Merge pull request #31 from cticenhour/sqa-doco

Fill in empty fields in SQA documentation

.coverage

@@ -6,7 +6,5 @@
 # - warn_new: Warns below this percentage of coverage for new lines added
 
 [default]
-# very low for now, but that's because there is no content in this app yet.
-# this should be upped as we add content.
-require_total = 87
+require_total = 90
 warn_new = 90

doc/config.yml

@@ -47,6 +47,11 @@ Extensions:
     MooseDocs.extensions.acronym:
         acronyms:
             framework: !include ${MOOSE_DIR}/framework/doc/acronyms.yml
+            fenix:
+                FENIX: Fusion ENergy Integrated multiphys-X
+                PIC: particle-in-cell
+                CFD: computational fluid dynamics
+                CAD: computer-aided design
     MooseDocs.extensions.sqa:
         active: true
         categories:

doc/content/sqa/fenix_rtm.md

@@ -1 +1,13 @@
-!template load file=sqa/app_rtm.md.template app=FENIX category=fenix
+!template load file=sqa/app_rtm.md.template app=FENIX category=fenix
+
+!template! item key=system-scope
+!include fenix_srs.md start=system-scope-begin end=system-scope-finish
+!template-end!
+
+!template! item key=system-purpose
+!include fenix_srs.md start=system-purpose-begin end=system-purpose-finish
+!template-end!
+
+!template! item key=log-revisions
+Currently, no errors in issue references related to the changelog have been discovered.
+!template-end!

doc/content/sqa/fenix_sdd.md

@@ -1 +1,57 @@
-!template load file=sqa/app_sdd.md.template app=FENIX category=fenix
+!template load file=sqa/app_sdd.md.template app=FENIX category=fenix
+
+!template! item key=introduction
+Many of the phenomena related to fusion energy systems depend on the solutions of multiple
+physics models, which can be described by partial differential equations that provide spatially- and
+temporally-varying values of solution variables. These models for individual physics often depend on
+each other. [!ac]({{app}}) relies on the MOOSE framework to solve these physics models, accounting
+for the couplings that may occur between them. This document describes the system design of [!ac]({{app}}).
+!template-end!
+
+!template! item key=system-scope
+!include fenix_srs.md start=system-scope-begin end=system-scope-finish
+!template-end!
+
+!template! item key=dependencies-and-limitations
+{{app}} inherits the [software dependencies of the MOOSE framework](framework_sdd.md#dependencies-and-limitations),
+with no additional dependencies.
+!template-end!
+
+!template! item key=design-stakeholders
+Stakeholders for [!ac]({{app}}) include several of the funding sources including [!ac](DOE) and [!ac](INL).
+However, since [!ac]({{app}}) is an open-source project, several universities, companies, and foreign
+governments have an interest in the development and maintenance of the [!ac]({{app}}) project.
+!template-end!
+
+!template! item key=system-design
+[!ac]({{app}}) relies on MOOSE to solve the coupled physics models underlying fusion energy systems,
+accounting for the couplings that may occur between various components and sub-systems of this class
+of devices. The design of MOOSE is based on the concept of modular code objects that define all of
+the aspects of the physics model. [!ac]({{app}}) follows this design, providing code objects that
+define specific aspects of the solutions for its physics that derive from the base classes defined
+by the MOOSE framework and the modules that it depends on. [!ac]({{app}}) provides specialized
+[UserObject](syntax/UserObjects/index.md) classes that compute data for velocity updating, charge
+accumulation, and [Ray](source/raytracing/Ray.md) data necessary for simple [!ac](PIC) simulations.
+It also provides specialized utilities for accumulating field data on rays. Much of the remaining
+functionality is provided by MOOSE modules (electromagnetics, ray tracing), the
+[Cardinal](https://cardinal.cels.anl.gov/) application ([!ac](CFD) and Monte Carlo radiation transport),
+and the [Tritium Migration Analysis Program Version 8 (TMAP8)](https://mooseframework.inl.gov/TMAP8)
+application (tritium migration) that [!ac]({{app}}) builds on.
+!template-end!
+
+!template! item key=system-structure
+[!ac]({{app}}) relies on the MOOSE framework to provide the core functionality of solving multiphysics problems
+using the finite element method. It also relies on the MOOSE modules for much of its core functionality.
+A summary listing of the current modules required for complete [!ac]({{app}}) operation are shown below:
+
+- [Electromagnetics](electromagnetics/index.md)
+- [Ray Tracing](ray_tracing/index.md)
+
+The structure of [!ac]({{app}}) is based on defining C++ classes that derive from classes in the MOOSE
+framework or modules that provide functionality that is specifically tailored to fusion device
+modeling and simulation. By using the interfaces defined in MOOSE base classes for these classes,
+[!ac]({{app}}) is able to rely on MOOSE to execute these models at the appropriate times during the
+simulation and use their results in the desired ways.
+!template-end!
+
+!syntax complete subsystems=False actions=False objects=False

doc/content/sqa/fenix_srs.md

@@ -1 +1,84 @@
-!template load file=sqa/app_srs.md.template app=FENIX category=fenix
+!template load file=sqa/app_srs.md.template app=FENIX category=fenix
+
+!template! item key=system-scope
+!! system-scope-begin
+FENIX is an application for performing system-level, engineering scale (i.e., at the scale of
+centimeters and meters), and microstructure-scale (i.e., at the scale of microns) multiphysics
+calculations related to fusion energy systems. These models often include highly coupled systems of
+equations related to plasma physics, electromagnetics, heat conduction, scalar transport, thermal
+hydraulics, [!ac](CFD), and thermomechanics, amongst others. Interfaces to other MOOSE-based codes,
+including tritium transport (TMAP8) and neutronics (Cardinal) are also included to support FENIX
+simulations. FENIX will enable high-fidelity modeling of irradiation levels and plasma exposure
+conditions of plasma facing components and their impact on heat and tritium distributions, as well
+as the resulting mechanical constraints experienced by the plasma facing components. The [syntax/MultiApps/index.md]
+is leveraged to allow for the multiscale, multiphysics coupling. Further, other MOOSE capabilities
+(such as the stochastic tools module) will eventually enable engineering studies, allowing for extended
+uncertainty quantification and risk analysis studies for particular system designs. Interfaces for
+[!ac](CAD) meshing workflows to model complex geometries are also included. FENIX therefore supports
+design, safety, engineering, and research projects.
+!! system-scope-finish
+!template-end!
+
+!template! item key=system-purpose
+!! system-purpose-begin
+The purpose of FENIX is to perform fully integrated, high-fidelity, multiphysics simulations of fusion
+energy systems and devices at different length scales with a variety of materials, system configurations,
+and component designs in order to better understand component degradation and operational impacts on
+system performance. FENIX's main goal is to bring together the combined multiphysics capabilities of
+the [!ac](MOOSE) ecosystem to provide an open platform for future research, safety assessment,
+engineering, and design studies of fusion energy systems.
+!! system-purpose-finish
+!template-end!
+
+!template! item key=assumptions-and-dependencies
+[!ac]({{app}}) has no constraints on hardware and software beyond those of the MOOSE framework and
+modules listed in their respective [!ac](SRS) documents, which are accessible through the links at
+the beginning of this document.
+
+[!ac]({{app}}) provides access to a number of code objects that perform computations, such as particle
+transport, material behavior, and boundary conditions. These objects each make their own physics-based
+assumptions, such as the units of the inputs and outputs. Those assumptions are described in the
+documentation for those individual objects.
+!template-end!
+
+!template! item key=user-characteristics
+[!ac]({{app}}) has three main classes of users:
+
+- +[!ac]({{app}}) Developers+: These are the core developers of [!ac]({{app}}). They are responsible
+  for designing, implementing, and maintaining the software, while following and enforcing its software
+  development standards.
+- +Developers+: These are scientists or engineers that modify or add capabilities to [!ac]({{app}})
+  for their own purposes, which may include research or extending its capabilities. They will typically
+  have a background in fusion energy sciences, plasma physics, tritium migration, radiation transport,
+  heat conduction, and/or material science as well as in modeling and simulation techniques, but may have
+  more limited background in code development using the C++ language. In many cases, these developers
+  will be encouraged to contribute code back to [!ac]({{app}}).
+- +Analysts+: These are users that run [!ac]({{app}}) to run simulations, but do not develop code.
+  The primary interface of these users with [!ac]({{app}}) is the input files that define their
+  simulations. These users may interact with developers of the system requesting new features and
+  reporting bugs found.
+!template-end!
+
+!template! item key=information-management
+[!ac]({{app}}) as well as the core MOOSE framework in its entirety will be made publicly available
+on an appropriate repository hosting site. Day-to-day backups and security services will be provided
+by the hosting service. More information about backups of the public repository on [!ac](INL)-hosted
+services can be found on the following page: [sqa/github_backup.md]
+!template-end!
+
+!template! item key=policies-and-regulations
+!include framework_srs.md start=policies-and-regulations-begin end=policies-and-regulations-finish
+!template-end!
+
+!template! item key=packaging
+No special requirements are needed for packaging or shipping any media containing the [!ac](MOOSE)
+and [!ac]({{app}}) source code. However, some [!ac](MOOSE)-based applications that use the [!ac]({{app}})
+code may be export-controlled, in which case all export control restrictions must be adhered to when
+packaging and shipping media.
+!template-end!
+
+!template! item key=reliability
+The regression test suite will cover at least 90% of all lines of code at all times. Known
+regressions will be recorded and tracked (see [#maintainability]) to an independent and
+satisfactory resolution.
+!template-end!

doc/content/sqa/fenix_vvr.md

@@ -1 +1,5 @@
-!template load file=sqa/app_vvr.md.template app=FENIX category=fenix
+!template load file=sqa/app_vvr.md.template app=FENIX category=fenix
+
+!template! item key=introduction
+The [!ac](VVR) for {{app}} provides evidence that {{app}} fulfills its intended purpose.
+!template-end!

doc/content/sqa/theory_manual.md

@@ -0,0 +1,3 @@
+# FENIX Theory Manual
+
+Documentation for all the theory supporting FENIX is contained in the [syntax/index.md] page.

doc/content/sqa/user_manual.md

@@ -0,0 +1,3 @@
+# FENIX User Manual
+
+Documentation for all FENIX input file objects, and how they can be used in the creation of a simulation, is contained in the [syntax/index.md] page.

doc/sqa_reports.yml

@@ -24,7 +24,8 @@ Documents:
     software_library_list: sqa/fenix_sll.md
     communication_and_contact_information: sqa/fenix_cci.md
     software_coding_standards: sqa/fenix_scs.md
-    log_default: WARNING
+    user_manual: sqa/user_manual.md
+    theory_manual: sqa/theory_manual.md
     show_warning: false
     working_dirs:
         - ${ROOT_DIR}/doc/content