From 78b7b70e2c062a9631952714595b01a9f3e6b80c Mon Sep 17 00:00:00 2001
From: renchao_lu <renchao.lu@gmail.com>
Date: Sat, 21 Sep 2019 15:40:06 +0200
Subject: [PATCH] [CL] Add Surface (definition and creation).
---
.../CreateChemicalSolverInterface.cpp | 7 +++
ChemistryLib/PhreeqcIOData/CreateSurface.cpp | 52 +++++++++++++++++++
ChemistryLib/PhreeqcIOData/CreateSurface.h | 29 +++++++++++
ChemistryLib/PhreeqcIOData/Surface.cpp | 27 ++++++++++
ChemistryLib/PhreeqcIOData/Surface.h | 46 ++++++++++++++++
5 files changed, 161 insertions(+)
create mode 100644 ChemistryLib/PhreeqcIOData/CreateSurface.cpp
create mode 100644 ChemistryLib/PhreeqcIOData/CreateSurface.h
create mode 100644 ChemistryLib/PhreeqcIOData/Surface.cpp
create mode 100644 ChemistryLib/PhreeqcIOData/Surface.h
diff --git a/ChemistryLib/CreateChemicalSolverInterface.cpp b/ChemistryLib/CreateChemicalSolverInterface.cpp
index 3f4a3d28253..489c91e1c30 100644
--- a/ChemistryLib/CreateChemicalSolverInterface.cpp
+++ b/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(
diff --git a/ChemistryLib/PhreeqcIOData/CreateSurface.cpp b/ChemistryLib/PhreeqcIOData/CreateSurface.cpp
new file mode 100644
index 00000000000..48be1050f6d
--- /dev/null
+++ b/ChemistryLib/PhreeqcIOData/CreateSurface.cpp
@@ -0,0 +1,52 @@
+/**
+ * \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
diff --git a/ChemistryLib/PhreeqcIOData/CreateSurface.h b/ChemistryLib/PhreeqcIOData/CreateSurface.h
new file mode 100644
index 00000000000..08da56da749
--- /dev/null
+++ b/ChemistryLib/PhreeqcIOData/CreateSurface.h
@@ -0,0 +1,29 @@
+/**
+ * \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
diff --git a/ChemistryLib/PhreeqcIOData/Surface.cpp b/ChemistryLib/PhreeqcIOData/Surface.cpp
new file mode 100644
index 00000000000..54d604d873c
--- /dev/null
+++ b/ChemistryLib/PhreeqcIOData/Surface.cpp
@@ -0,0 +1,27 @@
+/**
+ * \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
diff --git a/ChemistryLib/PhreeqcIOData/Surface.h b/ChemistryLib/PhreeqcIOData/Surface.h
new file mode 100644
index 00000000000..dddfac90415
--- /dev/null
+++ b/ChemistryLib/PhreeqcIOData/Surface.h
@@ -0,0 +1,46 @@
+/**
+ * \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
--
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