# Dynamics
[](https://pypi.python.org/pypi/atooms-dynamics/)
[](https://pypi.python.org/pypi/atooms-dynamics/)
[](https://en.wikipedia.org/wiki/GNU_General_Public_License)
[](https://mybinder.org/v2/git/https%3A%2F%2Fframagit.org%2Fatooms%2Fdynamics/HEAD?labpath=docs%2Findex.ipynb)
[](https://framagit.org/atooms/dynamics/badges/master/pipeline.svg)
[](https://framagit.org/atooms/dynamics/-/commits/master)
Newtonian and stochastic dynamics backends for atooms.
## Quick start
Run a molecular dynamics simulation of a Lennard-Jones system from an existing xyz file
```python
from atooms.trajectory import Trajectory
from atooms.simulation import Simulation
from atooms.dynamics.netwonian import VelocityVerlet
# Start from the last frame of input.xyz
trajectory = Trajectory('input.xyz')
system = trajectory[-1]
system.interaction = Interaction('lennard_jones')
backend = VelocityVerlet(system, timestep=0.002)
sim = Simulation(backend, steps=200)
sim.run()
```
Do the same via the API, storing configurations in `output.xyz`,
```python
from atooms.dynamics.api import md
md('input.xyz', 'output.xyz',
method='velocity-verlet', model='lennard_jones',
dt=0.002, nsteps=200, config_number=20)
```
or from the command line
```sh
md.py --method velocity-verlet -n 200 --dt 0.002 --config-number 20 input.xyz output.xyz
```
## Features
Integration algorithms (work in progress)
- Netwonian dynamics
- velocity-Verlet
- Nose-Poincaré
- Berendsen thermostat/barostat
- event-driven
- Stochastic dynamics
- overdamped Langevin dynamics
## Documentation
Check out the [tutorial](https://atooms.frama.io/dynamics/tutorial) for more examples and the [public API](https://atooms.frama.io/postprocessing/api/dynamics) for full details.
Org-mode and jupyter notebooks are available under `docs/`. You can run the tutorial interactively on [Binder]( https://mybinder.org/v2/git/https%3A%2F%2Fframagit.org%2Fatooms%2Fdynamics/HEAD?labpath=docs%2Findex.ipynb).
## Installation
From pypi
```
pip install atooms-dynamics
```
You can clone the code repository and install from source
```
git clone https://framagit.org/atooms/dynamics.git
cd dynamics
make install
```
## Contributing
Contributions to the project are welcome. If you wish to contribute, check out [these guidelines](https://framagit.org/atooms/atooms/-/blob/master/CONTRIBUTING.md).
## Authors
Daniele Coslovich: https://www.units.it/daniele.coslovich/
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"description": "# Dynamics\n\n[](https://pypi.python.org/pypi/atooms-dynamics/)\n[](https://pypi.python.org/pypi/atooms-dynamics/)\n[](https://en.wikipedia.org/wiki/GNU_General_Public_License)\n[](https://mybinder.org/v2/git/https%3A%2F%2Fframagit.org%2Fatooms%2Fdynamics/HEAD?labpath=docs%2Findex.ipynb)\n[](https://framagit.org/atooms/dynamics/badges/master/pipeline.svg)\n[](https://framagit.org/atooms/dynamics/-/commits/master)\n\nNewtonian and stochastic dynamics backends for atooms.\n\n## Quick start\n\nRun a molecular dynamics simulation of a Lennard-Jones system from an existing xyz file\n```python\nfrom atooms.trajectory import Trajectory\nfrom atooms.simulation import Simulation\nfrom atooms.dynamics.netwonian import VelocityVerlet\n\n# Start from the last frame of input.xyz\ntrajectory = Trajectory('input.xyz')\nsystem = trajectory[-1]\nsystem.interaction = Interaction('lennard_jones')\nbackend = VelocityVerlet(system, timestep=0.002)\nsim = Simulation(backend, steps=200)\nsim.run()\n```\n\nDo the same via the API, storing configurations in `output.xyz`,\n```python\nfrom atooms.dynamics.api import md\n\nmd('input.xyz', 'output.xyz',\n method='velocity-verlet', model='lennard_jones',\n dt=0.002, nsteps=200, config_number=20)\n```\n\nor from the command line\n```sh\nmd.py --method velocity-verlet -n 200 --dt 0.002 --config-number 20 input.xyz output.xyz\n```\n\n## Features\n\nIntegration algorithms (work in progress)\n\n- Netwonian dynamics\n - velocity-Verlet\n - Nose-Poincar\u00e9\n - Berendsen thermostat/barostat\n - event-driven\n- Stochastic dynamics\n - overdamped Langevin dynamics\n\n## Documentation\n\nCheck out the [tutorial](https://atooms.frama.io/dynamics/tutorial) for more examples and the [public API](https://atooms.frama.io/postprocessing/api/dynamics) for full details.\n\nOrg-mode and jupyter notebooks are available under `docs/`. You can run the tutorial interactively on [Binder]( https://mybinder.org/v2/git/https%3A%2F%2Fframagit.org%2Fatooms%2Fdynamics/HEAD?labpath=docs%2Findex.ipynb).\n\n## Installation\n\nFrom pypi\n```\npip install atooms-dynamics\n```\n\nYou can clone the code repository and install from source\n```\ngit clone https://framagit.org/atooms/dynamics.git\ncd dynamics\nmake install\n```\n\n## Contributing\n\nContributions to the project are welcome. If you wish to contribute, check out [these guidelines](https://framagit.org/atooms/atooms/-/blob/master/CONTRIBUTING.md).\n\n## Authors\n\nDaniele Coslovich: https://www.units.it/daniele.coslovich/\n\n\n",
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