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Set initial conditions for a GLM-AED simulation

Source: R/set_model_init.R
set_glm_init.Rd

Thin wrapper for editing the initial temperature/salinity profile and water-quality initial values of a GLM-AED hydrodynamic nml file in place, without needing an aeme object. Intended for a GLM-AED-only workflow where a user just wants to tweak initial conditions, run the model, and load the output.

Usage

set_glm_init(
  path_glm,
  temp = NULL,
  salt = NULL,
  wq_init = NULL,
  glm_file = find_glm_nml(path_glm)
)

Arguments

path_glm

filepath; directory containing the GLM-AED configuration

temp

numeric; new initial water temperature profile. Recycled to the number of depths in init_profiles. NULL (default) leaves it unchanged.

salt

numeric; new initial salinity profile, same recycling rule as temp. NULL (default) leaves it unchanged.

wq_init

named list; new initial values for water quality variables, e.g. list(NIT_amm = 0.5, CHM_oxy = 300). Names must match init_profiles$wq_names in the nml file. Each value is recycled across depths. NULL (default) leaves water quality initial values unchanged.

glm_file

filepath; path to the nml file to edit. Defaults to the GLM hydrodynamic nml (glm3.nml/glm4.nml) found in path_glm via find_glm_nml().

Value

invisibly, the updated nml object

Details

Existing profile depths (init_profiles$the_depths) are left unchanged – temp/salt/wq_init values are recycled (via rep_len()) across however many depths are already defined.

Examples

if (FALSE) { # \dontrun{
set_glm_init(path_glm, temp = seq(20, 10, length.out = 10))
set_glm_init(path_glm, wq_init = list(NIT_amm = 0.5, CHM_oxy = 300))
} # }