Merge pull request #27279 from farscape-project/amendment

Documentation fixes + skip initial residual evaluation for new apps

framework/doc/content/source/kernels/ADCoupledTimeDerivative.md

@@ -36,9 +36,7 @@ equations for phase field calculations. The syntax is simple, taking its type
 that the time derivative operator acts upon. Example syntax can be found in the
 kernel block below:
 
-!listing
-test/tests/kernels/coupled_time_derivative/ad_coupled_time_derivative_test.i
-block=Kernels
+!listing test/tests/kernels/coupled_time_derivative/ad_coupled_time_derivative_test.i block=Kernels
 
 !syntax parameters /Kernels/ADCoupledTimeDerivative
 

framework/doc/content/source/kernels/CoupledTimeDerivative.md

@@ -40,9 +40,7 @@ for phase field calculations. The syntax is simple, taking its type
 derivative operator acts upon. Example syntax can be found in the kernel block
 below:
 
-!listing
-test/tests/kernels/coupled_time_derivative/coupled_time_derivative_test.i
-block=Kernels
+!listing test/tests/kernels/coupled_time_derivative/coupled_time_derivative_test.i block=Kernels
 
 !syntax parameters /Kernels/CoupledTimeDerivative
 

framework/doc/content/source/kernels/FunctionDiffusion.md

@@ -5,17 +5,17 @@
 ## Overview
 
 !style halign=left
-The `FunctionDiffusion` object represents a Laplacian operator term with a function coefficient for 
+The `FunctionDiffusion` object represents a diffusion term with a function coefficient for
 scalar field variables. This term is
 
 \begin{equation}
-  f(\mathbf{r}, t) \nabla^2 v
+  - \nabla \cdot f(\mathbf{r}, t) \nabla v
 \end{equation}
 
 where
 
 - $v$ is a scalar field solution variable, and
-- $f(\mathbf{r}, t)$ is a scalar function serving as a coefficient.
+- $f(\mathbf{r}, t)$ is a scalar function serving as a diffusion coefficient.
 
 Note that the [!param](/Kernels/FunctionDiffusion/v) parameter is optional. If no variable is entered 
 there, then the kernel's nonlinear variable will be used in the operator as usual. 

framework/doc/content/source/kernels/GradField.md

@@ -9,15 +9,15 @@ The GradField object implements the following PDE term for coupled
 scalar-vector PDE systems:
 
 \begin{equation}
-  - k \nabla u,
+  - k \nabla v,
 \end{equation}
 
-where $k$ is a constant scalar coefficient and  $u$ is a scalar field variable.
+where $k$ is a constant scalar coefficient and  $v$ is a scalar field variable.
 Given vector test functions $\vec{\psi_i}$, the weak form, in inner-product
 notation, is given by:
 
 \begin{equation}
-  R_i(u) = (\nabla \cdot \vec{\psi_i}, k u) \quad \forall \vec{\psi_i}.
+  R_i(v) = (\nabla \cdot \vec{\psi_i}, k v) \quad \forall \vec{\psi_i}.
 \end{equation}
 
 ## Example Input File Syntax

framework/doc/content/source/kernels/MassLumpedTimeDerivative.md

@@ -7,7 +7,7 @@ helps ensure conservation of mass at a node. In a standard node-based Galerkin
 approximation, fluxes from spatial terms can be thought of as "entering"
 nodes. If there is no flux to a node, then the mass at that node should stay
 fixed. However, if the standard Galerkin method is applied to a time derivative
-term, $(\psi_i, \frac{\partial u_h}{\partial t}$ the corresponding coefficient
+term, $(\psi_i, \frac{\partial u_h}{\partial t})$ the corresponding coefficient
 matrix is tri-diagonal and the mass at a node is affected by fluxes to neighboring
 nodes. This can lead to violation of local mass conservation and generation of
 spurious oscillations with unphysical under- and over-shoot phenomena. Lumping
@@ -23,13 +23,13 @@ differential operator. We write our finite element solution as
 Substituting into our governing equation, we have:
 
 \begin{equation}
-  \sum u_j'\phi_j = Sum u_jA\phi_j
+  \sum u_j'\phi_j = \sum u_jA\phi_j
 \end{equation}
 
 Now we apply our test functions $\psi_i$ and integrate over the volume:
 
 \begin{equation}
-  \sum u_j' (\psi_i\phi_j) = \sum u_j (\psi_i, Au_j)
+  \sum u_j' (\psi_i,\phi_j) = \sum u_j (\psi_i, A\phi_j)
 \end{equation}
 
 After applying all of our test functions, we have the matrix system

framework/doc/content/source/kernels/MatDiffusion.md

@@ -4,7 +4,7 @@
 
 Implements the term
 \begin{equation}
-\nabla\cdot D(c,a,b,\dots) \nabla u,
+-\nabla\cdot D(c,a,b,\dots) \nabla u,
 \end{equation}
 where the diffusion coefficient $D$ (`diffusivity`) is provided by a `FunctionMaterial` function material (see `Phase Field Module` for more information), $u$ is the nonlinear variable the kernel is operating on.  
 

framework/src/kernels/FunctionDiffusion.C

@@ -16,7 +16,7 @@ InputParameters
 FunctionDiffusion::validParams()
 {
   InputParameters params = Diffusion::validParams();
-  params.addClassDescription("The Laplacian operator with a function coefficient.");
+  params.addClassDescription("Diffusion with a function coefficient.");
   params.addParam<FunctionName>("function", 1.0, "Function multiplier for diffusion term.");
   params.addCoupledVar("v",
                        "Coupled concentration variable for kernel to operate on; if this "

framework/src/kernels/GradField.C

@@ -17,7 +17,7 @@ GradField::validParams()
 {
   InputParameters params = VectorKernel::validParams();
   params.addClassDescription("The gradient operator optionally scaled by a constant scalar "
-                             "coefficient. Weak form: $(\\nabla \\cdot \\vec{\\psi_i}, k u)$.");
+                             "coefficient. Weak form: $(\\nabla \\cdot \\vec{\\psi_i}, k v)$.");
   params.addRequiredCoupledVar("coupled_scalar_variable", "The scalar field");
   params.addParam<Real>("coeff", 1.0, "The constant coefficient");
   return params;

modules/doc/content/citing.md

@@ -8,25 +8,25 @@ list of publications that have cited MOOSE, please refer to the [publications.md
 For all publications that use MOOSE or a MOOSE-based application please cite the following.
 
 ```tex
-@article{lindsay2022moose,
-   title = {2.0 - {MOOSE}: Enabling massively parallel multiphysics simulation},
-   author = {Alexander D. Lindsay and Derek R. Gaston and Cody J. Permann and Jason M. Miller and
-             David Andr{\v{s}} and Andrew E. Slaughter and Fande Kong and Joshua Hansel and
-             Robert W. Carlsen and Casey Icenhour and Logan Harbour and Guillaume L. Giudicelli
-             and Roy H. Stogner and Peter German and Jacob Badger and Sudipta Biswas and
-             Leora Chapuis and Christopher Green and Jason Hales and Tianchen Hu and Wen Jiang
-             and Yeon Sang Jung and Christopher Matthews and Yinbin Miao and April Novak and
-             John W. Peterson and Zachary M. Prince and Andrea Rovinelli and Sebastian Schunert
-             and Daniel Schwen and Benjamin W. Spencer and Swetha Veeraraghavan and Antonio Recuero
-             and Dewen Yushu and Yaqi Wang and Andy Wilkins and Christopher Wong},
-    year = {2022},
+@article{giudicelli2024moose,
+   title = {3.0 - {MOOSE}: Enabling massively parallel multiphysics simulations},
+   author = {Guillaume Giudicelli and Alexander Lindsay and Logan Harbour and Casey Icenhour and
+             Mengnan Li and Joshua E. Hansel and Peter German and Patrick Behne and Oana Marin and
+             Roy H. Stogner and Jason M. Miller and Daniel Schwen and Yaqi Wang and Lynn Munday and
+             Sebastian Schunert and Benjamin W. Spencer and Dewen Yushu and Antonio Recuero and
+             Zachary M. Prince and Max Nezdyur and Tianchen Hu and Yinbin Miao and
+             Yeon Sang Jung and Christopher Matthews and April Novak and Brandon Langley and
+             Timothy Truster and Nuno Nobre and Brian Alger and David Andr{\v{s}} and
+             Fande Kong and Robert Carlsen and Andrew E. Slaughter and John W. Peterson and
+             Derek Gaston and Cody Permann},
+    year = {2024},
  journal = {{SoftwareX}},
-  volume = {20},
-   pages = {101202},
+  volume = {26},
+   pages = {101690},
     issn = {2352-7110},
-     doi = {https://doi.org/10.1016/j.softx.2022.101202},
-     url = {https://www.sciencedirect.com/science/article/pii/S2352711022001200},
-keywords = {Multiphysics, Object-oriented, Finite-element, Framework},
+     doi = {https://doi.org/10.1016/j.softx.2024.101690},
+     url = {https://www.sciencedirect.com/science/article/pii/S235271102400061X},
+keywords = {Framework, Finite-element, Finite-volume, Parallel, Multiphysics, Multiscale},
 }
 ```
 

modules/doc/content/getting_started/examples_and_tutorials/examples/ex01_inputfile.md

@@ -10,7 +10,7 @@ $-\nabla \cdot \nabla u = 0 \in \Omega$, $u = 1$ on the bottom, $u = 0$ on the t
 $\nabla u \cdot \hat{n} = 0$ on the remaining boundaries.
 
 The weak form ([see Finite Elements Principles](finite_element_concepts/fem_principles.md)) of
-this equation, in inner-product notation, is given by: $\nabla \phi_i, \nabla u_h = 0 \quad
+this equation, in inner-product notation, is given by: $(\nabla \phi_i, \nabla u_h) = 0 \quad
 \forall  \phi_i$, where $\phi_i$ are the test functions and $u_h$ is the finite element solution.
 
 ## Input File Syntax
@@ -37,7 +37,6 @@ file itself:
 []
 ```
 
-<br>
 
 !media large_media/examples/mug_mesh.png
        caption=mug.e mesh file
@@ -108,7 +107,6 @@ make -j8
 This will generate the results file, out.e, as shown in [example-1-results]. This file may be viewed using
 Peacock or an external application that supports the Exodus II format (e.g., Paraview).
 
-<br>
 
 !media large_media/examples/ex01_results.png
        id=example-1-results

modules/doc/content/getting_started/examples_and_tutorials/examples/ex03_coupling.md

@@ -94,8 +94,6 @@ make -j8
 This will generate the results file, out.e, as shown in Figure 1 and 2. This file may be viewed
 using Peacock or an external application that supports the Exodus II format (e.g., Paraview).
 
-<div style="width:100%">
-
 !media large_media/examples/ex03_out_diffused.png
        caption=Figure 1: example 3 Results, "diffused variable"
        style=width:40%;display:inline-flex;margin-left:7%;
@@ -104,8 +102,6 @@ using Peacock or an external application that supports the Exodus II format (e.g
        caption=Figure 2: example 3 Results, "convected variable"
        style=width:40%;display:inline-flex;margin-left:7%;
 
-</div><br>
-
 # 1D exact solution
 
  A simplified 1D analog of this problem is given as follows, where $u(0)=0$ and $u(1)=1$:

modules/heat_transfer/doc/content/source/auxkernels/JouleHeatingHeatGeneratedAux.md

@@ -4,7 +4,7 @@
 
 ## Description
 
-The `JouleHeatingHeatGeneratedAux` AuxKernel is used to compute the heat generated by Joule heating. The heat (power per unit volume) is computed as $dP/dV= \bm{J} \cdot \bm{E} = E ^2 \sigma$, where $\bm{J} = \sigma \bm{E}$ is the current density, $\bm{E}$ is the electric field, and $ \sigma $ is the electrical conductivity.
+The `JouleHeatingHeatGeneratedAux` AuxKernel is used to compute the heat generated by Joule heating. The heat (power per unit volume) is computed as $dP/dV= \bm{J} \cdot \bm{E} = E ^2 \sigma$, where $\bm{J} = \sigma \bm{E}$ is the current density, $\bm{E}$ is the electric field, and $\sigma$ is the electrical conductivity.
 
 !syntax parameters /AuxKernels/JouleHeatingHeatGeneratedAux
 

stork/src/base/StorkApp.C.app

@@ -9,6 +9,7 @@ StorkApp::validParams()
 {
   InputParameters params = MooseApp::validParams();
   params.set<bool>("use_legacy_material_output") = false;
+  params.set<bool>("use_legacy_initial_residual_evaluation_bahavior") = false;
   return params;
 }
 
@@ -19,7 +20,7 @@ StorkApp::StorkApp(InputParameters parameters) : MooseApp(parameters)
 
 StorkApp::~StorkApp() {}
 
-void 
+void
 StorkApp::registerAll(Factory & f, ActionFactory & af, Syntax & s)
 {
   ModulesApp::registerAllObjects<StorkApp>(f, af, s);