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Update Initialization

Max Lübke 2024-04-08 11:35:40 +02:00
parent fdf6e6cb44
commit 71e901c63d
1 changed files with 6 additions and 15 deletions
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21
Initialization.md

@ -2,9 +2,7 @@
## 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.
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
# Define a setup list for simulation configuration
@ -30,7 +28,7 @@ Grid <- list(
pqc_db_string = character(), # Phreeqc database file as string
#---#
grid_def = matrix(), # Definition of the grid, containing IDs according to the Phreeqc input script
grid_size = numeric(), # Size of the grid in meters
grid_size = numeric(), # Size of the grid in meters (s_row x s_cols)
constant_cells = numeric(), # IDs of cells with constant concentration (PLACEHOLDER)
porosity = numeric(nrow * ncol) | numeric(1), # Porosity of the grid (PLACEHOLDER)
)
@ -38,9 +36,7 @@ Grid <- list(
## Diffusion
As the current code refactoring is still in progress, the diffusion setup is
focused on 2D grids. There is no support for 1D grids right now, but can be
implemented in the future quite easily.
As the current code refactoring is still in progress, the diffusion setup is focused on 2D grids. There is no support for 1D grids right now, but can be implemented in the future quite easily.
```r
Diffusion <- list(
@ -77,14 +73,9 @@ Diffusion <- list(
## Chemistry
I think we need to refactor the list of inputs. Maybe we should move the hook
functions into a separate input file and evaluete them at runtime.
I think we need to refactor the list of inputs. Maybe we should move the hook functions into a separate input file and evaluete them at runtime.
Instead of preprocessing them and write them to the simulation initialization
file, my suggestion is to output a template file after initialization, defining
all species and allowing the user to adjust significant digits for DHT and
Interpolation keys. This file can, when not edited in its definings etc, be read
by POET without any problems.
Instead of preprocessing them and write them to the simulation initialization file, my suggestion is to output a template file after initialization, defining all species and allowing the user to adjust significant digits for DHT and Interpolation keys. This file can, when not edited in its definings etc, be read by POET without any problems.
For the hook functions, I don't have a good idea right now.
@ -109,4 +100,4 @@ Runtime <- list(
store_result = TRUE, # Whether to store simulation results
out_save = numeric() # Optional: Iterations to save simulation results
)
```
```