Merge pull request idaholab#26803 from farscape-project/fix_makefile

Fix previous changes to the build system and some docs

framework/app.mk

@@ -209,7 +209,6 @@ app_LINK := $(foreach i, $(include_files), $(all_header_dir)/$(notdir $(i)))
 $(eval $(call all_header_dir_rule, $(all_header_dir)))
 $(call symlink_rules, $(all_header_dir), $(include_files))
 
-$(APPLICATION_NAME)_header_symlinks: $(all_header_dir) $(app_LINK)
 app_INCLUDE = -I$(all_header_dir)
 
 else # No Header Symlinks
@@ -258,7 +257,6 @@ else
 endif
 
 app_LIBS       += $(app_LIB)
-app_LIBS_other := $(filter-out $(app_LIB),$(app_LIBS))
 app_HEADERS    := $(app_HEADER) $(app_HEADERS)
 app_INCLUDES   += $(app_INCLUDE) $(ADDITIONAL_INCLUDES)
 app_DIRS       += $(APPLICATION_DIR)
@@ -291,7 +289,7 @@ ifeq ($(MOOSE_HEADER_SYMLINKS),true)
 # object files until all symlinking is completed. The first dependency in the
 # list below ensures this.
 
-$(all_app_objects) : | $(APPLICATION_NAME)_header_symlinks $(moose_config_symlink)
+$(all_app_objects) : | $(app_LINKS) $(moose_config_symlink)
 
 else
 

framework/doc/content/hit.md

@@ -179,7 +179,7 @@ hit common file1.i file2.i ... > common_parameters.i
 ```
 
 Will extract all parameters that are common to the specified input files (and
-have the same values). This can be used as the **first step** in factoring out
+have the same values). This can be used as the +first step+ in factoring out
 common settings into a single input file.
 
 ## `hit subtract` - Removing common parameters parameters
@@ -189,7 +189,7 @@ hit subtract simulation_1_full.i common_parameters.i > simulation_1.i
 ```
 
 removes the parameters in `common_parameters.i` from `simulation_1_full.i`,
-creating `simulation_1.i`. This is the **second step** in factoring out common
+creating `simulation_1.i`. This is the +second step+ in factoring out common
 parameters from a set of input files. The resulting file can be run as
 `./mooseapp-opt -i common.i simulation_1.i` and will result in the same
 simulation as `./mooseapp-opt -i simulation_1_full.i`.

framework/doc/content/source/auxkernels/AdvectiveFluxAux.md

@@ -7,11 +7,11 @@
 The `AdvectiveFluxAux` AuxKernel is used to compute a component of an advective flux vector. The flux is computed as
 
 !equation
-(\\vec{J} = \\vec{v} u \\cdot \\vec{n})
+\vec{J} \cdot \vec{n} = \vec{v} u \cdot \vec{n}
 
-where $\\vec{J}$ is the advection flux vector, $u$ is the advected quantity, $\\vec{v}$ is the velocity, and $\\vec{n}$ is the normal for the desired component which can be the x, y, z axis or the normal direction (only near boundaries).
+where $\vec{J}$ is the advection flux vector, $u$ is the advected quantity, $\vec{v}$ is the velocity, and $\vec{n}$ is the normal for the desired component which can be the x, y, z axis or the normal direction (only near boundaries).
 
-This auxkernel supports CONSTANT and FIRST MONOMIAL AuxVariable types. The advection velocity is required with [!param](/AuxKernels/AdvectiveFluxAux/vel_x) for advection flux calculation. [!param](/Postprocessors/SideAdvectiveFluxIntegral/vel_y) and [!param](/Postprocessors/SideAdvectiveFluxIntegral/vel_z) are needed for 2D and 3D simulations. The advected quantity can be either a variable[!param](/AuxKernels/AdvectiveFluxAux/advected_variable) or material property[!param](/AuxKernels/AdvectiveFluxAux/advected_mat_prop).
+This auxkernel supports CONSTANT and FIRST MONOMIAL AuxVariable types. The advection velocity is required with [!param](/AuxKernels/AdvectiveFluxAux/vel_x) for advection flux calculation. [!param](/Postprocessors/SideAdvectiveFluxIntegral/vel_y) and [!param](/Postprocessors/SideAdvectiveFluxIntegral/vel_z) are needed for 2D and 3D simulations. The advected quantity can be either a variable [!param](/AuxKernels/AdvectiveFluxAux/advected_variable) or material property [!param](/AuxKernels/AdvectiveFluxAux/advected_mat_prop).
 
 !alert warning
 The expression of the advective flux in this object is generic, as described, and may differ from the advective flux implemented in your physics implementation. If so, you may not use this object to compute the advective flux.

framework/doc/content/source/auxkernels/SecondTimeDerivativeAux.md

@@ -3,7 +3,7 @@
 !syntax description /AuxKernels/SecondTimeDerivativeAux
 
 The [!param](/AuxKernels/SecondTimeDerivativeAux/factor) multiplies the output of the second time derivative operation.
-The time derivative of the [!param](/AuxKernels/SecondTimeDerivativeAux/factor) is **not** computed.
+The time derivative of the [!param](/AuxKernels/SecondTimeDerivativeAux/factor) is +not+ computed.
 
 !alert warning
 The `SecondTimeDerivativeAux` can only output a non-zero time derivative when the [time integrator](syntax/Executioner/TimeIntegrator/index.md) has implemented the second time derivative. Only [CentralDifference.md] and [NewmarkBeta.md] have as of early 2023, but contributions are welcome!

framework/doc/content/source/auxkernels/TimeDerivativeAux.md

@@ -3,7 +3,7 @@
 !syntax description /AuxKernels/TimeDerivativeAux
 
 The [!param](/AuxKernels/TimeDerivativeAux/factor) multiplies the output of the time derivative operation.
-The time derivative of the [!param](/AuxKernels/TimeDerivativeAux/factor) is **not** computed.
+The time derivative of the [!param](/AuxKernels/TimeDerivativeAux/factor) is +not+ computed.
 
 !alert warning
 The `TimeDerivativeAux` is restricted to constructs for which the time derivative is computed by MOOSE. Time derivative

framework/doc/content/source/fvkernels/FVBodyForce.md

@@ -13,7 +13,7 @@ where $f$ is the source term (negative if a sink) and the second term on the
 left hand side represents the strong forms of other kernels.
 
 The Jacobian term for this kernel is zero: $\frac{\partial R_i(u_h)}{\partial u_j} = 0$, since
-it is assumed that $f$ **is not** a function of the unknown $u$.
+it is assumed that $f$ +is not+ a function of the unknown $u$.
 
 The force is constructed through a user supplied constant $c$,
 [function](/Functions/index.md) value evaluated at the current time and

framework/doc/content/source/geomsearch/GeometricSearchData.md

@@ -22,4 +22,4 @@
 - The non-quadrature based methods should be used for nodal objects such as:
     - [`NodeFaceConstraints`](Constraints/index.md) e.g. the `Contact` module's `MechanicalContactConstraint` object
     - [Nodal `AuxKernels`](AuxKernels/index.md) e.g. the nodal versions of [`GapValueAux`](/GapValueAux.md), [`NearestNodeDistanceAux`](/NearestNodeDistanceAux.md), and [`PenetrationAux`](/PenetrationAux.md)
-- geometric search objects like [`NearestNodeLocator`](/NearestNodeLocator.md) and [`PenetrationLocator`](/PenetrationLocator.md) should hold to their geometric purpose and **not** call algebraic APIs like `FEProblemBase::prepare` which will query `libMesh::DofObject` information. This information may or may not have been initialized at the time that geometric search objects are being updated, so any query attempt may result in failed assertions or segmentation faults.
+- geometric search objects like [`NearestNodeLocator`](/NearestNodeLocator.md) and [`PenetrationLocator`](/PenetrationLocator.md) should hold to their geometric purpose and +not+ call algebraic APIs like `FEProblemBase::prepare` which will query `libMesh::DofObject` information. This information may or may not have been initialized at the time that geometric search objects are being updated, so any query attempt may result in failed assertions or segmentation faults.

framework/doc/content/source/interfaces/TaggingInterface.md

@@ -11,7 +11,7 @@ This behavior can be modified by setting parameters in the object's blocks in th
 
 | Tag           | Description |
 |-              |            -|
-|vector_tags    | The tag for the vectors this object should fill |
-|extra_vector_tags | Add more vectors to fill beyond what is in `vector_tags` - useful for adding without overriding the defaults|
-|matrix_tags    | The tag for the matrices this object should fill |
-|extra_matrix_tags | Add more matrices to fill beyond what is in `matrix_tags` - useful for adding without overriding the defaults |
+| vector_tags    | The tag for the vectors this object should fill |
+| extra_vector_tags | Add more vectors to fill beyond what is in `vector_tags` - useful for adding without overriding the defaults |
+| matrix_tags    | The tag for the matrices this object should fill |
+| extra_matrix_tags | Add more matrices to fill beyond what is in `matrix_tags` - useful for adding without overriding the defaults |

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

@@ -8,7 +8,7 @@
 (\vec{u}^\ast, -\vec{f}),
 \end{equation}
 where $\vec{u}^\ast$ is the test functions of all the components of the array variable $\vec{u}$, and $\vec{f}$ is the body force functions whose size must agree with the number of components of the array variable.
-The Jacobian term for this kernel is zero since it is assumed that $\vec{f}$ **is not** a function of the unknown $\vec{u}$.
+The Jacobian term for this kernel is zero since it is assumed that $\vec{f}$ +is not+ a function of the unknown $\vec{u}$.
 
 ## Example Input Syntax
 

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

@@ -20,7 +20,7 @@ where the $\psi_i$ are the test functions, and $u_h$ are the trial solutions in
 the finite dimensional space $\mathcal{S}^h$ for the unknown ($u$).
 
 The Jacobian term for this kernel is zero: $\frac{\partial R_i(u_h)}{\partial u_j} = 0$, since
-it is assumed that $f$ **is not** a function of the unknown $u$.
+it is assumed that $f$ +is not+ a function of the unknown $u$.
 
 The force is constructed through a user supplied constant $c$,
 [function](/Functions/index.md) value evaluated at the current time and

framework/doc/content/source/positions/MultiAppPositions.md

@@ -9,7 +9,7 @@ the main app frame of reference. This position can be used to align the meshes f
 for outputting the `MultiApps` [Exodus results](Exodus.md) at the translated positions.
 
 !alert warning
-This should **not** be used to generate new `MultiApps`. The `MultiApps` have already
+This should +not+ be used to generate new `MultiApps`. The `MultiApps` have already
 been created when the positions are gathered.
 
 ## Example MultiApp File Syntax

framework/doc/content/source/relationshipmanagers/RelationshipManager.md

@@ -81,7 +81,7 @@ params.addRelationshipManager("ElementSideNeighborLayers",
 because there is a (default) 1 layer of side ghosting for all ghosting types
 (1 layer coupling ghosting <= 1 layer algebraic ghosting <= 1 layer geometric
 ghosting).
-The following RM set-up would be **invalid**:
+The following RM set-up would be +invalid+:
 
 ```c++
 params.addRelationshipManager(

framework/doc/content/source/timeintegrators/ExplicitTimeIntegrator.md

@@ -105,7 +105,7 @@ time (the time we are solving "from"):
 
 !listing framework/src/timeintegrators/ActuallyExplicitEuler.C line=timeOld
 
-However, `DirichletBC` derived boundary conditions need to use the **final** time,
+However, `DirichletBC` derived boundary conditions need to use the +final+ time,
 since the strong constraints they represent use the final time and are not affected
 by the time integrator. To achieve this, time is reset to the `_current_time` after
 the weak form residual evaluation and before `NodalBC` boundary condition application,

framework/doc/content/source/timesteppers/CompositionDT.md

@@ -7,7 +7,7 @@
 The `CompositionDT` TimeStepper takes multiple time steppers as input and computes the minimum time step size among all time steppers as output. If any time sequence stepper(s) is supplied for input, CompositionDT will compare the computed minimum time step size with the one needs to hit the time point, then select the smaller value as output. An optional parameter [!param](/Executioner/TimeSteppers/CompositionDT/lower_bound)is provided to set a lower bound for the computed time step size, and enable growth driven by a single time stepper.
 
 The composition rules are listed with priority rank:
-1. The time points from time sequence stepper(s) **must** be hit;
+1. The time points from time sequence stepper(s) +must+ be hit;
 2. The time step size can not go below the [!param](/Executioner/TimeSteppers/CompositionDT/lower_bound);
 3. Take the minimum time step value of all input time steppers.
 

framework/doc/content/source/utils/IndexableProperty.md

@@ -8,12 +8,12 @@ select a scalar component from the property value.
 
 | Material property type | `component` parameter example |
 | - | - |
-|`Real` | _none_ |
-|`RealVectorValue` | `component = 1`|
-|`std::vector<Real>` | `component = 7`|
-|`RankTwoTensor` | `component = "0 2"`|
-|`RankThreeTensor` | `component = "1 2 0"`|
-|`RankFourTensor` | `component = "1 0 1 2"`|
+| `Real` | _none_ |
+| `RealVectorValue` | `component = 1` |
+| `std::vector<Real>` | `component = 7` |
+| `RankTwoTensor` | `component = "0 2"` |
+| `RankThreeTensor` | `component = "1 2 0"` |
+| `RankFourTensor` | `component = "1 0 1 2"` |
 
 To use this utility class declare a member in your class header
 

framework/doc/content/source/utils/Units.md

@@ -21,7 +21,7 @@ The following units are currently supported
 
 | Symbol | Base units | Name | Description |
 | - | - | - | - |
-| `Ohm` | $\text{kg}\cdot \text{m}^{2}\cdot \text{s}^{-3}\cdot \text{A}^{-2}$ | Ohm | resistance, impedance, reactance|
+| `Ohm` | $\text{kg}\cdot \text{m}^{2}\cdot \text{s}^{-3}\cdot \text{A}^{-2}$ | Ohm | resistance, impedance, reactance |
 | `atm` | $101325\, \text{kg}\cdot \text{m}^{-1}\cdot \text{s}^{-2}$ | Standard atmosphere | pressure |
 | `eV` | $1.60218\cdot10^{-19}\, \text{kg}\cdot \text{m}^{2}\cdot \text{s}^{-2}$ | electron Volt | energy |
 | `erg` | $10^{-7}\, \text{kg}\cdot \text{m}^{2}\cdot \text{s}^{-2}$ | Erg | energy |
@@ -35,7 +35,7 @@ The following units are currently supported
 | `s` | $\text{s}$ | second | time |
 | `A` | $\text{A}$ | Ampere | electric current |
 | `K` | $\text{K}$ | Kelvin | temperature |
-| `mol` | $6.02214\cdot10^{23}\, \text{at}$ | mole | amount of substance|
+| `mol` | $6.02214\cdot10^{23}\, \text{at}$ | mole | amount of substance |
 | `cd` | $\text{cd}$ | candela | luminous intensity |
 | `N` | $\text{kg}\cdot \text{m}\cdot \text{s}^{-2}$ | Newton | force, weight |
 | `Pa` | $\text{kg}\cdot \text{m}^{-1}\cdot \text{s}^{-2}$ | Pascal | pressure, stress |
@@ -45,7 +45,7 @@ The following units are currently supported
 | `V` | $\text{kg}\cdot \text{m}^{2}\cdot \text{s}^{-3}\cdot \text{A}^{-1}$ | Volt | voltage (electrical potential), emf |
 | `F` | $\text{kg}^{-1}\cdot \text{m}^{-2}\cdot \text{s}^{4}\cdot \text{A}^{2}$ | Farad | capacitance |
 | `S` | $\text{kg}^{-1}\cdot \text{m}^{-2}\cdot \text{s}^{3}\cdot \text{A}^{2}$ | Siemens | electrical conductance |
-| `Wb` | $\text{kg}\cdot \text{m}^{2}\cdot \text{s}^{-2}\cdot \text{A}^{-1}$ | Weber | magnetic flux|
+| `Wb` | $\text{kg}\cdot \text{m}^{2}\cdot \text{s}^{-2}\cdot \text{A}^{-1}$ | Weber | magnetic flux |
 | `T` | $\text{kg}\cdot \text{s}^{-2}\cdot \text{A}^{-1}$ | Tesla | magnetic flux density |
 | `H` | $\text{kg}\cdot \text{m}^{2}\cdot \text{s}^{-2}\cdot \text{A}^{-2}$ | Henry | inductance |
 | `Ba` | $0.1\, \text{kg}\cdot \text{m}^{-1}\cdot \text{s}^{-2}$ | barye | Pressure |
@@ -58,7 +58,7 @@ The following units are currently supported
 | `BTU` | $1055.06\, \text{kg}\cdot \text{m}^{2}\cdot \text{s}^{-2}$ | ISO 31-4 British thermal unit | heat |
 | `bar` | $10^5\, \text{kg}\cdot \text{m}^{-1}\cdot \text{s}^{-2}$ | Bar | pressure, stress |
 | `h` | $3600\, \text{s}$ | hour | time |
-| `day` | $86400\, \text{s}$ | day | time (`d` would create an ambiguity between centi-day and candela)|
+| `day` | $86400\, \text{s}$ | day | time (`d` would create an ambiguity between centi-day and candela) |
 | `l` | $0.001\, \text{m}^{3}$ | liter | volume |
 | `u` | $1.66054\cdot10^{-27}\, \text{kg}^{3}$ | unified atomic mass unit | mass |
 | `at` | $\text{at}$ | atom | single count of substance |

framework/doc/content/source/vectorpostprocessors/LineMaterialRealSampler.md

@@ -7,7 +7,7 @@
 This class samples Real material properties for the integration points
 in all elements that are intersected by a user-defined line.
 
-The output to CSV is **by default** ordered as follows:
+The output to CSV is +by default+ ordered as follows:
 
 - rows are ordered by point sampled along the line
 

framework/doc/content/source/vectorpostprocessors/VectorMemoryUsage.md

@@ -6,12 +6,12 @@ This vector postprocessor generates multiple output columns with one row per MPI
 
 | Column name   | Description |
 |---------------|--------------|
-| `hardware_id` | Ranks with a common hardware ID share common RAM (i.e. are located on the same compute node)|
-| `total_ram`   | Total available RAM on the compute node the respective MPI rank is located on.|
-| `physical_mem` | Physical memory the current rank uses (default unit: MBs).|
-| `virtual_mem` | Virtual memory the current rank uses (the amount returned strongly depends on the operating system and does not reflect the physical RAM used by the simulation - default unit: MBs).|
-| `page_faults` | Number of hard page faults encountered by the MPI rank. This number is only available on Linux systems and indicates the amount of swap activity (indicating low performance due to insufficient available RAM)|
-| `node_utilization` | Indicates which fraction of the total RAM available on the compute node is occupied by MOOSE processes of the current simulation.|
+| `hardware_id` | Ranks with a common hardware ID share common RAM (i.e. are located on the same compute node) |
+| `total_ram`   | Total available RAM on the compute node the respective MPI rank is located on. |
+| `physical_mem` | Physical memory the current rank uses (default unit: MBs). |
+| `virtual_mem` | Virtual memory the current rank uses (the amount returned strongly depends on the operating system and does not reflect the physical RAM used by the simulation - default unit: MBs). |
+| `page_faults` | Number of hard page faults encountered by the MPI rank. This number is only available on Linux systems and indicates the amount of swap activity (indicating low performance due to insufficient available RAM) |
+| `node_utilization` | Indicates which fraction of the total RAM available on the compute node is occupied by MOOSE processes of the current simulation. |
 
 For a Postprocessor that provides min/max/average memory statistics see
 [`MemoryUsage`](/MemoryUsage.md).

framework/doc/content/syntax/AuxKernels/index.md

@@ -26,7 +26,7 @@ file snippet creates an auxiliary variable suitable for use with an `VectorAuxKe
 There are two flavors of AuxKernel objects: nodal and elemental. The distinction is based on the
 type of variable that is being operated on by the object. If the variable family is `LAGRANGE` or
 `LAGRANGE_VEC` then the AuxKernel will behave as nodal. If the variable family is `MONOMIAL` then
-the AuxKernel will behave as an elemental.
+the AuxKernel will behave as elemental.
 
 The difference is based on how the `computeValue` method of the object is called when the kernel
 is executed. In the nodal case the `computeValue` method will be executed on each +node+ within the

framework/doc/content/syntax/FunctorMaterials/index.md

@@ -17,7 +17,7 @@ All functor materials support caching in some capacity. This can avoid expensive
 disabled by default due to the potential memory cost. The reader is referred to the [Functors caching documentation](syntax/Functors/index.md#caching).
 
 !alert warning
-Functor material properties and regular material properties are generally **NOT** compatible with each other. Functor material properties can only be used as regular material properties using a
+Functor material properties and regular material properties are generally +NOT+ compatible with each other. Functor material properties can only be used as regular material properties using a
 [MaterialFunctorConverter.md] to process them.
 
 Functor materials are created within the `[FunctorMaterials]` block.

framework/doc/content/syntax/Mesh/index.md

@@ -279,7 +279,7 @@ We point out in this section a few things to look for.
   the flux will depend on the orientation of the sideset.
 - MOOSE generally does not support non-conformal meshes for regular kernels, except when they arise from online mesh refinement.
   When inspecting your mesh, you should not see any hanging nodes or surfaces not exactly touching. If you are using such
-  a mesh, you **MUST** use interface kernels, mortar or other advanced numerical treatments.
+  a mesh, you +MUST+ use interface kernels, mortar or other advanced numerical treatments.
 - Many physics will give better results with high element quality and smooth distributions of element volumes.
   You may examine the spatial distribution of these quantities using the [ElementQualityAux.md] and [VolumeAux.md]
   respectively.

framework/include/utils/InputParameters.h

@@ -153,7 +153,7 @@ class InputParameters : public Parameters
   /**
    * This method adds a parameter and documentation string to the InputParameters
    * object that will be extracted from the input file.  If the parameter is
-   * missing in the input file, and error will be thrown
+   * missing in the input file, an error will be thrown
    */
   template <typename T>
   void addRequiredParam(const std::string & name, const std::string & doc_string);