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https://github.com/aiidaplugins/aiida-lammps
LAMMPS plugin for AiiDA
https://github.com/aiidaplugins/aiida-lammps
aiida lammps plugin
Last synced: 1 day ago
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LAMMPS plugin for AiiDA
- Host: GitHub
- URL: https://github.com/aiidaplugins/aiida-lammps
- Owner: aiidaplugins
- License: mit
- Created: 2017-11-02T09:25:35.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2024-12-24T10:34:34.000Z (10 days ago)
- Last Synced: 2024-12-24T11:44:22.124Z (10 days ago)
- Topics: aiida, lammps, plugin
- Language: Python
- Homepage: https://aiida-lammps.readthedocs.io
- Size: 1.7 MB
- Stars: 25
- Watchers: 4
- Forks: 15
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://github.com/aiidaplugins/aiida-lammps)
[](https://codecov.io/gh/aiidaplugins/aiida-lammps)
[](https://pypi.python.org/pypi/aiida-lammps/)
[](https://github.com/ambv/black)
[](http://aiida-lammps.readthedocs.io/)
# AiiDA LAMMPS plugin
An [AiiDA](http://aiida-core.readthedocs.io/) plugin for the classical molecular dynamics code [LAMMPS](https://www.lammps.org).
This plugin contains 2 types of calculations:
- `lammps.base`: Calculation making use of parameter based input generation for single stage LAMMPS calculations.
- `lammps.raw`: Calculation making use of a pre-made LAMMPS input file.
The `lammps.base` is also used to handle three workflows:
- `lammps.base`: A workflow that can be used to submit any single stage LAMMPS calculation.
- `lammps.relax`: A workflow to submit a structural relaxation using LAMMPS.
- `lammps.md`: A workflow to submit a molecular dynamics calculation using LAMMPS.
- [AiiDA LAMMPS plugin](#aiida-lammps-plugin)
- [Installation](#installation)
- [Built-in Potential Support](#built-in-potential-support)
- [Examples](#examples)
- [Code Setup](#code-setup)
- [Structure Setup](#structure-setup)
- [Potential Setup](#potential-setup)
- [Force Calculation](#force-calculation)
- [Optimisation Calculation](#optimisation-calculation)
- [MD Calculation](#md-calculation)
- [Development](#development)
- [Coding Style Requirements](#coding-style-requirements)
- [Testing](#testing)
## Installation
To install a stable version from pypi:
```shell
pip install aiida-lammps
```
To install from source:
```shell
git clone https://github.com/aiidaplugins/aiida-lammps.git
pip install -e aiida-lammps
```
## Built-in Potential Support
The `lammps.base` calculation and associated workflows make use of the ``LammpsPotentialData`` data structure which is created by passing a potential file, plus some labelling parameters to it.
This data structure can be used to handle the following potential types:
- Single file potentials: Any potential that can be stored in a single file, e.g. [EAM](https://docs.lammps.org/pair_eam.html), [MEAM](https://docs.lammps.org/pair_meam.html), [Tersoff](https://docs.lammps.org/pair_tersoff.html) and [ReaxFF](https://docs.lammps.org/pair_reaxff.html).
- Directly parametrized potentials: Potentials whose parameters are directly given via ``pair_coeff`` in the input file, e.g [Born](https://docs.lammps.org/pair_born_gauss.html), [Lennard-Jones](https://docs.lammps.org/pair_line_lj.html) and [Yukawa](https://docs.lammps.org/pair_yukawa.html). These parameters should be written into a file that is then stored into a ``LammpsPotentialData`` node.
## Examples
More example calculations are found in the folder **/examples** as well as in the documentation. The examples touch some common cases for the usage of LAMMPS for a single stage calculation.
## Development
### Running tests
The test suite can be run in an isolated, virtual environment using `tox` (see `tox.ini` in the repo):
```shell
pip install tox
tox -e 3.9-aiida_lammps -- tests/
```
or directly:
```shell
pip install .[testing]
pytest -v
```
The tests require that both PostgreSQL and RabbitMQ are running.
If you wish to run an isolated RabbitMQ instance, see the `docker-compose.yml` file in the repo.
Some tests require that a `lammps` executable be present.
The easiest way to achieve this is to use Conda:
```shell
conda install lammps==2019.06.05
# this will install lmp_serial and lmp_mpi
```
You can specify a different executable name for LAMMPS with:
```shell
tox -e 3.9-aiida_lammps -- --lammps-exec lmp_exec
```
To output the results of calcjob executions to a specific directory:
```shell
pytest --lammps-workdir "test_workdir"
```
### Pre-commit
The code is formatted and linted using [pre-commit](https://pre-commit.com/), so that the code conform to the standard:
```shell
cd aiida-lammps
pre-commit run --all
```
or to automate runs, triggered before each commit:
```shell
pre-commit install
```
## License
The `aiida-lammps` plugin package is released under the MIT license. See the `LICENSE` file for more details.