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adimensional_system_solution_saver.cpp
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adimensional_system_solution_saver.cpp
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			/*-------------------------------------------------------------------------------

			Copyright (c) 2015 F. Georget <fabieng@princeton.edu>, Princeton University
			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 "adimensional_system_solution_saver.hpp"

			#include "adimensional_system_solution.hpp"

			#include "../../utils/log.hpp"
			#include "../../utils/dateandtime.hpp"
			#include "../../utils/io/yaml.hpp"
			#include <yaml-cpp/emitter.h>
			#include <yaml-cpp/yaml.h>

			#include <fstream>

			#include <chrono>
			#include <ctime>
			#include <stdexcept>

			#define SECTION_VALUES "solutions"
			#define VALUE_META_NAME "name"
			#define VALUE_META_DATE "date"
			#define VALUE_META_DATABASE "database"
			#define VALUE_META_DATABASE_VERSION "database_version"

			#define SECTION_MAIN "main_variables"
			#define SECTION_LOGGAMMA "log_gamma"
			#define SECTION_GAS "gas_fugacities"
			#define SECTION_SORBED "sorbed_molalities"
			#define SECTION_AQUEOUS "aqueous_molalities"

			#define VALUE_FREE_SURFACE "free_surface"
			#define VALUE_IONIC_STRENGTH "ionic_strength"
			#define VALUE_INERT "inert_vol_fraction"
			#define VALUE_COMPONENT "components"
			#define VALUE_AQUEOUS "aqueous"
			#define VALUE_MINERAL "minerals"

			namespace specmicp {


			//! \brief Serialize a solution as a YAML-formatted string
			std::string format_solution_yaml(
			const RawDatabasePtr& the_database,
			const AdimensionalSystemSolution& the_solution
			)
			{
			return AdimensionalSystemSolutionSaver(the_database).format_solution(the_solution);
			}

			//! \brief Serialize a solution and save it in a file
			void save_solution_yaml(
			const std::string& filename,
			const RawDatabasePtr& the_database,
			const AdimensionalSystemSolution& the_solution
			)
			{
			AdimensionalSystemSolutionSaver(the_database).save_solution(filename, the_solution);
			}

			//! \brief Read a solution from a JSON file
			AdimensionalSystemSolution parse_solution_yaml(
			const std::string& filename,
			const RawDatabasePtr& the_database
			)
			{
			return AdimensionalSystemSolutionSaver(the_database).parse_solution(filename);
			}


			//! \brief Read a solution from a JSON file
			AdimensionalSystemSolution parse_solution_yaml(
			std::istream& input,
			const RawDatabasePtr& the_database
			)
			{
			return AdimensionalSystemSolutionSaver(the_database).parse_solution(input);
			}


			void AdimensionalSystemSolutionSaver::save_solution(
			const std::string& filename,
			const AdimensionalSystemSolution& solution
			)
			{
			YAML::Emitter solution_yaml;
			io::configure_yaml_emitter(solution_yaml);
			set_yaml_emitter(solution, solution_yaml);
			io::save_yaml(filename, solution_yaml);
			}

			void AdimensionalSystemSolutionSaver::set_yaml_emitter(
			const AdimensionalSystemSolution& solution,
			YAML::Emitter& yaml_tree
			)
			{
			//# Fixme better str for the date
			yaml_tree << YAML::BeginMap;
			yaml_tree << YAML::Key << VALUE_META_DATE << YAML::Value << dateandtime::now();
			yaml_tree << YAML::Key << VALUE_META_DATABASE << YAML::Value << m_data->metadata.name;
			yaml_tree << YAML::Key << VALUE_META_DATABASE_VERSION << YAML::Value << m_data->metadata.version;

			yaml_tree << YAML::Key << SECTION_VALUES << YAML::Value;
			yaml_tree << YAML::BeginSeq;
			format_solution(solution, yaml_tree);
			yaml_tree << YAML::EndSeq;
			yaml_tree << YAML::EndMap;
			}

			std::string AdimensionalSystemSolutionSaver::format_solution(
			const AdimensionalSystemSolution& solution
			)
			{
			YAML::Emitter solution_yaml;
			io::configure_yaml_emitter(solution_yaml);
			set_yaml_emitter(solution, solution_yaml);
			if (solution_yaml.good())
			{
			throw std::runtime_error("Error in the emitter");
			}
			return std::string(solution_yaml.c_str());
			}

			//! \brief Save a set of solutions as a JSON file
			void AdimensionalSystemSolutionSaver::save_solutions(
			const std::string& filename,
			const std::vector<AdimensionalSystemSolution>& solutions
			)
			{
			YAML::Emitter yaml_tree;

			yaml_tree << YAML::BeginMap;
			yaml_tree << YAML::Key << VALUE_META_DATE << YAML::Value << dateandtime::now();
			yaml_tree << YAML::Key << VALUE_META_DATABASE << YAML::Value << m_data->metadata.name;
			yaml_tree << YAML::Key << VALUE_META_DATABASE_VERSION << YAML::Value << m_data->metadata.version;

			yaml_tree << YAML::Key << SECTION_VALUES << YAML::Value;
			yaml_tree << YAML::BeginSeq;
			for (std::size_t ind=0; ind<solutions.size(); ++ind)
			format_solution(solutions[ind], yaml_tree);
			yaml_tree << YAML::EndSeq;

			yaml_tree << YAML::EndMap;
			io::save_yaml(filename, yaml_tree);
			}



			void AdimensionalSystemSolutionSaver::format_solution(
			const AdimensionalSystemSolution& solution,
			YAML::Emitter& out
			)
			{
			out << YAML::BeginMap;
			format_main_variables(solution, out);
			format_aqueous_molalities(solution, out);
			format_loggamma(solution, out);
			out << YAML::Key << VALUE_IONIC_STRENGTH
			<< YAML::Value << solution.ionic_strength;
			format_gas_fugacities(solution, out);
			format_sorbed_molalities(solution, out);
			out << YAML::Key << VALUE_INERT
			<< YAML::Value << solution.inert_volume_fraction;
			out << YAML::EndMap;
			}

			AdimensionalSystemSolution
			AdimensionalSystemSolutionSaver::parse_solution(std::istream& input)
			{
			YAML::Node root = io::parse_yaml(input);
			parse_check_metadata(root);
			// TODO : error code management

			AdimensionalSystemSolution the_solution;

			io::check_mandatory_yaml_node(root, SECTION_VALUES, "__main__");
			if (root[SECTION_VALUES].Type() != YAML::NodeType::Sequence
			and root[SECTION_VALUES].size() < 1)
			{
			throw std::runtime_error("Expecting a non-zero list for section '" SECTION_VALUES "'.");
			}
			const YAML::Node& yaml_solution = root[SECTION_VALUES][0];
			parse_one_solution(yaml_solution, the_solution);

			return the_solution;
			}

			void AdimensionalSystemSolutionSaver::parse_one_solution(
			const YAML::Node& yaml_solution,
			AdimensionalSystemSolution& the_solution
			)
			{
			read_main_variables(yaml_solution, the_solution);
			read_aqueous_molalities(yaml_solution, the_solution);
			read_loggamma(yaml_solution, the_solution);
			read_gas_fugacities(yaml_solution, the_solution);
			read_sorbed_molalities(yaml_solution, the_solution);

			the_solution.inert_volume_fraction = io::get_yaml_mandatory<scalar_t>(yaml_solution, VALUE_INERT, "Solution");
			the_solution.ionic_strength =io::get_yaml_mandatory<scalar_t>(yaml_solution, VALUE_IONIC_STRENGTH, "Solution");

			the_solution.is_valid = true;
			}

			//! \brief Create a solution from a JSON file
			void AdimensionalSystemSolutionSaver::parse_solutions(
			const std::string& filename,
			std::vector<AdimensionalSystemSolution>& solutions_vector
			)
			{
			YAML::Node root = io::parse_yaml_file(filename);
			parse_check_metadata(root);
			// TODO : error code management

			io::check_mandatory_yaml_node(root, SECTION_VALUES, "__main__");
			if (root[SECTION_VALUES].Type() != YAML::NodeType::Sequence
			and root[SECTION_VALUES].size() < 1)
			{
			throw std::runtime_error("Expecting a non-zero list for section '" SECTION_VALUES "'.");
			}
			int nb_sol = root[SECTION_VALUES].size();
			solutions_vector.clear();
			solutions_vector.reserve(nb_sol);

			for (int ind=0; ind<nb_sol; ++ind)
			{
			AdimensionalSystemSolution the_solution;

			const YAML::Node& yaml_solution = root[SECTION_VALUES][ind];

			parse_one_solution(yaml_solution, the_solution);
			solutions_vector.emplace_back(std::move(the_solution));
			}
			}


			int AdimensionalSystemSolutionSaver::parse_check_metadata(const YAML::Node& root)
			{
			io::check_mandatory_yaml_node(root, VALUE_META_DATABASE, "__main__");
			if (root[VALUE_META_DATABASE].as<std::string>() != m_data->metadata.name)
			{
			WARNING << "SolutionSaver : The name of the database does not match the record in the solution !";
			return 1;
			}
			io::check_mandatory_yaml_node(root, VALUE_META_DATABASE_VERSION, "__main__");
			if (root[VALUE_META_DATABASE_VERSION].as<std::string>() != m_data->metadata.version)
			{
			WARNING << "SolutionSaver : The version of the databases does not match the record in the solution !";
			return 2;
			}
			return 0;
			}

			AdimensionalSystemSolution
			AdimensionalSystemSolutionSaver::parse_solution(const std::string& filename)
			{
			std::ifstream ofile(filename);
			AdimensionalSystemSolution the_solution = parse_solution(ofile);
			ofile.close();
			return the_solution;
			}


			void AdimensionalSystemSolutionSaver::format_main_variables(
			const AdimensionalSystemSolution& solution,
			YAML::Emitter& out)
			{
			out << YAML::Key << SECTION_MAIN << YAML::Value;
			out << YAML::BeginMap;
			out << YAML::Key << VALUE_COMPONENT << YAML::Value;
			out << YAML::BeginMap;
			for (auto component: m_data->range_component())
			{
			out << YAML::Key << m_data->get_label_component(component)
			<< YAML::Value << solution.main_variables(dof_component(component));
			}
			out << YAML::EndMap;
			out << YAML::Key << VALUE_FREE_SURFACE << YAML::Value << solution.main_variables(dof_surface());
			out << YAML::Key << VALUE_MINERAL << YAML::Value;
			out << YAML::BeginMap;
			for (auto mineral: m_data->range_mineral())
			{
			out << YAML::Key << m_data->get_label_mineral(mineral)
			<< YAML::Value << solution.main_variables(dof_mineral(mineral));
			}
			out << YAML::EndMap;
			out << YAML::EndMap;
			}

			void AdimensionalSystemSolutionSaver::format_aqueous_molalities(
			const AdimensionalSystemSolution& solution,
			YAML::Emitter& out
			)
			{
			out << YAML::Key << SECTION_AQUEOUS << YAML::Value;
			out << YAML::BeginMap;
			for (auto aqueous: m_data->range_aqueous())
			{
			out << YAML::Key << m_data->get_label_aqueous(aqueous)
			<< YAML::Value << solution.secondary_molalities(aqueous);
			}
			out << YAML::EndMap;
			}

			void AdimensionalSystemSolutionSaver::format_loggamma(
			const AdimensionalSystemSolution& solution,
			YAML::Emitter& out
			)
			{
			out << YAML::Key << SECTION_LOGGAMMA << YAML::Value;
			out << YAML::BeginMap;
			out << YAML::Key << VALUE_COMPONENT << YAML::Value;
			out << YAML::BeginMap;
			for (auto component: m_data->range_aqueous_component())
			{
			out << YAML::Key << m_data->get_label_component(component)
			<< YAML::Value << solution.log_gamma(dof_component_gamma(component));
			}
			out << YAML::EndMap;
			out << YAML::Key << VALUE_AQUEOUS << YAML::Value;
			out << YAML::BeginMap;
			for (auto aqueous: m_data->range_aqueous())
			{
			out << YAML::Key << m_data->get_label_aqueous(aqueous)
			<< YAML::Value << solution.log_gamma(dof_aqueous_gamma(aqueous));
			}
			out << YAML::EndMap;
			out << YAML::EndMap;
			}

			void AdimensionalSystemSolutionSaver::format_gas_fugacities(
			const AdimensionalSystemSolution& solution,
			YAML::Emitter& out
			)
			{
			out << YAML::Key << SECTION_GAS << YAML::Value;
			out << YAML::BeginMap;
			for (auto gas: m_data->range_gas())
			{
			out << YAML::Key << m_data->get_label_gas(gas)
			<< YAML::Value << solution.gas_fugacities(gas);
			}
			out << YAML::EndMap;
			}


			void AdimensionalSystemSolutionSaver::format_sorbed_molalities(
			const AdimensionalSystemSolution& solution,
			YAML::Emitter& out
			)
			{
			out << YAML::Key << SECTION_SORBED << YAML::Value;
			out << YAML::BeginMap;
			for (auto sorbed: m_data->range_sorbed())
			{
			out << YAML::Key << m_data->get_label_sorbed(sorbed)
			<< YAML::Value << solution.sorbed_molalities(sorbed);
			}
			out << YAML::EndMap;
			}

			void AdimensionalSystemSolutionSaver::read_main_variables(
			const YAML::Node& root,
			AdimensionalSystemSolution& solution
			)
			{
			// Initialization
			// --------------
			solution.main_variables = Vector(total_dofs());
			solution.main_variables(dof_water()) = 0;
			solution.main_variables(dof_electron()) = - INFINITY;
			for (auto id: m_data->range_aqueous_component())
			{
			solution.main_variables(dof_component(id)) = - INFINITY;
			}
			solution.main_variables(dof_surface()) = - INFINITY;
			for (auto mineral: m_data->range_mineral())
			{
			solution.main_variables(dof_mineral(mineral)) = 0;
			}
			// Parsing values
			// --------------
			io::check_mandatory_yaml_node(root, SECTION_MAIN, SECTION_VALUES);
			const YAML::Node& main = root[SECTION_MAIN];
			// components
			io::check_mandatory_yaml_node(main, VALUE_COMPONENT, SECTION_VALUES);
			const YAML::Node& components = main[VALUE_COMPONENT];
			for (auto& it: components)
			{
			const std::string label = it.first.as<std::string>();
			const index_t id = m_data->get_id_component(label);
			if (id == no_species)
			{
			throw std::invalid_argument("Component '" + label + "' does not exist in the database !");
			}
			try
			{
			solution.main_variables(dof_component(id)) = it.second.as<scalar_t>();
			}
			catch (YAML::BadConversion)
			{
			if (it.second.as<std::string>() == "-inf")
			{
			solution.main_variables(dof_component(id)) = - INFINITY;
			}
			}
			}
			// sorption
			solution.main_variables(dof_surface()) =
			io::get_yaml_optional<scalar_t>(main, VALUE_FREE_SURFACE, SECTION_MAIN, -INFINITY);
			// minerals
			io::check_mandatory_yaml_node(main, VALUE_MINERAL, SECTION_VALUES);
			const YAML::Node& minerals = main[VALUE_MINERAL];
			for (auto& it: minerals)
			{
			const std::string label = it.first.as<std::string>();
			const index_t id = m_data->get_id_mineral(label);
			if (id == no_species)
			{
			throw std::invalid_argument("Mineral '" + label + "' does not exist in the database !");
			}
			solution.main_variables(dof_mineral(id)) = it.second.as<scalar_t>();
			}
			}

			void AdimensionalSystemSolutionSaver::read_loggamma(
			const YAML::Node& root,
			AdimensionalSystemSolution& solution
			)
			{
			solution.log_gamma = Vector::Zero(m_data->nb_component()+m_data->nb_aqueous());
			io::check_mandatory_yaml_node(root, SECTION_LOGGAMMA, SECTION_VALUES);
			const YAML::Node& loggamma = root[SECTION_LOGGAMMA];
			// components
			io::check_mandatory_yaml_node(loggamma, VALUE_COMPONENT, SECTION_LOGGAMMA);
			const YAML::Node& components = loggamma[VALUE_COMPONENT];
			for (auto& it: components)
			{
			const std::string label = it.first.as<std::string>();
			const index_t id = m_data->get_id_component(label);
			if (id == no_species)
			{
			throw std::invalid_argument("Component '" + label + "' does not exist in the database !");
			}
			solution.log_gamma(dof_component_gamma(id)) = it.second.as<scalar_t>();
			}
			// aqueous
			io::check_mandatory_yaml_node(loggamma, VALUE_AQUEOUS, SECTION_LOGGAMMA);
			const YAML::Node& aqueous = loggamma[VALUE_AQUEOUS];
			for (auto& it: aqueous)
			{
			const std::string label = it.first.as<std::string>();
			const index_t id = m_data->get_id_aqueous(label);
			if (id == no_species)
			{
			throw std::invalid_argument("Aqueous '" + label + "' does not exist in the database !");
			}
			solution.log_gamma(dof_aqueous_gamma(id)) = it.second.as<scalar_t>();
			}
			}

			void AdimensionalSystemSolutionSaver::read_aqueous_molalities(
			const YAML::Node& root,
			AdimensionalSystemSolution &solution
			)
			{
			solution.secondary_molalities = Vector::Zero(m_data->nb_aqueous());
			io::check_mandatory_yaml_node(root, SECTION_AQUEOUS, SECTION_VALUES);
			const YAML::Node& aqueous_section = root[SECTION_AQUEOUS];
			for (auto& it: aqueous_section)
			{
			const std::string label = it.first.as<std::string>();
			const index_t id = m_data->get_id_aqueous(label);
			if (id == no_species)
			{
			throw std::invalid_argument("Secondary aqueous species '" + label + "' does not exist in the database !");
			}
			solution.secondary_molalities(id) = it.second.as<scalar_t>();
			}
			}

			void AdimensionalSystemSolutionSaver::read_gas_fugacities(
			const YAML::Node& root,
			AdimensionalSystemSolution& solution
			)
			{
			solution.gas_fugacities = Vector::Zero(m_data->nb_gas());
			io::check_mandatory_yaml_node(root, SECTION_GAS, SECTION_VALUES);
			const YAML::Node& gas_section = root[SECTION_GAS];
			for (auto& it: gas_section)
			{
			const std::string label = it.first.as<std::string>();
			const index_t id = m_data->get_id_gas(label);
			if (id == no_species)
			{
			throw std::invalid_argument("Gas '" + label + "' does not exist in the database !");
			}
			solution.gas_fugacities(id) = it.second.as<scalar_t>();
			}
			}

			void AdimensionalSystemSolutionSaver::read_sorbed_molalities(
			const YAML::Node& root,
			AdimensionalSystemSolution& solution
			)
			{
			solution.sorbed_molalities = Vector::Zero(m_data->nb_sorbed());
			io::check_mandatory_yaml_node(root, SECTION_SORBED, SECTION_VALUES);
			const YAML::Node& sorbed_section = root[SECTION_SORBED];
			for (auto& it: sorbed_section)
			{
			const std::string label = it.first.as<std::string>();
			const index_t id = m_data->get_id_sorbed(label);
			if (id == no_species)
			{
			throw std::invalid_argument("sorbed species '" + label + "' does not exist in the database !");
			}
			solution.sorbed_molalities(id) = it.second.as<scalar_t>();
			}
			}

			} //end namespace specmicp

specmicp/src/specmicp/adimensional/adimensional_system_solution_saver.cpp5a5d1f0d9096specmicp_bin

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specmicp/src/specmicp/adimensional/adimensional_system_solution_saver.cpp
5a5d1f0d9096specmicp_bin

adimensional_system_solution_saver.cpp
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