Revision 5b17b2bcb5d69d5e7597f2b2ca8802e222c3fb1a authored by wenqing on 01 November 2021, 17:23:02 UTC, committed by wenqing on 01 November 2021, 17:23:02 UTC
[GMSH2OGS] Added a test to test the conversion of linear elements See merge request ogs/ogs!3860
TH2MProcess.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 "TH2MProcess.h"
#include <cassert>
#include "MeshLib/Elements/Utils.h"
#include "NumLib/DOF/ComputeSparsityPattern.h"
#include "ProcessLib/Process.h"
#include "ProcessLib/TH2M/CreateLocalAssemblers.h"
#include "TH2MFEM.h"
#include "TH2MProcessData.h"
namespace ProcessLib
{
namespace TH2M
{
template <int DisplacementDim>
TH2MProcess<DisplacementDim>::TH2MProcess(
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,
TH2MProcessData<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);
// TODO (naumov) remove ip suffix. Probably needs modification of the mesh
// properties, s.t. there is no "overlapping" with cell/point data.
// See getOrCreateMeshProperty.
_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>(
"saturation_ip", 1 /*n components*/, integration_order,
_local_assemblers, &LocalAssemblerInterface::getSaturation));
_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 TH2MProcess<DisplacementDim>::isLinear() const
{
return false;
}
template <int DisplacementDim>
MathLib::MatrixSpecifications
TH2MProcess<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 == deformation_process_id)
{
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 TH2MProcess<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 gas pressure, which is the first
std::vector<MeshLib::MeshSubset> all_mesh_subsets{
*_mesh_subset_base_nodes};
// For capillary pressure, which is the second
all_mesh_subsets.push_back(*_mesh_subset_base_nodes);
// For temperature, which is the third
all_mesh_subsets.push_back(*_mesh_subset_base_nodes);
// For displacement.
std::generate_n(
std::back_inserter(all_mesh_subsets),
getProcessVariables(monolithic_process_id)[deformation_process_id]
.get()
.getNumberOfGlobalComponents(),
[&]() { return *_mesh_subset_all_nodes; });
std::vector<int> const vec_n_components{
n_gas_pressure_components, n_capillary_pressure_components,
n_temperature_components, n_displacement_components};
_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
{
OGS_FATAL("A Staggered version of TH2M is not implemented.");
}
}
template <int DisplacementDim>
void TH2MProcess<DisplacementDim>::initializeConcreteProcess(
NumLib::LocalToGlobalIndexMap const& dof_table,
MeshLib::Mesh const& mesh,
unsigned const integration_order)
{
const int mechanical_process_id =
_use_monolithic_scheme ? 0 : deformation_process_id;
const int deformation_variable_id =
_use_monolithic_scheme ? deformation_process_id : 0;
ProcessLib::TH2M::createLocalAssemblers<DisplacementDim,
TH2MLocalAssembler>(
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);
auto add_secondary_variable = [&](std::string const& name,
int const num_components,
auto get_ip_values_function)
{
_secondary_variables.addSecondaryVariable(
name,
makeExtrapolator(num_components, getExtrapolator(),
_local_assemblers,
std::move(get_ip_values_function)));
};
add_secondary_variable("sigma",
MathLib::KelvinVector::KelvinVectorType<
DisplacementDim>::RowsAtCompileTime,
&LocalAssemblerInterface::getIntPtSigma);
add_secondary_variable("epsilon",
MathLib::KelvinVector::KelvinVectorType<
DisplacementDim>::RowsAtCompileTime,
&LocalAssemblerInterface::getIntPtEpsilon);
add_secondary_variable("velocity_gas", mesh.getDimension(),
&LocalAssemblerInterface::getIntPtDarcyVelocityGas);
add_secondary_variable(
"velocity_liquid", mesh.getDimension(),
&LocalAssemblerInterface::getIntPtDarcyVelocityLiquid);
add_secondary_variable("saturation", 1,
&LocalAssemblerInterface::getIntPtSaturation);
add_secondary_variable("vapour_pressure", 1,
&LocalAssemblerInterface::getIntPtVapourPressure);
add_secondary_variable("porosity", 1,
&LocalAssemblerInterface::getIntPtPorosity);
add_secondary_variable("gas_density", 1,
&LocalAssemblerInterface::getIntPtGasDensity);
add_secondary_variable("solid_density", 1,
&LocalAssemblerInterface::getIntPtSolidDensity);
add_secondary_variable("liquid_density", 1,
&LocalAssemblerInterface::getIntPtLiquidDensity);
add_secondary_variable("mole_fraction_gas", 1,
&LocalAssemblerInterface::getIntPtMoleFractionGas);
add_secondary_variable("mass_fraction_gas", 1,
&LocalAssemblerInterface::getIntPtMassFractionGas);
add_secondary_variable(
"mass_fraction_liquid", 1,
&LocalAssemblerInterface::getIntPtMassFractionLiquid);
add_secondary_variable(
"relative_permeability_gas", 1,
&LocalAssemblerInterface::getIntPtRelativePermeabilityGas);
add_secondary_variable(
"relative_permeability_liquid", 1,
&LocalAssemblerInterface::getIntPtRelativePermeabilityLiquid);
add_secondary_variable("enthalpy_gas", 1,
&LocalAssemblerInterface::getIntPtEnthalpyGas);
add_secondary_variable("enthalpy_liquid", 1,
&LocalAssemblerInterface::getIntPtEnthalpyLiquid);
add_secondary_variable("enthalpy_solid", 1,
&LocalAssemblerInterface::getIntPtEnthalpySolid);
_process_data.element_saturation = MeshLib::getOrCreateMeshProperty<double>(
const_cast<MeshLib::Mesh&>(mesh), "saturation_avg",
MeshLib::MeshItemType::Cell, 1);
_process_data.gas_pressure_interpolated =
MeshLib::getOrCreateMeshProperty<double>(
const_cast<MeshLib::Mesh&>(mesh), "gas_pressure_interpolated",
MeshLib::MeshItemType::Node, 1);
_process_data.capillary_pressure_interpolated =
MeshLib::getOrCreateMeshProperty<double>(
const_cast<MeshLib::Mesh&>(mesh), "capillary_pressure_interpolated",
MeshLib::MeshItemType::Node, 1);
_process_data.liquid_pressure_interpolated =
MeshLib::getOrCreateMeshProperty<double>(
const_cast<MeshLib::Mesh&>(mesh), "liquid_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& _meshproperty =
*mesh.getProperties().template getPropertyVector<double>(name);
// The mesh property must be defined on integration points.
if (_meshproperty.getMeshItemType() !=
MeshLib::MeshItemType::IntegrationPoint)
{
continue;
}
auto const ip_meta_data = getIntegrationPointMetaData(mesh, name);
// Check the number of components.
if (ip_meta_data.n_components !=
_meshproperty.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,
_meshproperty.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, &_meshproperty[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 TH2MProcess<DisplacementDim>::initializeBoundaryConditions()
{
if (_use_monolithic_scheme)
{
initializeProcessBoundaryConditionsAndSourceTerms(
*_local_to_global_index_map, monolithic_process_id);
return;
}
// Staggered scheme:
OGS_FATAL("A Staggered version of TH2M is not implemented.");
}
template <int DisplacementDim>
void TH2MProcess<DisplacementDim>::setInitialConditionsConcreteProcess(
std::vector<GlobalVector*>& x, double const t, int const process_id)
{
if (process_id != 0)
{
return;
}
DBUG("Set initial conditions of TH2MProcess.");
GlobalExecutor::executeMemberOnDereferenced(
&LocalAssemblerInterface::setInitialConditions, _local_assemblers,
getDOFTable(process_id), *x[process_id], t, _use_monolithic_scheme,
process_id);
}
template <int DisplacementDim>
void TH2MProcess<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 TH2M");
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 TH2MProcess<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 TH2M for the monolithic scheme.");
dof_tables.emplace_back(*_local_to_global_index_map);
}
else
{
// For the staggered scheme
OGS_FATAL("A Staggered version of TH2M is not implemented.");
}
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 TH2MProcess<DisplacementDim>::preTimestepConcreteProcess(
std::vector<GlobalVector*> const& x, double const t, double const dt,
const int process_id)
{
DBUG("PreTimestep TH2MProcess.");
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 TH2MProcess<DisplacementDim>::postTimestepConcreteProcess(
std::vector<GlobalVector*> const& x, double const t, double const dt,
const int process_id)
{
DBUG("PostTimestep TH2MProcess.");
auto const dof_tables = getDOFTables(x.size());
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 TH2MProcess<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 TH2MProcess.");
auto const dof_tables = getDOFTables(x.size());
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>
TH2MProcess<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& TH2MProcess<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 <int DisplacementDim>
std::vector<NumLib::LocalToGlobalIndexMap const*>
TH2MProcess<DisplacementDim>::getDOFTables(int const number_of_processes) const
{
std::vector<NumLib::LocalToGlobalIndexMap const*> dof_tables;
dof_tables.reserve(number_of_processes);
std::generate_n(std::back_inserter(dof_tables), number_of_processes,
[&]() { return &getDOFTable(dof_tables.size()); });
return dof_tables;
}
template class TH2MProcess<2>;
template class TH2MProcess<3>;
} // namespace TH2M
} // namespace ProcessLib
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