Source code for moldesign.integrators.verlet

# Copyright 2016 Autodesk Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
import moldesign as mdt
from moldesign import units as u
from moldesign.molecules import Trajectory

from .base import IntegratorBase

def exports(o):
    return o
__all__ = []

[docs]class VelocityVerlet(IntegratorBase): def __init__(self, *args, **kwargs): super(VelocityVerlet, self).__init__(*args, **kwargs) # TODO: raise exception if any constraints are requested ...
[docs] def run(self, run_for): """ Users won't call this directly - instead, use Propagate position, momentum by a single timestep using velocity verlet :param run_for: number of timesteps OR amount of time to run for """ if not self._prepped: self.prep() nsteps = self.time_to_steps(run_for, self.params.timestep) # Set up trajectory and record the first frame self.mol.time = 0.0 * u.default.time self.traj = Trajectory(self.mol) self.mol.calculate() self.traj.new_frame() next_trajectory_frame = self.params.frame_interval # Dynamics loop for istep in xrange(nsteps): self.step() if istep + 1 >= next_trajectory_frame: self.traj.new_frame() next_trajectory_frame += self.params.frame_interval return self.traj
[docs] def prep(self): self.time = 0.0 * self.params.timestep self._prepped = True
[docs] def step(self): # Move momenta from t-dt to t-dt/2 phalf = self.mol.momenta + 0.5 * self.params.timestep * self.mol.calc_forces(wait=True) # Move positions from t-dt to t self.mol.positions += phalf * self.params.timestep / self.mol.dim_masses # Move momenta from t-dt/2 to t - triggers recomputed forces self.mol.momenta = phalf + 0.5 * self.params.timestep * self.mol.calc_forces(wait=True) self.time += self.params.timestep self.mol.time = self.time