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
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
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))
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))
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
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