Exemple #1
0
def add_rotational_velocity(atoms, rot_vel, axis, anchor):
    """
  Adds the rot_vel to the vel vector of atoms with respect
  to the rotation around axis and attached to anchor.
  """
    for atom in atoms:
        r_perp = v3.perpendicular(atom.pos - anchor, axis)
        v_tang_dir = v3.cross(axis, r_perp)
        v_tang_dir_len = v3.mag(v_tang_dir)
        if v3.is_similar_mag(v_tang_dir_len, 0):
            v_tang = v3.vector()
        else:
            v_new_len = rot_vel * v3.mag(r_perp)
            v_tang = v3.scale(v_tang_dir, v_new_len / v_tang_dir_len)
        atom.vel += v_tang
Exemple #2
0
def add_rotational_velocity(atoms, rot_vel, axis, anchor):
  """
  Adds the rot_vel to the vel vector of atoms with respect
  to the rotation around axis and attached to anchor.
  """
  for atom in atoms:
    r_perp = v3.perpendicular(atom.pos - anchor, axis)
    v_tang_dir = v3.cross(axis, r_perp)
    v_tang_dir_len = v3.mag(v_tang_dir)
    if v3.is_similar_mag(v_tang_dir_len, 0):
      v_tang = v3.vector()
    else:
      v_new_len = rot_vel * v3.mag(r_perp)
      v_tang = v3.scale(v_tang_dir, v_new_len/v_tang_dir_len)
    atom.vel += v_tang
Exemple #3
0
def anderson_velocity_scale(atoms, temperature, n_degree_of_freedom):
    """
  Scales the velocity of atoms such that average energy
  is consistent with the temperature.
  """
    # This is the classic Anderson approach to temperature
    # regulation. Whilst deterministic, can be easily trapped in
    # local minima.
    target_energy = mean_energy(temperature, n_degree_of_freedom)
    kin = kinetic_energy(atoms)
    if v3.is_similar_mag(kin, 0):
        gas_randomize(atoms, temperature)
    else:
        scaling_factor = math.sqrt(target_energy / kin)
        for atom in atoms:
            v3.set_vector(atom.vel, v3.scale(atom.vel, scaling_factor))
Exemple #4
0
def anderson_velocity_scale(atoms, temperature, n_degree_of_freedom):
  """
  Scales the velocity of atoms such that average energy
  is consistent with the temperature.
  """
  # This is the classic Anderson approach to temperature
  # regulation. Whilst deterministic, can be easily trapped in
  # local minima.
  target_energy = mean_energy(temperature, n_degree_of_freedom)
  kin = kinetic_energy(atoms)
  if v3.is_similar_mag(kin, 0):
    gas_randomize(atoms, temperature)
  else:
    scaling_factor = math.sqrt(target_energy / kin)
    for atom in atoms:
      v3.set_vector(atom.vel, v3.scale(atom.vel, scaling_factor))
Exemple #5
0
def rotational_velocity(atom, axis, anchor):
    """
  Returns the rotational velocity (rad/ps) of the atom connected
  to anchor around axis.
  """
    r = atom.pos - anchor
    r_perp = v3.perpendicular(r, axis)
    vel_perp = v3.perpendicular(atom.vel, axis)
    vel_tang = v3.perpendicular(vel_perp, r_perp)
    pos_ref = v3.cross(axis, r_perp)
    if v3.dot(vel_tang, pos_ref) < 0.0:
        sign = -1.0
    else:
        sign = 1.0
    if v3.is_similar_mag(v3.mag(r_perp), 0):
        result = 0.0
    else:
        result = sign * v3.mag(vel_tang) / v3.mag(r_perp)
    return result
Exemple #6
0
def rotational_velocity(atom, axis, anchor):
  """
  Returns the rotational velocity (rad/ps) of the atom connected
  to anchor around axis.
  """
  r = atom.pos - anchor
  r_perp = v3.perpendicular(r, axis)
  vel_perp = v3.perpendicular(atom.vel, axis)
  vel_tang = v3.perpendicular(vel_perp, r_perp)
  pos_ref = v3.cross(axis, r_perp)
  if v3.dot(vel_tang, pos_ref) < 0.0:
    sign = -1.0
  else:
    sign = 1.0
  if v3.is_similar_mag(v3.mag(r_perp), 0):
    result = 0.0
  else:
    result = sign * v3.mag(vel_tang) / v3.mag(r_perp)
  return result