From 9ad0eab91003edc3735cb26f13f60f73d3845f97 Mon Sep 17 00:00:00 2001
From: renchao_lu <renchao.lu@gmail.com>
Date: Sun, 31 May 2020 17:10:46 +0200
Subject: [PATCH] [CL] Remove mapping process id to component name.
---
.../CreateChemicalSolverInterface.cpp | 10 +--
ChemistryLib/CreateChemicalSolverInterface.h | 2 -
ChemistryLib/PhreeqcIO.cpp | 89 ++++++++-----------
ChemistryLib/PhreeqcIO.h | 6 +-
.../PhreeqcIOData/CreateAqueousSolution.cpp | 8 +-
.../PhreeqcIOData/CreateAqueousSolution.h | 8 +-
.../PhreeqcIOData/CreateSolutionComponent.cpp | 33 +------
.../PhreeqcIOData/CreateSolutionComponent.h | 5 +-
8 files changed, 43 insertions(+), 118 deletions(-)
diff --git a/ChemistryLib/CreateChemicalSolverInterface.cpp b/ChemistryLib/CreateChemicalSolverInterface.cpp
index bd080a09972..da0bb97b329 100644
--- a/ChemistryLib/CreateChemicalSolverInterface.cpp
+++ b/ChemistryLib/CreateChemicalSolverInterface.cpp
@@ -67,8 +67,6 @@ template <>
std::unique_ptr<ChemicalSolverInterface>
createChemicalSolverInterface<ChemicalSolver::Phreeqc>(
std::vector<std::unique_ptr<MeshLib::Mesh>> const& meshes,
- std::vector<std::pair<int, std::string>> const&
- process_id_to_component_name_map,
BaseLib::ConfigTree const& config, std::string const& output_directory)
{
auto mesh_name =
@@ -92,8 +90,7 @@ createChemicalSolverInterface<ChemicalSolver::Phreeqc>(
// solution
auto aqueous_solution = PhreeqcIOData::createAqueousSolution(
//! \ogs_file_param{prj__chemical_system__solution}
- config.getConfigSubtree("solution"),
- process_id_to_component_name_map);
+ config.getConfigSubtree("solution"));
// kinetic reactants
auto chemical_system_map =
@@ -158,16 +155,13 @@ createChemicalSolverInterface<ChemicalSolver::Phreeqc>(
std::move(path_to_database), std::move(aqueous_solutions),
std::move(equilibrium_reactants), std::move(kinetic_reactants),
std::move(reaction_rates), std::move(surface), std::move(user_punch),
- std::move(output), std::move(dump), std::move(knobs),
- process_id_to_component_name_map);
+ std::move(output), std::move(dump), std::move(knobs));
}
template <>
std::unique_ptr<ChemicalSolverInterface>
createChemicalSolverInterface<ChemicalSolver::PhreeqcKernel>(
std::vector<std::unique_ptr<MeshLib::Mesh>> const& meshes,
- std::vector<std::pair<int, std::string>> const&
- process_id_to_component_name_map,
BaseLib::ConfigTree const& config, std::string const& /*output_directory*/)
{
auto mesh = *meshes[0];
diff --git a/ChemistryLib/CreateChemicalSolverInterface.h b/ChemistryLib/CreateChemicalSolverInterface.h
index 39615caae60..16af2b92eb9 100644
--- a/ChemistryLib/CreateChemicalSolverInterface.h
+++ b/ChemistryLib/CreateChemicalSolverInterface.h
@@ -33,7 +33,5 @@ class ChemicalSolverInterface;
template <ChemicalSolver chemical_solver>
std::unique_ptr<ChemicalSolverInterface> createChemicalSolverInterface(
std::vector<std::unique_ptr<MeshLib::Mesh>> const& meshes,
- std::vector<std::pair<int, std::string>> const&
- process_id_to_component_name_map,
BaseLib::ConfigTree const& config, std::string const& output_directory);
} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIO.cpp b/ChemistryLib/PhreeqcIO.cpp
index 1735c5f6104..8f6999744f2 100644
--- a/ChemistryLib/PhreeqcIO.cpp
+++ b/ChemistryLib/PhreeqcIO.cpp
@@ -56,9 +56,7 @@ PhreeqcIO::PhreeqcIO(std::string const project_file_name,
std::unique_ptr<UserPunch>&& user_punch,
std::unique_ptr<Output>&& output,
std::unique_ptr<Dump>&& dump,
- Knobs&& knobs,
- std::vector<std::pair<int, std::string>> const&
- process_id_to_component_name_map)
+ Knobs&& knobs)
: _phreeqc_input_file(project_file_name + "_phreeqc.inp"),
_mesh(mesh),
_database(std::move(database)),
@@ -70,8 +68,7 @@ PhreeqcIO::PhreeqcIO(std::string const project_file_name,
_user_punch(std::move(user_punch)),
_output(std::move(output)),
_dump(std::move(dump)),
- _knobs(std::move(knobs)),
- _process_id_to_component_name_map(process_id_to_component_name_map)
+ _knobs(std::move(knobs))
{
// initialize phreeqc instance
if (CreateIPhreeqc() != phreeqc_instance_id)
@@ -159,61 +156,45 @@ void PhreeqcIO::setAqueousSolutionsOrUpdateProcessSolutions(
// Loop over transport process id map to retrieve component
// concentrations from process solutions or to update process solutions
// after chemical calculation by Phreeqc
- for (auto const& process_id_to_component_name_map_element :
- _process_id_to_component_name_map)
- {
- auto const& transport_process_id =
- process_id_to_component_name_map_element.first;
- auto const& transport_process_variable =
- process_id_to_component_name_map_element.second;
+ for (unsigned component_id = 0; component_id < components.size();
+ ++component_id)
+ {
+ auto& component = components[component_id];
auto& transport_process_solution =
- process_solutions[transport_process_id];
-
- auto component =
- std::find_if(components.begin(), components.end(),
- [&transport_process_variable](Component const& c) {
- return c.name == transport_process_variable;
- });
-
- if (component != components.end())
+ process_solutions[component_id + 1];
+ switch (status)
{
- switch (status)
- {
- case Status::SettingAqueousSolutions:
- // Set component concentrations.
- component->amount =
- transport_process_solution->get(global_id);
- break;
- case Status::UpdatingProcessSolutions:
- // Update solutions of component transport processes.
- transport_process_solution->set(global_id,
- component->amount);
- break;
- }
+ case Status::SettingAqueousSolutions:
+ // Set component concentrations.
+ component.amount =
+ transport_process_solution->get(global_id);
+ break;
+ case Status::UpdatingProcessSolutions:
+ // Update solutions of component transport processes.
+ transport_process_solution->set(global_id,
+ component.amount);
+ break;
}
+ }
- if (transport_process_variable == "H")
+ switch (status)
+ {
+ case Status::SettingAqueousSolutions:
{
- switch (status)
- {
- case Status::SettingAqueousSolutions:
- {
- // Set pH value by hydrogen concentration.
- aqueous_solution.pH = -std::log10(
- transport_process_solution->get(global_id));
- break;
- }
- case Status::UpdatingProcessSolutions:
- {
- // Update hydrogen concentration by pH value.
- auto hydrogen_concentration =
- std::pow(10, -aqueous_solution.pH);
- transport_process_solution->set(global_id,
- hydrogen_concentration);
- break;
- }
- }
+ // Set pH value by hydrogen concentration.
+ aqueous_solution.pH =
+ -std::log10(process_solutions.back()->get(global_id));
+ break;
+ }
+ case Status::UpdatingProcessSolutions:
+ {
+ // Update hydrogen concentration by pH value.
+ auto hydrogen_concentration =
+ std::pow(10, -aqueous_solution.pH);
+ process_solutions.back()->set(global_id,
+ hydrogen_concentration);
+ break;
}
}
}
diff --git a/ChemistryLib/PhreeqcIO.h b/ChemistryLib/PhreeqcIO.h
index 7bf70f58f5c..2db34efab46 100644
--- a/ChemistryLib/PhreeqcIO.h
+++ b/ChemistryLib/PhreeqcIO.h
@@ -53,9 +53,7 @@ public:
std::unique_ptr<UserPunch>&& user_punch,
std::unique_ptr<Output>&& output,
std::unique_ptr<Dump>&& dump,
- Knobs&& knobs,
- std::vector<std::pair<int, std::string>> const&
- process_id_to_component_name_map);
+ Knobs&& knobs);
void executeInitialCalculation(
std::vector<GlobalVector*>& process_solutions) override;
@@ -101,8 +99,6 @@ private:
std::unique_ptr<Output> const _output;
std::unique_ptr<Dump> const _dump;
Knobs const _knobs;
- std::vector<std::pair<int, std::string>> const&
- _process_id_to_component_name_map;
double _dt = std::numeric_limits<double>::quiet_NaN();
const int phreeqc_instance_id = 0;
};
diff --git a/ChemistryLib/PhreeqcIOData/CreateAqueousSolution.cpp b/ChemistryLib/PhreeqcIOData/CreateAqueousSolution.cpp
index 907eea1885e..70a7e2c6157 100644
--- a/ChemistryLib/PhreeqcIOData/CreateAqueousSolution.cpp
+++ b/ChemistryLib/PhreeqcIOData/CreateAqueousSolution.cpp
@@ -18,10 +18,7 @@ namespace ChemistryLib
{
namespace PhreeqcIOData
{
-AqueousSolution createAqueousSolution(
- BaseLib::ConfigTree const& config,
- std::vector<std::pair<int, std::string>> const&
- process_id_to_component_name_map)
+AqueousSolution createAqueousSolution(BaseLib::ConfigTree const& config)
{
//! \ogs_file_param{prj__chemical_system__solution__temperature}
auto const temperature = config.getConfigParameter<double>("temperature");
@@ -32,8 +29,7 @@ AqueousSolution createAqueousSolution(
//! \ogs_file_param{prj__chemical_system__solution__pe}
auto const pe = config.getConfigParameter<double>("pe");
- auto components =
- createSolutionComponents(config, process_id_to_component_name_map);
+ auto components = createSolutionComponents(config);
auto charge_balance = createChargeBalance(config);
diff --git a/ChemistryLib/PhreeqcIOData/CreateAqueousSolution.h b/ChemistryLib/PhreeqcIOData/CreateAqueousSolution.h
index 787d4196fb6..8e0d680f276 100644
--- a/ChemistryLib/PhreeqcIOData/CreateAqueousSolution.h
+++ b/ChemistryLib/PhreeqcIOData/CreateAqueousSolution.h
@@ -10,9 +10,6 @@
#pragma once
-#include <string>
-#include <vector>
-
namespace BaseLib
{
class ConfigTree;
@@ -24,9 +21,6 @@ namespace PhreeqcIOData
{
struct AqueousSolution;
-AqueousSolution createAqueousSolution(
- BaseLib::ConfigTree const& config,
- std::vector<std::pair<int, std::string>> const&
- process_id_to_component_name_map);
+AqueousSolution createAqueousSolution(BaseLib::ConfigTree const& config);
} // namespace PhreeqcIOData
} // namespace ChemistryLib
diff --git a/ChemistryLib/PhreeqcIOData/CreateSolutionComponent.cpp b/ChemistryLib/PhreeqcIOData/CreateSolutionComponent.cpp
index 66430c61ddb..44c0fce8422 100644
--- a/ChemistryLib/PhreeqcIOData/CreateSolutionComponent.cpp
+++ b/ChemistryLib/PhreeqcIOData/CreateSolutionComponent.cpp
@@ -11,16 +11,13 @@
#include "CreateSolutionComponent.h"
#include "AqueousSolution.h"
#include "BaseLib/ConfigTree.h"
-#include "BaseLib/Error.h"
namespace ChemistryLib
{
namespace PhreeqcIOData
{
std::vector<Component> createSolutionComponents(
- BaseLib::ConfigTree const& config,
- std::vector<std::pair<int, std::string>> const&
- process_id_to_component_name_map)
+ BaseLib::ConfigTree const& config)
{
std::vector<Component> components;
//! \ogs_file_param{prj__chemical_system__solution__components}
@@ -33,34 +30,6 @@ std::vector<Component> createSolutionComponents(
components.emplace_back(component_name);
}
- for (auto const& component : components)
- {
- auto process_id_to_component_name_map_element = std::find_if(
- process_id_to_component_name_map.begin(),
- process_id_to_component_name_map.end(),
- [&component](std::pair<int, std::string> const& map_element) {
- return map_element.second == component.name;
- });
-
- if (process_id_to_component_name_map_element ==
- process_id_to_component_name_map.end())
- {
- OGS_FATAL(
- "Component {:s} given in <solution>/<components> is not found "
- "in "
- "specified coupled processes (see "
- "<process>/<process_variables>/<concentration>).",
- component.name);
- }
- }
- if (components.size() + 1 != process_id_to_component_name_map.size())
- {
- OGS_FATAL(
- "The number of components given in <solution>/<components> is not "
- "in line with the number of transport processes - 1 which stands "
- "for the transport process of hydrogen.");
- }
-
return components;
}
} // namespace PhreeqcIOData
diff --git a/ChemistryLib/PhreeqcIOData/CreateSolutionComponent.h b/ChemistryLib/PhreeqcIOData/CreateSolutionComponent.h
index 66151c5d671..417450e9dac 100644
--- a/ChemistryLib/PhreeqcIOData/CreateSolutionComponent.h
+++ b/ChemistryLib/PhreeqcIOData/CreateSolutionComponent.h
@@ -10,7 +10,6 @@
#pragma once
-#include <string>
#include <vector>
namespace BaseLib
@@ -25,8 +24,6 @@ namespace PhreeqcIOData
struct Component;
std::vector<Component> createSolutionComponents(
- BaseLib::ConfigTree const& config,
- std::vector<std::pair<int, std::string>> const&
- process_id_to_component_name_map);
+ BaseLib::ConfigTree const& config);
} // namespace PhreeqcIOData
} // namespace ChemistryLib
--
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