PERTURBdyna: Dynamic solution of C, N, P and O2 dynamics in the sediment,...
In CNPDIA: Diagenetic Model with Simple Nitrogen, Carbon, Phosphorus Dynamics
Description
Usage
Arguments
Details
Value
Note
Author(s)
References
Examples
Description
CNPDIAperturb dynamically runs the CNPDIA model with event-like perturbations.
CNPDIAperturbSettings and CNPDIAperturbFluxes retrieve the settings and perturbation fluxes.
Usage
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CNPDIAperturb (parms = list(), times = 0:365, spinup = NULL, yini = NULL,
gridtype = 1, Grid = NULL, porosity = NULL, bioturbation = NULL,
irrigation = NULL, surface = NULL, diffusionfactor = NULL,
dynamicbottomwater = FALSE, perturbType = "mix",
perturbTimes = seq(from = 0, to = max(times), by = 365),
perturbDepth = 5, concfac = 1,
CfluxForc = NULL, FePfluxForc = NULL, CaPfluxForc = NULL,
O2bwForc = NULL, NO3bwForc = NULL, NO2bwForc = NULL,
NH3bwForc = NULL, ODUbwForc = NULL, PO4bwForc = NULL,
DICbwForc = NULL, wForc = NULL, biotForc = NULL,
irrForc = NULL, rFastForc = NULL, rSlowForc = NULL,
pFastForc = NULL, MPBprodForc = NULL, gasfluxForc = NULL,
HwaterForc = NULL, ratefactor = NULL, verbose = FALSE, ...)
mixSolid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5)
mixLiquid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5, BW)
erodeSolid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5)
erodeLiquid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5)
depositSolid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5, concfac = 1)
depositLiquid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5, BW)
CNPDIAperturbFluxes(out, which = NULL)
CNPDIAperturbSettings(out)
Arguments
parms
A list with parameter names and values. Possible parameters are:
Cflux, pFast, FePflux, CaPflux, rFast, rSlow, NCrFdet, NCrSdet, PCrFdet, PCrSdet,
BCupLiq, BCdownLiq, O2bw, NO3bw, NO2bw, NH3bw, ODUbw, PO4bw, DICbw, O2dw, NO3dw, NO2dw, NH3dw,
ODUdw, PO4dw, DICdw, w, biot, mixdepth, mixatt, irr, gasflux, MPBprod, kMPB, ksDIN
ksPO4 ksDIC NH3Ads, rnit, ksO2nitri, rODUox, ksO2oduox, ksO2oxic, ksNO3denit,
kinO2denit, kinNO3anox kinO2anox, pdepo, rdepo, temperature, salinity, TOC0,
rFePdesorp, rFePadsorp, rCaPprod, rCaPdiss, CPrCaP, por0, pordeep, porcoeff,
dilution, Hwater, Cfall, FePfall, CaPfall
See details of CNPDIAsolve.
gridtype
Type of grid: 1 for cartesian, 2 for cylindrical, 3 for spherical.
times
Output times for the dynamic run
spinup
Spinput times for the dynamic run; not used for output; the outputted simulation starts from the final values of the spinup run.
CfluxForc, FePfluxForc, CaPfluxForc
NULL or a list, detailing the forcing function for the deposition fluxes of organic carbon, FeP and CaP.
If NULL then the corresponding parameter value (Cflux, CaPflux, FePflux) is used.
If a list, it should contain either a data time series (list(data = )) or parameters determining the periodicity of the seasonal signal (defined as list(data = NULL, amp = 0, period = 365, phase = 0, pow = 1, min = 0). see details.
O2bwForc, NO3bwForc, NO2bwForc, NH3bwForc, ODUbwForc, PO4bwForc, DICbwForc
NULL or a list, detailing the forcing function for the boundary concentrations.
If NULL then the corresponding parameter value (O2bw, NO3bw, NO2bw, NH3bw, ODUbw, PO4bw, DICbw) is used.
If a list, it should contain either a data time series (list(data = )) or parameters determining the periodicity of the seasonal signal (defined as list(data = NULL, amp = 0, period = 365, phase = 0, pow = 1, min = 0). see details.
wForc, biotForc, irrForc
NULL or a list, detailing the forcing function forthe advection, bioturbation and irrigation rates (units of cm/d, cm2/d and /d).
If NULL then the corresponding parameter value (w, biot, irr) is used.
If a list, it should contain either a data time series (list(data = )) or parameters determining the periodicity of the seasonal signal (defined as list(data = NULL, amp = 0, period = 365, phase = 0, pow = 1, min = 0). see details.
rFastForc, rSlowForc, pFastForc, MPBprodForc
NULL or a list, detailing the forcing function forthe decay rate of fast and slow detritus, the fraction of fast detritus in organic flux and the maximal microphytobenthos production rate (units of /d, /d, - and mmolO2/m3/d).
If NULL then the corresponding parameter value (rFast, rSlow, pFast, MPBprod) is used.
If a list, it should contain either a data time series (list(data = )) or parameters determining the periodicity of the seasonal signal (defined as list(data = NULL, amp = 0, period = 365, phase = 0, pow = 1, min = 0). see details.
gasfluxForc
NULL or a list, detailing the forcing function for the intensity of exchange with the air (units of cm/d).
If NULL then the corresponding parameter value (gasflux) is used.
If a list, it should contain either a data time series (list(data = )) or parameters determining the periodicity of the seasonal signal (defined as list(data = NULL, amp = 0, period = 365, phase = 0, pow = 1, min = 0). see details.
A gasflux>0 represents exchange rate for O2 and DIC, not for other dissolved substances. There can still be deposition of C, FeP and CaP.
HwaterForc
NULL or a list, detailing the forcing function for the height of the water above the sediment - if dynamicbottomwater = TRUE.
If NULL then the corresponding parameter value (Hwater) is used.
If a list, it should contain either a data time series (list(data = )) or parameters determining the periodicity of the seasonal signal (defined as list(data = NULL, amp = 0, period = 365, phase = 0, pow = 1, min = 0). see details.
dynamicbottomwater
If TRUE, then the concentrations in the water overlying the sediment will also be dynamically described,
and with water height equal to Hwater. Note that this will slow down the simulation.
ratefactor
NULL or a list, detailing the forcing function for the biogeochemical rate multiplication factor. If not specified (or NULL), then it is assumed to be 1 and constant.
If a list, it should contain either a data time series (list(data = )) or parameters determining the periodicity of the seasonal signal (defined as list(data = NULL, amp = 0, period = 365, phase = 0, pow = 1, min = 0). see details.
Grid
If specified: either an object, as returned by setup.grid.1D from the package ReacTran,
a vector of length 101 with the transport distances (from mid to mid of layers, upper interface = diffusive boundary layer),
or one number with the constant layer thickness.
If NULL, it is defined as setup.grid.1D(x.up = 0, dx.1 = 0.01, N = 100, L = 100), i.e. the total length is 100 cm,
the first layer is 0.01 cm thick and layers are increasing with depth for 100 layers.
porosity
If specified, either an object with porosities ([-]) as returned by setup.prop.1D from the package ReacTran,
a vector of length 101 with the porosities defined at the layer interfaces, or one number with the constant porosity.
If NULL, it is defined by the parameters por0, pordeep and porcoeff as:
(pordeep + (por0 - pordeep) * exp(-pmax(0, x.int)/porcoeff)), where x.int is the distance, from the surface of the layer interface.
Note that the porosity values should be consistent withe the Grid - and should be inbetween 0 and 1.
bioturbation
If specified, either an object with bioturbation rates (units [cm2/d]) as returned by setup.prop.1D from the package ReacTran,
a vector of length 101 with the bioturbation defined at the layer interfaces, or one number with the constant bioturbation.
If NULL, it is defined by the parameters biot, mixdepth and mixatt as:
biot * exp(-pmax(0, (x.int-mixL)/mixatt), where x.int is the distance, from the surface of the layer interface.
Note that the bioturbation values should be consistent withe the Grid.
irrigation
If specified, either an object with irrigation rates (units [/d]) as returned by setup.prop.1D from the package ReacTran,
a vector of length 100 with the irrigation rates defined at the layer centres, or one number with the constant rates.
If NULL, it is defined by the parameters irr, mixdepth and mixatt as:
irr * exp(-pmax(0, (x-mixdepth)/mixxatt)), where x is the distance, from the surface, of the layer centres.
Note that the irrigation values should be consistent withe the Grid.
surface
If specified, either an object with surface areas (units [cm2]) as returned by setup.prop.1D from the package ReacTran,
a vector of length 101 with the surface areas defined at the layer interfaces, or one number with the constant surface area.
If NULL, it is defined by the parameter gridtype, and the Grid as:
surface = rep(1, 101) for gridtype == 1, surface = rev(2*pi*Grid$x.int) for gridtype == 2 and surface = rev(pi*(Grid$x.int)^2) for gridtype == 3.
Note that the surface values should be consistent withe the Grid.
diffusionfactor
The multiplication factor necessary to go from molecular diffusion to effective sediment diffusion, i.e. that takes into account tortuosity.
If specified, either an object with these factors ([-]) as returned by setup.prop.1D from the package ReacTran,
a vector of length 101 with these factors defined at the layer interfaces, or one number with the constant factor.
If NULL, it is set equal to the porosity. Note that the factors should be consistent withe the Grid.
yini
The condition at which to inialise the dynamic simulation, i.e. a vector or matrix, with the values of
FDET, SDET, O2, NO3, NO2, NH3, ODU, PO4, FeP, CaP, DIC, Pads, each in 100 layers, and in that order.
If NULL, the default, then the steady-state solution based on the mean forcing is used (and obtained with CNPDIAsolve) .
perturbType
how to perturb, one of "mix", "deposit", "erode". Several options can be chosen, in which case the perturbations will be done in the order defined.
perturbTimes
times at which the perturbations should take place. Either one value, or a vector of the same length as perturbType.
perturbDepth, depth
the depth of the perturbation, in cm.
concfac
only when perturbType = "deposit": the factor at which the available concentration should be increased or decreased.
C
The concentration vector to be perturbed; a vector that is compatible with grid (i.e. has the same length as grid$x.mid).
BW
The concentration in the overlying water, one value.
grid
a list as generated with setup.grid.1D[ReacTran] that contains the grid definition
por
the sediment porosity; either as generated with setup.prop.1D[ReacTran],
or a vector of length = length(C), or one value.
verbose
If TRUE, will write progession to the screen .
out
an output object returned by CNPDIAperturb or CNPDIAdyna.
which
if not NULL, a vector with names of the species from which to return the fluxes.
...
Any argument passed to the dynamic solver (ode.1D[deSolve])
Details
Several parameters can also be described as forcing functions. They are:
Cflux, FePflux, CaPflux, O2bw, NO3bw, NO2bw, NH3bw, ODUbw, PO4bw, DICbw, w,
biot, irr, rFast, rSlow, pFast, MPBprod, gasflux, Hwater.
The forcing functions are prescribed as a list that either contains a data series or specifies a periodic signal.
The list is defined as: list(data = NULL, amp = 0, period = 365, phase = 0, pow = 1, min = 0)
Forcing functions a data series are set with item data contains time series for the parameter - a matrix with times (first column) and values, second column. The values should be in the same units as the parameters.
The time series should embrace both arguments times and spinup.
if a periodic signal, the list should contain amp, period, phase, pow and min: parameters determining the periodicity of the seasonal signal in the same units as the parameters.
From this the forcing function time series is estimated, e.g. for CfluxForc as: max(min, Cflux*(1 + (amp*sin((times-phase)/period*2*pi))^pow), where Cflux is the parameter value. Used only if data is NULL. If amp = 0, or pow = 0, then the forcing will be kept constant and equal to the parameter value.
Value
CNPDIAperturb returns a matrix of type deSolve, as generated by the
solver ode.1D from R-package deSolve.
It contains several output columns, the first is time. The meaning and units of these columns can be assessed via the R-functions:
CNPDIAsvar(), CNPDIA1D(), CNPDIA0D(). See CNPDIA0D.
The instantaneous release/gain is saved in the attribute perturbFluxes and the settings in attribute perturbSettings. They can be retrieved with functions
CNPDIAperturbFluxes, and CNPDIAperturbSettings
Functions depositLiquid, depositSolid, mixLiquid, mixSolid, erodeLiquid, erodeSolid return
a list, with the values:
-
C, the altered concentration profile
-
Flux, the instantaneous gain in mass, estimated as (integral(Cnew) - integral(C)).
Note
The model application starts by estimating the steady-state condition
of the model. This steady-state condition is then used as a starting
condition for a dynamic simulation, with perturbations as provided in perturbTimes.
Mixing will homogenise the perturbed depth of the sediment (perturbType = "mix").
Erosion will remove the perturbed depth of the sediment (perturbType = "erode".
Deposition will add a layer of sediment (perturbType = "deposit".
All these events can be combined; the sequence of events is as provided, i.e.
perturbType = c("mix", "erode") will not give the same results as perturbType = c("erode", "mix").
Author(s)
Karline Soetaert
References
Soetaert K, PMJ Herman and JJ Middelburg, 1996a.
A model of early diagenetic processes from the shelf to abyssal depths.
Geochimica Cosmochimica Acta, 60(6):1019-1040.
Soetaert K, PMJ Herman and JJ Middelburg, 1996b.
Dynamic response of deep-sea sediments to seasonal variation: a model.
Limnol. Oceanogr. 41(8): 1651-1668.
Examples
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# ========================================
# One perturbation at the start
# ========================================
out <- CNPDIAperturb()
par(mar = c(3,3,3,3))
image2D(out, ylim = c(20, 0), mfrow = c(4, 3))
# ========================================
# Mixing at selected times
# ========================================
out2 <- CNPDIAperturb(perturbTime = c(0, 100, 200, 300),
perturbType = "mix", perturbDepth = 10)
image2D(out2, ylim = c(20, 0), mfrow = c(4, 3))
CNPDIAbudgetO2(out)
# ========================================
# Erosion at selected times
# ========================================
out3 <- CNPDIAperturb(perturbTime = c(0, 100, 200, 300),
perturbType = "erode", perturbDepth = 5)
image2D(out3, ylim = c(20, 0), mfrow = c(4, 3))
(PertFluxes <- CNPDIAperturbFluxes(out3))
CNPDIAperturbSettings(out3)
# ========================================
# Several subsequent perturbations
# ========================================
out4 <- CNPDIAperturb(perturbTime = c(0, 100, 200, 300),
perturbType = c("mix", "erode"), perturbDepth = c(10, 5))
image2D(out4, ylim = c(20, 0), mfrow = c(4, 3))
# ========================================
# Create perturbation profiles
# ========================================
# create reference solution
pm <- par(mfrow = c(1, 2))
DIA <- CNPDIAsolve()
# ------------------------
# perturb solid fraction
# ------------------------
SDET <- DIA$y[,"SDET"]
Grid <- DIA$Grid
por <- DIA$porosity
# perturb it
mix <- mixSolid (SDET, grid = Grid, por = por)
deposit <- depositSolid(SDET, grid = Grid, por = por)
erode <- erodeSolid (SDET, grid = Grid, por = por)
matplot(x = cbind(SDET, mix$C, erode$C, deposit$C), main = "Solid",
y = Grid$x.mid, type = "l", lwd = 3, ylim = c(20, 0))
legend("bottomright", col = 1:4, lty = 1:4,
legend = c("default", "mix", "erode", "deposit"))
cat("instantaneous fluxes, nmol/cm2\n", "mixing: ", mix$Flux,
"erosion: ", erode$Flux, "deposition: ", deposit$Flux, "\n")
# ------------------------
# perturb liquid fraction
# ------------------------
NO3 <- DIA$y[,"NO3"]
Grid <- DIA$Grid
por <- DIA$porosity
# perturb it
mix <- mixLiquid (NO3, grid = Grid, BW = 10, por = por)
deposit <- depositLiquid(NO3, grid = Grid, BW = 10, por = por)
erode <- erodeLiquid (NO3, grid = Grid, por = por)
matplot(x = cbind(NO3, mix$C, erode$C, deposit$C), main = "Liquid",
y = Grid$x.mid, type = "l", lwd = 3, ylim = c(20, 0))
legend("bottomright", col = 1:4, lty = 1:4,
legend = c("default", "mix", "erode", "deposit"))
cat("instantaneous fluxes, nmol/cm2\n", "mixing: ", mix$Flux,
"erosion: ", erode$Flux, "deposition: ", deposit$Flux)
par(mfrow = pm)
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Description Usage Arguments Details Value Note Author(s) References Examples
Description
CNPDIAperturb dynamically runs the CNPDIA model with event-like perturbations.
CNPDIAperturbSettings and CNPDIAperturbFluxes retrieve the settings and perturbation fluxes.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | CNPDIAperturb (parms = list(), times = 0:365, spinup = NULL, yini = NULL,
gridtype = 1, Grid = NULL, porosity = NULL, bioturbation = NULL,
irrigation = NULL, surface = NULL, diffusionfactor = NULL,
dynamicbottomwater = FALSE, perturbType = "mix",
perturbTimes = seq(from = 0, to = max(times), by = 365),
perturbDepth = 5, concfac = 1,
CfluxForc = NULL, FePfluxForc = NULL, CaPfluxForc = NULL,
O2bwForc = NULL, NO3bwForc = NULL, NO2bwForc = NULL,
NH3bwForc = NULL, ODUbwForc = NULL, PO4bwForc = NULL,
DICbwForc = NULL, wForc = NULL, biotForc = NULL,
irrForc = NULL, rFastForc = NULL, rSlowForc = NULL,
pFastForc = NULL, MPBprodForc = NULL, gasfluxForc = NULL,
HwaterForc = NULL, ratefactor = NULL, verbose = FALSE, ...)
mixSolid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5)
mixLiquid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5, BW)
erodeSolid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5)
erodeLiquid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5)
depositSolid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5, concfac = 1)
depositLiquid (C, depth = 5, grid = setup.grid.1D(N = 100, L = 30),
por = 0.5, BW)
CNPDIAperturbFluxes(out, which = NULL)
CNPDIAperturbSettings(out)
|
Arguments
parms |
A list with parameter names and values. Possible parameters are:
See details of CNPDIAsolve. |
gridtype |
Type of grid: |
times |
Output times for the dynamic run |
spinup |
Spinput times for the dynamic run; not used for output; the outputted simulation starts from the final values of the spinup run. |
CfluxForc, FePfluxForc, CaPfluxForc |
|
O2bwForc, NO3bwForc, NO2bwForc, NH3bwForc, ODUbwForc, PO4bwForc, DICbwForc |
|
wForc, biotForc, irrForc |
|
rFastForc, rSlowForc, pFastForc, MPBprodForc |
|
gasfluxForc |
|
HwaterForc |
|
dynamicbottomwater |
If TRUE, then the concentrations in the water overlying the sediment will also be dynamically described,
and with water height equal to |
ratefactor |
|
Grid |
If specified: either an object, as returned by |
porosity |
If specified, either an object with porosities ([-]) as returned by |
bioturbation |
If specified, either an object with bioturbation rates (units [cm2/d]) as returned by |
irrigation |
If specified, either an object with irrigation rates (units [/d]) as returned by |
surface |
If specified, either an object with surface areas (units [cm2]) as returned by Note that the surface values should be consistent withe the |
diffusionfactor |
The multiplication factor necessary to go from molecular diffusion to effective sediment diffusion, i.e. that takes into account tortuosity.
If specified, either an object with these factors ([-]) as returned by |
yini |
The condition at which to inialise the dynamic simulation, i.e. a vector or matrix, with the values of
|
perturbType |
how to perturb, one of "mix", "deposit", "erode". Several options can be chosen, in which case the perturbations will be done in the order defined. |
perturbTimes |
times at which the perturbations should take place. Either one value, or a vector of the same length as |
perturbDepth, depth |
the depth of the perturbation, in cm. |
concfac |
only when perturbType = "deposit": the factor at which the available concentration should be increased or decreased. |
C |
The concentration vector to be perturbed; a vector that is compatible with |
BW |
The concentration in the overlying water, one value. |
grid |
a list as generated with setup.grid.1D[ReacTran] that contains the grid definition |
por |
the sediment porosity; either as generated with setup.prop.1D[ReacTran],
or a vector of length = |
verbose |
If TRUE, will write progession to the screen . |
out |
an output object returned by CNPDIAperturb or CNPDIAdyna. |
which |
if not |
... |
Any argument passed to the dynamic solver (ode.1D[deSolve]) |
Details
Several parameters can also be described as forcing functions. They are:
Cflux, FePflux, CaPflux, O2bw, NO3bw, NO2bw, NH3bw, ODUbw, PO4bw, DICbw, w,
biot, irr, rFast, rSlow, pFast, MPBprod, gasflux, Hwater.
The forcing functions are prescribed as a list that either contains a data series or specifies a periodic signal.
The list is defined as: list(data = NULL, amp = 0, period = 365, phase = 0, pow = 1, min = 0)
Forcing functions a data series are set with item
datacontains time series for the parameter - a matrix with times (first column) and values, second column. The values should be in the same units as the parameters.The time series should embrace both arguments
timesandspinup.if a periodic signal, the list should contain
amp, period, phase, powandmin: parameters determining the periodicity of the seasonal signal in the same units as the parameters. From this the forcing function time series is estimated, e.g. for CfluxForc as:max(min, Cflux*(1 + (amp*sin((times-phase)/period*2*pi))^pow), whereCfluxis the parameter value. Used only ifdataisNULL. Ifamp= 0, orpow= 0, then the forcing will be kept constant and equal to the parameter value.
Value
CNPDIAperturb returns a matrix of type deSolve, as generated by the
solver ode.1D from R-package deSolve.
It contains several output columns, the first is time. The meaning and units of these columns can be assessed via the R-functions:
CNPDIAsvar(), CNPDIA1D(), CNPDIA0D(). See CNPDIA0D.
The instantaneous release/gain is saved in the attribute perturbFluxes and the settings in attribute perturbSettings. They can be retrieved with functions
CNPDIAperturbFluxes, and CNPDIAperturbSettings
Functions depositLiquid, depositSolid, mixLiquid, mixSolid, erodeLiquid, erodeSolid return
a list, with the values:
-
C, the altered concentration profile -
Flux, the instantaneous gain in mass, estimated as (integral(Cnew) - integral(C)).
Note
The model application starts by estimating the steady-state condition
of the model. This steady-state condition is then used as a starting
condition for a dynamic simulation, with perturbations as provided in perturbTimes.
Mixing will homogenise the perturbed depth of the sediment (perturbType = "mix").
Erosion will remove the perturbed depth of the sediment (perturbType = "erode".
Deposition will add a layer of sediment (perturbType = "deposit".
All these events can be combined; the sequence of events is as provided, i.e.
perturbType = c("mix", "erode") will not give the same results as perturbType = c("erode", "mix").
Author(s)
Karline Soetaert
References
Soetaert K, PMJ Herman and JJ Middelburg, 1996a. A model of early diagenetic processes from the shelf to abyssal depths. Geochimica Cosmochimica Acta, 60(6):1019-1040.
Soetaert K, PMJ Herman and JJ Middelburg, 1996b. Dynamic response of deep-sea sediments to seasonal variation: a model. Limnol. Oceanogr. 41(8): 1651-1668.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 | # ========================================
# One perturbation at the start
# ========================================
out <- CNPDIAperturb()
par(mar = c(3,3,3,3))
image2D(out, ylim = c(20, 0), mfrow = c(4, 3))
# ========================================
# Mixing at selected times
# ========================================
out2 <- CNPDIAperturb(perturbTime = c(0, 100, 200, 300),
perturbType = "mix", perturbDepth = 10)
image2D(out2, ylim = c(20, 0), mfrow = c(4, 3))
CNPDIAbudgetO2(out)
# ========================================
# Erosion at selected times
# ========================================
out3 <- CNPDIAperturb(perturbTime = c(0, 100, 200, 300),
perturbType = "erode", perturbDepth = 5)
image2D(out3, ylim = c(20, 0), mfrow = c(4, 3))
(PertFluxes <- CNPDIAperturbFluxes(out3))
CNPDIAperturbSettings(out3)
# ========================================
# Several subsequent perturbations
# ========================================
out4 <- CNPDIAperturb(perturbTime = c(0, 100, 200, 300),
perturbType = c("mix", "erode"), perturbDepth = c(10, 5))
image2D(out4, ylim = c(20, 0), mfrow = c(4, 3))
# ========================================
# Create perturbation profiles
# ========================================
# create reference solution
pm <- par(mfrow = c(1, 2))
DIA <- CNPDIAsolve()
# ------------------------
# perturb solid fraction
# ------------------------
SDET <- DIA$y[,"SDET"]
Grid <- DIA$Grid
por <- DIA$porosity
# perturb it
mix <- mixSolid (SDET, grid = Grid, por = por)
deposit <- depositSolid(SDET, grid = Grid, por = por)
erode <- erodeSolid (SDET, grid = Grid, por = por)
matplot(x = cbind(SDET, mix$C, erode$C, deposit$C), main = "Solid",
y = Grid$x.mid, type = "l", lwd = 3, ylim = c(20, 0))
legend("bottomright", col = 1:4, lty = 1:4,
legend = c("default", "mix", "erode", "deposit"))
cat("instantaneous fluxes, nmol/cm2\n", "mixing: ", mix$Flux,
"erosion: ", erode$Flux, "deposition: ", deposit$Flux, "\n")
# ------------------------
# perturb liquid fraction
# ------------------------
NO3 <- DIA$y[,"NO3"]
Grid <- DIA$Grid
por <- DIA$porosity
# perturb it
mix <- mixLiquid (NO3, grid = Grid, BW = 10, por = por)
deposit <- depositLiquid(NO3, grid = Grid, BW = 10, por = por)
erode <- erodeLiquid (NO3, grid = Grid, por = por)
matplot(x = cbind(NO3, mix$C, erode$C, deposit$C), main = "Liquid",
y = Grid$x.mid, type = "l", lwd = 3, ylim = c(20, 0))
legend("bottomright", col = 1:4, lty = 1:4,
legend = c("default", "mix", "erode", "deposit"))
cat("instantaneous fluxes, nmol/cm2\n", "mixing: ", mix$Flux,
"erosion: ", erode$Flux, "deposition: ", deposit$Flux)
par(mfrow = pm)
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