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)
mol.internas_ang(ang, nang)
mol.internas_dihe(dih, ndih)
# Calculation of the transpose Wilson Matrix
wilson, transp = my.matrix_transf(symb, bond, ang, dih)
# force field calculation
grad, pot = mol.potential(transp, Grad_st1, Hess_st1)
vect_ext = calc_grad_ext(mod_Fext, symb[anchor1].cart, symb[anchor2].cart)
grad_ext = flat_points(check_anchor(vect_ext, anchor1, anchor2, numat))
new_grad = grad + grad_ext
