->registerSynchronizer(communicator, *it);
}
}
mesh.sendEvent(new_nodes);
mesh.sendEvent(new_elements);
delete[] intersects_proc;
AKANTU_DEBUG_OUT();
return &communicator;
}
/* -------------------------------------------------------------------------- */
template GridSynchronizer *
GridSynchronizer::createGridSynchronizer<IntegrationPoint>(
Mesh & mesh, const SpatialGrid<IntegrationPoint> & grid, SynchronizerID id,
SynchronizerRegistry * synchronizer_registry,
const std::set<SynchronizationTag> & tags_to_register, MemoryID memory_id,
const bool register_to_event_manager);
template GridSynchronizer * GridSynchronizer::createGridSynchronizer<Element>(
Mesh & mesh, const SpatialGrid<Element> & grid, SynchronizerID id,
SynchronizerRegistry * synchronizer_registry,
const std::set<SynchronizationTag> & tags_to_register, MemoryID memory_id,
const bool register_to_event_manager);
-__END_AKANTU__
+} // akantu
diff --git a/src/synchronizer/grid_synchronizer.hh b/src/synchronizer/grid_synchronizer.hh
index cc0677855..431feaf04 100644
--- a/src/synchronizer/grid_synchronizer.hh
+++ b/src/synchronizer/grid_synchronizer.hh
@@ -1,99 +1,99 @@
/**
* @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__
-__BEGIN_AKANTU__
+namespace akantu {
class Mesh;
template <class T> class SpatialGrid;
class GridSynchronizer : public ElementSynchronizer {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
protected:
GridSynchronizer(Mesh & mesh, const ID & id = "grid_synchronizer",
MemoryID memory_id = 0,
const bool register_to_event_manager = true);
public:
virtual ~GridSynchronizer(){};
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/**
*Create the Grid Synchronizer:
*Compute intersection and send info to neighbours that will be stored in
*ghosts elements
*/
template <class E>
static GridSynchronizer *
createGridSynchronizer(Mesh & mesh, const SpatialGrid<E> & grid,
SynchronizerID id = "grid_synchronizer",
SynchronizerRegistry * synch_registry = NULL,
const std::set<SynchronizationTag> & tags_to_register =
std::set<SynchronizationTag>(),
MemoryID memory_id = 0,
const bool register_to_event_manager = true);
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:
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_GRID_SYNCHRONIZER_HH__ */
diff --git a/src/synchronizer/master_element_info_per_processor.cc b/src/synchronizer/master_element_info_per_processor.cc
index cc685c156..44560563c 100644
--- a/src/synchronizer/master_element_info_per_processor.cc
+++ b/src/synchronizer/master_element_info_per_processor.cc
@@ -1,490 +1,490 @@
/**
* @file master_element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Mar 11 14:57:13 2016
*
* @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 "element_group.hh"
#include "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
MasterElementInfoPerProc::MasterElementInfoPerProc(
ElementSynchronizer & synchronizer, UInt message_cnt, UInt root,
ElementType type, const MeshPartition & partition)
: ElementInfoPerProc(synchronizer, message_cnt, root, type),
partition(partition), all_nb_local_element(nb_proc, 0),
all_nb_ghost_element(nb_proc, 0), all_nb_element_to_send(nb_proc, 0) {
Vector<UInt> size(5);
size(0) = (UInt)type;
if (type != _not_defined) {
nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
nb_element = mesh.getNbElement(type);
const Array<UInt> & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const CSR<UInt> & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
for (UInt el = 0; el < nb_element; ++el) {
this->all_nb_local_element[partition_num(el)]++;
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el); ++part) {
this->all_nb_ghost_element[*part]++;
}
this->all_nb_element_to_send[partition_num(el)] +=
ghost_partition.getNbCols(el) + 1;
}
/// tag info
std::vector<std::string> tag_names;
this->getMeshData().getTagNames(tag_names, type);
this->nb_tags = tag_names.size();
size(4) = nb_tags;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
size(1) = this->all_nb_local_element[p];
size(2) = this->all_nb_ghost_element[p];
size(3) = this->all_nb_element_to_send[p];
AKANTU_DEBUG_INFO(
"Sending connectivities informations to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_SIZES)
<< ")");
comm.send(size, p,
Tag::genTag(this->rank, this->message_count, Tag::_SIZES));
} else {
this->nb_local_element = this->all_nb_local_element[p];
this->nb_ghost_element = this->all_nb_ghost_element[p];
}
}
} else {
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p != this->root) {
AKANTU_DEBUG_INFO(
"Sending empty connectivities informations to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_SIZES)
<< ")");
comm.send(size, p,
Tag::genTag(this->rank, this->message_count, Tag::_SIZES));
}
}
}
}
/* ------------------------------------------------------------------------ */
void MasterElementInfoPerProc::synchronizeConnectivities() {
const Array<UInt> & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const CSR<UInt> & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
std::vector<Array<UInt>> buffers(this->nb_proc);
auto conn_it = this->mesh.getConnectivity(this->type, _not_ghost)
.begin(this->nb_nodes_per_element);
auto conn_end = this->mesh.getConnectivity(this->type, _not_ghost)
.end(this->nb_nodes_per_element);
/// copying the local connectivity
auto part_it = partition_num.begin();
for (; conn_it != conn_end; ++conn_it, ++part_it) {
const auto & conn = *conn_it;
for (UInt i = 0; i < conn.size(); ++i) {
buffers[*part_it].push_back(conn[i]);
}
}
/// copying the connectivity of ghost element
conn_it = this->mesh.getConnectivity(this->type, _not_ghost)
.begin(this->nb_nodes_per_element);
for (UInt el = 0; conn_it != conn_end; ++el, ++conn_it) {
for (auto part = ghost_partition.begin(el); part != ghost_partition.end(el);
++part) {
UInt proc = *part;
const Vector<UInt> & conn = *conn_it;
for (UInt i = 0; i < conn.size(); ++i) {
buffers[proc].push_back(conn[i]);
}
}
}
#ifndef AKANTU_NDEBUG
for (UInt p = 0; p < this->nb_proc; ++p) {
UInt size = this->nb_nodes_per_element *
(this->all_nb_local_element[p] + this->all_nb_ghost_element[p]);
AKANTU_DEBUG_ASSERT(
buffers[p].getSize() == size,
"The connectivity data packed in the buffer are not correct");
}
#endif
/// send all connectivity and ghost information to all processors
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p != this->root) {
AKANTU_DEBUG_INFO(
"Sending connectivities to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_CONNECTIVITY)
<< ")");
requests.push_back(comm.asyncSend(
buffers[p], p,
Tag::genTag(this->rank, this->message_count, Tag::_CONNECTIVITY)));
}
}
Array<UInt> & old_nodes = this->getNodesGlobalIds();
/// create the renumbered connectivity
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(mesh, buffers[root], all_nb_local_element[root],
all_nb_ghost_element[root], type, old_nodes);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
}
/* ------------------------------------------------------------------------ */
void MasterElementInfoPerProc::synchronizePartitions() {
const Array<UInt> & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const CSR<UInt> & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
std::vector<Array<UInt>> buffers(this->partition.getNbPartition());
/// splitting the partition information to send them to processors
Vector<UInt> count_by_proc(nb_proc, 0);
for (UInt el = 0; el < nb_element; ++el) {
UInt proc = partition_num(el);
buffers[proc].push_back(ghost_partition.getNbCols(el));
UInt i(0);
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el); ++part, ++i) {
buffers[proc].push_back(*part);
}
}
for (UInt el = 0; el < nb_element; ++el) {
UInt i(0);
for (CSR<UInt>::const_iterator part = ghost_partition.begin(el);
part != ghost_partition.end(el); ++part, ++i) {
buffers[*part].push_back(partition_num(el));
}
}
#ifndef AKANTU_NDEBUG
for (UInt p = 0; p < this->nb_proc; ++p) {
AKANTU_DEBUG_ASSERT(
buffers[p].getSize() ==
(this->all_nb_ghost_element[p] + this->all_nb_element_to_send[p]),
"Data stored in the buffer are most probably wrong");
}
#endif
std::vector<CommunicationRequest> requests;
/// last data to compute the communication scheme
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p != this->root) {
AKANTU_DEBUG_INFO(
"Sending partition informations to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, this->message_count, Tag::_PARTITIONS)
<< ")");
requests.push_back(comm.asyncSend(
buffers[p], p,
Tag::genTag(this->rank, this->message_count, Tag::_PARTITIONS)));
}
}
if (Mesh::getSpatialDimension(this->type) ==
this->mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
this->fillCommunicationScheme(buffers[this->rank]);
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::synchronizeTags() {
AKANTU_DEBUG_IN();
if (this->nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
UInt mesh_data_sizes_buffer_length;
MeshData & mesh_data = this->getMeshData();
/// tag info
std::vector<std::string> tag_names;
mesh_data.getTagNames(tag_names, type);
// Make sure the tags are sorted (or at least not in random order),
// because they come from a map !!
std::sort(tag_names.begin(), tag_names.end());
// Sending information about the tags in mesh_data: name, data type and
// number of components of the underlying array associated to the current
// type
DynamicCommunicationBuffer mesh_data_sizes_buffer;
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
for (; names_it != names_end; ++names_it) {
mesh_data_sizes_buffer << *names_it;
mesh_data_sizes_buffer << mesh_data.getTypeCode(*names_it);
mesh_data_sizes_buffer << mesh_data.getNbComponent(*names_it, type);
}
mesh_data_sizes_buffer_length = mesh_data_sizes_buffer.getSize();
AKANTU_DEBUG_INFO(
"Broadcasting the size of the information about the mesh data tags: ("
<< mesh_data_sizes_buffer_length << ").");
comm.broadcast(mesh_data_sizes_buffer_length, root);
AKANTU_DEBUG_INFO(
"Broadcasting the information about the mesh data tags, addr "
<< (void *)mesh_data_sizes_buffer.storage());
if (mesh_data_sizes_buffer_length != 0)
comm.broadcast(mesh_data_sizes_buffer, root);
if (mesh_data_sizes_buffer_length != 0) {
// Sending the actual data to each processor
DynamicCommunicationBuffer * buffers =
new DynamicCommunicationBuffer[nb_proc];
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
// Loop over each tag for the current type
for (; names_it != names_end; ++names_it) {
// Type code of the current tag (i.e. the tag named *names_it)
this->fillTagBuffer(buffers, *names_it);
}
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
AKANTU_DEBUG_INFO("Sending "
<< buffers[p].getSize()
<< " bytes of mesh data to proc " << p << " TAG("
<< Tag::genTag(this->rank, this->message_count,
Tag::_MESH_DATA)
<< ")");
requests.push_back(comm.asyncSend(
buffers[p], p,
Tag::genTag(this->rank, this->message_count, Tag::_MESH_DATA)));
}
}
names_it = tag_names.begin();
// Loop over each tag for the current type
for (; names_it != names_end; ++names_it) {
// Reinitializing the mesh data on the master
this->fillMeshData(buffers[root], *names_it,
mesh_data.getTypeCode(*names_it),
mesh_data.getNbComponent(*names_it, type));
}
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
delete[] buffers;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
template <typename T>
void MasterElementInfoPerProc::fillTagBufferTemplated(
DynamicCommunicationBuffer * buffers, const std::string & tag_name) {
MeshData & mesh_data = this->getMeshData();
const Array<T> & data = mesh_data.getElementalDataArray<T>(tag_name, type);
const Array<UInt> & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const CSR<UInt> & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
// Not possible to use the iterator because it potentially triggers the
// creation of complex
// type templates (such as akantu::Vector< std::vector<Element> > which don't
// implement the right interface
// (e.g. operator<< in that case).
// typename Array<T>::template const_iterator< Vector<T> > data_it =
// data.begin(data.getNbComponent());
// typename Array<T>::template const_iterator< Vector<T> > data_end =
// data.end(data.getNbComponent());
const T * data_it = data.storage();
const T * data_end = data.storage() + data.getSize() * data.getNbComponent();
const UInt * part = partition_num.storage();
/// copying the data, element by element
for (; data_it != data_end; ++part) {
for (UInt j(0); j < data.getNbComponent(); ++j, ++data_it) {
buffers[*part] << *data_it;
}
}
data_it = data.storage();
/// copying the data for the ghost element
for (UInt el(0); data_it != data_end;
data_it += data.getNbComponent(), ++el) {
CSR<UInt>::const_iterator it = ghost_partition.begin(el);
CSR<UInt>::const_iterator end = ghost_partition.end(el);
for (; it != end; ++it) {
UInt proc = *it;
for (UInt j(0); j < data.getNbComponent(); ++j) {
buffers[proc] << data_it[j];
}
}
}
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::fillTagBuffer(
DynamicCommunicationBuffer * buffers, const std::string & tag_name) {
MeshData & mesh_data = this->getMeshData();
#define AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA(r, extra_param, elem) \
case BOOST_PP_TUPLE_ELEM(2, 0, elem): { \
this->fillTagBufferTemplated<BOOST_PP_TUPLE_ELEM(2, 1, elem)>(buffers, \
tag_name); \
break; \
}
MeshDataTypeCode data_type_code = mesh_data.getTypeCode(tag_name);
switch (data_type_code) {
BOOST_PP_SEQ_FOR_EACH(AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA, ,
AKANTU_MESH_DATA_TYPES)
default:
AKANTU_DEBUG_ERROR("Could not obtain the type of tag" << tag_name << "!");
break;
}
#undef AKANTU_DISTRIBUTED_SYNHRONIZER_TAG_DATA
}
/* -------------------------------------------------------------------------- */
void MasterElementInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
DynamicCommunicationBuffer * buffers =
new DynamicCommunicationBuffer[nb_proc];
typedef std::vector<std::vector<std::string>> ElementToGroup;
ElementToGroup element_to_group;
element_to_group.resize(nb_element);
GroupManager::const_element_group_iterator egi = mesh.element_group_begin();
GroupManager::const_element_group_iterator ege = mesh.element_group_end();
for (; egi != ege; ++egi) {
ElementGroup & eg = *(egi->second);
std::string name = egi->first;
ElementGroup::const_element_iterator eit =
eg.element_begin(type, _not_ghost);
ElementGroup::const_element_iterator eend =
eg.element_end(type, _not_ghost);
for (; eit != eend; ++eit) {
element_to_group[*eit].push_back(name);
}
eit = eg.element_begin(type, _not_ghost);
if (eit != eend)
const_cast<Array<UInt> &>(eg.getElements(type)).empty();
}
const Array<UInt> & partition_num =
this->partition.getPartition(this->type, _not_ghost);
const CSR<UInt> & ghost_partition =
this->partition.getGhostPartitionCSR()(this->type, _not_ghost);
/// preparing the buffers
const UInt * part = partition_num.storage();
/// copying the data, element by element
ElementToGroup::const_iterator data_it = element_to_group.begin();
ElementToGroup::const_iterator data_end = element_to_group.end();
for (; data_it != data_end; ++part, ++data_it) {
buffers[*part] << *data_it;
}
data_it = element_to_group.begin();
/// copying the data for the ghost element
for (UInt el(0); data_it != data_end; ++data_it, ++el) {
CSR<UInt>::const_iterator it = ghost_partition.begin(el);
CSR<UInt>::const_iterator end = ghost_partition.end(el);
for (; it != end; ++it) {
UInt proc = *it;
buffers[proc] << *data_it;
}
}
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < this->nb_proc; ++p) {
if (p == this->rank)
continue;
AKANTU_DEBUG_INFO("Sending element groups to proc "
<< p << " TAG("
<< Tag::genTag(this->rank, p, Tag::_ELEMENT_GROUP)
<< ")");
requests.push_back(comm.asyncSend(
buffers[p], p, Tag::genTag(this->rank, p, Tag::_ELEMENT_GROUP)));
}
this->fillElementGroupsFromBuffer(buffers[this->rank]);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
delete[] buffers;
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/synchronizer/mpi_type_wrapper.hh b/src/synchronizer/mpi_type_wrapper.hh
index cd58a6af9..4173d148e 100644
--- a/src/synchronizer/mpi_type_wrapper.hh
+++ b/src/synchronizer/mpi_type_wrapper.hh
@@ -1,109 +1,109 @@
/**
* @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 "aka_common.hh"
#include "static_communicator_mpi.hh"
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_MPI_TYPE_WRAPPER_HH__
#define __AKANTU_MPI_TYPE_WRAPPER_HH__
-__BEGIN_AKANTU__
+namespace akantu {
class MPITypeWrapper {
public:
MPITypeWrapper(StaticCommunicatorMPI & static_comm)
: static_comm(static_comm), communicator(MPI_COMM_WORLD), max_tag(0) {}
template <typename T> static inline MPI_Datatype getMPIDatatype();
inline void setMPICommunicator(MPI_Comm comm) {
communicator = comm;
int prank, psize;
MPI_Comm_rank(communicator, &prank);
MPI_Comm_size(communicator, &psize);
static_comm.setRank(prank);
static_comm.setSize(psize);
int flag;
int * value;
MPI_Comm_get_attr(comm, MPI_TAG_UB, &value, &flag);
AKANTU_DEBUG_ASSERT(flag, "No attribute MPI_TAG_UB.");
this->max_tag = *value;
}
inline MPI_Comm getMPICommunicator() const { return communicator; }
static MPI_Op getMPISynchronizerOperation(const SynchronizerOperation & op) {
return synchronizer_operation_to_mpi_op[op];
}
inline int getMaxTag() const { return this->max_tag; }
private:
StaticCommunicatorMPI & static_comm;
MPI_Comm communicator;
int max_tag;
static MPI_Op synchronizer_operation_to_mpi_op[_so_null + 1];
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_MPI_TYPE_WRAPPER_HH__ */
diff --git a/src/synchronizer/node_info_per_processor.cc b/src/synchronizer/node_info_per_processor.cc
index 25365bda2..5f461736c 100644
--- a/src/synchronizer/node_info_per_processor.cc
+++ b/src/synchronizer/node_info_per_processor.cc
@@ -1,500 +1,500 @@
/**
* @file node_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Mar 11 15:49:43 2016
*
* @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 "node_info_per_processor.hh"
#include "node_group.hh"
#include "node_synchronizer.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
NodeInfoPerProc::NodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: MeshAccessor(synchronizer.getMesh()), synchronizer(synchronizer),
comm(synchronizer.getCommunicator()), rank(comm.whoAmI()),
nb_proc(comm.getNbProc()), root(root), mesh(synchronizer.getMesh()),
spatial_dimension(synchronizer.getMesh().getSpatialDimension()),
message_count(message_cnt) {}
/* -------------------------------------------------------------------------- */
template <class CommunicationBuffer>
void NodeInfoPerProc::fillNodeGroupsFromBuffer(CommunicationBuffer & buffer) {
AKANTU_DEBUG_IN();
std::vector<std::vector<std::string>> node_to_group;
buffer >> node_to_group;
AKANTU_DEBUG_ASSERT(node_to_group.size() == mesh.getNbGlobalNodes(),
"Not the good amount of nodes where transmitted");
const auto & global_nodes = mesh.getGlobalNodesIds();
auto nbegin = global_nodes.begin();
auto nit = global_nodes.begin();
auto nend = global_nodes.end();
for (; nit != nend; ++nit) {
std::vector<std::string>::iterator it = node_to_group[*nit].begin();
std::vector<std::string>::iterator end = node_to_group[*nit].end();
for (; it != end; ++it) {
mesh.getNodeGroup(*it).add(nit - nbegin, false);
}
}
GroupManager::const_node_group_iterator ngi = mesh.node_group_begin();
GroupManager::const_node_group_iterator nge = mesh.node_group_end();
for (; ngi != nge; ++ngi) {
NodeGroup & ng = *(ngi->second);
ng.optimize();
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillNodesType() {
AKANTU_DEBUG_IN();
UInt nb_nodes = mesh.getNbNodes();
Array<NodeType> & nodes_type = this->getNodesType();
Array<UInt> nodes_set(nb_nodes);
nodes_set.set(0);
enum NodeSet {
NORMAL_SET = 1,
GHOST_SET = 2,
};
Array<bool> already_seen(nb_nodes, 1, false);
for (UInt g = _not_ghost; g <= _ghost; ++g) {
GhostType gt = (GhostType)g;
UInt set = NORMAL_SET;
if (gt == _ghost)
set = GHOST_SET;
already_seen.set(false);
Mesh::type_iterator it =
mesh.firstType(_all_dimensions, gt, _ek_not_defined);
Mesh::type_iterator end =
mesh.lastType(_all_dimensions, gt, _ek_not_defined);
for (; it != end; ++it) {
ElementType type = *it;
UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
UInt nb_element = mesh.getNbElement(type, gt);
Array<UInt>::const_vector_iterator conn_it =
mesh.getConnectivity(type, gt).begin(nb_nodes_per_element);
for (UInt e = 0; e < nb_element; ++e, ++conn_it) {
const Vector<UInt> & conn = *conn_it;
for (UInt n = 0; n < nb_nodes_per_element; ++n) {
AKANTU_DEBUG_ASSERT(conn(n) < nb_nodes,
"Node " << conn(n)
<< " bigger than number of nodes "
<< nb_nodes);
if (!already_seen(conn(n))) {
nodes_set(conn(n)) += set;
already_seen(conn(n)) = true;
}
}
}
}
}
for (UInt i = 0; i < nb_nodes; ++i) {
if (nodes_set(i) == NORMAL_SET)
nodes_type(i) = _nt_normal;
else if (nodes_set(i) == GHOST_SET)
nodes_type(i) = _nt_pure_gost;
else if (nodes_set(i) == (GHOST_SET + NORMAL_SET))
nodes_type(i) = _nt_master;
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void NodeInfoPerProc::fillCommunicationScheme(const Array<UInt> & master_info) {
AKANTU_DEBUG_IN();
Communications<UInt> & communications =
this->synchronizer.getCommunications();
{ // send schemes
auto it = master_info.begin_reinterpret(2, master_info.getSize() / 2);
auto end = master_info.end_reinterpret(2, master_info.getSize() / 2);
std::map<UInt, Array<UInt>> send_array_per_proc;
for (; it != end; ++it) {
const Vector<UInt> & send_info = *it;
send_array_per_proc[send_info(0)].push_back(send_info(1));
}
for (auto & send_schemes : send_array_per_proc) {
auto & scheme = communications.createSendScheme(send_schemes.first);
auto & sends = send_schemes.second;
std::sort(sends.begin(), sends.end());
std::transform(sends.begin(), sends.end(), sends.begin(),
[this](UInt g) -> UInt { return mesh.getNodeLocalId(g); });
scheme.copy(sends);
}
}
{ // receive schemes
const Array<NodeType> & nodes_type = this->getNodesType();
std::map<UInt, Array<UInt>> recv_array_per_proc;
UInt node = 0;
for (auto & node_type : nodes_type) {
if (Int(node_type) >= 0) {
recv_array_per_proc[node_type].push_back(mesh.getNodeGlobalId(node));
}
++node;
}
for (auto & recv_schemes : recv_array_per_proc) {
auto & scheme = communications.createRecvScheme(recv_schemes.first);
auto & recvs = recv_schemes.second;
std::sort(recvs.begin(), recvs.end());
std::transform(recvs.begin(), recvs.end(), recvs.begin(),
[this](UInt g) -> UInt { return mesh.getNodeLocalId(g); });
scheme.copy(recvs);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
MasterNodeInfoPerProc::MasterNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: NodeInfoPerProc(synchronizer, message_cnt, root) {
UInt nb_global_nodes = this->mesh.getNbGlobalNodes();
this->comm.broadcast(nb_global_nodes, this->root);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeNodes() {
this->nodes_per_proc.resize(nb_proc);
this->nb_nodes_per_proc.resize(nb_proc);
Array<Real> local_nodes(0, spatial_dimension);
Array<Real> & nodes = this->getNodes();
for (UInt p = 0; p < nb_proc; ++p) {
UInt nb_nodes = 0;
// UInt * buffer;
Array<Real> * nodes_to_send;
Array<UInt> & nodespp = nodes_per_proc[p];
if (p != root) {
nodes_to_send = new Array<Real>(0, spatial_dimension);
AKANTU_DEBUG_INFO("Receiving number of nodes from proc "
<< p << " " << Tag::genTag(p, 0, Tag::_NB_NODES));
comm.receive(nb_nodes, p, Tag::genTag(p, 0, Tag::_NB_NODES));
nodespp.resize(nb_nodes);
this->nb_nodes_per_proc(p) = nb_nodes;
AKANTU_DEBUG_INFO("Receiving list of nodes from proc "
<< p << " " << Tag::genTag(p, 0, Tag::_NODES));
comm.receive(nodespp, p, Tag::genTag(p, 0, Tag::_NODES));
} else {
Array<UInt> & local_ids = this->getNodesGlobalIds();
this->nb_nodes_per_proc(p) = local_ids.getSize();
nodespp.copy(local_ids);
nodes_to_send = &local_nodes;
}
Array<UInt>::const_scalar_iterator it = nodespp.begin();
Array<UInt>::const_scalar_iterator end = nodespp.end();
/// get the coordinates for the selected nodes
for (; it != end; ++it) {
Vector<Real> coord(nodes.storage() + spatial_dimension * *it,
spatial_dimension);
nodes_to_send->push_back(coord);
}
if (p != root) { /// send them for distant processors
AKANTU_DEBUG_INFO("Sending coordinates to proc "
<< p << " "
<< Tag::genTag(this->rank, 0, Tag::_COORDINATES));
comm.send(*nodes_to_send, p,
Tag::genTag(this->rank, 0, Tag::_COORDINATES));
delete nodes_to_send;
}
}
/// construct the local nodes coordinates
nodes.copy(local_nodes);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeTypes() {
// <global_id, <proc, local_id> >
std::multimap<UInt, std::pair<UInt, UInt>> nodes_to_proc;
std::vector<Array<NodeType>> nodes_type_per_proc(nb_proc);
// arrays containing pairs of (proc, node)
std::vector<Array<UInt>> nodes_to_send_per_proc(nb_proc);
for (UInt p = 0; p < nb_proc; ++p) {
nodes_type_per_proc[p].resize(nb_nodes_per_proc(p));
}
this->fillNodesType();
for (UInt p = 0; p < nb_proc; ++p) {
auto & nodes_types = nodes_type_per_proc[p];
if (p != root) {
AKANTU_DEBUG_INFO(
"Receiving first nodes types from proc "
<< p << " "
<< Tag::genTag(this->rank, this->message_count, Tag::_NODES_TYPE));
comm.receive(nodes_types, p, Tag::genTag(p, 0, Tag::_NODES_TYPE));
} else {
nodes_types.copy(this->getNodesType());
}
// stack all processors claiming to be master for a node
for (UInt local_node = 0; local_node < nb_nodes_per_proc(p); ++local_node) {
if (nodes_types(local_node) == _nt_master) {
UInt global_node = nodes_per_proc[p](local_node);
nodes_to_proc.insert(std::make_pair(global_node, std::make_pair(p, local_node)));
}
}
}
for (UInt i = 0; i < mesh.getNbGlobalNodes(); ++i) {
auto it_range = nodes_to_proc.equal_range(i);
if (it_range.first == nodes_to_proc.end() || it_range.first->first != i)
continue;
// pick the first processor out of the multi-map as the actual master
UInt master_proc = (it_range.first)->second.first;
for (auto it_node = it_range.first; it_node != it_range.second; ++it_node) {
UInt proc = it_node->second.first;
UInt node = it_node->second.second;
if (proc != master_proc) {
// store the info on all the slaves for a given master
nodes_type_per_proc[proc](node) = NodeType(master_proc);
nodes_to_send_per_proc[master_proc].push_back(proc);
nodes_to_send_per_proc[master_proc].push_back(i);
}
}
}
std::vector<CommunicationRequest> requests_send_type;
std::vector<CommunicationRequest> requests_send_master_info;
for (UInt p = 0; p < nb_proc; ++p) {
if (p != root) {
AKANTU_DEBUG_INFO("Sending nodes types to proc "
<< p << " "
<< Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
requests_send_type.push_back(
comm.asyncSend(nodes_type_per_proc[p], p,
Tag::genTag(this->rank, 0, Tag::_NODES_TYPE)));
auto & nodes_to_send = nodes_to_send_per_proc[p];
/// push back an element to avoid a send of size 0
nodes_to_send.push_back(-1);
AKANTU_DEBUG_INFO("Sending nodes master info to proc "
<< p << " "
<< Tag::genTag(this->rank, 1, Tag::_NODES_TYPE));
requests_send_master_info.push_back(
comm.asyncSend(nodes_to_send, p,
Tag::genTag(this->rank, 1, Tag::_NODES_TYPE)));
} else {
this->getNodesType().copy(nodes_type_per_proc[p]);
this->fillCommunicationScheme(nodes_to_send_per_proc[root]);
}
}
comm.waitAll(requests_send_type);
comm.freeCommunicationRequest(requests_send_type);
requests_send_type.clear();
comm.waitAll(requests_send_master_info);
comm.freeCommunicationRequest(requests_send_master_info);
}
/* -------------------------------------------------------------------------- */
void MasterNodeInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
UInt nb_total_nodes = mesh.getNbGlobalNodes();
DynamicCommunicationBuffer buffer;
typedef std::vector<std::vector<std::string>> NodeToGroup;
NodeToGroup node_to_group;
node_to_group.resize(nb_total_nodes);
GroupManager::const_node_group_iterator ngi = mesh.node_group_begin();
GroupManager::const_node_group_iterator nge = mesh.node_group_end();
for (; ngi != nge; ++ngi) {
NodeGroup & ng = *(ngi->second);
std::string name = ngi->first;
NodeGroup::const_node_iterator nit = ng.begin();
NodeGroup::const_node_iterator nend = ng.end();
for (; nit != nend; ++nit) {
node_to_group[*nit].push_back(name);
}
nit = ng.begin();
if (nit != nend)
ng.empty();
}
buffer << node_to_group;
std::vector<CommunicationRequest> requests;
for (UInt p = 0; p < nb_proc; ++p) {
if (p == this->rank)
continue;
AKANTU_DEBUG_INFO("Sending node groups to proc "
<< p << " "
<< Tag::genTag(this->rank, p, Tag::_NODE_GROUP));
requests.push_back(comm.asyncSend(
buffer, p, Tag::genTag(this->rank, p, Tag::_NODE_GROUP)));
}
this->fillNodeGroupsFromBuffer(buffer);
comm.waitAll(requests);
comm.freeCommunicationRequest(requests);
requests.clear();
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
SlaveNodeInfoPerProc::SlaveNodeInfoPerProc(NodeSynchronizer & synchronizer,
UInt message_cnt, UInt root)
: NodeInfoPerProc(synchronizer, message_cnt, root) {
UInt nb_global_nodes = 0;
comm.broadcast(nb_global_nodes, root);
this->setNbGlobalNodes(nb_global_nodes);
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeNodes() {
AKANTU_DEBUG_INFO("Sending list of nodes to proc "
<< root << " " << Tag::genTag(this->rank, 0, Tag::_NB_NODES)
<< " " << Tag::genTag(this->rank, 0, Tag::_NODES));
Array<UInt> & local_ids = this->getNodesGlobalIds();
Array<Real> & nodes = this->getNodes();
UInt nb_nodes = local_ids.getSize();
comm.send(nb_nodes, root, Tag::genTag(this->rank, 0, Tag::_NB_NODES));
comm.send(local_ids, root, Tag::genTag(this->rank, 0, Tag::_NODES));
/* --------<<<<-COORDINATES---------------------------------------------- */
nodes.resize(nb_nodes);
AKANTU_DEBUG_INFO("Receiving coordinates from proc "
<< root << " " << Tag::genTag(root, 0, Tag::_COORDINATES));
comm.receive(nodes, root, Tag::genTag(root, 0, Tag::_COORDINATES));
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeTypes() {
this->fillNodesType();
Array<NodeType> & nodes_types = this->getNodesType();
AKANTU_DEBUG_INFO("Sending first nodes types to proc "
<< root << ""
<< Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
comm.send(nodes_types, root, Tag::genTag(this->rank, 0, Tag::_NODES_TYPE));
AKANTU_DEBUG_INFO("Receiving nodes types from proc "
<< root << " " << Tag::genTag(root, 0, Tag::_NODES_TYPE));
comm.receive(nodes_types, root, Tag::genTag(root, 0, Tag::_NODES_TYPE));
AKANTU_DEBUG_INFO("Receiving nodes master info from proc "
<< root << " " << Tag::genTag(root, 1, Tag::_NODES_TYPE));
CommunicationStatus status;
comm.probe<UInt>(root, Tag::genTag(root, 1, Tag::_NODES_TYPE), status);
Array<UInt> nodes_master_info(status.getSize());
comm.receive(nodes_master_info, root,
Tag::genTag(root, 1, Tag::_NODES_TYPE));
nodes_master_info.resize(nodes_master_info.getSize() - 1);
this->fillCommunicationScheme(nodes_master_info);
}
/* -------------------------------------------------------------------------- */
void SlaveNodeInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
AKANTU_DEBUG_INFO("Receiving node groups from proc "
<< root << " "
<< Tag::genTag(root, this->rank, Tag::_NODE_GROUP));
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, this->rank, Tag::_NODE_GROUP),
status);
CommunicationBuffer buffer(status.getSize());
comm.receive(buffer, root, Tag::genTag(root, this->rank, Tag::_NODE_GROUP));
this->fillNodeGroupsFromBuffer(buffer);
AKANTU_DEBUG_OUT();
}
-__END_AKANTU__
+} // akantu
diff --git a/src/synchronizer/node_info_per_processor.hh b/src/synchronizer/node_info_per_processor.hh
index a3fe2ff0b..ca461d9d8 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 StaticCommunicator;
}
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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 StaticCommunicator & 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();
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();
private:
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_NODE_INFO_PER_PROCESSOR_HH__ */
diff --git a/src/synchronizer/real_static_communicator.hh b/src/synchronizer/real_static_communicator.hh
index b974d12ca..ea35d9dc3 100644
--- a/src/synchronizer/real_static_communicator.hh
+++ b/src/synchronizer/real_static_communicator.hh
@@ -1,153 +1,153 @@
/**
* @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__
-__BEGIN_AKANTU__
+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)) {}
// CommunicationRequest(CommunicationRequest & other)
// : request(std::move(other.request)) {}
// CommunicationRequest(CommunicationRequest && other)
// : request(std::move(other.request)) {}
// CommunicationRequest & operator=(CommunicationRequest & other) {
// request = std::move(other.request);
// return *this;
// }
// CommunicationRequest & operator=(CommunicationRequest && other) {
// request = std::move(other.request);
// return *this;
// }
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:
CommunicationStatus() : source(0), size(0), tag(0){};
AKANTU_GET_MACRO(Source, source, Int);
AKANTU_GET_MACRO(Size, size, UInt);
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;
UInt size;
Int tag;
};
/* -------------------------------------------------------------------------- */
/// Datatype to pack pairs for MPI_{MIN,MAX}LOC
template <typename T1, typename T2> struct SCMinMaxLoc {
T1 min_max;
T2 loc;
};
/* -------------------------------------------------------------------------- */
class StaticCommunicator;
/* -------------------------------------------------------------------------- */
class RealStaticCommunicator {
public:
RealStaticCommunicator(__attribute__((unused)) int & argc,
__attribute__((unused)) char **& argv) {
prank = -1;
psize = -1;
};
virtual ~RealStaticCommunicator(){};
friend class StaticCommunicator;
Int getNbProc() { return this->psize; }
Int whoAmI() { return this->prank; }
protected:
Int prank;
Int psize;
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_REAL_STATIC_COMMUNICATOR_HH__ */
diff --git a/src/synchronizer/slave_element_info_per_processor.cc b/src/synchronizer/slave_element_info_per_processor.cc
index 7263d6c36..78c764065 100644
--- a/src/synchronizer/slave_element_info_per_processor.cc
+++ b/src/synchronizer/slave_element_info_per_processor.cc
@@ -1,197 +1,197 @@
/**
* @file slave_element_info_per_processor.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date Fri Mar 11 14:59:21 2016
*
* @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 "element_info_per_processor.hh"
#include "element_synchronizer.hh"
#include "mesh_utils.hh"
#include "static_communicator.hh"
/* -------------------------------------------------------------------------- */
#include <algorithm>
#include <iostream>
#include <map>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
SlaveElementInfoPerProc::SlaveElementInfoPerProc(
ElementSynchronizer & synchronizer, UInt message_cnt, UInt root)
: ElementInfoPerProc(synchronizer, message_cnt, root, _not_defined) {
Vector<UInt> size(5);
comm.receive(size, this->root,
Tag::genTag(this->root, this->message_count, Tag::_SIZES));
this->type = (ElementType)size[0];
this->nb_local_element = size[1];
this->nb_ghost_element = size[2];
this->nb_element_to_receive = size[3];
this->nb_tags = size[4];
if (this->type != _not_defined)
this->nb_nodes_per_element = Mesh::getNbNodesPerElement(type);
}
/* -------------------------------------------------------------------------- */
bool SlaveElementInfoPerProc::needSynchronize() {
return this->type != _not_defined;
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeConnectivities() {
Array<UInt> local_connectivity(
(this->nb_local_element + this->nb_ghost_element) *
this->nb_nodes_per_element);
AKANTU_DEBUG_INFO("Receiving connectivities from proc " << root);
comm.receive(
local_connectivity, this->root,
Tag::genTag(this->root, this->message_count, Tag::_CONNECTIVITY));
Array<UInt> & old_nodes = this->getNodesGlobalIds();
AKANTU_DEBUG_INFO("Renumbering local connectivities");
MeshUtils::renumberMeshNodes(this->mesh, local_connectivity,
this->nb_local_element, this->nb_ghost_element,
this->type, old_nodes);
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizePartitions() {
Array<UInt> local_partitions(this->nb_element_to_receive +
this->nb_ghost_element * 2);
AKANTU_DEBUG_INFO("Receiving partition informations from proc " << root);
this->comm.receive(local_partitions, this->root,
Tag::genTag(root, this->message_count, Tag::_PARTITIONS));
if (Mesh::getSpatialDimension(this->type) ==
this->mesh.getSpatialDimension()) {
AKANTU_DEBUG_INFO("Creating communications scheme");
this->fillCommunicationScheme(local_partitions);
}
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeTags() {
AKANTU_DEBUG_IN();
if (this->nb_tags == 0) {
AKANTU_DEBUG_OUT();
return;
}
/* --------<<<<-TAGS------------------------------------------------- */
UInt mesh_data_sizes_buffer_length = 0;
CommunicationBuffer mesh_data_sizes_buffer;
AKANTU_DEBUG_INFO(
"Receiving the size of the information about the mesh data tags.");
comm.broadcast(mesh_data_sizes_buffer_length, root);
if (mesh_data_sizes_buffer_length != 0) {
mesh_data_sizes_buffer.resize(mesh_data_sizes_buffer_length);
AKANTU_DEBUG_INFO(
"Receiving the information about the mesh data tags, addr "
<< (void *)mesh_data_sizes_buffer.storage());
comm.broadcast(mesh_data_sizes_buffer, root);
AKANTU_DEBUG_INFO("Size of the information about the mesh data: "
<< mesh_data_sizes_buffer_length);
std::vector<std::string> tag_names;
std::vector<MeshDataTypeCode> tag_type_codes;
std::vector<UInt> tag_nb_component;
tag_names.resize(nb_tags);
tag_type_codes.resize(nb_tags);
tag_nb_component.resize(nb_tags);
CommunicationBuffer mesh_data_buffer;
UInt type_code_int;
for (UInt i(0); i < nb_tags; ++i) {
mesh_data_sizes_buffer >> tag_names[i];
mesh_data_sizes_buffer >> type_code_int;
tag_type_codes[i] = static_cast<MeshDataTypeCode>(type_code_int);
mesh_data_sizes_buffer >> tag_nb_component[i];
}
std::vector<std::string>::const_iterator names_it = tag_names.begin();
std::vector<std::string>::const_iterator names_end = tag_names.end();
CommunicationStatus mesh_data_comm_status;
AKANTU_DEBUG_INFO("Checking size of data to receive for mesh data TAG("
<< Tag::genTag(root, this->message_count, Tag::_MESH_DATA)
<< ")");
comm.probe<char>(root,
Tag::genTag(root, this->message_count, Tag::_MESH_DATA),
mesh_data_comm_status);
UInt mesh_data_buffer_size(mesh_data_comm_status.getSize());
AKANTU_DEBUG_INFO("Receiving "
<< mesh_data_buffer_size << " bytes of mesh data TAG("
<< Tag::genTag(root, this->message_count, Tag::_MESH_DATA)
<< ")");
mesh_data_buffer.resize(mesh_data_buffer_size);
comm.receive(mesh_data_buffer, root,
Tag::genTag(root, this->message_count, Tag::_MESH_DATA));
// Loop over each tag for the current type
UInt k(0);
for (; names_it != names_end; ++names_it, ++k) {
this->fillMeshData(mesh_data_buffer, *names_it, tag_type_codes[k],
tag_nb_component[k]);
}
}
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
void SlaveElementInfoPerProc::synchronizeGroups() {
AKANTU_DEBUG_IN();
StaticCommunicator & comm = StaticCommunicator::getStaticCommunicator();
UInt my_rank = comm.whoAmI();
AKANTU_DEBUG_INFO("Receiving element groups from proc "
<< root << " TAG("
<< Tag::genTag(root, my_rank, Tag::_ELEMENT_GROUP) << ")");
CommunicationStatus status;
comm.probe<char>(root, Tag::genTag(root, my_rank, Tag::_ELEMENT_GROUP),
status);
CommunicationBuffer buffer(status.getSize());
comm.receive(buffer, root, Tag::genTag(root, my_rank, Tag::_ELEMENT_GROUP));
this->fillElementGroupsFromBuffer(buffer);
AKANTU_DEBUG_OUT();
}
/* -------------------------------------------------------------------------- */
-__END_AKANTU__
+} // akantu
diff --git a/src/synchronizer/static_communicator.cc b/src/synchronizer/static_communicator.cc
index 89f93e134..501e94347 100644
--- a/src/synchronizer/static_communicator.cc
+++ b/src/synchronizer/static_communicator.cc
@@ -1,133 +1,133 @@
/**
* @file static_communicator.cc
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Tue Jan 19 2016
*
* @brief implementation of the common part of the static communicator
*
* @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 "static_communicator.hh"
#include "static_communicator_dummy.hh"
#ifdef AKANTU_USE_MPI
#include "static_communicator_mpi.hh"
#endif
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
/* -------------------------------------------------------------------------- */
bool StaticCommunicator::is_instantiated = false;
StaticCommunicator * StaticCommunicator::static_communicator = NULL;
UInt InternalCommunicationRequest::counter = 0;
/* -------------------------------------------------------------------------- */
InternalCommunicationRequest::InternalCommunicationRequest(UInt source, UInt dest)
: source(source), destination(dest) {
this->id = counter++;
}
/* -------------------------------------------------------------------------- */
InternalCommunicationRequest::~InternalCommunicationRequest() {}
/* -------------------------------------------------------------------------- */
void InternalCommunicationRequest::printself(std::ostream & stream, int indent) const {
std::string space;
for (Int i = 0; i < indent; i++, space += AKANTU_INDENT)
;
stream << space << "CommunicationRequest [" << std::endl;
stream << space << " + id : " << id << std::endl;
stream << space << " + source : " << source << std::endl;
stream << space << " + destination : " << destination << std::endl;
stream << space << "]" << std::endl;
}
/* -------------------------------------------------------------------------- */
StaticCommunicator::StaticCommunicator(int & argc, char **& argv,
CommunicatorType type) {
real_type = type;
#ifdef AKANTU_USE_MPI
if (type == _communicator_mpi) {
real_static_communicator = new StaticCommunicatorMPI(argc, argv);
} else {
#endif
real_static_communicator = new StaticCommunicatorDummy(argc, argv);
#ifdef AKANTU_USE_MPI
}
#endif
this->is_instantiated = true;
}
/* -------------------------------------------------------------------------- */
StaticCommunicator::~StaticCommunicator() {
FinalizeCommunicatorEvent * event = new FinalizeCommunicatorEvent(*this);
this->sendEvent(*event);
this->barrier();
delete event;
delete real_static_communicator;
is_instantiated = false;
StaticCommunicator::static_communicator = NULL;
}
/* -------------------------------------------------------------------------- */
StaticCommunicator &
StaticCommunicator::getStaticCommunicator(CommunicatorType type) {
AKANTU_DEBUG_IN();
if (!static_communicator) {
int nb_args = 0;
char ** null;
static_communicator = new StaticCommunicator(nb_args, null, type);
}
AKANTU_DEBUG_OUT();
return *static_communicator;
}
/* -------------------------------------------------------------------------- */
StaticCommunicator &
StaticCommunicator::getStaticCommunicator(int & argc, char **& argv,
CommunicatorType type) {
if (!static_communicator)
static_communicator = new StaticCommunicator(argc, argv, type);
return getStaticCommunicator(type);
}
/* -------------------------------------------------------------------------- */
StaticCommunicator * StaticCommunicator::getStaticCommunicatorDummy() {
int nb_args = 0;
char ** null;
return new StaticCommunicator(nb_args, null, _communicator_dummy);
}
-__END_AKANTU__
+} // akantu
diff --git a/src/synchronizer/static_communicator.hh b/src/synchronizer/static_communicator.hh
index 484b97adb..a1307f1fb 100644
--- a/src/synchronizer/static_communicator.hh
+++ b/src/synchronizer/static_communicator.hh
@@ -1,417 +1,417 @@
/**
* @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/>.
*
*/
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_STATIC_COMMUNICATOR_HH__
#define __AKANTU_STATIC_COMMUNICATOR_HH__
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_event_handler_manager.hh"
#include "communication_buffer.hh"
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
#define AKANTU_COMMUNICATOR_LIST_0 BOOST_PP_SEQ_NIL
#include "static_communicator_dummy.hh"
#define AKANTU_COMMUNICATOR_LIST_1 \
BOOST_PP_SEQ_PUSH_BACK( \
AKANTU_COMMUNICATOR_LIST_0, \
(_communicator_dummy, (StaticCommunicatorDummy, BOOST_PP_NIL)))
#if defined(AKANTU_USE_MPI)
#include "static_communicator_mpi.hh"
#define AKANTU_COMMUNICATOR_LIST_ALL \
BOOST_PP_SEQ_PUSH_BACK( \
AKANTU_COMMUNICATOR_LIST_1, \
(_communicator_mpi, (StaticCommunicatorMPI, BOOST_PP_NIL)))
#else
#define AKANTU_COMMUNICATOR_LIST_ALL AKANTU_COMMUNICATOR_LIST_1
#endif // AKANTU_COMMUNICATOR_LIST
#include "real_static_communicator.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class RealStaticCommunicator;
struct FinalizeCommunicatorEvent {
explicit FinalizeCommunicatorEvent(const StaticCommunicator & comm)
: communicator(comm) {}
const StaticCommunicator & communicator;
};
class CommunicatorEventHandler {
public:
virtual ~CommunicatorEventHandler() {}
virtual void onCommunicatorFinalize() { }
private:
inline void sendEvent(const FinalizeCommunicatorEvent &) {
onCommunicatorFinalize();
}
template <class EventHandler> friend class EventHandlerManager;
};
class StaticCommunicator
: public EventHandlerManager<CommunicatorEventHandler> {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
protected:
StaticCommunicator(int & argc, char **& argv,
CommunicatorType type = _communicator_mpi);
public:
virtual ~StaticCommunicator();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
/* Point to Point */
/* ------------------------------------------------------------------------ */
template <typename T>
inline void receive(Array<T> & values, Int sender, Int tag) const {
return this->receive(values.storage(),
values.getSize() * values.getNbComponent(), sender,
tag);
}
template <typename T>
inline void receive(Vector<T> & values, Int sender, Int tag) const {
return this->receive(values.storage(), values.size(), sender, tag);
}
template <typename T>
inline void receive(Matrix<T> & values, Int sender, Int tag) const {
return this->receive(values.storage(), values.size(), sender, tag);
}
template <bool is_static>
inline void receive(CommunicationBufferTemplated<is_static> & values,
Int sender, Int tag) const {
return this->receive(values.storage(), values.getSize(), sender, tag);
}
template <typename T>
inline void receive(T & values, Int sender, Int tag) const {
return this->receive(&values, 1, sender, tag);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void send(Array<T> & values, Int receiver, Int tag) const {
return this->send(values.storage(),
values.getSize() * values.getNbComponent(), receiver,
tag);
}
template <typename T>
inline void send(Vector<T> & values, Int receiver, Int tag) const {
return this->send(values.storage(), values.size(), receiver, tag);
}
template <typename T>
inline void send(Matrix<T> & values, Int receiver, Int tag) const {
return this->send(values.storage(), values.size(), receiver, tag);
}
template <bool is_static>
inline void send(CommunicationBufferTemplated<is_static> & values,
Int receiver, Int tag) const {
return this->send(values.storage(), values.getSize(), receiver, tag);
}
template <typename T>
inline void send(T & values, Int receiver, Int tag) const {
return this->send(&values, 1, receiver, tag);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline CommunicationRequest asyncSend(Array<T> & values, Int receiver,
Int tag) const {
return this->asyncSend(values.storage(),
values.getSize() * values.getNbComponent(), receiver,
tag);
}
template <typename T>
inline CommunicationRequest asyncSend(Vector<T> & values, Int receiver,
Int tag) const {
return this->asyncSend(values.storage(), values.size(), receiver, tag);
}
template <typename T>
inline CommunicationRequest asyncSend(Matrix<T> & values, Int receiver,
Int tag) const {
return this->asyncSend(values.storage(), values.size(), receiver, tag);
}
template <bool is_static>
inline CommunicationRequest
asyncSend(CommunicationBufferTemplated<is_static> & values, Int receiver,
Int tag) const {
return this->asyncSend(values.storage(), values.getSize(), receiver, tag);
}
template <typename T>
inline CommunicationRequest asyncSend(T & values, Int receiver,
Int tag) const {
return this->asyncSend(&values, 1, receiver, tag);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline CommunicationRequest asyncReceive(Array<T> & values, Int sender,
Int tag) const {
return this->asyncReceive(values.storage(),
values.getSize() * values.getNbComponent(),
sender, tag);
}
template <typename T, UInt ndim, class RetType>
inline CommunicationRequest
asyncReceive(TensorStorage<T, ndim, RetType> & values, Int sender,
Int tag) const {
return this->asyncReceive(values.storage(), values.size(), sender, tag);
}
template <bool is_static>
inline CommunicationRequest
asyncReceive(CommunicationBufferTemplated<is_static> & values, Int sender,
Int tag) const {
return this->asyncReceive(values.storage(), values.getSize(), sender, tag);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void probe(Int sender, Int tag, CommunicationStatus & status) const;
/* ------------------------------------------------------------------------ */
/* Collectives */
/* ------------------------------------------------------------------------ */
template <typename T>
inline void allReduce(Array<T> & values,
const SynchronizerOperation & op) const {
this->allReduce(values.storage(),
values.getSize() * values.getNbComponent(), op);
}
template <typename T>
inline void allReduce(Vector<T> & values,
const SynchronizerOperation & op) const {
this->allReduce(values.storage(), values.size(), op);
}
template <typename T>
inline void allReduce(Matrix<T> & values,
const SynchronizerOperation & op) const {
this->allReduce(values.storage(), values.size(), op);
}
template <typename T>
inline void allReduce(T & values, const SynchronizerOperation & op) const {
this->allReduce(&values, 1, op);
}
/* ------------------------------------------------------------------------ */
template <typename T> inline void allGather(Array<T> & values) const {
AKANTU_DEBUG_ASSERT(UInt(this->real_static_communicator->getNbProc()) ==
values.getSize(),
"The array size is not correct");
this->allGather(values.storage(), values.getNbComponent());
}
template <typename T> inline void allGather(Vector<T> & values) const {
AKANTU_DEBUG_ASSERT(UInt(this->real_static_communicator->getNbProc()) ==
values.size(),
"The array size is not correct");
this->allGather(values.storage(), 1);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void allGatherV(Array<T> & values, Array<Int> sizes) const {
this->allGatherV(values.storage(), sizes.storage());
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void reduce(Array<T> & values, const SynchronizerOperation & op,
int root = 0) const {
this->reduce(values.storage(), values.getSize() * values.getNbComponent(),
op, root);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void gather(Vector<T> & values, int root = 0) const {
this->gather(values.storage(), values.getNbComponent(), root);
}
template <typename T> inline void gather(T values, int root = 0) const {
this->gather(&values, 1, root);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void gather(Vector<T> & values, Array<T> & gathered) const {
AKANTU_DEBUG_ASSERT(values.getSize() == gathered.getNbComponent(),
"The array size is not correct");
gathered.resize(this->real_static_communicator->getNbProc());
this->gather(values.data(), values.getSize(), gathered.storage(),
gathered.getNbComponent());
}
template <typename T>
inline void gather(T values, Array<T> & gathered) const {
this->gather(&values, 1, gathered.storage(), 1);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void gatherV(Array<T> & values, Array<Int> sizes, int root = 0) const {
this->gatherV(values.storage(), sizes.storage(), root);
}
/* ------------------------------------------------------------------------ */
template <typename T>
inline void broadcast(Array<T> & values, int root = 0) const {
this->broadcast(values.storage(),
values.getSize() * values.getNbComponent(), root);
}
template <bool is_static>
inline void broadcast(CommunicationBufferTemplated<is_static> & values,
int root = 0) const {
this->broadcast(values.storage(), values.getSize(), root);
}
template <typename T> inline void broadcast(T & values, int root = 0) const {
this->broadcast(&values, 1, root);
}
/* ------------------------------------------------------------------------ */
inline void barrier() const;
/* ------------------------------------------------------------------------ */
/* Request handling */
/* ------------------------------------------------------------------------ */
inline bool testRequest(CommunicationRequest & request) const;
inline void wait(CommunicationRequest & request) const;
inline void waitAll(std::vector<CommunicationRequest> & requests) const;
inline UInt waitAny(std::vector<CommunicationRequest> & requests) const;
inline void freeCommunicationRequest(CommunicationRequest & request) const;
inline void
freeCommunicationRequest(std::vector<CommunicationRequest> & requests) const;
protected:
template <typename T>
inline void send(T * buffer, Int size, Int receiver, Int tag) const;
template <typename T>
inline void receive(T * buffer, Int size, Int sender, Int tag) const;
template <typename T>
inline CommunicationRequest asyncSend(T * buffer, Int size, Int receiver,
Int tag) const;
template <typename T>
inline CommunicationRequest asyncReceive(T * buffer, Int size, Int sender,
Int tag) const;
template <typename T>
inline void allReduce(T * values, int nb_values,
const SynchronizerOperation & op) const;
template <typename T> inline void allGather(T * values, int nb_values) const;
template <typename T>
inline void allGatherV(T * values, int * nb_values) const;
template <typename T>
inline void reduce(T * values, int nb_values,
const SynchronizerOperation & op, int root = 0) const;
template <typename T>
inline void gather(T * values, int nb_values, int root = 0) const;
template <typename T>
inline void gather(T * values, int nb_values, T * gathered,
int nb_gathered = 0) const;
template <typename T>
inline void gatherV(T * values, int * nb_values, int root = 0) const;
template <typename T>
inline void broadcast(T * values, int nb_values, int root = 0) const;
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
virtual Int getNbProc() const { return real_static_communicator->psize; };
virtual Int whoAmI() const { return real_static_communicator->prank; };
AKANTU_GET_MACRO(RealStaticCommunicator, *real_static_communicator,
const RealStaticCommunicator &);
AKANTU_GET_MACRO_NOT_CONST(RealStaticCommunicator, *real_static_communicator,
RealStaticCommunicator &);
template <class Comm> Comm & getRealStaticCommunicator() {
return dynamic_cast<Comm &>(*real_static_communicator);
}
static StaticCommunicator &
getStaticCommunicator(CommunicatorType type = _communicator_mpi);
static StaticCommunicator &
getStaticCommunicator(int & argc, char **& argv,
CommunicatorType type = _communicator_mpi);
static StaticCommunicator * getStaticCommunicatorDummy();
static bool isInstantiated() { return is_instantiated; };
int getMaxTag() const;
int getMinTag() const;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
static bool is_instantiated;
static StaticCommunicator * static_communicator;
RealStaticCommunicator * real_static_communicator;
CommunicatorType real_type;
};
/* -------------------------------------------------------------------------- */
/* Inline Functions ArrayBase */
/* -------------------------------------------------------------------------- */
inline std::ostream & operator<<(std::ostream & stream,
const CommunicationRequest & _this) {
_this.printself(stream);
return stream;
}
-__END_AKANTU__
+} // akantu
#include "static_communicator_inline_impl.hh"
#endif /* __AKANTU_STATIC_COMMUNICATOR_HH__ */
diff --git a/src/synchronizer/static_communicator_dummy.hh b/src/synchronizer/static_communicator_dummy.hh
index cc5748c2f..2e99950ec 100644
--- a/src/synchronizer/static_communicator_dummy.hh
+++ b/src/synchronizer/static_communicator_dummy.hh
@@ -1,122 +1,122 @@
/**
* @file static_communicator_dummy.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Fri Jun 18 2010
* @date last modification: Wed Jan 13 2016
*
* @brief Dummy communicator to make everything work im sequential
*
* @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_STATIC_COMMUNICATOR_DUMMY_HH__
#define __AKANTU_STATIC_COMMUNICATOR_DUMMY_HH__
/* -------------------------------------------------------------------------- */
#include "aka_common.hh"
#include "real_static_communicator.hh"
/* -------------------------------------------------------------------------- */
#include <cstring>
#include <vector>
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
class StaticCommunicatorDummy : public RealStaticCommunicator {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
StaticCommunicatorDummy(int & argc, char **& argv)
: RealStaticCommunicator(argc, argv) {
this->prank = 0;
this->psize = 1;
}
virtual ~StaticCommunicatorDummy() {}
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <typename T> void send(T *, Int, Int, Int) {}
template <typename T> void receive(T *, Int, Int, Int) {}
template <typename T> CommunicationRequest asyncSend(T *, Int, Int, Int) {
return std::shared_ptr<InternalCommunicationRequest>(
new InternalCommunicationRequest(0, 0));
}
template <typename T> CommunicationRequest asyncReceive(T *, Int, Int, Int) {
return std::shared_ptr<InternalCommunicationRequest>(
new InternalCommunicationRequest(0, 0));
}
template <typename T> inline void probe(Int, Int, CommunicationStatus &) {}
bool testRequest(CommunicationRequest &) { return true; }
void wait(CommunicationRequest &) {}
void waitAll(std::vector<CommunicationRequest> &) {}
UInt waitAny(std::vector<CommunicationRequest> &) { return UInt(-1); }
void barrier() {}
template <typename T>
void reduce(T *, int, const SynchronizerOperation &, int) {}
template <typename T>
void allReduce(T *, int, const SynchronizerOperation &) {}
template <typename T> inline void allGather(T *, int) {}
template <typename T> inline void allGatherV(T *, int *) {}
template <typename T> inline void gather(T *, int, int = 0) {}
template <typename T>
inline void gather(T * values, int nb_values, T * gathered, int) {
std::memcpy(gathered, values, nb_values);
}
template <typename T> inline void gatherV(T *, int *, int = 0) {}
template <typename T> inline void broadcast(T *, int, int = 0) {}
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/* ------------------------------------------------------------------------ */
int getMaxTag() { return std::numeric_limits<int>::max(); }
int getMinTag() { return 0; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
};
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_STATIC_COMMUNICATOR_DUMMY_HH__ */
diff --git a/src/synchronizer/static_communicator_mpi.cc b/src/synchronizer/static_communicator_mpi.cc
index af1f5a636..fb931b9d7 100644
--- a/src/synchronizer/static_communicator_mpi.cc
+++ b/src/synchronizer/static_communicator_mpi.cc
@@ -1,557 +1,557 @@
/**
* @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 <iostream>
/* -------------------------------------------------------------------------- */
#include "mpi_type_wrapper.hh"
#include "static_communicator_mpi.hh"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+namespace akantu {
MPI_Op MPITypeWrapper::synchronizer_operation_to_mpi_op[_so_null + 1] = {
MPI_SUM, MPI_MIN, MPI_MAX, MPI_PROD, MPI_LAND, MPI_BAND, MPI_LOR,
MPI_BOR, MPI_LXOR, MPI_BXOR, MPI_MINLOC, MPI_MAXLOC, MPI_OP_NULL};
class CommunicationRequestMPI : public InternalCommunicationRequest {
public:
CommunicationRequestMPI(UInt source, UInt dest);
MPI_Request & getMPIRequest() { return *request; };
private:
std::unique_ptr<MPI_Request> request;
};
/* -------------------------------------------------------------------------- */
/* Implementation */
/* -------------------------------------------------------------------------- */
CommunicationRequestMPI::CommunicationRequestMPI(UInt source, UInt dest)
: InternalCommunicationRequest(source, dest), request(new MPI_Request) {}
/* -------------------------------------------------------------------------- */
StaticCommunicatorMPI::StaticCommunicatorMPI(int & argc, char **& argv)
: RealStaticCommunicator(argc, argv) {
int is_initialized = false;
MPI_Initialized(&is_initialized);
if (!is_initialized) {
MPI_Init(&argc, &argv);
}
this->is_externaly_initialized = is_initialized;
mpi_data = new MPITypeWrapper(*this);
mpi_data->setMPICommunicator(MPI_COMM_WORLD);
}
/* -------------------------------------------------------------------------- */
StaticCommunicatorMPI::~StaticCommunicatorMPI() {
if (!this->is_externaly_initialized) {
MPI_Finalize();
delete this->mpi_data;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::send(T * buffer, Int size, Int receiver, Int tag) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Send(buffer, size, type, receiver, tag, communicator);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Send.");
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::receive(T * buffer, Int size, Int sender, Int tag) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
MPI_Status status;
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Recv(buffer, size, type, sender, tag, communicator, &status);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Recv.");
}
/* -------------------------------------------------------------------------- */
template <typename T>
CommunicationRequest StaticCommunicatorMPI::asyncSend(T * buffer, Int size,
Int receiver, Int tag) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
CommunicationRequestMPI * request =
new CommunicationRequestMPI(prank, receiver);
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
MPI_Request & req = request->getMPIRequest();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Isend(buffer, size, type, receiver, tag, communicator, &req);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Isend.");
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
CommunicationRequest StaticCommunicatorMPI::asyncReceive(T * buffer, Int size,
Int sender, Int tag) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
CommunicationRequestMPI * request =
new CommunicationRequestMPI(sender, prank);
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
MPI_Request & req = request->getMPIRequest();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Irecv(buffer, size, type, sender, tag, communicator, &req);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Irecv.");
return std::shared_ptr<InternalCommunicationRequest>(request);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::probe(Int sender, Int tag,
CommunicationStatus & status) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
MPI_Status mpi_status;
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Probe(sender, tag, communicator, &mpi_status);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Probe.");
MPI_Datatype type = MPITypeWrapper::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);
}
/* -------------------------------------------------------------------------- */
bool StaticCommunicatorMPI::testRequest(CommunicationRequest & request) {
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);
}
/* -------------------------------------------------------------------------- */
void StaticCommunicatorMPI::wait(CommunicationRequest & request) {
MPI_Status status;
CommunicationRequestMPI & req_mpi =
dynamic_cast<CommunicationRequestMPI &>(request.getInternal());
MPI_Request & req = req_mpi.getMPIRequest();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Wait(&req, &status);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Wait.");
}
/* -------------------------------------------------------------------------- */
void StaticCommunicatorMPI::waitAll(
std::vector<CommunicationRequest> & requests) {
MPI_Status status;
std::vector<CommunicationRequest>::iterator it;
for (it = requests.begin(); it != requests.end(); ++it) {
MPI_Request & req =
dynamic_cast<CommunicationRequestMPI &>(it->getInternal())
.getMPIRequest();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Wait(&req, &status);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Wait.");
}
}
/* -------------------------------------------------------------------------- */
UInt StaticCommunicatorMPI::waitAny(
std::vector<CommunicationRequest> & requests) {
MPI_Status status;
std::vector<MPI_Request> reqs(requests.size());
UInt r = 0;
for (auto it = requests.begin(); it != requests.end(); ++it, ++r) {
reqs[r] = static_cast<CommunicationRequestMPI *>(&it->getInternal())
->getMPIRequest();
}
int pos;
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Waitany(requests.size(), reqs.data(), &pos, &status);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Wait.");
if (pos != MPI_UNDEFINED) {
return pos;
} else {
return UInt(-1);
}
}
/* -------------------------------------------------------------------------- */
void StaticCommunicatorMPI::barrier() {
MPI_Comm communicator = mpi_data->getMPICommunicator();
MPI_Barrier(communicator);
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::reduce(T * values, int nb_values,
const SynchronizerOperation & op, int root) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Reduce(MPI_IN_PLACE, values, nb_values, type,
MPITypeWrapper::getMPISynchronizerOperation(op), root,
communicator);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Allreduce.");
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::allReduce(T * values, int nb_values,
const SynchronizerOperation & op) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Allreduce(MPI_IN_PLACE, values, nb_values, type,
MPITypeWrapper::getMPISynchronizerOperation(op),
communicator);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Allreduce.");
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::allGather(T * values, int nb_values) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Allgather(MPI_IN_PLACE, nb_values, type, values, nb_values, type,
communicator);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Allgather.");
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::allGatherV(T * values, int * nb_values) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
int * displs = new int[psize];
displs[0] = 0;
for (int i = 1; i < psize; ++i) {
displs[i] = displs[i - 1] + nb_values[i - 1];
}
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Allgatherv(MPI_IN_PLACE, *nb_values, type, values, nb_values, displs,
type, communicator);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Gather.");
delete[] displs;
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::gather(T * values, int nb_values, int root) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
T *send_buf = NULL, *recv_buf = NULL;
if (prank == root) {
send_buf = (T *)MPI_IN_PLACE;
recv_buf = values;
} else {
send_buf = values;
}
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Gather(send_buf, nb_values, type, recv_buf, nb_values, type, root,
communicator);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Gather.");
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::gather(T * values, int nb_values, T * gathered,
int nb_gathered) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
T * send_buf = values;
T * recv_buf = gathered;
if (nb_gathered == 0)
nb_gathered = nb_values;
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Gather(send_buf, nb_values, type, recv_buf, nb_gathered, type,
this->prank, communicator);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Gather.");
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::gatherV(T * values, int * nb_values, int root) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
int * displs = NULL;
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;
if (prank == root) {
send_buf = (T *)MPI_IN_PLACE;
recv_buf = values;
} else
send_buf = values;
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Gatherv(send_buf, *nb_values, type, recv_buf, nb_values, displs, type,
root, communicator);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Gather.");
if (prank == root) {
delete[] displs;
}
}
/* -------------------------------------------------------------------------- */
template <typename T>
void StaticCommunicatorMPI::broadcast(T * values, int nb_values, int root) {
MPI_Comm communicator = mpi_data->getMPICommunicator();
MPI_Datatype type = MPITypeWrapper::getMPIDatatype<T>();
#if !defined(AKANTU_NDEBUG)
int ret =
#endif
MPI_Bcast(values, nb_values, type, root, communicator);
AKANTU_DEBUG_ASSERT(ret == MPI_SUCCESS, "Error in MPI_Gather.");
}
/* -------------------------------------------------------------------------- */
int StaticCommunicatorMPI::getMaxTag() { return this->mpi_data->getMaxTag(); }
/* -------------------------------------------------------------------------- */
int StaticCommunicatorMPI::getMinTag() { return 0; }
/* -------------------------------------------------------------------------- */
// template<typename T>
// MPI_Datatype StaticCommunicatorMPI::getMPIDatatype() {
// return MPI_DATATYPE_NULL;
// }
template <> MPI_Datatype MPITypeWrapper::getMPIDatatype<char>() {
return MPI_CHAR;
}
template <> MPI_Datatype MPITypeWrapper::getMPIDatatype<float>() {
return MPI_FLOAT;
}
template <> MPI_Datatype MPITypeWrapper::getMPIDatatype<double>() {
return MPI_DOUBLE;
}
template <> MPI_Datatype MPITypeWrapper::getMPIDatatype<long double>() {
return MPI_LONG_DOUBLE;
}
template <> MPI_Datatype MPITypeWrapper::getMPIDatatype<signed int>() {
return MPI_INT;
}
template <> MPI_Datatype MPITypeWrapper::getMPIDatatype<NodeType>() {
return MPITypeWrapper::getMPIDatatype<Int>();
}
template <> MPI_Datatype MPITypeWrapper::getMPIDatatype<unsigned int>() {
return MPI_UNSIGNED;
}
template <> MPI_Datatype MPITypeWrapper::getMPIDatatype<signed long int>() {
return MPI_LONG;
}
template <> MPI_Datatype MPITypeWrapper::getMPIDatatype<unsigned long int>() {
return MPI_UNSIGNED_LONG;
}
template <>
MPI_Datatype MPITypeWrapper::getMPIDatatype<signed long long int>() {
return MPI_LONG_LONG;
}
template <>
MPI_Datatype MPITypeWrapper::getMPIDatatype<unsigned long long int>() {
return MPI_UNSIGNED_LONG_LONG;
}
template <>
MPI_Datatype MPITypeWrapper::getMPIDatatype<SCMinMaxLoc<double, int>>() {
return MPI_DOUBLE_INT;
}
template <>
MPI_Datatype MPITypeWrapper::getMPIDatatype<SCMinMaxLoc<float, int>>() {
return MPI_FLOAT_INT;
}
template <>
MPI_Datatype MPITypeWrapper::getMPIDatatype<bool>() {
return MPI_CXX_BOOL;
}
/* -------------------------------------------------------------------------- */
/* Template instantiation */
/* -------------------------------------------------------------------------- */
#define AKANTU_MPI_COMM_INSTANTIATE(T) \
template void StaticCommunicatorMPI::send<T>(T * buffer, Int size, \
Int receiver, Int tag); \
template void StaticCommunicatorMPI::receive<T>(T * buffer, Int size, \
Int sender, Int tag); \
template CommunicationRequest StaticCommunicatorMPI::asyncSend<T>( \
T * buffer, Int size, Int receiver, Int tag); \
template CommunicationRequest StaticCommunicatorMPI::asyncReceive<T>( \
T * buffer, Int size, Int sender, Int tag); \
template void StaticCommunicatorMPI::probe<T>(Int sender, Int tag, \
CommunicationStatus & status); \
template void StaticCommunicatorMPI::allGather<T>(T * values, \
int nb_values); \
template void StaticCommunicatorMPI::allGatherV<T>(T * values, \
int * nb_values); \
template void StaticCommunicatorMPI::gather<T>(T * values, int nb_values, \
int root); \
template void StaticCommunicatorMPI::gather<T>( \
T * values, int nb_values, T * gathered, int nb_gathered); \
template void StaticCommunicatorMPI::gatherV<T>(T * values, int * nb_values, \
int root); \
template void StaticCommunicatorMPI::broadcast<T>(T * values, int nb_values, \
int root); \
template void StaticCommunicatorMPI::allReduce<T>( \
T * values, int nb_values, const SynchronizerOperation & op)
AKANTU_MPI_COMM_INSTANTIATE(bool);
AKANTU_MPI_COMM_INSTANTIATE(Real);
AKANTU_MPI_COMM_INSTANTIATE(UInt);
AKANTU_MPI_COMM_INSTANTIATE(Int);
AKANTU_MPI_COMM_INSTANTIATE(char);
AKANTU_MPI_COMM_INSTANTIATE(NodeType);
template void StaticCommunicatorMPI::send<SCMinMaxLoc<Real, int>>(
SCMinMaxLoc<Real, int> * buffer, Int size, Int receiver, Int tag);
template void StaticCommunicatorMPI::receive<SCMinMaxLoc<Real, int>>(
SCMinMaxLoc<Real, int> * buffer, Int size, Int sender, Int tag);
template CommunicationRequest
StaticCommunicatorMPI::asyncSend<SCMinMaxLoc<Real, int>>(
SCMinMaxLoc<Real, int> * buffer, Int size, Int receiver, Int tag);
template CommunicationRequest
StaticCommunicatorMPI::asyncReceive<SCMinMaxLoc<Real, int>>(
SCMinMaxLoc<Real, int> * buffer, Int size, Int sender, Int tag);
template void StaticCommunicatorMPI::probe<SCMinMaxLoc<Real, int>>(
Int sender, Int tag, CommunicationStatus & status);
template void StaticCommunicatorMPI::allGather<SCMinMaxLoc<Real, int>>(
SCMinMaxLoc<Real, int> * values, int nb_values);
template void StaticCommunicatorMPI::allGatherV<SCMinMaxLoc<Real, int>>(
SCMinMaxLoc<Real, int> * values, int * nb_values);
template void StaticCommunicatorMPI::gather<SCMinMaxLoc<Real, int>>(
SCMinMaxLoc<Real, int> * values, int nb_values, int root);
template void StaticCommunicatorMPI::gatherV<SCMinMaxLoc<Real, int>>(
SCMinMaxLoc<Real, int> * values, int * nb_values, int root);
template void StaticCommunicatorMPI::broadcast<SCMinMaxLoc<Real, int>>(
SCMinMaxLoc<Real, int> * values, int nb_values, int root);
template void StaticCommunicatorMPI::allReduce<SCMinMaxLoc<Real, int>>(
SCMinMaxLoc<Real, int> * values, int nb_values,
const SynchronizerOperation & op);
#if AKANTU_INTEGER_SIZE > 4
AKANTU_MPI_COMM_INSTANTIATE(int);
#endif
-__END_AKANTU__
+} // akantu
diff --git a/src/synchronizer/static_communicator_mpi.hh b/src/synchronizer/static_communicator_mpi.hh
index 2e909abb3..b9df5f0c9 100644
--- a/src/synchronizer/static_communicator_mpi.hh
+++ b/src/synchronizer/static_communicator_mpi.hh
@@ -1,131 +1,131 @@
/**
* @file static_communicator_mpi.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Sun Sep 05 2010
* @date last modification: Tue Jan 19 2016
*
* @brief class handling parallel communication trough MPI
*
* @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_STATIC_COMMUNICATOR_MPI_HH__
#define __AKANTU_STATIC_COMMUNICATOR_MPI_HH__
/* -------------------------------------------------------------------------- */
#include "real_static_communicator.hh"
/* -------------------------------------------------------------------------- */
#include <vector>
-__BEGIN_AKANTU__
+namespace akantu {
class MPITypeWrapper;
/* -------------------------------------------------------------------------- */
class StaticCommunicatorMPI : public RealStaticCommunicator {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
public:
StaticCommunicatorMPI(int & argc, char **& argv);
virtual ~StaticCommunicatorMPI();
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
template <typename T> void send(T * buffer, Int size, Int receiver, Int tag);
template <typename T> void receive(T * buffer, Int size, Int sender, Int tag);
template <typename T>
CommunicationRequest asyncSend(T * buffer, Int size, Int receiver, Int tag);
template <typename T>
CommunicationRequest asyncReceive(T * buffer, Int size, Int sender, Int tag);
template <typename T>
void probe(Int sender, Int tag, CommunicationStatus & status);
template <typename T> void allGather(T * values, int nb_values);
template <typename T> void allGatherV(T * values, int * nb_values);
template <typename T> void gather(T * values, int nb_values, int root);
template <typename T>
void gather(T * values, int nb_values, T * gathered, int nb_gathered = 0);
template <typename T> void gatherV(T * values, int * nb_values, int root);
template <typename T> void broadcast(T * values, int nb_values, int root);
bool testRequest(CommunicationRequest & request);
void wait(CommunicationRequest & request);
void waitAll(std::vector<CommunicationRequest> & requests);
UInt waitAny(std::vector<CommunicationRequest> & requests);
void barrier();
template <typename T>
void reduce(T * values, int nb_values, const SynchronizerOperation & op,
int root);
template <typename T>
void allReduce(T * values, int nb_values, const SynchronizerOperation & op);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
const MPITypeWrapper & getMPITypeWrapper() const { return *mpi_data; }
MPITypeWrapper & getMPITypeWrapper() { return *mpi_data; }
int getMinTag();
int getMaxTag();
private:
void setRank(int prank) { this->prank = prank; }
void setSize(int psize) { this->psize = psize; }
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
private:
friend class MPITypeWrapper;
MPITypeWrapper * mpi_data;
bool is_externaly_initialized;
};
/* -------------------------------------------------------------------------- */
/* inline functions */
/* -------------------------------------------------------------------------- */
#include "static_communicator_mpi_inline_impl.hh"
-__END_AKANTU__
+} // akantu
#endif /* __AKANTU_STATIC_COMMUNICATOR_MPI_HH__ */
diff --git a/src/synchronizer/synchronizer_registry.cc b/src/synchronizer/synchronizer_registry.cc
index 11f1fc4e1..0c8ce1398 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"
/* -------------------------------------------------------------------------- */
-__BEGIN_AKANTU__
+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.");
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.");
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.");
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;
}
-__END_AKANTU__
+} // akantu