atooms-dynamics 0.2.0

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Dynamics

Netwonian and stochastic dynamics backends for atooms.

Quick start

Run a molecular dynamics simulation of a Lennard-Jones system from an existing xyz file

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,

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

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
• Stochastic dynamics
  • overdamped Langevin dynamics

Documentation

Check out the tutorial for more examples and the public API for full details.

The tutorial is also available as

• org-mode file
• pdf file
• jupyter notebook
• jupyter notebook on binder for interactive execution

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.

Authors

Daniele Coslovich: https://www.units.it/daniele.coslovich/