general_settings¶

These include several modules dealing with settings and other options.

settings¶

Settings for KIPET

class kipet.general_settings.settings.Settings(category='model')¶

This is a container for all of the options that can be used in Kipet Since it can be confusing due to the large number of options, this should make it easier for the user to see everything in one spot.

This class loads the default settings from the settings.yml file located in the directory wherever KIPET has been installed. If you really want to change this file, go ahead, but make sure that you save a copy of the original settings in case something goes wrong.

Methods

updated_settings()

__init__(category='model')¶: Settings object initialization that begins each time a ReactionModel instance is created.

update_settings(category, item, value)¶

Sets the default settings to some new value

This allows the user to make permanent changes to the settings file.

Warning

Careful! This may result in KIPET not working properly if you make a change that is incompatible!

Parameters

category (str) – The category containing the value to change
item (str) – The name of the setting to change
value (str) – The new value for the setting

Returns

None

property as_dicts¶

unit_base¶

Unit Base - Object for holding units and the unit registry

class kipet.general_settings.unit_base.UnitBase¶

Class to hold universal units and the unit registry

Parameters

ur (pint.UnitRegistry) – default unit registry
time (str) – time base
volume (str) – volume base
concentration (str) – concentration base

__init__()¶

Initialize the UnitBase for the ReactionModel

Parameters

ur (pint.UnitRegistry) – default unit registry
time (str) – time base
volume (str) – volume base
concentration (str) – concentration base

variable_names¶

General KIPET Model Varialbe names

class kipet.general_settings.variable_names.VariableNames¶

Names of the KIPET model variables

This provides a central location to reduce errors in developing KIPET modules by forcing a naming convention. It also provides useful collections of variables for use in many other functions.

This is not really needed by the user and should only be used by developers.

__init__()¶: Initialize self. See help(type(self)) for accurate signature.

property optimization_variables¶: These are the independent variables that need to be fixed in simulations

property time_dependent_variables¶

Property to return variables that are time dependent:

Defaults: [‘Z’, ‘dZdt’, ‘S’, ‘C’, ‘X’, ‘dXdt’, ‘U’, ‘Y’]
Return model_vars: The list of target variables
Return type: list

property modeled_states¶

Property to return variables that are modeled:

Defaults: [‘Z’, ‘dZdt’, ‘X’, ‘dXdt’]
Return model_vars: The list of target variables
Return type: list

property model_vars¶

Property to return component variables:

Defaults: [‘Z’, ‘X’, ‘P’, ‘Y’, ‘step’, ‘Const’]
Return model_vars: The list of target variables
Return type: list

property rate_vars¶

Property to return rate variables:

Return model_vars: The list of target variables
Return type: list

property plot_vars¶

Property to return plotted variables

Return model_vars: The list of target variables
Return type: list