void AssembleBoussinesqAppoximation_AD(MultiLevelProblem& ml_prob) {
// ml_prob is the global object from/to where get/set all the data
// level is the level of the PDE system to be assembled
// levelMax is the Maximum level of the MultiLevelProblem
// assembleMatrix is a flag that tells if only the residual or also the matrix should be assembled
// extract pointers to the several objects that we are going to use
TransientNonlinearImplicitSystem* mlPdeSys = &ml_prob.get_system<TransientNonlinearImplicitSystem> ("NS"); // pointer to the linear implicit system named "Poisson"
const unsigned level = mlPdeSys->GetLevelToAssemble();
Mesh* msh = ml_prob._ml_msh->GetLevel(level); // pointer to the mesh (level) object
elem* el = msh->el; // pointer to the elem object in msh (level)
MultiLevelSolution* mlSol = ml_prob._ml_sol; // pointer to the multilevel solution object
Solution* sol = ml_prob._ml_sol->GetSolutionLevel(level); // pointer to the solution (level) object
LinearEquationSolver* pdeSys = mlPdeSys->_LinSolver[level]; // pointer to the equation (level) object
bool assembleMatrix = mlPdeSys->GetAssembleMatrix();
// call the adept stack object
adept::Stack& s = FemusInit::_adeptStack;
if(assembleMatrix) s.continue_recording();
else s.pause_recording();
SparseMatrix* KK = pdeSys->_KK; // pointer to the global stifness matrix object in pdeSys (level)
NumericVector* RES = pdeSys->_RES; // pointer to the global residual vector object in pdeSys (level)
const unsigned dim = msh->GetDimension(); // get the domain dimension of the problem
unsigned dim2 = (3 * (dim - 1) + !(dim - 1)); // dim2 is the number of second order partial derivatives (1,3,6 depending on the dimension)
unsigned iproc = msh->processor_id(); // get the process_id (for parallel computation)
// reserve memory for the local standar vectors
const unsigned maxSize = static_cast< unsigned >(ceil(pow(3, dim))); // conservative: based on line3, quad9, hex27
//solution variable
unsigned solTIndex;
solTIndex = mlSol->GetIndex("T"); // get the position of "T" in the ml_sol object
unsigned solTType = mlSol->GetSolutionType(solTIndex); // get the finite element type for "T"
vector < unsigned > solVIndex(dim);
solVIndex[0] = mlSol->GetIndex("U"); // get the position of "U" in the ml_sol object
solVIndex[1] = mlSol->GetIndex("V"); // get the position of "V" in the ml_sol object
if(dim == 3) solVIndex[2] = mlSol->GetIndex("W"); // get the position of "V" in the ml_sol object
unsigned solVType = mlSol->GetSolutionType(solVIndex[0]); // get the finite element type for "u"
unsigned solPIndex;
solPIndex = mlSol->GetIndex("P"); // get the position of "P" in the ml_sol object
unsigned solPType = mlSol->GetSolutionType(solPIndex); // get the finite element type for "u"
unsigned solTPdeIndex;
solTPdeIndex = mlPdeSys->GetSolPdeIndex("T"); // get the position of "T" in the pdeSys object
// std::cout << solTIndex <<" "<<solTPdeIndex<<std::endl;
vector < unsigned > solVPdeIndex(dim);
solVPdeIndex[0] = mlPdeSys->GetSolPdeIndex("U"); // get the position of "U" in the pdeSys object
solVPdeIndex[1] = mlPdeSys->GetSolPdeIndex("V"); // get the position of "V" in the pdeSys object
if(dim == 3) solVPdeIndex[2] = mlPdeSys->GetSolPdeIndex("W");
unsigned solPPdeIndex;
solPPdeIndex = mlPdeSys->GetSolPdeIndex("P"); // get the position of "P" in the pdeSys object
vector < adept::adouble > solT; // local solution
vector < vector < adept::adouble > > solV(dim); // local solution
vector < adept::adouble > solP; // local solution
vector < double > solTold; // local solution
vector < vector < double > > solVold(dim); // local solution
vector < double > solPold; // local solution
vector< adept::adouble > aResT; // local redidual vector
vector< vector < adept::adouble > > aResV(dim); // local redidual vector
vector< adept::adouble > aResP; // local redidual vector
vector < vector < double > > coordX(dim); // local coordinates
unsigned coordXType = 2; // get the finite element type for "x", it is always 2 (LAGRANGE QUADRATIC)
solT.reserve(maxSize);
solTold.reserve(maxSize);
aResT.reserve(maxSize);
for(unsigned k = 0; k < dim; k++) {
solV[k].reserve(maxSize);
solVold[k].reserve(maxSize);
aResV[k].reserve(maxSize);
coordX[k].reserve(maxSize);
}
solP.reserve(maxSize);
solPold.reserve(maxSize);
aResP.reserve(maxSize);
vector <double> phiV; // local test function
vector <double> phiV_x; // local test function first order partial derivatives
vector <double> phiV_xx; // local test function second order partial derivatives
phiV.reserve(maxSize);
phiV_x.reserve(maxSize * dim);
phiV_xx.reserve(maxSize * dim2);
vector <double> phiT; // local test function
vector <double> phiT_x; // local test function first order partial derivatives
vector <double> phiT_xx; // local test function second order partial derivatives
phiT.reserve(maxSize);
phiT_x.reserve(maxSize * dim);
phiT_xx.reserve(maxSize * dim2);
double* phiP;
double weight; // gauss point weight
vector< int > sysDof; // local to global pdeSys dofs
sysDof.reserve((dim + 2) *maxSize);
vector< double > Res; // local redidual vector
Res.reserve((dim + 2) *maxSize);
vector < double > Jac;
Jac.reserve((dim + 2) *maxSize * (dim + 2) *maxSize);
if(assembleMatrix)
KK->zero(); // Set to zero all the entries of the Global Matrix
// element loop: each process loops only on the elements that owns
for(int iel = msh->_elementOffset[iproc]; iel < msh->_elementOffset[iproc + 1]; iel++) {
// element geometry type
short unsigned ielGeom = msh->GetElementType(iel);
unsigned nDofsT = msh->GetElementDofNumber(iel, solTType); // number of solution element dofs
unsigned nDofsV = msh->GetElementDofNumber(iel, solVType); // number of solution element dofs
unsigned nDofsP = msh->GetElementDofNumber(iel, solPType); // number of solution element dofs
unsigned nDofsX = msh->GetElementDofNumber(iel, coordXType); // number of coordinate element dofs
unsigned nDofsTVP = nDofsT + dim * nDofsV + nDofsP;
// resize local arrays
sysDof.resize(nDofsTVP);
solT.resize(nDofsV);
solTold.resize(nDofsV);
for(unsigned k = 0; k < dim; k++) {
solV[k].resize(nDofsV);
solVold[k].resize(nDofsV);
coordX[k].resize(nDofsX);
}
solP.resize(nDofsP);
solPold.resize(nDofsP);
aResT.resize(nDofsV); //resize
std::fill(aResT.begin(), aResT.end(), 0); //set aRes to zero
for(unsigned k = 0; k < dim; k++) {
aResV[k].resize(nDofsV); //resize
std::fill(aResV[k].begin(), aResV[k].end(), 0); //set aRes to zero
}
aResP.resize(nDofsP); //resize
std::fill(aResP.begin(), aResP.end(), 0); //set aRes to zero
// local storage of global mapping and solution
for(unsigned i = 0; i < nDofsT; i++) {
unsigned solTDof = msh->GetSolutionDof(i, iel, solTType); // global to global mapping between solution node and solution dof
solT[i] = (*sol->_Sol[solTIndex])(solTDof); // global extraction and local storage for the solution
solTold[i] = (*sol->_SolOld[solTIndex])(solTDof); // global extraction and local storage for the solution
sysDof[i] = pdeSys->GetSystemDof(solTIndex, solTPdeIndex, i, iel); // global to global mapping between solution node and pdeSys dofs
}
// local storage of global mapping and solution
for(unsigned i = 0; i < nDofsV; i++) {
unsigned solVDof = msh->GetSolutionDof(i, iel, solVType); // global to global mapping between solution node and solution dof
for(unsigned k = 0; k < dim; k++) {
solV[k][i] = (*sol->_Sol[solVIndex[k]])(solVDof); // global extraction and local storage for the solution
solVold[k][i] = (*sol->_SolOld[solVIndex[k]])(solVDof); // global extraction and local storage for the solution
sysDof[i + nDofsT + k * nDofsV] = pdeSys->GetSystemDof(solVIndex[k], solVPdeIndex[k], i, iel); // global to global mapping between solution node and pdeSys dof
}
}
for(unsigned i = 0; i < nDofsP; i++) {
unsigned solPDof = msh->GetSolutionDof(i, iel, solPType); // global to global mapping between solution node and solution dof
solP[i] = (*sol->_Sol[solPIndex])(solPDof); // global extraction and local storage for the solution
solPold[i] = (*sol->_SolOld[solPIndex])(solPDof); // global extraction and local storage for the solution
sysDof[i + nDofsT + dim * nDofsV] = pdeSys->GetSystemDof(solPIndex, solPPdeIndex, i, iel); // global to global mapping between solution node and pdeSys dof
}
// local storage of coordinates
for(unsigned i = 0; i < nDofsX; i++) {
unsigned coordXDof = msh->GetSolutionDof(i, iel, coordXType); // global to global mapping between coordinates node and coordinate dof
for(unsigned k = 0; k < dim; k++) {
coordX[k][i] = (*msh->_topology->_Sol[k])(coordXDof); // global extraction and local storage for the element coordinates
}
}
// start a new recording of all the operations involving adept::adouble variables
if(assembleMatrix) s.new_recording();
// *** Gauss point loop ***
for(unsigned ig = 0; ig < msh->_finiteElement[ielGeom][solVType]->GetGaussPointNumber(); ig++) {
// *** get gauss point weight, test function and test function partial derivatives ***
msh->_finiteElement[ielGeom][solTType]->Jacobian(coordX, ig, weight, phiT, phiT_x, phiT_xx);
msh->_finiteElement[ielGeom][solVType]->Jacobian(coordX, ig, weight, phiV, phiV_x, phiV_xx);
phiP = msh->_finiteElement[ielGeom][solPType]->GetPhi(ig);
// evaluate the solution, the solution derivatives and the coordinates in the gauss point
adept::adouble solT_gss = 0;
double solTold_gss = 0;
vector < adept::adouble > gradSolT_gss(dim, 0.);
vector < double > gradSolTold_gss(dim, 0.);
for(unsigned i = 0; i < nDofsT; i++) {
solT_gss += phiT[i] * solT[i];
solTold_gss += phiT[i] * solTold[i];
for(unsigned j = 0; j < dim; j++) {
gradSolT_gss[j] += phiT_x[i * dim + j] * solT[i];
gradSolTold_gss[j] += phiT_x[i * dim + j] * solTold[i];
}
}
vector < adept::adouble > solV_gss(dim, 0);
vector < double > solVold_gss(dim, 0);
vector < vector < adept::adouble > > gradSolV_gss(dim);
vector < vector < double > > gradSolVold_gss(dim);
for(unsigned k = 0; k < dim; k++) {
gradSolV_gss[k].resize(dim);
gradSolVold_gss[k].resize(dim);
std::fill(gradSolV_gss[k].begin(), gradSolV_gss[k].end(), 0);
std::fill(gradSolVold_gss[k].begin(), gradSolVold_gss[k].end(), 0);
}
for(unsigned i = 0; i < nDofsV; i++) {
for(unsigned k = 0; k < dim; k++) {
solV_gss[k] += phiV[i] * solV[k][i];
solVold_gss[k] += phiV[i] * solVold[k][i];
}
for(unsigned j = 0; j < dim; j++) {
for(unsigned k = 0; k < dim; k++) {
gradSolV_gss[k][j] += phiV_x[i * dim + j] * solV[k][i];
gradSolVold_gss[k][j] += phiV_x[i * dim + j] * solVold[k][i];
}
}
}
adept::adouble solP_gss = 0;
double solPold_gss = 0;
for(unsigned i = 0; i < nDofsP; i++) {
solP_gss += phiP[i] * solP[i];
solPold_gss += phiP[i] * solPold[i];
}
double alpha = 1.;
double beta = 1.;//40000.;
double Pr = 0.71;
double Ra = 340000;
double dt = mlPdeSys -> GetIntervalTime();
// *** phiT_i loop ***
for(unsigned i = 0; i < nDofsT; i++) {
adept::adouble Temp = 0.;
adept::adouble TempOld = 0.;
for(unsigned j = 0; j < dim; j++) {
Temp += 1. / sqrt(Ra * Pr) * alpha * phiT_x[i * dim + j] * gradSolT_gss[j];
Temp += phiT[i] * (solV_gss[j] * gradSolT_gss[j]);
TempOld += 1. / sqrt(Ra * Pr) * alpha * phiT_x[i * dim + j] * gradSolTold_gss[j];
TempOld += phiT[i] * (solVold_gss[j] * gradSolTold_gss[j]);
}
aResT[i] += (- (solT_gss - solTold_gss) * phiT[i] / dt - 0.5 * (Temp + TempOld)) * weight;
} // end phiT_i loop
// *** phiV_i loop ***
for(unsigned i = 0; i < nDofsV; i++) {
vector < adept::adouble > NSV(dim, 0.);
vector < double > NSVold(dim, 0.);
for(unsigned j = 0; j < dim; j++) {
for(unsigned k = 0; k < dim; k++) {
NSV[k] += sqrt(Pr / Ra) * phiV_x[i * dim + j] * (gradSolV_gss[k][j] + gradSolV_gss[j][k]);
NSV[k] += phiV[i] * (solV_gss[j] * gradSolV_gss[k][j]);
NSVold[k] += sqrt(Pr / Ra) * phiV_x[i * dim + j] * (gradSolVold_gss[k][j] + gradSolVold_gss[j][k]);
NSVold[k] += phiV[i] * (solVold_gss[j] * gradSolVold_gss[k][j]);
}
}
for(unsigned k = 0; k < dim; k++) {
NSV[k] += -solP_gss * phiV_x[i * dim + k];
NSVold[k] += -solPold_gss * phiV_x[i * dim + k];
}
NSV[1] += -beta * solT_gss * phiV[i];
NSVold[1] += -beta * solTold_gss * phiV[i];
for(unsigned k = 0; k < dim; k++) {
aResV[k][i] += (- (solV_gss[k] - solVold_gss[k]) * phiV[i] / dt - 0.5 * (NSV[k] + NSVold[k])) * weight;
}
} // end phiV_i loop
// *** phiP_i loop ***
for(unsigned i = 0; i < nDofsP; i++) {
for(int k = 0; k < dim; k++) {
aResP[i] += - (gradSolV_gss[k][k]) * phiP[i] * weight;
}
} // end phiP_i loop
} // end gauss point loop
//--------------------------------------------------------------------------------------------------------
// Add the local Matrix/Vector into the global Matrix/Vector
//copy the value of the adept::adoube aRes in double Res and store them in RES
Res.resize(nDofsTVP); //resize
for(int i = 0; i < nDofsT; i++) {
Res[i] = -aResT[i].value();
}
for(int i = 0; i < nDofsV; i++) {
for(unsigned k = 0; k < dim; k++) {
Res[ i + nDofsT + k * nDofsV ] = -aResV[k][i].value();
}
}
for(int i = 0; i < nDofsP; i++) {
Res[ i + nDofsT + dim * nDofsV ] = -aResP[i].value();
}
RES->add_vector_blocked(Res, sysDof);
//Extarct and store the Jacobian
if(assembleMatrix) {
Jac.resize(nDofsTVP * nDofsTVP);
// define the dependent variables
s.dependent(&aResT[0], nDofsT);
for(unsigned k = 0; k < dim; k++) {
s.dependent(&aResV[k][0], nDofsV);
}
s.dependent(&aResP[0], nDofsP);
// define the independent variables
s.independent(&solT[0], nDofsT);
for(unsigned k = 0; k < dim; k++) {
s.independent(&solV[k][0], nDofsV);
}
s.independent(&solP[0], nDofsP);
// get the and store jacobian matrix (row-major)
s.jacobian(&Jac[0] , true);
KK->add_matrix_blocked(Jac, sysDof, sysDof);
s.clear_independents();
s.clear_dependents();
}
} //end element loop for each process
RES->close();
if(assembleMatrix) {
KK->close();
}
// ***************** END ASSEMBLY *******************
}
void AssembleWillmoreFlow_AD(MultiLevelProblem& ml_prob) {
// ml_prob is the global object from/to where get/set all the data
// level is the level of the PDE system to be assembled
// levelMax is the Maximum level of the MultiLevelProblem
// assembleMatrix is a flag that tells if only the residual or also the matrix should be assembled
// call the adept stack object
adept::Stack& s = FemusInit::_adeptStack;
// extract pointers to the several objects that we are going to use
TransientNonlinearImplicitSystem* mlPdeSys = &ml_prob.get_system<TransientNonlinearImplicitSystem> ("Willmore"); // pointer to the linear implicit system named "Poisson"
const unsigned level = mlPdeSys->GetLevelToAssemble();
Mesh* msh = ml_prob._ml_msh->GetLevel(level); // pointer to the mesh (level) object
elem* el = msh->el; // pointer to the elem object in msh (level)
MultiLevelSolution* mlSol = ml_prob._ml_sol; // pointer to the multilevel solution object
Solution* sol = ml_prob._ml_sol->GetSolutionLevel(level); // pointer to the solution (level) object
LinearEquationSolver* pdeSys = mlPdeSys->_LinSolver[level]; // pointer to the equation (level) object
SparseMatrix* KK = pdeSys->_KK; // pointer to the global stifness matrix object in pdeSys (level)
NumericVector* RES = pdeSys->_RES; // pointer to the global residual vector object in pdeSys (level)
const unsigned dim = msh->GetDimension(); // get the domain dimension of the problem
unsigned iproc = msh->processor_id(); // get the process_id (for parallel computation)
//solution variable
unsigned solRIndex[3];
solRIndex[0] = mlSol->GetIndex("X"); // get the position of "X" in the ml_sol object
solRIndex[1] = mlSol->GetIndex("Y"); // get the position of "Y" in the ml_sol object
solRIndex[2] = mlSol->GetIndex("Z"); // get the position of "Z" in the ml_sol object
unsigned solRType[3];
solRType[0] = mlSol->GetSolutionType(solRIndex[0]); // get the finite element type for "R"
solRType[1] = mlSol->GetSolutionType(solRIndex[1]); // get the finite element type for "R"
solRType[2] = mlSol->GetSolutionType(solRIndex[2]); // get the finite element type for "R"
unsigned solRPdeIndex[3];
solRPdeIndex[0] = mlPdeSys->GetSolPdeIndex("X"); // get the position of "X" in the pdeSys object
solRPdeIndex[1] = mlPdeSys->GetSolPdeIndex("Y"); // get the position of "Y" in the pdeSys object
solRPdeIndex[2] = mlPdeSys->GetSolPdeIndex("Z"); // get the position of "Z" in the pdeSys object
vector < adept::adouble > solR[3]; // local solution
vector < double > solR_old[3];
unsigned solHIndex;
solHIndex = mlSol->GetIndex("H"); // get the position of "H" in the ml_sol object
unsigned solHType = mlSol->GetSolutionType(solHIndex); // get the finite element type for "H"
unsigned solHPdeIndex;
solHPdeIndex = mlPdeSys->GetSolPdeIndex("H"); // get the position of "H" in the pdeSys object
vector < adept::adouble > solH; // local solution
vector < vector < double > > x(dim); // local coordinates
unsigned xType = 2; // get the finite element type for "x", it is always 2 (LAGRANGE QUADRATIC)
vector< int > sysDof; // local to global pdeSys dofs
vector <double> phi; // local test function
vector <double> phi_x; // local test function first order partial derivatives
vector <double> phi_xx; // local test function second order partial derivatives
double weight; // gauss point weight
vector< double > Res; // local redidual vector
vector< adept::adouble > aResR[3]; // local redidual vector
vector< adept::adouble > aResH; // local redidual vector
// reserve memory for the local standar vectors
const unsigned maxSize = static_cast< unsigned >(ceil(pow(3, dim))); // conservative: based on line3, quad9, hex27
for (int i = 0; i < 3; i++) {
solR[i].reserve(maxSize);
solR_old[i].reserve(maxSize);
}
solH.reserve(maxSize);
for (unsigned i = 0; i < dim; i++)
x[i].reserve(maxSize);
sysDof.reserve(4 * maxSize);
phi.reserve(maxSize);
phi_x.reserve(maxSize * dim);
unsigned dim2 = (3 * (dim - 1) + !(dim - 1)); // dim2 is the number of second order partial derivatives (1,3,6 depending on the dimension)
phi_xx.reserve(maxSize * dim2);
Res.reserve(4 * maxSize);
for (int i = 0; i < 3; i++) {
aResR[i].reserve(maxSize);
}
aResH.reserve(maxSize);
vector < double > Jac; // local Jacobian matrix (ordered by column, adept)
Jac.reserve(4 * maxSize * 4 * maxSize);
KK->zero(); // Set to zero all the entries of the Global Matrix
// element loop: each process loops only on the elements that owns
for (int iel = msh->_elementOffset[iproc]; iel < msh->_elementOffset[iproc + 1]; iel++) {
short unsigned ielGeom = msh->GetElementType(iel);
unsigned nDofs = msh->GetElementDofNumber(iel, solHType); // number of solution element dofs
unsigned nDofs2 = msh->GetElementDofNumber(iel, xType); // number of coordinate element dofs
// resize local arrays
sysDof.resize(4 * nDofs);
for (int i = 0; i < 3; i++) {
solR[i].resize(nDofs);
solR_old[i].resize(nDofs);
}
solH.resize(nDofs);
for (int i = 0; i < dim; i++) {
x[i].resize(nDofs2);
}
Res.resize(4 * nDofs); //resize
for (int i = 0; i < 3; i++) {
aResR[i].resize(nDofs); //resize
}
aResH.resize(nDofs); //resize
for (int i = 0; i < 3; i++) {
std::fill(aResR[i].begin(), aResR[i].end(), 0); //set aRes to zero
}
std::fill(aResH.begin(), aResH.end(), 0); //set aRes to zero
// local storage of global mapping and solution
for (unsigned i = 0; i < nDofs; i++) {
unsigned solDof = msh->GetSolutionDof(i, iel, solHType); // global to global mapping between solution node and solution dof
for (int k = 0; k < 3; k++) {
solR[k][i] = (*sol->_Sol[solRIndex[k]])(solDof); // global extraction and local storage for the solution
solR_old[k][i] = (*sol->_SolOld[solRIndex[k]])(solDof); // global extraction and local storage for the solution
}
solH[i] = (*sol->_Sol[solHIndex])(solDof); // global extraction and local storage for the solution
for (int k = 0; k < 3; k++) {
sysDof[k * nDofs + i] = pdeSys->GetSystemDof(solRIndex[k], solRPdeIndex[k], i, iel); // global to global mapping between solution node and pdeSys dof
}
sysDof[3 * nDofs + i] = pdeSys->GetSystemDof(solHIndex, solHPdeIndex, i, iel); // global to global mapping between solution node and pdeSys dof
}
// local storage of coordinates
for (unsigned i = 0; i < nDofs2; i++) {
unsigned xDof = msh->GetSolutionDof(i, iel, xType); // global to global mapping between coordinates node and coordinate dof
for (unsigned idim = 0; idim < dim; idim++) {
x[idim][i] = (*msh->_topology->_Sol[idim])(xDof); // global extraction and local storage for the element coordinates
}
}
// start a new recording of all the operations involving adept::adouble variables
s.new_recording();
// *** Gauss point loop ***
for (unsigned ig = 0; ig < msh->_finiteElement[ielGeom][solHType]->GetGaussPointNumber(); ig++) {
// *** get gauss point weight, test function and test function partial derivatives ***
msh->_finiteElement[ielGeom][solHType]->Jacobian(x, ig, weight, phi, phi_x, phi_xx);
// evaluate the solution, the solution derivatives and the coordinates in the gauss point
adept::adouble solRGauss[3];
double solRGaussOld[3];
adept::adouble solRGauss_x[3][2];
adept::adouble solRGauss_xx[3][2][2];
adept::adouble sol_x[2];
sol_x[0] = sol_x[1] = 0.;
for (int k = 0; k < 3; k++) {
solRGauss[k] = 0.;
solRGaussOld[k] = 0.;
for (int i = 0; i < dim; i++) {
solRGauss_x[k][i] = 0.;
for (int j = 0; j < dim; j++) {
solRGauss_xx[k][i][j] = 0.;
}
}
}
adept::adouble solHGauss = 0;
adept::adouble solHGauss_x[2] = {0., 0.};
for (unsigned i = 0; i < nDofs; i++) {
for (int k = 0; k < 3; k++) {
solRGauss[k] += phi[i] * solR[k][i];
solRGaussOld[k] += phi[i] * solR_old[k][i];
}
solHGauss += phi[i] * solH[i];
for (unsigned u = 0; u < dim; u++) {
sol_x[u] += phi[i] * x[u][i];
}
for (unsigned u = 0; u < dim; u++) { // gradient
for (int k = 0; k < 3; k++) {
solRGauss_x[k][u] += phi_x[i * dim + u] * solR[k][i];
}
solHGauss_x[u] += phi_x[i * dim + u] * solH[i];
}
for (unsigned u = 0; u < dim; u++) { // hessian
for (unsigned v = 0; v < dim; v++) {
unsigned uvindex = 0; //_uu
if (u != v) uvindex = 2; //_uv or _vu
else if (u == 1) uvindex = 1; //_vv
for (int k = 0; k < 3; k++) {
solRGauss_xx[k][u][v] += phi_xx[i * dim2 + uvindex] * solR[k][i];
}
}
}
}
adept::adouble g[2][2];
g[0][0] = g[0][1] = g[1][0] = g[1][1] = 0.;
for (int k = 0; k < 3; k++) {
for (int u = 0; u < dim; u++) {
for (int v = 0; v < dim; v++) {
g[u][v] += solRGauss_x[k][u] * solRGauss_x[k][v];
}
}
}
adept::adouble detg = g[0][0] * g[1][1] - g[0][1] * g[1][0];
adept::adouble A = sqrt(detg);
adept::adouble gI[2][2];
gI[0][0] = g[1][1] / detg;
gI[0][1] = -g[0][1] / detg;
gI[1][0] = -g[1][0] / detg;
gI[1][1] = g[0][0] / detg;
adept::adouble N[3];
N[0] = (solRGauss_x[1][0] * solRGauss_x[2][1] - solRGauss_x[1][1] * solRGauss_x[2][0]) / A;
N[1] = (solRGauss_x[2][0] * solRGauss_x[0][1] - solRGauss_x[2][1] * solRGauss_x[0][0]) / A;
N[2] = (solRGauss_x[0][0] * solRGauss_x[1][1] - solRGauss_x[0][1] * solRGauss_x[1][0]) / A;
adept::adouble h[2][2];
h[0][0] = h[0][1] = h[1][0] = h[1][1] = 0.;
for (int k = 0; k < 3; k++) {
for (int u = 0; u < dim; u++) {
for (int v = 0; v < dim; v++) {
h[u][v] += solRGauss_xx[k][u][v] * N[k];
}
}
}
//adept::adouble K = cos(sol_x[0])/(a+cos(sol_x[0]));//(h[0][0]*h[1][1]-h[0][1]*h[1][0])/detg;
adept::adouble K = (h[0][0] * h[1][1] - h[0][1] * h[1][0]) / detg;
adept::adouble H_exact = 0.5 * (1. + cos(sol_x[0]) / (a + cos(sol_x[0])));
// *** phi_i loop ***
for (unsigned i = 0; i < nDofs; i++) {
for (int k = 0; k < 3; k++) {
for (int u = 0; u < dim; u++) {
adept::adouble AgIgradRgradPhi = 0;
for (int v = 0; v < dim; v++) {
AgIgradRgradPhi += A * gI[u][v].value() * solRGauss_x[k][v];
}
aResR[k][i] += AgIgradRgradPhi * phi_x[i * dim + u] * weight;
}
aResR[k][i] += 2.* A * solHGauss.value() * N[k] * phi[i] * weight;
}
for (int u = 0; u < dim; u++) {
adept::adouble AgIgradHgradPhi = 0;
for (int v = 0; v < dim; v++) {
AgIgradHgradPhi += A * gI[u][v].value() * solHGauss_x[v];
}
aResH[i] -= AgIgradHgradPhi * phi_x[i * dim + u] * weight;
}
aResH[i] += A * (-0 * (solRGauss[0] - solRGaussOld[0]) * N[0].value()
- 0 * (solRGauss[1] - solRGaussOld[1]) * N[1].value()
- 0 * (solRGauss[2] - solRGaussOld[2]) * N[2].value()
+ 2. * solHGauss * (solHGauss * solHGauss - K.value())) * phi[i] * weight;
} // end phi_i loop
} // end gauss point loop
//--------------------------------------------------------------------------------------------------------
// Add the local Matrix/Vector into the global Matrix/Vector
//copy the value of the adept::adoube aRes in double Res and store
for (int i = 0; i < nDofs; i++) {
for (int k = 0; k < 3; k++) {
Res[ k * nDofs + i] = -aResR[k][i].value();
}
Res[ 3 * nDofs + i] = -aResH[i].value();
}
RES->add_vector_blocked(Res, sysDof);
Jac.resize((4 * nDofs) * (4 * nDofs));
// define the dependent variables
for (int k = 0; k < 3; k++) {
s.dependent(&aResR[k][0], nDofs);
}
s.dependent(&aResH[0], nDofs);
// define the independent variables
for (int k = 0; k < 3; k++) {
s.independent(&solR[k][0], nDofs);
}
s.independent(&solH[0], nDofs);
// get the jacobian matrix (ordered by row)
s.jacobian(&Jac[0], true);
KK->add_matrix_blocked(Jac, sysDof, sysDof);
s.clear_independents();
s.clear_dependents();
} //end element loop for each process
RES->close();
KK->close();
// ***************** END ASSEMBLY *******************
}
//------------------------------------------------------------------------------------------------------------
void AssembleMatrixRes_VC(MultiLevelProblem &ml_prob) {
TransientNonlinearImplicitSystem* mlPdeSys = & ml_prob.get_system<TransientNonlinearImplicitSystem>("Timedep");
const unsigned level = mlPdeSys->GetLevelToAssemble();
MultiLevelSolution *ml_sol = ml_prob._ml_sol;
Solution* sol = ml_sol->GetSolutionLevel(level);
LinearEquationSolver* pdeSys = mlPdeSys->_LinSolver[level];
const char* pdename = mlPdeSys->name().c_str();
Mesh* msh = ml_prob._ml_msh->GetLevel(level);
elem* myel = msh->el;
SparseMatrix* JAC = pdeSys->_KK;
NumericVector* RES = pdeSys->_RES;
// data
const unsigned dim = msh->GetDimension();
const unsigned max_size = static_cast< unsigned >(ceil(pow(3, dim))); // conservative: based on line3, quad9, hex27
unsigned nel = msh->GetNumberOfElements();
unsigned igrid = msh->GetLevel();
unsigned iproc = msh->processor_id();
// time dep data
double dt = mlPdeSys->GetIntervalTime();
// double theta = 0.5;
//************** geometry (at dofs and quadrature points) *************************************
vector < vector < double > > coords_at_dofs(dim);
unsigned coords_fe_type = BIQUADR_FE; // get the finite element type for "x", it is always 2 (LAGRANGE BIQUADRATIC)
for (unsigned i = 0; i < coords_at_dofs.size(); i++) coords_at_dofs[i].reserve(max_size);
vector < double > coord_at_qp(dim);
//************* shape functions (at dofs and quadrature points) **************************************
const int solType_max = BIQUADR_FE; //biquadratic
double weight_qp; // gauss point weight
vector < vector < double > > phi_fe_qp(NFE_FAMS);
vector < vector < double > > phi_x_fe_qp(NFE_FAMS);
vector < vector < double > > phi_xx_fe_qp(NFE_FAMS);
for(int fe=0; fe < NFE_FAMS; fe++) {
phi_fe_qp[fe].reserve(max_size);
phi_x_fe_qp[fe].reserve(max_size*dim);
phi_xx_fe_qp[fe].reserve(max_size*(3*(dim-1)));
}
//***************************************************
//********* WHOLE SET OF VARIABLES ******************
//***************************************************
const unsigned int n_unknowns = mlPdeSys->GetSolPdeIndex().size();
vector < std::string > Solname(n_unknowns); Solname[0] = "u";
vector < unsigned > SolPdeIndex(n_unknowns);
vector < unsigned > SolIndex(n_unknowns);
vector < unsigned int > SolFEType(n_unknowns); //FEtype of each MultilevelSolution
vector < unsigned int > Sol_n_el_dofs(n_unknowns); //number of element dofs
std::fill(Sol_n_el_dofs.begin(), Sol_n_el_dofs.end(), 0);
for(unsigned ivar=0; ivar < n_unknowns; ivar++) {
SolPdeIndex[ivar] = mlPdeSys->GetSolPdeIndex( Solname[ivar].c_str() );
SolIndex[ivar] = ml_sol->GetIndex ( Solname[ivar].c_str() );
SolFEType[ivar] = ml_sol->GetSolutionType ( SolIndex[ivar]);
}
//------------ quantities (at quadrature points) ---------------------
vector<double> sol_qp(n_unknowns);
vector<double> sol_old_qp(n_unknowns);
vector< vector<double> > sol_grad_qp(n_unknowns);
vector< vector<double> > sol_old_grad_qp(n_unknowns);
std::fill(sol_qp.begin(), sol_qp.end(), 0.);
std::fill(sol_old_qp.begin(), sol_old_qp.end(), 0.);
for (unsigned k = 0; k < n_unknowns; k++) {
sol_grad_qp[k].resize(dim);
std::fill(sol_grad_qp[k].begin(), sol_grad_qp[k].end(), 0.);
sol_old_grad_qp[k].resize(dim);
std::fill(sol_old_grad_qp[k].begin(), sol_old_grad_qp[k].end(), 0.);
}
//----------- quantities (at dof objects) ------------------------------
vector < vector < double > > sol_eldofs(n_unknowns);
vector < vector < double > > sol_old_eldofs(n_unknowns);
for(int k=0; k<n_unknowns; k++) { sol_eldofs[k].reserve(max_size);
sol_old_eldofs[k].reserve(max_size);
}
//******** linear system *******************************************
vector < vector < int > > L2G_dofmap(n_unknowns); for(int i = 0; i < n_unknowns; i++) { L2G_dofmap[i].reserve(max_size); }
vector< int > L2G_dofmap_AllVars; L2G_dofmap_AllVars.reserve( n_unknowns*max_size );
vector< vector< double > > Res_el(n_unknowns);
vector< vector< vector< double > > > Jac_el(n_unknowns);
for(int i = 0; i < n_unknowns; i++) Res_el[i].reserve(max_size);
for(int i = 0; i < n_unknowns; i++) {
Jac_el[i].resize(n_unknowns);
for(int j = 0; j < n_unknowns; j++) {
Jac_el[i][j].reserve(max_size*max_size);
}
}
// Set to zero all the entries of the matrix
RES->zero();
JAC->zero();
const double deltat_term = 1.;
const double lapl_term = 1.;
const double delta_g_term = 1.;
// *** element loop ***
for (int iel = msh->_elementOffset[iproc]; iel < msh->_elementOffset[iproc+1]; iel++) {
short unsigned ielGeom = msh->GetElementType(iel); // element geometry type
//******************** GEOMETRY *********************
unsigned nDofx = msh->GetElementDofNumber(iel, coords_fe_type); // number of coordinate element dofs
for (int i = 0; i < dim; i++) coords_at_dofs[i].resize(nDofx);
// local storage of coordinates
for (unsigned i = 0; i < nDofx; i++) {
unsigned xDof = msh->GetSolutionDof(i, iel, coords_fe_type); // global to global mapping between coordinates node and coordinate dof
for (unsigned jdim = 0; jdim < dim; jdim++) {
coords_at_dofs[jdim][i] = (*msh->_topology->_Sol[jdim])(xDof); // global extraction and local storage for the element coordinates
}
}
//***************************************************
//all vars###################################################################
for (unsigned k = 0; k < n_unknowns; k++) {
unsigned ndofs_unk = msh->GetElementDofNumber(iel, SolFEType[k]);
Sol_n_el_dofs[k] = ndofs_unk;
sol_eldofs[k].resize(ndofs_unk);
sol_old_eldofs[k].resize(ndofs_unk);
L2G_dofmap[k].resize(ndofs_unk);
for (unsigned i = 0; i < ndofs_unk; i++) {
unsigned solDof = msh->GetSolutionDof(i, iel, SolFEType[k]); // global to global mapping between solution node and solution dof
// via local to global solution node
sol_eldofs[k][i] = (*sol->_Sol[SolIndex[k]])(solDof); // global extraction and local storage for the solution
sol_old_eldofs[k][i] = (*sol->_SolOld[SolIndex[k]])(solDof); // This is OLD in TIME, not in nonlinear loop
L2G_dofmap[k][i] = pdeSys->GetSystemDof(SolIndex[k], SolPdeIndex[k], i, iel); // global to global mapping between solution node and pdeSys dof
}
}
unsigned nDof_AllVars = 0;
for (unsigned k = 0; k < n_unknowns; k++) { nDof_AllVars += Sol_n_el_dofs[k]; }
// TODO COMPUTE MAXIMUM maximum number of element dofs for one scalar variable
int nDof_max = 0;
for (unsigned k = 0; k < n_unknowns; k++) {
if(Sol_n_el_dofs[k] > nDof_max) nDof_max = Sol_n_el_dofs[k];
}
for(int k = 0; k < n_unknowns; k++) {
L2G_dofmap[k].resize(Sol_n_el_dofs[k]);
Res_el[SolPdeIndex[k]].resize(Sol_n_el_dofs[k]);
memset(& Res_el[SolPdeIndex[k]][0], 0., Sol_n_el_dofs[k] * sizeof(double) );
Jac_el[SolPdeIndex[k]][SolPdeIndex[k]].resize(Sol_n_el_dofs[k] * Sol_n_el_dofs[k]);
memset(& Jac_el[SolPdeIndex[k]][SolPdeIndex[k]][0], 0., Sol_n_el_dofs[k] * Sol_n_el_dofs[k] * sizeof(double));
}
//all vars###################################################################
// *** quadrature loop ***
for(unsigned ig = 0; ig < ml_prob.GetQuadratureRule(ielGeom).GetGaussPointsNumber(); ig++) {
// *** get gauss point weight, test function and test function partial derivatives ***
for(int fe=0; fe < NFE_FAMS; fe++) {
msh->_finiteElement[ielGeom][fe]->Jacobian(coords_at_dofs,ig,weight_qp,phi_fe_qp[fe],phi_x_fe_qp[fe],phi_xx_fe_qp[fe]);
}
//HAVE TO RECALL IT TO HAVE BIQUADRATIC JACOBIAN
msh->_finiteElement[ielGeom][coords_fe_type]->Jacobian(coords_at_dofs,ig,weight_qp,phi_fe_qp[coords_fe_type],phi_x_fe_qp[coords_fe_type],phi_xx_fe_qp[coords_fe_type]);
//========= fill gauss value quantities ==================
std::fill(sol_qp.begin(), sol_qp.end(), 0.);
std::fill(sol_old_qp.begin(), sol_old_qp.end(), 0.);
for (unsigned k = 0; k < n_unknowns; k++) { std::fill(sol_grad_qp[k].begin(), sol_grad_qp[k].end(), 0.);
std::fill(sol_old_grad_qp[k].begin(), sol_old_grad_qp[k].end(), 0.);
}
for (unsigned k = 0; k < n_unknowns; k++) {
for (unsigned i = 0; i < Sol_n_el_dofs[k]; i++) {
sol_qp[k] += sol_eldofs[k][i] * phi_fe_qp[SolFEType[k]][i];
sol_old_qp[k] += sol_old_eldofs[k][i] * phi_fe_qp[SolFEType[k]][i];
for (unsigned d = 0; d < dim; d++) { sol_grad_qp[k][d] += sol_eldofs[k][i] * phi_x_fe_qp[SolFEType[k]][i * dim + d];
sol_old_grad_qp[k][d] += sol_old_eldofs[k][i] * phi_x_fe_qp[SolFEType[k]][i * dim + d];
}
}
}
//========= fill gauss value quantities ==================
// *** phi_i loop ***
for(unsigned i = 0; i < nDof_max; i++) {
//BEGIN RESIDUALS A block ===========================
double Lap_rhs_i = 0.;
double Lap_old_rhs_i = 0.;
for(unsigned d = 0; d < dim; d++) {
Lap_rhs_i += phi_x_fe_qp[SolFEType[0]][i * dim + d] * sol_grad_qp[0][d];
Lap_old_rhs_i += phi_x_fe_qp[SolFEType[0]][i * dim + d] * sol_old_grad_qp[0][d];
}
Res_el[SolPdeIndex[0]][i] += - weight_qp * (
delta_g_term * Singularity::function(sol_qp[0]) * Singularity::g_vc(sol_qp[0]) * phi_fe_qp[ SolFEType[0] ][i]
- delta_g_term * Singularity::function(sol_qp[0]) * Singularity::g_vc(sol_old_qp[0]) * phi_fe_qp[ SolFEType[0] ][i]
+ deltat_term * Singularity::function(sol_qp[0]) * dt * phi_fe_qp[ SolFEType[0] ][i]
+ lapl_term * dt * Lap_rhs_i
);
//END RESIDUALS A block ===========================
// *** phi_j loop ***
for(unsigned j = 0; j<nDof_max; j++) {
double Lap_mat_i_j = 0.;
for(unsigned d = 0; d < dim; d++) Lap_mat_i_j += phi_x_fe_qp[SolFEType[0]][i * dim + d] *
phi_x_fe_qp[SolFEType[0]][j * dim + d];
Jac_el[SolPdeIndex[0]][SolPdeIndex[0]][i * Sol_n_el_dofs[0] + j] += weight_qp * (
+ delta_g_term * phi_fe_qp[ SolFEType[0] ][i] * Singularity::derivative( phi_fe_qp[ SolFEType[0] ][j] ) * phi_fe_qp[ SolFEType[0] ][j] * Singularity::g_vc( phi_fe_qp[ SolFEType[0] ][j] )
+ delta_g_term * phi_fe_qp[ SolFEType[0] ][i] * Singularity::function ( phi_fe_qp[ SolFEType[0] ][j] ) * Singularity::g_vc_derivative( phi_fe_qp[ SolFEType[0] ][j] ) * phi_fe_qp[ SolFEType[0] ][j]
- delta_g_term * phi_fe_qp[ SolFEType[0] ][i] * Singularity::derivative( phi_fe_qp[ SolFEType[0] ][j] ) * phi_fe_qp[ SolFEType[0] ][j] * Singularity::g_vc( sol_old_qp[0] )
+ deltat_term * phi_fe_qp[ SolFEType[0] ][i] * Singularity::derivative( phi_fe_qp[ SolFEType[0] ][j] ) * phi_fe_qp[ SolFEType[0] ][j] * dt
+ lapl_term * dt * Lap_mat_i_j
);
} //end phij loop
} //end phii loop
} // end gauss point loop
//--------------------------------------------------------------------------------------------------------
//Sum the local matrices/vectors into the Global Matrix/Vector
for(unsigned ivar=0; ivar < n_unknowns; ivar++) {
RES->add_vector_blocked(Res_el[SolPdeIndex[ivar]],L2G_dofmap[ivar]);
JAC->add_matrix_blocked(Jac_el[SolPdeIndex[ivar]][SolPdeIndex[ivar]],L2G_dofmap[ivar],L2G_dofmap[ivar]);
}
//--------------------------------------------------------------------------------------------------------
} //end list of elements loop for each subdomain
JAC->close();
RES->close();
// ***************** END ASSEMBLY *******************
}
