https://gitlab.opengeosys.org/ogs/ogs.git
Tip revision: e8b2807fcb4e30cbab03736efd92539dd1ba4ca1 authored by Norbert Grunwald on 20 September 2021, 13:10:09 UTC
update tests.cmake to inclide phase transition dissolution tst
update tests.cmake to inclide phase transition dissolution tst
Tip revision: e8b2807
ThermoHydroMechanicsProcess.cpp
/**
* \file
* \copyright
* Copyright (c) 2012-2021, OpenGeoSys Community (http://www.opengeosys.org)
* Distributed under a Modified BSD License.
* See accompanying file LICENSE.txt or
* http://www.opengeosys.org/project/license
*
*/
#include "ThermoHydroMechanicsProcess.h"
#include <cassert>
#include "MeshLib/Elements/Utils.h"
#include "NumLib/DOF/ComputeSparsityPattern.h"
#include "ProcessLib/Process.h"
#include "ProcessLib/ThermoHydroMechanics/CreateLocalAssemblers.h"
#include "ThermoHydroMechanicsFEM.h"
#include "ThermoHydroMechanicsProcessData.h"
namespace ProcessLib
{
namespace ThermoHydroMechanics
{
template <int DisplacementDim>
ThermoHydroMechanicsProcess<DisplacementDim>::ThermoHydroMechanicsProcess(
std::string name,
MeshLib::Mesh& mesh,
std::unique_ptr<ProcessLib::AbstractJacobianAssembler>&& jacobian_assembler,
std::vector<std::unique_ptr<ParameterLib::ParameterBase>> const& parameters,
unsigned const integration_order,
std::vector<std::vector<std::reference_wrapper<ProcessVariable>>>&&
process_variables,
ThermoHydroMechanicsProcessData<DisplacementDim>&& process_data,
SecondaryVariableCollection&& secondary_variables,
bool const use_monolithic_scheme)
: Process(std::move(name), mesh, std::move(jacobian_assembler), parameters,
integration_order, std::move(process_variables),
std::move(secondary_variables), use_monolithic_scheme),
_process_data(std::move(process_data))
{
_nodal_forces = MeshLib::getOrCreateMeshProperty<double>(
mesh, "NodalForces", MeshLib::MeshItemType::Node, DisplacementDim);
_hydraulic_flow = MeshLib::getOrCreateMeshProperty<double>(
mesh, "HydraulicFlow", MeshLib::MeshItemType::Node, 1);
_integration_point_writer.emplace_back(
std::make_unique<IntegrationPointWriter>(
"sigma_ip",
static_cast<int>(mesh.getDimension() == 2 ? 4 : 6) /*n components*/,
integration_order, _local_assemblers,
&LocalAssemblerInterface::getSigma));
_integration_point_writer.emplace_back(
std::make_unique<IntegrationPointWriter>(
"epsilon_ip",
static_cast<int>(mesh.getDimension() == 2 ? 4 : 6) /*n components*/,
integration_order, _local_assemblers,
&LocalAssemblerInterface::getEpsilon));
}
template <int DisplacementDim>
bool ThermoHydroMechanicsProcess<DisplacementDim>::isLinear() const
{
return false;
}
template <int DisplacementDim>
MathLib::MatrixSpecifications
ThermoHydroMechanicsProcess<DisplacementDim>::getMatrixSpecifications(
const int process_id) const
{
// For the monolithic scheme or the M process (deformation) in the staggered
// scheme.
if (_use_monolithic_scheme || process_id == 2)
{
auto const& l = *_local_to_global_index_map;
return {l.dofSizeWithoutGhosts(), l.dofSizeWithoutGhosts(),
&l.getGhostIndices(), &this->_sparsity_pattern};
}
// For staggered scheme and T or H process (pressure).
auto const& l = *_local_to_global_index_map_with_base_nodes;
return {l.dofSizeWithoutGhosts(), l.dofSizeWithoutGhosts(),
&l.getGhostIndices(), &_sparsity_pattern_with_linear_element};
}
template <int DisplacementDim>
void ThermoHydroMechanicsProcess<DisplacementDim>::constructDofTable()
{
// Create single component dof in every of the mesh's nodes.
_mesh_subset_all_nodes =
std::make_unique<MeshLib::MeshSubset>(_mesh, _mesh.getNodes());
// Create single component dof in the mesh's base nodes.
_base_nodes = MeshLib::getBaseNodes(_mesh.getElements());
_mesh_subset_base_nodes =
std::make_unique<MeshLib::MeshSubset>(_mesh, _base_nodes);
// TODO move the two data members somewhere else.
// for extrapolation of secondary variables of stress or strain
std::vector<MeshLib::MeshSubset> all_mesh_subsets_single_component{
*_mesh_subset_all_nodes};
_local_to_global_index_map_single_component =
std::make_unique<NumLib::LocalToGlobalIndexMap>(
std::move(all_mesh_subsets_single_component),
// by location order is needed for output
NumLib::ComponentOrder::BY_LOCATION);
if (_use_monolithic_scheme)
{
// For temperature, which is the first
std::vector<MeshLib::MeshSubset> all_mesh_subsets{
*_mesh_subset_base_nodes};
// For pressure, which is the second
all_mesh_subsets.push_back(*_mesh_subset_base_nodes);
// For displacement.
const int monolithic_process_id = 0;
std::generate_n(std::back_inserter(all_mesh_subsets),
getProcessVariables(monolithic_process_id)[2]
.get()
.getNumberOfGlobalComponents(),
[&]() { return *_mesh_subset_all_nodes; });
std::vector<int> const vec_n_components{1, 1, DisplacementDim};
_local_to_global_index_map =
std::make_unique<NumLib::LocalToGlobalIndexMap>(
std::move(all_mesh_subsets), vec_n_components,
NumLib::ComponentOrder::BY_LOCATION);
assert(_local_to_global_index_map);
}
else
{
// For displacement equation.
const int process_id = 2;
std::vector<MeshLib::MeshSubset> all_mesh_subsets;
std::generate_n(std::back_inserter(all_mesh_subsets),
getProcessVariables(process_id)[0]
.get()
.getNumberOfGlobalComponents(),
[&]() { return *_mesh_subset_all_nodes; });
std::vector<int> const vec_n_components{DisplacementDim};
_local_to_global_index_map =
std::make_unique<NumLib::LocalToGlobalIndexMap>(
std::move(all_mesh_subsets), vec_n_components,
NumLib::ComponentOrder::BY_LOCATION);
// For pressure equation or temperature equation.
// Collect the mesh subsets with base nodes in a vector.
std::vector<MeshLib::MeshSubset> all_mesh_subsets_base_nodes{
*_mesh_subset_base_nodes};
_local_to_global_index_map_with_base_nodes =
std::make_unique<NumLib::LocalToGlobalIndexMap>(
std::move(all_mesh_subsets_base_nodes),
// by location order is needed for output
NumLib::ComponentOrder::BY_LOCATION);
_sparsity_pattern_with_linear_element = NumLib::computeSparsityPattern(
*_local_to_global_index_map_with_base_nodes, _mesh);
assert(_local_to_global_index_map);
assert(_local_to_global_index_map_with_base_nodes);
}
}
template <int DisplacementDim>
void ThermoHydroMechanicsProcess<DisplacementDim>::initializeConcreteProcess(
NumLib::LocalToGlobalIndexMap const& dof_table,
MeshLib::Mesh const& mesh,
unsigned const integration_order)
{
const int mechanical_process_id = _use_monolithic_scheme ? 0 : 2;
const int deformation_variable_id = _use_monolithic_scheme ? 2 : 0;
ProcessLib::ThermoHydroMechanics::createLocalAssemblers<
DisplacementDim, ThermoHydroMechanicsLocalAssembler>(
mesh.getDimension(), mesh.getElements(), dof_table,
// use displacement process variable to set shape function order
getProcessVariables(mechanical_process_id)[deformation_variable_id]
.get()
.getShapeFunctionOrder(),
_local_assemblers, mesh.isAxiallySymmetric(), integration_order,
_process_data);
_secondary_variables.addSecondaryVariable(
"sigma",
makeExtrapolator(MathLib::KelvinVector::KelvinVectorType<
DisplacementDim>::RowsAtCompileTime,
getExtrapolator(), _local_assemblers,
&LocalAssemblerInterface::getIntPtSigma));
_secondary_variables.addSecondaryVariable(
"epsilon",
makeExtrapolator(MathLib::KelvinVector::KelvinVectorType<
DisplacementDim>::RowsAtCompileTime,
getExtrapolator(), _local_assemblers,
&LocalAssemblerInterface::getIntPtEpsilon));
_secondary_variables.addSecondaryVariable(
"velocity",
makeExtrapolator(mesh.getDimension(), getExtrapolator(),
_local_assemblers,
&LocalAssemblerInterface::getIntPtDarcyVelocity));
_process_data.pressure_interpolated =
MeshLib::getOrCreateMeshProperty<double>(
const_cast<MeshLib::Mesh&>(mesh), "pressure_interpolated",
MeshLib::MeshItemType::Node, 1);
_process_data.temperature_interpolated =
MeshLib::getOrCreateMeshProperty<double>(
const_cast<MeshLib::Mesh&>(mesh), "temperature_interpolated",
MeshLib::MeshItemType::Node, 1);
// Set initial conditions for integration point data.
for (auto const& ip_writer : _integration_point_writer)
{
// Find the mesh property with integration point writer's name.
auto const& name = ip_writer->name();
if (!mesh.getProperties().existsPropertyVector<double>(name))
{
continue;
}
auto const& mesh_property =
*mesh.getProperties().template getPropertyVector<double>(name);
// The mesh property must be defined on integration points.
if (mesh_property.getMeshItemType() !=
MeshLib::MeshItemType::IntegrationPoint)
{
continue;
}
auto const ip_meta_data = getIntegrationPointMetaData(mesh, name);
// Check the number of components.
if (ip_meta_data.n_components !=
mesh_property.getNumberOfGlobalComponents())
{
OGS_FATAL(
"Different number of components in meta data ({:d}) than in "
"the integration point field data for '{:s}': {:d}.",
ip_meta_data.n_components, name,
mesh_property.getNumberOfGlobalComponents());
}
// Now we have a properly named vtk's field data array and the
// corresponding meta data.
std::size_t position = 0;
for (auto& local_asm : _local_assemblers)
{
std::size_t const integration_points_read =
local_asm->setIPDataInitialConditions(
name, &mesh_property[position],
ip_meta_data.integration_order);
if (integration_points_read == 0)
{
OGS_FATAL(
"No integration points read in the integration point "
"initial conditions set function.");
}
position += integration_points_read * ip_meta_data.n_components;
}
}
// Initialize local assemblers after all variables have been set.
GlobalExecutor::executeMemberOnDereferenced(
&LocalAssemblerInterface::initialize, _local_assemblers,
*_local_to_global_index_map);
}
template <int DisplacementDim>
void ThermoHydroMechanicsProcess<
DisplacementDim>::initializeBoundaryConditions()
{
if (_use_monolithic_scheme)
{
const int process_id_of_thermohydromechancs = 0;
initializeProcessBoundaryConditionsAndSourceTerms(
*_local_to_global_index_map, process_id_of_thermohydromechancs);
return;
}
// Staggered scheme:
// for the equations of heat transport
const int thermal_process_id = 0;
initializeProcessBoundaryConditionsAndSourceTerms(
*_local_to_global_index_map_with_base_nodes, thermal_process_id);
// for the equations of mass balance
const int hydraulic_process_id = 1;
initializeProcessBoundaryConditionsAndSourceTerms(
*_local_to_global_index_map_with_base_nodes, hydraulic_process_id);
// for the equations of deformation.
const int mechanical_process_id = 2;
initializeProcessBoundaryConditionsAndSourceTerms(
*_local_to_global_index_map, mechanical_process_id);
}
template <int DisplacementDim>
void ThermoHydroMechanicsProcess<DisplacementDim>::assembleConcreteProcess(
const double t, double const dt, std::vector<GlobalVector*> const& x,
std::vector<GlobalVector*> const& xdot, int const process_id,
GlobalMatrix& M, GlobalMatrix& K, GlobalVector& b)
{
DBUG("Assemble the equations for ThermoHydroMechanics");
std::vector<std::reference_wrapper<NumLib::LocalToGlobalIndexMap>>
dof_table = {std::ref(*_local_to_global_index_map)};
ProcessLib::ProcessVariable const& pv = getProcessVariables(process_id)[0];
GlobalExecutor::executeSelectedMemberDereferenced(
_global_assembler, &VectorMatrixAssembler::assemble, _local_assemblers,
pv.getActiveElementIDs(), dof_table, t, dt, x, xdot, process_id, M, K,
b);
}
template <int DisplacementDim>
void ThermoHydroMechanicsProcess<DisplacementDim>::
assembleWithJacobianConcreteProcess(
const double t, double const dt, std::vector<GlobalVector*> const& x,
std::vector<GlobalVector*> const& xdot, const double dxdot_dx,
const double dx_dx, int const process_id, GlobalMatrix& M,
GlobalMatrix& K, GlobalVector& b, GlobalMatrix& Jac)
{
std::vector<std::reference_wrapper<NumLib::LocalToGlobalIndexMap>>
dof_tables;
// For the monolithic scheme
if (_use_monolithic_scheme)
{
DBUG(
"Assemble the Jacobian of ThermoHydroMechanics for the monolithic "
"scheme.");
dof_tables.emplace_back(*_local_to_global_index_map);
}
else
{
// For the staggered scheme
if (process_id == 0)
{
DBUG(
"Assemble the Jacobian equations of heat transport process in "
"ThermoHydroMechanics for the staggered scheme.");
}
else if (process_id == 1)
{
DBUG(
"Assemble the Jacobian equations of liquid fluid process in "
"ThermoHydroMechanics for the staggered scheme.");
}
else
{
DBUG(
"Assemble the Jacobian equations of mechanical process in "
"ThermoHydroMechanics for the staggered scheme.");
}
dof_tables.emplace_back(*_local_to_global_index_map_with_base_nodes);
dof_tables.emplace_back(*_local_to_global_index_map_with_base_nodes);
dof_tables.emplace_back(*_local_to_global_index_map);
}
ProcessLib::ProcessVariable const& pv = getProcessVariables(process_id)[0];
GlobalExecutor::executeSelectedMemberDereferenced(
_global_assembler, &VectorMatrixAssembler::assembleWithJacobian,
_local_assemblers, pv.getActiveElementIDs(), dof_tables, t, dt, x, xdot,
dxdot_dx, dx_dx, process_id, M, K, b, Jac);
auto copyRhs = [&](int const variable_id, auto& output_vector)
{
if (_use_monolithic_scheme)
{
transformVariableFromGlobalVector(b, variable_id, dof_tables[0],
output_vector,
std::negate<double>());
}
else
{
transformVariableFromGlobalVector(b, 0, dof_tables[process_id],
output_vector,
std::negate<double>());
}
};
if (_use_monolithic_scheme || process_id == 1)
{
copyRhs(0, *_hydraulic_flow);
}
if (_use_monolithic_scheme || process_id == 2)
{
copyRhs(1, *_nodal_forces);
}
}
template <int DisplacementDim>
void ThermoHydroMechanicsProcess<DisplacementDim>::preTimestepConcreteProcess(
std::vector<GlobalVector*> const& x, double const t, double const dt,
const int process_id)
{
DBUG("PreTimestep ThermoHydroMechanicsProcess.");
if (hasMechanicalProcess(process_id))
{
ProcessLib::ProcessVariable const& pv =
getProcessVariables(process_id)[0];
GlobalExecutor::executeSelectedMemberOnDereferenced(
&LocalAssemblerInterface::preTimestep, _local_assemblers,
pv.getActiveElementIDs(), *_local_to_global_index_map,
*x[process_id], t, dt);
}
}
template <int DisplacementDim>
void ThermoHydroMechanicsProcess<DisplacementDim>::postTimestepConcreteProcess(
std::vector<GlobalVector*> const& x, double const t, double const dt,
const int process_id)
{
if (process_id != 0)
{
return;
}
DBUG("PostTimestep ThermoHydroMechanicsProcess.");
std::vector<NumLib::LocalToGlobalIndexMap const*> dof_tables;
auto const n_processes = x.size();
dof_tables.reserve(n_processes);
for (std::size_t process_id = 0; process_id < n_processes; ++process_id)
{
dof_tables.push_back(&getDOFTable(process_id));
}
ProcessLib::ProcessVariable const& pv = getProcessVariables(process_id)[0];
GlobalExecutor::executeSelectedMemberOnDereferenced(
&LocalAssemblerInterface::postTimestep, _local_assemblers,
pv.getActiveElementIDs(), dof_tables, x, t, dt);
}
template <int DisplacementDim>
void ThermoHydroMechanicsProcess<DisplacementDim>::
postNonLinearSolverConcreteProcess(GlobalVector const& x,
GlobalVector const& xdot, const double t,
double const dt, const int process_id)
{
if (!hasMechanicalProcess(process_id))
{
return;
}
DBUG("PostNonLinearSolver ThermoHydroMechanicsProcess.");
// Calculate strain, stress or other internal variables of mechanics.
ProcessLib::ProcessVariable const& pv = getProcessVariables(process_id)[0];
GlobalExecutor::executeSelectedMemberOnDereferenced(
&LocalAssemblerInterface::postNonLinearSolver, _local_assemblers,
pv.getActiveElementIDs(), getDOFTable(process_id), x, xdot, t, dt,
_use_monolithic_scheme, process_id);
}
template <int DisplacementDim>
void ThermoHydroMechanicsProcess<DisplacementDim>::
computeSecondaryVariableConcrete(double const t, double const dt,
std::vector<GlobalVector*> const& x,
GlobalVector const& x_dot,
const int process_id)
{
if (process_id != 0)
{
return;
}
DBUG("Compute the secondary variables for ThermoHydroMechanicsProcess.");
std::vector<NumLib::LocalToGlobalIndexMap const*> dof_tables;
auto const n_processes = x.size();
dof_tables.reserve(n_processes);
for (std::size_t process_id = 0; process_id < n_processes; ++process_id)
{
dof_tables.push_back(&getDOFTable(process_id));
}
ProcessLib::ProcessVariable const& pv = getProcessVariables(process_id)[0];
GlobalExecutor::executeSelectedMemberOnDereferenced(
&LocalAssemblerInterface::computeSecondaryVariable, _local_assemblers,
pv.getActiveElementIDs(), dof_tables, t, dt, x, x_dot, process_id);
}
template <int DisplacementDim>
std::tuple<NumLib::LocalToGlobalIndexMap*, bool> ThermoHydroMechanicsProcess<
DisplacementDim>::getDOFTableForExtrapolatorData() const
{
const bool manage_storage = false;
return std::make_tuple(_local_to_global_index_map_single_component.get(),
manage_storage);
}
template <int DisplacementDim>
NumLib::LocalToGlobalIndexMap const&
ThermoHydroMechanicsProcess<DisplacementDim>::getDOFTable(
const int process_id) const
{
if (hasMechanicalProcess(process_id))
{
return *_local_to_global_index_map;
}
// For the equation of pressure
return *_local_to_global_index_map_with_base_nodes;
}
template class ThermoHydroMechanicsProcess<2>;
template class ThermoHydroMechanicsProcess<3>;
} // namespace ThermoHydroMechanics
} // namespace ProcessLib