Source code for ase.md.nvtberendsen

"""Berendsen NVT dynamics class."""

import numpy as np
from ase.md.md import MolecularDynamics
from ase.parallel import world


[docs]class NVTBerendsen(MolecularDynamics): def __init__(self, atoms, timestep, temperature=None, taut=None, fixcm=True, *, temperature_K=None, trajectory=None, logfile=None, loginterval=1, communicator=world, append_trajectory=False): """Berendsen (constant N, V, T) molecular dynamics. Parameters: atoms: Atoms object The list of atoms. timestep: float The time step in ASE time units. temperature: float The desired temperature, in Kelvin. temperature_K: float Alias for *temperature* taut: float Time constant for Berendsen temperature coupling in ASE time units. fixcm: bool (optional) If True, the position and momentum of the center of mass is kept unperturbed. Default: True. trajectory: Trajectory object or str (optional) Attach trajectory object. If *trajectory* is a string a Trajectory will be constructed. Use *None* for no trajectory. logfile: file object or str (optional) If *logfile* is a string, a file with that name will be opened. Use '-' for stdout. loginterval: int (optional) Only write a log line for every *loginterval* time steps. Default: 1 append_trajectory: boolean (optional) Defaults to False, which causes the trajectory file to be overwriten each time the dynamics is restarted from scratch. If True, the new structures are appended to the trajectory file instead. """ MolecularDynamics.__init__(self, atoms, timestep, trajectory, logfile, loginterval, append_trajectory=append_trajectory) if taut is None: raise TypeError("Missing 'taut' argument.") self.taut = taut self.temperature = self._process_temperature(temperature, temperature_K, 'K') self.fix_com = fixcm # will the center of mass be held fixed? self.communicator = communicator def set_taut(self, taut): self.taut = taut def get_taut(self): return self.taut def set_temperature(self, temperature=None, *, temperature_K=None): self.temperature = self._process_temperature(temperature, temperature_K, 'K') def get_temperature(self): return self.temperature def set_timestep(self, timestep): self.dt = timestep def get_timestep(self): return self.dt def scale_velocities(self): """ Do the NVT Berendsen velocity scaling """ tautscl = self.dt / self.taut old_temperature = self.atoms.get_temperature() scl_temperature = np.sqrt(1.0 + (self.temperature / old_temperature - 1.0) * tautscl) # Limit the velocity scaling to reasonable values if scl_temperature > 1.1: scl_temperature = 1.1 if scl_temperature < 0.9: scl_temperature = 0.9 p = self.atoms.get_momenta() p = scl_temperature * p self.atoms.set_momenta(p) return def step(self, forces=None): """Move one timestep forward using Berenden NVT molecular dynamics.""" self.scale_velocities() # one step velocity verlet atoms = self.atoms if forces is None: forces = atoms.get_forces(md=True) p = self.atoms.get_momenta() p += 0.5 * self.dt * forces if self.fix_com: # calculate the center of mass # momentum and subtract it psum = p.sum(axis=0) / float(len(p)) p = p - psum self.atoms.set_positions( self.atoms.get_positions() + self.dt * p / self.atoms.get_masses()[:, np.newaxis]) # We need to store the momenta on the atoms before calculating # the forces, as in a parallel Asap calculation atoms may # migrate during force calculations, and the momenta need to # migrate along with the atoms. For the same reason, we # cannot use self.masses in the line above. self.atoms.set_momenta(p) forces = self.atoms.get_forces(md=True) atoms.set_momenta(self.atoms.get_momenta() + 0.5 * self.dt * forces) return forces