ThermochimicaDataBase< is_nodal > Class Template Reference

User object that performs a Gibbs energy minimization at each node by calling the Thermochimica code. More...

#include <ThermochimicaData.h>

Inheritance diagram for ThermochimicaDataBase< is_nodal >:

Classes
struct	Data

Public Member Functions
	ThermochimicaDataBase (const InputParameters &parameters)
	~ThermochimicaDataBase ()
virtual void	initialize () override
virtual void	execute () override
virtual void	finalize () override
virtual void	threadJoin (const UserObject &) override
void	reinitDataMooseFromTc ()
	Function to get re-initialization data from Thermochimica and save it in member variables of this UserObject. More...
void	reinitDataMooseToTc ()
	Function to load re-initialization data saved in this UserObject back into Thermochimica. More...
const Data &	getNodalData (dof_id_type id) const
const Data &	getElementData (dof_id_type id) const
const Data &	getData (dof_id_type id) const

Static Public Member Functions
static InputParameters	validParams ()

Protected Types
enum	ReinitializationType { ReinitializationType::NONE, ReinitializationType::TIME, ReinitializationType::NODE }
enum	OutputMassUnit { OutputMassUnit::MOLES, OutputMassUnit::FRACTION }
	Mass unit for output species. More...

Protected Member Functions
void	server ()
template<typename T >
void	expect (T expect_msg)
template<typename T >
void	notify (T send_msg)

Protected Attributes
const VariableValue &	_pressure
const VariableValue &	_temperature
const std::size_t	_n_phases
const std::size_t	_n_species
const std::size_t	_n_elements
const std::size_t	_n_vapor_species
const std::size_t	_n_phase_elements
const std::size_t	_n_potentials
std::vector< const VariableValue * >	_el
const ChemicalCompositionAction &	_action
std::vector< unsigned int >	_el_ids
enum ThermochimicaDataBase::ReinitializationType	_reinit
const std::vector< std::string > &	_ph_names
const std::vector< std::string > &	_element_potentials
const std::vector< std::pair< std::string, std::string > > &	_species_phase_pairs
const std::vector< std::pair< std::string, std::string > > &	_vapor_phase_pairs
const std::vector< std::pair< std::string, std::string > > &	_phase_element_pairs
std::unordered_map< dof_id_type, Data >	_data
	Nodal data (Used only for reinitialization) More...
std::vector< MooseWritableVariable * >	_ph
	Writable phase amount variables. More...
std::vector< MooseWritableVariable * >	_sp
	Writable species amount variables. More...
std::vector< MooseWritableVariable * >	_vp
	Writable vapour pressures for each element. More...
std::vector< MooseWritableVariable * >	_el_pot
	Writable chemical potential variables for each element. More...
std::vector< MooseWritableVariable * >	_el_ph
	Writable variable for molar amounts of each element in specified phase. More...
enum ThermochimicaDataBase::OutputMassUnit	_output_mass_unit
int	_socket
	communication socket More...
pid_t	_pid
	child PID More...
dof_id_type *	_shared_dofid_mem
	shared memory pointer for dof_id_type values More...
Real *	_shared_real_mem
	shared memory pointer for Real values More...
dof_id_type	_current_id
const bool	_output_element_potentials
	Element chemical potential output. More...
const bool	_output_vapor_pressures
const bool	_output_element_phases

Detailed Description

template<bool is_nodal>
class ThermochimicaDataBase< is_nodal >

User object that performs a Gibbs energy minimization at each node by calling the Thermochimica code.

This object can only be added through the ChemicalCompositionAction which also sets up the variables for the calculation.

Definition at line 30 of file ThermochimicaData.h.

Member Enumeration Documentation

OutputMassUnit

template<bool is_nodal>

enum ThermochimicaDataBase::OutputMassUnit

strongprotected

Mass unit for output species.

Enumerator
MOLES
FRACTION

Definition at line 134 of file ThermochimicaData.h.

{ MOLES, FRACTION } _output_mass_unit;

ReinitializationType

template<bool is_nodal>

enum ThermochimicaDataBase::ReinitializationType

strongprotected

Enumerator
NONE
TIME
NODE

Definition at line 101 of file ThermochimicaData.h.

{ NONE, TIME, NODE } _reinit;

Constructor & Destructor Documentation

ThermochimicaDataBase()

template<bool is_nodal>

ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase

(

const InputParameters &

parameters

)

Definition at line 77 of file ThermochimicaData.C.

  : ThermochimicaDataBaseParent<is_nodal>(parameters),
    _pressure(coupledValue("pressure")),
    _temperature(coupledValue("temperature")),
    _n_phases(coupledComponents("output_phases")),
    _n_species(coupledComponents("output_species")),
    _n_elements(coupledComponents("elements")),
    _n_vapor_species(coupledComponents("output_vapor_pressures")),
    _n_phase_elements(coupledComponents("output_element_phases")),
    _n_potentials(coupledComponents("output_element_potentials")),
    _el(_n_elements),
    _action(*parameters.getCheckedPointerParam<ChemicalCompositionAction *>(
        "_chemical_composition_action")),
    _el_ids(_action.elementIDs()),
    _reinit(parameters.get<MooseEnum>("reinit_type").getEnum<ReinitializationType>()),
    _ph_names(_action.phases()),
    _element_potentials(_action.elementPotentials()),
    _species_phase_pairs(_action.speciesPhasePairs()),
    _vapor_phase_pairs(_action.vaporPhasePairs()),
    _phase_element_pairs(_action.phaseElementPairs()),
    _output_element_potentials(isCoupled("output_element_potentials")),
    _output_vapor_pressures(isCoupled("output_vapor_pressures")),
    _output_element_phases(isCoupled("output_element_phases")),
    _ph(_n_phases),
    _sp(_n_species),
    _vp(_n_vapor_species),
    _el_pot(_n_potentials),
    _el_ph(_n_phase_elements),
    _output_mass_unit(parameters.get<MooseEnum>("output_species_unit").getEnum<OutputMassUnit>())
{
  ThermochimicaUtils::checkLibraryAvailability(*this);

  if (_el_ids.size() != _n_elements)
    mooseError("Element IDs size does not match number of elements.");
  for (const auto i : make_range(_n_elements))
    _el[i] = &coupledValue("elements", i);

  if (isParamValid("output_phases"))
  {
    if (_ph_names.size() != _n_phases)
      mooseError("Phase names vector size does not match number of phases.");

    for (const auto i : make_range(_n_phases))
      _ph[i] = &writableVariable("output_phases", i);
  }

  if (isParamValid("output_species"))
  {
    if (_species_phase_pairs.size() != _n_species)
      mooseError("Species name vector size does not match number of output species.");

    for (const auto i : make_range(_n_species))
      _sp[i] = &writableVariable("output_species", i);
  }

  if (isParamValid("output_vapor_pressures"))
  {
    if (_vapor_phase_pairs.size() != _n_vapor_species)
      mooseError("Vapor species name vector size does not match number of output vapor species.");

    for (const auto i : make_range(_n_vapor_species))
      _vp[i] = &writableVariable("output_vapor_pressures", i);
  }

  if (isParamValid("output_element_phases"))
  {
    if (_phase_element_pairs.size() != _n_phase_elements)
      mooseError("Element phase vector size does not match number of output elements in phases");

    for (const auto i : make_range(_n_phase_elements))
      _el_ph[i] = &writableVariable("output_element_phases", i);
  }

  if (isParamValid("output_element_potentials"))
  {
    if (_element_potentials.size() != _n_potentials)
      mooseError("Element potentials vector size does not match number of element potentials "
                 "specified for output.");

    for (const auto i : make_range(_n_potentials))
      _el_pot[i] = &writableVariable("output_element_potentials", i);
  }
  // buffer size
  const auto dofid_size = std::max(/* send */ 1, /* receive */ 0);
  const auto real_size =
      std::max(/* send */ 2 + _n_elements,
               /* receive */ _n_phases + _n_species + _element_potentials.size() +
                   _n_vapor_species + _n_phase_elements);

  // set up shared memory for communication with child process
  auto shared_mem =
      static_cast<std::byte *>(mmap(nullptr,
                                    dofid_size * sizeof(dof_id_type) + real_size * sizeof(Real),
                                    PROT_READ | PROT_WRITE,
                                    MAP_ANONYMOUS | MAP_SHARED,
                                    -1 /* fd */,
                                    0 /* offset */));
  if (shared_mem == MAP_FAILED)
    mooseError("Failed to allocate shared memory for thermochimica IPC.");

  // set up buffer partitions
  _shared_dofid_mem = reinterpret_cast<dof_id_type *>(shared_mem);
  _shared_real_mem = reinterpret_cast<Real *>(shared_mem + dofid_size * sizeof(dof_id_type));

  // set up a bidirectional communication socket
  int sockets[2];
  if (socketpair(AF_UNIX, SOCK_STREAM, 0, sockets) < 0)
    mooseError("Failed to create socketpair for thermochimica IPC.");

  // fork child process that will manage thermochimica calls
  _pid = fork();
  if (_pid < 0)
    mooseError("Fork failed for thermochimica library.");
  if (_pid == 0)
  {
    // here we are in the child process
    _socket = sockets[0];
    // clean exit upon SIGTERM (mainly for Civet code coverage)
    signal(SIGTERM, ThermochimicaDataBase_handler);

#ifdef THERMOCHIMICA_ENABLED
    // Initialize database in Thermochimica
    if (isParamValid("thermofile"))
    {
      const auto thermo_file = this->template getParam<FileName>("thermofile");

      if (thermo_file.length() > 1024)
        this->paramError("thermofile",
                         "Path exceeds Thermochimica's maximal permissible length of 1024 with ",
                         thermo_file.length(),
                         " characters: ",
                         thermo_file);

      Thermochimica::setThermoFilename(thermo_file);

      // Read in thermodynamics model, only once
      Thermochimica::parseThermoFile();

      const auto idbg = Thermochimica::checkInfoThermo();
      if (idbg != 0)
        this->paramError("thermofile", "Thermochimica data file cannot be parsed. ", idbg);
    }
#endif

    while (true)
      server();
  }

  // parent process continues here
  _socket = sockets[1];
}

~ThermochimicaDataBase()

template<bool is_nodal>

ThermochimicaDataBase< is_nodal >::~ThermochimicaDataBase

(

)

Definition at line 230 of file ThermochimicaData.C.

{
  if (_pid)
    kill(_pid, SIGTERM);
}

Member Function Documentation

execute()

template<bool is_nodal>

void ThermochimicaDataBase< is_nodal >::execute ( )

overridevirtual

Definition at line 269 of file ThermochimicaData.C.

{
  // either one DOF at a node or (currently) one DOF for constant monomial FV!
  // This is enforced automatically by the ChemicalComposition action, which creates the correct
  // variables.
  const unsigned int qp = 0;

  // store current dofID
  if constexpr (is_nodal)
    _shared_dofid_mem[0] = this->_current_node->id();
  else
    _shared_dofid_mem[0] = this->_current_elem->id();

  // store all required data in shared memory
  _shared_real_mem[0] = _temperature[qp];
  _shared_real_mem[1] = _pressure[qp];
  for (const auto i : make_range(_n_elements))
    _shared_real_mem[2 + i] = (*_el[i])[qp];

  // message child process to trigger calculation
  notify('A');

  // and wait for the child process to signal end of calculation
  expect('B');

  // unpack data from shared memory
  std::size_t idx = 0;

  for (const auto i : make_range(_n_phases))
    _ph[i]->setDofValue(_shared_real_mem[idx++], qp);

  for (const auto i : make_range(_n_species))
    _sp[i]->setDofValue(_shared_real_mem[idx++], qp);

  if (_output_element_potentials)
    for (const auto i : index_range(_element_potentials))
      _el_pot[i]->setDofValue(_shared_real_mem[idx++], qp);

  if (_output_vapor_pressures)
    for (const auto i : make_range(_n_vapor_species))
      _vp[i]->setDofValue(_shared_real_mem[idx++], qp);

  if (_output_element_phases)
    for (const auto i : make_range(_n_phase_elements))
      _el_ph[i]->setDofValue(_shared_real_mem[idx++], qp);
}

expect()

template<bool is_nodal>

template<typename T >

void ThermochimicaDataBase< is_nodal >::expect ( T  expect_msg )

protected

Definition at line 245 of file ThermochimicaData.C.

{
  T msg;
  while (read(_socket, &msg, sizeof(T)) == 0)
  {
    if (errno == EAGAIN)
      continue;
    mooseError("Read error waiting for '", expect_msg, "' ", errno, ' ', strerror(errno));
  }
  if (msg != expect_msg)
    mooseError("Expected '", expect_msg, "' but received '", msg, "'");
}

finalize()

template<bool is_nodal>

virtual void ThermochimicaDataBase< is_nodal >::finalize ( )

inlineoverridevirtual

Definition at line 39 of file ThermochimicaData.h.

{}

getData()

template<bool is_nodal>

const ThermochimicaDataBase< is_nodal >::Data & ThermochimicaDataBase< is_nodal >::getData

(

dof_id_type

id

)

const

Definition at line 607 of file ThermochimicaData.C.

{
  const auto it = _data.find(id);
  if (it == _data.end())
  {
    if constexpr (is_nodal)
      mooseError("Unable to look up data for node ", id);
    else
      mooseError("Unable to look up data for element ", id);
  }
  return it->second;
}

getElementData()

template<bool is_nodal>

const ThermochimicaDataBase< is_nodal >::Data & ThermochimicaDataBase< is_nodal >::getElementData

(

dof_id_type

id

)

const

Definition at line 598 of file ThermochimicaData.C.

{
  if constexpr (is_nodal)
    mooseError("Requesting per element data from a nodal object.");
  return this->getData(element_id);
}

getNodalData()

template<bool is_nodal>

const ThermochimicaDataBase< is_nodal >::Data & ThermochimicaDataBase< is_nodal >::getNodalData

(

dof_id_type

id

)

const

Definition at line 589 of file ThermochimicaData.C.

{
  if constexpr (!is_nodal)
    mooseError("Requesting nodal data from an element object.");
  return this->getData(node_id);
}

initialize()

template<bool is_nodal>

void ThermochimicaDataBase< is_nodal >::initialize ( )

overridevirtual

Definition at line 238 of file ThermochimicaData.C.

{
}

notify()

template<bool is_nodal>

template<typename T >

void ThermochimicaDataBase< is_nodal >::notify ( T  send_msg )

protected

Definition at line 261 of file ThermochimicaData.C.

{
  if (write(_socket, &send_msg, sizeof(T)) != sizeof(T))
    mooseError("Failed to notify thermochimica library child process.");
}

reinitDataMooseFromTc()

template<bool is_nodal>

void ThermochimicaDataBase< is_nodal >::reinitDataMooseFromTc

(

)

Function to get re-initialization data from Thermochimica and save it in member variables of this UserObject.

Definition at line 525 of file ThermochimicaData.C.

{
#ifdef THERMOCHIMICA_ENABLED
  auto & d = _data[_current_id];

  if (_reinit != ReinitializationType::NONE)
  {
    Thermochimica::saveReinitData();
    auto data = Thermochimica::getReinitData();

    if (_reinit == ReinitializationType::TIME)
    {
      d._assemblage = std::move(data.assemblage);
      d._moles_phase = std::move(data.molesPhase);
      d._element_potential = std::move(data.elementPotential);
      d._chemical_potential = std::move(data.chemicalPotential);
      d._mol_fraction = std::move(data.moleFraction);
      d._elements_used = std::move(data.elementsUsed);
      d._reinit_available = data.reinitAvailable;
    }
  }
#endif
}

reinitDataMooseToTc()

template<bool is_nodal>

void ThermochimicaDataBase< is_nodal >::reinitDataMooseToTc

(

)

Function to load re-initialization data saved in this UserObject back into Thermochimica.

Definition at line 551 of file ThermochimicaData.C.

{
#ifdef THERMOCHIMICA_ENABLED
  // Tell Thermochimica whether a re-initialization is requested for this calculation
  switch (_reinit)
  {
    case ReinitializationType::NONE:
      Thermochimica::setReinitRequested(false);
      break;
    default:
      Thermochimica::setReinitRequested(true);
  }
  // If we have re-initialization data and want a re-initialization, then
  // load data into Thermochimica
  auto it = _data.find(_current_id);

  if (it != _data.end() &&
      _reinit == ReinitializationType::TIME) // If doing previous timestep reinit
  {
    auto & d = it->second;
    if (d._reinit_available)
    {
      Thermochimica::resetReinit();
      Thermochimica::ReinitializationData data;
      data.assemblage = d._assemblage;
      data.molesPhase = d._moles_phase;
      data.elementPotential = d._element_potential;
      data.chemicalPotential = d._chemical_potential;
      data.moleFraction = d._mol_fraction;
      data.elementsUsed = d._elements_used;
      Thermochimica::setReinitData(data);
    }
  }
#endif
}

server()

template<bool is_nodal>

void ThermochimicaDataBase< is_nodal >::server ( )

protected

Definition at line 318 of file ThermochimicaData.C.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

{
  // wait for message from parent process
  expect('A');

#ifdef THERMOCHIMICA_ENABLED
  // fetch data from shared memory
  _current_id = _shared_dofid_mem[0];

  auto temperature = _shared_real_mem[0];
  auto pressure = _shared_real_mem[1];

  // Set temperature and pressure for thermochemistry solver
  Thermochimica::setTemperaturePressure(temperature, pressure);

  // Reset all element masses to 0
  Thermochimica::setElementMass(0, 0.0);

  // Set element masses
  for (const auto i : make_range(_n_elements))
    Thermochimica::setElementMass(_el_ids[i], _shared_real_mem[2 + i]);

  // Optionally ask for a re-initialization (if reinit_requested == true)
  reinitDataMooseToTc();

  // Calculate thermochemical equilibrium
  Thermochimica::thermochimica();

  // Check for error status
  auto idbg = Thermochimica::checkInfoThermo();
  if (idbg != 0)
    // error out for now, but we should send a code to the parent process
    mooseError("Thermochimica error ", idbg);

  // Save data for future reinits
  reinitDataMooseFromTc();

  // Get requested phase indices if phase concentration output was requested
  // i.e. if output_phases is coupled
  auto moles_phase = Thermochimica::getMolesPhase();

  std::size_t idx = 0;

  for (const auto i : make_range(_n_phases))
  {
    // Is this maybe constant? No it isn't for now
    auto [index, idbg] = Thermochimica::getPhaseIndex(_ph_names[i]);
    if (idbg != 0)
      mooseError("Failed to get index of phase '", _ph_names[i], "'");
    // Convert from 1-based (fortran) to 0-based (c++) indexing
    if (index - 1 < 0)
      _shared_real_mem[idx] = 0.0;
    else
      _shared_real_mem[idx] = moles_phase[index - 1];
    idx++;
  }

  auto db_phases = Thermochimica::getPhaseNamesSystem();
  auto getSpeciesMoles =
      [this, moles_phase, db_phases](const std::string phase,
                                     const std::string species) -> std::pair<double, int>
  {
    Real value = 0.0;
    int code = 0;

    auto [index, idbg] = Thermochimica::getPhaseIndex(phase);

    if (Thermochimica::isPhaseMQM(
            std::distance(db_phases.begin(), std::find(db_phases.begin(), db_phases.end(), phase))))
    {
      auto [fraction, idbg] = Thermochimica::getMqmqaPairMolFraction(phase, species);

      switch (_output_mass_unit)
      {
        case OutputMassUnit::FRACTION:
        {
          value = fraction;
          code = idbg;
          break;
        }
        case OutputMassUnit::MOLES:
        {
          auto [molesPair, idbgPair] = Thermochimica::getMqmqaMolesPairs(phase);
          value = molesPair * fraction;
          code = idbg + idbgPair;
          break;
        }
        default:
          break;
      }
    }
    else
    {
      auto [fraction, idbg] = Thermochimica::getOutputMolSpeciesPhase(phase, species);
      switch (_output_mass_unit)
      {
        case OutputMassUnit::FRACTION:
        {
          value = fraction;
          code = idbg;
          break;
        }
        case OutputMassUnit::MOLES:
        {
          value = index >= 1 ? moles_phase[index - 1] * fraction : 0.0;
          code = idbg;
          break;
        }
        default:
          break;
      }
    }
    return {value, code};
  };

  for (const auto i : make_range(_n_species))
  {
    auto [fraction, idbg] = getSpeciesMoles(
        _species_phase_pairs[i].first,
        _species_phase_pairs[i].second); // can we somehow use IDs instead of strings here?

    if (idbg == 0)
      _shared_real_mem[idx] = fraction;
    else if (idbg == 1)
      _shared_real_mem[idx] = 0.0;
#ifndef NDEBUG
    else
      mooseError("Failed to get phase speciation for phase '",
                 _species_phase_pairs[i].first,
                 "' and species '",
                 _species_phase_pairs[i].second,
                 "'. Thermochimica returned ",
                 idbg);
#endif
    idx++;
  }

  if (_output_element_potentials)
    for (const auto i : index_range(_element_potentials))
    {
      auto [potential, idbg] = Thermochimica::getOutputChemPot(_element_potentials[i]);
      if (idbg == 0)
        _shared_real_mem[idx] = potential;
      else if (idbg == 1)
        // element not present, just leave this at 0 for now
        _shared_real_mem[idx] = 0.0;
#ifndef NDEBUG
      else if (idbg == -1)
        mooseError("Failed to get element potential for element '",
                   _element_potentials[i],
                   "'. Thermochimica returned ",
                   idbg);
#endif
      idx++;
    }

  if (_output_vapor_pressures)
    for (const auto i : make_range(_n_vapor_species))
    {
      auto [fraction, moles, idbg] =
          Thermochimica::getOutputMolSpecies(_vapor_phase_pairs[i].second);
      libmesh_ignore(moles);

      if (idbg == 0)
        _shared_real_mem[idx] = fraction * pressure;
      else if (idbg == 1)
        _shared_real_mem[idx] = 0.0;
#ifndef NDEBUG
      else
        mooseError("Failed to get vapor pressure for phase '",
                   _vapor_phase_pairs[i].first,
                   "' and species '",
                   _vapor_phase_pairs[i].second,
                   "'. Thermochimica returned ",
                   idbg);
#endif
      idx++;
    }

  if (_output_element_phases)
    for (const auto i : make_range(_n_phase_elements))
    {
      auto [moles, idbg] = Thermochimica::getElementMolesInPhase(_phase_element_pairs[i].second,
                                                                 _phase_element_pairs[i].first);

      if (idbg == 0)
        _shared_real_mem[idx] = moles;
      else if (idbg == 1)
        _shared_real_mem[idx] = 0.0;
#ifndef NDEBUG
      else
        mooseError("Failed to get moles of element '",
                   _phase_element_pairs[i].second,
                   "' in phase '",
                   _phase_element_pairs[i].first,
                   "'. Thermochimica returned ",
                   idbg);
#endif
      idx++;
    }
#endif
  // Send message back to parent process
  notify('B');
}

threadJoin()

template<bool is_nodal>

virtual void ThermochimicaDataBase< is_nodal >::threadJoin ( const UserObject &  )

inlineoverridevirtual

Definition at line 40 of file ThermochimicaData.h.

{}

validParams()

template<bool is_nodal>

InputParameters ThermochimicaDataBase< is_nodal >::validParams ( )

static

Definition at line 31 of file ThermochimicaData.C.

{
  InputParameters params = ThermochimicaDataBaseParent<is_nodal>::validParams();

  if constexpr (is_nodal)
    ThermochimicaUtils::addClassDescription(
        params, "Provides access to Thermochimica-calculated data at nodes.");
  else
    ThermochimicaUtils::addClassDescription(
        params, "Provides access to Thermochimica-calculated data at elements.");

  params.addRequiredCoupledVar("elements", "Amounts of elements");
  params.addRequiredCoupledVar("temperature", "Coupled temperature");
  params.addCoupledVar("pressure", 1.0, "Pressure");

  MooseEnum reinit_type("none time nodal", "nodal");
  params.addParam<MooseEnum>(
      "reinit_type", reinit_type, "Reinitialization scheme to use with Thermochimica");

  params.addCoupledVar("output_element_potentials", "Chemical potentials of elements");
  params.addCoupledVar("output_phases", "Amounts of phases to be output");
  params.addCoupledVar("output_species", "Amounts of species to be output");
  params.addCoupledVar("output_vapor_pressures", "Vapour pressures of species to be output");
  params.addCoupledVar("output_element_phases",
                       "Elements whose molar amounts in specific phases are requested");

  MooseEnum mUnit_op("mole_fraction moles", "moles");
  params.addParam<MooseEnum>(
      "output_species_unit", mUnit_op, "Mass unit for output species: mole_fractions or moles");

  if constexpr (is_nodal)
    params.set<bool>("unique_node_execute") = true;

  params.addPrivateParam<ChemicalCompositionAction *>("_chemical_composition_action");
  params.addParam<FileName>("thermofile",
                            "Thermodynamic file to be used for Thermochimica calculations");
  return params;
}

Member Data Documentation

_action

template<bool is_nodal>

const ChemicalCompositionAction& ThermochimicaDataBase< is_nodal >::_action

protected

Definition at line 97 of file ThermochimicaData.h.

_current_id

template<bool is_nodal>

dof_id_type ThermochimicaDataBase< is_nodal >::_current_id

protected

Definition at line 149 of file ThermochimicaData.h.

_data

template<bool is_nodal>

std::unordered_map<dof_id_type, Data> ThermochimicaDataBase< is_nodal >::_data

protected

Nodal data (Used only for reinitialization)

Definition at line 110 of file ThermochimicaData.h.

_el

template<bool is_nodal>

std::vector<const VariableValue *> ThermochimicaDataBase< is_nodal >::_el

protected

Definition at line 95 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_el_ids

template<bool is_nodal>

std::vector<unsigned int> ThermochimicaDataBase< is_nodal >::_el_ids

protected

Definition at line 98 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_el_ph

template<bool is_nodal>

std::vector<MooseWritableVariable *> ThermochimicaDataBase< is_nodal >::_el_ph

protected

Writable variable for molar amounts of each element in specified phase.

Definition at line 131 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_el_pot

template<bool is_nodal>

std::vector<MooseWritableVariable *> ThermochimicaDataBase< is_nodal >::_el_pot

protected

Writable chemical potential variables for each element.

Definition at line 128 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_element_potentials

template<bool is_nodal>

const std::vector<std::string>& ThermochimicaDataBase< is_nodal >::_element_potentials

protected

Definition at line 104 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_n_elements

template<bool is_nodal>

const std::size_t ThermochimicaDataBase< is_nodal >::_n_elements

protected

Definition at line 90 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_n_phase_elements

template<bool is_nodal>

const std::size_t ThermochimicaDataBase< is_nodal >::_n_phase_elements

protected

Definition at line 92 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_n_phases

template<bool is_nodal>

const std::size_t ThermochimicaDataBase< is_nodal >::_n_phases

protected

Definition at line 88 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_n_potentials

template<bool is_nodal>

const std::size_t ThermochimicaDataBase< is_nodal >::_n_potentials

protected

Definition at line 93 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_n_species

template<bool is_nodal>

const std::size_t ThermochimicaDataBase< is_nodal >::_n_species

protected

Definition at line 89 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_n_vapor_species

template<bool is_nodal>

const std::size_t ThermochimicaDataBase< is_nodal >::_n_vapor_species

protected

Definition at line 91 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_output_element_phases

template<bool is_nodal>

const bool ThermochimicaDataBase< is_nodal >::_output_element_phases

protected

Definition at line 115 of file ThermochimicaData.h.

_output_element_potentials

template<bool is_nodal>

const bool ThermochimicaDataBase< is_nodal >::_output_element_potentials

protected

Element chemical potential output.

Definition at line 113 of file ThermochimicaData.h.

_output_mass_unit

template<bool is_nodal>

enum ThermochimicaDataBase::OutputMassUnit ThermochimicaDataBase< is_nodal >::_output_mass_unit

protected

_output_vapor_pressures

template<bool is_nodal>

const bool ThermochimicaDataBase< is_nodal >::_output_vapor_pressures

protected

Definition at line 114 of file ThermochimicaData.h.

_ph

template<bool is_nodal>

std::vector<MooseWritableVariable *> ThermochimicaDataBase< is_nodal >::_ph

protected

Writable phase amount variables.

Definition at line 119 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_ph_names

template<bool is_nodal>

const std::vector<std::string>& ThermochimicaDataBase< is_nodal >::_ph_names

protected

Definition at line 103 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_phase_element_pairs

template<bool is_nodal>

const std::vector<std::pair<std::string, std::string> >& ThermochimicaDataBase< is_nodal >::_phase_element_pairs

protected

Definition at line 107 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_pid

template<bool is_nodal>

pid_t ThermochimicaDataBase< is_nodal >::_pid

protected

child PID

Definition at line 140 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_pressure

template<bool is_nodal>

const VariableValue& ThermochimicaDataBase< is_nodal >::_pressure

protected

Definition at line 85 of file ThermochimicaData.h.

_reinit

template<bool is_nodal>

enum ThermochimicaDataBase::ReinitializationType ThermochimicaDataBase< is_nodal >::_reinit

protected

_shared_dofid_mem

template<bool is_nodal>

dof_id_type* ThermochimicaDataBase< is_nodal >::_shared_dofid_mem

protected

shared memory pointer for dof_id_type values

Definition at line 143 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_shared_real_mem

template<bool is_nodal>

Real* ThermochimicaDataBase< is_nodal >::_shared_real_mem

protected

shared memory pointer for Real values

Definition at line 146 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_socket

template<bool is_nodal>

int ThermochimicaDataBase< is_nodal >::_socket

protected

communication socket

Definition at line 137 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_sp

template<bool is_nodal>

std::vector<MooseWritableVariable *> ThermochimicaDataBase< is_nodal >::_sp

protected

Writable species amount variables.

Definition at line 122 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_species_phase_pairs

template<bool is_nodal>

const std::vector<std::pair<std::string, std::string> >& ThermochimicaDataBase< is_nodal >::_species_phase_pairs

protected

Definition at line 105 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_temperature

template<bool is_nodal>

const VariableValue& ThermochimicaDataBase< is_nodal >::_temperature

protected

Definition at line 86 of file ThermochimicaData.h.

_vapor_phase_pairs

template<bool is_nodal>

const std::vector<std::pair<std::string, std::string> >& ThermochimicaDataBase< is_nodal >::_vapor_phase_pairs

protected

Definition at line 106 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

_vp

template<bool is_nodal>

std::vector<MooseWritableVariable *> ThermochimicaDataBase< is_nodal >::_vp

protected

Writable vapour pressures for each element.

Definition at line 125 of file ThermochimicaData.h.

Referenced by ThermochimicaDataBase< is_nodal >::ThermochimicaDataBase().

---

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

• chemical_reactions/include/userobjects/ThermochimicaData.h
• chemical_reactions/src/userobjects/ThermochimicaData.C