berni 0.2.0

Database of interaction models for molecular dynamics and Monte Carlo simulations

Berni

A database of interaction models and trajectory samples for molecular dynamics and Monte Carlo simulations. Berni can export interaction models to a range of simulation backends, such as atooms, LAMMPS, RUMD.

Quick start

Get info on the available models

import berni
for model in berni.models:
    print(f'- "{model["name"]}": {model["description"]}')

- "bernu_hiwatari_hansen_pastore": Binary soft-sphere mixture with size ratio of 1.4
- "coslovich_pastore": Short-ranged pairwise-additive model for silica
- "dellavalle_gazzillo_frattini_pastore": Binary Lennard-Jones mixture model for NiY alloys
- "gaussian_core": One-component Gaussian core model with long-range cutoff
- "grigera_cavagna_giardina_parisi": Binary soft-sphere mixture with size ratio of 1.2 and smooth cutoff
- "harmonic_spheres": Binary mixture of harmonic spheres with size ratio of 1.4
- "kob_andersen": Binary Kob-Andersen Lennard-Jones mixture
- "kob_andersen_2": Ternary Kob-Andersen Lennard-Jones mixture
- "lennard_jones": One-component Lennard-Jones model
- "roux_barrat_hansen": Binary soft-sphere mixture with size ratio of 1.2
- "roy_heyde_heuer-II": Variant of roy_heyde_heuer with optimized parameters               
- "roy_heyde_heuer": 2d model of a silica bilayer
- "wahnstrom": Binary Lennard-Jones mixture with size ratio of 1.2

Get a specific model as a dictionary in the default schema

berni.models.get("lennard_jones")

Print the qualified names of the available samples

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

coslovich_pastore-488db481cdac35e599922a26129c3e35.xyz
lennard_jones-13ce47602b259f7802e89e23ffd57f19.xyz
roy_heyde_heuer-II-b8d70742799933357ea83314590d2b4d.xyz
lennard_jones-5cc3b80bc415fa5c262e83410ca65779.xyz
kob_andersen-8f4a9fe755e5c1966c10b50c9a53e6bf.xyz
bernu_hiwatari_hansen_pastore-f61d7e58b9656cf9640f6e5754441930.xyz
grigera_cavagna_giardina_parisi-0ac97fa8c69c320e48bd1fca80855e8a.xyz

Get a local copy of a Lennard-Jones fluid sample

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

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

Export a model for a simulation backend

berni.models.export("kob_andersen", backend='lammps')

pair_style lj/cut 1.0
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 1 2 1.5 0.8 2.0
pair_coeff 2 2 0.5 0.88 2.2
pair_modify shift yes

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/