void ComputeFullJacobianThread::computeJacobian() { std::vector<std::pair<MooseVariable *, MooseVariable *> > & ce = _fe_problem.couplingEntries(_tid); for (std::vector<std::pair<MooseVariable *, MooseVariable *> >::iterator it = ce.begin(); it != ce.end(); ++it) { MooseVariable & ivariable = *(*it).first; MooseVariable & jvariable = *(*it).second; unsigned int ivar = ivariable.number(); unsigned int jvar = jvariable.number(); if (ivariable.activeOnSubdomain(_subdomain) && jvariable.activeOnSubdomain(_subdomain)) { // only if there are dofs for j-variable (if it is subdomain restricted var, there may not be any) const std::vector<KernelBase *> & kernels = _sys._kernels[_tid].activeVar(ivar); for (std::vector<KernelBase *>::const_iterator kt = kernels.begin(); kt != kernels.end(); ++kt) { KernelBase * kernel = *kt; if ((kernel->variable().number() == ivar) && kernel->isImplicit()) { kernel->subProblem().prepareShapes(jvar, _tid); kernel->computeOffDiagJacobian(jvar); } } } } const std::vector<MooseVariableScalar *> & scalar_vars = _sys.getScalarVariables(_tid); if (scalar_vars.size() > 0) { // go over nl-variables (non-scalar) const std::vector<MooseVariable *> & vars = _sys.getVariables(_tid); for (std::vector<MooseVariable *>::const_iterator it = vars.begin(); it != vars.end(); it++) { MooseVariable & ivar = *(*it); if (ivar.activeOnSubdomain(_subdomain) > 0) { // for each variable get the list of active kernels const std::vector<KernelBase *> & kernels = _sys._kernels[_tid].activeVar(ivar.number()); for (std::vector<KernelBase *>::const_iterator kt = kernels.begin(); kt != kernels.end(); ++kt) { KernelBase * kernel = *kt; if (kernel->isImplicit()) { // now, get the list of coupled scalar vars and compute their off-diag jacobians const std::vector<MooseVariableScalar *> coupled_scalar_vars = kernel->getCoupledMooseScalarVars(); for (std::vector<MooseVariableScalar *>::const_iterator jt = coupled_scalar_vars.begin(); jt != coupled_scalar_vars.end(); jt++) { MooseVariableScalar & jvar = *(*jt); // Do: dvar / dscalar_var if (_sys.hasScalarVariable(jvar.name())) // want to process only nl-variables (not aux ones) kernel->computeOffDiagJacobianScalar(jvar.number()); } } } } } } }