rmt_create_rct creates an RMT3DMS rct object.

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.

Value

an object of class rct

Details

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

See also