diff --git a/src/database/database.cpp b/src/database/database.cpp
index 6c6394d..d7ee771 100644
--- a/src/database/database.cpp
+++ b/src/database/database.cpp
@@ -1,172 +1,176 @@
/*-------------------------------------------------------------------------------
Copyright (c) 2014,2015 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 "database.hpp"
#include "selector.hpp"
#include "switch_basis.hpp"
#include "mineral_selector.hpp"
#include "yaml_reader.hpp"
#include "oxydo_selector.hpp"
#include "appender.hpp"
#include "yaml_writer.hpp"
namespace specmicp {
namespace database {
// Implementation note
// --------------------
// This class does not contain any major algorithm
// Instead it calls the database modules methods
// This is done in the source file to reduce compilation dependancy
// and avoid exporting too many symbols
//
// This class should only contains short functions.
void Database::parse_database(std::string filepath)
{
DataReaderYaml reader(filepath);
set_database(reader.get_database());
}
void Database::parse_database(std::istream& input)
{
DataReaderYaml reader(input);
set_database(reader.get_database());
}
void Database::remove_components(const std::vector<std::string>& labels_components_to_remove)
{
std::vector<index_t> id_components_to_remove;
id_components_to_remove.reserve(labels_components_to_remove.size());
for (auto it: labels_components_to_remove)
{
id_components_to_remove.push_back(safe_component_label_to_id(it));
}
remove_components(id_components_to_remove);
}
void Database::remove_components(const std::vector<index_t>& id_components_to_remove)
{
DatabaseSelector selector(data);
selector.remove_component(id_components_to_remove);
}
void Database::keep_only_components(const std::vector<std::string>& labels_components_to_keep)
{
std::vector<index_t> id_components_to_keep;
id_components_to_keep.reserve(labels_components_to_keep.size());
for (auto it: labels_components_to_keep)
{
id_components_to_keep.push_back(safe_component_label_to_id(it));
}
keep_only_components(id_components_to_keep);
}
void Database::keep_only_components(const std::vector<index_t>& id_components_to_keep)
{
DatabaseSelector selector(data);
selector.keep_only_component(id_components_to_keep);
}
void Database::minerals_keep_only(const std::vector<std::string>& minerals_to_keep)
{
MineralSelector(data).keep_only(minerals_to_keep);
}
void Database::minerals_keep_only(const std::vector<index_t>& minerals_to_keep)
{
MineralSelector(data).keep_only(minerals_to_keep);
}
void Database::swap_components(const std::map<std::string, std::string>& swap_to_make)
{
BasisSwitcher(data).swap_components(swap_to_make);
}
void Database::remove_gas_phases()
{
DatabaseSelector(data).remove_all_gas();
}
void Database::add_gas_phases(const std::string &gas_input)
{
DataAppender(data).add_gas(gas_input);
}
void Database::remove_solid_phases()
{
MineralSelector(data).remove_all_minerals();
}
void Database::add_solid_phases(const std::string &solid_phases_input)
{
DataAppender(data).add_minerals(solid_phases_input);
}
void Database::remove_sorbed_species()
{
DatabaseSelector(data).remove_all_sorbed();
}
void Database::add_sorbed_species(const std::string& sorbed_input)
{
DataAppender(data).add_sorbed(sorbed_input);
}
void Database::remove_compounds()
{
DatabaseSelector(data).remove_all_compounds();
}
void Database::add_compounds(const std::string& compounds_input)
{
DataAppender(data).add_compounds(compounds_input);
}
+void Database::remove_half_cell_reactions()
+{
+ OxydoSelector(data).remove_half_cells();
+}
void Database::remove_half_cell_reactions(const std::vector<std::string>& list_components)
{
OxydoSelector(data).remove_half_cells(list_components);
}
void Database::remove_half_cell_reactions(const std::vector<index_t>& list_id_components)
{
OxydoSelector(data).remove_half_cells(list_id_components);
}
void Database::save(const std::string& filename)
{
DatabaseWriterYaml(data).write(filename);
}
} // end namespace database
} // end namespace specmicp
diff --git a/src/database/database.hpp b/src/database/database.hpp
index 40e8611..de53720 100644
--- a/src/database/database.hpp
+++ b/src/database/database.hpp
@@ -1,181 +1,183 @@
/*-------------------------------------------------------------------------------
Copyright (c) 2014,2015 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.
-----------------------------------------------------------------------------*/
#ifndef SPECMICP_DATABASE_DATABASE_HPP
#define SPECMICP_DATABASE_DATABASE_HPP
//! \file src/database/database.hpp
//! \brief Database management
#include "module.hpp"
#include <map>
namespace specmicp {
//! \namespace specmicp::database
//! \brief Database management
namespace database {
//! \brief Prepare the database for the simulation.
//!
//! This is the class that should be used to handle the database.
//! It does not contain the data, only the algorithms.
//!
//! \ingroup specmicp_api
class SPECMICP_DLL_PUBLIC Database: public DatabaseModule
{
public:
//! \brief Default constructor
//!
//! the method parse_database must be called to parse the json database
Database() {}
//! \brief Initialise the database py parsing 'filepath'
Database(std::string filepath) {
parse_database(filepath);
}
//! \brief initialise the database with the raw database
Database(std::shared_ptr<DataContainer> raw_data):
DatabaseModule(raw_data)
{}
//! \brief Parse the database 'filepath'
void parse_database(std::string filepath);
//! \brief Parse the database from a stream
void parse_database(std::istream& input);
//! \brief Return the database
//!
//! Return a smart pointer of a DataCotnainer instance
//! Note : this is a read write access, be careful
std::shared_ptr<DataContainer> get_database() {return data;}
//! \brief Change the basis
//!
//! @param new_basis list of id of the new basis
//!
//! The new basis is a list of id, id = id_component for no swapping
//! or id = id_aqueous + nb_component for swapping a secondary species
void switch_basis(std::vector<index_t>& new_basis);
//! \brief Swap some component in the basis
//! \param swap_to_make a map where the keys are the current
//! component and the values are the new component
void swap_components(const std::map<std::string, std::string>& swap_to_make);
//! \brief Remove components not present in the system
//!
//! "H2O" and "E[-]" cannot be removed from the database.
//!
//! \param labels_components_to_remove list of labels of the component to remove from the basis
void remove_components(const std::vector<std::string>& labels_components_to_remove);
//! \brief Remove components not present in the system
//!
//! "H2O" and "E[-]" cannot be removed from the database.
//!
//! \param id_components_to_remove list of id of the component to remove from the basis
void remove_components(const std::vector<index_t>& id_components_to_remove);
//! \brief Keep only components in the id_components_to_keep list
//!
//! "H2O" and "E[-]" will always be kept in the database.
//!
//! \param id_components_to_keep list of id of the component to keep in the basis
void keep_only_components(const std::vector<index_t>& id_components_to_keep);
//! \brief Keep only components in the labels_components_to_keep list
//!
//! "H2O" and "E[-]" will always be kept in the database.
//!
//! \param labels_components_to_keep list of labels of the component to keep in the basis
void keep_only_components(const std::vector<std::string>& labels_components_to_keep);
//! \brief Keep only some minerals at equilibrium
//!
//! The effect is to flag all the other minerals as "kinetic"
void minerals_keep_only(const std::vector<std::string>& minerals_to_keep);
//! \brief Keep only some minerals at equilibrium
//!
//! The effect is to flag all the other minerals as "kinetic"
void minerals_keep_only(const std::vector<index_t>& minerals_to_keep);
//! \brief Remove all gas species
void remove_gas_phases();
//! \brief Add gas phases into the database
//!
//! The input is a JSON list of gas (formated like the database)
void add_gas_phases(const std::string& gas_input);
//! \brief Remove all solid phases
void remove_solid_phases();
//! \brief Add some solid phases into the database
//!
//! The input is a JSON list of minerals (formated like the database)
void add_solid_phases(const std::string& solid_phases_input);
//! \brief Remove all sorbed species
void remove_sorbed_species();
//! \brief Add sorbed species into the database
//!
//! The input is a JSON list of sorbed species (formated like the database)
void add_sorbed_species(const std::string& sorbed_species_input);
//! \brief Remove the compounds
void remove_compounds();
//! \brief Add some compounds into the database
//!
//! The input is a JSON list of compounds (formated like the database)
void add_compounds(const std::string& solid_phases_input);
+ //! \brief Remove all the half-cells reactions
+ void remove_half_cell_reactions();
//! \brief Remove the half-cells reactions for components in 'list_components'
void remove_half_cell_reactions(const std::vector<std::string>& list_components);
//! \brief Remove the half-cells reactions for components in 'list_id_components'
void remove_half_cell_reactions(const std::vector<index_t>& list_id_components);
//! \brief Freeze the database
void freeze() {data->freeze_db();}
//! \brief Save the database on disk
void save(const std::string& filename);
};
} // end namespace database
} // end namespace specmicp
#endif // SPECMICP_DATABASE_DATABASE_HPP
diff --git a/src/database/oxydo_selector.cpp b/src/database/oxydo_selector.cpp
index 02d5d10..9a6e31d 100644
--- a/src/database/oxydo_selector.cpp
+++ b/src/database/oxydo_selector.cpp
@@ -1,97 +1,136 @@
/*-------------------------------------------------------------------------------
Copyright (c) 2014,2015 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 "oxydo_selector.hpp"
namespace specmicp {
namespace database {
+//! \brief Remove the half-cells reaction in 'slist'
+void remove_half_cells_secondary(
+ ReactiveSpeciesList* slist
+ );
+
//! \brief Remove the half-cells reaction corresponding to list_components in 'slist'
void remove_half_cells_secondary(
ReactiveSpeciesList* slist,
- const std::vector<index_t>& list_components);
+ const std::vector<index_t>& list_components
+ );
void OxydoSelector::remove_half_cells(const std::vector<std::string>& list_components)
{
std::vector<index_t> list_id_components(list_components.size());
for (auto i=0; i<list_components.size(); ++i)
{
list_id_components[i] = safe_component_label_to_id(list_components[i]);
}
remove_half_cells(list_id_components);
}
void OxydoSelector::remove_half_cells(const std::vector<index_t>& list_components)
{
remove_half_cells_secondary(&(data->aqueous), list_components);
remove_half_cells_secondary(&(data->sorbed), list_components);
remove_half_cells_secondary(&(data->gas), list_components);
remove_half_cells_secondary(&(data->minerals), list_components);
remove_half_cells_secondary(&(data->minerals_kinetic), list_components);
}
+void OxydoSelector::remove_half_cells()
+{
+ remove_half_cells_secondary(&(data->aqueous));
+ remove_half_cells_secondary(&(data->sorbed));
+ remove_half_cells_secondary(&(data->gas));
+ remove_half_cells_secondary(&(data->minerals));
+ remove_half_cells_secondary(&(data->minerals_kinetic));
+}
//! \brief Remove the half-cells reaction for the aqueous species
void remove_half_cells_secondary(
ReactiveSpeciesList* slist,
- const std::vector<index_t>& list_components)
+ const std::vector<index_t>& list_components
+ )
{
// first we select the species to remove
std::vector<bool> to_remove(slist->size(), false);
-
for (auto id: slist->range())
{
if (slist->nu_ji(id, DataContainer::electron_index()) == 0.0) continue;
for (const auto& component: list_components)
{
if (slist->nu_ji(id, component) != 0.0)
to_remove[id] = true;
}
}
// then we remove them, in two steps
- const auto nb_to_keep = std::count(to_remove.cbegin(), to_remove.cend(), false);
auto new_j = 0;
// 1) first we copy data in the beginning of the arrays
for (index_t j: slist->range())
{
if (to_remove[j]) continue;
slist->move_erase(j, new_j);
++new_j;
}
- specmicp_assert(new_j == nb_to_keep);
// 2) then we resize the arrays
- slist->resize(nb_to_keep);
+ slist->resize(new_j);
+ slist->set_valid();
+}
+
+//! \brief Remove the half-cells reaction for the aqueous species
+void remove_half_cells_secondary(
+ ReactiveSpeciesList* slist
+ )
+{
+ // first we select the species to remove
+ std::vector<bool> to_remove(slist->size(), false);
+
+ for (auto id: slist->range())
+ {
+ if (slist->nu_ji(id, DataContainer::electron_index()) != 0.0)
+ to_remove[id] = true;
+ }
+
+ auto new_j = 0;
+ // 1) first we copy data in the beginning of the arrays
+ for (index_t j: slist->range())
+ {
+ if (to_remove[j]) continue;
+ slist->move_erase(j, new_j);
+ ++new_j;
+ }
+ // 2) then we resize the arrays
+ slist->resize(new_j);
slist->set_valid();
}
} // end namespace database
} // end namespace specmicp
diff --git a/src/database/oxydo_selector.hpp b/src/database/oxydo_selector.hpp
index 5dd72c8..b66e4d5 100644
--- a/src/database/oxydo_selector.hpp
+++ b/src/database/oxydo_selector.hpp
@@ -1,64 +1,66 @@
/*-------------------------------------------------------------------------------
Copyright (c) 2014,2015 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.
-----------------------------------------------------------------------------*/
#ifndef SPECMICP_DATABASE_OXYDOSELECTOR_HPP
#define SPECMICP_DATABASE_OXYDOSELECTOR_HPP
//! \file oxydo_selector.hpp
//! \brief Remove half-cells reactions
#include "module.hpp"
namespace specmicp {
namespace database {
//! \class OxydoSelector
//! \brief Remove half cells reaction for for given components
//!
class OxydoSelector: public DatabaseModule
{
public:
OxydoSelector(RawDatabasePtr thedata):
DatabaseModule(thedata)
{}
+ //! \brief Remove all half-cells reaction
+ void remove_half_cells();
//! \brief Remove the halfs-cells reaction for components in 'list_components'
void remove_half_cells(const std::vector<std::string>& list_components);
//! \brief Remove the halfs-cells reaction for components in 'list_components'
void remove_half_cells(const std::vector<index_t>& list_components);
};
} // end namespace database
} // end namespace specmicp
#endif // SPECMICP_DATABASE_MINERALSELECTOR_HPP