def step(self, f):
""" move one timestep forward using Berenden NPT molecular dynamics."""
NVTBerendsen.scale_velocities(self)
self.scale_positions_and_cell()
#one step velocity verlet
atoms = self.atoms
p = self.atoms.get_momenta()
p += 0.5 * self.dt * f
if self.fixcm:
# 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)
f = self.atoms.get_forces()
atoms.set_momenta(self.atoms.get_momenta() + 0.5 * self.dt * f)
return f
def step(self, f):
""" move one timestep forward using Berenden NPT molecular dynamics."""
NVTBerendsen.scale_velocities(self)
self.scale_positions_and_cell()
#one step velocity verlet
atoms = self.atoms
p = self.atoms.get_momenta()
p += 0.5 * self.dt * f
if self.fixcm:
# 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)
f = self.atoms.get_forces()
atoms.set_momenta(self.atoms.get_momenta() + 0.5 * self.dt * f)
return f
