Input Scripts

In the following the expected schemes of the input scripts is described. Therefore, each section of the input script gets its own chapter. All sections should return a list as results, which are concatenated to one setup list at the end of the file. All values must have the same name in order to get parsed by POET.

Grid initialization

name	type	description
`n_cells`	Numeric Vector	Number of cells in each direction
`s_cells`	Numeric Vector	Spatial resolution of grid in each direction
`type`	String	Type of initialization, can be set to scratch, phreeqc or rds
`init_cell`	Data Frame	Containing all exactly one value per species to initialize the field.
`props`	String Vector	Names of all species
`database`	String	Path to Phreeqc database
`input_script`	String	Path to Phreeqc initial script

Diffusion parameters

name	type	description
`init`	Named Numeric Vector	Initial state for each diffused species
`vecinj`	Data Frame	Defining all boundary conditions row wise
`vecinj_inner`	List of Triples	Inner boundaries
`vecinj_index`	List of 4 elements	Ghost nodes boundary conditions
`alpha`	Named Numeric Vector	Constant alpha for each species

Remark on boundary conditions

Each boundary condition should be defined in vecinj as a data frame, where one row holds one boundary condition.

To define inner (constant) boundary conditions, use a list of triples in vecinj_inner, where each triples is defined by (i,x,y). i is defining the boundary condition, referencing to the row in vecinj. x and y coordinates then defining the position inside the grid.

Ghost nodes are set by vecinj_index which is a list containing boundaries for each celestial direction (important: named by N, E, S, W). Each direction is a numeric vector, also representing a row index of the vecinj data frame for each ghost node, starting at the left-most and upper cell respectively. By setting the boundary condition to 0, the ghost node is set as closed boundary.

Example

Suppose you have a vecinj data frame defining 2 boundary conditions and a grid consisting of 10 \times 10 grid cells. Grid cell (1,1) should be set to the first boundary condition and (5,6) to the second. Also, all boundary conditions for the ghost nodes should be closed. Except the southern boundary, which should be set to the first boundary condition injection. The following setup describes how to setup your initial script, where n and m are the grids cell count for each direction (n = m = 10):

vecinj_inner <- list (
  l1 = c(1, 1, 1),
  l2 = c(2, 5, 6)
)

vecinj_index <- list(
  "N" = rep(0, n),
  "E" = rep(0, m),
  "S" = rep(1, n),
  "W" = rep(0, m)
)

Chemistry parameters

name	type	description
`database`	String	Path to the Phreeqc database
`input_script`	String	Path the the Phreeqc input script

Final setup

name	type	description
`grid`	List	Grid parameter list
`diffusion`	List	Diffusion parameter list
`chemistry`	List	Chemistry parameter list
`iterations`	Numeric Value	Count of iterations
`timesteps`	Numeric Vector	`\Delta t` to use for specific iteration
`store_result`	Boolean	Indicates if results should be stored
`out_save`	Numeric Vector	optional: At which iteration the states should be stored

DHT setup

name	type	description
`signif_vector`	Numeric Vector	Indicates significant digits to use for DHT rounding. Order of `props` vector.
`prop_type`	String Vector	Set type of species for rounding, can be left blank or set to act or ignore

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