Docs and sqa changes (idaholab#21885)

modules/optimization/doc/config.yml

@@ -1,45 +1,47 @@
 Content:
-  - ${ROOT_DIR}/examples
-  - ${ROOT_DIR}/doc/content
-  - ${MOOSE_DIR}/framework/doc/content
-  - ${MOOSE_DIR}/modules/heat_conduction/doc/content
-  - ${MOOSE_DIR}/modules/stochastic_tools/doc/content
-  - ${MOOSE_DIR}/modules/ray_tracing/doc/content
-  - ${MOOSE_DIR}/modules/tensor_mechanics/doc/content
+  - framework/doc/content
+  - modules/heat_conduction/doc/content
+  - modules/stochastic_tools/doc/content
+
+>>>>>>> 46426fd27e (Docs and sqa changes (#21885))
 Renderer:
   type: MooseDocs.base.MaterializeRenderer
 
 Extensions:
   MooseDocs.extensions.navigation:
-    name: Isopod
-    repo: https://github.com/zachmprince/isopod
+    name: MOOSE Optimization Module
+    repo: https://github.com/idaholab/moose
+    home: /modules/optimization/index.md
     menu:
-      Theory: getting_started/InvOptTheory.md
+      Getting Started:
+        Theory: getting_started/InvOptTheory.md
+        Running Optimization Problems: getting_started/RunningOptimization.md
+        Input Structure: getting_started/OptimizationInputStructure.md
+      Syntax: syntax/index.md
       Examples: examples/index.md
       Syntax: syntax/index.md
 
   MooseDocs.extensions.appsyntax:
-    executable: ${ROOT_DIR}
+    executable: ${MOOSE_DIR}.modules/optimize
     remove:
       framework: !include ${MOOSE_DIR}/framework/doc/remove.yml
+    includes:
+        - framework/include
+        - modules/optimization/include
+        - modules/heat_conduction/include
+        - modules/stochastic_tools/include
 
   MooseDocs.extensions.common:
     shortcuts: !include ${MOOSE_DIR}/framework/doc/globals.yml
-
   MooseDocs.extensions.acronym:
     acronyms: !include ${MOOSE_DIR}/framework/doc/acronyms.yml
-
   MooseDocs.extensions.template:
         active: True
   MooseDocs.extensions.sqa:
       active: False
       reports: !include ${ROOT_DIR}/doc/sqa_reports.yml
-      repos:
-          default: https://github.com/idaholab/isopod
-          moose: https://github.com/idaholab/moose
       categories:
-          framework: !include ${MOOSE_DIR}/framework/doc/sqa_framework.yml
-          stochastic_tools: !include ${MOOSE_DIR}/modules/stochastic_tools/doc/sqa_stochastic_tools.yml
-          heat_conduction: !include ${MOOSE_DIR}/modules/heat_conduction/doc/sqa_heat_conduction.yml
-          tensor_mechanics: !include ${MOOSE_DIR}/modules/tensor_mechanics/doc/sqa_tensor_mechanics.yml
-          isopod: !include ${ROOT_DIR}/doc/sqa_isopod.yml
+          framework: !include framework/doc/sqa_framework.yml
+          optimization: !include modules/stochastic_tools/doc/sqa_optimization.yml
+          stochastic_tools: !include modules/stochastic_tools/doc/sqa_stochastic_tools.yml
+          heat_conduction: !include modules/heat_conduction/doc/sqa_heat_conduction.yml

modules/optimization/doc/content/getting_started/OptimizationInputStructure.md

@@ -0,0 +1,110 @@
+# Input File Structure
+
+## Basic Syntax
+
+The input file used by Isopod (or any MOOSE application) is broken into
+sections or blocks identified with square brackets. The type of input block is
+placed in the opening brackets, and empty brackets mark the end of the block.
+
+```text
+[BlockName]
+    <block lines and subblocks>
+[]
+```
+
+Each block may contain an arbitrary number of line commands to define
+parameters related to that block. They can also optionally contain one
+or more subblocks, which may in turn contain their own nested subblocks.
+Subblocks are opened and closed with the following syntax:
+
+```text
+[./subblock_name]
+    <line commands>
+[../]
+```
+
+Note that all subblocks contained within a given block must have unique
+names (within the opening [] brackets).
+
+Parameters are defined with line commands, and are given as key/value
+pairs separated by an equals sign (=). They specify parameters to be
+used by the object being described.  The key is a string (no
+whitespace), and the value may be a string, an integer, a real number,
+or a list of strings, integers, or real numbers.  Lists are given
+in single quotes and are separated by whitespace.
+
+The following are examples of line commands for a single parameter and
+for a list of parameters:
+
+```text
+single_parameter = 2.3
+list_of_parameters = '1.0 2.3 3.7'
+```
+
+Blocks and subblocks at any level can contain line commands, which must
+be appropriate for the scope of the block containing them. Most of the
+time, blocks are used to create instances of MOOSE objects, and contain
+a ```type = ``` parameter to specify the type of MOOSE object to be
+created. The name of the MOOSE object specified in the parameter
+corresponds to the name of the class in the C++ source code.
+
+Each object type has a unique set of input parameters that are valid for
+specifying the behavior of that object. Some parameters are required,
+and some are optional, and revert to default behavior if they are not
+specified.  An error message is generated if a line command does not
+apply within the scope in which it is provided. Repeating a line within
+a block also results in an error.
+
+In this document, line commands are shown with the keyword, an equal
+sign, and, in angle brackets, the value. If a default value exists for
+that line command, it is shown in parentheses.
+
+In the initial description of a block, line commands common to all
+subblocks will be described. Those line commands are then omitted from
+the description of the subblocks but are nonetheless valid line commands
+for those subblocks.
+
+The name of a subblock (`[./<name>]`) is arbitrary. However, these
+names should be chosen to be meaningful because they can be used to
+refer to those entities elsewhere in the input file. Not every created
+entity is referenced elsewhere, but a name must be created for every
+entity regardless.
+
+## Summary of MOOSE Object Types
+
+MOOSE is an objected-oriented system with well-defined interfaces for
+applications to define their own physics-specific code modules. The
+following is a listing of the major types of MOOSE objects used by Isopod:
+
+- Variable
+- Kernel
+- AuxVariable
+- AuxKernel
+- Material
+- BoundaryCondition
+- Function
+- Postprocessor
+- VectorPostprocessor
+- Constraint
+- Damper
+
+Specialized versions of these object types are implemented to provide
+the functionality needed to model physics of interest for Isopod.
+
+## Isopod Syntax Page
+
+A complete listing of all input syntax options in MOOSE is available on
+[the MOOSE Documentation page](http://mooseframework.org/documentation/).
+See the section on Input File Documentation. Note also that you can run
+
+```text
+isopod-opt --dump
+```
+
+to get a list of valid input options for Isopod.
+
+## Units
+
+Isopod can be run using any unit system preferred by the
+user. Empirical models within Isopod that depend on a specific unit
+system are noted in this documentation.

modules/optimization/doc/content/getting_started/RunningOptimization.md

@@ -0,0 +1,176 @@
+# Obtaining and Running Isopod
+
+## Checking Out the Code
+
+Isopod uses the git revision control system, and its repository is
+hosted on GitHub at [https://github.com/idaholab/isopod](https://github.com/idaholab/isopod).
+The following steps are required for the initial checkout of
+the code:
+
+First, create a GitHub account and add an SSH key to your GitHub profile. Note that
+this is not completely necessary, as you can check out the code without a GitHub
+account using the https protocol.  However, using ssh with a GitHub account is recommended,
+as it makes it easier to contribute to the code later on. The instructions provided here just
+document the steps to take, and more detailed information
+on using ssh keys with GitHub is available [here](https://help.github.com/articles/connecting-to-github-with-ssh/).
+
+First generate a public/private keypair and show the generated public key by
+typing the following in a terminal:
+
+```bash
+ssh-keygen -t rsa -C "your_email"
+cat ~/.ssh/id_rsa.pub
+```
+
+Then copy and paste the key to the 'SSH and GPG keys' section under the 'Settings' menu
+in your GitHub user profile. Next clone the Isopod repository. This assumes
+that you want the code to be in a directory named `projects` in your home directory, which
+you have already created:
+
+```bash
+cd ~/projects/
+git clone git@github.com:idaholab/isopod.git
+```
+
+Isopod requires a checkout of the MOOSE repository to link against. By default, the Isopod
+build process looks for that in a directory called `moose` located in the same directory
+that contains the `isopod` directory. Clone the MOOSE repository using the following command:
+
+```bash
+cd ~/projects/
+git clone git@github.com:idaholab/moose.git
+```
+
+After doing this, the `~/projects` directory should contain `isopod` and `moose` subdirectories:
+```bash
+$ ls ~/projects/
+isopod moose
+```
+
+It is necessary to build libMesh within the MOOSE repository before building any application:
+
+```bash
+cd ~/projects/moose/scripts
+./update_and_rebuild_libmesh.sh
+```
+
+On a multiprocessor machine, this process can optionally be done in parallel by setting
+the `JOBS` environment variable equal to the number of processors to be used. For example, to 
+build using 8 processors, the libMesh build script can be run as follows:
+```bash
+JOBS=8 ./update_and_rebuild_libmesh.sh
+```
+
+Once libMesh has compiled successfully, you may now compile Isopod:
+
+```bash
+cd ~/projects/isopod/
+make (add -jn to run on multiple "n" processors)
+```
+
+Once Isopod has compiled successfully, it is recommended to run the tests
+to make sure the version of the code you have is running correctly.
+
+```bash
+cd ~/projects/isopod/
+./run_test (add -jn to run "n" jobs at one time)
+```
+
+## Updating Isopod
+
+If it has been some time since you have checked out the code an update
+will be required to gain access to the new features in Isopod.
+First update Isopod:
+
+```bash
+cd ~/projects/isopod/
+git pull --rebase
+```
+
+Then update MOOSE:
+
+```bash
+cd ~/projects/moose/
+git pull --rebase
+```
+
+Next rebuild libMesh:
+
+```bash
+cd ~/projects/moose/scripts/
+./update_and_rebuild_libmesh.sh
+```
+
+And finally recompile Isopod:
+
+```bash
+cd ~/projects/isopod/
+make (add -jn to run on multiple "n" processors)
+```
+
+## Executing Isopod
+
+When first starting out with Isopod, it is recommended to start from an
+example problem similar to the problem that you are trying to solve.
+Multiple examples can be found in isopod/test/tests/.
+It may be worth running the example problems to see how the code works
+and modifying input parameters to see how the run time, results and
+convergence behavior change.
+
+To demonstrate running Isopod, consider running one of the regression tests:
+
+```bash
+cd isopod/test/tests/concrete_ASR_swelling
+# To run with one processor
+~/projects/isopod/isopod-opt -i asr_confined.i
+# To run in parallel (2 processors)
+mpiexec -n 2 ~/projects/isopod/isopod-opt -i asr_confined.i
+```
+
+Note that the procedure for running this model in parallel is shown only
+for illustrative purposes. This particular model is quite small, and would
+not benefit from being run in parallel, although it can be run that way.
+
+## Input to Isopod
+
+Isopod simulation models are defined by the user through a text file
+that defines the parameters of the run.  This text file specifies the
+set of code objects that are composed together to simulate a physical
+problem, and provides parameters that control how those objects behave
+and interact with each other.  This text file can be prepared using any
+text editor.
+
+In addition to the text file describing the model parameters, Isopod also
+requires a definition of the finite element mesh on which the physics
+equations are solved. The mesh can be generated internally by Isopod using
+parameters defined in Isopod's input file for very simple geometries, or can
+be read from a file as defined in the Isopod input file. Isopod supports the
+full set of mesh file formats supported by MOOSE, although the most common
+mesh format is the ExodusII format.
+
+## Post Processing
+
+Isopod typically writes solution data to an ExodusII file. Data may also
+be written in other formats, a simple comma separated file giving global
+data being the most common.
+
+Several options exist for viewing ExodusII results files. These include
+commercial as well as open-source tools. One good choice is ParaView,
+which is open-source.
+
+ParaView is available on a variety of platforms. It is capable of
+displaying node and element data in several ways. It will also produce
+line plots of global data or data from a particular node or element.
+Detailed information on ParaView is available on its project
+[website](https://www.paraview.org).
+
+## Graphical User Interface
+
+It is worth noting that a graphical user interface (GUI) exists for all
+MOOSE-based applications. This GUI is named Peacock. Information about
+Peacock and how to set it up for use may be found on
+[the MOOSE wiki page](http://mooseframework.org/wiki/Peacock).
+
+Peacock may be used to generate a text input file. It is also capable of
+submitting the analysis. It also provides basic post processing
+capabilities.

modules/optimization/doc/content/sqa/index.md

@@ -1 +1 @@
-!template load file=app_index.md.template app=Isopod category=isopod
+!template load file=app_index.md.template app=Optimization category=optimization

modules/optimization/doc/content/sqa/optimization_far.md

@@ -0,0 +1 @@
+!template load file=app_far.md.template app=Optimization category=optimization

modules/optimization/doc/content/sqa/optimization_rtm.md

@@ -0,0 +1 @@
+!template load file=app_rtm.md.template app=Optimization category=optimization

modules/optimization/doc/content/sqa/optimization_sdd.md

@@ -0,0 +1 @@
+!template load file=app_sdd.md.template app=Optimization category=optimization

modules/optimization/doc/content/sqa/optimization_sll.md

@@ -0,0 +1 @@
+!template load file=app_sll.md.template app=Optimization category=optimization

modules/optimization/doc/content/sqa/optimization_srs.md

@@ -0,0 +1 @@
+!template load file=app_srs.md.template app=Optimization category=optimization

modules/optimization/doc/content/sqa/optimization_ssr.md

@@ -0,0 +1 @@
+!template load file=app_ssr.md.template app=Optimization category=optimization

modules/optimization/doc/content/sqa/optimization_stp.md

@@ -0,0 +1 @@
+!template load file=app_stp.md.template app=Optimization category=optimization

modules/optimization/doc/content/sqa/optimization_vvr.md

@@ -0,0 +1 @@
+!template load file=app_vvr.md.template app=Optimization category=optimization

modules/optimization/doc/sqa_optimization.yml

@@ -0,0 +1,10 @@
+directories:
+    - ${MOOSE_DIR}/modules/optimization/test/tests
+specs:
+    - tests
+dependencies:
+    - framework
+    - heat_conduction
+    - stochastic_tools
+repo: moose
+reports: !include ${MOOSE_DIR}/modules/optimization/doc/sqa_reports.yml