def CBsys(
pHtot=None,
DIC=None,
CO2=None,
HCO3=None,
CO3=None,
TA=None,
fCO2=None,
pCO2=None,
BT=None,
BO3=None,
BO4=None,
ABT=None,
ABO3=None,
ABO4=None,
dBT=None,
dBO3=None,
dBO4=None,
alphaB=None,
T_in=25.0,
S_in=35.0,
P_in=None,
T_out=None,
S_out=None,
P_out=None,
Ca=None,
Mg=None,
TP=0.0,
TSi=0.0,
TS=None,
TF=None,
pHsws=None,
pHfree=None,
pHNBS=None,
Ks=None,
pdict=None,
unit="umol",
):
"""
Calculate carbon, boron and boron isotope chemistry of seawater from a minimal parameter set.
Constants calculated by MyAMI model (Hain et al, 2015; doi:10.1002/2014GB004986).
Speciation calculations from Zeebe & Wolf-Gladrow (2001; ISBN:9780444509468) Appendix B
pH is Total scale.
Inputs must either be single values, arrays of equal length or a mixture of both.
If you use arrays of unequal length, it won't work.
Note: Special Case! If pH is not known, you must provide either:
- Two of [DIC, CO2, HCO3, CO3], and one of [BT, BO3, BO4]
- One of [DIC, CO2, HCO3, CO3], and TA and BT
- Two of [BT, BO3, BO4] and one of [DIC, CO2, HCO3, CO3]
Isotopes will only be calculated if one of [ABT, ABO3, ABO4, dBT, dBO3, dBO4]
is provided.
Error propagation:
If inputs are ufloat or uarray (from uncertainties package) errors will
be propagated through all calculations, but:
**WARNING** Error propagation NOT IMPLEMENTED for carbon system calculations
with zero-finders (i.e. when pH is not given; cases 2-5 and 10-15).
Concentration Units
+++++++++++++++++++
* Ca and Mg must be in molar units.
* All other units must be the same, and can be specified in the 'unit' variable. Defaults to umolar.
* Isotopes can be in A (11B / BT) or d (delta). Either specified, both returned.
Parameters
----------
pH, DIC, CO2, HCO3, CO3, TA : array-like
Carbon system parameters. Two of these must be provided.
If TA is specified, a B species must also be specified.
pH, BT, BO3, BO4 : array-like
Boron system parameters. Two of these must be provided.
pH, ABT, ABO3, ABO4, dBT, dBO3, dBO4 : array-like
Boron isotope system parameters. pH and one other
parameter must be provided.
alphaB : array-like
Alpha value describing B fractionation (1.0XXX).
If missing, it's calculated using the temperature
sensitive formulation of Honisch et al (2008)
T, S : array-like
Temperature in Celcius and Salinity in PSU.
Used in calculating MyAMI constants.
P : array-like
Pressure in Bar.
Used in calculating MyAMI constants.
unit : str
Concentration units of C and B parameters (all must be in
the same units).
Can be 'mol', 'mmol', 'umol', 'nmol', 'pmol' or 'fmol'.
Used in calculating Alkalinity. Default is 'umol'.
Ca, Mg : arra-like
The [Ca] and [Mg] of the seawater, * in mol / kg *.
Used in calculating MyAMI constants.
Ks : dict
A dictionary of constants. Must contain keys
'K1', 'K2', 'KB' and 'KW'.
If None, Ks are calculated using MyAMI model.
pdict : dict
Optionally, you can provide some or all parameters as a dict,
with keys the same as the parameter names above. Any parameters
included in the dict will overwrite manually specified
parameters. This is particularly useful if you're including
this in other code.
Returns
-------
dict(/Bunch) containing all calculated parameters.
"""
# Bunch inputs
ps = Bunch(locals())
if isinstance(pdict, dict):
ps.update(pdict)
# convert unit to multiplier
udict = {
"mol": 1.0,
"mmol": 1.0e3,
"umol": 1.0e6,
"nmol": 1.0e9,
"pmol": 1.0e12,
"fmol": 1.0e15,
}
if isinstance(ps.unit, str):
ps.unit = udict[ps.unit]
elif isinstance(ps.unit, (int, float)):
ps.unit = unit
upar = [
"DIC",
"CO2",
"HCO3",
"CO3",
"TA",
"fCO2",
"pCO2",
"BT",
"BO3",
"BO4",
"TP",
"TSi",
]
for p in upar:
if ps[p] is not None:
ps[p] = np.divide(ps[p], ps.unit) # convert to molar
# reassign unit, convert back at end
orig_unit = ps.unit
ps.unit = 1.0
# Conserved seawater chemistry
if ps.TS is None:
ps.TS = calc_TS(ps.S_in)
if ps.TF is None:
ps.TF = calc_TF(ps.S_in)
# Calculate Ks
ps.Ks = calc_Ks(ps.T_in, ps.S_in, ps.P_in, ps.Mg, ps.Ca, ps.TS, ps.TF,
ps.Ks)
# Calculate pH scales (does nothing if none pH given)
ps.update(
calc_pH_scales(
ps.pHtot,
ps.pHfree,
ps.pHsws,
ps.pHNBS,
ps.TS,
ps.TF,
ps.T_in + 273.15,
ps.S_in,
ps.Ks,
))
# if fCO2 is given but CO2 is not, calculate CO2
if ps.CO2 is None:
if ps.fCO2 is not None:
ps.CO2 = fCO2_to_CO2(ps.fCO2, ps.Ks)
elif ps.pCO2 is not None:
ps.CO2 = fCO2_to_CO2(pCO2_to_fCO2(ps.pCO2, ps.T_in), ps.Ks)
# if no B info provided, assume modern conc.
nBspec = NnotNone(ps.BT, ps.BO3, ps.BO4)
if nBspec == 0:
ps.BT = calc_TB(ps.S_in)
elif isinstance(BT, (int, float)):
ps.BT = ps.BT * ps.S_in / 35.0
# count number of not None C parameters
nCspec = NnotNone(ps.DIC, ps.CO2, ps.HCO3, ps.CO3) # used below
# if pH is given, it's easy
if ps.pHtot is not None or nBspec == 2:
ps.update(
calc_B_species(pHtot=ps.pHtot,
BT=ps.BT,
BO3=ps.BO3,
BO4=ps.BO4,
Ks=ps.Ks))
ps.update(
calc_C_species(
pHtot=ps.pHtot,
DIC=ps.DIC,
CO2=ps.CO2,
HCO3=ps.HCO3,
CO3=ps.CO3,
TA=ps.TA,
fCO2=ps.fCO2,
pCO2=ps.pCO2,
T_in=ps.T_in,
BT=ps.BT,
TP=ps.TP,
TSi=ps.TSi,
TS=ps.TS,
TF=ps.TF,
Ks=ps.Ks,
))
# if not, this section works out the order that things should be calculated in.
# Special case: if pH is missing, must have:
# a) two C or one C and both TA and BT
# b) two B (above)
# c) one pH-dependent B, one pH-dependent C... But that's cray...
# (c not implemented!)
elif (nCspec == 2) | ((nCspec == 1) &
(NnotNone(ps.TA, ps.BT) == 2)): # case A
ps.update(
calc_C_species(
pHtot=ps.pHtot,
DIC=ps.DIC,
CO2=ps.CO2,
HCO3=ps.HCO3,
CO3=ps.CO3,
TA=ps.TA,
fCO2=ps.fCO2,
pCO2=ps.pCO2,
T_in=ps.T_in,
BT=ps.BT,
TP=ps.TP,
TSi=ps.TSi,
TS=ps.TS,
TF=ps.TF,
Ks=ps.Ks,
))
ps.update(
calc_B_species(pHtot=ps.pHtot,
BT=ps.BT,
BO3=ps.BO3,
BO4=ps.BO4,
Ks=ps.Ks))
# elif nBspec == 2: # case B -- moved up
# ps.update(calc_B_species(pHtot=ps.pHtot, BT=ps.BT, BO3=ps.BO3, BO4=ps.BO4, Ks=ps.Ks))
# ps.update(calc_C_species(pHtot=ps.pHtot, DIC=ps.DIC, CO2=ps.CO2,
# HCO3=ps.HCO3, CO3=ps.CO3, TA=ps.TA,
# fCO2=ps.fCO2, pCO2=ps.pCO2,
# T_in=ps.T_in, BT=ps.BT, TP=ps.TP, TSi=ps.TSi,
# TS=ps.TS, TF=ps.TF, Ks=ps.Ks)) # then C
else: # if neither condition is met, throw an error
raise ValueError(
("Impossible! You haven't provided enough parameters.\n" +
"If you don't know pH, you must provide either:\n" +
" - Two of [DIC, CO2, HCO3, CO3], and one of [BT, BO3, BO4]\n" +
" - One of [DIC, CO2, HCO3, CO3], and TA and BT\n" +
" - Two of [BT, BO3, BO4] and one of [DIC, CO2, HCO3, CO3]"))
ps["revelle_factor"] = calc_revelle_factor(
TA=ps.TA,
DIC=ps.DIC,
BT=ps.BT,
TP=ps.TP,
TSi=ps.TSi,
TS=ps.TS,
TF=ps.TF,
Ks=ps.Ks,
)
# If any isotope parameter specified, calculate the isotope systen.
if NnotNone(ps.ABT, ps.ABO3, ps.ABO4, ps.dBT, ps.dBO3, ps.dBO4) != 0:
ps.update(ABsys(pdict=ps))
# Calculate Isotopes
if ps.dBT is None and ps.dBO3 is None and ps.dBO4 is None:
ps.dBT = 0
# if deltas provided, calculate corresponding As
if ps.dBT is not None:
ps.ABT = d11_2_A11(ps.dBT)
if ps.dBO3 is not None:
ps.ABO3 = d11_2_A11(ps.dBO3)
if ps.dBO4 is not None:
ps.ABO4 = d11_2_A11(ps.dBO4)
# calculate alpha
ps.alphaB = alphaB_calc(ps.T_in)
if ps.pHtot is not None and ps.ABT is not None:
ps.H = ch(ps.pHtot)
elif ps.pHtot is not None and ps.ABO3 is not None:
ps.ABT = pH_ABO3(ps.pHtot, ps.ABO3, ps.Ks, ps.alphaB)
elif ps.pHtot is not None and ps.ABO4 is not None:
ps.ABT = pH_ABO3(ps.pHtot, ps.ABO4, ps.Ks, ps.alphaB)
else:
raise ValueError("pH must be determined to calculate isotopes.")
if ps.ABO3 is None:
ps.ABO3 = cABO3(ps.H, ps.ABT, ps.Ks, ps.alphaB)
if ps.ABO4 is None:
ps.ABO4 = cABO4(ps.H, ps.ABT, ps.Ks, ps.alphaB)
if ps.dBT is None:
ps.dBT = A11_2_d11(ps.ABT)
if ps.dBO3 is None:
ps.dBO3 = A11_2_d11(ps.ABO3)
if ps.dBO4 is None:
ps.dBO4 = A11_2_d11(ps.ABO4)
# clean up output
outputs = [
"BAlk",
"BT",
"CAlk",
"CO2",
"CO3",
"DIC",
"H",
"HCO3",
"HF",
"HSO4",
"Hfree",
"Ks",
"OH",
"PAlk",
"SiAlk",
"TA",
"TF",
"TP",
"TS",
"TSi",
"fCO2",
"pCO2",
"pHfree",
"pHsws",
"pHtot",
"pHNBS",
"BO3",
"BO4",
"ABO3",
"ABO4",
"dBO3",
"dBO4",
]
for k in outputs:
if not isinstance(ps[k], np.ndarray):
# convert all outputs to (min) 1D numpy arrays.
ps[k] = np.array(ps[k], ndmin=1)
# Handle Units
for p in upar + [
"CAlk", "BAlk", "PAlk", "SiAlk", "OH", "HSO4", "HF", "Hfree"
]:
ps[p] *= orig_unit # convert back to input units
# Recursive approach to calculate output params.
# if output conditions specified, calculate outputs.
if ps.T_out is not None or ps.S_out is not None or ps.P_out is not None:
if ps.T_out is None:
ps.T_out = ps.T_in
if ps.S_out is None:
ps.S_out = ps.S_in
if ps.P_out is None:
ps.P_out = ps.P_in
# assumes conserved alkalinity
out_cond = CBsys(
TA=ps.TA,
DIC=ps.DIC,
BT=ps.BT,
T_in=ps.T_out,
S_in=ps.S_out,
P_in=ps.P_out,
unit=ps.unit,
)
# Calculate pH scales (does nothing if no pH given)
out_cond.update(
calc_pH_scales(
out_cond.pHtot,
out_cond.pHfree,
out_cond.pHsws,
out_cond.pHNBS,
out_cond.TS,
out_cond.TF,
out_cond.T_in + 273.15,
out_cond.S_in,
out_cond.Ks,
))
# rename parameters in output conditions
ps.update({k + "_out": out_cond[k] for k in outputs})
# remove some superfluous outputs
rem = ["pdict", "unit"]
for r in rem:
if r in ps:
del ps[r]
return ps
def Csys(
pHtot=None,
DIC=None,
CO2=None,
HCO3=None,
CO3=None,
TA=None,
fCO2=None,
pCO2=None,
BT=None,
Ca=None,
Mg=None,
T_in=25.0,
S_in=35.0,
P_in=None,
T_out=None,
S_out=None,
P_out=None,
TP=0.0,
TSi=0.0,
TS=None,
TF=None,
pHsws=None,
pHfree=None,
pHNBS=None,
Ks=None,
pdict=None,
unit="umol",
):
"""
Calculate the carbon chemistry of seawater from a minimal parameter set.
Constants calculated by MyAMI model (Hain et al, 2015; doi:10.1002/2014GB004986).
Speciation calculations from Zeebe & Wolf-Gladrow (2001; ISBN:9780444509468) Appendix B
pH is Total scale.
Inputs must either be single values, arrays of equal length or a mixture of both.
If you use arrays of unequal length, it won't work.
Error propagation:
If inputs are ufloat or uarray (from uncertainties package) errors will
be propagated through all calculations, but:
**WARNING** Error propagation NOT IMPLEMENTED for carbon system calculations
with zero-finders (i.e. when pH is not given; cases 2-5 and 10-15).
Concentration Units
+++++++++++++++++++
* Ca and Mg must be in molar units.
* All other units must be the same, and can be specified in the 'unit' variable. Defaults to umolar.
Parameters
----------
pH, DIC, CO2, HCO3, CO3, TA : array-like
Carbon system parameters. Two of these must be provided.
BT : array-like
Total B at Salinity = 35, used in Alkalinity calculations.
Ca, Mg : arra-like
The [Ca] and [Mg] of the seawater, in mol / kg.
Used in calculating MyAMI constants.
T_in, S_in : array-like
Temperature in Celcius and Salinity in PSU that the
measurements were conducted under.
Used in calculating constants.
P_in : array-like
Pressure in Bar that the measurements were conducted under.
Used in pressure-correcting constants.
T_out, S_out : array-like
Temperature in Celcius and Salinity in PSU of the desired
output conditions.
Used in calculating constants.
P_in : array-like
Pressure in Bar of the desired output conditions.
Used in pressure-correcting constants.
unit : str
Concentration units of C and B parameters (all must be in
the same units).
Can be 'mol', 'mmol', 'umol', 'nmol', 'pmol' or 'fmol'.
Used in calculating Alkalinity. Default is 'umol'.
Ks : dict
A dictionary of constants. Must contain keys
'K1', 'K2', 'KB' and 'KW'.
If None, Ks are calculated using MyAMI model.
pdict : dict
Optionally, you can provide some or all parameters as a dict,
with keys the same as the parameter names above. Any parameters
included in the dict will overwrite manually specified
parameters. This is particularly useful if you're including
this in other code.
Returns
-------
dict(/Bunch) containing all calculated parameters.
"""
# Bunch inputs
ps = Bunch(locals())
if isinstance(pdict, dict):
ps.update(pdict)
# convert unit to multiplier
udict = {
"mol": 1.0,
"mmol": 1.0e3,
"umol": 1.0e6,
"nmol": 1.0e9,
"pmol": 1.0e12,
"fmol": 1.0e15,
}
if isinstance(ps.unit, str):
ps.unit = udict[ps.unit]
# elif isinstance(ps.unit, (int, float)):
# ps.unit = ps.unit
if ps.unit != 1:
upar = [
"DIC", "TA", "CO2", "HCO3", "CO3", "BT", "fCO2", "pCO2", "TP",
"TSi"
]
for p in upar:
if ps[p] is not None:
ps[p] = np.divide(ps[p], ps.unit) # convert to molar
# Conserved seawater chemistry
if ps.TS is None:
ps.TS = calc_TS(ps.S_in)
if ps.TF is None:
ps.TF = calc_TF(ps.S_in)
if ps.BT is None:
ps.BT = calc_TB(ps.S_in)
# elif isinstance(BT, (int, float)):
# ps.BT = ps.BT * ps.S_in / 35.
# Calculate Ks at input conditions
ps.Ks = calc_Ks(ps.T_in, ps.S_in, ps.P_in, ps.Mg, ps.Ca, ps.TS, ps.TF,
ps.Ks)
# Calculate pH scales at input conditions (does nothing if no pH given)
ps.update(
calc_pH_scales(
ps.pHtot,
ps.pHfree,
ps.pHsws,
ps.pHNBS,
ps.TS,
ps.TF,
ps.T_in + 273.15,
ps.S_in,
ps.Ks,
))
# calculate C system at input conditions
ps.update(
calc_C_species(
pHtot=ps.pHtot,
DIC=ps.DIC,
CO2=ps.CO2,
HCO3=ps.HCO3,
CO3=ps.CO3,
TA=ps.TA,
fCO2=ps.fCO2,
pCO2=ps.pCO2,
T_in=ps.T_in,
BT=ps.BT,
TP=ps.TP,
TSi=ps.TSi,
TS=ps.TS,
TF=ps.TF,
Ks=ps.Ks,
))
ps["revelle_factor"] = calc_revelle_factor(
TA=ps.TA,
DIC=ps.DIC,
BT=ps.BT,
TP=ps.TP,
TSi=ps.TSi,
TS=ps.TS,
TF=ps.TF,
Ks=ps.Ks,
)
# calculate pHs on all scales, if not done before.
if ps.pHNBS is None:
# Calculate pH on all scales
ps.update(
calc_pH_scales(
ps.pHtot,
ps.pHfree,
ps.pHsws,
ps.pHNBS,
ps.TS,
ps.TF,
ps.T_in + 273.15,
ps.S_in,
ps.Ks,
))
# clean up output
for k in [
"BT",
"CO2",
"CO3",
"Ca",
"DIC",
"H",
"HCO3",
"Mg",
"S_in",
"T_in",
"TA",
"CAlk",
"PAlk",
"SiAlk",
"OH",
]:
if not isinstance(ps[k], np.ndarray):
# convert all outputs to (min) 1D numpy arrays.
ps[k] = np.array(ps[k], ndmin=1)
if ps.unit != 1:
for p in upar + [
"CAlk", "BAlk", "PAlk", "SiAlk", "OH", "HSO4", "HF", "Hfree"
]:
ps[p] *= ps.unit # convert back to input units
# Calculate Output Conditions
# ===========================
if ps.T_out is not None or ps.S_out is not None or ps.P_out is not None:
if ps.T_out is None:
ps.T_out = ps.T_in
if ps.S_out is None:
ps.S_out = ps.S_in
if ps.P_out is None:
ps.P_out = ps.P_in
# assumes conserved alkalinity and DIC
out_cond = Csys(
TA=ps.TA,
DIC=ps.DIC,
T_in=ps.T_out,
S_in=ps.S_out,
P_in=ps.P_out,
unit=ps.unit,
)
# Calculate pH scales at output conditions (does nothing if no pH given)
out_cond.update(
calc_pH_scales(
out_cond.pHtot,
out_cond.pHfree,
out_cond.pHsws,
out_cond.pHNBS,
out_cond.TS,
out_cond.TF,
out_cond.T_in + 273.15,
out_cond.S_in,
out_cond.Ks,
))
# rename parameters in output conditions
outputs = [
"BAlk",
"BT",
"CAlk",
"CO2",
"CO3",
"DIC",
"H",
"HCO3",
"HF",
"HSO4",
"Hfree",
"Ks",
"OH",
"PAlk",
"SiAlk",
"TA",
"TF",
"TP",
"TS",
"TSi",
"fCO2",
"pCO2",
"pHfree",
"pHsws",
"pHtot",
"pHNBS",
]
ps.update({k + "_out": out_cond[k] for k in outputs})
# remove some superfluous outputs
rem = ["pdict"]
for r in rem:
if r in ps:
del ps[r]
return ps