pytheriak 1.2.0

Python wrapper functions for Theriak-Domino.

pytheriak

Python wrapper functions for Theriak-Domino.

Installation

You can install the package from pypi.org. Run the following to install:

pip install pytheriak

Usage

Run theriak from your python script

Import the wrapper module.

from pytheriak import wrapper

First, create a TherCaller-object.
The programs_dir must be set to the Programs directory of your Theriak-Domino installation. Specify the database (ensure that you correctly specify the file extension e.g., .txt or .bs). Specify your version of Theriak-Domino for completeness.
To run Theriak from Python, the database file should be in the same directory as your python script. On Windows you must also have a theriak.ini in the directory.

theriak = wrapper.TherCaller(programs_dir="..\Programs",
                             database="a database file",
                             theriak_version="v2023.01.02beta")

As input for Theriak define:

1. Pressure in bars.

pressure = 4000

2. Temperature in degree celsius.

temperature = 550

3. Bulk composition following the Theriak-Domino format: Elements in uppercase followed by (number of moles).

bulk = "AL(2)SI(1)O(?)"

Then call minimisation() on the TherCaller-object.

rock, element_list = theriak.minimisation(pressure, temperature, bulk)

This method returns a Rock-object containing all the properties of the minimised system and an element list. The list acts as an element - index lookup table for all compositional vectors of the Rock (bulk and phase compositions).

Access the properties of the Rock-object

An easy way to checkout all accessible properties is looking at the object's attributes using ...

dir(rock)

Useful rock properties are:

rock.g_system                   # Gibbs free energy of the system [J]
rock.bulk_composition_moles     # Bulk composition [mol]
rock.mineral_assemblage         # List of stable solid phases
...

Mineral (and fluid) assemblage contain Mineral- and Fluid-Objects which hold the phase related properties.

mineral = rock.mineral_assemblage[i]

mineral.name                    # Phase name from database
mineral.n                       # Amount of phase [mol]
mineral.composition_apfu        # Mineral composition [apfu]
...

A quick, easy and pythonic way to retrieve properties is using list comprehensions.

[mineral.name for mineral in rock.mineral_assemblage]
[mineral.composition_apfu for mineral in rock.mineral_assemblage]

Cite pytheriak

The pytheriak package is registered on Zenodo. If you use pytheriak in your research, please cite it using the following DOI:

License

Theriak-Domino/pytheriak is licensed under the GNU General Public License v3.0. See LICENSE for more details.