Update SQA docs

(refs idaholab#156)

doc/config.yml

@@ -71,11 +71,13 @@ Extensions:
                     - tests
                 directories:
                     - ${ROOT_DIR}/test/tests
+                reports: !include ${ROOT_DIR}/doc/sqa_reports.yml
             blackbear:
                 specs:
                     - tests
                 directories:
                     - ${BLACKBEAR_DIR}/test/tests
+                reports: !include ${BLACKBEAR_DIR}/doc/sqa_reports.yml
             framework: !include ${MOOSE_DIR}/framework/doc/sqa_framework.yml
             tensor_mechanics: !include ${MOOSE_DIR}/modules/tensor_mechanics/doc/sqa_tensor_mechanics.yml
             stochastic_tools: !include ${MOOSE_DIR}/modules/stochastic_tools/doc/sqa_stochastic_tools.yml

doc/content/sqa/index.md

@@ -1,32 +1 @@
-# Software Quality
-
-## Initiation
-
-- [Safety Software Determination (SSD)](https://jwebapps3.inl.gov/SafeSWDetermination/OfficialRecord?ssdNumber=SSD-000642)
-- [Quality Level Determination (QLD; ALL-000834)](https://edmvaultprd.inl.gov/edm17l/29442/7360459.pdf)
-- [Enterprise Architecture Entry](https://itarchitecture.inl.gov/pls/earch1/appreport.init_hist_report?app_id=382105&prevNext=EQ)
-
-## Planning
-
-- [Software Quality Assurance for Modeling and Simulation Software (PLN-4005)](https://inl-edms/pls/inl_docs/doc_3?f_doc=PLN-4005)
-
-## Requirements
-
-- [System Requirement Specification (SRS)](sqa/mastodon_srs.md)
-
-## Design
-
-- [System Design Description (SDD)](sqa/mastodon_sdd.md)
-
-## Testing
-
-- [Software Test Plan (STP)](sqa/mastodon_stp.md)
-- [Requirements Traceability Matrix (RTM)](sqa/mastodon_rtm.md)
-- [Verification and Validation Results Report](sqa/mastodon_vvr.md)
-
-## Other Documentation
-
-- [Theory Manual](manuals/theory/index.md)
-- [User Manual](manuals/user/index.md)
-
-!sqa report
+!template load file=app_index.md.template app=MASTODON category=mastodon

doc/content/sqa/mastodon_srs.md

@@ -1,126 +1 @@
-!!template load file=app_srs.md.template app=MASTODON category=mastodon
-
-!!!
-!SQA-load system_requirements_specification.md
-
-!SQA-template-item project_description
-
-!alert construction
-Work in Progress
-
-The template for this page is currently under development, the completed SRS is available
-as a pdf here: [MASTODON SRS](https://hpcgitlab.inl.gov/idaholab/mastodon/uploads/d50895b47f1cf489b504bf3036d79bae/MastodonSoftwareRequirementsSpecification.pdf).
-
-MASTODON is a nonlinear, three-dimensional seismic soil-structure interaction analysis framework.
-
-!END-template-item
-
-!SQA-template-item system_scope
-
-Multi-hazard Analysis for STOchastic time-DOmaiN phenomena (MASTODON) is a finite element application
-that analyzes the response of 3-D soil-structure systems to earthquakes. MASTODON currently focuses
-on the simulation of seismic events and has the capability to perform extensive 'source-to-site'
-simulations including earthquake fault rupture, nonlinear wave propagation and nonlinear
-soil-structure interaction (NLSSI) analysis. MASTODON is being developed to be a dynamic
-probabilistic risk assessment framework that enables analysts to not only perform deterministic
-analyses, but also easily perform probabilistic or stochastic simulations for the purpose of risk
-assessment.
-
-MASTODON is a MOOSE-based application and performs finite-element analysis of the dynamics of solids,
-mechanics of interfaces and porous media flow. It is equipped with numerical material models of dry
-and saturated soils including a nonlinear hysteretic soil model, and a uP-U model for saturated
-soil, as well as structural materials such as reinforced concrete. It is also equipped with
-interface models that simulate gapping, sliding and uplift at the interfaces of solid media such as
-the foundation-soil interface of structures. MASTODON also includes absorbing boundary models for
-the simulation of infinite or semi-infinite domains, fault rupture model for seismic source
-simulation, and the domain reduction method for the input of complex, three dimensional wave fields.
-Since MASTODON is a MOOSE-based application, it can efficiently solve problems using either standard
-workstations or very large high-performance computers.
-
-!END-template-item
-
-!SQA-template-item system_context
-
-!alert construction
-Under Development
-
-The current MOOSE template for the SRS is not complete and the sections do not align with
-the SRS for {{PROJECT}}. As development continues sections will be more configurable to meet
-the needs of application.
-
-!END-template-item
-
-!SQA-template-item system_requirements
-
-### Technical and Functional Requirements
-
-!SQA-requirement-list title=Time Integration
-    F1.1 The system shall be capable of performing time integration using the Newmark Beta method
-    F1.2 The system shall be capable of performing time integration using the HHT method
-
-!SQA-requirement-list title=Small Strain Damping
-    F2.1 The system shall allow Rayleigh damping
-    F2.2 The system shall allow frequency-independent damping
-
-!SQA-requirement-list title=Soil Layers and Meshing
-    F3.1 The system shall allow automatic mesh adaptivity to maintain a user-defined number of solid hexagonal elements per wavelength
-    F3.2 The system shall allow automatic mesh generation based on a user-defined dynamic shear wave velocity
-    F3.3 The system shall allow for scenarios with both horizontal and non-horizontal soil layers
-
-!SQA-requirement-list title=Material Models
-    F4.1 The system shall simulate a linear elastic material
-    F4.2 The system shall simulate a nonlinear soil material (ISoil)
-
-!SQA-requirement-list title=Foundation-Soil Interface Models
-    F5.1 The system shall allow for the simulation of a foundation-soil interface using the thin-layer method
-    F5.2 The system shall allow for the simulation of a foundation-soil interface using cyclic frictional contact algorithms
-
-!SQA-requirement-list title=Special Boundary Conditions
-    F6.1 The system shall allow Domain Reduction Method (DRM)
-    F6.2 The system shall allow non-reflecting boundary conditions
-    F6.3 The system shall allow a preset acceleration boundary condition
-    F6.4 The system shall allow a seismic force boundary condition
-
-!SQA-requirement-list title=Earthquake Fault Rupture
-    F7.1 The system shall allow for fault rupture using multiple point sources
-
-!SQA-requirement-list title=Post-Processing
-    F8.1 The system shall allow the calculation of response histories. Acceleration, velocity, and displacement time histories are used by analysts to evaluate structural response.
-    F8.2 The system shall allow the calculation of response spectra
-    F8.3 The system shall allow for the calculation of Housner Spectrum Index (HSI)
-
-### Design Inputs, Outputs and Design Constraints
-
-!SQA-requirement-list title=Design Inputs
-    DI1.1 The system shall use the input file syntax as defined by MOOSE
-    DI1.2 The system shall employ the dynamic time domain input file. Uses time integration.
-    DI1.3 The system shall allow the location of the interfaces to be provided as input for scenarios with horizontal soil layers
-    DI1.4 The system shall allow images (.jpg, .png, etc.) of the soil profile to be provided as input for mesh generation for scenarios where the soil layers are non-horizontal and non-planar
-
-!SQA-requirement-list title=Design Constraints
-    DC1.1 The system shall be implemented in MOOSE, INL's HPC development and runtime framework
-    DC1.2 The system shall be written with object oriented programming language C++
-
-!SQA-requirement-list title=Output File Structure
-    DO1.1 The system shall use the output capabilities of MOOSE framework
-    DO1.2 The system shall provide the PRA output (file structure TBD)
-
-### System Interfaces
-
-!SQA-requirement-list
-    SI1.1 MOOSE
-    SI1.2 BlackBear
-
-### Installation Considerations
-
-Detailed installation instructions, including the following installation considerations, will be included in the MASTODON User's Manual.
-
-!SQA-requirement-list
-    IC1.1 The user shall obtain a valid license.
-    IC1.2 MOOSE Environment Setup:  The user's system environment must be set up for MOOSE.
-    IC1.3 Code repository access: The user must establish a secure connection between their computer and the system where the source code repository is hosted.
-    IC1.4 Code Checkout:  It is necessary to build LibMesh before building any application.  Once LibMesh has been successfully compiled, the system can be compiled.
-    IC1.5 Verification Testing:  Once the system has been compiled successfully, it is required to run the tests to make sure the version of the code installed is running correctly.
-
-!END-template-item
-!!!
+!template load file=app_srs.md.template app=MASTODON category=mastodon

doc/content/sqa/mastodon_stp.md

@@ -1 +1 @@
-!!template load file=app_stp.md.template app=MASTODON category=MastodonApp
+!template load file=app_stp.md.template app=MASTODON category=mastodon

doc/content/sqa/v_and_v/materials/isoil/darendeli.md

@@ -47,7 +47,7 @@ The hysteresis stress-strain curve in the ZX plane is shown in [darendeli-hyster
               id=darendeli-hysteresis-loop
               caption=Plot of the element hysteresis stress-strain curve in the ZX plane over the duration of the simulation.
 
-Since the engineering strain in the ZX plane, $\gamma_{zx}$, is equal to two times the tensor shear strain, $\epsilon_{zx}$, it was necessary to multiply the strains output by MOOSE TensorMechanics by two to get the shear stresses, $\tau_{zx}$, which correspond to those determined by [shear]. Next, the engineering shear stress-strain curve was superimposed over the 100 points, calculated by hand with [shear], as shown in [darendeli-backbone-curve]. The backbone curve was obtained in MOOSE by sampling the data during the initial load cycle, i.e., from 3 seconds to 4 seconds (see [#problem-statement]). It is clear from [darendeli-backbone-curve] that the analytical solution of the Darendeli model was consistent with the MASTODON one.
+Since the engineering strain in the ZX plane, $\gamma_{zx}$, is equal to two times the tensor shear strain, $\epsilon_{zx}$, it was necessary to multiply the strains output by MOOSE TensorMechanics by two to get the shear stresses, $\tau_{zx}$, which correspond to those determined by [shear]. Next, the engineering shear stress-strain curve was superimposed over the 100 points, calculated by hand with [shear], as shown in [darendeli-backbone-curve]. The backbone curve was obtained in MOOSE by sampling the data during the initial load cycle, i.e., from 3 seconds to 4 seconds (see [isoil/problem_statement.md]). It is clear from [darendeli-backbone-curve] that the analytical solution of the Darendeli model was consistent with the MASTODON one.
 
 !media media/materials/isoil/darendeli_backbone.png
        id=darendeli-backbone-curve

doc/content/sqa/v_and_v/materials/isoil/gqh.md

@@ -69,7 +69,7 @@ The hysteresis stress-strain curve in the ZX plane is shown in [gqh-hysteresis-l
               id=gqh-hysteresis-loop
               caption=Plot of the element hysteresis stress-strain curve in the ZX plane over the duration of the simulation.
 
-Since the engineering strain in the ZX plane, $\gamma_{zx}$, is equal to two times the tensor shear strain, $\epsilon_{zx}$, it was necessary to multiply the strains output by MOOSE TensorMechanics by two to get the shear stresses, $\tau_{zx}$, which correspond to those determined by [backbone]. Next, the engineering shear stress-strain curve was superimposed over the 100 points, calculated by hand with [curve] and [backbone], as shown in [gqh-backbone-curve]. The backbone curve was obtained in MOOSE by sampling the data during the initial load cycle, i.e., from 3 seconds to 4 seconds (see [#problem-statement]). It is clear from [gqh-backbone-curve] that the analytical solution of the GQ/H model was consistent with the MASTODON one.
+Since the engineering strain in the ZX plane, $\gamma_{zx}$, is equal to two times the tensor shear strain, $\epsilon_{zx}$, it was necessary to multiply the strains output by MOOSE TensorMechanics by two to get the shear stresses, $\tau_{zx}$, which correspond to those determined by [backbone]. Next, the engineering shear stress-strain curve was superimposed over the 100 points, calculated by hand with [curve] and [backbone], as shown in [gqh-backbone-curve]. The backbone curve was obtained in MOOSE by sampling the data during the initial load cycle, i.e., from 3 seconds to 4 seconds (see [isoil/problem_statement.md]). It is clear from [gqh-backbone-curve] that the analytical solution of the GQ/H model was consistent with the MASTODON one.
 
 !media media/materials/isoil/GQH_backbone.png
        id=gqh-backbone-curve

doc/content/sqa/v_and_v/materials/isoil/pressure_dependency.md

@@ -26,7 +26,7 @@ To conserve dynamic equilibrium in the first time-step, the element was initiali
 \sigma_{initial}=[-12613\,\,\,\,0\,\,\,\,0\,\,\,\,0\,\,\,\,-12613\,\,\,\,0\,\,\,\,0\,\,\,\,0\,\,\,\,-29430]^{\mathrm{T}}\,\,\,\text{Pa}
 \end{equation}
 
-Then a body force equal to three times the force of gravity was applied thereby increasing the vertical pressure experienced by the element. Finally a ramp displacement was applied in the manner described in [#problem-statement].
+Then a body force equal to three times the force of gravity was applied thereby increasing the vertical pressure experienced by the element. Finally a ramp displacement was applied in the manner described in [isoil/problem_statement.md].
 
 I-Soil is capable of varying the shear yield strength and the shear modulus as a function of engineering strain, $\gamma$, mean effective stress, $p$, a specified reference pressure, $p_{ref}$, and a tension pressure cutoff value, $p_0<0$. Assuming positive compression, MASTODON computes the mean effective stress as
 
@@ -65,7 +65,7 @@ The five cases described in [strength-cases] were used to investigate the behavi
 
 #### Results
 
-The engineering shear stress-strain backbone curve results for Cases 1, 2, and 3 are presented in [strength-comparison1], and those for Cases 2, 4, and 5 are presented in [strength-comparison2]. Both figures show their results along with the user-defined backbone curve shown in [p-ref-backbone-input]. The backbone curves were obtained in MOOSE by sampling the data during the initial load cycle, i.e., from 3 seconds to 4 seconds (see [#problem-statement]). It can be seen in [strength-comparison1] and [strength-comparison2] that MASTODON effectively modifies the shear strength. In some cases, stiffness changes on those strain increments for which the mean effective stress exceeds $\tau_{y}(p,\gamma)$ can also be observed in these two figures, even though $b=0$. This is reasoned by the fact that, at a constant rate of strain, a change in strength of a material naturally (and numerically) leads to one in stiffness.
+The engineering shear stress-strain backbone curve results for Cases 1, 2, and 3 are presented in [strength-comparison1], and those for Cases 2, 4, and 5 are presented in [strength-comparison2]. Both figures show their results along with the user-defined backbone curve shown in [p-ref-backbone-input]. The backbone curves were obtained in MOOSE by sampling the data during the initial load cycle, i.e., from 3 seconds to 4 seconds (see [isoil/problem_statement.md]). It can be seen in [strength-comparison1] and [strength-comparison2] that MASTODON effectively modifies the shear strength. In some cases, stiffness changes on those strain increments for which the mean effective stress exceeds $\tau_{y}(p,\gamma)$ can also be observed in these two figures, even though $b=0$. This is reasoned by the fact that, at a constant rate of strain, a change in strength of a material naturally (and numerically) leads to one in stiffness.
 
 !media media/materials/isoil/pressure_dependent_strength1.png
        id=strength-comparison1
@@ -94,7 +94,7 @@ The three cases described in [stiffness-cases] were used to investigate the beha
 
 #### Results
 
-The engineering shear stress-strain backbone curve results for all cases are presented in [stiffness-comparison]. The results are shown along with the user-defined backbone curve shown in [p-ref-backbone-input]. The backbone curves were obtained in MOOSE by sampling the data during the initial load cycle, i.e., from 3 seconds to 4 seconds (see [#problem-statement]). It can be seen in [stiffness-comparison] that MASTODON effectively modifies the shear modulus. For reasons similar to why the curves shown in [strength-comparison1] and [strength-comparison2] exhibit stiffness changes, strength changes, particularly at the lower strains of Case 1 and Case 2, can also be observed in this figure, even though $a_{0}=1$, $a_{1}=0$, and $a_{2}=0$. However, the ultimate shear strength at which the material completely fails, which corresponds to the maximum stress value defined by the backbone curve ([p-ref-backbone-input]), remains the same.
+The engineering shear stress-strain backbone curve results for all cases are presented in [stiffness-comparison]. The results are shown along with the user-defined backbone curve shown in [p-ref-backbone-input]. The backbone curves were obtained in MOOSE by sampling the data during the initial load cycle, i.e., from 3 seconds to 4 seconds (see [isoil/problem_statement.md]). It can be seen in [stiffness-comparison] that MASTODON effectively modifies the shear modulus. For reasons similar to why the curves shown in [strength-comparison1] and [strength-comparison2] exhibit stiffness changes, strength changes, particularly at the lower strains of Case 1 and Case 2, can also be observed in this figure, even though $a_{0}=1$, $a_{1}=0$, and $a_{2}=0$. However, the ultimate shear strength at which the material completely fails, which corresponds to the maximum stress value defined by the backbone curve ([p-ref-backbone-input]), remains the same.
 
 !media media/materials/isoil/pressure_dependent_stiffness.png
        id=stiffness-comparison
@@ -118,7 +118,7 @@ The two cases described in [strength-stiffness-cases] were used to simultaneousl
 
 #### Results
 
-The engineering shear stress-strain backbone curve results for both cases are presented in [strength-stiffness-comparison]. The results are shown along with the user-defined backbone curve shown in [p-ref-backbone-input]. The backbone curves were obtained in MOOSE by sampling the data during the initial load cycle, i.e., from 3 seconds to 4 seconds (see [#problem-statement]). It can be seen in [strength-stiffness-comparison] that MASTODON effectively modifies both the strength and stiffness for a particular strain increment. Specifically, one should compare the curve shown in this figure to those in [strength-comparison1], [strength-comparison2], and [stiffness-comparison].
+The engineering shear stress-strain backbone curve results for both cases are presented in [strength-stiffness-comparison]. The results are shown along with the user-defined backbone curve shown in [p-ref-backbone-input]. The backbone curves were obtained in MOOSE by sampling the data during the initial load cycle, i.e., from 3 seconds to 4 seconds (see [isoil/problem_statement.md]). It can be seen in [strength-stiffness-comparison] that MASTODON effectively modifies both the strength and stiffness for a particular strain increment. Specifically, one should compare the curve shown in this figure to those in [strength-comparison1], [strength-comparison2], and [stiffness-comparison].
 
 !media media/materials/isoil/stiffness_and_strength_pressure_dependency.png
        id=strength-stiffness-comparison