R/run_example_sim.R

In USGS-R/glmtools: Tools for working with the General Lake Model (GLM)

#'Run example simulation 
#'@param sim_folder the directory where simulation files will be copied/moved to. 
#'If missing, will use a temporary directory 
#'@param verbose should operations and output of GLM be shown
#'@keywords methods
#'@seealso \code{\link[GLM3r]{run_glm}}
#'@importFrom GLM3r run_glm
#'@author
#'Jordan S. Read, Luke A. Winslow
#'@examples 
#'run_example_sim(verbose = FALSE)
#'\dontrun{
#'run_example_sim('~/Desktop/GLM_sims')
#'}    
#'@export
run_example_sim = function(sim_folder, verbose = TRUE){
  
  if (missing(sim_folder)){
    sim_folder <- tempdir() #simulation path
    if(verbose){cat('sim_folder argument missing, using temp directory: ', sim_folder,'\n\n')}
  }
  glmtools_folder = system.file('extdata', package = 'glmtools')
  file.copy(list.files(glmtools_folder,full.names = TRUE), sim_folder, overwrite = TRUE)
  field_file <- file.path(sim_folder, 'LakeMendota_field_data_hours.csv')
  nml_file <- file.path(sim_folder, 'glm3.nml')
  driver_file <- file.path(sim_folder, 'LakeMendota_NLDAS.csv')
  
  nc_out = 'output'
  nc_file <- file.path(sim_folder, paste0(nc_out, '.nc'))

  
  nml <- read_nml() # read in default nml from GLM3r
  # Set new nml paramters
  nml <- set_nml(nml, arg_list = list('Kw'=0.331, 'lake_name'='Mendota', 
                               'bsn_vals' = 15,
                               'H' = c(301.712, 303.018285714286, 304.324571428571, 305.630857142857, 306.937142857143, 308.243428571429, 309.549714285714, 310.856, 312.162285714286, 313.468571428571, 314.774857142857, 316.081142857143, 317.387428571429, 318.693714285714, 320),
                               'A' = c(0, 45545.8263571429, 91091.6527142857, 136637.479071429, 182183.305428571, 227729.131785714, 273274.958142857, 318820.7845, 364366.610857143, 409912.437214286, 455458.263571429, 501004.089928571, 546549.916285714, 592095.742642857, 637641.569),
                               'start' = '2015-04-01 12:00:00',
                               'stop' = '2015-07-30 12:00:00',
                               'dt' = 3600, 
                               'out_fn' = nc_out,
                               'nsave' = 24, 
                               'num_depths' = 3,
                               'lake_depth' = 18.288,
                               'the_depths' = c(0, 0.2, 18.288),
                               'the_temps' = c(3, 4, 4),
                               'the_sals' = c(0, 0, 0),
                               'subdaily' = TRUE,
                               'meteo_fl' = 'LakeMendota_NLDAS.csv',
															 'max_layer_thick' = 3,
															 'sw_factor' = 1.08,
															 'coef_wind_stir' = 0.402,
															 'coef_mix_hyp' = 0.2,
															 'coef_mix_KH' = 0.1,
															 'cd' = 0.0013,
															 'ce' = 0.00132,
															 'sed_temp_mean' = c(4.5,10),
															 'sed_temp_amplitude' = c(4,3),
															 'min_layer_thick' = 0.1,
															 'coef_mix_conv' = 0.20,
                               'num_outlet' = 0))

  if(verbose){cat('writing nml file to ', nml_file,'\n')}
  write_nml(glm_nml = nml, file = nml_file)  

  GLM3r::run_glm(sim_folder = sim_folder, verbose = TRUE)
  
  if(verbose){cat('simulation complete. \n*.nc output located in ', nc_file,'\n')}
  
  return(sim_folder)
}