Calculates the carbonate chemistry after changes in pCO2 generated by gas bubbling
pgas(flag, var1, var2, pCO2g, S=35, T=20, P=0, Pt=0, Sit=0, k1k2="x",
kf="x", ks="d", pHscale="T", b="u74", eos = "eos80", long = 1e+20, lat = 1e+20)The function returns a data frame containing the following columns:
The initial or final state water
Salinity
Temperature in degrees Celsius
Pressure in bar
pH
CO2 concentration (mol/kg)
pCO2, CO2 partial pressure (\(\mu\)atm)
fCO2, CO2 fugacity (\(\mu\)atm)
HCO3 concentration (mol/kg)
CO3 concentration (mol/kg)
DIC concentration (mol/kg)
ALK, total alkalinity (mol/kg)
Omega aragonite, aragonite saturation state
Omega calcite, calcite saturation state
select the couple of variables available. The flags which can be used are:
flag = 1 pH and CO2 given
flag = 2 CO2 and HCO3 given
flag = 3 CO2 and CO3 given
flag = 4 CO2 and ALK given
flag = 5 CO2 and DIC given
flag = 6 pH and HCO3 given
flag = 7 pH and CO3 given
flag = 8 pH and ALK given
flag = 9 pH and DIC given
flag = 10 HCO3 and CO3 given
flag = 11 HCO3 and ALK given
flag = 12 HCO3 and DIC given
flag = 13 CO3 and ALK given
flag = 14 CO3 and DIC given
flag = 15 ALK and DIC given
flag = 21 pCO2 and pH given
flag = 22 pCO2 and HCO3 given
flag = 23 pCO2 and CO3 given
flag = 24 pCO2 and ALK given
flag = 25 pCO2 and DIC given
Value of the first variable in mol/kg, except for pH and for pCO2 in \(\mu\)atm
Value of the second variable in mol/kg, except for pH
CO2 partial pressure of the gas used for bubbling in \(\mu\)atm
Salinity
Temperature in degrees Celsius
Hydrostatic pressure in bar (surface = 0)
Concentration of total phosphate in mol/kg
Concentration of total silicate in mol/kg
"cw" for using K1 and K2 from Cai & Wang (1998), "l" from Lueker et al. (2000), "m02" from Millero et al. (2002), "m06" from Millero et al. (2006), "m10" from Millero (2010), "mp2" from Mojica Prieto et al. (2002), "p18" from Papadimitriou et al. (2018), "r" from Roy et al. (1993), "sb21" from Shockman & Byrne (2021), "s20" from Sulpis et al. (2020), and "w14" from Waters et al. (2014). "x" is the default flag; the default value is then "l", except if T is outside the range 2 to 35oC and/or S is outside the range 19 to 43. In these cases, the default value is "w14".
"pf" for using Kf from Perez and Fraga (1987) and "dg" for using Kf from Dickson and Riley (1979 in Dickson and Goyet, 1994). "x" is the default flag; the default value is then "pf", except if T is outside the range 9 to 33oC and/or S is outside the range 10 to 40. In these cases, the default is "dg".
"d" for using Ks from Dickon (1990), "k" for using Ks from Khoo et al. (1977), default is "d"
"T" for the total scale, "F" for the free scale and "SWS" for using the seawater scale, default is "T" (total scale)
Concentration of total boron. "l10" for the Lee et al. (2010) formulation or "u74" for the Uppstrom (1974) formulation, default is "u74".
"teos10" to specify T and S according to Thermodynamic Equation Of Seawater - 2010 (TEOS-10); "eos80" to specify T and S according to EOS-80.
longitude of data point, used when eos parameter is "teos10" as a conversion parameter from absolute to practical salinity.
latitude of data point, used when eos parameter is "teos10".
Jean-Pierre Gattuso and Heloise Lavigne jean-pierre.gattuso@imev-mer.fr
The Lueker et al. (2000) constants for K1 and K2, the Perez and Fraga (1987) constant for Kf and the Dickson (1990) constant for Ks are recommended by Dickson et al. (2007). It is, however, critical to consider that each formulation is only valid for specific ranges of temperature and salinity:
For K1 and K2:
Cai and Wang (1998): S ranging between 0 and 40 and T ranging between 0.2 and 30oC.
Lueker et al. (2000): S ranging between 19 and 43 and T ranging between 2 and 35oC.
Millero et al. (2002): S ranging from 34 to 37 and T ranging between -1.6 and 35oC.
Millero et al. (2006): S ranging between 0.1 and 50 and T ranging between 1 and 50oC.
Millero (2010): S ranging between 1 and 50 and T ranging between 0 and 50oC. Millero (2010) provides a K1 and K2 formulation for the seawater, total and free pH scales. Therefore, when this method is used and if P=0, K1 and K2 are computed with the formulation corresponding to the pH scale given in the flag "pHscale".
Mojica Prieto et al. (2002): S ranging from 5 to 42 and T ranging between 0 and 45oC.
Papadimitriou et al. (2018): S ranging from 33 to 100 and T ranging between -6 to 25oC.
Roy et al. (1993): S ranging between 5 and 45 and T ranging between 0 and 45oC.
Shockman & Byrne (2021): for K2, S ranging from 19.6 to 41 and T ranging between 15 to 35oC. For K1, formulation is that of Waters et al.
Sulpis et al. (2020): S ranging from 30.7 to 37.6 and T ranging between -1.7 to 31.8oC.
Waters et al.(2014): S ranging between 1 and 50 and T ranging between 0 and 50oC. Waters (2014) provides a K1 and K2 formulation for the seawater, total and free pH scales. Therefore, when this method is used and if P=0, K1 and K2 are computed with the formulation corresponding to the pH scale given in the flag "pHscale".
For Kf:
Perez and Fraga (1987): S ranging between 10 and 40 and T ranging between 9 and 33oC.
Dickson and Riley (1979 in Dickson and Goyet, 1994): S ranging between 0 and 45 and T ranging between 0 and 45oC.
For Ks:
Dickson (1990): S ranging between 5 and 45 and T ranging between 0 and 45oC.
Khoo et al. (1977): S ranging between 20 and 45 and T ranging between 5 and 40oC.
The arguments can be given as a unique number or as vectors. If the lengths of the vectors are different, the longer vector is retained and only the first value of the other vectors is used. It is recommended to use either vectors with the same dimension or one vector for one argument and numbers for the other arguments.
Pressure corrections and pH scale:
For K0, the pressure correction term of Weiss (1974) is used.
For K1, K2, pK1, pK2, pK3, Kw, Kb, Khs and Ksi, the pressure correction was applied on the seawater scale. Hence, if needed, values were first transformed from the total scale to the seawater scale, the pressure correction applied as described by Millero (1995), and the value was transformed back to the required scale (T, F or SWS).
For Kf, the pressure correction was applied on the free scale. The formulation of Dickson and Riley (1979 in Dickson and Goyet, 1994) provides Kf on the free scale but that of Perez and Fraga (1987) provides it on the total scale. Hence, in that case, Kf was first transformed from the total scale to the free scale. With both formulations, the pressure correction was applied as described by Millero (1995), and the value was transformed back to the required scale (T, F or SWS).
For Ks, the pressure correction was applied on the free scale. The pressure correction was applied as described by Millero (1995), and the value was transformed back to the required scale (T, F or SWS).
For Kn, The pressure correction was applied on the seawater scale. The pressure correction was applied as described by Millero (1995), and the value was transformed back to the required scale (T, F or SWS).
long and lat are used as conversion parameters from absolute to practical salinity: when seawater is not of standard composition, practical salinity alone is not sufficient to compute absolute salinity and vice-versa. One needs to know the density. When long and lat are given, density is inferred from WOA silicate concentration at given location. When they are not, an arbitrary geographic point is chosen: mid equatorial Atlantic. Note that this implies an error on computed salinity up to 0.02 g/kg.
Cai W. J., and Wang Y., 1998. The chemistry, fluxes, and sources of carbon dioxide in the estuarine waters of the Satilla and Altamaha Rivers, Georgia. Limnology and Oceanography 43, 657-668.
Dickson A. G. and Riley J. P., 1979 The estimation of acid dissociation constants in seawater media from potentiometric titrations with strong base. I. The ionic product of water. Marine Chemistry 7, 89-99.
Dickson A. G., 1990 Standard potential of the reaction: AgCI(s) + 1/2H2(g) = Ag(s) + HCI(aq), and the standard acidity constant of the ion HSO4 in synthetic sea water from 273.15 to 318.15 K. Journal of Chemical Thermodynamics 22, 113-127.
Dickson A. G., Sabine C. L. and Christian J. R., 2007 Guide to best practices for ocean CO2 measurements. PICES Special Publication 3, 1-191.
Gattuso J.-P. and Lavigne H, 2009 Perturbation experiments to investigate the impact of ocean acidification: approaches and software tools. Biogeosciences 6, 4413-4439.
Khoo H. K., Ramette R. W., Culberson C. H. and Bates R. G., 1977 Determination of Hydrogen Ion Concentration in Seawater from 5 to 40oC: Standard Potentials at Salinities from 20 to 45. Analytical Chemistry 49, 29-34.
Lee K., Tae-Wook K., Byrne R.H., Millero F.J., Feely R.A. and Liu Y-M, 2010 The universal ratio of the boron to chlorinity for the North Pacific and North Atlantoc oceans. Geochimica et Cosmochimica Acta 74 1801-1811.
Millero F. J., 1995 Thermodynamics of the carbon dioxide system in the oceans. Geochimica Cosmochimica Acta 59: 661-677.
Millero F. J., 2010 Carbonate constant for estuarine waters. Marine and Freshwater Research 61: 139-142.
Millero F. J., Graham T. B., Huang F., Bustos-Serrano H. and Pierrot D., 2006. Dissociation constants of carbonic acid in seawater as a function of salinity and temperature. Marine Chemistry 100, 80-84.
Orr J. C., Epitalon J.-M. and Gattuso J.-P., 2015. Comparison of seven packages that compute ocean carbonate chemistry. Biogeosciences 12, 1483-1510.
Uppstrom L.R., 1974 The boron/chlorinity ratio of the deep-sea water from the Pacific Ocean. Deep-Sea Research I 21 161-162.
Waters, J., Millero, F. J., and Woosley, R. J., 2014. Corrigendum to ``The free proton concentration scale for seawater pH'', [MARCHE: 149 (2013) 8-22], Marine Chemistry 165, 66-67.
pgas(flag=15, var1=2302e-6, var2=2050e-6, pCO2g=750, S=35, T=20, P=0,
Pt=0, Sit=0, pHscale="T", kf="pf", k1k2="l", ks="d", b="u74")
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