Set up new website built on MooseDocs system

.github/workflows/auto-update-gh-pages.yml

@@ -1,7 +1,7 @@
 # This GitHub Action automatically updates built Doxygen files for Moltres' documentation
 # on `https://arfc.github.io/moltres/` every time a new pull request is merged into devel.
 
-name: Doxygen & Github Pages Action
+name: Doxygen & MooseDocs & Github Pages Action
 
 # Activate on pushes and pull requests into devel
 on:
@@ -16,17 +16,38 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-
-      # Generate Doxygen output files in ./docs directory using Doxyfile in base directory
+
+      # Generate Doxygen html files in ./doc/content/doxygen directory using Doxyfile in
+      # base directory
       - name: Doxygen Action
         uses: mattnotmitt/doxygen-action@v1
         with:
           working-directory: .
 
-      # Merge Doxygen output files in ./docs into gh-pages branch base directory
+      # Install MOOSE Conda environment & build combined MooseDocs/Doxygen html files into
+      # ./doc/html
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          channels: conda-forge,https://conda.software.inl.gov/public
+          activate-environment: moose-env
+      - shell: bash -l {0}
+        run: |
+          conda deactivate
+          conda activate moose-env
+          mamba install moose-tools=2021.07.14 moose-libmesh=2021.07.14
+          conda deactivate
+          conda activate moose-env
+          git submodule init && git submodule update
+          make -j 2
+          cd doc
+          ./moosedocs.py build --destination html
+
+      # Merge MooseDocs and Doxygen html files in ./doc/html into gh-pages branch base directory
       - name: GitHub Pages action
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./docs
+          publish_dir: ./doc/html
           commit_message: ${{ github.event.head_commit.message }}
+

Doxyfile

@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = docs
+OUTPUT_DIRECTORY       = doc/content/doxygen
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and

README.md

@@ -4,18 +4,18 @@
 Moltres
 =====
 
-Moltres is a MOOSE-application code designed for simulation of molten salt
-reactors.
+Moltres is an open-source MOOSE-application code designed for simulation of molten salt
+reactors and other advanced reactors.
 
-## Use
+## Documentation
 
-Moltres documentation can be found
-[here](http://arfc.github.io/software/moltres). Doxygen pages are
-[here](https://arfc.github.io/moltres/classes.html). Outlines of the kernels and boundary
+Moltres documentation can be found at
+[https://arfc.github.io/software/moltres](https://arfc.github.io/software/moltres).
+Outlines of the kernels and boundary
 conditions used to construct the Moltres governing equations can be found on the
-[Moltres wiki](http://arfc.github.io/software/moltres/wiki/). Breakdown of a
+[Moltres wiki](https://arfc.github.io/software/moltres/wiki/). Breakdown of a
 full-fledged Moltres input file can be found
-[here](http://arfc.github.io/software/moltres/wiki/input_example/). New Moltres
+[here](https://arfc.github.io/software/moltres/wiki/input_example/). New Moltres
 users who have never used MOOSE before are encouraged to check-out the MOOSE
 [website](https://mooseframework.inl.gov/) and
 workshop [slides](https://mooseframework.inl.gov/workshop/index.html#/) for
@@ -24,32 +24,8 @@ underlying Moltres components.
 
 ## Install
 
-Moltres relies on the MOOSE framework. We suggest that users install the MOOSE 
-environment using Conda Packages by following the instructions in the `Install 
-MOOSE Conda Packages` section of
-https://mooseframework.inl.gov/getting_started/installation/conda.html.
-The Moltres repository contains MOOSE and Squirrel as Git
-submodules, therefore there is no need to clone MOOSE into a separate directory.
-Instead, users can install Moltres by running the following commands in a shell
-after changing into the directory which will hold the Moltres directory (perhaps `~/projects`):
-
-```bash
-git clone https://github.com/arfc/moltres
-cd moltres
-git submodule init
-git submodule update
-make -j8
-```
-
-You may also compile a debug version of Moltres by replacing the last line in 
-the code block above with `METHOD=dbg make
--j8`. Note that you should replace `8` with the number of processors available
-on your machine.
-
-## Testing
-
-To ensure that Moltres is functioning properly, run `./run_tests -j8` from the
-root of the Moltres directory.
+Installation instructions can be found at
+[https://arfc.github.io/moltres/getting_started/installation.html](https://arfc.github.io/moltres/getting_started/installation.html)
 
 ## Development
 
@@ -65,5 +41,4 @@ A full list of contributing guidelines can be found
 
 ## Contact
 
-Please post to our discussion list at
-moltres-users@googlegroups.com.
+Please post to our GitHub Discussions tab.

doc/config.yml

@@ -3,15 +3,11 @@ Content:
         root_dir: ${ROOT_DIR}/doc/content
     moose:
         root_dir: ${MOOSE_DIR}/framework/doc/content
-        content:
-            - js/*
-            - css/*
-            - contrib/**
-            - media/**
-            - templates/stubs/*
 
 Renderer:
     type: MooseDocs.base.MaterializeRenderer
+    extra-css:
+        - css/moltres.css
 
 Extensions:
     MooseDocs.extensions.template:
@@ -20,12 +16,30 @@ Extensions:
         name: Moltres
         repo: https://github.com/arfc/moltres
         menu:
-            Getting Started: getting_started.md
-            Documentation: source/index.md
-            Help: help.md
+            Getting Started:
+                Install Moltres: getting_started/installation.md
+                Tutorials: getting_started/tutorials.md
+            Documentation:
+                Moltres Syntax: syntax/index.md
+                MOOSE Syntax: https://mooseframework.inl.gov/source/index.html
+                Moltres Doxygen: doxygen/classes.html
+                MOOSE Doxygen: https://mooseframework.inl.gov/docs/doxygen/moose/classes.html
+                Contributing: development/contributing.md
+                List of Publications: publications.md
+            Help:
+                Moltres Discussion Forum: https://github.com/arfc/moltres/discussions
+                MOOSE Discussion Forum: https://github.com/idaholab/moose/discussions
             Citing: citing.md
     MooseDocs.extensions.appsyntax:
         executable: ${ROOT_DIR}
-        remove: !include ${MOOSE_DIR}/framework/doc/remove.yml
         includes:
             - include
+        remove: !include ${MOOSE_DIR}/framework/doc/remove.yml
+        unregister: !include ${MOOSE_DIR}/framework/doc/unregister.yml
+    MooseDocs.extensions.acronym:
+        acronyms: !include ${MOOSE_DIR}/framework/doc/acronyms.yml
+    MooseDocs.extensions.common:
+        shortcuts:
+            framework: !include ${MOOSE_DIR}/framework/doc/globals.yml
+    MooseDocs.extensions.bibtex:
+        active: True

doc/content/bib/conference-publications.bib

@@ -0,0 +1,29 @@
+
+@inproceedings{park_multiphysics_2021,
+	address = {Virtual Meeting},
+	series = {Reactor {Analysis} {Methods} - {I}},
+	title = {Multiphysics {Benchmark} {Results} from {Moltres}},
+	url = {https://www.ans.org/meetings/am2021/session/view-587/},
+	booktitle = {Proceedings of the 2021 {ANS} {Virtual} {Annual} {Meeting}},
+	publisher = {American Nuclear Society},
+	author = {Park, Sun Myung and Huff, Kathryn D},
+	month = jun,
+	year = {2021},
+	note = {(Submitted before May 2021)},
+	file = {Park and Huff - 2021 - Multiphysics Benchmark Results from Moltres.pdf:C\:\\Users\\Sun Myung\\Zotero\\storage\\DI37TPGK\\Park and Huff - 2021 - Multiphysics Benchmark Results from Moltres.pdf:application/pdf;Reactor Analysis Methods - I -- ANS / Meetings / 2021 ANS Virtual Annual Meeting / Technical Sessions:C\:\\Users\\Sun Myung\\Zotero\\storage\\PSC9JE66\\view-587.html:text/html},
+}
+
+@inproceedings{park_safety_2019,
+	address = {Seattle, WA, United States},
+	title = {Safety {Analysis} of the {Molten} {Salt} {Fast} {Reactor} {Fuel} {Composition} using {Moltres}},
+	url = {http://epubs.ans.org/?a=47030},
+	doi = {10.31224/osf.io/7ce89},
+	abstract = {The Molten Salt Fast Reactor (MSFR) has garnered much interest for its inherent safety and sustainbility features. The MSFR can adopt a closed thorium fuel cycle for sustainable operation through the breeding of 233 U from 232 Th. The fuel composition changes significantly over the course of its lifespan. In this study, we investigated the steady state and transient behavior of the MSFR using Moltres, a coupled neutronics/thermal-hydraulics code developed within the Multiphysics Object Oriented Simulation Environment (MOOSE) framework. Three different fuel compositions, start-up, early-life, and equilibrium, were examined for potentially dangerous core temperature excursions during a unprotected loss of heat sink (ULOHS) accident. The six-group and total neutron flux distributions showed good agreement with SERPENT and published MSFR results, while the temperature distribution and total power showed discrepancies which can be attributed toknown sources of error. For the transient behavior under the ULOHS scenario, while the transition time towards the new steady state core temperature is also in good agreement with existing MSFR simulations by Fiorina et al., Moltres under-estimated the temperature rise by a factor of ten, due to the same sources of error affecting the steady state results. While an MSFR loaded with start-up fuel composition operates at a higher temperature than with the other two fuel compositions, all three cases were shown to be inherently safe due to thestrong negative temperature feedback.},
+	urldate = {2019-11-05},
+	booktitle = {Proceedings of {GLOBAL} {International} {Fuel} {Cycle} {Conference}},
+	publisher = {American Nuclear Society},
+	author = {Park, Sun Myung and Rykhlevskii, Andrei and Huff, Kathryn},
+	month = sep,
+	year = {2019},
+	file = {Park et al. - 2019 - Safety Analysis of Molten Salt Fast Reactor Fuel C.pdf:C\:\\Users\\Sun Myung\\Zotero\\storage\\EXYUTUGW\\Park et al. - 2019 - Safety Analysis of Molten Salt Fast Reactor Fuel C.pdf:application/pdf},
+}

doc/content/bib/journal-publications.bib

@@ -0,0 +1,79 @@
+@article{park_verification_2022,
+	title = {Verification of moltres for multiphysics simulations of fast-spectrum molten salt reactors},
+	volume = {173},
+	issn = {03064549},
+	url = {https://linkinghub.elsevier.com/retrieve/pii/S0306454922001463},
+	doi = {10.1016/j.anucene.2022.109111},
+	abstract = {Modeling strongly coupled neutronics and thermal–hydraulics in liquid-fueled MSRs requires robust and flexible multiphysics software for accurate simulations at reasonable computational costs. In this paper, we present Moltres and its neutronics and thermal–hydraulics modeling capabilities relevant to multiphysics reactor analysis. As a MOOSE-based application, Moltres provides various multiphysics coupling schemes and time-stepping methods, including fully coupled solves with implicit time-stepping. We verified Moltres’ MSR modeling capabilities against a multiphysics numerical benchmark developed for software dedicated to modeling fast-spectrum MSRs. The results show that Moltres performed comparably to participating software packages in the benchmark; the majority of the relevant quantities fell within one standard deviation of the benchmark average. Among the participating multiphysics tools in the benchmark, Moltres agrees closest to the multiphysics tool from the Delft University of Technology due to similarities in the numerical solution techniques and meshing schemes.},
+	language = {en},
+	urldate = {2022-04-26},
+	journal = {Annals of Nuclear Energy},
+	author = {Park, Sun Myung and Munk, Madicken},
+	month = aug,
+	year = {2022},
+	pages = {109111},
+	file = {Park and Munk - 2022 - Verification of moltres for multiphysics simulatio.pdf:C\:\\Users\\Sun Myung\\Zotero\\storage\\PHNTVU4R\\Park and Munk - 2022 - Verification of moltres for multiphysics simulatio.pdf:application/pdf},
+}
+
+@article{lindsay_introduction_2018,
+	title = {Introduction to {Moltres}: {An} application for simulation of {Molten} {Salt} {Reactors}},
+	volume = {114},
+	issn = {0306-4549},
+	shorttitle = {Introduction to {Moltres}},
+	url = {https://linkinghub.elsevier.com/retrieve/pii/S0306454917304760},
+	doi = {10.1016/j.anucene.2017.12.025},
+	abstract = {Moltres is a new physics application for modeling coupled physics in fluid-fuelled, molten salt reactors. This paper describes its neutronics model, thermal hydraulics model, and their coupling in the MOOSE framework. Neutron and precursor equations are implemented using an action system that allows use of an arbitrary number of groups with no change in the input card. Results for many-channel configurations in 2D-axisymmetric and 3D coordinates are presented and compared against other coupled models as well as the Molten Salt Reactor Experiment.},
+	language = {en},
+	urldate = {2018-01-08},
+	journal = {Annals of Nuclear Energy},
+	author = {Lindsay, Alexander and Ridley, Gavin and Rykhlevskii, Andrei and Huff, Kathryn},
+	month = apr,
+	year = {2018},
+	keywords = {agent based modeling, Finite elements, Hydrologic contaminant transport, MOOSE, Multiphysics, nuclear engineering, Nuclear fuel cycle, Object orientation, Parallel computing, Reactor physics, repository, Simulation, Systems analysis},
+	pages = {530--540},
+	annote = {2d prescribed},
+	file = {Lindsay et al. - 2018 - Introduction to Moltres An application for simula.pdf:C\:\\Users\\Sun Myung\\Zotero\\storage\\RCWUNGTP\\Lindsay et al. - 2018 - Introduction to Moltres An application for simula.pdf:application/pdf;Lindsay et al. - 2018 - Introduction to Moltres An application for simula.pdf:C\:\\Users\\Sun Myung\\Zotero\\storage\\3GEC6NQ9\\Lindsay et al. - 2018 - Introduction to Moltres An application for simula.pdf:application/pdf;Moltres.pdf:C\:\\Users\\Sun Myung\\Zotero\\storage\\4XDXRICB\\Moltres.pdf:application/pdf;ScienceDirect Full Text PDF:C\:\\Users\\Sun Myung\\Zotero\\storage\\E2T9U5IX\\Lindsay et al. - 2018 - Introduction to Moltres An application for simula.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Sun Myung\\Zotero\\storage\\3DT9TEY3\\S0306454917304760.html:text/html},
+}
+
+@article{lindsay_moltres_2018,
+	title = {Moltres: finite element based simulation of molten salt reactors},
+	volume = {3},
+	shorttitle = {Moltres},
+	doi = {10.21105/joss.00298},
+	abstract = {Moltres is a physics application for multiphysics modeling of fluid-fueled molten salt reactors
+(MSRs) (Lindsay et al. 2018). It couples equations for neutron diffusion, thermal
+hydraulics, and delayed neutron precursor transport. Neutron diffusion and precursor
+transport equations are set-up using an action system that allows the user to use an arbitrary
+number of neutron energy and precursor groups respectively with minimal input
+changes. Moltres sits on top of the Multi-physics Object-Oriented Simulation Environment
+(Gaston et al. 2015) and hence uses the finite element method to discretize the
+governing partial differential equations. In general the resulting system of non-linear algebraic
+equations is linearized using the Newton-Raphson method and then solved using
+the Portable, Extensible Toolkit for Scientific Computation (Balay et al. 2017). Assembly
+of the Jacobian and residual, and the linear solve are parallelized using MPI which
+allows Moltres to be run in massively parallel environments. Runs on the Blue Waters
+supercomputer at Illinois have utilized up to 608 cores.
+Moltres and MOOSE allow use of different basis functions for different system variables.
+Because of the purely diffusive nature of the neutron diffusion equations, neutron fluxes are
+typically discretized using continuous first-degree Lagrange polynomials and the degrees of
+freedom are associated with mesh nodes. The temperature variable may also be discretized
+with a continuous Lagrange basis, or a discontinuous basis of arbitrary degree monomials
+may be employed depending on the relative balance of heat convection to conduction. The
+purely hyperbolic precursor transport is currently discretized using constant monomials,
+which is equivalent to a first-order finite volume discretization. Moltres supports both
+segregated (through Picard iteration) and monolithic solutions of the equation system.
+However, due to the feedback between the power spectrum and temperature dependence
+of macroscopic cross-sections, monolithic solves have demonstrated superior robustness
+with segregated techniques often unable to converge to a solution. This result emphasizes
+the importance of a fully coupled multi-physics framework like the one that Moltres and
+MOOSE provide and suggests that iteratively coupling codes devoted to single physics
+(Kópházi, Lathouwers, and Kloosterman 2009) may result in limited flexibility.},
+	number = {21},
+	urldate = {2018-01-08},
+	journal = {The Journal of Open Source Software},
+	author = {Lindsay, Alexander and Huff, Kathryn},
+	month = jan,
+	year = {2018},
+	pages = {1--2},
+	file = {Full Text PDF:C\:\\Users\\Sun Myung\\Zotero\\storage\\MJIZZW4P\\Lindsay and Huff - 2018 - Moltres finite element based simulation of molten.pdf:application/pdf;Snapshot:C\:\\Users\\Sun Myung\\Zotero\\storage\\E3ARQ46H\\joss.html:text/html},
+}