Source code for ase.md.langevin

"""Langevin dynamics class."""

import numpy as np

from ase.md.md import MolecularDynamics
from ase.parallel import world


[docs]class Langevin(MolecularDynamics): """Langevin (constant N, V, T) molecular dynamics. Usage: Langevin(atoms, dt, temperature, friction) atoms The list of atoms. dt The time step. temperature The desired temperature, in energy units. friction A friction coefficient, typically 1e-4 to 1e-2. fixcm If True, the position and momentum of the center of mass is kept unperturbed. Default: True. rng Random number generator, by default numpy.random. Must have a standard_normal method matching the signature of numpy.random.standard_normal. The temperature and friction are normally scalars, but in principle one quantity per atom could be specified by giving an array. RATTLE constraints can be used with these propagators, see: E. V.-Eijnden, and G. Ciccotti, Chem. Phys. Lett. 429, 310 (2006) The propagator is Equation 23 (Eq. 39 if RATTLE constraints are used) of the above reference. That reference also contains another propagator in Eq. 21/34; but that propagator is not quasi-symplectic and gives a systematic offset in the temperature at large time steps. This dynamics accesses the atoms using Cartesian coordinates.""" # Helps Asap doing the right thing. Increment when changing stuff: _lgv_version = 3 def __init__(self, atoms, timestep, temperature, friction, fixcm=True, trajectory=None, logfile=None, loginterval=1, communicator=world, rng=np.random, append_trajectory=False): self.temp = temperature self.fr = friction self.fixcm = fixcm # will the center of mass be held fixed? self.communicator = communicator self.rng = rng MolecularDynamics.__init__(self, atoms, timestep, trajectory, logfile, loginterval, append_trajectory=append_trajectory) self.updatevars() def todict(self): d = MolecularDynamics.todict(self) d.update({'temperature': self.temp, 'friction': self.fr, 'fix-cm': self.fixcm}) return d def set_temperature(self, temperature): self.temp = temperature self.updatevars() def set_friction(self, friction): self.fr = friction self.updatevars() def set_timestep(self, timestep): self.dt = timestep self.updatevars() def updatevars(self): dt = self.dt T = self.temp fr = self.fr masses = self.masses sigma = np.sqrt(2 * T * fr / masses) self.c1 = dt / 2. - dt * dt * fr / 8. self.c2 = dt * fr / 2 - dt * dt * fr * fr / 8. self.c3 = np.sqrt(dt) * sigma / 2. - dt**1.5 * fr * sigma / 8. self.c5 = dt**1.5 * sigma / (2 * np.sqrt(3)) self.c4 = fr / 2. * self.c5 def step(self, f=None): atoms = self.atoms natoms = len(atoms) if f is None: f = atoms.get_forces() # This velocity as well as xi, eta and a few other variables are stored # as attributes, so Asap can do its magic when atoms migrate between # processors. self.v = atoms.get_velocities() self.xi = self.rng.standard_normal(size=(natoms, 3)) self.eta = self.rng.standard_normal(size=(natoms, 3)) # When holonomic constraints for rigid linear triatomic molecules are # present, ask the constraints to redistribute xi and eta within each # triple defined in the constraints. This is needed to achieve the # correct target temperature. for constraint in self.atoms.constraints: if hasattr(constraint, 'redistribute_forces_md'): constraint.redistribute_forces_md(atoms, self.xi, rand=True) constraint.redistribute_forces_md(atoms, self.eta, rand=True) if self.communicator is not None: self.communicator.broadcast(self.xi, 0) self.communicator.broadcast(self.eta, 0) # First halfstep in the velocity. self.v += (self.c1 * f / self.masses - self.c2 * self.v + self.c3 * self.xi - self.c4 * self.eta) # Full step in positions x = atoms.get_positions() if self.fixcm: old_cm = atoms.get_center_of_mass() # Step: x^n -> x^(n+1) - this applies constraints if any. atoms.set_positions(x + self.dt * self.v + self.c5 * self.eta) if self.fixcm: new_cm = atoms.get_center_of_mass() d = old_cm - new_cm # atoms.translate(d) # Does not respect constraints atoms.set_positions(atoms.get_positions() + d) # recalc velocities after RATTLE constraints are applied self.v = (self.atoms.get_positions() - x - self.c5 * self.eta) / self.dt f = atoms.get_forces(md=True) # Update the velocities self.v += (self.c1 * f / self.masses - self.c2 * self.v + self.c3 * self.xi - self.c4 * self.eta) if self.fixcm: # subtract center of mass vel v_cm = self._get_com_velocity() self.v -= v_cm # Second part of RATTLE taken care of here atoms.set_momenta(self.v * self.masses) return f def _get_com_velocity(self): """Return the center of mass velocity. Internal use only. This function can be reimplemented by Asap. """ return np.dot(self.masses.flatten(), self.v) / self.masses.sum()