Description Usage Arguments Details Value Author(s) References See Also Examples
Calculates the molecular and ionic diffusion coefficients in m2/sec, for several inorganic species in seawater at a given salinity, temperature, and pressure.
Based on Chapter 4 in Boudreau (1997)
1 2 3 4 5 6 7 8 9 10 11 | diffcoeff(S = 35, t = 25, P = 1.013253,
species = c("H2O", "O2", "CO2", "H2", "CH4", "DMS",
"He", "Ne", "Ar", "Kr", "Xe", "Rn",
"N2", "H2S", "NH3", "NO", "N2O", "CO", "SO2",
"OH", "F", "Cl", "Br", "I",
"HCO3", "CO3", "H2PO4", "HPO4", "PO4",
"HS", "HSO3", "SO3", "HSO4", "SO4", "IO3", "NO2", "NO3",
"H", "Li", "Na", "K", "Cs","Ag","NH4",
"Ca", "Mg", "Fe", "Mn", "Ba", "Be", "Cd", "Co",
"Cu", "Hg", "Ni", "Sr", "Pb", "Ra", "Zn", "Al", "Ce",
"La", "Pu", "H3PO4", "BOH3", "BOH4", "H4SiO4"))
|
S |
Salinity, -, |
t |
Temperature, degrees C, |
P |
True pressure, bar, |
species |
character vector with the names of the chemical species whose diffusion coefficient should be calculated. |
To correct for salinity, the Stokes-Einstein relationship is used. This is not quite accurate, but is at least consistent.
H_3PO_4 : Least (1984) determined D(H3PO4) at 25 deg C and 0 S. Assume that this value can be scaled by the Stokes-Einstein relationship to any other temperature.
B(OH)_3 : Mackin (1986) determined D(B(OH)3) at 25 deg C and about 29.2 S. Assume that this value can be scaled by the Stokes-Einstein relationship to any other temperature.
B(OH)_4 : No information on this species. Boudreau and Canfield (1988) assume it is 12.5% smaller than B(OH)3.
H_4SiO_4 : Wollast and Garrels (1971) found D(H4SiO4) at 25 deg C and 36.1 ppt S. Assume that this value can be scaled by the Stokes-Einstein relationship to any other temperature.
Arguments salinity, temperature or pressure can be vectors. In order to avoid
confusion, S, t and P must have either same length or length 1. More flexible
combinationsare of course possible with expand.grid
A data.frame
with the diffusion coefficients m2/sec
of the selected chemical species.
Filip Meysman <filip.meysman@nioz.nl>, Karline Soetaert <karline.soetaert@nioz.nl>
Based on Chapter 4 in Boudreau (1997) :
Boudreau BP, 1997. Diagenetic Models and their Implementation. Modelling Transport and Reactions in Aquatic Sediments. Springer. Berlin.
who cites:
for self-diffusion coefficient H2O:
Cohen MH and Turnbull D. 1959. Molecular transport in liquids and glasses. Journal of chemical physics 31 (5): 1164-1169
Krynicki K, Green CD and Sawyer DW, 1978. Pressure and temperature-dependence of self-diffusion in water. Faraday discussions 66: 199-208
for gases O2 and CO2:
Novel relation by Boudreau (1997) based on new compilation of data
for gases He, Ne, Kr, Xe, Rn, H2, CH4:
Jahne B, Heinz G, and Dietrich W, 1987. Measurements of the diffusion coefficients of sparingly soluble gases in water. J. Geophys. Res., 92:10,767-10,776.
for Ar:
Ohsumi T and Horibe Y, 1984. Diffusivity of He and Ar in deep-sea sediments, Earth and Planetary Science Letters 70, 61-68.
for DMS:
Saltzman ES, King DB, Holmen K, and Leck C, 1993. Experimental Determination of the Diffusion Coefficient of Dimethylsulfide in Water, J. Geophys. Res., 98(C9), 16, 481-486.
for other gases (N2, H2S, NH3, NO, N2O, CO, SO2):
Wilke CR and Chang P, 1955. Correlation of diffusion coefficients in dilute solutions. Aiche journal 1 (2): 264-270
with the correction proposed by
Hayduk W and Laudie H, 1974. Prediction of diffusion-coefficients for nonelectrolytes in dilute aqueous-solutions. Aiche journal 20 (3): 611-615
for ions:
Hayduk W and Laudie H, 1974. Prediction of diffusion-coefficients for nonelectrolytes in dilute aqueous-solutions. Aiche journal 20 (3): 611-615
for H3PO4, B(OH)3, B(OH)4, H4SiO4 : see details
coriolis
, viscosity
,
ssd2rad
, vertmean
,
gravity
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 | diffcoeff(S = 15, t = 15)*1e4*3600*24 # cm2/day
diffcoeff(t = 10, species = "O2") # m2/s
difftemp <- diffcoeff(t = 0:30)[,1:13]
matplot(0:30, difftemp, xlab = "temperature", ylab = "m2/s",
main = "Molecular/ionic diffusion", type = "l",
col = 1:13, lty = 1:13)
legend("topleft", ncol = 2, cex = 0.8, title = "mean",
col = 1:13, lty = 1:13,
legend = cbind(names(difftemp),
format(colMeans(difftemp), digits = 4)))
## vector-valued salinity
select <- c("O2", "CO2", "NH3", "NH4", "NO3")
diffsal <- diffcoeff(S = 0:35, species = select)
matplot(0:35, diffsal, xlab = "salinity", ylab = "m2/s",
main = "Molecular/ionic diffusion", type = "l",
col = 1:length(select), lty = 1:length(select))
legend("topleft", ncol = 2, cex = 0.8, title = "mean",
col = 1:length(select), lty = 1:length(select),
legend = cbind(select, format(colMeans(diffsal), digits = 4)))
## vector-valued temperature
difftemp <- diffcoeff(S = 1, t=1:20, species = select)
matplot(1:20, difftemp, xlab = "temperature", ylab = "m2/s",
main = "Molecular/ionic diffusion", type = "l",
col = 1:length(select), lty = 1:length(select))
legend("topleft", ncol = 2, cex = 0.8, title = "mean",
col = 1:length(select), lty = 1:length(select),
legend = cbind(select, format(colMeans(difftemp), digits = 4)))
## combination of S and t
diffsaltemp <- diffcoeff(S = rep(c(1, 35), each = 20),
t = rep(1:20, 2), species = select)
|
Loading required package: shape
Loading required package: seacarb
Loading required package: oce
Loading required package: testthat
Loading required package: gsw
Attaching package: 'marelac'
The following objects are masked from 'package:oce':
coriolis, gravity
H2O O2 CO2 H2 CH4 DMS He Ne
1 1.478897 1.570625 1.241991 3.429952 1.198804 0.8770747 5.186823 2.749411
Ar Kr Xe Rn N2 H2S NH3 NO
1 1.554712 1.166917 0.9126865 0.8079991 1.190863 1.180685 1.467438 1.500764
N2O CO SO2 OH F Cl Br I
1 1.164872 1.195 1.03556 3.543847 0.9577852 1.354384 1.391657 1.364436
HCO3 CO3 H2PO4 HPO4 PO4 HS HSO3 SO3
1 0.7693272 0.6126977 0.6168857 0.495435 0.3991121 1.214088 0.8836584 0.7379176
HSO4 SO4 IO3 NO2 NO3 H Li Na
1 0.8874275 0.700226 0.7069267 1.278582 1.283189 6.510175 0.6738419 0.8807268
K Cs Ag NH4 Ca Mg Fe Mn
1 0.8807268 1.385375 1.106039 1.314599 0.5264259 0.4682133 0.4657005 0.4610938
Ba Be Cd Co Cu Hg Ni
1 0.5611859 0.3911549 0.4682133 0.4682133 0.4824524 0.5653738 0.4447608
Sr Pb Ra Zn Al Ce La Pu
1 0.5214003 0.62233 0.5775189 0.4669569 0.4497863 0.4116759 0.4037188 0.3777535
H3PO4 BOH3 BOH4 H4SiO4
1 0.555835 0.7602404 0.6652104 0.6882134
O2
1 1.539783e-09
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