# Source code architecture # Model components Persephone is divided into four components, three of which are semi-independent submodels: 1. `core`: This is the foundation of the model software, which sets up and executes simulation runs. It also reads in the configuration file and landscape maps, and provides data output functionality. 2. `nature`: This is an individual-based model of species in agricultural landscapes. It defines the [`Animal`](@ref) agent type, and a set of macros that can be used to rapidly create new species. It also includes ecological process functions that are useful for all species. 3. `farm`: This is an agent-based model of farmer decision making. It is not yet implemented, but will provide the [`Farmer`](@ref) agent type. 4. `crop`: This is a mathematical growth model for various crops. It is not yet implemented, but already provides the agent type [`FarmPlot`](@ref), representing one field and its associated extent and crop type. Conceptually, `core` provides functionality that is needed by all of the submodels. Decisions made by `Farmer`s affect the `FarmPlot`s they own, and (directly or indirectly) the `Animal`s in the model landscape. # Important implementation details 1. **The `model` object:** A cursory reading of the source code will quickly show that most functions take an `AgentBaseModel` object as one of their arguments. This is the key data structure of [Agents.jl](https://juliadynamics.github.io/Agents.jl/stable/tutorial/#.-The-model-1), and holds all state that is in any way relevant to a simulation run. (Persephone has a strict "no global state" policy to avoid state-dependent bugs and allow parallelisation.) The model object gives access to all agent instances (via `model[id]`, where `id` is the unique identifier of this agent). It also stores the configuration (`model.settings`), the landscape (`model.landscape`, a matrix of [`Pixel`](@ref) objects that store the local land cover, amongst other things), and the current simulation date (`model.date`). 2. **Model configuration/the [`@param`](@ref) macro:** The model is configured via a [TOML](https://toml.io/en/) file, the default version of which is at `src/parameters.toml`. An individual run can be configured using a user-defined configuration file, commandline arguments, or function calls (when Persephone is used as a package rather than an application). During a model run, the `@param(parameter)` macro can be used as a short-hand for `model.settings["parameter"]`. Note that parameter names are prepended with the name of the component they are associated with. For example, the `outdir` parameter belongs to the `[core]` section of the TOML file, and must therefore be referenced as `@param(core.outdir)`. (See `src/core/input.jl` for details.) 3. **Output data:** Persephone can output model data into text files with a specified frequency (daily, monthly, yearly, or at the simulation end). Submodels can use [`newdataoutput!`](@ref) to plug into this system. For an example of how to use this, see `src/nature/ecologicaldata.jl`. (See `src/core/output.jl` for details.) 4. **Farm events:** The [`FarmEvent`](@ref) struct is used to communicate farming-related events between submodels. An event can be triggered with `createevent!()` and affects all pixels within a `FarmPlot`. (See `src/core/landscape.jl` for details.) 5. **Random numbers and logging:** By default in Julia, the random number generator (RNG) and the system logger are two globally accessible variables. As Persephone needs to avoid all global data (as this would interfere with parallel runs), the `model` object stores a local logger and a local RNG. *Whenever you need to use a random number, you must use the `model.rng`! The easiest way to do this is with the [`@rand`](@ref) and [`@shuffle!`](@ref) macros.* The local logger generally does not change the way the model uses [log statements](https://docs.julialang.org/en/v1/stdlib/Logging/), this is only important in some functions in `src/core/simulation.jl`. 6. **Working with agents:** For more information about working with agent objects, see the [Agents.jl API](https://juliadynamics.github.io/Agents.jl/stable/api/).