In the Hamilton-Jacobi equation, we take the partial time derivative of the action. But the action comes from integrating the Lagrangian over time, so time seems to just be a dummy variable here and hence I do not understand how we can partial differentiate $S$ with respect to time? A simple example would also be helpful.
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The action functional and Hamilton's principal function are two different mathematical objects related to the same physical quantity. The action along a trajectory $\gamma:[t_1,t_2]\rightarrow Q$ is given by $$ S[\gamma] = \int_{t_1}^{t_2}L(\gamma(t'),\dot\gamma(t'),t')dt' $$ whereas the pricipal function is the solution of the Hamilton-Jacobi equation $$ H(q,\nabla S(q,t),t) + \frac{\partial S}{\partial t}(q,t) = 0 $$ If you denote by $\gamma_{q,t}$ the solution of the Euler-Lagrange equations with $$ \gamma_{q,t}(t_0)=q_0\\ \gamma_{q,t}(t)=q $$ then $$ S(q,t):=S[\gamma_{q,t}]=\int_{t_0}^{t}L(\gamma_{q,t}(t'),\dot\gamma_{q,t}(t'),t')dt' $$ will solve the Hamilton-Jacobi equation. On the flip side, for the pricipal function we have $$ \frac{d}{dt}S(\gamma(t),t)=L(\gamma(t),\dot\gamma(t),t) $$ and thus $$ S[\gamma]=S(\gamma(t_2),t_2)-S(\gamma(t_1),t_1) $$ Note that the last two equations only hold for trajectories with $$ \frac{\partial L}{\partial\dot q}(\gamma(t),\dot\gamma(t),t) = \nabla S(\gamma(t),t) $$ Geometrically, the choice of integration constants of the principal function selects a leave of a foliation of phase space, which corresponds to the choice of initial condition $\gamma_q(t_0)=q_0$ from above. |
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I) At least three different quantities in physics are customary called an action and denoted with the letter $S$.
II) Example: A non-relativistic free particle in 1 dimension.
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