Refactor output classes

[wtraylor]

These are some ideas I had for improving performance and flexibility of output classes.

Collect output in structs of arrays instead of averaging it all the time ⇒ shift paradigm from “array of structs” to “struct of arrays”! Data are stored in std::unordered_map<Output::Variable, std::vector<double> >, where Variable is an enum class. Make sure that no new elements in the map can be created after construction. Only new values should be appended.

• Create enum class Output::Variable for all possible output variables.
  • Or should we have on HabitatVariable and one HerbivoreVariable type?
• Create class Fauna::Output::AggUnitDatum:
  • contains one HerbivoreData for each HFT plus one HabitatData + name of aggregation unit.
  • Each tuple is for one day and one habitat.
  • The AggUnitDatum::habitat_data member variable should be the only HabitatData object that is ever created for this aggregation unit. No copying of data!
  • AggUnitDatum::retrieve() resets all arrays and retrieves the mean in one single datum for each variable.
  • Reserve the data vectors in with a precalculated size:
    • Size for HerbivoreData: HFTs × habitats × days
    • Size for HabitatData: habitats × days
    • The count should be calculated by a framework function (which knows parameters and HFT list).
    • The number of habitats in each aggregation unit must be estimated based on the maximum number per aggregation unit encountered so far.
    • The number of days is simply based on the output.interval option.
• Create class Fauna::Output::HabitatData:
  • contains an array for each value that is stored in the old HabitatData.
  • All arrays are guaranteed to be always of the same length.
  • HabitatData::aggregate() is for both spatial and temporal aggregation.
• Create class Fauna::Output::HerbivoreData: Parallel to the new HabitatData.
  • HerbivoreData::aggregate_within_habitat() calculates the average spatially within one habitat.
  • HerbivoreData::aggregate() is for both spatial (between habitats) and temporal (between days) aggregation.
• Replace HerbivoreInterface::get_output() with HerbivoreInterface::append_output(Output::HerbivoreData&)
  • This adds output from the herbivore to the struct of arrays (std::unordered_map)
  • Only append to those variables that are required for output.
• Do the same for Habitat::append_output(Output::HabitatData&).
• From the framework, call HerbivoreInterface::append_output() within each habitat in each day and then append the result to the AggUnitDatum.

[wtraylor]

The output data classes are currently always in a consistent state. With every new datum, the total average is recalculated.
This is a great waste of computing power.
It would be a lot more efficient to first gather a long series of data, and finally calculate the mean or sum.