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aqueous_pressure_equation.cpp
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			/* =============================================================================

			Copyright (c) 2014 - 2016
			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
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			(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
			LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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			(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 "aqueous_pressure_equation.hpp"
			#include "variables_box.hpp"
			#include "transport_constraints.hpp"

			#include "../../../dfpm/meshes/mesh1d.hpp"
			#include "../../../utils/compat.hpp"
			#include "../../../physics/constants.hpp"
			#include "../../../physics/maths.hpp"

			#include "../../../dfpmsolver/parabolic_driver.hpp"

			namespace specmicp {

			namespace dfpmsolver {

			// explicit template instanciation
			template class ParabolicDriver<reactmicp::systems::unsaturated::AqueousGasTransportEquation>;

			} //end namespace dfpmsolver

			namespace reactmicp {
			namespace systems {
			namespace unsaturated {

			static constexpr index_t no_equation {-1};
			static constexpr index_t no_eq_no_var {-2};
			static constexpr index_t not_initialized {-5};

			struct SPECMICP_DLL_LOCAL AqueousGasTransportEquation::AqueousGasTransportEquationImpl
			{
			mesh::Mesh1DPtr m_mesh;
			LiquidGasAqueousVariableBox m_vars;
			std::vector<index_t> m_ideq;

			mesh::Mesh1D* mesh() {return m_mesh.get();}
			LiquidAqueousComponentVariableBox& vars() {return m_vars;}

			bool node_has_equation(index_t node) {
			return m_ideq[node] > no_equation;
			}

			bool node_can_flux(index_t node) {
			return m_ideq[node] > no_eq_no_var;
			}

			index_t id_equation(index_t node) {
			return m_ideq[node];
			}

			void fix_node(index_t node) {
			m_ideq[node] = no_equation;
			}

			void gas_node(index_t node) {
			m_ideq[node] = no_eq_no_var;
			}

			AqueousGasTransportEquationImpl(
			mesh::Mesh1DPtr the_mesh,
			LiquidGasAqueousVariableBox the_vars
			):
			m_mesh(the_mesh),
			m_vars(the_vars),
			m_ideq(the_mesh->nb_nodes(), not_initialized)
			{}

			void compute_transport_rate(scalar_t dt, const Vector& displacment);
			};

			AqueousGasTransportEquation::AqueousGasTransportEquation(mesh::Mesh1DPtr the_mesh,
			LiquidGasAqueousVariableBox& variables,
			const TransportConstraints& constraints):
			base(the_mesh->nb_nodes()),
			m_impl(make_unique<AqueousGasTransportEquationImpl>(the_mesh, variables))
			{
			number_equations(constraints);
			}

			AqueousGasTransportEquation::~AqueousGasTransportEquation() = default;


			index_t AqueousGasTransportEquation::id_equation_impl(index_t id_dof)
			{
			const auto id_eq = m_impl->id_equation(id_dof);
			return (id_eq>no_equation)?id_eq:no_equation;
			}

			mesh::Mesh1D* AqueousGasTransportEquation::get_mesh_impl()
			{
			return m_impl->mesh();
			}


			void AqueousGasTransportEquation::pre_nodal_residual_hook_impl(
			index_t node, const Vector& displacement)
			{}
			void AqueousGasTransportEquation::pre_residual_hook_impl(const Vector& displacement)
			{}
			void AqueousGasTransportEquation::post_residual_hook_impl(const Vector& displacement)
			{}

			//! \brief Compute the residuals inside 'element'
			void AqueousGasTransportEquation::residuals_element_impl(
			index_t element,
			const Vector& displacement,
			const Vector& velocity,
			Eigen::Vector2d& element_residual,
			bool use_chemistry_rate
			)
			{
			element_residual.setZero();

			mesh::Mesh1D* m_mesh = m_impl->mesh();
			LiquidGasAqueousVariableBox& vars = m_impl->m_vars;
			const scalar_t& rt = vars.constants.rt;

			const scalar_t mass_coeff_0 = m_mesh->get_volume_cell_element(element, 0);
			const scalar_t mass_coeff_1 = m_mesh->get_volume_cell_element(element, 1);

			const index_t node_0 = m_mesh->get_node(element, 0);
			const index_t node_1 = m_mesh->get_node(element, 1);

			scalar_t flux_0 = 0.0;
			scalar_t flux_1 = 0.0;

			if (m_impl->node_can_flux(node_0) and m_impl->node_can_flux(node_1))
			{
			// Diffusion Cw
			const scalar_t coeff_diff_0 = vars.liquid_diffusivity(node_0)
			* vars.relative_liquid_diffusivity(node_0);
			const scalar_t coeff_diff_1 = vars.liquid_diffusivity(node_1)
			* vars.relative_liquid_diffusivity(node_1);

			const scalar_t coeff_diff = average<Average::harmonic>(
			coeff_diff_0, coeff_diff_1);

			const scalar_t diff_aq = (displacement(node_1)
			- displacement(node_0)
			);
			const scalar_t diff_flux = coeff_diff * diff_aq/ m_mesh->get_dx(element);

			// advection
			if (vars.advection_flux(element) < 0)
			{
			flux_0 = -vars.advection_flux(element)*diff_aq;
			}
			else if (vars.advection_flux(element) > 0)
			{
			flux_1 = -vars.advection_flux(element)*diff_aq;
			}
			flux_0 += diff_flux;
			flux_1 -= diff_flux;
			}

			const scalar_t coeff_diff_gas_0 = vars.resistance_gas_diffusivity(node_0)
			* vars.relative_gas_diffusivity(node_0);
			const scalar_t coeff_diff_gas_1 = vars.resistance_gas_diffusivity(node_1)
			* vars.relative_gas_diffusivity(node_1);

			const scalar_t coeff_diff_gas = vars.binary_diffusion_coefficient *
			average<Average::harmonic>(coeff_diff_gas_0, coeff_diff_gas_1);

			const scalar_t diff_flux_gas = coeff_diff_gas*(
			vars.partial_pressure(node_1) - vars.partial_pressure(node_0))
			/ m_mesh->get_dx(element)
			/ rt;

			flux_0 += diff_flux_gas;
			flux_0 *= m_mesh->get_face_area(element);
			flux_1 -= diff_flux_gas;
			flux_1 *= m_mesh->get_face_area(element);

			// transient
			if (m_impl->node_has_equation(node_0))
			{
			const scalar_t porosity_0 = vars.porosity(node_0);
			const scalar_t aq_tot_conc_0 = displacement(node_0);
			const scalar_t saturation_0 = vars.saturation(node_0);

			const scalar_t transient_0 =
			porosity_0 * aq_tot_conc_0 * vars.saturation.velocity(node_0)
			+ saturation_0 * aq_tot_conc_0 * vars.porosity.velocity(node_0)
			+ porosity_0 * saturation_0 * velocity(node_0);

			scalar_t res = mass_coeff_0*transient_0 - flux_0;

			if (use_chemistry_rate)
			{
			const scalar_t chemistry_0 =
			vars.aqueous_concentration.chemistry_rate(node_0)
			+ vars.solid_concentration.chemistry_rate(node_0)
			+ vars.partial_pressure.chemistry_rate(node_0);
			res -= mass_coeff_0*chemistry_0;
			}
			element_residual(0) = res/get_scaling();

			}

			if (m_impl->node_has_equation(node_1))
			{
			const scalar_t porosity_1 = vars.porosity(node_1);
			const scalar_t aq_tot_conc_1 = displacement(node_1);
			const scalar_t saturation_1 = vars.saturation(node_1);

			const scalar_t transient_1 =
			porosity_1 * aq_tot_conc_1 * vars.saturation.velocity(node_1)
			+ saturation_1 * aq_tot_conc_1 * vars.porosity.velocity(node_1)
			+ porosity_1 * saturation_1 * velocity(node_1);
			scalar_t res = mass_coeff_1*transient_1 - flux_1;

			if (use_chemistry_rate)
			{
			const scalar_t chemistry_1 =
			vars.aqueous_concentration.chemistry_rate(node_1)
			+ vars.solid_concentration.chemistry_rate(node_1)
			+ vars.partial_pressure.chemistry_rate(node_1);
			res -= mass_coeff_1*chemistry_1;
			}
			element_residual(1) = res/get_scaling();
			}

			}

			void AqueousGasTransportEquation::number_equations(const TransportConstraints& constraints)
			{
			for (int fixed_node: constraints.fixed_nodes())
			{
			m_impl->fix_node(fixed_node);
			}
			for (int gas_node: constraints.gas_nodes())
			{
			m_impl->gas_node(gas_node);
			}
			index_t neq = 0;
			for (index_t node: m_impl->mesh()->range_nodes())
			{
			if (m_impl->m_ideq[node] == not_initialized)
			{
			m_impl->m_ideq[node] = neq;
			++neq;
			}
			}
			register_number_equations(neq);
			}

			void AqueousGasTransportEquation::compute_transport_rate(
			scalar_t dt,
			const Vector& displacement
			)
			{
			m_impl->compute_transport_rate(dt, displacement);
			}

			void AqueousGasTransportEquation::AqueousGasTransportEquationImpl::compute_transport_rate(
			scalar_t dt,
			const Vector& displacement)
			{
			MainVariable& aqueous_concentration = m_vars.aqueous_concentration;
			const MainVariable& saturation = m_vars.saturation;
			const MainVariable& solid_conc = m_vars.solid_concentration;
			const MainVariable& pressure = m_vars.partial_pressure;
			const SecondaryTransientVariable& porosity = m_vars.porosity;

			for (index_t node: m_mesh->range_nodes())
			{
			if (! node_has_equation(node)) continue;

			const scalar_t transient = (
			( porosity(node)
			* saturation(node)
			* displacement(node))
			- ( porosity.predictor(node)
			* aqueous_concentration.predictor(node)
			* saturation.predictor(node))
			) / dt;

			const scalar_t chem_rates = (
			saturation.chemistry_rate(node)
			+ solid_conc.chemistry_rate(node)
			+ pressure.chemistry_rate(node)
			);

			aqueous_concentration.transport_fluxes(node) = transient - chem_rates;
			}
			}


			} //end namespace unsaturated
			} //end namespace systems
			} //end namespace reactmicp
			} //end namespace specmicp

specmicp/src/reactmicp/systems/unsaturated/aqueous_pressure_equation.cppefe3e6ff717dyaml/safe

aqueous_pressure_equation.cppView Options

specmicp/src/reactmicp/systems/unsaturated/aqueous_pressure_equation.cpp
efe3e6ff717dyaml/safe

aqueous_pressure_equation.cpp
View Options