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adamantine.hh
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adamantine.hh
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/* Copyright (c) 2016 - 2024, the adamantine authors.
*
* This file is subject to the Modified BSD License and may not be distributed
* without copyright and license information. Please refer to the file LICENSE
* for the text and further information on this license.
*/
#ifndef ADAMANTINE_HH
#define ADAMANTINE_HH
#include <DataAssimilator.hh>
#include <ExperimentalData.hh>
#include <Geometry.hh>
#include <MaterialProperty.hh>
#include <MechanicalPhysics.hh>
#include <PointCloud.hh>
#include <PostProcessor.hh>
#include <RayTracing.hh>
#include <ThermalPhysics.hh>
#include <ThermalPhysicsInterface.hh>
#include <Timer.hh>
#include <ensemble_management.hh>
#include <experimental_data_utils.hh>
#include <material_deposition.hh>
#include <types.hh>
#include <utils.hh>
#include <deal.II/base/index_set.h>
#include <deal.II/base/mpi.h>
#include <deal.II/base/symmetric_tensor.h>
#include <deal.II/base/types.h>
#include <deal.II/distributed/cell_data_transfer.templates.h>
#include <deal.II/distributed/solution_transfer.h>
#include <deal.II/grid/filtered_iterator.h>
#include <deal.II/grid/grid_refinement.h>
#include <deal.II/lac/trilinos_sparse_matrix.h>
#include <deal.II/lac/vector_operation.h>
#include <deal.II/numerics/error_estimator.h>
#include <boost/archive/text_iarchive.hpp>
#include <boost/archive/text_oarchive.hpp>
#include <boost/property_tree/ptree.hpp>
#include <fstream>
#include <limits>
#include <memory>
#include <string>
#include <type_traits>
#include <unordered_map>
#ifdef ADAMANTINE_WITH_CALIPER
#include <caliper/cali.h>
#endif
#include <cmath>
#include <iostream>
template <
int dim, int p_order, typename MaterialStates, typename MemorySpaceType,
std::enable_if_t<
std::is_same<MemorySpaceType, dealii::MemorySpace::Host>::value, int> =
0>
void output_pvtu(
adamantine::PostProcessor<dim> &post_processor, unsigned int n_time_step,
double time,
std::unique_ptr<
adamantine::ThermalPhysicsInterface<dim, MemorySpaceType>> const
&thermal_physics,
dealii::LinearAlgebra::distributed::Vector<double, MemorySpaceType>
&temperature,
std::unique_ptr<adamantine::MechanicalPhysics<dim, p_order, MaterialStates,
MemorySpaceType>> const
&mechanical_physics,
dealii::LA::distributed::Vector<double, dealii::MemorySpace::Host>
&displacement,
adamantine::MaterialProperty<dim, p_order, MaterialStates,
MemorySpaceType> const &material_properties,
std::vector<adamantine::Timer> &timers)
{
#ifdef ADAMANTINE_WITH_CALIPER
CALI_CXX_MARK_FUNCTION;
#endif
timers[adamantine::output].start();
if (thermal_physics)
{
thermal_physics->get_affine_constraints().distribute(temperature);
if (mechanical_physics)
{
mechanical_physics->get_affine_constraints().distribute(displacement);
post_processor.template write_output<typename Kokkos::View<
double **, typename MemorySpaceType::kokkos_space>::array_layout>(
n_time_step, time, temperature, displacement,
mechanical_physics->get_stress_tensor(),
material_properties.get_state(), material_properties.get_dofs_map(),
material_properties.get_dof_handler());
}
else
{
post_processor.template write_thermal_output<typename Kokkos::View<
double **, typename MemorySpaceType::kokkos_space>::array_layout>(
n_time_step, time, temperature, material_properties.get_state(),
material_properties.get_dofs_map(),
material_properties.get_dof_handler());
}
}
else
{
mechanical_physics->get_affine_constraints().distribute(displacement);
post_processor.template write_mechanical_output<typename Kokkos::View<
double **, typename MemorySpaceType::kokkos_space>::array_layout>(
n_time_step, time, displacement,
mechanical_physics->get_stress_tensor(),
material_properties.get_state(), material_properties.get_dofs_map(),
material_properties.get_dof_handler());
}
timers[adamantine::output].stop();
}
template <
int dim, int p_order, typename MaterialStates, typename MemorySpaceType,
std::enable_if_t<
std::is_same<MemorySpaceType, dealii::MemorySpace::Default>::value,
int> = 0>
void output_pvtu(
adamantine::PostProcessor<dim> &post_processor, unsigned int n_time_step,
double time,
std::unique_ptr<
adamantine::ThermalPhysicsInterface<dim, MemorySpaceType>> const
&thermal_physics,
dealii::LinearAlgebra::distributed::Vector<double, MemorySpaceType>
&temperature,
std::unique_ptr<adamantine::MechanicalPhysics<dim, p_order, MaterialStates,
MemorySpaceType>> const
&mechanical_physics,
dealii::LA::distributed::Vector<double, dealii::MemorySpace::Host>
&displacement,
adamantine::MaterialProperty<dim, p_order, MaterialStates,
MemorySpaceType> const &material_properties,
std::vector<adamantine::Timer> &timers)
{
#ifdef ADAMANTINE_WITH_CALIPER
CALI_CXX_MARK_FUNCTION;
#endif
timers[adamantine::output].start();
auto state = material_properties.get_state();
auto state_host = Kokkos::create_mirror_view_and_copy(
dealii::MemorySpace::Host::kokkos_space{}, state);
if (thermal_physics)
{
dealii::LinearAlgebra::distributed::Vector<double,
dealii::MemorySpace::Host>
temperature_host(temperature.get_partitioner());
temperature_host.import(temperature, dealii::VectorOperation::insert);
thermal_physics->get_affine_constraints().distribute(temperature_host);
if (mechanical_physics)
{
mechanical_physics->get_affine_constraints().distribute(displacement);
post_processor.template write_output<typename Kokkos::View<
double **, typename MemorySpaceType::kokkos_space>::array_layout>(
n_time_step, time, temperature_host, displacement,
mechanical_physics->get_stress_tensor(), state_host,
material_properties.get_dofs_map(),
material_properties.get_dof_handler());
}
else
{
post_processor.template write_thermal_output<typename Kokkos::View<
double **, typename MemorySpaceType::kokkos_space>::array_layout>(
n_time_step, time, temperature_host, state_host,
material_properties.get_dofs_map(),
material_properties.get_dof_handler());
}
}
else
{
mechanical_physics->get_affine_constraints().distribute(displacement);
post_processor.template write_mechanical_output<typename Kokkos::View<
double **, typename MemorySpaceType::kokkos_space>::array_layout>(
n_time_step, time, displacement,
mechanical_physics->get_stress_tensor(), state_host,
material_properties.get_dofs_map(),
material_properties.get_dof_handler());
}
timers[adamantine::output].stop();
}
// inlining this function so we can have in the header
inline void initialize_timers(MPI_Comm const &communicator,
std::vector<adamantine::Timer> &timers)
{
timers.push_back(adamantine::Timer(communicator, "Main"));
timers.push_back(adamantine::Timer(communicator, "Refinement"));
timers.push_back(adamantine::Timer(communicator, "Add Material, Search"));
timers.push_back(adamantine::Timer(communicator, "Add Material, Activate"));
timers.push_back(
adamantine::Timer(communicator, "Data Assimilation, Exp. Data"));
timers.push_back(
adamantine::Timer(communicator, "Data Assimilation, DOF Mapping"));
timers.push_back(
adamantine::Timer(communicator, "Data Assimilation, Cov. Sparsity"));
timers.push_back(
adamantine::Timer(communicator, "Data Assimilation, Exp. Cov."));
timers.push_back(
adamantine::Timer(communicator, "Data Assimilation, Update Ensemble"));
timers.push_back(adamantine::Timer(communicator, "Evolve One Time Step"));
timers.push_back(adamantine::Timer(
communicator, "Evolve One Time Step: evaluate_thermal_physics"));
timers.push_back(adamantine::Timer(
communicator, "Evolve One Time Step: id_minus_tau_J_inverse"));
timers.push_back(adamantine::Timer(
communicator, "Evolve One Time Step: evaluate_material_properties"));
timers.push_back(adamantine::Timer(communicator, "Output"));
}
template <int dim, int p_order, int fe_degree, typename MaterialStates,
typename MemorySpaceType, typename QuadratureType>
std::unique_ptr<adamantine::ThermalPhysicsInterface<dim, MemorySpaceType>>
initialize(MPI_Comm const &communicator,
boost::property_tree::ptree const &database,
adamantine::Geometry<dim> &geometry,
adamantine::MaterialProperty<dim, p_order, MaterialStates,
MemorySpaceType> &material_properties)
{
return std::make_unique<
adamantine::ThermalPhysics<dim, p_order, fe_degree, MaterialStates,
MemorySpaceType, QuadratureType>>(
communicator, database, geometry, material_properties);
}
template <int dim, int p_order, int fe_degree, typename MaterialStates,
typename MemorySpaceType>
std::unique_ptr<adamantine::ThermalPhysicsInterface<dim, MemorySpaceType>>
initialize_quadrature(
std::string const &quadrature_type, MPI_Comm const &communicator,
boost::property_tree::ptree const &database,
adamantine::Geometry<dim> &geometry,
adamantine::MaterialProperty<dim, p_order, MaterialStates, MemorySpaceType>
&material_properties)
{
if (quadrature_type.compare("gauss") == 0)
return initialize<dim, p_order, fe_degree, MaterialStates, MemorySpaceType,
dealii::QGauss<1>>(communicator, database, geometry,
material_properties);
else
{
adamantine::ASSERT_THROW(quadrature_type.compare("lobatto") == 0,
"quadrature should be Gauss or Lobatto.");
return initialize<dim, p_order, fe_degree, MaterialStates, MemorySpaceType,
dealii::QGaussLobatto<1>>(communicator, database,
geometry, material_properties);
}
}
template <int dim, int p_order, typename MaterialStates,
typename MemorySpaceType>
std::unique_ptr<adamantine::ThermalPhysicsInterface<dim, MemorySpaceType>>
initialize_thermal_physics(
unsigned int fe_degree, std::string const &quadrature_type,
MPI_Comm const &communicator, boost::property_tree::ptree const &database,
adamantine::Geometry<dim> &geometry,
adamantine::MaterialProperty<dim, p_order, MaterialStates, MemorySpaceType>
&material_properties)
{
switch (fe_degree)
{
case 1:
{
return initialize_quadrature<dim, p_order, 1, MaterialStates,
MemorySpaceType>(
quadrature_type, communicator, database, geometry, material_properties);
}
case 2:
{
return initialize_quadrature<dim, p_order, 2, MaterialStates,
MemorySpaceType>(
quadrature_type, communicator, database, geometry, material_properties);
}
case 3:
{
return initialize_quadrature<dim, p_order, 3, MaterialStates,
MemorySpaceType>(
quadrature_type, communicator, database, geometry, material_properties);
}
case 4:
{
return initialize_quadrature<dim, p_order, 4, MaterialStates,
MemorySpaceType>(
quadrature_type, communicator, database, geometry, material_properties);
}
default:
{
adamantine::ASSERT_THROW(fe_degree == 5,
"fe_degree should be between 1 and 5.");
return initialize_quadrature<dim, p_order, 5, MaterialStates,
MemorySpaceType>(
quadrature_type, communicator, database, geometry, material_properties);
}
}
}
template <int dim, int p_order, typename MaterialStates,
typename MemorySpaceType>
void refine_and_transfer(
std::unique_ptr<adamantine::ThermalPhysicsInterface<dim, MemorySpaceType>>
&thermal_physics,
adamantine::MaterialProperty<dim, p_order, MaterialStates, MemorySpaceType>
&material_properties,
dealii::DoFHandler<dim> &dof_handler,
dealii::LA::distributed::Vector<double, MemorySpaceType> &solution)
{
#ifdef ADAMANTINE_WITH_CALIPER
CALI_CXX_MARK_FUNCTION;
#endif
// TODO transfer mechanical data is present, need to be aware that the data
// does not exist on some cells because it's liquid
dealii::parallel::distributed::Triangulation<dim> &triangulation =
dynamic_cast<dealii::parallel::distributed::Triangulation<dim> &>(
const_cast<dealii::Triangulation<dim> &>(
dof_handler.get_triangulation()));
// Update the material state from the ThermalOperator to MaterialProperty
// because, for now, we need to use state from MaterialProperty to perform the
// transfer to the refined mesh.
thermal_physics->set_state_to_material_properties();
// Transfer of the solution
dealii::parallel::distributed::SolutionTransfer<
dim, dealii::LA::distributed::Vector<double, dealii::MemorySpace::Host>>
solution_transfer(dof_handler);
// Transfer material state
unsigned int const direction_data_size = 2;
unsigned int const phase_history_data_size = 1;
unsigned int constexpr n_material_states = MaterialStates::n_material_states;
std::vector<std::vector<double>> data_to_transfer;
std::vector<double> dummy_cell_data(n_material_states + direction_data_size +
phase_history_data_size,
std::numeric_limits<double>::infinity());
auto state_host = Kokkos::create_mirror_view_and_copy(
Kokkos::HostSpace{}, material_properties.get_state());
unsigned int cell_id = 0;
unsigned int activated_cell_id = 0;
for (auto const &cell : dof_handler.active_cell_iterators())
{
if (cell->is_locally_owned())
{
std::vector<double> cell_data(n_material_states + direction_data_size +
phase_history_data_size);
for (unsigned int i = 0; i < n_material_states; ++i)
cell_data[i] = state_host(i, cell_id);
if (cell->active_fe_index() == 0)
{
cell_data[n_material_states] =
thermal_physics->get_deposition_cos(activated_cell_id);
cell_data[n_material_states + 1] =
thermal_physics->get_deposition_sin(activated_cell_id);
if (thermal_physics->get_has_melted(activated_cell_id))
cell_data[n_material_states + direction_data_size] = 1.0;
else
cell_data[n_material_states + direction_data_size] = 0.0;
++activated_cell_id;
}
else
{
cell_data[n_material_states] = std::numeric_limits<double>::infinity();
cell_data[n_material_states + 1] =
std::numeric_limits<double>::infinity();
cell_data[n_material_states + direction_data_size] =
std::numeric_limits<double>::infinity();
}
data_to_transfer.push_back(cell_data);
++cell_id;
}
else
{
data_to_transfer.push_back(dummy_cell_data);
}
}
// Prepare the Triangulation and the diffent data transfer objects for
// refinement
triangulation.prepare_coarsening_and_refinement();
// Prepare for refinement of the solution
dealii::LA::distributed::Vector<double, dealii::MemorySpace::Host>
solution_host;
if constexpr (std::is_same_v<MemorySpaceType, dealii::MemorySpace::Host>)
{
// We need to apply the constraints before the mesh transfer
thermal_physics->get_affine_constraints().distribute(solution);
// We need to update the ghost values before we can do the interpolation on
// the new mesh.
solution.update_ghost_values();
solution_transfer.prepare_for_coarsening_and_refinement(solution);
}
else
{
solution_host.reinit(solution.get_partitioner());
solution_host.import(solution, dealii::VectorOperation::insert);
// We need to apply the constraints before the mesh transfer
thermal_physics->get_affine_constraints().distribute(solution_host);
// We need to update the ghost values before we can do the interpolation on
// the new mesh.
solution_host.update_ghost_values();
solution_transfer.prepare_for_coarsening_and_refinement(solution_host);
}
dealii::parallel::distributed::CellDataTransfer<
dim, dim, std::vector<std::vector<double>>>
cell_data_trans(triangulation);
cell_data_trans.prepare_for_coarsening_and_refinement(data_to_transfer);
#ifdef ADAMANTINE_WITH_CALIPER
CALI_MARK_BEGIN("refine triangulation");
#endif
// Execute the refinement
triangulation.execute_coarsening_and_refinement();
#ifdef ADAMANTINE_WITH_CALIPER
CALI_MARK_END("refine triangulation");
#endif
// Update the AffineConstraints and resize the solution
thermal_physics->setup_dofs();
thermal_physics->initialize_dof_vector(0., solution);
// Update MaterialProperty DoFHandler and resize the state vectors
material_properties.reinit_dofs();
// Interpolate the solution
if constexpr (std::is_same_v<MemorySpaceType, dealii::MemorySpace::Host>)
{
solution_transfer.interpolate(solution);
}
else
{
solution_host.reinit(solution.get_partitioner());
solution_transfer.interpolate(solution_host);
solution.import(solution_host, dealii::VectorOperation::insert);
}
// Unpack the material state and repopulate the material state
std::vector<std::vector<double>> transferred_data(
triangulation.n_active_cells(),
std::vector<double>(n_material_states + direction_data_size +
phase_history_data_size));
cell_data_trans.unpack(transferred_data);
auto state = material_properties.get_state();
state_host = Kokkos::create_mirror_view(state);
unsigned int total_cell_id = 0;
cell_id = 0;
std::vector<double> transferred_cos;
std::vector<double> transferred_sin;
std::vector<bool> has_melted;
for (auto const &cell : dof_handler.active_cell_iterators())
{
if (cell->is_locally_owned())
{
for (unsigned int i = 0; i < n_material_states; ++i)
{
state_host(i, cell_id) = transferred_data[total_cell_id][i];
}
if (cell->active_fe_index() == 0)
{
transferred_cos.push_back(
transferred_data[total_cell_id][n_material_states]);
transferred_sin.push_back(
transferred_data[total_cell_id][n_material_states + 1]);
// Convert from double back to bool
if (transferred_data[total_cell_id]
[n_material_states + direction_data_size] > 0.5)
has_melted.push_back(true);
else
has_melted.push_back(false);
}
++cell_id;
}
++total_cell_id;
}
// Update the deposition cos and sin
thermal_physics->set_material_deposition_orientation(transferred_cos,
transferred_sin);
// Update the melted indicator
thermal_physics->set_has_melted_vector(has_melted);
// Copy the data back to material_property
Kokkos::deep_copy(state, state_host);
// Update the material states in the ThermalOperator
thermal_physics->get_state_from_material_properties();
#if ADAMANTINE_DEBUG
// Check that we are not losing material
cell_id = 0;
for (auto const &cell : dof_handler.active_cell_iterators())
{
if (cell->is_locally_owned())
{
double material_ratio = 0.;
for (unsigned int i = 0; i < n_material_states; ++i)
{
material_ratio += state_host(i, cell_id);
}
ASSERT(std::abs(material_ratio - 1.) < 1e-14, "Material is lost.");
++cell_id;
}
}
#endif
}
template <int dim>
std::vector<typename dealii::parallel::distributed::Triangulation<
dim>::active_cell_iterator>
compute_cells_to_refine(
dealii::parallel::distributed::Triangulation<dim> &triangulation,
double const time, double const next_refinement_time,
unsigned int const n_time_steps,
std::vector<std::shared_ptr<adamantine::HeatSource<dim>>> &heat_sources,
double const current_source_height, double const refinement_beam_cutoff)
{
// Compute the position of the beams between time and next_refinement_time and
// refine the mesh where the source is greater than refinement_beam_cutoff.
// This cut-off is due to the fact that the source is gaussian and thus never
// strictly zero. If the beams intersect, some cells will appear twice in the
// vector. This is not a problem.
std::vector<typename dealii::parallel::distributed::Triangulation<
dim>::active_cell_iterator>
cells_to_refine;
for (unsigned int i = 0; i < n_time_steps; ++i)
{
double const current_time = time + static_cast<double>(i) /
static_cast<double>(n_time_steps) *
(next_refinement_time - time);
for (auto &beam : heat_sources)
{
beam->update_time(current_time);
for (auto cell : dealii::filter_iterators(
triangulation.active_cell_iterators(),
dealii::IteratorFilters::LocallyOwnedCell()))
{
// Check the value at the center of the cell faces. For most cases this
// should be sufficient, but if the beam is small compared to the
// coarsest mesh we may need to add other points to check (e.g.
// quadrature points, vertices).
for (unsigned int f = 0; f < cell->reference_cell().n_faces(); ++f)
{
if (beam->value(cell->face(f)->center(), current_source_height) >
refinement_beam_cutoff)
{
cells_to_refine.push_back(cell);
break;
}
}
}
}
}
return cells_to_refine;
}
template <int dim, int p_order, int fe_degree, typename MaterialStates,
typename MemorySpaceType>
void refine_mesh(
std::unique_ptr<adamantine::ThermalPhysicsInterface<dim, MemorySpaceType>>
&thermal_physics,
adamantine::MaterialProperty<dim, p_order, MaterialStates, MemorySpaceType>
&material_properties,
dealii::LA::distributed::Vector<double, MemorySpaceType> &solution,
std::vector<std::shared_ptr<adamantine::HeatSource<dim>>> &heat_sources,
double const time, double const next_refinement_time,
unsigned int const time_steps_refinement,
boost::property_tree::ptree const &refinement_database)
{
#ifdef ADAMANTINE_WITH_CALIPER
CALI_CXX_MARK_FUNCTION;
#endif
dealii::DoFHandler<dim> &dof_handler = thermal_physics->get_dof_handler();
dealii::parallel::distributed::Triangulation<dim> &triangulation =
dynamic_cast<dealii::parallel::distributed::Triangulation<dim> &>(
const_cast<dealii::Triangulation<dim> &>(
dof_handler.get_triangulation()));
// Refine the mesh along the trajectory of the sources.
double current_source_height =
dynamic_cast<
adamantine::ThermalPhysics<dim, p_order, fe_degree, MaterialStates,
MemorySpaceType, dealii::QGauss<1>> *>(
thermal_physics.get())
? dynamic_cast<adamantine::ThermalPhysics<
dim, p_order, fe_degree, MaterialStates, MemorySpaceType,
dealii::QGauss<1>> *>(thermal_physics.get())
->get_current_source_height()
: dynamic_cast<adamantine::ThermalPhysics<
dim, p_order, fe_degree, MaterialStates, MemorySpaceType,
dealii::QGaussLobatto<1>> *>(thermal_physics.get())
->get_current_source_height();
// PropertyTreeInput refinement.n_refinements
unsigned int const n_refinements =
refinement_database.get("n_refinements", 2);
// PropertyTreeInput refinement.beam_cutoff
const double refinement_beam_cutoff =
refinement_database.get<double>("beam_cutoff", 1.0e-15);
for (unsigned int i = 0; i < n_refinements; ++i)
{
// Compute the cells to be refined.
std::vector<typename dealii::parallel::distributed::Triangulation<
dim>::active_cell_iterator>
cells_to_refine = compute_cells_to_refine(
triangulation, time, next_refinement_time, time_steps_refinement,
heat_sources, current_source_height, refinement_beam_cutoff);
// PropertyTreeInput refinement.coarsen_after_beam
const bool coarsen_after_beam =
refinement_database.get<bool>("coarsen_after_beam", false);
// If coarsening is allowed, set the coarsening flag everywhere
if (coarsen_after_beam)
{
for (auto cell : dealii::filter_iterators(
triangulation.active_cell_iterators(),
dealii::IteratorFilters::LocallyOwnedCell()))
{
if (cell->level() > 0)
cell->set_coarsen_flag();
}
}
// Flag the cells for refinement.
for (auto &cell : cells_to_refine)
{
if (coarsen_after_beam)
cell->clear_coarsen_flag();
cell->set_refine_flag();
}
// Execute the refinement and transfer the solution onto the new mesh.
refine_and_transfer(thermal_physics, material_properties, dof_handler,
solution);
}
// Recompute the inverse of the mass matrix
thermal_physics->compute_inverse_mass_matrix();
}
template <int dim, int p_order, typename MaterialStates,
typename MemorySpaceType>
void refine_mesh(
std::unique_ptr<adamantine::ThermalPhysicsInterface<dim, MemorySpaceType>>
&thermal_physics,
adamantine::MaterialProperty<dim, p_order, MaterialStates, MemorySpaceType>
&material_properties,
dealii::LA::distributed::Vector<double, MemorySpaceType> &solution,
std::vector<std::shared_ptr<adamantine::HeatSource<dim>>> &heat_sources,
double const time, double const next_refinement_time,
unsigned int const time_steps_refinement,
boost::property_tree::ptree const &refinement_database)
{
if (!thermal_physics)
return;
switch (thermal_physics->get_fe_degree())
{
case 1:
{
refine_mesh<dim, p_order, 1, MaterialStates>(
thermal_physics, material_properties, solution, heat_sources, time,
next_refinement_time, time_steps_refinement, refinement_database);
break;
}
case 2:
{
refine_mesh<dim, p_order, 2, MaterialStates>(
thermal_physics, material_properties, solution, heat_sources, time,
next_refinement_time, time_steps_refinement, refinement_database);
break;
}
case 3:
{
refine_mesh<dim, p_order, 3, MaterialStates>(
thermal_physics, material_properties, solution, heat_sources, time,
next_refinement_time, time_steps_refinement, refinement_database);
break;
}
case 4:
{
refine_mesh<dim, p_order, 4, MaterialStates>(
thermal_physics, material_properties, solution, heat_sources, time,
next_refinement_time, time_steps_refinement, refinement_database);
break;
}
case 5:
{
refine_mesh<dim, p_order, 5, MaterialStates>(
thermal_physics, material_properties, solution, heat_sources, time,
next_refinement_time, time_steps_refinement, refinement_database);
break;
}
default:
{
adamantine::ASSERT_THROW(false, "fe_degree should be between 1 and 5.");
}
}
}
template <int dim, int p_order, typename MaterialStates,
typename MemorySpaceType>
std::pair<dealii::LinearAlgebra::distributed::Vector<double,
dealii::MemorySpace::Host>,
dealii::LinearAlgebra::distributed::Vector<double,
dealii::MemorySpace::Host>>
run(MPI_Comm const &communicator, boost::property_tree::ptree const &database,
std::vector<adamantine::Timer> &timers)
{
#ifdef ADAMANTINE_WITH_CALIPER
CALI_CXX_MARK_FUNCTION;
#endif
// Create the Geometry
boost::property_tree::ptree geometry_database =
database.get_child("geometry");
adamantine::Geometry<dim> geometry(communicator, geometry_database);
// Create the MaterialProperty
boost::property_tree::ptree material_database =
database.get_child("materials");
adamantine::MaterialProperty<dim, p_order, MaterialStates, MemorySpaceType>
material_properties(communicator, geometry.get_triangulation(),
material_database);
// Extract the physics property tree
boost::property_tree::ptree physics_database = database.get_child("physics");
bool const use_thermal_physics = physics_database.get<bool>("thermal");
[[maybe_unused]] bool const use_mechanical_physics =
physics_database.get<bool>("mechanical");
// Extract the discretization property tree
boost::property_tree::ptree discretization_database =
database.get_child("discretization");
// Extract the post-processor property tree
boost::property_tree::ptree post_processor_database =
database.get_child("post_processor");
// Extract the verbosity
// PropertyTreeInput verbose_output
bool const verbose_output = database.get("verbose_output", false);
// Create ThermalPhysics if necessary
std::unique_ptr<adamantine::ThermalPhysicsInterface<dim, MemorySpaceType>>
thermal_physics;
std::vector<std::shared_ptr<adamantine::HeatSource<dim>>> heat_sources;
if (use_thermal_physics)
{
// PropertyTreeInput discretization.thermal.fe_degree
unsigned int const fe_degree =
discretization_database.get<unsigned int>("thermal.fe_degree");
// PropertyTreeInput discretization.thermal.quadrature
std::string quadrature_type =
discretization_database.get("thermal.quadrature", "gauss");
thermal_physics = initialize_thermal_physics<dim>(
fe_degree, quadrature_type, communicator, database, geometry,
material_properties);
heat_sources = thermal_physics->get_heat_sources();
post_processor_database.put("thermal_output", true);
}
// PropertyTreeInput materials.initial_temperature
double const initial_temperature =
material_database.get("initial_temperature", 300.);
// Get the reference temperature(s) for the substrate and deposited
// material(s)
std::vector<double> material_reference_temps;
// PropertyTreeInput materials.n_materials
unsigned int const n_materials =
material_database.get<unsigned int>("n_materials");
for (unsigned int i = 0; i < n_materials; ++i)
{
// Use the solidus as the reference temperature, in the future we may want
// to use something else
// PropertyTreeInput materials.material_n.solidus
double const reference_temperature = material_database.get<double>(
"material_" + std::to_string(i) + ".solidus");
material_reference_temps.push_back(reference_temperature);
}
material_reference_temps.push_back(initial_temperature);
// Create MechanicalPhysics
std::unique_ptr<adamantine::MechanicalPhysics<dim, p_order, MaterialStates,
MemorySpaceType>>
mechanical_physics;
if (use_mechanical_physics)
{
// PropertyTreeInput discretization.mechanical.fe_degree
unsigned int const fe_degree =
discretization_database.get<unsigned int>("mechanical.fe_degree");
mechanical_physics = std::make_unique<adamantine::MechanicalPhysics<
dim, p_order, MaterialStates, MemorySpaceType>>(
communicator, fe_degree, geometry, material_properties,
material_reference_temps);
post_processor_database.put("mechanical_output", true);
}
// Create PostProcessor
std::unique_ptr<adamantine::PostProcessor<dim>> post_processor;
bool thermal_output = post_processor_database.get("thermal_output", false);
bool mechanical_output =
post_processor_database.get("mechanical_output", false);
if ((thermal_output) && (mechanical_output))
{
post_processor = std::make_unique<adamantine::PostProcessor<dim>>(
communicator, post_processor_database,
thermal_physics->get_dof_handler(),
mechanical_physics->get_dof_handler());
}
else
{
post_processor = std::make_unique<adamantine::PostProcessor<dim>>(
communicator, post_processor_database,
thermal_output ? thermal_physics->get_dof_handler()
: mechanical_physics->get_dof_handler());
}
// Get the checkpoint and restart subtrees
boost::optional<boost::property_tree::ptree const &>
checkpoint_optional_database = database.get_child_optional("checkpoint");
boost::optional<boost::property_tree::ptree const &>
restart_optional_database = database.get_child_optional("restart");
unsigned int time_steps_checkpoint = std::numeric_limits<unsigned int>::max();
std::string checkpoint_filename;
bool checkpoint_overwrite = true;
if (checkpoint_optional_database)
{
auto checkpoint_database = checkpoint_optional_database.get();
// PropertyTreeInput checkpoint.time_steps_between_checkpoint
time_steps_checkpoint =
checkpoint_database.get<unsigned int>("time_steps_between_checkpoint");
// PropertyTreeInput checkpoint.filename_prefix
checkpoint_filename =
checkpoint_database.get<std::string>("filename_prefix");
// PropertyTreeInput checkpoint.overwrite_files
checkpoint_overwrite = checkpoint_database.get<bool>("overwrite_files");
}
bool restart = false;
std::string restart_filename;
if (restart_optional_database)
{
restart = true;
auto restart_database = restart_optional_database.get();
// PropertyTreeInput restart.filename_prefix
restart_filename = restart_database.get<std::string>("filename_prefix");
}
dealii::LA::distributed::Vector<double, MemorySpaceType> temperature;
dealii::LA::distributed::Vector<double, dealii::MemorySpace::Host>
displacement;
if (use_thermal_physics)
{
if (restart == false)
{
thermal_physics->setup();
thermal_physics->initialize_dof_vector(initial_temperature, temperature);
}
else
{
#ifdef ADAMANTINE_WITH_CALIPER
CALI_MARK_BEGIN("restart from file");
#endif
thermal_physics->load_checkpoint(restart_filename, temperature);
#ifdef ADAMANTINE_WITH_CALIPER
CALI_MARK_END("restart from file");
#endif
}
}
if (use_mechanical_physics)
{
// We currently do not support restarting the mechanical simulation.
adamantine::ASSERT_THROW(
restart == false,
"Mechanical simulation cannot be restarted from a file");
if (use_thermal_physics)
{
// Thermo-mechanical simulation
dealii::LA::distributed::Vector<double, dealii::MemorySpace::Host>
temperature_host(temperature.get_partitioner());
temperature_host.import(temperature, dealii::VectorOperation::insert);
mechanical_physics->setup_dofs(thermal_physics->get_dof_handler(),
temperature_host,
thermal_physics->get_has_melted_vector());
}
else
{
// Mechanical only simulation
mechanical_physics->setup_dofs();
}
displacement = mechanical_physics->solve();
}
unsigned int progress = 0;
unsigned int n_time_step = 0;
double time = 0.;
double activation_time_end = -1.;
unsigned int const rank =
dealii::Utilities::MPI::this_mpi_process(communicator);
if (restart == true)
{
if (rank == 0)
{
std::cout << "Restarting from file" << std::endl;
}
std::ifstream file{restart_filename + "_time.txt"};
boost::archive::text_iarchive ia{file};
ia >> time;
ia >> n_time_step;
}
// PropertyTreeInput geometry.deposition_time
double const activation_time =
geometry_database.get<double>("deposition_time", 0.);
// Output the initial solution
output_pvtu(*post_processor, n_time_step, time, thermal_physics, temperature,
mechanical_physics, displacement, material_properties, timers);
++n_time_step;
// Create the bounding boxes used for material deposition
auto [material_deposition_boxes, deposition_times, deposition_cos,
deposition_sin] =
adamantine::create_material_deposition_boxes<dim>(geometry_database,
heat_sources);
// Extract the time-stepping database
boost::property_tree::ptree time_stepping_database =
database.get_child("time_stepping");
// PropertyTreeInput time_stepping.time_step
double time_step = time_stepping_database.get<double>("time_step");
// PropertyTreeInput time_stepping.duration
double const duration = time_stepping_database.get<double>("duration");
// Extract the refinement database
boost::property_tree::ptree refinement_database =
database.get_child("refinement");
// PropertyTreeInput refinement.time_steps_between_refinement
unsigned int const time_steps_refinement =
refinement_database.get("time_steps_between_refinement", 10);
// PropertyTreeInput post_processor.time_steps_between_output
unsigned int const time_steps_output =
post_processor_database.get("time_steps_between_output", 1);
// PropertyTreeInput materials.new_material_temperature
double const new_material_temperature =
database.get("materials.new_material_temperature", 300.);
#ifdef ADAMANTINE_WITH_CALIPER
CALI_CXX_MARK_LOOP_BEGIN(main_loop_id, "main_loop");
#endif
while (time < duration)
{
#ifdef ADAMANTINE_WITH_CALIPER
CALI_CXX_MARK_LOOP_ITERATION(main_loop_id, n_time_step - 1);
#endif
if ((time + time_step) > duration)
time_step = duration - time;
// Refine the mesh after time_steps_refinement time steps.
if (((n_time_step % time_steps_refinement) == 0) && use_thermal_physics)
{
timers[adamantine::refine].start();
double next_refinement_time = time + time_steps_refinement * time_step;
refine_mesh(thermal_physics, material_properties, temperature,
heat_sources, time, next_refinement_time,
time_steps_refinement, refinement_database);
timers[adamantine::refine].stop();
if ((rank == 0) && (verbose_output == true))
std::cout << "n_dofs: " << thermal_physics->get_dof_handler().n_dofs()
<< std::endl;
}
// Add material if necessary.
// We use an epsilon to get the "expected" behavior when the deposition
// time and the time match should match exactly but don't because of
// floating point accuracy.
timers[adamantine::add_material_activate].start();
if (time > activation_time_end)
{
double const eps = time_step / 1e10;
auto activation_start =
std::lower_bound(deposition_times.begin(), deposition_times.end(),
time - eps) -
deposition_times.begin();