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122 lines
2.7 KiB
R
122 lines
2.7 KiB
R
## Time-stamp: "Last modified 2023-08-22 12:44:53 mluebke"
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#################################################################
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## Section 1 ##
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## Grid initialization ##
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#################################################################
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n <- 5
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m <- 5
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(n, m)
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)
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##################################################################
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## Section 2 ##
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## Advection parameters ##
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##################################################################
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## initial conditions
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## HACK: We need the chemical initialization here, as chem module initialization
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## depends on transport until now. This will change in the future.
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init_adv <- c(
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"H" = 110.124,
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"O" = 55.0622,
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"Charge" = -1.216307659761E-09,
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"C(4)" = 1.230067028174E-04,
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"Ca" = 1.230067028174E-04,
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"Cl" = 0,
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"Mg" = 0
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)
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## list of boundary conditions/inner nodes
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vecinj_adv <- list(
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list(
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"H" = 110.124,
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"O" = 55.0622,
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"Charge" = -1.217e-09,
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"C(4)" = 0,
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"Ca" = 0,
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"Cl" = 0,
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"Mg" = 0
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),
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list(
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"H" = 110.683,
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"O" = 55.3413,
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"Charge" = 1.90431e-16,
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"C(4)" = 0,
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"Ca" = 0,
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"Cl" = 0.002,
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"Mg" = 0.001
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)
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)
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vecinj_inner <- list(
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l1 = c(2, 1, 1)
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)
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# Create a list to store grid cell information
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flux_list <- list()
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# Function to get the index of a grid cell given its row and column
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get_index <- function(row, col) {
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index <- (row - 1) * m + col
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if (index < 1) {
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index <- -1
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} else if (index > n * m) {
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index <- -1
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}
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return(index)
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}
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flux_val <- 1
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# Loop through each row and column to populate the flux_list
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for (row in 1:n) {
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for (col in 1:m) {
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index <- get_index(row, col)
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# Initialize the connections for the current cell
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flux <- c()
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# Check and add connections to the east, south, west, and north cells
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# east
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flux <- c(flux, -flux_val)
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# south
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flux <- c(flux, -flux_val)
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# west
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flux <- c(flux, flux_val)
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# north
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flux <- c(flux, flux_val)
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# Store the connections in the flux_list
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flux_list[[index]] <- flux
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}
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}
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vecinj <- do.call(rbind.data.frame, vecinj_adv)
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names(vecinj) <- names(init_adv)
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advection <- list(
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init = init_adv,
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vecinj = vecinj,
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vecinj_inner = vecinj_inner,
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const_flux = flux_list
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)
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#################################################################
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## Section 4 ##
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## Putting all those things together ##
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#################################################################
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setup <- list(
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grid = grid,
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advection = advection
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)
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