diff --git a/ChemistryLib/CreateChemicalSolverInterface.cpp b/ChemistryLib/CreateChemicalSolverInterface.cpp
index 7212fda32ab4c663ea10b9492a85469358048a1a..11f677e6121ea016ae1645a21061241a5b3681f6 100644
--- a/ChemistryLib/CreateChemicalSolverInterface.cpp
+++ b/ChemistryLib/CreateChemicalSolverInterface.cpp
@@ -17,17 +17,13 @@
#include "Common/CreateReactionRate.h"
#include "MeshLib/Mesh.h"
#include "PhreeqcIO.h"
-#include "PhreeqcIOData/AqueousSolution.h"
-#include "PhreeqcIOData/CreateAqueousSolution.h"
-#include "PhreeqcIOData/CreateEquilibriumReactants.h"
-#include "PhreeqcIOData/CreateKineticReactant.h"
+#include "PhreeqcIOData/ChemicalSystem.h"
+#include "PhreeqcIOData/CreateChemicalSystem.h"
#include "PhreeqcIOData/CreateKnobs.h"
#include "PhreeqcIOData/CreateOutput.h"
#include "PhreeqcIOData/CreateSurface.h"
#include "PhreeqcIOData/CreateUserPunch.h"
#include "PhreeqcIOData/Dump.h"
-#include "PhreeqcIOData/EquilibriumReactant.h"
-#include "PhreeqcIOData/KineticReactant.h"
#include "PhreeqcIOData/Knobs.h"
#include "PhreeqcIOData/ReactionRate.h"
#include "PhreeqcIOData/Surface.h"
@@ -87,32 +83,18 @@ createChemicalSolverInterface<ChemicalSolver::Phreeqc>(
auto path_to_database = parseDatabasePath(config);
- // solution
- auto aqueous_solution = PhreeqcIOData::createAqueousSolution(
- //! \ogs_file_param{prj__chemical_system__solution}
- config.getConfigSubtree("solution"));
-
- // kinetic reactants
+ // chemical system
auto chemical_system_map =
*mesh.getProperties().template getPropertyVector<std::size_t>(
"bulk_node_ids", MeshLib::MeshItemType::Node, 1);
-
- auto kinetic_reactants = PhreeqcIOData::createKineticReactants(
- //! \ogs_file_param{prj__chemical_system__kinetic_reactants}
- config.getConfigSubtreeOptional("kinetic_reactants"), *meshes[0],
- chemical_system_map);
+ auto chemical_system = PhreeqcIOData::createChemicalSystem(
+ config, *meshes[0], chemical_system_map);
// rates
auto reaction_rates = createReactionRates<PhreeqcIOData::ReactionRate>(
//! \ogs_file_param{prj__chemical_system__rates}
config.getConfigSubtreeOptional("rates"));
- // equilibrium reactants
- auto equilibrium_reactants = PhreeqcIOData::createEquilibriumReactants(
- //! \ogs_file_param{prj__chemical_system__equilibrium_reactants}
- config.getConfigSubtreeOptional("equilibrium_reactants"), *meshes[0],
- chemical_system_map);
-
// surface
auto surface = PhreeqcIOData::createSurface(
//! \ogs_file_param{prj__chemical_system__surface}
@@ -138,22 +120,15 @@ createChemicalSolverInterface<ChemicalSolver::Phreeqc>(
config.getConfigSubtreeOptional("user_punch"), *meshes[0]);
// output
- auto const& components = aqueous_solution.components;
auto const use_high_precision =
//! \ogs_file_param{prj__chemical_system__use_high_precision}
config.getConfigParameter<bool>("use_high_precision", true);
auto output = PhreeqcIOData::createOutput(
- components, equilibrium_reactants, kinetic_reactants, user_punch,
- use_high_precision, project_file_name);
-
- auto const num_chemical_systems = mesh.getNumberOfBaseNodes();
- std::vector<PhreeqcIOData::AqueousSolution> aqueous_solutions(
- num_chemical_systems, aqueous_solution);
+ *chemical_system, user_punch, use_high_precision, project_file_name);
return std::make_unique<PhreeqcIOData::PhreeqcIO>(
std::move(project_file_name), *meshes[mesh.getID()],
- std::move(path_to_database), std::move(aqueous_solutions),
- std::move(equilibrium_reactants), std::move(kinetic_reactants),
+ std::move(path_to_database), std::move(chemical_system),
std::move(reaction_rates), std::move(surface), std::move(user_punch),
std::move(output), std::move(dump), std::move(knobs));
}
diff --git a/ChemistryLib/PhreeqcIO.cpp b/ChemistryLib/PhreeqcIO.cpp
index cb6088a50e719a9712214df1d00c986d5412ac16..d6345eaa231593bca05fb0c337aecfcfa682ed2a 100644
--- a/ChemistryLib/PhreeqcIO.cpp
+++ b/ChemistryLib/PhreeqcIO.cpp
@@ -20,6 +20,7 @@
#include "BaseLib/ConfigTreeUtil.h"
#include "MeshLib/Mesh.h"
#include "PhreeqcIOData/AqueousSolution.h"
+#include "PhreeqcIOData/ChemicalSystem.h"
#include "PhreeqcIOData/Dump.h"
#include "PhreeqcIOData/EquilibriumReactant.h"
#include "PhreeqcIOData/KineticReactant.h"
@@ -48,9 +49,7 @@ std::ostream& operator<<(std::ostream& os,
PhreeqcIO::PhreeqcIO(std::string const project_file_name,
MeshLib::Mesh const& mesh,
std::string&& database,
- std::vector<AqueousSolution>&& aqueous_solutions,
- std::vector<EquilibriumReactant>&& equilibrium_reactants,
- std::vector<KineticReactant>&& kinetic_reactants,
+ std::unique_ptr<ChemicalSystem>&& chemical_system,
std::vector<ReactionRate>&& reaction_rates,
std::vector<SurfaceSite>&& surface,
std::unique_ptr<UserPunch>&& user_punch,
@@ -60,9 +59,7 @@ PhreeqcIO::PhreeqcIO(std::string const project_file_name,
: _phreeqc_input_file(project_file_name + "_phreeqc.inp"),
_mesh(mesh),
_database(std::move(database)),
- _aqueous_solutions(std::move(aqueous_solutions)),
- _equilibrium_reactants(std::move(equilibrium_reactants)),
- _kinetic_reactants(std::move(kinetic_reactants)),
+ _chemical_system(std::move(chemical_system)),
_reaction_rates(std::move(reaction_rates)),
_surface(std::move(surface)),
_user_punch(std::move(user_punch)),
diff --git a/ChemistryLib/PhreeqcIO.h b/ChemistryLib/PhreeqcIO.h
index 1835c743aa7eb2cbf69c9e35801f936ee9a35f0c..4c59ca563b295b92f38f76e7ebc2aa1066177baf 100644
--- a/ChemistryLib/PhreeqcIO.h
+++ b/ChemistryLib/PhreeqcIO.h
@@ -24,9 +24,7 @@ namespace ChemistryLib
{
namespace PhreeqcIOData
{
-struct AqueousSolution;
-struct EquilibriumReactant;
-struct KineticReactant;
+struct ChemicalSystem;
struct ReactionRate;
struct Output;
struct SurfaceSite;
@@ -45,9 +43,7 @@ public:
PhreeqcIO(std::string const project_file_name,
MeshLib::Mesh const& mesh,
std::string&& database,
- std::vector<AqueousSolution>&& aqueous_solutions,
- std::vector<EquilibriumReactant>&& equilibrium_reactants,
- std::vector<KineticReactant>&& kinetic_reactants,
+ std::unique_ptr<ChemicalSystem>&& chemical_system,
std::vector<ReactionRate>&& reaction_rates,
std::vector<SurfaceSite>&& surface,
std::unique_ptr<UserPunch>&& user_punch,
@@ -92,9 +88,7 @@ private:
MeshLib::Mesh const& _mesh;
std::string const _database;
- std::vector<AqueousSolution> _aqueous_solutions;
- std::vector<EquilibriumReactant> _equilibrium_reactants;
- std::vector<KineticReactant> _kinetic_reactants;
+ std::unique_ptr<ChemicalSystem> _chemical_system;
std::vector<ReactionRate> const _reaction_rates;
std::vector<SurfaceSite> const _surface;
std::unique_ptr<UserPunch> _user_punch;
diff --git a/ChemistryLib/PhreeqcIOData/ChemicalSystem.h b/ChemistryLib/PhreeqcIOData/ChemicalSystem.h
new file mode 100644
index 0000000000000000000000000000000000000000..596c4ad2f63f5e566da37b9df8647bfe0f0c982e
--- /dev/null
+++ b/ChemistryLib/PhreeqcIOData/ChemicalSystem.h
@@ -0,0 +1,45 @@
+/**
+ * \file
+ * \copyright
+ * Copyright (c) 2012-2020, OpenGeoSys Community (http://www.opengeosys.org)
+ * Distributed under a Modified BSD License.
+ * See accompanying file LICENSE.txt or
+ * http://www.opengeosys.org/project/license
+ *
+ */
+
+#pragma once
+
+#include <memory>
+#include <vector>
+
+#include "AqueousSolution.h"
+#include "EquilibriumReactant.h"
+#include "KineticReactant.h"
+
+namespace MeshLib
+{
+class Mesh;
+}
+
+namespace ChemistryLib
+{
+namespace PhreeqcIOData
+{
+struct ChemicalSystem
+{
+ ChemicalSystem(std::unique_ptr<AqueousSolution>&& aqueous_solution_,
+ std::vector<KineticReactant>&& kinetic_reactants_,
+ std::vector<EquilibriumReactant>&& equilibrium_reactants_)
+ : aqueous_solution(std::move(aqueous_solution_)),
+ kinetic_reactants(std::move(kinetic_reactants_)),
+ equilibrium_reactants(std::move(equilibrium_reactants_))
+ {
+ }
+
+ std::unique_ptr<AqueousSolution> aqueous_solution;
+ std::vector<KineticReactant> kinetic_reactants;
+ std::vector<EquilibriumReactant> equilibrium_reactants;
+};
+} // namespace PhreeqcIOData
+} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/CreateChemicalSystem.cpp b/ChemistryLib/PhreeqcIOData/CreateChemicalSystem.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..f8cc8ee7612f6b1ee6f821542f936ef8f8c3ffa8
--- /dev/null
+++ b/ChemistryLib/PhreeqcIOData/CreateChemicalSystem.cpp
@@ -0,0 +1,50 @@
+/**
+ * \file
+ * \copyright
+ * Copyright (c) 2012-2020, OpenGeoSys Community (http://www.opengeosys.org)
+ * Distributed under a Modified BSD License.
+ * See accompanying file LICENSE.txt or
+ * http://www.opengeosys.org/project/license
+ *
+ */
+
+#include "CreateChemicalSystem.h"
+#include "BaseLib/ConfigTree.h"
+#include "ChemicalSystem.h"
+#include "CreateAqueousSolution.h"
+#include "CreateEquilibriumReactants.h"
+#include "CreateKineticReactant.h"
+#include "EquilibriumReactant.h"
+#include "KineticReactant.h"
+
+namespace ChemistryLib
+{
+namespace PhreeqcIOData
+{
+std::unique_ptr<ChemicalSystem> createChemicalSystem(
+ BaseLib::ConfigTree const& config, MeshLib::Mesh const& mesh,
+ MeshLib::PropertyVector<std::size_t> const& chemical_system_map)
+{
+ // solution
+ auto aqueous_solution = createAqueousSolution(
+ //! \ogs_file_param{prj__chemical_system__solution}
+ config.getConfigSubtree("solution"), mesh, chemical_system_map);
+
+ // kinetic reactants
+ auto kinetic_reactants = createKineticReactants(
+ //! \ogs_file_param{prj__chemical_system__kinetic_reactants}
+ config.getConfigSubtreeOptional("kinetic_reactants"), mesh,
+ chemical_system_map);
+
+ // equilibrium reactants
+ auto equilibrium_reactants = createEquilibriumReactants(
+ //! \ogs_file_param{prj__chemical_system__equilibrium_reactants}
+ config.getConfigSubtreeOptional("equilibrium_reactants"), mesh,
+ chemical_system_map);
+
+ return std::make_unique<ChemicalSystem>(std::move(aqueous_solution),
+ std::move(kinetic_reactants),
+ std::move(equilibrium_reactants));
+}
+} // namespace PhreeqcIOData
+} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/CreateChemicalSystem.h b/ChemistryLib/PhreeqcIOData/CreateChemicalSystem.h
new file mode 100644
index 0000000000000000000000000000000000000000..59962d127534d1407aaa6c0b6c5eca093220276b
--- /dev/null
+++ b/ChemistryLib/PhreeqcIOData/CreateChemicalSystem.h
@@ -0,0 +1,38 @@
+/**
+ * \file
+ * \copyright
+ * Copyright (c) 2012-2020, OpenGeoSys Community (http://www.opengeosys.org)
+ * Distributed under a Modified BSD License.
+ * See accompanying file LICENSE.txt or
+ * http://www.opengeosys.org/project/license
+ *
+ */
+
+#pragma once
+
+#include <memory>
+
+namespace BaseLib
+{
+class ConfigTree;
+}
+
+namespace MeshLib
+{
+class Mesh;
+
+template <typename PROP_VAL_TYPE>
+class PropertyVector;
+} // namespace MeshLib
+
+namespace ChemistryLib
+{
+namespace PhreeqcIOData
+{
+struct ChemicalSystem;
+
+std::unique_ptr<ChemicalSystem> createChemicalSystem(
+ BaseLib::ConfigTree const& config, MeshLib::Mesh const& mesh,
+ MeshLib::PropertyVector<std::size_t> const& chemical_system_map);
+} // namespace PhreeqcIOData
+} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/CreateOutput.cpp b/ChemistryLib/PhreeqcIOData/CreateOutput.cpp
index b34b7441de62e752121ca7a35ce885069992fe2a..70561477c1aa51b16fc56697e3e376876b9f6cba 100644
--- a/ChemistryLib/PhreeqcIOData/CreateOutput.cpp
+++ b/ChemistryLib/PhreeqcIOData/CreateOutput.cpp
@@ -12,8 +12,8 @@
#include <numeric>
#include "AqueousSolution.h"
+#include "ChemicalSystem.h"
#include "CreateOutput.h"
-#include "EquilibriumReactant.h"
#include "KineticReactant.h"
#include "UserPunch.h"
@@ -22,13 +22,14 @@ namespace ChemistryLib
namespace PhreeqcIOData
{
std::unique_ptr<Output> createOutput(
- std::vector<Component> const& components,
- std::vector<EquilibriumReactant> const& equilibrium_reactants,
- std::vector<KineticReactant> const& kinetic_reactants,
+ ChemicalSystem const& chemical_system,
std::unique_ptr<UserPunch> const& user_punch,
bool const use_high_precision,
std::string const& project_file_name)
{
+ auto const& components = chemical_system.aqueous_solution->components;
+ auto const& equilibrium_reactants = chemical_system.equilibrium_reactants;
+ auto const& kinetic_reactants = chemical_system.kinetic_reactants;
// Mark which phreeqc output items will be held.
std::vector<OutputItem> accepted_items{{"pH", ItemType::pH},
{"pe", ItemType::pe}};
diff --git a/ChemistryLib/PhreeqcIOData/CreateOutput.h b/ChemistryLib/PhreeqcIOData/CreateOutput.h
index 1f542fc764dff989f1c2b555e6d0d4d3c0564c60..25663db4be0cbd814a41bb156d481453347f5c65 100644
--- a/ChemistryLib/PhreeqcIOData/CreateOutput.h
+++ b/ChemistryLib/PhreeqcIOData/CreateOutput.h
@@ -18,15 +18,11 @@ namespace ChemistryLib
namespace PhreeqcIOData
{
struct Output;
-struct Component;
-struct EquilibriumReactant;
-struct KineticReactant;
+struct ChemicalSystem;
struct UserPunch;
std::unique_ptr<Output> createOutput(
- std::vector<Component> const& components,
- std::vector<EquilibriumReactant> const& equilibrium_reactants,
- std::vector<KineticReactant> const& kinetic_reactants,
+ ChemicalSystem const& chemical_system,
std::unique_ptr<UserPunch> const& user_punch,
bool const use_high_precision,
std::string const& project_file_name);