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/*
Copyright (C) 2011 - 2017 by the authors of the ASPECT code.
This file is part of ASPECT.
ASPECT is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2, or (at your option)
any later version.
ASPECT is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with ASPECT; see the file LICENSE. If not see
<http://www.gnu.org/licenses/>.
*/
#include <aspect/simulator.h>
#include <aspect/global.h>
#include <aspect/assembly.h>
#include <aspect/utilities.h>
#include <aspect/melt.h>
#include <aspect/free_surface.h>
#include <aspect/geometry_model/initial_topography_model/zero_topography.h>
#include <deal.II/base/index_set.h>
#include <deal.II/base/conditional_ostream.h>
#include <deal.II/base/quadrature_lib.h>
#include <deal.II/base/signaling_nan.h>
#include <deal.II/lac/constraint_matrix.h>
#include <deal.II/lac/block_sparsity_pattern.h>
#include <deal.II/lac/sparsity_tools.h>
#include <deal.II/grid/grid_tools.h>
#include <deal.II/dofs/dof_renumbering.h>
#include <deal.II/dofs/dof_accessor.h>
#include <deal.II/dofs/dof_tools.h>
#include <deal.II/fe/fe_q.h>
#include <deal.II/fe/fe_dgq.h>
#include <deal.II/fe/fe_dgp.h>
#include <deal.II/fe/fe_values.h>
#include <deal.II/fe/mapping_q.h>
#include <deal.II/fe/mapping_cartesian.h>
#include <deal.II/numerics/error_estimator.h>
#include <deal.II/numerics/derivative_approximation.h>
#include <deal.II/numerics/vector_tools.h>
#include <deal.II/distributed/solution_transfer.h>
#include <deal.II/distributed/grid_refinement.h>
#include <fstream>
#include <iostream>
#include <iomanip>
#include <locale>
#include <string>
namespace aspect
{
namespace
{
/**
* Return whether t is an element of the given container object.
*/
template <typename Container>
bool is_element (const typename Container::value_type &t,
const Container &container)
{
for (typename Container::const_iterator p = container.begin();
p != container.end();
++p)
if (*p == t)
return true;
return false;
}
/**
* Helper function to construct the final std::vector of FEVariable before
* it is used to construct the Introspection object. Create the default
* setup based on parameters followed by a signal to allow modifications.
*/
template <int dim>
std::vector<VariableDeclaration<dim> > construct_variables(const Parameters<dim> ¶meters,
SimulatorSignals<dim> &signals,
std_cxx11::shared_ptr<MeltHandler<dim> > &melt_handler)
{
std::vector<VariableDeclaration<dim> > variables
= construct_default_variables (parameters);
if (melt_handler)
melt_handler->edit_finite_element_variables (parameters, variables);
signals.edit_finite_element_variables(variables);
return variables;
}
/**
* Helper function to construct mapping for the model.
* The mapping is given by a degree four MappingQ for the case
* of a curved mesh, and a cartesian mapping for a rectangular mesh that is
* not deformed. Use a MappingQ1 if the mesh is deformed.
* If a free surface is enabled, each mapping is later swapped out for a
* MappingQ1Eulerian, which allows for mesh deformation during the
* computation.
*/
template <int dim>
Mapping<dim> *construct_mapping(const GeometryModel::Interface<dim> &geometry_model,
const InitialTopographyModel::Interface<dim> &initial_topography_model)
{
if (geometry_model.has_curved_elements())
return new MappingQ<dim>(4, true);
if (dynamic_cast<const InitialTopographyModel::ZeroTopography<dim>*>(&initial_topography_model) != 0)
return new MappingCartesian<dim>();
return new MappingQ1<dim>();
}
}
/**
* Constructor of the IntermediaryConstructorAction class. Since the
* class has no members, there is nothing to initialize -- all we
* need to do is execute the 'action' argument.
*/
template <int dim>
Simulator<dim>::IntermediaryConstructorAction::
IntermediaryConstructorAction (std_cxx11::function<void ()> action)
{
action();
}
/**
* Constructor. Initialize all member variables.
**/
template <int dim>
Simulator<dim>::Simulator (const MPI_Comm mpi_communicator_,
ParameterHandler &prm)
:
assemblers (new internal::Assembly::AssemblerLists<dim>()),
parameters (prm, mpi_communicator_),
melt_handler (parameters.include_melt_transport ? new MeltHandler<dim> (prm) : NULL),
post_signal_creation(
std_cxx11::bind (&internals::SimulatorSignals::call_connector_functions<dim>,
std_cxx11::ref(signals))),
introspection (construct_variables<dim>(parameters, signals, melt_handler), parameters),
mpi_communicator (Utilities::MPI::duplicate_communicator (mpi_communicator_)),
iostream_tee_device(std::cout, log_file_stream),
iostream_tee_stream(iostream_tee_device),
pcout (iostream_tee_stream,
(Utilities::MPI::
this_mpi_process(mpi_communicator)
== 0)),
computing_timer (mpi_communicator,
pcout,
TimerOutput::never,
TimerOutput::wall_times),
initial_topography_model(InitialTopographyModel::create_initial_topography_model<dim>(prm)),
geometry_model (GeometryModel::create_geometry_model<dim>(prm)),
// make sure the parameters object gets a chance to
// parse those parameters that depend on symbolic names
// for boundary components
post_geometry_model_creation_action (std_cxx11::bind (&Parameters<dim>::parse_geometry_dependent_parameters,
std_cxx11::ref(parameters),
std_cxx11::ref(prm),
std_cxx11::cref(*geometry_model))),
material_model (MaterialModel::create_material_model<dim>(prm)),
gravity_model (GravityModel::create_gravity_model<dim>(prm)),
// create a boundary composition model, but only if we actually need
// it. otherwise, allow the user to simply specify nothing at all
boundary_composition (parameters.fixed_composition_boundary_indicators.empty()
?
0
:
BoundaryComposition::create_boundary_composition<dim>(prm)),
prescribed_stokes_solution (PrescribedStokesSolution::create_prescribed_stokes_solution<dim>(prm)),
adiabatic_conditions (AdiabaticConditions::create_adiabatic_conditions<dim>(prm)),
time (numbers::signaling_nan<double>()),
time_step (0),
old_time_step (0),
timestep_number (0),
triangulation (mpi_communicator,
typename Triangulation<dim>::MeshSmoothing
(Triangulation<dim>::smoothing_on_refinement |
Triangulation<dim>::smoothing_on_coarsening),
parallel::distributed::Triangulation<dim>::mesh_reconstruction_after_repartitioning),
mapping(construct_mapping<dim>(*geometry_model,*initial_topography_model)),
// define the finite element
finite_element(introspection.get_fes(), introspection.get_multiplicities()),
dof_handler (triangulation),
last_pressure_normalization_adjustment (numbers::signaling_nan<double>()),
rebuild_stokes_matrix (true),
assemble_newton_stokes_matrix (true),
assemble_newton_stokes_system (false),
rebuild_stokes_preconditioner (true)
{
if (Utilities::MPI::this_mpi_process(mpi_communicator) == 0)
{
// only open the log file on processor 0, the other processors won't be
// writing into the stream anyway
log_file_stream.open((parameters.output_directory + "log.txt").c_str(),
parameters.resume_computation ? std::ios_base::app : std::ios_base::out);
// we already printed the header to the screen, so here we just dump it
// into the log file.
print_aspect_header(log_file_stream);
}
computing_timer.enter_section("Initialization");
// first do some error checking for the parameters we got
{
// make sure velocity and traction boundary indicators don't appear in multiple lists
std::set<types::boundary_id> boundary_indicator_lists[6]
= { parameters.zero_velocity_boundary_indicators,
parameters.tangential_velocity_boundary_indicators,
parameters.free_surface_boundary_indicators,
std::set<types::boundary_id>() // to be prescribed velocity and traction boundary indicators
};
// sets of the boundary indicators only (no selectors and values)
std::set<types::boundary_id> velocity_bi;
std::set<types::boundary_id> traction_bi;
for (std::map<types::boundary_id,std::pair<std::string, std::string> >::const_iterator
p = parameters.prescribed_velocity_boundary_indicators.begin();
p != parameters.prescribed_velocity_boundary_indicators.end();
++p)
velocity_bi.insert(p->first);
for (std::map<types::boundary_id,std::pair<std::string, std::string> >::const_iterator
r = parameters.prescribed_traction_boundary_indicators.begin();
r != parameters.prescribed_traction_boundary_indicators.end();
++r)
traction_bi.insert(r->first);
// are there any indicators that occur in both the prescribed velocity and traction list?
std::set<types::boundary_id> intersection;
std::set_intersection (velocity_bi.begin(),
velocity_bi.end(),
traction_bi.begin(),
traction_bi.end(),
std::inserter(intersection, intersection.end()));
// if so, do they have different selectors?
if (!intersection.empty())
{
for (std::set<types::boundary_id>::const_iterator
it = intersection.begin();
it != intersection.end();
++it)
{
std::set<char> velocity_selector;
std::set<char> traction_selector;
for (std::string::const_iterator
it_selector = parameters.prescribed_velocity_boundary_indicators[*it].first.begin();
it_selector != parameters.prescribed_velocity_boundary_indicators[*it].first.end();
++it_selector)
velocity_selector.insert(*it_selector);
for (std::string::const_iterator
it_selector = parameters.prescribed_traction_boundary_indicators[*it].first.begin();
it_selector != parameters.prescribed_traction_boundary_indicators[*it].first.end();
++it_selector)
traction_selector.insert(*it_selector);
// if there are no selectors specified, throw exception
AssertThrow(!velocity_selector.empty() || !traction_selector.empty(),
ExcMessage ("Boundary indicator <"
+
Utilities::int_to_string(*it)
+
"> with symbolic name <"
+
geometry_model->translate_id_to_symbol_name (*it)
+
"> is listed as having both "
"velocity and traction boundary conditions in the input file."));
std::set<char> intersection_selector;
std::set_intersection (velocity_selector.begin(),
velocity_selector.end(),
traction_selector.begin(),
traction_selector.end(),
std::inserter(intersection_selector, intersection_selector.end()));
// if the same selectors are specified, throw exception
AssertThrow(intersection_selector.empty(),
ExcMessage ("Selectors of boundary indicator <"
+
Utilities::int_to_string(*it)
+
"> with symbolic name <"
+
geometry_model->translate_id_to_symbol_name (*it)
+
"> are listed as having both "
"velocity and traction boundary conditions in the input file."));
}
}
// remove correct boundary indicators that occur in both the velocity and the traction set
// but have different selectors
std::set<types::boundary_id> union_set;
std::set_union (velocity_bi.begin(),
velocity_bi.end(),
traction_bi.begin(),
traction_bi.end(),
std::inserter(union_set, union_set.end()));
// assign the prescribed boundary indicator list to the boundary_indicator_lists
boundary_indicator_lists[3] = union_set;
// for each combination of boundary indicator lists, make sure that the
// intersection is empty
for (unsigned int i=0; i<sizeof(boundary_indicator_lists)/sizeof(boundary_indicator_lists[0]); ++i)
for (unsigned int j=i+1; j<sizeof(boundary_indicator_lists)/sizeof(boundary_indicator_lists[0]); ++j)
{
std::set<types::boundary_id> intersection;
std::set_intersection (boundary_indicator_lists[i].begin(),
boundary_indicator_lists[i].end(),
boundary_indicator_lists[j].begin(),
boundary_indicator_lists[j].end(),
std::inserter(intersection, intersection.end()));
// if the same indicators are specified for different boundary conditions, throw exception
AssertThrow (intersection.empty(),
ExcMessage ("Boundary indicator <"
+
Utilities::int_to_string(*intersection.begin())
+
"> with symbolic name <"
+
geometry_model->translate_id_to_symbol_name (*intersection.begin())
+
"> is listed as having more "
"than one type of velocity or traction boundary condition in the input file."));
}
// Check that the periodic boundaries do not have other boundary conditions set
typedef std::set< std::pair< std::pair< types::boundary_id, types::boundary_id>, unsigned int> >
periodic_boundary_set;
periodic_boundary_set pbs = geometry_model->get_periodic_boundary_pairs();
for (periodic_boundary_set::iterator p = pbs.begin(); p != pbs.end(); ++p)
{
// Throw error if we are trying to use the same boundary for more than one boundary condition
AssertThrow( is_element( (*p).first.first, parameters.fixed_temperature_boundary_indicators ) == false &&
is_element( (*p).first.second, parameters.fixed_temperature_boundary_indicators ) == false &&
is_element( (*p).first.first, parameters.fixed_composition_boundary_indicators ) == false &&
is_element( (*p).first.second, parameters.fixed_composition_boundary_indicators ) == false &&
is_element( (*p).first.first, boundary_indicator_lists[0] ) == false && // zero velocity
is_element( (*p).first.second, boundary_indicator_lists[0] ) == false && // zero velocity
is_element( (*p).first.first, boundary_indicator_lists[1] ) == false && // tangential velocity
is_element( (*p).first.second, boundary_indicator_lists[1] ) == false && // tangential velocity
is_element( (*p).first.first, boundary_indicator_lists[2] ) == false && // free surface
is_element( (*p).first.second, boundary_indicator_lists[2] ) == false && // free surface
is_element( (*p).first.first, boundary_indicator_lists[3] ) == false && // prescribed traction or velocity
is_element( (*p).first.second, boundary_indicator_lists[3] ) == false, // prescribed traction or velocity
ExcMessage("Periodic boundaries must not have boundary conditions set."));
}
const std::set<types::boundary_id> all_boundary_indicators
= geometry_model->get_used_boundary_indicators();
if (parameters.nonlinear_solver!=NonlinearSolver::Advection_only)
{
// next make sure that all listed indicators are actually used by
// this geometry
for (unsigned int i=0; i<sizeof(boundary_indicator_lists)/sizeof(boundary_indicator_lists[0]); ++i)
for (typename std::set<types::boundary_id>::const_iterator
p = boundary_indicator_lists[i].begin();
p != boundary_indicator_lists[i].end(); ++p)
AssertThrow (all_boundary_indicators.find (*p)
!= all_boundary_indicators.end(),
ExcMessage ("One of the boundary indicators listed in the input file "
"is not used by the geometry model."));
}
else
{
// next make sure that there are no listed indicators
for (unsigned int i = 0; i<sizeof(boundary_indicator_lists)/sizeof(boundary_indicator_lists[0]); ++i)
AssertThrow (boundary_indicator_lists[i].empty(),
ExcMessage ("With solver type Advection only, one cannot set boundary conditions for velocity."));
}
// now do the same for the fixed temperature indicators and the
// compositional indicators
for (typename std::set<types::boundary_id>::const_iterator
p = parameters.fixed_temperature_boundary_indicators.begin();
p != parameters.fixed_temperature_boundary_indicators.end(); ++p)
AssertThrow (all_boundary_indicators.find (*p)
!= all_boundary_indicators.end(),
ExcMessage ("One of the fixed boundary temperature indicators listed in the input file "
"is not used by the geometry model."));
for (typename std::set<types::boundary_id>::const_iterator
p = parameters.fixed_composition_boundary_indicators.begin();
p != parameters.fixed_composition_boundary_indicators.end(); ++p)
AssertThrow (all_boundary_indicators.find (*p)
!= all_boundary_indicators.end(),
ExcMessage ("One of the fixed boundary composition indicators listed in the input file "
"is not used by the geometry model."));
}
// if any plugin wants access to the Simulator by deriving from SimulatorAccess, initialize it and
// call the initialize() functions immediately after.
//
// up front, we can not know whether a plugin derives from
// SimulatorAccess. all we have is a pointer to the base class of
// each plugin type (the 'Interface' class in the namespace
// corresponding to each plugin type), but this base class is not
// derived from SimulatorAccess. in order to find out whether a
// concrete plugin derives from this base (interface) class AND
// the SimulatorAccess class via multiple inheritance, we need to
// do a sideways dynamic_cast to this putative sibling of the
// interface class, and investigate if the dynamic_cast
// succeeds. if it succeeds, the dynamic_cast returns a non-NULL
// result, and we can test this in an if-statement. there is a nice
// idiom whereby we can write
// if (SiblingClass *ptr = dynamic_cast<SiblingClass*>(ptr_to_base))
// ptr->do_something()
// where we declare a variable *inside* the 'if' condition, and only
// enter the code block guarded by the 'if' in case the so-declared
// variable evaluates to something non-zero, which here means that
// the dynamic_cast succeeded and returned the address of the sibling
// object.
//
// we also need to let all models parse their parameters. this is done *after* setting
// up their SimulatorAccess base class so that they can query, for example, the
// geometry model's description of symbolic names for boundary parts. note that
// the geometry model is the only model whose run time parameters are already read
// at the time it is created
if (SimulatorAccess<dim> *sim = dynamic_cast<SimulatorAccess<dim>*>(initial_topography_model.get()))
sim->initialize_simulator (*this);
initial_topography_model->initialize ();
if (SimulatorAccess<dim> *sim = dynamic_cast<SimulatorAccess<dim>*>(geometry_model.get()))
sim->initialize_simulator (*this);
geometry_model->initialize ();
if (SimulatorAccess<dim> *sim = dynamic_cast<SimulatorAccess<dim>*>(material_model.get()))
sim->initialize_simulator (*this);
material_model->parse_parameters (prm);
material_model->initialize ();
heating_model_manager.initialize_simulator (*this);
heating_model_manager.parse_parameters (prm);
if (SimulatorAccess<dim> *sim = dynamic_cast<SimulatorAccess<dim>*>(gravity_model.get()))
sim->initialize_simulator (*this);
gravity_model->parse_parameters (prm);
gravity_model->initialize ();
// Create the initial condition plugins
initial_temperature_manager.initialize_simulator(*this);
initial_temperature_manager.parse_parameters (prm);
// Create the initial composition plugins
initial_composition_manager.initialize_simulator(*this);
initial_composition_manager.parse_parameters (prm);
// create a boundary temperature manager, but only if we actually need
// it. otherwise, allow the user to simply specify nothing at all
if (!parameters.fixed_temperature_boundary_indicators.empty())
{
boundary_temperature_manager.initialize_simulator (*this);
boundary_temperature_manager.parse_parameters (prm);
}
if (boundary_composition.get())
{
if (SimulatorAccess<dim> *sim = dynamic_cast<SimulatorAccess<dim>*>(boundary_composition.get()))
sim->initialize_simulator (*this);
boundary_composition->parse_parameters (prm);
boundary_composition->initialize ();
}
// Make sure we only have a prescribed Stokes plugin if needed
if (parameters.nonlinear_solver==NonlinearSolver::Advection_only)
{
AssertThrow(prescribed_stokes_solution.get()!=NULL,
ExcMessage("For 'Advection only' solver you need to provide a Stokes plugin")
);
}
else
{
AssertThrow(prescribed_stokes_solution.get()==NULL,
ExcMessage("The prescribed stokes plugin you selected only works with solver type 'Advection only' ")
);
}
if (SimulatorAccess<dim> *sim = dynamic_cast<SimulatorAccess<dim>*>(prescribed_stokes_solution.get()))
sim->initialize_simulator (*this);
if (prescribed_stokes_solution.get())
{
prescribed_stokes_solution->parse_parameters (prm);
prescribed_stokes_solution->initialize ();
}
if (SimulatorAccess<dim> *sim = dynamic_cast<SimulatorAccess<dim>*>(adiabatic_conditions.get()))
sim->initialize_simulator (*this);
adiabatic_conditions->parse_parameters (prm);
adiabatic_conditions->initialize ();
// Initialize the free surface handler
if (parameters.free_surface_enabled)
{
// It should be possible to make the free surface work with any of a number of nonlinear
// schemes, but I do not see a way to do it in generality --IR
AssertThrow( parameters.nonlinear_solver == NonlinearSolver::IMPES ||
parameters.nonlinear_solver == NonlinearSolver::iterated_Stokes,
ExcMessage("The free surface scheme is only implemented for the IMPES or Iterated Stokes solver") );
// Pressure normalization doesn't really make sense with a free surface, and if we do
// use it, we can run into problems with geometry_model->depth().
AssertThrow ( parameters.pressure_normalization == "no",
ExcMessage("The free surface scheme can only be used with no pressure normalization") );
// Allocate the FreeSurfaceHandler object
free_surface.reset( new FreeSurfaceHandler<dim>( *this, prm ) );
}
// Initialize the melt handler
if (parameters.include_melt_transport)
{
AssertThrow( !parameters.use_discontinuous_temperature_discretization &&
!parameters.use_discontinuous_composition_discretization,
ExcMessage("Melt transport can not be used with discontinuous elements.") );
AssertThrow( !parameters.free_surface_enabled,
ExcMessage("Melt transport together with a free surface has not been tested.") );
melt_handler->initialize_simulator (*this);
}
postprocess_manager.initialize_simulator (*this);
postprocess_manager.parse_parameters (prm);
mesh_refinement_manager.initialize_simulator (*this);
mesh_refinement_manager.parse_parameters (prm);
termination_manager.initialize_simulator (*this);
termination_manager.parse_parameters (prm);
lateral_averaging.initialize_simulator (*this);
geometry_model->create_coarse_mesh (triangulation);
global_Omega_diameter = GridTools::diameter (triangulation);
for (std::map<types::boundary_id,std::pair<std::string,std::string> >::const_iterator
p = parameters.prescribed_velocity_boundary_indicators.begin();
p != parameters.prescribed_velocity_boundary_indicators.end();
++p)
{
BoundaryVelocity::Interface<dim> *bv
= BoundaryVelocity::create_boundary_velocity<dim>
(p->second.second);
boundary_velocity[p->first].reset (bv);
if (SimulatorAccess<dim> *sim = dynamic_cast<SimulatorAccess<dim>*>(bv))
sim->initialize_simulator(*this);
bv->parse_parameters (prm);
bv->initialize ();
}
for (std::map<types::boundary_id,std::pair<std::string,std::string> >::const_iterator
p = parameters.prescribed_traction_boundary_indicators.begin();
p != parameters.prescribed_traction_boundary_indicators.end();
++p)
{
BoundaryTraction::Interface<dim> *bv
= BoundaryTraction::create_boundary_traction<dim>
(p->second.second);
boundary_traction[p->first].reset (bv);
if (SimulatorAccess<dim> *sim = dynamic_cast<SimulatorAccess<dim>*>(bv))
sim->initialize_simulator(*this);
bv->parse_parameters (prm);
bv->initialize ();
}
// determine how to treat the pressure. we have to scale it for the solver
// to make velocities and pressures of roughly the same (numerical) size,
// and we may have to fix up the right hand side vector before solving for
// compressible models if there are no in-/outflow boundaries
pressure_scaling = material_model->reference_viscosity() / geometry_model->length_scale();
std::set<types::boundary_id> open_velocity_boundary_indicators
= geometry_model->get_used_boundary_indicators();
for (std::map<types::boundary_id,std::pair<std::string,std::string> >::const_iterator
p = parameters.prescribed_velocity_boundary_indicators.begin();
p != parameters.prescribed_velocity_boundary_indicators.end();
++p)
open_velocity_boundary_indicators.erase (p->first);
for (std::set<types::boundary_id>::const_iterator
p = parameters.zero_velocity_boundary_indicators.begin();
p != parameters.zero_velocity_boundary_indicators.end();
++p)
open_velocity_boundary_indicators.erase (*p);
for (std::set<types::boundary_id>::const_iterator
p = parameters.tangential_velocity_boundary_indicators.begin();
p != parameters.tangential_velocity_boundary_indicators.end();
++p)
open_velocity_boundary_indicators.erase (*p);
// We need to do the RHS compatibility modification, if the model is
// compressible or compatible (in the case of melt transport), and
// there is no open boundary to balance the pressure.
do_pressure_rhs_compatibility_modification = ((material_model->is_compressible() && !parameters.include_melt_transport)
||
(parameters.include_melt_transport && !material_model->is_compressible()))
&&
(open_velocity_boundary_indicators.size() == 0);
// make sure that we don't have to fill every column of the statistics
// object in each time step.
statistics.set_auto_fill_mode(true);
// finally produce a record of the run-time parameters by writing
// the currently used values into a file
// Only write the parameter files on the root node to avoid file system conflicts
if (Utilities::MPI::this_mpi_process(mpi_communicator) == 0)
{
std::ofstream prm_out ((parameters.output_directory + "parameters.prm").c_str());
AssertThrow (prm_out,
ExcMessage (std::string("Could not open file <") +
parameters.output_directory + "parameters.prm>."));
prm.print_parameters(prm_out, ParameterHandler::Text);
}
if (Utilities::MPI::this_mpi_process(mpi_communicator) == 0)
{
std::ofstream prm_out ((parameters.output_directory + "parameters.tex").c_str());
AssertThrow (prm_out,
ExcMessage (std::string("Could not open file <") +
parameters.output_directory + "parameters.tex>."));
prm.print_parameters(prm_out, ParameterHandler::LaTeX);
}
// check that the setup of equations, material models, and heating terms is consistent
check_consistency_of_formulation();
// now that all member variables have been set up, also
// connect the functions that will actually do the assembly
set_assemblers();
computing_timer.exit_section();
}
/**
* Destructor.
*/
template <int dim>
Simulator<dim>::~Simulator ()
{
// wait if there is a thread that's still writing the statistics
// object (set from the output_statistics() function)
output_statistics_thread.join();
}
namespace
{
/**
* Conversion object where one can provide a function that returns
* a tensor for the velocity at a given point and it returns something
* that matches the dealii::Function interface with a number of output
* components equal to the number of components of the finite element
* in use.
*/
template <int dim>
class VectorFunctionFromVelocityFunctionObject : public Function<dim>
{
public:
/**
* Given a function object that takes a Point and returns a Tensor<1,dim>,
* convert this into an object that matches the Function@<dim@>
* interface.
*
* @param n_components total number of components of the finite element system.
* @param function_object The function that will form one component
* of the resulting Function object.
*/
VectorFunctionFromVelocityFunctionObject (const unsigned int n_components,
const std_cxx11::function<Tensor<1,dim> (const Point<dim> &)> &function_object);
/**
* Return the value of the
* function at the given
* point. Returns the value the
* function given to the constructor
* produces for this point.
*/
virtual double value (const Point<dim> &p,
const unsigned int component = 0) const;
/**
* Return all components of a
* vector-valued function at a
* given point.
*
* <tt>values</tt> shall have the right
* size beforehand,
* i.e. #n_components.
*/
virtual void vector_value (const Point<dim> &p,
Vector<double> &values) const;
private:
/**
* The function object which we call when this class's value() or
* value_list() functions are called.
**/
const std_cxx11::function<Tensor<1,dim> (const Point<dim> &)> function_object;
};
template <int dim>
VectorFunctionFromVelocityFunctionObject<dim>::
VectorFunctionFromVelocityFunctionObject
(const unsigned int n_components,
const std_cxx11::function<Tensor<1,dim> (const Point<dim> &)> &function_object)
:
Function<dim>(n_components),
function_object (function_object)
{
}
template <int dim>
double
VectorFunctionFromVelocityFunctionObject<dim>::value (const Point<dim> &p,
const unsigned int component) const
{
Assert (component < this->n_components,
ExcIndexRange (component, 0, this->n_components));
if (component < dim)
{
const Tensor<1,dim> v = function_object(p);
return v[component];
}
else
return 0;
}
template <int dim>
void
VectorFunctionFromVelocityFunctionObject<dim>::
vector_value (const Point<dim> &p,
Vector<double> &values) const
{
AssertDimension(values.size(), this->n_components);
// set everything to zero, and then the right components to their correct values
values = 0;
const Tensor<1,dim> v = function_object(p);
for (unsigned int d=0; d<dim; ++d)
values(d) = v[d];
}
}
template <int dim>
void
Simulator<dim>::
start_timestep ()
{
// first produce some output for the screen to show where we are
if (parameters.convert_to_years == true)
pcout << "*** Timestep " << timestep_number
<< ": t=" << time/year_in_seconds
<< " years"
<< std::endl;
else
pcout << "*** Timestep " << timestep_number
<< ": t=" << time
<< " seconds"
<< std::endl;
nonlinear_iteration = 0;
// then interpolate the current boundary velocities. copy constraints
// into current_constraints and then add to current_constraints
compute_current_constraints ();
// If needed, construct sparsity patterns and matrices with the current
// constraints. Of course we need to force assembly too.
if (rebuild_sparsity_and_matrices)
{
rebuild_sparsity_and_matrices = false;
setup_system_matrix (introspection.index_sets.system_partitioning);
setup_system_preconditioner (introspection.index_sets.system_partitioning);
rebuild_stokes_matrix = rebuild_stokes_preconditioner = true;
}
// TODO: do this in a more efficient way (TH)? we really only need
// to make sure that the time dependent velocity boundary conditions
// end up in the right hand side in the right way; we currently do
// that by re-assembling the entire system
if (!boundary_velocity.empty())
rebuild_stokes_matrix = rebuild_stokes_preconditioner = true;
// notify different system components that we started the next time step
// TODO: implement this for all plugins that might need it at one place.
// Temperature BC are currently updated in compute_current_constraints
material_model->update();
gravity_model->update();
heating_model_manager.update();
adiabatic_conditions->update();
mesh_refinement_manager.update();
if (prescribed_stokes_solution.get())
prescribed_stokes_solution->update();
// do the same for the traction boundary conditions and other things
// that end up in the bilinear form. we update those that end up in
// the constraints object when calling compute_current_constraints()
// above
for (typename std::map<types::boundary_id,std_cxx11::shared_ptr<BoundaryTraction::Interface<dim> > >::iterator
p = boundary_traction.begin();
p != boundary_traction.end(); ++p)
p->second->update ();
}
template <int dim>
void
Simulator<dim>::
compute_current_constraints ()
{
current_constraints.clear ();
current_constraints.reinit (introspection.index_sets.system_relevant_set);
current_constraints.merge (constraints);
{
// set the current time and do the interpolation
// for the prescribed velocity fields
for (typename std::map<types::boundary_id,std_cxx11::shared_ptr<BoundaryVelocity::Interface<dim> > >::iterator
p = boundary_velocity.begin();
p != boundary_velocity.end(); ++p)
{
p->second->update ();
VectorFunctionFromVelocityFunctionObject<dim> vel
(introspection.n_components,
std_cxx11::bind (static_cast<Tensor<1,dim> (BoundaryVelocity::Interface<dim>::*)(
const types::boundary_id,
const Point<dim> &) const> (&BoundaryVelocity::Interface<dim>::boundary_velocity),
p->second,
p->first,
std_cxx11::_1));
// here we create a mask for interpolate_boundary_values out of the 'selector'
std::vector<bool> mask(introspection.component_masks.velocities.size(), false);
const std::string &comp = parameters.prescribed_velocity_boundary_indicators[p->first].first;
if (comp.length()>0)
{
for (std::string::const_iterator direction=comp.begin(); direction!=comp.end(); ++direction)
{
switch (*direction)
{
case 'x':
mask[introspection.component_indices.velocities[0]] = true;
break;
case 'y':
mask[introspection.component_indices.velocities[1]] = true;
break;
case 'z':
// we must be in 3d, or 'z' should never have gotten through
Assert (dim==3, ExcInternalError());
if (dim==3)
mask[introspection.component_indices.velocities[2]] = true;
break;
default:
Assert (false, ExcInternalError());
}
}
}
else
{
// no mask given -- take all velocities
for (unsigned int i=0; i<introspection.component_masks.velocities.size(); ++i)
mask[i]=introspection.component_masks.velocities[i];
}
VectorTools::interpolate_boundary_values (*mapping,
dof_handler,
p->first,
vel,
current_constraints,
mask);
}
}
// If there is a fixed boundary temperature,
// update the temperature boundary condition.
boundary_temperature_manager.update();
// if using continuous temperature FE, do the same for the temperature variable:
// evaluate the current boundary temperature and add these constraints as well
if (!parameters.use_discontinuous_temperature_discretization)
{
// obtain the boundary indicators that belong to Dirichlet-type
// temperature boundary conditions and interpolate the temperature
// there
for (std::set<types::boundary_id>::const_iterator
p = parameters.fixed_temperature_boundary_indicators.begin();
p != parameters.fixed_temperature_boundary_indicators.end(); ++p)
{
Assert (is_element (*p, geometry_model->get_used_boundary_indicators()),
ExcInternalError());
VectorTools::interpolate_boundary_values (*mapping,
dof_handler,
*p,
VectorFunctionFromScalarFunctionObject<dim>(std_cxx11::bind (&BoundaryTemperature::Manager<dim>::boundary_temperature,
std_cxx11::cref(boundary_temperature_manager),
*p,
std_cxx11::_1),
introspection.component_masks.temperature.first_selected_component(),
introspection.n_components),
current_constraints,
introspection.component_masks.temperature);
}
}
// If there are fixed boundary compositions,
// update the composition boundary condition.
if (boundary_composition.get())
boundary_composition->update();
// now do the same for the composition variable:
if (!parameters.use_discontinuous_composition_discretization)
{
// obtain the boundary indicators that belong to Dirichlet-type
// composition boundary conditions and interpolate the composition
// there
for (unsigned int c=0; c<introspection.n_compositional_fields; ++c)
for (std::set<types::boundary_id>::const_iterator
p = parameters.fixed_composition_boundary_indicators.begin();
p != parameters.fixed_composition_boundary_indicators.end(); ++p)
{
Assert (is_element (*p, geometry_model->get_used_boundary_indicators()),
ExcInternalError());
VectorTools::interpolate_boundary_values (*mapping,
dof_handler,
*p,
VectorFunctionFromScalarFunctionObject<dim>(std_cxx11::bind (&BoundaryComposition::Interface<dim>::boundary_composition,
std_cxx11::cref(*boundary_composition),
*p,
std_cxx11::_1,
c),
introspection.component_masks.compositional_fields[c].first_selected_component(),
introspection.n_components),
current_constraints,
introspection.component_masks.compositional_fields[c]);
}
}
// let plugins add more constraints if they so choose, then close the
// constraints object
signals.post_constraints_creation(*this, current_constraints);
current_constraints.close();
}
template <int dim>
void
Simulator<dim>::
setup_system_matrix (const std::vector<IndexSet> &system_partitioning)
{
system_matrix.clear ();