GeochemistryFormattedOutput Namespace Reference

Functions
std::string	reaction (const DenseMatrix< Real > &stoi, unsigned row, const std::vector< std::string > &names, Real stoi_tol=1.0E-6, int precision=4)
	Returns a nicely formatted string corresponding to the reaction defined by the given row of the stoichiometric matrix. More...

Function Documentation

reaction()

std::string GeochemistryFormattedOutput::reaction	(	const DenseMatrix< Real > &	stoi,
		unsigned	row,
		const std::vector< std::string > &	names,
		Real	stoi_tol = 1.0E-6,
		int	precision = 4
	)

Returns a nicely formatted string corresponding to the reaction defined by the given row of the stoichiometric matrix.

For instance, if stoi(row, :) = (1, 2, 1E-5, -0.333333333333) and names = ["H2O", "H+", "HCO3-", "O2(aq)"] then this function will return "H2O + 2*H+ - 0.333*O2(aq)" if stoi_tol=1E-4 and precision = 3

Parameters

stoi	matrix stoichiometric coefficients
row	row of stoi which defines the reaction of interest
names	names of the basis species
stoi_tol	Any stoichiometric coefficients of magnitude less than this value will not appear in the returned string
precision	Maximum number of digits written for each stoichiometric coefficient in the returned string

Definition at line 15 of file GeochemistryFormattedOutput.C.

Referenced by GeochemistryConsoleOutput::output(), GeochemistryConsoleOutput::outputNernstInfo(), GeochemicalModelInterrogator::outputReaction(), GeochemicalDatabaseReader::printReactions(), and TEST().

{
  if (row >= stoi.m())
    mooseError("GeochemistryFormattedOutput::reaction called with stoichiometric matrix having ",
               stoi.m(),
               " rows, but row = ",
               row);
  const unsigned num_cols = stoi.n();
  if (num_cols != names.size())
    mooseError("GeochemistryFormattedOutput::reaction called with stoichiometric matrix having ",
               num_cols,
               " columns, but names has size ",
               names.size());
  std::stringstream ss;
  ss << std::setprecision(precision);
  bool printed_something = false;
  for (unsigned i = 0; i < num_cols; ++i)
    if (stoi(row, i) > stoi_tol)
    {
      if (!printed_something)
      {
        ss << stoi(row, i) << "*" << names[i];
        printed_something = true;
      }
      else
        ss << " + " << stoi(row, i) << "*" << names[i];
    }
    else if (stoi(row, i) < -stoi_tol)
    {
      if (!printed_something)
      {
        ss << "-" << -stoi(row, i) << "*" << names[i];
        printed_something = true;
      }
      else
        ss << " - " << -stoi(row, i) << "*" << names[i];
    }
  return ss.str();
}