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dof_manager.hh
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/**
* @file dof_manager.hh
*
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Tue Aug 18 2015
* @date last modification: Wed Feb 21 2018
*
* @brief Class handling the different types of dofs
*
* @section LICENSE
*
* Copyright (©) 2015-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu is distributed in the hope that it will be useful, but WITHOUT ANY
* WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
* A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_factory.hh"
#include "aka_memory.hh"
#include "mesh.hh"
/* -------------------------------------------------------------------------- */
#include <map>
#include <set>
/* -------------------------------------------------------------------------- */
#ifndef __AKANTU_DOF_MANAGER_HH__
#define __AKANTU_DOF_MANAGER_HH__
namespace akantu {
class TermsToAssemble;
class NonLinearSolver;
class TimeStepSolver;
class SparseMatrix;
class SolverVector;
} // namespace akantu
namespace akantu {
class DOFManager : protected Memory, protected MeshEventHandler {
/* ------------------------------------------------------------------------ */
/* Constructors/Destructors */
/* ------------------------------------------------------------------------ */
protected:
struct DOFData;
public:
DOFManager(const ID & id = "dof_manager", const MemoryID & memory_id = 0);
DOFManager(Mesh & mesh, const ID & id = "dof_manager",
const MemoryID & memory_id = 0);
~DOFManager() override;
/* ------------------------------------------------------------------------ */
/* Methods */
/* ------------------------------------------------------------------------ */
public:
/// register an array of degree of freedom
virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const DOFSupportType & support_type);
/// the dof as an implied type of _dst_nodal and is defined only on a subset
/// of nodes
virtual void registerDOFs(const ID & dof_id, Array<Real> & dofs_array,
const ID & group_support);
/// register an array of previous values of the degree of freedom
virtual void registerDOFsPrevious(const ID & dof_id,
Array<Real> & dofs_array);
/// register an array of increment of degree of freedom
virtual void registerDOFsIncrement(const ID & dof_id,
Array<Real> & dofs_array);
/// register an array of derivatives for a particular dof array
virtual void registerDOFsDerivative(const ID & dof_id, UInt order,
Array<Real> & dofs_derivative);
/// register array representing the blocked degree of freedoms
virtual void registerBlockedDOFs(const ID & dof_id,
Array<bool> & blocked_dofs);
/// Assemble an array to the global residual array
virtual void assembleToResidual(const ID & dof_id,
Array<Real> & array_to_assemble,
Real scale_factor = 1.);
/// Assemble an array to the global lumped matrix array
virtual void assembleToLumpedMatrix(const ID & dof_id,
Array<Real> & array_to_assemble,
const ID & lumped_mtx,
Real scale_factor = 1.);
/**
* Assemble elementary values to a local array of the size nb_nodes *
* nb_dof_per_node. The dof number is implicitly considered as
* conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayLocalArray(
const Array<Real> & elementary_vect, Array<Real> & array_assembeled,
const ElementType & type, const GhostType & ghost_type,
Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d.
* With 0 < n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalArrayToResidual(
const ID & dof_id, const Array<Real> & elementary_vect,
const ElementType & type, const GhostType & ghost_type,
Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to a global array corresponding to a lumped
* matrix
*/
virtual void assembleElementalArrayToLumpedMatrix(
const ID & dof_id, const Array<Real> & elementary_vect,
const ID & lumped_mtx, const ElementType & type,
const GhostType & ghost_type, Real scale_factor = 1.,
const Array<UInt> & filter_elements = empty_filter);
/**
* Assemble elementary values to the global residual array. The dof number is
* implicitly considered as conn(el, n) * nb_nodes_per_element + d. With 0 <
* n < nb_nodes_per_element and 0 < d < nb_dof_per_node
**/
virtual void assembleElementalMatricesToMatrix(
const ID & matrix_id, const ID & dof_id,
const Array<Real> & elementary_mat, const ElementType & type,
const GhostType & ghost_type = _not_ghost,
const MatrixType & elemental_matrix_type = _symmetric,
const Array<UInt> & filter_elements = empty_filter) = 0;
/// multiply a vector by a matrix and assemble the result to the residual
virtual void assembleMatMulVectToResidual(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) = 0;
/// multiply a vector by a matrix and assemble the result to the residual
virtual void assembleMatMulVectToArray(const ID & dof_id, const ID & A_id,
const Array<Real> & x,
Array<Real> & array,
Real scale_factor = 1) = 0;
/// multiply the dofs by a matrix and assemble the result to the residual
virtual void assembleMatMulDOFsToResidual(const ID & A_id,
Real scale_factor = 1);
/// multiply a vector by a lumped matrix and assemble the result to the
/// residual
virtual void assembleLumpedMatMulVectToResidual(const ID & dof_id,
const ID & A_id,
const Array<Real> & x,
Real scale_factor = 1) = 0;
/// assemble coupling terms between to dofs
virtual void assemblePreassembledMatrix(const ID & dof_id_m,
const ID & dof_id_n,
const ID & matrix_id,
const TermsToAssemble & terms) = 0;
/// sets the residual to 0
virtual void clearResidual();
/// sets the matrix to 0
virtual void clearMatrix(const ID & mtx);
/// sets the lumped matrix to 0
virtual void clearLumpedMatrix(const ID & mtx);
virtual void applyBoundary(const ID & matrix_id = "J") = 0;
/// extract a lumped matrix part corresponding to a given dof
virtual void getLumpedMatrixPerDOFs(const ID & dof_id, const ID & lumped_mtx,
Array<Real> & lumped);
/// splits the solution storage from a global view to the per dof storages
void splitSolutionPerDOFs();
private:
/// dispatch the creation of the dof data and register it
DOFData & getNewDOFDataInternal(const ID & dof_id);
protected:
/// common function to help registering dofs the return values are the add new
/// numbers of local dofs, pure local dofs, and system size
virtual std::tuple<UInt, UInt, UInt>
registerDOFsInternal(const ID & dof_id, Array<Real> & dofs_array);
/// minimum functionality to implement per derived version of the DOFManager
/// to allow the splitSolutionPerDOFs function to work
virtual void getSolutionPerDOFs(const ID & dof_id,
Array<Real> & solution_array);
/// fill a Vector with the equation numbers corresponding to the given
/// connectivity
inline void extractElementEquationNumber(const Array<Int> & equation_numbers,
const Vector<UInt> & connectivity,
UInt nb_degree_of_freedom,
Vector<Int> & local_equation_number);
/* ------------------------------------------------------------------------ */
/* Accessors */
/* ------------------------------------------------------------------------ */
public:
/// Get the location type of a given dof
inline bool isLocalOrMasterDOF(UInt local_dof_num);
/// Answer to the question is a dof a slave dof ?
inline bool isSlaveDOF(UInt local_dof_num);
/// Answer to the question is a dof a slave dof ?
inline bool isPureGhostDOF(UInt local_dof_num);
/// tells if the dof manager knows about a global dof
bool hasGlobalEquationNumber(Int global) const;
/// return the local index of the global equation number
inline Int globalToLocalEquationNumber(Int global) const;
/// converts local equation numbers to global equation numbers;
inline Int localToGlobalEquationNumber(Int local) const;
/// get the array of dof types (use only if you know what you do...)
inline NodeFlag getDOFFlag(Int local_id) const;
/// Global number of dofs
AKANTU_GET_MACRO(SystemSize, this->system_size, UInt);
/// Local number of dofs
AKANTU_GET_MACRO(LocalSystemSize, this->local_system_size, UInt);
/// Pure local number of dofs
AKANTU_GET_MACRO(PureLocalSystemSize, this->pure_local_system_size, UInt);
/// Retrieve all the registered DOFs
std::vector<ID> getDOFIDs() const;
/* ------------------------------------------------------------------------ */
/* DOFs and derivatives accessors */
/* ------------------------------------------------------------------------ */
/// Get a reference to the registered dof array for a given id
inline Array<Real> & getDOFs(const ID & dofs_id);
/// Get the support type of a given dof
inline DOFSupportType getSupportType(const ID & dofs_id) const;
/// are the dofs registered
inline bool hasDOFs(const ID & dofs_id) const;
/// Get a reference to the registered dof derivatives array for a given id
inline Array<Real> & getDOFsDerivatives(const ID & dofs_id, UInt order);
/// Does the dof has derivatives
inline bool hasDOFsDerivatives(const ID & dofs_id, UInt order) const;
/// Get a reference to the blocked dofs array registered for the given id
inline const Array<bool> & getBlockedDOFs(const ID & dofs_id) const;
/// Does the dof has a blocked array
inline bool hasBlockedDOFs(const ID & dofs_id) const;
/// Get a reference to the registered dof increment array for a given id
inline Array<Real> & getDOFsIncrement(const ID & dofs_id);
/// Does the dof has a increment array
inline bool hasDOFsIncrement(const ID & dofs_id) const;
/// Does the dof has a previous array
inline Array<Real> & getPreviousDOFs(const ID & dofs_id);
/// Get a reference to the registered dof array for previous step values a
/// given id
inline bool hasPreviousDOFs(const ID & dofs_id) const;
/// saves the values from dofs to previous dofs
virtual void savePreviousDOFs(const ID & dofs_id);
/// Get a reference to the solution array registered for the given id
inline const Array<Real> & getSolution(const ID & dofs_id) const;
/// Get a reference to the solution array registered for the given id
inline Array<Real> & getSolution(const ID & dofs_id);
/* ------------------------------------------------------------------------ */
/* Matrices accessors */
/* ------------------------------------------------------------------------ */
/// Get an instance of a new SparseMatrix
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const MatrixType & matrix_type) = 0;
/// Get an instance of a new SparseMatrix as a copy of the SparseMatrix
/// matrix_to_copy_id
virtual SparseMatrix & getNewMatrix(const ID & matrix_id,
const ID & matrix_to_copy_id) = 0;
protected:
/* ------------------------------------------------------------------------ */
/// register a matrix
SparseMatrix & registerSparseMatrix(const ID & matrix_id,
std::unique_ptr<SparseMatrix> & matrix);
/// register a lumped matrix (aka a Vector)
SolverVector & registerLumpedMatrix(const ID & matrix_id,
std::unique_ptr<SolverVector> & matrix);
/// register a non linear solver instantiated by a derived class
NonLinearSolver &
registerNonLinearSolver(const ID & non_linear_solver_id,
std::unique_ptr<NonLinearSolver> & non_linear_solver);
/// register a time step solver instantiated by a derived class
TimeStepSolver &
registerTimeStepSolver(const ID & time_step_solver_id,
std::unique_ptr<TimeStepSolver> & time_step_solver);
template <class NLSType, class DMType>
NonLinearSolver & registerNonLinearSolver(DMType & dm, const ID & id,
const NonLinearSolverType & type) {
ID non_linear_solver_id = this->id + ":nls:" + id;
std::unique_ptr<NonLinearSolver> nls = std::make_unique<NLSType>(
dm, type, non_linear_solver_id, this->memory_id);
return this->registerNonLinearSolver(non_linear_solver_id, nls);
}
template <class TSSType, class DMType>
TimeStepSolver & registerTimeStepSolver(DMType & dm, const ID & id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver) {
ID time_step_solver_id = this->id + ":tss:" + id;
std::unique_ptr<TimeStepSolver> tss = std::make_unique<TSSType>(
dm, type, non_linear_solver, time_step_solver_id, this->memory_id);
return this->registerTimeStepSolver(time_step_solver_id, tss);
}
template <class MatType, class DMType>
SparseMatrix & registerSparseMatrix(DMType & dm, const ID & id,
const MatrixType & matrix_type) {
ID matrix_id = this->id + ":mtx:" + id;
std::unique_ptr<SparseMatrix> sm =
std::make_unique<MatType>(dm, matrix_type, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
template <class MatType>
SparseMatrix & registerSparseMatrix(const ID & id,
const ID & matrix_to_copy_id) {
ID matrix_id = this->id + ":mtx:" + id;
auto & sm_to_copy =
dynamic_cast<MatType &>(this->getMatrix(matrix_to_copy_id));
std::unique_ptr<SparseMatrix> sm =
std::make_unique<MatType>(sm_to_copy, matrix_id);
return this->registerSparseMatrix(matrix_id, sm);
}
template <class MatType, class DMType>
SolverVector & registerLumpedMatrix(DMType & dm, const ID & id) {
ID matrix_id = this->id + ":lumped_mtx:" + id;
std::unique_ptr<SolverVector> sm = std::make_unique<MatType>(dm, matrix_id);
return this->registerLumpedMatrix(matrix_id, sm);
}
protected:
virtual void makeConsistentForPeriodicity(const ID & dof_id,
SolverVector & array) = 0;
virtual void assembleToGlobalArray(const ID & dof_id,
const Array<Real> & array_to_assemble,
SolverVector & global_array,
Real scale_factor) = 0;
virtual void getArrayPerDOFs(const ID & dof_id, const SolverVector & global,
Array<Real> & local) = 0;
public:
/// Get the reference of an existing matrix
SparseMatrix & getMatrix(const ID & matrix_id);
/// check if the given matrix exists
bool hasMatrix(const ID & matrix_id) const;
/// Get an instance of a new lumped matrix
virtual SolverVector & getNewLumpedMatrix(const ID & matrix_id) = 0;
/// Get the lumped version of a given matrix
const SolverVector & getLumpedMatrix(const ID & matrix_id) const;
/// Get the lumped version of a given matrix
SolverVector & getLumpedMatrix(const ID & matrix_id);
/// check if the given matrix exists
bool hasLumpedMatrix(const ID & matrix_id) const;
/* ------------------------------------------------------------------------ */
/* Non linear system solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a non linear solver
virtual NonLinearSolver & getNewNonLinearSolver(
const ID & nls_solver_id,
const NonLinearSolverType & _non_linear_solver_type) = 0;
/// get instance of a non linear solver
virtual NonLinearSolver & getNonLinearSolver(const ID & nls_solver_id);
/// check if the given solver exists
bool hasNonLinearSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
/* Time-Step Solver */
/* ------------------------------------------------------------------------ */
/// Get instance of a time step solver
virtual TimeStepSolver &
getNewTimeStepSolver(const ID & time_step_solver_id,
const TimeStepSolverType & type,
NonLinearSolver & non_linear_solver) = 0;
/// get instance of a time step solver
virtual TimeStepSolver & getTimeStepSolver(const ID & time_step_solver_id);
/// check if the given solver exists
bool hasTimeStepSolver(const ID & solver_id) const;
/* ------------------------------------------------------------------------ */
const Mesh & getMesh() {
if (mesh) {
return *mesh;
} else {
AKANTU_EXCEPTION("No mesh registered in this dof manager");
}
}
/* ------------------------------------------------------------------------ */
AKANTU_GET_MACRO(Communicator, communicator, const auto &);
AKANTU_GET_MACRO_NOT_CONST(Communicator, communicator, auto &);
/* ------------------------------------------------------------------------ */
AKANTU_GET_MACRO(Solution, *(solution.get()), const auto &);
AKANTU_GET_MACRO_NOT_CONST(Solution, *(solution.get()), auto &);
AKANTU_GET_MACRO(Residual, *(residual.get()), const auto &);
AKANTU_GET_MACRO_NOT_CONST(Residual, *(residual.get()), auto &);
/* ------------------------------------------------------------------------ */
/* MeshEventHandler interface */
/* ------------------------------------------------------------------------ */
protected:
friend class GlobalDOFInfoDataAccessor;
/// helper function for the DOFManager::onNodesAdded method
virtual std::pair<UInt, UInt> updateNodalDOFs(const ID & dof_id,
const Array<UInt> & nodes_list);
template <typename Func>
auto countDOFsForNodes(const DOFData & dof_data, UInt nb_nodes,
Func && getNode);
void updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local, UInt nb_nodes,
const std::function<UInt(UInt)> & getNode);
void updateDOFsData(DOFData & dof_data, UInt nb_new_local_dofs,
UInt nb_new_pure_local);
auto computeFirstDOFIDs(UInt nb_new_local_dofs, UInt nb_new_pure_local);
/// resize all the global information and takes the needed measure like
/// cleaning matrices profiles
virtual void resizeGlobalArrays();
public:
/// function to implement to react on akantu::NewNodesEvent
void onNodesAdded(const Array<UInt> & nodes_list,
const NewNodesEvent & event) override;
/// function to implement to react on akantu::RemovedNodesEvent
void onNodesRemoved(const Array<UInt> & nodes_list,
const Array<UInt> & new_numbering,
const RemovedNodesEvent & event) override;
/// function to implement to react on akantu::NewElementsEvent
void onElementsAdded(const Array<Element> & elements_list,
const NewElementsEvent & event) override;
/// function to implement to react on akantu::RemovedElementsEvent
void onElementsRemoved(const Array<Element> & elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const RemovedElementsEvent & event) override;
/// function to implement to react on akantu::ChangedElementsEvent
void onElementsChanged(const Array<Element> & old_elements_list,
const Array<Element> & new_elements_list,
const ElementTypeMapArray<UInt> & new_numbering,
const ChangedElementsEvent & event) override;
protected:
inline DOFData & getDOFData(const ID & dof_id);
inline const DOFData & getDOFData(const ID & dof_id) const;
template <class _DOFData>
inline _DOFData & getDOFDataTyped(const ID & dof_id);
template <class _DOFData>
inline const _DOFData & getDOFDataTyped(const ID & dof_id) const;
virtual std::unique_ptr<DOFData> getNewDOFData(const ID & dof_id) = 0;
/* ------------------------------------------------------------------------ */
/* Class Members */
/* ------------------------------------------------------------------------ */
protected:
/// dof representations in the dof manager
struct DOFData {
DOFData() = delete;
explicit DOFData(const ID & dof_id);
virtual ~DOFData();
/// DOF support type (nodal, general) this is needed to determine how the
/// dof are shared among processors
DOFSupportType support_type;
ID group_support;
/// Degree of freedom array
Array<Real> * dof{nullptr};
/// Blocked degree of freedoms array
Array<bool> * blocked_dofs{nullptr};
/// Degree of freedoms increment
Array<Real> * increment{nullptr};
/// Degree of freedoms at previous step
Array<Real> * previous{nullptr};
/// Solution associated to the dof
Array<Real> solution;
/* ---------------------------------------------------------------------- */
/* data for dynamic simulations */
/* ---------------------------------------------------------------------- */
/// Degree of freedom derivatives arrays
std::vector<Array<Real> *> dof_derivatives;
/* ---------------------------------------------------------------------- */
/// number of dofs to consider locally for this dof id
UInt local_nb_dofs{0};
/// Number of purely local dofs
UInt pure_local_nb_dofs{0};
/// number of ghost dofs
UInt ghosts_nb_dofs{0};
/// local numbering equation numbers
Array<Int> local_equation_number;
/// associated node for _dst_nodal dofs only
Array<UInt> associated_nodes;
};
/// type to store dofs information
using DOFStorage = std::map<ID, std::unique_ptr<DOFData>>;
/// type to store all the matrices
using SparseMatricesMap = std::map<ID, std::unique_ptr<SparseMatrix>>;
/// type to store all the lumped matrices
using LumpedMatricesMap = std::map<ID, std::unique_ptr<SolverVector>>;
/// type to store all the non linear solver
using NonLinearSolversMap = std::map<ID, std::unique_ptr<NonLinearSolver>>;
/// type to store all the time step solver
using TimeStepSolversMap = std::map<ID, std::unique_ptr<TimeStepSolver>>;
/// store a reference to the dof arrays
DOFStorage dofs;
/// list of sparse matrices that where created
SparseMatricesMap matrices;
/// list of lumped matrices
LumpedMatricesMap lumped_matrices;
/// non linear solvers storage
NonLinearSolversMap non_linear_solvers;
/// time step solvers storage
TimeStepSolversMap time_step_solvers;
/// reference to the underlying mesh
Mesh * mesh{nullptr};
/// Total number of degrees of freedom (size with the ghosts)
UInt local_system_size{0};
/// Number of purely local dofs (size without the ghosts)
UInt pure_local_system_size{0};
/// Total number of degrees of freedom
UInt system_size{0};
/// rhs to the system of equation corresponding to the residual linked to the
/// different dofs
std::unique_ptr<SolverVector> residual;
/// solution of the system of equation corresponding to the different dofs
std::unique_ptr<SolverVector> solution;
/// define the dofs type, local, shared, ghost
Array<NodeFlag> dofs_flag;
/// equation number in global numbering
Array<Int> global_equation_number;
using equation_numbers_map = std::unordered_map<Int, Int>;
/// dual information of global_equation_number
equation_numbers_map global_to_local_mapping;
/// Communicator used for this manager, should be the same as in the mesh if a
/// mesh is registered
Communicator & communicator;
/// accumulator to know what would be the next global id to use
UInt first_global_dof_id{0};
private:
/// This is for unit testing
friend class DOFManagerTester;
};
using DefaultDOFManagerFactory =
Factory<DOFManager, ID, const ID &, const MemoryID &>;
using DOFManagerFactory =
Factory<DOFManager, ID, Mesh &, const ID &, const MemoryID &>;
} // namespace akantu
#include "dof_manager_inline_impl.cc"
#endif /* __AKANTU_DOF_MANAGER_HH__ */
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