DRW: Dynamic Random Walk aqueous contaminant transport solution
In CJBarry/DRW: Dynamic Random Walk

Description Usage Arguments Value Examples

Dynamic Random Walk aqueous contaminant transport solution

DRW(rootname, description, mfdir = ".", mfdata, wtop, dis, bas, wel, hds, cbb,
  cbf, newcbf = TRUE, source.term, STna.rm = FALSE, porosity, start.t,
  end.t, dt, D, vdepD, Rf = 1, lambda = 0, decay.sorbed = FALSE, cd, mm,
  minnp = 100L, maxnp, Ndp = 2L, init = NULL, nc.to.mf = 1L,
  plot.state = TRUE, keep.MF.cellref = TRUE, time.mismatch.tol = 0.001,
  ..., keepMPfiles = FALSE)

`rootname`	character string; the rootname for the results file (`".rds"` is automatically affixed)
`description`	character string; a description of this model run, for future reference
`mfdir`	character string; path to the directory holding all the MODFLOW input and output files; the function navigates to this directory so that extended file paths for MODFLOW files needn't be specified
`mfdata`	NetCDF object, list of NetCDF objects or character string[Nmfds]; the MODFLOW data sets in NetCDF form (see `GW.nc`), either as NetCDF objects (see `open.nc`) or as character string file paths; this function may use a series of MODFLOW models with identical spatial co-ordinates and grids and with time periods that lead on from one another, thus a historic flow model may seamlessly be linked to a recent flow model, for example
`wtop`	NetCDF object, list of NetCDF objects or character string [Nmfds]; NetCDF data sets of the cell-by-cell top of water in each cell (the lower out of head and cell top); if character string file names are used, the files needn't exist beforehand as they can be created using `get.wtop.nc`
`dis`	character string [Nmfds]; file paths to DIS package files corresponding to the MODFLOW data sets in mfdata (note, this cannot be a list of DIS.MFpackage objects, as the file names are needed for MODPATH)
`bas`	BAS.MFpackage object (or list thereof) or character string [Nmfds]; the BAS packages corresponding to mfdata (see `read.BAS`); only the `$IBOUND` element is used
`wel`	Optional: WEL.MFpackage object (or list thereof) or character string [Nmfds]; the WEL packages corresponding to mfdata (see `read.WEL`); this information is only used for plotting, and plotting does not depend on it
`hds, cbb`	character string [Nmfds]; the head save and cell-by-cell budget files corresponding to mfdata; although this information is in mfdata, MODPATH needs to know where the original HDS files are
`cbf`	character string [Nmfds]; the composite budget file names created by MODPATH 5; if these files don't already exist or `newcbf = TRUE`, MODPATH 5 will write these files afresh
`newcbf`	logical [1]; Whether MODPATH 5 should rewrite the CBF file. If you have modified the MODFLOW model since the last DRW run, then you should set this to `TRUE` (the default), but this can be time-consuming, so if you know it is not needed, set to `FALSE`. The CBF will only ever be written for the first time step using a particular MODFLOW data set.
`source.term`	data.table, data.frame, DNAPLSourceTerm object, or list of any combination of these; information about the transient point releases in the system; if a data table or frame, columns should be: x, y (location in the same absolute co-ordinate system as `mfdata`), L (MODFLOW layer), zo (z-offset within layer) and J (list of functions of one variable, time, returning values representing source term flux, in units of mass per time OR numeric values representing constant release rates in units of mass per time)
`STna.rm`	logical [1]; if `TRUE`, any `NA` values resulting from the source term functions (within the model time frame) are ignored and treated as 0, otherwise an error will occur if `NA`s are found.
`porosity`	numeric [1], numeric [NLAY] or numeric array [NCOL, NROW, NLAY]; the porosity (fractional, 0 to 1), either as uniform value, layer-by-layer values or a 3D array of cell-by-cell values matching the MODFLOW grid dimensions
`start.t, end.t`	numeric [1]; start and end times of the model (the `td` function may be useful)
`dt`	numeric [1]; time step size
`D`	numeric [2 or 3]; simplified dispersivity/ dispersion coefficient tensor, giving longitudinal, transverse and optionally vertical components
`vdepD`	logical [1]; `TRUE` if the dispersion coefficient is velocity-dependent, in which case `D` is taken to represent dispersivity, with units of length
`Rf`	numeric [1]; retardation factor (1 - (bulk_density times K_d)/(effective_porosity))
`lambda`	numeric [1]; first-order degradation constant (log(2)/half_life)
`decay.sorbed`	logical [1]; `TRUE` if first-order degradation affects sorbed contaminant (not yet implemented)
`cd`	numeric [2]; horizontal and vertical coalescing search radii (see `coalesce`)
`mm`	numeric [1]; minimum mass of particles after coalescing (see `coalesce`)
`minnp`	integer [1]; minimum number of particles on which to perform coalescing
`maxnp`	integer [1]; maximum number of particles after coalescing (see `coalesce`)
`Ndp`	integer [1]; number of pairs of particles to spawn to model the dispersion of contaminant mass
`init`	`NULL`, a DRWmodel object or a character string giving the RDS file name in which a DRWmodel object is stored; another DRW model run to use as the initial state for the current model; the time step just before `start.t` is used as the initial state, modifying the time step times as necessary
`nc.to.mf`	integer [`length(mfdata)`]; the MODFLOW model that is related to by each NetCDF dataset in `mfdata`; normally this will be 1, 2, 3 ..., but sometimes a large MODFLOW model may be split into multiple NetCDF datasets (see `GW.nc`), in which case it will be something like 1, 1, 1 ...; for the most common case in which there is only one MODFLOW model used, the default value of 1 is appropriate
`plot.state`	logical [1]; if `TRUE`, a summary plot of the model state will be shown after each time step (generally, not costly in terms of run time)
`keep.MF.cellref`	logical [2]; if `TRUE`, the final results for mobile and immobile particles will retain MODFLOW column (C), row (R), dataset (mfds) and time step (mfts) references
`time.mismatch.tol`	numeric [1]; various time comparisons are made during the model in order to check consistency, such as checking that the end time of one MODFLOW dataset matches the start time of the next; time.mismatch.tol gives the tolerance used in these comparisons in calls to `all.equal`
`...`	graphical parameters such as `xlim` (not axis labels, titles, `asp` or `zlim`)
`keepMPfiles`	logical [1]; use for debugging when MODPATH not working: doesn't delete the MODPATH files

A DRWmodel object, invisibly. The result is also saved to file: paste0(rootname, ".rds").

library(data.table)

# single point source which ceases after t = 10000
mfdir <- system.file(package = "DRW")
demoDRW <- DRW("DRW_EXAMPLE", "demo", mfdir,
               "drw_mf_demo.nc", "drw_mf_demo_wtop.nc",
               "drw_mf_demo.dis", "drw_mf_demo.bas", "drw_mf_demo.wel",
               "drw_mf_demo.hds", "drw_mf_demo.cbb", "DRWtest.cbf",
               newcbf = TRUE,
               source.term = data.table(x = 625, y = 825,
                                        L = 1L, zo = .5,
                                        J = function(t){
                                          if(t < 1e4) 1 else 0
                                        }),
               porosity = .1,
               start.t = 9000, end.t = 11000, dt = 200,
               D = c(10, 1), vdepD = TRUE,
               cd = c(20, 10), mm = 1e-7, minnp = 100L, maxnp = 2e4L,
               Ndp = 4L)