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:

Isotropic Langevin barostat npt.npt_langevin_isotropic_step() [4, 5]
Anisotropic Langevin barostat (independent cell lengths)
npt.npt_langevin_anisotropic_step() [4, 5]
Isotropic Nosé-Hoover barostat npt.npt_nose_hoover_isotropic_step() from [10]
Isotropic C-Rescale barostat npt.npt_crescale_isotropic_step()
from [6, 8, 9]
Triclinic C-Rescale barostat (cell lengths and angles)
npt.npt_crescale_triclinic_step() from [7, 8, 9]

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].

[10]Tuckerman, Mark E., et al. “A Liouville-operator derived measure-preserving: integrator for molecular dynamics simulations in the isothermal-isobaric ensemble.” Journal of Physics A: Mathematical and General 39.19 (2006): 5629-5651.

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.
`INTEGRATOR_KWARG_UNITS`	Unit-carrying kwargs of each integrator, derived at import time from the `TimeArg`/`InverseTimeArg`/`PressureArg`/`InversePressureArg` annotations on the registered init/step functions.

Classes

`Integrator`	Enumeration of available molecular dynamics (MD) integrators.
`IntegratorKwargUnits`	Metadata for integrator parameters carrying physical units.
`unit_kwargs`	dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object's (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list. For example: dict(one=1, two=2).

Modules

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