Update Initialization

Initialization.md

@@ -5,15 +5,16 @@
 The _setup_ list holds all values, which can be parsed by poet. It's divided into components of POET e.g. _chemistry_, _diffusion_ etc. and hold metadata information like _timestep_ of each iteration, count of _iterations_ etc.
 
 ```r
-setup <- list(
- grid = list(), # see section Grid
- diffusion = list(), # see section Diffusion
- advection = list(), # not yet implemented (WIP)
- chemistry = list(), # see section chemistry
- iterations = integer, # Count of iterations
- timesteps = vector, # timestepping for each iteration
- store_result = boolean, # Set to TRUE, if output should be written to .rds file
- out_save = vector # optional: Define iterations, when to write .rds file
+# Define a setup list for simulation configuration
+simulation_setup <- list(
+grid = list(),                    # Parameters related to the grid structure
+diffusion = list(),               # Parameters related to diffusion processes
+advection = list(),               # Parameters related to advection processes (Work in progress)
+chemistry = list(),               # Parameters related to chemical processes
+iterations = 0,                   # Total number of iterations
+timesteps = numeric(),            # Time step size for each iteration
+store_result = FALSE,             # Whether to store simulation results
+out_save = numeric()              # Optional: Iterations to save simulation results
 )
 ```