Refactor diffusion_setup boundaries in Initialization.md

Initialization.md

@@ -37,23 +37,27 @@ grid_setup <- list(
 
 ```r
 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()
+    boundaries = list(                  # Define boundary conditions for diffusion
+        "N" = list(
+            "cell" = numeric(),         # Define the cell ID; counting begins @ 1 
+            "sol_id" = numeric(),       # Define the Phreeqc solution ID for the boundary
+        ),
+        # Only those boundaries needs to be defined, which are constant 
+        "E" = list(...),                
+        # You can also leave sides out -> closed boundary on complete side
     ),
-    to_transport = character(),         # Define the species to transport
-    alphax = list(                      # Define the diffusion coefficient in x-direction
-        matrix(),
-        matrix(),
+    # alphas can be set by a list of matrices for ALL species to transport
+    alphax = list(                      
+        matrix(nrow, ncol),
+        matrix(nrow, ncol),
         ...
-    ),
-    alphay = list(                      # Define the diffusion coefficient in y-direction
-        matrix(),
-        matrix(),
-        ...
-    )
+    ), 
+    # or by defining a single matrix for all species, assuming homogenous diffusion coefficients among species at the same cell
+    alphax = matrix(nrow, ncol),
+    # or by defining a single value, which acts as a homogeneous diffusion coefficient for all species and cells
+    alphax = numeric(),
+    # ---- 
+    alphay = alphax # See documentation for alphax
 )
 ```