void VariableBuilder::add_vars_to_system( MultiphysicsSystem& system,
const std::vector<std::string>& var_names,
const std::string& fe_family,
const std::string& order,
std::vector<VariableIndex>& var_indices,
const std::set<libMesh::subdomain_id_type>& subdomain_ids )
{
const unsigned int n_vars = var_names.size();
// Setup var_indices
libmesh_assert( var_indices.empty() );
var_indices.resize(n_vars);
if( subdomain_ids.empty() )
for( unsigned int v = 0; v < n_vars; v++ )
var_indices[v] = system.add_variable( var_names[v],
libMesh::Utility::string_to_enum<GRINSEnums::Order>(order),
libMesh::Utility::string_to_enum<GRINSEnums::FEFamily>(fe_family) );
else
for( unsigned int v = 0; v < n_vars; v++ )
var_indices[v] = system.add_variable( var_names[v],
libMesh::Utility::string_to_enum<GRINSEnums::Order>(order),
libMesh::Utility::string_to_enum<GRINSEnums::FEFamily>(fe_family),
&subdomain_ids );
}
void AverageNusseltNumber::init( const GetPot& input, const MultiphysicsSystem& system )
{
// Grab temperature variable index
std::string T_var_name = input("Physics/VariableNames/Temperature",
T_var_name_default);
this->_T_var = system.variable_number(T_var_name);
return;
}
void Vorticity::init( const GetPot& input, const MultiphysicsSystem& system )
{
// Grab velocity variable indices
std::string u_var_name = input("Physics/VariableNames/u_velocity", u_var_name_default);
std::string v_var_name = input("Physics/VariableNames/v_velocity", v_var_name_default);
this->_u_var = system.variable_number(u_var_name);
this->_v_var = system.variable_number(v_var_name);
return;
}
void PrescribedVectorValueDirichletOldStyleBCFactory::add_funcs( const GetPot& input,
MultiphysicsSystem& system,
const std::string& input_string,
const std::vector<std::string>& var_names,
libMesh::CompositeFunction<libMesh::Number>& composite_func ) const
{
for( unsigned int n = 0; n < var_names.size(); n++ )
{
std::vector<VariableIndex> dbc_vars(1,system.variable_number(var_names[n]));
libMesh::Number value = input(input_string, 0.0, n);
libMesh::ConstFunction<libMesh::Number> const_func(value);
composite_func.attach_subfunction(const_func, dbc_vars);
}
}
void AverageNusseltNumber::init
(const GetPot& input,
const MultiphysicsSystem& system,
unsigned int /*qoi_num*/ )
{
this->set_parameter
( _k, input, "QoI/NusseltNumber/thermal_conductivity", -1.0 );
this->set_parameter
( _scaling, input, "QoI/NusseltNumber/scaling", 1.0 );
if( this->_k < 0.0 )
{
std::cerr << "Error: thermal conductivity for AverageNusseltNumber must be positive." << std::endl
<< "Found k = " << _k << std::endl;
libmesh_error();
}
// Read boundary ids for which we want to compute
int num_bcs = input.vector_variable_size("QoI/NusseltNumber/bc_ids");
if( num_bcs <= 0 )
{
std::cerr << "Error: Must specify at least one boundary id to compute"
<< " average Nusselt number." << std::endl
<< "Found: " << num_bcs << std::endl;
libmesh_error();
}
for( int i = 0; i < num_bcs; i++ )
{
_bc_ids.insert( input("QoI/NusseltNumber/bc_ids", -1, i ) );
}
// Grab temperature variable index
std::string T_var_name = input( "Physics/VariableNames/Temperature",
T_var_name_default );
this->_T_var = system.variable_number(T_var_name);
return;
}
void ParameterManager::initialize
( const GetPot& input,
const std::string & parameters_varname,
MultiphysicsSystem & system,
CompositeQoI * qoi)
{
const unsigned int n_parameters =
input.vector_variable_size(parameters_varname);
libmesh_assert(n_parameters);
this->parameter_name_list.resize(n_parameters);
this->parameter_vector.clear();
for (unsigned int i=0; i != n_parameters; ++i)
{
std::string param_name =
input(parameters_varname, std::string(), i);
this->parameter_name_list[i] = param_name;
libMesh::ParameterMultiAccessor<libMesh::Number> *next_param =
new libMesh::ParameterMultiAccessor<libMesh::Number>();
// We always have Physics solving for u
system.register_parameter(param_name, *next_param);
// We don't always have QoIs when solving for du/dp
if (qoi)
qoi->register_parameter(param_name, *next_param);
if (next_param->size() == 0)
{
std::cout << "No parameters named " << param_name <<
" found in active Physics or QoIs" << std::endl;
libmesh_error();
}
this->parameter_vector.push_back
(libMesh::UniquePtr<libMesh::ParameterAccessor<libMesh::Number> >
(next_param));
}
}
void ConstantFunctionDirichletBCFactory::add_found_vars( const GetPot& input,
MultiphysicsSystem& system,
const std::string& section,
const std::set<std::string>& vars_found,
libMesh::CompositeFunction<libMesh::Number>& composite_func,
std::set<std::string>& vars_added ) const
{
libMesh::Number invalid_num = std::numeric_limits<libMesh::Number>::max();
for( std::set<std::string>::const_iterator var = vars_found.begin();
var != vars_found.end(); ++var )
{
std::vector<VariableIndex> var_idx(1,system.variable_number(*var));
libMesh::Number value = input(section+"/"+(*var),invalid_num);
libMesh::ConstFunction<libMesh::Number> const_func(value);
composite_func.attach_subfunction(const_func,var_idx);
}
vars_added = vars_found;
}
libMesh::UniquePtr<FunctionType>
ParsedFunctionDirichletOldStyleBCFactory<FunctionType>::build_func( const GetPot& input,
MultiphysicsSystem& system,
std::vector<std::string>& var_names,
const std::string& section )
{
libmesh_assert_equal_to( var_names.size(), 1 );
std::vector<VariableIndex> dbc_vars(1,system.variable_number(var_names[0]));
std::string section_str = section+"/"+DirichletBCFactoryFunctionOldStyleBase<FunctionType>::_value_var_old_style;
std::string expression = input(section_str,"DIE!",DirichletBCFactoryFunctionOldStyleBase<FunctionType>::_value_idx_old_style);
libMesh::UniquePtr<FunctionType> all_funcs = this->build_composite_func();
typedef typename TypeFrom<FunctionType>::to_composite composite_type;
composite_type * composite_func =
libMesh::cast_ptr<composite_type *>(all_funcs.get());
composite_func->attach_subfunction
(TypeFrom<FunctionType>::to_parsed(system, expression), dbc_vars);
return all_funcs;
}
void PostProcessedQuantities<NumericType>::init_quantities( const MultiphysicsSystem& multiphysics_system,
libMesh::System& output_system,
const unsigned int component )
{
switch( component )
{
case(PERFECT_GAS_DENSITY):
{
if( !multiphysics_system.has_physics(low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< low_mach_navier_stokes
<< " enable for perfect gas density calculation."
<< std::endl;
libmesh_error();
}
_quantity_var_map.insert
( std::make_pair(output_system.add_variable("rho", libMesh::FIRST),
PERFECT_GAS_DENSITY) );
_cache.add_quantity(Cache::PERFECT_GAS_DENSITY);
}
break;
case(MIXTURE_DENSITY):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for mixture gas density calculation."
<< std::endl;
libmesh_error();
}
_quantity_var_map.insert
( std::make_pair(output_system.add_variable("rho", libMesh::FIRST),
MIXTURE_DENSITY) );
_cache.add_quantity(Cache::MIXTURE_DENSITY);
}
break;
case(PERFECT_GAS_VISCOSITY):
{
libmesh_not_implemented();
}
break;
case(SPECIES_VISCOSITY):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for species viscosity calculation."
<< std::endl;
libmesh_error();
}
for( unsigned int s = 0; s < _species_names.size(); s++ )
{
VariableIndex var = output_system.add_variable
("mu_"+_species_names[s], libMesh::FIRST);
_species_var_map.insert( std::make_pair(var, s) );
_quantity_var_map.insert( std::make_pair(var, SPECIES_VISCOSITY) );
}
// We need T, p0, and mass fractions too
_cache.add_quantity(Cache::TEMPERATURE);
_cache.add_quantity(Cache::THERMO_PRESSURE);
_cache.add_quantity(Cache::MASS_FRACTIONS);
_cache.add_quantity(Cache::SPECIES_VISCOSITY);
}
break;
case(MIXTURE_VISCOSITY):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for mixture viscosity calculation."
<< std::endl;
libmesh_error();
}
_quantity_var_map.insert
( std::make_pair(output_system.add_variable("mu", libMesh::FIRST),
MIXTURE_VISCOSITY) );
_cache.add_quantity(Cache::MIXTURE_VISCOSITY);
}
break;
case(PERFECT_GAS_THERMAL_CONDUCTIVITY):
{
libmesh_not_implemented();
}
break;
case(SPECIES_THERMAL_CONDUCTIVITY):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for species thermal conductivity calculation."
<< std::endl;
libmesh_error();
}
for( unsigned int s = 0; s < _species_names.size(); s++ )
{
VariableIndex var = output_system.add_variable
("k_"+_species_names[s], libMesh::FIRST);
_species_var_map.insert( std::make_pair(var, s) );
_quantity_var_map.insert( std::make_pair(var, SPECIES_THERMAL_CONDUCTIVITY) );
}
_cache.add_quantity(Cache::SPECIES_THERMAL_CONDUCTIVITY);
}
break;
case(MIXTURE_THERMAL_CONDUCTIVITY):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for mixture thermal conductivity calculation."
<< std::endl;
libmesh_error();
}
_quantity_var_map.insert
( std::make_pair(output_system.add_variable("k", libMesh::FIRST),
MIXTURE_THERMAL_CONDUCTIVITY) );
_cache.add_quantity(Cache::MIXTURE_THERMAL_CONDUCTIVITY);
}
break;
case(PERFECT_GAS_SPECIFIC_HEAT_P):
{
libmesh_not_implemented();
}
break;
case(SPECIES_SPECIFIC_HEAT_P):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for species cp calculation."
<< std::endl;
libmesh_error();
}
for( unsigned int s = 0; s < _species_names.size(); s++ )
{
VariableIndex var = output_system.add_variable
("cp_"+_species_names[s], libMesh::FIRST);
_species_var_map.insert( std::make_pair(var, s) );
_quantity_var_map.insert( std::make_pair(var, SPECIES_SPECIFIC_HEAT_P) );
}
_cache.add_quantity(Cache::SPECIES_SPECIFIC_HEAT_P);
}
break;
case(MIXTURE_SPECIFIC_HEAT_P):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for mixture cp calculation."
<< std::endl;
libmesh_error();
}
_quantity_var_map.insert
( std::make_pair(output_system.add_variable("cp", libMesh::FIRST),
MIXTURE_SPECIFIC_HEAT_P) );
_cache.add_quantity(Cache::MIXTURE_SPECIFIC_HEAT_P);
}
break;
case(PERFECT_GAS_SPECIFIC_HEAT_V):
{
libmesh_not_implemented();
}
break;
case(SPECIES_SPECIFIC_HEAT_V):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for species cv calculation."
<< std::endl;
libmesh_error();
}
for( unsigned int s = 0; s < _species_names.size(); s++ )
{
VariableIndex var = output_system.add_variable
("cv_"+_species_names[s], libMesh::FIRST);
_species_var_map.insert( std::make_pair(var, s) );
_quantity_var_map.insert( std::make_pair(var, SPECIES_SPECIFIC_HEAT_V) );
}
_cache.add_quantity(Cache::SPECIES_SPECIFIC_HEAT_V);
}
break;
case(MIXTURE_SPECIFIC_HEAT_V):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for mixture cv calculation."
<< std::endl;
libmesh_error();
}
_quantity_var_map.insert
( std::make_pair(output_system.add_variable("cp", libMesh::FIRST),
MIXTURE_SPECIFIC_HEAT_V) );
_cache.add_quantity(Cache::MIXTURE_SPECIFIC_HEAT_V);
}
break;
case(MOLE_FRACTIONS):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for mole fraction calculation."
<< std::endl;
libmesh_error();
}
for( unsigned int s = 0; s < _species_names.size(); s++ )
{
VariableIndex var = output_system.add_variable
("X_"+_species_names[s], libMesh::FIRST);
_species_var_map.insert( std::make_pair(var, s) );
_quantity_var_map.insert( std::make_pair(var, MOLE_FRACTIONS) );
}
_cache.add_quantity(Cache::MOLE_FRACTIONS);
}
break;
case(SPECIES_ENTHALPY):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for omega_dot calculation."
<< std::endl;
libmesh_error();
}
for( unsigned int s = 0; s < _species_names.size(); s++ )
{
VariableIndex var = output_system.add_variable
("h_"+_species_names[s], libMesh::FIRST);
_species_var_map.insert( std::make_pair(var, s) );
_quantity_var_map.insert( std::make_pair(var, SPECIES_ENTHALPY) );
}
// We need T too
_cache.add_quantity(Cache::TEMPERATURE);
_cache.add_quantity(Cache::SPECIES_ENTHALPY);
}
break;
case(OMEGA_DOT):
{
if( !multiphysics_system.has_physics(reacting_low_mach_navier_stokes) )
{
std::cerr << "Error: Must have "<< reacting_low_mach_navier_stokes
<< " enable for omega_dot calculation."
<< std::endl;
libmesh_error();
}
for( unsigned int s = 0; s < _species_names.size(); s++ )
{
VariableIndex var = output_system.add_variable
("omega_"+_species_names[s], libMesh::FIRST);
_species_var_map.insert( std::make_pair(var, s) );
_quantity_var_map.insert( std::make_pair(var, OMEGA_DOT) );
}
// We need T, p0, and mass fractions too
_cache.add_quantity(Cache::TEMPERATURE);
_cache.add_quantity(Cache::THERMO_PRESSURE);
_cache.add_quantity(Cache::MASS_FRACTIONS);
_cache.add_quantity(Cache::MIXTURE_DENSITY);
_cache.add_quantity(Cache::MIXTURE_GAS_CONSTANT);
_cache.add_quantity(Cache::MOLAR_DENSITIES);
_cache.add_quantity(Cache::SPECIES_NORMALIZED_ENTHALPY_MINUS_NORMALIZED_ENTROPY);
_cache.add_quantity(Cache::OMEGA_DOT);
}
break;
default:
{
std::cerr << "Error: Invalid quantity " << component << std::endl;
libmesh_error();
}
} // end switch
return;
}
void OverlappingFluidSolidMap::build_maps( MultiphysicsSystem & system,
const libMesh::PointLocatorBase & point_locator,
const std::set<libMesh::subdomain_id_type> & solid_ids,
const std::set<libMesh::subdomain_id_type> & fluid_ids,
const DisplacementVariable & solid_disp_vars )
{
const libMesh::MeshBase & mesh = system.get_mesh();
libMesh::UniquePtr<libMesh::DiffContext> raw_context = system.build_context();
libMesh::UniquePtr<libMesh::FEMContext> fem_context( libMesh::cast_ptr<libMesh::FEMContext *>(raw_context.release()) );
if( !mesh.is_serial() )
libmesh_error_msg("ERROR: build_maps currently only implemented for ReplicatedMesh!");
for( std::set<libMesh::subdomain_id_type>::const_iterator solid_id_it = solid_ids.begin();
solid_id_it != solid_ids.end(); ++solid_id_it )
for( libMesh::MeshBase::const_element_iterator e = mesh.active_subdomain_elements_begin(*solid_id_it);
e != mesh.active_local_subdomain_elements_end(*solid_id_it);
++e )
{
// Convenience
const libMesh::Elem * solid_elem = *e;
// Setup FEMContext for computing solid displacements
const std::vector<libMesh::Point>& qpoints =
fem_context->get_element_fe(solid_disp_vars.u(),2)->get_xyz();
fem_context->get_element_fe(solid_disp_vars.u(),2)->get_phi();
fem_context->pre_fe_reinit(system,solid_elem);
fem_context->elem_fe_reinit();
// Find what fluid element contains each of the quadrature points and cache
for( unsigned int qp = 0; qp < qpoints.size(); qp++ )
{
libMesh::Real u_disp = 0;
libMesh::Real v_disp = 0;
libMesh::Real w_disp = 0;
fem_context->interior_value(solid_disp_vars.u(), qp, u_disp);
if( solid_disp_vars.dim() >= 2 )
fem_context->interior_value(solid_disp_vars.v(), qp, v_disp);
if( solid_disp_vars.dim() == 3 )
fem_context->interior_value(solid_disp_vars.w(), qp, w_disp);
libMesh::Point U( u_disp, v_disp, w_disp );
// We need to look for overlap with *displaced* solid point
libMesh::Point x = qpoints[qp]+U;
const libMesh::Elem * fluid_elem = point_locator( x, &fluid_ids );
if( !fluid_elem )
libmesh_error_msg("ERROR: Could not find fluid element for given displacement! Likely solid displaced off the fluid mesh!");
// Now add to the solid elem->overlapping fluid elems map, but only if
// the solid elem belongs to this processor
{
std::map<libMesh::dof_id_type,std::vector<unsigned int> > & fluid_elem_map =
_solid_to_fluid_map[solid_elem->id()];
// The solid quadrature point that are in this overlapping fluid/solid element pair
std::vector<unsigned int>& solid_qps = fluid_elem_map[fluid_elem->id()];
solid_qps.push_back(qp);
}
// Now add to the fluid elem->overlapping solid elems map, but only if
// the fluid elem belongs to this processor
{
std::map<libMesh::dof_id_type,std::vector<unsigned int> > & solid_elem_map =
_fluid_to_solid_map[fluid_elem->id()];
// The solid quadrature point that are in this overlapping fluid/solid element pair
std::vector<unsigned int>& solid_qps = solid_elem_map[solid_elem->id()];
solid_qps.push_back(qp);
}
}
}
}
void OldStyleBCBuilder::build_bcs( const GetPot& input, MultiphysicsSystem& system,
std::vector<SharedPtr<NeumannBCContainer> >& neumann_bcs )
{
// Warn about deprecation of this horrid style
{
std::string warning = "WARNING: Specifying boundary conditions in the\n";
warning += " Physics sections is DEPRECATED! Please\n";
warning += " update your input file to new the newer\n";
warning += " style. See the examples for an illustration.\n";
grins_warning(warning);
}
libMesh::DofMap& dof_map = system.get_dof_map();
const PhysicsList& physics_list = system.get_physics_list();
std::set<std::string> basic_physics;
this->build_basic_physics(basic_physics);
std::set<std::string> vel_and_temp_physics;
this->build_vel_and_temp_physics(vel_and_temp_physics);
std::set<std::string> reacting_physics;
this->build_reacting_physics(reacting_physics);
for( PhysicsListIter physics_iter = physics_list.begin();
physics_iter != physics_list.end();
physics_iter++ )
{
std::string physics_name = physics_iter->first;
std::string raw_physics_name = PhysicsNaming::extract_physics(physics_name);
std::string section_name = "Physics/"+physics_name;
if( basic_physics.find( raw_physics_name ) != basic_physics.end() )
{
this->construct_bcs_old_style(input,
system,
raw_physics_name,
section_name,
"bc_ids",
"bc_types",
"bc_values",
"bc_variables",
dof_map,
neumann_bcs);
}
if( (vel_and_temp_physics.find( raw_physics_name ) != vel_and_temp_physics.end()) ||
(reacting_physics.find( raw_physics_name ) != reacting_physics.end()) )
{
this->construct_bcs_old_style(input,
system,
raw_physics_name,
section_name,
"vel_bc_ids",
"vel_bc_types",
"vel_bc_values",
"vel_bc_variables",
dof_map,
neumann_bcs);
this->construct_bcs_old_style(input,
system,
raw_physics_name,
section_name,
"temp_bc_ids",
"temp_bc_types",
"temp_bc_values",
"temp_bc_variables",
dof_map,
neumann_bcs);
}
if( reacting_physics.find( raw_physics_name ) != reacting_physics.end() )
{
this->construct_bcs_old_style(input,
system,
raw_physics_name,
section_name,
"species_bc_ids",
"species_bc_types",
"species_bc_values",
"species_bc_variables",
dof_map,
neumann_bcs);
}
}
}