chloride.cpp
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chloride.cpp
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	/* =============================================================================

	Copyright (c) 2014-2017 F. Georget <fabieng@princeton.edu> Princeton University
	Copyright (c) 2017-2019 F. Georget <fabien.georget@epfl.ch> EPFL
	All rights reserved.


	Redistribution and use in source and binary forms, with or without modification,
	are permitted provided that the following conditions are met:

	1. Redistributions of source code must retain the above copyright notice,
	this list of conditions and the following disclaimer.

	2. Redistributions in binary form must reproduce the above copyright notice,
	this list of conditions and the following disclaimer in the documentation
	and/or other materials provided with the distribution.

	3. Neither the name of the copyright holder nor the names of its
	contributors may be used to endorse or promote products derived from this
	software without specific prior written permission.

	* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
	AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
	IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
	DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
	ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
	(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
	LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
	ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
	(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *

	============================================================================= */

	//! \file bin/reactmicp/chloride.cpp
	//! \brief Main file for the chloride system executable



	#include "app_core.hpp"

	#include "specmicp_common/types.hpp"

	#include "specmicp_common/plugins/plugin_manager.hpp"
	#include "specmicp_common/io/yaml.hpp"
	#include "specmicp_common/io/safe_config.hpp"
	#include "specmicp_common/compat.hpp"
	#include "specmicp_common/log.hpp"
	#include "specmicp_common/filesystem.hpp"
	#include "specmicp_common/string_algorithms.hpp"
	#include "specmicp_common/openmp_support.hpp"
	#include "specmicp_common/io/all_io_files.hpp"

	#include "specmicp_common/physics/io/configuration.hpp"
	#include "specmicp_database/io/configuration.hpp"
	#include "dfpm/io/configuration.hpp"
	#include "specmicp_common/io/configuration.hpp"
	#include "reactmicp/io/configuration_common.hpp"

	#include "specmicp/io/print.hpp"
	#include "dfpm/io/print.hpp"
	#include "specmicp_database/io/print.hpp"

	#include "reactmicp/reactmicp_chloride.hpp"
	#include "dfpm/solver/parabolic_structs.hpp"

	#include "specmicp_common/config.h"

	#include <string>
	#include <memory>
	#include <stdexcept>
	#include <iostream>


	#include "specmicp_common/io/config_yaml_sections.h"
	#include "specmicp_common/plugins/plugin_modules_names.h"


	using namespace specmicp;
	using namespace specmicp::reactmicp;
	using namespace specmicp::reactmicp::systems::chloride;

	//! \brief Headers printed in console
	const char* welcome =
	R"(===============================
	= Reactmicp - Chloride =
	===============================
	(C) copyright 2014-2017 F.Georget, Princeton University
	(C) copyright 2017-2019 F.Georget, EPFL

	version: not good enough yet
	)";


	//! \brief Main loop
	int main (int argc, char* argv[]);



	//! \brief Specialization of SystemApp for the Unsaturated system
	class SystemAppChloride:
	public SystemApp
	{
	public:
	SystemAppChloride():
	SystemApp()
	{}

	void print_welcome() override {
	std::cout << welcome << std::endl;
	}
	std::string driver_identification() {
	return "ReactMiCP Chloride System";
	}

	void init_plugin_manager() override;

	void init_simul_data(const std::vector<std::string> &db_dirs) override;

	void init_staggers() override;

	void check_init_data() override;

	void init_output(const std::string& working_dir);

	solver::VariablesBasePtr get_variables() override {
	return m_simul_data.variables;
	}

	private:
	void init_variables();

	void init_transport_stagger(io::YAMLConfigHandle& config_staggers);
	void init_chem_stagger(io::YAMLConfigHandle& config_staggers);
	void init_upscaling_stagger(io::YAMLConfigHandle& config_staggers);

	SimulationData m_simul_data;
	std::unique_ptr<io::ChlorideHDF5Saver> m_saver;
	};

	// Main

	int main(int argc, char *argv[])
	{
	MainApp app;
	SystemAppChloride system_app;

	int retcode = app.run(system_app, argc, argv);

	return retcode;
	}

	//
	void SystemAppChloride::init_plugin_manager()
	{
	init_plugin_manager_base({
	SPC_PLUGIN_REACTMICP_CHLORIDE_VARIABLES,
	SPC_PLUGIN_REACTMICP_CHLORIDE_UPSCALING
	});
	}

	void SystemAppChloride::init_simul_data(const std::vector<std::string> &db_dirs)
	{

	m_simul_data.units = get_units_from_config();
	m_simul_data.raw_data = get_database_from_config(db_dirs);
	m_simul_data.mesh1d = get_mesh_from_config();
	init_variables();

	m_simul_data.raw_data->freeze_db();
	io::print_db_to_conf_log(m_simul_data.raw_data.get());

	m_simul_data.bcs = io::configure_chloride_boundary_conditions(
	m_simul_data.mesh1d,
	m_simul_data.raw_data,
	get_config().get_section(SPC_CF_S_BOUNDARYCONDITIONS)
	);
	for (auto dof: m_simul_data.bcs->get_fixed_dofs()) {
	std::cout << " - " << dof << std::endl;
	}
	m_all_io_files->sync();
	}

	void SystemAppChloride::init_staggers()
	{
	SPC_CONF_LOG << "\n\n" << SPC_CONF_LOG_SECTION
	<< "\n= Staggers initialization =\n"
	<< SPC_CONF_LOG_SECTION;

	auto config_staggers = get_config().get_section(SPC_CF_S_STAGGERS);

	auto* vars = m_simul_data.variables.get();

	init_upscaling_stagger(config_staggers);
	m_staggers.upscaling->initialize(vars);

	init_chem_stagger(config_staggers);
	m_staggers.chemistry->initialize(vars);

	init_transport_stagger(config_staggers);
	auto tc_stagger = std::static_pointer_cast<ChlorideTransportStagger>(m_staggers.transport);
	tc_stagger->register_chemistry_stagger(
	std::static_pointer_cast<ChlorideChemistryStaggerBase>(m_staggers.chemistry));
	m_staggers.transport->initialize(vars);

	m_staggers.upscaling->register_transport_stagger(m_staggers.transport);
	m_staggers.upscaling->register_chemistry_stagger(m_staggers.chemistry);
	}

	void SystemAppChloride::check_init_data()
	{
	// todo
	}

	void SystemAppChloride::init_output(const std::string& working_dir)
	{
	if (m_config->has_section(SPC_CF_S_REACTOUTPUT)) {
	auto conf = m_config->get_section(SPC_CF_S_REACTOUTPUT);
	// main output file
	auto type = conf.get_optional_attribute<std::string>(
	SPC_CF_S_REACTOUTPUT_A_TYPE, SPC_CF_S_REACTOUTPUT_A_TYPE_V_HDF5);
	if (type == SPC_CF_V_DEFAULT) type = SPC_CF_S_REACTOUTPUT_A_TYPE_V_HDF5;
	if (type != SPC_CF_S_REACTOUTPUT_A_TYPE_V_HDF5) {
	conf.report_error(
	io::YAMLConfigError::InvalidArgument,
	"Only hdf5 is accepted for attribute "
	SPC_CF_S_REACTOUTPUT_A_TYPE " for now.");
	}
	auto filepath = conf.get_required_attribute<std::string>(
	SPC_CF_S_REACTOUTPUT_A_FILEPATH);
	if (not working_dir.empty() and not utils::is_path_absolute(filepath)) {
	filepath = utils::complete_path(working_dir, filepath);
	}
	m_all_io_files->add_solution(io::output_file(IO_FILE_OUTPUT, filepath));

	m_saver = make_unique<io::ChlorideHDF5Saver>(
	filepath, m_simul_data.variables);

	auto* saver_ptr = m_saver.get();
	auto out_pol = [saver_ptr](
	scalar_t timestep,
	solver::VariablesBasePtr _) {
	saver_ptr->save_timestep(timestep);
	};
	m_saver->save_timestep(0.0);
	m_runner->set_output_policy(out_pol);

	// database output
	database::Database db_manager(m_simul_data.raw_data);
	auto db_path = conf.get_attribute<std::string>(SPC_CF_S_REACTOUTPUT_A_DATABASE);
	if (not working_dir.empty() and not utils::is_path_absolute(db_path)) {
	db_path = utils::complete_path(working_dir, db_path);
	}
	db_manager.save(db_path);
	m_all_io_files->add_database(io::output_file(IO_FILE_WORK_DB, db_path));
	}

	const auto iter_path = m_runner->get_iter_file_path();
	if (not iter_path.empty()) {
	m_all_io_files->add_log_file(
	io::output_file(IO_ITER_FILE, iter_path));
	}
	m_all_io_files->sync();
	}

	void SystemAppChloride::init_variables()
	{

	SPC_CONF_LOG << "Variables initialization\n"
	<< SPC_CONF_LOG_SECTION;
	auto config = get_config().get_section(SPC_CF_S_REACTMICPVARIABLES);


	auto type = config.get_optional_attribute<std::string>(
	SPC_CF_S_REACTMICPVARIABLES_A_TYPE, SPC_CF_V_PLUGIN);
	if (type == SPC_CF_V_DEFAULT) type = SPC_CF_V_PLUGIN;
	if (type != SPC_CF_V_PLUGIN) {
	config.report_error(
	io::YAMLConfigError::InvalidArgument,
	"Only accepted value for attribute '"
	SPC_CF_S_REACTMICPVARIABLES_A_TYPE
	"' is '" SPC_CF_V_PLUGIN "'."
	);
	}
	auto plugin_name = get_plugin_name(config);
	auto& plugin_manager = plugins::get_plugin_manager();
	std::unique_ptr<InitializeVariables> initializer =
	plugin_manager.get_object<InitializeVariables>(
	SPC_PLUGIN_REACTMICP_CHLORIDE_VARIABLES,
	plugin_name
	);
	if (initializer == nullptr) {
	CRITICAL << "No variable initializer found";
	throw std::runtime_error("No variable initializer found");
	}
	m_simul_data.variables = initializer->initialize_variables(
	m_simul_data.raw_data,
	m_simul_data.mesh1d,
	m_simul_data.units,
	config
	);
	}

	void SystemAppChloride::init_transport_stagger(io::YAMLConfigHandle& config_staggers)
	{

	SPC_CONF_LOG << "\n\n --> Transport stagger <-- \n"
	<< SPC_CONF_LOG_SECTION;
	// No conf
	// -------
	if (not config_staggers.has_section(SPC_CF_S_STAGGERS_SS_TRANSPORTSTAGGER)) {
	m_staggers.transport = ChlorideTransportStagger::make(
	m_simul_data.variables,
	m_simul_data.bcs
	);
	return;
	}
	// Conf is given
	auto transport_conf = config_staggers.get_section(
	SPC_CF_S_STAGGERS_SS_TRANSPORTSTAGGER);
	std::shared_ptr<ChlorideTransportStagger> stagger = ChlorideTransportStagger::make(
	m_simul_data.variables,
	m_simul_data.bcs
	);
	dfpmsolver::ParabolicDriverOptions default_opts = stagger->get_options();
	if (transport_conf.has_section(SPC_CF_S_STAGGERS_SS_TRANSPORTSTAGGER_SS_DEFAULT_OPTS))
	{
	io::configure_transport_options(
	default_opts,
	transport_conf.get_section(SPC_CF_S_STAGGERS_SS_TRANSPORTSTAGGER_SS_DEFAULT_OPTS)
	);
	}
	SPC_CONF_LOG << "\nDefault transport options\n"
	<< SPC_CONF_LOG_HLINE;
	std::ostringstream msg;
	io::print_transport_options(default_opts, msg);
	SPC_CONF_LOG << msg.str() << SPC_CONF_LOG_HLINE;

	stagger->get_options() = default_opts;
	m_staggers.transport = stagger;


	}

	void SystemAppChloride::init_chem_stagger(io::YAMLConfigHandle& config_staggers)
	{
	SPC_CONF_LOG << "\n\n --> Chemistry stagger <-- \n"
	<< SPC_CONF_LOG_SECTION;
	// no conf
	// -------
	if (not config_staggers.has_section(SPC_CF_S_STAGGERS_SS_CHEMISTRYSTAGGER)) {
	auto opts = systems::EquilibriumOptionsVector::make(
	m_simul_data.mesh1d->nb_nodes());
	opts->get("default").units_set = m_simul_data.units;
	m_staggers.chemistry = ChlorideEquilibriumStagger::make(
	m_simul_data.variables,
	m_simul_data.bcs,
	opts
	);

	return;
	}
	// conf is given
	// --------------
	auto conf_chem = config_staggers.get_section(SPC_CF_S_STAGGERS_SS_CHEMISTRYSTAGGER);
	auto type = conf_chem.get_optional_attribute<std::string>(
	SPC_CF_S_STAGGERS_SS_CHEMISTRYSTAGGER_A_TYPE,
	SPC_CF_S_STAGGERS_SS_CHEMISTRYSTAGGER_A_TYPE_V_EQUILIBRIUM);
	if (type == SPC_CF_V_DEFAULT)
	type = SPC_CF_S_STAGGERS_SS_CHEMISTRYSTAGGER_A_TYPE_V_EQUILIBRIUM;
	if (type !=SPC_CF_S_STAGGERS_SS_CHEMISTRYSTAGGER_A_TYPE_V_EQUILIBRIUM) {
	CRITICAL << "Unknown chemistry stagger";
	throw std::invalid_argument("Only equilibrium stagger supported.");
	}
	SPC_CONF_LOG << "Use equilibrium stagger";
	std::shared_ptr<systems::EquilibriumOptionsVector> opts {nullptr};
	if (conf_chem.has_section(SPC_CF_S_STAGGERS_SS_CHEMISTRYSTAGGER_SS_EQUILIBRIUM_OPTS)) {
	opts = io::configure_equilibrium_options(
	m_simul_data.mesh1d->nb_nodes(),
	m_simul_data.units,
	conf_chem.get_section(SPC_CF_S_STAGGERS_SS_CHEMISTRYSTAGGER_SS_EQUILIBRIUM_OPTS)
	);
	} else {
	SPC_CONF_LOG << " Use default options ";
	opts = systems::EquilibriumOptionsVector::make(m_simul_data.mesh1d->nb_nodes());
	SPC_CONF_LOG << "Default SpecMiCP options : ";
	std::ostringstream msg;
	io::print_specmicp_options(msg, opts->get("default"));
	SPC_CONF_LOG << msg.str() << "\n" << SPC_CONF_LOG_HLINE;

	}
	SPC_CONF_LOG << SPC_CONF_LOG_HLINE;
	m_staggers.chemistry = ChlorideEquilibriumStagger::make(
	m_simul_data.variables,
	m_simul_data.bcs,
	opts
	);
	}

	void SystemAppChloride::init_upscaling_stagger(io::YAMLConfigHandle& config_staggers)
	{
	SPC_CONF_LOG << "\n\n --> Upscaling stagger <-- \n"
	<< SPC_CONF_LOG_SECTION;

	auto conf = config_staggers.get_section(SPC_CF_S_STAGGERS_SS_UPSCALINGSTAGGER);
	auto type = conf.get_optional_attribute<std::string>(
	SPC_CF_S_STAGGERS_SS_UPSCALINGSTAGGER_A_TYPE,
	SPC_CF_V_PLUGIN);
	// only plugin accepted for now
	if (type == SPC_CF_V_DEFAULT) type = SPC_CF_V_PLUGIN;
	if (type != SPC_CF_V_PLUGIN) {
	conf.report_error(
	io::YAMLConfigError::InvalidArgument,
	"Invalid argument for attribute '"
	SPC_CF_A_TYPE
	"' only value accepted is '" SPC_CF_V_PLUGIN "'.");
	}
	auto plugin_name = get_plugin_name(conf);
	auto& plugin_manager = plugins::get_plugin_manager();
	auto upscaling_factory = plugin_manager.get_object<UpscalingStaggerFactory>(
	SPC_PLUGIN_REACTMICP_CHLORIDE_UPSCALING, plugin_name);
	if (upscaling_factory == nullptr) {
	CRITICAL << "No upscaling stagger factory found";
	throw std::runtime_error("No upscaling stagger factory found");
	}
	SPC_CONF_LOG << SPC_CONF_LOG_HLINE;
	m_staggers.upscaling = upscaling_factory->get_upscaling_stagger(
	m_simul_data, std::move(conf));
	}

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