R/mcnp_si_sp_RD.R

In markhogue/radsafer: Radiation Safety

#' Produce MCNP source terms from ICRP 107 data except beta
#' @family mcnp tools
#' @seealso  [mcnp_sdef_erg_hist()] if radioactive emission data is available in histogram form and needs formatting for MCNP input.
#'
#' @description 
#' #' `r lifecycle::badge("deprecated")`:
#' This function is deprecated 
#' and will be removed in a future package revision. 
#' For now, it is still usable. 
#' The replacement, `mcnp_sdef_erg_line` is the same function,
#' renamed to be consistent with the name of function 
#' `mcnp_sdef_erg_hist`.
#'
#' @param desired_RN Radionuclide in form "Ba-137m"
#' @param rad_type Radiation type, leave NULL if selecting photons or
#' select from:
#' 'X' for X-Ray
#' 'G' for Gamma
#' 'AE' for Auger Electron
#' 'IE' for Internal Conversion Electron
#' 'A' for Alpha
#' 'AR' for Alpha Recoil
#' 'B-' for Beta Negative
#' 'AQ' for Annihilation Quanta
#' 'B+' for Beta Positive
#' 'PG' for Prompt Gamma
#' 'DG' for Delayed Gamma
#' 'DB' for Delayed Beta
#' 'FF' for Fission Fragment
#' 'N' for Neutron
#' @param photon 'Y' to select all rad_types that are photons
#' @param cut minimum energy, defaults to 1e-3 MeV
#' @param erg.dist energy distribution number for MCNP input
#' @param my_dir Optional directory. The function will write an output text file, si_sp.txt to the working directory by default.
#' @param write_permit Set this to 'y' to allow writing output to your directory.
#' @return a data frame can be saved to memory if desired (i.e. by my_file <- mcnp_si_sp_RD(...)).
#' For use with MCNP, a text file, 'si_sp.txt' is written to working directory.
#' If file already exists, it is appended. The file contains all
#' emission energies in the si 'card' and the Line indicator, L is included,
#' e.g. si1  L  0.01 (showing a first energy of 0.01 MeV).
#' This is followed by the emission probability of each si entry.
#' An additional text entry is made summing up the probabilities.
#'
#' @examples
#' \dontrun{
#' mcnp_si_sp_RD("Co-60", photon = TRUE, cut = 0.01, erg.dist = 13)
#' mcnp_si_sp_RD("Sr-90", rad_type = "B-", cut = 0.01, erg.dist = 15)
#' mcnp_si_sp_RD("Am-241", rad_type = "A", cut = 0.01, erg.dist = 23)
#' }
#' @export
mcnp_si_sp_RD <- function(desired_RN, rad_type = NULL, photon = FALSE, cut = 1e-3, erg.dist = 1, my_dir = NULL, write_permit = "n") {
  if (is.null(my_dir)) my_dir <- getwd()
  
  rt_allowed <- c("X", "G", "AE", "IE", "A", "AR", "B-", "AQ", "B+", "PG", "DG", "DB", "FF", "N")
  stop_flag <- FALSE
  # Checks for valid arguments~~~~~~~~~~~~~~ Is rad_type valid?
  if (!is.null(rad_type)) {
    if (!rad_type %in% rt_allowed) {
      cat("Invalid specification for rad_type.\n")
      cat("Please enter one of these: \n")
      cat(rt_allowed)
      cat(" (in quotes) or NULL and select photon = TRUE")
    }
  }
  # Are both rad_type and photon selected?
  if (!is.null(rad_type) & photon == TRUE) {
    cat("Enter either rad_type = 'a rad_type', or photon = TRUE, but not both.")
    return()
  }

  # end of argument checks~~~~~~~~~~~~~~~~

  # all betas use ICRP_07.BET others ICRP_07.RAD
  dat_set <- "R"
  if (!is.null(rad_type)) {
    if (rad_type %in% c("B-", "B+", "DB")) {
      dat_set <- "B"
    }
  }

  if (dat_set == "B") {
    si.sp <- RadData::ICRP_07.BET[which(RadData::ICRP_07.BET$RN == desired_RN), ]
  }

  if (dat_set == "R") {
    si.sp <- RadData::ICRP_07.RAD[which(RadData::ICRP_07.RAD$RN ==
      desired_RN), ]

    if (photon == TRUE) {
      si.sp <- si.sp[which(si.sp$is_photon == TRUE), ]
    }

    if (photon == FALSE) {
      si.sp <- si.sp[which(si.sp$code_AN == rad_type), ]
    }
  }


  if (photon == TRUE) {
    si.sp <- RadData::ICRP_07.RAD[which(RadData::ICRP_07.RAD$RN == desired_RN), ]

    si.sp <- si.sp[which(si.sp$is_photon == TRUE), ]
  }

  # check for no matches
  if (is.na(si.sp[1, 1])) {
    oops <- "No matches"
    stop_flag <- TRUE
  }
  if (stop_flag) {
    return(oops)
  }

  # apply cutoff
  si.sp <- si.sp[which(si.sp$E_MeV > cut), ]

  # Create matrix for formatting.
  add.NA <- function(n) (6 - (n %% 6)) * ((n %% 6) != 0)
  na.num <- add.NA(length(si.sp$E_MeV))

  # na.num <- 6 - (length(si.sp$E_MeV) %% 6)
  prob.sum <- ifelse(dat_set == "B",
    "see branching ratio",
    sum(si.sp$prob)
  )

  si <- as.data.frame(matrix(c(si.sp$E_MeV, rep("$", na.num)),
    ncol = 6, byrow = TRUE
  ))

  si$V7 <- c(rep("&", nrow(si) - 1), "$")
  si <- data.frame(si$V1, si$V2, si$V3, si$V4, si$V5, si$V6, si$V7)
  if (dat_set == "B") {
    sp <- as.data.frame(matrix(c(si.sp$A, rep("$", na.num)),
      ncol = 6,
      byrow = TRUE
    ))
  }
  
  if (dat_set == "R") {
    sp <- as.data.frame(matrix(c(
      si.sp$prob,
      rep("$", na.num)
    ),
    ncol = 6,
    byrow = TRUE
    ))
  }
  sp$V7 <- c(rep("&", nrow(sp) - 1), "$")
  sp <- data.frame(sp$V1, sp$V2, sp$V3, sp$V4, sp$V5, sp$V6, sp$V7)
  #
  # write output si output
  if (write_permit  == "y") {
    utils::write.table(data.frame(text = "c"), "si_sp.txt",
    col.names = FALSE,
    row.names = FALSE,
    append = TRUE,
    quote = FALSE
  )
  }
  dist_type <- "L"
  if (dat_set == "B") {
    dist_type <- "A"
  }
  r_type_text <- as.character(rad_type)
  if (photon == TRUE) {
    r_type_text <- "photon"
  }
  
  if (write_permit  == "y") {
    utils::write.table(data.frame(text = paste0(
    "si",
    erg.dist, " ", dist_type, " & ", "$", desired_RN,
    ", radiation type= ", r_type_text
  )), "si_sp.txt",
  col.names = FALSE,
  row.names = FALSE,
  append = TRUE,
  quote = FALSE
  )
  
  utils::write.table(data.frame(text = paste0(
    "c  energy cut off at ",
    cut, " MeV "
  )),
  "si_sp.txt",
  col.names = FALSE,
  row.names = FALSE,
  append = TRUE,
  quote = FALSE
  )

  readr::write_delim(data.frame(si),
    "si_sp.txt",
    col_names = FALSE,
    append = TRUE
  )

  # sp output
  utils::write.table(data.frame(text = "c"),
    "si_sp.txt",
    col.names = FALSE,
    row.names = FALSE,
    append = TRUE,
    quote = FALSE
  )

  utils::write.table(data.frame(text = paste0(
    "sp",
    erg.dist, " & ", "$",
    desired_RN, ", radiation type= ",
    r_type_text, " sum of probs = ",
    prob.sum
  )), "si_sp.txt",
  col.names = FALSE,
  row.names = FALSE,
  append = TRUE,
  quote = FALSE
  )

  readr::write_delim(data.frame(sp),
    "si_sp.txt",
    col_names = FALSE,
    append = TRUE
  )
  cat("\n")
  cat(paste0(
    "The output is appeneded to file, si_sp.txt, in your working directory, ",
    my_dir, "."
  ))
  cat("\n")
}
  # return a data frame to allow plots, etc.
  si.sp
}