NOX::Abstract::Group::ReturnType
LOCA::Homotopy::Group::computeNewton(Teuchos::ParameterList& params)
{
if (isValidNewton)
return NOX::Abstract::Group::Ok;
string callingFunction =
"LOCA::Homotopy::Group::computeNewton()";
NOX::Abstract::Group::ReturnType status, finalStatus;
if (newtonVecPtr == Teuchos::null)
newtonVecPtr = gVecPtr->clone(NOX::ShapeCopy);
finalStatus = computeF();
globalData->locaErrorCheck->checkReturnType(finalStatus, callingFunction);
status = computeJacobian();
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status, finalStatus,
callingFunction);
status = applyJacobianInverse(params, *gVecPtr, *newtonVecPtr);
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status, finalStatus,
callingFunction);
newtonVecPtr->scale(-1.0);
isValidNewton = true;
return finalStatus;
}
bool Model::
computeCOM(Vector & com, Matrix * opt_jcom) const
{
com = Vector::Zero(3);
if (opt_jcom) {
*opt_jcom = Matrix::Zero(3, ndof_);
}
double mtotal(0);
for (size_t ii(0); ii < ndof_; ++ii) {
taoDNode * const node(kgm_tree_->info[ii].node);
deVector3 wpos;
wpos.multiply(node->frameGlobal()->rotation(), *(node->center()));
wpos += node->frameGlobal()->translation();
if (opt_jcom) {
Matrix wjcom;
if ( ! computeJacobian(node, wpos[0], wpos[1], wpos[2], wjcom)) {
return false;
}
*opt_jcom += *(node->mass()) * wjcom.block(0, 0, 3, wjcom.cols());
}
wpos *= *(node->mass());
mtotal += *(node->mass());
com += Vector::Map(&wpos[0], 3);
}
if (fabs(mtotal) > 1e-3) {
com /= mtotal;
if (opt_jcom) {
*opt_jcom /= mtotal;
}
}
return true;
}
void SurfaceBasis<EvalT, Traits>::evaluateFields(typename Traits::EvalData workset)
{
for (std::size_t cell(0); cell < workset.numCells; ++cell) {
// for the reference geometry
// compute the mid-plane coordinates
computeReferenceMidplaneCoords(referenceCoords, refMidplaneCoords);
// compute basis vectors
computeReferenceBaseVectors(refMidplaneCoords, refBasis);
// compute the dual
computeDualBaseVectors(refMidplaneCoords, refBasis, refNormal, refDualBasis);
// compute the Jacobian
computeJacobian(refBasis, refDualBasis, refArea);
if (needCurrentBasis) {
// for the current configuration
// compute the mid-plane coordinates
computeCurrentMidplaneCoords(currentCoords, currentMidplaneCoords);
// compute base vectors
computeCurrentBaseVectors(currentMidplaneCoords, currentBasis);
}
}
}
void
ADNodalBCTempl<T, compute_stage>::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
auto ad_offset = jvar * _sys.getMaxVarNDofsPerNode();
auto residual = computeQpResidual();
const std::vector<dof_id_type> & cached_rows = _var.dofIndices();
// Note: this only works for Lagrange variables...
dof_id_type cached_col = _current_node->dof_number(_sys.number(), jvar, 0);
// Cache the user's computeQpJacobian() value for later use.
for (auto tag : _matrix_tags)
if (_sys.hasMatrix(tag))
for (size_t i = 0; i < cached_rows.size(); ++i)
_fe_problem.assembly(0).cacheJacobianContribution(
cached_rows[i],
cached_col,
conversionHelper(residual, i).derivatives()[ad_offset + i],
tag);
}
}
Vector2d leastSquareSolverCalib::pointAlignerLoop( Vector2d &x, MatrixXd &Z, int iterations, Vector2d &result)
{
result=x;
MatrixXd H(2,2);
H.setZero();
MatrixXd b(2,1);
b.setZero();
Vector2d X;
std::cout << Z.transpose()<< std::endl;
for(int i = 0; i < iterations; i++){
std::cout<<"iteration "<<i <<std::endl;
X=x;
for(int j=0;j<Z.cols();j++){
Matrix2d J = computeJacobian(j,Z);
Vector2d e=computeError(j,Z);
std:: cout << "error: "<< e<< std::endl<<std::endl;
H+=J.transpose()*J;
b+=J.transpose()*e;
}
}
Vector2d dx;
std::cout << "H: "<<std::endl<<H<<std::endl<<std::endl<<std::endl;
std::cout << "b: "<<std::endl<<b<<std::endl;
LDLT<MatrixXd> ldlt(-H);
dx=ldlt.solve(b); // using a LDLT factorizationldlt;
return dx;
}
CMUK_ERROR_CODE cmuk::computeFootDK( LegIndex leg,
const vec3f& q,
mat3f* jac,
vec3f* pos,
vec4f* orient,
mat3f* axes ) const {
if (!jac) {
return CMUK_INSUFFICIENT_ARGUMENTS;
}
Transform3f t[4];
CMUK_ERROR_CODE e = computeLegTransforms( leg, q, t );
if (e != CMUK_OKAY) { return e; }
mat3f a;
computeJointAxes( t, &a );
const vec3f& fpos = t[3].translation();
computeJacobian( t, a, fpos, jac );
if (pos) { *pos = fpos; }
if (orient) { *orient = t[3].rotation(); }
if (axes) { *axes = a; }
return CMUK_OKAY;
}
CMUK_ERROR_CODE cmuk::computePointDK( LegIndex leg,
JointOffset link,
const vec3f& q,
const vec3f& p,
mat3f* jac,
mat3f* axes) const {
if ((int)link < HIP_RX_OFFSET || (int)link >= NUM_OFFSETS) {
return CMUK_BAD_JOINT_OFFSET;
}
if (!jac) {
return CMUK_INSUFFICIENT_ARGUMENTS;
}
Transform3f t[4];
CMUK_ERROR_CODE e = computeLegTransforms( leg, q, t );
if (e != CMUK_OKAY) { return e; }
mat3f a;
computeJointAxes( t, &a );
computeJacobian( t, a, p, jac, link );
if (axes) { *axes = a; }
return CMUK_OKAY;
}
void
ADIntegratedBCTempl<T, compute_stage>::computeJacobianBlock(MooseVariableFEBase & jvar)
{
auto jvar_num = jvar.number();
if (jvar_num == _var.number())
computeJacobian();
else
{
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar_num);
if (jvar.phiFaceSize() != ke.n())
return;
size_t ad_offset = jvar_num * _sys.getMaxVarNDofsPerElem();
for (_i = 0; _i < _test.size(); _i++)
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
{
DualReal residual = _ad_JxW[_qp] * _coord[_qp] * computeQpResidual();
for (_j = 0; _j < jvar.phiFaceSize(); _j++)
ke(_i, _j) += residual.derivatives()[ad_offset + _j];
}
}
}
void
DiracKernel::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
{
computeJacobian();
}
else
{
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar);
const std::vector<unsigned int> * multiplicities = _drop_duplicate_points ? NULL : &_local_dirac_kernel_info.getPoints()[_current_elem].second;
unsigned int local_qp = 0;
Real multiplicity = 1.0;
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
{
_current_point = _physical_point[_qp];
if (isActiveAtPoint(_current_elem, _current_point))
{
if (!_drop_duplicate_points)
multiplicity = (*multiplicities)[local_qp++];
for (_i=0; _i<_test.size(); _i++)
for (_j=0; _j<_phi.size(); _j++)
ke(_i, _j) += multiplicity * computeQpOffDiagJacobian(jvar);
}
}
}
}
NOX::Abstract::Group::ReturnType
LOCA::Homotopy::Group::computeGradient()
{
if (isValidGradient)
return NOX::Abstract::Group::Ok;
string callingFunction =
"LOCA::Homotopy::Group::computeGradient()";
NOX::Abstract::Group::ReturnType status, finalStatus;
if (gradVecPtr == Teuchos::null)
gradVecPtr = gVecPtr->clone(NOX::ShapeCopy);
finalStatus = computeF();
globalData->locaErrorCheck->checkReturnType(finalStatus, callingFunction);
status = computeJacobian();
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status, finalStatus,
callingFunction);
status = applyJacobianTranspose(*gVecPtr, *gradVecPtr);
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status, finalStatus,
callingFunction);
return finalStatus;
}
//Evaluate the constraints for Chompification
void TSRConstraint::evaluateConstraints(const MatX& qt,
MatX& h,
MatX& H)
{
//the pos is equivalent to the position of the
// end-effector in the robot frame.
double xyzrpy[6];
//the position of the ee.
Transform pos;
//get the position of the ee
forwardKinematics( qt, pos );
//get the position of the ee in the TSR frame
endeffectorToTSRFrame( pos, xyzrpy );
//the dimensionality of the configuration space
size_t DoF = qt.size() ;
//format h (constraint value vector).
if (size_t(h.rows()) != _dim_constraint || h.cols() != 1)
{
h.resize(_dim_constraint, 1);
}
int current_dim = 0;
std::vector< int > active_dims;
for ( int i = 0; i < _dim_constraint; i ++ )
{
const int dim = _dimension_id[i];
//if the robot's position goes over the TSR's upper bound:
if ( xyzrpy[dim] > _Bw(dim, 1) ){
h(current_dim) = xyzrpy[ dim ] - _Bw(dim, 1);
active_dims.push_back( dim );
current_dim ++;
}
//if the robot's position goes below the TSR's lower bound:
else if ( xyzrpy[dim] < _Bw( dim, 0 ) ){
h(current_dim) = xyzrpy[ dim ] - _Bw(dim, 0);
active_dims.push_back( dim );
current_dim ++;
}
}
if ( current_dim != _dim_constraint ){
h.conservativeResize( current_dim, 1 );
}
if ( H.rows() != current_dim || size_t( H.cols() ) != DoF ){
H.resize( current_dim, DoF );
}
computeJacobian( qt, pos, H, active_dims );
}
vec& LinkedTreeRobot::getQDot(const vec& desired, vec& qdot, vec& axes) {
vec P(3 * _numEffectors);
getEffectorPositions(P); // position of the effectors currently
vec F = clamp(desired - P, 0.5);
mat J;
computeJacobian(desired, J, axes);
mat Jc;
//cout << "++ Going to compute constraint jacobian ++" << endl;
computeConstraintJacobian(desired, axes, Jc);
//cout << "++ Finished computed constraint jacobian ++" << endl;
//cout << "Jc:" << endl << Jc << endl;
vec ga = trans(J) * F;
//cout << "ga:" << endl << ga << endl;
vec gc;
if (Jc.n_elem == 0 || is_all_zeros(Jc)) // no constraints, or all constraints OK
gc.zeros(ga.n_elem);
else {
vec b = -Jc * ga;
//cout << "b:" << endl << b << endl;
mat JcT = trans(Jc);
mat A = Jc * JcT;
//cout << "A:" << endl << A << endl;
vec d;
mat U, V;
if (!svd(U, d, V, A))
cerr << "could not compute SVD" << endl;
//cout << "U:" << endl << U << endl;
//cout << "V:" << endl << V << endl;
//cout << "d:" << endl << d << endl;
//vec lambda = V * inv(D) * trans(U) * b; // too naive
vec utb = trans(U) * b;
vec dinv_ut_b(d.n_elem);
dinv_ut_b.zeros();
for (size_t d_idx = 0; d_idx < d.n_elem; d_idx++) {
double elem = d[d_idx];
if (!double_equals(elem, 0.0))
dinv_ut_b[d_idx] = 1.0 / elem * utb[d_idx];
}
gc = JcT * (V * dinv_ut_b); // Jc^T * lambda
}
qdot = ga + gc; // qdot
return qdot;
}
CMUK_ERROR_CODE cmuk::computePointFootDK( LegIndex leg,
JointOffset link,
const vec3f& q,
const vec3f& p,
mat3f* jac,
vec3f* fpos,
float* det,
float det_tol,
float lambda ) const {
if ((int)link < HIP_RX_OFFSET || (int)link >= NUM_OFFSETS) {
return CMUK_BAD_JOINT_OFFSET;
}
if (!jac) {
return CMUK_INSUFFICIENT_ARGUMENTS;
}
if (link == FOOT_OFFSET) { link = KNEE_RY_OFFSET; }
Transform3f t[4];
CMUK_ERROR_CODE e = computeLegTransforms( leg, q, t );
if (e != CMUK_OKAY) { return e; }
mat3f a;
computeJointAxes( t, &a );
mat3f J_p, J_f, J_f_inv;
vec3f f;
f = t[3].translation();
computeJacobian( t, a, f, &J_f );
computeJacobian( t, a, p, &J_p, link );
CMUK_ERROR_CODE err = computeDKInverse( J_f, &J_f_inv,
det, det_tol, lambda );
*jac = J_p * J_f_inv;
if (fpos) { *fpos = f; }
return err;
}
bool Model::
computeJacobian(taoDNode const * node,
Matrix & jacobian) const
{
if ( ! node) {
return false;
}
deVector3 const & gpos(node->frameGlobal()->translation());
return computeJacobian(node, gpos[0], gpos[1], gpos[2], jacobian);
}
void
StressDivergenceRZ::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
if (_volumetric_locking_correction)
{
// calculate volume averaged value of shape function derivative
_avg_grad_test.resize(_test.size());
for (_i = 0; _i < _test.size(); _i++)
{
_avg_grad_test[_i].resize(2);
_avg_grad_test[_i][_component] = 0.0;
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
{
if (_component == 0)
_avg_grad_test[_i][_component] += (_grad_test[_i][_qp](_component) + _test[_i][_qp] / _q_point[_qp](0)) * _JxW[_qp] * _coord[_qp];
else
_avg_grad_test[_i][_component] += _grad_test[_i][_qp](_component) * _JxW[_qp] * _coord[_qp];
}
_avg_grad_test[_i][_component] /= _current_elem_volume;
}
_avg_grad_phi.resize(_phi.size());
for (_i = 0; _i < _phi.size(); _i++)
{
_avg_grad_phi[_i].resize(3);
for (unsigned int component = 0; component < 2; component++)
{
_avg_grad_phi[_i][component] = 0.0;
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
{
if (component == 0)
_avg_grad_phi[_i][component] += (_grad_phi[_i][_qp](component) + _phi[_i][_qp] / _q_point[_qp](0)) * _JxW[_qp] * _coord[_qp];
else
_avg_grad_phi[_i][component] += _grad_phi[_i][_qp](component) * _JxW[_qp] * _coord[_qp];
}
_avg_grad_phi[_i][component] /= _current_elem_volume;
}
}
}
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar);
for (_i = 0; _i < _test.size(); _i++)
for (_j = 0; _j < _phi.size(); _j++)
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpOffDiagJacobian(jvar);
}
}
float OptSO3::conjugateGradientCUDA_impl(Matrix3f& R, float res0, uint32_t N,
uint32_t maxIter)
{
Timer t0;
Matrix3f G_prev, G, H, M_t_min, J;
// Matrix3f R = R0;
vector<float> res(1,res0);
#ifndef NDEBUG
cout<<"N="<<N<<endl;
cout<<"R0="<<endl<<R<<endl;
cout<<"residual 0 = "<<res[0]<<endl;
#endif
//float ts[10] = {0.0,0.1,0.2,0.3,0.4,0.5,0.7,1.0,1.5,2.0};
//float ts[10] = {0.0,0.01,0.02,0.03,0.04,0.05,0.07,.1,.2,.3};
Timer t1;
for(uint32_t i =0; i<maxIter; ++i)
{
computeJacobian(J,R,N);
#ifndef NDEBUG
cout<<"J="<<endl<<J<<endl;
#endif
t0.toctic("--- jacobian ");
updateGandH(G,G_prev,H,R,J,M_t_min,i%3 == 0); // want first iteration to reset H
#ifndef NDEBUG
cout<<(i%3 == 2)<<endl;
cout<<"R="<<endl<<R<<endl;
cout<<"G="<<endl<<G<<endl;
cout<<"H="<<endl<<H<<endl;
#endif
t0.toctic("--- update G and H ");
float f_t_min = linesearch(R,M_t_min,H,N,t_max_,dt_);
t0.toctic("--- linesearch ");
if(f_t_min == 999999.0f) break;
res.push_back(f_t_min);
float dresidual = res[res.size()-2] - res[res.size()-1];
if( abs(dresidual) < 1e-7 )
{
cout<<"converged after "<<res.size()<<" delta residual "
<< dresidual <<" residual="<<res[res.size()-1]<<endl;
break;
}else{
cout<<"delta residual " << dresidual
<<" residual="<<res[res.size()-1]<<endl;
}
}
dtCG_ = t1.toc();
// R0 = R; // update R
return res.back();
}
void
StressDivergenceTruss::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
{
computeJacobian();
}
else
{
unsigned int coupled_component = 0;
bool active(false);
if ( _xdisp_coupled && jvar == _xdisp_var )
{
coupled_component = 0;
active = true;
}
else if ( _ydisp_coupled && jvar == _ydisp_var )
{
coupled_component = 1;
active = true;
}
else if ( _zdisp_coupled && jvar == _zdisp_var )
{
coupled_component = 2;
active = true;
}
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar);
if (active)
{
ColumnMajorMatrix stiff_global(3,3);
computeStiffness( stiff_global );
for (_i=0; _i<_test.size(); _i++)
{
for (_j=0; _j<_phi.size(); _j++)
{
int sign( _i == _j ? 1 : -1 );
ke(_i,_j) += sign * stiff_global(_component, coupled_component);
}
}
}
else if ( false ) // Need some code here for coupling with temperature
{
}
}
}
double TimeModeProposal::computeLogJacobian()
{
double k = rateParameter(_event);
double T = _event->getTimeToTip();
double jacobian = computeJacobian(k, T);
double logJacobian = std::log(jacobian);
if (_lastTimeModeProposal == TimeConstant) {
return logJacobian;
} else {
return -logJacobian;
}
}
void
ComputeJacobianThread::onElement(const Elem *elem)
{
_fe_problem.prepare(elem, _tid);
_fe_problem.reinitElem(elem, _tid);
_fe_problem.reinitMaterials(_subdomain, _tid);
if (_sys.getScalarVariables(_tid).size() > 0)
_fe_problem.reinitOffDiagScalars(_tid);
computeJacobian();
_fe_problem.swapBackMaterials(_tid);
}
void
KernelGrad::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
DenseMatrix<Number> & Ke = _assembly.jacobianBlock(_var.number(), jvar);
for (_j = 0; _j < _phi.size(); _j++)
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
for (_i = 0; _i < _test.size(); _i++)
Ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpOffDiagJacobian(jvar);
}
}
void
NodalKernel::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
_qp = 0;
Real cached_val = computeQpOffDiagJacobian(jvar);
dof_id_type cached_row = _var.nodalDofIndex();
// Note: this only works for Lagrange variables...
dof_id_type cached_col = _current_node->dof_number(_sys.number(), jvar, 0);
_assembly.cacheJacobianContribution(cached_row, cached_col, cached_val);
}
}
void
NodalBC::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
_qp = 0;
Real cached_val = computeQpOffDiagJacobian(jvar);
dof_id_type cached_row = _var.nodalDofIndex();
// Note: this only works for Lagrange variables...
dof_id_type cached_col = _current_node->dof_number(_sys.number(), jvar, 0);
// Cache the user's computeQpJacobian() value for later use.
_fe_problem.assembly(0).cacheNodalBCJacobianEntry(cached_row, cached_col, cached_val);
}
}
NOX::Abstract::Group::ReturnType
LOCA::Homotopy::DeflatedGroup::
computeNewton(Teuchos::ParameterList& params)
{
if (isValidNewton)
return NOX::Abstract::Group::Ok;
string callingFunction =
"LOCA::Homotopy::DeflatedGroup::computeNewton()";
NOX::Abstract::Group::ReturnType finalStatus = NOX::Abstract::Group::Ok;
NOX::Abstract::Group::ReturnType status;
// Make sure F is valid
if (!isF()) {
status = computeF();
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status,
finalStatus,
callingFunction);
}
// Make sure Jacobian is valid
if (!isJacobian()) {
status = computeJacobian();
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status,
finalStatus,
callingFunction);
}
// zero out newton vec -- used as initial guess for some linear solvers
newtonMultiVec.init(0.0);
status = applyJacobianInverseMultiVector(params, fMultiVec,
newtonMultiVec);
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status,
finalStatus,
callingFunction);
newtonMultiVec.scale(-1.0);
isValidNewton = true;
return finalStatus;
}
void
StressDivergence::computeOffDiagJacobian(MooseVariableFEBase & jvar)
{
size_t jvar_num = jvar.number();
if (jvar_num == _var.number())
computeJacobian();
else
{
if (_volumetric_locking_correction)
{
// calculate volume averaged value of shape function derivative
_avg_grad_test.resize(_test.size());
for (_i = 0; _i < _test.size(); _i++)
{
_avg_grad_test[_i].resize(3);
_avg_grad_test[_i][_component] = 0.0;
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
_avg_grad_test[_i][_component] +=
_grad_test[_i][_qp](_component) * _JxW[_qp] * _coord[_qp];
_avg_grad_test[_i][_component] /= _current_elem_volume;
}
_avg_grad_phi.resize(jvar.phiSize());
for (_i = 0; _i < jvar.phiSize(); _i++)
{
_avg_grad_phi[_i].resize(3);
for (unsigned int component = 0; component < _mesh.dimension(); component++)
{
_avg_grad_phi[_i][component] = 0.0;
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
_avg_grad_phi[_i][component] += _grad_phi[_i][_qp](component) * _JxW[_qp] * _coord[_qp];
_avg_grad_phi[_i][component] /= _current_elem_volume;
}
}
}
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar_num);
for (_i = 0; _i < _test.size(); _i++)
for (_j = 0; _j < jvar.phiSize(); _j++)
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
ke(_i, _j) += _JxW[_qp] * _coord[_qp] * computeQpOffDiagJacobian(jvar_num);
}
}
NOX::Abstract::Group::ReturnType
LOCA::LAPACK::Group::computeComplex(double frequency)
{
string callingFunction = "LOCA::LAPACK::computeComplex()";
#ifdef HAVE_TEUCHOS_COMPLEX
NOX::Abstract::Group::ReturnType finalStatus;
freq = frequency;
// Compute Jacobian
finalStatus = computeJacobian();
globalData->locaErrorCheck->checkReturnType(finalStatus, callingFunction);
// Compute Mass matrix
bool res =
locaProblemInterface.computeShiftedMatrix(0.0, 1.0, xVector,
shiftedSolver.getMatrix());
// Compute complex matrix
NOX::LAPACK::Matrix<double>& jacobianMatrix = jacSolver.getMatrix();
NOX::LAPACK::Matrix<double>& massMatrix = shiftedSolver.getMatrix();
NOX::LAPACK::Matrix< std::complex<double> >& complexMatrix =
complexSolver.getMatrix();
int n = jacobianMatrix.numRows();
for (int j=0; j<n; j++) {
for (int i=0; i<n; i++) {
complexMatrix(i,j) =
std::complex<double>(jacobianMatrix(i,j), frequency*massMatrix(i,j));
}
}
if (finalStatus == NOX::Abstract::Group::Ok && res)
isValidComplex = true;
if (res)
return finalStatus;
else
return NOX::Abstract::Group::Failed;
#else
globalData->locaErrorCheck->throwError(
callingFunction,
"TEUCHOS_COMPLEX must be enabled for complex support! Reconfigure with -D Teuchos_ENABLE_COMPLEX");
return NOX::Abstract::Group::BadDependency;
#endif
}
NOX::Abstract::Group::ReturnType
LOCA::TurningPoint::MooreSpence::ExtendedGroup::computeNewton(
Teuchos::ParameterList& params)
{
if (isValidNewton)
return NOX::Abstract::Group::Ok;
string callingFunction =
"LOCA::TurningPoint::MooreSpence::ExtendedGroup::computeNewton()";
NOX::Abstract::Group::ReturnType finalStatus = NOX::Abstract::Group::Ok;
NOX::Abstract::Group::ReturnType status;
// Make sure F is valid
if (!isF()) {
status = computeF();
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status,
finalStatus,
callingFunction);
}
// Make sure Jacobian is valid
if (!isJacobian()) {
status = computeJacobian();
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status,
finalStatus,
callingFunction);
}
// zero out newton vec -- used as initial guess for some linear solvers
newtonMultiVec.init(0.0);
// solve using contiguous
status = solverStrategy->solve(params, *ffMultiVec, newtonMultiVec);
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status, finalStatus,
callingFunction);
newtonMultiVec.scale(-1.0);
isValidNewton = true;
return finalStatus;
}
void
DGKernel::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
// Compute element-element Jacobian
computeOffDiagElemNeighJacobian(Moose::ElementElement,jvar);
// Compute element-neighbor Jacobian
computeOffDiagElemNeighJacobian(Moose::ElementNeighbor,jvar);
// Compute neighbor-element Jacobian
computeOffDiagElemNeighJacobian(Moose::NeighborElement,jvar);
// Compute neighbor-neighbor Jacobian
computeOffDiagElemNeighJacobian(Moose::NeighborNeighbor,jvar);
}
}
NOX::Abstract::Group::ReturnType
LOCA::Homotopy::DeflatedGroup::
computeGradient()
{
if (isValidGradient)
return NOX::Abstract::Group::Ok;
string callingFunction =
"LOCA::Homotopy::DeflatedGroup::computeGradient()";
NOX::Abstract::Group::ReturnType finalStatus = NOX::Abstract::Group::Ok;
NOX::Abstract::Group::ReturnType status;
// Make sure F is valid
if (!isF()) {
status = computeF();
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status,
finalStatus,
callingFunction);
}
// Make sure Jacobian is valid
if (!isJacobian()) {
status = computeJacobian();
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status,
finalStatus,
callingFunction);
}
// Compute J^T*f for homotopy group
status = applyJacobianTranspose(*fVec, *gradientVec);
finalStatus =
globalData->locaErrorCheck->combineAndCheckReturnTypes(status,
finalStatus,
callingFunction);
isValidGradient = true;
return finalStatus;
}
void
DiracKernel::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
{
computeJacobian();
}
else
{
DenseMatrix<Number> & ke = _assembly.jacobianBlock(_var.number(), jvar);
for (_qp = 0; _qp < _qrule->n_points(); _qp++)
{
_current_point = _physical_point[_qp];
if (isActiveAtPoint(_current_elem, _current_point))
for (_i=0; _i<_test.size(); _i++)
for (_j=0; _j<_phi.size(); _j++)
ke(_i, _j) += computeQpOffDiagJacobian(jvar);
}
}
}
void
NodalBC::computeOffDiagJacobian(unsigned int jvar)
{
if (jvar == _var.number())
computeJacobian();
else
{
_qp = 0;
Real cached_val = 0.0;
cached_val = computeQpOffDiagJacobian(jvar);
dof_id_type cached_row = _var.nodalDofIndex();
// Note: this only works for Lagrange variables...
dof_id_type cached_col = _current_node->dof_number(_sys.number(), jvar, 0);
// Cache the user's computeQpJacobian() value for later use.
for (auto tag : _matrix_tags)
if (_sys.hasMatrix(tag))
_fe_problem.assembly(0).cacheJacobianContribution(cached_row, cached_col, cached_val, tag);
}
}