GapHeatTransfer::GapHeatTransfer(const std::string & name, InputParameters parameters)
:IntegratedBC(name, parameters),
_gap_type_set(false),
_gap_type(Moose::COORD_XYZ),
_quadrature(getParam<bool>("quadrature")),
_slave_flux(!_quadrature ? &_sys.getVector("slave_flux") : NULL),
_gap_conductance(getMaterialProperty<Real>("gap_conductance"+getParam<std::string>("appended_property_name"))),
_gap_conductance_dT(getMaterialProperty<Real>("gap_conductance"+getParam<std::string>("appended_property_name")+"_dT")),
_min_gap(getParam<Real>("min_gap")),
_max_gap(getParam<Real>("max_gap")),
_gap_temp(0),
_gap_distance(88888),
_edge_multiplier(1.0),
_has_info(false),
_xdisp_coupled(isCoupled("disp_x")),
_ydisp_coupled(isCoupled("disp_y")),
_zdisp_coupled(isCoupled("disp_z")),
_xdisp_var(_xdisp_coupled ? coupled("disp_x") : 0),
_ydisp_var(_ydisp_coupled ? coupled("disp_y") : 0),
_zdisp_var(_zdisp_coupled ? coupled("disp_z") : 0),
_gap_distance_value(_quadrature ? _zero : coupledValue("gap_distance")),
_gap_temp_value(_quadrature ? _zero : coupledValue("gap_temp")),
_penetration_locator(!_quadrature ? NULL : &getQuadraturePenetrationLocator(parameters.get<BoundaryName>("paired_boundary"),
getParam<std::vector<BoundaryName> >("boundary")[0],
Utility::string_to_enum<Order>(parameters.get<MooseEnum>("order")))),
_warnings(getParam<bool>("warnings"))
{
if (_quadrature)
{
if (!parameters.isParamValid("paired_boundary"))
mooseError(std::string("No 'paired_boundary' provided for ") + _name);
}
else
{
if (!isCoupled("gap_distance"))
mooseError(std::string("No 'gap_distance' provided for ") + _name);
if (!isCoupled("gap_temp"))
mooseError(std::string("No 'gap_temp' provided for ") + _name);
}
}
ForchheimerMass::ForchheimerMass(const InputParameters & parameters) :
Kernel(parameters),
// Coupled gradients
_grad_u_vel(coupledGradient("u")),
_grad_v_vel(coupledGradient("v")),
_grad_w_vel(coupledGradient("w")),
_grad_p(coupledGradient("p")),
// Coupled variables
_u_vel(coupledValue("u")),
_v_vel(coupledValue("v")),
_w_vel(coupledValue("w")),
_p(coupledValue("p")),
// Density from Richards
_density(getUserObject<RichardsDensity>("gas_density_userobject")),
// Variable numberings
_u_vel_var_number(coupled("u")),
_v_vel_var_number(coupled("v")),
_w_vel_var_number(coupled("w")),
_p_var_number(coupled("p"))
{
}
FunctionMaterialBase::FunctionMaterialBase(const std::string & name,
InputParameters parameters) :
DerivativeMaterialInterface<Material>(name, parameters),
_F_name(getParam<std::string>("f_name")),
_prop_F(&declareProperty<Real>(_F_name)),
_number_of_nl_variables(_fe_problem.getNonlinearSystem().nVariables()),
_arg_index(_number_of_nl_variables)
{
// loop counters
unsigned int i, j, k;
// fetch names and numbers of all coupled variables
_mapping_is_unique = true;
for (std::set<std::string>::const_iterator it = _pars.coupledVarsBegin(); it != _pars.coupledVarsEnd(); ++it)
{
std::map<std::string, std::vector<MooseVariable *> >::iterator vars = _coupled_vars.find(*it);
// no MOOSE variable was provided for this coupling, skip derivatives w.r.t. this variable
if (vars == _coupled_vars.end())
continue;
// check if we have a 1:1 mapping between parameters and variables
if (vars->second.size() != 1)
_mapping_is_unique = false;
// iterate over all components
for (unsigned int j = 0; j < vars->second.size(); ++j)
{
// make sure each nonlinear variable is coupled in only once
if (std::find(_arg_names.begin(), _arg_names.end(), vars->second[j]->name()) != _arg_names.end())
mooseError("A nonlinear variable can only be coupled in once.");
// insert the map values
//unsigned int number = vars->second[j]->number();
unsigned int number = coupled(*it, j);
_arg_names.push_back(vars->second[j]->name());
_arg_numbers.push_back(number);
_arg_param_names.push_back(*it);
// populate number -> arg index lookup table skipping aux variables
if (number < _number_of_nl_variables)
_arg_index[number] = _args.size();
// get variable value
_args.push_back(&coupledValue(*it, j));
}
}
_nargs = _arg_names.size();
// check number of coupled variables
if (_nargs == 0)
mooseError("Need at least one couple variable for Function Materials.");
}
JouleHeatingSource::JouleHeatingSource(const InputParameters & parameters)
: DerivativeMaterialInterface<JvarMapKernelInterface<HeatSource>>(parameters),
_grad_elec(coupledGradient("elec")),
_elec_var(coupled("elec")),
_elec_cond(getMaterialProperty<Real>("electrical_conductivity")),
_delec_cond_dT(getMaterialPropertyDerivative<Real>("electrical_conductivity", _var.name())),
_delec_cond_darg(_coupled_moose_vars.size())
{
for (unsigned int i = 0; i < _delec_cond_darg.size(); ++i)
_delec_cond_darg[i] = &getMaterialPropertyDerivative<Real>("electrical_conductivity",
_coupled_moose_vars[i]->name());
}
PorousFlow2PhasePP::PorousFlow2PhasePP(const InputParameters & parameters) :
PorousFlowVariableBase(parameters),
_phase0_porepressure_nodal(coupledNodalValue("phase0_porepressure")),
_phase0_porepressure_qp(coupledValue("phase0_porepressure")),
_phase0_gradp_qp(coupledGradient("phase0_porepressure")),
_phase0_porepressure_varnum(coupled("phase0_porepressure")),
_p0var(_dictator_UO.isPorousFlowVariable(_phase0_porepressure_varnum) ? _dictator_UO.porousFlowVariableNum(_phase0_porepressure_varnum) : 0),
_phase1_porepressure_nodal(coupledNodalValue("phase1_porepressure")),
_phase1_porepressure_qp(coupledValue("phase1_porepressure")),
_phase1_gradp_qp(coupledGradient("phase1_porepressure")),
_phase1_porepressure_varnum(coupled("phase1_porepressure")),
_p1var(_dictator_UO.isPorousFlowVariable(_phase1_porepressure_varnum) ? _dictator_UO.porousFlowVariableNum(_phase1_porepressure_varnum) : 0),
_tvar(_dictator_UO.isPorousFlowVariable(_temperature_varnum) ? _dictator_UO.porousFlowVariableNum(_temperature_varnum) : 0)
{
if (_dictator_UO.numPhases() != 2)
mooseError("The Dictator announces that the number of phases is " << _dictator_UO.numPhases() << " whereas PorousFlow2PhasePP can only be used for 2-phase simulation. When you have an efficient government, you have a dictatorship.");
}
RichardsHalfGaussianSinkFlux::RichardsHalfGaussianSinkFlux(const InputParameters & parameters)
: SideIntegralVariablePostprocessor(parameters),
_feproblem(dynamic_cast<FEProblemBase &>(_subproblem)),
_maximum(getParam<Real>("max")),
_sd(getParam<Real>("sd")),
_centre(getParam<Real>("centre")),
_richards_name_UO(getUserObject<RichardsVarNames>("richardsVarNames_UO")),
_pvar(_richards_name_UO.richards_var_num(coupled("variable"))),
_m_func(getFunction("multiplying_fcn")),
_pp(getMaterialProperty<std::vector<Real>>("porepressure"))
{
}
ComputeExternalGrainForceAndTorque::ComputeExternalGrainForceAndTorque(const InputParameters & parameters) :
DerivativeMaterialInterface<ShapeElementUserObject>(parameters),
GrainForceAndTorqueInterface(),
_c_name(getVar("c", 0)->name()),
_c_var(coupled("c")),
_dF_name(getParam<MaterialPropertyName>("force_density")),
_dF(getMaterialPropertyByName<std::vector<RealGradient> >(_dF_name)),
_dFdc(getMaterialPropertyByName<std::vector<RealGradient> >(propertyNameFirst(_dF_name, _c_name))),
_op_num(coupledComponents("etas")),
_grain_tracker(getUserObject<GrainTrackerInterface>("grain_data")),
_vals_var(_op_num),
_vals_name(_op_num),
_dFdeta(_op_num)
{
for (unsigned int i = 0; i < _op_num; ++i)
{
_vals_var[i] = coupled("etas", i);
_vals_name[i] = getVar("etas", i)->name();
_dFdeta[i] = &getMaterialPropertyByName<std::vector<RealGradient> >(propertyNameFirst(_dF_name, _vals_name[i]));
}
}
DesorptionToPorespace::DesorptionToPorespace(const std::string & name,
InputParameters parameters) :
Kernel(name,parameters),
_conc_val(&coupledValue("conc_var")),
_conc_var(coupled("conc_var")),
_desorption_time_const(getMaterialProperty<Real>("desorption_time_const")),
_adsorption_time_const(getMaterialProperty<Real>("adsorption_time_const")),
_equilib_conc(getMaterialProperty<Real>("desorption_equilib_conc")),
_equilib_conc_prime(getMaterialProperty<Real>("desorption_equilib_conc_prime"))
{
}
OrderParameterFunctionMaterial::OrderParameterFunctionMaterial(const std::string & name,
InputParameters parameters) :
DerivativeMaterialInterface<Material>(name, parameters),
_eta(coupledValue("eta")),
_eta_var(coupled("eta")),
_eta_name(getVar("eta", 0)->name()),
_function_name(getParam<std::string>("function_name")),
_prop_f(declareProperty<Real>(_function_name)),
_prop_df(declarePropertyDerivative<Real>(_function_name, _eta_name)),
_prop_d2f(declarePropertyDerivative<Real>(_function_name, _eta_name, _eta_name))
{
}
ACMultiInterface::ACMultiInterface(const InputParameters & parameters) :
Kernel(parameters),
_num_etas(coupledComponents("etas")),
_eta(_num_etas),
_grad_eta(_num_etas),
_eta_vars(_fe_problem.getNonlinearSystem().nVariables(), -1),
_kappa_names(getParam<std::vector<MaterialPropertyName> >("kappa_names")),
_kappa(_num_etas),
_L(getMaterialProperty<Real>("mob_name"))
{
if (_num_etas != _kappa_names.size())
mooseError("Supply the same nummber of etas and kappa_names.");
unsigned int nvariables = _fe_problem.getNonlinearSystem().nVariables();
int a = -1;
for (unsigned int i = 0; i < _num_etas; ++i)
{
// get all order parameters and their gradients
_eta[i] = &coupledValue("etas", i);
_grad_eta[i] = &coupledGradient("etas", i);
// populate lookup table form jvar to _eta index
unsigned int var = coupled("etas", i);
if (var < nvariables)
_eta_vars[var] = i;
// get the index of the variable the kernel is operating on
if (coupled("etas", i) == _var.number())
a = i;
// get gradient prefactors
_kappa[i] = &getMaterialPropertyByName<Real>(_kappa_names[i]);
}
if (a < 0)
mooseError("Kernel variable must be listed in etas for ACMultiInterface kernel " << name());
else
_a = a;
}
INSSplitMomentum::INSSplitMomentum(const InputParameters & parameters)
: Kernel(parameters),
// Coupled variables
_u_vel(coupledValue("u")),
_v_vel(_mesh.dimension() >= 2 ? coupledValue("v") : _zero),
_w_vel(_mesh.dimension() == 3 ? coupledValue("w") : _zero),
_a1(coupledValue("a1")),
_a2(_mesh.dimension() >= 2 ? coupledValue("a2") : _zero),
_a3(_mesh.dimension() == 3 ? coupledValue("a3") : _zero),
// Gradients
_grad_u_vel(coupledGradient("u")),
_grad_v_vel(_mesh.dimension() >= 2 ? coupledGradient("v") : _grad_zero),
_grad_w_vel(_mesh.dimension() == 3 ? coupledGradient("w") : _grad_zero),
// Variable numberings
_u_vel_var_number(coupled("u")),
_v_vel_var_number(_mesh.dimension() >= 2 ? coupled("v") : libMesh::invalid_uint),
_w_vel_var_number(_mesh.dimension() == 3 ? coupled("w") : libMesh::invalid_uint),
_a1_var_number(coupled("a1")),
_a2_var_number(_mesh.dimension() >= 2 ? coupled("a2") : libMesh::invalid_uint),
_a3_var_number(_mesh.dimension() == 3 ? coupled("a3") : libMesh::invalid_uint),
// Required parameters
_gravity(getParam<RealVectorValue>("gravity")),
_component(getParam<unsigned>("component")),
// Material properties
_mu(getMaterialProperty<Real>("mu_name")),
_rho(getMaterialProperty<Real>("rho_name"))
{
}
ContactMaster::ContactMaster(const InputParameters & parameters) :
DiracKernel(parameters),
_component(getParam<unsigned int>("component")),
_model(contactModel(getParam<std::string>("model"))),
_formulation(contactFormulation(getParam<std::string>("formulation"))),
_normalize_penalty(getParam<bool>("normalize_penalty")),
_penetration_locator(getPenetrationLocator(getParam<BoundaryName>("boundary"),
getParam<BoundaryName>("slave"),
Utility::string_to_enum<Order>(getParam<MooseEnum>("order")))),
_penalty(getParam<Real>("penalty")),
_friction_coefficient(getParam<Real>("friction_coefficient")),
_tension_release(getParam<Real>("tension_release")),
_capture_tolerance(getParam<Real>("capture_tolerance")),
_updateContactSet(true),
_residual_copy(_sys.residualGhosted()),
_x_var(isCoupled("disp_x") ? coupled("disp_x") : libMesh::invalid_uint),
_y_var(isCoupled("disp_y") ? coupled("disp_y") : libMesh::invalid_uint),
_z_var(isCoupled("disp_z") ? coupled("disp_z") : libMesh::invalid_uint),
_mesh_dimension(_mesh.dimension()),
_vars(_x_var, _y_var, _z_var),
_nodal_area_var(getVar("nodal_area", 0)),
_aux_system(_nodal_area_var->sys()),
_aux_solution(_aux_system.currentSolution())
{
if (parameters.isParamValid("tangential_tolerance"))
_penetration_locator.setTangentialTolerance(getParam<Real>("tangential_tolerance"));
if (parameters.isParamValid("normal_smoothing_distance"))
_penetration_locator.setNormalSmoothingDistance(getParam<Real>("normal_smoothing_distance"));
if (parameters.isParamValid("normal_smoothing_method"))
_penetration_locator.setNormalSmoothingMethod(parameters.get<std::string>("normal_smoothing_method"));
if (_model == CM_GLUED ||
(_model == CM_COULOMB && _formulation == CF_DEFAULT))
_penetration_locator.setUpdate(false);
if (_friction_coefficient < 0)
mooseError("The friction coefficient must be nonnegative");
}
// DEPRECATED CONSTRUCTOR
StressDivergencePFFracTensors::StressDivergencePFFracTensors(const std::string & deprecated_name, InputParameters parameters) :
StressDivergenceTensors(deprecated_name, parameters),
_c_coupled(isCoupled("c")),
_c_var(_c_coupled ? coupled("c") : 0)
{
if (_c_coupled)
{
if (!isParamValid("pff_jac_prop_name"))
mooseError("StressDivergencePFFracTensors: Provide pff_jac_prop_name that contains d_stress_d_c: Coupled variable only used in Jacobian evaluation");
else
_d_stress_dc = &getMaterialProperty<RankTwoTensor>("pff_jac_prop_name");
}
}
CoupledTPBPotentialYSZQS::CoupledTPBPotentialYSZQS(const InputParameters & parameters) :
Kernel(parameters),
_s0(getParam<Real>("s0")),
_z(getParam<Real>("z")),
_F(getParam<Real>("F")),
_R(getParam<Real>("R")),
_T(getParam<Real>("T")),
_func_phi_LSM(getFunction("function_phi_LSM")),
_pO2_CE(getParam<Real>("pO2_CE")),
_num_p_O2(coupled("p_O2")),
_p_O2(coupledValue("p_O2"))
{
}
INSProjection::INSProjection(const std::string & name, InputParameters parameters) :
Kernel(name, parameters),
// Coupled variables
_a1(coupledValue("a1")),
_a2(_mesh.dimension() >= 2 ? coupledValue("a2") : _zero),
_a3(_mesh.dimension() == 3 ? coupledValue("a3") : _zero),
// Gradients
_grad_p(coupledGradient("p")),
// Variable numberings
_a1_var_number(coupled("a1")),
_a2_var_number(_mesh.dimension() >= 2 ? coupled("a2") : libMesh::invalid_uint),
_a3_var_number(_mesh.dimension() == 3 ? coupled("a3") : libMesh::invalid_uint),
_p_var_number(coupled("p")),
// Required parameters
_rho(getParam<Real>("rho")),
_component(getParam<unsigned>("component"))
{
}
ExcitationReaction::ExcitationReaction(const InputParameters & parameters)
: Kernel(parameters),
_r_units(1. / getParam<Real>("position_units")),
_n_gas(getMaterialProperty<Real>("n_gas")),
_diffem(getMaterialProperty<Real>("diffem")),
_muem(getMaterialProperty<Real>("muem")),
_alpha_source(getMaterialProperty<Real>("alpha_ex")),
// _alpha_sink(getMaterialProperty<Real>("alpha_dex")),
_d_iz_d_actual_mean_en(getMaterialProperty<Real>("d_iz_d_actual_mean_en")),
_d_muem_d_actual_mean_en(getMaterialProperty<Real>("d_muem_d_actual_mean_en")),
_d_diffem_d_actual_mean_en(getMaterialProperty<Real>("d_diffem_d_actual_mean_en")),
_mean_en(coupledValue("mean_en")),
_grad_potential(coupledGradient("potential")),
_em(coupledValue("em")),
_grad_em(coupledGradient("em")),
_mean_en_id(coupled("mean_en")),
_potential_id(coupled("potential")),
_em_id(coupled("em")),
_reactant(getParam<bool>("reactant"))
{
}
LowMachPreconditioner::LowMachPreconditioner(const InputParameters & parameters) :
Kernel(parameters),
// Coupled auxilary variables
_rhoA(coupledValue("rhoA")),
_rhouA_x(coupledValue("rhouA_x")),
_rhouA_y(_mesh.dimension()>=2 ? coupledValue("rhouA_y") : _zero),
_rhouA_z(_mesh.dimension()==3 ? coupledValue("rhouA_z") : _zero),
_pressure_old(coupledValueOld("pressure")),
_pressure_older(coupledValueOlder("pressure")),
_area(coupledValue("area")),
// Equation of state:
_eos(getUserObject<EquationOfState>("eos")),
// Parameters:
_Mach_ref(getParam<Real>("Mach_nb_ref")),
// Parameters for jacobian:
_rhoA_nb(coupled("rhoA")),
_rhouA_x_nb(coupled("rhouA_x")),
_rhouA_y_nb(isCoupled("rhouA_y") ? coupled("rhouA_y") : -1),
_rhouA_z_nb(isCoupled("rhouA_z") ? coupled("rhouA_z") : -1)
{}
MechanicalContactConstraint::MechanicalContactConstraint(const std::string & name, InputParameters parameters) :
NodeFaceConstraint(name, parameters),
_component(getParam<unsigned int>("component")),
_model(contactModel(getParam<std::string>("model"))),
_formulation(contactFormulation(getParam<std::string>("formulation"))),
_normalize_penalty(getParam<bool>("normalize_penalty")),
_penalty(getParam<Real>("penalty")),
_friction_coefficient(getParam<Real>("friction_coefficient")),
_tension_release(getParam<Real>("tension_release")),
_update_contact_set(true),
_time_last_called(-std::numeric_limits<Real>::max()),
_residual_copy(_sys.residualGhosted()),
_x_var(isCoupled("disp_x") ? coupled("disp_x") : 99999),
_y_var(isCoupled("disp_y") ? coupled("disp_y") : 99999),
_z_var(isCoupled("disp_z") ? coupled("disp_z") : 99999),
_mesh_dimension(_mesh.dimension()),
_vars(_x_var, _y_var, _z_var),
_nodal_area_var(getVar("nodal_area", 0)),
_aux_system( _nodal_area_var->sys() ),
_aux_solution( _aux_system.currentSolution() )
{
_overwrite_slave_residual = false;
if (parameters.isParamValid("tangential_tolerance"))
_penetration_locator.setTangentialTolerance(getParam<Real>("tangential_tolerance"));
if (parameters.isParamValid("normal_smoothing_distance"))
_penetration_locator.setNormalSmoothingDistance(getParam<Real>("normal_smoothing_distance"));
if (parameters.isParamValid("normal_smoothing_method"))
_penetration_locator.setNormalSmoothingMethod(parameters.get<std::string>("normal_smoothing_method"));
if (_model == CM_GLUED ||
(_model == CM_COULOMB && _formulation == CF_DEFAULT))
_penetration_locator.setUpdate(false);
if (_friction_coefficient < 0)
mooseError("The friction coefficient must be nonnegative");
}
ElectronAdvectionDoNothingBC::ElectronAdvectionDoNothingBC(const InputParameters & parameters) :
IntegratedBC(parameters),
_position_units(1./getParam<Real>("position_units")),
_muem(getMaterialProperty<Real>("muem")),
_d_muem_d_actual_mean_en(getMaterialProperty<Real>("d_muem_d_actual_mean_en")),
_sign(getMaterialProperty<Real>("sgnem")),
// Coupled variables
_potential_id(coupled("potential")),
_grad_potential(coupledGradient("potential")),
_mean_en(coupledValue("mean_en")),
_mean_en_id(coupled("mean_en")),
_d_actual_mean_en_d_mean_en(0),
_d_muem_d_mean_en(0),
_d_actual_mean_en_d_u(0),
_d_muem_d_u(0)
{
}
RigidBodyModesRZ::RigidBodyModesRZ(const InputParameters & parameters) :
NodalUserObject(parameters),
_subspace_name(parameters.get<std::string>("subspace_name")),
_subspace_indices(parameters.get<std::vector<unsigned int> >("subspace_indices")),
_disp_r_i(coupled("disp_r")),
_disp_z_i(coupled("disp_z"))
{
if (_subspace_indices.size() != 1) {
std::stringstream err;
err << "Expected 1 RZ rigid body mode, got " << _subspace_indices.size() << " instead\n";
mooseError(err.str());
}
for (unsigned int i = 0; i < _subspace_indices.size(); ++i)
{
if (_subspace_indices[i] >= _fe_problem.subspaceDim(_subspace_name))
{
std::stringstream err;
err << "Invalid " << i << "-th " << _subspace_name << " index " << _subspace_indices[i] << "; must be < " << _fe_problem.subspaceDim(_subspace_name) << "\n";
mooseError(err.str());
}
}
}
TwoSpeciesSource::TwoSpeciesSource(const InputParameters & parameters) :
// You must call the constructor of the base class first
Kernel(parameters),
_Distribution(getFunction("Distribution")),
_neutronflux_var(coupled("neutron_flux")),
_neutronflux(coupledValue("neutron_flux")),
_species_j1(coupledValue("species_j1")),
_c1(getParam<Real>("c1")),
_c2(getParam<Real>("c2")),
_cross1(getMaterialProperty<Real>("Pu239_absorption")),
_cross2(getMaterialProperty<Real>("Pu239_capture")),//test,calcu should be 4 kernels
_expansion_factor(getMaterialProperty<Real>("expansion_factor"))
{}
ElectronsFromIonizationLFA::ElectronsFromIonizationLFA(const InputParameters & parameters) :
Kernel(parameters),
_diffem(getMaterialProperty<Real>("diffem")),
_muem(getMaterialProperty<Real>("muem")),
_iz_coeff_efield_a(getMaterialProperty<Real>("iz_coeff_efield_a")),
_iz_coeff_efield_b(getMaterialProperty<Real>("iz_coeff_efield_b")),
_iz_coeff_efield_c(getMaterialProperty<Real>("iz_coeff_efield_c")),
_grad_potential(coupledGradient("potential")),
_potential_id(coupled("potential"))
{
}
INSChorinCorrector::INSChorinCorrector(const InputParameters & parameters) :
Kernel(parameters),
// Current velocities
_u_vel_star(coupledValue("u_star")),
_v_vel_star(_mesh.dimension() >= 2 ? coupledValue("v_star") : _zero),
_w_vel_star(_mesh.dimension() == 3 ? coupledValue("w_star") : _zero),
// Pressure gradient
_grad_p(coupledGradient("p")),
// Variable numberings
_u_vel_star_var_number(coupled("u_star")),
_v_vel_star_var_number(_mesh.dimension() >= 2 ? coupled("v_star") : libMesh::invalid_uint),
_w_vel_star_var_number(_mesh.dimension() == 3 ? coupled("w_star") : libMesh::invalid_uint),
_p_var_number(coupled("p")),
// Required parameters
_rho(getParam<Real>("rho")),
_component(getParam<unsigned>("component"))
{
}
FlowProperties::FlowProperties(const InputParameters & parameters)
:Material(parameters),
_molecular_wieght(getParam<std::vector<Real> >("molecular_wieght")),
_comp_heat_capacity(getParam<std::vector<Real> >("comp_heat_capacity")),
_comp_ref_viscosity(getParam<std::vector<Real> >("comp_ref_viscosity")),
_comp_ref_temp(getParam<std::vector<Real> >("comp_ref_temp")),
_comp_Sutherland_const(getParam<std::vector<Real> >("comp_Sutherland_const")),
_flow_rate(getParam<Real>("flow_rate")),
_column_length(getParam<Real>("column_length")),
_velocity(declareProperty<Real>("velocity")),
_gas_density(declareProperty<Real>("gas_density")),
_gas_viscosity(declareProperty<Real>("gas_viscosity")),
_gas_heat_capacity(declareProperty<Real>("gas_heat_capacity")),
_gas_molecular_wieght(declareProperty<Real>("gas_molecular_wieght")),
_inner_dia(getMaterialProperty<Real>("inner_dia")),
_porosity(getMaterialProperty<Real>("porosity")),
_pellet_density(getMaterialProperty<Real>("pellet_density")),
_pellet_heat_capacity(getMaterialProperty<Real>("pellet_heat_capacity")),
_heat_retardation(declareProperty<Real>("heat_retardation")),
_molecular_diffusion(declareProperty<std::vector<Real> >("molecular_diffusion")),
_dispersion(declareProperty<std::vector<Real> >("dispersion")),
_retardation(declareProperty<std::vector<Real> >("retardation")),
_temperature(coupledValue("temperature")),
_total_pressure(coupledValue("total_pressure"))
{
unsigned int n = coupledComponents("coupled_gases");
_index.resize(n);
_gas_conc.resize(n);
_solid_conc.resize(n);
_solid_perturb.resize(n);
for (unsigned int i = 0; i<_gas_conc.size(); ++i)
{
_index[i] = coupled("coupled_gases",i); //may only be useful for compute Jacobian Off Diagonal (see ~/projects/truck/moose/modules/chemical_reactions/ .../ CoupledConvectionReactionSub.C)
_gas_conc[i] = &coupledValue("coupled_gases",i);
_solid_conc[i] = &coupledValue("coupled_adsorption",i);
_solid_perturb[i] = &coupledValue("coupled_perturbation",i);
}
/*
Note: When using _gas_conc[i], it must be appropriately dereferenced as follows...
(*_gas_conc[i])[_qp] = concentration of species i at node _qp
Opposite for materials
_molecular_diffusion[_qp][i] = Dm[_qp][i]
*/
}
KKSCHBulk::KKSCHBulk(const InputParameters & parameters) :
CHBulk(parameters),
// number of coupled variables (ca, args_a[])
_nvar(_coupled_moose_vars.size()),
_ca_var(coupled("ca")),
_ca_name(getVar("ca", 0)->name()),
_cb_var(coupled("cb")),
_cb_name(getVar("cb", 0)->name()),
_prop_h(getMaterialProperty<Real>("h_name")),
_second_derivative_Fa(getMaterialPropertyDerivative<Real>("fa_name", _ca_name, _ca_name)),
_second_derivative_Fb(getMaterialPropertyDerivative<Real>("fb_name", _cb_name, _cb_name))
{
// reserve space for derivatives
_second_derivatives.resize(_nvar);
_third_derivatives.resize(_nvar);
_third_derivatives_ca.resize(_nvar);
_grad_args.resize(_nvar);
// Iterate over all coupled variables
for (unsigned int i = 0; i < _nvar; ++i)
{
MooseVariable *cvar = this->_coupled_moose_vars[i];
// get the second derivative material property (TODO:warn)
_second_derivatives[i] = &getMaterialPropertyDerivative<Real>("fa_name", _ca_name, cvar->name());
// get the third derivative material properties
_third_derivatives[i].resize(_nvar);
for (unsigned int j = 0; j < _nvar; ++j)
_third_derivatives[i][j] = &getMaterialPropertyDerivative<Real>("fa_name", _ca_name, cvar->name(), _coupled_moose_vars[j]->name());
// third derivative for the on-diagonal jacobian
_third_derivatives_ca[i] = &getMaterialPropertyDerivative<Real>("fa_name", _ca_name, cvar->name(), _ca_name);
// get the gradient
_grad_args[i] = &(cvar->gradSln());
}
}
ExampleShapeSideIntegratedBC::ExampleShapeSideIntegratedBC(const InputParameters & parameters)
: NonlocalIntegratedBC(parameters),
_num_shp(getUserObject<NumShapeSideUserObject>("num_user_object")),
_num_shp_integral(_num_shp.getIntegral()),
_num_shp_jacobian(_num_shp.getJacobian()),
_denom_shp(getUserObject<DenomShapeSideUserObject>("denom_user_object")),
_denom_shp_integral(_denom_shp.getIntegral()),
_denom_shp_jacobian(_denom_shp.getJacobian()),
_var_dofs(_var.dofIndices()),
_v_var(coupled("v")),
_v_dofs(getVar("v", 0)->dofIndices()),
_Vb(getParam<Real>("Vb"))
{
}
CoupledKernelGradTest::CoupledKernelGradTest(const InputParameters & parameters)
: KernelGrad(parameters), _var2(coupledValue("var2")), _var2_num(coupled("var2"))
{
std::vector<Real> a(getParam<std::vector<Real>>("vel"));
if (a.size() != 2)
{
mooseError("ERROR: CoupledKernelGradTest only implemented for 2D, vel is not size 2");
}
_beta = RealVectorValue(a[0], a[1]);
// Test coupling error
if (getParam<bool>("test_coupling_error"))
coupledGradient("var_undeclared");
}
PorousFlow2PhasePS::PorousFlow2PhasePS(const InputParameters & parameters) :
PorousFlowVariableBase(parameters),
_phase0_porepressure_nodal(coupledNodalValue("phase0_porepressure")),
_phase0_porepressure_qp(coupledValue("phase0_porepressure")),
_phase0_gradp_qp(coupledGradient("phase0_porepressure")),
_phase0_porepressure_varnum(coupled("phase0_porepressure")),
_pvar(_dictator.isPorousFlowVariable(_phase0_porepressure_varnum) ? _dictator.porousFlowVariableNum(_phase0_porepressure_varnum) : 0),
_phase1_saturation_nodal(coupledNodalValue("phase1_saturation")),
_phase1_saturation_qp(coupledValue("phase1_saturation")),
_phase1_grads_qp(coupledGradient("phase1_saturation")),
_phase1_saturation_varnum(coupled("phase1_saturation")),
_svar(_dictator.isPorousFlowVariable(_phase1_saturation_varnum) ? _dictator.porousFlowVariableNum(_phase1_saturation_varnum) : 0),
_tvar(_dictator.isPorousFlowVariable(_temperature_varnum) ? _dictator.porousFlowVariableNum(_temperature_varnum) : 0),
_pc(getParam<Real>("pc"))
{
if (_dictator.numPhases() != 2)
mooseError("The Dictator proclaims that the number of phases is " << _dictator.numPhases() << " whereas PorousFlow2PhasePS can only be used for 2-phase simulation. Be aware that the Dictator has noted your mistake.");
}
PorousFlowDesorpedMassTimeDerivative::PorousFlowDesorpedMassTimeDerivative(
const InputParameters & parameters)
: TimeKernel(parameters),
_dictator(getUserObject<PorousFlowDictator>("PorousFlowDictator")),
_conc_var_number(coupled("conc_var")),
_conc(coupledValue("conc_var")),
_conc_old(coupledValueOld("conc_var")),
_porosity(getMaterialProperty<Real>("PorousFlow_porosity_qp")),
_porosity_old(getMaterialPropertyOld<Real>("PorousFlow_porosity_qp")),
_dporosity_dvar(getMaterialProperty<std::vector<Real>>("dPorousFlow_porosity_qp_dvar")),
_dporosity_dgradvar(
getMaterialProperty<std::vector<RealGradient>>("dPorousFlow_porosity_qp_dgradvar"))
{
}
DCIonBC::DCIonBC(const InputParameters & parameters) :
IntegratedBC(parameters),
_mu(getMaterialProperty<Real>("mu"+_var.name())),
_sgn(getMaterialProperty<Real>("sgn"+_var.name())),
// _vthermal_ip(getMaterialProperty<Real>("vthermal_ip")),
_a(0.0),
_r_units(1. / getParam<Real>("position_units")),
// coupled variables
_grad_potential(coupledGradient("potential")),
_potential_id(coupled("potential"))
{}