From b7f268eef73320a4e5ac767a7ef17558cf04606a Mon Sep 17 00:00:00 2001
From: renchao_lu <renchao.lu@gmail.com>
Date: Fri, 1 Jan 2021 21:07:15 +0100
Subject: [PATCH] [MPL] Rename amount as molality.
---
ChemistryLib/PhreeqcIO.cpp | 40 ++++++++++---------
ChemistryLib/PhreeqcIOData/ChemicalSystem.cpp | 4 +-
.../CreateEquilibriumReactants.cpp | 12 +++---
.../PhreeqcIOData/CreateKineticReactant.cpp | 10 ++---
.../PhreeqcIOData/EquilibriumReactant.cpp | 4 +-
.../PhreeqcIOData/EquilibriumReactant.h | 12 +++---
.../PhreeqcIOData/KineticReactant.cpp | 2 +-
ChemistryLib/PhreeqcIOData/KineticReactant.h | 12 +++---
MaterialLib/MPL/PropertyType.h | 14 +++----
9 files changed, 55 insertions(+), 55 deletions(-)
diff --git a/ChemistryLib/PhreeqcIO.cpp b/ChemistryLib/PhreeqcIO.cpp
index 91711e29547..d1515e5d244 100644
--- a/ChemistryLib/PhreeqcIO.cpp
+++ b/ChemistryLib/PhreeqcIO.cpp
@@ -51,29 +51,30 @@ std::ostream& operator<<(std::ostream& os,
}
template <typename Reactant>
-void setReactantAmount(Reactant& reactant,
- GlobalIndexType const& chemical_system_id,
- MaterialPropertyLib::Phase const& solid_phase,
- ParameterLib::SpatialPosition const& pos, double const t)
+void setReactantMolality(Reactant& reactant,
+ GlobalIndexType const& chemical_system_id,
+ MaterialPropertyLib::Phase const& solid_phase,
+ ParameterLib::SpatialPosition const& pos,
+ double const t)
{
auto const& solid_constituent = solid_phase.component(reactant.name);
- auto const amount =
- solid_constituent.property(MaterialPropertyLib::PropertyType::amount)
+ auto const molality =
+ solid_constituent.property(MaterialPropertyLib::PropertyType::molality)
.template initialValue<double>(pos, t);
- (*reactant.amount)[chemical_system_id] = amount;
+ (*reactant.molality)[chemical_system_id] = molality;
}
template <typename Reactant>
-static double averageReactantAmount(
+static double averageReactantMolality(
Reactant const& reactant,
std::vector<GlobalIndexType> const& chemical_system_indices)
{
double const sum = std::accumulate(
chemical_system_indices.begin(), chemical_system_indices.end(), 0.0,
[&](double const s, GlobalIndexType const id) {
- return s + (*reactant.amount)[id];
+ return s + (*reactant.molality)[id];
});
return sum / chemical_system_indices.size();
}
@@ -151,14 +152,14 @@ void PhreeqcIO::initializeChemicalSystemConcrete(
auto const& solid_phase = medium->phase("Solid");
for (auto& kinetic_reactant : _chemical_system->kinetic_reactants)
{
- setReactantAmount(kinetic_reactant, chemical_system_id, solid_phase,
- pos, t);
+ setReactantMolality(kinetic_reactant, chemical_system_id, solid_phase,
+ pos, t);
}
for (auto& equilibrium_reactant : _chemical_system->equilibrium_reactants)
{
- setReactantAmount(equilibrium_reactant, chemical_system_id, solid_phase,
- pos, t);
+ setReactantMolality(equilibrium_reactant, chemical_system_id,
+ solid_phase, pos, t);
}
}
@@ -530,7 +531,7 @@ std::istream& operator>>(std::istream& in, PhreeqcIO& phreeqc_io)
equilibrium_reactants.end(), compare_by_name,
"Could not find equilibrium reactant '" + item_name +
"'.");
- (*equilibrium_reactant.amount)[chemical_system_id] =
+ (*equilibrium_reactant.molality)[chemical_system_id] =
accepted_items[item_id];
break;
}
@@ -541,7 +542,7 @@ std::istream& operator>>(std::istream& in, PhreeqcIO& phreeqc_io)
kinetic_reactants.begin(), kinetic_reactants.end(),
compare_by_name,
"Could not find kinetic reactant '" + item_name + "'.");
- (*kinetic_reactant.amount)[chemical_system_id] =
+ (*kinetic_reactant.molality)[chemical_system_id] =
accepted_items[item_id];
break;
}
@@ -585,14 +586,15 @@ void PhreeqcIO::computeSecondaryVariable(
{
for (auto& kinetic_reactant : _chemical_system->kinetic_reactants)
{
- (*kinetic_reactant.amount_avg)[ele_id] =
- averageReactantAmount(kinetic_reactant, chemical_system_indices);
+ (*kinetic_reactant.mesh_prop_molality)[ele_id] =
+ averageReactantMolality(kinetic_reactant, chemical_system_indices);
}
for (auto& equilibrium_reactant : _chemical_system->equilibrium_reactants)
{
- (*equilibrium_reactant.amount_avg)[ele_id] = averageReactantAmount(
- equilibrium_reactant, chemical_system_indices);
+ (*equilibrium_reactant.mesh_prop_molality)[ele_id] =
+ averageReactantMolality(equilibrium_reactant,
+ chemical_system_indices);
}
}
} // namespace PhreeqcIOData
diff --git a/ChemistryLib/PhreeqcIOData/ChemicalSystem.cpp b/ChemistryLib/PhreeqcIOData/ChemicalSystem.cpp
index 669c57d3b88..6a7286fb1c9 100644
--- a/ChemistryLib/PhreeqcIOData/ChemicalSystem.cpp
+++ b/ChemistryLib/PhreeqcIOData/ChemicalSystem.cpp
@@ -38,12 +38,12 @@ void ChemicalSystem::initialize(std::size_t const num_chemical_systems)
for (auto& kinetic_reactant : kinetic_reactants)
{
- kinetic_reactant.amount->resize(num_chemical_systems);
+ kinetic_reactant.molality->resize(num_chemical_systems);
}
for (auto& equilibrium_reactant : equilibrium_reactants)
{
- equilibrium_reactant.amount->resize(num_chemical_systems);
+ equilibrium_reactant.molality->resize(num_chemical_systems);
}
}
} // namespace PhreeqcIOData
diff --git a/ChemistryLib/PhreeqcIOData/CreateEquilibriumReactants.cpp b/ChemistryLib/PhreeqcIOData/CreateEquilibriumReactants.cpp
index 198f4f59896..8455a6f23a9 100644
--- a/ChemistryLib/PhreeqcIOData/CreateEquilibriumReactants.cpp
+++ b/ChemistryLib/PhreeqcIOData/CreateEquilibriumReactants.cpp
@@ -42,17 +42,15 @@ std::vector<EquilibriumReactant> createEquilibriumReactants(
equilibrium_reactant_config.getConfigParameter<double>(
"saturation_index");
- auto amount = MeshLib::getOrCreateMeshProperty<double>(
+ auto molality = MeshLib::getOrCreateMeshProperty<double>(
mesh, name, MeshLib::MeshItemType::IntegrationPoint, 1);
- auto mesh_prop_amount = MeshLib::getOrCreateMeshProperty<double>(
+ auto mesh_prop_molality = MeshLib::getOrCreateMeshProperty<double>(
mesh, name + "_avg", MeshLib::MeshItemType::Cell, 1);
- mesh_prop_amount->resize(mesh.getNumberOfElements());
+ mesh_prop_molality->resize(mesh.getNumberOfElements());
- equilibrium_reactants.emplace_back(std::move(name),
- amount,
- mesh_prop_amount,
- saturation_index);
+ equilibrium_reactants.emplace_back(
+ std::move(name), molality, mesh_prop_molality, saturation_index);
}
return equilibrium_reactants;
diff --git a/ChemistryLib/PhreeqcIOData/CreateKineticReactant.cpp b/ChemistryLib/PhreeqcIOData/CreateKineticReactant.cpp
index a063b340b30..8ab72618334 100644
--- a/ChemistryLib/PhreeqcIOData/CreateKineticReactant.cpp
+++ b/ChemistryLib/PhreeqcIOData/CreateKineticReactant.cpp
@@ -50,12 +50,12 @@ std::vector<KineticReactant> createKineticReactants(
//! \ogs_file_param{prj__chemical_system__kinetic_reactants__kinetic_reactant__fix_amount}
reactant_config.getConfigParameter<bool>("fix_amount", false);
- auto amount = MeshLib::getOrCreateMeshProperty<double>(
+ auto molality = MeshLib::getOrCreateMeshProperty<double>(
mesh, name, MeshLib::MeshItemType::IntegrationPoint, 1);
- auto mesh_prop_amount = MeshLib::getOrCreateMeshProperty<double>(
+ auto mesh_prop_molality = MeshLib::getOrCreateMeshProperty<double>(
mesh, name + "_avg", MeshLib::MeshItemType::Cell, 1);
- mesh_prop_amount->resize(mesh.getNumberOfElements());
+ mesh_prop_molality->resize(mesh.getNumberOfElements());
if (chemical_formula.empty() && fix_amount)
{
@@ -66,8 +66,8 @@ std::vector<KineticReactant> createKineticReactants(
kinetic_reactants.emplace_back(std::move(name),
std::move(chemical_formula),
- amount,
- mesh_prop_amount,
+ molality,
+ mesh_prop_molality,
std::move(parameters),
fix_amount);
}
diff --git a/ChemistryLib/PhreeqcIOData/EquilibriumReactant.cpp b/ChemistryLib/PhreeqcIOData/EquilibriumReactant.cpp
index f6ff1020f85..89c88653a11 100644
--- a/ChemistryLib/PhreeqcIOData/EquilibriumReactant.cpp
+++ b/ChemistryLib/PhreeqcIOData/EquilibriumReactant.cpp
@@ -19,8 +19,8 @@ namespace PhreeqcIOData
void EquilibriumReactant::print(std::ostream& os,
std::size_t const global_id) const
{
- os << name << " " << saturation_index << " "
- << (*amount)[global_id] << "\n";
+ os << name << " " << saturation_index << " " << (*molality)[global_id]
+ << "\n";
}
} // namespace PhreeqcIOData
} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/EquilibriumReactant.h b/ChemistryLib/PhreeqcIOData/EquilibriumReactant.h
index 3ef18ab9e9c..c502f756d05 100644
--- a/ChemistryLib/PhreeqcIOData/EquilibriumReactant.h
+++ b/ChemistryLib/PhreeqcIOData/EquilibriumReactant.h
@@ -29,12 +29,12 @@ namespace PhreeqcIOData
struct EquilibriumReactant
{
EquilibriumReactant(std::string name_,
- MeshLib::PropertyVector<double>* amount_,
- MeshLib::PropertyVector<double>* amount_avg_,
+ MeshLib::PropertyVector<double>* molality_,
+ MeshLib::PropertyVector<double>* mesh_prop_molality_,
double saturation_index_)
: name(std::move(name_)),
- amount(amount_),
- amount_avg(amount_avg_),
+ molality(molality_),
+ mesh_prop_molality(mesh_prop_molality_),
saturation_index(saturation_index_)
{
}
@@ -42,8 +42,8 @@ struct EquilibriumReactant
void print(std::ostream& os, std::size_t const global_id) const;
std::string const name;
- MeshLib::PropertyVector<double>* amount;
- MeshLib::PropertyVector<double>* amount_avg;
+ MeshLib::PropertyVector<double>* molality;
+ MeshLib::PropertyVector<double>* mesh_prop_molality;
double const saturation_index;
static const ItemType item_type = ItemType::EquilibriumReactant;
};
diff --git a/ChemistryLib/PhreeqcIOData/KineticReactant.cpp b/ChemistryLib/PhreeqcIOData/KineticReactant.cpp
index 18db0961fe7..ac8b6fe83d8 100644
--- a/ChemistryLib/PhreeqcIOData/KineticReactant.cpp
+++ b/ChemistryLib/PhreeqcIOData/KineticReactant.cpp
@@ -26,7 +26,7 @@ void KineticReactant::print(std::ostream& os,
os << "-formula " << chemical_formula << "\n";
}
- os << "-m " << (*amount)[global_id] << "\n";
+ os << "-m " << (*molality)[global_id] << "\n";
if (!parameters.empty())
{
diff --git a/ChemistryLib/PhreeqcIOData/KineticReactant.h b/ChemistryLib/PhreeqcIOData/KineticReactant.h
index 40c9af5b6f4..b104206f71f 100644
--- a/ChemistryLib/PhreeqcIOData/KineticReactant.h
+++ b/ChemistryLib/PhreeqcIOData/KineticReactant.h
@@ -26,14 +26,14 @@ struct KineticReactant
{
KineticReactant(std::string name_,
std::string chemical_formula_,
- MeshLib::PropertyVector<double>* amount_,
- MeshLib::PropertyVector<double>* amount_avg_,
+ MeshLib::PropertyVector<double>* molality_,
+ MeshLib::PropertyVector<double>* mesh_prop_molality_,
std::vector<double>&& parameters_,
bool const fix_amount_)
: name(std::move(name_)),
chemical_formula(std::move(chemical_formula_)),
- amount(amount_),
- amount_avg(amount_avg_),
+ molality(molality_),
+ mesh_prop_molality(mesh_prop_molality_),
parameters(std::move(parameters_)),
fix_amount(fix_amount_)
{
@@ -43,8 +43,8 @@ struct KineticReactant
std::string const name;
std::string const chemical_formula;
- MeshLib::PropertyVector<double>* amount;
- MeshLib::PropertyVector<double>* amount_avg;
+ MeshLib::PropertyVector<double>* molality;
+ MeshLib::PropertyVector<double>* mesh_prop_molality;
std::vector<double> const parameters;
bool const fix_amount;
static const ItemType item_type = ItemType::KineticReactant;
diff --git a/MaterialLib/MPL/PropertyType.h b/MaterialLib/MPL/PropertyType.h
index 55a7adb99c0..554e7a52bb1 100644
--- a/MaterialLib/MPL/PropertyType.h
+++ b/MaterialLib/MPL/PropertyType.h
@@ -35,7 +35,6 @@ namespace MaterialPropertyLib
enum PropertyType : int
{
acentric_factor,
- amount,
binary_interaction_coefficient,
biot_coefficient,
bishops_effective_stress,
@@ -58,6 +57,7 @@ enum PropertyType : int
heat_capacity,
/// used to compute the hydrodynamic dispersion tensor.
longitudinal_dispersivity,
+ molality,
molar_mass,
mole_fraction,
/// used to compute the hydrodynamic dispersion tensor.
@@ -182,6 +182,11 @@ inline PropertyType convertStringToProperty(std::string const& inString)
{
return PropertyType::longitudinal_dispersivity;
}
+ // TODO (renchao): add property "volume fraction"
+ if (boost::iequals(inString, "molality"))
+ {
+ return PropertyType::molality;
+ }
if (boost::iequals(inString, "molar_mass"))
{
return PropertyType::molar_mass;
@@ -290,11 +295,6 @@ inline PropertyType convertStringToProperty(std::string const& inString)
{
return PropertyType::viscosity;
}
- // TODO (renchao): replace property "amount" with volume fraction
- if (boost::iequals(inString, "amount"))
- {
- return PropertyType::amount;
- }
OGS_FATAL(
"The property name '{:s}' does not correspond to any known property",
@@ -306,7 +306,6 @@ inline PropertyType convertStringToProperty(std::string const& inString)
static const std::array<std::string, PropertyType::number_of_properties>
property_enum_to_string{{"acentric_factor",
- "amount",
"binary_interaction_coefficient",
"biot_coefficient",
"bishops_effective_stress",
@@ -327,6 +326,7 @@ static const std::array<std::string, PropertyType::number_of_properties>
"fredlund_parameters",
"heat_capacity",
"longitudinal_dispersivity",
+ "molality",
"molar_mass",
"mole_fraction",
"molecular_diffusion",
--
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