[![Test][test_badge]][test_workflow]
# compaction: Compact layers of sediment
Compact a column of sediment following Bahr et al., 2001.
Cite as,
```bibtex
@article{bahr2001exponential,
title={Exponential approximations to compacted sediment porosity profiles},
author={Bahr, David B and Hutton, Eric WH and Syvitski, James PM and Pratson, Lincoln F},
journal={Computers \& Geosciences},
volume={27},
number={6},
pages={691--700},
year={2001},
publisher={Pergamon}
}
```
## Requirements
*Compaction* requires Python 3.
Apart from Python, *Compaction* has a number of other requirements, all of which
can be obtained through either *pip* or *conda*, that will be automatically
installed when you install *Compaction*.
To see a full listing of the requirements, have a look at the project's
*requirements.txt* file.
If you are a developer of *Compaction* you will also want to install
additional dependencies for running *Compaction*'s tests to make sure
that things are working as they should. These dependencies are listed
in *requirements-testing.txt*.
## Installation
To install *Compaction*, first create a new environment in
which *Compaction* will be installed. This, although not necessary, will
isolate the installation so that there won't be conflicts with your
base *Python* installation. This can be done with *conda* as:
```bash
conda create -n compaction python=3
conda activate compaction
```
## Stable Release
*Compaction*, and its dependencies, can be installed either with *pip*
or *conda*. Using *pip*:
```bash
pip install compaction
```
Using *conda*:
```bash
conda install compaction -c conda-forge
```
### From Source
After downloading the *Compaction* source code, run the following from
*Compaction*'s top-level folder (the one that contains *setup.py*) to
install *Compaction* into the current environment:
```bash
pip install -e .
```
## Input Files
### Configuration File
The main *Compaction* input file is a yaml-formatted text file that lists
constants used by *Compaction*. Running the following will print a sample
*Compaction* configuration file:
```
compact show config
```
```yaml
c: 5.0e-08
porosity_max: 0.5
porosity_min: 0.0
rho_grain: 2650.0
rho_void: 1000.0
```
### Porosity File
The *Compaction* porosity file defines initial porosity of each of the
sediment layers to be compacted as a two-column CSV file. The first
column is layer thickness (in meters) and the second the porosity of
the sediment in that layer. A sample porosity file can be obtained with:
```bash
compact show porosity
```
```
# Layer Thickness [m], Porosity [-]
100.0,0.5
100.0,0.5
100.0,0.5
```
## Output File
The output file of *Compaction* is a porosity file of the same form as
the input porosity file - a CSV file of layer thickness and porosity.
## Examples
To run a simulation using the sample input files described above, you first
need to create a set of sample files:
```
sequence setup example
```
```
example/sequence.yaml
```
You can now run the simulation:
```bash
sequence run example/sequence.yaml
```
```
# Layer Thickness [m], Porosity [-]
100.0,0.5
96.18666488709239,0.4801774231522433
92.78860257194452,0.4611407154102571
```
[test_badge]: https://github.com/mcflugen/compaction/actions/workflows/test.yml/badge.svg
[test_workflow]: https://github.com/mcflugen/compaction/actions/workflows/test.yml
# Credits
## Development Lead
* [Eric Hutton](https://github.com/mcflugen)
# Contributors
None yet. Why not be the first?
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