About pyAp

pyAp is a python package for calculating magmatic volatile, trace element concentrations, and oxygen fugacity using mineral apatite. More modules will be added in the future.

Code authors: Weiran Li (University of Hong Kong) & Yishen Zhang (Rice University)

Introduction

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

  • ApThermo: a thermodynamic model for calculating melt H 2 O (and CO 2 ) concentrations (following Li & Costa, 2020, 2023, GCA)

    • Inputs: Apatite F, Cl and H 2 O (if available) concentrations; Temperature and melt Cl and/or F concentrations (for calculating melt water)

    • Outputs: Apatite stoichiometry (atom per fomula unit); Exchange coefficients for OH-Cl and/or OH-F; H 2 O concentrations in the melt

  • ApREE: a lattice strain-thermodynamic model for calculating melt trace element (including REEs) concentrations and oxygen fugacity ( f O 2) (following Li et al, 2023, CMP)

    • Inputs: Trace element concentrations in apatite and melt (be it melt inclusions/groundmass/whole rock)

    • Outputs: Partition coefficients of unmeasured trace elements; oxygen fugacity of the melt (if Eu was measured)

Citing pyAp

If you use this package please cite our publications for specific models:

ApThermo:

[1] Li, W. & Costa, F. (2020) A thermodynamic model for F-Cl-OH partitioning between apatite and melt including non-ideal mixing and applications to constraining melt volatile budgets, Geochimica et Cosmochimica Acta 269, 203–222. https://doi.org/10.1016/j.gca.2019.10.035

[2] Li, W., & Costa, F. (2023). Corrigendum to” A thermodynamic model for F-Cl-OH partitioning between silicate melts and apatite including non-ideal mixing with application to constraining melt volatile budgets”[Geochim. Cosmochim. Acta 269 (2020) 203-222]. Geochimica et Cosmochimica Acta, 347, 125-125.

ApREE:

Li, W., Costa, F, Oppenheimer, C. & Nagashima K. (2023) Volatile and trace element partitioning between apatite and alkaline melts. Contributions to Mineralogy and Petrology 178 (2), 9. https://doi.org/10.1007/s00410-022-01985-8

You are encouraged to cite the specific version of the package you used. The DOI of the first zenodo release (v0.1) is: 10.5281/zenodo.6228767