ASPECT

Classes  
struct  AdvectionField 
struct  IntermediaryConstructorAction 
Public Types  
using  NonlinearSolver = typename Parameters< dim >::NonlinearSolver 
using  NullspaceRemoval = typename Parameters< dim >::NullspaceRemoval 
Public Member Functions  
Simulator (const MPI_Comm mpi_communicator, ParameterHandler &prm)  
~Simulator ()  
void  run () 
void  write_plugin_graph (std::ostream &output_stream) const 
Static Public Member Functions  
static void  declare_parameters (ParameterHandler &prm) 
Private Member Functions  
Toplevel functions in the overall flow of the numerical  
algorithm  
void  setup_dofs () 
void  setup_introspection () 
void  set_initial_temperature_and_compositional_fields () 
void  compute_initial_pressure_field () 
void  compute_initial_velocity_boundary_constraints (AffineConstraints< double > &constraints) 
void  compute_current_velocity_boundary_constraints (AffineConstraints< double > &constraints) 
void  compute_current_constraints () 
double  compute_pressure_scaling_factor () const 
void  start_timestep () 
void  solve_timestep () 
void  solve_single_advection_single_stokes () 
void  solve_no_advection_iterated_stokes () 
void  solve_no_advection_single_stokes () 
void  solve_first_timestep_only_single_stokes () 
void  solve_iterated_advection_and_stokes () 
void  solve_single_advection_iterated_stokes () 
void  solve_no_advection_iterated_defect_correction_stokes () 
void  solve_single_advection_iterated_defect_correction_stokes () 
void  solve_iterated_advection_and_defect_correction_stokes () 
void  solve_iterated_advection_and_newton_stokes (bool use_newton_iterations) 
void  solve_single_advection_and_iterated_newton_stokes (bool use_newton_iterations) 
void  solve_single_advection_no_stokes () 
void  solve_no_advection_no_stokes () 
void  build_stokes_preconditioner () 
void  build_advection_preconditioner (const AdvectionField &advection_field, aspect::LinearAlgebra::PreconditionILU &preconditioner, const double diagonal_strengthening) 
void  assemble_stokes_system () 
double  assemble_and_solve_temperature (const double &initial_residual=0, double *residual=nullptr) 
std::vector< double >  assemble_and_solve_composition (const std::vector< double > &initial_residual={}, std::vector< double > *residual=nullptr) 
double  assemble_and_solve_stokes (const double &initial_nonlinear_residual=0, double *nonlinear_residual=nullptr) 
void  do_one_defect_correction_Stokes_step (DefectCorrectionResiduals &dcr, const bool use_picard) 
void  assemble_advection_system (const AdvectionField &advection_field) 
double  solve_advection (const AdvectionField &advection_field) 
DEAL_II_DEPRECATED void  interpolate_particle_properties (const AdvectionField &advection_field) 
void  interpolate_particle_properties (const std::vector< AdvectionField > &advection_fields) 
std::pair< double, double >  solve_stokes () 
std::pair< double, double >  solve_stokes_block_gmg () 
void  postprocess () 
void  refine_mesh (const unsigned int max_grid_level) 
Functions used in saving the state of the program and  
restarting from a saved state  
void  create_snapshot () 
void  resume_from_snapshot () 
template<class Archive >  
void  serialize (Archive &ar, const unsigned int version) 
Functions used in setting up linear systems  
Table< 2, DoFTools::Coupling >  setup_system_matrix_coupling () const 
void  setup_system_matrix (const std::vector< IndexSet > &system_partitioning) 
void  setup_system_preconditioner (const std::vector< IndexSet > &system_partitioning) 
Helper functions  
void  make_pressure_rhs_compatible (LinearAlgebra::BlockVector &vector) 
template<typename T >  
void  get_artificial_viscosity (Vector< T > &viscosity_per_cell, const AdvectionField &advection_field, const bool skip_interior_cells=false) const 
void  compute_Vs_anomaly (Vector< float > &values) const 
void  compute_Vp_anomaly (Vector< float > &values) const 
double  normalize_pressure (LinearAlgebra::BlockVector &vector) const 
void  denormalize_pressure (const double pressure_adjustment, LinearAlgebra::BlockVector &vector, const LinearAlgebra::BlockVector &relevant_vector) const 
void  apply_limiter_to_dg_solutions (const AdvectionField &advection_field) 
void  compute_reactions () 
void  update_solution_vectors_with_reaction_results (const unsigned int block_index, const LinearAlgebra::BlockVector &distributed_vector, const LinearAlgebra::BlockVector &distributed_reaction_vector) 
void  initialize_current_linearization_point () 
void  interpolate_material_output_into_advection_field (const AdvectionField &adv_field) 
void  interpolate_onto_velocity_system (const TensorFunction< 1, dim > &func, LinearAlgebra::Vector &vec) 
void  setup_nullspace_constraints (AffineConstraints< double > &constraints) 
void  remove_nullspace (LinearAlgebra::BlockVector &relevant_dst, LinearAlgebra::BlockVector &tmp_distributed_stokes) 
RotationProperties< dim >  compute_net_angular_momentum (const bool use_constant_density, const LinearAlgebra::BlockVector &solution, const bool limit_to_top_faces=false) const 
void  remove_net_angular_momentum (const bool use_constant_density, LinearAlgebra::BlockVector &relevant_dst, LinearAlgebra::BlockVector &tmp_distributed_stokes, const bool limit_to_top_faces=false) 
void  replace_outflow_boundary_ids (const unsigned int boundary_id_offset) 
void  restore_outflow_boundary_ids (const unsigned int boundary_id_offset) 
void  remove_net_linear_momentum (const bool use_constant_density, LinearAlgebra::BlockVector &relevant_dst, LinearAlgebra::BlockVector &tmp_distributed_stokes) 
double  get_maximal_velocity (const LinearAlgebra::BlockVector &solution) const 
double  get_entropy_variation (const double average_field, const AdvectionField &advection_field) const 
std::pair< double, double >  get_extrapolated_advection_field_range (const AdvectionField &advection_field) const 
void  exchange_refinement_flags () 
void  maybe_write_timing_output () const 
bool  maybe_write_checkpoint (const time_t last_checkpoint_time, const bool force_writing_checkpoint) 
bool  maybe_do_initial_refinement (const unsigned int max_refinement_level) 
void  maybe_refine_mesh (const double new_time_step, unsigned int &max_refinement_level) 
void  advance_time (const double step_size) 
double  compute_viscosity (internal::Assembly::Scratch::AdvectionSystem< dim > &scratch, const double global_u_infty, const double global_field_variation, const double average_field, const double global_entropy_variation, const double cell_diameter, const AdvectionField &advection_field) const 
void  compute_advection_system_residual (internal::Assembly::Scratch::AdvectionSystem< dim > &scratch, const double average_field, const AdvectionField &advection_field, double &max_residual, double &max_velocity, double &max_density, double &max_specific_heat, double &conductivity) const 
bool  stokes_matrix_depends_on_solution () const 
bool  stokes_A_block_is_symmetric () const 
void  check_consistency_of_formulation () 
void  select_default_solver_and_averaging () 
void  check_consistency_of_boundary_conditions () const 
double  compute_initial_newton_residual (const LinearAlgebra::BlockVector &linearized_stokes_initial_guess) 
double  compute_Eisenstat_Walker_linear_tolerance (const bool EisenstatWalkerChoiceOne, const double maximum_linear_stokes_solver_tolerance, const double linear_stokes_solver_tolerance, const double stokes_residual, const double newton_residual, const double newton_residual_old) 
void  output_statistics () 
double  compute_initial_stokes_residual () 
Friends  
class  boost::serialization::access 
class  SimulatorAccess< dim > 
class  MeshDeformation::MeshDeformationHandler< dim > 
class  VolumeOfFluidHandler< dim > 
class  StokesMatrixFreeHandler< dim > 
template<int dimension, int velocity_degree>  
class  StokesMatrixFreeHandlerImplementation 
struct  Parameters< dim > 
Variables that have to do with input, output, parallel  
communication and interfacing with other parts of the program.  
using  TeeDevice = boost::iostreams::tee_device< std::ostream, std::ofstream > 
using  TeeStream = boost::iostreams::stream< TeeDevice > 
Parameters< dim >  parameters 
std::unique_ptr< MeltHandler< dim > >  melt_handler 
std::unique_ptr< NewtonHandler< dim > >  newton_handler 
SimulatorSignals< dim >  signals 
const IntermediaryConstructorAction  post_signal_creation 
std::unique_ptr< VolumeOfFluidHandler< dim > >  volume_of_fluid_handler 
Introspection< dim >  introspection 
MPI_Comm  mpi_communicator 
std::ofstream  log_file_stream 
TeeDevice  iostream_tee_device 
TeeStream  iostream_tee_stream 
ConditionalOStream  pcout 
TableHandler  statistics 
std::size_t  statistics_last_write_size 
std::size_t  statistics_last_hash 
TimerOutput  computing_timer 
Timer  wall_timer 
double  total_walltime_until_last_snapshot 
std::thread  output_statistics_thread 
This is the main class of ASPECT. It implements the overall simulation algorithm using the numerical methods discussed in the papers and manuals that accompany ASPECT.
Definition at line 187 of file simulator.h.
using aspect::Simulator< dim >::NonlinearSolver = typename Parameters<dim>::NonlinearSolver 
Import Nonlinear Solver type.
Definition at line 253 of file simulator.h.
using aspect::Simulator< dim >::NullspaceRemoval = typename Parameters<dim>::NullspaceRemoval 
Import nullspace removal type.
Definition at line 258 of file simulator.h.

private 
Definition at line 1883 of file simulator.h.

private 
Definition at line 1884 of file simulator.h.
aspect::Simulator< dim >::Simulator  (  const MPI_Comm  mpi_communicator, 
ParameterHandler &  prm  
) 
Constructor.
mpi_communicator  The MPI communicator on which this class is to work. The class creates a clone of the actual communicator to make its communications private from the rest of the world. 
prm  The runtime parameter object from which this class obtains its settings. 
This function is implemented in source/simulator/core.cc
.
aspect::Simulator< dim >::~Simulator  (  ) 
Destructor. Destroy what needs to be destroyed after waiting for all threads that may still be doing something in the background.

static 
Declare the runtime parameters this class takes, and call the respective declare_parameters
functions of the namespaces that describe geometries, material models, etc.
prm  The object in which the runtime parameters are to be declared. 
This function is implemented in source/simulator/parameters.cc
.
void aspect::Simulator< dim >::run  (  ) 
The function that runs the overall algorithm. It contains the loop over all time steps as well as the logic of what to do when before the loop starts and within the time loop.
This function is implemented in source/simulator/core.cc
.
void aspect::Simulator< dim >::write_plugin_graph  (  std::ostream &  output_stream  )  const 
Write a connection graph of all of the plugins we know about, in the format that the programs dot and neato understand. This allows for a visualization of how all of the plugins that ASPECT knows about are interconnected, and connect to other parts of the ASPECT code.
This function is implemented in source/simulator/helper_functions.cc
.
output_stream  The stream to write the output to. 

private 
The function that sets up the DoFHandler objects, It also sets up the various partitioners and computes those constraints on the Stokes variable and temperature that are the same between all time steps.
This function is implemented in source/simulator/core.cc
.

private 
This function initializes the variables of the introspection object. It is called by setup_dofs() right after distributing degrees of freedom since this is when all of the information is available.
This function is implemented in source/simulator/core.cc
.

private 
A function that is responsible for initializing the temperature/compositional field before the first time step. The temperature field then serves as the temperature from which the velocity is computed during the first time step, and is subsequently overwritten by the temperature field one gets by advancing by one time step.
This function is implemented in source/simulator/initial_conditions.cc
.

private 
A function that initializes the pressure variable before the first time step. It does so by either interpolating (for continuous pressure finite elements) or projecting (for discontinuous elements) the adiabatic pressure computed from the material model.
Note that the pressure so set is overwritten by the pressure in fact computed during the first time step. We need this function, however, so that the evaluation of pressuredependent coefficients (e.g. pressure dependent densities or thermal coefficients) during the first time step has some useful pressure to start with.
This function is implemented in source/simulator/initial_conditions.cc
.

private 
Fill the given constraints
with constraints coming from the velocity boundary conditions that do not change over time. This function is used by setup_dofs();

private 
Fill the given constraints
with constraints coming from the velocity boundary conditions that do can change over time. This function is used by compute_current_constraints().

private 
Given the 'constraints' member that contains all constraints that are independent of the time (e.g., hanging node constraints, tangential flow constraints, etc), copy it over to 'current_constraints' and add to the latter all constraints that do depend on time such as temperature or velocity Dirichlet boundary conditions. This function is therefore called at the beginning of every time step in start_timestep(), but also when setting up the initial values.
This function is implemented in source/simulator/core.cc
.

private 
Compute the factor by which we scale the second of the Stokes equations (the "pressure scaling factor"). We compute the factor by taking the logarithmic average of the viscosities we find on the cells in this domain and dividing this average by a reference length scale provided by the used geometry model.
This function returns the pressure scaling variable.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Do some housekeeping at the beginning of each time step. This includes generating some screen output, adding some information to the statistics file, and interpolating timedependent boundary conditions specific to this particular time step (the time independent boundary conditions, for example for hanging nodes or for tangential flow, are computed only once per mesh in setup_dofs()).
This function is implemented in source/simulator/core.cc
.

private 
Do the various steps necessary to assemble and solve the things necessary in each time step.
This function is implemented in source/simulator/core.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
If `single Advection, single Stokes' is selected as the nonlinear solver scheme, no nonlinear iterations are done, and the temperature, compositional fields and Stokes equations are solved exactly once per time step, one after the other.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `no Advection, iterated Stokes' scheme only solves the Stokes system and ignores compositions and the temperature equation (careful, the material model must not depend on the temperature; mostly useful for Stokes benchmarks).
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `no Advection, single Stokes' scheme only solves the Stokes system and ignores compositions and the temperature equation.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `first timestep only, single Stokes' scheme only solves the Stokes system, for the initial timestep. This results in a `steady state' velocity field for particle calculations.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `iterated Advection and Stokes' scheme iterates by alternating the solution of the temperature, composition and Stokes systems. This is essentially a type of Picard iterations for the whole system of equations.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `single Advection, iterated Stokes' scheme solves the temperature and composition equations once at the beginning of each time step and then iterates out the solution of the Stokes equation using Picard iterations.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `no Advection, iterated defect correction Stokes' scheme does not solve the temperature and composition equations but only iterates out the solution of the Stokes equation using Defect Correction (DC) Picard iterations.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `single Advection, iterated defect correction Stokes' scheme solves the temperature and composition equations once at the beginning of each time step and then iterates out the solution of the Stokes equation using Defect Correction (DC) Picard iterations.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `iterated Advection and defect correction Stokes' scheme iterates over both the temperature and composition equations and the Stokes equations at the same time. The Stokes equation is iterated out using the Defect Correction (DC) form of the Picard iterations.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `iterated Advection and Newton Stokes' scheme iterates over solving the temperature, composition, and Stokes equations just like `iterated Advection and Stokes', but for the Stokes system it is able to switch from a defect correction form of Picard iterations to Newton iterations after a certain tolerance or number of iterations is reached. This can greatly improve the convergence rate for particularly nonlinear viscosities.
use_newton_iterations  Sets whether this function should only use defect correction iterations (use_newton_iterations = false) or also use Newton iterations (use_newton_iterations = true). 
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `single Advection, iterated Newton Stokes' scheme solves the temperature and composition equations once at the beginning of each time step and then iterates out the solution of the Stokes equation using Newton iterations. For the Stokes system it is able to switch from a defect correction form of Picard iterations to Newton iterations after a certain tolerance or number of iterations is reached. This can greatly improve the convergence rate for particularly nonlinear viscosities.
use_newton_iterations  Sets whether this function should only use defect correction iterations (use_newton_iterations = false) or also use Newton iterations (use_newton_iterations = true). 
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `single Advection, no Stokes' scheme only solves the temperature and other advection systems and instead of solving for the Stokes system, a prescribed velocity and pressure is used."
This function is implemented in source/simulator/solver_schemes.cc
.

private 
This function implements one scheme for the various steps necessary to assemble and solve the nonlinear problem.
The `no Advection, no Stokes' scheme skips solving the temperature, composition and Stokes equations, which permits to go directly to postprocessing after setting up the initial condition.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
Initiate the assembly of the Stokes preconditioner matrix via assemble_stokes_preconditioner(), then set up the data structures to actually build a preconditioner from this matrix.
This function is implemented in source/simulator/assembly.cc
.

private 
Initialize the preconditioner for the advection equation of field index.
This function is implemented in source/simulator/assembly.cc
.

private 
Initiate the assembly of the Stokes matrix and right hand side.
This function is implemented in source/simulator/assembly.cc
.

private 
Assemble and solve the temperature equation. This function returns the residual after solving.
If the residual
argument is not a nullptr
, the function computes the residual and puts it into this variable. The function returns the current residual divided by the initial residual given as the first argument. The two arguments may point to the same variable, in which case the function first computes the residual and at the end scales that residual by itself, thus returning 1.0.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
Solve the composition equations with whatever method is selected (fields or particles). This function returns the residuals for all fields after solving.
If the residual
argument is not a nullptr
, the function computes the residual and puts it into this variable. The function returns the current residual divided by the initial residual given as the first argument. The two arguments may point to the same variable, in which case the function first computes the residual and at the end scales that residual by itself, thus returning 1.0.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
Assemble and solve the Stokes equation. This function returns the nonlinear residual after solving.
If the residual
argument is not a nullptr
, the function computes the residual and puts it into this variable. The function returns the current residual divided by the initial residual given as the first argument. The two arguments may point to the same variable, in which case the function first computes the residual and at the end scales that residual by itself, thus returning 1.0.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
Do one step of the defect correction form of the Stokes equation; i.e., assemble and solve the defect correction equations. This function takes a structure of DefectCorrectionResiduals which contains information about different residuals. The information in this structure is updated by this function. The parameter use_picard forces the use of the defect correction Picard iteration, if set to 'true' no Newton derivatives are added to the matrix.
This function is implemented in source/simulator/solver_schemes.cc
.

private 
Initiate the assembly of one advection matrix and right hand side and build a preconditioner for the matrix.
This function is implemented in source/simulator/assembly.cc
.

private 
Solve one block of the temperature/composition linear system. Return the initial nonlinear residual, i.e., if the linear system to be solved is \(Ax=b\), then return \(\Ax_0b\\) where \(x_0\) is the initial guess for the solution variable and is taken from the current_linearization_point member variable.
This function is implemented in source/simulator/solver.cc
.

private 
Interpolate a particular particle property to the solution field.

private 
Interpolate the corresponding particle properties into the given advection_fields
solution fields.

private 
Solve the Stokes linear system.
The function returns two pieces of information as a pair of doubles:
current_linearization_point
member variable. For the purpose of this function, this residual is computed only from the velocity and pressure equations (i.e., for the 2x2 block system involving the velocity and pressure variables). A rationale for why this number is computed is given below.The two values are used in nonlinear solver schemes to assess how accurate the solution was before the current solve (for the first element of the returned pair) and how accurately the next iteration will have to be solved (for the second element of the pair) when using the EisenstatWalker method.
current_linearization_point
is the solution of the previous iteration (or the solution extrapolated from the previous time steps, if this is the first nonlinear iteration). Let us call this solution \(x_k\) as above, where \(x\) is a twocomponent block vector that consists of velocity and pressure. This function then assumes that we have already built the system matrix \(A_k=A(x_k)\) and \(F_k=F(x_k)\), both linearized around the previous solution. The function solves the linear system \(A_k x_{k+1} = F_k\) for the solution \(x_{k+1}\). If the linear system were solved exactly, then that would imply that the linear residual \(\A_k x_{k+1}  F_k\\) were zero, or at least small. In other words, its size does not tell us anything about how accurately we have solved the nonlinear system. On the other hand, the nonlinear residual \(\A_k x_k  F_k\\) tells us something about how accurately the previous guess \(x_k\) already solved the nonlinear system. Consequently, this is what this function returns. (In some sense, this is not really what we are interested in: it tells us how accurate the solution already was, and if it was already pretty accurate, then we may not want to actually solve for \(x_{k+1}\). But, this would require that this function receives a tolerance so that it can bail out early without actually solving for \(x_{k+1}\) if the tolerance is already reached. This function does not actually do that – in some sense, one may argue that if we have already built the matrix and right hand side, we may as well solve with them, whether or not the solution was already good. If it happens to have been good already, then it will be even better after the solve. If it was not good enough yet, then we have to solve anyway.) In contrast to all of this, if we are using a Newton solver, then \(x_{k+1}\) is actually the Newton update vector, for which we have no initial guess other than the zero vector. In this case, the function simply returns \(\F_k\\) as the first element of the pair, where \(F_k=F(x_k)\) is the residual vector for the previous solution \(x_k\).This function is implemented in source/simulator/solver.cc
.

private 
Solve the Stokes system using a block preconditioner and GMG.

private 
This function is called at the end of every time step. It runs all the postprocessors that have been listed in the input parameter file (see the manual) in turn. In particular, this usually includes generating graphical output every few time steps.
The function also updates the statistics output file at the end of each time step.
This function is implemented in source/simulator/core.cc
.

private 
Refine the mesh according to error indicators calculated by compute_refinement_criterion(), set up all necessary data structures on this new mesh, and interpolate the old solutions onto the new mesh.
[in]  max_grid_level  The maximum refinement level of the mesh. This is the sum of the initial global refinement and the initial adaptive refinement (as provided by the user in the input file) and in addition it gets increased by one at each additional refinement time. 
This function is implemented in source/simulator/core.cc
.

private 
Save the state of this program to a set of files in the output directory. In reality, however, only some variables are stored (in particular the mesh, the solution vectors, etc) whereas others can either be regenerated (matrices, DoFHandler objects, etc) or are read from the input parameter file. See the manual for more information.
This function is implemented in source/simulator/checkpoint_restart.cc
.

private 
Restore the state of this program from a set of files in the output directory. In reality, however, only some variables are stored (in particular the mesh, the solution vectors, etc) whereas others can either be regenerated (matrices, DoFHandler objects, etc) or are read from the input parameter file. See the manual for more information. This function only restores those variables that can neither be regenerated from other information nor are read from the input parameter file.
This function is implemented in source/simulator/checkpoint_restart.cc
.

private 
Save a number of variables using BOOST serialization mechanism.
This function is implemented in source/simulator/checkpoint_restart.cc
.

private 
Determine which of the components of our finiteelement system couple to each other. Depending on which equations are solved and which solver is used this varies widely.
This function is implemented in source/simulator/core.cc
.

private 
Set up the size and structure of the matrix used to store the elements of the linear system.
This function is implemented in source/simulator/core.cc
.

private 
Set up the size and structure of the matrix used to store the elements of the matrix that is used to build the preconditioner for the system. This matrix is only used for the Stokes system, so while it has the size of the whole system, it only has entries in the velocity and pressure blocks.
This function is implemented in source/simulator/core.cc
.

private 
Determine, based on the runtime parameters of the current simulation, which functions need to be called in order to assemble linear systems, matrices, and right hand side vectors.
This function is implemented in source/simulator/assembly.cc
.

private 
Determine, based on the runtime parameters of the current simulation, which functions need to be called in order to assemble linear systems, matrices, and right hand side vectors for the advection. This function is used by both the default full Stokes solver and the Newton solvers, but not by the twophase flow solver.
This function is implemented in source/simulator/assembly.cc
.

private 
Determine, based on the runtime parameters of the current simulation, which functions need to be called in order to assemble linear systems, matrices, and right hand side vectors for the default full Stokes solver i.e. without considering twophase flow, or Newton solvers.
This function is implemented in source/simulator/assembly.cc
.

private 
Initiate the assembly of the preconditioner for the Stokes system.
This function is implemented in source/simulator/assembly.cc
.

private 
Compute the integrals for the preconditioner for the Stokes system on a single cell.
This function is implemented in source/simulator/assembly.cc
.

private 
Copy the contribution to the preconditioner for the Stokes system from a single cell into the global matrix that stores these elements.
This function is implemented in source/simulator/assembly.cc
.

private 
Compute the integrals for the Stokes matrix and right hand side on a single cell.
This function is implemented in source/simulator/assembly.cc
.

private 
Copy the contribution to the Stokes system from a single cell into the global matrix that stores these elements.
This function is implemented in source/simulator/assembly.cc
.

private 
Compute the integrals for one advection matrix and right hand side on the faces of a single cell.
This function is implemented in source/simulator/assembly.cc
.

private 
Compute the integrals for one advection matrix and right hand side on a single cell.
This function is implemented in source/simulator/assembly.cc
.

private 
Copy the contribution to the advection system from a single cell into the global matrix that stores these elements.
This function is implemented in source/simulator/assembly.cc
.

private 
This routine adjusts the second block of the right hand side of a Stokes system (containing the term that comes from compressibility, so that the system becomes compatible: \(0=\int div u = \int g\). The vector to adjust is given as the argument of this function. This function makes use of the helper vector pressure_shape_function_integrals that contains \(h_i=(q_i,1)\) with the pressure functions \(q_i\) and we adjust the right hand side \(g\) by \(h_i \int g / \Omega\).
The purpose of this function is described in the second paper on the numerical methods in ASPECT.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Fills a vector with the artificial viscosity for the temperature or composition on each local cell.
viscosity_per_cell  Output vector 
advection_field  Determines whether this variable should select the temperature field or a compositional field. 
skip_interior_cells  A boolean flag. If set to true the function will only compute the artificial viscosity in cells at boundaries. 

private 
Compute the seismic shear wave speed, Vs anomaly per element. we compute the anomaly by computing a smoothed (over 200 km or so) laterally averaged temperature profile and associated seismic velocity that is then subtracted from the seismic velocity at the current pressure temperature conditions
values  The output vector of depth averaged values. The function takes the preexisting size of this vector as the number of depth slices. 

private 
Compute the seismic pressure wave speed, Vp anomaly per element. we compute the anomaly by computing a smoothed (over 200 km or so) laterally averaged temperature profile and associated seismic velocity that is then subtracted from the seismic velocity at the current pressure temperature conditions
This function is implemented in source/simulator/helper_functions.cc
.
values  The output vector of depth averaged values. The function takes the preexisting size of this vector as the number of depth slices. 

private 
Adjust the pressure variable (which is only determined up to a constant by the equations, though its value may enter traction boundary conditions) by adding a constant to it in such a way that the pressure on the surface or within the entire volume has a known average value. The point of this function is that the pressure that results from solving the linear system may not coincide with what we think of as the "physical pressure"; in particular, we typically think of the pressure as zero (on average) along the surface because it is the sum of the hydrostatic and dynamic pressure, where the former is thought of as zero along the surface. This function therefore converts from the "mathematical" pressure to the "physical" pressure so that all following postprocessing steps can use the latter.
In the case of the surface average, whether a face is part of the surface is determined by asking whether its depth of its midpoint (as determined by the geometry model) is less than 1/3*1/sqrt(dim1)*diameter of the face. For reasonably curved boundaries, this rules out side faces that are perpendicular to the surface boundary but includes those faces that are along the boundary even if the real boundary is curved.
Whether the pressure should be normalized based on the surface or volume average is decided by a parameter in the input file.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Invert the action of the normalize_pressure() function above. This means that we move from a pressure that satisfies the pressure normalization (e.g., has a zero average pressure, or a zero average surface pressure) to one that does not actually satisfy this normalization, and this doesn't seem to make sense because we are not interested in such a pressure.
Indeed, this function is only called at the very beginning of solve_stokes() before we compute the initial (linear) residual of the linear system \(Ax=b\) that corresponds to the Stokes system, where \(x\) is the variable for which the pressure is adjusted back to the "wrong" form. Because stokes_system() calls normalize_pressure() at the end of its operations, no such "wrong" pressure ever escapes the realm of solve_stokes(). The "wrong" pressure is then used for two purposes in that function: (i) To compute the initial Stokes residual, which makes sense because it can only be zero (if we solved the same linear system twice) if we reuse the exact same pressure as we got from the previous solve – i.e., before we called normalize_pressure() at the end of the solve. (ii) To initialize the solution vector before calling the GMRES solver, which also makes sense because the best guess vector for GMRES is the one that had previously come out of GMRES, namely the one on which we later called normalize_pressure().
This function modifies vector
inplace. In some cases, we need locally_relevant values of the pressure. To avoid creating a new vector and transferring data, this function uses a second vector with relevant dofs (relevant_vector
) for accessing these pressure values. Both vector
and relevant_vector
are expected to already contain the correct pressure values.
pressure_adjustment
function argument that would typically have been computed and returned by the normalize_pressure() function. This value is typically stored in the member variable last_pressure_normalization_adjustment
, but the current function doesn't read this variable but instead gets the adjustment variable from the given argument.This function is implemented in source/simulator/helper_functions.cc
.

private 
Apply the bound preserving limiter to the discontinuous Galerkin solutions: i.e., given two fixed upper and lower bound [min, max], after applying the limiter, the discontinuous Galerkin solution will stay in the prescribed bounds.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Compute the reactions in case of operator splitting: Using the current solution vector, this function makes a number of time steps determined by the size of the reaction time step, and solves a system of coupled ordinary differential equations for the reactions between compositional fields and temperature in each of them. To do that, is uses the reaction rates outputs from the material and heating models used in the computation. The solution vector is then updated with the new values of temperature and composition after the reactions.
As the ordinary differential equation in any given point is independent from the solution at all other points, we do not have to assemble a matrix, but just need to loop over all node locations for the temperature and compositional fields and compute the update to the solution.
The function also updates the old solution vectors with the reaction update so that the advection time stepping scheme will have the correct field terms for the righthand side when assembling the advection system.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Update the indicated block of the solution vector with the corresponding block of the handed over distributed_vector
. Also update reaction_vector with the corresponding block of distributed_reaction_vector
.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Initialize the current linearization point vector from the old solution vector(s). Depending on the time of the call this can be simply a copy of the solution of the last timestep, or a linear extrapolation of old and old_old timestep to the new timestep.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Interpolate material model outputs onto an advection field (temperature or composition). For the field identified by the AdvectionField adv_field
, this function asks the material model to fill a MaterialModel::MaterialModelOutputs object that has an attached MaterialModel::PrescribedFieldOutputs "additional outputs" object (for composition) or an attached MaterialModel::PrescribedTemperatureOutputs (for temperature). The MaterialModel::MaterialModelInputs object passed to the material model then contains the support points of the advection field, thereby allowing the outputs to be interpolated to the finite element space and consequently into the solution vector. This is useful for advection fields whose advection mode is set to Parameters::AdvectionFieldMethod::prescribed_field or Parameters::AdvectionFieldMethod::prescribed_field_with_diffusion.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Interpolate the given function onto the velocity FE space and write it into the given vector.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Add constraints to the given constraints
object that are required for unique solvability of the velocity block based on the nullspace removal settings.
This method will add a zero Dirichlet constraint for the first velocity unknown in the domain for each velocity component, which is later being processed for translational or linear momentum removal. This avoids breakdowns of the linear solvers that otherwise occurred in some instances.

private 
Eliminate the nullspace of the velocity in the given vector. Both vectors are expected to contain the up to date data.
relevant_dst  locally relevant vector for the whole FE, will be filled at the end. 
tmp_distributed_stokes  only contains velocity and pressure. 
This function is implemented in source/simulator/nullspace.cc
.

private 
Compute the angular momentum and other rotation properties of the velocities in the given solution vector.
use_constant_density  determines whether to use a constant density (which corresponds to computing a net rotation instead of net angular momentum). 
solution  Solution vector to compute the properties for. 
limit_to_top_faces  allows to only compute the net angular momentum (or net rotation) of the top surface. 
This function is implemented in source/simulator/nullspace.cc
.

private 
Remove the angular momentum of the given vector
use_constant_density  determines whether to use a constant density (which corresponds to removing a net rotation instead of net angular momentum). 
relevant_dst  locally relevant vector for the whole FE, will be filled at the end. 
tmp_distributed_stokes  only contains velocity and pressure. 
limit_to_top_faces  allows to only remove the net angular momentum (or net rotation) of the top surface. This can be useful to compare surface motions against plate reconstructions in no net rotation reference frames. 
This function is implemented in source/simulator/nullspace.cc
.

private 
Offset the boundary id of all faces located on an outflow boundary by a fixed value given by the input parameter boundary_id_offset
.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Undo the offset of the boundary ids done in replace_outflow_boundary_ids by resetting all boundary ids to their original value.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Remove the linear momentum of the given vector
use_constant_density  determines whether to use a constant density (which corresponds to removing a net translation instead of net linear momentum). 
relevant_dst  locally relevant vector for the whole FE, will be filled at the end. 
tmp_distributed_stokes  only contains velocity and pressure. 
This function is implemented in source/simulator/nullspace.cc
.

private 
Compute the maximal velocity throughout the domain. This is needed to compute the size of the time step.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Compute the variation (i.e., the difference between maximal and minimal value) of the entropy \((T\bar T)^2\) where \(\bar T\) is the average temperature throughout the domain given as argument to this function.
This function is used in computing the artificial diffusion stabilization term.
This function is implemented in source/simulator/assembly.cc
.

private 
Compute the minimal and maximal temperature throughout the domain from a solution vector extrapolated from the previous time steps. This is needed to compute the artificial diffusion stabilization terms.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Exchange coarsen/refinement flags set between processors so that we have the correct settings on all ghost cells.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Check if timing output should be written in this timestep, and if so write it.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Check if a checkpoint should be written in this timestep. If so create one. Returns whether a checkpoint was written.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Check if we should do an initial refinement cycle in this timestep. This will only be checked in timestep 0, afterwards the variable pre_refinement_step variable is invalidated, and this function will return without doing refinement. An initial refinement cycle is different from a regular one, because time is not increased. Instead the same timestep is solved using the new mesh. Therefore, only output timing information and postprocessor output if required in the input file. But always output statistics (to have a history of the number of cells in the statistics file). This function returns whether an initial refinement was done.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Check if refinement is requested in this timestep. If so: Refine mesh. The max_refinement_level
might be increased from this time on if this is an additional refinement cycle.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Advance the current time by the given step_size
and update the solution vectors as needed.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Compute the artificial diffusion coefficient value on a cell given the values and gradients of the solution passed as arguments.
This function is implemented in source/simulator/assembly.cc
.

private 
Compute the residual of one advection equation to be used for the artificial diffusion coefficient value on a cell given the values and gradients of the solution passed as arguments.
This function is implemented in source/simulator/assembly.cc
.

private 
Return whether the Stokes matrix depends on the values of the solution at the previous time step. This is the case is the coefficients that appear in the matrix (i.e., the viscosity and, in the case of a compressible model, the density) depend on the solution.
This function exists to ensure that the Stokes matrix is rebuilt in time steps where it may have changed, while we want to save the effort of rebuilding it whenever we don't need to.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Return whether to the best of our knowledge the A block of the Stokes system is symmetric. This is the case for most models, except if additional nonsymmetric terms are added by special assemblers (e.g., the free surface stabilization term).
This function is implemented in source/simulator/helper_functions.cc
.

private 
This function checks that the userselected formulations of the equations are consistent with the other inputs. If an incorrect selection is detected it throws an exception. It for example assures that correct heating terms are selected, and the material model supports the selection of the mass conservation formulation (e.g. incompressible)). If the parameter 'parameters.formulation' is set to 'custom' it only ensures very basic consistency.
This function is implemented in source/simulator/helper_functions.cc
.

private 
This function checks if the default solver and/or material averaging were selected and if so, determines the appropriate solver and/or averaging option.

private 
This function checks that the userselected boundary conditions do not contain contradictions. If an incorrect selection is detected it throws an exception. This for example assures that not both velocity and traction boundary conditions are prescribed at the same boundary, and that no boundary temperatures are prescribed at a periodic boundary.
This function is implemented in source/simulator/helper_functions.cc
.

private 
Computes the initial Newton residual.

private 
This function computes the Eisenstat Walker linear tolerance used for the Newton iterations in the `iterated Advection and Newton Stokes' and `single Advection, iterated Newton Stokes' solver schemes. The Eisenstat and Walker (1996) method is used for determining the linear tolerance of the iteration after the first iteration. The paper gives two preferred choices of computing this tolerance. Both choices are implemented here with the suggested parameter values and safeguards.

private 
This function is called at the end of each time step and writes the statistics object that contains data like the current time, the number of linear solver iterations, and whatever the postprocessors have generated, to disk.
This function is implemented in source/simulator/helper_functions.cc
.

private 
This routine computes the initial (nonlinear) Stokes residual that is needed as a convergence criterion in models with solver schemes that do nonlinear iterations. We calculate it in the same way as the tolerance for the linear solver, using the norm of the pressure RHS for the pressure part and a residual with zero velocity for the velocity part to get the part of the RHS not balanced by the static pressure.
This function is implemented in source/simulator/helper_functions.cc
.

friend 
Definition at line 2180 of file simulator.h.

friend 
Definition at line 2181 of file simulator.h.

friend 
Definition at line 2182 of file simulator.h.

friend 
Definition at line 2183 of file simulator.h.

friend 
Definition at line 2184 of file simulator.h.

friend 
Definition at line 2186 of file simulator.h.

friend 
Definition at line 2187 of file simulator.h.

private 
A member variable that tracks whether we are completely done with initialization and have started the time loop. This variable needs to be the first one that is initialized in the constructor, so that its value correctly tracks the status of the overall object. As a consequence, it has to be the first one declared in this class.
The variable is set to true
just before we start the time stepping loop, but may be temporarily reset to false
if, for example, we are during the initial mesh refinement steps where we start the time loop, but then go back to initialization steps (mesh refinement, interpolation of initial conditions, etc.) before restarting the time loop.
This variable is queried by SimulatorAccess::simulator_is_past_initialization().
Definition at line 420 of file simulator.h.

private 
A member variable that stores, for the current simulation, what functions need to be called in order to assemble linear systems, matrices, and right hand side vectors.
One would probably want this variable to just be a member of type Assemblers::Manager<dim>, but this requires that this type is declared in the current scope, and that would require including <simulator/assemblers/interface.h> which we don't want because it's big. Consequently, we just store a pointer to such an object, and create the object pointed to at the top of set_assemblers().
Definition at line 1102 of file simulator.h.

private 
Definition at line 1843 of file simulator.h.

private 
Unique pointer for an instance of the MeltHandler. This way, if we do not need the machinery for doing melt stuff, we do not even allocate it.
Definition at line 1850 of file simulator.h.

private 
Unique pointer for an instance of the NewtonHandler. This way, if we do not need the machinery for doing Newton stuff, we do not even allocate it.
Definition at line 1857 of file simulator.h.

private 
Definition at line 1859 of file simulator.h.

private 
Definition at line 1861 of file simulator.h.

private 
Unique pointer for an instance of the VolumeOfFluidHandler. This way, if we do not need the machinery for doing volume_of_fluid stuff, we do not even allocate it.
Located here due to needing signals access
Definition at line 1870 of file simulator.h.

private 
Definition at line 1872 of file simulator.h.

private 
Definition at line 1875 of file simulator.h.

private 
This stream will log into the file output/log.txt (used automatically by pcout).
Definition at line 1881 of file simulator.h.

private 
Definition at line 1886 of file simulator.h.

private 
Definition at line 1887 of file simulator.h.

private 
Output stream for logging information. Will only output on processor 0.
Definition at line 1893 of file simulator.h.

private 
An object that stores a bunch of statistics such as the number of linear solver iterations, the time corresponding to each time step, etc, as well as whatever the various postprocessors want to put into it.
This variable is written to disk after every time step, by the Simulator::output_statistics() function.
Definition at line 1904 of file simulator.h.

private 
The following two variables keep track which parts of the statistics object have already been written. This is because the TableHandler class has no way to keep track what it has already written, and so we can not just append the last row of the table to the output file. Rather, we keep track how many bytes we already wrote, and a hash of what they contained, and if these somany bytes have not changed between the previous and current write operation, then we only open the file in 'append' mode to add the new bytes from the last row. If what we would write now has changed from what we wrote back then in the first somany bytes (e.g., because column widths of the table have changed), then we just replace the previous file by the current table contents in their entirety.
Definition at line 1920 of file simulator.h.

private 
Definition at line 1921 of file simulator.h.

mutableprivate 
Definition at line 1923 of file simulator.h.

private 
A timer used to track the current wall time since the last snapshot (or since the program started).
Definition at line 1929 of file simulator.h.

private 
The total wall time that has elapsed up to the last snapshot that was created.
Definition at line 1935 of file simulator.h.

private 
In output_statistics(), where we output the statistics object above, we do the actual writing on a separate thread. This variable is the handle we get for this thread so that we can wait for it to finish, either if we want to write the statistics object for the next thread, or if we want to terminate altogether.
Definition at line 1944 of file simulator.h.

private 
Definition at line 1954 of file simulator.h.

private 
Definition at line 1955 of file simulator.h.

private 
Definition at line 1956 of file simulator.h.

private 
Definition at line 1957 of file simulator.h.

private 
Definition at line 1958 of file simulator.h.

private 
Definition at line 1959 of file simulator.h.

private 
Definition at line 1960 of file simulator.h.

private 
Definition at line 1961 of file simulator.h.

private 
The following two variables are pointers to objects that describe the initial temperature and composition values. The Simulator class itself releases these pointers once they are no longer needed, somewhere during the first time step once it is known that they are no longer needed. However, plugins can have their own shared pointers to these objects, and the lifetime of the objects pointed to is then until the last of these plugins gets deleted.
Definition at line 1973 of file simulator.h.

private 
Definition at line 1974 of file simulator.h.

private 
Definition at line 1976 of file simulator.h.

private 
Definition at line 1991 of file simulator.h.

private 
Definition at line 1992 of file simulator.h.

private 
Definition at line 1993 of file simulator.h.

private 
The worlds holding different sets of particles
Definition at line 1998 of file simulator.h.

private 
Definition at line 2007 of file simulator.h.

private 
Definition at line 2008 of file simulator.h.

private 
Definition at line 2009 of file simulator.h.

private 
Definition at line 2010 of file simulator.h.

private 
Definition at line 2011 of file simulator.h.

private 
Definition at line 2012 of file simulator.h.

private 
Definition at line 2013 of file simulator.h.

private 
Definition at line 2022 of file simulator.h.

private 
Definition at line 2031 of file simulator.h.

private 
Definition at line 2040 of file simulator.h.

private 
Definition at line 2041 of file simulator.h.

private 
Definition at line 2042 of file simulator.h.

private 
Definition at line 2044 of file simulator.h.

private 
Definition at line 2045 of file simulator.h.

private 
Pointer to the Mapping object used by the finite elements when going from the reference cell to the cell in the computational domain. We use a pointer since different mapping objects may be useful. In particular, when the mesh is deformable we use a MappingQ1Eulerian object to describe the mesh deformation, swapping it in for the original MappingQ or MappingCartesian object.
Definition at line 2055 of file simulator.h.

private 
Definition at line 2057 of file simulator.h.

private 
Definition at line 2059 of file simulator.h.

private 
Definition at line 2061 of file simulator.h.

private 
Constraint objects. The first of these describes all constraints that are not time dependent (e.g., hanging nodes, nonormalflux constraints), whereas the second one is initialized at the top of every time step by copying from the first and then adding to it constraints that are time dependent (e.g., time dependent velocity or temperature boundary conditions).
'constraints' is computed in setup_dofs(), 'current_constraints' is done in compute_current_constraints().
Definition at line 2074 of file simulator.h.

private 
Definition at line 2075 of file simulator.h.

private 
A place to store the latest correction computed by normalize_pressure(). We store this so we can undo the correction in denormalize_pressure().
Definition at line 2081 of file simulator.h.

private 
Scaling factor for the pressure as explained in the Kronbichler/Heister/Bangerth paper to ensure that the linear system that results from the Stokes equations is well conditioned.
Definition at line 2088 of file simulator.h.

private 
A variable that determines whether we need to do the correction of the Stokes right hand side vector to ensure that the average divergence is zero. This is necessary for compressible models, but only if there are no in/outflow boundaries.
Definition at line 2096 of file simulator.h.

private 
An object that contains the entries of the system matrix. It has a size equal to the total number of degrees of freedom, but since we typically do not solve for all variables at once, the content of the matrix at any given time is only appropriate for the part of the system we are currently solving.
Definition at line 2116 of file simulator.h.

private 
This vector is used for the weighted BFBT preconditioner. It stores the inverted lumped velocity mass matrix.
Definition at line 2122 of file simulator.h.

private 
An object that contains the entries of preconditioner matrices for the system matrix. It has a size equal to the total number of degrees of freedom, but is only used for the Stokes system (that's the only part of the system where we use a matrix for preconditioning that is different from the matrix we solve). Consequently, the blocks in rows and columns corresponding to temperature or compositional fields are left empty when building the sparsity pattern of this matrix in the Simulator::setup_system_preconditioner() function.
Definition at line 2136 of file simulator.h.

private 
Definition at line 2138 of file simulator.h.

private 
Definition at line 2139 of file simulator.h.

private 
Definition at line 2140 of file simulator.h.

private 
Definition at line 2141 of file simulator.h.

private 
Definition at line 2143 of file simulator.h.

private 
Definition at line 2146 of file simulator.h.

private 
Definition at line 2149 of file simulator.h.

private 
Definition at line 2153 of file simulator.h.

private 
Definition at line 2154 of file simulator.h.

private 
Definition at line 2156 of file simulator.h.

private 
Definition at line 2157 of file simulator.h.

private 
Definition at line 2158 of file simulator.h.

private 
Definition at line 2159 of file simulator.h.

private 
Definition at line 2160 of file simulator.h.

private 
Unique pointer for an instance of the MeshDeformationHandler. this way, if we do not need the machinery for doing mesh deformation stuff, we do not even allocate it.
Definition at line 2173 of file simulator.h.

private 
Unique pointer for the matrixfree Stokes solver
Definition at line 2178 of file simulator.h.