pyAp package

pyAp.ApStoic module

Weiran Li & Yishen Zhang

2022-07-08, v0.2

Please cite the paper below if you use “ApThermo” in your research:

Li and Costa (2020, GCA) https://doi.org/10.1016/j.gca.2019.10.035

pyAp.ApStoic.stoi_(data, assume_oxy=26)

function to test apatite stoichiometry

Parameters:

data: :class: pandas.Dataframe oxygen number: default is 26 for FAp, and 25 for OHAp [Use “ApStoic_Ketcham.py” if you wish to use oxygen number depending on the crystal composition (between 25-26) following Ketcham2015]

Return:

res_apfu: :class: pandas.Dataframe

saved csv file

pyAp.ApTernary module

Weiran Li & Yishen Zhang

2022-02-20, v0.2

Please cite the paper below if you use “ApThermo” in your research:

Li and Costa (2020, GCA) https://doi.org/10.1016/j.gca.2019.10.035

pyAp.ApTernary.ternary(ax)

Function for apatite ternary plot on an axis (“ax” as input).

The figure where the axis is located needs to be defined outside of this function.

pyAp.pyAp_tools module

Weiran Li & Yishen Zhang

2022-02-20, v0.2

pyAp.pyAp_tools.ap_mc(comp, std, i, mc)

MC calculation model for pyAp

Parameters:

comp: :class: pandas.Dataframe std: :class: pandas.Dataframe i: :class: numpy.array

index for iteration

mc: :class: numpy.array

number of monte carlo simulation

Returns:

df: :class: pandas.Dataframe

expanded dataframe after monte carlo simulation

pyAp.pyAp_tools.load_animation()

pyAp.pyAp_tools.yes_or_no(question)

pyAp.pyApthermo module

Weiran Li & Yishen Zhang

2022-07-08, v0.2

Please cite the paper below if you use “ApThermo” in your research:

Li and Costa (2020, GCA) https://doi.org/10.1016/j.gca.2019.10.035

class pyAp.pyApthermo.ApThermo(inputs, cal_H2O=True, cal_gamma=False)

Bases: object

calculate exchange coefficients (Kd) and melt water contents using apatite

Input values should be filled in the provided excel spreadsheet.

!! Do NOT change the column header names in the input file, as this code reads the data according to those names (it’s okay to change column orders).

Parameters (“inputs”)

Inputs have to follow this order: “XF”, “XCL”, “T,C”, “MELTF”, “MELTCL”, “MELTCOMP”,

For Kd calculation: * XF : mole fraction of F in apatite (can be calculated from “pyAp/ApStoic.py”) * XCL : mole fraction of Cl in apatite * “T,C” : temperature in celsius degree

For water calculation (if “cal_H2O==True”): * MELTF : F concentration in the melt, in wt% * MELTCL : Cl concentration in the melt, in wt% * MELTCOMP: Melt composition (for choosing water speciation model)

Switches (conditions for calculation)

For water speciation: “highP” , “highT” (see below)

“cal_H2O”choose whether to calculate melt water contents

default = True

“cal_gamma”: choose whether to calculate activity coefficients of F, Cl, OH in the melt (for further calculations beyond this model)

default = False

Kd()

calculate exchange coefficients Kd using apatite F-Cl-OH composition, and temperature (T)

return Kds for OH-Cl, OH-F, Cl-F, and activity coefficients (gamma) for OH, F, Cl

conversion(moleOH_melt, k2)

convert melt OH (moles) to melt total H2O (wt%)

return total H2O concentration (wt%) in the melt

meltH2O()

calculate water concentrations in the melt (wt%) using OH/Cl and/or OH/F in the melt and the “conversion” func written above

return all results: melt water estimates, KDs, gammas

Module contents

pyAp

pyAp is a python package for calculating magmatic volatile, trace element concentrations, and oxygen fugacity using mineral apatite.

It includes multiple apatite-based models developed by W. Li and co-authors, including:

ApThermo: a thermodynamic model for calculating melt H2O (and CO2) concentrations (following Li & Costa, 2020, GCA) ApREE2O3: a lattice strain-thermodynamic model for calculating melt trace element (including REE) concentrations and oxygen fugacity (fO2) (following Li et al, in review)

More modules will be added in the future (ApTimer - Li et al. 2020 EPSL; ApZone - Li et al. in prep).