When finding the discrete energy states of a operator I have been taught to use the time-independent Schrodinger equation which restates the definition of eigenvalues and eigenvectors. What I don’t understand is why the eigenvalues are the energy states, is there firstly a mathematical reason and secondly a physical reason?
Does this arise from Hamiltonian or Lagrangian mechanics which I am not familiar with?
Answer
As has been remarked by others and explained clearly, and mathematically, the eigenvalues are important because a) they allow you to solve the time-dependent equation, i.e., solve for the evolution of the system and b) a state which belongs to the eigenvalue $E$, i.e., as we say, a state which is an eigenstate with eigenvalue $E$, has an expectation value of the energy operator which is easy to see has to be $E$ itself. But those explanations are advanced and rely on the maths. And they do not explain why $E$ should be considered 'an energy level'. At some risk, I will try to answer your question more physically.
What is the physical reason why the energy states of a system, e.g., an atom, are the eigenvalues of the operator $H$ that appears in the time-independent Schroedinger equation? Well, first, note that it's absolutely the same $H$ that appears in the time-dependent Schrodinger equation, $$H\cdot \psi = -i{\partial \psi \over \partial t}$$ which controls the rate of change of $\psi$.
The answer doesn't come from the classical Hamiltonian or Lagrangian mechanics, but from the then-new quantum properties of Nature. A non-classical feature of QM is that some states are stationary, which means they do not change in time. E.g., the electron in a Bohr orbit is actually not moving, not orbiting at all, and this solves the classical paradoxes about the atom (why the rotating charge doesn't radiate its energy away and fall into the centre).
The first key point is that an eigenstate is a stationary state: what is the explanation for this? well, Schroedinger's time dependent equation clearly says that, up to a constant of proportionality, the time-rate of change of any state $\psi$ is found by applying the operator $H$ (the Hamiltonian: we do not yet know it is also the energy operator) to it: the new vector or function $H\cdot\psi$ is the change in $\psi$ per unit time. Obviously if this is zero, $\psi$ does not change (this was the only classical possibility). But also if $H\cdot\psi$ is even a non-zero multiple of $\psi$, call it $E\psi$, then $\psi$ plus this rate of change is still a multiple of $\psi$, so as time goes on, $\psi$ changes in a trivial fashion: just to another multiple of itself. In QM, a multiple of the wave function represents the same quantum state, so we see the quantum state does not change.
Now the next key point is that a state with a definite energy value must be stationary. Why? In QM, it is not automatic that a system has a definite value of a physical quantity, but if it does, that means its measurement always leads to the same answer, so there is no uncertainty. So if there is no uncertainty in the energy, by Heisenberg's uncertainty principle there must be infinite uncertainty in something else, whatever is 'conjugate' to energy. And that is time. You cannot tell the time using this system, which implies it is not changing. So it is stationary. (remember, we are not assuming that $H$ is also the energy operator and we are not assuming the formula for expectations).
Thus being an eigenstate of $H$ implies $\psi$ is stationary. And having a definite energy value implies it is stationary. Being physicists, we now conclude that being an eigenstate implies it has a definite energy value, which answers your question, and these are the 'energy levels' of a system such as an atom: a system, even an atom, might not possess a definite energy, but if it doesn't, it won't be stationary, and being microscopic, the time-scale in which it will evolve will be so rapid we are unlikely to be able to observe its energy, or even care (since it won't be relevant to molecules or chemistry). So, 'most' atoms for which we can actually measure their energy must be stationary: this is 'why' the definite values of energy which a stationary state can possess are called the 'energy levels' of the system, and historically were discovered first, before Schroedingers equation. From a human perspective, most atoms that we care about spend most of their time that matters to us in an approximately stationary state.
In case you are wondering why time is the conjugate to energy, whereas Heisenberg's original analysis of his uncertainty principle showed that position was conjugate to momentum, we rely on relativity: time is just another coordinate of space-time, and so is analogous to position. And in relativistic mechanics, momentum in a spatial direction is analogous to energy (or mass, same thing). In the standard relativistic equation $$p^2-m^2=E^2,$$ we see that momentum ($p$) and mass $m$ are symmetric (except for the negative sign) with each other. So since momentum is conjugate to position, $m$ or energy must be conjugate to time. For this reason, Bohr was able to extend Heisenberg's analysis, of the uncertainty relations between measurements of position and measurements of momentum, to show the same relations between energy and time.
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