ReadExodusMeshVars Class Reference

Utility function to read a single variable off an Exodus mesh for optimization problem This class will read initial conditions and bounds from an exodus file and make sure they have the same order in the parameter reporter between the main and subapp when using ParameterMeshOptimization. More...

#include <ReadExodusMeshVars.h>

Public Member Functions
	ReadExodusMeshVars (const libMesh::FEType &param_type, const std::string &exodus_mesh, const std::string var_name)
std::vector< Real >	getParameterValues (const unsigned int timestep) const
	Initializes parameter data and sets bounds in the main optmiization application getParameterValues is only used by ParameterMeshOptimization. More...

Private Attributes
libMesh::Parallel::Communicator	_communicator
libMesh::ReplicatedMesh	_mesh
std::unique_ptr< libMesh::EquationSystems >	_eq
libMesh::System *	_sys
std::unique_ptr< libMesh::ExodusII_IO >	_exodusII_io
const std::string	_var_name
	variable name read from Exodus mesh More...

Detailed Description

Utility function to read a single variable off an Exodus mesh for optimization problem This class will read initial conditions and bounds from an exodus file and make sure they have the same order in the parameter reporter between the main and subapp when using ParameterMeshOptimization.

Definition at line 30 of file ReadExodusMeshVars.h.

Constructor & Destructor Documentation

ReadExodusMeshVars()

ReadExodusMeshVars::ReadExodusMeshVars	(	const libMesh::FEType &	param_type,
		const std::string &	exodus_mesh,
		const std::string	var_name
	)

Definition at line 22 of file ReadExodusMeshVars.C.

  : _communicator(MPI_COMM_SELF), _mesh(_communicator), _var_name(var_name)
{
  _mesh.allow_renumbering(false);
  _mesh.prepare_for_use();
  _exodusII_io = std::make_unique<ExodusII_IO>(_mesh);
  _exodusII_io->read(exodus_mesh);
  _mesh.read(exodus_mesh);
  // Create system to store parameter values
  _eq = std::make_unique<EquationSystems>(_mesh);
  _sys = &_eq->add_system<ExplicitSystem>("_reading_exodus_mesh_var");

  // Make Exodus vars for equation system
  const std::vector<std::string> & all_nodal(_exodusII_io->get_nodal_var_names());
  const std::vector<std::string> & all_elemental(_exodusII_io->get_elem_var_names());

  std::string nodal_variable;
  std::string elemental_variable;

  if (std::find(all_nodal.begin(), all_nodal.end(), _var_name) != all_nodal.end())
    nodal_variable = _var_name;
  if (std::find(all_elemental.begin(), all_elemental.end(), _var_name) != all_elemental.end())
    elemental_variable = _var_name;

  // Add the parameter variable to system
  // All parameters in a group will be the same type, only one of these loops will do anything
  // If it tries to add the wrong type, will throw a libmesh error
  if (!nodal_variable.empty())
    _sys->add_variable(_var_name, param_type);
  if (!elemental_variable.empty())
    _sys->add_variable(_var_name, param_type);
  // Initialize the equations systems
  _eq->init();

  if (nodal_variable.empty() && elemental_variable.empty())
  {
    std::string out("\n  Parameter Requested: " + var_name);
    out += "\n  Exodus Nodal Variables: ";
    for (const auto & var : all_nodal)
      out += var + " ";
    out += "\n  Exodus Elemental Variables: ";
    for (const auto & var : all_elemental)
      out += var + " ";
    mooseError("Exodus file did not contain the parameter name being intitialized.", out);
  }
}

Member Function Documentation

getParameterValues()

std::vector< Real > ReadExodusMeshVars::getParameterValues

(

const unsigned int

timestep

)

const

Initializes parameter data and sets bounds in the main optmiization application getParameterValues is only used by ParameterMeshOptimization.

Parameters

timestep

timestep to read variable off mesh

Returns

vector of variables read off mesh at timestep

Definition at line 72 of file ReadExodusMeshVars.C.

Referenced by ParameterMeshOptimization::parseExodusData().

{
  // get the exodus variable and put it into the equation system.
  unsigned int step_to_read = _exodusII_io->get_num_time_steps();
  if (time_step <= step_to_read)
    step_to_read = time_step;
  else if (time_step != std::numeric_limits<unsigned int>::max())
    mooseError("Invalid value passed as \"time_step\". Expected a valid integer "
               "less than ",
               _exodusII_io->get_num_time_steps(),
               ", received ",
               time_step);

  // Store Exodus variable on the equation system.
  // This will give it the same order as other functions reading variables from the same exodus mesh
  const std::vector<std::string> & all_nodal(_exodusII_io->get_nodal_var_names());
  const std::vector<std::string> & all_elemental(_exodusII_io->get_elem_var_names());
  // determine what kind of variable you are trying to read from mesh
  if (std::find(all_nodal.begin(), all_nodal.end(), _var_name) != all_nodal.end())
    _exodusII_io->copy_nodal_solution(*_sys, _var_name, _var_name, step_to_read);
  else if (std::find(all_elemental.begin(), all_elemental.end(), _var_name) != all_elemental.end())
    _exodusII_io->copy_elemental_solution(*_sys, _var_name, _var_name, step_to_read);

  // Update the equations systems
  _sys->update();

  // Now read the Exodus variable from the equation system into a vector for the reporter
  const unsigned short int var_id = _sys->variable_number(_var_name);
  std::set<dof_id_type> var_indices;
  _sys->local_dof_indices(var_id, var_indices); // Everything is local so this is fine
  std::vector<dof_id_type> var_indices_vector(var_indices.begin(), var_indices.end());

  std::vector<Real> parameter_values;
  _sys->solution->localize(parameter_values, var_indices_vector);
  return parameter_values;
}

Member Data Documentation

_communicator

libMesh::Parallel::Communicator ReadExodusMeshVars::_communicator

private

Definition at line 45 of file ReadExodusMeshVars.h.

_eq

std::unique_ptr<libMesh::EquationSystems> ReadExodusMeshVars::_eq

private

Definition at line 47 of file ReadExodusMeshVars.h.

Referenced by ReadExodusMeshVars().

_exodusII_io

std::unique_ptr<libMesh::ExodusII_IO> ReadExodusMeshVars::_exodusII_io

private

Definition at line 49 of file ReadExodusMeshVars.h.

Referenced by getParameterValues(), and ReadExodusMeshVars().

_mesh

libMesh::ReplicatedMesh ReadExodusMeshVars::_mesh

private

Definition at line 46 of file ReadExodusMeshVars.h.

Referenced by ReadExodusMeshVars().

_sys

libMesh::System* ReadExodusMeshVars::_sys

private

Definition at line 48 of file ReadExodusMeshVars.h.

Referenced by getParameterValues(), and ReadExodusMeshVars().

_var_name

const std::string ReadExodusMeshVars::_var_name

private

variable name read from Exodus mesh

Definition at line 52 of file ReadExodusMeshVars.h.

Referenced by getParameterValues(), and ReadExodusMeshVars().

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The documentation for this class was generated from the following files:

• optimization/include/utils/ReadExodusMeshVars.h
• optimization/src/utils/ReadExodusMeshVars.C