PourPy.system

Created on Mon Jul 24 09:50:23 2023

@author: fabioenricofurcas

Classes

System

System class that contains all required physiochemical parameters, elements and reacion constituents nessecary to create a pourbaix diagram.

Module Contents

class PourPy.system.System(filename=None)

System class that contains all required physiochemical parameters, elements and reacion constituents nessecary to create a pourbaix diagram.

reactions = []

elements

property temperature

Get the system temperature.

Returns:: Temperature in degrees Kelvin.
Return type:: float

property pressure

Get the system pressure.

Returns:: Pressure in bar.
Return type:: float

property pHmin

Get the minimum pH value of the system.

Returns:: Minimum pH value.
Return type:: float

property pHmax

Get the maximum pH value of the system.

Returns:: Maximum pH value.
Return type:: float

property Emin

Get the minimum electrode potential value of the system.

Returns:: Minimum electrode potential value in volts vs. SHE.
Return type:: float

property Emax

Get the maximum electrode potential value of the system.

Returns:: Maximum electrode potential value in volts vs. SHE.
Return type:: float

property reference_electrode

Get the reference electrode information.

Returns:: A tuple containing the reference electrode abbreviation and potential difference.
Return type:: tuple

set_database(database)

__str__()

Generate a string of the System object containing all chemical reactions, its temperature and pressure.

Returns:: String representation of the System.
Return type:: str

initialize()

Initialize all chemical reactions included in the system using its current physiochemical parameters.

Returns:: None
Return type:: None

write_parameters_to_file(filename)

Writes a dictionary of standard system parameters and physical constants into a JSON file.

Parameters:

filename (str) – Name of the JSON file to write parameters to.
R (float) – Ideal gas constant R = 8.31446262 J/mol/K.
F (float) – Faraday constant F = 96485.3321 A*s/mol.
T0 (float) – Standard temperature T0 = 298.15 degree Kelvin.
P0 (float) – Standard pressure P0 = 1.00 bar.
Reference_abbreviation (str) – Abbreviation of the reference electrode.
dE (float) – Potential difference of the reference electrode in volts vs. the standard hydrogen electrode.
T (float) – Temperature in degree Kelvin.
P (float) – Pressure in bar.
pHmin (float) – Minimum pH of the diagram.
pHmax (float) – Maximum pH of the diagram.
Emin (float) – Minimum potential of the diagram in volts vs. SHE.
Emax (float) – Maximum potential of the diagram in volts vs. SHE.

read_parameters_from_file(filename)

Reads system parameters from a JSON file.

Parameters:: filename (str) – Name of the JSON file to read parameters from.
Returns:: None
Return type:: None

property pHs

Get the system pH range.

Returns:: A tuple containing the minimum and maximum pH values.
Return type:: tuple

property electrode_potentials

Get the electrode potential range of the system and automatically check which value is the lower one an which one corresponds to the upper limit.

Returns:: A tuple containing the minimum and maximum electrode potentials.
Return type:: tuple

property reference_abbreviation

Get the abbreviation of the reference electrode.

Returns:: Abbreviation of the reference electrode.
Return type:: str

property deltaE

Get the potential difference of the reference electrode in volts vs. the standard hydrogen electrode.

Returns:: Potential difference in volts.
Return type:: float

add_elements(elements: list)

Adds elements to the chemical system.

Parameters:: elements (list) – List of chemical elements in the system.

abstractmethod add_reactions(reactions)

_(reactions: list)

Adds reactions to the chemical system.

Parameters:: reactions (list) – List of chemical reactions in the system.

read_reactions_from_file(filename: str)

Reads the reactions from a file and adds reactions to the chemical system

Parameters:: filename (str) – filename with reactions

set_aqueous_activity(element: str, activity: float)

Modifies the aqueous activity of singular elements previously defined to be included in the chemical system.

Parameters:

element (str) – Chemical element in the system.
activity (float) – Chemical activity of element.

_get_elements(elements)

Validates the user-input list of chemical elements and updates the dictionary in system_parameters.json to include a dictionary of elements together with their aqueous activities.

Parameters:: elements (list) – List of chemical elements in the system.
Raises:: ValueError – Error raised if the list of elements provided contains entries that are not in element_list of know and supported elements.
Returns:: Dictionary of validated elements as keys and standard aqueous activities as values.
Return type:: dict

construct_reactions_from_reactants(reactants: dict)

Validates the user-input reactants and constructs reactions from reactants from a dictionary containing the reactants and their corresponding activities.

Parameters:: reactants (dict) – A dictionary of reactants (species) as keys and their corresponding activities as values.
Returns:: A Reaction object created based on the provided reactants and activities.
Return type:: Reaction
Raises:: ValueError – If any reactant contains elements not yet added to the system.

_get_reactions(reactions)

Validates the user-input list of chemical reactions to appear on the Pourbaix diagram.

Parameters:: reactions (list) – List of chemical reactions in the system.
Raises:: ValueError – Error raised if list entries are not in the form of a dictionary. Further error validation upon creating the reaction() object from each entry provided.
Returns:: List of chemical reaction objects featuring the systems potential and pH limits as well as the temperature and pressure.
Return type:: list

_set_aqueous_activity(element: str, activity: float) → dict

Validates the user-input element and corresponding chemical activity and updates the dictionary in system_parameters.json.

Parameters:

element (str) – Chemical element whose activity is modified.
activity (float) – Chemical activity of the element.

Raises:

ValueError – Error raised if element provided is not part of the chemical system.

Returns:

Dictionary of elements as keys and updated standard aqueous activities as values.

Return type:

dict