void
AddCoupledSolidKinSpeciesAction::act()
{
mooseDoOnce(printReactions());
std::vector<bool> primary_participation(_primary_species.size(), false);
std::vector<std::string> solid_kin_species(_reactions.size());
std::vector<Real> weight;
// Loop through reactions
for (unsigned int j = 0; j < _reactions.size(); ++j)
{
std::vector<std::string> tokens;
// Parsing each reaction
MooseUtils::tokenize(_reactions[j], tokens, 1, "+=");
if (tokens.size() == 0)
mooseError("Empty reaction specified.");
std::vector<Real> stos(tokens.size() - 1);
std::vector<VariableName> rxn_species(tokens.size() - 1);
for (unsigned int k = 0; k < tokens.size(); ++k)
{
std::vector<std::string> stos_primary_species;
MooseUtils::tokenize(tokens[k], stos_primary_species, 1, "()");
if (stos_primary_species.size() == 2)
{
Real coef;
std::istringstream iss(stos_primary_species[0]);
iss >> coef;
stos[k] = coef;
rxn_species[k] = stos_primary_species[1];
// Check the participation of primary species
for (unsigned int i = 0; i < _primary_species.size(); ++i)
if (rxn_species[k] == _primary_species[i])
primary_participation[i] = true;
}
else
solid_kin_species[j] = stos_primary_species[0];
}
void
AddCoupledSolidKinSpeciesKernelsAction::act()
{
std::vector<NonlinearVariableName> vars = getParam<std::vector<NonlinearVariableName> >("primary_species");
std::vector<std::string> reactions = getParam<std::vector<std::string> >("kin_reactions");
Moose::out<< "Solid kinetic reaction list:" << "\n";
for (unsigned int i=0; i < reactions.size(); i++)
{
Moose::out<< reactions[i] << "\n";
}
for (unsigned int i=0; i < vars.size(); i++)
{
Moose::out << "primary species - " << vars[i] << "\n";
std::vector<bool> primary_participation(reactions.size(), false);
std::vector<std::string> solid_kin_species(reactions.size());
std::vector<Real> weight;
for (unsigned int j=0; j < reactions.size(); j++)
{
std::vector<std::string> tokens;
// Parsing each reaction
MooseUtils::tokenize(reactions[j], tokens, 1, "+=");
std::vector<Real> stos(tokens.size()-1);
std::vector<std::string> rxn_vars(tokens.size()-1);
for (unsigned int k=0; k < tokens.size(); k++)
{
Moose::out << tokens[k] << "\t";
std::vector<std::string> stos_vars;
MooseUtils::tokenize(tokens[k], stos_vars, 1, "()");
if (stos_vars.size() == 2)
{
Real coef;
std::istringstream iss(stos_vars[0]);
iss >> coef;
stos[k] = coef;
rxn_vars[k] = stos_vars[1];
Moose::out << "stochiometric: " << stos[k] << "\t";
Moose::out << "reactant: " << rxn_vars[k] << "\n";
// Check the participation of primary species
if (rxn_vars[k] == vars[i]) primary_participation[j] = true;
}
else
{
solid_kin_species[j] = stos_vars[0];
}
}
// Done parsing, recorded stochiometric and variables into separate arrays
Moose::out << "whether primary present (0 is not): " << primary_participation[j] << "\n";
if (primary_participation[j])
{
// Assigning the stochiometrics based on parsing
for (unsigned int m=0; m < rxn_vars.size(); m++)
{
if (rxn_vars[m] == vars[i])
{
weight.push_back(stos[m]);
Moose::out << "weight for " << rxn_vars[m] <<" : " << weight[weight.size()-1] << "\n";
}
}
Moose::out << "solid kinetic species: " << solid_kin_species[j] << "\n";
std::vector<VariableName> coupled_var(1);
coupled_var[0] = solid_kin_species[j];
// Building kernels for solid kinetic species
InputParameters params_kin = _factory.getValidParams("CoupledBEKinetic");
params_kin.set<NonlinearVariableName>("variable") = vars[i];
params_kin.set<std::vector<Real> >("weight") = weight;
params_kin.set<std::vector<VariableName> >("v") = coupled_var;
_problem->addKernel("CoupledBEKinetic", vars[i]+"_"+solid_kin_species[j]+"_kin", params_kin);
Moose::out << vars[i]+"_"+solid_kin_species[j]+"_kin" << "\n";
params_kin.print();
}
}
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 == "-")