run_MC_CW_IRSL_TUN.R

#' @title Run Monte-Carlo Simulation for CW-IRSL (tunnelling transitions)
#'
#' @description Runs a Monte-Carlo (MC) simulation of continuous wave infrared stimulated luminescence
#' (CW-IRSL) using the model for tunnelling transitions. Tunnelling refers to quantum mechanical
#' tunnelling processes from the excited state of the trap,
#' into a recombination centre.
#'
#' @details
#'
#' **The model**
#'
#' \deqn{
#' I_{TUN}(r',t) = -dn/dt = A * exp(-(\rho')^{-1/3} * r')* n (r',t)
#' }
#'
#'Where in the function: \cr
#' A := effective optical excitation rate for the tunnelling process (s^-1) \cr
#' r' := the dimensionless tunnelling radius \cr
#' \eqn{\rho}' := `rho'` the dimensionless density of recombination centres (see Huntley (2006)) \cr
#' t := time (s) \cr
#' n := the instantaneous number of electrons corresponding to the radius r' at time t
#'
#' @param A [numeric] (**required**): The effective optical excitation rate for the tunnelling process
#' (`s^-1`).
#'
#' @param rho [numeric] (**required**): The density of recombination centres
#' (defined as \eqn{\rho}' in Huntley 2006) (dimensionless).
#'
#' @param times [numeric] (**required**): The sequence of time steps within the simulation (s).
#'
#' @param clusters [numeric] (*with default*): The number of created clusters for the MC runs. The input can be the output of [create_ClusterSystem]. In that case `n_filled` indicate absolute numbers of a system.
#'
#' @param N_e [numeric] (*width default*): The total number of electron traps available (dimensionless).
#' Can be a vector of `length(clusters)`, shorter values are recycled.
#'
#' @param r_c [numeric] (*with default*): Critical distance (>0) that must be provided if the
#' sample has been thermally and/or optically pretreated. This parameter expresses the fact
#' that electron-hole pairs within a critical radius `r_c` have already recombined.
#'
#' @param delta.r [numeric] (*with default*): Increments of the dimensionless distance parameter r'
#'
#' @param method [character] (*with default*): Sequential `'seq'` or parallel `'par'`processing. In
#' the parallel mode the function tries to run the simulation on multiple CPU cores (if available) with
#' a positive effect on the computation time.
#'
#' @param output [character] (*with default*): output is either the `'signal'` (the default) or
#' `'remaining_e'` (the remaining charges/electrons in the trap)
#'
#' @param \dots further arguments, such as `cores` to control the number of used CPU cores or `verbose` to silence the terminal
#'
#' @return This function returns an object of class `RLumCarlo_Model_Output` which
#' is a [list] consisting of an [array] with dimension length(times) x length(r) x clusters
#' and a [numeric] time vector.
#'
#' @section Function version: 0.2.0
#'
#' @author Johannes Friedrich, University of Bayreuth (Germany),
#' Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany)
#'
#' @references
#' Huntley, D.J., 2006. An explanation of the power-law decay of luminescence.
#' Journal of Physics: Condensed Matter, 18(4), 1359.
#'
#' Pagonis, V., Friedrich, J., Discher, M., Müller-Kirschbaum, A., Schlosser, V., Kreutzer, S.,
#' Chen, R. and Schmidt, C., 2019. Excited state luminescence signals from a random distribution of defects:
#' A new Monte Carlo simulation approach for feldspar.
#' Journal of Luminescence 207, 266–272. \doi{10.1016/j.jlumin.2018.11.024}
#'
#' **Further reading**
#'
#' Aitken, M.J., 1985. Thermoluminescence dating. Academic Press.
#'
#' Jain, M., Guralnik, B., Andersen, M.T., 2012. Stimulated luminescence emission from
#' localized recombination in randomly distributed defects.
#' Journal of Physics: Condensed Matter 24, 385402.
#'
#' Chen, R., McKeever, S.W.S., 1997. Theory of Thermoluminescence and Related Phenomena.
#' WORLD SCIENTIFIC. \doi{10.1142/2781}
#'
#' @examples
#' run_MC_CW_IRSL_TUN(
#'  A = 0.8,
#'  rho = 1e-4,
#'  times = 0:50,
#'  r_c = 0.05,
#'  delta.r = 0.1,
#'  method = "seq",
#'  clusters = 10,
#'   output = "signal") %>%
#'  plot_RLumCarlo(norm = TRUE, legend = TRUE)
#'
#' @keywords models data
#' @encoding UTF-8
#' @md
#' @export
run_MC_CW_IRSL_TUN <- function(
  A,
  rho,
  times,
  clusters = 10,
  r_c = 0,
  delta.r = 0.1,
  N_e = 200,
  method = "seq",
  output = "signal",
  ...){

# Integrity checks ----------------------------------------------------------------------------
  if(!output %in% c("signal", "remaining_e"))
    stop("[run_MC_CW_IRSL_TUN()] Allowed keywords for 'output' are either 'signal' or 'remaining_e'!",
         call. = FALSE)

# Register multi-core back end ----------------------------------------------------------------
cl <- .registerClusters(method, ...)
on.exit(parallel::stopCluster(cl))

# Setting parameters --------------------------------------------------------------------------
r <- seq(abs(r_c[1]), 2, abs(delta.r[1]))

# Enable dosimetric cluster system -----------------------------------------
if(class(clusters)[1] == "RLumCarlo_ClusterSystem"){
  N_e <- .distribute_electrons(
    clusters = clusters,
    N_system = N_e[1])[["e_in_cluster"]]
  clusters <- clusters$cl_groups

}

# Expand parameters -------------------------------------------------------
N_e <- rep(N_e, length.out = max(clusters))

# Run model -----------------------------------------------------------------------------------
temp <- foreach(
  c = 1:max(clusters),
  .packages = 'RLumCarlo',
  .combine = 'comb_array',
  .multicombine = TRUE
) %dopar% {
  results <- MC_C_CW_IRSL_TUN(
    times = times,
    N_e = N_e[c],
    r = r,
    rho = rho[1],
    A = A[1]
  )

  return(results[[output]])

}  # end c-loop

# Return --------------------------------------------------------------------------------------
.return_ModelOutput(signal = temp, time = times)
}