pyfastchem 4.0.3

FastChem, an ultra-fast equilibrium chemistry

FastChem 4

An ultra-fast equilibrium chemistry code for gas and condensed phases

Authors: Daniel Kitzmann, Joachim Stock

Overview

FastChem is an equilibrium chemistry code that calculates the chemical composition of the gas and condensed phase for given temperatures and pressures. The calculation of the gas phase is based on a semi-analytic approach, described in detail in Stock et al. (2018) and Stock et al. (2022). FastChem Cond (version 3) adds condensation to the code, computing chemical compositions using equilibrium condensation or the rainout approximation commonly used in the field of exoplanets and brown dwarfs, as described in Kitzmann, Stock & Patzer (2024). The current version FastChem 4 resolved convergence issues in both gas phase and condensate calculations and added a wide range of new elements and chemical species.

The code is written in object-oriented C++. The current version uses log-based element densities as primary variables, which avoids numerical underflow and allows FastChem to converge at temperatures as low as 1 K (without ions). Overall, the model has been successfully tested for temperatures from 100 K to 6000 K and pressures from 1e-13 bar to 1000 bar for solar element abundances.

Besides the actual FastChem model, we provide a C++ stand-alone version in the model_src folder that allows to calculate the equilibrium chemistry for a given temperature-pressure structure. In addition, we provide the Python interface PyFastChem.

Installation

PyFastChem (Python)

The easiest way to install FastChem is via pip:

pip install pyfastchem

On most platforms, this will download a pre-compiled package, so no compiler is needed.

Building from source (C++)

mkdir build && cd build
cmake ..
make -j

This produces the fastchem executable and the fastchem_lib library. To also build the Python wrapper via CMake:

cmake -DUSE_PYTHON=ON ..
make -j

PyFastChem

FastChem includes the Python interface PyFastChem that allows running the C++ code as a normal Python module. We provide several examples that show how to call FastChem from within a Python script, including iterating over different metallicity values or C/O ratios, and computing chemical compositions with condensation. The Python examples can be found in the python directory.

Notes on Apple Silicon

Previous versions of FastChem relied on long double (quadruple) precision for convergence at low temperatures. Since Apple Silicon (Mx) processors have no hardware support for quadruple-precision arithmetic, this caused convergence issues on these machines. The current version of FastChem has been redesigned to work fully in double precision, resolving this limitation.

OpenMP on macOS

FastChem automatically runs multiple calculations in parallel using OpenMP. Apple's default compiler (Apple Clang) does not ship with OpenMP support. To enable OpenMP parallelisation on macOS, install libomp via Homebrew:

brew install libomp

CMake and the Python build system (setup.py) will automatically detect and use it.

User Guide

FastChem comes with a user guide available at: https://newstrangeworlds.github.io/FastChem/

It describes the installation and usage of FastChem and covers both the C++ stand-alone version and the Python interface. The manual also contains detailed information on the internal interface functions that the FastChem object class and its Python interface provide.

Updated chemistry data

This FastChem release contains updated chemistry data, including new elements, gas-phase species, and condensates. As part of the update, some gas-phase isomers have been renamed. Since by default the gas-phase species in FastChem use the Hill notation, isomers were identified with an underscore. For example, HCN was declared as C1H1N1_1, while the isomer HNC was C1H1N1_2. In the new FastChem database, isomers now contain their actual molecular formular as part of the Hill notation. So, HCN is now referred to by C1H1N1_hcn, while HNC is C1H1N1_hnc. The same applies to AlOH (Al1H1O1_aloh), OAlH (Al1H1O1_oalh), SSF2 (F2S2_ssf2), and FS2F (F2S2_fs2f). The new function ConvertToHill notation automatically converts these isomers to the internal FastChem notation properly.

References

If you use FastChem in your work, please cite the relevant papers:

• FastChem (original method): Stock, J. W., Kitzmann, D., Patzer, A. B. C., & Sedlmayr, E. 2018, MNRAS, 479, 865. DOI: 10.1093/mnras/sty1531

• FastChem 2 (improved gas-phase solver): Stock, J. W., Kitzmann, D., & Patzer, A. B. C. 2022, MNRAS, 517, 4070. DOI: 10.1093/mnras/stac2623

• FastChem Cond (condensation & rainout): Kitzmann, D., Stock, J. W., & Patzer, A. B. C. 2024, MNRAS, 527, 7263. DOI: 10.1093/mnras/stad3515

BibTeX entries

@article{Stock2018,
  author  = {Stock, J. W. and Kitzmann, D. and Patzer, A. B. C. and Sedlmayr, E.},
  title   = {{FastChem: A computer program for efficient complex chemical equilibrium calculations in the neutral/ionized gas phase with applications to stellar and planetary atmospheres}},
  journal = {Monthly Notices of the Royal Astronomical Society},
  year    = {2018},
  volume  = {479},
  pages   = {865--874},
  doi     = {10.1093/mnras/sty1531}
}

@article{Stock2022,
  author  = {Stock, J. W. and Kitzmann, D. and Patzer, A. B. C.},
  title   = {{FastChem 2: an improved computer program to determine the gas-phase chemical equilibrium composition for arbitrary element distributions}},
  journal = {Monthly Notices of the Royal Astronomical Society},
  year    = {2022},
  volume  = {517},
  pages   = {4070--4080},
  doi     = {10.1093/mnras/stac2623}
}

@article{Kitzmann2024,
  author  = {Kitzmann, D. and Stock, J. W. and Patzer, A. B. C.},
  title   = {{FastChem Cond: equilibrium chemistry with condensation and rainout for cool planetary and stellar environments}},
  journal = {Monthly Notices of the Royal Astronomical Society},
  year    = {2024},
  volume  = {527},
  pages   = {7263--7283},
  doi     = {10.1093/mnras/stad3515}
}

Licence

This project is Copyright (c) Daniel Kitzmann and Joachim Stock.

FastChem is released under the GNU General Public Licence (GPL) 3.0. It can be freely copied, edited, and re-distributed. If the code is re-distributed it has to be released under at least a GPL 3.0 licence as well. The full licence can be found in the repository licence.md file.

The user guide is released under the Creative Commons Licence (CC BY SA). Licensees may copy and distribute the work and make derivative works based on it only if they give the authors (Daniel Kitzmann & Joachim Stock) the credits by providing a reference to the original guide and this GitHub repository. Licensees may also distribute derivative works only under a license identical to ("not more restrictive than") the license that governs the original work.