I'm trying to follow a derivation of the Euler-Lagrange equation at the continuum limit, and find some details hard to understand. The 1D lattice has a mono-atomic basis with atomic spacing $\mathfrak{a}$ and atom mass being $m$. The relative displacement of the nth atom is $\delta \eta_{n}$. The Lagrangian at the discrete limit is written as
$$\begin{aligned} \mathfrak{L} &=\sum_{n=1}^{N} \mathfrak{a} \frac{1}{2}\left[\frac{m}{\mathfrak{a}}\left(\delta \dot{\eta}_{n}\right)^{2}-\kappa \mathfrak{a}\left(\frac{\delta \eta_{n+1}-\delta \eta_{n}}{\mathfrak{a}}\right)^{2}-\frac{m}{\mathfrak{a}} \Omega^{2}\left(\delta \eta_{n}\right)^{2}\right] \\ &=: \sum_{n=1}^{N} \mathfrak{a} L_{n} \end{aligned}$$
where $\kappa$ and $\Omega^2$ are the strength of the atomic bonding and the external field, respectively. At the limit of $N\rightarrow\infty$, the time derivative of the relative displacement $\delta \eta_{n}$ at time $t$ has been replaced by the value of the time derivative $\left(\partial_{t} \varphi\right)$ at the space-time coordinate $(x, t)$. And we have periodic boundary condition of
$$\varphi(x+L, t)=\varphi(x, t), \quad x \in] 0, L], \quad \forall t \in \mathbb{R}.$$
If we let
$$\mu:=\frac{m}{\mathfrak{a}}, \quad Y:=\kappa \mathfrak{a}$$
and replace the discrete sum $\sum_{n}$ by the integral $\int \mathrm{d} x /\mathfrak{a}$ over the semi-open interval $] 0, L]$, then we write the Lagrangian as
$$\begin{aligned} \mathfrak{L}=& \int_{0}^{L} \mathrm{d} x \frac{1}{2}\left[\mu\left(\frac{\partial \varphi}{\partial t}\right)^{2}-Y\left(\frac{\partial \varphi}{\partial x}\right)^{2}-\mu \Omega^{2} \varphi^{2}\right] \\ =&: \int_{0}^{L} \mathrm{d} x \mathcal{L} \end{aligned}.$$
where $\mathcal{L}$ is the "Lagrangian density". From Christopher Mudry's book one obtains the continuum limit of Euler-Lagrange equations as
$$\partial_{t} \frac{\delta \mathcal{L}(x, t)}{\delta\left(\partial_{t} \varphi\right)(y, t)}+\partial_{x} \frac{\delta \mathcal{L}(x, t)}{\delta\left(\partial_{x} \varphi\right)(y, t)}=\frac{\delta \mathcal{L}(x, t)}{\delta \varphi(y, t)}\tag{1}.$$
To get (1) I first expand $\mathcal{L}$ in terms of $\varphi,\left(\partial_{x} \varphi\right),$ and $\left(\partial_{t} \varphi\right)$ to give
$$\begin{aligned} \delta \mathcal{L} &=\mathcal{L}\left[\varphi+\delta \varphi,\left(\partial_{x} \varphi\right)+\delta\left(\partial_{x} \varphi\right),\left(\partial_{t} \varphi\right)+\delta\left(\partial_{t} \varphi\right)\right]-\mathcal{L}\left[\varphi,\left(\partial_{x} \varphi\right),\left(\partial_{t} \varphi\right)\right] \\ &=\frac{\partial \mathcal{L}}{\partial \varphi} \delta \varphi+\frac{\partial \mathcal{L}}{\partial\left(\partial_{x} \varphi\right)} \delta\left(\partial_{x} \varphi\right)+\frac{\partial \mathcal{L}}{\partial\left(\partial_{t} \varphi\right)} \delta\left(\partial_{t} \varphi\right)+\cdots \end{aligned}\tag{2}.$$
Ignore the higher-order terms in (2) and notice that $\delta\partial_x\varphi=\partial_x\delta\varphi$, we can integrate (2) by parts to give
$$ \begin{aligned} \delta\mathfrak{L}&=\int^L_0dx\delta\mathcal{L}\\ &=\int^L_0dx\{\frac{\partial\mathcal{L}}{\partial\varphi}\delta\varphi+\partial_x\left(\frac{\partial\mathcal{L}}{\partial(\partial_x\varphi)}\delta\varphi\right)+\partial_t\left(\frac{\partial\mathcal{L}}{\partial(\partial_t\varphi)}\delta\varphi\right)-\delta\varphi\partial_x(\frac{\partial\mathcal{L}}{\partial(\partial_x\varphi)})-\delta\varphi\partial_t(\frac{\partial\mathcal{L}}{\partial(\partial_t\varphi)})\} \end{aligned}\tag{3}. $$
In order to get (1) from (3), the following integral must be satisfied:
$$\int^L_0dx\partial_x\left(\frac{\partial \mathcal{L}}{\partial\left(\partial_{x} \varphi\right)} \delta \varphi\right)=\left[\frac{\partial \mathcal{L}}{\partial\left(\partial_{x} \varphi\right)} \delta \varphi\right]^L_0=0\tag{5},$$
$$\int^L_0dx\partial_t\left(\frac{\partial \mathcal{L}}{\partial\left(\partial_{t} \varphi\right)} \delta \varphi\right)=\frac{d}{dt}\int^L_0dx\left(\frac{\partial \mathcal{L}}{\partial\left(\partial_{t} \varphi\right)} \delta \varphi\right)=0\tag{6}.$$
While I have no problem with (5) as we don't change the endpoints, I don't know why Eqn. (6) is valid. Is it just because we treat time $t$ as a fixed parameter in (6)?