int main(int argc, char** argv) {
double br=0.;
if (argc>1) br=0.1;
M5T const m(br);
Basic3DVector<float> axis(0.5,1.,1);
Surface::RotationType rot(axis,0.5*M_PI);
std::cout << rot << std::endl;
Surface::PositionType pos( 0., 0., 0.);
Plane plane(pos,rot);
LocalTrajectoryParameters tpl(-1./3.5, 1.,1., 0.,0.,1.);
GlobalVector mg = plane.toGlobal(tpl.momentum());
GlobalTrajectoryParameters tpg(pos,mg,-1., &m);
double curv = tpg.transverseCurvature();
std::cout << curv << " " << mg.mag() << std::endl;
std::cout << tpg.position() << " " << tpg.momentum() << std::endl;
GlobalTrajectoryParameters tpg0(tpg);
//HelixForwardPlaneCrossing::PositionType zero(0.,0.,0.);
GlobalPoint zero(0.,0.,0.);
std::cout << std::endl;
void Process::setInitialConditions(const int process_id, double const t,
GlobalVector& x)
{
// getDOFTableOfProcess can be overloaded by the specific process.
auto const& dof_table_of_process = getDOFTable(process_id);
auto const& per_process_variables = _process_variables[process_id];
for (std::size_t variable_id = 0;
variable_id < per_process_variables.size();
variable_id++)
{
SpatialPosition pos;
auto const& pv = per_process_variables[variable_id];
DBUG("Set the initial condition of variable %s of process %d.",
pv.get().getName().data(), process_id);
auto const& ic = pv.get().getInitialCondition();
auto const num_comp = pv.get().getNumberOfComponents();
for (int component_id = 0; component_id < num_comp; ++component_id)
{
auto const& mesh_subset =
dof_table_of_process.getMeshSubset(variable_id, component_id);
auto const mesh_id = mesh_subset.getMeshID();
for (auto const* node : mesh_subset.getNodes())
{
MeshLib::Location const l(mesh_id, MeshLib::MeshItemType::Node,
node->getID());
pos.setNodeID(node->getID());
auto const& ic_value = ic(t, pos);
auto global_index =
std::abs(dof_table_of_process.getGlobalIndex(l, variable_id,
component_id));
#ifdef USE_PETSC
// The global indices of the ghost entries of the global
// matrix or the global vectors need to be set as negative
// values for equation assembly, however the global indices
// start from zero. Therefore, any ghost entry with zero
// index is assigned an negative value of the vector size
// or the matrix dimension. To assign the initial value for
// the ghost entries, the negative indices of the ghost
// entries are restored to zero.
if (global_index == x.size())
global_index = 0;
#endif
x.set(global_index, ic_value[component_id]);
}
}
}
}
// TODO that essentially duplicates code which is also present in ProcessOutput.
double getNodalValue(GlobalVector const& x, MeshLib::Mesh const& mesh,
NumLib::LocalToGlobalIndexMap const& dof_table,
std::size_t const node_id,
std::size_t const global_component_id)
{
MeshLib::Location const l{mesh.getID(), MeshLib::MeshItemType::Node,
node_id};
auto const index = dof_table.getLocalIndex(
l, global_component_id, x.getRangeBegin(), x.getRangeEnd());
return x.get(index);
}
void Process::setInitialConditions(double const t, GlobalVector& x)
{
DBUG("Set initial conditions.");
SpatialPosition pos;
for (int variable_id = 0;
variable_id < static_cast<int>(_process_variables.size());
++variable_id)
{
ProcessVariable& pv = _process_variables[variable_id];
auto const& ic = pv.getInitialCondition();
auto const num_comp = pv.getNumberOfComponents();
for (int component_id = 0; component_id < num_comp; ++component_id)
{
auto const& mesh_subsets =
_local_to_global_index_map->getMeshSubsets(variable_id,
component_id);
for (auto const& mesh_subset : mesh_subsets)
{
auto const mesh_id = mesh_subset->getMeshID();
for (auto const* node : mesh_subset->getNodes())
{
MeshLib::Location const l(
mesh_id, MeshLib::MeshItemType::Node, node->getID());
pos.setNodeID(node->getID());
auto const& ic_value = ic(t, pos);
auto global_index =
std::abs(_local_to_global_index_map->getGlobalIndex(
l, variable_id, component_id));
#ifdef USE_PETSC
// The global indices of the ghost entries of the global matrix
// or the global vectors need to be set as negative values for
// equation assembly, however the global indices start from
// zero. Therefore, any ghost entry with zero index is assigned
// an negative value of the vector size or the matrix dimension.
// To assign the initial value for the ghost entries, the
// negative indices of the ghost entries are restored to zero.
if (global_index == x.size())
global_index = 0;
#endif
x.set(global_index, ic_value[component_id]);
}
}
}
}
}
void SmallDeformationNonlocalProcess<DisplacementDim>::
assembleWithJacobianConcreteProcess(const double t, GlobalVector const& x,
GlobalVector const& xdot,
const double dxdot_dx,
const double dx_dx, GlobalMatrix& M,
GlobalMatrix& K, GlobalVector& b,
GlobalMatrix& Jac)
{
DBUG("AssembleWithJacobian SmallDeformationNonlocalProcess.");
std::vector<std::reference_wrapper<NumLib::LocalToGlobalIndexMap>>
dof_table = {std::ref(*_local_to_global_index_map)};
const int process_id = 0;
ProcessLib::ProcessVariable const& pv = getProcessVariables(process_id)[0];
// Call global assembler for each local assembly item.
GlobalExecutor::executeSelectedMemberDereferenced(
_global_assembler, &VectorMatrixAssembler::assembleWithJacobian,
_local_assemblers, pv.getActiveElementIDs(), dof_table, t, x, xdot,
dxdot_dx, dx_dx, M, K, b, Jac, _coupled_solutions);
b.copyValues(*_nodal_forces);
std::transform(_nodal_forces->begin(), _nodal_forces->end(),
_nodal_forces->begin(), [](double val) { return -val; });
}
void VectorMatrixAssembler::preAssemble(
const std::size_t mesh_item_id, LocalAssemblerInterface& local_assembler,
const NumLib::LocalToGlobalIndexMap& dof_table, const double t,
const GlobalVector& x)
{
auto const indices = NumLib::getIndices(mesh_item_id, dof_table);
auto const local_x = x.get(indices);
local_assembler.preAssemble(t, local_x);
}
void oldCode(const GlobalPoint & P1, const GlobalPoint & P2) {
typedef TkRotation<double> Rotation;
typedef Basic2DVector<double> Point2D;
GlobalVector aX = GlobalVector( P1.x(), P1.y(), 0.).unit();
GlobalVector aY( -aX.y(), aX.x(), 0.);
GlobalVector aZ( 0., 0., 1.);
TkRotation<double > theRotation = Rotation(aX,aY,aZ);
PointUV p1(Point2D(P1.x(),P1.y()), &theRotation);
PointUV p2(Point2D(P2.x(),P2.y()), &theRotation);
std::cout << "\nold for " << P1 <<", " << P2 << std::endl;
std::cout << theRotation << std::endl;
std::cout << p1.u() << " " << p1.v() << std::endl;
std::cout << p2.u() << " " << p2.v() << std::endl;
std::cout << p1.unmap() << std::endl;
std::cout << p2.unmap() << std::endl;
}
Eigen::Vector3d HTProcess::getFlux(std::size_t element_id,
MathLib::Point3d const& p,
double const t,
GlobalVector const& x) const
{
// fetch local_x from primary variable
std::vector<GlobalIndexType> indices_cache;
auto const r_c_indices = NumLib::getRowColumnIndices(
element_id, *_local_to_global_index_map, indices_cache);
std::vector<double> local_x(x.get(r_c_indices.rows));
return _local_assemblers[element_id]->getFlux(p, t, local_x);
}
void getVectorValues(
GlobalVector const& x,
NumLib::LocalToGlobalIndexMap::RowColumnIndices const& r_c_indices,
std::vector<double>& local_x)
{
auto const& indices = r_c_indices.rows;
local_x.clear();
local_x.reserve(indices.size());
for (auto i : indices)
{
local_x.emplace_back(x.get(i));
}
}
void PhaseFieldProcess<DisplacementDim>::assembleWithJacobianConcreteProcess(
const double t, GlobalVector const& x, GlobalVector const& xdot,
const double dxdot_dx, const double dx_dx, 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("AssembleJacobian PhaseFieldProcess for the monolithic scheme.");
dof_tables.emplace_back(*_local_to_global_index_map);
}
else
{
// For the staggered scheme
if (_coupled_solutions->process_id == 1)
{
DBUG(
"Assemble the Jacobian equations of phase field in "
"PhaseFieldProcess for the staggered scheme.");
}
else
{
DBUG(
"Assemble the Jacobian equations of deformation in "
"PhaseFieldProcess for the staggered scheme.");
}
dof_tables.emplace_back(*_local_to_global_index_map);
dof_tables.emplace_back(*_local_to_global_index_map_single_component);
}
// Call global assembler for each local assembly item.
GlobalExecutor::executeMemberDereferenced(
_global_assembler, &VectorMatrixAssembler::assembleWithJacobian,
_local_assemblers, dof_tables, t, x, xdot, dxdot_dx, dx_dx, M, K, b,
Jac, _coupled_solutions);
if (!_use_monolithic_scheme && (_coupled_solutions->process_id == 0))
{
b.copyValues(*_nodal_forces);
std::transform(_nodal_forces->begin(), _nodal_forces->end(),
_nodal_forces->begin(), [](double val) { return -val; });
}
}
NumLib::IterationResult TESProcess::postIterationConcreteProcess(
GlobalVector const& x)
{
bool check_passed = true;
if (!Trafo::constrained)
{
// bounds checking only has to happen if the vapour mass fraction is
// non-logarithmic.
std::vector<GlobalIndexType> indices_cache;
std::vector<double> local_x_cache;
std::vector<double> local_x_prev_ts_cache;
auto check_variable_bounds = [&](std::size_t id,
TESLocalAssemblerInterface& loc_asm) {
auto const r_c_indices = NumLib::getRowColumnIndices(
id, *this->_local_to_global_index_map, indices_cache);
local_x_cache = x.get(r_c_indices.rows);
local_x_prev_ts_cache = _x_previous_timestep->get(r_c_indices.rows);
if (!loc_asm.checkBounds(local_x_cache, local_x_prev_ts_cache))
check_passed = false;
};
GlobalExecutor::executeDereferenced(check_variable_bounds,
_local_assemblers);
}
if (!check_passed)
return NumLib::IterationResult::REPEAT_ITERATION;
// TODO remove
DBUG("ts %lu iteration %lu (in current ts: %lu) try %u accepted",
_assembly_params.timestep, _assembly_params.total_iteration,
_assembly_params.iteration_in_current_timestep,
_assembly_params.number_of_try_of_iteration);
_assembly_params.number_of_try_of_iteration = 0;
return NumLib::IterationResult::SUCCESS;
}
void VectorMatrixAssembler::assemble(
const std::size_t mesh_item_id, LocalAssemblerInterface& local_assembler,
std::vector<std::reference_wrapper<NumLib::LocalToGlobalIndexMap>> const&
dof_tables,
const double t, const GlobalVector& x, GlobalMatrix& M, GlobalMatrix& K,
GlobalVector& b, CoupledSolutionsForStaggeredScheme const* const cpl_xs)
{
std::vector<std::vector<GlobalIndexType>> indices_of_processes;
indices_of_processes.reserve(dof_tables.size());
for (std::size_t i = 0; i < dof_tables.size(); i++)
{
indices_of_processes.emplace_back(
NumLib::getIndices(mesh_item_id, dof_tables[i].get()));
}
auto const& indices = (cpl_xs == nullptr)
? indices_of_processes[0]
: indices_of_processes[cpl_xs->process_id];
_local_M_data.clear();
_local_K_data.clear();
_local_b_data.clear();
if (cpl_xs == nullptr)
{
auto const local_x = x.get(indices);
local_assembler.assemble(t, local_x, _local_M_data, _local_K_data,
_local_b_data);
}
else
{
auto local_coupled_xs0 =
getPreviousLocalSolutions(*cpl_xs, indices_of_processes);
auto local_coupled_xs =
getCurrentLocalSolutions(*cpl_xs, indices_of_processes);
ProcessLib::LocalCoupledSolutions local_coupled_solutions(
cpl_xs->dt, cpl_xs->process_id, std::move(local_coupled_xs0),
std::move(local_coupled_xs));
local_assembler.assembleForStaggeredScheme(t, _local_M_data,
_local_K_data, _local_b_data,
local_coupled_solutions);
}
auto const num_r_c = indices.size();
auto const r_c_indices =
NumLib::LocalToGlobalIndexMap::RowColumnIndices(indices, indices);
if (!_local_M_data.empty())
{
auto const local_M = MathLib::toMatrix(_local_M_data, num_r_c, num_r_c);
M.add(r_c_indices, local_M);
}
if (!_local_K_data.empty())
{
auto const local_K = MathLib::toMatrix(_local_K_data, num_r_c, num_r_c);
K.add(r_c_indices, local_K);
}
if (!_local_b_data.empty())
{
assert(_local_b_data.size() == num_r_c);
b.add(indices, _local_b_data);
}
}
void VectorMatrixAssembler::assembleWithJacobian(
std::size_t const mesh_item_id, LocalAssemblerInterface& local_assembler,
std::vector<std::reference_wrapper<NumLib::LocalToGlobalIndexMap>> const&
dof_tables,
const double t, GlobalVector const& x, GlobalVector const& xdot,
const double dxdot_dx, const double dx_dx, GlobalMatrix& M, GlobalMatrix& K,
GlobalVector& b, GlobalMatrix& Jac,
CoupledSolutionsForStaggeredScheme const* const cpl_xs)
{
std::vector<std::vector<GlobalIndexType>> indices_of_processes;
indices_of_processes.reserve(dof_tables.size());
for (std::size_t i = 0; i < dof_tables.size(); i++)
{
indices_of_processes.emplace_back(
NumLib::getIndices(mesh_item_id, dof_tables[i].get()));
}
auto const& indices = (cpl_xs == nullptr)
? indices_of_processes[0]
: indices_of_processes[cpl_xs->process_id];
auto const local_xdot = xdot.get(indices);
_local_M_data.clear();
_local_K_data.clear();
_local_b_data.clear();
_local_Jac_data.clear();
if (cpl_xs == nullptr)
{
auto const local_x = x.get(indices);
_jacobian_assembler->assembleWithJacobian(
local_assembler, t, local_x, local_xdot, dxdot_dx, dx_dx,
_local_M_data, _local_K_data, _local_b_data, _local_Jac_data);
}
else
{
auto local_coupled_xs0 =
getPreviousLocalSolutions(*cpl_xs, indices_of_processes);
auto local_coupled_xs =
getCurrentLocalSolutions(*cpl_xs, indices_of_processes);
ProcessLib::LocalCoupledSolutions local_coupled_solutions(
cpl_xs->dt, cpl_xs->process_id, std::move(local_coupled_xs0),
std::move(local_coupled_xs));
_jacobian_assembler->assembleWithJacobianForStaggeredScheme(
local_assembler, t, local_xdot, dxdot_dx, dx_dx, _local_M_data,
_local_K_data, _local_b_data, _local_Jac_data,
local_coupled_solutions);
}
auto const num_r_c = indices.size();
auto const r_c_indices =
NumLib::LocalToGlobalIndexMap::RowColumnIndices(indices, indices);
if (!_local_M_data.empty())
{
auto const local_M = MathLib::toMatrix(_local_M_data, num_r_c, num_r_c);
M.add(r_c_indices, local_M);
}
if (!_local_K_data.empty())
{
auto const local_K = MathLib::toMatrix(_local_K_data, num_r_c, num_r_c);
K.add(r_c_indices, local_K);
}
if (!_local_b_data.empty())
{
assert(_local_b_data.size() == num_r_c);
b.add(indices, _local_b_data);
}
if (!_local_Jac_data.empty())
{
auto const local_Jac =
MathLib::toMatrix(_local_Jac_data, num_r_c, num_r_c);
Jac.add(r_c_indices, local_Jac);
}
else
{
OGS_FATAL(
"No Jacobian has been assembled! This might be due to programming "
"errors in the local assembler of the current process.");
}
}
void LocalLinearLeastSquaresExtrapolator::extrapolateElement(
std::size_t const element_index,
const unsigned num_components,
ExtrapolatableElementCollection const& extrapolatables,
const double t,
GlobalVector const& current_solution,
LocalToGlobalIndexMap const& dof_table,
GlobalVector& counts)
{
auto const& integration_point_values =
extrapolatables.getIntegrationPointValues(
element_index, t, current_solution, dof_table,
_integration_point_values_cache);
auto const& N_0 = extrapolatables.getShapeMatrix(element_index, 0);
auto const num_nodes = static_cast<unsigned>(N_0.cols());
auto const num_values =
static_cast<unsigned>(integration_point_values.size());
if (num_values % num_components != 0)
OGS_FATAL(
"The number of computed integration point values is not divisable "
"by the number of num_components. Maybe the computed property is "
"not a %d-component vector for each integration point.",
num_components);
// number of integration points in the element
const auto num_int_pts = num_values / num_components;
if (num_int_pts < num_nodes)
OGS_FATAL(
"Least squares is not possible if there are more nodes than"
"integration points.");
auto const pair_it_inserted = _qr_decomposition_cache.emplace(
std::make_pair(num_nodes, num_int_pts), CachedData{});
auto& cached_data = pair_it_inserted.first->second;
if (pair_it_inserted.second)
{
DBUG("Computing new singular value decomposition");
// interpolation_matrix * nodal_values = integration_point_values
// We are going to pseudo-invert this relation now using singular value
// decomposition.
auto& interpolation_matrix = cached_data.A;
interpolation_matrix.resize(num_int_pts, num_nodes);
interpolation_matrix.row(0) = N_0;
for (unsigned int_pt = 1; int_pt < num_int_pts; ++int_pt)
{
auto const& shp_mat =
extrapolatables.getShapeMatrix(element_index, int_pt);
assert(shp_mat.cols() == num_nodes);
// copy shape matrix to extrapolation matrix row-wise
interpolation_matrix.row(int_pt) = shp_mat;
}
// JacobiSVD is extremely reliable, but fast only for small matrices.
// But we usually have small matrices and we don't compute very often.
// Cf.
// http://eigen.tuxfamily.org/dox/group__TopicLinearAlgebraDecompositions.html
//
// Decomposes interpolation_matrix = U S V^T.
Eigen::JacobiSVD<Eigen::MatrixXd> svd(
interpolation_matrix, Eigen::ComputeThinU | Eigen::ComputeThinV);
auto const& S = svd.singularValues();
auto const& U = svd.matrixU();
auto const& V = svd.matrixV();
// Compute and save the pseudo inverse V * S^{-1} * U^T.
auto const rank = svd.rank();
assert(rank == num_nodes);
// cf. http://eigen.tuxfamily.org/dox/JacobiSVD_8h_source.html
cached_data.A_pinv.noalias() = V.leftCols(rank) *
S.head(rank).asDiagonal().inverse() *
U.leftCols(rank).transpose();
}
else if (cached_data.A.row(0) != N_0)
{
OGS_FATAL("The cached and the passed shapematrices differ.");
}
auto const& global_indices =
_dof_table_single_component(element_index, 0).rows;
if (num_components == 1)
{
auto const integration_point_values_vec =
MathLib::toVector(integration_point_values);
// Apply the pre-computed pseudo-inverse.
Eigen::VectorXd const nodal_values =
cached_data.A_pinv * integration_point_values_vec;
// TODO does that give rise to PETSc problems? E.g., writing to ghost
// nodes? Furthermore: Is ghost nodes communication necessary for PETSc?
_nodal_values->add(global_indices, nodal_values);
counts.add(global_indices,
std::vector<double>(global_indices.size(), 1.0));
}
else
{
auto const integration_point_values_mat = MathLib::toMatrix(
integration_point_values, num_components, num_int_pts);
// Apply the pre-computed pseudo-inverse.
Eigen::MatrixXd const nodal_values =
cached_data.A_pinv * integration_point_values_mat.transpose();
std::vector<GlobalIndexType> indices;
indices.reserve(num_components * global_indices.size());
// _nodal_values is ordered location-wise
for (unsigned comp = 0; comp < num_components; ++comp)
{
for (auto i : global_indices)
{
indices.push_back(num_components * i + comp);
}
}
// Nodal_values are passed as a raw pointer, because PETScVector and
// EigenVector implementations differ slightly.
_nodal_values->add(indices, nodal_values.data());
counts.add(indices, std::vector<double>(indices.size(), 1.0));
}
}