diff --git a/ChemistryLib/CreateOutput.cpp b/ChemistryLib/CreateOutput.cpp
index e0678dd1c48f5823dbc84c6860b4ebc3cf37d0ef..310a2037b74c3fa60b55521e3156ae17c85fd95e 100644
--- a/ChemistryLib/CreateOutput.cpp
+++ b/ChemistryLib/CreateOutput.cpp
@@ -22,13 +22,19 @@ std::unique_ptr<Output> createOutput(
std::vector<OutputItem> accepted_items{{"pH", ItemType::pH},
{"pe", ItemType::pe}};
for (auto const& component : components)
+ {
accepted_items.emplace_back(component.name, ItemType::Component);
+ }
for (auto const& equilibrium_phase : equilibrium_phases)
+ {
accepted_items.emplace_back(equilibrium_phase.name,
ItemType::EquilibriumPhase);
+ }
for (auto const& kinetic_reactant : kinetic_reactants)
+ {
accepted_items.emplace_back(kinetic_reactant.name,
ItemType::KineticReactant);
+ }
// Record ids of which phreeqc output items will be dropped.
BasicOutputSetups basic_output_setups(project_file_name);
diff --git a/ChemistryLib/CreatePhreeqcIO.cpp b/ChemistryLib/CreatePhreeqcIO.cpp
index dd5ed3a468a88748d848fc05e77f068a4f8b7530..95a0ecd7c5d51877dceeef49ee5623a461606d1e 100644
--- a/ChemistryLib/CreatePhreeqcIO.cpp
+++ b/ChemistryLib/CreatePhreeqcIO.cpp
@@ -65,18 +65,22 @@ std::unique_ptr<PhreeqcIO> createPhreeqcIO(
if (process_id_to_component_name_map_element ==
process_id_to_component_name_map.end())
+ {
OGS_FATAL(
"Component %s given in <solution>/<components> is not found in "
"specified coupled processes (see "
"<process>/<process_variables>/<concentration>).",
component.name.c_str());
+ }
}
if (components_per_chem_sys.size() + 1 !=
process_id_to_component_name_map.size())
+ {
OGS_FATAL(
"The number of components given in <solution>/<components> is not "
"in line with the number of transport processes - 1 which stands "
"for the transport process of hydrogen.");
+ }
std::vector<AqueousSolution> aqueous_solutions(
num_chemical_systems, aqueous_solution_per_chem_sys);
diff --git a/ChemistryLib/Output.cpp b/ChemistryLib/Output.cpp
index 6eed8b29076c27dbad6113f8aad2535a783ed449..64593e54754665ea5c905a0806d55a370e4eba08 100644
--- a/ChemistryLib/Output.cpp
+++ b/ChemistryLib/Output.cpp
@@ -41,7 +41,9 @@ std::ofstream& operator<<(std::ofstream& out, Output const& output)
output.getOutputItemsByItemType(ItemType::Component);
out << "-totals";
for (auto const& component_item : component_items)
+ {
out << " " << component_item.name;
+ }
out << "\n";
auto const equilibrium_phase_items =
@@ -50,7 +52,9 @@ std::ofstream& operator<<(std::ofstream& out, Output const& output)
{
out << "-equilibrium_phases";
for (auto const& equilibrium_phase_item : equilibrium_phase_items)
+ {
out << " " << equilibrium_phase_item.name;
+ }
out << "\n";
}
@@ -60,7 +64,9 @@ std::ofstream& operator<<(std::ofstream& out, Output const& output)
{
out << "-kinetic_reactants";
for (auto const& kinetic_reactant_item : kinetic_reactant_items)
+ {
out << " " << kinetic_reactant_item.name;
+ }
out << "\n";
}
diff --git a/ChemistryLib/PhreeqcIO.cpp b/ChemistryLib/PhreeqcIO.cpp
index 6a3580b6de1d8ce1a7dfc890c3ddad1d2174384e..faa62265ad133f4b8da8aa64c24c6b1cddb255bf 100644
--- a/ChemistryLib/PhreeqcIO.cpp
+++ b/ChemistryLib/PhreeqcIO.cpp
@@ -118,14 +118,18 @@ void PhreeqcIO::writeInputsToFile()
std::ofstream out(_phreeqc_input_file, std::ofstream::out);
if (!out)
+ {
OGS_FATAL("Could not open file '%s' for writing phreeqc inputs.",
_phreeqc_input_file.c_str());
+ }
out << *this;
if (!out)
+ {
OGS_FATAL("Failed in generating phreeqc input file '%s'.",
_phreeqc_input_file.c_str());
+ }
out.close();
}
@@ -188,9 +192,11 @@ void PhreeqcIO::execute()
// load a specific database in the working directory
if (!database_loaded(instance_id))
+ {
OGS_FATAL(
"Failed in loading the specified thermodynamic database file: %s.",
_database.c_str());
+ }
SetSelectedOutputFileOn(instance_id, 1);
@@ -213,14 +219,18 @@ void PhreeqcIO::readOutputsFromFile()
std::ifstream in(phreeqc_result_file);
if (!in)
+ {
OGS_FATAL("Could not open phreeqc result file '%s'.",
phreeqc_result_file.c_str());
+ }
in >> *this;
if (!in)
+ {
OGS_FATAL("Error when reading phreeqc result file '%s'",
phreeqc_result_file.c_str());
+ }
in.close();
}
@@ -244,10 +254,12 @@ std::ifstream& operator>>(std::ifstream& in, PhreeqcIO& phreeqc_io)
// Get calculation result of the solution after the reaction
if (!std::getline(in, line))
+ {
OGS_FATAL(
"Error when reading calculation result of Solution %u after "
"the reaction.",
chemical_system_id);
+ }
std::vector<double> accepted_items;
std::vector<std::string> items;
@@ -259,7 +271,9 @@ std::ifstream& operator>>(std::ifstream& in, PhreeqcIO& phreeqc_io)
{
if (std::find(dropped_item_ids.begin(), dropped_item_ids.end(),
item_id) == dropped_item_ids.end())
+ {
accepted_items.push_back(std::stod(items[item_id]));
+ }
}
assert(accepted_items.size() == output.accepted_items.size());
diff --git a/ChemistryLib/PhreeqcIOData/AqueousSolution.cpp b/ChemistryLib/PhreeqcIOData/AqueousSolution.cpp
index 6680a4d45362733834e12373930aae53c9617046..8867e80dd97f30618d8d33a1b243e750f9a02654 100644
--- a/ChemistryLib/PhreeqcIOData/AqueousSolution.cpp
+++ b/ChemistryLib/PhreeqcIOData/AqueousSolution.cpp
@@ -48,14 +48,20 @@ AqueousSolution createAqueousSolution(BaseLib::ConfigTree const& config)
if (means_of_adjusting_charge_in_str)
{
if (*means_of_adjusting_charge_in_str == "pH")
+ {
means_of_adjusting_charge = MeansOfAdjustingCharge::pH;
+ }
else if (*means_of_adjusting_charge_in_str == "pe")
+ {
means_of_adjusting_charge = MeansOfAdjustingCharge::pe;
+ }
else
+ {
OGS_FATAL(
"Error in specifying means of adjusting charge. Achieving "
"charge balance is currently supported with the way of "
"adjusting pH value or pe value.");
+ }
}
else
{
@@ -99,7 +105,9 @@ std::ofstream& operator<<(std::ofstream& out,
out << "units mol/kgw\n";
for (auto const& component : aqueous_solution.components)
+ {
out << component.name << " " << component.amount << "\n";
+ }
return out;
}
diff --git a/ChemistryLib/PhreeqcIOData/EquilibriumPhase.cpp b/ChemistryLib/PhreeqcIOData/EquilibriumPhase.cpp
index 05888627e5c31889eeffd6f4354318488b63b344..e92d7b06641f0aa324344167422677da626e0602 100644
--- a/ChemistryLib/PhreeqcIOData/EquilibriumPhase.cpp
+++ b/ChemistryLib/PhreeqcIOData/EquilibriumPhase.cpp
@@ -18,7 +18,9 @@ std::vector<EquilibriumPhase> createEquilibriumPhases(
boost::optional<BaseLib::ConfigTree> const& config)
{
if (!config)
+ {
return {};
+ }
std::vector<EquilibriumPhase> equilibrium_phases;
for (
diff --git a/ChemistryLib/PhreeqcIOData/KineticReactant.cpp b/ChemistryLib/PhreeqcIOData/KineticReactant.cpp
index 6f6c76b5d201da80f271af86f9d4ff1e27fad59a..e4e39a22a9e32a2fa516a6e1aec873124a72d317 100644
--- a/ChemistryLib/PhreeqcIOData/KineticReactant.cpp
+++ b/ChemistryLib/PhreeqcIOData/KineticReactant.cpp
@@ -18,7 +18,9 @@ std::vector<KineticReactant> createKineticReactants(
boost::optional<BaseLib::ConfigTree> const& config)
{
if (!config)
+ {
return {};
+ }
std::vector<KineticReactant> kinetic_reactants;
for (
@@ -58,7 +60,9 @@ std::ofstream& operator<<(std::ofstream& out,
{
out << "-parms";
for (auto const& parameter : kinetic_reactant.parameters)
+ {
out << " " << parameter;
+ }
out << "\n";
}
}
diff --git a/ChemistryLib/PhreeqcIOData/ReactionRate.cpp b/ChemistryLib/PhreeqcIOData/ReactionRate.cpp
index ee967a4037131410677b9980fa75b41839690387..00331c51f0e172ef32f1668a5ef749af7299f8aa 100644
--- a/ChemistryLib/PhreeqcIOData/ReactionRate.cpp
+++ b/ChemistryLib/PhreeqcIOData/ReactionRate.cpp
@@ -18,7 +18,9 @@ std::vector<ReactionRate> createReactionRates(
boost::optional<BaseLib::ConfigTree> const& config)
{
if (!config)
+ {
return {};
+ }
std::vector<ReactionRate> reaction_rates;
for (auto const& rate_config :
@@ -37,7 +39,9 @@ std::vector<ReactionRate> createReactionRates(
auto const& expression_statement :
//! \ogs_file_param{prj__chemical_system__rates__rate__expression__statement}
expression_config.getConfigParameterList<std::string>("statement"))
+ {
expression_statements.push_back(expression_statement);
+ }
reaction_rates.emplace_back(std::move(kinetic_reactant),
std::move(expression_statements));