def calculate_dissolved_volatiles(self,pressure,sample,X_fluid=1.0,**kwargs):
"""Calculates the dissolved CO2 concentration using Eqn (3) of Dixon (1997).
Parameters
----------
pressure float
Total pressure in bars.
sample Sample class
Magma major element composition.
X_fluid float
The mol fraction of CO2 in the fluid.
Returns
-------
float
The CO2 concentration in wt%.
"""
if X_fluid < 0 or X_fluid > 1:
raise core.InputError("X_fluid must have a value between 0 and 1.")
if pressure < 0:
raise core.InputError("Pressure must be positive.")
# if type(sample) != dict and type(sample) != pd.core.series.Series:
# raise core.InputError("sample must be a dict or pandas Series")
if sample.check_oxide('SiO2') == False:
raise core.InputError("sample must contain SiO2.")
if pressure == 0:
return 0
XCO3 = self.molfrac_molecular(pressure=pressure,sample=sample,X_fluid=X_fluid,**kwargs)
return (4400 * XCO3) / (36.594- 44*XCO3) # Following Dixon 1997 setting Mr as constant
def calculate_saturation_pressure(self, sample, **kwargs):
""" Calculates the pressure at which a pure H2O fluid is saturated, for the given
sample composition and H2O concentration. Calls the scipy.root_scalar routine, which makes
repeated calls to the calculate_dissolved_volatiles method.
Parameters
----------
sample Sample class
Magma major element composition (including H2O).
Returns
-------
float
Saturation pressure in bar
"""
if sample.check_oxide('H2O') == False:
raise core.InputError("sample must contain H2O")
if sample.get_composition('H2O') < 0:
raise core.InputError(
"H2O concentration must be greater than 0 wt%.")
if sample.get_composition('H2O') < self.calculate_dissolved_volatiles(
sample=sample, pressure=0, **kwargs):
return np.nan
try:
satP = root_scalar(self.root_saturation_pressure,
bracket=[1e-15, 1e5],
args=(sample, kwargs)).root
except:
w.warn("Saturation pressure not found.",
RuntimeWarning,
stacklevel=2)
satP = np.nan
return satP
def calculate_saturation_pressure(self, sample, X_fluid=1.0, **kwargs):
"""
Calculates the pressure at which a pure H2O fluid is saturated, for the given sample
composition and H2O concentration. Calls the scipy.root_scalar routine, which makes
repeated called to the calculate_dissolved_volatiles method.
Parameters
----------
sample Sample class
Magma major element composition (including H2O).
X_fluid float
The mole fraction of H2O in the fluid. Default is 1.0.
Returns
-------
float
Calculated saturation pressure in bars.
"""
if sample.check_oxide('H2O') is False:
raise core.InputError("sample must contain H2O")
if sample.get_composition('H2O') < 0:
raise core.InputError(
"H2O concentration must be greater than 0 wt%.")
try:
satP = root_scalar(self.root_saturation_pressure,
x0=100.0,
x1=1000.0,
args=(sample, kwargs)).root
except Exception:
w.warn("Saturation pressure not found.",
RuntimeWarning,
stacklevel=2)
satP = np.nan
return np.real(satP)
def calculate_dissolved_volatiles(self,pressure,sample,X_fluid=1.0,**kwargs):
"""Calculates the dissolved H2O concentration using Eqns (5) and (6) of Dixon (1997).
Parameters
----------
pressure float
Total pressure in bars.
sample Sample class
Magma major element composition.
X_fluid float
The mol fraction of H2O in the fluid.
Returns
-------
float
The H2O concentration in wt%.
"""
if isinstance(sample,sample_class.Sample) == False:
raise core.InputError("Sample must be an instance of the Sample class.")
if sample.check_oxide('SiO2') == False:
raise core.InputError("sample must contain SiO2.")
if pressure < 0:
raise core.InputError("Pressure must be positive")
if X_fluid < 0 or X_fluid > 1:
raise core.InputError("X_fluid must have a value between 0 and 1.")
if pressure == 0:
return 0
XH2O = self.molfrac_molecular(pressure=pressure,sample=sample,X_fluid=X_fluid,**kwargs)
XOH = self.XOH(pressure=pressure,sample=sample,X_fluid=X_fluid,**kwargs)
XB = XH2O + 0.5*XOH
return 1801.5*XB/(36.594-18.579*XB) # Following Dixon spreadsheet
def NBO_O(self, sample, coeffs='webapp'):
"""
Calculates NBO/O according to Appendix A.1. of Iacono-Marziano et al. (2012). NBO/O
is calculated on either a hydrous or anhyrous basis, as set when initialising the
Model class.
Parameters
----------
sample pandas Series or dict
Major element oxides in wt% (including H2O if using the hydrous parameterization).
coeffs str
One of:
- 'webapp' or 'manuscript' to include H2O in NBO/O
- 'anhydrous' to exclude H2O from NBO/O
Returns
-------
float
NBO/O.
"""
if isinstance(sample, sample_class.Sample) is False:
raise core.InputError(
"Sample must be an instance of the Sample class.")
if all(
sample.check_oxide(ox) for ox in [
'K2O', 'Na2O', 'CaO', 'MgO', 'FeO', 'Al2O3', 'SiO2', 'TiO2'
]) is False:
raise core.InputError(
"Sample must contain K2O, Na2O, CaO, MgO, FeO, Al2O3, SiO2, "
"and TiO2.")
X = sample.get_composition(units='mol_oxides',
oxide_masses=self.IM_oxideMasses)
if 'Fe2O3' in X:
Fe2O3 = X['Fe2O3']
else:
Fe2O3 = 0
NBO = 2 * (X['K2O'] + X['Na2O'] + X['CaO'] + X['MgO'] + X['FeO'] +
2 * Fe2O3 - X['Al2O3'])
Ox = (2 * X['SiO2'] + 2 * X['TiO2'] + 3 * X['Al2O3'] + X['MgO'] +
X['FeO'] + 2 * Fe2O3 + X['CaO'] + X['Na2O'] + X['K2O'])
if coeffs == 'webapp' or coeffs == 'manuscript':
if 'H2O' not in X:
raise core.InputError(
"sample must contain H2O if using the hydrous"
" parameterization.")
NBO = NBO + 2 * X['H2O']
Ox = Ox + X['H2O']
return NBO / Ox
def check_inputs(custom_H2O, custom_CO2):
if custom_H2O is not None:
if custom_CO2 is None:
raise core.InputError("If x data is passed, y data must also be passed.")
else:
if len(custom_H2O) == len(custom_CO2):
pass
else:
raise core.InputError("x and y data must be same length")
if custom_CO2 is not None:
if custom_H2O is None:
raise core.InputError("If y data is passed, x data must also be passed.")
def calculate_saturation_pressure(self,
temperature,
sample,
X_fluid=1.0,
**kwargs):
"""
Calculates the pressure at which a an CO2-bearing fluid is saturated. Calls the
scipy.root_scalar routine, which makes repeated called to the
calculate_dissolved_volatiles method.
Parameters
----------
sample: Sample class
Magma major element composition.
temperature float
Temperature in degrees C.
X_fluid float
OPTIONAL. Default is 0. Mole fraction of CO2 in the H2O-CO2 fluid.
Returns
-------
float
Calculated saturation pressure in bars.
"""
temperatureK = temperature + 273.15
if temperatureK <= 0.0:
raise core.InputError("Temperature must be greater than 0K.")
if X_fluid < 0 or X_fluid > 1:
raise core.InputError("X_fluid must have a value between 0 and 1.")
if isinstance(sample, sample_class.Sample) is False:
raise core.InputError(
"Sample must be an instance of the Sample class.")
if sample.check_oxide('CO2') is False:
raise core.InputError("sample must contain CO2.")
if sample.get_composition('CO2') < 0.0:
raise core.InputError(
"Dissolved CO2 concentration must be greater than 0 wt%.")
try:
satP = root_scalar(self.root_saturation_pressure,
args=(temperature, sample, X_fluid, kwargs),
x0=10.0,
x1=2000.0).root
except Exception:
w.warn("Saturation pressure not found.",
RuntimeWarning,
stacklevel=2)
satP = np.nan
return np.real(satP)
def calculate_dissolved_volatiles(self,
pressure,
sample,
X_fluid=1.0,
**kwargs):
"""Calculates the dissolved H2O concentration using Eqn (9) of Shishkina et al. (2014).
Parameters
----------
pressure float
Total pressure in bars
sample Sample class
Magma major element composition.
X_fluid float
The mol fraction of H2O in the fluid
Returns
-------
float
The H2O concentration in wt%
"""
if isinstance(sample, sample_class.Sample) == False:
raise core.InputError(
"Sample must be an instance of the Sample class.")
if sample.check_oxide('Na2O') == False or sample.check_oxide(
'K2O') == False:
raise core.InputError("Na2O and K2O must be present in sample.")
if pressure < 0:
raise core.InputError("Pressure must be positive.")
_mols = sample.get_composition(units='mol_cations')
_mol_volatiles = 0
if 'H' in _mols:
_mol_volatiles += _mols['H']
if 'C' in _mols:
_mol_volatiles += _mols['C']
total_alkalis = (_mols['Na'] + _mols['K']) / (1 - _mol_volatiles)
fugacity = self.fugacity_model.fugacity(pressure,
X_fluid=X_fluid,
**kwargs)
a = 3.36e-7 * (fugacity / 10)**3 - 2.33e-4 * (
fugacity / 10)**2 + 0.0711 * (fugacity / 10) - 1.1309
b = -1.2e-5 * (fugacity / 10)**2 + 0.0196 * (fugacity / 10) + 1.1297
return a * total_alkalis + b
def NBO_O(self, sample, hydrous_coeffs=True):
"""
Calculates NBO/O according to Appendix A.1. of Iacono-Marziano et al. (2012). NBO/O
is calculated on either a hydrous or anhyrous basis, as set when initialising the
Model class.
Parameters
----------
sample pandas Series or dict
Major element oxides in wt% (including H2O if using the hydrous parameterization).
Returns
-------
float
NBO/O.
"""
if isinstance(sample, sample_class.Sample) == False:
raise core.InputError(
"Sample must be an instance of the Sample class.")
if all(
sample.check_oxide(ox) for ox in [
'K2O', 'Na2O', 'CaO', 'MgO', 'FeO', 'Al2O3', 'SiO2', 'TiO2'
]) == False:
raise core.InputError(
"sample must contain K2O, Na2O, CaO, MgO, FeO, Al2O3, SiO2, and TiO2."
)
# X = sample.get_composition(units='mol_oxides',normalization='additionalvolatiles')
X = sample.get_composition(units='mol_oxides')
if 'Fe2O3' in X:
Fe2O3 = X['Fe2O3']
else:
Fe2O3 = 0
NBO = 2 * (X['K2O'] + X['Na2O'] + X['CaO'] + X['MgO'] + X['FeO'] +
2 * Fe2O3 - X['Al2O3'])
O = 2 * X['SiO2'] + 2 * X['TiO2'] + 3 * X['Al2O3'] + X['MgO'] + X[
'FeO'] + 2 * Fe2O3 + X['CaO'] + X['Na2O'] + X['K2O']
if hydrous_coeffs == True:
if 'H2O' not in X:
raise core.InputError(
"sample must contain H2O if using the hydrous parameterization."
)
NBO = NBO + 2 * X['H2O']
O = O + X['H2O']
return NBO / O
def scatterplot(custom_x, custom_y, xlabel=None, ylabel=None, **kwargs):
"""
Custom x-y plotting using VESIcal's built-in plot() function, built
Matplotlib's plot and scatter functions.
Parameters
----------
custom_x: list
List of groups of x-values to plot as points or lines
custom_y: list
List of groups of y-values to plot as points or lines
xlabel: str
OPTIONAL. What to display along the x-axis.
ylabel: str
OPTIONAL. What to display along the y-axis.
kwargs:
Can take in any key word agruments that can be passed to `plot()`.
Returns
-------
fig, ax matplotlib objects
X-y plot with custom x and y axis values and labels.
"""
if isinstance(custom_x, list) and isinstance(custom_y, list):
if len(custom_x) != len(custom_y):
raise core.InputError("X and y lists must be same length")
if xlabel is not None:
if isinstance(xlabel, str):
pass
else:
raise core.InputError("xlabel must be string")
if ylabel is not None:
if isinstance(ylabel, str):
pass
else:
raise core.InputError("ylabel must be string")
return plot(custom_x=custom_x,
custom_y=custom_y,
xlabel=xlabel,
ylabel=ylabel,
**kwargs)
def set_default_normalization(self, default_normalization):
""" Set the default type of normalization to use with the get_composition() method.
Parameters
----------
default_normalization: str
The type of normalization to apply to the data. One of:
- 'none' (no normalization)
- 'standard' (default): Normalizes an input composition to 100%.
- 'fixedvolatiles': Normalizes major element oxides to 100 wt%, including volatiles.
The volatile wt% will remain fixed, whilst the other major element oxides are reduced
proportionally so that the total is 100 wt%.
- 'additionalvolatiles': Normalises major element oxide wt% to 100%, assuming it is
volatile-free. If H2O or CO2 are passed to the function, their un-normalized values will
be retained in addition to the normalized non-volatile oxides, summing to >100%.
"""
if default_normalization in [
'none', 'standard', 'fixedvolatiles', 'additionalvolatiles'
]:
self.default_normalization = default_normalization
else:
raise core.InputError(
"The normalization method must be one of 'none', 'standard', 'fixedvolatiles',\
or 'additionalvolatiles'.")
def PiStar(self, sample):
"""Shishkina et al. (2014) Eq (11)
Calculates the Pi* parameter for use in calculating CO2 solubility.
Parameters
----------
sample: Sample class
The magma composition stored in a Sample class.
Returns
-------
float
The value of the Pi* compositional parameter.
"""
_mols = sample.get_composition(units='mol_cations')
if all(cation in _mols for cation in
['Ca', 'K', 'Na', 'Mg', 'Fe', 'Si', 'Al']) == False:
raise core.InputError(
"To calculate PiStar, values for CaO, K2O, Na2O, MgO, FeO, SiO2, and Al2O3\
must be provided in sample.")
_pi = (_mols['Ca'] + 0.8*_mols['K'] + 0.7*_mols['Na'] + 0.4*_mols['Mg'] + 0.4*_mols['Fe'])/\
(_mols['Si']+_mols['Al'])
return _pi
def calculate_saturation_pressure(self, temperature, sample, **kwargs):
"""
Calculates the pressure at which a pure H2O fluid is saturated, for the given sample
composition and H2O concentration. Calls the scipy.root_scalar routine, which makes
repeated called to the calculate_dissolved_volatiles method.
Parameters
----------
temperature float
The temperature of the system in C.
sample pandas Series or dict
Major element oxides in wt% (including H2O).
X_fluid float
The mole fraction of H2O in the fluid. Default is 1.0.
Returns
-------
float
Calculated saturation pressure in bars.
"""
if isinstance(sample, sample_class.Sample) is False:
raise core.InputError(
"Sample must be an instance of the Sample class.")
if sample.check_oxide('H2O') is False:
raise core.InputError("sample must contain H2O.")
if sample.get_composition('H2O') < 0.0:
raise core.InputError("Dissolved H2O must be greater than 0 wt%.")
try:
# Checks whether the upper bound for the numerical solver returns a positive H2O
# concentration, and if it doesn't, it will progressively decrease the bound until
# it does.
upperbound = 1e5
while self.calculate_dissolved_volatiles(upperbound, temperature,
sample, **kwargs) < 0:
upperbound = upperbound * 0.9
satP = root_scalar(self.root_saturation_pressure,
args=(temperature, sample, kwargs),
bracket=[1e-15, upperbound]).root
except Exception:
w.warn("Saturation pressure not found.",
RuntimeWarning,
stacklevel=2)
satP = np.nan
return satP
def calculate_saturation_pressure(self,
sample,
temperature=1200,
X_fluid=1.0,
**kwargs):
"""
Calculates the pressure at which a pure CO2 fluid is saturated, for the given sample
composition and CO2 concentration. Calls the scipy.root_scalar routine, which makes
repeated called to the calculate_dissolved_volatiles method.
Parameters
----------
temperature float
The temperature of the system in C.
sample: Sample class
Magma major element composition (including CO2).
X_fluid float
The mole fraction of H2O in the fluid. Default is 1.0.
Returns
-------
float
Calculated saturation pressure in bars.
"""
if X_fluid < 0 or X_fluid > 1:
raise core.InputError("X_fluid must have a value between 0 and 1.")
if isinstance(sample, sample_class.Sample) is False:
raise core.InputError(
"Sample must be an instance of the Sample class.")
if sample.check_oxide('CO2') is False:
raise core.InputError("sample must contain CO2.")
if sample.get_composition('CO2') < 0.0:
raise core.InputError(
"Dissolved CO2 concentration must be greater than 0 wt%.")
try:
satP = root_scalar(self.root_saturation_pressure,
args=(temperature, sample, X_fluid, kwargs),
x0=1000.0,
x1=2000.0).root
except Exception:
w.warn("Saturation pressure not found.",
RuntimeWarning,
stacklevel=2)
satP = np.nan
return satP
def check_colors(custom_colors):
if custom_colors == "VESIcal":
use_colors = color_list
elif isinstance(custom_colors, list):
use_colors = custom_colors
else:
raise core.InputError("Argument custom_colors must be type list. Just passing one item? Try putting square brackets, [], around it.")
return use_colors
def calculate_dissolved_volatiles(self,
pressure,
sample,
X_fluid=1,
**kwargs):
""" Calculates the dissolved CO2 concentration in wt%, using equation (13) of Shishkina et al. (2014).
Parameters
----------
pressure: float
(Total) pressure in bars.
sample: Sample class
Magma composition.
X_fluid: float
The mol-fraction of the fluid that is CO2. Default is 1, i.e. a pure CO2 fluid.
Returns
-------
float
The dissolved CO2 concentration in wt%.
"""
if X_fluid < 0 or X_fluid > 1:
raise core.InputError("X_fluid must have a value between 0 and 1.")
if pressure < 0:
raise core.InputError("pressure must be a positive value.")
PiStar = self.PiStar(sample)
fugacity = self.fugacity_model.fugacity(pressure=pressure,
X_fluid=X_fluid,
**kwargs)
A = 1.150
B = 6.71
C = -1.345
if fugacity == 0:
return 0
else:
return np.exp(A * np.log(fugacity / 10) + B * PiStar + C) / 1e4
def calculate_saturation_pressure(self, temperature, sample, **kwargs):
"""
Calculates the pressure at which a pure CO2 fluid is saturated, for the given sample
composition and CO2 concentration. Calls the scipy.root_scalar routine, which makes
repeated called to the calculate_dissolved_volatiles method.
Parameters
----------
temperature float
The temperature of the system in C.
sample Sample class
Magma major element composition (including CO2).
Returns
-------
float
Calculated saturation pressure in bars.
"""
if temperature <= 0:
raise core.InputError("Temperature must be greater than 0K.")
if isinstance(sample, sample_class.Sample) is False:
raise core.InputError(
"Sample must be an instance of the Sample class.")
if sample.check_oxide('CO2') is False:
raise core.InputError("sample must contain CO2")
if sample.get_composition('CO2') < 0:
raise core.InputError("Dissolved CO2 must be greater than 0 wt%.")
try:
satP = root_scalar(self.root_saturation_pressure,
args=(temperature, sample, kwargs),
bracket=[1e-15, 1e5]).root
except Exception:
w.warn("Saturation pressure not found.",
RuntimeWarning,
stacklevel=2)
satP = np.nan
return satP
def _normalize_FixedVolatiles(self, composition, units='wtpt_oxides'):
"""
Normalizes major element oxides to 100 wt%, including volatiles. The volatile
wt% will remain fixed, whilst the other major element oxides are reduced proportionally
so that the total is 100 wt%.
Intended to be called only by the get_composition() method.
Parameters
----------
composition: pandas Series
Major element composition
units: str
The units of composition. Should be one of:
- wtpt_oxides (default)
- mol_oxides
- mol_cations
Returns
-------
pandas Series
Normalized major element oxides.
"""
comp = composition.copy()
normalized = pd.Series({}, dtype=float)
volatiles = 0
if 'CO2' in list(comp.index):
volatiles += comp['CO2']
if 'H2O' in list(comp.index):
volatiles += comp['H2O']
for ox in list(comp.index):
if ox != 'H2O' and ox != 'CO2':
normalized[ox] = comp[ox]
if units == 'wtpt_oxides':
normalized = normalized / np.sum(normalized) * (100 - volatiles)
elif units == 'mol_oxides' or units == 'mol_cations':
normalized = normalized / np.sum(normalized) * (1 - volatiles)
else:
raise core.InputError(
"Units must be one of 'wtpt_oxides', 'mol_oxides', or 'mol_cations'."
)
if 'CO2' in list(comp.index):
normalized['CO2'] = comp['CO2']
if 'H2O' in list(comp.index):
normalized['H2O'] = comp['H2O']
return normalized
def __init__(self,
sample,
model='MagmaSat',
silence_warnings=False,
**kwargs):
"""
Initializes the calculation.
Parameters
----------
sample: Sample class
The rock composition as a Sample object.
model: string or Model class
Which model to use for the calculation. If passed a string, it
will look up the name in the default_models dictionary. Default is
MagmaSat.
silence_warnings: bool
Silence warnings about calibration ranges. Default is False.
preprocess_sample: bool
Before running the calculation, run the sample through the
preprocessing routine. As of Feb 2021 this functionality should be
redundant.
"""
self.model_name = model
if model == 'MagmaSat':
self.model = magmasat.MagmaSat()
elif type(model) == str:
if model in models.default_models.keys():
self.model = models.default_models[model]
else:
raise core.InputError("The model name given is not recognised."
" Run the method get_model_names() to "
"find allowed names.")
else:
self.model = model
self.sample = sample
self.result = self.calculate(sample=self.sample, **kwargs)
self.calib_check = self.check_calibration_range(sample=self.sample,
**kwargs)
if self.calib_check is not None and silence_warnings is False:
if self.calib_check != '':
w.warn(self.calib_check, RuntimeWarning)
def _normalize_AdditionalVolatiles(self, composition, units='wtpt_oxides'):
"""
Normalises major element oxide wt% to 100%, assuming it is volatile-free. If
H2O or CO2 are passed to the function, their un-normalized values will be retained
in addition to the normalized non-volatile oxides, summing to >100%.
Intended to be called only by the get_composition() method.
Parameters
----------
composition: pandas.Series
Major element composition
units: str
The units of composition. Should be one of:
- wtpt_oxides (default)
- mol_oxides
- mol_cations
Returns
-------
pandas.Series
Normalized major element oxides.
"""
comp = composition.copy()
normalized = pd.Series({}, dtype=float)
for ox in list(comp.index):
if ox != 'H2O' and ox != 'CO2':
normalized[ox] = comp[ox]
if units == 'wtpt_oxides':
normalized = normalized / np.sum(normalized) * 100
elif units == 'mol_oxides' or units == 'mol_cations':
normalized = normalized / np.sum(normalized)
else:
raise core.InputError(
"Units must be one of 'wtpt_oxides', 'mol_oxides', or 'mol_cations'."
)
if 'H2O' in comp.index:
normalized['H2O'] = comp['H2O']
if 'CO2' in comp.index:
normalized['CO2'] = comp['CO2']
return normalized
def calculate(self,
sample,
pressure='saturation',
fractionate_vapor=0.0,
final_pressure=100.0,
**kwargs):
check = getattr(self.model, "calculate_degassing_path", None)
if callable(check):
data = self.model.calculate_degassing_path(
sample=sample,
pressure=pressure,
fractionate_vapor=fractionate_vapor,
final_pressure=final_pressure,
**kwargs)
return data
else:
raise core.InputError(
"This model does not have a calculate_isobars_and_isopleths method built in, most likely because it is a pure fluid model."
)
def set_default_units(self, default_units):
""" Set the default units of composition to return when using the get_composition() method.
Parameters
----------
default_units str
The type of composition to return, one of:
- wtpt_oxides (default)
- mol_oxides
- mol_cations
- mol_singleO
"""
if default_units in [
'wtpt_oxides', 'mol_oxides', 'mol_cations', 'mol_singleO'
]:
self.default_units = default_units
else:
raise core.InputError(
"The units must be one of 'wtpt_oxides','mol_oxides','mol_cations','mol_singleO'."
)
def calculate(self,
sample,
pressure_list,
isopleth_list=[0, 1],
points=101,
**kwargs):
check = getattr(self.model, "calculate_isobars_and_isopleths", None)
if callable(check):
# samplenorm = sample.copy()
# samplenorm = normalize_AdditionalVolatiles(samplenorm)
isobars, isopleths = self.model.calculate_isobars_and_isopleths(
sample=self.sample,
pressure_list=pressure_list,
isopleth_list=isopleth_list,
points=points,
**kwargs)
return isobars, isopleths
else:
raise core.InputError(
"This model does not have a calculate_isobars_and_isopleths method built in, most likely because it is a pure fluid model."
)
def _normalize_Standard(self, composition, units='wtpt_oxides'):
"""
Normalizes the given composition to 100 wt%, including volatiles. This method
is intended only to be called by the get_composition() method.
Parameters
----------
composition: pandas.Series
A rock composition with oxide names as keys and concentrations as values.
units: str
The units of composition. Should be one of:
- wtpt_oxides (default)
- mol_oxides
- mol_cations
Returns
-------
pandas.Series
Normalized oxides in wt%.
"""
comp = composition.copy()
comp = dict(comp)
if units == 'wtpt_oxides':
normed = pd.Series(
{k: 100.0 * v / sum(comp.values())
for k, v in comp.items()})
elif units == 'mol_oxides' or units == 'mol_cations':
normed = pd.Series(
{k: v / sum(comp.values())
for k, v in comp.items()})
else:
raise core.InputError(
"Units must be one of 'wtpt_oxides', 'mol_oxides', or 'mol_cations'."
)
return normed
def change_composition(self,
new_composition,
units='wtpt_oxides',
inplace=True):
"""
Change the concentration of some component of the composition.
If the units are moles, they are read as moles relative to the present composition,
i.e. if you wish to double the moles of MgO, if the present content is 0.1 moles,
you should provide {'MgO':0.2}. The composition will then be re-normalized. If the
original composition was provided in un-normalized wt%, the unnormalized total will
be lost.
Parameters
----------
new_composition: dict or pandas.Series
The components to be updated.
units: str
The units of new_composition. Should be one of:
- wtpt_oxides (default)
- mol_oxides
- mol_cations
inplace: bool
If True the object will be modified in place. If False, a copy of the Sample
object will be created, modified, and then returned.
Returns
-------
Sample class
Modified Sample class.
"""
# if new_composition is pandas.Series, convert to dict
if isinstance(new_composition, pd.Series):
new_composition = dict(new_composition)
if inplace == False:
newsample = deepcopy(self)
return newsample.change_composition(new_composition, units=units)
if units == 'wtpt_oxides':
for ox in new_composition:
self._composition[ox] = new_composition[ox]
elif units == 'mol_oxides':
_comp = self.get_composition(units='mol_oxides')
for ox in new_composition:
_comp[ox] = new_composition[ox]
self._composition = self._molOxides_to_wtpercentOxides(_comp)
elif units == 'mol_cations':
_comp = self.get_composition(units='mol_cations')
for el in new_composition:
_comp[el] = new_composition[el]
self._composition = self._molCations_to_wtpercentOxides(_comp)
else:
raise core.InputError(
"Units must be one of 'wtpt_oxides', 'mol_oxides', or 'mol_cations'."
)
return self
def __init__(self,
composition,
units='wtpt_oxides',
default_normalization='none',
default_units='wtpt_oxides'):
""" Initialises the sample class.
The composition is stored as wtpt. If the composition
is provided as wtpt, no normalization will be applied. If the composition is supplied as
mols, the composition will be normalized to 100 wt%.
Parameters
----------
composition dict or pandas.Series
The composition of the sample in the format specified by the composition_type
parameter. Default is oxides in wtpt.
units str
Specifies the units and type of compositional information passed in the
composition parameter. Choose from 'wtpt_oxides', 'mol_oxides', 'mol_cations'.
default_normalization: None or str
The type of normalization to apply to the data by default. One of:
- None (no normalization)
- 'standard' (default): Normalizes an input composition to 100%.
- 'fixedvolatiles': Normalizes major element oxides to 100 wt%, including volatiles.
The volatile wt% will remain fixed, whilst the other major element oxides are reduced
proportionally so that the total is 100 wt%.
- 'additionalvolatiles': Normalises major element oxide wt% to 100%, assuming it is
volatile-free. If H2O or CO2 are passed to the function, their un-normalized values will
be retained in addition to the normalized non-volatile oxides, summing to >100%.
default_units str
The type of composition to return by default, one of:
- wtpt_oxides (default)
- mol_oxides
- mol_cations
- mol_singleO
"""
composition = deepcopy(composition)
if isinstance(composition, dict):
composition = pd.Series(composition, dtype='float64')
elif isinstance(composition, pd.Series) == False:
raise core.InputError(
"The composition must be given as either a dictionary or a pandas Series."
)
if units == 'wtpt_oxides':
self._composition = composition
elif units == 'mol_oxides':
self._composition = self._molOxides_to_wtpercentOxides(composition)
elif units == 'mol_cations':
self._composition = self._molCations_to_wtpercentOxides(
composition)
else:
raise core.InputError(
"Units must be one of 'wtpt_oxides', 'mol_oxides', or 'mol_cations'."
)
self.set_default_normalization(default_normalization)
self.set_default_units(default_units)
def get_composition(self,
species=None,
normalization=None,
units=None,
exclude_volatiles=False,
asSampleClass=False):
""" Returns the composition in the format requested, normalized as requested.
Parameters
----------
species: NoneType or str
The name of the oxide or cation to return the concentration of. If NoneType (default) the
whole composition will be returned as a pandas.Series. If an oxide is passed, the value in
wtpt will be returned unless units is set to 'mol_oxides', even if the default units for the
sample object are mol_oxides. If an element is passed, the concentration will be returned as
mol_cations, unless 'mol_singleO' is specified as units, even if the default units for the
sample object are mol_singleO. Unless normalization is specified in the method call, none
will be applied.
normalization: NoneType or str
The type of normalization to apply to the data. One of:
- 'none' (no normalization)
- 'standard' (default): Normalizes an input composition to 100%.
- 'fixedvolatiles': Normalizes major element oxides to 100 wt%, including volatiles.
The volatile wt% will remain fixed, whilst the other major element oxides are reduced
proportionally so that the total is 100 wt%.
- 'additionalvolatiles': Normalises major element oxide wt% to 100%, assuming it is
volatile-free. If H2O or CO2 are passed to the function, their un-normalized values will
be retained in addition to the normalized non-volatile oxides, summing to >100%.
If NoneType is passed the default normalization option will be used (self.default_normalization).
units: NoneType or str
The units of composition to return, one of:
- wtpt_oxides (default)
- mol_oxides
- mol_cations
- mol_singleO
If NoneType is passed the default units option will be used (self.default_type).
exclude_volatiles bool
If True, volatiles will be excluded from the returned composition, prior to normalization and
conversion.
asSampleClass: bool
If True, the sample composition will be returned as a sample class, with default options. In this case
any normalization instructions will be ignored.
Returns
-------
pandas.Series, float, or Sample class
The sample composition, as specified.
"""
# Fetch the default return types if not specified in function call
if normalization == None and species == None:
normalization = self.default_normalization
if units == None and species == None:
units = self.default_units
# Check whether to exclude volatiles
# note that here composition is gotten as wtpt_oxides
if exclude_volatiles == True:
composition = self._composition.copy()
if 'H2O' in composition.index:
composition = composition.drop(index='H2O')
if 'CO2' in composition.index:
composition = composition.drop(index='CO2')
else:
composition = self._composition.copy()
# Check for a species being provided, if so, work out which units to return.
if isinstance(species, str):
if species in composition.index: # if the requested species has a value, proceed
if species in core.oxides:
if units in ['mol_cations, mol_singleO'] or units == None:
units = 'wtpt_oxides'
elif species in core.cations_to_oxides:
if units in ['wtpt_oxides', 'mol_oxides'] or units == None:
units = 'mol_cations'
else:
raise core.InputError(
species +
" was not recognised, check spelling, capitalization and stoichiometry."
)
if normalization == None:
normalization = 'none'
else:
return 0.0 # if the requested species has no set value, return a float of 0.0
elif species != None:
raise core.InputError(
"Species must be either a string or a NoneType.")
# Get the requested type of composition
if units == 'wtpt_oxides':
converted = composition
elif units == 'mol_oxides':
converted = self._wtpercentOxides_to_molOxides(composition)
elif units == 'mol_cations':
converted = self._wtpercentOxides_to_molCations(composition)
elif units == 'mol_singleO':
converted = self._wtpercentOxides_to_molSingleO(composition)
else:
raise core.InputError(
"The units must be one of 'wtpt_oxides', 'mol_oxides', 'mol_cations', \
or 'mol_singleO'.")
# Do requested normalization
if normalization == 'none':
final = converted
elif normalization == 'standard':
final = self._normalize_Standard(converted, units=units)
elif normalization == 'fixedvolatiles':
final = self._normalize_FixedVolatiles(converted, units=units)
elif normalization == 'additionalvolatiles':
final = self._normalize_AdditionalVolatiles(converted, units=units)
else:
raise core.InputError(
"The normalization method must be one of 'none', 'standard', 'fixedvolatiles',\
or 'additionalvolatiles'.")
if species == None:
if asSampleClass == False:
return final
else:
return Sample(final)
elif isinstance(species, str):
if asSampleClass == True:
w.warn(
"Cannot return single species as Sample class. Returning as float.",
RuntimeWarning,
stacklevel=2)
return final[species]
def calculate_dissolved_volatiles(self,
pressure,
temperature,
sample,
X_fluid=1,
coeffs='webapp',
**kwargs):
"""
Calculates the dissolved CO2 concentration, using Eq (12) of Iacono-Marziano et al. (2012).
If using the hydrous parameterization, it will use the scipy.root_scalar routine to find
the root of the root_dissolved_volatiles method.
Parameters
----------
pressure float
Total pressure in bars.
temperature float
Temperature in C
sample Sample class
Magma major element composition.
X_fluid float
Mole fraction of H2O in the fluid. Default is 1.0.
coeffs str
Which set of coefficients should be used for H2O calculations:
- 'webapp' (default) for the hydrous NBO/O parameterisation coefficients used in the
Iacono-Marziano webapp.
- 'manuscript' for the hydrous NBO/O parameterisation coefficients given in the
Iacono-Marziano et al. (2012) manuscript.
- 'anhydrous' for the anhydrous NBO/O parameterisation coefficients given in the
Iacono-Marziano et al. (2012) manuscript.
Returns
-------
float
Dissolved H2O concentration in wt%.
"""
if coeffs not in ['webapp', 'manuscript', 'anhydrous']:
raise core.InputError(
"The coeffs argument must be one of 'webapp', 'manuscript', "
"or 'anhydrous'")
temperature = temperature + 273.15 # translate T from C to K
if isinstance(sample, sample_class.Sample) is False:
raise core.InputError(
"Sample must be an instance of the Sample class.")
if pressure < 0:
raise core.InputError("Pressure must be positive.")
if temperature <= 0:
raise core.InputError("Temperature must be greater than 0K.")
if X_fluid < 0 or X_fluid > 1:
raise core.InputError("X_fluid must have a value between 0 and 1.")
if pressure == 0:
return 0
if coeffs == 'webapp' or coeffs == 'manuscript':
im_h2o_model = water()
h2o = im_h2o_model.calculate_dissolved_volatiles(
pressure=pressure,
temperature=temperature - 273.15,
sample=sample,
X_fluid=1 - X_fluid,
coeffs=coeffs,
**kwargs)
sample_h2o = sample.change_composition({'H2O': h2o}, inplace=False)
d = np.array([-16.4, 4.4, -17.1, 22.8])
a = 1.0
b = 17.3
B = -6.0
C = 0.12
NBO_O = self.NBO_O(sample=sample_h2o, coeffs=coeffs)
else:
im_h2o_model = water()
h2o = im_h2o_model.calculate_dissolved_volatiles(
pressure=pressure,
temperature=temperature - 273.15,
sample=sample,
X_fluid=1 - X_fluid,
coeffs=coeffs,
**kwargs)
sample_h2o = sample.change_composition({'H2O': h2o}, inplace=False)
d = np.array([2.3, 3.8, -16.3, 20.1])
a = 1.0
b = 15.8
B = -5.3
C = 0.14
NBO_O = self.NBO_O(sample=sample, coeffs=coeffs)
fugacity = self.fugacity_model.fugacity(pressure=pressure,
X_fluid=X_fluid,
temperature=temperature -
273.15,
**kwargs)
if fugacity == 0:
return 0
molarProps = sample_h2o.get_composition(
units='mol_oxides', oxide_masses=self.IM_oxideMasses)
if all(ox in molarProps for ox in [
'Al2O3', 'CaO', 'K2O', 'Na2O', 'FeO', 'MgO', 'Na2O', 'K2O'
]) is False:
raise core.InputError(
"sample must contain Al2O3, CaO, K2O, Na2O, FeO, MgO, Na2O, "
"and K2O.")
if 'Fe2O3' in molarProps:
Fe2O3 = molarProps['Fe2O3']
else:
Fe2O3 = 0
x = list()
if 'H2O' in molarProps:
x.append(molarProps['H2O'])
else:
x.append(0.0)
x.append(molarProps['Al2O3'] /
(molarProps['CaO'] + molarProps['K2O'] + molarProps['Na2O']))
x.append((molarProps['FeO'] + Fe2O3 * 2 + molarProps['MgO']))
x.append((molarProps['Na2O'] + molarProps['K2O']))
x = np.array(x)
CO3 = np.exp(
np.sum(x * d) + a * np.log(fugacity) + b * NBO_O + B +
C * pressure / temperature)
CO2 = CO3 / 1e4
return CO2
def calculate_dissolved_volatiles(self,
pressure,
temperature,
sample,
X_fluid=1.0,
coeffs='webapp',
**kwargs):
"""
Calculates the dissolved H2O concentration, using Eq (13) of Iacono-Marziano et al. (2012).
If using the hydrous parameterization, it will use the scipy.root_scalar routine to find
the root of the root_dissolved_volatiles method.
Parameters
----------
pressure float
Total pressure in bars.
temperature float
Temperature in C
sample pandas Series or dict
Major element oxides in wt%.
X_fluid float
Mole fraction of H2O in the fluid. Default is 1.0.
coeffs str
Which set of coefficients should be used in the calculations:
- 'webapp' (default) for the hydrous NBO/O parameterisation coefficients used in
the Iacono-Marziano webapp.
- 'manuscript' for the hydrous NBO/O parameterisation coefficients given in the
Iacono-Marziano et al. (2012) manuscript, but were incorrect (pers.comm.).
- 'anhydrous' for the anhydrous NBO/O parameterisation coefficients given in the
Iacono-Marziano et al. (2012) manuscript.
Returns
-------
float
Dissolved H2O concentration in wt%.
"""
if coeffs not in ['webapp', 'manuscript', 'anhydrous']:
raise core.InputError(
"The coeffs argument must be one of 'webapp', 'manuscript', "
"or 'anhydrous'")
temperature = temperature + 273.15 # translate T from C to K
if isinstance(sample, sample_class.Sample) is False:
raise core.InputError(
"Sample must be an instance of the Sample class.")
if pressure < 0:
raise core.InputError("Pressure must be positive.")
if X_fluid < 0 or X_fluid > 1:
raise core.InputError("X_fluid must have a value between 0 and 1.")
if pressure == 0:
return 0
if coeffs == 'webapp' or coeffs == 'manuscript':
if X_fluid == 0:
return 0
H2O = root_scalar(self.root_dissolved_volatiles,
args=(pressure, temperature, sample, X_fluid,
coeffs, kwargs),
x0=1.0,
x1=2.0).root
return H2O
else:
a = 0.54
b = 1.24
B = -2.95
C = 0.02
fugacity = self.fugacity_model.fugacity(pressure=pressure,
X_fluid=X_fluid,
temperature=temperature -
273.15,
**kwargs)
if fugacity == 0:
return 0
NBO_O = self.NBO_O(sample=sample, coeffs=coeffs)
H2O = np.exp(a * np.log(fugacity) + b * NBO_O + B +
C * pressure / temperature)
return H2O
def calculate_dissolved_volatiles(self,
pressure,
temperature=1200,
sample=None,
X_fluid=1.0,
**kwargs):
"""
Calclates the dissolved CO2 concentration using (Eqns) 2-7 or 10-11 from Allison et al.
(2019).
Parameters
----------
pressure float
Pressure in bars.
temperature float
Temperature in C.
sample NoneType or Sample class
Magma major element composition. Not required for this model, therefore None may be
passed.
X_fluid float
The mole fraction of CO2 in the fluid. Default is 1.0.
Returns
-------
float
Dissolved CO2 concentration in wt%.
"""
# temperature = 1200 #temp in degrees C
temperature = temperature + 273.15 # translate T from C to K
if pressure < 0.0:
raise core.InputError("Pressure must be positive.")
if X_fluid < 0 or X_fluid > 1:
raise core.InputError("X_fluid must have a value between 0 and 1.")
if self.model_fit not in ['power', 'thermodynamic']:
raise core.InputError(
"model_fit must be one of 'power', or 'thermodynamic'.")
if self.model_loc not in [
'sunset', 'sfvf', 'erebus', 'vesuvius', 'etna', 'stromboli'
]:
raise core.InputError(
"model_loc must be one of 'sunset', 'sfvf', 'erebus', ",
"'vesuvius', 'etna', or 'stromboli'.")
if pressure == 0:
return 0
if self.model_fit == 'thermodynamic':
P0 = 1000 # bar
params = dict({
'sunset': [16.4, -14.67],
'sfvf': [15.02, -14.87],
'erebus': [15.83, -14.65],
'vesuvius': [24.42, -14.04],
'etna': [21.59, -14.28],
'stromboli': [14.93, -14.68]
})
DV = params[self.model_loc][0]
lnK0 = params[self.model_loc][1]
lnK = lnK0 - (pressure - P0) * DV / (10 * 8.3141 * temperature)
fCO2 = self.fugacity_model.fugacity(pressure=pressure,
temperature=temperature -
273.15,
X_fluid=X_fluid,
**kwargs)
Kf = np.exp(lnK) * fCO2
XCO3 = Kf / (1 - Kf)
FWone = 36.594
wtCO2 = (44.01 * XCO3) / ((44.01 * XCO3) +
(1 - XCO3) * FWone) * 100
return wtCO2
if self.model_fit == 'power':
params = dict({
'stromboli': [1.05, 0.883],
'etna': [2.831, 0.797],
'vesuvius': [4.796, 0.754],
'sfvf': [3.273, 0.74],
'sunset': [4.32, 0.728],
'erebus': [5.145, 0.713]
})
fCO2 = self.fugacity_model.fugacity(pressure=pressure,
temperature=temperature -
273.15,
X_fluid=X_fluid,
**kwargs)
return params[self.model_loc][0] * fCO2**params[
self.model_loc][1] / 1e4
