#include <fem_system.h>
Inherits DifferentiableSystem.
Inherited by ContinuationSystem.
typedef FEMSystem sys_type
typedef DifferentiableSystem Parent
typedef std::map< std::string, SparseMatrix< Number > * >::iterator matrices_iterator
typedef std::map< std::string, SparseMatrix< Number > * >::const_iterator const_matrices_iterator
typedef std::map< std::string, NumericVector< Number > * >::iterator vectors_iterator
typedef std::map< std::string, NumericVector< Number > * >::const_iterator const_vectors_iterator
FEMSystem (EquationSystems &es, const std::string &name, const unsigned int number)
virtual ~FEMSystem ()
virtual void clear ()
virtual void assembly (bool get_residual, bool get_jacobian)
virtual void solve ()
virtual void time_evolving (unsigned int var)
virtual void mesh_x_position (unsigned int sysnum, unsigned int var)
virtual void mesh_y_position (unsigned int sysnum, unsigned int var)
virtual void mesh_z_position (unsigned int sysnum, unsigned int var)
void mesh_position_get ()
void mesh_position_set ()
virtual bool eulerian_residual (bool request_jacobian, DiffContext &context)
virtual bool mass_residual (bool request_jacobian, DiffContext &context)
virtual AutoPtr< DiffContext > build_context ()
virtual void init_context (DiffContext &)
virtual void postprocess ()
virtual void assemble_qoi ()
virtual void assemble_qoi_derivative ()
virtual void reinit ()
virtual void assemble ()
virtual bool element_time_derivative (bool request_jacobian, DiffContext &)
virtual bool element_constraint (bool request_jacobian, DiffContext &)
virtual bool side_time_derivative (bool request_jacobian, DiffContext &)
virtual bool side_constraint (bool request_jacobian, DiffContext &)
virtual void element_postprocess (DiffContext &)
virtual void side_postprocess (DiffContext &)
virtual void element_qoi (DiffContext &)
virtual void element_qoi_derivative (DiffContext &)
virtual void side_qoi (DiffContext &)
virtual void side_qoi_derivative (DiffContext &)
virtual bool side_mass_residual (bool request_jacobian, DiffContext &)
virtual void adjoint_solve ()
virtual void qoi_parameter_sensitivity (std::vector< Number * > ¶meters, std::vector< Number > &sensitivities)
sys_type & system ()
virtual std::string system_type () const
SparseMatrix< Number > & add_matrix (const std::string &mat_name)
bool have_matrix (const std::string &mat_name) const
const SparseMatrix< Number > & get_matrix (const std::string &mat_name) const
SparseMatrix< Number > & get_matrix (const std::string &mat_name)
unsigned int n_matrices () const
void init ()
virtual void update ()
virtual bool compare (const System &other_system, const Real threshold, const bool verbose) const
const std::string & name () const
void project_solution (Number fptr(const Point &p, const Parameters ¶meters, const std::string &sys_name, const std::string &unknown_name), Gradient gptr(const Point &p, const Parameters ¶meters, const std::string &sys_name, const std::string &unknown_name), Parameters ¶meters) const
void project_vector (Number fptr(const Point &p, const Parameters ¶meters, const std::string &sys_name, const std::string &unknown_name), Gradient gptr(const Point &p, const Parameters ¶meters, const std::string &sys_name, const std::string &unknown_name), Parameters ¶meters, NumericVector< Number > &new_vector) const
unsigned int number () const
void update_global_solution (std::vector< Number > &global_soln) const
void update_global_solution (std::vector< Number > &global_soln, const unsigned int dest_proc) const
const MeshBase & get_mesh () const
MeshBase & get_mesh ()
const DofMap & get_dof_map () const
DofMap & get_dof_map ()
const EquationSystems & get_equation_systems () const
EquationSystems & get_equation_systems ()
bool active () const
void activate ()
void deactivate ()
vectors_iterator vectors_begin ()
const_vectors_iterator vectors_begin () const
vectors_iterator vectors_end ()
const_vectors_iterator vectors_end () const
NumericVector< Number > & add_vector (const std::string &vec_name, const bool projections=true)
bool & project_solution_on_reinit (void)
bool have_vector (const std::string &vec_name) const
const NumericVector< Number > & get_vector (const std::string &vec_name) const
NumericVector< Number > & get_vector (const std::string &vec_name)
const NumericVector< Number > & get_vector (const unsigned int vec_num) const
NumericVector< Number > & get_vector (const unsigned int vec_num)
const std::string & vector_name (const unsigned int vec_num)
NumericVector< Number > & get_adjoint_solution ()
const NumericVector< Number > & get_adjoint_solution () const
unsigned int n_vectors () const
unsigned int n_vars () const
unsigned int n_dofs () const
unsigned int n_active_dofs () const
unsigned int n_constrained_dofs () const
unsigned int n_local_dofs () const
unsigned int add_variable (const std::string &var, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=NULL)
unsigned int add_variable (const std::string &var, const Order order=FIRST, const FEFamily=LAGRANGE, const std::set< subdomain_id_type > *const active_subdomains=NULL)
const Variable & variable (unsigned int var) const
bool has_variable (const std::string &var) const
const std::string & variable_name (const unsigned int i) const
unsigned short int variable_number (const std::string &var) const
const FEType & variable_type (const unsigned int i) const
const FEType & variable_type (const std::string &var) const
Real calculate_norm (NumericVector< Number > &v, unsigned int var=0, FEMNormType norm_type=L2) const
Real calculate_norm (NumericVector< Number > &v, const SystemNorm &norm) const
void read_header (Xdr &io, const std::string &version, const bool read_header=true, const bool read_additional_data=true, const bool read_legacy_format=false)
void read_legacy_data (Xdr &io, const bool read_additional_data=true)
void read_serialized_data (Xdr &io, const bool read_additional_data=true)
void read_parallel_data (Xdr &io, const bool read_additional_data)
void write_header (Xdr &io, const std::string &version, const bool write_additional_data) const
void write_serialized_data (Xdr &io, const bool write_additional_data=true) const
void write_parallel_data (Xdr &io, const bool write_additional_data) const
std::string get_info () const
void attach_init_function (void fptr(EquationSystems &es, const std::string &name))
void attach_assemble_function (void fptr(EquationSystems &es, const std::string &name))
void attach_constraint_function (void fptr(EquationSystems &es, const std::string &name))
void attach_QOI_function (void fptr(EquationSystems &es, const std::string &name))
void attach_QOI_derivative (void fptr(EquationSystems &es, const std::string &name))
virtual void user_initialization ()
virtual void user_assembly ()
virtual void user_constrain ()
virtual void user_QOI ()
virtual void user_QOI_derivative ()
virtual void re_update ()
virtual void restrict_vectors ()
virtual void prolong_vectors ()
Number current_solution (const unsigned int global_dof_number) const
void local_dof_indices (const unsigned int var, std::set< unsigned int > &var_indices) const
void zero_variable (NumericVector< Number > &v, unsigned int var_num) const
static std::string get_info ()
static void print_info ()
static unsigned int n_objects ()
bool fe_reinit_during_postprocess
int extra_quadrature_order
Real numerical_jacobian_h
Real verify_analytic_jacobians
bool compute_internal_sides
bool postprocess_sides
bool assemble_qoi_sides
AutoPtr< TimeSolver > time_solver
Real time
Real deltat
bool print_solution_norms
bool print_solutions
bool print_residual_norms
bool print_residuals
bool print_jacobian_norms
bool print_jacobians
bool print_element_jacobians
bool use_fixed_solution
SparseMatrix< Number > * matrix
NumericVector< Number > * rhs
bool assemble_before_solve
AutoPtr< NumericVector< Number > > solution
AutoPtr< NumericVector< Number > > current_local_solution
Number qoi
typedef bool(TimeSolver::* TimeSolverResPtr )(bool, DiffContext &)
typedef std::map< std::string, std::pair< unsigned int, unsigned int > > Counts
virtual void init_data ()
void numerical_jacobian (TimeSolverResPtr res, FEMContext &context)
void numerical_elem_jacobian (FEMContext &context)
void numerical_side_jacobian (FEMContext &context)
virtual void init_matrices ()
void project_vector (NumericVector< Number > &) const
void project_vector (const NumericVector< Number > &, NumericVector< Number > &) const
void increment_constructor_count (const std::string &name)
void increment_destructor_count (const std::string &name)
unsigned int _mesh_sys
unsigned int _mesh_x_var
unsigned int _mesh_y_var
unsigned int _mesh_z_var
std::vector< bool > _time_evolving
static Counts _counts
static Threads::atomic< unsigned int > _n_objects
static Threads::spin_mutex _mutex
This class provides a specific system class. It aims at nonlinear implicit systems, requiring only a cell residual calculation from the user. Note that still additional vectors/matrices may be added, as offered in the class ExplicitSystem.
This class is part of the new DifferentiableSystem framework, which is still experimental. Users of this framework should beware of bugs and future API changes.
Author:
Definition at line 52 of file fem_system.h.
Definition at line 112 of file implicit_system.h.
Definition at line 279 of file system.h.
Definition at line 105 of file reference_counter.h.
Definition at line 111 of file implicit_system.h.
Reimplemented from DifferentiableSystem.
Reimplemented in ContinuationSystem.
Definition at line 77 of file fem_system.h.
Reimplemented from DifferentiableSystem.
Reimplemented in ContinuationSystem.
Definition at line 72 of file fem_system.h.
Definition at line 281 of file fem_system.h.
Definition at line 278 of file system.h.
Definition at line 41 of file fem_system.C.
: Parent(es, name, number),
fe_reinit_during_postprocess(true),
extra_quadrature_order(0),
numerical_jacobian_h(1.e-6),
verify_analytic_jacobians(0.0),
_mesh_sys(libMesh::invalid_uint),
_mesh_x_var(libMesh::invalid_uint),
_mesh_y_var(libMesh::invalid_uint),
_mesh_z_var(libMesh::invalid_uint)
{
}
Definition at line 57 of file fem_system.C.
References clear().
{
this->clear();
}
Definition at line 1103 of file system.h.
References System::_active.
{
_active = true;
}
Definition at line 1095 of file system.h.
References System::_active.
{
return _active;
}
Definition at line 168 of file implicit_system.C.
References ImplicitSystem::_can_add_matrices, ImplicitSystem::_matrices, and ImplicitSystem::have_matrix().
Referenced by ImplicitSystem::add_system_matrix(), EigenTimeSolver::init(), and NewmarkSystem::NewmarkSystem().
{
// only add matrices before initializing...
if (!_can_add_matrices)
{
std::cerr << 'ERROR: Too late. Cannot add matrices to the system after initialization'
<< std::endl
<< ' any more. You should have done this earlier.'
<< std::endl;
libmesh_error();
}
// Return the matrix if it is already there.
if (this->have_matrix(mat_name))
return *(_matrices[mat_name]);
// Otherwise build the matrix and return it.
SparseMatrix<Number>* buf = SparseMatrix<Number>::build().release();
_matrices.insert (std::make_pair (mat_name, buf));
return *buf;
}
Definition at line 652 of file system.C.
References System::_dof_map, System::_variable_numbers, System::_variables, System::n_vars(), System::number(), System::variable_name(), and System::variable_type().
Referenced by System::add_variable(), ErrorVector::plot_error(), and System::read_header().
{
// Make sure the variable isn't there already
// or if it is, that it's the type we want
for (unsigned int v=0; v<this->n_vars(); v++)
if (this->variable_name(v) == var)
{
if (this->variable_type(v) == type)
return _variables[v].number();
std::cerr << 'ERROR: incompatible variable '
<< var
<< ' has already been added for this system!'
<< std::endl;
libmesh_error();
}
const unsigned int curr_n_vars = this->n_vars();
// Add the variable to the list
_variables.push_back((active_subdomains == NULL) ?
Variable(var, curr_n_vars, type) :
Variable(var, curr_n_vars, type, *active_subdomains));
libmesh_assert ((curr_n_vars+1) == this->n_vars());
_variable_numbers[var] = curr_n_vars;
// Add the variable to the _dof_map
_dof_map->add_variable (_variables.back());
// Return the number of the new variable
return curr_n_vars;
}
Definition at line 691 of file system.C.
References System::add_variable().
{
return this->add_variable(var,
FEType(order, family),
active_subdomains);
}
By default vectors added by add_vector are projected to changed grids by reinit(). To zero them instead (more efficient), pass 'false' as the second argument
Definition at line 530 of file system.C.
References System::_can_add_vectors, System::_vector_projections, System::_vectors, System::have_vector(), NumericVector< T >::init(), System::n_dofs(), System::n_local_dofs(), and libMeshEnums::PARALLEL.
Referenced by ExplicitSystem::add_system_rhs(), NonlinearImplicitSystem::adjoint_solve(), NewtonSolver::adjoint_solve(), LinearImplicitSystem::adjoint_solve(), UnsteadySolver::init(), ContinuationSystem::init_data(), NewmarkSystem::NewmarkSystem(), System::read_header(), FrequencySystem::set_frequencies(), FrequencySystem::set_frequencies_by_range(), and FrequencySystem::set_frequencies_by_steps().
{
// Return the vector if it is already there.
if (this->have_vector(vec_name))
return *(_vectors[vec_name]);
// Otherwise build the vector
NumericVector<Number>* buf = NumericVector<Number>::build().release();
_vectors.insert (std::make_pair (vec_name, buf));
_vector_projections.insert (std::make_pair (vec_name, projections));
// Initialize it if necessary
if (!_can_add_vectors)
buf->init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
return *buf;
}
FIXME - transient adjoint solves are not yet implemented.
Reimplemented from ExplicitSystem.
Definition at line 112 of file diff_system.C.
References DifferentiableSystem::time_solver.
{
time_solver->adjoint_solve();
}
Reimplemented from ImplicitSystem.
Definition at line 98 of file diff_system.C.
References DifferentiableSystem::assembly().
{
this->assembly(true, true);
}
Users may have to override this function for quantities of interest that are not expressible as a sum of element qois.
Reimplemented from ExplicitSystem.
Definition at line 486 of file fem_system.C.
References MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), DifferentiableSystem::assemble_qoi_sides, build_context(), DifferentiableSystem::compute_internal_sides, FEMContext::elem, DifferentiableSystem::element_qoi(), System::get_mesh(), Elem::n_sides(), Elem::neighbor(), System::qoi, FEMContext::reinit(), FEMContext::side, FEMContext::side_fe, DifferentiableSystem::side_qoi(), and System::update().
{
START_LOG('assemble_qoi()', 'FEMSystem');
const MeshBase& mesh = this->get_mesh();
this->update();
AutoPtr<DiffContext> con = this->build_context();
FEMContext &_femcontext = libmesh_cast_ref<FEMContext&>(*con);
// the quantity of interest is assumed to be a sum of element and
// side terms
qoi = 0;
// Loop over every active mesh element on this processor
MeshBase::const_element_iterator el =
mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_el =
mesh.active_local_elements_end();
for ( ; el != end_el; ++el)
{
_femcontext.reinit(*this, *el);
this->element_qoi(_femcontext);
for (_femcontext.side = 0;
_femcontext.side != _femcontext.elem->n_sides();
++_femcontext.side)
{
// Don't compute on non-boundary sides unless requested
if (!assemble_qoi_sides ||
(!compute_internal_sides &&
_femcontext.elem->neighbor(_femcontext.side) != NULL))
continue;
std::map<FEType, FEBase *>::iterator fe_end =
_femcontext.side_fe.end();
for (std::map<FEType, FEBase *>::iterator i =
_femcontext.side_fe.begin();
i != fe_end; ++i)
{
i->second->reinit(_femcontext.elem, _femcontext.side);
}
this->side_qoi(_femcontext);
}
}
Parallel::sum(qoi);
STOP_LOG('assemble_qoi()', 'FEMSystem');
}
Users may have to override this function for quantities of interest that are not expressible as a sum of element qois.
Reimplemented from ExplicitSystem.
Definition at line 543 of file fem_system.C.
References MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), NumericVector< T >::add_vector(), DifferentiableSystem::assemble_qoi_sides, build_context(), DifferentiableSystem::compute_internal_sides, DofMap::constrain_element_vector(), DiffContext::dof_indices, FEMContext::elem, DiffContext::elem_residual, DifferentiableSystem::element_qoi_derivative(), System::get_dof_map(), System::get_mesh(), Elem::n_sides(), Elem::neighbor(), FEMContext::reinit(), ExplicitSystem::rhs, FEMContext::side, FEMContext::side_fe, DifferentiableSystem::side_qoi_derivative(), System::update(), and NumericVector< T >::zero().
{
START_LOG('assemble_qoi_derivative()', 'FEMSystem');
const MeshBase& mesh = this->get_mesh();
this->update();
AutoPtr<DiffContext> con = this->build_context();
FEMContext &_femcontext = libmesh_cast_ref<FEMContext&>(*con);
// In case there's already a rhs in use
rhs->zero();
// Loop over every active mesh element on this processor
MeshBase::const_element_iterator el =
mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_el =
mesh.active_local_elements_end();
for ( ; el != end_el; ++el)
{
_femcontext.reinit(*this, *el);
this->element_qoi_derivative(_femcontext);
for (_femcontext.side = 0;
_femcontext.side != _femcontext.elem->n_sides();
++_femcontext.side)
{
// Don't compute on non-boundary sides unless requested
if (!assemble_qoi_sides ||
(!compute_internal_sides &&
_femcontext.elem->neighbor(_femcontext.side) != NULL))
continue;
std::map<FEType, FEBase *>::iterator fe_end =
_femcontext.side_fe.end();
for (std::map<FEType, FEBase *>::iterator i =
_femcontext.side_fe.begin();
i != fe_end; ++i)
{
i->second->reinit(_femcontext.elem, _femcontext.side);
}
this->side_qoi_derivative(_femcontext);
}
this->get_dof_map().constrain_element_vector
(_femcontext.elem_residual, _femcontext.dof_indices, false);
this->rhs->add_vector (_femcontext.elem_residual,
_femcontext.dof_indices);
}
STOP_LOG('assemble_qoi_derivative()', 'FEMSystem');
}
Implements DifferentiableSystem.
Definition at line 78 of file fem_system.C.
References MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), DenseMatrix< T >::add(), SparseMatrix< T >::add_matrix(), NumericVector< T >::add_vector(), build_context(), SparseMatrix< T >::close(), NumericVector< T >::close(), DifferentiableSystem::compute_internal_sides, DofMap::constrain_element_matrix(), DofMap::constrain_element_matrix_and_vector(), DofMap::constrain_element_vector(), DiffContext::dof_indices, FEMContext::elem, DiffContext::elem_jacobian, DiffContext::elem_residual, FEMContext::elem_side_fe_reinit(), AutoPtr< Tp >::get(), System::get_dof_map(), System::get_mesh(), DofObject::id(), SparseMatrix< T >::l1_norm(), NumericVector< T >::l1_norm(), DenseMatrix< T >::l1_norm(), ImplicitSystem::matrix, std::max(), Elem::n_sides(), Elem::neighbor(), numerical_elem_jacobian(), numerical_side_jacobian(), DifferentiableSystem::print_element_jacobians, DifferentiableSystem::print_jacobian_norms, DifferentiableSystem::print_jacobians, DifferentiableSystem::print_residual_norms, DifferentiableSystem::print_residuals, DifferentiableSystem::print_solution_norms, DifferentiableSystem::print_solutions, FEMContext::reinit(), ExplicitSystem::rhs, FEMContext::side, System::solution, DenseMatrix< T >::swap(), DifferentiableSystem::time_solver, System::update(), verify_analytic_jacobians, DenseMatrix< T >::zero(), NumericVector< T >::zero(), and SparseMatrix< T >::zero().
Referenced by ContinuationSystem::continuation_solve(), and ContinuationSystem::solve_tangent().
{
libmesh_assert(get_residual || get_jacobian);
std::string log_name;
if (get_residual && get_jacobian)
log_name = 'assembly()';
else if (get_residual)
log_name = 'assembly(get_residual)';
else
log_name = 'assembly(get_jacobian)';
START_LOG(log_name, 'FEMSystem');
const MeshBase& mesh = this->get_mesh();
// this->get_vector('_nonlinear_solution').localize
// (*current_local_nonlinear_solution,
// dof_map.get_send_list());
this->update();
if (print_solution_norms)
{
// this->get_vector('_nonlinear_solution').close();
this->solution->close();
std::cout << '|U| = '
// << this->get_vector('_nonlinear_solution').l1_norm()
<< this->solution->l1_norm()
<< std::endl;
}
if (print_solutions)
{
unsigned int old_precision = std::cout.precision();
std::cout.precision(16);
// std::cout << 'U = [' << this->get_vector('_nonlinear_solution')
std::cout << 'U = [' << *(this->solution)
<< '];' << std::endl;
std::cout.precision(old_precision);
}
// Is this definitely necessary? [RHS]
if (get_jacobian)
matrix->zero();
if (get_residual)
rhs->zero();
// Stupid C++ lets you set *Real* verify_analytic_jacobians = true!
if (verify_analytic_jacobians > 0.5)
{
std::cerr << 'WARNING! verify_analytic_jacobians was set '
<< 'to absurdly large value of '
<< verify_analytic_jacobians << std::endl;
std::cerr << 'Resetting to 1e-6!' << std::endl;
verify_analytic_jacobians = 1e-6;
}
// In time-dependent problems, the nonlinear function we're trying
// to solve at each timestep may depend on the particular solver
// we're using
libmesh_assert (time_solver.get() != NULL);
AutoPtr<DiffContext> con = this->build_context();
FEMContext &_femcontext = libmesh_cast_ref<FEMContext&>(*con);
// Build the residual and jacobian contributions on every active
// mesh element on this processor
MeshBase::const_element_iterator el =
mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_el =
mesh.active_local_elements_end();
for ( ; el != end_el; ++el)
{
_femcontext.reinit(*this, *el);
bool jacobian_computed =
time_solver->element_residual(get_jacobian, _femcontext);
// Compute a numeric jacobian if we have to
if (get_jacobian && !jacobian_computed)
{
// Make sure we didn't compute a jacobian and lie about it
libmesh_assert(_femcontext.elem_jacobian.l1_norm() == 0.0);
// Logging of numerical jacobians is done separately
this->numerical_elem_jacobian(_femcontext);
}
// Compute a numeric jacobian if we're asked to verify the
// analytic jacobian we got
if (get_jacobian && jacobian_computed &&
verify_analytic_jacobians != 0.0)
{
DenseMatrix<Number> analytic_jacobian(_femcontext.elem_jacobian);
_femcontext.elem_jacobian.zero();
// Logging of numerical jacobians is done separately
this->numerical_elem_jacobian(_femcontext);
Real analytic_norm = analytic_jacobian.l1_norm();
Real numerical_norm = _femcontext.elem_jacobian.l1_norm();
// If we can continue, we'll probably prefer the analytic jacobian
analytic_jacobian.swap(_femcontext.elem_jacobian);
// The matrix 'analytic_jacobian' will now hold the error matrix
analytic_jacobian.add(-1.0, _femcontext.elem_jacobian);
Real error_norm = analytic_jacobian.l1_norm();
Real relative_error = error_norm /
std::max(analytic_norm, numerical_norm);
if (relative_error > verify_analytic_jacobians)
{
std::cerr << 'Relative error ' << relative_error
<< ' detected in analytic jacobian on element '
<< _femcontext.elem->id() << '!' << std::endl;
unsigned int old_precision = std::cout.precision();
std::cout.precision(16);
std::cout << 'J_analytic ' << _femcontext.elem->id() << ' = '
<< _femcontext.elem_jacobian << std::endl;
analytic_jacobian.add(1.0, _femcontext.elem_jacobian);
std::cout << 'J_numeric ' << _femcontext.elem->id() << ' = '
<< analytic_jacobian << std::endl;
std::cout.precision(old_precision);
libmesh_error();
}
}
for (_femcontext.side = 0;
_femcontext.side != _femcontext.elem->n_sides();
++_femcontext.side)
{
// Don't compute on non-boundary sides unless requested
if (!compute_internal_sides &&
_femcontext.elem->neighbor(_femcontext.side) != NULL)
continue;
// Any mesh movement has already been done (and restored,
// if the TimeSolver isn't broken), but
// reinitializing the side FE objects is still necessary
_femcontext.elem_side_fe_reinit();
DenseMatrix<Number> old_jacobian;
// If we're in DEBUG mode, we should always verify that the
// user's side_residual function doesn't alter our existing
// jacobian and then lie about it
#ifndef DEBUG
// Even if we're not in DEBUG mode, when we're verifying
// analytic jacobians we'll want to verify each side's
// jacobian contribution separately
if (verify_analytic_jacobians != 0.0 && get_jacobian)
#endif // ifndef DEBUG
{
old_jacobian = _femcontext.elem_jacobian;
_femcontext.elem_jacobian.zero();
}
jacobian_computed =
time_solver->side_residual(get_jacobian, _femcontext);
// Compute a numeric jacobian if we have to
if (get_jacobian && !jacobian_computed)
{
// In DEBUG mode, we've already set elem_jacobian == 0,
// so we can make sure side_residual didn't compute a
// jacobian and lie about it
#ifdef DEBUG
libmesh_assert(_femcontext.elem_jacobian.l1_norm() == 0.0);
#endif
// Logging of numerical jacobians is done separately
this->numerical_side_jacobian(_femcontext);
// If we're in DEBUG mode or if
// verify_analytic_jacobians is on, we've moved
// elem_jacobian's accumulated values into old_jacobian.
// Now let's add them back.
#ifndef DEBUG
if (verify_analytic_jacobians != 0.0)
#endif // ifndef DEBUG
_femcontext.elem_jacobian += old_jacobian;
}
// Compute a numeric jacobian if we're asked to verify the
// analytic jacobian we got
if (get_jacobian && jacobian_computed &&
verify_analytic_jacobians != 0.0)
{
DenseMatrix<Number> analytic_jacobian(_femcontext.elem_jacobian);
_femcontext.elem_jacobian.zero();
// Logging of numerical jacobians is done separately
this->numerical_side_jacobian(_femcontext);
Real analytic_norm = analytic_jacobian.l1_norm();
Real numerical_norm = _femcontext.elem_jacobian.l1_norm();
// If we can continue, we'll probably prefer the analytic jacobian
analytic_jacobian.swap(_femcontext.elem_jacobian);
// The matrix 'analytic_jacobian' will now hold the error matrix
analytic_jacobian.add(-1.0, _femcontext.elem_jacobian);
Real error_norm = analytic_jacobian.l1_norm();
Real relative_error = error_norm /
std::max(analytic_norm, numerical_norm);
if (relative_error > verify_analytic_jacobians)
{
std::cerr << 'Relative error ' << relative_error
<< ' detected in analytic jacobian on element '
<< _femcontext.elem->id()
<< ', side '
<< _femcontext.side << '!' << std::endl;
unsigned int old_precision = std::cout.precision();
std::cout.precision(16);
std::cout << 'J_analytic ' << _femcontext.elem->id() << ' = '
<< _femcontext.elem_jacobian << std::endl;
analytic_jacobian.add(1.0, _femcontext.elem_jacobian);
std::cout << 'J_numeric ' << _femcontext.elem->id() << ' = '
<< analytic_jacobian << std::endl;
std::cout.precision(old_precision);
libmesh_error();
}
// Once we've verified a side, we'll want to add back the
// rest of the accumulated jacobian
_femcontext.elem_jacobian += old_jacobian;
}
// In DEBUG mode, we've set elem_jacobian == 0, and we
// may still need to add the old jacobian back
#ifdef DEBUG
if (get_jacobian && jacobian_computed &&
verify_analytic_jacobians == 0.0)
{
_femcontext.elem_jacobian += old_jacobian;
}
#endif // ifdef DEBUG
}
#ifdef LIBMESH_ENABLE_AMR
// We turn off the asymmetric constraint application;
// enforce_constraints_exactly() should be called in the solver
if (get_residual && get_jacobian)
this->get_dof_map().constrain_element_matrix_and_vector
(_femcontext.elem_jacobian, _femcontext.elem_residual,
_femcontext.dof_indices, false);
else if (get_residual)
this->get_dof_map().constrain_element_vector
(_femcontext.elem_residual, _femcontext.dof_indices, false);
else if (get_jacobian)
this->get_dof_map().constrain_element_matrix
(_femcontext.elem_jacobian, _femcontext.dof_indices, false);
#endif // #ifdef LIBMESH_ENABLE_AMR
if (get_jacobian && print_element_jacobians)
{
unsigned int old_precision = std::cout.precision();
std::cout.precision(16);
std::cout << 'J_elem ' << _femcontext.elem->id() << ' = '
<< _femcontext.elem_jacobian << std::endl;
std::cout.precision(old_precision);
}
if (get_jacobian)
this->matrix->add_matrix (_femcontext.elem_jacobian,
_femcontext.dof_indices);
if (get_residual)
this->rhs->add_vector (_femcontext.elem_residual,
_femcontext.dof_indices);
}
if (get_residual && print_residual_norms)
{
this->rhs->close();
std::cout << '|F| = ' << this->rhs->l1_norm() << std::endl;
}
if (get_residual && print_residuals)
{
this->rhs->close();
unsigned int old_precision = std::cout.precision();
std::cout.precision(16);
std::cout << 'F = [' << *(this->rhs) << '];' << std::endl;
std::cout.precision(old_precision);
}
if (get_jacobian && print_jacobian_norms)
{
this->matrix->close();
std::cout << '|J| = ' << this->matrix->l1_norm() << std::endl;
}
if (get_jacobian && print_jacobians)
{
this->matrix->close();
unsigned int old_precision = std::cout.precision();
std::cout.precision(16);
std::cout << 'J = [' << *(this->matrix) << '];' << std::endl;
std::cout.precision(old_precision);
}
STOP_LOG(log_name, 'FEMSystem');
}
Definition at line 1084 of file system.C.
References System::_assemble_system.
{
libmesh_assert (fptr != NULL);
_assemble_system = fptr;
}
Definition at line 1094 of file system.C.
References System::_constrain_system.
{
libmesh_assert (fptr != NULL);
_constrain_system = fptr;
}
Definition at line 1074 of file system.C.
References System::_init_system.
{
libmesh_assert (fptr != NULL);
_init_system = fptr;
}
Definition at line 1114 of file system.C.
References System::_qoi_evaluate_derivative.
{
libmesh_assert (fptr != NULL);
_qoi_evaluate_derivative = fptr;
}
Definition at line 1104 of file system.C.
References System::_qoi_evaluate.
{
libmesh_assert (fptr != NULL);
_qoi_evaluate = fptr;
}
For most problems, the default FEMSystem implementation is correct; users who subclass FEMContext will need to also reimplement this method to build it.
Reimplemented from DifferentiableSystem.
Definition at line 724 of file fem_system.C.
Referenced by assemble_qoi(), assemble_qoi_derivative(), assembly(), mesh_position_get(), mesh_position_set(), and postprocess().
{
return AutoPtr<DiffContext>(new FEMContext(*this));
}
Definition at line 824 of file system.C.
References libMeshEnums::DISCRETE_L1, libMeshEnums::DISCRETE_L2, libMeshEnums::DISCRETE_L_INF, System::discrete_var_norm(), libMeshEnums::L2, and System::n_vars().
Referenced by AdaptiveTimeSolver::calculate_norm(), and UnsteadySolver::du().
{
//short circuit to save time
if(norm_type == DISCRETE_L1 ||
norm_type == DISCRETE_L2 ||
norm_type == DISCRETE_L_INF)
return discrete_var_norm(v,var,norm_type);
// Not a discrete norm
std::vector<FEMNormType> norms(this->n_vars(), L2);
std::vector<Real> weights(this->n_vars(), 0.0);
norms[var] = norm_type;
weights[var] = 1.0;
Real val = this->calculate_norm(v, SystemNorm(norms, weights));
return val;
}
Definition at line 845 of file system.C.
References System::_dof_map, MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), TypeTensor< T >::add_scaled(), TypeVector< T >::add_scaled(), FEBase::build(), FEType::default_quadrature_rule(), libMeshEnums::DISCRETE_L1, libMeshEnums::DISCRETE_L2, libMeshEnums::DISCRETE_L_INF, System::discrete_var_norm(), DofMap::dof_indices(), AutoPtr< Tp >::get(), System::get_dof_map(), System::get_mesh(), libMeshEnums::H1, libMeshEnums::H1_SEMINORM, libMeshEnums::H2, libMeshEnums::H2_SEMINORM, SystemNorm::is_discrete(), NumericVector< T >::l1_norm(), libMeshEnums::L2, NumericVector< T >::l2_norm(), libmesh_norm(), NumericVector< T >::linfty_norm(), NumericVector< T >::localize(), MeshBase::mesh_dimension(), System::n_vars(), libMeshEnums::SERIAL, NumericVector< T >::size(), TypeTensor< T >::size_sq(), TypeVector< T >::size_sq(), SystemNorm::type(), DofMap::variable_type(), SystemNorm::weight(), and SystemNorm::weight_sq().
{
// This function must be run on all processors at once
parallel_only();
START_LOG ('calculate_norm()', 'System');
// Zero the norm before summation
Real v_norm = 0.;
if (norm.is_discrete())
{
STOP_LOG ('calculate_norm()', 'System');
//Check to see if all weights are 1.0
unsigned int check_var = 0;
for (; check_var != this->n_vars(); ++check_var)
if(norm.weight(check_var) != 1.0)
break;
//All weights were 1.0 so just do the full vector discrete norm
if(check_var == this->n_vars())
{
FEMNormType norm_type = norm.type(0);
if(norm_type == DISCRETE_L1)
return v.l1_norm();
if(norm_type == DISCRETE_L2)
return v.l2_norm();
if(norm_type == DISCRETE_L_INF)
return v.linfty_norm();
else
libmesh_error();
}
for (unsigned int var=0; var != this->n_vars(); ++var)
{
// Skip any variables we don't need to integrate
if (norm.weight(var) == 0.0)
continue;
v_norm += norm.weight(var) * discrete_var_norm(v, var, norm.type(var));
}
return v_norm;
}
// Localize the potentially parallel vector
AutoPtr<NumericVector<Number> > local_v = NumericVector<Number>::build();
local_v->init(v.size(), true, SERIAL);
v.localize (*local_v, _dof_map->get_send_list());
unsigned int dim = this->get_mesh().mesh_dimension();
// Loop over all variables
for (unsigned int var=0; var != this->n_vars(); ++var)
{
// Skip any variables we don't need to integrate
if (norm.weight(var) == 0.0)
continue;
const FEType& fe_type = this->get_dof_map().variable_type(var);
AutoPtr<QBase> qrule =
fe_type.default_quadrature_rule (dim);
AutoPtr<FEBase> fe
(FEBase::build(dim, fe_type));
fe->attach_quadrature_rule (qrule.get());
const std::vector<Real>& JxW = fe->get_JxW();
const std::vector<std::vector<Real> >* phi = NULL;
if (norm.type(var) == H1 ||
norm.type(var) == H2 ||
norm.type(var) == L2)
phi = &(fe->get_phi());
const std::vector<std::vector<RealGradient> >* dphi = NULL;
if (norm.type(var) == H1 ||
norm.type(var) == H2 ||
norm.type(var) == H1_SEMINORM)
dphi = &(fe->get_dphi());
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
const std::vector<std::vector<RealTensor> >* d2phi = NULL;
if (norm.type(var) == H2 ||
norm.type(var) == H2_SEMINORM)
d2phi = &(fe->get_d2phi());
#endif
std::vector<unsigned int> dof_indices;
// Begin the loop over the elements
MeshBase::const_element_iterator el =
this->get_mesh().active_local_elements_begin();
const MeshBase::const_element_iterator end_el =
this->get_mesh().active_local_elements_end();
for ( ; el != end_el; ++el)
{
const Elem* elem = *el;
fe->reinit (elem);
this->get_dof_map().dof_indices (elem, dof_indices, var);
const unsigned int n_qp = qrule->n_points();
const unsigned int n_sf = dof_indices.size();
// Begin the loop over the Quadrature points.
for (unsigned int qp=0; qp<n_qp; qp++)
{
if (norm.type(var) == H1 ||
norm.type(var) == H2 ||
norm.type(var) == L2)
{
Number u_h = 0.;
for (unsigned int i=0; i != n_sf; ++i)
u_h += (*phi)[i][qp] * (*local_v)(dof_indices[i]);
v_norm += norm.weight_sq(var) *
JxW[qp] * libmesh_norm(u_h);
}
if (norm.type(var) == H1 ||
norm.type(var) == H2 ||
norm.type(var) == H1_SEMINORM)
{
Gradient grad_u_h;
for (unsigned int i=0; i != n_sf; ++i)
grad_u_h.add_scaled((*dphi)[i][qp], (*local_v)(dof_indices[i]));
v_norm += norm.weight_sq(var) *
JxW[qp] * grad_u_h.size_sq();
}
#ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
if (norm.type(var) == H2 ||
norm.type(var) == H2_SEMINORM)
{
Tensor hess_u_h;
for (unsigned int i=0; i != n_sf; ++i)
hess_u_h.add_scaled((*d2phi)[i][qp], (*local_v)(dof_indices[i]));
v_norm += norm.weight_sq(var) *
JxW[qp] * hess_u_h.size_sq();
}
#endif
}
}
}
Parallel::sum(v_norm);
STOP_LOG ('calculate_norm()', 'System');
return std::sqrt(v_norm);
}
Reimplemented from DifferentiableSystem.
Reimplemented in ContinuationSystem.
Definition at line 64 of file fem_system.C.
References DifferentiableSystem::clear().
Referenced by ContinuationSystem::clear(), and ~FEMSystem().
{
Parent::clear();
}
Definition at line 380 of file system.C.
References System::_can_add_vectors, System::_sys_name, System::_vectors, AutoPtr< Tp >::get(), System::get_vector(), System::n_vectors(), System::name(), and System::solution.
Referenced by EquationSystems::compare().
{
// we do not care for matrices, but for vectors
libmesh_assert (!_can_add_vectors);
libmesh_assert (!other_system._can_add_vectors);
if (verbose)
{
std::cout << ' Systems '' << _sys_name << ''' << std::endl;
std::cout << ' comparing matrices not supported.' << std::endl;
std::cout << ' comparing names...';
}
// compare the name: 0 means identical
const int name_result = _sys_name.compare(other_system.name());
if (verbose)
{
if (name_result == 0)
std::cout << ' identical.' << std::endl;
else
std::cout << ' names not identical.' << std::endl;
std::cout << ' comparing solution vector...';
}
// compare the solution: -1 means identical
const int solu_result = solution->compare (*other_system.solution.get(),
threshold);
if (verbose)
{
if (solu_result == -1)
std::cout << ' identical up to threshold.' << std::endl;
else
std::cout << ' first difference occured at index = '
<< solu_result << '.' << std::endl;
}
// safety check, whether we handle at least the same number
// of vectors
std::vector<int> ov_result;
if (this->n_vectors() != other_system.n_vectors())
{
if (verbose)
{
std::cout << ' Fatal difference. This system handles '
<< this->n_vectors() << ' add'l vectors,' << std::endl
<< ' while the other system handles '
<< other_system.n_vectors()
<< ' add'l vectors.' << std::endl
<< ' Aborting comparison.' << std::endl;
}
return false;
}
else if (this->n_vectors() == 0)
{
// there are no additional vectors...
ov_result.clear ();
}
else
{
// compare other vectors
for (const_vectors_iterator pos = _vectors.begin();
pos != _vectors.end(); ++pos)
{
if (verbose)
std::cout << ' comparing vector ''
<< pos->first << '' ...';
// assume they have the same name
const NumericVector<Number>& other_system_vector =
other_system.get_vector(pos->first);
ov_result.push_back(pos->second->compare (other_system_vector,
threshold));
if (verbose)
{
if (ov_result[ov_result.size()-1] == -1)
std::cout << ' identical up to threshold.' << std::endl;
else
std::cout << ' first difference occured at' << std::endl
<< ' index = ' << ov_result[ov_result.size()-1] << '.' << std::endl;
}
}
} // finished comparing additional vectors
bool overall_result;
// sum up the results
if ((name_result==0) && (solu_result==-1))
{
if (ov_result.size()==0)
overall_result = true;
else
{
bool ov_identical;
unsigned int n = 0;
do
{
ov_identical = (ov_result[n]==-1);
n++;
}
while (ov_identical && n<ov_result.size());
overall_result = ov_identical;
}
}
else
overall_result = false;
if (verbose)
{
std::cout << ' finished comparisons, ';
if (overall_result)
std::cout << 'found no differences.' << std::endl << std::endl;
else
std::cout << 'found differences.' << std::endl << std::endl;
}
return overall_result;
}
Definition at line 115 of file system.C.
References System::current_local_solution, and System::n_dofs().
Referenced by ExactSolution::_compute_error(), UniformRefinementEstimator::_estimate_error(), HPCoarsenTest::add_projection(), JumpErrorEstimator::estimate_error(), ExactErrorEstimator::estimate_error(), eulerian_residual(), PatchRecoveryErrorEstimator::EstimateError::operator()(), FEMContext::reinit(), HPCoarsenTest::select_refinement(), VTKIO::solution_to_vtk(), EnsightIO::write_scalar_ascii(), and EnsightIO::write_vector_ascii().
{
// Check the sizes
libmesh_assert (global_dof_number < _dof_map->n_dofs());
libmesh_assert (global_dof_number < current_local_solution->size());
return (*current_local_solution)(global_dof_number);
}
Definition at line 1111 of file system.h.
References System::_active.
{
_active = false;
}
Users may need to reimplement this for their particular PDE. To implement the constraint 0 = G(u), the user should examine u = elem_solution and add (G(u), phi_i) to elem_residual.
Definition at line 136 of file diff_system.h.
Referenced by SteadySolver::element_residual(), EulerSolver::element_residual(), Euler2Solver::element_residual(), and EigenTimeSolver::element_residual().
{
return request_jacobian;
}
Definition at line 204 of file diff_system.h.
Referenced by postprocess().
{}
Definition at line 216 of file diff_system.h.
Referenced by assemble_qoi().
{}
Definition at line 222 of file diff_system.h.
Referenced by assemble_qoi_derivative().
{}
Users need to reimplement this for their particular PDE. To implement the physics model du/dt = F(u), the user should examine u = elem_solution and add (F(u), phi_i) to elem_residual.
Definition at line 119 of file diff_system.h.
Referenced by SteadySolver::element_residual(), EulerSolver::element_residual(), Euler2Solver::element_residual(), and EigenTimeSolver::element_residual().
{
return request_jacobian;
}
This function assumes that the user's time derivative equations (except for any equations involving unknown mesh xyz coordinates themselves) are expressed in an Eulerian frame of reference, and that the user is satisfied with an unstabilized convection term. Lagrangian equations will probably require overriding eulerian_residual() with a blank function; ALE or stabilized formulations will require reimplementing eulerian_residual() entirely.
Reimplemented from DifferentiableSystem.
Definition at line 846 of file fem_system.C.
References _mesh_sys, _mesh_x_var, _mesh_y_var, _mesh_z_var, DifferentiableSystem::_time_evolving, System::current_solution(), DifferentiableSystem::deltat, DiffContext::dof_indices_var, DiffContext::elem_subjacobians, DiffContext::elem_subresiduals, FEMContext::element_fe_var, FEMContext::element_qrule, AutoPtr< Tp >::get(), FEMContext::interior_gradient(), libMesh::invalid_uint, libmesh_real(), QBase::n_points(), System::n_vars(), System::number(), UnsteadySolver::old_nonlinear_solution(), and DifferentiableSystem::time_solver.
{
// Only calculate a mesh movement residual if it's necessary
if (_mesh_sys == libMesh::invalid_uint)
return request_jacobian;
FEMContext &context = libmesh_cast_ref<FEMContext&>(c);
// This function only supports fully coupled mesh motion for now
libmesh_assert(_mesh_sys == this->number());
unsigned int n_qpoints = context.element_qrule->n_points();
const unsigned int n_x_dofs = (_mesh_x_var == libMesh::invalid_uint) ?
0 : context.dof_indices_var[_mesh_x_var].size();
const unsigned int n_y_dofs = (_mesh_y_var == libMesh::invalid_uint) ?
0 : context.dof_indices_var[_mesh_y_var].size();
const unsigned int n_z_dofs = (_mesh_z_var == libMesh::invalid_uint) ?
0 : context.dof_indices_var[_mesh_z_var].size();
const unsigned int mesh_xyz_var = n_x_dofs ? _mesh_x_var :
(n_y_dofs ? _mesh_y_var :
(n_z_dofs ? _mesh_z_var :
libMesh::invalid_uint));
// If we're our own _mesh_sys, we'd better be in charge of
// at least one coordinate, and we'd better have the same
// FE type for all coordinates we are in charge of
libmesh_assert(mesh_xyz_var != libMesh::invalid_uint);
libmesh_assert(!n_x_dofs || context.element_fe_var[_mesh_x_var] ==
context.element_fe_var[mesh_xyz_var]);
libmesh_assert(!n_y_dofs || context.element_fe_var[_mesh_y_var] ==
context.element_fe_var[mesh_xyz_var]);
libmesh_assert(!n_z_dofs || context.element_fe_var[_mesh_z_var] ==
context.element_fe_var[mesh_xyz_var]);
const std::vector<std::vector<Real> > &psi =
context.element_fe_var[mesh_xyz_var]->get_phi();
for (unsigned int var = 0; var != this->n_vars(); ++var)
{
// Mesh motion only affects time-evolving variables
if (!_time_evolving[var])
continue;
// The mesh coordinate variables themselves are Lagrangian,
// not Eulerian, and no convective term is desired.
if (_mesh_sys == this->number() &&
(var == _mesh_x_var ||
var == _mesh_y_var ||
var == _mesh_z_var))
continue;
// Some of this code currently relies on the assumption that
// we can pull mesh coordinate data from our own system
if (_mesh_sys != this->number())
libmesh_not_implemented();
// This residual should only be called by unsteady solvers:
// if the mesh is steady, there's no mesh convection term!
UnsteadySolver *unsteady =
dynamic_cast<UnsteadySolver *>(this->time_solver.get());
if (!unsteady)
return request_jacobian;
const std::vector<Real> &JxW =
context.element_fe_var[var]->get_JxW();
const std::vector<std::vector<Real> > &phi =
context.element_fe_var[var]->get_phi();
const std::vector<std::vector<RealGradient> > &dphi =
context.element_fe_var[var]->get_dphi();
const unsigned int n_u_dofs = context.dof_indices_var[var].size();
DenseSubVector<Number> &Fu = *context.elem_subresiduals[var];
DenseSubMatrix<Number> &Kuu = *context.elem_subjacobians[var][var];
DenseSubMatrix<Number> *Kux = n_x_dofs ?
context.elem_subjacobians[var][_mesh_x_var] : NULL;
DenseSubMatrix<Number> *Kuy = n_y_dofs ?
context.elem_subjacobians[var][_mesh_y_var] : NULL;
DenseSubMatrix<Number> *Kuz = n_z_dofs ?
context.elem_subjacobians[var][_mesh_z_var] : NULL;
std::vector<Real> delta_x(n_x_dofs, 0.);
std::vector<Real> delta_y(n_y_dofs, 0.);
std::vector<Real> delta_z(n_z_dofs, 0.);
for (unsigned int i = 0; i != n_x_dofs; ++i)
{
unsigned int j = context.dof_indices_var[_mesh_x_var][i];
delta_x[i] = libmesh_real(this->current_solution(j)) -
libmesh_real(unsteady->old_nonlinear_solution(j));
}
for (unsigned int i = 0; i != n_y_dofs; ++i)
{
unsigned int j = context.dof_indices_var[_mesh_y_var][i];
delta_y[i] = libmesh_real(this->current_solution(j)) -
libmesh_real(unsteady->old_nonlinear_solution(j));
}
for (unsigned int i = 0; i != n_z_dofs; ++i)
{
unsigned int j = context.dof_indices_var[_mesh_z_var][i];
delta_z[i] = libmesh_real(this->current_solution(j)) -
libmesh_real(unsteady->old_nonlinear_solution(j));
}
for (unsigned int qp = 0; qp != n_qpoints; ++qp)
{
Gradient grad_u = context.interior_gradient(var, qp);
RealGradient convection(0.);
for (unsigned int i = 0; i != n_x_dofs; ++i)
convection(0) += delta_x[i] * psi[i][qp];
for (unsigned int i = 0; i != n_y_dofs; ++i)
convection(1) += delta_y[i] * psi[i][qp];
for (unsigned int i = 0; i != n_z_dofs; ++i)
convection(2) += delta_z[i] * psi[i][qp];
for (unsigned int i = 0; i != n_u_dofs; ++i)
{
Number JxWxPhiI = JxW[qp] * phi[i][qp];
Fu(i) += (convection * grad_u) * JxWxPhiI;
if (request_jacobian)
{
Number JxWxPhiI = JxW[qp] * phi[i][qp];
for (unsigned int j = 0; j != n_u_dofs; ++j)
Kuu(i,j) += JxWxPhiI * (convection * dphi[j][qp]);
Number JxWxPhiIoverDT = JxWxPhiI/this->deltat;
Number JxWxPhiIxDUDXoverDT = JxWxPhiIoverDT * grad_u(0);
for (unsigned int j = 0; j != n_x_dofs; ++j)
(*Kux)(i,j) += JxWxPhiIxDUDXoverDT * psi[j][qp];
Number JxWxPhiIxDUDYoverDT = JxWxPhiIoverDT * grad_u(1);
for (unsigned int j = 0; j != n_y_dofs; ++j)
(*Kuy)(i,j) += JxWxPhiIxDUDYoverDT * psi[j][qp];
Number JxWxPhiIxDUDZoverDT = JxWxPhiIoverDT * grad_u(2);
for (unsigned int j = 0; j != n_z_dofs; ++j)
(*Kuz)(i,j) += JxWxPhiIxDUDZoverDT * psi[j][qp];
}
}
}
}
return request_jacobian;
}
Definition at line 637 of file system.C.
References System::get_vector().
Referenced by AdjointResidualErrorEstimator::estimate_error().
{
// Get the adjoint solution using the get_vector function declared above
return this->get_vector('adjoint_solution');
}
Definition at line 645 of file system.C.
References System::get_vector().
{
return this->get_vector('adjoint_solution');
}
Definition at line 1079 of file system.h.
References System::_dof_map.
Referenced by __libmesh_petsc_diff_solver_jacobian(), __libmesh_petsc_diff_solver_residual(), ExactSolution::_compute_error(), UniformRefinementEstimator::_estimate_error(), HPCoarsenTest::add_projection(), PetscDiffSolver::adjoint_solve(), NewtonSolver::adjoint_solve(), assemble_qoi_derivative(), assembly(), EquationSystems::build_discontinuous_solution_vector(), EquationSystems::build_solution_vector(), System::calculate_norm(), DofMap::enforce_constraints_exactly(), JumpErrorEstimator::estimate_error(), ExactErrorEstimator::estimate_error(), System::get_info(), EigenSystem::init_data(), ImplicitSystem::init_matrices(), System::local_dof_indices(), DofMap::max_constraint_error(), mesh_position_get(), UnsteadySolver::old_nonlinear_solution(), System::ProjectVector::operator()(), PatchRecoveryErrorEstimator::EstimateError::operator()(), ErrorVector::plot_error(), System::project_vector(), FEMContext::reinit(), EquationSystems::reinit(), HPCoarsenTest::select_refinement(), UnsteadySolver::solve(), PetscDiffSolver::solve(), NewtonSolver::solve(), EnsightIO::write_scalar_ascii(), and EnsightIO::write_vector_ascii().
{
return *_dof_map;
}
Definition at line 1087 of file system.h.
References System::_dof_map.
{
return *_dof_map;
}
Definition at line 252 of file system.h.
References System::_equation_systems.
Referenced by UniformRefinementEstimator::_estimate_error(), LinearImplicitSystem::adjoint_solve(), NewmarkSystem::clear(), FrequencySystem::clear_all(), ExactErrorEstimator::find_squared_element_error(), FrequencySystem::init_data(), FrequencySystem::n_frequencies(), FrequencySystem::set_current_frequency(), FrequencySystem::set_frequencies(), FrequencySystem::set_frequencies_by_range(), FrequencySystem::set_frequencies_by_steps(), NewmarkSystem::set_newmark_parameters(), NonlinearImplicitSystem::set_solver_parameters(), LinearImplicitSystem::solve(), FrequencySystem::solve(), and EigenSystem::solve().
{ return _equation_systems; }
Definition at line 257 of file system.h.
References System::_equation_systems.
{ return _equation_systems; }
Definition at line 1001 of file system.C.
References Utility::enum_to_string< FEFamily >(), Utility::enum_to_string< InfMapType >(), Utility::enum_to_string< Order >(), FEType::family, System::get_dof_map(), FEType::inf_map, System::n_constrained_dofs(), System::n_dofs(), System::n_local_dofs(), System::n_vars(), System::n_vectors(), System::name(), FEType::order, FEType::radial_family, FEType::radial_order, System::system_type(), System::variable_name(), and DofMap::variable_type().
{
std::ostringstream out;
const std::string& sys_name = this->name();
out << ' System '' << sys_name << ''
<< ' Type '' << this->system_type() << ''
<< ' Variables=';
for (unsigned int vn=0; vn<this->n_vars(); vn++)
out << ''' << this->variable_name(vn) << '' ';
out << ';
out << ' Finite Element Types=';
#ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
for (unsigned int vn=0; vn<this->n_vars(); vn++)
out << '''
<< Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_type(vn).family)
<< '' ';
#else
for (unsigned int vn=0; vn<this->n_vars(); vn++)
{
out << '''
<< Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_type(vn).family)
<< '', ''
<< Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_type(vn).radial_family)
<< '' ';
}
out << ' << ' Infinite Element Mapping=';
for (unsigned int vn=0; vn<this->n_vars(); vn++)
out << '''
<< Utility::enum_to_string<InfMapType>(this->get_dof_map().variable_type(vn).inf_map)
<< '' ';
#endif
out << ';
out << ' Approximation Orders=';
for (unsigned int vn=0; vn<this->n_vars(); vn++)
{
#ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
out << '''
<< Utility::enum_to_string<Order>(this->get_dof_map().variable_type(vn).order)
<< '' ';
#else
out << '''
<< Utility::enum_to_string<Order>(this->get_dof_map().variable_type(vn).order)
<< '', ''
<< Utility::enum_to_string<Order>(this->get_dof_map().variable_type(vn).radial_order)
<< '' ';
#endif
}
out << ';
out << ' n_dofs()=' << this->n_dofs() << ';
out << ' n_local_dofs()=' << this->n_local_dofs() << ';
#ifdef LIBMESH_ENABLE_AMR
out << ' n_constrained_dofs()=' << this->n_constrained_dofs() << ';
#endif
out << ' ' << 'n_vectors()=' << this->n_vectors() << ';
// out << ' ' << 'n_additional_matrices()=' << this->n_additional_matrices() << ';
return out.str();
}
Definition at line 45 of file reference_counter.C.
References ReferenceCounter::_counts, and Quality::name().
Referenced by ReferenceCounter::print_info().
{
#if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
std::ostringstream out;
out << '
<< ' ----------------------------------------------------------------------------
<< '| Reference count information |
<< ' ---------------------------------------------------------------------------- ;
for (Counts::iterator it = _counts.begin();
it != _counts.end(); ++it)
{
const std::string name(it->first);
const unsigned int creations = it->second.first;
const unsigned int destructions = it->second.second;
out << '| ' << name << ' reference count information:
<< '| Creations: ' << creations << '
<< '| Destructions: ' << destructions << ';
}
out << ' ---------------------------------------------------------------------------- ;
return out.str();
#else
return '';
#endif
}
Definition at line 212 of file implicit_system.C.
References ImplicitSystem::_matrices.
{
// Make sure the matrix exists
matrices_iterator pos = _matrices.find (mat_name);
if (pos == _matrices.end())
{
std::cerr << 'ERROR: matrix '
<< mat_name
<< ' does not exist in this system!'
<< std::endl;
libmesh_error();
}
return *(pos->second);
}
Definition at line 193 of file implicit_system.C.
References ImplicitSystem::_matrices.
Referenced by PetscDiffSolver::adjoint_solve(), NewtonSolver::adjoint_solve(), LinearImplicitSystem::adjoint_solve(), NewmarkSystem::compute_matrix(), NewtonSolver::solve(), LinearImplicitSystem::solve(), EigenTimeSolver::solve(), and NewmarkSystem::update_rhs().
{
// Make sure the matrix exists
const_matrices_iterator pos = _matrices.find (mat_name);
if (pos == _matrices.end())
{
std::cerr << 'ERROR: matrix '
<< mat_name
<< ' does not exist in this system!'
<< std::endl;
libmesh_error();
}
return *(pos->second);
}
Definition at line 1063 of file system.h.
References System::_mesh.
Referenced by ExactSolution::_compute_error(), HPCoarsenTest::add_projection(), assemble_qoi(), assemble_qoi_derivative(), assembly(), System::calculate_norm(), PatchRecoveryErrorEstimator::estimate_error(), JumpErrorEstimator::estimate_error(), ExactErrorEstimator::estimate_error(), AdjointResidualErrorEstimator::estimate_error(), System::init_data(), EigenSystem::init_data(), ImplicitSystem::init_matrices(), System::local_dof_indices(), DofMap::max_constraint_error(), mesh_position_get(), mesh_position_set(), System::ProjectVector::operator()(), PatchRecoveryErrorEstimator::EstimateError::operator()(), postprocess(), System::project_vector(), System::read_header(), System::read_legacy_data(), System::read_parallel_data(), System::read_serialized_vector(), HPSingularity::select_refinement(), HPCoarsenTest::select_refinement(), System::write_header(), System::write_parallel_data(), System::write_serialized_vector(), and System::zero_variable().
{
return _mesh;
}
Definition at line 1071 of file system.h.
References System::_mesh.
{
return _mesh;
}
Definition at line 551 of file system.C.
References System::_vectors.
Referenced by UniformRefinementEstimator::_estimate_error(), UnsteadySolver::advance_timestep(), AdaptiveTimeSolver::advance_timestep(), System::compare(), UnsteadySolver::du(), System::get_adjoint_solution(), NewmarkSystem::initial_conditions(), UnsteadySolver::solve(), TwostepTimeSolver::solve(), FrequencySystem::solve(), NewmarkSystem::update_rhs(), and NewmarkSystem::update_u_v_a().
{
// Make sure the vector exists
const_vectors_iterator pos = _vectors.find(vec_name);
if (pos == _vectors.end())
{
std::cerr << 'ERROR: vector '
<< vec_name
<< ' does not exist in this system!'
<< std::endl;
libmesh_error();
}
return *(pos->second);
}
Definition at line 570 of file system.C.
References System::_vectors.
{
// Make sure the vector exists
vectors_iterator pos = _vectors.find(vec_name);
if (pos == _vectors.end())
{
std::cerr << 'ERROR: vector '
<< vec_name
<< ' does not exist in this system!'
<< std::endl;
libmesh_error();
}
return *(pos->second);
}
Definition at line 589 of file system.C.
References System::vectors_begin(), and System::vectors_end().
{
const_vectors_iterator v = vectors_begin();
const_vectors_iterator v_end = vectors_end();
unsigned int num = 0;
while((num<vec_num) && (v!=v_end))
{
num++;
++v;
}
libmesh_assert(v!=v_end);
return *(v->second);
}
Definition at line 605 of file system.C.
References System::vectors_begin(), and System::vectors_end().
{
vectors_iterator v = vectors_begin();
vectors_iterator v_end = vectors_end();
unsigned int num = 0;
while((num<vec_num) && (v!=v_end))
{
num++;
++v;
}
libmesh_assert(v!=v_end);
return *(v->second);
}
Definition at line 703 of file system.C.
References System::_variable_numbers.
Referenced by GMVIO::copy_nodal_solution().
{
return _variable_numbers.count(var);
}
Definition at line 199 of file implicit_system.h.
References ImplicitSystem::_matrices.
Referenced by ImplicitSystem::add_matrix(), PetscDiffSolver::adjoint_solve(), NewtonSolver::adjoint_solve(), LinearImplicitSystem::adjoint_solve(), EigenTimeSolver::init(), NewtonSolver::solve(), and LinearImplicitSystem::solve().
{
return (_matrices.count(mat_name));
}
Definition at line 1173 of file system.h.
References System::_vectors.
Referenced by System::add_vector().
{
return (_vectors.count(vec_name));
}
Definition at line 149 of file reference_counter.h.
References ReferenceCounter::_counts, Quality::name(), and Threads::spin_mtx.
Referenced by ReferenceCountedObject< Value >::ReferenceCountedObject().
{
Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
std::pair<unsigned int, unsigned int>& p = _counts[name];
p.first++;
}
Definition at line 167 of file reference_counter.h.
References ReferenceCounter::_counts, Quality::name(), and Threads::spin_mtx.
Referenced by ReferenceCountedObject< Value >::~ReferenceCountedObject().
{
Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
std::pair<unsigned int, unsigned int>& p = _counts[name];
p.second++;
}
Definition at line 156 of file system.C.
References System::init_data(), System::n_vars(), and System::user_initialization().
{
// First initialize any required data
this->init_data();
//If no variables have been added to this system
//don't do anything
if(!this->n_vars())
return;
// Then call the user-provided intialization function
this->user_initialization();
}
Reimplemented from DifferentiableSystem.
Definition at line 731 of file fem_system.C.
References DifferentiableSystem::_time_evolving, FEMContext::element_fe_var, DifferentiableSystem::init_context(), and System::n_vars().
Referenced by mesh_position_get().
{
Parent::init_context(c);
FEMContext &context = libmesh_cast_ref<FEMContext&>(c);
// Make sure we're prepared to do mass integration
for (unsigned int var = 0; var != this->n_vars(); ++var)
if (_time_evolving[var])
{
context.element_fe_var[var]->get_JxW();
context.element_fe_var[var]->get_phi();
}
}
Reimplemented from DifferentiableSystem.
Reimplemented in ContinuationSystem.
Definition at line 71 of file fem_system.C.
References DifferentiableSystem::init_data().
Referenced by ContinuationSystem::init_data().
{
// First initialize LinearImplicitSystem data
Parent::init_data();
}
Definition at line 92 of file implicit_system.C.
References ImplicitSystem::_can_add_matrices, ImplicitSystem::_matrices, DofMap::attach_matrix(), DofMap::compute_sparsity(), System::get_dof_map(), System::get_mesh(), SparseMatrix< T >::initialized(), and ImplicitSystem::matrix.
Referenced by ImplicitSystem::init_data(), and ImplicitSystem::reinit().
{
libmesh_assert (matrix != NULL);
// Check for quick return in case the system matrix
// (and by extension all the matrices) has already
// been initialized
if (matrix->initialized())
return;
// Get a reference to the DofMap
DofMap& dof_map = this->get_dof_map();
// no chance to add other matrices
_can_add_matrices = false;
// Tell the matrices about the dof map, and vice versa
for (matrices_iterator pos = _matrices.begin();
pos != _matrices.end(); ++pos)
{
libmesh_assert (!pos->second->initialized());
dof_map.attach_matrix (*(pos->second));
}
// Compute the sparsity pattern for the current
// mesh and DOF distribution. This also updates
// additional matrices,
DofMap now knows them
dof_map.compute_sparsity (this->get_mesh());
// Initialize matrices
for (matrices_iterator pos = _matrices.begin();
pos != _matrices.end(); ++pos)
pos->second->init ();
// Set the additional matrices to 0.
for (matrices_iterator pos = _matrices.begin();
pos != _matrices.end(); ++pos)
pos->second->zero ();
}
Definition at line 730 of file system.C.
References MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), DofMap::dof_indices(), DofMap::end_dof(), DofMap::first_dof(), System::get_dof_map(), and System::get_mesh().
Referenced by System::discrete_var_norm().
{
// Make sure the set is clear
var_indices.clear();
std::vector<unsigned int> dof_indices;
// Begin the loop over the elements
MeshBase::const_element_iterator el =
this->get_mesh().active_local_elements_begin();
const MeshBase::const_element_iterator end_el =
this->get_mesh().active_local_elements_end();
const unsigned int
first_local = this->get_dof_map().first_dof(),
end_local = this->get_dof_map().end_dof();
for ( ; el != end_el; ++el)
{
const Elem* elem = *el;
this->get_dof_map().dof_indices (elem, dof_indices, var);
for(unsigned int i=0; i<dof_indices.size(); i++)
{
unsigned int dof = dof_indices[i];
//If the dof is owned by the local processor
if(first_local <= dof && dof < end_local)
var_indices.insert(dof_indices[i]);
}
}
}
Most problems can use the FEMSystem::mass_residual implementation, which calculates the residual (u, phi_i) and jacobian (phi_i, phi_j); few users will need to reimplement this themselves. Using a custom mass matrix (e.g. for divergence-free elements or mass lumping) requires reimplementing mass_residual().
Reimplemented from DifferentiableSystem.
Definition at line 1003 of file fem_system.C.
References DifferentiableSystem::_time_evolving, DiffContext::dof_indices_var, DiffContext::elem_solution_derivative, DiffContext::elem_subjacobians, DiffContext::elem_subresiduals, FEMContext::element_fe_var, FEMContext::element_qrule, FEMContext::interior_value(), System::n_dofs(), QBase::n_points(), and System::n_vars().
{
FEMContext &context = libmesh_cast_ref<FEMContext&>(c);
unsigned int n_qpoints = context.element_qrule->n_points();
for (unsigned int var = 0; var != this->n_vars(); ++var)
{
if (!_time_evolving[var])
continue;
const std::vector<Real> &JxW =
context.element_fe_var[var]->get_JxW();
const std::vector<std::vector<Real> > &phi =
context.element_fe_var[var]->get_phi();
const unsigned int n_dofs = context.dof_indices_var[var].size();
DenseSubVector<Number> &Fu = *context.elem_subresiduals[var];
DenseSubMatrix<Number> &Kuu = *context.elem_subjacobians[var][var];
for (unsigned int qp = 0; qp != n_qpoints; ++qp)
{
Number u = context.interior_value(var, qp);
Number JxWxU = JxW[qp] * u;
for (unsigned int i = 0; i != n_dofs; ++i)
{
Fu(i) += JxWxU * phi[i][qp];
if (request_jacobian && context.elem_solution_derivative)
{
libmesh_assert (context.elem_solution_derivative == 1.0);
Number JxWxPhiI = JxW[qp] * phi[i][qp];
Kuu(i,i) += JxWxPhiI * phi[i][qp];
for (unsigned int j = i+1; j < n_dofs; ++j)
{
Number Kij = JxWxPhiI * phi[j][qp];
Kuu(i,j) += Kij;
Kuu(j,i) += Kij;
}
}
}
}
}
return request_jacobian;
}
Definition at line 792 of file fem_system.C.
References _mesh_sys, _mesh_x_var, _mesh_y_var, _mesh_z_var, MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), build_context(), DofMap::dof_indices(), DiffContext::dof_indices_var, FEMContext::elem, FEMContext::elem_position_get(), DiffContext::elem_subsolutions, System::get_dof_map(), System::get_mesh(), init_context(), libMesh::invalid_uint, System::n_vars(), System::number(), System::solution, and System::update().
{
// This function makes no sense unless we've already picked out some
// variable(s) to reflect mesh position coordinates
if (_mesh_sys == libMesh::invalid_uint)
libmesh_error();
// We currently assume mesh variables are in our own system
if (_mesh_sys != this->number())
libmesh_not_implemented();
// Loop over every active mesh element on this processor
const MeshBase& mesh = this->get_mesh();
const DofMap& dof_map = this->get_dof_map();
MeshBase::const_element_iterator el =
mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_el =
mesh.active_local_elements_end();
AutoPtr<DiffContext> con = this->build_context();
FEMContext &_femcontext = libmesh_cast_ref<FEMContext&>(*con);
this->init_context(_femcontext);
// Get the solution's mesh variables from every element
for ( ; el != end_el; ++el)
{
_femcontext.elem = *el;
// Initialize the per-variable data for elem.
for (unsigned int i=0; i != this->n_vars(); ++i)
{
dof_map.dof_indices (_femcontext.elem,
_femcontext.dof_indices_var[i], i);
}
_femcontext.elem_position_get();
if (_mesh_x_var != libMesh::invalid_uint)
this->solution->insert(*_femcontext.elem_subsolutions[_mesh_x_var],
_femcontext.dof_indices_var[_mesh_x_var]);
if (_mesh_y_var != libMesh::invalid_uint)
this->solution->insert(*_femcontext.elem_subsolutions[_mesh_y_var],
_femcontext.dof_indices_var[_mesh_y_var]);
if (_mesh_z_var != libMesh::invalid_uint)
this->solution->insert(*_femcontext.elem_subsolutions[_mesh_z_var],
_femcontext.dof_indices_var[_mesh_z_var]);
}
// And make sure the current_local_solution is up to date too
this->update();
}
Definition at line 392 of file fem_system.C.
References _mesh_sys, MeshBase::active_elements_begin(), MeshBase::active_elements_end(), build_context(), FEMContext::elem, FEMContext::elem_position_set(), System::get_mesh(), Elem::has_children(), MeshBase::is_serial(), System::number(), and FEMContext::reinit().
Referenced by solve().
{
// If we don't need to move the mesh, we're done
if (_mesh_sys != this->number())
return;
const MeshBase& mesh = this->get_mesh();
// This code won't work on a parallelized mesh yet -
// it won't get ancestor elements right.
libmesh_assert(mesh.is_serial());
AutoPtr<DiffContext> con = this->build_context();
FEMContext &_femcontext = libmesh_cast_ref<FEMContext&>(*con);
// Move every mesh element we can
MeshBase::const_element_iterator el =
mesh.active_elements_begin();
const MeshBase::const_element_iterator end_el =
mesh.active_elements_end();
for ( ; el != end_el; ++el)
{
_femcontext.reinit(*this, *el);
// This code won't handle moving subactive elements
libmesh_assert(!_femcontext.elem->has_children());
_femcontext.elem_position_set(0.);
}
}
The system with mesh coordinate data (which may be this system itself, for fully coupled moving mesh problems) is currently assumed to have new (end of time step) mesh coordinates stored in solution, old (beginning of time step) mesh coordinates stored in _old_nonlinear_solution, and constant velocity motion during each time step.
Activating this function ensures that local (but not neighbor!) element geometry is correctly repositioned when evaluating element residuals.
Definition at line 756 of file fem_system.C.
References _mesh_sys, _mesh_x_var, libMesh::invalid_uint, and System::number().
{
if (_mesh_sys != libMesh::invalid_uint && _mesh_sys != sysnum)
libmesh_error();
if (sysnum != this->number())
libmesh_not_implemented();
_mesh_sys = sysnum;
_mesh_x_var = var;
}
Definition at line 768 of file fem_system.C.
References _mesh_sys, _mesh_y_var, libMesh::invalid_uint, and System::number().
{
if (_mesh_sys != libMesh::invalid_uint && _mesh_sys != sysnum)
libmesh_error();
if (sysnum != this->number())
libmesh_not_implemented();
_mesh_sys = sysnum;
_mesh_y_var = var;
}
Definition at line 780 of file fem_system.C.
References _mesh_sys, _mesh_z_var, libMesh::invalid_uint, and System::number().
{
if (_mesh_sys != libMesh::invalid_uint && _mesh_sys != sysnum)
libmesh_error();
if (sysnum != this->number())
libmesh_not_implemented();
_mesh_sys = sysnum;
_mesh_z_var = var;
}
Definition at line 1165 of file system.h.
References System::n_constrained_dofs(), and System::n_dofs().
{
return this->n_dofs() - this->n_constrained_dofs();
}
Definition at line 93 of file system.C.
References System::_dof_map.
Referenced by System::get_info(), and System::n_active_dofs().
{
#ifdef LIBMESH_ENABLE_AMR
return _dof_map->n_constrained_dofs();
#else
return 0;
#endif
}
Definition at line 86 of file system.C.
References System::_dof_map.
Referenced by System::add_vector(), System::current_solution(), System::get_info(), System::init_data(), mass_residual(), System::n_active_dofs(), System::ProjectVector::operator()(), System::project_vector(), System::read_legacy_data(), System::reinit(), System::restrict_vectors(), and UnsteadySolver::solve().
{
return _dof_map->n_dofs();
}
Definition at line 108 of file system.C.
References System::_dof_map, and libMesh::processor_id().
Referenced by System::add_vector(), System::get_info(), System::init_data(), System::project_vector(), System::read_serialized_blocked_dof_objects(), System::reinit(), System::restrict_vectors(), and UnsteadySolver::solve().
{
return _dof_map->n_dofs_on_processor (libMesh::processor_id());
}
Definition at line 206 of file implicit_system.h.
References ImplicitSystem::_matrices.
{
return _matrices.size();
}
Definition at line 76 of file reference_counter.h.
References ReferenceCounter::_n_objects.
Referenced by System::read_serialized_blocked_dof_objects(), and System::write_serialized_blocked_dof_objects().
{ return _n_objects; }
Definition at line 1119 of file system.h.
References System::_variables.
Referenced by UniformRefinementEstimator::_estimate_error(), System::add_variable(), EquationSystems::build_discontinuous_solution_vector(), EquationSystems::build_solution_vector(), System::calculate_norm(), DiffContext::DiffContext(), JumpErrorEstimator::estimate_error(), ExactErrorEstimator::estimate_error(), ErrorEstimator::estimate_errors(), eulerian_residual(), ExactSolution::ExactSolution(), FEMContext::FEMContext(), System::get_info(), System::init(), init_context(), DifferentiableSystem::init_data(), mass_residual(), mesh_position_get(), System::ProjectVector::operator()(), PatchRecoveryErrorEstimator::EstimateError::operator()(), System::project_vector(), System::re_update(), System::read_header(), System::read_legacy_data(), System::read_parallel_data(), System::read_serialized_vector(), System::reinit(), FEMContext::reinit(), EquationSystems::reinit(), HPCoarsenTest::select_refinement(), VTKIO::solution_to_vtk(), TecplotIO::write_ascii(), TecplotIO::write_binary(), System::write_header(), System::write_parallel_data(), System::write_serialized_vector(), and System::zero_variable().
{
return _variables.size();
}
Definition at line 1181 of file system.h.
References System::_vectors.
Referenced by ExplicitSystem::add_system_rhs(), System::compare(), System::get_info(), System::read_header(), and System::write_header().
{
return _vectors.size();
}
Definition at line 1047 of file system.h.
References System::_sys_name.
Referenced by System::compare(), ExactErrorEstimator::estimate_error(), ExactSolution::ExactSolution(), ExactErrorEstimator::find_squared_element_error(), System::get_info(), System::ProjectVector::operator()(), System::project_vector(), FrequencySystem::solve(), System::user_assembly(), System::user_constrain(), System::user_initialization(), System::user_QOI(), System::user_QOI_derivative(), TecplotIO::write_binary(), System::write_header(), System::write_parallel_data(), and System::write_serialized_data().
{
return _sys_name;
}
Definition at line 1055 of file system.h.
References System::_sys_number.
Referenced by System::add_variable(), eulerian_residual(), mesh_position_get(), mesh_position_set(), mesh_x_position(), mesh_y_position(), mesh_z_position(), numerical_jacobian(), System::read_legacy_data(), System::read_parallel_data(), System::read_serialized_blocked_dof_objects(), HPCoarsenTest::select_refinement(), System::write_parallel_data(), System::write_serialized_blocked_dof_objects(), and System::zero_variable().
{
return _sys_number;
}
Definition at line 706 of file fem_system.C.
References TimeSolver::element_residual(), and numerical_jacobian().
Referenced by assembly().
{
START_LOG('numerical_elem_jacobian()', 'FEMSystem');
this->numerical_jacobian(&TimeSolver::element_residual, context);
STOP_LOG('numerical_elem_jacobian()', 'FEMSystem');
}
Definition at line 603 of file fem_system.C.
References _mesh_sys, _mesh_x_var, _mesh_y_var, _mesh_z_var, DiffContext::dof_indices, DiffContext::dof_indices_var, FEMContext::elem, DiffContext::elem_jacobian, DiffContext::elem_residual, DiffContext::elem_solution, Elem::hmin(), libMesh::invalid_uint, libmesh_real(), System::number(), numerical_jacobian_h, Elem::point(), and DenseVector< T >::zero().
Referenced by numerical_elem_jacobian(), and numerical_side_jacobian().
{
// Logging is done by numerical_elem_jacobian
// or numerical_side_jacobian
DenseVector<Number> original_residual(context.elem_residual);
DenseVector<Number> backwards_residual(context.elem_residual);
DenseMatrix<Number> numerical_jacobian(context.elem_jacobian);
#ifdef DEBUG
DenseMatrix<Number> old_jacobian(context.elem_jacobian);
#endif
Real numerical_point_h = 0.;
if (_mesh_sys == this->number())
numerical_point_h = numerical_jacobian_h * context.elem->hmin();
for (unsigned int j = 0; j != context.dof_indices.size(); ++j)
{
// Take the 'minus' side of a central differenced first derivative
Number original_solution = context.elem_solution(j);
context.elem_solution(j) -= numerical_jacobian_h;
// Make sure to catch any moving mesh terms
// FIXME - this could be less ugly
Real *coord = NULL;
if (_mesh_sys == this->number())
{
if (_mesh_x_var != libMesh::invalid_uint)
for (unsigned int k = 0;
k != context.dof_indices_var[_mesh_x_var].size(); ++k)
if (context.dof_indices_var[_mesh_x_var][k] ==
context.dof_indices[j])
coord = &(context.elem->point(k)(0));
if (_mesh_y_var != libMesh::invalid_uint)
for (unsigned int k = 0;
k != context.dof_indices_var[_mesh_y_var].size(); ++k)
if (context.dof_indices_var[_mesh_y_var][k] ==
context.dof_indices[j])
coord = &(context.elem->point(k)(1));
if (_mesh_z_var != libMesh::invalid_uint)
for (unsigned int k = 0;
k != context.dof_indices_var[_mesh_z_var].size(); ++k)
if (context.dof_indices_var[_mesh_z_var][k] ==
context.dof_indices[j])
coord = &(context.elem->point(k)(2));
}
if (coord)
{
// We have enough information to scale the perturbations
// here appropriately
context.elem_solution(j) = original_solution - numerical_point_h;
*coord = libmesh_real(context.elem_solution(j));
}
context.elem_residual.zero();
((*time_solver).*(res))(false, context);
#ifdef DEBUG
libmesh_assert(old_jacobian == context.elem_jacobian);
#endif
backwards_residual = context.elem_residual;
// Take the 'plus' side of a central differenced first derivative
context.elem_solution(j) = original_solution + numerical_jacobian_h;
if (coord)
{
context.elem_solution(j) = original_solution + numerical_point_h;
*coord = libmesh_real(context.elem_solution(j));
}
context.elem_residual.zero();
((*time_solver).*(res))(false, context);
#ifdef DEBUG
libmesh_assert(old_jacobian == context.elem_jacobian);
#endif
context.elem_solution(j) = original_solution;
if (coord)
{
*coord = libmesh_real(context.elem_solution(j));
for (unsigned int i = 0; i != context.dof_indices.size(); ++i)
{
numerical_jacobian(i,j) =
(context.elem_residual(i) - backwards_residual(i)) /
2. / numerical_point_h;
}
}
else
{
for (unsigned int i = 0; i != context.dof_indices.size(); ++i)
{
numerical_jacobian(i,j) =
(context.elem_residual(i) - backwards_residual(i)) /
2. / numerical_jacobian_h;
}
}
}
context.elem_residual = original_residual;
context.elem_jacobian = numerical_jacobian;
}
Definition at line 715 of file fem_system.C.
References numerical_jacobian(), and TimeSolver::side_residual().
Referenced by assembly().
{
START_LOG('numerical_side_jacobian()', 'FEMSystem');
this->numerical_jacobian(&TimeSolver::side_residual, context);
STOP_LOG('numerical_side_jacobian()', 'FEMSystem');
}
Implements DifferentiableSystem.
Definition at line 426 of file fem_system.C.
References MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), build_context(), DifferentiableSystem::compute_internal_sides, FEMContext::elem, DifferentiableSystem::element_postprocess(), fe_reinit_during_postprocess, System::get_mesh(), Elem::n_sides(), Elem::neighbor(), DifferentiableSystem::postprocess_sides, FEMContext::reinit(), FEMContext::side, FEMContext::side_fe, DifferentiableSystem::side_postprocess(), and System::update().
{
START_LOG('postprocess()', 'FEMSystem');
const MeshBase& mesh = this->get_mesh();
this->update();
AutoPtr<DiffContext> con = this->build_context();
FEMContext &_femcontext = libmesh_cast_ref<FEMContext&>(*con);
// Loop over every active mesh element on this processor
MeshBase::const_element_iterator el =
mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_el =
mesh.active_local_elements_end();
for ( ; el != end_el; ++el)
{
_femcontext.reinit(*this, *el);
// Optionally initialize all the interior FE objects on elem.
// if (fe_reinit_during_postprocess)
// _femcontext.elem_fe_reinit();
this->element_postprocess(_femcontext);
for (_femcontext.side = 0;
_femcontext.side != _femcontext.elem->n_sides();
++_femcontext.side)
{
// Don't compute on non-boundary sides unless requested
if (!postprocess_sides ||
(!compute_internal_sides &&
_femcontext.elem->neighbor(_femcontext.side) != NULL))
continue;
// Optionally initialize all the interior FE objects on elem/side.
// Logging of FE::reinit is done in the FE functions
if (fe_reinit_during_postprocess)
{
std::map<FEType, FEBase *>::iterator fe_end =
_femcontext.side_fe.end();
for (std::map<FEType, FEBase *>::iterator i =
_femcontext.side_fe.begin();
i != fe_end; ++i)
{
i->second->reinit(_femcontext.elem, _femcontext.side);
}
}
this->side_postprocess(_femcontext);
}
}
STOP_LOG('postprocess()', 'FEMSystem');
}
Definition at line 83 of file reference_counter.C.
References ReferenceCounter::get_info().
{
#if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
std::cout << ReferenceCounter::get_info();
#endif
}
This method projects an analytic function onto the solution via L2 projections and nodal interpolations on each element.
Definition at line 237 of file system_projection.C.
References System::current_local_solution, System::project_vector(), and System::solution.
{
this->project_vector(fptr, gptr, parameters, *solution);
solution->localize(*current_local_solution);
}
Definition at line 319 of file system.h.
References System::_solution_projection.
Referenced by UniformRefinementEstimator::_estimate_error().
{ return _solution_projection; }
This method projects an analytic function via L2 projections and nodal interpolations on each element.
Definition at line 258 of file system_projection.C.
References NumericVector< T >::close(), DofMap::enforce_constraints_exactly(), FEType::family, System::get_dof_map(), System::get_mesh(), libMesh::n_processors(), System::n_vars(), System::name(), Threads::parallel_for(), libMesh::processor_id(), libMeshEnums::SCALAR, DofMap::SCALAR_dof_indices(), NumericVector< T >::set(), System::Variable::type(), System::variable(), and System::variable_name().
Referenced by System::project_solution(), System::project_vector(), and System::restrict_vectors().
{
START_LOG ('project_vector()', 'System');
Threads::parallel_for (ConstElemRange (this->get_mesh().active_local_elements_begin(),
this->get_mesh().active_local_elements_end(),
1000),
ProjectSolution(*this,
fptr,
gptr,
parameters,
new_vector)
);
// Also, load values into the SCALAR dofs
// Note: We assume that all SCALAR dofs are on the
// processor with highest ID
if(libMesh::processor_id() == (libMesh::n_processors()-1))
{
const DofMap& dof_map = this->get_dof_map();
for (unsigned int var=0; var<this->n_vars(); var++)
if(this->variable(var).type().family == SCALAR)
{
std::vector<unsigned int> SCALAR_indices;
dof_map.SCALAR_dof_indices (SCALAR_indices, var);
const unsigned int n_SCALAR_dofs = SCALAR_indices.size();
for (unsigned int i=0; i<n_SCALAR_dofs; i++)
{
const unsigned int index = SCALAR_indices[i];
// We pass the point (i,0,0) to the fptr to distinguish
// the different scalars within the SCALAR variable
Point p_i(i,0,0);
new_vector.set( index, fptr(p_i,
parameters,
this->name(),
this->variable_name(var))
);
}
}
}
new_vector.close();
#ifdef LIBMESH_ENABLE_AMR
this->get_dof_map().enforce_constraints_exactly(*this, &new_vector);
#endif
STOP_LOG('project_vector()', 'System');
}
Definition at line 43 of file system_projection.C.
References NumericVector< T >::clone(), and System::project_vector().
{
// Create a copy of the vector, which currently
// contains the old data.
AutoPtr<NumericVector<Number> >
old_vector (vector.clone());
// Project the old vector to the new vector
this->project_vector (*old_vector, vector);
}
This method projects the vector via L2 projections or nodal interpolations on each element.
This method projects a solution from an old mesh to a current, refined mesh. The input vector old_v gives the solution on the old mesh, while the new_v gives the solution (to be computed) on the new mesh.
Definition at line 60 of file system_projection.C.
References NumericVector< T >::clear(), NumericVector< T >::close(), DofMap::enforce_constraints_exactly(), FEType::family, AutoPtr< Tp >::get(), System::get_dof_map(), System::get_mesh(), libMeshEnums::GHOSTED, NumericVector< T >::init(), NumericVector< T >::local_size(), NumericVector< T >::localize(), System::n_dofs(), System::n_local_dofs(), libMesh::n_processors(), System::n_vars(), libMeshEnums::PARALLEL, Threads::parallel_for(), Threads::parallel_reduce(), libMesh::processor_id(), libMeshEnums::SCALAR, DofMap::SCALAR_dof_indices(), System::BuildProjectionList::send_list, libMeshEnums::SERIAL, NumericVector< T >::set(), NumericVector< T >::size(), System::Variable::type(), NumericVector< T >::type(), System::BuildProjectionList::unique(), and System::variable().
{
START_LOG ('project_vector()', 'System');
new_v.clear();
#ifdef LIBMESH_ENABLE_AMR
// Resize the new vector and get a serial version.
NumericVector<Number> *new_vector_ptr = NULL;
AutoPtr<NumericVector<Number> > new_vector_built;
NumericVector<Number> *local_old_vector;
AutoPtr<NumericVector<Number> > local_old_vector_built;
const NumericVector<Number> *old_vector_ptr = NULL;
ConstElemRange active_local_elem_range
(this->get_mesh().active_local_elements_begin(),
this->get_mesh().active_local_elements_end());
// If the old vector was uniprocessor, make the new
// vector uniprocessor
if (old_v.type() == SERIAL)
{
new_v.init (this->n_dofs(), false, SERIAL);
new_vector_ptr = &new_v;
old_vector_ptr = &old_v;
}
// Otherwise it is a parallel, distributed vector, which
// we need to localize.
else if (old_v.type() == PARALLEL)
{
// Build a send list for efficient localization
BuildProjectionList projection_list(*this);
Threads::parallel_reduce (active_local_elem_range,
projection_list);
// Create a sorted, unique send_list
projection_list.unique();
new_v.init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
new_vector_built = NumericVector<Number>::build();
local_old_vector_built = NumericVector<Number>::build();
new_vector_ptr = new_vector_built.get();
local_old_vector = local_old_vector_built.get();
new_vector_ptr->init(this->n_dofs(), false, SERIAL);
local_old_vector->init(old_v.size(), false, SERIAL);
old_v.localize(*local_old_vector, projection_list.send_list);
local_old_vector->close();
old_vector_ptr = local_old_vector;
}
else if (old_v.type() == GHOSTED)
{
// Build a send list for efficient localization
BuildProjectionList projection_list(*this);
Threads::parallel_reduce (active_local_elem_range,
projection_list);
// Create a sorted, unique send_list
projection_list.unique();
new_v.init (this->n_dofs(), this->n_local_dofs(),
this->get_dof_map().get_send_list(), false, GHOSTED);
local_old_vector_built = NumericVector<Number>::build();
new_vector_ptr = &new_v;
local_old_vector = local_old_vector_built.get();
local_old_vector->init(old_v.size(), old_v.local_size(),
projection_list.send_list, false, GHOSTED);
old_v.localize(*local_old_vector, projection_list.send_list);
local_old_vector->close();
old_vector_ptr = local_old_vector;
}
else // unknown old_v.type()
{
std::cerr << 'ERROR: Unknown old_v.type() == ' << old_v.type()
<< std::endl;
libmesh_error();
}
// Note that the above will have zeroed the new_vector.
// Just to be sure, assert that new_vector_ptr and old_vector_ptr
// were successfully set before trying to deref them.
libmesh_assert(new_vector_ptr);
libmesh_assert(old_vector_ptr);
NumericVector<Number> &new_vector = *new_vector_ptr;
const NumericVector<Number> &old_vector = *old_vector_ptr;
Threads::parallel_for (active_local_elem_range,
ProjectVector(*this,
old_vector,
new_vector)
);
// Copy the SCALAR dofs from old_vector to new_vector
// Note: We assume that all SCALAR dofs are on the
// processor with highest ID
if(libMesh::processor_id() == (libMesh::n_processors()-1))
{
const DofMap& dof_map = this->get_dof_map();
for (unsigned int var=0; var<this->n_vars(); var++)
if(this->variable(var).type().family == SCALAR)
{
// We can just map SCALAR dofs directly across
std::vector<unsigned int> new_SCALAR_indices, old_SCALAR_indices;
dof_map.SCALAR_dof_indices (new_SCALAR_indices, var, false);
dof_map.SCALAR_dof_indices (old_SCALAR_indices, var, true);
const unsigned int new_n_dofs = new_SCALAR_indices.size();
for (unsigned int i=0; i<new_n_dofs; i++)
{
new_vector.set( new_SCALAR_indices[i], old_vector(old_SCALAR_indices[i]) );
}
}
}
new_vector.close();
// If the old vector was serial, we probably need to send our values
// to other processors
//
// FIXME: I'm not sure how to make a NumericVector do that without
// creating a temporary parallel vector to use localize! - RHS
if (old_v.type() == SERIAL)
{
AutoPtr<NumericVector<Number> > dist_v = NumericVector<Number>::build();
dist_v->init(this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
dist_v->close();
for (unsigned int i=0; i!=dist_v->size(); i++)
if (new_vector(i) != 0.0)
dist_v->set(i, new_vector(i));
dist_v->close();
dist_v->localize (new_v, this->get_dof_map().get_send_list());
new_v.close();
}
// If the old vector was parallel, we need to update it
// and free the localized copies
else if (old_v.type() == PARALLEL)
{
// We may have to set dof values that this processor doesn't
// own in certain special cases, like LAGRANGE FIRST or
// HERMITE THIRD elements on second-order meshes
for (unsigned int i=0; i!=new_v.size(); i++)
if (new_vector(i) != 0.0)
new_v.set(i, new_vector(i));
new_v.close();
}
this->get_dof_map().enforce_constraints_exactly(*this, &new_v);
#else
// AMR is disabled: simply copy the vector
new_v = old_v;
#endif // #ifdef LIBMESH_ENABLE_AMR
STOP_LOG('project_vector()', 'System');
}
Definition at line 253 of file system.C.
References System::restrict_vectors().
Referenced by EquationSystems::reinit().
{
#ifdef LIBMESH_ENABLE_AMR
// Currently project_vector handles both restriction and prolongation
this->restrict_vectors();
#endif
}
FIXME - transient sensitivities are not yet implemented. TODO - Simultaneous sensitivity calculations for multiple QoIs are not yet implemented. Analytic options for partial derivatives are not yet implemented.
Reimplemented from ExplicitSystem.
Definition at line 120 of file diff_system.C.
{
// Get ready to fill in senstivities:
sensitivities.clear();
sensitivities.resize(parameters.size(), 0);
// An introduction to the problem:
//
// Residual R(u(p),p) = 0
// partial R / partial u = J = system matrix
//
// This implies that:
// d/dp(R) = 0
// (partial R / partial p) +
// (partial R / partial u) * (partial u / partial p) = 0
// We first do an adjoint solve:
// J^T * z = (partial q / partial u)
this->adjoint_solve();
// We use the identities:
// dq/dp = (partial q / partial p) + (partial q / partial u) *
// (partial u / partial p)
// dq/dp = (partial q / partial p) + (J^T * z) *
// (partial u / partial p)
// dq/dp = (partial q / partial p) + z * J *
// (partial u / partial p)
// Leading to our final formula:
// dq/dp = (partial q / partial p) - z * (partial R / partial p)
for (unsigned int i=0; i != parameters.size(); ++i)
{
// We currently get partial derivatives via central differencing
Number delta_p = 1e-6;
// (partial q / partial p) ~= (q(p+dp)-q(p-dp))/(2*dp)
// (partial R / partial p) ~= (rhs(p+dp) - rhs(p-dp))/(2*dp)
Number old_parameter = *parameters[i];
// Number old_qoi = this->qoi;
*parameters[i] = old_parameter - delta_p;
this->assemble_qoi();
Number qoi_minus = this->qoi;
this->assembly(true, false);
this->rhs->close();
AutoPtr<NumericVector<Number> > partialR_partialp = this->rhs->clone();
*partialR_partialp *= -1;
*parameters[i] = old_parameter + delta_p;
this->assemble_qoi();
Number qoi_plus = this->qoi;
Number partialq_partialp = (qoi_plus - qoi_minus) / (2.*delta_p);
this->assembly(true, false);
this->rhs->close();
*partialR_partialp += *this->rhs;
*partialR_partialp /= (2.*delta_p);
// Don't leave the parameter changed
*parameters[i] = old_parameter;
sensitivities[i] = partialq_partialp -
partialR_partialp->dot(this->get_adjoint_solution());
}
// All parameters have been reset.
// Don't leave the qoi or system changed - principle of least
// surprise.
this->assembly(true, false);
this->rhs->close();
this->assemble_qoi();
}
Definition at line 312 of file system.C.
References System::current_local_solution, Utility::iota(), System::n_vars(), and System::solution.
{
//const std::vector<unsigned int>& send_list = _dof_map->get_send_list ();
// If this system is empty... don't do anything!
if(!this->n_vars())
return;
// Explicitly build a send_list
std::vector<unsigned int> send_list(solution->size());
Utility::iota (send_list.begin(), send_list.end(), 0);
// Check sizes
libmesh_assert (current_local_solution->size() == solution->size());
// Not true with ghosted vectors
// libmesh_assert (current_local_solution->local_size() == solution->size());
libmesh_assert (!send_list.empty());
libmesh_assert (send_list.size() <= solution->size());
// Create current_local_solution from solution. This will
// put a local copy of solution into current_local_solution.
solution->localize (*current_local_solution, send_list);
}
Definition at line 78 of file system_io.C.
References System::_additional_data_written, System::_can_add_vectors, System::add_variable(), System::add_vector(), System::clear(), Xdr::data(), FEType::family, System::get_mesh(), FEType::inf_map, MeshBase::mesh_dimension(), libMeshEnums::MONOMIAL, System::n_vars(), System::n_vectors(), libMesh::on_command_line(), FEType::order, libMesh::processor_id(), FEType::radial_family, FEType::radial_order, Xdr::reading(), and libMeshEnums::XYZ.
Referenced by EquationSystems::_read_impl().
{
// This method implements the input of a
// System object, embedded in the output of
// an EquationSystems<T_sys>. This warrants some
// documentation. The output file essentially
// consists of 5 sections:
//
// for this system
//
// 5.) The number of variables in the system (unsigned int)
//
// for each variable in the system
//
// 6.) The name of the variable (string)
//
// 7.) Combined in an FEType:
// - The approximation order(s) of the variable
// (Order Enum, cast to int/s)
// - The finite element family/ies of the variable
// (FEFamily Enum, cast to int/s)
//
// end variable loop
//
// 8.) The number of additional vectors (unsigned int),
//
// for each additional vector in the system object
//
// 9.) the name of the additional vector (string)
//
// end system
libmesh_assert (io.reading());
// Possibly clear data structures and start from scratch.
if (read_header)
this->clear ();
// Figure out if we need to read infinite element information.
// This will be true if the version string contains ' with infinite elements'
const bool read_ifem_info =
(version.rfind(' with infinite elements') < version.size()) ||
libMesh::on_command_line ('--read_ifem_systems');
{
// 5.)
// Read the number of variables in the system
unsigned int n_vars=0;
if (libMesh::processor_id() == 0) io.data (n_vars);
Parallel::broadcast(n_vars);
for (unsigned int var=0; var<n_vars; var++)
{
// 6.)
// Read the name of the var-th variable
std::string var_name;
if (libMesh::processor_id() == 0) io.data (var_name);
Parallel::broadcast(var_name);
// 7.)
// Read the approximation order(s) of the var-th variable
int order=0;
if (libMesh::processor_id() == 0) io.data (order);
Parallel::broadcast(order);
// do the same for infinite element radial_order
int rad_order=0;
if (read_ifem_info)
{
if (libMesh::processor_id() == 0) io.data(rad_order);
Parallel::broadcast(rad_order);
}
// Read the finite element type of the var-th variable
int fam=0;
if (libMesh::processor_id() == 0) io.data (fam);
Parallel::broadcast(fam);
FEType type;
type.order = static_cast<Order>(order);
type.family = static_cast<FEFamily>(fam);
// Check for incompatibilities. The shape function indexing was
// changed for the monomial and xyz finite element families to
// simplify extension to arbitrary p. The consequence is that
// old restart files will not be read correctly. This is expected
// to be an unlikely occurance, but catch it anyway.
if (read_legacy_format)
if ((type.family == MONOMIAL || type.family == XYZ) &&
((type.order > 2 && this->get_mesh().mesh_dimension() == 2) ||
(type.order > 1 && this->get_mesh().mesh_dimension() == 3)))
{
libmesh_here();
std::cout << '*****************************************************************
<< '* WARNING: reading a potentially incompatible restart file!!! *
<< '* contact libmesh-users@lists.sourceforge.net for more details *
<< '*****************************************************************'
<< std::endl;
}
// Read additional information for infinite elements
int radial_fam=0;
int i_map=0;
if (read_ifem_info)
{
if (libMesh::processor_id() == 0) io.data (radial_fam);
Parallel::broadcast(radial_fam);
if (libMesh::processor_id() == 0) io.data (i_map);
Parallel::broadcast(i_map);
}
#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
type.radial_order = static_cast<Order>(rad_order);
type.radial_family = static_cast<FEFamily>(radial_fam);
type.inf_map = static_cast<InfMapType>(i_map);
#endif
if (read_header)
this->add_variable (var_name, type);
}
}
// 8.)
// Read the number of additional vectors.
unsigned int n_vectors=0;
if (libMesh::processor_id() == 0) io.data (n_vectors);
Parallel::broadcast(n_vectors);
// If n_vectors > 0, this means that write_additional_data
// was true when this file was written. We will need to
// make use of this fact later.
if (n_vectors > 0)
this->_additional_data_written = true;
for (unsigned int vec=0; vec<n_vectors; vec++)
{
// 9.)
// Read the name of the vec-th additional vector
std::string vec_name;
if (libMesh::processor_id() == 0) io.data (vec_name);
Parallel::broadcast(vec_name);
if (read_additional_data)
{
// sanity checks
libmesh_assert(this->_can_add_vectors);
// Some systems may have added their own vectors already
// libmesh_assert(this->_vectors.count(vec_name) == 0);
this->add_vector(vec_name);
}
}
}
Definition at line 241 of file system_io.C.
References System::_additional_data_written, System::_vectors, MeshBase::active_elements_begin(), MeshBase::active_elements_end(), Xdr::data(), System::get_mesh(), DofObject::invalid_id, System::n_dofs(), System::n_vars(), MeshBase::nodes_begin(), MeshBase::nodes_end(), System::number(), libMesh::processor_id(), Xdr::reading(), System::solution, and libMesh::zero.
{
libmesh_deprecated();
// This method implements the output of the vectors
// contained in this System object, embedded in the
// output of an EquationSystems<T_sys>.
//
// 10.) The global solution vector, re-ordered to be node-major
// (More on this later.)
//
// for each additional vector in the object
//
// 11.) The global additional vector, re-ordered to be
// node-major (More on this later.)
libmesh_assert (io.reading());
// read and reordering buffers
std::vector<Number> global_vector;
std::vector<Number> reordered_vector;
// 10.)
// Read and set the solution vector
{
if (libMesh::processor_id() == 0) io.data (global_vector);
Parallel::broadcast(global_vector);
// Remember that the stored vector is node-major.
// We need to put it into whatever application-specific
// ordering we may have using the dof_map.
reordered_vector.resize(global_vector.size());
//std::cout << 'global_vector.size()=' << global_vector.size() << std::endl;
//std::cout << 'this->n_dofs()=' << this->n_dofs() << std::endl;
libmesh_assert (global_vector.size() == this->n_dofs());
unsigned int cnt=0;
const unsigned int sys = this->number();
const unsigned int n_vars = this->n_vars();
for (unsigned int var=0; var<n_vars; var++)
{
// First reorder the nodal DOF values
{
MeshBase::node_iterator
it = this->get_mesh().nodes_begin(),
end = this->get_mesh().nodes_end();
for (; it != end; ++it)
for (unsigned int index=0; index<(*it)->n_comp(sys,var); index++)
{
libmesh_assert ((*it)->dof_number(sys, var, index) !=
DofObject::invalid_id);
libmesh_assert (cnt < global_vector.size());
reordered_vector[(*it)->dof_number(sys, var, index)] =
global_vector[cnt++];
}
}
// Then reorder the element DOF values
{
MeshBase::element_iterator
it = this->get_mesh().active_elements_begin(),
end = this->get_mesh().active_elements_end();
for (; it != end; ++it)
for (unsigned int index=0; index<(*it)->n_comp(sys,var); index++)
{
libmesh_assert ((*it)->dof_number(sys, var, index) !=
DofObject::invalid_id);
libmesh_assert (cnt < global_vector.size());
reordered_vector[(*it)->dof_number(sys, var, index)] =
global_vector[cnt++];
}
}
}
*(this->solution) = reordered_vector;
}
// For each additional vector, simply go through the list.
// ONLY attempt to do this IF additional data was actually
// written to the file for this system (controlled by the
// _additional_data_written flag).
if (this->_additional_data_written)
{
std::map<std::string, NumericVector<Number>* >::iterator
pos = this->_vectors.begin();
for (; pos != this->_vectors.end(); ++pos)
{
// 11.)
// Read the values of the vec-th additional vector.
// Prior do _not_ clear, but fill with zero, since the
// additional vectors _have_ to have the same size
// as the solution vector
std::fill (global_vector.begin(), global_vector.end(), libMesh::zero);
if (libMesh::processor_id() == 0) io.data (global_vector);
Parallel::broadcast(global_vector);
// If read_additional_data==true, then we will keep this vector, otherwise
// we are going to throw it away.
if (read_additional_data)
{
// Remember that the stored vector is node-major.
// We need to put it into whatever application-specific
// ordering we may have using the dof_map.
std::fill (reordered_vector.begin(),
reordered_vector.end(),
libMesh::zero);
reordered_vector.resize(global_vector.size());
libmesh_assert (global_vector.size() == this->n_dofs());
unsigned int cnt=0;
const unsigned int sys = this->number();
const unsigned int n_vars = this->n_vars();
for (unsigned int var=0; var<n_vars; var++)
{
// First reorder the nodal DOF values
{
MeshBase::node_iterator
it = this->get_mesh().nodes_begin(),
end = this->get_mesh().nodes_end();
for (; it!=end; ++it)
for (unsigned int index=0; index<(*it)->n_comp(sys,var); index++)
{
libmesh_assert ((*it)->dof_number(sys, var, index) !=
DofObject::invalid_id);
libmesh_assert (cnt < global_vector.size());
reordered_vector[(*it)->dof_number(sys, var, index)] =
global_vector[cnt++];
}
}
// Then reorder the element DOF values
{
MeshBase::element_iterator
it = this->get_mesh().active_elements_begin(),
end = this->get_mesh().active_elements_end();
for (; it!=end; ++it)
for (unsigned int index=0; index<(*it)->n_comp(sys,var); index++)
{
libmesh_assert ((*it)->dof_number(sys, var, index) !=
DofObject::invalid_id);
libmesh_assert (cnt < global_vector.size());
reordered_vector[(*it)->dof_number(sys, var, index)] =
global_vector[cnt++];
}
}
}
// use the overloaded operator=(std::vector) to assign the values
*(pos->second) = reordered_vector;
}
}
} // end if (_additional_data_written)
}
This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.
9.) The global solution vector, re-ordered to be node-major (More on this later.)
for each additional vector in the object
10.) The global additional vector, re-ordered to be node-major (More on this later.)
Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will read XDR or ASCII files with no changes.
Definition at line 419 of file system_io.C.
References System::_vectors, Xdr::data(), System::get_mesh(), DofObject::invalid_id, Xdr::is_open(), System::n_vars(), System::number(), Xdr::reading(), and System::solution.
{
libmesh_assert (io.reading());
libmesh_assert (io.is_open());
// build the ordered nodes and element maps.
// when writing/reading parallel files we need to iterate
// over our nodes/elements in order of increasing global id().
// however, this is not guaranteed to be ordering we obtain
// by using the node_iterators/element_iterators directly.
// so build a set, sorted by id(), that provides the ordering.
// further, for memory economy build the set but then transfer
// its contents to vectors, which will be sorted.
std::vector<const DofObject*> ordered_nodes, ordered_elements;
{
std::set<const DofObject*, CompareDofObjectsByID>
ordered_nodes_set (this->get_mesh().local_nodes_begin(),
this->get_mesh().local_nodes_end());
ordered_nodes.insert(ordered_nodes.end(),
ordered_nodes_set.begin(),
ordered_nodes_set.end());
}
{
std::set<const DofObject*, CompareDofObjectsByID>
ordered_elements_set (this->get_mesh().local_elements_begin(),
this->get_mesh().local_elements_end());
ordered_elements.insert(ordered_elements.end(),
ordered_elements_set.begin(),
ordered_elements_set.end());
}
std::vector<Number> io_buffer;
// 9.)
//
// Actually read the solution components
// for the ith system to disk
io.data(io_buffer);
const unsigned int sys_num = this->number();
const unsigned int n_vars = this->n_vars();
unsigned int cnt=0;
// Loop over each variable and each node, and read out the value.
for (unsigned int var=0; var<n_vars; var++)
{
// First read the node DOF values
for (std::vector<const DofObject*>::const_iterator
it = ordered_nodes.begin(); it != ordered_nodes.end(); ++it)
for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
{
libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
DofObject::invalid_id);
libmesh_assert (cnt < io_buffer.size());
this->solution->set((*it)->dof_number(sys_num, var, comp), io_buffer[cnt++]);
}
// Then read the element DOF values
for (std::vector<const DofObject*>::const_iterator
it = ordered_elements.begin(); it != ordered_elements.end(); ++it)
for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
{
libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
DofObject::invalid_id);
libmesh_assert (cnt < io_buffer.size());
this->solution->set((*it)->dof_number(sys_num, var, comp), io_buffer[cnt++]);
}
}
// Only read additional vectors if wanted
if (read_additional_data)
{
std::map<std::string, NumericVector<Number>* >::const_iterator
pos = _vectors.begin();
for(; pos != this->_vectors.end(); ++pos)
{
cnt=0;
io_buffer.clear();
// 10.)
//
// Actually read the additional vector components
// for the ith system to disk
io.data(io_buffer);
// Loop over each variable and each node, and read out the value.
for (unsigned int var=0; var<n_vars; var++)
{
// First read the node DOF values
for (std::vector<const DofObject*>::const_iterator
it = ordered_nodes.begin(); it != ordered_nodes.end(); ++it)
for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
{
libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
DofObject::invalid_id);
libmesh_assert (cnt < io_buffer.size());
this->solution->set((*it)->dof_number(sys_num, var, comp), io_buffer[cnt++]);
}
// Then read the element DOF values
for (std::vector<const DofObject*>::const_iterator
it = ordered_elements.begin(); it != ordered_elements.end(); ++it)
for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
{
libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
DofObject::invalid_id);
libmesh_assert (cnt < io_buffer.size());
this->solution->set((*it)->dof_number(sys_num, var, comp), io_buffer[cnt++]);
}
}
}
}
}
Definition at line 559 of file system_io.C.
References System::_vectors, Xdr::comment(), libMesh::processor_id(), System::read_serialized_vector(), and System::solution.
{
// This method implements the input of the vectors
// contained in this System object, embedded in the
// output of an EquationSystems<T_sys>.
//
// 10.) The global solution vector, re-ordered to be node-major
// (More on this later.)
//
// for each additional vector in the object
//
// 11.) The global additional vector, re-ordered to be
// node-major (More on this later.)
parallel_only();
std::string comment;
// 10.)
// Read the global solution vector
{
this->read_serialized_vector(io, *this->solution);
// get the comment
if (libMesh::processor_id() == 0)
io.comment (comment);
}
// 11.)
// Only read additional vectors if wanted
if (read_additional_data)
{
std::map<std::string, NumericVector<Number>* >::const_iterator
pos = _vectors.begin();
for(; pos != this->_vectors.end(); ++pos)
{
this->read_serialized_vector(io, *pos->second);
// get the comment
if (libMesh::processor_id() == 0)
io.comment (comment);
}
}
}
Reimplemented from ImplicitSystem.
Definition at line 67 of file diff_system.C.
References ImplicitSystem::reinit(), and DifferentiableSystem::time_solver.
{
Parent::reinit();
time_solver->reinit();
}
Definition at line 217 of file system.C.
References System::_dof_map, System::_solution_projection, System::_vector_projections, System::_vectors, System::current_local_solution, libMeshEnums::GHOSTED, NumericVector< T >::init(), System::n_dofs(), System::n_local_dofs(), libMeshEnums::PARALLEL, System::project_vector(), and System::solution.
Referenced by System::prolong_vectors(), and EquationSystems::reinit().
{
#ifdef LIBMESH_ENABLE_AMR
// Restrict the _vectors on the coarsened cells
for (vectors_iterator pos = _vectors.begin(); pos != _vectors.end(); ++pos)
{
NumericVector<Number>* v = pos->second;
if (_vector_projections[pos->first])
this->project_vector (*v);
else
v->init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
}
const std::vector<unsigned int>& send_list = _dof_map->get_send_list ();
// Restrict the solution on the coarsened cells
if (_solution_projection)
this->project_vector (*solution);
#ifdef LIBMESH_ENABLE_GHOSTED
current_local_solution->init(this->n_dofs(),
this->n_local_dofs(), send_list,
false, GHOSTED);
#else
current_local_solution->init(this->n_dofs());
#endif
if (_solution_projection)
solution->localize (*current_local_solution, send_list);
#endif // LIBMESH_ENABLE_AMR
}
Users may need to reimplement this for their particular PDE depending on the boundary conditions.
Definition at line 176 of file diff_system.h.
Referenced by SteadySolver::side_residual(), EulerSolver::side_residual(), Euler2Solver::side_residual(), and EigenTimeSolver::side_residual().
{
return request_jacobian;
}
For most problems, the default implementation of 'do nothing' is correct; users with boundary conditions including time derivatives may need to reimplement this themselves.
Definition at line 294 of file diff_system.h.
Referenced by EulerSolver::side_residual(), Euler2Solver::side_residual(), and EigenTimeSolver::side_residual().
{
return request_jacobian;
}
Definition at line 210 of file diff_system.h.
Referenced by postprocess().
{}
Definition at line 228 of file diff_system.h.
Referenced by assemble_qoi().
{}
Definition at line 235 of file diff_system.h.
Referenced by assemble_qoi_derivative().
{}
Users may need to reimplement this for their particular PDE depending on the boundary conditions.
Definition at line 160 of file diff_system.h.
Referenced by SteadySolver::side_residual(), EulerSolver::side_residual(), Euler2Solver::side_residual(), and EigenTimeSolver::side_residual().
{
return request_jacobian;
}
For moving mesh systems, this also translates the mesh to the solution position.
Reimplemented from DifferentiableSystem.
Reimplemented in ContinuationSystem.
Definition at line 383 of file fem_system.C.
References mesh_position_set(), and DifferentiableSystem::solve().
{
Parent::solve();
this->mesh_position_set();
}
Reimplemented from ExplicitSystem.
Reimplemented in LinearImplicitSystem, and NonlinearImplicitSystem.
Definition at line 71 of file implicit_system.h.
{ return *this; }
Returns:
Reimplemented from ExplicitSystem.
Reimplemented in FrequencySystem, LinearImplicitSystem, NewmarkSystem, and NonlinearImplicitSystem.
Definition at line 106 of file implicit_system.h.
{ return 'Implicit'; }
Most derived systems will not have to reimplment this function; however any system which reimplements mass_residual() may have to reimplement time_evolving() to prepare data structures.
Reimplemented from DifferentiableSystem.
Definition at line 748 of file fem_system.C.
References DifferentiableSystem::time_evolving().
{
// Call the parent function
Parent::time_evolving(var);
}
Definition at line 293 of file system.C.
References System::_dof_map, System::current_local_solution, and System::solution.
Referenced by __libmesh_petsc_diff_solver_jacobian(), __libmesh_petsc_diff_solver_residual(), UniformRefinementEstimator::_estimate_error(), PetscDiffSolver::adjoint_solve(), NonlinearImplicitSystem::adjoint_solve(), NewtonSolver::adjoint_solve(), LinearImplicitSystem::adjoint_solve(), assemble_qoi(), assemble_qoi_derivative(), assembly(), Problem_Interface::computeF(), GMVIO::copy_nodal_solution(), mesh_position_get(), postprocess(), NonlinearImplicitSystem::solve(), NewtonSolver::solve(), LinearImplicitSystem::solve(), and ExplicitSystem::solve().
{
const std::vector<unsigned int>& send_list = _dof_map->get_send_list ();
// Check sizes
libmesh_assert (current_local_solution->size() == solution->size());
// More processors than elements => empty send_list
// libmesh_assert (!send_list.empty());
libmesh_assert (send_list.size() <= solution->size());
// Create current_local_solution from solution. This will
// put a local copy of solution into current_local_solution.
// Only the necessary values (specified by the send_list)
// are copied to minimize communication
solution->localize (*current_local_solution, send_list);
}
Definition at line 511 of file system.C.
References System::solution.
Referenced by ExactSolution::_compute_error(), EquationSystems::build_discontinuous_solution_vector(), EquationSystems::build_solution_vector(), and ExactErrorEstimator::estimate_error().
{
global_soln.resize (solution->size());
solution->localize (global_soln);
}
Definition at line 520 of file system.C.
References System::solution.
{
global_soln.resize (solution->size());
solution->localize_to_one (global_soln, dest_proc);
}
Definition at line 1133 of file system.C.
References System::_assemble_system, System::_equation_systems, and System::name().
Referenced by System::assemble().
{
// Call the user-provided assembly function,
// if it was provided
if (_assemble_system != NULL)
this->_assemble_system (_equation_systems, this->name());
}
Definition at line 1143 of file system.C.
References System::_constrain_system, System::_equation_systems, and System::name().
Referenced by System::init_data(), and EquationSystems::reinit().
{
// Call the user-provided constraint function,
// if it was provided
if(_constrain_system!= NULL)
this->_constrain_system(_equation_systems, this->name());
}
Definition at line 1124 of file system.C.
References System::_equation_systems, System::_init_system, and System::name().
Referenced by System::init(), and NewmarkSystem::initial_conditions().
{
// Call the user-provided intialization function,
// if it was provided
if (_init_system != NULL)
this->_init_system (_equation_systems, this->name());
}
Definition at line 1153 of file system.C.
References System::_equation_systems, System::_qoi_evaluate, and System::name().
Referenced by System::assemble_qoi().
{
// Call the user-provided quantity of interest function,
// if it was provided
if(_qoi_evaluate != NULL)
this->_qoi_evaluate(_equation_systems, this->name());
}
Definition at line 1163 of file system.C.
References System::_equation_systems, System::_qoi_evaluate_derivative, and System::name().
Referenced by System::assemble_qoi_derivative().
{
// Call the user-provided quantity of interest derivative,
// if it was provided
if(_qoi_evaluate_derivative != NULL)
this->_qoi_evaluate_derivative(_equation_systems, this->name());
}
Definition at line 1127 of file system.h.
References System::_variables.
Referenced by EquationSystems::build_solution_vector(), and System::project_vector().
{
libmesh_assert (i < _variables.size());
return _variables[i];
}
Definition at line 1137 of file system.h.
References System::_variables.
Referenced by System::add_variable(), KellyErrorEstimator::boundary_side_integration(), DiscontinuityMeasure::boundary_side_integration(), ExactErrorEstimator::estimate_error(), ExactSolution::ExactSolution(), System::get_info(), System::ProjectVector::operator()(), System::project_vector(), VTKIO::solution_to_vtk(), and System::write_header().
{
libmesh_assert (i < _variables.size());
return _variables[i].name();
}
Definition at line 710 of file system.C.
References System::_variable_numbers, and System::_variables.
Referenced by ExactSolution::_compute_error(), GMVIO::copy_nodal_solution(), ExactErrorEstimator::estimate_error(), ExactErrorEstimator::find_squared_element_error(), System::variable_type(), EnsightIO::write_scalar_ascii(), and EnsightIO::write_vector_ascii().
{
// Make sure the variable exists
std::map<std::string, unsigned short int>::const_iterator
pos = _variable_numbers.find(var);
if (pos == _variable_numbers.end())
{
std::cerr << 'ERROR: variable '
<< var
<< ' does not exist in this system!'
<< std::endl;
libmesh_error();
}
libmesh_assert (_variables[pos->second].name() == var);
return pos->second;
}
Definition at line 1157 of file system.h.
References System::_variables, and System::variable_number().
{
return _variables[this->variable_number(var)].type();
}
Definition at line 1147 of file system.h.
References System::_variables.
Referenced by System::add_variable(), EquationSystems::build_discontinuous_solution_vector(), EquationSystems::build_solution_vector(), GMVIO::copy_nodal_solution(), FEMContext::FEMContext(), System::write_header(), EnsightIO::write_scalar_ascii(), and EnsightIO::write_vector_ascii().
{
libmesh_assert (i < _variables.size());
return _variables[i].type();
}
Definition at line 621 of file system.C.
References System::vectors_begin(), and System::vectors_end().
{
const_vectors_iterator v = vectors_begin();
const_vectors_iterator v_end = vectors_end();
unsigned int num = 0;
while((num<vec_num) && (v!=v_end))
{
num++;
++v;
}
libmesh_assert(v!=v_end);
return v->first;
}
Definition at line 1187 of file system.h.
References System::_vectors.
Referenced by UniformRefinementEstimator::_estimate_error(), System::get_vector(), VTKIO::system_vectors_to_vtk(), and System::vector_name().
{
return _vectors.begin();
}
Definition at line 1193 of file system.h.
References System::_vectors.
{
return _vectors.begin();
}
Definition at line 1205 of file system.h.
References System::_vectors.
{
return _vectors.end();
}
Definition at line 1199 of file system.h.
References System::_vectors.
Referenced by UniformRefinementEstimator::_estimate_error(), System::get_vector(), VTKIO::system_vectors_to_vtk(), and System::vector_name().
{
return _vectors.end();
}
This method implements the output of a System object, embedded in the output of an EquationSystems<T_sys>. This warrants some documentation. The output of this part consists of 5 sections:
for this system
5.) The number of variables in the system (unsigned int)
for each variable in the system
6.) The name of the variable (string)
7.) Combined in an FEType:
end variable loop
8.) The number of additional vectors (unsigned int),
for each additional vector in the system object
9.) the name of the additional vector (string)
end system
Definition at line 815 of file system_io.C.
References System::_vectors, Xdr::data(), FEType::family, System::get_mesh(), FEType::inf_map, System::n_vars(), System::n_vectors(), System::name(), FEType::order, MeshBase::processor_id(), FEType::radial_family, FEType::radial_order, System::variable_name(), System::variable_type(), and Xdr::writing().
{
libmesh_assert (io.writing());
// Only write the header information
// if we are processor 0.
if (this->get_mesh().processor_id() != 0)
return;
std::string comment;
char buf[80];
// 5.)
// Write the number of variables in the system
{
// set up the comment
comment = '# No. of Variables in System '';
comment += this->name();
comment += ''';
unsigned int n_vars = this->n_vars();
io.data (n_vars, comment.c_str());
}
for (unsigned int var=0; var<this->n_vars(); var++)
{
// 6.)
// Write the name of the var-th variable
{
// set up the comment
comment = '# Name, Variable No. ';
std::sprintf(buf, '%d', var);
comment += buf;
comment += ', System '';
comment += this->name();
comment += ''';
std::string var_name = this->variable_name(var);
io.data (var_name, comment.c_str());
}
// 7.)
// Write the approximation order of the var-th variable
// in this system
{
// set up the comment
comment = '# Approximation Order, Variable '';
std::sprintf(buf, '%s', this->variable_name(var).c_str());
comment += buf;
comment += '', System '';
comment += this->name();
comment += ''';
int order = static_cast<int>(this->variable_type(var).order);
io.data (order, comment.c_str());
}
#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
// do the same for radial_order
{
comment = '# Radial Approximation Order, Variable '';
std::sprintf(buf, '%s', this->variable_name(var).c_str());
comment += buf;
comment += '', System '';
comment += this->name();
comment += ''';
int rad_order = static_cast<int>(this->variable_type(var).radial_order);
io.data (rad_order, comment.c_str());
}
#endif
// Write the Finite Element type of the var-th variable
// in this System
{
// set up the comment
comment = '# FE Family, Variable '';
std::sprintf(buf, '%s', this->variable_name(var).c_str());
comment += buf;
comment += '', System '';
comment += this->name();
comment += ''';
const FEType& type = this->variable_type(var);
int fam = static_cast<int>(type.family);
io.data (fam, comment.c_str());
#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
comment = '# Radial FE Family, Variable '';
std::sprintf(buf, '%s', this->variable_name(var).c_str());
comment += buf;
comment += '', System '';
comment += this->name();
comment += ''';
int radial_fam = static_cast<int>(type.radial_family);
io.data (radial_fam, comment.c_str());
comment = '# Infinite Mapping Type, Variable '';
std::sprintf(buf, '%s', this->variable_name(var).c_str());
comment += buf;
comment += '', System '';
comment += this->name();
comment += ''';
int i_map = static_cast<int>(type.inf_map);
io.data (i_map, comment.c_str());
#endif
}
} // end of the variable loop
// 8.)
// Write the number of additional vectors in the System.
// If write_additional_data==false, then write zero for
// the number of additional vectors.
{
{
// set up the comment
comment = '# No. of Additional Vectors, System '';
comment += this->name();
comment += ''';
unsigned int n_vectors = write_additional_data ? this->n_vectors () : 0;
io.data (n_vectors, comment.c_str());
}
if (write_additional_data)
{
std::map<std::string, NumericVector<Number>* >::const_iterator
vec_pos = this->_vectors.begin();
unsigned int cnt=0;
for (; vec_pos != this->_vectors.end(); ++vec_pos)
{
// 9.)
// write the name of the cnt-th additional vector
comment = '# Name of ';
std::sprintf(buf, '%d', cnt++);
comment += buf;
comment += 'th vector';
std::string vec_name = vec_pos->first;
io.data (vec_name, comment.c_str());
}
}
}
}
This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.
9.) The global solution vector, re-ordered to be node-major (More on this later.)
for each additional vector in the object
10.) The global additional vector, re-ordered to be node-major (More on this later.)
Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will read XDR or ASCII files with no changes.
This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.
9.) The global solution vector, re-ordered to be node-major (More on this later.)
for each additional vector in the object
10.) The global additional vector, re-ordered to be node-major (More on this later.)
Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will read XDR or ASCII files with no changes.
Definition at line 1213 of file system_io.C.
References System::_vectors, Xdr::data(), System::get_mesh(), DofObject::invalid_id, System::n_vars(), System::name(), System::number(), System::solution, and Xdr::writing().
{
std::string comment;
libmesh_assert (io.writing());
std::vector<Number> io_buffer; io_buffer.reserve(this->solution->local_size());
// build the ordered nodes and element maps.
// when writing/reading parallel files we need to iterate
// over our nodes/elements in order of increasing global id().
// however, this is not guaranteed to be ordering we obtain
// by using the node_iterators/element_iterators directly.
// so build a set, sorted by id(), that provides the ordering.
// further, for memory economy build the set but then transfer
// its contents to vectors, which will be sorted.
std::vector<const DofObject*> ordered_nodes, ordered_elements;
{
std::set<const DofObject*, CompareDofObjectsByID>
ordered_nodes_set (this->get_mesh().local_nodes_begin(),
this->get_mesh().local_nodes_end());
ordered_nodes.insert(ordered_nodes.end(),
ordered_nodes_set.begin(),
ordered_nodes_set.end());
}
{
std::set<const DofObject*, CompareDofObjectsByID>
ordered_elements_set (this->get_mesh().local_elements_begin(),
this->get_mesh().local_elements_end());
ordered_elements.insert(ordered_elements.end(),
ordered_elements_set.begin(),
ordered_elements_set.end());
}
const unsigned int sys_num = this->number();
const unsigned int n_vars = this->n_vars();
// Loop over each variable and each node, and write out the value.
for (unsigned int var=0; var<n_vars; var++)
{
// First write the node DOF values
for (std::vector<const DofObject*>::const_iterator
it = ordered_nodes.begin(); it != ordered_nodes.end(); ++it)
for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
{
//std::cout << '(*it)->id()=' << (*it)->id() << std::endl;
libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
DofObject::invalid_id);
io_buffer.push_back((*this->solution)((*it)->dof_number(sys_num, var, comp)));
}
// Then write the element DOF values
for (std::vector<const DofObject*>::const_iterator
it = ordered_elements.begin(); it != ordered_elements.end(); ++it)
for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
{
libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
DofObject::invalid_id);
io_buffer.push_back((*this->solution)((*it)->dof_number(sys_num, var, comp)));
}
}
// 9.)
//
// Actually write the reordered solution vector
// for the ith system to disk
// set up the comment
{
comment = '# System '';
comment += this->name();
comment += '' Solution Vector';
}
io.data (io_buffer, comment.c_str());
// Only write additional vectors if wanted
if (write_additional_data)
{
std::map<std::string, NumericVector<Number>* >::const_iterator
pos = _vectors.begin();
for(; pos != this->_vectors.end(); ++pos)
{
io_buffer.clear(); io_buffer.reserve( pos->second->local_size());
// Loop over each variable and each node, and write out the value.
for (unsigned int var=0; var<n_vars; var++)
{
// First write the node DOF values
for (std::vector<const DofObject*>::const_iterator
it = ordered_nodes.begin(); it != ordered_nodes.end(); ++it)
for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
{
libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
DofObject::invalid_id);
io_buffer.push_back((*pos->second)((*it)->dof_number(sys_num, var, comp)));
}
// Then write the element DOF values
for (std::vector<const DofObject*>::const_iterator
it = ordered_elements.begin(); it != ordered_elements.end(); ++it)
for (unsigned int comp=0; comp<(*it)->n_comp(sys_num, var); comp++)
{
libmesh_assert ((*it)->dof_number(sys_num, var, comp) !=
DofObject::invalid_id);
io_buffer.push_back((*pos->second)((*it)->dof_number(sys_num, var, comp)));
}
}
// 10.)
//
// Actually write the reordered additional vector
// for this system to disk
// set up the comment
{
comment = '# System '';
comment += this->name();
comment += '' Additional Vector '';
comment += pos->first;
comment += ''';
}
io.data (io_buffer, comment.c_str());
}
}
}
This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.
9.) The global solution vector, re-ordered to be node-major (More on this later.)
for each additional vector in the object
10.) The global additional vector, re-ordered to be node-major (More on this later.)
Definition at line 1370 of file system_io.C.
References System::_vectors, Xdr::comment(), System::name(), libMesh::processor_id(), System::solution, and System::write_serialized_vector().
{
parallel_only();
std::string comment;
this->write_serialized_vector(io, *this->solution);
// set up the comment
if (libMesh::processor_id() == 0)
{
comment = '# System '';
comment += this->name();
comment += '' Solution Vector';
io.comment (comment);
}
// Only write additional vectors if wanted
if (write_additional_data)
{
std::map<std::string, NumericVector<Number>* >::const_iterator
pos = _vectors.begin();
for(; pos != this->_vectors.end(); ++pos)
{
this->write_serialized_vector(io, *pos->second);
// set up the comment
if (libMesh::processor_id() == 0)
{
comment = '# System '';
comment += this->name();
comment += '' Additional Vector '';
comment += pos->first;
comment += ''';
io.comment (comment);
}
}
}
}
Definition at line 763 of file system.C.
References MeshBase::active_local_elements_begin(), MeshBase::active_local_elements_end(), DofObject::dof_number(), System::get_mesh(), MeshBase::local_nodes_begin(), MeshBase::local_nodes_end(), DofObject::n_comp(), System::n_vars(), System::number(), and NumericVector< T >::set().
{
/* Make sure the call makes sense. */
libmesh_assert(var_num<this->n_vars());
/* Get a reference to the mesh. */
const MeshBase& mesh = this->get_mesh();
/* Check which system we are. */
const unsigned int sys_num = this->number();
/* Loop over nodes. */
{
MeshBase::const_node_iterator it = mesh.local_nodes_begin();
const MeshBase::const_node_iterator end_it = mesh.local_nodes_end();
for ( ; it != end_it; ++it)
{
const Node* node = *it;
unsigned int n_comp = node->n_comp(sys_num,var_num);
for(unsigned int i=0; i<n_comp; i++)
{
const unsigned int index = node->dof_number(sys_num,var_num,i);
v.set(index,0.0);
}
}
}
/* Loop over elements. */
{
MeshBase::const_element_iterator it = mesh.active_local_elements_begin();
const MeshBase::const_element_iterator end_it = mesh.active_local_elements_end();
for ( ; it != end_it; ++it)
{
const Elem* elem = *it;
unsigned int n_comp = elem->n_comp(sys_num,var_num);
for(unsigned int i=0; i<n_comp; i++)
{
const unsigned int index = elem->dof_number(sys_num,var_num,i);
v.set(index,0.0);
}
}
}
}
Definition at line 110 of file reference_counter.h.
Referenced by ReferenceCounter::get_info(), ReferenceCounter::increment_constructor_count(), and ReferenceCounter::increment_destructor_count().
Definition at line 307 of file fem_system.h.
Referenced by eulerian_residual(), mesh_position_get(), mesh_position_set(), mesh_x_position(), mesh_y_position(), mesh_z_position(), and numerical_jacobian().
Definition at line 307 of file fem_system.h.
Referenced by eulerian_residual(), mesh_position_get(), mesh_x_position(), and numerical_jacobian().
Definition at line 307 of file fem_system.h.
Referenced by eulerian_residual(), mesh_position_get(), mesh_y_position(), and numerical_jacobian().
Definition at line 307 of file fem_system.h.
Referenced by eulerian_residual(), mesh_position_get(), mesh_z_position(), and numerical_jacobian().
Definition at line 123 of file reference_counter.h.
Definition at line 118 of file reference_counter.h.
Referenced by ReferenceCounter::n_objects(), ReferenceCounter::ReferenceCounter(), and ReferenceCounter::~ReferenceCounter().
Definition at line 424 of file diff_system.h.
Referenced by DifferentiableSystem::clear(), eulerian_residual(), init_context(), DifferentiableSystem::init_data(), mass_residual(), and DifferentiableSystem::time_evolving().
You will only want to set this to false if you need direct control over when the system is assembled, and are willing to track the state of its assembly yourself. An example of such a case is an implicit system with multiple right hand sides. In this instance, a single assembly would likely be followed with multiple calls to solve.
The frequency system and Newmark system have their own versions of this flag, called _finished_assemble, which might be able to be replaced with this more general concept.
Definition at line 713 of file system.h.
Referenced by NonlinearImplicitSystem::adjoint_solve(), LinearImplicitSystem::adjoint_solve(), LinearImplicitSystem::solve(), and EigenSystem::solve().
Definition at line 199 of file diff_system.h.
Referenced by assemble_qoi(), and assemble_qoi_derivative().
Definition at line 147 of file diff_system.h.
Referenced by assemble_qoi(), assemble_qoi_derivative(), assembly(), and postprocess().
Definition at line 740 of file system.h.
Referenced by UniformRefinementEstimator::_estimate_error(), NonlinearImplicitSystem::adjoint_solve(), System::clear(), Problem_Interface::computeF(), System::current_solution(), ExactErrorEstimator::estimate_error(), System::init_data(), System::project_solution(), System::re_update(), System::reinit(), System::restrict_vectors(), and System::update().
Definition at line 365 of file diff_system.h.
Referenced by UnsteadySolver::advance_timestep(), EulerSolver::element_residual(), Euler2Solver::element_residual(), eulerian_residual(), EulerSolver::side_residual(), Euler2Solver::side_residual(), UnsteadySolver::solve(), and TwostepTimeSolver::solve().
Definition at line 247 of file fem_system.h.
Referenced by FEMContext::FEMContext().
Definition at line 236 of file fem_system.h.
Definition at line 156 of file implicit_system.h.
Referenced by __libmesh_petsc_diff_solver_jacobian(), ImplicitSystem::add_system_matrix(), PetscDiffSolver::adjoint_solve(), NonlinearImplicitSystem::adjoint_solve(), NewtonSolver::adjoint_solve(), LinearImplicitSystem::adjoint_solve(), ImplicitSystem::assemble(), assembly(), ImplicitSystem::clear(), NewmarkSystem::compute_matrix(), ContinuationSystem::continuation_solve(), ImplicitSystem::init_matrices(), PetscDiffSolver::solve(), NonlinearImplicitSystem::solve(), NewtonSolver::solve(), LinearImplicitSystem::solve(), FrequencySystem::solve(), EigenTimeSolver::solve(), and ContinuationSystem::solve_tangent().
Definition at line 254 of file fem_system.h.
Referenced by numerical_jacobian().
Definition at line 192 of file diff_system.h.
Definition at line 402 of file diff_system.h.
Definition at line 392 of file diff_system.h.
Definition at line 397 of file diff_system.h.
Definition at line 382 of file diff_system.h.
Definition at line 387 of file diff_system.h.
Definition at line 371 of file diff_system.h.
Definition at line 377 of file diff_system.h.
Definition at line 745 of file system.h.
Referenced by assemble_qoi(), and ExplicitSystem::assemble_qoi().
Definition at line 132 of file explicit_system.h.
Referenced by __libmesh_petsc_diff_solver_residual(), ExplicitSystem::add_system_rhs(), PetscDiffSolver::adjoint_solve(), NonlinearImplicitSystem::adjoint_solve(), NewtonSolver::adjoint_solve(), LinearImplicitSystem::adjoint_solve(), ImplicitSystem::assemble(), ExplicitSystem::assemble_qoi(), assemble_qoi_derivative(), ExplicitSystem::assemble_qoi_derivative(), assembly(), ExplicitSystem::clear(), ContinuationSystem::continuation_solve(), NewtonSolver::line_search(), PetscDiffSolver::solve(), NonlinearImplicitSystem::solve(), NewtonSolver::solve(), LinearImplicitSystem::solve(), FrequencySystem::solve(), ContinuationSystem::solve_tangent(), and NewmarkSystem::update_rhs().
Definition at line 728 of file system.h.
Referenced by __libmesh_petsc_diff_solver_jacobian(), __libmesh_petsc_diff_solver_residual(), ExactSolution::_compute_error(), UniformRefinementEstimator::_estimate_error(), PetscDiffSolver::adjoint_solve(), UnsteadySolver::advance_timestep(), AdaptiveTimeSolver::advance_timestep(), ContinuationSystem::apply_predictor(), assembly(), System::clear(), System::compare(), Problem_Interface::computeF(), ContinuationSystem::continuation_solve(), GMVIO::copy_nodal_solution(), UnsteadySolver::du(), DofMap::enforce_constraints_exactly(), PatchRecoveryErrorEstimator::estimate_error(), JumpErrorEstimator::estimate_error(), ExactErrorEstimator::estimate_error(), EigenSystem::get_eigenpair(), System::init_data(), ContinuationSystem::initialize_tangent(), DofMap::max_constraint_error(), mesh_position_get(), ErrorVector::plot_error(), System::project_solution(), System::re_update(), System::read_legacy_data(), System::read_parallel_data(), System::read_serialized_data(), System::reinit(), System::restrict_vectors(), ContinuationSystem::save_current_solution(), VTKIO::solution_to_vtk(), TwostepTimeSolver::solve(), PetscDiffSolver::solve(), NonlinearImplicitSystem::solve(), NewtonSolver::solve(), LinearImplicitSystem::solve(), FrequencySystem::solve(), ContinuationSystem::solve_tangent(), System::update(), System::update_global_solution(), ContinuationSystem::update_solution(), NewmarkSystem::update_u_v_a(), System::write_parallel_data(), and System::write_serialized_data().
Definition at line 359 of file diff_system.h.
Referenced by UnsteadySolver::advance_timestep(), AdaptiveTimeSolver::advance_timestep(), and TwostepTimeSolver::solve().
Definition at line 351 of file diff_system.h.
Referenced by DifferentiableSystem::adjoint_solve(), assembly(), ContinuationSystem::continuation_solve(), eulerian_residual(), DifferentiableSystem::init_data(), DifferentiableSystem::reinit(), DifferentiableSystem::solve(), and ContinuationSystem::solve_tangent().
Definition at line 411 of file diff_system.h.
Referenced by DifferentiableSystem::clear(), DiffContext::DiffContext(), SteadySolver::element_residual(), EulerSolver::element_residual(), Euler2Solver::element_residual(), FEMContext::reinit(), SteadySolver::side_residual(), EulerSolver::side_residual(), and Euler2Solver::side_residual().
If verify_analytic_jacobian is equal to the positive value tol, then any time a full analytic element jacobian can be calculated it will be tested against a numerical jacobian on the same element, and the program will abort if the relative error (in matrix l1 norms) exceeds tol.
Definition at line 269 of file fem_system.h.
Referenced by assembly().
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