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app_core.cpp
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app_core.cpp
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/* =============================================================================
Copyright (c) 2014-2017 F. Georget <fabieng@princeton.edu> Princeton University
Copyright (c) 2017-2018 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. *
============================================================================= */
#include "app_core.hpp"
#include "specmicp_common/physics/units.hpp"
#include "specmicp_common/log.hpp"
#include "specmicp_common/compat.hpp"
#include "specmicp_common/openmp_support.hpp"
#include "specmicp_common/cli/parser.hpp"
#include "specmicp_common/filesystem.hpp"
#include "specmicp_database/data_container.hpp"
#include "specmicp_database/io/configuration.hpp"
#include "specmicp_common/io/config_yaml_sections.h"
#include "specmicp_common/io/configuration.hpp"
#include "specmicp_common/physics/io/configuration.hpp"
#include "specmicp_common/physics/io/units.hpp"
#include "dfpm/io/configuration.hpp"
#include "reactmicp/io/configuration.hpp"
#include "reactmicp/solver/reactive_transport_solver.hpp"
#include "reactmicp/solver/reactive_transport_solver_structs.hpp"
#include "specmicp_common/plugins/plugin_modules_names.h"
#include "specmicp_common/plugins/module_base.hpp"
#include "specmicp_common/plugins/plugin_manager.hpp"
#include <iostream>
// ==================== //
// Main App //
// ==================== //
MainApp::MainApp() {}
MainApp::~MainApp() = default;
int MainApp::run(SystemApp& system_app, int argc, char* argv[])
{
system_app.print_welcome();
init_logger(&std::cout, logger::Warning);
CliOptions cli_opts = CliOptions::parse_cli(argc, argv);
if (cli_opts.done)
{
return EXIT_SUCCESS;
}
// db dirs contain the directories when the database is searched
std::vector<std::string> db_dirs = cli_opts.get_db_dirs();
// Configuration File
// ------------------
system_app.init_input_file(cli_opts.input_filepath);
system_app.init_simul_info(cli_opts.working_dir);
system_app.init_alliofiles(cli_opts);
if (cli_opts.clean_outputs) {
if (cli_opts.only_pretend) {
return EXIT_SUCCESS; // Do not panic, just for fun
}
system_app.clean_output_files();
return EXIT_SUCCESS; // just cleaning, nothing more to run
}
system_app.init_conf_logger();
system_app.init_logger();
system_app.init_plugin_manager();
// openmp initialization
// ---------------------
utils::initialize_parallel();
// Simulation Data and Staggers
// ----------------------------
system_app.init_simul_data(db_dirs);
// Staggers
// -------
system_app.init_staggers();
// Check the variables
// -------------------
system_app.check_init_data();
// Solver
// ------
system_app.init_solver();
system_app.init_runner();
system_app.init_output(cli_opts.working_dir);
if (not cli_opts.only_pretend) {
system_app.run();
}
return EXIT_SUCCESS;
}
// ==================== //
// CLI options //
// ==================== //
CliOptions CliOptions::parse_cli(int argc, char *argv[])
{
CliOptions opts;
// CLI options
cli::CommandLineParser parser;
parser.add_option('i', "input",
cli::ValueType::string,
"input_file (yaml format)");
parser.add_option('d', "database_dir",
std::string(""),
"directory where database are stored");
parser.add_option('w', "workdir",
utils::get_current_directory(),
"working directory");
parser.add_option('o', "overwrite", false,
"If true, allow overwrite of previous simulation");
parser.add_option('c', "clean", false,
"Clean previous output files");
parser.add_option('p', "pretend", false,
"Dry-run, do not run simulation");
parser.set_help_message("ReactMiCP Unsaturated System");
const auto ret_parse = parser.parse(argc, argv);
if (ret_parse > 0) {
opts.done = true;
}
opts.input_filepath = parser.get_option<cli::ValueType::string>("input");
opts.database_dir = parser.get_option<cli::ValueType::string>("database_dir");
opts.working_dir = parser.get_option<cli::ValueType::string>("workdir");
opts.allow_overwrite = parser.get_option<cli::ValueType::boolean>("overwrite");
opts.clean_outputs = parser.get_option<cli::ValueType::boolean>("clean");
opts.only_pretend = parser.get_option<cli::ValueType::boolean>("pretend");
return opts;
}
std::vector<std::string> CliOptions::get_db_dirs() const
{
std::vector<std::string> db_dirs;
if (not database_dir.empty()) {db_dirs.push_back(database_dir);}
db_dirs.push_back(utils::get_current_directory());
io::add_db_dirs_from_env(db_dirs);
if (not working_dir.empty()) {db_dirs.push_back(working_dir);}
return db_dirs;
}
// ==================== //
// SystemApp //
// ==================== //
void SystemApp::init_input_file(const std::string& input_filepath)
{
m_config = io::YAMLConfigFile::make(input_filepath);
}
void SystemApp::init_simul_info(const std::string& working_dir)
{
m_simul_info = make_unique<solver::SimulationInformation>("", 0);
*m_simul_info = io::configure_simulation_information(
m_config->get_section(SPC_CF_S_SIMULINFO));
m_simul_info->working_dir = working_dir;
}
void SystemApp::init_alliofiles(const CliOptions& cli_opts)
{
io::AllIOFilesMode flag = io::AllIOFilesMode::ErrorIfExist;
if (cli_opts.allow_overwrite) {
flag = io::AllIOFilesMode::Write;
} else if (cli_opts.clean_outputs ){
flag = io::AllIOFilesMode::Read;
}
auto io_file_path = m_simul_info->complete_filepath("io", "yml");
m_all_io_files = make_unique<io::AllIOFiles>(io_file_path, flag);
m_all_io_files->add_configuration_file(io::input_file(IO_INPUT, cli_opts.input_filepath));
}
void SystemApp::init_conf_logger()
{
if (m_config->has_section(SPC_CF_S_CONF_LOGS)) {
m_out_conf_logger = io::configure_conf_log(
m_config->get_section(SPC_CF_S_CONF_LOGS),
m_all_io_files.get() // log file registered here
);
}
SPC_CONF_LOG << "Running " << this->driver_identification();
}
void SystemApp::init_logger()
{
if (m_config->has_section(SPC_CF_S_LOGS)) {
m_out_logger = io::configure_log(
m_config->get_section(SPC_CF_S_LOGS),
m_all_io_files.get() // log file registered here
);
}
}
void SystemApp::init_solver()
{
m_solver = make_unique<solver::ReactiveTransportSolver>(
m_staggers.transport, m_staggers.chemistry, m_staggers.upscaling);
io::configure_reactmicp_options(
m_solver->get_options(),
m_config->get_section(SPC_CF_S_REACTMICP)
);
SPC_CONF_LOG << "\n\n++ ReactMiCP ++\n"
<< SPC_CONF_LOG_SECTION
<< "\n ReactMiCP options\n"
<< SPC_CONF_LOG_HLINE;
std::ostringstream msg;
io::print_reactmicp_options(msg, m_solver->get_options());
SPC_CONF_LOG << msg.str();
}
void SystemApp::init_runner()
{
m_runner = make_unique<solver::ReactiveTransportRunner>(
*m_solver,
1.0, 10.0, // dummy value, set later
*m_simul_info);
io::configure_reactmicp_timestepper(
m_runner->get_timestepper_options(),
m_config->get_section(SPC_CF_S_TIMESTEPPER)
);
}
void SystemApp::run()
{
// run info
auto run_section = m_config->get_section(SPC_CF_S_RUN);
auto run_until = run_section.get_required_attribute<scalar_t>(
SPC_CF_S_RUN_A_RUNUNTIL);
// At this point we assume it's safe to destroy the config
// to get information about unread keys
m_config.reset(nullptr);
m_runner->run_until(run_until, get_variables());
}
void SystemApp::clean_output_files()
{
m_all_io_files->clean_output_files();
m_all_io_files.reset(nullptr);
}
void SystemApp::init_plugin_manager_base(std::vector<std::string> plugin_modules)
{
SPC_CONF_LOG << SPC_CONF_LOG_SECTION
<< "\nInitialize plugin manager\n"
<< SPC_CONF_LOG_HLINE;
plugins::PluginManager& plugin_manager = plugins::get_plugin_manager();
for (auto& module: plugin_modules)
{
SPC_CONF_LOG << "Registering module " + module;
plugin_manager.register_module(module,
make_unique<plugins::ModuleBase>());
}
if (m_config->has_section(SPC_CF_S_PLUGINS)) {
io::configure_plugin_manager(m_config->get_section(SPC_CF_S_PLUGINS));
}
auto dirs = plugin_manager.get_plugin_directories();
if (not dirs.empty()) {
SPC_CONF_LOG << "plugin path : ";
for (auto dir: dirs) {
SPC_CONF_LOG << " - " << dir;
}
}
SPC_CONF_LOG << SPC_CONF_LOG_HLINE;
}
units::UnitsSet SystemApp::get_units_from_config()
{
units::UnitsSet t_units;
if (m_config->has_section(SPC_CF_S_UNITS))
{
t_units = io::configure_units(
m_config->get_section(SPC_CF_S_UNITS));
}
SPC_CONF_LOG << SPC_CONF_LOG_HLINE
<< "\nUnits :"
<< "\n - length : " << io::to_string(t_units.length)
<< "\n - mass : " << io::to_string(t_units.mass)
<< "\n - quantity : " << io::to_string(t_units.quantity)
<< "\n" << SPC_CONF_LOG_HLINE;
return t_units;
}
database::RawDatabasePtr SystemApp::get_database_from_config(
const std::vector<std::string> &db_dirs)
{
auto& config = get_config();
SPC_CONF_LOG << "Database initialization\n";
RawDatabasePtr raw_data = io::configure_database(
config.get_section(SPC_CF_S_DATABASE),
db_dirs
);
auto& metadata = raw_data->metadata;
m_all_io_files->add_database(
io::input_file(IO_FILE_INIT_DB, metadata.path,
metadata.name + " - " + metadata.version
));
SPC_CONF_LOG << SPC_CONF_LOG_HLINE;
if (not raw_data->is_valid()) {
CRITICAL << "Invalid database from the configuration.";
throw std::runtime_error("Database parsed from the configuration has"
" been detected to be invalid. Abort.");
}
return raw_data;
}
mesh::Mesh1DPtr SystemApp::get_mesh_from_config()
{
SPC_CONF_LOG << "Mesh initialization\n"
<< SPC_CONF_LOG_SECTION;
auto mesh1d =
io::configure_mesh(m_config->get_section(SPC_CF_S_MESH));
SPC_CONF_LOG << SPC_CONF_LOG_HLINE;
return mesh1d;
}
std::string get_plugin_name(io::YAMLConfigHandle& conf)
{
std::string plugin_name = conf.get_required_attribute<std::string>(
SPC_CF_A_PLUGIN_NAME);
SPC_CONF_LOG << "Use plugin " << plugin_name;
plugins::PluginManager& plugin_manager = plugins::get_plugin_manager();
auto extra_plugin_file = conf.get_optional_attribute<std::string>(
SPC_CF_A_PLUGIN_FILE, "");
if (extra_plugin_file != "") {
SPC_CONF_LOG << "Load plugin file " << extra_plugin_file;
auto retcode = plugin_manager.load_plugin(extra_plugin_file);
if (not retcode) {
CRITICAL << "Failed to load plugin file : " << extra_plugin_file << std::endl;
std::runtime_error("Fail to load plugin file : "
+ extra_plugin_file + ".");
}
}
return plugin_name;
}

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