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specmicp/src/reactmicp/systems/diffusion/diffusion_numbering.cpp
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diffusion_numbering.cpp
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/*-------------------------------------------------------
- Module : reactmicp/systems/diffusion
- File : diffusion_numbering.cpp
- 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 "diffusion_numbering.hpp"
#include "reactmicp/meshes/mesh1d.hpp"
namespace specmicp {
namespace reactmicp {
namespace systems {
namespace diffusion {
// Boundary Condition
void BoundaryCondition::fix_all()
{
if (not composition.is_valid())
throw std::runtime_error("The composition has not been correctly initialized");
std::shared_ptr<database::DataContainer> data = composition.get_database();
component.reserve(data->nb_component - 1);
tot_mobile_concentration.reserve(data->nb_component -1);
mineral.reserve(data->nb_mineral);
for (int comp: data->range_aqueous_component())
{
component.push_back(comp);
tot_mobile_concentration.push_back(comp);
}
for (int min: data->range_mineral())
{
mineral.push_back(min);
}
}
// Diffusion numbering
DiffusionNumbering::DiffusionNumbering(ind_t number_nodes,
ind_t number_aqueous_component,
ind_t number_mineral, const ListBoundaryCondition &list_bc, Variables &variable):
nb_aq_component(number_aqueous_component), nb_mineral(number_mineral),
nb_ndf(2*number_aqueous_component+number_mineral),
m_ideq(nb_ndf, number_nodes)
{
number_equations(list_bc, variable);
}
void DiffusionNumbering::number_equations(const ListBoundaryCondition& list_bc,
Variables& variable)
{
initialize_variable(variable);
// First we parse the bcs, to find the correct bc to apply
parse_bcs(list_bc, variable);
// Then we number the equations
do_numbering();
}
void DiffusionNumbering::initialize_variable(Variables& variable)
{
variable.displacement = Vector::Zero(m_ideq.rows()*m_ideq.cols());
variable.velocity = Vector::Zero(m_ideq.rows()*m_ideq.cols());
}
void DiffusionNumbering::parse_bcs(const ListBoundaryCondition& list_bc,
Variables& variable)
{
variable.displacement.setZero();
variable.velocity.setZero();
m_ideq.setZero();
m_nodes_with_bc.reserve(list_bc.size());
for (BoundaryCondition bc: list_bc)
{
const ind_t node = bc.node;
m_nodes_with_bc.push_back(node);
for (ind_t component: bc.tot_mobile_concentration)
{
m_ideq(get_ndof_diffusion(component), node) = no_equation;
mobile_total_concentration(node, component, variable) = bc.composition.total_aqueous_concentration_component(component);
}
for (ind_t component: bc.component)
{
m_ideq(get_ndof_massbalance(component), node) = no_equation;
component_concentration(node, component, variable) = std::log10(bc.composition.molality_component(component));
}
for (ind_t mineral: bc.mineral)
{
m_ideq(get_ndof_mineral(mineral), node) = no_equation;
mole_mineral(node, mineral, variable) = bc.composition.moles_mineral(mineral);
}
}
//
for (int node=0; node<m_ideq.cols(); ++node)
{
for (ind_t component=1; component<5; ++component)
{
// m_ideq(get_ndof_diffusion(component), node) = no_equation;
// m_ideq(get_ndof_massbalance(component), node) = no_equation;
}
for (ind_t mineral=0; mineral<5; ++mineral)
{
// m_ideq(get_ndof_mineral(mineral), node) = no_equation;
}
}
}
void DiffusionNumbering::do_numbering()
{
ind_t neq = 0;
for (ind_t node=0; node<m_ideq.cols(); ++node)
{
for (ind_t df=0; df<get_ndf(); ++df)
{
if (m_ideq(df, node) != no_equation)
{
m_ideq(df, node) = neq;
++neq;
}
}
}
nb_neq = neq;
}
//! \brief Return true if the node has a boundary condition
double DiffusionNumbering::node_has_bc(ind_t node)
{
auto search = std::find(m_nodes_with_bc.begin(), m_nodes_with_bc.end(), node);
if (search == m_nodes_with_bc.end()) return false;
else return true;
}
} // end namespace diffusion
} // end namespace systems
} // end namespace reactmicp
} // end namespace specmicp
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