docs(laneEmdenVariationalForm): updated to match MFEM sign convention more closley
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@@ -84,7 +84,7 @@ Now we exploit the linearity of summation and integration to move the sums out o
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\end{align}
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We will now define $M_{kj}$, $D_{\ell j}$, and $Q_{\ell i}$ such that
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\begin{align}
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M_{kj} &\equiv \int_{\Omega}\nabla \psi_{k}^{\theta}\cdot \vec{N}_{j}^{\phi}dV \\
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M_{kj} &\equiv -\int_{\Omega}\nabla \psi_{k}^{\theta}\cdot \vec{N}_{j}^{\phi}dV \\
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D_{\ell j} &\equiv \int_{\Omega}\vec{\psi}_{\ell}^{\phi}\cdot\vec{N}_{j}^{\phi}dV \\
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Q_{\ell i} &\equiv \int_{\Omega}\vec{\psi}_{\ell}^{\phi}\cdot\nabla N_{i}^{\theta} dV
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\end{align}
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@@ -96,18 +96,18 @@ f(\bar{\theta}) \equiv \int_{\Omega}\psi_{k}^{\theta}\left(\theta_{h}\right)^{n}
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\end{align}
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We can write the variational form of our system of equations as
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\begin{align}
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-\sum_{j=1}^{N_{dof}^{\phi}}\phi_{j}M_{kj} + f(\bar{\theta)} &= 0 \\
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\sum_{j=1}^{N_{dof}^{\phi}}\phi_{j}M_{kj} + f(\bar{\theta)} &= 0 \\
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\sum_{j=1}^{N^{\phi}_{dof}}\phi_{j}D_{\ell j} - \sum_{i=1}^{N_{dof}^{\theta}}\theta_{i}Q_{\ell i} &= 0
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\end{align}
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Or using the notation we defined
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\begin{align}
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-\mathbf{M}\bar{\phi} + f(\bar{\theta}) &= 0 \\
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\mathbf{M}\bar{\phi} + f(\bar{\theta}) &= 0 \\
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\mathbf{D}\bar{\phi} - \mathbf{Q}\bar{\theta} &= 0
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\end{align}
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We can then set this up as a matrix operation
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\begin{align}
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\begin{bmatrix}
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0 & -\mathbf{M} \\
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0 & \mathbf{M} \\
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-\mathbf{Q} & \mathbf{D}
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\end{bmatrix}
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\begin{bmatrix}
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@@ -126,7 +126,7 @@ From this form we can easily see that the residual matrix is
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\begin{align}
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R &= \begin{bmatrix}
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f(\bar{\theta}) - M\bar{\phi} \\
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f(\bar{\theta}) + M\bar{\phi} \\
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D\bar{\phi} - Q\bar{\theta}
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\end{bmatrix}
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\end{align}
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@@ -144,11 +144,11 @@ in our Newton-Raphson method. Generally the Jacobian is the matrix of partial de
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So then the Jacobian is
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\begin{align}
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J &= \begin{bmatrix}
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\frac{\partial}{\partial \theta}\left(f(\theta) - M\phi\right) & \frac{\partial}{\partial \phi}\left(f(\theta) - M\phi\right) \\
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\frac{\partial}{\partial \theta}\left(f(\theta) + M\phi\right) & \frac{\partial}{\partial \phi}\left(f(\theta) + M\phi\right) \\
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\frac{\partial}{\partial \theta}\left(D\phi - Q\theta\right) & \frac{\partial}{\partial \phi}\left(D\phi - Q\theta\right)
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\end{bmatrix} \\
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J &= \begin{bmatrix}
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\frac{df}{d\theta} - \phi\frac{\partial M}{\partial \theta} & -M-\phi\frac{\partial M}{\partial \phi} \\
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\frac{df}{d\theta} + \phi\frac{\partial M}{\partial \theta} & M+\phi\frac{\partial M}{\partial \phi} \\
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-Q - \theta\frac{\partial Q}{\partial \theta} & D + \phi\frac{\partial D}{\partial \phi} - \theta\frac{\partial Q}{\partial \phi}
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\end{bmatrix}
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\end{align}
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@@ -156,7 +156,7 @@ So then the Jacobian is
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Finally, we know that the matrices $M$, $D$, and $Q$ are constant with respect to $\theta$ and $\phi$. Therefore, we can drop the partial derivatives with respect to $\theta$ and $\phi$ from the Jacobian. This gives us
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\begin{align}
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\mathbf{J} &= \begin{bmatrix}
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\frac{df}{d\theta} & -M \\
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\frac{df}{d\theta} & M \\
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-Q & D
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\end{bmatrix}
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\end{align}
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@@ -164,9 +164,9 @@ Finally, we know that the matrices $M$, $D$, and $Q$ are constant with respect t
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\noindent In a fully assembled, distritized form this will look like
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\begin{align}
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\mathbf{J} = \begin{bmatrix} \frac{df}{d\theta}_{00} & \dots & \frac{df}{d\theta}_{0n_{\theta}} & -M_{00} & \dots & -M_{0n_{\phi}} \\
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\mathbf{J} = \begin{bmatrix} \frac{df}{d\theta}_{00} & \dots & \frac{df}{d\theta}_{0n_{\theta}} & M_{00} & \dots & M_{0n_{\phi}} \\
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\vdots & \ddots & & \vdots & \ddots & \\
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\frac{df}{d\theta}_{n_{\theta}0} & & \frac{df}{d\theta}_{n_{\theta}n_{\theta}} & -M_{n_{\theta}0} & & -M_{n_{\theta}n_{\phi}} \\
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\frac{df}{d\theta}_{n_{\theta}0} & & \frac{df}{d\theta}_{n_{\theta}n_{\theta}} & M_{n_{\theta}0} & & M_{n_{\theta}n_{\phi}} \\
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-Q_{00} & \dots & -Q_{0n_{\theta}} & D_{00} & \dots & D_{0n_{\phi}} \\
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\vdots & \ddots & & \vdots & \ddots & \\
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-Q_{n_{\phi}0} & & -Q_{n_{\phi}n_{\theta}} & D_{n_{\phi}0} & & D_{n_{\phi}n_{\phi}}
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