| Name | pytheriak JSON |
| Version |
1.1.1
JSON |
| download |
| home_page | |
| Summary | Python wrapper functions for Theriak-Domino. |
| upload_time | 2024-02-11 13:11:38 |
| maintainer | |
| docs_url | None |
| author | Philip Hartmeier |
| requires_python | >=3.10,<4.0 |
| license | GPL-3.0-or-later |
| keywords |
|
| VCS |
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No requirements were recorded.
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# pytheriak
[](https://doi.org/10.5281/zenodo.7945482)
Python wrapper functions for Theriak-Domino.
## Installation
[](https://pypi.python.org/pypi/pytheriak)
[](https://pypi.python.org/pypi/pytheriak/)
You can install the package from pypi.org.
Run the following to install:
```python
pip install pytheriak
```
## Usage
### Run theriak from your python script
Import the wrapper module.
```python
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.
```python
theriak = wrapper.TherCaller(programs_dir="..\Programs",
database="a database file",
theriak_version="v2023.01.02beta")
```
As input for Theriak define:\
1. Pressure in bars.
```python
pressure = 4000
```
2. Temperature in degree celsius.
```python
temperature = 550
```
3. Bulk composition following the Theriak-Domino format: Elements in uppercase followed by (number of moles).
```python
bulk = "AL(2)SI(1)O(?)"
```
Then call minimisation() on the TherCaller-object.
```python
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 ...
```python
dir(rock)
```
Useful rock properties are:
```python
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.
```python
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.
```python
[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:
[](https://doi.org/10.5281/zenodo.7945482)
## License
Theriak-Domino/pytheriak is licensed under the GNU General Public License v3.0. See [LICENSE](LICENSE) for more details.
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"description": "# pytheriak\n[](https://doi.org/10.5281/zenodo.7945482)\n\nPython wrapper functions for Theriak-Domino.\n\n## Installation\n[](https://pypi.python.org/pypi/pytheriak)\n[](https://pypi.python.org/pypi/pytheriak/)\n\nYou can install the package from pypi.org.\nRun the following to install:\n\n```python\npip install pytheriak\n```\n\n## Usage\n\n### Run theriak from your python script\n\nImport the wrapper module.\n\n```python\nfrom pytheriak import wrapper\n```\nFirst, create a TherCaller-object.\\\nThe `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.\\\nTo 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.\n```python\ntheriak = wrapper.TherCaller(programs_dir=\"..\\Programs\",\n database=\"a database file\",\n theriak_version=\"v2023.01.02beta\")\n```\nAs input for Theriak define:\\\n1. Pressure in bars.\n```python\npressure = 4000\n```\n2. Temperature in degree celsius.\n```python\ntemperature = 550\n```\n3. Bulk composition following the Theriak-Domino format: Elements in uppercase followed by (number of moles).\n```python\nbulk = \"AL(2)SI(1)O(?)\"\n```\nThen call minimisation() on the TherCaller-object.\n```python\nrock, element_list = theriak.minimisation(pressure, temperature, bulk)\n```\nThis 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).\n\n### Access the properties of the Rock-object\n\nAn easy way to checkout all accessible properties is looking at the object's attributes using ...\n```python\ndir(rock)\n```\nUseful rock properties are:\n```python\nrock.g_system # Gibbs free energy of the system [J]\nrock.bulk_composition_moles # Bulk composition [mol]\nrock.mineral_assemblage # List of stable solid phases\n...\n```\nMineral (and fluid) assemblage contain Mineral- and Fluid-Objects which hold the phase related properties.\n```python\nmineral = rock.mineral_assemblage[i]\n\nmineral.name # Phase name from database\nmineral.n # Amount of phase [mol]\nmineral.composition_apfu # Mineral composition [apfu]\n...\n```\nA quick, easy and pythonic way to retrieve properties is using list comprehensions.\n```python\n[mineral.name for mineral in rock.mineral_assemblage]\n[mineral.composition_apfu for mineral in rock.mineral_assemblage]\n```\n\n## Cite pytheriak\n\nThe pytheriak package is registered on Zenodo. If you use pytheriak in your research, please cite it using the following DOI:\n\n[](https://doi.org/10.5281/zenodo.7945482)\n\n## License\n\nTheriak-Domino/pytheriak is licensed under the GNU General Public License v3.0. See [LICENSE](LICENSE) for more details.\n",
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