torch_sim.integrators

Integrators for molecular dynamics simulations.

This module provides a collection of integrators for molecular dynamics simulations, supporting NVE (microcanonical), NVT (canonical), and NPT (isothermal-isobaric) ensembles. Each integrator handles batched simulations efficiently using PyTorch tensors and supports periodic boundary conditions.

NVE:

• Velocity Verlet integrator for constant energy simulations nve.nve_step()

NVT:

• Velocity Rescaling thermostat integrator

  nvt.nvt_vrescale_step() [1]

• Langevin thermostat integrator nvt.nvt_langevin_step()

  using BAOAB scheme [2]

• Nosé-Hoover thermostat integrator nvt.nvt_nose_hoover_step() from [3]

NPT:

• Langevin barostat integrator npt.npt_langevin_step() [4, 5]

• Nosé-Hoover barostat integrator npt.npt_nose_hoover_step() from [3]

• Isotropic C-Rescale barostat integrator npt.npt_crescale_isotropic_step()

from [6, 8, 9] - C-Rescale barostat integrator npt.npt_crescale_anisotropic_step() from [7, 8, 9]. Available implementations include isotropic and anisotropic cell rescaling, allowing to change cell lengths, and potentially angles as well.

References

[1] Bussi G, Donadio D, Parrinello M. “Canonical sampling through velocity rescaling.”

The Journal of chemical physics, 126(1), 014101 (2007).

[2] Leimkuhler B, Matthews C.2016 Efficient molecular dynamics using geodesic

integration and solvent-solute splitting. Proc. R. Soc. A 472: 20160138

[3] Martyna, G. J., Tuckerman, M. E., Tobias, D. J., & Klein, M. L. (1996).

Explicit reversible integrators for extended systems dynamics. Molecular Physics, 87(5), 1117-1157.

[4] Grønbech-Jensen, N., & Farago, O. (2014).

Constant pressure and temperature discrete-time Langevin molecular dynamics. The Journal of chemical physics, 141(19).

[5] LAMMPS: https://docs.lammps.org/fix_press_langevin.html [6] Bernetti, Mattia, and Giovanni Bussi.

“Pressure control using stochastic cell rescaling.” The Journal of Chemical Physics 153.11 (2020).

[7] Del Tatto, Vittorio, et al. “Molecular dynamics of solids at

constant pressure and stress using anisotropic stochastic cell rescaling.” Applied Sciences 12.3 (2022): 1139.

[8] Bussi Anisotropic C-Rescale SimpleMD implementation:

https://github.com/bussilab/crescale/blob/master/simplemd_anisotropic/simplemd.cpp

[9] Supplementary Information for [6].

Examples

>>> import torch_sim as ts
>>> state = ts.nvt_langevin_init(initial_state, model, kT=300.0 * units.temperature)
>>> for _ in range(1000):
...     state = ts.nvt_langevin_step(
...         state, model, dt=1e-3 * units.time, kT=300.0 * units.temperature
...     )

Notes

All integrators support batched operations for efficient parallel simulation of multiple systems.

Module Attributes

INTEGRATOR_REGISTRY

Integrator registry - maps integrator names to (init_fn, step_fn) pairs.

Classes

Integrator

Enumeration of available molecular dynamics (MD) integrators.

Modules

md	Core molecular dynamics state and operations.
npt	Implementations of NPT integrators.
nve	Implementations of NVE integrators.
nvt	Implementations of NVT integrators.