Atooms database

A database of interaction models and trajectory samples for classical molecular dynamics and Monte Carlo simulations.

Quick start

List the available models

from atooms import database
for model in database.models:
    print(model["name"])

Gaussian core
Bernu-Hiwatari-Hansen-Pastore
Kob-Andersen
Lennard-Jones
Dellavalle-Gazzillo-Frattini-Pastore
Roux-Barrat-Hansen
Coslovich-Pastore
Grigera-Cavagna-Giardina-Parisi
harmonic spheres
Wahnstrom

Print all the available samples

for sample in database.samples:
    print(sample["path"])

coslovich_pastore/0_488db481cdac35e599922a26129c3e35.xyz
kob_andersen/0_8f4a9fe755e5c1966c10b50c9a53e6bf.xyz
grigera_cavagna_giardina_parisi/0_0ac97fa8c69c320e48bd1fca80855e8a.xyz
lennard_jones/0_5cc3b80bc415fa5c262e83410ca65779.xyz
lennard_jones/0_13ce47602b259f7802e89e23ffd57f19.xyz
bernu_hiwatari_hansen_pastore/0_f61d7e58b9656cf9640f6e5754441930.xyz

Get a local copy of a Lennard-Jones fluid sample

local_file = database.samples.copy("lennard_jones/0_5cc3b80bc415fa5c262e83410ca65779.xyz")

The local_file can then be used to start a simulation or further analysis using atooms packages.

Documentation

Check out the documentation for full details.

Installation

Clone the code repository and install from source

git clone https://framagit.org/atooms/database.git
cd database
pip install .

Install atooms-database with pip

pip install atooms-database

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/