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Commit 198b41dd authored by renchao.lu's avatar renchao.lu
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[CL] Replace with chemical system index map.

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ChemistryLib/PhreeqcIO.cpp
+ 197
− 188
View file @ 198b41dd
...@@ -242,81 +242,83 @@ std::ostream& operator<<(std::ostream& os, PhreeqcIO const& phreeqc_io) ...@@ -242,81 +242,83 @@ std::ostream& operator<<(std::ostream& os, PhreeqcIO const& phreeqc_io)
os << reaction_rates << "\n"; os << reaction_rates << "\n";
} }
std::size_t const num_chemical_systems = for (std::size_t mesh_item_id = 0;
phreeqc_io._mesh.getNumberOfBaseNodes(); mesh_item_id < phreeqc_io.chemical_system_index_map.size();
++mesh_item_id)
auto const chemical_system_map =
*phreeqc_io._mesh.getProperties()
.template getPropertyVector<std::size_t>(
"bulk_node_ids", MeshLib::MeshItemType::Node, 1);
for (std::size_t local_id = 0; local_id < num_chemical_systems; ++local_id)
{ {
auto const global_id = chemical_system_map[local_id]; auto const& local_chemical_system =
os << "SOLUTION " << global_id + 1 << "\n"; phreeqc_io.chemical_system_index_map[mesh_item_id];
phreeqc_io._chemical_system->aqueous_solution->print(os, local_id); for (std::size_t ip = 0; ip < local_chemical_system.size(); ++ip)
auto const& dump = phreeqc_io._dump;
if (dump)
{ {
auto const& aqueous_solutions_prev = dump->aqueous_solutions_prev; auto const& chemical_system_id = local_chemical_system[ip];
if (!aqueous_solutions_prev.empty())
os << "SOLUTION " << chemical_system_id + 1 << "\n";
phreeqc_io._chemical_system->aqueous_solution->print(
os, chemical_system_id);
auto const& dump = phreeqc_io._dump;
if (dump)
{ {
os << aqueous_solutions_prev[local_id] << "\n\n"; auto const& aqueous_solutions_prev =
dump->aqueous_solutions_prev;
if (!aqueous_solutions_prev.empty())
{
os << aqueous_solutions_prev[chemical_system_id] << "\n\n";
}
} }
}
os << "USE solution none" << "\n"; os << "USE solution none" << "\n";
os << "END" << "\n\n"; os << "END" << "\n\n";
os << "USE solution " << global_id + 1 << "\n\n"; os << "USE solution " << chemical_system_id + 1 << "\n\n";
auto const& equilibrium_reactants = auto const& equilibrium_reactants =
phreeqc_io._chemical_system->equilibrium_reactants; phreeqc_io._chemical_system->equilibrium_reactants;
if (!equilibrium_reactants.empty()) if (!equilibrium_reactants.empty())
{
os << "EQUILIBRIUM_PHASES " << global_id + 1 << "\n";
for (auto const& equilibrium_reactant : equilibrium_reactants)
{ {
equilibrium_reactant.print(os, global_id); os << "EQUILIBRIUM_PHASES " << chemical_system_id + 1 << "\n";
for (auto const& equilibrium_reactant : equilibrium_reactants)
{
equilibrium_reactant.print(os, chemical_system_id);
}
os << "\n";
} }
os << "\n";
}
auto const& kinetic_reactants = auto const& kinetic_reactants =
phreeqc_io._chemical_system->kinetic_reactants; phreeqc_io._chemical_system->kinetic_reactants;
if (!kinetic_reactants.empty()) if (!kinetic_reactants.empty())
{
os << "KINETICS " << global_id + 1 << "\n";
for (auto const& kinetic_reactant : kinetic_reactants)
{ {
kinetic_reactant.print(os, global_id); os << "KINETICS " << chemical_system_id + 1 << "\n";
for (auto const& kinetic_reactant : kinetic_reactants)
{
kinetic_reactant.print(os, chemical_system_id);
}
os << "-steps " << phreeqc_io._dt << "\n" << "\n";
} }
os << "-steps " << phreeqc_io._dt << "\n" << "\n";
}
auto const& surface = phreeqc_io._surface; auto const& surface = phreeqc_io._surface;
if (!surface.empty()) if (!surface.empty())
{ {
os << "SURFACE " << global_id + 1 << "\n"; os << "SURFACE " << chemical_system_id + 1 << "\n";
std::size_t aqueous_solution_id = std::size_t aqueous_solution_id =
dump->aqueous_solutions_prev.empty() dump->aqueous_solutions_prev.empty()
? global_id + 1 ? chemical_system_id + 1
: num_chemical_systems + global_id + 1; : phreeqc_io._num_chemical_systems +
os << "-equilibrate with solution " << aqueous_solution_id << "\n"; chemical_system_id + 1;
os << "-sites_units DENSITY" os << "-equilibrate with solution " << aqueous_solution_id << "\n";
<< "\n"; os << "-sites_units DENSITY" << "\n";
os << surface << "\n"; os << surface << "\n";
os << "SAVE solution " << global_id + 1 << "\n"; os << "SAVE solution " << chemical_system_id + 1 << "\n";
} }
os << "END" << "\n\n"; os << "END" << "\n\n";
}
} }
auto const& dump = phreeqc_io._dump; auto const& dump = phreeqc_io._dump;
if (dump) if (dump)
{ {
dump->print(os, num_chemical_systems); dump->print(os, phreeqc_io._num_chemical_systems);
} }
return os; return os;
...@@ -371,150 +373,157 @@ std::istream& operator>>(std::istream& in, PhreeqcIO& phreeqc_io) ...@@ -371,150 +373,157 @@ std::istream& operator>>(std::istream& in, PhreeqcIO& phreeqc_io)
auto const& surface = phreeqc_io._surface; auto const& surface = phreeqc_io._surface;
int const num_skipped_lines = surface.empty() ? 1 : 2; int const num_skipped_lines = surface.empty() ? 1 : 2;
std::size_t const num_chemical_systems = for (std::size_t mesh_item_id = 0;
phreeqc_io._mesh.getNumberOfBaseNodes(); mesh_item_id < phreeqc_io.chemical_system_index_map.size();
++mesh_item_id)
auto const chemical_system_map =
*phreeqc_io._mesh.getProperties()
.template getPropertyVector<std::size_t>(
"bulk_node_ids", MeshLib::MeshItemType::Node, 1);
for (std::size_t local_id = 0; local_id < num_chemical_systems; ++local_id)
{ {
auto const global_id = chemical_system_map[local_id]; auto const& local_chemical_system =
// Skip equilibrium calculation result of initial solution phreeqc_io.chemical_system_index_map[mesh_item_id];
for (int i = 0; i < num_skipped_lines; ++i) for (std::size_t ip = 0; ip < local_chemical_system.size(); ++ip)
{ {
in.ignore(std::numeric_limits<std::streamsize>::max(), '\n'); auto const& chemical_system_id = local_chemical_system[ip];
}
// Get calculation result of the solution after the reaction // Skip equilibrium calculation result of initial solution
if (!std::getline(in, line)) for (int i = 0; i < num_skipped_lines; ++i)
{ {
OGS_FATAL( in.ignore(std::numeric_limits<std::streamsize>::max(), '\n');
"Error when reading calculation result of Solution {:d} after " }
"the reaction.",
global_id);
}
std::vector<double> accepted_items; // Get calculation result of the solution after the reaction
std::vector<std::string> items; if (!std::getline(in, line))
boost::trim_if(line, boost::is_any_of("\t "));
boost::algorithm::split(items, line, boost::is_any_of("\t "),
boost::token_compress_on);
for (int item_id = 0; item_id < static_cast<int>(items.size());
++item_id)
{
if (std::find(dropped_item_ids.begin(), dropped_item_ids.end(),
item_id) == dropped_item_ids.end())
{ {
double value; OGS_FATAL(
try "Error when reading calculation result of Solution {:d} "
{ "after "
value = std::stod(items[item_id]); "the reaction.",
} chemical_system_id);
catch (const std::invalid_argument& e) }
{
OGS_FATAL( std::vector<double> accepted_items;
"Invalid argument. Could not convert string '{:s}' to " std::vector<std::string> items;
"double for chemical system {:d}, column {:d}. " boost::trim_if(line, boost::is_any_of("\t "));
"Exception " boost::algorithm::split(items, line, boost::is_any_of("\t "),
"'{:s}' was thrown.", boost::token_compress_on);
items[item_id], global_id, item_id, e.what()); for (int item_id = 0; item_id < static_cast<int>(items.size());
} ++item_id)
catch (const std::out_of_range& e) {
if (std::find(dropped_item_ids.begin(), dropped_item_ids.end(),
item_id) == dropped_item_ids.end())
{ {
OGS_FATAL( double value;
"Out of range error. Could not convert string '{:s}' " try
"to " {
"double for chemical system {:d}, column {:d}. " value = std::stod(items[item_id]);
"Exception " }
"'{:s}' was thrown.", catch (const std::invalid_argument& e)
items[item_id], global_id, item_id, e.what()); {
OGS_FATAL(
"Invalid argument. Could not convert string '{:s}' "
"to double for chemical system {:d}, column {:d}. "
"Exception '{:s}' was thrown.",
items[item_id], chemical_system_id + 1, item_id,
e.what());
}
catch (const std::out_of_range& e)
{
OGS_FATAL(
"Out of range error. Could not convert string "
"'{:s}' to double for chemical system {:d}, column "
"{:d}. Exception '{:s}' was thrown.",
items[item_id], chemical_system_id + 1, item_id,
e.what());
}
accepted_items.push_back(value);
} }
accepted_items.push_back(value);
} }
} assert(accepted_items.size() == output.accepted_items.size());
assert(accepted_items.size() == output.accepted_items.size());
auto& aqueous_solution =
auto& aqueous_solution = phreeqc_io._chemical_system->aqueous_solution; phreeqc_io._chemical_system->aqueous_solution;
auto& components = aqueous_solution->components; auto& components = aqueous_solution->components;
auto& equilibrium_reactants = auto& equilibrium_reactants =
phreeqc_io._chemical_system->equilibrium_reactants; phreeqc_io._chemical_system->equilibrium_reactants;
auto& kinetic_reactants = auto& kinetic_reactants =
phreeqc_io._chemical_system->kinetic_reactants; phreeqc_io._chemical_system->kinetic_reactants;
auto& user_punch = phreeqc_io._user_punch; auto& user_punch = phreeqc_io._user_punch;
for (int item_id = 0; item_id < static_cast<int>(accepted_items.size()); for (int item_id = 0;
++item_id) item_id < static_cast<int>(accepted_items.size());
{ ++item_id)
auto const& accepted_item = output.accepted_items[item_id]; {
auto const& item_name = accepted_item.name; auto const& accepted_item = output.accepted_items[item_id];
auto const& item_name = accepted_item.name;
auto compare_by_name = [&item_name](auto const& item) { auto compare_by_name = [&item_name](auto const& item) {
return item.name == item_name; return item.name == item_name;
}; };
switch (accepted_item.item_type) switch (accepted_item.item_type)
{
case ItemType::pH:
{ {
// Update pH value case ItemType::pH:
aqueous_solution->pH->set(local_id, {
// Update pH value
aqueous_solution->pH->set(chemical_system_id,
accepted_items[item_id]);
break;
}
case ItemType::pe:
{
// Update pe value
(*aqueous_solution->pe)[chemical_system_id] =
accepted_items[item_id];
break;
}
case ItemType::Component:
{
// Update component concentrations
auto& component = BaseLib::findElementOrError(
components.begin(), components.end(),
compare_by_name,
"Could not find component '" + item_name + "'.");
component.amount->set(chemical_system_id,
accepted_items[item_id]); accepted_items[item_id]);
break; break;
} }
case ItemType::pe: case ItemType::EquilibriumReactant:
{ {
// Update pe value // Update amounts of equilibrium reactant
(*aqueous_solution->pe)[global_id] = auto& equilibrium_reactant =
accepted_items[item_id]; BaseLib::findElementOrError(
break; equilibrium_reactants.begin(),
} equilibrium_reactants.end(), compare_by_name,
case ItemType::Component: "Could not find equilibrium reactant '" +
{ item_name + "'.");
// Update component concentrations (*equilibrium_reactant.amount)[chemical_system_id] =
auto& component = BaseLib::findElementOrError( accepted_items[item_id];
components.begin(), components.end(), compare_by_name, break;
"Could not find component '" + item_name + "'."); }
component.amount->set(local_id, accepted_items[item_id]); case ItemType::KineticReactant:
break; {
} // Update amounts of kinetic reactants
case ItemType::EquilibriumReactant: auto& kinetic_reactant = BaseLib::findElementOrError(
{ kinetic_reactants.begin(), kinetic_reactants.end(),
// Update amounts of equilibrium reactant compare_by_name,
auto& equilibrium_reactant = BaseLib::findElementOrError( "Could not find kinetic reactant '" + item_name +
equilibrium_reactants.begin(), "'.");
equilibrium_reactants.end(), compare_by_name, (*kinetic_reactant.amount)[chemical_system_id] =
"Could not find equilibrium reactant '" + item_name + accepted_items[item_id];
"'."); break;
(*equilibrium_reactant.amount)[global_id] = }
accepted_items[item_id]; case ItemType::SecondaryVariable:
break; {
} assert(user_punch);
case ItemType::KineticReactant: auto& secondary_variables =
{ user_punch->secondary_variables;
// Update amounts of kinetic reactants // Update values of secondary variables
auto& kinetic_reactant = BaseLib::findElementOrError( auto& secondary_variable = BaseLib::findElementOrError(
kinetic_reactants.begin(), kinetic_reactants.end(), secondary_variables.begin(),
compare_by_name, secondary_variables.end(), compare_by_name,
"Could not find kinetic reactant '" + item_name + "'."); "Could not find secondary variable '" + item_name +
(*kinetic_reactant.amount)[global_id] = "'.");
accepted_items[item_id]; (*secondary_variable.value)[chemical_system_id] =
break; accepted_items[item_id];
} break;
case ItemType::SecondaryVariable: }
{
assert(user_punch);
auto& secondary_variables = user_punch->secondary_variables;
// Update values of secondary variables
auto& secondary_variable = BaseLib::findElementOrError(
secondary_variables.begin(), secondary_variables.end(),
compare_by_name,
"Could not find secondary variable '" + item_name +
"'.");
(*secondary_variable.value)[global_id] =
accepted_items[item_id];
break;
} }
} }
} }
......
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