NutMEG.culture package¶
Subpackages¶
- NutMEG.culture.base_organism package
- Subpackages
- Submodules
- NutMEG.culture.base_organism.CHNOPSexchanger module
- NutMEG.culture.base_organism.base_organism module
- NutMEG.culture.base_organism.base_organism_dbhelper module
- NutMEG.culture.base_organism.maintainer module
- NutMEG.culture.base_organism.respirator module
- Module contents
- NutMEG.culture.colony package
- NutMEG.culture.horde package
- NutMEG.culture.organism package
- NutMEG.culture.saved_organisms package
Submodules¶
NutMEG.culture.culture module¶
Module to manage all organism behaviour in NutMEG. A culture can contain one or more hordes and colonies, each of those based on (or including) a base_organism. Each horde/organism requires a maintainer, respirator and CHNOPSexchanger object (or, they can just use the default).
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class
NutMEG.culture.culture.culture(hordes=[], colonies=[], lite=False)¶ Bases:
objectClass to contain all organisms in the ecosystem, separated into hordes and colonies.
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hordes¶ List of different hordes in the system
- Type
lst
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colonies¶ List of different colonies in the system
- Type
lst
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lite¶ Whether the colonies are lite or not. lite colonies are not yet supported so please leave this as the default (False)
- Type
bool, optional
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output¶ Helper instance for generating the output and database filling info.
- Type
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all()¶ Return a list of hosted organisms in the order, hordes, colonies.
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full_output()¶ generate a full dictionary of everything being monitored in the culture, for every colony and horde.
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full_output_datatypes()¶ Return the name and type of all parameters output monitors. Useful for database building.
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get_growth_rates()¶ Return a list of the growth rates of the hosted organisms in the order hordes, colonies.
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get_maintenance_fractions()¶ Return a list of the maintenance fractions of the hosted organisms in the order hordes, colonies.
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get_metabolic_rates()¶ Return a list of the metabolic rates of the hosted organisms in the order hordes, colonies.
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get_population(inactive=False)¶ Return the total number of hosted organisms
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get_total_mass(inactive=False)¶ Return the total mass of the hosted organisms
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get_total_volume(inactive=False)¶ Return the total volume of the hosted organisms
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getmin_timestep(factorup=1.01)¶ Return the smallest time step for all of the organisms.
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lite= False¶
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refresh_output()¶ Refresh all of the data output dictionaries in the culture
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take_step(t)¶ Advance all organisms by the passed time step
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