AddCoupledSolidKinSpeciesAction::AddCoupledSolidKinSpeciesAction(const InputParameters & params)
: Action(params),
_primary_species(getParam<std::vector<NonlinearVariableName>>("primary_species")),
_secondary_species(getParam<std::vector<AuxVariableName>>("secondary_species")),
_kinetic_species_involved(_primary_species.size()),
_weights(_primary_species.size()),
_input_reactions(getParam<std::string>("kin_reactions")),
_logk(getParam<std::vector<Real>>("log10_keq")),
_r_area(getParam<std::vector<Real>>("specific_reactive_surface_area")),
_ref_kconst(getParam<std::vector<Real>>("kinetic_rate_constant")),
_e_act(getParam<std::vector<Real>>("activation_energy")),
_gas_const(getParam<Real>("gas_constant")),
_ref_temp(getParam<std::vector<Real>>("reference_temperature")),
_sys_temp(getParam<std::vector<VariableName>>("system_temperature"))
{
// Note: as the reaction syntax has changed, check to see if the old syntax has
// been used and throw an informative error. The number of = signs should be one
// more than the number of commas, while the smallest number of spaces possible is 2
bool old_syntax = false;
if (std::count(_input_reactions.begin(), _input_reactions.end(), '=') !=
std::count(_input_reactions.begin(), _input_reactions.end(), ',') + 1)
old_syntax = true;
if (std::count(_input_reactions.begin(), _input_reactions.end(), ' ') < 2)
old_syntax = true;
if (old_syntax)
mooseError("Old solid kinetic reaction syntax present.\nReactions should now be comma "
"separated, and must have spaces between species and +/-/= operators.\n"
"See #9972 for details");
// Parse the kinetic reactions
pcrecpp::RE re_reactions("(.+?)" // A single reaction (any character until the comma delimiter)
"(?:,\\s*|$)" // comma or end of string
,
pcrecpp::RE_Options().set_extended(true));
pcrecpp::RE re_terms("(\\S+)");
pcrecpp::RE re_coeff_and_species("(?: \\(? (.*?) \\)? )" // match the leading coefficent
"([A-Za-z].*)" // match the species
,
pcrecpp::RE_Options().set_extended(true));
pcrecpp::StringPiece input(_input_reactions);
pcrecpp::StringPiece single_reaction, term;
std::string single_reaction_str;
// Parse reaction network to extract each individual reaction
while (re_reactions.FindAndConsume(&input, &single_reaction_str))
_reactions.push_back(single_reaction_str);
_num_reactions = _reactions.size();
if (_num_reactions == 0)
mooseError("No solid kinetic reaction provided!");
// Start parsing each reaction
for (unsigned int i = 0; i < _num_reactions; ++i)
{
single_reaction = _reactions[i];
// Capture all of the terms
std::string species, coeff_str;
Real coeff;
int sign = 1;
bool secondary = false;
std::vector<Real> local_stos;
std::vector<VariableName> local_species_list;
// Find every single term in this reaction (species and operators)
while (re_terms.FindAndConsume(&single_reaction, &term))
{
// Separating the stoichiometric coefficients from species
if (re_coeff_and_species.PartialMatch(term, &coeff_str, &species))
{
if (coeff_str.length())
coeff = std::stod(coeff_str);
else
coeff = 1.0;
coeff *= sign;
if (secondary)
_solid_kinetic_species.push_back(species);
else
{
local_stos.push_back(coeff);
local_species_list.push_back(species);
}
}
// Finding the operators and assign value of -1.0 to "-" sign
else if (term == "+" || term == "=" || term == "-")
{
if (term == "-")
{
sign = -1;
term = "+";
}
if (term == "=")
secondary = true;
}
else
mooseError("Error parsing term: ", term.as_string());
}
_stos.push_back(local_stos);
_primary_species_involved.push_back(local_species_list);
}
// Start picking out primary species and coupled primary species and assigning
// corresponding stoichiomentric coefficients
for (unsigned int i = 0; i < _primary_species.size(); ++i)
for (unsigned int j = 0; j < _num_reactions; ++j)
{
for (unsigned int k = 0; k < _primary_species_involved[j].size(); ++k)
if (_primary_species_involved[j][k] == _primary_species[i])
{
_weights[i].push_back(_stos[j][k]);
_kinetic_species_involved[i].push_back(_solid_kinetic_species[j]);
}
}
// Print out details of the solid kinetic reactions to the console
_console << "Solid kinetic reactions:\n";
for (unsigned int i = 0; i < _num_reactions; ++i)
_console << " Reaction " << i + 1 << ": " << _reactions[i] << "\n";
_console << "\n";
// Check that all secondary species read from the reaction network have been added
// as AuxVariables. Note: can't sort the _solid_kinetic_species vector as it throws
// out the species and coefficient vectors so use std::is_permutation
if (!std::is_permutation(
_secondary_species.begin(), _secondary_species.end(), _solid_kinetic_species.begin()))
mooseError("All solid kinetic species must be added as secondary species");
// Check that the size of property vectors is equal to the number of reactions
if (_logk.size() != _num_reactions)
mooseError("The number of values entered for log10_keq is not equal to the number of solid "
"kinetic reactions");
if (_r_area.size() != _num_reactions)
mooseError("The number of values entered for specific_reactive_surface_area is not equal to "
"the number of solid kinetic reactions");
if (_ref_kconst.size() != _num_reactions)
mooseError("The number of values entered for kinetic_rate_constant is not equal to the number "
"of solid kinetic reactions");
if (_e_act.size() != _num_reactions)
mooseError("The number of values entered for activation_energy is not equal to the number of "
"solid kinetic reactions");
if (_ref_temp.size() != _num_reactions)
mooseError("The number of values entered for reference_temperature is not equal to the number "
"of solid kinetic reactions");
}
void
AddCoupledEqSpeciesKernelsAction::act()
{
// Reading primary species and reaction network from the input file
std::vector<NonlinearVariableName> vars =
getParam<std::vector<NonlinearVariableName>>("primary_species");
std::string reactions = getParam<std::string>("reactions");
// Getting ready for the parsing system
pcrecpp::RE re_reactions(
"(.*?)" // the reaction network (any character until the equilibrium coefficient appears)
"\\s" // word boundary
"(" // start capture
"-?" // optional minus sign
"\\d+(?:\\.\\d*)?" // digits followed by optional decimal and more 0 or more digits
")"
"\\b" // word boundary
"(?:\\s+|$)" // eat the whitespace
,
pcrecpp::RE_Options().set_extended(true));
pcrecpp::RE re_terms("(\\S+)");
pcrecpp::RE re_coeff_and_species("(?: \\(? (.*?) \\)? )" // match the leading coefficent
"([A-Za-z].*)" // match the species
,
pcrecpp::RE_Options().set_extended(true));
pcrecpp::StringPiece input(reactions);
pcrecpp::StringPiece single_reaction, term;
Real equal_coeff;
std::vector<std::vector<bool>> primary_participation(vars.size());
std::vector<string> eq_species;
std::vector<Real> weight;
std::vector<Real> eq_const;
std::vector<std::vector<Real>> sto_u(vars.size());
std::vector<std::vector<std::vector<Real>>> sto_v(vars.size());
std::vector<std::vector<std::vector<VariableName>>> coupled_v(vars.size());
std::vector<std::vector<Real>> stos;
std::vector<std::vector<std::string>> primary_species_involved;
unsigned int n_reactions = 0;
// Start parsing
// Going into every single reaction
std::ostringstream oss;
while (re_reactions.FindAndConsume(&input, &single_reaction, &equal_coeff))
{
n_reactions += 1;
oss << "\n\n" << n_reactions << "_th reaction: " << single_reaction << std::endl;
eq_const.push_back(equal_coeff);
oss << "\nEquilibrium: " << eq_const[n_reactions - 1] << std::endl;
// capture all of the terms
std::string species, coeff_str;
Real coeff;
int sign = 1;
bool secondary = false;
std::vector<Real> local_stos;
std::vector<std::string> local_species_list;
// Going to find every single term in this reaction, sto_species combos and operators
while (re_terms.FindAndConsume(&single_reaction, &term))
{
// Separating the sto from species
if (re_coeff_and_species.PartialMatch(term, &coeff_str, &species))
{
if (coeff_str.length())
{
std::istringstream iss(coeff_str);
iss >> coeff;
}
else
coeff = 1.0;
coeff *= sign;
if (secondary)
eq_species.push_back(species);
else
{
local_stos.push_back(coeff);
local_species_list.push_back(species);
oss << "\nSpecies: " << species << "\n"
<< "Coeff: " << coeff << std::endl;
}
}
// Finding the operators and assign value of -1.0 to "-" sign
else if (term == "+" || term == "=" || term == "-")