//------------------------------------------------------------------------------------------------------------
void AssembleMatrixResNS(MultiLevelProblem &ml_prob){
//pointers
TransientNonlinearImplicitSystem& my_nnlin_impl_sys = ml_prob.get_system<TransientNonlinearImplicitSystem>("Navier-Stokes");
const unsigned level = my_nnlin_impl_sys.GetLevelToAssemble();
const unsigned gridn = my_nnlin_impl_sys.GetLevelMax();
bool assemble_matrix = my_nnlin_impl_sys.GetAssembleMatrix();
MultiLevelSolution *ml_sol = ml_prob._ml_sol;
Solution* mysolution = ml_sol->GetSolutionLevel(level);
LinearEquationSolver* mylsyspde = my_nnlin_impl_sys._LinSolver[level];
const char* pdename = my_nnlin_impl_sys.name().c_str();
Mesh* mymsh = ml_prob._ml_msh->GetLevel(level);
elem* myel = mymsh->el;
SparseMatrix* myKK = mylsyspde->_KK;
NumericVector* myRES = mylsyspde->_RES;
//data
double dt = my_nnlin_impl_sys.GetIntervalTime();
double theta = 0.5;
const unsigned dim = mymsh->GetDimension();
unsigned nel= mymsh->GetNumberOfElements();
unsigned igrid= mymsh->GetLevel();
unsigned iproc = mymsh->processor_id();
double ILambda = 0.;
double IRe = ml_prob.parameters.get<Fluid>("Fluid").get_IReynolds_number();
bool penalty = true; // mylsyspde->GetStabilization();
const bool symm_mat = false; // mylsyspde->GetMatrixProperties();
const bool NavierStokes = true;
unsigned nwtn_alg = 1;
bool newton = (nwtn_alg==0) ? 0:1;
// solution and coordinate variables
const char Solname[4][2] = {"U","V","W","P"};
vector < unsigned > SolPdeIndex(dim+1);
vector < unsigned > SolIndex(dim+1);
vector< vector < double> > coordinates(dim);
for(unsigned ivar=0; ivar<dim; ivar++) {
SolPdeIndex[ivar]=my_nnlin_impl_sys.GetSolPdeIndex(&Solname[ivar][0]);
SolIndex[ivar]=ml_sol->GetIndex(&Solname[ivar][0]);
}
SolPdeIndex[dim]=my_nnlin_impl_sys.GetSolPdeIndex(&Solname[3][0]);
SolIndex[dim]=ml_sol->GetIndex(&Solname[3][0]);
//solution order
unsigned order_ind2 = ml_sol->GetSolutionType(SolIndex[0]);
unsigned order_ind1 = ml_sol->GetSolutionType(SolIndex[dim]);
// declare
vector < int > metis_node2;
vector < int > node1;
vector< vector< int > > KK_dof(dim+1);
vector <double> phi2;
vector <double> gradphi2;
vector <double> nablaphi2;
const double *phi1;
double Weight2;
double normal[3];
vector< vector< double > > F(dim+1);
vector< vector< vector< double > > > B(dim+1);
// reserve
const unsigned max_size = static_cast< unsigned > (ceil(pow(3,dim)));
metis_node2.reserve(max_size);
node1.reserve( static_cast< unsigned > (ceil(pow(2,dim))));
for(int i=0;i<dim;i++) {
coordinates[i].reserve(max_size);
}
phi2.reserve(max_size);
gradphi2.reserve(max_size*dim);
nablaphi2.reserve(max_size*(3*(dim-1)));
for(int i=0;i<dim;i++) {
KK_dof[i].reserve(max_size);
}
for(int i=0;i<dim+1;i++) F[i].reserve(max_size);
if(assemble_matrix){
for(int i=0;i<dim+1;i++){
B[i].resize(dim+1);
for(int j=0;j<dim+1;j++){
B[i][j].reserve(max_size*max_size);
}
}
}
vector < double > Sol(dim+1);
vector < vector < double > > gradSol(dim);
for(int i=0;i<dim;i++) {
gradSol[i].resize(dim);
}
vector < double > SolOld(dim+1);
vector < vector < double > > gradSolOld(dim);
for(int i=0;i<dim;i++) {
gradSolOld[i].resize(dim);
}
//vector < double > AccSol(dim);
// Set to zeto all the entries of the matrix
if(assemble_matrix) myKK->zero();
// *** element loop ***
for (int iel=mymsh->_elementOffset[iproc]; iel < mymsh->_elementOffset[iproc+1]; iel++) {
unsigned kel = mymsh->IS_Mts2Gmt_elem[iel];
short unsigned kelt= mymsh->GetElementType(kel);
unsigned nve2=mymsh->GetElementDofNumber(kel,order_ind2);
unsigned nve1=mymsh->GetElementDofNumber(kel,order_ind1);
//set to zero all the entries of the FE matrices
metis_node2.resize(nve2);
node1.resize(nve1);
phi2.resize(nve2);
gradphi2.resize(nve2*dim);
nablaphi2.resize(nve2*(3*(dim-1)));
for(int ivar=0; ivar<dim; ivar++) {
coordinates[ivar].resize(nve2);
KK_dof[ivar].resize(nve2);
F[SolPdeIndex[ivar]].resize(nve2);
memset(&F[SolPdeIndex[ivar]][0],0,nve2*sizeof(double));
if(assemble_matrix){
B[SolPdeIndex[ivar]][SolPdeIndex[ivar]].resize(nve2*nve2);
B[SolPdeIndex[ivar]][SolPdeIndex[dim]].resize(nve2*nve1);
B[SolPdeIndex[dim]][SolPdeIndex[ivar]].resize(nve1*nve2);
memset(&B[SolPdeIndex[ivar]][SolPdeIndex[ivar]][0],0,nve2*nve2*sizeof(double));
memset(&B[SolPdeIndex[ivar]][SolPdeIndex[dim]][0],0,nve2*nve1*sizeof(double));
memset(&B[SolPdeIndex[dim]][SolPdeIndex[ivar]][0],0,nve1*nve2*sizeof(double));
}
}
KK_dof[dim].resize(nve1);
F[SolPdeIndex[dim]].resize(nve1);
memset(&F[SolPdeIndex[dim]][0],0,nve1*sizeof(double));
if(assemble_matrix*nwtn_alg==2){
for(int ivar=0; ivar<dim; ivar++) {
for(int ivar2=1; ivar2<dim; ivar2++) {
B[SolPdeIndex[ivar]][SolPdeIndex[(ivar+ivar2)%dim]].resize(nve2*nve2);
memset(&B[SolPdeIndex[ivar]][SolPdeIndex[(ivar+ivar2)%dim]][0],0,nve2*nve2*sizeof(double));
}
}
}
if(assemble_matrix*penalty){
B[SolPdeIndex[dim]][SolPdeIndex[dim]].resize(nve1*nve1,0.);
memset(&B[SolPdeIndex[dim]][SolPdeIndex[dim]][0],0,nve1*nve1*sizeof(double));
}
for( unsigned i=0;i<nve2;i++){
unsigned inode=myel->GetElementVertexIndex(kel,i)-1u;
unsigned inode_metis=mymsh->GetSolutionDof(inode,2);
metis_node2[i]=inode_metis;
for(unsigned ivar=0; ivar<dim; ivar++) {
coordinates[ivar][i]=(*mymsh->_topology->_Sol[ivar])(inode_metis);
KK_dof[ivar][i]=mylsyspde->GetSystemDof(SolIndex[ivar],SolPdeIndex[ivar],inode);
}
}
for(unsigned i=0;i<nve1;i++) {
unsigned inode=(order_ind1<dim)?(myel->GetElementVertexIndex(kel,i)-1u):(kel+i*nel);
node1[i]=inode;
KK_dof[dim][i]=mylsyspde->GetSystemDof(SolIndex[dim],SolPdeIndex[dim],inode);
}
if(igrid==gridn || !myel->GetRefinedElementIndex(kel)) {
// *** Gauss poit loop ***
for(unsigned ig=0;ig < ml_prob._ml_msh->_finiteElement[kelt][order_ind2]->GetGaussPointNumber(); ig++) {
// *** get Jacobian and test function and test function derivatives ***
ml_prob._ml_msh->_finiteElement[kelt][order_ind2]->Jacobian(coordinates,ig,Weight2,phi2,gradphi2,nablaphi2);
phi1=ml_prob._ml_msh->_finiteElement[kelt][order_ind1]->GetPhi(ig);
//velocity variable
for(unsigned ivar=0; ivar<dim; ivar++) {
Sol[ivar]=0.;
SolOld[ivar]=0.;
//AccSol[ivar]=0.;
for(unsigned ivar2=0; ivar2<dim; ivar2++){
gradSol[ivar][ivar2]=0;
gradSolOld[ivar][ivar2]=0;
}
unsigned SolIndex=ml_sol->GetIndex(&Solname[ivar][0]);
unsigned SolType =ml_sol->GetSolutionType(&Solname[ivar][0]);
for(unsigned i=0; i<nve2; i++) {
double soli = (*mysolution->_Sol[SolIndex])(metis_node2[i]);
double sololdi = (*mysolution->_SolOld[SolIndex])(metis_node2[i]);
Sol[ivar]+=phi2[i]*soli;
SolOld[ivar]+=phi2[i]*sololdi;
for(unsigned ivar2=0; ivar2<dim; ivar2++){
gradSol[ivar][ivar2] += gradphi2[i*dim+ivar2]*soli;
gradSolOld[ivar][ivar2] += gradphi2[i*dim+ivar2]*sololdi;
}
}
}
//pressure variable
Sol[dim]=0;
unsigned SolIndex=ml_sol->GetIndex(&Solname[3][0]);
unsigned SolType=ml_sol->GetSolutionType(&Solname[3][0]);
for(unsigned i=0; i<nve1; i++){
unsigned sol_dof = mymsh->GetSolutionDof(node1[i],SolType);
double soli = (*mysolution->_Sol[SolIndex])(sol_dof);
Sol[dim]+=phi1[i]*soli;
}
// *** phi_i loop ***
for(unsigned i=0; i<nve2; i++){
//BEGIN RESIDUALS A block ===========================
for(unsigned ivar=0; ivar<dim; ivar++) {
double Adv_rhs=0;
double Adv_old_rhs=0;
double Lap_rhs=0;
double Lap_old_rhs=0;
for(unsigned ivar2=0; ivar2<dim; ivar2++) {
Lap_rhs += gradphi2[i*dim+ivar2]*gradSol[ivar][ivar2];
Lap_old_rhs += gradphi2[i*dim+ivar2]*gradSolOld[ivar][ivar2];
Adv_rhs += Sol[ivar2]*gradSol[ivar][ivar2];
Adv_old_rhs += SolOld[ivar2]*gradSolOld[ivar][ivar2];
}
F[SolPdeIndex[ivar]][i]+= ( -theta*dt*IRe*Lap_rhs // Laplacian
-(1.-theta)*dt*IRe*Lap_old_rhs // Laplacian
-theta*dt*NavierStokes*Adv_rhs*phi2[i] // advection
-(1.-theta)*dt*NavierStokes*Adv_old_rhs*phi2[i] // advection
+dt*Sol[dim]*gradphi2[i*dim+ivar] // pressure
-(Sol[ivar] - SolOld[ivar])*phi2[i] // acceleration
)*Weight2;
}
//END RESIDUALS A block ===========================
if(assemble_matrix){
// *** phi_j loop ***
for(unsigned j=0; j<nve2; j++) {
double Lap=0;
double Adv1=0;
double Adv2 = phi2[i]*phi2[j]*Weight2;
double Mass = phi2[i]*phi2[j]*Weight2;
for(unsigned ivar=0; ivar<dim; ivar++) {
// Laplacian
Lap += gradphi2[i*dim+ivar]*gradphi2[j*dim+ivar]*Weight2;
// advection term I
Adv1 += Sol[ivar]*gradphi2[j*dim+ivar]*phi2[i]*Weight2;
}
for(unsigned ivar=0; ivar<dim; ivar++) {
B[SolPdeIndex[ivar]][SolPdeIndex[ivar]][i*nve2+j] += theta*dt*IRe*Lap + theta*dt*NavierStokes*newton*Adv1 + Mass;
if(nwtn_alg==2){
// Advection term II
B[SolPdeIndex[ivar]][SolPdeIndex[ivar]][i*nve2+j] += theta*dt*Adv2*gradSol[ivar][ivar];
for(unsigned ivar2=1; ivar2<dim; ivar2++) {
B[SolPdeIndex[ivar]][SolPdeIndex[(ivar+ivar2)%dim]][i*nve2+j] += theta*dt*Adv2*gradSol[ivar][(ivar+ivar2)%dim];
}
}
}
} //end phij loop
// *** phi1_j loop ***
for(unsigned j=0; j<nve1; j++){
for(unsigned ivar=0; ivar<dim; ivar++) {
B[SolPdeIndex[ivar]][SolPdeIndex[dim]][i*nve1+j] -= dt*gradphi2[i*dim+ivar]*phi1[j]*Weight2;
}
} //end phi1_j loop
} // endif assemble_matrix
} //end phii loop
// *** phi1_i loop ***
for(unsigned i=0; i<nve1; i++){
//BEGIN RESIDUALS B block ===========================
double div = 0;
for(unsigned ivar=0; ivar<dim; ivar++) {
div += gradSol[ivar][ivar];
}
F[SolPdeIndex[dim]][i]+= dt*(phi1[i]*div +penalty*ILambda*phi1[i]*Sol[dim])*Weight2;
//END RESIDUALS B block ===========================
if(assemble_matrix){
// *** phi_j loop ***
for(unsigned j=0; j<nve2; j++) {
for(unsigned ivar=0; ivar<dim; ivar++) {
B[SolPdeIndex[dim]][SolPdeIndex[ivar]][i*nve2+j]-= dt*phi1[i]*gradphi2[j*dim+ivar]*Weight2;
}
} //end phij loop
} // endif assemble_matrix
} //end phi1_i loop
if(assemble_matrix * penalty){ //block nve1 nve1
// *** phi_i loop ***
for(unsigned i=0; i<nve1; i++){
// *** phi_j loop ***
for(unsigned j=0; j<nve1; j++){
B[SolPdeIndex[dim]][SolPdeIndex[dim]][i*nve1+j]-= dt*ILambda*phi1[i]*phi1[j]*Weight2;
}
}
} //end if penalty
} // end gauss point loop
//--------------------------------------------------------------------------------------------------------
// Boundary Integral --> to be added
//number of faces for each type of element
// if (igrid==gridn || !myel->GetRefinedElementIndex(kel) ) {
//
// unsigned nfaces = myel->GetElementFaceNumber(kel);
//
// // loop on faces
// for(unsigned jface=0;jface<nfaces;jface++){
//
// // look for boundary faces
// if(myel->GetFaceElementIndex(kel,jface)<0){
// for(unsigned ivar=0; ivar<dim; ivar++) {
// ml_prob.ComputeBdIntegral(pdename, &Solname[ivar][0], kel, jface, level, ivar);
// }
// }
// }
// }
//--------------------------------------------------------------------------------------------------------
} // endif single element not refined or fine grid loop
//--------------------------------------------------------------------------------------------------------
//Sum the local matrices/vectors into the Global Matrix/Vector
for(unsigned ivar=0; ivar<dim; ivar++) {
myRES->add_vector_blocked(F[SolPdeIndex[ivar]],KK_dof[ivar]);
if(assemble_matrix){
myKK->add_matrix_blocked(B[SolPdeIndex[ivar]][SolPdeIndex[ivar]],KK_dof[ivar],KK_dof[ivar]);
myKK->add_matrix_blocked(B[SolPdeIndex[ivar]][SolPdeIndex[dim]],KK_dof[ivar],KK_dof[dim]);
myKK->add_matrix_blocked(B[SolPdeIndex[dim]][SolPdeIndex[ivar]],KK_dof[dim],KK_dof[ivar]);
if(nwtn_alg==2){
for(unsigned ivar2=1; ivar2<dim; ivar2++) {
myKK->add_matrix_blocked(B[SolPdeIndex[ivar]][SolPdeIndex[(ivar+ivar2)%dim]],KK_dof[ivar],KK_dof[(ivar+ivar2)%dim]);
}
}
}
}
//Penalty
if(assemble_matrix*penalty) myKK->add_matrix_blocked(B[SolPdeIndex[dim]][SolPdeIndex[dim]],KK_dof[dim],KK_dof[dim]);
myRES->add_vector_blocked(F[SolPdeIndex[dim]],KK_dof[dim]);
//--------------------------------------------------------------------------------------------------------
} //end list of elements loop for each subdomain
if(assemble_matrix) myKK->close();
myRES->close();
// ***************** END ASSEMBLY *******************
}
void AssembleBilaplaceProblem_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
// call the adept stack object
adept::Stack& s = FemusInit::_adeptStack;
// extract pointers to the several objects that we are going to use
NonLinearImplicitSystem* mlPdeSys = &ml_prob.get_system<NonLinearImplicitSystem> ("Poisson"); // 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 soluIndex;
soluIndex = mlSol->GetIndex("u"); // get the position of "u" in the ml_sol object
unsigned soluType = mlSol->GetSolutionType(soluIndex); // get the finite element type for "u"
unsigned soluPdeIndex;
soluPdeIndex = mlPdeSys->GetSolPdeIndex("u"); // get the position of "u" in the pdeSys object
vector < adept::adouble > solu; // local solution
unsigned solvIndex;
solvIndex = mlSol->GetIndex("v"); // get the position of "v" in the ml_sol object
unsigned solvType = mlSol->GetSolutionType(solvIndex); // get the finite element type for "v"
unsigned solvPdeIndex;
solvPdeIndex = mlPdeSys->GetSolPdeIndex("v"); // get the position of "v" in the pdeSys object
vector < adept::adouble > solv; // 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 > aResu; // local redidual vector
vector< adept::adouble > aResv; // 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
solu.reserve(maxSize);
solv.reserve(maxSize);
for (unsigned i = 0; i < dim; i++)
x[i].reserve(maxSize);
sysDof.reserve(2 * 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(2 * maxSize);
aResu.reserve(maxSize);
aResv.reserve(maxSize);
vector < double > Jac; // local Jacobian matrix (ordered by column, adept)
Jac.reserve(4 * maxSize * 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, soluType); // number of solution element dofs
unsigned nDofs2 = msh->GetElementDofNumber(iel, xType); // number of coordinate element dofs
// resize local arrays
sysDof.resize(2 * nDofs);
solu.resize(nDofs);
solv.resize(nDofs);
for (int i = 0; i < dim; i++) {
x[i].resize(nDofs2);
}
aResu.assign(nDofs, 0.); //resize
aResv.assign(nDofs, 0.); //resize
// local storage of global mapping and solution
for (unsigned i = 0; i < nDofs; i++) {
unsigned solDof = msh->GetSolutionDof(i, iel, soluType); // global to global mapping between solution node and solution dof
solu[i] = (*sol->_Sol[soluIndex])(solDof); // global extraction and local storage for the solution
solv[i] = (*sol->_Sol[solvIndex])(solDof); // global extraction and local storage for the solution
sysDof[i] = pdeSys->GetSystemDof(soluIndex, soluPdeIndex, i, iel); // global to global mapping between solution node and pdeSys dof
sysDof[nDofs + i] = pdeSys->GetSystemDof(solvIndex, solvPdeIndex, 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 jdim = 0; jdim < dim; jdim++) {
x[jdim][i] = (*msh->_topology->_Sol[jdim])(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][soluType]->GetGaussPointNumber(); ig++) {
// *** get gauss point weight, test function and test function partial derivatives ***
msh->_finiteElement[ielGeom][soluType]->Jacobian(x, ig, weight, phi, phi_x, phi_xx);
// evaluate the solution, the solution derivatives and the coordinates in the gauss point
adept::adouble soluGauss = 0;
vector < adept::adouble > soluGauss_x(dim, 0.);
adept::adouble solvGauss = 0;
vector < adept::adouble > solvGauss_x(dim, 0.);
vector < double > xGauss(dim, 0.);
for (unsigned i = 0; i < nDofs; i++) {
soluGauss += phi[i] * solu[i];
solvGauss += phi[i] * solv[i];
for (unsigned jdim = 0; jdim < dim; jdim++) {
soluGauss_x[jdim] += phi_x[i * dim + jdim] * solu[i];
solvGauss_x[jdim] += phi_x[i * dim + jdim] * solv[i];
xGauss[jdim] += x[jdim][i] * phi[i];
}
}
// *** phi_i loop ***
for (unsigned i = 0; i < nDofs; i++) {
adept::adouble Laplace_u = 0.;
adept::adouble Laplace_v = 0.;
for (unsigned jdim = 0; jdim < dim; jdim++) {
Laplace_u += - phi_x[i * dim + jdim] * soluGauss_x[jdim];
Laplace_v += - phi_x[i * dim + jdim] * solvGauss_x[jdim];
}
double exactSolValue = GetExactSolutionValue(xGauss);
double pi = acos(-1.);
aResv[i] += (solvGauss * phi[i] - Laplace_u) * weight;
aResu[i] += (4.*pi * pi * pi * pi * exactSolValue * phi[i] - Laplace_v) * 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
Res.resize(2 * nDofs);
for (int i = 0; i < nDofs; i++) {
Res[i] = -aResu[i].value();
Res[nDofs + i] = -aResv[i].value();
}
RES->add_vector_blocked(Res, sysDof);
Jac.resize( 4 * nDofs * nDofs );
// define the dependent variables
s.dependent(&aResu[0], nDofs);
s.dependent(&aResv[0], nDofs);
// define the independent variables
s.independent(&solu[0], nDofs);
s.independent(&solv[0], nDofs);
// get the jacobian matrix (ordered by column)
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 ETD(MultiLevelProblem& ml_prob)
{
const unsigned& NLayers = NumberOfLayers;
adept::Stack& s = FemusInit::_adeptStack;
LinearImplicitSystem* mlPdeSys = &ml_prob.get_system<LinearImplicitSystem> ("SW"); // pointer to the linear implicit system named "Poisson"
unsigned level = ml_prob._ml_msh->GetNumberOfLevels() - 1u;
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)
NumericVector* EPS = pdeSys->_EPS; // 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)
unsigned nprocs = msh->n_processors(); // get the process_id (for parallel computation)
//solution variable
std::vector < unsigned > solIndexh(NLayers);
std::vector < unsigned > solPdeIndexh(NLayers);
std::vector < unsigned > solIndexv(NLayers);
std::vector < unsigned > solPdeIndexv(NLayers);
std::vector < unsigned > solIndexHT(NLayers);
std::vector < unsigned > solPdeIndexHT(NLayers);
std::vector < unsigned > solIndexT(NLayers);
vector< int > l2GMap; // local to global mapping
for(unsigned i = 0; i < NLayers; i++) {
char name[10];
sprintf(name, "h%d", i);
solIndexh[i] = mlSol->GetIndex(name); // get the position of "hi" in the sol object
solPdeIndexh[i] = mlPdeSys->GetSolPdeIndex(name); // get the position of "hi" in the pdeSys object
sprintf(name, "v%d", i);
solIndexv[i] = mlSol->GetIndex(name); // get the position of "vi" in the sol object
solPdeIndexv[i] = mlPdeSys->GetSolPdeIndex(name); // get the position of "vi" in the pdeSys object
sprintf(name, "HT%d", i);
solIndexHT[i] = mlSol->GetIndex(name); // get the position of "Ti" in the sol object
solPdeIndexHT[i] = mlPdeSys->GetSolPdeIndex(name); // get the position of "Ti" in the pdeSys object
sprintf(name, "T%d", i);
solIndexT[i] = mlSol->GetIndex(name); // get the position of "Ti" in the sol object
}
unsigned solTypeh = mlSol->GetSolutionType(solIndexh[0]); // get the finite element type for "hi"
unsigned solTypev = mlSol->GetSolutionType(solIndexv[0]); // get the finite element type for "vi"
unsigned solTypeHT = mlSol->GetSolutionType(solIndexHT[0]); // get the finite element type for "Ti"
vector < double > x; // local coordinates
vector< vector < adept::adouble > > solh(NLayers); // local coordinates
vector< vector < adept::adouble > > solv(NLayers); // local coordinates
vector< vector < adept::adouble > > solHT(NLayers); // local coordinates
vector< vector < double > > solT(NLayers); // local coordinates
vector< vector < bool > > bdch(NLayers); // local coordinates
vector< vector < bool > > bdcv(NLayers); // local coordinates
vector< vector < bool > > bdcHT(NLayers); // local coordinates
unsigned xType = 2; // get the finite element type for "x", it is always 2 (LAGRANGE QUADRATIC)
vector < vector< adept::adouble > > aResh(NLayers);
vector < vector< adept::adouble > > aResv(NLayers);
vector < vector< adept::adouble > > aResHT(NLayers);
KK->zero();
RES->zero();
double maxWaveSpeed = 0.;
double dx;
for(unsigned k=0; k<NumberOfLayers; k++){
for(unsigned i = msh->_dofOffset[solTypeHT][iproc]; i < msh->_dofOffset[solTypeHT][iproc + 1]; i++){
double valueT = (*sol->_Sol[solIndexT[k]])(i);
double valueH = (*sol->_Sol[solIndexh[k]])(i);
double valueHT = valueT * valueH;
sol->_Sol[solIndexHT[k]]->set(i, valueHT);
}
sol->_Sol[solIndexHT[k]]->close();
}
for(int iel = msh->_elementOffset[iproc]; iel < msh->_elementOffset[iproc + 1]; iel++) {
short unsigned ielGeom = msh->GetElementType(iel);
unsigned nDofh = msh->GetElementDofNumber(iel, solTypeh); // number of solution element dofs
unsigned nDofv = msh->GetElementDofNumber(iel, solTypev); // number of solution element dofs
unsigned nDofHT = msh->GetElementDofNumber(iel, solTypeHT); // number of coordinate element dofs
unsigned nDofx = msh->GetElementDofNumber(iel, xType); // number of coordinate element dofs
unsigned nDofs = nDofh + nDofv + nDofHT;
// resize local arrays
l2GMap.resize(NLayers * (nDofs) );
for(unsigned i = 0; i < NLayers; i++) {
solh[i].resize(nDofh);
solv[i].resize(nDofv);
solHT[i].resize(nDofHT);
solT[i].resize(nDofHT);
bdch[i].resize(nDofh);
bdcv[i].resize(nDofv);
bdcHT[i].resize(nDofHT);
aResh[i].resize(nDofh); //resize
std::fill(aResh[i].begin(), aResh[i].end(), 0); //set aRes to zero
aResv[i].resize(nDofv); //resize
std::fill(aResv[i].begin(), aResv[i].end(), 0); //set aRes to zero
aResHT[i].resize(nDofHT); //resize
std::fill(aResHT[i].begin(), aResHT[i].end(), 0); //set aRes to zero
}
x.resize(nDofx);
//local storage of global mapping and solution
for(unsigned i = 0; i < nDofh; i++) {
unsigned solDofh = msh->GetSolutionDof(i, iel, solTypeh); // global to global mapping between solution node and solution dof
for(unsigned j = 0; j < NLayers; j++) {
solh[j][i] = (*sol->_Sol[solIndexh[j]])(solDofh); // global extraction and local storage for the solution
bdch[j][i] = ( (*sol->_Bdc[solIndexh[j]])(solDofh) < 1.5) ? true : false;
l2GMap[ j * nDofs + i] = pdeSys->GetSystemDof(solIndexh[j], solPdeIndexh[j], i, iel); // global to global mapping between solution node and pdeSys dof
}
}
for(unsigned i = 0; i < nDofv; i++) {
unsigned solDofv = msh->GetSolutionDof(i, iel, solTypev); // global to global mapping between solution node and solution dof
for(unsigned j = 0; j < NLayers; j++) {
solv[j][i] = (*sol->_Sol[solIndexv[j]])(solDofv); // global extraction and local storage for the solution
bdcv[j][i] = ( (*sol->_Bdc[solIndexv[j]])(solDofv) < 1.5) ? true : false;
l2GMap[ j * nDofs + nDofh + i] = pdeSys->GetSystemDof(solIndexv[j], solPdeIndexv[j], i, iel); // global to global mapping between solution node and pdeSys dof
}
}
for(unsigned i = 0; i < nDofHT; i++) {
unsigned solDofHT = msh->GetSolutionDof(i, iel, solTypeHT); // global to global mapping between solution node and solution dof
unsigned solDofh = msh->GetSolutionDof(i, iel, solTypeh);
for(unsigned j = 0; j < NLayers; j++) {
solHT[j][i] = (*sol->_Sol[solIndexHT[j]])(solDofHT); // global extraction and local storage for the solution
solT[j][i] = (*sol->_Sol[solIndexT[j]])(solDofHT); // global extraction and local storage for the solution
bdcHT[j][i] = ( (*sol->_Bdc[solIndexHT[j]])(solDofHT) < 1.5) ? true : false;
l2GMap[ j * nDofs + nDofh + nDofv + i] = pdeSys->GetSystemDof(solIndexHT[j], solPdeIndexHT[j], i, iel); // global to global mapping between solution node and pdeSys dof
//std::cout << solT[j][i] << " ";
}
}
s.new_recording();
for(unsigned i = 0; i < nDofx; i++) {
unsigned xDof = msh->GetSolutionDof(i, iel, xType); // global to global mapping between coordinates node and coordinate dof
x[i] = (*msh->_topology->_Sol[0])(xDof); // global extraction and local storage for the element coordinates
}
double xmid = 0.5 * (x[0] + x[1]);
//std::cout << xmid << std::endl;
double zz = sqrt(aa * aa - xmid * xmid); // z coordinate of points on sphere
double dd = aa * acos((zz * z_c) / (aa * aa)); // distance to center point on sphere [m]
double hh = 1 - dd * dd / (bb * bb);
double b = ( H_shelf + H_0 / 2 * (1 + tanh(hh / phi)) );
double hTot = 0.;
double beta = 0.2;
std::vector < adept::adouble > P(NLayers);
for(unsigned k = 0; k < NLayers; k++) {
hTot += solh[k][0].value();
adept::adouble rhok = rho1[k] - beta * solT[k][0];
P[k] = - rhok * 9.81 * b; // bottom topography
for( unsigned j = 0; j < NLayers; j++){
adept::adouble rhoj = (j <= k) ? (rho1[j] - beta * solT[j][0]) : rhok;
P[k] += rhoj * 9.81 * solh[j][0];
}
P[k] /= 1024;
}
std::vector < double > hALE(NLayers, 0.);
hALE[0] = hRest[0] + (hTot - b);
for(unsigned k = 1; k < NLayers - 1; k++){
hALE[k] = hRest[k];
}
hALE[NLayers - 1] = b - hRest[NLayers - 1];
std::vector < double > w(NLayers+1, 0.);
dx = x[1] - x[0];
for(unsigned k = NLayers; k>1; k--){
w[k-1] = w[k] - solh[k-1][0].value() * (solv[k-1][1].value() - solv[k-1][0].value() )/dx- ( hALE[k-1] - solh[k-1][0].value()) / dt;
//std::cout << hALE[k-1] << " " << w[k-1] << " ";
}
//std::cout<<std::endl;
std::vector < adept::adouble > zMid(NLayers);
for(unsigned k = 0; k < NLayers; k++) {
zMid[k] = -b + solh[k][0]/2;
for(unsigned i = k+1; i < NLayers; i++) {
zMid[k] += solh[i][0];
}
}
double celerity = sqrt( 9.81 * hTot);
for(unsigned i = 0; i<NLayers; i++){
double vmid = 0.5 * ( solv[i][0].value() + solv[i][1].value() );
maxWaveSpeed = ( maxWaveSpeed > fabs(vmid) + fabs(celerity) )? maxWaveSpeed : fabs(vmid) + fabs(celerity);
}
for(unsigned k = 0; k < NLayers; k++) {
if(!bdch[k][0]) {
for (unsigned j = 0; j < nDofv; j++) {
double sign = ( j == 0) ? 1. : -1;
aResh[k][0] += sign * solh[k][0] * solv[k][j] / dx;
}
aResh[k][0] += w[k+1] - w[k];
}
adept::adouble vMid = 0.5 * (solv[k][0] + solv[k][1]);
adept::adouble fv = 0.5 * vMid * vMid + P[k];
for (unsigned i = 0; i < nDofv; i++) {
if(!bdcv[k][i]) {
double sign = ( i == 0) ? -1. : 1;
aResv[k][i] += sign * fv / dx;
if ( k > 0 ){
aResv[k][i] -= 0.5 * ( w[k] * 0.5 * ( solv[k-1][i] - solv[k][i] ) / (0.5 * ( solh[k-1][0] + solh[k][0] ) ) );
}
if (k < NLayers - 1) {
aResv[k][i] -= 0.5 * ( w[k+1] * 0.5 * ( solv[k][i] - solv[k+1][i] ) / (0.5 * ( solh[k][0] + solh[k+1][0] ) ) );
}
//aResv[k][i] += sign * 9.81 * rho1[k] / 1024. * zMid[k] / dx;
}
}
if(!bdcHT[k][0]) {
for (unsigned j = 0; j < nDofv; j++) {
double sign = ( j == 0) ? 1. : -1;
aResHT[k][0] += sign * solv[k][j] * solHT[k][0] / dx;
}
if(k<NLayers-1){
aResHT[k][0] += w[k+1] * 0.5 * (solHT[k][0]/solh[k][0] + solHT[k+1][0]/solh[k+1][0]);
//aResHT[k][0] += w[k+1] * 0.5 * (solT[k][0] + solT[k+1][0]);
}
if( k > 0){
aResHT[k][0] -= w[k] * 0.5 * (solHT[k-1][0]/solh[k-1][0] + solHT[k][0]/solh[k][0] );
//aResHT[k][0] -= w[k] * 0.5 * (solT[k-1][0] + solT[k][0]);
}
}
}
vector< double > Res(NLayers * nDofs); // local redidual vector
unsigned counter = 0;
for(unsigned k = 0; k < NLayers; k++) {
for(int i = 0; i < nDofh; i++) {
Res[counter] = aResh[k][i].value();
counter++;
}
for(int i = 0; i < nDofv; i++) {
Res[counter] = aResv[k][i].value();
counter++;
}
for(int i = 0; i < nDofHT; i++) {
Res[counter] = aResHT[k][i].value();
counter++;
}
}
RES->add_vector_blocked(Res, l2GMap);
for(unsigned k = 0; k < NLayers; k++) {
// define the dependent variables
s.dependent(&aResh[k][0], nDofh);
s.dependent(&aResv[k][0], nDofv);
s.dependent(&aResHT[k][0], nDofHT);
// define the independent variables
s.independent(&solh[k][0], nDofh);
s.independent(&solv[k][0], nDofv);
s.independent(&solHT[k][0], nDofHT);
}
// get the jacobian matrix (ordered by row major )
vector < double > Jac(NLayers * nDofs * NLayers * nDofs);
s.jacobian(&Jac[0], true);
//store K in the global matrix KK
KK->add_matrix_blocked(Jac, l2GMap, l2GMap);
s.clear_independents();
s.clear_dependents();
}
RES->close();
KK->close();
// PetscViewer viewer;
// PetscViewerDrawOpen(PETSC_COMM_WORLD,NULL,NULL,0,0,900,900,&viewer);
// PetscObjectSetName((PetscObject)viewer,"FSI matrix");
// PetscViewerPushFormat(viewer,PETSC_VIEWER_DRAW_LG);
// MatView((static_cast<PetscMatrix*>(KK))->mat(),viewer);
// double a;
// std::cin>>a;
//
// abort();
MFN mfn;
Mat A = (static_cast<PetscMatrix*>(KK))->mat();
FN f, f1, f2, f3 , f4;
std::cout << "dt = " << dt << " dx = "<< dx << " maxWaveSpeed = "<<maxWaveSpeed << std::endl;
//dt = 100.;
Vec v = (static_cast< PetscVector* >(RES))->vec();
Vec y = (static_cast< PetscVector* >(EPS))->vec();
MFNCreate( PETSC_COMM_WORLD, &mfn );
MFNSetOperator( mfn, A );
MFNGetFN( mfn, &f );
// FNCreate(PETSC_COMM_WORLD, &f1);
// FNCreate(PETSC_COMM_WORLD, &f2);
// FNCreate(PETSC_COMM_WORLD, &f3);
// FNCreate(PETSC_COMM_WORLD, &f4);
//
// FNSetType(f1, FNEXP);
//
// FNSetType(f2, FNRATIONAL);
// double coeff1[1] = { -1};
// FNRationalSetNumerator(f2, 1, coeff1);
// FNRationalSetDenominator(f2, 0, PETSC_NULL);
//
// FNSetType( f3, FNCOMBINE );
//
// FNCombineSetChildren(f3, FN_COMBINE_ADD, f1, f2);
//
// FNSetType(f4, FNRATIONAL);
// double coeff2[2] = {1., 0.};
// FNRationalSetNumerator(f4, 2, coeff2);
// FNRationalSetDenominator(f4, 0, PETSC_NULL);
//
// FNSetType( f, FNCOMBINE );
//
// FNCombineSetChildren(f, FN_COMBINE_DIVIDE, f3, f4);
FNPhiSetIndex(f,1);
FNSetType( f, FNPHI );
// FNView(f,PETSC_VIEWER_STDOUT_WORLD);
FNSetScale( f, dt, dt);
MFNSetFromOptions( mfn );
MFNSolve( mfn, v, y);
MFNDestroy( &mfn );
// FNDestroy(&f1);
// FNDestroy(&f2);
// FNDestroy(&f3);
// FNDestroy(&f4);
sol->UpdateSol(mlPdeSys->GetSolPdeIndex(), EPS, pdeSys->KKoffset);
unsigned solIndexeta = mlSol->GetIndex("eta");
unsigned solIndexb = mlSol->GetIndex("b");
sol->_Sol[solIndexeta]->zero();
for(unsigned k=0;k<NumberOfLayers;k++){
sol->_Sol[solIndexeta]->add(*sol->_Sol[solIndexh[k]]);
}
sol->_Sol[solIndexeta]->add(-1,*sol->_Sol[solIndexb]);
for(unsigned k=0; k<NumberOfLayers; k++){
for(unsigned i = msh->_dofOffset[solTypeHT][iproc]; i < msh->_dofOffset[solTypeHT][iproc + 1]; i++){
double valueHT = (*sol->_Sol[solIndexHT[k]])(i);
double valueH = (*sol->_Sol[solIndexh[k]])(i);
double valueT = valueHT/valueH;
sol->_Sol[solIndexT[k]]->set(i, valueT);
}
sol->_Sol[solIndexT[k]]->close();
}
}
void AssemblePoisson_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
NonLinearImplicitSystem* mlPdeSys = &ml_prob.get_system<NonLinearImplicitSystem> ("Poisson"); // 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 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 solUIndex;
solUIndex = mlSol->GetIndex ("U"); // get the position of "U" in the ml_sol object = 0
unsigned solUType = mlSol->GetSolutionType (solUIndex); // get the finite element type for "T"
unsigned solUPdeIndex;
solUPdeIndex = mlPdeSys->GetSolPdeIndex ("U"); // get the position of "U" in the pdeSys object = 0
vector < adept::adouble > solU; // local solution
vector< adept::adouble > aResU; // local redidual vector
unsigned solVIndex;
solVIndex = mlSol->GetIndex ("V");
unsigned solVType = mlSol->GetSolutionType (solVIndex);
unsigned solVPdeIndex;
solVPdeIndex = mlPdeSys->GetSolPdeIndex ("V");
vector < adept::adouble > solV; // local solution
vector< adept::adouble > aResV; // local redidual vector
vector < vector < double > > crdX (dim); // local coordinates
unsigned crdXType = 2; // get the finite element type for "x", it is always 2 (LAGRANGE QUADRATIC)
solU.reserve (maxSize);
aResU.reserve (maxSize);
solV.reserve (maxSize);
aResV.reserve (maxSize);
for (unsigned k = 0; k < dim; k++) {
crdX[k].reserve (maxSize);
}
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
phi.reserve (maxSize);
phi_x.reserve (maxSize * dim);
phi_xx.reserve (maxSize * dim2);
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);
double weight; // gauss point weight
vector< int > sysDof; // local to global pdeSys dofs
sysDof.reserve (2 * maxSize);
vector< double > Res; // local residual vector
Res.reserve (2 * maxSize);
vector < double > Jac;
Jac.reserve (4 * maxSize * 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); // element geometry type
unsigned nDofsU = msh->GetElementDofNumber (iel, solUType); // number of solution element dofs
unsigned nDofsV = msh->GetElementDofNumber (iel, solVType);
unsigned nDofsX = msh->GetElementDofNumber (iel, crdXType); // number of solution element dofs
// resize local arrays
sysDof.resize (nDofsU + nDofsV);
solU.resize (nDofsU);
solV.resize (nDofsV);
for (unsigned k = 0; k < dim; k++) {
crdX[k].resize (nDofsX);
}
aResU.assign (nDofsU, 0);
aResV.assign (nDofsV, 0);
// local storage of global mapping and solution
for (unsigned i = 0; i < nDofsU; i++) {
unsigned solUDof = msh->GetSolutionDof (i, iel, solUType); // local to global mapping of the solution U
solU[i] = (*sol->_Sol[solUIndex]) (solUDof); // value of the solution U in the dofs
sysDof[i] = pdeSys->GetSystemDof (solUIndex, solUPdeIndex, i, iel); // local to global mapping between solution U and system
}
for (unsigned i = 0; i < nDofsV; i++) {
unsigned solVDof = msh->GetSolutionDof (i, iel, solVType);
solV[i] = (*sol->_Sol[solVIndex]) (solVDof);
sysDof[i + nDofsU] = pdeSys->GetSystemDof (solVIndex, solVPdeIndex, i, iel);
}
// local storage of coordinates
for (unsigned i = 0; i < nDofsX; i++) {
unsigned coordXDof = msh->GetSolutionDof (i, iel, crdXType); // local to global mapping of the coordinate X[dim]
for (unsigned k = 0; k < dim; k++) {
crdX[k][i] = (*msh->_topology->_Sol[k]) (coordXDof); // value of the solution X[dim]
}
}
s.new_recording();
// *** Gauss point loop *** //
for (unsigned ig = 0; ig < msh->_finiteElement[ielGeom][solUType]->GetGaussPointNumber(); ig++) {
// *** get gauss point weight, test function and test function partial derivatives ***
msh->_finiteElement[ielGeom][solUType]->Jacobian (crdX, ig, weight, phi, phi_x, phi_xx);
msh->_finiteElement[ielGeom][solVType]->Jacobian (crdX, ig, weight, phiV, phiV_x, phiV_xx);
adept::adouble solUig = 0; // solution U in the gauss point
vector < adept::adouble > gradSolUig (dim, 0.); // gradient of solution U in the gauss point
for (unsigned i = 0; i < nDofsU; i++) {
solUig += phi[i] * solU[i];
for (unsigned j = 0; j < dim; j++) {
gradSolUig[j] += phi_x[i * dim + j] * solU[i];
}
}
adept::adouble solVig = 0; // solution V in the gauss point
vector < adept::adouble > gradSolVig (dim, 0.); // gradient of solution U in the gauss point
for (unsigned i = 0; i < nDofsV; i++) {
solVig += phiV[i] * solV[i];
for (unsigned j = 0; j < dim; j++) {
gradSolVig[j] += phiV_x[i * dim + j] * solV[i];
}
}
double nu = 1.;
// *** phiU_i loop ***
for (unsigned i = 0; i < nDofsU; i++) {
adept::adouble LaplaceU = 0.;
for (unsigned j = 0; j < dim; j++) {
LaplaceU -= nu * phi_x[i * dim + j] * gradSolUig[j];
}
aResU[i] += (phi[i] - LaplaceU) * weight;
} // end phiU_i loop
for (unsigned i = 0; i < nDofsV; i++) {
adept::adouble LaplaceV = 0.;
for (unsigned j = 0; j < dim; j++) {
LaplaceV -= nu * phiV_x[i * dim + j] * gradSolVig[j];
}
aResV[i] += (phiV[i] * solUig - LaplaceV) * weight;
} // end phiV_i loop
} // end gauss point loop
// } // endif single element not refined or fine grid 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 (nDofsU + nDofsV); //resize
for (int i = 0; i < nDofsU; i++) {
Res[i] = -aResU[i].value();
}
for (int i = 0; i < nDofsV; i++) {
Res[i + nDofsU] = -aResV[i].value();
}
RES->add_vector_blocked (Res, sysDof);
//Extarct and store the Jacobian
Jac.resize ( (nDofsU + nDofsV) * (nDofsU + nDofsV));
// define the dependent variables
s.dependent (&aResU[0], nDofsU);
s.dependent (&aResV[0], nDofsV);
// define the independent variables
s.independent (&solU[0], nDofsU);
s.independent (&solV[0], nDofsV);
// 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();
KK->close();
// ***************** END ASSEMBLY *******************
}
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
NonLinearImplicitSystem* mlPdeSys = &ml_prob.get_system<NonLinearImplicitSystem> ("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< 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);
aResT.reserve(maxSize);
for(unsigned k = 0; k < dim; k++) {
solV[k].reserve(maxSize);
aResV[k].reserve(maxSize);
coordX[k].reserve(maxSize);
}
solP.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);
for(unsigned k = 0; k < dim; k++) {
solV[k].resize(nDofsV);
coordX[k].resize(nDofsX);
}
solP.resize(nDofsP);
aResT.resize(nDofsT); //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
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
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
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;
vector < adept::adouble > gradSolT_gss(dim, 0.);
for(unsigned i = 0; i < nDofsT; i++) {
solT_gss += phiT[i] * solT[i];
for(unsigned j = 0; j < dim; j++) {
gradSolT_gss[j] += phiT_x[i * dim + j] * solT[i];
}
}
vector < adept::adouble > solV_gss(dim, 0);
vector < vector < adept::adouble > > gradSolV_gss(dim);
for(unsigned k = 0; k < dim; k++) {
gradSolV_gss[k].resize(dim);
std::fill(gradSolV_gss[k].begin(), gradSolV_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];
}
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];
}
}
}
adept::adouble solP_gss = 0;
for(unsigned i = 0; i < nDofsP; i++) {
solP_gss += phiP[i] * solP[i];
}
double alpha = 1.;
double beta = 1.;//40000.;
double Pr = 1. / 10;
double Ra = 10000;
// *** phiT_i loop ***
for(unsigned i = 0; i < nDofsT; i++) {
adept::adouble Temp = 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]);
}
aResT[i] += - Temp * weight;
} // end phiT_i loop
// *** phiV_i loop ***
for(unsigned i = 0; i < nDofsV; i++) {
vector < adept::adouble > NSV(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]);
}
}
for(unsigned k = 0; k < dim; k++) {
NSV[k] += -solP_gss * phiV_x[i * dim + k];
}
NSV[1] += -beta * solT_gss * phiV[i];
for(unsigned k = 0; k < dim; k++) {
aResV[k][i] += - NSV[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 AssembleBoussinesqAppoximation(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
NonLinearImplicitSystem* mlPdeSys = &ml_prob.get_system<NonLinearImplicitSystem> ("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
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 < double > solT; // local solution
vector < vector < double > > solV(dim); // local solution
vector < double > solP; // local solution
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);
for(unsigned k = 0; k < dim; k++) {
solV[k].reserve(maxSize);
coordX[k].reserve(maxSize);
}
solP.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
//BEGIN element loop
for(int iel = msh->_elementOffset[iproc]; iel < msh->_elementOffset[iproc + 1]; iel++) {
//BEGIN local dof number extraction
unsigned nDofsT = msh->GetElementDofNumber(iel, solTType); //temperature
unsigned nDofsV = msh->GetElementDofNumber(iel, solVType); //velocity
unsigned nDofsP = msh->GetElementDofNumber(iel, solPType); //pressure
unsigned nDofsX = msh->GetElementDofNumber(iel, coordXType); // coordinates
unsigned nDofsTVP = nDofsT + dim * nDofsV + nDofsP; // all solutions
//END local dof number extraction
//BEGIN memory allocation
Res.resize(nDofsTVP);
std::fill(Res.begin(), Res.end(), 0);
Jac.resize(nDofsTVP * nDofsTVP);
std::fill(Jac.begin(), Jac.end(), 0);
sysDof.resize(nDofsTVP);
solT.resize(nDofsV);
for(unsigned k = 0; k < dim; k++) {
solV[k].resize(nDofsV);
coordX[k].resize(nDofsX);
}
solP.resize(nDofsP);
//END memory allocation
//BEGIN global to local extraction
for(unsigned i = 0; i < nDofsT; i++) { //temperature
unsigned solTDof = msh->GetSolutionDof(i, iel, solTType); //local to global solution dof
solT[i] = (*sol->_Sol[solTIndex])(solTDof); //global to local solution value
sysDof[i] = pdeSys->GetSystemDof(solTIndex, solTPdeIndex, i, iel); //local to global system dof
}
for(unsigned i = 0; i < nDofsV; i++) { //velocity
unsigned solVDof = msh->GetSolutionDof(i, iel, solVType); //local to global solution dof
for(unsigned k = 0; k < dim; k++) {
solV[k][i] = (*sol->_Sol[solVIndex[k]])(solVDof); //global to local solution value
sysDof[i + nDofsT + k * nDofsV] = pdeSys->GetSystemDof(solVIndex[k], solVPdeIndex[k], i, iel); //local to global system dof
}
}
for(unsigned i = 0; i < nDofsP; i++) { //pressure
unsigned solPDof = msh->GetSolutionDof(i, iel, solPType); //local to global solution dof
solP[i] = (*sol->_Sol[solPIndex])(solPDof); //global to local solution value
sysDof[i + nDofsT + dim * nDofsV] = pdeSys->GetSystemDof(solPIndex, solPPdeIndex, i, iel); //local to global system dof
}
for(unsigned i = 0; i < nDofsX; i++) { //coordinates
unsigned coordXDof = msh->GetSolutionDof(i, iel, coordXType); //local to global coordinate dof
for(unsigned k = 0; k < dim; k++) {
coordX[k][i] = (*msh->_topology->_Sol[k])(coordXDof); //global to local coordinate value
}
}
//END global to local extraction
//BEGIN Gauss point loop
short unsigned ielGeom = msh->GetElementType(iel);
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
double solT_gss = 0;
vector < double > gradSolT_gss(dim, 0.);
for(unsigned i = 0; i < nDofsT; i++) {
solT_gss += phiT[i] * solT[i];
for(unsigned j = 0; j < dim; j++) {
gradSolT_gss[j] += phiT_x[i * dim + j] * solT[i];
}
}
vector < double > solV_gss(dim, 0);
vector < vector < double > > gradSolV_gss(dim);
for(unsigned k = 0; k < dim; k++) {
gradSolV_gss[k].resize(dim);
std::fill(gradSolV_gss[k].begin(), gradSolV_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];
}
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];
}
}
}
double solP_gss = 0;
for(unsigned i = 0; i < nDofsP; i++) {
solP_gss += phiP[i] * solP[i];
}
double alpha = 1.;
double beta = 1.;//40000.;
double Pr = Prandtl;
double Ra = Rayleigh;
//BEGIN phiT_i loop: Energy balance
for(unsigned i = 0; i < nDofsT; i++) {
unsigned irow = i;
for(unsigned k = 0; k < dim; k++) {
Res[irow] += -alpha / sqrt(Ra * Pr) * phiT_x[i * dim + k] * gradSolT_gss[k] * weight;
Res[irow] += -phiT[i] * solV_gss[k] * gradSolT_gss[k] * weight;
if(assembleMatrix) {
unsigned irowMat = irow * nDofsTVP;
for(unsigned j = 0; j < nDofsT; j++) {
Jac[ irowMat + j ] += alpha / sqrt(Ra * Pr) * phiT_x[i * dim + k] * phiT_x[j * dim + k] * weight;
Jac[ irowMat + j ] += phiT[i] * solV_gss[k] * phiT_x[j * dim + k] * weight;
}
for(unsigned j = 0; j < nDofsV; j++) {
unsigned jcol = nDofsT + k * nDofsV + j;
Jac[ irowMat + jcol ] += phiT[i] * phiV[j] * gradSolT_gss[k] * weight;
}
}
}
}
//END phiT_i loop
//BEGIN phiV_i loop: Momentum balance
for(unsigned i = 0; i < nDofsV; i++) {
for(unsigned k = 0; k < dim; k++) {
unsigned irow = nDofsT + k * nDofsV + i;
for(unsigned l = 0; l < dim; l++) {
Res[irow] += -sqrt(Pr / Ra) * phiV_x[i * dim + l] * (gradSolV_gss[k][l] + gradSolV_gss[l][k]) * weight;
Res[irow] += -phiV[i] * solV_gss[l] * gradSolV_gss[k][l] * weight;
}
Res[irow] += solP_gss * phiV_x[i * dim + k] * weight;
if(k == 1) {
Res[irow] += beta * solT_gss * phiV[i] * weight;
}
if(assembleMatrix) {
unsigned irowMat = nDofsTVP * irow;
for(unsigned l = 0; l < dim; l++) {
for(unsigned j = 0; j < nDofsV; j++) {
unsigned jcol1 = (nDofsT + k * nDofsV + j);
unsigned jcol2 = (nDofsT + l * nDofsV + j);
Jac[ irowMat + jcol1] += sqrt(Pr / Ra) * phiV_x[i * dim + l] * phiV_x[j * dim + l] * weight;
Jac[ irowMat + jcol2] += sqrt(Pr / Ra) * phiV_x[i * dim + l] * phiV_x[j * dim + k] * weight;
Jac[ irowMat + jcol1] += phiV[i] * solV_gss[l] * phiV_x[j * dim + l] * weight;
Jac[ irowMat + jcol2] += phiV[i] * phiV[j] * gradSolV_gss[k][l] * weight;
}
}
for(unsigned j = 0; j < nDofsP; j++) {
unsigned jcol = (nDofsT + dim * nDofsV) + j;
Jac[ irowMat + jcol] += - phiV_x[i * dim + k] * phiP[j] * weight;
}
if(k == 1) {
for(unsigned j = 0; j < nDofsT; j++) {
Jac[ irowMat + j ] += -beta * phiV[i] * phiT[j] * weight;
}
}
}
}
}
//END phiV_i loop
//BEGIN phiP_i loop: mass balance
for(unsigned i = 0; i < nDofsP; i++) {
unsigned irow = nDofsT + dim * nDofsV + i;
for(int k = 0; k < dim; k++) {
Res[irow] += (gradSolV_gss[k][k]) * phiP[i] * weight;
if(assembleMatrix) {
unsigned irowMat = nDofsTVP * irow;
for(unsigned j = 0; j < nDofsV; j++) {
unsigned jcol = (nDofsT + k * nDofsV + j);
Jac[ irowMat + jcol ] += - phiP[i] * phiV_x[j * dim + k] * weight;
}
}
}
}
//END phiP_i loop
}
//END Gauss point loop
//BEGIN local to global Matrix/Vector assembly
RES->add_vector_blocked(Res, sysDof);
if(assembleMatrix) {
KK->add_matrix_blocked(Jac, sysDof, sysDof);
}
//END local to global Matrix/Vector assembly
}
//END element loop
RES->close();
if(assembleMatrix) {
KK->close();
}
// ***************** END ASSEMBLY *******************
}
//------------------------------------------------------------------------------------------------------------
void AssemblePoissonMatrixandRhs(MultiLevelProblem& ml_prob) {
//pointers and references
LinearImplicitSystem& mylin_impl_sys = ml_prob.get_system<LinearImplicitSystem>("Poisson");
const unsigned level = mylin_impl_sys.GetLevelToAssemble();
//bool assemble_matrix = mylin_impl_sys.GetAssembleMatrix();
Solution* mysolution = ml_prob._ml_sol->GetSolutionLevel(level);
LinearEquationSolver* mylsyspde = mylin_impl_sys._LinSolver[level];
Mesh* mymsh = ml_prob._ml_msh->GetLevel(level);
elem* myel = mymsh->el;
SparseMatrix* myKK = mylsyspde->_KK;
NumericVector* myRES = mylsyspde->_RES;
MultiLevelSolution* ml_sol = ml_prob._ml_sol;
//data
const unsigned dim = mymsh->GetDimension();
unsigned nel = mymsh->GetNumberOfElements();
unsigned igrid = mymsh->GetLevel();
unsigned iproc = mymsh->processor_id();
//solution variable
unsigned SolIndex;
unsigned SolPdeIndex;
SolIndex = ml_sol->GetIndex("Sol");
SolPdeIndex = mylin_impl_sys.GetSolPdeIndex("Sol");
//solution order
unsigned order_ind = ml_sol->GetSolutionType(SolIndex);
//coordinates
vector< vector < double> > coordinates(dim);
// declare
vector< int > metis_node;
vector< int > KK_dof;
vector <double> phi;
vector <double> gradphi;
vector <double> nablaphi;
double weight;
vector< double > F;
vector< double > B;
vector<double> normal(3.0);
double src_term = 0.;
vector<double> xyzt(4, 0.);
ParsedFunction* bdcfunc = NULL;
// reserve
const unsigned max_size = static_cast< unsigned >(ceil(pow(3, dim)));
metis_node.reserve(max_size);
KK_dof.reserve(max_size);
for (int i = 0; i < dim; i++)
coordinates[i].reserve(max_size);
phi.reserve(max_size);
gradphi.reserve(max_size * dim);
unsigned nabla_dim = (3 * (dim - 1) + !(dim - 1));
nablaphi.reserve(max_size * nabla_dim);
F.reserve(max_size);
B.reserve(max_size * max_size);
// Set to zeto all the entries of the Global Matrix
myKK->zero();
// *** element loop ***
for (int iel = mymsh->_elementOffset[iproc]; iel < mymsh->_elementOffset[iproc + 1]; iel++) {
short unsigned ielt = mymsh->GetElementType(iel);
unsigned nve = mymsh->GetElementDofNumber(iel, order_ind);
unsigned nve2 = mymsh->GetElementDofNumber(iel, 2);
// resize
metis_node.resize(nve);
KK_dof.resize(nve);
for (int i = 0; i < dim; i++) {
coordinates[i].resize(nve);
}
// set to zero all the entries of the FE matrices
F.resize(nve);
memset(&F[0], 0, nve * sizeof(double));
B.assign(nve * nve, 0.);
// get local to global mappings
for (unsigned i = 0; i < nve2; i++) {
unsigned inode_coord_metis = mymsh->GetSolutionDof(i, iel, 2);
for (unsigned ivar = 0; ivar < dim; ivar++) {
coordinates[ivar][i] = (*mymsh->_topology->_Sol[ivar])(inode_coord_metis);
}
if (i < nve) {
metis_node[i] = mymsh->GetSolutionDof(i, iel, order_ind);
KK_dof[i] = mylsyspde->GetSystemDof(SolIndex, SolPdeIndex, i, iel);
}
}
// *** Gauss point loop ***
// Supg stabilization tau evaluation
double V[3] = {0., 0., 0.};
double nu = 1.;
if (dim == 1) {
V[0] = 1.;
nu = 0.01;
}
else if (dim == 2) {
// nu=0.0001;
// V[0]=sqrt(2)/2;
// V[1]=-sqrt(2)/2;
nu = 1.;
V[0] = 0.;
V[1] = 0.;
}
else if (dim == 3) {
nu = 1.;
V[0] = V[1] = V[2] = 0.;
}
double barNu = 0.;
double vL2Norm2 = 0.;
for (int i = 0; i < dim; i++) {
vL2Norm2 += V[i] * V[i];
unsigned ip = referenceElementDirection[ielt][i][1];
unsigned im = referenceElementDirection[ielt][i][0];
double VxiHxi = 0.;
for (int j = 0; j < dim; j++) {
VxiHxi += (coordinates[j][ip] - coordinates[j][im]) * V[j];
}
double PeXi = VxiHxi / (2.*nu);
double barXi = (fabs(PeXi) < 1.0e-10) ? 0. : 1. / tanh(PeXi) - 1. / PeXi;
barNu += barXi * VxiHxi / 2.;
}
double supgTau = (vL2Norm2 > 1.0e-15) ? barNu / vL2Norm2 : 0.;
// End Stabilization stabilization tau evaluation
for (unsigned ig = 0; ig < mymsh->_finiteElement[ielt][order_ind]->GetGaussPointNumber(); ig++) {
// *** get Jacobian and test function and test function derivatives ***
mymsh->_finiteElement[ielt][order_ind]->Jacobian(coordinates, ig, weight, phi, gradphi, nablaphi);
//current solution
double SolT = 0;
vector < double > gradSolT(dim, 0.);
vector < double > NablaSolT(dim, 0.);
xyzt.assign(4, 0.);
unsigned SolType = ml_sol->GetSolutionType("Sol");
for (unsigned i = 0; i < nve; i++) {
double soli = (*mysolution->_Sol[SolIndex])(metis_node[i]);
for (unsigned ivar = 0; ivar < dim; ivar++) {
xyzt[ivar] += coordinates[ivar][i] * phi[i];
}
SolT += phi[i] * soli;
for (unsigned ivar2 = 0; ivar2 < dim; ivar2++) {
gradSolT[ivar2] += gradphi[i * dim + ivar2] * soli;
NablaSolT[ivar2] += nablaphi[i * nabla_dim + ivar2] * soli;
}
}
// *** phi_i loop ***
for (unsigned i = 0; i < nve; i++) {
//BEGIN RESIDUALS A block ===========================
double advRhs = 0.;
double lapRhs = 0.;
double resRhs = 0.;
double supgPhi = 0.;
for (unsigned ivar = 0; ivar < dim; ivar++) {
lapRhs += nu * gradphi[i * dim + ivar] * gradSolT[ivar];
advRhs += V[ivar] * gradSolT[ivar] * phi[i];
resRhs += -nu * NablaSolT[ivar] + V[ivar] * gradSolT[ivar];
supgPhi += (V[ivar] * gradphi[i * dim + ivar] + nu * nablaphi[i * nabla_dim + ivar]) * supgTau;
}
src_term = fpsource(&xyzt[0]);
F[i] += (src_term * phi[i] - lapRhs - advRhs
+ (src_term - resRhs) * supgPhi) * weight;
//END RESIDUALS A block ===========================
// *** phi_j loop ***
for (unsigned j = 0; j < nve; j++) {
double lap = 0;
double adv = 0;
for (unsigned ivar = 0; ivar < dim; ivar++) {
lap += nu * (gradphi[i * dim + ivar] * gradphi[j * dim + ivar]
- nablaphi[j * nabla_dim + ivar] * supgPhi) * weight;
adv += V[ivar] * gradphi[j * dim + ivar] * (phi[i] + supgPhi) * weight;
}
B[i * nve + j] += lap + adv ;
} // end phij loop
} // end phii loop
} // end gauss point loop
if (ml_prob._ml_sol->_useParsedBCFunction) {
//number of faces for each type of element
unsigned nfaces = mymsh->GetElementFaceNumber(iel);
// loop on faces
for (unsigned jface = 0; jface < nfaces; jface++) {
// look for boundary faces
if (myel->GetBoundaryIndex(iel, jface) > 0) {
unsigned int faceIndex = myel->GetBoundaryIndex(iel, jface);
if (ml_sol->GetBoundaryCondition("Sol", faceIndex - 1u) == NEUMANN && !ml_sol->Ishomogeneous("Sol", faceIndex - 1u)) {
bdcfunc = (ParsedFunction*)(ml_sol->GetBdcFunction("Sol", faceIndex - 1u));
unsigned nve = mymsh->GetElementFaceDofNumber(iel, jface, order_ind);
const unsigned felt = mymsh->GetElementFaceType(iel, jface);
for (unsigned i = 0; i < nve; i++) {
unsigned ilocal = mymsh->GetLocalFaceVertexIndex(iel, jface, i);
unsigned inode_coord_metis = mymsh->GetSolutionDof(ilocal, iel, 2);
for (unsigned ivar = 0; ivar < dim; ivar++) {
coordinates[ivar][i] = (*mymsh->_topology->_Sol[ivar])(inode_coord_metis);
}
}
if (felt != 6) {
for (unsigned igs = 0; igs < mymsh->_finiteElement[felt][order_ind]->GetGaussPointNumber(); igs++) {
mymsh->_finiteElement[felt][order_ind]->JacobianSur(coordinates, igs, weight, phi, gradphi, normal);
xyzt.assign(4, 0.);
for (unsigned i = 0; i < nve; i++) {
for (unsigned ivar = 0; ivar < dim; ivar++) {
xyzt[ivar] += coordinates[ivar][i] * phi[i];
}
}
// *** phi_i loop ***
for (unsigned i = 0; i < nve; i++) {
double surfterm_g = (*bdcfunc)(&xyzt[0]);
double bdintegral = phi[i] * surfterm_g * weight;
unsigned int ilocalnode = mymsh->GetLocalFaceVertexIndex(iel, jface, i);
F[ilocalnode] += bdintegral;
}
}
}
else { // 1D : the side elems are points and does not still exist the point elem
// in 1D it is only one point
xyzt[0] = coordinates[0][0];
xyzt[1] = 0.;
xyzt[2] = 0.;
xyzt[3] = 0.;
double bdintegral = (*bdcfunc)(&xyzt[0]);
unsigned int ilocalnode = mymsh->GetLocalFaceVertexIndex(iel, jface, 0);
F[ilocalnode] += bdintegral;
}
}
}
}
}
else {
double tau = 0.;
std::vector< double > xx(dim, 0.);
vector < double > normal(dim, 0);
// loop on faces
for (unsigned jface = 0; jface < mymsh->GetElementFaceNumber(iel); jface++) {
// look for boundary faces
if (myel->GetFaceElementIndex(iel, jface) < 0) {
unsigned int faceIndex = myel->GetBoundaryIndex(iel, jface);
if (!ml_sol->GetBdcFunction()(xx, "Sol", tau, faceIndex, 0.) && tau != 0.) {
unsigned nve = mymsh->GetElementFaceDofNumber(iel, jface, order_ind);
const unsigned felt = mymsh->GetElementFaceType(iel, jface);
for (unsigned i = 0; i < nve; i++) {
unsigned int ilocal = mymsh->GetLocalFaceVertexIndex(iel, jface, i);
unsigned inode = mymsh->GetSolutionDof(ilocal, iel, 2);
for (unsigned idim = 0; idim < dim; idim++) {
coordinates[idim][i] = (*mymsh->_topology->_Sol[idim])(inode);
}
}
for (unsigned igs = 0; igs < mymsh->_finiteElement[felt][order_ind]->GetGaussPointNumber(); igs++) {
mymsh->_finiteElement[felt][order_ind]->JacobianSur(coordinates, igs, weight, phi, gradphi, normal);
// *** phi_i loop ***
for (unsigned i = 0; i < nve; i++) {
double value = phi[i] * tau * weight;
unsigned int ilocal = mymsh->GetLocalFaceVertexIndex(iel, jface, i);
F[ilocal] += value;
}
}
}
}
}
}
//--------------------------------------------------------------------------------------------------------
//Sum the local matrices/vectors into the global Matrix/vector
myRES->add_vector_blocked(F, KK_dof);
myKK->add_matrix_blocked(B, KK_dof, KK_dof);
} //end list of elements loop for each subdomain
myRES->close();
myKK->close();
// ***************** END ASSEMBLY *******************
}
void AssembleProblem(MultiLevelProblem& ml_prob) {
// ************** J dx = f - J x_old ******************
// 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
NonLinearImplicitSystemWithPrimalDualActiveSetMethod* mlPdeSys = &ml_prob.get_system<NonLinearImplicitSystemWithPrimalDualActiveSetMethod> ("OptSys");
const unsigned level = mlPdeSys->GetLevelToAssemble();
const bool assembleMatrix = mlPdeSys->GetAssembleMatrix();
Mesh* msh = ml_prob._ml_msh->GetLevel(level);
MultiLevelSolution* ml_sol = ml_prob._ml_sol;
Solution* sol = ml_prob._ml_sol->GetSolutionLevel(level);
LinearEquationSolver* pdeSys = mlPdeSys->_LinSolver[level];
SparseMatrix* KK = pdeSys->_KK;
NumericVector* RES = pdeSys->_RES;
const unsigned dim = msh->GetDimension(); // get the domain dimension of the problem
const unsigned dim2 = (3 * (dim - 1) + !(dim - 1)); // dim2 is the number of second order partial derivatives (1,3,6 depending on the dimension)
const unsigned max_size = static_cast< unsigned >(ceil(pow(3, dim))); // conservative: based on line3, quad9, hex27
const unsigned iproc = msh->processor_id();
//************** geometry (at dofs) *************************************
vector < vector < double > > coords_at_dofs(dim);
vector < unsigned int > SolFEType_domain(dim);
for (unsigned d = 0; d < dim; d++) SolFEType_domain[d] = BIQUADR_FE;
for (unsigned i = 0; i < coords_at_dofs.size(); i++) coords_at_dofs[i].reserve(max_size);
//************** geometry (at quadrature points) *************************************
vector < double > coord_at_qp(dim);
//************** geometry phi **************************
vector < vector < double > > phi_fe_qp_domain(dim);
vector < vector < double > > phi_x_fe_qp_domain(dim);
vector < vector < double > > phi_xx_fe_qp_domain(dim);
for(int fe = 0; fe < dim; fe++) {
phi_fe_qp_domain[fe].reserve(max_size);
phi_x_fe_qp_domain[fe].reserve(max_size * dim);
phi_xx_fe_qp_domain[fe].reserve(max_size * dim2);
}
//***************************************************
//********* WHOLE SET OF VARIABLES ******************
//***************************************************
const unsigned int n_unknowns = mlPdeSys->GetSolPdeIndex().size();
enum Sol_pos{pos_state = 0, pos_ctrl, pos_adj, pos_mu}; //these are known at compile-time
//right now this is the same as Sol_pos = SolPdeIndex, but now I want to have flexible rows and columns
// the ROW index corresponds to the EQUATION we want to solve
// the COLUMN index corresponds to the column variables
// Now, first of all we have to make sure that the Sparsity pattern is correctly built...
// This means that we should write the Sparsity pattern with COLUMNS independent of ROWS!
// But that implies that the BOUNDARY CONDITIONS will be enforced in OFF-DIAGONAL BLOCKS!
// In fact, having the row order be different from the column order implies that the diagonal blocks would be RECTANGULAR.
// Although this is in principle possible, I would avoid doing that for now.
// const unsigned int pos_state = mlPdeSys->GetSolPdeIndex("state"); //these are known at run-time, so they are slower
// const unsigned int pos_ctrl = mlPdeSys->GetSolPdeIndex("control"); //these are known at run-time, so they are slower
// const unsigned int pos_adj = mlPdeSys->GetSolPdeIndex("adjoint"); //these are known at run-time, so they are slower
// const unsigned int pos_mu = mlPdeSys->GetSolPdeIndex("mu"); //these are known at run-time, so they are slower
assert(pos_state == mlPdeSys->GetSolPdeIndex("state"));
assert(pos_ctrl == mlPdeSys->GetSolPdeIndex("control"));
assert(pos_adj == mlPdeSys->GetSolPdeIndex("adjoint"));
assert(pos_mu == mlPdeSys->GetSolPdeIndex("mu"));
//***************************************************
const int solFEType_max = BIQUADR_FE; //biquadratic
vector < std::string > Solname(n_unknowns);
Solname[pos_state] = "state";
Solname[pos_ctrl] = "control";
Solname[pos_adj] = "adjoint";
Solname[pos_mu] = "mu";
//***************************************************
vector < unsigned int > SolPdeIndex(n_unknowns); //index as in the row/column of the matrix (diagonal blocks are square)
vector < unsigned int > SolIndex(n_unknowns); //index as in the MultilevelSolution vector
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() );
assert(ivar == SolPdeIndex[ivar]);
SolIndex[ivar] = ml_sol->GetIndex ( Solname[ivar].c_str() );
SolFEType[ivar] = ml_sol->GetSolutionType ( SolIndex[ivar]);
}
//************* shape functions (at dofs and quadrature points) **************************************
double weight_qp;
vector < vector < double > > phi_fe_qp(n_unknowns);
vector < vector < double > > phi_x_fe_qp(n_unknowns);
vector < vector < double > > phi_xx_fe_qp(n_unknowns);
vector < vector < vector < double > > > phi_x_fe_qp_vec(n_unknowns);
for(int fe = 0; fe < n_unknowns; 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 * dim2);
phi_x_fe_qp_vec[fe].resize(dim);
for(int d = 0; d < dim; d++) {
phi_x_fe_qp_vec[fe][d].reserve(max_size);
}
}
//----------- quantities (at dof objects) ------------------------------
vector < vector < double > > sol_eldofs(n_unknowns);
for(int k=0; k<n_unknowns; k++) sol_eldofs[k].reserve(max_size);
//************** act flag (at dof objects) ****************************
std::string act_flag_name = "act_flag";
unsigned int solIndex_act_flag = ml_sol->GetIndex(act_flag_name.c_str());
unsigned int solFEType_act_flag = ml_sol->GetSolutionType(solIndex_act_flag);
if(sol->GetSolutionTimeOrder(solIndex_act_flag) == 2) {
*(sol->_SolOld[solIndex_act_flag]) = *(sol->_Sol[solIndex_act_flag]);
}
//********* variables for ineq constraints (at dof objects) *****************
const int ineq_flag = INEQ_FLAG;
const double c_compl = C_COMPL;
vector < double/*int*/ > sol_actflag; sol_actflag.reserve(max_size); //flag for active set
vector < double > ctrl_lower; ctrl_lower.reserve(max_size);
vector < double > ctrl_upper; ctrl_upper.reserve(max_size);
//------------ quantities (at quadrature points) ---------------------
vector<double> sol_qp(n_unknowns);
vector< vector<double> > sol_grad_qp(n_unknowns);
std::fill(sol_qp.begin(), sol_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.);
}
//******* EQUATION RELATED STUFF ********************************************
int m_b_f[n_unknowns][n_unknowns];
m_b_f[pos_state][pos_state] = 1; //nonzero
m_b_f[pos_state][pos_ctrl] = 0; //THIS IS ZERO IN NON-LIFTING APPROACHES (there are also pieces that go on top on blocks that are already meant to be different from zero)
m_b_f[pos_state][pos_adj] = 1; //nonzero
m_b_f[pos_state][pos_mu] = 0; //this is zero without state constraints
m_b_f[pos_ctrl][pos_state] = 0;//THIS IS ZERO IN NON-LIFTING APPROACHES
m_b_f[pos_ctrl][pos_ctrl] = 1;//nonzero
m_b_f[pos_ctrl][pos_adj] = 1;//nonzero
m_b_f[pos_ctrl][pos_mu] = 1;//nonzero
m_b_f[pos_adj][pos_state] = 1; //nonzero
m_b_f[pos_adj][pos_ctrl] = 1; //nonzero
m_b_f[pos_adj][pos_adj] = 0; //this must always be zero
m_b_f[pos_adj][pos_mu] = 0; //this must always be zero
m_b_f[pos_mu][pos_state] = 0; //this is zero without state constraints
m_b_f[pos_mu][pos_ctrl] = 1; //nonzero
m_b_f[pos_mu][pos_adj] = 0; //this must always be zero
m_b_f[pos_mu][pos_mu] = 1; //nonzero
//***************************************************
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< double > Res; Res.reserve( n_unknowns*max_size );
vector< double > Jac; Jac.reserve( n_unknowns*max_size * n_unknowns*max_size);
//***************************************************
//********************* DATA ************************
double alpha = ALPHA_CTRL_VOL;
double beta = BETA_CTRL_VOL;
double penalty_strong = 10e+14;
//***************************************************
RES->zero();
if (assembleMatrix) KK->zero();
// element loop: each process loops only on the elements that it owns
for (int iel = msh->_elementOffset[iproc]; iel < msh->_elementOffset[iproc + 1]; iel++) {
short unsigned ielGeom = msh->GetElementType(iel); // element geometry type
//******************** GEOMETRY *********************
for (unsigned jdim = 0; jdim < dim; jdim++) {
unsigned nDofx = msh->GetElementDofNumber(iel, SolFEType_domain[jdim]);
coords_at_dofs[jdim].resize(nDofx);
// local storage of coordinates
for (unsigned i = 0; i < coords_at_dofs[jdim].size(); i++) {
unsigned xDof = msh->GetSolutionDof(i, iel, SolFEType_domain[jdim]); // global to global mapping between coordinates node and coordinate dof
coords_at_dofs[jdim][i] = (*msh->_topology->_Sol[jdim])(xDof); // global extraction and local storage for the element coordinates
}
}
// elem average point
vector < double > elem_center(dim);
for (unsigned j = 0; j < dim; j++) { elem_center[j] = 0.; }
for (unsigned j = 0; j < dim; j++) {
for (unsigned i = 0; i < coords_at_dofs[j].size(); i++) {
elem_center[j] += coords_at_dofs[j][i];
}
}
for (unsigned j = 0; j < dim; j++) { elem_center[j] = elem_center[j]/coords_at_dofs[j].size(); }
//***************************************************
//****** set target domain flag *********************
int target_flag = 0;
target_flag = ElementTargetFlag(elem_center);
//***************************************************
//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);
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
L2G_dofmap[k][i] = pdeSys->GetSystemDof(SolIndex[k], SolPdeIndex[k], i, iel); // global to global mapping between solution node and pdeSys dof
}
}
//all vars###################################################################
for (unsigned k = 0; k < n_unknowns; k++) {
for(int d = 0; d < dim; d++) {
phi_x_fe_qp_vec[k][d].resize(Sol_n_el_dofs[k]);
}
}
//************** update active set flag for current nonlinear iteration ****************************
// 0: inactive; 1: active_a; 2: active_b
assert(Sol_n_el_dofs[pos_mu] == Sol_n_el_dofs[pos_ctrl]);
sol_actflag.resize(Sol_n_el_dofs[pos_mu]);
ctrl_lower.resize(Sol_n_el_dofs[pos_mu]);
ctrl_upper.resize(Sol_n_el_dofs[pos_mu]);
std::fill(sol_actflag.begin(), sol_actflag.end(), 0);
std::fill(ctrl_lower.begin(), ctrl_lower.end(), 0.);
std::fill(ctrl_upper.begin(), ctrl_upper.end(), 0.);
for (unsigned i = 0; i < sol_actflag.size(); i++) {
std::vector<double> node_coords_i(dim,0.);
for (unsigned d = 0; d < dim; d++) node_coords_i[d] = coords_at_dofs[d][i];
ctrl_lower[i] = InequalityConstraint(node_coords_i,false);
ctrl_upper[i] = InequalityConstraint(node_coords_i,true);
if ( (sol_eldofs[pos_mu][i] + c_compl * (sol_eldofs[pos_ctrl][i] - ctrl_lower[i] )) < 0 ) sol_actflag[i] = 1;
else if ( (sol_eldofs[pos_mu][i] + c_compl * (sol_eldofs[pos_ctrl][i] - ctrl_upper[i] )) > 0 ) sol_actflag[i] = 2;
}
//************** act flag ****************************
unsigned nDof_act_flag = msh->GetElementDofNumber(iel, solFEType_act_flag); // number of solution element dofs
for (unsigned i = 0; i < nDof_act_flag; i++) {
unsigned solDof_mu = msh->GetSolutionDof(i, iel, solFEType_act_flag);
(sol->_Sol[solIndex_act_flag])->set(solDof_mu,sol_actflag[i]);
}
//******************** ALL VARS *********************
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];
}
Res.resize(nDof_AllVars); std::fill(Res.begin(), Res.end(), 0.);
Jac.resize(nDof_AllVars * nDof_AllVars); std::fill(Jac.begin(), Jac.end(), 0.);
L2G_dofmap_AllVars.resize(0);
for (unsigned k = 0; k < n_unknowns; k++) L2G_dofmap_AllVars.insert(L2G_dofmap_AllVars.end(),L2G_dofmap[k].begin(),L2G_dofmap[k].end());
//***************************************************
//***** set control flag ****************************
int control_el_flag = 0;
control_el_flag = ControlDomainFlag_internal_restriction(elem_center);
std::vector<int> control_node_flag(Sol_n_el_dofs[pos_ctrl],0);
if (control_el_flag == 1) std::fill(control_node_flag.begin(), control_node_flag.end(), 1);
//***************************************************
// *** Gauss point loop ***
for (unsigned ig = 0; ig < msh->_finiteElement[ielGeom][solFEType_max]->GetGaussPointNumber(); ig++) {
// *** get gauss point weight, test function and test function partial derivatives ***
for(unsigned int k = 0; k < n_unknowns; k++) {
msh->_finiteElement[ielGeom][SolFEType[k]]->Jacobian(coords_at_dofs, ig, weight_qp, phi_fe_qp[k], phi_x_fe_qp[k], phi_xx_fe_qp[k]);
}
for (unsigned k = 0; k < n_unknowns; k++) {
for(unsigned int d = 0; d < dim; d++) {
for(unsigned int i = 0; i < Sol_n_el_dofs[k]; i++) {
phi_x_fe_qp_vec[k][d][i] = phi_x_fe_qp[k][i * dim + d];
}
}
}
//HAVE TO RECALL IT TO HAVE BIQUADRATIC JACOBIAN
for (unsigned int d = 0; d < dim; d++) {
msh->_finiteElement[ielGeom][SolFEType_domain[d]]->Jacobian(coords_at_dofs, ig, weight_qp, phi_fe_qp_domain[d], phi_x_fe_qp_domain[d], phi_xx_fe_qp_domain[d]);
}
//========= fill gauss value xyz ==================
std::fill(coord_at_qp.begin(), coord_at_qp.end(), 0.);
for (unsigned d = 0; d < dim; d++) {
for (unsigned i = 0; i < coords_at_dofs[d].size(); i++) {
coord_at_qp[d] += coords_at_dofs[d][i] * phi_fe_qp_domain[d][i];
}
}
//========= fill gauss value xyz ==================
//========= fill gauss value quantities ==================
std::fill(sol_qp.begin(), sol_qp.end(), 0.);
for (unsigned k = 0; k < n_unknowns; k++) { std::fill(sol_grad_qp[k].begin(), sol_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[k][i];
for (unsigned d = 0; d < dim; d++) sol_grad_qp[k][d] += sol_eldofs[k][i] * phi_x_fe_qp[k][i * dim + d];
}
}
//========= fill gauss value quantities ==================
//==========FILLING THE EQUATIONS ===========
for (unsigned i = 0; i < nDof_max; i++) {
//======================Residuals=======================
// ===============
Res[ assemble_jacobian<double,double>::res_row_index(Sol_n_el_dofs,pos_state,i) ] += - weight_qp * (target_flag * phi_fe_qp[pos_state][i] * (
m_b_f[pos_state][pos_state] * sol_qp[pos_state]
- DesiredTarget(coord_at_qp) )
+ m_b_f[pos_state][pos_adj] * ( assemble_jacobian<double,double>::laplacian_row(phi_x_fe_qp_vec, sol_grad_qp, pos_state, pos_adj, i, dim)
- sol_qp[pos_adj] * nonlin_term_derivative(phi_fe_qp[pos_state][i]) * sol_qp[pos_ctrl]) );
// ==============
if ( control_el_flag == 1) Res[ assemble_jacobian<double,double>::res_row_index(Sol_n_el_dofs,pos_ctrl,i) ] += /*(control_node_flag[i]) **/ - weight_qp * (
+ m_b_f[pos_ctrl][pos_ctrl] * alpha * phi_fe_qp[pos_ctrl][i] * sol_qp[pos_ctrl]
+ m_b_f[pos_ctrl][pos_ctrl] * beta * assemble_jacobian<double,double>::laplacian_row(phi_x_fe_qp_vec, sol_grad_qp, pos_ctrl, pos_ctrl, i, dim)
- m_b_f[pos_ctrl][pos_adj] * phi_fe_qp[pos_ctrl][i] * sol_qp[pos_adj] * nonlin_term_function(sol_qp[pos_state])
);
else if ( control_el_flag == 0) Res[ assemble_jacobian<double,double>::res_row_index(Sol_n_el_dofs,pos_ctrl,i) ] += /*(1 - control_node_flag[i]) **/ m_b_f[pos_ctrl][pos_ctrl] * (- penalty_strong) * (sol_eldofs[pos_ctrl][i]);
// =============
Res[ assemble_jacobian<double,double>::res_row_index(Sol_n_el_dofs,pos_adj,i) ] += - weight_qp * ( + m_b_f[pos_adj][pos_state] * assemble_jacobian<double,double>::laplacian_row(phi_x_fe_qp_vec, sol_grad_qp, pos_adj, pos_state, i, dim)
- m_b_f[pos_adj][pos_ctrl] * phi_fe_qp[pos_adj][i] * sol_qp[pos_ctrl] * nonlin_term_function(sol_qp[pos_state])
);
//======================End Residuals=======================
if (assembleMatrix) {
// *** phi_j loop ***
for (unsigned j = 0; j < nDof_max; j++) {
//============ delta_state row ============================
Jac[ assemble_jacobian<double,double>::jac_row_col_index(Sol_n_el_dofs, nDof_AllVars, pos_state, pos_state, i, j) ] +=
m_b_f[pos_state][pos_state] * weight_qp * target_flag * phi_fe_qp[pos_state][j] * phi_fe_qp[pos_state][i];
Jac[ assemble_jacobian<double,double>::jac_row_col_index(Sol_n_el_dofs, nDof_AllVars, pos_state, pos_adj, i, j) ] +=
m_b_f[pos_state][pos_adj] * weight_qp * (
assemble_jacobian<double,double>::laplacian_row_col(phi_x_fe_qp_vec,phi_x_fe_qp_vec, pos_state, pos_adj, i, j, dim)
- phi_fe_qp[pos_adj][j] *
nonlin_term_derivative(phi_fe_qp[pos_state][i]) *
sol_qp[pos_ctrl]
);
//=========== delta_control row ===========================
if ( control_el_flag == 1) {
Jac[ assemble_jacobian<double,double>::jac_row_col_index(Sol_n_el_dofs, nDof_AllVars, pos_ctrl, pos_ctrl, i, j) ] +=
m_b_f[pos_ctrl][pos_ctrl] * ( control_node_flag[i]) * weight_qp * (
beta * control_el_flag * assemble_jacobian<double,double>::laplacian_row_col(phi_x_fe_qp_vec,phi_x_fe_qp_vec, pos_ctrl, pos_ctrl, i, j, dim)
+ alpha * control_el_flag * phi_fe_qp[pos_ctrl][i] * phi_fe_qp[pos_ctrl][j]
);
Jac[ assemble_jacobian<double,double>::jac_row_col_index(Sol_n_el_dofs, nDof_AllVars, pos_ctrl, pos_adj, i, j) ] += m_b_f[pos_ctrl][pos_adj] * control_node_flag[i] * weight_qp * (
- phi_fe_qp[pos_ctrl][i] *
phi_fe_qp[pos_adj][j] *
nonlin_term_function(sol_qp[pos_state])
);
}
else if ( control_el_flag == 0 && i == j) {
Jac[ assemble_jacobian<double,double>::jac_row_col_index(Sol_n_el_dofs, nDof_AllVars, pos_ctrl, pos_ctrl, i, j) ] += m_b_f[pos_ctrl][pos_ctrl] * (1 - control_node_flag[i]) * penalty_strong;
}
//=========== delta_adjoint row ===========================
Jac[ assemble_jacobian<double,double>::jac_row_col_index(Sol_n_el_dofs, nDof_AllVars, pos_adj, pos_state, i, j) ] += m_b_f[pos_adj][pos_state] * weight_qp * (
assemble_jacobian<double,double>::laplacian_row_col(phi_x_fe_qp_vec,phi_x_fe_qp_vec, pos_adj, pos_state, i, j, dim)
- phi_fe_qp[pos_adj][i] *
nonlin_term_derivative(phi_fe_qp[pos_state][j]) *
sol_qp[pos_ctrl]
);
Jac[ assemble_jacobian<double,double>::jac_row_col_index(Sol_n_el_dofs, nDof_AllVars, pos_adj, pos_ctrl, i, j) ] += m_b_f[pos_adj][pos_ctrl] * weight_qp * (
- phi_fe_qp[pos_adj][i] *
phi_fe_qp[pos_ctrl][j] *
nonlin_term_function(sol_qp[pos_state])
);
} // end phi_j loop
} // endif assemble_matrix
} // end phi_i loop
} // end gauss point loop
//std::vector<double> Res_ctrl (Sol_n_el_dofs[pos_ctrl]); std::fill(Res_ctrl.begin(),Res_ctrl.end(), 0.);
for (unsigned i = 0; i < sol_eldofs[pos_ctrl].size(); i++) {
unsigned n_els_that_node = 1;
if ( control_el_flag == 1) {
// Res[Sol_n_el_dofs[pos_state] + i] += - ( + n_els_that_node * ineq_flag * sol_eldofs[pos_mu][i] /*- ( 0.4 + sin(M_PI * x[0][i]) * sin(M_PI * x[1][i]) )*/ );
// Res_ctrl[i] = Res[Sol_n_el_dofs[pos_state] + i];
}
}
//========== end of integral-based part
RES->add_vector_blocked(Res, L2G_dofmap_AllVars);
if (assembleMatrix) KK->add_matrix_blocked(Jac, L2G_dofmap_AllVars, L2G_dofmap_AllVars);
//========== dof-based part, without summation
//============= delta_mu row ===============================
std::vector<double> Res_mu (Sol_n_el_dofs[pos_mu]); std::fill(Res_mu.begin(),Res_mu.end(), 0.);
for (unsigned i = 0; i < sol_actflag.size(); i++) {
if (sol_actflag[i] == 0) { //inactive
Res_mu [i] = (- ineq_flag) * ( 1. * sol_eldofs[pos_mu][i] );
// Res_mu [i] = Res[res_row_index(Sol_n_el_dofs,pos_mu,i)];
}
else if (sol_actflag[i] == 1) { //active_a
Res_mu [i] = (- ineq_flag) * c_compl * ( sol_eldofs[pos_ctrl][i] - ctrl_lower[i]);
}
else if (sol_actflag[i] == 2) { //active_b
Res_mu [i] = (- ineq_flag) * c_compl * ( sol_eldofs[pos_ctrl][i] - ctrl_upper[i]);
}
}
RES->insert(Res_mu, L2G_dofmap[pos_mu]);
//============= delta_ctrl - mu ===============================
KK->matrix_set_off_diagonal_values_blocked(L2G_dofmap[pos_ctrl], L2G_dofmap[pos_mu], m_b_f[pos_ctrl][pos_mu] * ineq_flag * 1.);
//============= delta_mu - ctrl row ===============================
for (unsigned i = 0; i < sol_actflag.size(); i++) if (sol_actflag[i] != 0 ) sol_actflag[i] = m_b_f[pos_mu][pos_ctrl] * ineq_flag * c_compl;
KK->matrix_set_off_diagonal_values_blocked(L2G_dofmap[pos_mu], L2G_dofmap[pos_ctrl], sol_actflag);
//============= delta_mu - mu row ===============================
for (unsigned i = 0; i < sol_actflag.size(); i++) sol_actflag[i] = m_b_f[pos_mu][pos_mu] * ( ineq_flag * (1 - sol_actflag[i]/c_compl) + (1-ineq_flag) * 1. ); //can do better to avoid division, maybe use modulo operator
KK->matrix_set_off_diagonal_values_blocked(L2G_dofmap[pos_mu], L2G_dofmap[pos_mu], sol_actflag );
} //end element loop for each process
RES->close();
if (assembleMatrix) KK->close();
// std::ostringstream mat_out; mat_out << ml_prob.GetFilesHandler()->GetOutputPath() << "/" << "jacobian" << mlPdeSys->GetNonlinearIt() << ".txt";
// KK->print_matlab(mat_out.str(),"ascii");
// KK->print();
// ***************** END ASSEMBLY *******************
unsigned int global_ctrl_size = pdeSys->KKoffset[pos_ctrl+1][iproc] - pdeSys->KKoffset[pos_ctrl][iproc];
std::vector<double> one_times_mu(global_ctrl_size, 0.);
std::vector<int> positions(global_ctrl_size);
// double position_mu_i;
for (unsigned i = 0; i < positions.size(); i++) {
positions[i] = pdeSys->KKoffset[pos_ctrl][iproc] + i;
// position_mu_i = pdeSys->KKoffset[pos_mu][iproc] + i;
// std::cout << position_mu_i << std::endl;
one_times_mu[i] = m_b_f[pos_ctrl][pos_mu] * ineq_flag * 1. * (*sol->_Sol[SolIndex[pos_mu]])(i/*position_mu_i*/) ;
}
RES->add_vector_blocked(one_times_mu, positions);
// RES->print();
return;
}
void AssembleMatrixResNS(MultiLevelProblem &ml_prob){
adept::Stack & adeptStack = FemusInit::_adeptStack;
clock_t AssemblyTime=0;
clock_t start_time, end_time;
//pointers and references
NonLinearImplicitSystem& my_nnlin_impl_sys = ml_prob.get_system<NonLinearImplicitSystem>("Navier-Stokes");
const unsigned level = my_nnlin_impl_sys.GetLevelToAssemble();
const unsigned gridn = my_nnlin_impl_sys.GetLevelMax();
bool assemble_matrix = my_nnlin_impl_sys.GetAssembleMatrix();
MultiLevelSolution* ml_sol = ml_prob._ml_sol;
Solution* mysolution = ml_sol->GetSolutionLevel(level);
LinearEquationSolver* myLinEqSolver = my_nnlin_impl_sys._LinSolver[level];
Mesh *mymsh = ml_prob._ml_msh->GetLevel(level);
elem *myel = mymsh->el;
SparseMatrix *myKK = myLinEqSolver->_KK;
NumericVector *myRES = myLinEqSolver->_RES;
const unsigned dim = mymsh->GetDimension();
const unsigned nabla_dim = 3*(dim-1);
const unsigned max_size = static_cast< unsigned > (ceil(pow(3,dim)));
// local objects
vector<adept::adouble> SolVAR(dim+1);
vector<vector<adept::adouble> > GradSolVAR(dim+1);
vector<vector<adept::adouble> > NablaSolVAR(dim+1);
for(int i=0;i<dim+1;i++){
GradSolVAR[i].resize(dim);
NablaSolVAR[i].resize(nabla_dim);
}
vector <double > phi;
vector <adept::adouble> gradphi;
vector <adept::adouble> nablaphi;
adept::adouble Weight;
phi.reserve(max_size);
gradphi.reserve(max_size*dim);
nablaphi.reserve(max_size*nabla_dim);
vector <double > phi1;
vector <adept::adouble> gradphi1;
vector <adept::adouble> nablaphi1;
adept::adouble Weight1;
phi1.reserve(max_size);
gradphi1.reserve(max_size*dim);
nablaphi1.reserve(max_size*nabla_dim);
vector <vector < adept::adouble> > vx(dim);
vector <vector < adept::adouble> > vx_face(dim);
for(int i=0;i<dim;i++){
vx[i].reserve(max_size);
vx_face[i].resize(9);
}
vector< vector< adept::adouble > > Soli(dim+1);
vector< vector< int > > dofsVAR(dim+1);
for(int i=0;i<dim+1;i++){
Soli[i].reserve(max_size);
dofsVAR[i].reserve(max_size);
}
vector< vector< double > > Rhs(dim+1);
vector< vector< adept::adouble > > aRhs(dim+1);
for(int i=0;i<dim+1;i++){
aRhs[i].reserve(max_size);
Rhs[i].reserve(max_size);
}
vector < int > dofsAll;
dofsAll.reserve(max_size*(dim+1));
vector < double > KKloc;
KKloc.reserve(dim*max_size*(dim+1)*dim*max_size*(dim+1));
vector < double > Jac;
Jac.reserve(dim*max_size*(dim+1)*dim*max_size*(dim+1));
// ------------------------------------------------------------------------
// Physical parameters
double rhof = ml_prob.parameters.get<Fluid>("Fluid").get_density();
double IRe = ml_prob.parameters.get<Fluid>("Fluid").get_IReynolds_number();
double betans = 1.;
// gravity
double _gravity[3]={0.,0.,0.};
double DRe = 1+(counter*counter)*5;
//double DRe=150;
IRe =( DRe*(counter+1) < 10000 )? 1./(DRe*(counter+1)):1./10000.;
cout<<"iteration="<<counter<<" Reynolds Number = "<<1./IRe<<endl;
counter++;
// -----------------------------------------------------------------
// space discretization parameters
unsigned SolType2 = ml_sol->GetSolutionType(ml_sol->GetIndex("U"));
unsigned SolType1 = ml_sol->GetSolutionType(ml_sol->GetIndex("P"));
unsigned SolTypeVx = 2;
// mesh and procs
unsigned nel = mymsh->GetNumberOfElements();
unsigned igrid = mymsh->GetLevel();
unsigned iproc = mymsh->processor_id();
//----------------------------------------------------------------------------------
//variable-name handling
const char varname[4][3] = {"U","V","W","P"};
vector <unsigned> indexVAR(dim+1);
vector <unsigned> indVAR(dim+1);
vector <unsigned> SolType(dim+1);
for(unsigned ivar=0; ivar<dim; ivar++) {
indVAR[ivar]=ml_sol->GetIndex(&varname[ivar][0]);
SolType[ivar]=ml_sol->GetSolutionType(&varname[ivar][0]);
indexVAR[ivar]=my_nnlin_impl_sys.GetSolPdeIndex(&varname[ivar][0]);
}
indVAR[dim]=ml_sol->GetIndex(&varname[3][0]);
SolType[dim]=ml_sol->GetSolutionType(&varname[3][0]);
indexVAR[dim]=my_nnlin_impl_sys.GetSolPdeIndex(&varname[3][0]);
unsigned indLmbd=ml_sol->GetIndex("lmbd");
//----------------------------------------------------------------------------------
start_time=clock();
myKK->zero();
// *** element loop ***
for(int iel=mymsh->_elementOffset[iproc]; iel < mymsh->_elementOffset[iproc+1]; iel++) {
unsigned kel = mymsh->IS_Mts2Gmt_elem[iel];
short unsigned kelt = mymsh->GetElementType(kel);
unsigned nve2 = mymsh->GetElementDofNumber(kel,SolType2);
unsigned nve1 = mymsh->GetElementDofNumber(kel,SolType1);
unsigned nveVx = mymsh->GetElementDofNumber(kel,SolTypeVx);
// *******************************************************************************************************
//cout<<SolType1<<" "<<SolType2<<" "<<SolTypeVx<<" "<<nve1<<" "<<nve2<<" "<<nveVx<<endl;
//Rhs
for(int i=0; i<dim; i++) {
dofsVAR[i].resize(nve2);
Soli[indexVAR[i]].resize(nve2);
aRhs[indexVAR[i]].resize(nve2);
Rhs[indexVAR[i]].resize(nve2);
}
dofsVAR[dim].resize(nve1);
Soli[indexVAR[dim]].resize(nve1);
aRhs[indexVAR[dim]].resize(nve1);
Rhs[indexVAR[dim]].resize(nve1);
dofsAll.resize(0);
KKloc.resize((dim*nve2+nve1)*(dim*nve2+nve1));
Jac.resize((dim*nve2+nve1)*(dim*nve2+nve1));
// ----------------------------------------------------------------------------------------
// coordinates
for(int i=0;i<dim;i++){
vx[i].resize(nveVx);
}
for (unsigned i=0;i<nveVx;i++) {
unsigned inode=myel->GetMeshDof(kel,i,SolTypeVx);
unsigned inode_Metis=mymsh->GetSolutionDof(inode,SolTypeVx);
for(int j=0; j<dim; j++) {
//coordinates
vx[j][i]= (*mymsh->_topology->_Sol[j])(inode_Metis);
}
}
// Velocity
for (unsigned i=0;i<nve2;i++) {
unsigned inode=myel->GetMeshDof(kel,i,SolType2);
unsigned inode_Metis=mymsh->GetSolutionDof(inode,SolType2);
for(int j=0; j<dim; j++) {
// velocity dofs
Soli[indexVAR[j]][i] = (*mysolution->_Sol[indVAR[j]])(inode_Metis);
dofsVAR[j][i] = myLinEqSolver->GetSystemDof(indVAR[j],indexVAR[j],inode);
aRhs[indexVAR[j]][i] = 0.;
}
}
// Pressure dofs
for (unsigned i=0;i<nve1;i++) {
unsigned inode=myel->GetMeshDof(kel,i,SolType1);
unsigned inode_Metis =mymsh->GetSolutionDof(inode,SolType1);
Soli[indexVAR[dim]][i] = (*mysolution->_Sol[indVAR[dim]])(inode_Metis);
dofsVAR[dim][i]=myLinEqSolver->GetSystemDof(indVAR[dim],indexVAR[dim],inode);
aRhs[indexVAR[dim]][i] = 0.;
}
// build dof composition
for(int idim=0;idim<dim;idim++){
dofsAll.insert( dofsAll.end(), dofsVAR[idim].begin(), dofsVAR[idim].end() );
}
dofsAll.insert( dofsAll.end(), dofsVAR[dim].begin(), dofsVAR[dim].end() );
if (igrid==gridn || !myel->GetRefinedElementIndex(kel) ) {
adeptStack.new_recording();
// *** Gauss point loop ***
adept::adouble hk;
for (unsigned ig=0;ig < mymsh->_finiteElement[kelt][SolType2]->GetGaussPointNumber(); ig++) {
// *** get Jacobian and test function and test function derivatives in the moving frame***
mymsh->_finiteElement[kelt][SolType2]->Jacobian(vx,ig,Weight,phi,gradphi,nablaphi);
mymsh->_finiteElement[kelt][SolType1]->Jacobian(vx,ig,Weight1,phi1,gradphi1,nablaphi1);
for(int i=0;i<nve1;i++){
for(int j=0;j<nabla_dim;j++){
//cout<<nablaphi[i*nabla_dim+j]<<" ";
}
//cout<<endl;
}
//cout<<endl;
if(ig==0){
double referenceElementArea[6]={8, 1./6., 1., 4., 1., 2.};
double GaussWeight = mymsh->_finiteElement[kelt][SolType2]->GetGaussWeight(ig);
double area=referenceElementArea[kelt]*Weight.value()/GaussWeight;
hk = pow(area,1./dim);
//cout<<hk<<" ";
}
// velocity: solution, gradient and laplace
for(int i=0; i<dim; i++){
SolVAR[i]=0.;
for(int j=0; j<dim; j++) {
GradSolVAR[i][j]=0.;
}
for(int j=0; j<nabla_dim; j++) {
NablaSolVAR[i][j]=0.;
}
for (unsigned inode=0; inode<nve2; inode++) {
adept::adouble soli = Soli[indexVAR[i]][inode];
SolVAR[i]+=phi[inode]*soli;
for(int j=0; j<dim; j++) {
GradSolVAR[i][j]+=gradphi[inode*dim+j]*soli;
}
for(int j=0; j<nabla_dim; j++) {
NablaSolVAR[i][j]+=nablaphi[inode*nabla_dim+j]*soli;
}
}
}
// pressure, solution and gradient
SolVAR[dim]=0.;
for(int j=0; j<dim; j++) {
GradSolVAR[dim][j]=0.;
}
for (unsigned inode=0; inode<nve1; inode++) {
adept::adouble soli = Soli[indexVAR[dim]][inode];
SolVAR[dim]+=phi1[inode]*soli;
for(int j=0; j<dim; j++) {
GradSolVAR[dim][j]+=gradphi1[inode*dim+j]*soli;
}
}
bool Tezduyare=0;
bool FrancaAndFrey=!Tezduyare;
if( Tezduyare ){
//BEGIN TAU_SUPG, TAU_PSPG EVALUATION
// ******** T.E. Tezduyar, S. Mittal, S.E. Ray and R. Shih *****************************
// Computer Methods in Applied Mechanics and Engineering 95 (1992) 221-242 North-Holland
// *************************************************************************************
// velocity
vector < adept::adouble > u(dim);
for(int ivar=0; ivar<dim; ivar++){
u[ivar]=SolVAR[ivar];
}
// speed
adept::adouble uL2Norm=0.;
for(int ivar=0;ivar<dim;ivar++){
uL2Norm += u[ivar]*u[ivar];
}
uL2Norm=sqrt(uL2Norm);
adept::adouble tauSupg=0.;
adept::adouble tauPspg=0.;
if( uL2Norm/(2.*IRe) > 1.0e-10){
// velocity direction s = u/|u|
vector < adept::adouble > s(dim);
for(int ivar=0;ivar<dim;ivar++)
s[ivar]=u[ivar]/uL2Norm;
// element lenght h(s) = 2. ( \sum_i |s . gradphi_i | )^(-1)
adept::adouble h=0.;
for (unsigned i=0; i<nve2; i++) {
adept::adouble sDotGradphi=0.;
for(int ivar=0; ivar<dim; ivar++)
sDotGradphi += s[ivar]*gradphi[i*dim+ivar];
//Start WARNING!!! do not change the following if into h += fabs(sDotGradphi).
//Adept does not like it, and convergence is bad
if( sDotGradphi.value() < 0.)
h -= sDotGradphi;
else
h += sDotGradphi;
//End WARNING
}
h = 2./h;
//tauSupg
adept::adouble Reu = 1./3.*(uL2Norm*h)/(2.*IRe);
adept::adouble zReu = (Reu.value() < 1.)? Reu : 1.;
tauSupg = h / (2.*uL2Norm)*zReu;
uL2Norm=0.01;
h = 2.*hk/sqrt(acos(-1.));
Reu = 1./3.*(uL2Norm*h)/(2.*IRe);
zReu = (Reu.value() < 1.)? Reu : 1.;
tauPspg = h / (2.*uL2Norm)*zReu;
}
//END TAU_SUPG, TAU_PSPG EVALUATION
//BEGIN FLUID ASSEMBLY
{
vector < adept::adouble > Res(dim,0.);
for(unsigned ivar=0; ivar<dim; ivar++) {
Res[ivar] += 0. - GradSolVAR[dim][ivar];
for(unsigned jvar=0; jvar<dim; jvar++) {
unsigned kvar;
if(ivar == jvar) kvar = jvar;
else if (1 == ivar + jvar ) kvar = dim; // xy
else if (2 == ivar + jvar ) kvar = dim+2; // xz
else if (3 == ivar + jvar ) kvar = dim+1; // yz
Res[ivar] += - SolVAR[jvar]*GradSolVAR[ivar][jvar]
+ IRe * ( NablaSolVAR[ivar][jvar] + NablaSolVAR[jvar][kvar] );
}
}
adept::adouble div_vel=0.;
for(int ivar=0; ivar<dim; ivar++) {
div_vel +=GradSolVAR[ivar][ivar];
}
//BEGIN redidual momentum block
for (unsigned i=0; i<nve2; i++){
for(unsigned ivar=0; ivar<dim; ivar++) {
adept::adouble Advection = 0.;
adept::adouble Laplacian = 0.;
adept::adouble phiSupg=0.;
for(unsigned jvar=0; jvar<dim; jvar++) {
unsigned kvar;
if(ivar == jvar) kvar = jvar;
else if (1 == ivar + jvar ) kvar = dim; // xy
else if (2 == ivar + jvar ) kvar = dim+2; // xz
else if (3 == ivar + jvar ) kvar = dim+1; // yz
Advection += SolVAR[jvar]*GradSolVAR[ivar][jvar]*phi[i];
Laplacian += IRe*gradphi[i*dim+jvar]*(GradSolVAR[ivar][jvar]+GradSolVAR[jvar][ivar]);
phiSupg += ( SolVAR[jvar]*gradphi[i*dim+jvar] ) * tauSupg;
}
aRhs[indexVAR[ivar]][i]+= ( - Advection - Laplacian
+ SolVAR[dim] * gradphi[i*dim+ivar]
+ Res[ivar] * phiSupg ) * Weight;
}
}
//END redidual momentum block
//BEGIN continuity block
for (unsigned i=0; i<nve1; i++) {
adept::adouble MinusGradPhi1DotRes = 0.;
for(int ivar=0;ivar<dim;ivar++){
MinusGradPhi1DotRes += -gradphi1[i*dim+ivar] * Res[ivar] * tauPspg;
}
aRhs[indexVAR[dim]][i] += ( - (-div_vel) * phi1[i] + MinusGradPhi1DotRes ) * Weight;
}
//END continuity block
}
//END FLUID ASSEMBLY
}
else if(FrancaAndFrey){
//BEGIN TAU_SUPG EVALUATION
// ********************************* Tau_Supg FRANCA and FREY **************************
// Computer Methods in Applied Mechanics and Engineering 99 (1992) 209-233 North-Holland
// *************************************************************************************
// velocity
// double Ck[6][3]={{1.,1.,1.},{1.,1.,1.},{1.,1.,1.},{0.5, 11./270., 11./270.},{0.,1./42.,1./42.},{1.,1.,1.}};
vector < adept::adouble > a(dim);
for(int ivar=0; ivar<dim; ivar++){
a[ivar]=SolVAR[ivar];
}
// speed
adept::adouble aL2Norm=0.;
for(int ivar=0;ivar<dim;ivar++){
aL2Norm += a[ivar]*a[ivar];
}
aL2Norm=sqrt(aL2Norm);
adept::adouble deltaSupg=0.;
double sqrtlambdak = (*mysolution->_Sol[indLmbd])(iel);
adept::adouble tauSupg=1. / ( sqrtlambdak*sqrtlambdak *4.*IRe);
adept::adouble Rek = aL2Norm / ( 4.*sqrtlambdak*IRe);
/*adept::adouble mk=std::min(1./3., 2.*Ck[kelt][SolType2]);
adept::adouble Rek = mk * aL2Norm * hk / ( 4.*IRe);
adept::adouble tauSupg = (mk*hk*hk/2.) / ( 4.*IRe);
*/
if( Rek > 1.0e-15){
adept::adouble xiRek = ( Rek >= 1. ) ? 1.:Rek;
tauSupg = xiRek/(aL2Norm*sqrtlambdak);
deltaSupg = (xiRek*aL2Norm)/sqrtlambdak;
// tauSupg = hk / (2.*aL2Norm)*xiRek;
// double lambda=1.;
// deltaSupg = lambda*aL2Norm*hk*xiRek;
}
//END TAU_SUPG EVALUATION ============
//BEGIN FLUID ASSEMBLY ============
{
vector < adept::adouble > Res(dim,0.);
for(unsigned ivar=0; ivar<dim; ivar++) {
Res[ivar] += 0. - GradSolVAR[dim][ivar];
for(unsigned jvar=0; jvar<dim; jvar++) {
unsigned kvar;
if(ivar == jvar) kvar = jvar;
else if (1 == ivar + jvar ) kvar = dim; // xy
else if (2 == ivar + jvar ) kvar = dim+2; // xz
else if (3 == ivar + jvar ) kvar = dim+1; // yz
Res[ivar] += - SolVAR[jvar]*GradSolVAR[ivar][jvar]
+ IRe * ( NablaSolVAR[ivar][jvar] + NablaSolVAR[jvar][kvar] );
}
}
adept::adouble div_vel=0.;
for(int ivar=0; ivar<dim; ivar++) {
div_vel +=GradSolVAR[ivar][ivar];
}
//BEGIN redidual momentum block
for (unsigned i=0; i<nve2; i++){
for(unsigned ivar=0; ivar<dim; ivar++) {
adept::adouble Advection = 0.;
adept::adouble Laplacian = 0.;
adept::adouble phiSupg=0.;
for(unsigned jvar=0; jvar<dim; jvar++) {
unsigned kvar;
if(ivar == jvar) kvar = jvar;
else if (1 == ivar + jvar ) kvar = dim; // xy
else if (2 == ivar + jvar ) kvar = dim+2; // xz
else if (3 == ivar + jvar ) kvar = dim+1; // yz
Advection += SolVAR[jvar]*GradSolVAR[ivar][jvar]*phi[i];
Laplacian += IRe*gradphi[i*dim+jvar]*(GradSolVAR[ivar][jvar]+GradSolVAR[jvar][ivar]);
phiSupg += ( SolVAR[jvar]*gradphi[i*dim+jvar] ) * tauSupg;
aRhs[indexVAR[ivar]][i] += Res[ivar] * (-IRe * nablaphi[i*nabla_dim+jvar])* tauSupg * Weight;
aRhs[indexVAR[jvar]][i] += Res[ivar] * (-IRe * nablaphi[i*nabla_dim+kvar])* tauSupg * Weight;
}
aRhs[indexVAR[ivar]][i]+= ( - Advection - Laplacian
+ ( SolVAR[dim] - deltaSupg * div_vel) * gradphi[i*dim+ivar]
+ Res[ivar] * phiSupg ) * Weight;
}
}
//END redidual momentum block
//BEGIN continuity block
for (unsigned i=0; i<nve1; i++) {
adept::adouble MinusGradPhi1DotRes = 0.;
for(int ivar=0;ivar<dim;ivar++){
MinusGradPhi1DotRes += -gradphi1[i*dim+ivar] * Res[ivar] * tauSupg;
}
aRhs[indexVAR[dim]][i] += ( - (-div_vel) * phi1[i] + MinusGradPhi1DotRes ) * Weight;
}
//END continuity block ===========================
}
//END FLUID ASSEMBLY ============
}
}
}
//BEGIN local to global assembly
//copy adouble aRhs into double Rhs
for (unsigned i=0;i<dim;i++) {
for(int j=0; j<nve2; j++) {
Rhs[indexVAR[i]][j] = aRhs[indexVAR[i]][j].value();
}
}
for (unsigned j=0;j<nve1;j++) {
Rhs[indexVAR[dim]][j] = aRhs[indexVAR[dim]][j].value();
}
for(int i=0; i<dim+1; i++) {
myRES->add_vector_blocked(Rhs[indexVAR[i]],dofsVAR[i]);
}
//Store equations
for(int i=0; i<dim; i++) {
adeptStack.dependent(&aRhs[indexVAR[i]][0], nve2);
adeptStack.independent(&Soli[indexVAR[i]][0], nve2);
}
adeptStack.dependent(&aRhs[indexVAR[dim]][0], nve1);
adeptStack.independent(&Soli[indexVAR[dim]][0], nve1);
adeptStack.jacobian(&Jac[0]);
unsigned nveAll=(dim*nve2+nve1);
for (int inode=0;inode<nveAll;inode++){
for (int jnode=0;jnode<nveAll;jnode++){
KKloc[inode*nveAll+jnode]=-Jac[jnode*nveAll+inode];
}
}
myKK->add_matrix_blocked(KKloc,dofsAll,dofsAll);
adeptStack.clear_independents();
adeptStack.clear_dependents();
//END local to global assembly
} //end list of elements loop
myKK->close();
myRES->close();
// *************************************
end_time=clock();
AssemblyTime+=(end_time-start_time);
// ***************** END ASSEMBLY RESIDUAL + MATRIX *******************
}
/**
* This function assemble the stiffnes matrix KK and the residual vector Res
* Using automatic differentiation for Newton iterative scheme
* J(u0) w = - F(u0) ,
* with u = u0 + w
* - F = f(x) - J u = Res
* J = \grad_u F
*
* thus
* J w = f(x) - J u0
**/
void AssemblePoissonProblem_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
LinearImplicitSystem* mlPdeSys = &ml_prob.get_system<LinearImplicitSystem> ("Poisson"); // 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 dim2 = (3 * (dim - 1) + !(dim - 1)); // dim2 is the number of second order partial derivatives (1,3,6 depending on the dimension)
const unsigned maxSize = static_cast< unsigned >(ceil(pow(3, dim))); // conservative: based on line3, quad9, hex27
unsigned iproc = msh->processor_id(); // get the process_id (for parallel computation)
//solution variable
unsigned soluIndex;
soluIndex = mlSol->GetIndex("u"); // get the position of "u" in the ml_sol object
unsigned soluType = mlSol->GetSolutionType(soluIndex); // get the finite element type for "u"
unsigned soluPdeIndex;
soluPdeIndex = mlPdeSys->GetSolPdeIndex("u"); // get the position of "u" in the pdeSys object
vector < adept::adouble > solu; // local solution
solu.reserve(maxSize);
vector < vector < double > > x(dim); // local coordinates
unsigned xType = 2; // get the finite element type for "x", it is always 2 (LAGRANGE QUADRATIC)
for (unsigned i = 0; i < dim; i++) {
x[i].reserve(maxSize);
}
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
phi.reserve(maxSize);
phi_x.reserve(maxSize * dim);
phi_xx.reserve(maxSize * dim2);
vector< adept::adouble > aRes; // local redidual vector
aRes.reserve(maxSize);
vector< int > l2GMap; // local to global mapping
l2GMap.reserve(maxSize);
vector< double > Res; // local redidual vector
Res.reserve(maxSize);
vector < double > Jac;
Jac.reserve(maxSize * 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 nDofu = msh->GetElementDofNumber(iel, soluType); // number of solution element dofs
unsigned nDofx = msh->GetElementDofNumber(iel, xType); // number of coordinate element dofs
// resize local arrays
l2GMap.resize(nDofu);
solu.resize(nDofu);
for (int i = 0; i < dim; i++) {
x[i].resize(nDofx);
}
aRes.resize(nDofu); //resize
std::fill(aRes.begin(), aRes.end(), 0); //set aRes to zero
// local storage of global mapping and solution
for (unsigned i = 0; i < nDofu; i++) {
unsigned solDof = msh->GetSolutionDof(i, iel, soluType); // global to global mapping between solution node and solution dof
solu[i] = (*sol->_Sol[soluIndex])(solDof); // global extraction and local storage for the solution
l2GMap[i] = pdeSys->GetSystemDof(soluIndex, soluPdeIndex, i, iel); // global to global mapping between solution node and pdeSys dof
}
// local storage of coordinates
for (unsigned i = 0; i < nDofx; i++) {
unsigned xDof = msh->GetSolutionDof(i, iel, xType); // global to global mapping between coordinates node and coordinate dof
for (unsigned jdim = 0; jdim < dim; jdim++) {
x[jdim][i] = (*msh->_topology->_Sol[jdim])(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][soluType]->GetGaussPointNumber(); ig++) {
// *** get gauss point weight, test function and test function partial derivatives ***
msh->_finiteElement[ielGeom][soluType]->Jacobian(x, ig, weight, phi, phi_x, phi_xx);
// evaluate the solution, the solution derivatives and the coordinates in the gauss point
adept::adouble solu_gss = 0;
vector < adept::adouble > gradSolu_gss(dim, 0.);
vector < double > x_gss(dim, 0.);
for (unsigned i = 0; i < nDofu; i++) {
solu_gss += phi[i] * solu[i];
for (unsigned jdim = 0; jdim < dim; jdim++) {
gradSolu_gss[jdim] += phi_x[i * dim + jdim] * solu[i];
x_gss[jdim] += x[jdim][i] * phi[i];
}
}
// *** phi_i loop ***
for (unsigned i = 0; i < nDofu; i++) {
adept::adouble laplace = 0.;
for (unsigned jdim = 0; jdim < dim; jdim++) {
laplace += phi_x[i * dim + jdim] * gradSolu_gss[jdim];
}
double srcTerm = - GetExactSolutionLaplace(x_gss);
aRes[i] += (srcTerm * phi[i] - laplace) * 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
Res.resize(nDofu); //resize
for (int i = 0; i < nDofu; i++) {
Res[i] = - aRes[i].value();
}
RES->add_vector_blocked(Res, l2GMap);
// define the dependent variables
s.dependent(&aRes[0], nDofu);
// define the independent variables
s.independent(&solu[0], nDofu);
// get the jacobian matrix (ordered by row major )
Jac.resize(nDofu * nDofu); //resize
s.jacobian(&Jac[0], true);
//store K in the global matrix KK
KK->add_matrix_blocked(Jac, l2GMap, l2GMap);
s.clear_independents();
s.clear_dependents();
} //end element loop for each process
RES->close();
KK->close();
// ***************** END ASSEMBLY *******************
}
//------------------------------------------------------------------------------------------------------------
void AssembleMatrixResT(MultiLevelProblem &ml_prob){
//pointers and references
LinearImplicitSystem& mylin_impl_sys = ml_prob.get_system<LinearImplicitSystem>("Temperature");
const unsigned level = mylin_impl_sys.GetLevelToAssemble();
const unsigned gridn = mylin_impl_sys.GetLevelMax();
bool assemble_matrix = mylin_impl_sys.GetAssembleMatrix();
Solution* mysolution = ml_prob._ml_sol->GetSolutionLevel(level);
LinearEquationSolver* mylsyspde = mylin_impl_sys._LinSolver[level];
Mesh* mymsh = ml_prob._ml_msh->GetLevel(level);
elem* myel = mymsh->el;
SparseMatrix* myKK = mylsyspde->_KK;
NumericVector* myRES = mylsyspde->_RES;
MultiLevelSolution* ml_sol = ml_prob._ml_sol;
//data
const unsigned dim = mymsh->GetDimension();
unsigned nel = mymsh->GetNumberOfElements();
unsigned igrid = mymsh->GetLevel();
unsigned iproc = mymsh->processor_id();
double IPe = 1./(ml_prob.parameters.get<Fluid>("Fluid").get_Peclet_number());
//solution variable
unsigned SolIndex;
unsigned SolPdeIndex;
SolIndex=ml_sol->GetIndex("T");
SolPdeIndex=mylin_impl_sys.GetSolPdeIndex("T");
//solution order
unsigned order_ind = ml_sol->GetSolutionType(SolIndex);
//unsigned end_ind = order_ind;
//coordinates
vector< vector < double> > coordinates(dim);
//const char coordinate_name[3][2] = {"X","Y","Z"};
//vector < unsigned > coordinate_Index(dim);
// for(unsigned ivar=0; ivar<dim; ivar++) {
// coordinate_Index[ivar]=ivar;//ml_prob.GetIndex(coordinate_name[ivar]);
// }
// declare
vector< int > metis_node;
vector< int > KK_dof;
vector <double> phi;
vector <double> gradphi;
vector <double> nablaphi;
double weight;
vector< double > F;
vector< double > B;
// reserve
const unsigned max_size = static_cast< unsigned > (ceil(pow(3,dim)));
metis_node.reserve(max_size);
KK_dof.reserve(max_size);
for(int i=0;i<dim;i++)
coordinates[i].reserve(max_size);
phi.reserve(max_size);
gradphi.reserve(max_size*dim);
nablaphi.reserve(max_size*(3*(dim-1)));
F.reserve(max_size);
B.reserve(max_size*max_size);
// Set to zeto all the entries of the Global Matrix
if(assemble_matrix) myKK->zero();
// *** element loop ***
for (int iel=mymsh->_elementOffset[iproc]; iel < mymsh->_elementOffset[iproc+1]; iel++) {
unsigned kel = mymsh->IS_Mts2Gmt_elem[iel];
short unsigned kelt=mymsh->GetElementType(kel);
unsigned nve=mymsh->GetElementDofNumber(kel,order_ind);
// resize
metis_node.resize(nve);
KK_dof.resize(nve);
phi.resize(nve);
gradphi.resize(nve*dim);
nablaphi.resize(nve*(3*(dim-1)));
for(int i=0;i<dim;i++){
coordinates[i].resize(nve);
}
// set to zero all the entries of the FE matrices
F.resize(nve);
memset(&F[0],0,nve*sizeof(double));
if(assemble_matrix){
B.resize(nve*nve);
memset(&B[0],0,nve*nve*sizeof(double));
}
// get local to global mappings
for( unsigned i=0;i<nve;i++){
unsigned inode=myel->GetElementVertexIndex(kel,i)-1u;
unsigned inode_coord_metis=mymsh->GetSolutionDof(inode,2);
metis_node[i]=mymsh->GetSolutionDof(inode,order_ind);
for(unsigned ivar=0; ivar<dim; ivar++) {
coordinates[ivar][i]=(*mymsh->_topology->_Sol[ivar])(inode_coord_metis);
}
KK_dof[i]=mylsyspde->GetSystemDof(SolIndex,SolPdeIndex,inode);
}
if(igrid==gridn || !myel->GetRefinedElementIndex(kel)) {
// *** Gauss poit loop ***
for(unsigned ig=0;ig < ml_prob._ml_msh->_finiteElement[kelt][order_ind]->GetGaussPointNumber(); ig++) {
// *** get Jacobian and test function and test function derivatives ***
ml_prob._ml_msh->_finiteElement[kelt][order_ind]->Jacobian(coordinates,ig,weight,phi,gradphi,nablaphi);
//Temperature and velocity current solution
double SolT=0;
vector < double > gradSolT(dim,0.);
for(unsigned ivar=0; ivar<dim; ivar++){
gradSolT[ivar]=0;
}
vector < double > SolU(dim,0.);
vector < unsigned > SolIndexU(dim);
SolIndexU[0]=ml_sol->GetIndex("U");
SolIndexU[1]=ml_sol->GetIndex("V");
if(dim==3) SolIndexU[2]=ml_sol->GetIndex("W");
unsigned SolType=ml_sol->GetSolutionType("T");
for(unsigned i=0; i<nve; i++) {
double soli = (*mysolution->_Sol[SolIndex])(metis_node[i]);
SolT+=phi[i]*soli;
for(unsigned ivar=0; ivar<dim; ivar++) gradSolT[ivar] += gradphi[i*dim+ivar]*soli;
for(int j=0;j<dim;j++) {
SolU[j]+=phi[i]*(*mysolution->_Sol[SolIndexU[j]])(metis_node[i]);
}
}
// *** phi_i loop ***
for(unsigned i=0; i<nve; i++){
//BEGIN RESIDUALS A block ===========================
double Adv_rhs=0;
double Lap_rhs=0;
for(unsigned ivar=0; ivar<dim; ivar++) {
Lap_rhs += gradphi[i*dim+ivar]*gradSolT[ivar];
Adv_rhs += SolU[ivar]*gradSolT[ivar];
}
F[i]+= (-IPe*Lap_rhs-Adv_rhs*phi[i])*weight;
//END RESIDUALS A block ===========================
if(assemble_matrix){
// *** phi_j loop ***
for(unsigned j=0; j<nve; j++) {
double Lap=0;
double Adv1=0;
for(unsigned ivar=0; ivar<dim; ivar++) {
// Laplacian
Lap += gradphi[i*dim+ivar]*gradphi[j*dim+ivar]*weight;
// advection term I
Adv1 += SolU[ivar]*gradphi[j*dim+ivar]*phi[i]*weight;
}
B[i*nve+j] += IPe*Lap + Adv1;
} // end phij loop
} // end phii loop
} // endif assemble_matrix
} // end gauss point loop
} // endif single element not refined or fine grid loop
//--------------------------------------------------------------------------------------------------------
//Sum the local matrices/vectors into the global Matrix/vector
myRES->add_vector_blocked(F,KK_dof);
if(assemble_matrix) myKK->add_matrix_blocked(B,KK_dof,KK_dof);
} //end list of elements loop for each subdomain
myRES->close();
if(assemble_matrix) myKK->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 AssembleMatrixResSteadyStokes(MultiLevelProblem &ml_prob){
//pointers
LinearImplicitSystem& my_lin_impl_sys = ml_prob.get_system<LinearImplicitSystem>("Stokes");
const unsigned level = my_lin_impl_sys.GetLevelToAssemble();
const unsigned gridn = my_lin_impl_sys.GetLevelMax();
bool assemble_matrix = my_lin_impl_sys.GetAssembleMatrix();
Solution* mysolution = ml_prob._ml_sol->GetSolutionLevel(level);
LinearEquationSolver* mylsyspde = my_lin_impl_sys._LinSolver[level];
const char* pdename = my_lin_impl_sys.name().c_str();
MultiLevelSolution* ml_sol=ml_prob._ml_sol;
Mesh* mymsh = ml_prob._ml_msh->GetLevel(level);
elem* myel = mymsh->el;
SparseMatrix* myKK = mylsyspde->_KK;
NumericVector* myRES = mylsyspde->_RES;
//data
const unsigned dim = mymsh->GetDimension();
unsigned nel= mymsh->GetNumberOfElements();
unsigned igrid= mymsh->GetLevel();
unsigned iproc = mymsh->processor_id();
double ILambda= 0;
double IRe = ml_prob.parameters.get<Fluid>("Fluid").get_IReynolds_number();
bool penalty = true;
const bool symm_mat = false;
// solution and coordinate variables
const char Solname[4][2] = {"U","V","W","P"};
vector < unsigned > SolPdeIndex(dim+1);
vector < unsigned > SolIndex(dim+1);
vector< vector < double> > coordinates(dim);
for(unsigned ivar=0; ivar<dim; ivar++) {
SolPdeIndex[ivar]=my_lin_impl_sys.GetSolPdeIndex(&Solname[ivar][0]);
SolIndex[ivar]=ml_sol->GetIndex(&Solname[ivar][0]);
}
SolPdeIndex[dim]=my_lin_impl_sys.GetSolPdeIndex(&Solname[3][0]);
SolIndex[dim]=ml_sol->GetIndex(&Solname[3][0]);
//solution order
unsigned order_ind_vel = ml_sol->GetSolutionType(SolIndex[0]);
unsigned order_ind_p = ml_sol->GetSolutionType(SolIndex[dim]);
double alpha = 0.;
if(order_ind_p == order_ind_vel && order_ind_vel == 0) // if pressure and velocity are both linear, we need stabilization
{
alpha = 0.013333;
}
// declare
vector < int > metis_node2;
vector < int > node1;
vector< vector< int > > KK_dof(dim+1);
vector <double> phi2;
vector <double> gradphi2;
vector <double> nablaphi2;
const double *phi1;
double Weight2;
double normal[3];
vector< vector< double > > F(dim+1);
vector< vector< vector< double > > > B(dim+1);
// reserve
const unsigned max_size = static_cast< unsigned > (ceil(pow(3,dim)));
metis_node2.reserve(max_size);
node1.reserve( static_cast< unsigned > (ceil(pow(2,dim))));
for(int i=0;i<dim;i++) {
coordinates[i].reserve(max_size);
}
phi2.reserve(max_size);
gradphi2.reserve(max_size*dim);
nablaphi2.reserve(max_size*(3*(dim-1)));
for(int i=0;i<dim;i++) {
KK_dof[i].reserve(max_size);
}
for(int i=0;i<dim+1;i++) F[i].reserve(max_size);
if(assemble_matrix){
for(int i=0;i<dim+1;i++){
B[i].resize(dim+1);
for(int j=0;j<dim+1;j++){
B[i][j].reserve(max_size*max_size);
}
}
}
vector < double > SolVAR(dim+1);
vector < vector < double > > gradSolVAR(dim);
for(int i=0;i<dim;i++) {
gradSolVAR[i].resize(dim);
}
// Set to zeto all the entries of the matrix
if(assemble_matrix) myKK->zero();
// *** element loop ***
for (int iel=mymsh->_elementOffset[iproc]; iel < mymsh->_elementOffset[iproc+1]; iel++) {
unsigned kel = mymsh->IS_Mts2Gmt_elem[iel];
short unsigned kelt=myel->GetElementType(kel);
unsigned nve2=myel->GetElementDofNumber(kel,order_ind_vel);
unsigned nve1=myel->GetElementDofNumber(kel,order_ind_p);
//set to zero all the entries of the FE matrices
metis_node2.resize(nve2);
node1.resize(nve1);
phi2.resize(nve2);
gradphi2.resize(nve2*dim);
nablaphi2.resize(nve2*(3*(dim-1)));
for(int ivar=0; ivar<dim; ivar++) {
coordinates[ivar].resize(nve2);
KK_dof[ivar].resize(nve2);
F[SolPdeIndex[ivar]].resize(nve2);
memset(&F[SolPdeIndex[ivar]][0],0,nve2*sizeof(double));
if(assemble_matrix){
B[SolPdeIndex[ivar]][SolPdeIndex[ivar]].resize(nve2*nve2);
B[SolPdeIndex[ivar]][SolPdeIndex[dim]].resize(nve2*nve1);
B[SolPdeIndex[dim]][SolPdeIndex[ivar]].resize(nve1*nve2);
memset(&B[SolPdeIndex[ivar]][SolPdeIndex[ivar]][0],0,nve2*nve2*sizeof(double));
memset(&B[SolPdeIndex[ivar]][SolPdeIndex[dim]][0],0,nve2*nve1*sizeof(double));
memset(&B[SolPdeIndex[dim]][SolPdeIndex[ivar]][0],0,nve1*nve2*sizeof(double));
}
}
KK_dof[dim].resize(nve1);
F[SolPdeIndex[dim]].resize(nve1);
memset(&F[SolPdeIndex[dim]][0],0,nve1*sizeof(double));
if(assemble_matrix*penalty){
B[SolPdeIndex[dim]][SolPdeIndex[dim]].resize(nve1*nve1,0.);
memset(&B[SolPdeIndex[dim]][SolPdeIndex[dim]][0],0,nve1*nve1*sizeof(double));
}
for( unsigned i=0;i<nve2;i++){
unsigned inode=myel->GetElementVertexIndex(kel,i)-1u;
unsigned inode_coord_metis=mymsh->GetSolutionDof(inode,2);
metis_node2[i]=mymsh->GetSolutionDof(inode,order_ind_vel);
for(unsigned ivar=0; ivar<dim; ivar++) {
coordinates[ivar][i]=(*mymsh->_topology->_Sol[ivar])(inode_coord_metis);
KK_dof[ivar][i]=mylsyspde->GetSystemDof(SolIndex[ivar],SolPdeIndex[ivar],inode);
}
}
double hk = sqrt( (coordinates[0][2] - coordinates[0][0])*(coordinates[0][2] - coordinates[0][0]) +
(coordinates[1][2] - coordinates[1][0])*(coordinates[1][2] - coordinates[1][0]) );
for(unsigned i=0;i<nve1;i++) {
unsigned inode=(order_ind_p<dim)?(myel->GetElementVertexIndex(kel,i)-1u):(kel+i*nel);
node1[i]=inode;
KK_dof[dim][i]=mylsyspde->GetSystemDof(SolIndex[dim],SolPdeIndex[dim],inode);
}
if(igrid==gridn || !myel->GetRefinedElementIndex(kel)) {
// *** Gauss poit loop ***
for(unsigned ig=0;ig < ml_prob._ml_msh->_finiteElement[kelt][order_ind_vel]->GetGaussPointNumber(); ig++) {
// *** get Jacobian and test function and test function derivatives ***
ml_prob._ml_msh->_finiteElement[kelt][order_ind_vel]->Jacobian(coordinates,ig,Weight2,phi2,gradphi2,nablaphi2);
phi1=ml_prob._ml_msh->_finiteElement[kelt][order_ind_p]->GetPhi(ig);
double GradSolP[3] = {0.,0.,0.};
//velocity variable
for(unsigned ivar=0; ivar<dim; ivar++) {
SolVAR[ivar]=0;
for(unsigned ivar2=0; ivar2<dim; ivar2++){
gradSolVAR[ivar][ivar2]=0;
}
unsigned SolIndex=ml_sol->GetIndex(&Solname[ivar][0]);
unsigned SolType=ml_sol->GetSolutionType(&Solname[ivar][0]);
for(unsigned i=0; i<nve2; i++) {
double soli = (*mysolution->_Sol[SolIndex])(metis_node2[i]);
SolVAR[ivar]+=phi2[i]*soli;
for(unsigned ivar2=0; ivar2<dim; ivar2++){
gradSolVAR[ivar][ivar2] += gradphi2[i*dim+ivar2]*soli;
}
}
}
//pressure variable
SolVAR[dim]=0;
unsigned SolIndex=ml_sol->GetIndex(&Solname[3][0]);
unsigned SolType=ml_sol->GetSolutionType(&Solname[3][0]);
for(unsigned i=0; i<nve1; i++){
unsigned sol_dof = mymsh->GetSolutionDof(node1[i],SolType);
double soli = (*mysolution->_Sol[SolIndex])(sol_dof);
SolVAR[dim]+=phi1[i]*soli;
for(unsigned ivar2=0; ivar2<dim; ivar2++){
GradSolP[ivar2] += gradphi2[i*dim+ivar2]*soli;
}
}
// std::cout << " 0: " << GradSolP[0] << " 1: " << GradSolP[1] << std::endl;
// *** phi_i loop ***
for(unsigned i=0; i<nve2; i++){
//BEGIN RESIDUALS A block ===========================
for(unsigned ivar=0; ivar<dim; ivar++) {
double Lap_rhs=0;
for(unsigned ivar2=0; ivar2<dim; ivar2++) {
Lap_rhs += gradphi2[i*dim+ivar2]*gradSolVAR[ivar][ivar2];
}
F[SolPdeIndex[ivar]][i]+= (-IRe*Lap_rhs + SolVAR[dim]*gradphi2[i*dim+ivar])*Weight2;
}
//END RESIDUALS A block ===========================
if(assemble_matrix){
// *** phi_j loop ***
for(unsigned j=0; j<nve2; j++) {
double Lap=0;
for(unsigned ivar=0; ivar<dim; ivar++) {
// Laplacian
Lap += gradphi2[i*dim+ivar]*gradphi2[j*dim+ivar]*Weight2;
}
for(unsigned ivar=0; ivar<dim; ivar++) {
B[SolPdeIndex[ivar]][SolPdeIndex[ivar]][i*nve2+j] += IRe*Lap;
}
} //end phij loop
// *** phi1_j loop ***
for(unsigned j=0; j<nve1; j++){
for(unsigned ivar=0; ivar<dim; ivar++) {
B[SolPdeIndex[ivar]][SolPdeIndex[dim]][i*nve1+j] -= gradphi2[i*dim+ivar]*phi1[j]*Weight2;
}
} //end phi1_j loop
} // endif assemble_matrix
} //end phii loop
// *** phi1_i loop ***
for(unsigned i=0; i<nve1; i++){
//BEGIN RESIDUALS B block ===========================
double div = 0;
for(unsigned ivar=0; ivar<dim; ivar++) {
div += gradSolVAR[ivar][ivar];
}
F[SolPdeIndex[dim]][i]+= (phi1[i]*div + /*penalty*ILambda*phi1[i]*SolVAR[dim]*/
+ 0.*((hk*hk)/(4.*IRe))*alpha*(GradSolP[0]*gradphi2[i*dim + 0] + GradSolP[1]*gradphi2[i*dim + 1]) )*Weight2;
//END RESIDUALS B block ===========================
if(assemble_matrix){
// *** phi_j loop ***
for(unsigned j=0; j<nve2; j++) {
for(unsigned ivar=0; ivar<dim; ivar++) {
B[SolPdeIndex[dim]][SolPdeIndex[ivar]][i*nve2+j]-= phi1[i]*gradphi2[j*dim+ivar]*Weight2;
}
} //end phij loop
} // endif assemble_matrix
} //end phi1_i loop
if(assemble_matrix * penalty){ //block nve1 nve1
// *** phi_i loop ***
for(unsigned i=0; i<nve1; i++){
// *** phi_j loop ***
for(unsigned j=0; j<nve1; j++){
//B[SolPdeIndex[dim]][SolPdeIndex[dim]][i*nve1+j]-= ILambda*phi1[i]*phi1[j]*Weight2;
for(unsigned ivar=0; ivar<dim; ivar++) {
B[SolPdeIndex[dim]][SolPdeIndex[dim]][i*nve1+j] -= ((hk*hk)/(4.*IRe))*alpha*(gradphi2[i*dim + ivar]*gradphi2[j*dim + ivar])*Weight2;
}
}
}
} //end if penalty
} // end gauss point loop
//--------------------------------------------------------------------------------------------------------
// Boundary Integral --> to be added
//number of faces for each type of element
// if (igrid==gridn || !myel->GetRefinedElementIndex(kel) ) {
//
// unsigned nfaces = myel->GetElementFaceNumber(kel);
//
// // loop on faces
// for(unsigned jface=0;jface<nfaces;jface++){
//
// // look for boundary faces
// if(myel->GetFaceElementIndex(kel,jface)<0){
// for(unsigned ivar=0; ivar<dim; ivar++) {
// ml_prob.ComputeBdIntegral(pdename, &Solname[ivar][0], kel, jface, level, ivar);
// }
// }
// }
// }
//--------------------------------------------------------------------------------------------------------
} // endif single element not refined or fine grid loop
//--------------------------------------------------------------------------------------------------------
//Sum the local matrices/vectors into the Global Matrix/Vector
for(unsigned ivar=0; ivar<dim; ivar++) {
myRES->add_vector_blocked(F[SolPdeIndex[ivar]],KK_dof[ivar]);
if(assemble_matrix){
myKK->add_matrix_blocked(B[SolPdeIndex[ivar]][SolPdeIndex[ivar]],KK_dof[ivar],KK_dof[ivar]);
myKK->add_matrix_blocked(B[SolPdeIndex[ivar]][SolPdeIndex[dim]],KK_dof[ivar],KK_dof[dim]);
myKK->add_matrix_blocked(B[SolPdeIndex[dim]][SolPdeIndex[ivar]],KK_dof[dim],KK_dof[ivar]);
}
}
//Penalty
if(assemble_matrix*penalty) myKK->add_matrix_blocked(B[SolPdeIndex[dim]][SolPdeIndex[dim]],KK_dof[dim],KK_dof[dim]);
myRES->add_vector_blocked(F[SolPdeIndex[dim]],KK_dof[dim]);
//--------------------------------------------------------------------------------------------------------
} //end list of elements loop for each subdomain
if(assemble_matrix) myKK->close();
myRES->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 *******************
}
//------------------------------------------------------------------------------------------------------------
void AssemblePoissonMatrixandRhs(MultiLevelProblem& ml_prob) {
//pointers and references
LinearImplicitSystem& mylin_impl_sys = ml_prob.get_system<LinearImplicitSystem>("Poisson");
const unsigned level = mylin_impl_sys.GetLevelToAssemble();
Solution* mysolution = ml_prob._ml_sol->GetSolutionLevel(level);
LinearEquationSolver* mylsyspde = mylin_impl_sys._LinSolver[level];
Mesh* mymsh = ml_prob._ml_msh->GetLevel(level);
elem* myel = mymsh->el;
SparseMatrix* myKK = mylsyspde->_KK;
NumericVector* myRES = mylsyspde->_RES;
MultiLevelSolution* ml_sol = ml_prob._ml_sol;
//data
const unsigned dim = mymsh->GetDimension();
unsigned nel = mymsh->GetNumberOfElements();
unsigned igrid = mymsh->GetLevel();
unsigned iproc = mymsh->processor_id();
//solution variable
unsigned SolIndex;
unsigned SolPdeIndex;
SolIndex = ml_sol->GetIndex("Sol");
SolPdeIndex = mylin_impl_sys.GetSolPdeIndex("Sol");
//solution order
unsigned order_ind = ml_sol->GetSolutionType(SolIndex);
//coordinates
vector< vector < double> > coordinates(dim);
// declare
vector< int > metis_node;
vector< int > KK_dof;
vector <double> phi;
vector <double> gradphi;
vector <double> nablaphi;
double weight;
vector< double > F;
vector< double > B;
vector<double> normal(3.0);
double src_term = 0.;
vector<double> xyzt(4, 0.);
ParsedFunction* bdcfunc = NULL;
// reserve
const unsigned max_size = static_cast< unsigned >(ceil(pow(3, dim)));
metis_node.reserve(max_size);
KK_dof.reserve(max_size);
for (int i = 0; i < dim; i++)
coordinates[i].reserve(max_size);
phi.reserve(max_size);
gradphi.reserve(max_size * dim);
nablaphi.reserve(max_size * (3 * (dim - 1) + !(dim - 1)));
F.reserve(max_size);
B.reserve(max_size * max_size);
// Set to zeto all the entries of the Global Matrix
myKK->zero();
// *** element loop ***
for (int iel = mymsh->_elementOffset[iproc]; iel < mymsh->_elementOffset[iproc + 1]; iel++) {
short unsigned ielt = myel->GetElementType(iel);
unsigned nve = myel->GetElementDofNumber(iel, order_ind);
// resize
metis_node.resize(nve);
KK_dof.resize(nve);
phi.resize(nve);
gradphi.resize(nve * dim);
nablaphi.resize(nve * (3 * (dim - 1) + !(dim - 1)));
for (int i = 0; i < dim; i++) {
coordinates[i].resize(nve);
}
// set to zero all the entries of the FE matrices
F.resize(nve);
memset(&F[0], 0, nve * sizeof(double));
B.resize(nve * nve);
memset(&B[0], 0, nve * nve * sizeof(double));
// get local to global mappings
for (unsigned i = 0; i < nve; i++) {
unsigned inode_coord_metis = mymsh->GetSolutionDof(i, iel, 2);
metis_node[i] = mymsh->GetSolutionDof(i, iel, order_ind);
for (unsigned ivar = 0; ivar < dim; ivar++) {
coordinates[ivar][i] = (*mymsh->_topology->_Sol[ivar])(inode_coord_metis);
}
KK_dof[i] = mylsyspde->GetSystemDof(SolIndex, SolPdeIndex, i, iel);
}
// *** Gauss poit loop ***
for (unsigned ig = 0; ig < ml_prob._ml_msh->_finiteElement[ielt][order_ind]->GetGaussPointNumber(); ig++) {
// *** get Jacobian and test function and test function derivatives ***
ml_prob._ml_msh->_finiteElement[ielt][order_ind]->Jacobian(coordinates, ig, weight, phi, gradphi, nablaphi);
//current solution
double SolT = 0;
vector < double > gradSolT(dim, 0.);
for (unsigned ivar = 0; ivar < dim; ivar++) {
gradSolT[ivar] = 0;
}
xyzt.assign(4, 0.);
unsigned SolType = ml_sol->GetSolutionType("Sol");
for (unsigned i = 0; i < nve; i++) {
double soli = (*mysolution->_Sol[SolIndex])(metis_node[i]);
for (unsigned ivar = 0; ivar < dim; ivar++) {
xyzt[ivar] += coordinates[ivar][i] * phi[i];
}
SolT += phi[i] * soli;
for (unsigned ivar2 = 0; ivar2 < dim; ivar2++) gradSolT[ivar2] += gradphi[i * dim + ivar2] * soli;
}
// *** phi_i loop ***
for (unsigned i = 0; i < nve; i++) {
//BEGIN RESIDUALS A block ===========================
double Adv_rhs = 0;
double Lap_rhs = 0;
for (unsigned ivar = 0; ivar < dim; ivar++) {
Lap_rhs += gradphi[i * dim + ivar] * gradSolT[ivar];
}
//src_term = Source(xyzt);
#ifdef HAVE_FPARSER
//src_term = fpsource.Eval(xyzt);
src_term = fpsource(&xyzt[0]);
#endif
F[i] += (-Lap_rhs + src_term * phi[i]) * weight;
//END RESIDUALS A block ===========================
// *** phi_j loop ***
for (unsigned j = 0; j < nve; j++) {
double Lap = 0;
double Adv1 = 0;
for (unsigned ivar = 0; ivar < dim; ivar++) {
// Laplacian
Lap += gradphi[i * dim + ivar] * gradphi[j * dim + ivar] * weight;
}
B[i * nve + j] += Lap;
} // end phij loop
} // endif assemble_matrix
} // end gauss point loop
//number of faces for each type of element
//number of faces for each type of element
unsigned nfaces = myel->GetElementFaceNumber(iel);
// loop on faces
for (unsigned jface = 0; jface < nfaces; jface++) {
// look for boundary faces
if (myel->GetBoundaryIndex(iel, jface) > 0) {
unsigned int faceIndex = myel->GetBoundaryIndex(iel, jface) - 1u;
if (ml_sol->GetBoundaryCondition("Sol", faceIndex) == NEUMANN && !ml_sol->Ishomogeneous("Sol", faceIndex)) {
bdcfunc = (ParsedFunction*)(ml_sol->GetBdcFunction("Sol", faceIndex));
unsigned nve = mymsh->el->GetElementFaceDofNumber(iel, jface, order_ind);
const unsigned felt = mymsh->el->GetElementFaceType(iel, jface);
for (unsigned i = 0; i < nve; i++) {
unsigned ilocal = mymsh->el->GetLocalFaceVertexIndex(iel, jface, i);
unsigned inode_coord_metis = mymsh->GetSolutionDof(ilocal, iel, 2);
for (unsigned ivar = 0; ivar < dim; ivar++) {
coordinates[ivar][i] = (*mymsh->_topology->_Sol[ivar])(inode_coord_metis);
}
}
if (felt != 6)
{
for (unsigned igs = 0; igs < ml_prob._ml_msh->_finiteElement[felt][order_ind]->GetGaussPointNumber(); igs++) {
ml_prob._ml_msh->_finiteElement[felt][order_ind]->JacobianSur(coordinates, igs, weight, phi, gradphi, normal);
xyzt.assign(4, 0.);
for (unsigned i = 0; i < nve; i++) {
for (unsigned ivar = 0; ivar < dim; ivar++) {
xyzt[ivar] += coordinates[ivar][i] * phi[i];
}
}
// *** phi_i loop ***
for (unsigned i = 0; i < nve; i++) {
double surfterm_g = (*bdcfunc)(&xyzt[0]);
double bdintegral = phi[i] * surfterm_g * weight;
unsigned int ilocalnode = mymsh->el->GetLocalFaceVertexIndex(iel, jface, i);
F[ilocalnode] += bdintegral;
}
}
}
else // 1D : the side elems are points and does not still exist the point elem
{
// in 1D it is only one point
xyzt[0] = coordinates[0][0];
xyzt[1] = 0.;
xyzt[2] = 0.;
xyzt[3] = 0.;
double bdintegral = (*bdcfunc)(&xyzt[0]);
unsigned int ilocalnode = mymsh->el->GetLocalFaceVertexIndex(iel, jface, 0);
F[ilocalnode] += bdintegral;
}
}
}
}
//--------------------------------------------------------------------------------------------------------
//Sum the local matrices/vectors into the global Matrix/vector
myRES->add_vector_blocked(F, KK_dof);
myKK->add_matrix_blocked(B, KK_dof, KK_dof);
} //end list of elements loop for each subdomain
myRES->close();
myKK->close();
// ***************** END ASSEMBLY *******************
}