Esempio n. 1
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def pH_scale_converter(pH, scale, Temp, Sal, Press=None, TS=None, TF=None):
    """
    Returns pH on all scales.
    """
    pH_scales = ["Total", "FREE", "SWS", "NBS"]
    if scale not in pH_scales:
        raise ValueError("scale must be one of Total, NBS, SWS or FREE.")
    if TS is None:
        TS = calc_TS(Sal)
    if TF is None:
        TF = calc_TF(Sal)
    TempK = Temp + 273.15

    Ks = calc_Ks_TS(Temp, Sal, Press)

    inp = [None, None, None, None]
    inp[np.argwhere(scale == np.array(pH_scales))[0, 0]] = pH

    return calc_pH_scales(*inp, TS, TF, TempK, Sal, Ks)
Esempio n. 2
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def calc_Ks_TS(T, S, P, Ks={}):
    """
    Helper function to calculate Ks given only T(C), S and P.

    If Ks is a dict, the Ks provided in the dict are used
    transparrently (i.e. no pressure modification).
    """
    Mg = 0.0528171
    Ca = 0.0102821

    if isinstance(Ks, dict):
        given_Ks = Ks

    Ks = MyAMI_K_calc(TempC=T, Sal=S, P=P, Mg=Mg, Ca=Ca)

    # non-MyAMI Constants
    Ks.update(calc_KPs(T, S, P))
    Ks.update(calc_KF(T, S, P))
    Ks.update(calc_KSi(T, S, P))

    # pH conversions to total scale.
    #   - KP1, KP2, KP3 are all on SWS
    #   - KSi is on SWS
    #   - MyAMI KW is on SWS... DOES THIS MATTER?

    TS = calc_TS(S)
    TF = calc_TF(S)
    SWStoTOT = (1 + TS / Ks.KSO4) / (1 + TS / Ks.KSO4 + TF / Ks.KF)
    # FREEtoTOT = 1 + 'T_' + mode]S / Ks.KSO4
    conv = ["KP1", "KP2", "KP3", "KSi", "KW"]
    for c in conv:
        Ks[c] *= SWStoTOT

    Ks.update(given_Ks)

    return Ks
Esempio n. 3
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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
Esempio n. 4
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def ABsys(
    pHtot=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,
    Ca=None,
    Mg=None,
    TS=None,
    TF=None,
    pHsws=None,
    pHfree=None,
    pHNBS=None,
    Ks=None,
    pdict=None,
):
    """
    Calculate the 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).

    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.

    Concentration Units
    +++++++++++++++++++
    * 'A' is fractional abundance (11B / BT)
    * 'd' are delta values
    Either specified, both returned.

    Parameters
    ----------
    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.
    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)

    # 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 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)

    for k in [
            "ABO3",
            "ABO4",
            "ABT",
            "Ca",
            "H",
            "Mg",
            "S_in",
            "T_in",
            "alphaB",
            "dBO3",
            "dBO4",
            "dBT",
            "pHtot",
    ]:
        if not isinstance(ps[k], np.ndarray):
            # convert all outputs to (min) 1D numpy arrays.
            ps[k] = np.array(ps[k], ndmin=1)

    # remove some superfluous outputs
    rem = ["pdict"]
    for r in rem:
        if r in ps:
            del ps[r]

    return ps
Esempio n. 5
0
def Bsys(
    pHtot=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,
    TS=None,
    TF=None,
    pHsws=None,
    pHfree=None,
    pHNBS=None,
    Ks=None,
    pdict=None,
):
    """
    Calculate the boron 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).

    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.

    Concentration Units
    +++++++++++++++++++
    * All concentrations must be in the same units. Returned in the same units as inputs.

    Parameters
    ----------
    pH, BT, BO3, BO4 : array-like
        Boron system parameters. Two of these must be provided.
    dBT, dBO3, dBO4, ABT, ABO3, ABO4 : array-like
        delta (d) or fractional abundance (A) values for the Boron
        isotope system. One of these must be provided.
    alphaB : array-like
        The alpha value for BO3-BO4 isotope fractionation.
    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.
    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.
    """
    # input checks
    if NnotNone(BT, BO3, BO4) < 1:
        raise ValueError("Must provide at least one of BT, BO3 or BO4")
    if NnotNone(dBT, dBO3, dBO4, ABT, ABO3, ABO4) < 1:
        raise ValueError(
            "Must provide one of dBT, dBO3, dBO4, ABT, ABO3 or ABO4")

    # Bunch inputs
    ps = Bunch(locals())
    if isinstance(pdict, dict):
        ps.update(pdict)

    # 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,
        ))

    ps.update(
        calc_B_species(pHtot=ps.pHtot,
                       BT=ps.BT,
                       BO3=ps.BO3,
                       BO4=ps.BO4,
                       Ks=ps.Ks))

    # If pH not calced yet, calculate on all scales
    if ps.pHtot is None:
        ps.pHtot = np.array(cp(ps.H), ndmin=1)
        # Calculate other pH 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,
            ))

    # 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))

    for k in ["BT", "H", "BO3", "BO4", "Ca", "Mg", "S_in", "T_in"]:
        # convert all outputs to (min) 1D numpy arrays.
        if not isinstance(ps[k], np.ndarray):
            # convert all outputs to (min) 1D numpy arrays.
            ps[k] = np.array(ps[k], ndmin=1)

    # remove some superfluous outputs
    rem = ["pdict"]
    for r in rem:
        if r in ps:
            del ps[r]

    return ps
Esempio n. 6
0
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
Esempio n. 7
0
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=25.,
          S=35.,
          P=None,
          Ca=None,
          Mg=None,
          TP=0.,
          TSi=0.,
          pHsws=None,
          pHfree=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.,
        'mmol': 1.e3,
        'umol': 1.e6,
        'nmol': 1.e9,
        'pmol': 1.e12,
        'fmol': 1.e15
    }
    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, so conversions aren't repeated by Csys
    orig_unit = ps.unit
    ps.unit = 1.

    # determin max lengths
    kexcl = ['Ks', 'pdict', 'unit']
    ks = [k for k in ps.keys() if k not in kexcl]
    L = maxL(*[ps[k] for k in ks])
    # make inputs same length
    for k in ks:
        if ps[k] is not None:
            if isinstance(ps[k], (int, float)):
                ps[k] = np.full(L, ps[k])

    # Conserved seawater chemistry
    if 'TS' not in ps:
        ps.TS = calc_TS(ps.S)
    if 'TF' not in ps:
        ps.TF = calc_TF(ps.S)

    # Calculate Ks
    ps.Ks = get_Ks(ps)

    # Calculate pH scales (does nothing if none pH given)
    ps.update(
        calc_pH_scales(ps.pHtot, ps.pHfree, ps.pHsws, ps.TS, ps.TF, 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), 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)
    elif isinstance(BT, (int, float)):
        ps.BT = ps.BT * ps.S / 35.

    # This section works out the order that things should be calculated in.
    # Special case: if pH is missing, must have:
    #   a) two C
    #   b) two B
    #   c) one pH-dependent B, one pH-dependent C... But that's cray...
    #      (c not implemented!)
    if ps.pHtot is None:
        nCspec = NnotNone(ps.DIC, ps.CO2, ps.HCO3, ps.CO3)
        # a) if there are 2 C species, or one C species and TA and BT
        if ((nCspec == 2) | ((nCspec == 1) & (NnotNone(ps.TA, ps.BT) == 2))):
            ps.update(Csys(pdict=ps))  # calculate C first
            ps.update(Bsys(pdict=ps))  # then B
            # Note on the peculiar syntax here:
            #  ps is a dict of parameters, where
            #  everything that needs to be calculated
            #  is None.
            #  We give this to the [N]sys function
            #  as pdict, which passes the paramters from THIS
            #  function to [N]sys.
            #  As the output of Csys is also a dict (Bunch)
            #  with exactly the same form as ps, we can then
            #  use the .update attribute of ps to update
            #  all the paramters that were calculated by
            #  Csyst.
            #  Thus, all calculation is incremental, working
            #  with the same parameter set. As dicts are
            #  mutable, this has the added benefit of the
            #  parameters only being stored in memory once.
            if ps.TA is None:
                (ps.TA, ps.CAlk, ps.BAlk, ps.PAlk, ps.SiAlk, ps.OH, ps.Hfree,
                 ps.HSO4, ps.HF) = cTA(H=ps.H,
                                       DIC=ps.DIC,
                                       BT=ps.BT,
                                       TP=ps.TP,
                                       TSi=ps.TSi,
                                       TS=ps.TS,
                                       TF=ps.TF,
                                       Ks=ps.Ks,
                                       mode='multi')
                # necessary becayse TA in Csys fails if there's no BT
        # b) if there are 2 B species
        elif nBspec == 2:
            ps.update(Bsys(pdict=ps))  # calculate B first
            ps.update(Csys(pdict=ps))  # 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]"))

    else:  # if we DO have pH, it's dead easy!
        ps.update(Bsys(pdict=ps))  # calculate B first
        ps.update(Csys(pdict=ps))  # then C

    for p in upar + [
            'CAlk', 'BAlk', 'PAlk', 'SiAlk', 'OH', 'HSO4', 'HF', 'Hfree'
    ]:
        ps[p] *= orig_unit  # convert back to input units

        # remove some superfluous outputs
    rem = ['pdict', 'unit']
    for r in rem:
        if r in ps:
            del ps[r]

    return ps
Esempio n. 8
0
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=25.,
         S=35.,
         P=None,
         TP=0.,
         TSi=0.,
         pHsws=None,
         pHfree=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, 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'.
    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.,
        'mmol': 1.e3,
        'umol': 1.e6,
        'nmol': 1.e9,
        'pmol': 1.e12,
        'fmol': 1.e15
    }
    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 'TS' not in ps:
        ps.TS = calc_TS(ps.S)
    if 'TF' not in ps:
        ps.TF = calc_TF(ps.S)
    if ps.BT is None:
        ps.BT = calc_TB(ps.S)
    elif isinstance(BT, (int, float)):
        ps.BT = ps.BT * ps.S / 35.

    # Calculate Ks
    ps.Ks = get_Ks(ps)

    # Calculate pH scales (does nothing if no pH given)
    ps.update(
        calc_pH_scales(ps.pHtot, ps.pHfree, ps.pHsws, ps.TS, ps.TF, 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), ps.Ks)

    # Carbon System Calculations (from Zeebe & Wolf-Gladrow, Appendix B)
    # 1. CO2 and pH
    if ps.CO2 is not None and ps.pHtot is not None:
        ps.H = ch(ps.pHtot)
        ps.DIC = CO2_pH(ps.CO2, ps.pHtot, ps.Ks)
    # 2. ps.CO2 and ps.HCO3
    elif ps.CO2 is not None and ps.HCO3 is not None:
        ps.H = CO2_HCO3(ps.CO2, ps.HCO3, ps.Ks)
        ps.DIC = CO2_pH(ps.CO2, cp(ps.H), ps.Ks)
    # 3. ps.CO2 and ps.CO3
    elif ps.CO2 is not None and ps.CO3 is not None:
        ps.H = CO2_CO3(ps.CO2, ps.CO3, ps.Ks)
        ps.DIC = CO2_pH(ps.CO2, cp(ps.H), ps.Ks)
    # 4. ps.CO2 and ps.TA
    elif ps.CO2 is not None and ps.TA is not None:
        # unit conversion because OH and H wrapped
        # up in TA fns - all need to be in same units.
        ps.pHtot = CO2_TA(CO2=ps.CO2,
                          TA=ps.TA,
                          BT=ps.BT,
                          TP=ps.TP,
                          TSi=ps.TSi,
                          TS=ps.TS,
                          TF=ps.TF,
                          Ks=ps.Ks)
        ps.H = ch(ps.pHtot)
        ps.DIC = CO2_pH(ps.CO2, ps.pHtot, ps.Ks)
    # 5. ps.CO2 and ps.DIC
    elif ps.CO2 is not None and ps.DIC is not None:
        ps.H = CO2_DIC(ps.CO2, ps.DIC, ps.Ks)
    # 6. ps.pHtot and ps.HCO3
    elif ps.pHtot is not None and ps.HCO3 is not None:
        ps.H = ch(ps.pHtot)
        ps.DIC = pH_HCO3(ps.pHtot, ps.HCO3, ps.Ks)
    # 7. ps.pHtot and ps.CO3
    elif ps.pHtot is not None and ps.CO3 is not None:
        ps.H = ch(ps.pHtot)
        ps.DIC = pH_CO3(ps.pHtot, ps.CO3, ps.Ks)
    # 8. ps.pHtot and ps.TA
    elif ps.pHtot is not None and ps.TA is not None:
        ps.H = ch(ps.pHtot)
        ps.DIC = pH_TA(pH=ps.pHtot,
                       TA=ps.TA,
                       BT=ps.BT,
                       TP=ps.TP,
                       TSi=ps.TSi,
                       TS=ps.TS,
                       TF=ps.TF,
                       Ks=ps.Ks)
    # 9. ps.pHtot and ps.DIC
    elif ps.pHtot is not None and ps.DIC is not None:
        ps.H = ch(ps.pHtot)
    # 10. ps.HCO3 and ps.CO3
    elif ps.HCO3 is not None and ps.CO3 is not None:
        ps.H = HCO3_CO3(ps.HCO3, ps.CO3, ps.Ks)
        ps.DIC = pH_CO3(cp(ps.H), ps.CO3, ps.Ks)
    # 11. ps.HCO3 and ps.TA
    elif ps.HCO3 is not None and ps.TA is not None:
        Warning(
            'Nutrient alkalinity not implemented for this input combination.\nCalculations use only C and B alkalinity.'
        )
        ps.H = HCO3_TA(ps.HCO3, ps.TA, ps.BT, ps.Ks)
        ps.DIC = pH_HCO3(cp(ps.H), ps.HCO3, ps.Ks)
    # 12. ps.HCO3 amd ps.DIC
    elif ps.HCO3 is not None and ps.DIC is not None:
        ps.H = HCO3_DIC(ps.HCO3, ps.DIC, ps.Ks)
    # 13. ps.CO3 and ps.TA
    elif ps.CO3 is not None and ps.TA is not None:
        Warning(
            'Nutrient alkalinity not implemented for this input combination.\nCalculations use only C and B alkalinity.'
        )
        ps.H = CO3_TA(ps.CO3, ps.TA, ps.BT, ps.Ks)
        ps.DIC = pH_CO3(cp(ps.H), ps.CO3, ps.Ks)
    # 14. ps.CO3 and ps.DIC
    elif ps.CO3 is not None and ps.DIC is not None:
        ps.H = CO3_DIC(ps.CO3, ps.DIC, ps.Ks)
    # 15. ps.TA and ps.DIC
    elif ps.TA is not None and ps.DIC is not None:
        ps.pHtot = TA_DIC(TA=ps.TA,
                          DIC=ps.DIC,
                          BT=ps.BT,
                          TP=ps.TP,
                          TSi=ps.TSi,
                          TS=ps.TS,
                          TF=ps.TF,
                          Ks=ps.Ks)
        ps.H = ch(ps.pHtot)

    # The above makes sure that DIC and H are known,
    # this next bit calculates all the missing species
    # from DIC and H.
    if ps.CO2 is None:
        ps.CO2 = cCO2(ps.H, ps.DIC, ps.Ks)
    if ps.fCO2 is None:
        ps.fCO2 = CO2_to_fCO2(ps.CO2, ps.Ks)
    if ps.pCO2 is None:
        ps.pCO2 = fCO2_to_pCO2(ps.fCO2, ps.T)
    if ps.HCO3 is None:
        ps.HCO3 = cHCO3(ps.H, ps.DIC, ps.Ks)
    if ps.CO3 is None:
        ps.CO3 = cCO3(ps.H, ps.DIC, ps.Ks)
    # Always calculate elements of alkalinity
    try:
        # necessary for use with CBsyst in special cases
        # where BT is not known before Csys is run.
        (ps.TA, ps.CAlk, ps.BAlk, ps.PAlk, ps.SiAlk, ps.OH, ps.Hfree, ps.HSO4,
         ps.HF) = cTA(H=ps.H,
                      DIC=ps.DIC,
                      BT=ps.BT,
                      TP=ps.TP,
                      TSi=ps.TSi,
                      TS=ps.TS,
                      TF=ps.TF,
                      Ks=ps.Ks,
                      mode='multi')
    except TypeError:
        pass
    if ps.pHtot is None:
        ps.pHtot = np.array(cp(ps.H), ndmin=1)
        # Calculate other pH scales
        ps.update(
            calc_pH_scales(ps.pHtot, ps.pHfree, ps.pHsws, ps.TS, ps.TF, ps.Ks))

    # clean up for output
    for k in [
            'BT', 'CO2', 'CO3', 'Ca', 'DIC', 'H', 'HCO3', 'Mg', 'S', 'T', '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

    # remove some superfluous outputs
    rem = ['pdict']
    for r in rem:
        if r in ps:
            del ps[r]

    return ps
Esempio n. 9
0
def Bsys(pHtot=None,
         BT=None,
         BO3=None,
         BO4=None,
         ABT=None,
         ABO3=None,
         ABO4=None,
         dBT=None,
         dBO3=None,
         dBO4=None,
         alphaB=None,
         T=25.,
         S=35.,
         P=None,
         Ca=None,
         Mg=None,
         pHsws=None,
         pHfree=None,
         Ks=None,
         pdict=None):
    """
    Calculate the boron 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).

    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.

    Concentration Units
    +++++++++++++++++++
    * All concentrations must be in the same units. Returned in the same units as inputs.

    Parameters
    ----------
    pH, BT, BO3, BO4 : array-like
        Boron system parameters. Two of these must be provided.
    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.
    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)

    # Conserved seawater chemistry
    if 'TS' not in ps:
        ps.TS = calc_TS(ps.S)
    if 'TF' not in ps:
        ps.TF = calc_TF(ps.S)

    # if neither Ca nor Mg provided, use default Ks
    ps.Ks = get_Ks(ps)

    # Calculate pH scales (does nothing if none pH given)
    ps.update(
        calc_pH_scales(ps.pHtot, ps.pHfree, ps.pHsws, ps.TS, ps.TF, ps.Ks))

    # B system calculations
    if ps.pHtot is not None and ps.BT is not None:
        ps.H = ch(ps.pHtot)
    elif ps.BT is not None and ps.BO3 is not None:
        ps.H = BT_BO3(ps.BT, ps.BO3, ps.Ks)
    elif ps.BT is not None and ps.BO4 is not None:
        ps.H = BT_BO4(ps.BT, ps.BO4, ps.Ks)
    elif ps.BO3 is not None and ps.BO4 is not None:
        ps.BT = ps.BO3 + ps.BO3
        ps.H = BT_BO3(ps.BT, ps.BO3, ps.Ks)
    elif ps.pHtot is not None and ps.BO3 is not None:
        ps.H = ch(ps.pHtot)
        ps.BT = pH_BO3(ps.pHtot, ps.BO3, ps.Ks)
    elif ps.pHtot is not None and ps.BO4 is not None:
        ps.H = ch(ps.pHtot)
        ps.BT = pH_BO4(ps.pHtot, ps.BO4, ps.Ks)

    # The above makes sure that BT and H are known,
    # this next bit calculates all the missing species
    # from BT and H.
    if ps.BO3 is None:
        ps.BO3 = cBO3(ps.BT, ps.H, ps.Ks)
    if ps.BO4 is None:
        ps.BO4 = cBO4(ps.BT, ps.H, ps.Ks)
    if ps.pHtot is None:
        ps.pHtot = np.array(cp(ps.H), ndmin=1)
        # Calculate other pH scales
        ps.update(
            calc_pH_scales(ps.pHtot, ps.pHfree, ps.pHsws, ps.TS, ps.TF, ps.Ks))

    if NnotNone(ps.ABT, ps.ABO3, ps.ABO4, ps.dBT, ps.dBO3, ps.dBO4) != 0:
        ps.update(ABsys(pdict=ps))

    for k in ['BT', 'H', 'BO3', 'BO4', 'Ca', 'Mg', 'S', 'T']:
        # convert all outputs to (min) 1D numpy arrays.
        if not isinstance(ps[k], np.ndarray):
            # convert all outputs to (min) 1D numpy arrays.
            ps[k] = np.array(ps[k], ndmin=1)

    # remove some superfluous outputs
    rem = ['pdict']
    for r in rem:
        if r in ps:
            del ps[r]

    return ps