nonbond 0.1.0

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Nonbond

Nonbond is an ASE (Atomic Simulation Environment) calculator designed for computing non-bonded interactions.
Currently, it is primarily intended for use in specific contexts such as GCMC simulations, as it outputs only the total energy and per-atom energies (forces are not yet implemented).

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🧩 Features

• Lennard-Jones (LJ) potential energy calculations
• Efficient long-range Coulomb interaction algorithms
• Fast neighbor list construction using PyTorch and vesin
• GPU acceleration via PyTorch

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🧠 Requirements

• Python ≥ 3.12
• ASE ≥ 3.26.0
• torch-pme ≥ 0.3.2
• vesin-torch ≥ 0.4.2
• PyTorch (latest stable version recommended)

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⚙️ Installation

Install via pip:

pip install nonbond

🚀 Example

from ase import Atoms
from nonbond import Nonbond
import numpy as np

# Define Lennard-Jones parameters for SPC/E water
epsilon = {
    'Ow': 0.15535,
    'Hw': 0.0,
}

sigma = {
    'Ow': 3.16600,
    'Hw': 1.0,
}

# Create calculator
calc = Nonbond(
    epsilon=epsilon,
    sigma=sigma,
    rc=14.0,
    charge_method='ewald',  # Options: 'direct', 'ewald', 'pme', 'p3m'
    accuracy=1e-5
)

# Build an SPC/E water molecule
atoms = Atoms(
    'OH2',
    positions=[
        [0.00000, -0.06461, 0.00000],
        [0.81649,  0.51275, 0.00000],
        [-0.81649, 0.51275, 0.00000]
    ],
    cell=[40.0, 40.0, 40.0],
    pbc=True
)

# Assign atom types and charges
atoms.set_array('type', np.array(['Ow', 'Hw', 'Hw']))
atoms.set_initial_charges([-0.8476, 0.4238, 0.4238])

# Attach calculator and compute energy
atoms.calc = calc
energy = atoms.get_potential_energy()
print(f"Potential energy: {energy:.6f} eV")

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📝 Notes

• Only energy calculations are currently supported.
• Force and stress tensor support will be added in future releases.