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Database.md
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Database.md
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			# Database {#database}

			[TOC]

			This page describes the specmicp::database module and how to set up a database.

			# Introduction {#introduction}


			The term database is used in SpecMiCP to denotes the thermodynamic database.
			The thermodynamic database contains the information about the species and
			chemical reactions. The database is encoded as a JSON file.

			The database module is divided into two main parts, the data container
			(specmicp::database::DataContainer) and the database manager
			(specmicp::database::Database).
			The data container is shared by many objects through a shared pointer
			(specmicp::RawDatabasePtr).

			The creation and modification of the database should be done through the
			database manager.

			# Creating and customizing the database {#managing}


			## Parsing the database {#parsing}

			The database can be created with the database manager :

			~~~~~~~{.cpp}
			specmicp::database::Database database_manager(path_to_the_database);
			~~~~~~~

			## Customization of the database {#customization}

			The database can be adapted to the simulation through the methods defined by
			specmicp::database::Database.
			The actual implementation of this algorithm are done by the different modules
			in the specmicp::database namespace.
			However, their direct use should be avoided and the methods provided by the
			\link specmicp::database::Database Database \endlink shoudl be used instead.

			The only exception is the specmicp::database::AqueousSelector that should
			normally not be used.

			### Swapping the components

			The basis is defined in the JSON database but may be changed at the beginning
			of the simulation.
			Swapping the components may be done to help the convergence in the simulation.
			It is done by using the member function
			specmicp::database::Database::swap_components.

			~~~~~~~~{.cpp}
			database_manager.swap_components({
			{"H[+]", "HO[-]"},
			{"Si(OH)4", "SiO(OH)3[-]"}
			});
			~~~~~~~~

			Due to the use of the complementarity condition, the database do not need to be
			changed during the simulation \cite Georget2015.

			Note : liquid water "H2O" and the electron "E[-]" are fixed in the database and
			can NOT be swapped.

			### Removing components

			Not all components are needed in every computation. The basis can be reduced by
			using one of this four methods

			- specmicp::database::Database::keep_only_components(const
			std::vector<index_t>&)
			- specmicp::database::Database::keep_only_components(const
			std::vector<std::string>&)
			- specmicp::database::Database::remove_components(const
			std::vector<index_t>&)
			- specmicp::database::Database::remove_components(const
			std::vector<std::string>&)

			The liquid water ("H2O") and the electron ("E[-]) cannot be removed from the
			database.

			The following code keep 5 components in the database (include "H2O" and "E[-]")
			:

			~~~~~~~~~~~{.cpp}
			database_manager.keep_only_components({
			"HO[-]", "Ca[2+]", "SiO(OH)3[-]"
			});
			~~~~~~~~~~~

			### Setting the list of solid phases

			It is not always desirable to include all the solid phases in the computation.
			The list of solid phases to take into account in the speciation solver can be
			set with the specmicp::database::Database::minerals_keep_only() method.

			~~~~~~~~~~{.cpp}
			database_manager.minerals_keep_only({
			"Portlandite", "SiO2(am)", "CSHjennite"
			});
			~~~~~~~~~~

			The function is overloaded and can be given a list of id instead
			(specmicp::database::Database::minerals_keep_only(const std::vector<index_t>&)).

			### Adding species

			At the beginning of the simulation the user can add solid phases, gases or
			sorbed species in the database.
			The methods [add_solid_phases()](@ref
			specmicp::database::Database::add_solid_phases),
			[add_gas_phases()](@ref specmicp::database::Database::add_gas_phases), and
			[add_sorbed_species()](@ref specmicp::database::Database::add_sorbed_species)
			are used to add species in the database.

			Their argument is a JSON formatted string. For a description of the format, see
			the format section below.

			Example :

			~~~~~~~{.cpp}
			std::string gas_appendix_database = R"plop(
			[
			{
			"label": "CO2(g)",
			"composition": "CO2(aq)",
			"log_k": -1.468
			}
			]
			)plop";
			database_manager.add_gas_phases(gas_appendix_database)
			~~~~~~~

			## Obtaining the raw database {#container}

			Once the database is prepared, a pointer to the raw database can be obtained
			with the specmicp::database::Database::get_database() method.

			\code{.cpp}
			specmicp::RawDatabasePtr raw_data = database_manager.get_database()
			\endcode

			## Freezing and validating the database {#validation}

			The consistency of the database is a requirement for the computation.
			This consistency can be check with the
			specmicp::database::DataContainer::is_valid() function.
			It checks if all of the species list of the database are valid.
			It does not check the values, just that the modification algorithms happened
			according to plan.

			~~~~~~~{.cpp}
			if (not raw_data->is_valid())
			throw std::runtime_error("Doomed, we are doomed my friends")
			~~~~~~~

			The check is not run automatically in non-debug mode but it is recommended to
			used it at least once in a simulation.

			To detect any undesired modification, the database can be frozen.
			To do so call the method specmicp::database::DataContainer::freeze_db().
			It does not prevent any modification to the database, but any call to
			[is_valid()](@ref specmicp::database::DataContainer::is_valid)
			will check that the database has not changed since the call to [freeze_db()
			](@ref specmicp::database::DataContainer#freeze_db).
			The definition of "No changes" is quite loose and again the numericals values
			are not checked, only the names of the species in the database.

			~~~~~~~{.cpp}
			raw_data->freeze_db()
			// code
			if (not raw_data->is_valid())
			throw std::runtime_error("Doomed, we are doomed my friends, the database has
			changed.")
			~~~~~~~

			To avoid any undesired modification of the values, the getter methods defined
			in specmicp::database::DataContainer are read-only.
			Any modification of the values is non-obvious and thus is considered to be
			voluntary.

			## Saving the database {#saving}

			The database can be saved in the JSON format for inspection or later use.

			~~~~~~~{.cpp}
			specmicp:database::DatabaseManager database_manager = ...
			// obtain and transform the database
			database_manager.save("file_where_db_is_saved.dat")
			~~~~~~~

			The database is human and machine readable. It can be parsed by SpecMiCP to run further computations.


			# Labels and IDs {#using}

			Outside of the programs/solver the main use of the database is to make the link
			between the ID and the label of the species.
			The ID of the species is simply its position in a vector.
			The label of a species is its name in the database.
			For efficiency reasons, in the computation the ID of the species are used.
			However in the setup and the post-processing of a simulation using the labels
			improves the readability and the robustness and should be used.

			The format of a label is described [here](#format_label).

			Note 0 : The IDs are not unique. They are unique per types of species. For
			example, the first species in all the list have ID "0".

			Note 1 : The C convention is used, the first ID is "0". For exemple water
			("H2O") has ID "0" in the basis.

			Note 2 : There is three sets of 'ID' that should not be confused :

			- ID : this is the ID of a species in the database
			- dof : this is the degree of freedom of a variable in a program to solve
			- ideq : ID of an equation, this is the row for a varaible/equation in the
			linear system to solve

			The user should only worry about the first one. To implement a new equation and

			Note 3: The algorithms seems to be stable and the ID are predictable. However,
			this is not a guarantee and the user should used the methods described in this
			section to find the ID of a species.

			## label to ID {#ID}

			There is two versions available, a 'safe' and 'unsafe' versions.
			The safe version (prefixed with safe_) will throw std::runtime_error if the
			label does not exist.
			The unsafe version will return specmicp::no_species if the species does not
			exist.

			Safe versions :

			- [safe_component_label_to_id()](@ref
			specmicp::database::Database::safe_component_label_to_id)
			- [safe_aqueous_label_to_id()](@ref
			specmicp::database::Database::safe_aqueous_label_to_id)
			- [safe_mineral_label_to_id()](@ref
			specmicp::database::Database::safe_mineral_label_to_id)
			- [safe_mineral_kinetic_label_to_id()](@ref
			specmicp::database::Database::safe_mineral_kinetic_label_to_id)
			- [safe_gas_label_to_id()](@ref
			specmicp::database::Database::safe_gas_label_to_id)
			- [safe_sorbed_label_to_id()](@ref
			specmicp::database::Database::safe_sorbed_label_to_id)

			Unsafe versions :

			- [component_label_to_id()](@ref
			specmicp::database::Database::component_label_to_id)
			- [aqueous_label_to_id()](@ref
			specmicp::database::Database::aqueous_label_to_id)
			- [mineral_label_to_id()](@ref
			specmicp::database::Database::mineral_label_to_id)
			- [mineral_kinetic_label_to_id()](@ref
			specmicp::database::Database::mineral_kinetic_label_to_id)
			- [gas_label_to_id()](@ref specmicp::database::Database::gas_label_to_id)
			- [sorbed_label_to_id()](@ref
			specmicp::database::Database::sorbed_label_to_id)

			## ID to label {#label}

			These methods return the label of a species given its ID and its type.
			There is no safe and unsafe version, it is up to the user to ensure that the id
			is valid.
			In debug mode, the bounds are check using an assertion.

			Available methods :

			- [component_id_to_label()](@ref
			specmicp::database::Database::component_id_to_label)
			- [aqueous_id_to_label()](@ref
			specmicp::database::Database::aqueous_id_to_label)
			- [mineral_id_to_label()](@ref
			specmicp::database::Database::mineral_id_to_label)
			- [mineral_kinetic_id_to_label()](@ref
			specmicp::database::Database::mineral_kinetic_id_to_label)
			- [gas_id_to_label()](@ref specmicp::database::Database::gas_id_to_label)
			- [sorbed_id_to_label()](@ref
			specmicp::database::Database::sorbed_id_to_label)

			## low-level {#label_low}

			In the computation, it is not necessary to create a [database manager](@ref
			specmicp::database::Database) to obtain the labels and IDs.
			The user may use the methods defined by specmicp::database::DataContainer
			The following methods are available :

			### ID to label

			- [get_id_component(const std::string& label)](@ref
			specmicp::database::DataContainer::get_id_component)
			- [get_id_aqueous(const std::string& label)](@ref
			specmicp::database::DataContainer::get_id_aqueous)
			- [get_id_mineral(const std::string& label)](@ref
			specmicp::database::DataContainer::get_id_mineral)
			- [get_id_mineral_kinetic(const std::string& label)](@ref
			specmicp::database::DataContainer::get_id_mineral_kinetic)
			- [get_id_gas(const std::string& label)](@ref
			specmicp::database::DataContainer::get_id_gas)
			- [get_id_sorbed(const std::string& label)](@ref
			specmicp::database::DataContainer::get_id_sorbed)

			### label to ID

			- [get_label_component(index_t id)](@ref
			specmicp::database::DataContainer::get_label_component)
			- [get_label_aqueous(index_t id)](@ref
			specmicp::database::DataContainer::get_label_aqueous)
			- [get_label_mineral(index_t id)](@ref
			specmicp::database::DataContainer::get_label_mineral)
			- [get_label_mineral_kinetic(index_t id)](@ref
			specmicp::database::DataContainer::get_label_mineral_kinetic)
			- [get_label_gas(index_t id)](@ref
			specmicp::database::DataContainer::get_label_gas)
			- [get_label_sorbed(index_t id)](@ref
			specmicp::database::DataContainer::get_label_sorbed)

			### Size

			The number of species in a list can be obtained through the following functions
			:

			- [nb_component()](@ref specmicp::database::DataContainer::nb_component)
			- [nb_aqueous()](@ref specmicp::database::DataContainer::nb_aqueous)
			- [nb_mineral()](@ref specmicp::database::DataContainer::nb_mineral)
			- [nb_mineral_kinetic()](@ref
			specmicp::database::DataContainer::nb_mineral_kinetic)
			- [nb_gas()](@ref specmicp::database::DataContainer::nb_gas)
			- [nb_sorbed()](@ref specmicp::database::DataContainer::nb_sorbed)

			The maximum index ist the number of species - 1.

			### Range

			To iterate other a list of species the following methods are defined :

			- [range_component()](@ref
			specmicp::database::DataContainer::range_component)
			- [range_aqueous_component()](@ref
			specmicp::database::DataContainer::range_aqueous_component)
			- [range_aqueous()](@ref specmicp::database::DataContainer::range_aqueous)
			- [range_mineral()](@ref specmicp::database::DataContainer::range_mineral)
			- [range_mineral_kinetic()](@ref
			specmicp::database::DataContainer::range_mineral_kinetic)
			- [range_gas()](@ref specmicp::database::DataContainer::range_gas)
			- [range_sorbed()](@ref specmicp::database::DataContainer::range_sorbed)


			The [range_aqueous_component()](@ref
			specmicp::database::DataContainer::range_aqueous_component) method do not
			include the water ("H2O") and the electron ("E[-]").

			The following example print the labels of the aqueous species :

			~~~~~~~~{.cpp}
			std::cout << "List of Aqueous species : \n";
			for (auto id: raw_data->range_aqueous())
			std::cout << " - " << raw_data->get_label_aqueous(id) << "\n";
			std::cout << std::endl;
			~~~~~~~~

			# Thermodynamics data {#thermo}

			The database contains the stoichiometric coefficients, the equilibrium
			constant, the non ideal aqueous solutions parameters, the molar volume, etc.
			In short, all the thermodynamics data needed for the computations. The complete
			description of the available data can be find [here](@ref
			specmicp::database::DataContainer).

			Note : the thermodynamics data is only available through the
			[DataContainer](@ref specmicp::database::DataContainer) class, not the
			[Database](@ref specmicp::database::Database) class which is reserved for the
			[customization algorithms](#managing).

			# Format of a database {#jsonformat}

			The database is saved as a JSON file. JSON is a concise format to exchange data.
			This section describes the format of the database.

			The database is a list of sections :

			~~~~~{.js}
			{
			"Metadata": {...},
			"Basis" [...],
			"Aqueous": [...],
			"Minerals": [...],
			("Gas": [...],)
			("Sorbed": [...],)
			"References: [...]
			}
			~~~~~

			where `(<name> : <value>)` denotes an optional section.

			The JSON format is extensible and extra information can be included into the
			database. However, they will be ignored by SpecMiCP.

			The format of the database was chosen to avoid any ambiguity and obtained a
			database that is easily parsed in opposition of other tools.
			The objective is that other tools are able to implement a parser for the same
			format.

			## Labels {#format_label}

			A label is formatted as : `<name>[<charge>]`.
			The charge consist of a number and a sign. If the number is 1 it can be omited.
			If the charge is 0, the brackets can be omited.
			For example, the following labels are valid :

			- `H2O`
			- `E[-]`
			- `HO[-]`
			- `Ca[2+]`
			- `Al(OH)4`
			- `AlO(OH)3[-]`
			- `AlO2(OH)2[2-]`

			## Chemical reactions {#format_equations}

			A chemical reactions in the database always denotes the dissociation of the
			species (decomplexation, dissolution, ...), for this reason, in the JSON file
			it is called a composition.
			A composition is simply a comma-separated list of a species preceded by a
			stoichiometric coefficient.
			A stoichiometric coefficient is a sign (`+`/`-`) followed by a number. If the
			sign is `+` it can be omitted.
			If the number is `1` it can be omitted.

			Examples :

			`Al(OH)4[-]` : `Al[3+], 4 H2O, -4 H[+]`

			`S2O3[2-]` : `2.00 SO4[2-], 10.00 H[+], 8.00 E[-], -5.00 H2O`

			The charged neutrality of the equation is tested during the parsing of the
			database.

			## Metadata section {#format_metadata}

			This section describes meta-information such as the name and the version of the
			database.


			~~~~~~~~{.js}
			"Metadata": {
			"name": <name>,
			"version": <version>
			},
			~~~~~~~~

			JSON is an extensible format and the user may add a changelog entry to describe
			the modifications made at each version.

			## Basis section {#format_basis}

			This section defines the basis used to build the database. It is a list of
			entry formatted as :

			~~~~~~~~{.js}
			{
			"label": <label>,
			"molar_mass": <molar mass>, // g/mol
			"activity": {
			"a": <ion size parameter>,
			"b": <b-dot parameter>
			}
			},
			~~~~~~~~

			The molar_mass is the Molar Mass of the species in g/mol.
			The optional activity array contains the parameters for the non ideal aqueous
			solution model.
			a is the ion size parameter (in nanometer) and b is the b-dot parameter.

			The activity coefficient is build as

			\f[
			\log \gamma_k = - \frac{A z_k^2 \sqrt{I}}{1 + a B \sqrt{I}} + b I
			\f]
			where \f$I\f$ is the ionic strength and \f$z_k\f$ is the charge for species k.


			The first two species in the basis must be `H2O` and `E[-]`.

			Example of a simple basis :

			~~~~~~~{.js}
			{
			"label": "H2O",
			"molar_mass": 18.015 // g/mol
			},
			{
			"label": "E[-]",
			"molar_mass": 0.00
			},
			{
			"label": "H[+]",
			"molar_mass": 1.008,
			"activity": {
			"a": 9.00,
			"b": 0.00
			}
			},
			{
			"label": "Al[3+]",
			"molar_mass": 26.982,
			"activity": {
			"a": 6.65,
			"b": 0.19
			}
			},
			~~~~~~~

			## Aqueous section {#format_aqueous}

			The aqueous section is a list of aqueous species. An aqueous species is an
			entry formatted as follow :


			~~~~~~~~{.js}
			{
			"label": <label>,
			"composition": <dissociation reaction>,
			"log_k": <log_10 of the equilibrium constant>,
			"activity": {
			"a": <ion size parameter>,
			"b": <b-dot parameter>
			}
			}
			~~~~~~~~

			The composition is the dissociation of `<label>` into the species of the basis,
			and `log_k` is the logarithm in base 10 of the corresponding equilibrium.

			Note : In PHREEQC, the equation for an aqueous species is the complexation
			reaction and thus it's log_k is the negative of SpecMiCP !

			## Mineral section {#format_mineral}

			The `Minerals` section is a list of mineral species. A mineral species entry
			is formatted as follow :

			~~~~~~~{.js}
			{
			"label": <label>,
			"composition": <dissolution reaction>,
			"log_k": <log_k>,
			"molar_volume": <molar_volume>, //cm^3/mol
			"flag_kinetic": <0 or 1>
			},
			~~~~~~~

			`label`, `composition` and `log_k` follow the same rules as the same fields of
			an [aqueous species](#format_aqueous).

			`molar_volume` is the molar volume (in \f$\textrm{cm}^3 / \textrm{mol}\f$) of
			the solid phase. This field is optional.
			However if the solid phase is at equilibrium and used with
			specmicp::AdimensionalSystem, an error will be raised.

			`flag_kinetic` should be set to 1 if the corresponding solid phase is not at
			equilibrium in the system. Of o, this field may be omitted.
			The set of solid phase at equilibrium can be further restricted in a simulation
			by using the specmicp::database::Database::minerals_keep_only() method.


			## Gas section {#format_gas}

			This section is optional. It consists of a list of gas. A gas entry is
			formatted as follow :

			~~~~~~~{.js}
			{
			"label": <label>,
			"composition": <dissolution reaction>,
			"log_k": <log_k>,
			},
			~~~~~~~

			`label`, `composition` and `log_k` follow the same rules as the same fields of
			an [aqueous species](#format_aqueous).


			## Sorbed section {#format_sorbed}

			This section is optional. It consists of list of sorbed species. A sorbed
			species entry is formatted as follow :

			~~~~~~~{.js}
			{
			"label": <label>,
			"composition": <dissolution reaction>,
			"nb_sites_occupied": <number>,
			"log_k": <log_k>,
			},
			~~~~~~~

			`label`, `composition` and `log_k` follow the same rules as the same fields of
			an [aqueous species](#format_aqueous).

			`nb_sites_occupied` is the number of surface sorption sites occupied by the
			sorbed species.

			## References section {#format_references}

			The `References` is not parsed by SpecMiCP but can be used to store the
			citations for the values used in the database.
			The section is a list of citations entry formatted as followed :

			~~~~~~~{.js}
			{
			"key": <key>,
			"description": <description>,
			}
			~~~~~~~

			This citation can be used in the species entries with a `references` field
			containing a list of references key.
			These entries may be used to keep track of the values and facilitates their
			validations.

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