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The total flux ($\Phi$ ) through an solenoidal inductor of length $l$ and $N$ turns is proportional to the current through the inductor and the inductance $L$ of the inductor according to $$\Phi =L \cdot I $$ $$\Rightarrow \Phi =\frac{\pi r^2\mu_0 N^2 }{l}\cdot I \tag{1}$$ Clearly, in this case, if we double the amount of turns (whilst holding the length and current constant) we increase the total flux by a factor of 4. This is because the inductance of a solenoid depends quadratically on $N$. Now I have just learnt about the concept of reluctance (denoted $R$) and magnetomotive force (denoted $m.m.f$) where $m.m.f$ is defined to be $m.m.f \equiv N\cdot I$. These two quantities are related to each other by the total flux via the formula $$m.m.f = R\cdot \Phi \tag{2}$$ Now applying the above formula (eq 2) to the case of the solenoidal inductor, if we hold the current constant but double the number of turns (N) of the inductor, the $m.m.f$ only doubles (since $m.m.f \equiv N\cdot I$). But according to equation (1), the total flux must quadruple since $\Phi \propto N^2$. Thus in order for equation (2) to remain valid, the reluctance must necessarily half. That is, in order for equations 1 and 2 to be simultaneously valid, the reluctance must be inversely proportional to the number of turns so that $R\propto \frac{1}{N}$. However, everywhere I look, I find that reluctance is always given by equations that are independent of $N$. For instance, wikipedia states that $R=\frac{l}{\mu A}$. How can this be? How can equations 1 and 2 be simultaneously true whilst reluctance is independent of $N$? Any help on this issue would be most appreciated!

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Reluctance is independent of the number of turns. Your confusion results from the fact that people use the word flux to refer to two closely related but different quantities. Recall that magnetic flux is the integral of $\vec B$ through a surface. To speak of a flux, we must first define what this surface is. In the analysis of magnetic circuits, this surface is usually the cross section of a relevant part of the magnetic circuit. In this case, this would be the cross section of the inductor winding with area $\pi r^2$. With this definition, the flux is $\Phi_1 = \pi r^2 B$ where $\vec B$ is the magnetic field within the coil (assumed uniform here for simplicity). From the reluctance of the magnetic circuit, we have $\mathcal F=\mathcal R\Phi_1 $, where $\mathcal F=NI$ is the mmf and $\mathcal R$ is the reluctance.

The other magnetic flux we may speak of is the one through the winding, more relevant for electrical analysis, e.g. through the definition of inductance. Consider the loop formed by the coil, including whatever external circuit it may be connected to. This loop is the boundary of a surface, and it is this surface through which we calculate the flux to define inductance, because this is the flux whose rate of change gives the electromotive force along the loop. It is not necessarily easy to visualize this, but each magnetic field line in the inductor core intersects the surface bounded by the loop $N$ times, so the flux is $\Phi_2=N\pi r^2B=N\Phi_1.$ Inductance is calculated as $L =\Phi_2/I$.

Putting everything together, $$L=\frac {\Phi_2} I = \frac {N\Phi_1} I = \frac {N^2} {\mathcal R}$$ which is proportional to $N^2$, as expected.

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The source of your confusion is that you are not considering the magnetic flux linked to the solenoid circuit rather you need to consider the magnetic flux linked with the material of the core of the solenoid.
The solenoid produces a magnetic field $B=\mu N I /L$ and this produces a magnetic flux through the material of its core of $\Phi = BA = \mu N I A /L$ where $A$ is the cross-sectional area of the core.

Thus the equation $\text{mmf}= R_{\rm m} \Phi$ is to do with the magnetic circuit containing the core whereas the equation $\Phi = LI$ is to do with the electrical circuit of which the solenoid is a part.

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