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You can use the method system of class IntegratedGeodesic. For instance, the following code displays the geodesic equation for the round metric of the 2-sphere in polar coordinates $(\theta,\phi)$:

sage: M = manifolds.Sphere(2)
sage: p = M.point((pi/2, pi))
sage: v0 = M.vector(p, (1, 1))
sage: lbda = var('lbda', latex_name=r'\lambda')
sage: C = M.integrated_geodesic(M.metric(), (lbda, 0, 1), v0)
sage: C.system()[0]
[Dphi^2*cos(theta)*sin(theta), -2*Dphi*Dtheta*cos(theta)/sin(theta)]

The two items in the output list are the values of $\ddot\theta$ and $\ddot\phi$, with Dtheta standing for $\dot\theta$ and Dphi standing for $\dot\phi$ and the dot denotes the derivative with respect to the geodesic parameter $\lambda$.