pyAp

Code authors: Dr. Weiran (Alex) Li (weiranli@hku.hk; University of Hong Kong) & Dr. Yishen (Eason) Zhang (Rice University)

Introduction

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.

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 (Li & Costa, 2020, 2023, GCA; see citations below).

  • Inputs: Apatite F, Cl and H₂O (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; H₂O concentrations in the melt.

• ApREE: a lattice strain-thermodynamic model for calculating melt trace element (including REE) concentrations and oxygen fugacity (fO₂) (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).

Documentation

Full documentation, further information about the package, and a tutorial for getting started are provided at pyap.readthedocs.io

Installation

pyAp can be installed by running python setup.py install in the package depository using command line commands.

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