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588 | // *****************************************************************************
/*!
\file src/PDE/Transport/DGTransport.hpp
\copyright 2012-2015 J. Bakosi,
2016-2018 Los Alamos National Security, LLC.,
2019-2021 Triad National Security, LLC.
All rights reserved. See the LICENSE file for details.
\brief Scalar transport using disccontinous Galerkin discretization
\details This file implements the physics operators governing transported
scalars using disccontinuous Galerkin discretization.
*/
// *****************************************************************************
#ifndef DGTransport_h
#define DGTransport_h
#include <vector>
#include <array>
#include <limits>
#include <cmath>
#include <unordered_set>
#include <map>
#include "Macro.hpp"
#include "Exception.hpp"
#include "Vector.hpp"
#include "Inciter/Options/BC.hpp"
#include "UnsMesh.hpp"
#include "Integrate/Basis.hpp"
#include "Integrate/Quadrature.hpp"
#include "Integrate/Initialize.hpp"
#include "Integrate/Mass.hpp"
#include "Integrate/Surface.hpp"
#include "Integrate/Boundary.hpp"
#include "Integrate/Volume.hpp"
#include "Riemann/Upwind.hpp"
#include "Reconstruction.hpp"
#include "Limiter.hpp"
#include "PrefIndicator.hpp"
namespace inciter {
extern ctr::InputDeck g_inputdeck;
namespace dg {
//! \brief Transport equation used polymorphically with tk::DGPDE
//! \details The template argument(s) specify policies and are used to configure
//! the behavior of the class. The policies are:
//! - Physics - physics configuration, see PDE/Transport/Physics.h
//! - Problem - problem configuration, see PDE/Transport/Problem.h
//! \note The default physics is DGAdvection, set in
//! inciter::deck::check_transport()
template< class Physics, class Problem >
class Transport {
private:
using eq = tag::transport;
public:
//! Constructor
//! \param[in] c Equation system index (among multiple systems configured)
explicit Transport( ncomp_t c ) :
m_physics( Physics() ),
m_problem( Problem() ),
m_system( c ),
m_ncomp(
g_inputdeck.get< tag::component >().get< eq >().at(c) ),
m_offset(
g_inputdeck.get< tag::component >().offset< eq >(c) )
{
// associate boundary condition configurations with state functions, the
// order in which the state functions listed matters, see ctr::bc::Keys
brigand::for_each< ctr::bc::Keys >( ConfigBC< eq >( m_system, m_bc,
{ dirichlet
, invalidBC // Symmetry BC not implemented
, inlet
, outlet
, invalidBC // Characteristic BC not implemented
, extrapolate } ) );
m_problem.errchk( m_system, m_ncomp );
}
//! Find the number of primitive quantities required for this PDE system
//! \return The number of primitive quantities required to be stored for
//! this PDE system
std::size_t nprim() const
{
// transport does not need/store any primitive quantities currently
return 0;
}
//! Find the number of materials set up for this PDE system
//! \return The number of materials set up for this PDE system
std::size_t nmat() const
{
return m_ncomp;
}
//! Assign number of DOFs per equation in the PDE system
//! \param[in,out] numEqDof Array storing number of Dofs for each PDE
//! equation
void numEquationDofs(std::vector< std::size_t >& numEqDof) const
{
// all equation-dofs initialized to ndofs
for (std::size_t i=0; i<m_ncomp; ++i) {
numEqDof.push_back(g_inputdeck.get< tag::discr, tag::ndof >());
}
}
//! Determine elements that lie inside the user-defined IC box
void IcBoxElems( const tk::Fields&,
std::size_t,
std::vector< std::unordered_set< std::size_t > >& ) const
{}
//! Initalize the transport equations for DG
//! \param[in] L Element mass matrix
//! \param[in] inpoel Element-node connectivity
//! \param[in] coord Array of nodal coordinates
//! \param[in,out] unk Array of unknowns
//! \param[in] t Physical time
//! \param[in] nielem Number of internal elements
void
initialize(
const tk::Fields& L,
const std::vector< std::size_t >& inpoel,
const tk::UnsMesh::Coords& coord,
const std::vector< std::unordered_set< std::size_t > >& /*inbox*/,
tk::Fields& unk,
tk::real t,
const std::size_t nielem ) const
{
tk::initialize( m_system, m_ncomp, m_offset, L, inpoel, coord,
Problem::initialize, unk, t, nielem );
}
//! Compute the left hand side mass matrix
//! \param[in] geoElem Element geometry array
//! \param[in,out] l Block diagonal mass matrix
void lhs( const tk::Fields& geoElem, tk::Fields& l ) const {
const auto ndof = g_inputdeck.get< tag::discr, tag::ndof >();
tk::mass( m_ncomp, m_offset, ndof, geoElem, l );
}
//! Update the interface cells to first order dofs
//! \details This function resets the high-order terms in interface cells,
//! and is currently not used in transport.
void updateInterfaceCells( tk::Fields&,
std::size_t,
std::vector< std::size_t >& ) const {}
//! Update the primitives for this PDE system
//! \details This function computes and stores the dofs for primitive
//! quantities, which are currently unused for transport.
void updatePrimitives( const tk::Fields&,
const tk::Fields&,
const tk::Fields&,
tk::Fields&,
std::size_t ) const {}
//! Clean up the state of trace materials for this PDE system
//! \details This function cleans up the state of materials present in trace
//! quantities in each cell. This is currently unused for transport.
void cleanTraceMaterial( const tk::Fields&,
tk::Fields&,
tk::Fields&,
std::size_t ) const {}
//! Reconstruct second-order solution from first-order
//! \param[in] t Physical time
//! \param[in] geoFace Face geometry array
//! \param[in] geoElem Element geometry array
//! \param[in] fd Face connectivity and boundary conditions object
//! \param[in] esup Elements-surrounding-nodes connectivity
//! \param[in] inpoel Element-node connectivity
//! \param[in] coord Array of nodal coordinates
//! \param[in,out] U Solution vector at recent time step
//! \param[in,out] P Primitive vector at recent time step
void reconstruct( tk::real t,
const tk::Fields& geoFace,
const tk::Fields& geoElem,
const inciter::FaceData& fd,
const std::map< std::size_t, std::vector< std::size_t > >&
esup,
const std::vector< std::size_t >& inpoel,
const tk::UnsMesh::Coords& coord,
tk::Fields& U,
tk::Fields& P ) const
{
const auto rdof = g_inputdeck.get< tag::discr, tag::rdof >();
// do reconstruction only if P0P1
if (rdof == 4 && g_inputdeck.get< tag::discr, tag::ndof >() == 1) {
const auto nelem = fd.Esuel().size()/4;<--- Variable 'nelem' is assigned a value that is never used.
const auto intsharp = g_inputdeck.get< tag::param, tag::transport,<--- Variable 'intsharp' is assigned a value that is never used.
tag::intsharp >()[m_system];
Assert( U.nprop() == rdof*m_ncomp, "Number of components in solution "
"vector must equal "+ std::to_string(rdof*m_ncomp) );
Assert( fd.Inpofa().size()/3 == fd.Esuf().size()/2,
"Mismatch in inpofa size" );
// allocate and initialize matrix and vector for reconstruction
std::vector< std::array< std::array< tk::real, 3 >, 3 > >
lhs_ls( nelem, {{ {{0.0, 0.0, 0.0}},
{{0.0, 0.0, 0.0}},
{{0.0, 0.0, 0.0}} }} );
// specify how many variables need to be reconstructed
std::array< std::size_t, 2 > varRange {{0, m_ncomp-1}};
std::vector< std::vector< std::array< tk::real, 3 > > >
rhs_ls( nelem, std::vector< std::array< tk::real, 3 > >
( m_ncomp,
{{ 0.0, 0.0, 0.0 }} ) );
// reconstruct x,y,z-derivatives of unknowns
// 0. get lhs matrix, which is only geometry dependent
tk::lhsLeastSq_P0P1(fd, geoElem, geoFace, lhs_ls);
// 1. internal face contributions
tk::intLeastSq_P0P1( m_offset, rdof, fd, geoElem, U, rhs_ls, varRange );
// 2. boundary face contributions
for (const auto& b : m_bc)
tk::bndLeastSqConservedVar_P0P1( m_system, m_ncomp, m_offset, rdof,
b.first, fd, geoFace, geoElem, t, b.second, P, U, rhs_ls, varRange );
// 3. solve 3x3 least-squares system
tk::solveLeastSq_P0P1( m_offset, rdof, lhs_ls, rhs_ls, U, varRange );
for (std::size_t e=0; e<nelem; ++e)
{
std::vector< std::size_t > matInt(m_ncomp, 0);
std::vector< tk::real > alAvg(m_ncomp, 0.0);
for (std::size_t k=0; k<m_ncomp; ++k)
alAvg[k] = U(e, k*rdof, m_offset);
auto intInd = interfaceIndicator(m_ncomp, alAvg, matInt);
if ((intsharp > 0) && intInd)
{
// Reconstruct second-order dofs of volume-fractions in Taylor space
// using nodal-stencils, for a good interface-normal estimate
tk::recoLeastSqExtStencil( rdof, m_offset, e, esup, inpoel, geoElem,
U, varRange );
}
}
// 4. transform reconstructed derivatives to Dubiner dofs
tk::transform_P0P1( m_offset, rdof, nelem, inpoel, coord, U, varRange );
}
}
//! Limit second-order solution
//! \param[in] t Physical time
//! \param[in] geoFace Face geometry array
//! \param[in] geoElem Element geometry array
//! \param[in] fd Face connectivity and boundary conditions object
//! \param[in] esup Elements surrounding points
//! \param[in] inpoel Element-node connectivity
//! \param[in] coord Array of nodal coordinates
//! \param[in] ndofel Vector of local number of degrees of freedome
// //! \param[in] gid Local->global node id map
// //! \param[in] bid Local chare-boundary node ids (value) associated to
// //! global node ids (key)
// //! \param[in] uNodalExtrm Chare-boundary nodal extrema for conservative
// //! variables
//! \param[in,out] U Solution vector at recent time step
void limit( [[maybe_unused]] tk::real t,
[[maybe_unused]] const tk::Fields& geoFace,
const tk::Fields& geoElem,
const inciter::FaceData& fd,
const std::map< std::size_t, std::vector< std::size_t > >& esup,
const std::vector< std::size_t >& inpoel,
const tk::UnsMesh::Coords& coord,
const std::vector< std::size_t >& ndofel,
const std::vector< std::size_t >&,
const std::unordered_map< std::size_t, std::size_t >&,
const std::vector< std::vector<tk::real> >&,
const std::vector< std::vector<tk::real> >&,
tk::Fields& U,
tk::Fields&,
std::vector< std::size_t >& ) const
{
const auto limiter = g_inputdeck.get< tag::discr, tag::limiter >();
if (limiter == ctr::LimiterType::WENOP1)
WENO_P1( fd.Esuel(), m_offset, U );
else if (limiter == ctr::LimiterType::SUPERBEEP1)
Superbee_P1( fd.Esuel(), inpoel, ndofel, m_offset, coord, U );
else if (limiter == ctr::LimiterType::VERTEXBASEDP1)
VertexBasedTransport_P1( esup, inpoel, ndofel, fd.Esuel().size()/4,
m_system, m_offset, geoElem, coord, U );
}
//! Compute right hand side
//! \param[in] t Physical time
//! \param[in] geoFace Face geometry array
//! \param[in] geoElem Element geometry array
//! \param[in] fd Face connectivity and boundary conditions object
//! \param[in] inpoel Element-node connectivity
//! \param[in] coord Array of nodal coordinates
//! \param[in] U Solution vector at recent time step
//! \param[in] P Primitive vector at recent time step
//! \param[in] ndofel Vector of local number of degrees of freedom
//! \param[in,out] R Right-hand side vector computed
void rhs( tk::real t,
const tk::Fields& geoFace,
const tk::Fields& geoElem,
const inciter::FaceData& fd,
const std::vector< std::size_t >& inpoel,
const std::vector< std::unordered_set< std::size_t > >&,
const tk::UnsMesh::Coords& coord,
const tk::Fields& U,
const tk::Fields& P,
const std::vector< std::size_t >& ndofel,
tk::Fields& R ) const
{
const auto ndof = g_inputdeck.get< tag::discr, tag::ndof >();<--- Variable 'ndof' is assigned a value that is never used.
const auto rdof = g_inputdeck.get< tag::discr, tag::rdof >();<--- Variable 'rdof' is assigned a value that is never used.
const auto intsharp = g_inputdeck.get< tag::param, tag::transport,<--- Variable 'intsharp' is assigned a value that is never used.
tag::intsharp >()[m_system];
Assert( U.nunk() == P.nunk(), "Number of unknowns in solution "
"vector and primitive vector at recent time step incorrect" );
Assert( U.nunk() == R.nunk(), "Number of unknowns in solution "
"vector and right-hand side at recent time step incorrect" );
Assert( U.nprop() == rdof*m_ncomp, "Number of components in solution "
"vector must equal "+ std::to_string(rdof*m_ncomp) );
Assert( P.nprop() == 0, "Number of components in primitive "
"vector must equal "+ std::to_string(0) );
Assert( R.nprop() == ndof*m_ncomp, "Number of components in right-hand "
"side vector must equal "+ std::to_string(ndof*m_ncomp) );
Assert( fd.Inpofa().size()/3 == fd.Esuf().size()/2,
"Mismatch in inpofa size" );
// set rhs to zero
R.fill(0.0);
// empty vector for non-conservative terms. This vector is unused for
// linear transport since, there are no non-conservative terms in the
// system of PDEs.
std::vector< std::vector < tk::real > > riemannDeriv;
std::vector< std::vector< tk::real > > vriem;
std::vector< std::vector< tk::real > > riemannLoc;
// compute internal surface flux integrals
tk::surfInt( m_system, m_ncomp, m_offset, t, ndof, rdof, inpoel, coord,
fd, geoFace, geoElem, Upwind::flux,
Problem::prescribedVelocity, U, P, ndofel, R, vriem,
riemannLoc, riemannDeriv, intsharp );
if(ndof > 1)
// compute volume integrals
tk::volInt( m_system, m_ncomp, m_offset, t, ndof, rdof,
fd.Esuel().size()/4, inpoel, coord, geoElem, flux,
Problem::prescribedVelocity, U, P, ndofel, R, intsharp );
// compute boundary surface flux integrals
for (const auto& b : m_bc)
tk::bndSurfInt( m_system, m_ncomp, m_offset, ndof, rdof, b.first, fd,
geoFace, geoElem, inpoel, coord, t, Upwind::flux,
Problem::prescribedVelocity, b.second, U, P, ndofel, R, vriem,
riemannLoc, riemannDeriv, intsharp );
}
//! Evaluate the adaptive indicator and mark the ndof for each element
//! \param[in] nunk Number of unknowns
//! \param[in] coord Array of nodal coordinates
//! \param[in] inpoel Element-node connectivity
//! \param[in] fd Face connectivity and boundary conditions object
//! \param[in] unk Array of unknowns
//! \param[in] indicator p-refinement indicator type
//! \param[in] ndof Number of degrees of freedom in the solution
//! \param[in] ndofmax Max number of degrees of freedom for p-refinement
//! \param[in] tolref Tolerance for p-refinement
//! \param[in,out] ndofel Vector of local number of degrees of freedome
void eval_ndof( std::size_t nunk,
[[maybe_unused]] const tk::UnsMesh::Coords& coord,
[[maybe_unused]] const std::vector< std::size_t >& inpoel,
const inciter::FaceData& fd,
const tk::Fields& unk,
inciter::ctr::PrefIndicatorType indicator,
std::size_t ndof,
std::size_t ndofmax,
tk::real tolref,
std::vector< std::size_t >& ndofel ) const
{
const auto& esuel = fd.Esuel();
if(indicator == inciter::ctr::PrefIndicatorType::SPECTRAL_DECAY)
spectral_decay( 1, nunk, esuel, unk, ndof, ndofmax, tolref, ndofel );
else
Throw( "No such adaptive indicator type" );
}
//! Compute the minimum time step size
// //! \param[in] U Solution vector at recent time step
// //! \param[in] coord Mesh node coordinates
// //! \param[in] inpoel Mesh element connectivity
//! \return Minimum time step size
tk::real dt( const std::array< std::vector< tk::real >, 3 >& /*coord*/,
const std::vector< std::size_t >& /*inpoel*/,
const inciter::FaceData& /*fd*/,
const tk::Fields& /*geoFace*/,
const tk::Fields& /*geoElem*/,
const std::vector< std::size_t >& /*ndofel*/,
const tk::Fields& /*U*/,
const tk::Fields&,
const std::size_t /*nielem*/ ) const
{
tk::real mindt = std::numeric_limits< tk::real >::max();
return mindt;
}
//! Return analytic field names to be output to file
//! \return Vector of strings labelling analytic fields output in file
std::vector< std::string > analyticFieldNames() const {
std::vector< std::string > n;
auto depvar = g_inputdeck.get< tag::param, eq, tag::depvar >()[m_system];
for (ncomp_t c=0; c<m_ncomp; ++c)
n.push_back( depvar + std::to_string(c) + "_analytic" );
return n;
}
//! Return surface field output going to file
std::vector< std::vector< tk::real > >
surfOutput( const std::map< int, std::vector< std::size_t > >&,
tk::Fields& ) const
{
std::vector< std::vector< tk::real > > s; // punt for now
return s;
}
//! Return time history field names to be output to file
//! \return Vector of strings labelling time history fields output in file
std::vector< std::string > histNames() const {
std::vector< std::string > s; // punt for now
return s;
}
//! Return names of integral variables to be output to diagnostics file
//! \return Vector of strings labelling integral variables output
std::vector< std::string > names() const {
std::vector< std::string > n;
const auto& depvar =
g_inputdeck.get< tag::param, eq, tag::depvar >().at(m_system);
// construct the name of the numerical solution for all components
for (ncomp_t c=0; c<m_ncomp; ++c)
n.push_back( depvar + std::to_string(c) );
return n;
}
//! Return analytic solution (if defined by Problem) at xi, yi, zi, t
//! \param[in] xi X-coordinate at which to evaluate the analytic solution
//! \param[in] yi Y-coordinate at which to evaluate the analytic solution
//! \param[in] zi Z-coordinate at which to evaluate the analytic solution
//! \param[in] t Physical time at which to evaluate the analytic solution
//! \return Vector of analytic solution at given spatial location and time
std::vector< tk::real >
analyticSolution( tk::real xi, tk::real yi, tk::real zi, tk::real t ) const
{ return Problem::analyticSolution( m_system, m_ncomp, xi, yi, zi, t ); }
//! Return analytic solution for conserved variables
//! \param[in] xi X-coordinate at which to evaluate the analytic solution
//! \param[in] yi Y-coordinate at which to evaluate the analytic solution
//! \param[in] zi Z-coordinate at which to evaluate the analytic solution
//! \param[in] t Physical time at which to evaluate the analytic solution
//! \return Vector of analytic solution at given location and time
std::vector< tk::real >
solution( tk::real xi, tk::real yi, tk::real zi, tk::real t ) const
{ return Problem::initialize( m_system, m_ncomp, xi, yi, zi, t ); }
//! Return time history field output evaluated at time history points
//! \param[in] h History point data
std::vector< std::vector< tk::real > >
histOutput( const std::vector< HistData >& h,
const std::vector< std::size_t >&,
const tk::UnsMesh::Coords&,
const tk::Fields&,
const tk::Fields& ) const
{
std::vector< std::vector< tk::real > > Up(h.size()); //punt for now
return Up;
}
private:
const Physics m_physics; //!< Physics policy
const Problem m_problem; //!< Problem policy
const ncomp_t m_system; //!< Equation system index
const ncomp_t m_ncomp; //!< Number of components in this PDE
const ncomp_t m_offset; //!< Offset this PDE operates from
//! BC configuration
BCStateFn m_bc;
//! Evaluate physical flux function for this PDE system
//! \param[in] ncomp Number of scalar components in this PDE system
//! \param[in] ugp Numerical solution at the Gauss point at which to
//! evaluate the flux
//! \param[in] v Prescribed velocity evaluated at the Gauss point at which
//! to evaluate the flux
//! \return Flux vectors for all components in this PDE system
//! \note The function signature must follow tk::FluxFn
static tk::FluxFn::result_type
flux( ncomp_t,
ncomp_t ncomp,
const std::vector< tk::real >& ugp,
const std::vector< std::array< tk::real, 3 > >& v )
{
Assert( ugp.size() == ncomp, "Size mismatch" );
Assert( v.size() == ncomp, "Size mismatch" );
std::vector< std::array< tk::real, 3 > > fl( ugp.size() );
for (ncomp_t c=0; c<ncomp; ++c)
fl[c] = {{ v[c][0] * ugp[c], v[c][1] * ugp[c], v[c][2] * ugp[c] }};
return fl;
}
//! \brief Boundary state function providing the left and right state of a
//! face at extrapolation boundaries
//! \param[in] ul Left (domain-internal) state
//! \return Left and right states for all scalar components in this PDE
//! system
//! \note The function signature must follow tk::StateFn
static tk::StateFn::result_type
extrapolate( ncomp_t, ncomp_t, const std::vector< tk::real >& ul,
tk::real, tk::real, tk::real, tk::real,
const std::array< tk::real, 3 >& )
{
return {{ ul, ul }};
}
//! \brief Boundary state function providing the left and right state of a
//! face at extrapolation boundaries
//! \param[in] ul Left (domain-internal) state
//! \return Left and right states for all scalar components in this PDE
//! system
//! \note The function signature must follow tk::StateFn
static tk::StateFn::result_type
inlet( ncomp_t, ncomp_t, const std::vector< tk::real >& ul,
tk::real, tk::real, tk::real, tk::real,
const std::array< tk::real, 3 >& )
{
auto ur = ul;
std::fill( begin(ur), end(ur), 0.0 );
return {{ ul, std::move(ur) }};
}
//! \brief Boundary state function providing the left and right state of a
//! face at outlet boundaries
//! \param[in] ul Left (domain-internal) state
//! \return Left and right states for all scalar components in this PDE
//! system
//! \note The function signature must follow tk::StateFn
static tk::StateFn::result_type
outlet( ncomp_t, ncomp_t, const std::vector< tk::real >& ul,
tk::real, tk::real, tk::real, tk::real,
const std::array< tk::real, 3 >& )
{
return {{ ul, ul }};
}
//! \brief Boundary state function providing the left and right state of a
//! face at Dirichlet boundaries
//! \param[in] system Equation system index
//! \param[in] ncomp Number of scalar components in this PDE system
//! \param[in] ul Left (domain-internal) state
//! \param[in] x X-coordinate at which to compute the states
//! \param[in] y Y-coordinate at which to compute the states
//! \param[in] z Z-coordinate at which to compute the states
//! \param[in] t Physical time
//! \return Left and right states for all scalar components in this PDE
//! system
//! \note The function signature must follow tk::StateFn
static tk::StateFn::result_type
dirichlet( ncomp_t system, ncomp_t ncomp, const std::vector< tk::real >& ul,
tk::real x, tk::real y, tk::real z, tk::real t,
const std::array< tk::real, 3 >& )
{
return {{ ul, Problem::initialize( system, ncomp, x, y, z, t ) }};
}
};
} // dg::
} // inciter::
#endif // DGTransport_h
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