From d652be41e2058b0cd9bb17d40a49bab1f9f5ea5c Mon Sep 17 00:00:00 2001
From: renchao_lu <renchao.lu@gmail.com>
Date: Sat, 13 Jul 2019 16:27:52 +0200
Subject: [PATCH] [CL] Pass mesh information for creating PhreeqcIO instance.
---
Applications/ApplicationsLib/ProjectData.cpp | 4 ++--
ChemistryLib/CreatePhreeqcIO.cpp | 17 +++++++----------
ChemistryLib/CreatePhreeqcIO.h | 7 ++++++-
3 files changed, 15 insertions(+), 13 deletions(-)
diff --git a/Applications/ApplicationsLib/ProjectData.cpp b/Applications/ApplicationsLib/ProjectData.cpp
index 7189bc26a34..a6f3693eebf 100644
--- a/Applications/ApplicationsLib/ProjectData.cpp
+++ b/Applications/ApplicationsLib/ProjectData.cpp
@@ -1043,8 +1043,8 @@ void ProjectData::parseChemicalSystem(
component_transport_process->getProcessIDToComponentNameMap();
_chemical_system = ChemistryLib::createPhreeqcIO(
- _mesh_vec[0]->getNumberOfBaseNodes(),
- process_id_to_component_name_map, *config, output_directory);
+ *_mesh_vec[0], process_id_to_component_name_map, *config,
+ output_directory);
}
else
{
diff --git a/ChemistryLib/CreatePhreeqcIO.cpp b/ChemistryLib/CreatePhreeqcIO.cpp
index 61b542d0f3e..1799565dbbd 100644
--- a/ChemistryLib/CreatePhreeqcIO.cpp
+++ b/ChemistryLib/CreatePhreeqcIO.cpp
@@ -11,6 +11,7 @@
#include "BaseLib/Error.h"
#include "CreateOutput.h"
#include "CreatePhreeqcIO.h"
+#include "MeshLib/Mesh.h"
#include "PhreeqcIO.h"
#include "PhreeqcIOData/AqueousSolution.h"
#include "PhreeqcIOData/CreateAqueousSolution.h"
@@ -24,13 +25,13 @@
namespace ChemistryLib
{
std::unique_ptr<PhreeqcIO> createPhreeqcIO(
- std::size_t const num_nodes,
+ MeshLib::Mesh const& mesh,
std::vector<std::pair<int, std::string>> const&
process_id_to_component_name_map,
BaseLib::ConfigTree const& config,
std::string const& output_directory)
{
- auto const& num_chemical_systems = num_nodes;
+ auto const num_chemical_systems = mesh.getNumberOfBaseNodes();
// database
//! \ogs_file_param{prj__chemical_system__database}
@@ -88,18 +89,14 @@ std::unique_ptr<PhreeqcIO> createPhreeqcIO(
num_chemical_systems, aqueous_solution_per_chem_sys);
// equilibrium phases
- auto const equilibrium_phases_per_chem_sys = createEquilibriumPhases(
+ auto equilibrium_phases = createEquilibriumPhases(
//! \ogs_file_param{prj__chemical_system__equilibrium_phases}
- config.getConfigSubtreeOptional("equilibrium_phases"));
- std::vector<std::vector<EquilibriumPhase>> equilibrium_phases(
- num_chemical_systems, equilibrium_phases_per_chem_sys);
+ config.getConfigSubtreeOptional("equilibrium_phases"), mesh);
// kinetic reactants
- auto const kinetic_reactants_per_chem_sys = createKineticReactants(
+ auto kinetic_reactants = createKineticReactants(
//! \ogs_file_param{prj__chemical_system__kinetic_reactants}
- config.getConfigSubtreeOptional("kinetic_reactants"));
- std::vector<std::vector<KineticReactant>> kinetic_reactants(
- num_chemical_systems, kinetic_reactants_per_chem_sys);
+ config.getConfigSubtreeOptional("kinetic_reactants"), mesh);
// rates
auto reaction_rates = createReactionRates(
diff --git a/ChemistryLib/CreatePhreeqcIO.h b/ChemistryLib/CreatePhreeqcIO.h
index 46652a3d1bf..addc2bfabef 100644
--- a/ChemistryLib/CreatePhreeqcIO.h
+++ b/ChemistryLib/CreatePhreeqcIO.h
@@ -13,6 +13,11 @@
#include "PhreeqcIO.h"
+namespace MeshLib
+{
+class Mesh;
+}
+
namespace BaseLib
{
class ConfigTree;
@@ -26,7 +31,7 @@ class Process;
namespace ChemistryLib
{
std::unique_ptr<PhreeqcIO> createPhreeqcIO(
- std::size_t const num_nodes,
+ MeshLib::Mesh const& mesh,
std::vector<std::pair<int, std::string>> const&
process_id_to_component_name_map,
BaseLib::ConfigTree const& config,
--
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