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Update diffusion and chemistry setup in Initialization.md

Max Lübke 2024-03-06 15:53:17 +01:00
parent 8beb3a15ba
commit 7fc5e1078f
1 changed files with 17 additions and 4 deletions
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21
Initialization.md

@ -36,20 +36,20 @@ grid_setup <- list(
## Diffusion
```r
diffusion <- list(
boundaries = list( # Define boundary conditions for diffusion, 0 = closed, > 0 ID of Phreeqc ID
diffusion_setup <- list(
boundaries = list( # Define boundary conditions for diffusion, 0 = closed, > 0 ID of Phreeqc ID
"N" = numeric(),
"E" = numeric(),
"S" = numeric(),
"W" = numeric()
),
to_transport = character(), # Define the species to transport
alphax = list( # Define the diffusion coefficient in x-direction
alphax = list( # Define the diffusion coefficient in x-direction
matrix(),
matrix(),
...
),
alphay = list( # Define the diffusion coefficient in y-direction
alphay = list( # Define the diffusion coefficient in y-direction
matrix(),
matrix(),
...
@ -58,3 +58,16 @@ diffusion <- list(
```
## Chemistry
```r
chemistry_setup <- list(
dht_species = numeric(), # optional: Named vector with species to use with significant digits for DHT key rounding
pht_species = numeric(), # optional: Named vector with species to use with significant digits for Interpolation key rounding
hooks = list( # optional: List of hooks to run before and after certain steps
dht_fill = logical() <- function(numeric(), numeric()), # function to run before writing DHT
dht_fuzz = numeric() <- function(numeric()), # function to run before reading DHT
interp_pre_func = numeric() <- function(numeric(), list()), # function to run before interpolation
interp_post_func = logical() <- function(numeric()) # function to run after interpolation
)
)
```