Update Initialization

Initialization.md

@@ -0,0 +1,24 @@
+# Naming and Type conventions
+
+## Setup list
+
+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
+)
+```
+
+## Grid (Geometry)
+
+## Diffusion
+
+## Chemistry

Initialization.org

@@ -1,14 +0,0 @@
-* Naming and Type conventions
-
-** Grid (Geometry)
-
-** Diffusion
-
-** Chemistry
-
-#+BEGIN_SRC R
-setup <- list(
- diffusion = list ()
- ...
-)
-#+END_SRC