Metadata-Version: 2.1
Name: pytoughreact
Version: 1.0.3
Summary: Python Library for automating reaction simulations using TOUGHREACT, TMVOC and TMVOC-BIO
Author-email: Temitope Ajayi <ajayi_temmy@yahoo.com>
Maintainer-email: Temitope Ajayi <ajayi_temmy@yahoo.com>
License: MIT License
        
        Copyright (c) 2023 Temitope Ajayi
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: repository, https://github.com/temmy222/PyTOUGHREACT
Keywords: biodegradation,reactive transport,automation,uncertainty quantification
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy >=1
Requires-Dist: scipy >=1
Requires-Dist: vtk >=1
Requires-Dist: matplotlib >=3
Requires-Dist: pandas >=1
Requires-Dist: PyTOUGH

# PyTOUGHREACT


- [PyTOUGHREACT](#pytoughreact)
  - [Installation](#installation)
  - [Usage](#usage)
  - [Contributing](#contributing)
  - [Documentation](#documentation)
  - [License](#license)
  - [Tests](#tests)


PyTOUGHREACT is a Python package for automating reactive transport simulations including biodegradation reactions.
It makes use of TOUGHREACT, TMVOC and TMVOCBIO executables for running the simulations. These executables are interfaced
with python to automate the runs. It will be particularly useful for uncertainty quantifications, sensitivity 
analysis without the need to have a lot of files stored on your local computer. It builds on the PyTOUGH software which processes for the TOUGH2 executables.

## Installation

PyTOUGHREACT is available on PyPI which is a repository of softwares built with the Python Programming Language. Before installing PyTOUGHREACT, it is required to have Python >=3.7 installed on your local computer. Python can be downloaded from the [python.org](python.org) website and installing it by following the instructions. Windows users should ensure that the path to the python is set in the environment variable to ensure availability everywhere.

Use the package manager [pip](https://pip.pypa.io/en/stable/) to install PyTOUGHREACT.

```bash
pip install pytoughreact
```

The package can also be forked from this GitHub page and installation performed using

```bash
python setup.py install  or py setup.py install
```

Because pytoughreact requires PyTOUGH and PyTOUGH is not uploaded to PyPI, it is required to download the zip folder of PyTOUGH from the GitHub repository https://github.com/acroucher/PyTOUGH. Unzip the folder and place in your current working directory. Change directory into the PyTOUGH folder and run python setup.py install or pip install on the command line. With PyTOUGH installed, PyTOUGHREACT is ready to be used as a package.

## Usage

```python
import os
from mulgrids import mulgrid
from pytoughreact.writers.react_writing import t2react
from pytoughreact.pytough_wrapper.wrapper.reactgrid import t2reactgrid
from pytoughreact.pytough_wrapper.wrapper.reactzone import t2zone
from pytoughreact.chemical.chemical_composition import PrimarySpecies, WaterComp, Water, ReactGas
from pytoughreact.chemical.mineral_composition import MineralComp
from pytoughreact.chemical.mineral_zone import MineralZone
from pytoughreact.chemical.mineral_description import Mineral
from pytoughreact.constants.default_minerals import get_kinetics_minerals, get_specific_mineral
from pytoughreact.writers.chemical_writing import t2chemical
from pytoughreact.writers.solute_writing import t2solute
from t2grids import rocktype

#__________________________________FLOW.INP____________________________________________
length = 0.1
nblks = 1
dx = [length / nblks] * nblks
dy = [0.5]
dz = [0.5] * 1
geo = mulgrid().rectangular(dx, dy, dz)
geo.write('geom.dat')

react = t2react()
react.title = 'Reaction example'

react.multi = {'num_components': 1, 'num_equations': 1, 'num_phases': 2,
               'num_secondary_parameters': 6}

react.grid = t2reactgrid().fromgeo(geo)

react.parameter.update(
    {'print_level': 4,
     'max_timesteps': 9999,
     'tstop': 8640,
     'const_timestep': 10.,
     'print_interval': 1,
     'gravity': 9.81,
     'relative_error': 1e-5,
     'phase_index': 2,
     'default_incons': [1.013e5, 25]})

sand = rocktype('ROCK1', 0, 2600, 0.1, [6.51e-12, 6.51e-12, 6.51e-12], 0.0, 952.9)

react.grid.delete_rocktype('dfalt')
react.grid.add_rocktype(sand)

for blk in react.grid.blocklist[0:]:
    blk.rocktype = react.grid.rocktype[sand.name]


zone1 = t2zone('zone1')

react.grid.add_zone(zone1)

for blk in react.grid.blocklist[0:]:
    blk.zone = react.grid.zone[zone1.name]

react.start = True

react.write('flow.inp')

#____________________________________CHEMICAL.INP________________________________________
h2o = PrimarySpecies('h2o', 0)
h = PrimarySpecies('h+', 0)
na = PrimarySpecies('na+', 0)
cl = PrimarySpecies('cl-', 0)
hco3 = PrimarySpecies('hco3-', 0)
ca = PrimarySpecies('ca+2', 0)
so4 = PrimarySpecies('so4-2', 0)
mg = PrimarySpecies('mg+2', 0)
h4sio4 = PrimarySpecies('h4sio4', 0)
al = PrimarySpecies('al+3', 0)
fe = PrimarySpecies('fe+2', 0)
hs = PrimarySpecies('hs-', 0)

all_species = [h2o, h,na, cl, hco3, ca, so4, mg, h4sio4, al, fe, hs]

h2o_comp1 = WaterComp(h2o, 1, 1.0000E+00, 1.000000E+00)
h_comp1 = WaterComp(h, 1, 1E-7, 1E-7)
na_comp1 = WaterComp(na, 1, 1E-10, 2.93E-2)
cl_comp1 = WaterComp(cl, 1, 1E-10, 1.08E-3)
hco3_comp1 = WaterComp(hco3, 1, 1E-10, 2.21E-08)
ca_comp1 = WaterComp(ca, 1, 1E-10, 5.9E-03)
so4_comp1 = WaterComp(so4, 1, 1E-10, 6.94E-3)
mg_comp1 = WaterComp(mg, 1, 1E-10, 2.54E-8)
h4sio4_comp1 = WaterComp(h4sio4, 1, 1E-10, 1E-10)
al_comp1 = WaterComp(al, 1, 1E-10, 9.96E-5)
fe_comp1 = WaterComp(fe, 1, 1E-10, 9.7E-9)
hs_comp1 = WaterComp(hs, 1, 1E-10, 1E-10)

initial_water_zone1 = Water([h2o_comp1, h_comp1, na_comp1, cl_comp1, hco3_comp1, ca_comp1, so4_comp1, mg_comp1, h4sio4_comp1, al_comp1, fe_comp1, hs_comp1], 25, 200)

mineral_list = ['c3fh6', 'tobermorite', 'calcite', 'csh' , 'portlandite', 'ettringite', 'katoite', 'hydrotalcite']
all_minerals = get_kinetics_minerals(mineral_list)


c3fh6_zone1 = MineralComp(get_specific_mineral(mineral_list[0]), 0.1, 0, 0.0E-00, 20000.0, 0)
tobermorite_zone1 = MineralComp(get_specific_mineral(mineral_list[1]), 0.05, 0, 0.0E-00, 20000.0, 0)
calcite_zone1 = MineralComp(get_specific_mineral(mineral_list[2]), 0.4, 1, 0.0E-00, 260.0, 0)
csh_zone1 = MineralComp(get_specific_mineral(mineral_list[3]), 0.1, 1, 0.0E-00, 20000.0, 0)
portlandite_zone1 = MineralComp(get_specific_mineral(mineral_list[4]), 0.1, 1, 0.0E-00, 1540.0, 0)
ettringite_zone1 = MineralComp(get_specific_mineral(mineral_list[5]), 0.1, 1, 0.0E-00, 20000.0, 0)
katoite_zone1 = MineralComp(get_specific_mineral(mineral_list[6]), 0.1, 1, 0.0E-00, 570.0, 0)
hydrotalcite_zone1 = MineralComp(get_specific_mineral(mineral_list[7]), 0.05, 1, 0.0E-00, 1000.0, 0)

initial_co2 = ReactGas('co2(g)', 0, 1.1)
ijgas = [[initial_co2], []]

zone1.water = [[initial_water_zone1], []]
zone1.gas = [[initial_co2], []]
mineral_zone1 = MineralZone([c3fh6_zone1, tobermorite_zone1, calcite_zone1, csh_zone1, portlandite_zone1, ettringite_zone1, katoite_zone1, hydrotalcite_zone1])
zone1.mineral_zone = mineral_zone1

writeChemical = t2chemical(t2reactgrid=react.grid)
writeChemical.minerals = all_minerals
writeChemical.title = 'Automating Tough react'
writeChemical.primary_aqueous = all_species
writeChemical.gases = initial_co2
writeChemical.write()

#____________________________________SOLUTE.INP__________________________________________
writeSolute = t2solute(writeChemical)
writeSolute.nodes_to_write = [0]
masa = writeSolute.getgrid_info()
writeSolute.write()

#___________________________________ RUN SIMULATION ______________________________________
react.run(simulator='treacteos1.exe', runlocation=os.getcwd())


```

## Contributing
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Contributing to the code would involve you following the below procedures to quickly get started

1. Clone the repo using preferred cloning method
2. Install the library to enable you able to use the test example using

```python
pip install -e .
```
3. Modify the code 
4. Run tests: Tests are conducted with pytest. Flake8 is also used to ensure code readability

```python
pytest
```
5. Make a pull request after passing all tests

## Documentation
Documentation can be found here https://pytoughreact.readthedocs.io/en/latest/ 


## License
[MIT](https://choosealicense.com/licenses/mit/)

## Tests

![Tests](https://github.com/temmy222/PyTOUGHREACT/actions/workflows/tests.yml/badge.svg)
![JOSS Article](https://github.com/temmy222/PyTOUGHREACT/actions/workflows/draft-pdf.yml/badge.svg)
![Dependabot](https://img.shields.io/badge/dependabot-025E8C?style=for-the-badge&logo=dependabot&logoColor=white)
![GitHub contributors](https://img.shields.io/github/contributors/temmy222/PyTOUGHREACT)
![PyPI - Version](https://img.shields.io/pypi/v/PyTOUGHREACT)
![PyPI - License](https://img.shields.io/pypi/l/pytoughreact)
