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aiida-gromacs-0.0.1
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مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
A plugin for using GROMACS with AiiDA for molecular dymanics simulations.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | aiida-gromacs-0.0.1 |
| نام | aiida-gromacs |
| نسخه کتابخانه | 0.0.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | James Gebbie-Rayet |
| ایمیل نویسنده | james.gebbie@stfc.ac.uk |
| آدرس صفحه اصلی | https://github.com/jimboid/aiida-gromacs |
| آدرس اینترنتی | https://pypi.org/project/aiida-gromacs/ |
| مجوز | MIT |
[](https://github.com/jimboid/aiida-gromacs/actions)
[](https://coveralls.io/github/jimboid/aiida-gromacs?branch=master)
[](http://aiida-gromacs.readthedocs.io/)
[](https://badge.fury.io/py/aiida-gromacs)
# aiida-gromacs
A plugin for using GROMACS with AiiDA for molecular dymanics simulations.
This plugin is the default output of the
[AiiDA plugin cutter](https://github.com/aiidateam/aiida-plugin-cutter),
intended to help developers get started with their AiiDA plugins.
## Repository contents
* [`.github/`](.github/): [Github Actions](https://github.com/features/actions) configuration
* [`ci.yml`](.github/workflows/ci.yml): runs tests, checks test coverage and builds documentation at every new commit
* [`publish-on-pypi.yml`](.github/workflows/publish-on-pypi.yml): automatically deploy git tags to PyPI - just generate a [PyPI API token](https://pypi.org/help/#apitoken) for your PyPI account and add it to the `pypi_token` secret of your github repository
* [`aiida_gromacs/`](aiida_gromacs/): The main source code of the plugin package
* [`data/`](aiida_gromacs/data/): A new `DiffParameters` data class, used as input to the `DiffCalculation` `CalcJob` class
* [`calculations.py`](aiida_gromacs/calculations.py): A new `DiffCalculation` `CalcJob` class
* [`cli.py`](aiida_gromacs/cli.py): Extensions of the `verdi data` command line interface for the `DiffParameters` class
* [`helpers.py`](aiida_gromacs/helpers.py): Helpers for setting up an AiiDA code for `diff` automatically
* [`parsers.py`](aiida_gromacs/parsers.py): A new `Parser` for the `DiffCalculation`
* [`docs/`](docs/): A documentation template ready for publication on [Read the Docs](http://aiida-diff.readthedocs.io/en/latest/)
* [`examples/`](examples/): An example of how to submit a calculation using this plugin
* [`tests/`](tests/): Basic regression tests using the [pytest](https://docs.pytest.org/en/latest/) framework (submitting a calculation, ...). Install `pip install -e .[testing]` and run `pytest`.
* [`.coveragerc`](.coveragerc): Configuration of [coverage.py](https://coverage.readthedocs.io/en/latest) tool reporting which lines of your plugin are covered by tests
* [`.gitignore`](.gitignore): Telling git which files to ignore
* [`.pre-commit-config.yaml`](.pre-commit-config.yaml): Configuration of [pre-commit hooks](https://pre-commit.com/) that sanitize coding style and check for syntax errors. Enable via `pip install -e .[pre-commit] && pre-commit install`
* [`.readthedocs.yml`](.readthedocs.yml): Configuration of documentation build for [Read the Docs](https://readthedocs.org/)
* [`LICENSE`](LICENSE): License for your plugin
* [`MANIFEST.in`](MANIFEST.in): Configure non-Python files to be included for publication on [PyPI](https://pypi.org/)
* [`README.md`](README.md): This file
* [`conftest.py`](conftest.py): Configuration of fixtures for [pytest](https://docs.pytest.org/en/latest/)
* [`pytest.ini`](pytest.ini): Configuration of [pytest](https://docs.pytest.org/en/latest/) test discovery
* [`setup.json`](setup.json): Plugin metadata for registration on [PyPI](https://pypi.org/) and the [AiiDA plugin registry](https://aiidateam.github.io/aiida-registry/) (including entry points)
* [`setup.py`](setup.py): Installation script for pip / [PyPI](https://pypi.org/)
See also the following video sequences from the 2019-05 AiiDA tutorial:
* [aiida-diff setup.json](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=240s)
* [run aiida-diff example calculation](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=403s)
* [aiida-diff CalcJob plugin](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=685s)
* [aiida-diff Parser plugin](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=936s)
* [aiida-diff computer/code helpers](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1238s)
* [aiida-diff input data (with validation)](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1353s)
* [aiida-diff cli](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1621s)
* [aiida-diff tests](https://www.youtube.com/watch?v=2CxiuiA1uVs&t=1931s)
* [Adding your plugin to the registry](https://www.youtube.com/watch?v=760O2lDB-TM&t=112s)
* [pre-commit hooks](https://www.youtube.com/watch?v=760O2lDB-TM&t=333s)
For more information, see the [developer guide](https://aiida-diff.readthedocs.io/en/latest/developer_guide) of your plugin.
## Features
* Add input files using `SinglefileData`:
```python
SinglefileData = DataFactory('singlefile')
inputs['file1'] = SinglefileData(file='/path/to/file1')
inputs['file2'] = SinglefileData(file='/path/to/file2')
```
* Specify command line options via a python dictionary and `DiffParameters`:
```python
d = { 'ignore-case': True }
DiffParameters = DataFactory('gromacs')
inputs['parameters'] = DiffParameters(dict=d)
```
* `DiffParameters` dictionaries are validated using [voluptuous](https://github.com/alecthomas/voluptuous).
Find out about supported options:
```python
DiffParameters = DataFactory('gromacs')
print(DiffParameters.schema.schema)
```
## Installation
```shell
pip install aiida-gromacs
verdi quicksetup # better to set up a new profile
verdi plugin list aiida.calculations # should now show your calclulation plugins
```
## Usage
Here goes a complete example of how to submit a test calculation using this plugin.
A quick demo of how to submit a calculation:
```shell
verdi daemon start # make sure the daemon is running
cd examples
./example_01.py # run test calculation
verdi process list -a # check record of calculation
```
The plugin also includes verdi commands to inspect its data types:
```shell
verdi data gromacs list
verdi data gromacs export <PK>
```
## Development
```shell
git clone https://github.com/jimboid/aiida-gromacs .
cd aiida-gromacs
pip install -e .[pre-commit,testing] # install extra dependencies
pre-commit install # install pre-commit hooks
pytest -v # discover and run all tests
```
See the [developer guide](http://aiida-gromacs.readthedocs.io/en/latest/developer_guide/index.html) for more information.
## License
MIT
## Contact
james.gebbie@stfc.ac.uk
نحوه نصب
نصب پکیج whl aiida-gromacs-0.0.1:
pip install aiida-gromacs-0.0.1.whl
نصب پکیج tar.gz aiida-gromacs-0.0.1:
pip install aiida-gromacs-0.0.1.tar.gz