Source code for ase.md.bussi

# fmt: off

"""Bussi NVT dynamics class."""

import math

import numpy as np

from ase import units
from ase.md.verlet import VelocityVerlet




class Bussi(VelocityVerlet):
    """Bussi stochastic velocity rescaling (NVT) molecular dynamics.

    Based on the paper from Bussi et al., J. Chem. Phys. 126, 014101 (2007)
    (also available from https://arxiv.org/abs/0803.4060).
    """

    def __init__(
        self,
        atoms,
        timestep,
        temperature_K,
        taut,
        rng=None,
        **kwargs,
    ):
        """
        Parameters
        ----------
        atoms : Atoms
            The atoms object.
        timestep : float
            The time step in ASE time units.
        temperature_K : float
            The desired temperature, in Kelvin.
        taut : float
            Time constant for Bussi temperature coupling in ASE time units.
        rng : RNG object, optional
            Random number generator, by default numpy.random.
        **kwargs : dict, optional
            Additional arguments are passed to
            :class:~ase.md.md.MolecularDynamics base class.
        """
        super().__init__(atoms, timestep, **kwargs)

        self.temp = temperature_K * units.kB
        self.taut = taut
        if rng is None:
            self.rng = np.random
        else:
            self.rng = rng

        self.ndof = self.atoms.get_number_of_degrees_of_freedom()

        self.target_kinetic_energy = 0.5 * self.temp * self.ndof

        if np.isclose(
            self.atoms.get_kinetic_energy(), 0.0, rtol=0, atol=1e-12
        ):
            raise ValueError(
                "Initial kinetic energy is zero. "
                "Please set the initial velocities before running Bussi NVT."
            )

        self._exp_term = math.exp(-self.dt / self.taut)
        self._masses = self.atoms.get_masses()[:, np.newaxis]

        self.transferred_energy = 0.0

    def scale_velocities(self):
        """Do the NVT Bussi stochastic velocity scaling."""
        kinetic_energy = self.atoms.get_kinetic_energy()
        alpha = self.calculate_alpha(kinetic_energy)

        momenta = self.atoms.get_momenta()
        self.atoms.set_momenta(alpha * momenta)

        self.transferred_energy += (alpha**2 - 1.0) * kinetic_energy

    def calculate_alpha(self, kinetic_energy):
        """Calculate the scaling factor alpha using equation (A7)
        from the Bussi paper."""

        energy_scaling_term = (
            (1 - self._exp_term)
            * self.target_kinetic_energy
            / kinetic_energy
            / self.ndof
        )

        # R1 in Eq. (A7)
        noisearray = self.rng.standard_normal(size=(1,))
        # ASE mpi interfaces can only broadcast arrays, not scalars
        self.comm.broadcast(noisearray, 0)
        normal_noise = noisearray[0]

        # \sum_{i=2}^{Nf} R_i^2 in Eq. (A7)
        # 2 * standard_gamma(n / 2) is equal to chisquare(n)
        sum_of_noises = 2.0 * self.rng.standard_gamma(0.5 * (self.ndof - 1))

        return math.sqrt(
            self._exp_term
            + energy_scaling_term * (sum_of_noises + normal_noise**2)
            + 2
            * normal_noise
            * math.sqrt(self._exp_term * energy_scaling_term)
        )

    def step(self, forces=None):
        """Move one timestep forward using Bussi NVT molecular dynamics."""
        self.scale_velocities()
        return super().step(forces)