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/*************************************************************************
* Copyright (C) 2013 by T. Sweijen (T.sweijen@uu.nl) *
* *
* This program is free software; it is licensed under the terms of the *
* GNU General Public License v2 or later. See file LICENSE for details. *
*************************************************************************/
#ifdef YADE_CGAL
#ifdef FLOW_ENGINE
// #define SOLUTE_FLOW
#ifdef SOLUTE_FLOW
#include "FlowEngine_SoluteFlowEngineT.hpp"
#include <Eigen/Sparse>
namespace yade { // Cannot have #include directive inside.
class SoluteCellInfo : public FlowCellInfo_SoluteFlowEngineT {
public:
Real solute_concentration;
SoluteCellInfo(void)
: FlowCellInfo_SoluteFlowEngineT()
{
solute_concentration = 0;
}
inline Real& solute(void) { return solute_concentration; }
inline const Real& solute(void) const { return solute_concentration; }
inline void getInfo(const SoluteCellInfo& otherCellInfo)
{
FlowCellInfo_SoluteFlowEngineT::getInfo(otherCellInfo);
solute() = otherCellInfo.solute();
}
};
typedef TemplateFlowEngine_SoluteFlowEngineT<SoluteCellInfo, FlowVertexInfo_SoluteFlowEngineT> SoluteFlowEngineT;
REGISTER_SERIALIZABLE(SoluteFlowEngineT);
YADE_PLUGIN((SoluteFlowEngineT));
class SoluteFlowEngine : public SoluteFlowEngineT {
public:
void initializeSoluteTransport();
void soluteTransport();
double getConcentration(unsigned int id) { return solver->T[solver->currentTes].cellHandles[id]->info().solute(); }
double insertConcentration(unsigned int id, double conc)
{
solver->T[solver->currentTes].cellHandles[id]->info().solute() = conc;
return conc;
}
void soluteBC(unsigned int bc_id1, unsigned int bc_id2, double bc_concentration1, double bc_concentration2, unsigned int s);
double getConcentrationPlane(double Yobs, double Yr, int xyz);
double getAverageConcentration();
///Elaborate the description as you wish
// clang-format off
YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(SoluteFlowEngine,SoluteFlowEngineT,"A variant of :yref:`FlowEngine` with solute transport).",
///No additional variable yet, else input here
// ((Vector3r, gradP, Vector3r::Zero(),,"Macroscopic pressure gradient"))
((double,DiffusionCoefficient,0,,"Diffusion coefficient for molecular diffusion"))
,,,
.def("soluteTransport",&SoluteFlowEngine::soluteTransport,"Solute transport (advection and diffusion) engine for diffusion use a diffusion coefficient (D) other than 0.")
.def("getConcentration",&SoluteFlowEngine::getConcentration,(boost::python::arg("id")),"get concentration of pore with ID")
.def("insertConcentration",&SoluteFlowEngine::insertConcentration,(boost::python::arg("id"),boost::python::arg("conc")),"Insert Concentration (ID, Concentration)")
.def("solute_BC",&SoluteFlowEngine::soluteBC,(boost::python::arg("bc_id1"),boost::python::arg("bc_id2"),boost::python::arg("bc_concentration1"),boost::python::arg("bc_concentration2"),boost::python::arg("s")),"Enter X,Y,Z for concentration observation'.")
.def("initializeSoluteTransport",&SoluteFlowEngine::initializeSoluteTransport,"Initialize Solute Transport")
.def("getConcentrationPlane",&SoluteFlowEngine::getConcentrationPlane,(boost::python::arg("Yobs"),boost::python::arg("Yr"),boost::python::arg("xyz")),"get concentration of pore with ID")
.def("getAverageConcentration",&SoluteFlowEngine::getAverageConcentration,"The the volume averaged concentration")
)
// clang-format on
};
REGISTER_SERIALIZABLE(SoluteFlowEngine);
// PeriodicFlowEngine::~PeriodicFlowEngine(){}
void SoluteFlowEngine::initializeSoluteTransport()
{
FOREACH(CellHandle & cell, solver->T[solver->currentTes].cellHandles) { cell->info().solute() = 0.0; }
}
void SoluteFlowEngine::soluteTransport()
{
double deltatime = scene->dt;
//soluteTransport is a function to solve transport of solutes for advection (+diffusion).
//Call this function with a pyRunner in the python script, implement a diffusion coefficient and a dt.
//Optimalization has to be done such that the coefficient matrix is not solved for each time step,only after triangulation.
//Extensive testing has to be done to check its ability to simulate a deforming porous media.
double coeff = 0.00; //Ratio of dt and void volume
double coeff1 = 0.00; //Coefficient for off-diagonal element
double coeff2 = 0.00; //Coefficient for diagonal element
double qin = 0.00; //Flux into the pore per pore throat
double Qout = 0.0; //Total Flux out of the pore
double dt = 1e9;
double invdistance = 0.0; //Fluid facet area divided by pore throat length for each pore throat
double invdistancelocal = 0.0; //Sum of invdistance
//Set vectors & matrix
int ncells = solver->T[solver->currentTes].cellHandles.size();
Eigen::SparseMatrix<double, Eigen::ColMajor> Aconc(ncells, ncells);
typedef Eigen::Triplet<double> ETriplet2;
std::vector<ETriplet2> tripletList2;
Eigen::SparseLU<Eigen::SparseMatrix<double, Eigen::ColMajor>, Eigen::COLAMDOrdering<int>> eSolver2;
// Prepare (copy) concentration vector
VectorXr eb2(ncells);
VectorXr ex2(ncells);
FOREACH(CellHandle & cell, solver->T[solver->currentTes].cellHandles) { eb2[cell->info().id] = cell->info().solute(); }
// Fill coefficient matrix
FOREACH(CellHandle & cell, solver->T[solver->currentTes].cellHandles)
{
cell->info().invVoidVolume() = 1.0 / (std::abs(cell->info().volume()) - std::abs(solver->volumeSolidPore(cell)));
for (unsigned int ngb = 0; ngb < 4; ngb++) {
CGT::Point& p2 = cell->neighbor(ngb)->info();
CGT::Point& p1 = cell->info();
CGT::CVector l = p1 - p2;
CGT::Real fluidSurf = sqrt(cell->info().facetSurfaces[ngb].squared_length()) * cell->info().facetFluidSurfacesRatio[ngb];
invdistancelocal = (fluidSurf / sqrt(l.squared_length()));
invdistance += (fluidSurf / sqrt(l.squared_length()));
coeff = deltatime * cell->info().invVoidVolume();
qin = std::abs(cell->info().kNorm()[ngb]) * (cell->neighbor(ngb)->info().p() - cell->info().p());
dt = std::min((std::abs(cell->info().volume()) - std::abs(solver->volumeSolidPore(cell))) / std::abs(qin), dt);
Qout = Qout + qin; //max(qin,0.0);
coeff1 = -1 * coeff
* (qin
+ DiffusionCoefficient
* invdistancelocal); //(std::abs(max(qin,0.0))-(DiffusionCoefficient*invdistancelocal)); //off-diagonal
if (coeff1 != 0.0) { tripletList2.push_back(ETriplet2(cell->info().id, cell->neighbor(ngb)->info().id, coeff1)); }
}
coeff2 = 1.0 + (coeff * Qout) + (coeff * DiffusionCoefficient * invdistance); //diagonal
tripletList2.push_back(ETriplet2(cell->info().id, cell->info().id, coeff2));
Qout = 0.0;
invdistancelocal = 0.0;
invdistance = 0.0;
}
//Solve Matrix
Aconc.setFromTriplets(tripletList2.begin(), tripletList2.end());
//if (eSolver2.signDeterminant() < 1){cerr << "determinant is negative!!!!!!! " << eSolver2.signDeterminant()<<endl;}
//eSolver2.setPivotThreshold(10e-8);
eSolver2.analyzePattern(Aconc);
eSolver2.factorize(Aconc);
eSolver2.compute(Aconc);
ex2 = eSolver2.solve(eb2);
//Copy data to concentration array
FOREACH(CellHandle & cell, solver->T[solver->currentTes].cellHandles) { cell->info().solute() = ex2[cell->info().id]; }
tripletList2.clear();
if (dt != 1e9) { scene->dt = dt; }
}
void SoluteFlowEngine::soluteBC(unsigned int bcid1, unsigned int bcid2, double bcconcentration1, double bcconcentration2, unsigned int s)
{
//Boundary conditions according to soluteTransport.
//It simply assigns boundary concentrations to cells with a common vertices (e.g. infinite large sphere which makes up the boundary condition in flowEngine)
//s is a switch, if 0 only bc_id1 is used (advection only). If >0 than both bc_id1 and bc_id2 are used.
//NOTE (bruno): cell cirulators can be use to get all cells having bcid2 has a vertex more efficiently (see e.g. FlowBoundingSphere.ipp:721)
FOREACH(CellHandle & cell, solver->T[solver->currentTes].cellHandles)
{
for (unsigned int ngb = 0; ngb < 4; ngb++) {
if (cell->vertex(ngb)->info().id() == bcid1) { cell->info().solute() = bcconcentration1; }
if (s > 0) {
if (cell->vertex(ngb)->info().id() == bcid2) { cell->info().solute() = bcconcentration2; }
}
}
}
}
double SoluteFlowEngine::getConcentrationPlane(double Yobs, double Yr, int xyz)
{
//Get the concentration within a certain plane (Y_obs), whilst the cells are located in a small volume around this plane
//The concentration in cells are weighed for their distance to the observation point
//for a point on the x-axis (xyz=0), point on the y-axis (xyz=1), point on the z-axis (xyz=2)
double sumConcentration = 0.0;
double sumFraction = 0.0;
double concentration = 0.0;
//Find cells within designated volume
FOREACH(CellHandle & cell, solver->T[solver->currentTes].cellHandles)
{
CGT::Point& p1 = cell->info();
if (std::abs(p1[xyz]) < std::abs(std::abs(Yobs) + std::abs(Yr))) {
if (std::abs(p1[xyz]) > std::abs(std::abs(Yobs) - std::abs(Yr))) {
sumConcentration += cell->info().solute() * (1 - (std::abs(p1[xyz]) - std::abs(Yobs)) / std::abs(Yr));
sumFraction += (1 - (std::abs(p1[xyz]) - std::abs(Yobs)) / std::abs(Yr));
}
}
}
concentration = sumConcentration / sumFraction;
return concentration;
}
double SoluteFlowEngine::getAverageConcentration()
{
//Get volume-averaged concentration
double summConc = 0.0, summVol = 0.0;
FOREACH(CellHandle & cell, solver->T[solver->currentTes].cellHandles)
{
if (!cell->info().isFictious) {
summConc += cell->info().solute() * (std::abs(cell->info().volume()) - std::abs(solver->volumeSolidPore(cell)));
summVol += (std::abs(cell->info().volume()) - std::abs(solver->volumeSolidPore(cell)));
}
}
return (summConc / summVol);
}
YADE_PLUGIN((SoluteFlowEngine));
} // namespace yade
#endif //SOLUTE_FLOW
#endif //FLOW_ENGINE
#endif /* YADE_CGAL */
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