Adds page skeletons

LLNL · Jan 3, 2024 · 0063aac · 0063aac
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diff --git a/_config.yml b/_config.yml
@@ -75,6 +75,7 @@ kramdown:
   syntax_highlighter_opts:
     # Use existing pygments syntax highlighting css
     css_class: 'highlight'
+  toc_levels: 1..1
 
 # Set the Sass partials directory, as we're using @imports
 sass:

diff --git a/_index.html b/_index.html
diff --git a/_layouts/default.html b/_layouts/default.html
@@ -30,12 +30,12 @@ <h1 class="site-name"><a href="{{ site.baseurl }}/">{{ site.name }}</a></h1>
             <nav>
 <!--              <a href="{{ site.baseurl }}/">Home</a> -->
               <a href="{{ site.baseurl }}/getting-started">Getting Started</a>
-              <a href="{{ site.baseurl }}/tools">Tools</a>
+<!--              <a href="{{ site.baseurl }}/tools">Tools</a>-->
               <a href="{{ site.baseurl }}/contributing">Contributing</a>
-              <a href="{{ site.baseurl }}/issues">Known Issues & FAQ</a>
-              <a href="{{ site.baseurl }}/_posts">Changelog</a>
-              <a href="{{ site.baseurl }}/acknowledgements">Acknowledgements</a>
+              <a href="{{ site.baseurl }}/resources">Resources</a>
+              <a href="{{ site.baseurl }}/citing">Citation</a> 
               <a href="{{ site.baseurl }}/about">About</a>
+              <a href="{{ site.baseurl }}/_posts">Changelog</a>
             </nav>
           </header>
         </div>

diff --git a/_pages/about.md b/_pages/about.md
@@ -3,4 +3,59 @@ layout: page
 title: About
 permalink: /about/
 ---
+* TOC
+{:toc}
 
+# Method of solution
+A fully implicit numerical algorithm is used that allows both Newton-like iterations to steady state 
+and time-dependent solutions with large time-steps.  A preconditioning matrix is obtained by approximate 
+(ILUT) inversion of a numerical finite-difference Jacobian, which is then used in a Newton-Krylov 
+solution algorithm. A finite-volume differencing algorithm is used. Over 95% of the coding is in 
+Fortran with the remainder being C.
+
+# Related and auxiliary software
+
+Although UEDGE is written in Fortran, for efficient execution and analysis of results, it utilizes 
+either Python or BASIS scripting shells. Python is easily available for many platforms 
+(http://www.Python.org/). The features and availability of BASIS are described in "Basis Manual Set" 
+by P.F. Dubois, Z.C. Motteler, et al., Lawrence Livermore National Laboratory report UCRL-MA-118541, 
+June, 2002 and http://basis.llnl.gov/), however, BASIS is deprecated. Contact one of the UEDGE developers
+if you insist on running it within that environment. 
+The Python version of UEDGE uses the same source files but utilizes Forthon to produce a Python-compatible 
+source.  Forthon has been developed by D.P. Grote (see http://hifweb.lbl.gov/Forthon/ and Grote et al. 
+in the references below), and it is freely available. The graphics can be performed by any package importable 
+to Python, such as PYGIST.  The parallel version of UEDGE available through Python also uses the PETSc linear 
+algebra solver whose development has been led by ANL (https://www.mcs.anl.gov/petsc/).
+
+UEDGE can also be coupled to other codes.  An excellent example is couplling to the DUSTT code from
+UCSD (contact [email protected]) that follows the trajectories and ablation of dust particles in
+the background UEDGE plasma and provides impurity sources to UEDGE.  For an example, see R. Smirnov
+et al., Phys. Plasmas 22 (2015) 012506.
+
+# Authors contributing to V7 release
+T.D. Rognlien, I. Joseph, W.H. Meyer, M.E. Rensink, and M.V. Umansky, LLNL  
+([email protected], [email protected], [email protected], [email protected], [email protected])
+
+# Acknowledgements to previous contributors
+P.N. Brown, R.H. Cohen, D.P. Grote, A.C. Hindmarsh, L.L. LoDestro, J.L. Milovich, 
+A. Pankin, G.D. Porter, and G.R. Smith, all presently or formerly at LLNL; M. McCourt, 
+L.C. McInnes, and H. Zhang, ANL; J.R. Cary, A.H. Hakim, S.E. Kruger, and A. Pankin, Tech-X; 
+D.A. Knoll, INEEL; D.P. Stotler, PPPL; B.J. Braams, retired, IAEA; A.Yu. Pigarov and 
+R. Smirnov, UCSD; J.D. Elder, U. Toronto; M. Groth, Aalto Univ.; and R.B. Campbell, Sandia.
+
+# References
+**_UEDGE development_**   
+T.D. Rognlien, J.L. Milovich, M.E. Rensink, and G.D. Porter, J. Nucl. Mat. 196-198 (1992) 347-351.  
+G.R. Smith, P.N. Brown, R.B. Campbell, D.A. Knoll, P.R. McHugh, M.E. Rensink, and T.D. Rognlien, J. Nucl. Mater. 220-222 (1995) 1024.  
+M.E. Rensink and T.D. Rognlien, J. Nucl. Mater. 266-269 (1999) 1180.  
+T.D. Rognlien, D.D. Ryutov, N. Mattor, and G.D. Porter, Phys. Plasmas 6, (1999) 1851.  
+T.D. Rognlien, M.E. Rensink, and G.R. Smith, "User manual for the UEDGE edge-plasma transport code," January 2000, LLNL Rpt. UCRL-ID-137121, lastest revision May 1, 2013.  
+
+**_Forthon development_** 
+D. P. Grote, A. Friedman, I. Haber, "Methods used in WARP3d, a Three-Dimensional PIC/Accelerator Code", Proceedings of the 1996 Computational Accelerator Physics Conference, AIP Conference Proceedings 391, p. 51.  
+See also: http://hifweb.lbl.gov/Forthon/  .
+
+**_FACETS project_**    
+J.R. Cary, J. Candy, R.H. Cohen et al., J. Phys.: Conf. Ser. 125 (2008) 012040.  
+A.H. Hakim, T.D. Rognlien, R.J. Groebner et al., Phys. Plasmas 19 (2012) 032505.  
+M. McCourt, T.D. Rognlien, L.C. McInnes, and H. Zhang, Computational Science & Discovery 5 (2012) 014012.  
diff --git a/_pages/acknowledgements.md → _pages/citing.md b/_pages/acknowledgements.md → _pages/citing.md
@@ -1,7 +1,7 @@
 ---
 layout: page
-title: Acknowledgments
-permalink: /acknowledgements/
+title: Citing the use of UEDGE 
+permalink: /citing/
 ---
 
 ## If using LLNL branch

diff --git a/_pages/contributing.md b/_pages/contributing.md
@@ -3,13 +3,16 @@ layout: page
 title: Contributing
 permalink: /contributing/
 ---
+* TOC
+{:toc}
 
-## Best practices
 
-### Develop on public forks
+# Best practices
 
-### Supply working examples
+## Develop on public forks
 
-### Allow maintainers to edit PRs
+## Supply working examples
 
-## Testing 
+## Allow maintainers to edit PRs
+
+# Testing 
diff --git a/_pages/getting-started.md b/_pages/getting-started.md
@@ -4,16 +4,25 @@ title: Getting started with UEDGE
 permalink: /getting-started/
 ---
 
-## Installation
+* <h6>TOC</h6>
+{:toc}
 
-### Pip install
+# Branches and versions
 
-### Building UEDGE
+## Master branch
 
-## Quickstart Guide
+## Develop branch
 
-## Instructions
+# Installation
 
-## UEDGE Manual
+## Pip install
+
+## Building UEDGE
+
+# Quickstart Guide
+
+# Instructions
+
+# UEDGE Manual
 
 
diff --git a/_pages/issues.md b/_pages/issues.md
diff --git a/_pages/resources.md b/_pages/resources.md
@@ -0,0 +1,17 @@
+---
+layout: page
+title: Resources
+permalink: /resources/
+---
+* TOC
+{:toc}
+
+# Known Issues
+
+# FAQ
+
+# The UEDGE Toolbox
+
+# Wiki
+
+# Discussion
diff --git a/index.md b/index.md
@@ -2,4 +2,6 @@
 layout: default
 ---
 
-# Welcome to UEDGE
+UEDGE is an interactive suite of physics packages using the Python or BASIS scripting systems. The original (circa 2007) Python version was further developed under the FACETS SciDAC project [Cary 2008, McCourt 2012]. The plasma is described by time-dependent 2D plasma fluid equations that include equations for density, velocity, ion temperature, electron temperature, electrostatic potential, and gas density in the edge region of a magnetic fusion energy confinement device. slab, cylindrical, and toroidal geometries are allowed, and closed and open magnetic field-line regions are included. Classical transport is assumed along magnetic field lines, and anomalous transport is assumed across field lines.  Multi-charge state impurities can be included with the corresponding line-radiation energy loss. 
+
+