[CL] Add Surface (definition and creation).

ChemistryLib/CreateChemicalSolverInterface.cpp

@@ -17,10 +17,12 @@
 #include "PhreeqcIOData/CreateEquilibriumPhase.h"
 #include "PhreeqcIOData/CreateKineticReactant.h"
 #include "PhreeqcIOData/CreateOutput.h"
+#include "PhreeqcIOData/CreateSurface.h"
 #include "PhreeqcIOData/CreateUserPunch.h"
 #include "PhreeqcIOData/EquilibriumPhase.h"
 #include "PhreeqcIOData/KineticReactant.h"
 #include "PhreeqcIOData/ReactionRate.h"
+#include "PhreeqcIOData/Surface.h"
 #include "PhreeqcIOData/UserPunch.h"
 #include "PhreeqcKernel.h"
 #include "PhreeqcKernelData/AqueousSolution.h"
@@ -90,6 +92,11 @@ createChemicalSolverInterface<ChemicalSolver::Phreeqc>(
         //! \ogs_file_param{prj__chemical_system__equilibrium_phases}
         config.getConfigSubtreeOptional("equilibrium_phases"), mesh);
 
+    // surface
+    auto surface = PhreeqcIOData::createSurface(
+        //! \ogs_file_param{prj__chemical_system__surface}
+        config.getConfigSubtreeOptional("surface"));
+
     // output
     auto const& components = aqueous_solution.components;
     auto const project_file_name = BaseLib::joinPaths(

ChemistryLib/PhreeqcIOData/CreateSurface.cpp

+/**
+ * \copyright
+ * Copyright (c) 2012-2019, 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 <boost/optional/optional.hpp>
+
+#include "BaseLib/ConfigTree.h"
+#include "Surface.h"
+
+namespace ChemistryLib
+{
+namespace PhreeqcIOData
+{
+std::vector<SurfaceSite> createSurface(
+    boost::optional<BaseLib::ConfigTree> const& config)
+{
+    if (!config)
+        return {};
+
+    std::vector<SurfaceSite> surface;
+    for (auto const& site_config :
+         //! \ogs_file_param{prj__chemical_system__surface__site}
+         config->getConfigSubtreeList("site"))
+    {
+        //! \ogs_file_param{prj__chemical_system__surface__site__mineral}
+        auto mineral = site_config.getConfigParameter<std::string>("mineral");
+
+        auto const site_density =
+            //! \ogs_file_param{prj__chemical_system__surface__site__site_density}
+            site_config.getConfigParameter<double>("site_density");
+
+        auto const specific_surface_area =
+            //! \ogs_file_param{prj__chemical_system__surface__site__specific_surface_area}
+            site_config.getConfigParameter<double>("specific_surface_area");
+
+        auto const mass =
+            //! \ogs_file_param{prj__chemical_system__surface__site__mass}
+            site_config.getConfigParameter<double>("mass");
+
+        surface.emplace_back(
+            std::move(mineral), site_density, specific_surface_area, mass);
+    }
+
+    return surface;
+}
+}  // namespace PhreeqcIOData
+}  // namespace ChemistryLib

ChemistryLib/PhreeqcIOData/CreateSurface.h

+/**
+ * \copyright
+ * Copyright (c) 2012-2019, 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 <boost/optional/optional_fwd.hpp>
+#include <vector>
+
+namespace BaseLib
+{
+class ConfigTree;
+}
+
+namespace ChemistryLib
+{
+namespace PhreeqcIOData
+{
+struct SurfaceSite;
+
+std::vector<SurfaceSite> createSurface(
+    boost::optional<BaseLib::ConfigTree> const& config);
+}  // namespace PhreeqcIOData
+}  // namespace ChemistryLib

ChemistryLib/PhreeqcIOData/Surface.cpp

+/**
+ * \copyright
+ * Copyright (c) 2012-2019, 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 <ostream>
+
+#include "Surface.h"
+
+namespace ChemistryLib
+{
+namespace PhreeqcIOData
+{
+std::ostream& operator<<(std::ostream& os, SurfaceSite const& surface_site)
+{
+    os << surface_site.mineral.c_str() << " " << surface_site.site_density
+       << " " << surface_site.specific_surface_area << " " << surface_site.mass
+       << "\n";
+
+    return os;
+}
+}  // namespace PhreeqcIOData
+}  // namespace ChemistryLib

ChemistryLib/PhreeqcIOData/Surface.h

+/**
+ * \copyright
+ * Copyright (c) 2012-2019, 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 <iosfwd>
+#include <string>
+
+namespace BaseLib
+{
+class ConfigTree;
+}
+
+namespace ChemistryLib
+{
+namespace PhreeqcIOData
+{
+struct SurfaceSite
+{
+    SurfaceSite(std::string&& mineral_,
+                double const site_density_,
+                double const specific_surface_area_,
+                double const mass_)
+        : mineral(std::move(mineral_)),
+          site_density(site_density_),
+          specific_surface_area(specific_surface_area_),
+          mass(mass_)
+    {
+    }
+
+    friend std::ostream& operator<<(std::ostream& os,
+                                    SurfaceSite const& surface_site);
+
+    std::string const mineral;
+    double const site_density;
+    double const specific_surface_area;
+    double const mass;
+};
+}  // namespace PhreeqcIOData
+}  // namespace ChemistryLib