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adimensional_system_pcfm.cpp
665b1c9415f6configuration

adimensional_system_pcfm.cpp
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			/*-------------------------------------------------------

			Copyright (c) 2014,2015 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 "adimensional_system_pcfm.hpp"
			#include "adimensional_system.hpp"

			#include <iostream>
			#include "utils/log.hpp"

			namespace specmicp {

			// AdimensionalSystemPCFM

			AdimensionalSystemPCFM::AdimensionalSystemPCFM(std::shared_ptr<AdimensionalSystem> program):
			m_data(program->get_database()),
			m_program(program)
			{
			check_validity();
			}

			AdimensionalSystemPCFM::AdimensionalSystemPCFM(
			std::shared_ptr<AdimensionalSystem> program,
			const PCFMOptions& options):
			OptionsHandler<PCFMOptions>(options),
			m_data(program->get_database()),
			m_program(program)
			{
			check_validity();
			}

			bool AdimensionalSystemPCFM::check_validity()
			{
			bool is_valid = true;
			if (m_program->water_equation_type() != WaterEquationType::NoEquation)
			{
			ERROR << "The implementation of the positive continuous fraction method does not compute the conservation of water";
			is_valid = false;
			}
			if (m_program->get_database()->nb_mineral() != 0.0)
			{
			WARNING << "The implementation of the positive continuous fraction method does not compute the solid phase assemblage";
			is_valid = false;
			}
			return is_valid;
			}

			PCFMReturnCode AdimensionalSystemPCFM::solve(Vector &x)
			{
			index_t cnt = 0;
			m_errors.setZero(m_program->total_variables());

			while (cnt < get_options().max_iterations)
			{
			one_iteration(x);

			scalar_t error = m_errors.lpNorm<Eigen::Infinity>();
			DEBUG << "PCFM error : " << error << " ?< " << get_options().tolerance;
			if (not std::isfinite(error))
			return PCFMReturnCode::Error;
			if (error < get_options().tolerance)
			return PCFMReturnCode::Success;
			++cnt;
			}
			if (cnt == get_options().max_iterations)
			return PCFMReturnCode::MaxIterationsReached;
			return PCFMReturnCode::NotConvergedYet;
			}

			void AdimensionalSystemPCFM::one_iteration(Vector &x)
			{
			m_program->set_secondary_concentration(x);
			m_program->set_sorbed_concentrations(x);
			for (index_t component: m_data->range_aqueous_component())
			{
			if (m_program->ideq_paq(component) != no_equation)
			{
			solve_component(component, x);
			}
			}
			if (m_program->ideq_surf() != no_equation)
			{
			solve_surface(x);
			}
			}

			void AdimensionalSystemPCFM::solve_component(index_t component, Vector& x)
			{
			specmicp_assert(component > 0 and component < m_data->nb_component() and "Must be an aqueous component");
			specmicp_assert(m_program->ideq_paq(component) != no_equation and "No corresponding equation for this component");
			specmicp_assert(m_program->aqueous_component_equation_type(component) == AqueousComponentEquationType::MassConservation);
			const scalar_t total_concentration = m_program->total_concentration_bc(component);

			scalar_t conc_w = m_program->density_water()*m_program->saturation_water(x);

			scalar_t sum_reac = conc_w*m_program->component_molality(x, component);
			scalar_t sum_prod = 0.0;


			// compute the lhs and rhs of the mass balance so that every contribution is positive
			if (total_concentration >= 0)
			{
			sum_prod += total_concentration;
			}
			else
			{
			sum_reac -= total_concentration;
			}

			for (index_t aqueous: m_data->range_aqueous())
			{
			if (m_data->nu_aqueous(aqueous, component) > 0)
			sum_reac += conc_wm_data->nu_aqueous(aqueous, component)m_program->secondary_molality(aqueous);
			else
			sum_prod -= conc_wm_data->nu_aqueous(aqueous, component)m_program->secondary_molality(aqueous);
			}
			for (index_t sorbed: m_data->range_sorbed())
			{
			if (m_data->nu_sorbed(sorbed, component) > 0)
			sum_reac += m_data->nu_sorbed(sorbed, component)*m_program->sorbed_species_concentration(sorbed);
			else
			sum_prod -= m_data->nu_sorbed(sorbed, component)*m_program->sorbed_species_concentration(sorbed);
			}
			specmicp_assert(std::isfinite(sum_reac));
			specmicp_assert(sum_reac > 0.0 && "Sum of reactants concentration should be positive");
			specmicp_assert(sum_prod > 0.0 && "Sum of products should be positive");
			// compute the step size
			scalar_t theta;
			const scalar_t factor = (sum_prod/sum_reac);
			if (sum_reac > sum_prod)
			theta = 0.9 - 0.8*factor;
			else
			theta = 0.9 - 0.8/factor;
			//
			theta *= get_options().theta_factor;
			scalar_t new_conc = (1-theta + thetafactor)m_program->component_molality(x, component);
			x(m_program->ideq_paq(component)) = std::log10(new_conc);

			m_errors(m_program->ideq_paq(component)) = std::abs(sum_reac - sum_prod)/(sum_reac + sum_prod);
			}

			void AdimensionalSystemPCFM::solve_surface(Vector& x)
			{
			specmicp_assert(m_program->ideq_surf() != no_equation);
			specmicp_assert(m_program->surface_total_concentration() > 0);
			scalar_t sum_prod = m_program->surface_total_concentration();
			scalar_t sum_reac = m_program->free_sorption_site_concentration(x);

			for (index_t sorbed: m_data->range_sorbed())
			{
			sum_reac += m_data->nb_sorption_sites(sorbed)*m_program->sorbed_species_concentration(sorbed);
			}

			specmicp_assert(std::isfinite(sum_reac));
			specmicp_assert(sum_reac > 0.0 && "Sum of reactants concentration should be positive");
			specmicp_assert(sum_prod > 0.0 && "Sum of products should be positive");
			scalar_t theta;
			const scalar_t factor = (sum_prod/sum_reac);
			if (sum_reac > sum_prod)
			theta = 0.9 - 0.8*factor;
			else
			theta = 0.9 - 0.8/factor;
			//
			theta *= get_options().theta_factor;
			scalar_t new_conc = (1-theta + thetafactor)m_program->free_sorption_site_concentration(x);
			x(m_program->ideq_surf()) = std::log10(new_conc);

			m_errors(m_program->ideq_surf()) = std::abs(sum_reac - sum_prod)/(sum_reac + sum_prod);
			}

			} // end namespace specmicp

specmicp/src/specmicp/adimensional/adimensional_system_pcfm.cpp665b1c9415f6configuration

adimensional_system_pcfm.cppView Options

specmicp/src/specmicp/adimensional/adimensional_system_pcfm.cpp
665b1c9415f6configuration

adimensional_system_pcfm.cpp
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