provide additional test input script

test/CMakeLists.txt

@@ -7,7 +7,7 @@ target_link_libraries(testPOET doctest poetlib)
 target_include_directories(testPOET PRIVATE "${PROJECT_SOURCE_DIR}/src")
 
 get_filename_component(TEST_RInsideSourceFile "RInsidePOET_funcs.R" REALPATH)
-get_filename_component(TEST_SampleInputScript "${PROJECT_SOURCE_DIR}/bench/dolo/dolo_adv.R" REALPATH)
+get_filename_component(TEST_SampleInputScript "${PROJECT_SOURCE_DIR}/test/advection/dolo_adv.R" REALPATH)
 configure_file(testDataStructures.hpp.in testDataStructures.hpp)
 target_include_directories(testPOET PRIVATE "${CMAKE_CURRENT_BINARY_DIR}")
 

test/advection/dolo_adv.R

@@ -0,0 +1,121 @@
+## Time-stamp: "Last modified 2023-08-22 12:44:53 mluebke"
+
+#################################################################
+##                          Section 1                          ##
+##                     Grid initialization                     ##
+#################################################################
+
+n <- 5
+m <- 5
+
+grid <- list(
+  n_cells = c(n, m),
+  s_cells = c(n, m)
+)
+
+##################################################################
+##                          Section 2                           ##
+##                     Advection parameters                     ##
+##################################################################
+
+## initial conditions
+
+## HACK: We need the chemical initialization here, as chem module initialization
+## depends on transport until now. This will change in the future.
+init_adv <- c(
+  "H" = 110.124,
+  "O" = 55.0622,
+  "Charge" = -1.216307659761E-09,
+  "C(4)" = 1.230067028174E-04,
+  "Ca" = 1.230067028174E-04,
+  "Cl" = 0,
+  "Mg" = 0
+)
+
+## list of boundary conditions/inner nodes
+vecinj_adv <- list(
+  list(
+    "H" = 110.124,
+    "O" = 55.0622,
+    "Charge" = -1.217e-09,
+    "C(4)" = 0,
+    "Ca" = 0,
+    "Cl" = 0,
+    "Mg" = 0
+  ),
+  list(
+    "H" = 110.683,
+    "O" = 55.3413,
+    "Charge" = 1.90431e-16,
+    "C(4)" = 0,
+    "Ca" = 0,
+    "Cl" = 0.002,
+    "Mg" = 0.001
+  )
+)
+
+vecinj_inner <- list(
+  l1 = c(2, 1, 1)
+)
+
+# Create a list to store grid cell information
+flux_list <- list()
+
+# Function to get the index of a grid cell given its row and column
+get_index <- function(row, col) {
+  index <- (row - 1) * m + col
+  if (index < 1) {
+    index <- -1
+  } else if (index > n * m) {
+    index <- -1
+  }
+  return(index)
+}
+
+flux_val <- 1
+
+# Loop through each row and column to populate the flux_list
+for (row in 1:n) {
+  for (col in 1:m) {
+    index <- get_index(row, col)
+
+    # Initialize the connections for the current cell
+    flux <- c()
+
+    # Check and add connections to the east, south, west, and north cells
+    # east
+    flux <- c(flux, -flux_val)
+
+    # south
+    flux <- c(flux, -flux_val)
+
+    # west
+    flux <- c(flux, flux_val)
+
+    # north
+    flux <- c(flux, flux_val)
+
+    # Store the connections in the flux_list
+    flux_list[[index]] <- flux
+  }
+}
+
+vecinj <- do.call(rbind.data.frame, vecinj_adv)
+names(vecinj) <- names(init_adv)
+
+advection <- list(
+  init = init_adv,
+  vecinj = vecinj,
+  vecinj_inner = vecinj_inner,
+  const_flux = flux_list
+)
+
+#################################################################
+##                          Section 4                          ##
+##              Putting all those things together              ##
+#################################################################
+
+setup <- list(
+  grid = grid,
+  advection = advection
+)

test/advection/testAdvection.cpp

@@ -1,4 +1,5 @@
 #include "testDataStructures.hpp"
+
 #include <cstddef>
 #include <poet/AdvectionModule.hpp>
 #include <string>