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specmicp/src/reactmicp/io/saturated_react.cpp
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saturated_react.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
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 "saturated_react.hpp"
#include <iostream>
#include <fstream>
#include <chrono>
#include <ctime>
#include "../../dfpm/meshes/mesh1d.hpp"
#include "../../specmicp/adimensional/adimensional_system_solution_extractor.hpp"
#include "../../utils/dateandtime.hpp"
#include "../../physics/io/units.hpp"
#include "../systems/saturated_react/variables.hpp"
#include "../../utils/io/csv_formatter.hpp"
#include "../../dfpm/io/meshes.hpp"
#include "../../utils/compat.hpp"
#include "../../database/database_holder.hpp"
using namespace specmicp::reactmicp::systems::satdiff;
namespace specmicp {
namespace io {
void print_csv_header(CSVFile& ofile)
{
ofile.insert_comment_line("ReactMiCP");
ofile.insert_comment_line("---------");
ofile.insert_comment_date();
}
void print_components_total_aqueous_concentration(
RawDatabasePtr the_database,
SaturatedVariablesPtr variables,
mesh::Mesh1DPtr the_mesh,
const units::UnitsSet& units_set,
CSVFile& ofile
)
{
print_csv_header(ofile);
ofile.insert_comment_line("Total aqueous concentrations profiles");
ofile.insert_comment_line( "length unit : " + io::length_unit_to_string(units_set.length));
ofile.insert_comment_line( "concentration unit : mol/" + io::volume_unit_to_string(units_set.length));
ofile << "Position";
for (index_t component: the_database->range_aqueous_component())
{
ofile.separator();
ofile << the_database->get_label_component(component);
}
ofile.eol();
for (index_t node: the_mesh->range_nodes())
{
ofile << the_mesh->get_position(node);
for (index_t component: the_database->range_aqueous_component())
{
ofile.separator();
ofile << variables->aqueous_concentration(node, component);
}
ofile.eol();
}
ofile.flush();
}
//! \brief Print the total aqueous concentrations in the CSV format in the file 'filepath'
void print_components_total_aqueous_concentration(
RawDatabasePtr the_database,
SaturatedVariablesPtr variables,
mesh::Mesh1DPtr the_mesh,
const units::UnitsSet& units_set,
const std::string& filepath
)
{
CSVFile ofile(filepath);
print_components_total_aqueous_concentration(the_database, variables, the_mesh, units_set, ofile);
}
//! \brief Print the total solid concentrations in the CSV format in 'ofile'
void print_components_total_solid_concentration(
RawDatabasePtr the_database,
SaturatedVariablesPtr variables,
mesh::Mesh1DPtr the_mesh,
const units::UnitsSet& units_set,
CSVFile& ofile
)
{
print_csv_header(ofile);
ofile.insert_comment_line( "length unit : " + io::length_unit_to_string(units_set.length));
ofile.insert_comment_line( "concentration unit : mol/" + io::volume_unit_to_string(units_set.length));
ofile << "Position";
for (index_t component: the_database->range_aqueous_component())
{
ofile.separator();
ofile << the_database->get_label_component(component);
}
ofile.eol();
for (index_t node: the_mesh->range_nodes())
{
ofile << the_mesh->get_position(node);
for (index_t component: the_database->range_aqueous_component())
{
ofile.separator();
ofile << variables->solid_concentration(node, component);
}
ofile.eol();
}
ofile.flush();
}
//! \brief Print the total solid concentrations in the CSV format in the file 'filepath'
void print_components_total_solid_concentration(
RawDatabasePtr the_database,
SaturatedVariablesPtr variables,
mesh::Mesh1DPtr the_mesh,
const units::UnitsSet& units_set,
const std::string& filepath
)
{
CSVFile ofile(filepath);
print_components_total_solid_concentration(the_database, variables, the_mesh, units_set, ofile);
}
//! \brief Print the solid phases profiles in 'ofile'
inline void print_minerals_profile(RawDatabasePtr the_database,
SaturatedVariablesPtr variables,
mesh::Mesh1DPtr the_mesh,
const units::UnitsSet& units_set,
CSVFile& ofile
)
{
print_csv_header(ofile);
ofile.insert_comment_line("Solid phase profiles");
ofile.insert_comment_line( "length unit : " + io::length_unit_to_string(units_set.length));
ofile << "Position";
for (index_t mineral: the_database->range_mineral())
{
ofile.separator();
ofile << the_database->get_label_mineral(mineral);
}
ofile.separator();
ofile << "Porosity";
ofile.separator();
ofile << "pH";
ofile.eol();
for (index_t node: the_mesh->range_nodes())
{
ofile << the_mesh->get_position(node);
AdimensionalSystemSolutionExtractor extractor(variables->equilibrium_solution(node), the_database, units::UnitsSet());
for (index_t mineral: the_database->range_mineral())
{
ofile.separator();
ofile << extractor.volume_fraction_mineral(mineral);
}
ofile.separator();
ofile << variables->porosity(node);
ofile.separator();
ofile << extractor.pH();
ofile.eol();
}
ofile.flush();
}
//! \brief Print the solid phases profiles in 'filepath'
void print_minerals_profile(
RawDatabasePtr the_database,
SaturatedVariablesPtr variables,
mesh::Mesh1DPtr the_mesh,
const units::UnitsSet& units_set,
const std::string& filepath
)
{
CSVFile ofile(filepath);
print_minerals_profile(
the_database,
variables,
the_mesh,
units_set,
ofile
);
}
// declaration of implementation
// =============================
//! \brief The implementation details of OutputNodalVariables
//!
//! \internal
struct OutputNodalVariables::OutputNodalVariablesImpl: public database::DatabaseHolder
{
using equilibrium_var_f = std::function<scalar_t (AdimensionalSystemSolutionExtractor*)> ;
OutputNodalVariablesImpl(
const RawDatabasePtr& the_database,
const mesh::Mesh1DPtr& the_mesh,
const units::UnitsSet& the_units):
database::DatabaseHolder(the_database),
m_mesh(the_mesh),
m_units(the_units)
{}
// attributes
mesh::Mesh1DPtr m_mesh;
units::UnitsSet m_units;
std::vector<index_t> m_index_aqueous {};
std::vector<index_t> m_index_solid {};
std::vector<index_t> m_index_conc {};
CSVFile m_out_poro {};
CSVFile m_out_diffusivity {};
std::vector<CSVFile> m_out_aqueous {};
std::vector<CSVFile> m_out_solid {};
std::vector<CSVFile> m_out_conc {};
std::vector<CSVFile> m_out_equilibrium_vars {};
std::vector<equilibrium_var_f> m_func_equilibrium_vars {};
std::vector<CSVFile> m_out_custom {};
std::vector<custom_f> m_func_custom {};
// functions
void print_csv_column_headers(CSVFile& out);
void register_porosity(const std::string& filepath);
void register_diffusion_coefficient(const std::string &filepath);
void register_total_aqueous_concentration(
index_t component,
const std::string& filepath
);
void register_total_concentration(
index_t component,
const std::string& filepath
);
void register_total_solid_concentration(
index_t component,
const std::string& filepath
);
void register_molality_component(
index_t component,
const std::string& filepath);
void register_pH(const std::string& filepath);
void register_volume_fraction_mineral(
index_t mineral,
const std::string& filepath
);
void register_saturation_index_mineral_kinetic(
index_t mineral_kinetic,
const std::string& filepath);
void register_custom_function(
custom_f getter_function,
const std::string& filepath,
const std::string& msg
);
void output(scalar_t time, SaturatedVariablesPtr var);
};
// Main functions
// ===============
OutputNodalVariables::OutputNodalVariables(
RawDatabasePtr the_database,
mesh::Mesh1DPtr the_mesh,
const units::UnitsSet& the_units
):
m_impl(make_unique<OutputNodalVariablesImpl>(the_database, the_mesh, the_units))
{}
OutputNodalVariables::~OutputNodalVariables() = default;
void OutputNodalVariables::register_porosity(const std::string &filepath)
{
m_impl->register_porosity(filepath);
}
void OutputNodalVariables::register_diffusion_coefficient(const std::string &filepath)
{
m_impl->register_diffusion_coefficient(filepath);
}
void OutputNodalVariables::register_total_aqueous_concentration(
index_t component,
const std::string& filepath
)
{
specmicp_assert_component_bounds(component, m_impl->get_database());
m_impl->register_total_aqueous_concentration(component, filepath);
}
void OutputNodalVariables::register_total_concentration(
index_t component,
const std::string& filepath
)
{
specmicp_assert_component_bounds(component, m_impl->get_database());
m_impl->register_total_concentration(component, filepath);
}
void OutputNodalVariables::register_total_solid_concentration(
index_t component,
const std::string& filepath
)
{
specmicp_assert_component_bounds(component, m_impl->get_database());
m_impl->register_total_solid_concentration(component, filepath);
}
void OutputNodalVariables::register_molality_component(
index_t component,
const std::string& filepath
)
{
specmicp_assert_component_bounds(component, m_impl->get_database());
m_impl->register_molality_component(component, filepath);
}
void OutputNodalVariables::register_pH(const std::string& filepath)
{
m_impl->register_pH(filepath);
}
void OutputNodalVariables::register_volume_fraction_mineral(index_t mineral, const std::string& filepath)
{
specmicp_assert_mineral_bounds(mineral, m_impl->get_database());
m_impl->register_volume_fraction_mineral(mineral, filepath);
}
void OutputNodalVariables::register_saturation_index_mineral_kinetic(
index_t mineral_kinetic,
const std::string& filepath
)
{
specmicp_assert_mineral_kinetic_bounds(mineral_kinetic, m_impl->get_database());
m_impl->register_saturation_index_mineral_kinetic(mineral_kinetic, filepath);
}
void OutputNodalVariables::register_custom_function(
custom_f getter_function,
const std::string& filepath,
const std::string& msg
)
{
m_impl->register_custom_function(getter_function, filepath, msg);
}
void OutputNodalVariables::output(scalar_t time, reactmicp::solver::VariablesBasePtr var)
{
SaturatedVariablesPtr true_var = cast_var_from_base(var);
m_impl->output(time, true_var);
}
std::function<void (scalar_t, reactmicp::solver::VariablesBasePtr)> OutputNodalVariables::get_output_for_reactmicp()
{
return std::bind(std::mem_fn<void (scalar_t, reactmicp::solver::VariablesBasePtr)>(
&OutputNodalVariables::output),
this, std::placeholders::_1, std::placeholders::_2);
}
RawDatabasePtr OutputNodalVariables::get_database()
{
return m_impl->get_database();
}
// #########################################
//
// Implementation
//
// ##########################################
void OutputNodalVariables::OutputNodalVariablesImpl::print_csv_column_headers(CSVFile& out)
{
out.insert_comment_unit("time", "s");
out.insert_comment_unit("length", io::length_unit_to_string(m_units.length));
out << "Time";
for (index_t node: m_mesh->range_nodes())
{
out.separator();
out << m_mesh->get_position(node);
}
out.eol();
}
void OutputNodalVariables::OutputNodalVariablesImpl::register_porosity(
const std::string &filepath
)
{
m_out_poro.open(filepath);
m_out_poro.insert_comment_line("ReactMiCP - porosity");
m_out_poro.insert_comment_date();
print_csv_column_headers(m_out_poro);
}
void OutputNodalVariables::OutputNodalVariablesImpl::register_diffusion_coefficient(
const std::string &filepath
)
{
m_out_diffusivity.open(filepath);
m_out_diffusivity.insert_comment_line("ReactMiCP - diffusion coefficient");
m_out_diffusivity.insert_comment_date();
m_out_diffusivity.insert_comment_unit("diffusion coefficient", io::surface_unit_to_string(m_units.length)+"/s");
print_csv_column_headers(m_out_diffusivity);
}
void OutputNodalVariables::OutputNodalVariablesImpl::register_total_aqueous_concentration(
index_t component,
const std::string& filepath
)
{
m_index_aqueous.push_back(component);
m_out_aqueous.emplace_back(filepath);
auto i = m_out_aqueous.size() - 1;
m_out_aqueous[i].open(filepath);
m_out_aqueous[i].insert_comment_line("ReactMiCP - aqueous concentration");
m_out_aqueous[i].insert_comment_date();
m_out_aqueous[i].insert_comment_unit("Concentration", "mol/"+io::volume_unit_to_string(m_units.length));
print_csv_column_headers(m_out_aqueous[i]);
}
void OutputNodalVariables::OutputNodalVariablesImpl::register_total_concentration(
index_t component,
const std::string& filepath
)
{
m_index_conc.push_back(component);
m_out_conc.emplace_back(filepath);
auto i = m_out_conc.size() - 1;
m_out_conc[i].open(filepath);
m_out_conc[i].insert_comment_line("ReactMiCP - Total concentration");
m_out_conc[i].insert_comment_date();
m_out_conc[i].insert_comment_unit("Concentration", "mol/"+io::volume_unit_to_string(m_units.length));
print_csv_column_headers(m_out_conc[i]);
}
void OutputNodalVariables::OutputNodalVariablesImpl::register_total_solid_concentration(
index_t component,
const std::string& filepath
)
{
m_index_solid.push_back(component);
m_out_solid.emplace_back(filepath);
auto i = m_out_solid.size() - 1;
m_out_solid[i].insert_comment_line("ReactMiCP - solid concentration");
m_out_solid[i].insert_comment_date();
m_out_solid[i].insert_comment_unit("Concentration", "mol/"+io::volume_unit_to_string(m_units.length));
print_csv_column_headers(m_out_solid[i]);
}
void OutputNodalVariables::OutputNodalVariablesImpl::register_molality_component(
index_t component,
const std::string& filepath
)
{
m_func_equilibrium_vars.emplace_back(std::bind(
std::mem_fn(&AdimensionalSystemSolutionExtractor::molality_component),
std::placeholders::_1,
component
));
m_out_equilibrium_vars.emplace_back(filepath);
auto i = m_out_equilibrium_vars.size() -1;
m_out_equilibrium_vars[i].insert_comment_line("ReactMiCP - molality component "+m_data->get_label_component(component));
m_out_equilibrium_vars[i].insert_comment_date();
m_out_equilibrium_vars[i].insert_comment_unit("molality", "mol/kg");
print_csv_column_headers(m_out_equilibrium_vars[i]);
}
void OutputNodalVariables::OutputNodalVariablesImpl::register_pH(
const std::string& filepath
)
{
m_func_equilibrium_vars.emplace_back(std::bind(
std::mem_fn(&AdimensionalSystemSolutionExtractor::pH),
std::placeholders::_1
));
m_out_equilibrium_vars.emplace_back(filepath);
auto i = m_out_equilibrium_vars.size() -1;
m_out_equilibrium_vars[i].insert_comment_line("ReactMiCP - pH");
m_out_equilibrium_vars[i].insert_comment_date();
print_csv_column_headers(m_out_equilibrium_vars[i]);
}
void OutputNodalVariables::OutputNodalVariablesImpl::register_volume_fraction_mineral(
index_t mineral,
const std::string& filepath
)
{
m_func_equilibrium_vars.emplace_back(std::bind(
std::mem_fn(&AdimensionalSystemSolutionExtractor::volume_fraction_mineral),
std::placeholders::_1,
mineral
));
m_out_equilibrium_vars.emplace_back(filepath);
auto i = m_out_equilibrium_vars.size() -1;
m_out_equilibrium_vars[i].insert_comment_line("ReactMiCP - volume fraction mineral "+m_data->get_label_mineral(mineral));
m_out_equilibrium_vars[i].insert_comment_date();
print_csv_column_headers(m_out_equilibrium_vars[i]);
}
void OutputNodalVariables::OutputNodalVariablesImpl::register_saturation_index_mineral_kinetic(
index_t mineral_kinetic,
const std::string& filepath)
{
m_func_equilibrium_vars.emplace_back(std::bind(
std::mem_fn(&AdimensionalSystemSolutionExtractor::saturation_index_kinetic),
std::placeholders::_1,
mineral_kinetic
));
m_out_equilibrium_vars.emplace_back(filepath);
auto i = m_out_equilibrium_vars.size() -1;
m_out_equilibrium_vars[i].insert_comment_line("ReactMiCP - Saturation index mineral "
+ m_data->get_label_mineral_kinetic(mineral_kinetic));
m_out_equilibrium_vars[i].insert_comment_date();
print_csv_column_headers(m_out_equilibrium_vars[i]);
}
void OutputNodalVariables::OutputNodalVariablesImpl::register_custom_function(
custom_f getter_function,
const std::string& filepath,
const std::string& msg
)
{
m_func_custom.push_back(getter_function);
m_out_custom.emplace_back(filepath);
auto i = m_out_custom.size() -1;
CSVFile& out = m_out_custom[i];
out.insert_comment_line("ReactMiCP");
out.insert_comment_line(msg);
out.insert_comment_date();
print_csv_column_headers(out);
}
void OutputNodalVariables::OutputNodalVariablesImpl::output(scalar_t time, SaturatedVariablesPtr variables)
{
// upscaling
// ---------
if (m_out_poro.is_open())
{
m_out_poro << time;
for (index_t node: m_mesh->range_nodes())
{
m_out_poro.separator();
m_out_poro << variables->porosity(node);
}
m_out_poro.endl();
}
if (m_out_diffusivity.is_open())
{
m_out_diffusivity << time;
for (index_t node: m_mesh->range_nodes())
{
m_out_diffusivity.separator();
m_out_diffusivity << variables->diffusion_coefficient(node);
}
m_out_diffusivity.endl();
}
// equilibrium vars
// ----------------
if (m_out_equilibrium_vars.size() > 0)
{
for (std::vector<CSVFile>::size_type var=0; var< m_out_equilibrium_vars.size(); ++var)
{
m_out_equilibrium_vars[var] << time;
}
for (index_t node: m_mesh->range_nodes())
{
AdimensionalSystemSolutionExtractor extr(variables->equilibrium_solution(node), m_data, m_units);
for (std::vector<CSVFile>::size_type var=0; var< m_out_equilibrium_vars.size(); ++var)
{
m_out_equilibrium_vars[var].separator();
m_out_equilibrium_vars[var] << m_func_equilibrium_vars[var](&extr);
}
}
for (std::vector<CSVFile>::size_type var=0; var< m_out_equilibrium_vars.size(); ++var)
{
m_out_equilibrium_vars[var].endl();
}
}
// nodal vars
// -----------
for (std::vector<CSVFile>::size_type aqueous=0; aqueous< m_index_aqueous.size(); ++aqueous)
{
m_out_aqueous[aqueous] << time;
}
for (std::vector<CSVFile>::size_type solid=0; solid< m_index_solid.size(); ++solid)
{
m_out_solid[solid] << time;
}
for (std::vector<CSVFile>::size_type tot=0; tot< m_index_conc.size(); ++tot)
{
m_out_conc[tot] << time;
}
for (index_t node: m_mesh->range_nodes())
{
for (std::vector<CSVFile>::size_type aqueous=0; aqueous< m_index_aqueous.size(); ++aqueous)
{
m_out_aqueous[aqueous].separator();
m_out_aqueous[aqueous] << variables->aqueous_concentration(node, m_index_aqueous[aqueous]);
}
for (std::vector<CSVFile>::size_type solid=0; solid< m_index_solid.size(); ++solid)
{
m_out_solid[solid].separator();
m_out_solid[solid] << variables->solid_concentration(node, m_index_solid[solid]);
}
for (std::vector<CSVFile>::size_type tot=0; tot< m_index_conc.size(); ++tot)
{
m_out_conc[tot].separator();
m_out_conc[tot] << variables->porosity(node)*variables->aqueous_concentration(node, m_index_conc[tot])
+ variables->solid_concentration(node, m_index_conc[tot]);
}
}
for (std::vector<CSVFile>::size_type aqueous=0; aqueous< m_index_aqueous.size(); ++aqueous)
{
m_out_aqueous[aqueous].endl();
}
for (std::vector<CSVFile>::size_type solid=0; solid< m_index_solid.size(); ++solid)
{
m_out_solid[solid].endl();
}
for (std::vector<CSVFile>::size_type tot=0; tot< m_index_conc.size(); ++tot)
{
m_out_conc[tot].endl();
}
// custom functions
for (std::vector<CSVFile>::size_type var=0; var< m_out_custom.size(); ++var)
{
auto& out = m_out_custom[var];
out << time;
for (index_t node: m_mesh->range_nodes())
{
out.separator();
out << m_func_custom[var](node, variables);
}
out.endl();
}
}
} // end namespace io
} // end namespace specmicp
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