rmt_create_rct: Create an 'RMT3DMS' rct object

In rogiersbart/RMT3DMS: Pre- and post-processing of MT3DMS & MT3D-USGS files

Description

rmt_create_rct creates an RMT3DMS rct object.

Usage

rmt_create_rct(
  btn,
  isothm = 0,
  ireact = 0,
  irctop = 2,
  igetsc = 0,
  ireaction = 0,
  rhob = 157,
  prsity2 = 0.1,
  srconc = as.list(rep(0, btn$ncomp)),
  sp1 = as.list(rep(0, btn$ncomp)),
  sp1im = as.list(rep(0, btn$ncomp)),
  sp2 = as.list(rep(0, btn$ncomp)),
  rc1 = as.list(rep(0, btn$ncomp)),
  rc2 = as.list(rep(0, btn$ncomp)),
  rc3 = as.list(rep(0, btn$ncomp)),
  yld = rep(1, btn$ncomp - 1),
  ied = 1,
  iea = 2,
  f = 1,
  rec_filename = "reaction_module.dat",
  ned = 1,
  nea = 5,
  nspecial = 0,
  ifesld = 0,
  ispec = rep(0, nspecial),
  specialispec = rep("SOLID", nspecial),
  efcmax = rep(0, nspecial),
  hsc = rep(0.5, nea),
  ic = rep(0.01, nea),
  decayrate = matrix(0.0186, nrow = nea, ncol = ned),
  yieldc = matrix(1, nrow = nea + ned, ncol = ned)
)

Arguments

btn	RMT3DMS btn object
isothm	integer flag to set type of sorption (or dual-domain mass transfer). See MT3DMS/MT3D-USGS manual. Defaults to 0.
ireact	integer flag indicating which type of kinetic rate reaction is simulated. See MT3DMS/MT3D-USGS manual. Defaults to 0.
irctop	integer flag indicating how reaction variables are entered. See MT3DMS/MT3D-USGS manual. Defaults to 2 (as 3D-arrays).
igetsc	integer flag specifying if initial concentration of nonequilibrium sorbed or immobile phases should be read. See MT3DMS/MT3D-USGS manual. Defaults to 0 (not read).
ireaction	MT3D-USGS only. Integer flag specifying a reaction module. See MT3D-USGS manual. Defaults to 0 (no reaction module.
rhob	3d array with bulk density of aquifer medium. Defaults to 157 for all cells.
prsity2	3d array with porosity values for the immobile domain. Defaults to 0.1 for all cells.
srconc	list with ncomp 3d arrays specifying the initial sorbed concentrations if igetsc > 0. Defaults to 0 for all cells.
sp1	list with ncomp 3d arrays specifying the first sorption parameter. See MT3DMS/MT3D-USGS manual. Defaults to 0.
sp1im	list with ncomp 3d arrays speciyfing the immobile domain distribution coefficient for sorption. See MT3DMS/MT3D-USGS manual. Defaults to 0.
sp2	list with ncomp 3d arrays specifying the second sorption or dual-domain model parameter. See MT3DMS/MT3D-USGS manual. Defaults to 0.
rc1	list with ncomp 3d arrays specifying the primary kinetic parameter. See MT3DMS/MT3D-USGS manual. Defaults to 0.
rc2	list with ncomp 3d arrays specifying the secondary kinetic parameter.See MT3DMS/MT3D-USGS manual. Defaults to 0.
rc3	list with ncomp 3d arrays specifying the half-saturation constants when ireact = 2. Defaults to 0.
yld	numeric vector of length ncomp - 1 with the yield coefficients between species when ireact = 3. ncomp should be larger than 1 when this feature is used. See MT3DMS/MT3D-USGS manual.
ied	integer species number representing the electron donor in a EA/ED reaction (ireaction = 1).
iea	integer species number representing the electron acceptor in a EA/ED reaction (ireaction = 1).
f	stoiciometric ratio in the simulated equation ED + F*EA -> Product (ireaction = 1).
rec_filename	character, name of the input file that will provide parameter information when ireaction = 2. Defaults to 'reaction_module.dat'.
ned	number of electron donors when ireaction = 2.
nea	number of electron acceptors when ireaction = 2.
nspecial	number of special cases when ireaction = 2.
ifesld	integer flag specifying if solid phase Fe(III) is simulated. Defaults to 0 (not simulated).
ispec	numeric vector of length nspecial specifying the sequential order of the species treated as special case.
specialispec	character vector of length nspecial specifying the keyword of the species treated as special case. See MT3D-USGS manual.
efcmax	numeric vector of length nspecial specifying the maximum express field capacity (EFC) of the species treated as special case. See MT3D-USGS manual.
hsc	numeric vector of length nea with the half-saturation constants.
ic	numeric vector of length nea with the inhibition constants.
decayrate	matrix with nea rows and ned columns specifying the decay rates of each EA corresponding to each ED.
yieldc	matrix with nea + ned rows and ned columns specifying the yield coefficient of each component corresponding to each ED.

Details

If irctop < 2, all 3D variables should be given as 1D vectors with one value per layer.

Value

an object of class rct

See Also

rmt_read_rct, rmt_write_rct

rogiersbart/RMT3DMS documentation built on Oct. 16, 2021, 9:45 a.m.