for n in range(numat):
symb[n].vel.x = my.random_maxwell(symb[n], 2 * T)
symb[n].vel.y = my.random_maxwell(symb[n], 2 * T)
symb[n].vel.z = my.random_maxwell(symb[n], 2 * T)
while t_heat <= time / my.au_time:
Mass_total = sum(symb[k].mass for k in range(numat))
MC_vel_X = sum(symb[k].mass * symb[k].vel.x
for k in xrange(numat)) / Mass_total
MC_vel_Y = sum(symb[k].mass * symb[k].vel.y
for k in xrange(numat)) / Mass_total
MC_vel_Z = sum(symb[k].mass * symb[k].vel.z
for k in xrange(numat)) / Mass_total
angular_vel = my.Inertia_matrix(symb)
rot_comp = [
my.cross(angular_vel, [symb[k].cart.x, symb[k].cart.y, symb[k].cart.z])
for k in range(numat)
]
for i in xrange(numat):
symb[i].vel.x = symb[i].vel.x - MC_vel_X - rot_comp[i][0]
symb[i].vel.y = symb[i].vel.y - MC_vel_Y - rot_comp[i][1]
symb[i].vel.z = symb[i].vel.z - MC_vel_Z - rot_comp[i][2]
my.nose_hoover_1(symb, dt, thermo, T, numat)
# Transformation to internal coordinates
mol.cart = [var.cart for var in symb]
mol.internas_bonds(bond, nbond)
