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Run AEME models

Source: R/run_aeme.R
run_dy_cd.Rd

These functions provide a unified interface for running external hydrodynamic or biogeochemical lake models from within R. Each function moves into the appropriate simulation directory, executes the model's command-line binary, prints progress messages, and reports whether the model run completed successfully. The functions are intended to be called for their side effects: they do not return model results directly, but instead produce model output files in the simulation folder.

Usage

run_dy_cd(
  sim_folder,
  verbose = FALSE,
  debug = FALSE,
  args = character(),
  timeout = Inf,
  version = getOption("AEME.dyresm_version", default = NULL)
)

run_glm_aed(
  sim_folder,
  verbose = FALSE,
  debug = FALSE,
  config_file = find_glm_nml(sim_folder),
  args = character(),
  timeout = Inf,
  version = getOption("AEME.glm_version", default = NULL)
)

run_gotm_wet(
  sim_folder,
  verbose = FALSE,
  debug = FALSE,
  config_file = "gotm.yaml",
  args = character(),
  timeout = Inf,
  version = getOption("AEME.gotm_version", default = NULL)
)

run_simstrat_aed2(
  sim_folder,
  verbose = FALSE,
  debug = FALSE,
  config_file = "simstrat.par",
  args = character(),
  timeout = Inf,
  version = getOption("AEME.simstrat_version", default = NULL)
)

run_simstrat_aed(
  sim_folder,
  verbose = FALSE,
  debug = FALSE,
  config_file = "simstrat.par",
  args = character(),
  timeout = Inf,
  version = getOption("AEME.simstrat_aed_version", default = NULL)
)

Arguments

sim_folder

the directory where simulation files are contained

verbose

Logical: Should output of model be shown

debug

Logical; save debug file. DYRESM only.

args

character vector of additional command-line arguments to pass to the model executable. Currently only used for GLM-AED. Options are: "–xdisp" to plot the model output using the plots.nml settings.

timeout

timeout in seconds, ignored if 0. This is a limit for the elapsed time running command in a separate process. Fractions of seconds are ignored.

version

character; specific version of the model to run. If not provided, the default version bundled with the package will be used. For GLM-AED and GOTM-WET, this can also be set via the AEME.glm_version or AEME.gotm_version options, respectively. For DYRESM-CAEDYM, use AEME.dyresm_version. Currently, only GLM-AED support version selection; GOTM-WET and DYRESM-CAEDYM always uses the bundled version.

config_file

character; path to the model's main configuration file, passed to the model executable on the command line. Defaults to the hydrodynamic configuration file within sim_folder: the GLM nml file (see find_glm_nml()) for GLM-AED, "gotm.yaml" for GOTM-WET, and "simstrat.par" for Simstrat-AED2. Not used by DYRESM-CAEDYM, which reads several files derived from the .stg file present in sim_folder.

Value

Invisibly returns NULL.