berni 0.0.1

Database of interaction models for molecular dynamics and Monte Carlo simulations

Berni

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

Quick start

Print all the available models

import berni
for model in berni.models:
    print(model["name"])

gaussian_core
coslovich_pastore
bernu_hiwatari_hansen_pastore
lennard_jones
kob_andersen
roux_barrat_hansen
grigera_cavagna_giardina_parisi
harmonic_spheres
kob_andersen_2
dellavalle_gazzillo_frattini_pastore
wahnstrom
kob_andersen
coslovich_pastore

Get a model

berni.models.get("lennard_jones")

Print all the available samples

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

lennard_jones-13ce47602b259f7802e89e23ffd57f19.xyz
grigera_cavagna_giardina_parisi-0ac97fa8c69c320e48bd1fca80855e8a.xyz
coslovich_pastore-488db481cdac35e599922a26129c3e35.xyz
lennard_jones-5cc3b80bc415fa5c262e83410ca65779.xyz
kob_andersen-8f4a9fe755e5c1966c10b50c9a53e6bf.xyz
bernu_hiwatari_hansen_pastore-f61d7e58b9656cf9640f6e5754441930.xyz

Get a local copy of a Lennard-Jones fluid sample

local_file = berni.models.get("lennard_jones-5cc3b80bc415fa5c262e83410ca65779.xyz")

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

Documentation

Check out the documentation for full details.

Installation

Clone the code repository and install from source

git clone https://framagit.org/coslo/berni.git
cd sample
make install

Install berni with pip

pip install berni

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/