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adimensional_system_solver.cpp
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adimensional_system_solver.cpp
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			/*-------------------------------------------------------

			- Module : specmicp
			- File : reduced_system_solver
			- Author : Fabien Georget

			Copyright (c) 2014, Fabien 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:
			* Redistributions of source code must retain the above copyright
			notice, this list of conditions and the following disclaimer.
			* 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.
			* Neither the name of the Princeton University 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 OWNER 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 "micpsolver/micpsolver.hpp"

			#include "adimensional_system_solver.hpp"
			#include "specmicp/adimensional/adimensional_system_solution.hpp"
			#include "adimensional_system_pcfm.hpp"

			#include "utils/log.hpp"

			namespace specmicp {

			// constructor
			// -----------

			AdimensionalSystemSolver::AdimensionalSystemSolver(RawDatabasePtr data,
			const AdimensionalSystemConstraints& constraints,
			AdimensionalSystemSolverOptions options
			):
			OptionsHandler<AdimensionalSystemSolverOptions>(options),
			m_data(data),
			m_system(std::make_shared<AdimensionalSystem>(
			data,
			constraints,
			options.system_options
			)),
			m_var(Vector::Zero(data->nb_component+data->nb_mineral))
			{}

			AdimensionalSystemSolver::AdimensionalSystemSolver(RawDatabasePtr data,
			const AdimensionalSystemConstraints& constraints,
			const AdimensionalSystemSolution& previous_solution,
			AdimensionalSystemSolverOptions options
			):
			OptionsHandler<AdimensionalSystemSolverOptions>(options),
			m_data(data),
			m_system(std::make_shared<AdimensionalSystem>(
			data,
			constraints,
			previous_solution,
			options.system_options
			)),
			m_var(Vector::Zero(data->nb_component+data->nb_mineral))
			{}

			AdimensionalSystemSolution AdimensionalSystemSolver::get_raw_solution(Vector& x)
			{
			set_true_variable_vector(x);
			return m_system->get_solution(x, m_var);
			}

			// Solving the system
			// ------------------

			micpsolver::MiCPPerformance AdimensionalSystemSolver::solve(Vector& x, bool init)
			{
			m_system->set_units(get_options().units_set);
			if (init)
			{
			m_system->reasonable_starting_guess(x);
			if (get_options().use_pcfm)
			{
			run_pcfm(x);
			}
			}
			else if (get_options().force_pcfm)
			{
			run_pcfm(x);
			}
			set_true_variable_vector(x);
			micpsolver::MiCPPerformance perf = solve_system();
			int cnt = 0;
			while (perf.return_code < micpsolver::MiCPSolverReturnCode::Success // != micpsolver::MiCPSolverReturnCode::ResidualMinimized
			and get_options().allow_restart
			and cnt < 3)
			{
			WARNING << "Failed to solve the system ! Return code :"
			<< (int) perf.return_code
			<< ". We shake it up and start again";
			const scalar_t save_penalization_factor = get_options().solver_options.penalization_factor;
			const scalar_t save_factor_descent = get_options().solver_options.factor_descent_condition;
			const bool save_scaling = get_options().solver_options.use_scaling;
			get_options().solver_options.factor_descent_condition *= 1e-2;
			get_options().solver_options.use_scaling = true;
			if (save_penalization_factor == 1)
			get_options().solver_options.penalization_factor = 0.8;
			set_return_vector(x);
			m_system->reasonable_restarting_guess(x);
			if (get_options().use_pcfm or get_options().force_pcfm)
			run_pcfm(x);
			set_true_variable_vector(x);
			micpsolver::MiCPPerformance perf2 = solve_system();
			get_options().solver_options.penalization_factor = save_penalization_factor;
			get_options().solver_options.factor_descent_condition = save_factor_descent;
			get_options().solver_options.use_scaling = save_scaling;
			perf += perf2;
			++cnt;
			}
			if (perf.return_code > micpsolver::MiCPSolverReturnCode::NotConvergedYet) set_return_vector(x);
			return perf;
			}


			micpsolver::MiCPPerformance AdimensionalSystemSolver::solve_system()
			{
			micpsolver::MiCPSolver<AdimensionalSystem> solver(m_system);
			solver.set_options(get_options().solver_options);
			solver.solve(m_var);
			return solver.get_perfs();

			}

			// Variables management
			// ---------------------

			void AdimensionalSystemSolver::set_true_variable_vector(const Vector& x)
			{
			const std::vector<index_t>& non_active_component = m_system->get_non_active_component();
			if ((non_active_component.size() == 0)
			and
			(m_system->ideq_surf() != no_equation))
			{
			// we still copy the data, if we failed to solve the problem, we can restart
			if (m_system->is_active_component(0))
			m_var = x; // direct copy
			else
			m_var = x.block(1, 0, x.rows()-1, 1);
			for (int i=0; i<m_var.rows(); ++i)
			{
			if (m_var(i) == -HUGE_VAL) // check for previously undefined value
			{
			m_var(i) = m_system->get_options().new_component_concentration;
			}
			}
			}
			else // remove the dof that are not part of the problem
			{
			uindex_t new_i = 0;
			if (m_system->is_active_component(0))
			{
			m_var(0) = x(m_system->dof_water());
			++new_i;
			}
			for (index_t i: m_data->range_aqueous_component())
			{
			auto it = std::find(non_active_component.begin(), non_active_component.end(),i);
			if (it != non_active_component.end()) continue;
			scalar_t value = x(m_system->dof_component(i));
			if (value == -HUGE_VAL) // check for previously undefined value
			{
			value = m_system->get_options().new_component_concentration;
			}
			m_var(new_i) = value;
			++new_i;
			}
			if (m_system->ideq_surf() != no_equation)
			{
			m_var(new_i) = x(m_system->dof_surface());
			++new_i;
			}

			for (index_t m: m_data->range_mineral())
			{
			bool to_keep = true;
			for (auto it=non_active_component.begin(); it!=non_active_component.end(); ++it)
			{
			if (m_data->nu_mineral(m, *it) != 0) to_keep = false;
			}
			if (to_keep)
			{
			m_var(new_i) = x(m_system->dof_mineral(m));
			++new_i;
			}
			}
			m_var.conservativeResize(new_i);
			specmicp_assert(new_i == (unsigned) m_system->total_variables());
			}
			}


			void AdimensionalSystemSolver::set_return_vector(Vector& x)
			{
			const std::vector<index_t>& non_active_component = m_system->get_non_active_component();
			if (non_active_component.size() == 0 and m_system->ideq_surf() != no_equation) // shortcut
			{
			if (m_system->is_active_component(0))
			x = m_var; //direct copy
			else
			x.block(1, 0, x.rows()-1, 1) = m_var;
			// at that point we should have the correct solution
			}
			else
			{
			uindex_t new_i = 0;
			if (m_system->is_active_component(0))
			{
			x(m_system->dof_water()) = m_var(new_i);
			++new_i;
			}
			else
			{
			x(m_system->dof_water()) = m_system->saturation_water(x);
			}
			for (index_t i: m_data->range_aqueous_component())
			{
			auto it = std::find(non_active_component.begin(), non_active_component.end(),i);
			if (it != non_active_component.end())
			{
			x(m_system->dof_component(i)) = -HUGE_VAL;
			continue;
			}
			x(m_system->dof_component(i)) = m_var(new_i) ;
			++new_i;
			}
			if (m_system->ideq_surf() != no_equation)
			{
			x(m_system->dof_surface()) = m_var(new_i);
			++new_i;
			}
			else
			x(m_system->dof_surface()) = -HUGE_VAL;
			for (index_t m: m_data->range_mineral())
			{
			bool to_keep = true;
			for (const index_t& k: non_active_component)
			{
			if (m_data->nu_mineral(m, k) != 0.0) to_keep = false;
			}
			if (to_keep)
			{
			x(m_system->dof_mineral(m)) =m_var(new_i);
			++new_i;
			}
			else
			{
			x(m_system->dof_mineral(m)) = 0.0;
			}
			}
			}
			}

			// PCFM
			// ----

			void AdimensionalSystemSolver::run_pcfm(Vector &x)
			{
			DEBUG << "Start PCFM initialization.";

			// we set up the true variable
			set_true_variable_vector(x);
			// The residual is computed to have some point of comparison
			Vector residuals(m_system->total_variables());
			residuals.setZero();
			m_system->get_residuals(m_var, residuals);
			const scalar_t res_0 = residuals.norm();

			// the pcfm iterations are executed
			AdimensionalSystemPCFM pcfm_solver(m_system);
			PCFMReturnCode retcode = pcfm_solver.solve(m_var);
			// Check the answer
			if (retcode < PCFMReturnCode::Success)
			{
			// small prograss is still good enough
			m_system->get_residuals(m_var, residuals);
			const scalar_t final_residual = residuals.norm();
			DEBUG << "Final pcfm residuals : " << final_residual << " <? " << res_0;
			if (std::isfinite(final_residual) and final_residual < res_0)
			retcode = PCFMReturnCode::Success;
			}
			// if we did a good job, use the solution as initial state
			if (retcode == PCFMReturnCode::Success)
			{
			DEBUG << "Successful PCFM iterations.";
			set_return_vector(x);
			}
			else // we reset
			{
			DEBUG << "Unsuccessful PCFM iterations. The problem is reset to the initial state.";
			set_true_variable_vector(x);
			m_system->set_secondary_variables(m_var);
			}
			}

			// Initialisation of variables
			// ---------------------------

			void AdimensionalSystemSolver::initialise_variables(
			Vector& x,
			scalar_t volume_fraction_water,
			std::map<std::string, scalar_t> log_molalities,
			std::map<std::string, scalar_t> volume_fraction_minerals,
			scalar_t log_free_sorption_site_concentration
			)
			{
			m_system->reasonable_starting_guess(x);

			database::Database database(m_data);

			if (volume_fraction_water < 0 or volume_fraction_water > 1)
			{
			WARNING << "Initial guess for the volume fraction of water is not between 0 and 1";
			}
			x(m_system->dof_water()) = volume_fraction_water;
			for (auto pair: log_molalities)
			{
			index_t idc = database.component_label_to_id(pair.first);
			if (idc == no_species or idc == 0)
			{
			throw std::invalid_argument("This is not an aqueous component : "+pair.first);
			}
			if (pair.second > 0)
			{
			WARNING << "Initial molality for : " << pair.first << "is bigger than 1 molal.";
			}
			x(m_system->dof_component(idc)) = pair.second;
			}
			for (auto pair: volume_fraction_minerals)
			{
			index_t idm = database.mineral_label_to_id(pair.first);
			if (idm == no_species )
			{
			throw std::invalid_argument("This is not a mineral at equilibrium : "+pair.first);
			}
			if (pair.second < 0 or pair.second > 1)
			{
			WARNING << "Initial volume fraction for : " << pair.first << "is not between 0 and 1.";
			}
			x(m_system->dof_mineral(idm)) = pair.second;
			}
			if (log_free_sorption_site_concentration != 0.0)
			x(m_system->dof_surface()) = log_free_sorption_site_concentration;

			}

			void AdimensionalSystemSolver::initialise_variables(Vector& x,
			scalar_t volume_fraction_water,
			scalar_t log_molalities
			)
			{
			m_system->reasonable_starting_guess(x);

			if (volume_fraction_water < 0 or volume_fraction_water > 1)
			{
			WARNING << "Initial guess for the volume fraction of water is not between 0 and 1";
			}
			x(m_system->dof_water()) = volume_fraction_water;

			if (log_molalities > 0)
			{
			WARNING << "Initial molality for : " << log_molalities << "is bigger than 1 molal.";
			}
			x.segment(1, m_data->nb_component-1).setConstant(log_molalities);
			}


			void AdimensionalSystemSolver::initialise_variables(Vector& x,
			scalar_t volume_fraction_water,
			scalar_t log_molalities,
			scalar_t log_free_sorption_site_concentration
			)
			{
			initialise_variables(x, volume_fraction_water, log_molalities);
			x(m_system->dof_surface()) = log_free_sorption_site_concentration;
			}
			} // end namespace specmicp

specmicp/src/specmicp/adimensional/adimensional_system_solver.cpp9cf41f6dfb45chloride

adimensional_system_solver.cppView Options

specmicp/src/specmicp/adimensional/adimensional_system_solver.cpp
9cf41f6dfb45chloride

adimensional_system_solver.cpp
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