Index (chemmisol-java 0.1 API)

A C D F G L M P R S U V
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

addComponent(ChemicalComponent) - Method in class ummisco.gama.chemmisol.ChemicalSystem: Adds a component to this chemical system.
addReaction(Reaction) - Method in class ummisco.gama.chemmisol.ChemicalSystem: Adds a new reaction to the chemical system.
addReagent(String, int, Phase) - Method in class ummisco.gama.chemmisol.Reaction: Adds a reagent to this reaction.
addReagent(Reagent) - Method in class ummisco.gama.chemmisol.Reaction: Adds a reagent to this reaction.
addSpecies(ChemicalSpecies) - Method in class ummisco.gama.chemmisol.ChemicalSystem: Adds a species to this chemical system.
AQUEOUS - Enum constant in enum ummisco.gama.chemmisol.Phase: An aqueous chemical entity lives in a solution with a given volume.

C

ChemicalComponent - Class in ummisco.gama.chemmisol: Represents a chemical component.
ChemicalComponent(String, Phase, double) - Constructor for class ummisco.gama.chemmisol.ChemicalComponent: Initializes a chemical component associated to a new ChemicalSpecies with the specified name and phase.
ChemicalComponent(ChemicalSpecies, double) - Constructor for class ummisco.gama.chemmisol.ChemicalComponent: Initializes a chemical component associated to the specified species.
ChemicalEntity - Class in ummisco.gama.chemmisol: Represents a chemical entity with a name and a phase.
ChemicalEntity(String, Phase) - Constructor for class ummisco.gama.chemmisol.ChemicalEntity: Initializes a Chemical entity.
ChemicalSpecies - Class in ummisco.gama.chemmisol: Represents a chemical species living in a chemical system.
ChemicalSpecies(String, Phase) - Constructor for class ummisco.gama.chemmisol.ChemicalSpecies: Initializes a ChemicalSpecies with an initial null concentration.
ChemicalSystem - Class in ummisco.gama.chemmisol: Describes a chemical system, where components reacts to form other chemical species according to chemical reactions.
ChemicalSystem() - Constructor for class ummisco.gama.chemmisol.ChemicalSystem: Initializes a default chemical system.
ChemicalSystem(double, double, double) - Constructor for class ummisco.gama.chemmisol.ChemicalSystem: Initializes a mineral chemical system.
ChemicalSystem.ChemmisolCoreException - Exception in ummisco.gama.chemmisol: Wrapper around exceptions thrown by the native chemmisol-cpp library.
Chemmisol - Class in ummisco.gama.chemmisol: Main Chemmisol helper class, that defines static methods to load the native chemmisol-cpp library from different places.
Chemmisol() - Constructor for class ummisco.gama.chemmisol.Chemmisol
CHEMMISOL - Static variable in class ummisco.gama.chemmisol.Chemmisol: chemmisol library name.
CHEMMISOL_JAVA - Static variable in class ummisco.gama.chemmisol.Chemmisol: chemmisol-java library name.
close() - Method in class ummisco.gama.chemmisol.ChemicalSystem
concentration(String) - Method in class ummisco.gama.chemmisol.ChemicalSystem: Gets the concentration of the species with the specified name directly from the native chemmisol-cpp library.

D

dispose() - Method in class ummisco.gama.chemmisol.ChemicalSystem: Releases C++ memory resources used by this ChemicalSystem instance.

F

fixPH(double) - Method in class ummisco.gama.chemmisol.ChemicalSystem: Fixes the pH in a default component named "H+".
fixPH(double, ChemicalComponent) - Method in class ummisco.gama.chemmisol.ChemicalSystem: Fixes the pH, using the provided component as the chemical component representing the H+ ions.

G

getCoefficient() - Method in class ummisco.gama.chemmisol.Reagent: Gets the stoichiometric coefficient associated to this reagent.
getConcentration() - Method in class ummisco.gama.chemmisol.ChemicalSpecies: Gets the current concentration of this chemical species.
getLogK() - Method in class ummisco.gama.chemmisol.Reaction: Gets the base 10 logarithm of this reaction.
getName() - Method in class ummisco.gama.chemmisol.ChemicalComponent: Gets the name of the component, i.e. the name of its associated species.
getName() - Method in class ummisco.gama.chemmisol.ChemicalEntity: Gets the name of the chemical entity.
getName() - Method in class ummisco.gama.chemmisol.Reaction: Gets the name of this reaction.
getPhase() - Method in class ummisco.gama.chemmisol.ChemicalComponent: Gets the phase of the species associated to this component.
getPhase() - Method in class ummisco.gama.chemmisol.ChemicalEntity: Gets the phase of the chemical entity.
getReagents() - Method in class ummisco.gama.chemmisol.Reaction: Gets the current list of reagents of this reaction.
getSpecies() - Method in class ummisco.gama.chemmisol.ChemicalComponent: Gets the species associated to this component.
getTotalConcentration() - Method in class ummisco.gama.chemmisol.ChemicalComponent: Gets the total concentration of this component.

L

loadChemmisolLibrariesFromFile(Path) - Static method in class ummisco.gama.chemmisol.Chemmisol: Loads the chemmisol and chemmisol-java libraries from the file system.
loadChemmisolLibrariesFromFiles(Path, Path) - Static method in class ummisco.gama.chemmisol.Chemmisol: Loads the chemmisol and chemmisol-java libraries from the file system.
loadChemmisolLibrariesFromProperties(Class<?>, String, String) - Static method in class ummisco.gama.chemmisol.Chemmisol: Loads the chemmisol and chemmisol-java libraries from the path represented by the property named lib_directory_property in the project_properties file loaded from the specified class.
loadChemmisolLibrariesFromResource(Class<?>) - Static method in class ummisco.gama.chemmisol.Chemmisol: Loads the chemmisol and chemmisol-java libraries from the resources of the specified class.
loadChemmisolLibrariesFromResource(Class<?>, String) - Static method in class ummisco.gama.chemmisol.Chemmisol: Loads the chemmisol and chemmisol-java libraries from the resource_path resource folder of the clazz class.
loadChemmisolLibrariesFromResource(Class<?>, String, Class<?>, String) - Static method in class ummisco.gama.chemmisol.Chemmisol: Loads the chemmisol library from the resource_path_to_chemmisol resource folder of the clazz1 class, and loads the chemmisol-java library from the resource_path_to_chemmisol_java resource folder of the clazz2 class.

M

MINERAL - Enum constant in enum ummisco.gama.chemmisol.Phase: A mineral chemical entity is a surface complex fixed at the surface of a mineral.

P

Phase - Enum in ummisco.gama.chemmisol: Describes the phase of a chemical entity.

R

Reaction - Class in ummisco.gama.chemmisol: Describes a reaction that transforms reactants into products.
Reaction(String, double) - Constructor for class ummisco.gama.chemmisol.Reaction: Initializes a new Reaction.
reactionQuotient(String) - Method in class ummisco.gama.chemmisol.ChemicalSystem: Returns the reaction quotient of the reaction named reaction_name in this chemical system.
reactionQuotient(Reaction) - Method in class ummisco.gama.chemmisol.ChemicalSystem: Returns the reaction quotient of the specified reaction.
Reagent - Class in ummisco.gama.chemmisol: Chemical entity that represents a reagent of a reaction.
Reagent(String, int, Phase) - Constructor for class ummisco.gama.chemmisol.Reagent: Initializes a Reagent.

S

setCoefficient(int) - Method in class ummisco.gama.chemmisol.Reagent: Sets the stoichiometric coefficient associated to this reagent.
setConcentration(double) - Method in class ummisco.gama.chemmisol.ChemicalSpecies: Sets the current concentration of the chemical species.
setName(String) - Method in class ummisco.gama.chemmisol.ChemicalEntity: Sets the name of the chemical entity.
setTotalConcentration(ChemicalComponent, double) - Method in class ummisco.gama.chemmisol.ChemicalSystem: Sets the total concentration of the provided component.
setUp() - Method in class ummisco.gama.chemmisol.ChemicalSystem: Sets up the system so that it is ready to be solved.
sitesQuantity() - Method in class ummisco.gama.chemmisol.ChemicalSystem: Returns the total quantity of sites of the surface complex, computed from the solid_concentration, specific_surface_area and site_concentration parameters specified in the ChemicalSystem definition.
solve() - Method in class ummisco.gama.chemmisol.ChemicalSystem: Solves the equilibrium state of this chemical system using the native chemmisol-cpp solver.
Solvent - Class in ummisco.gama.chemmisol: Describes a solvent (such as H2O), that is a chemical component always in excess, with a fixed concentration and activity.
Solvent(String) - Constructor for class ummisco.gama.chemmisol.Solvent: Initializes a new solvent.
SOLVENT - Enum constant in enum ummisco.gama.chemmisol.Phase: A solvent is always in excess and has a fixed concentration and activity.

U

ummisco.gama.chemmisol - package ummisco.gama.chemmisol

V

valueOf(String) - Static method in enum ummisco.gama.chemmisol.Phase: Returns the enum constant of this type with the specified name.
values() - Static method in enum ummisco.gama.chemmisol.Phase: Returns an array containing the constants of this enum type, in the order they are declared.

A C D F G L M P R S U V
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form