References updated

FESTUNG · May 14, 2018 · 652c628 · 652c628
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diff --git a/README.md b/README.md
@@ -13,15 +13,19 @@ FESTUNG relies on fully vectorized matrix/vector operations to deliver optimized
 ## Usage
 To check out the latest version, run 
 
-    git clone https://github.com/FESTUNG/project.git
+```bash
+git clone --recursive https://github.com/FESTUNG/project.git
+```
 
 Model problems are defined following a generic [solver structure](doxygen/solverStructure.md).
 Have a look at the implementation of the standard (element-based) DG discretizations of linear advection (folders `advection` for time-explicit and `advection_implicit` for time-implicit) or the LDG discretization of the diffusion operator (folder `diffusion`).
 A hybridized DG discretization of linear advection can be found in the folder `hdg_advection`.
 
 Start the computation for any of these problems using `main(<folder name>)`, for example
 
-    $ main('advection')
+```bash
+main('advection')
+```
 
 Output files are written in [VTK format](http://www.vtk.org/VTK/img/file-formats.pdf) or [TecPlot ASCII file format](http://paulbourke.net/dataformats/tp/) and can be visualized, e.g., using [Paraview](http://www.paraview.org/).
 
@@ -31,7 +35,9 @@ When developing code for or with FESTUNG we suggest to stick to the [Naming conv
 ## Documentation
 All routines are carefully documented in the Doxygen format, which allows to produce [this documentation](https://www1.am.uni-erlangen.de/FESTUNG). It can be generated by calling 
 
-    $ doxygen doxyfileFESTUNG
+```bash
+doxygen
+```
 
 in the main directory.
 
@@ -49,7 +55,8 @@ FESTUNGs main developers are [Florian Frank](http://frank.ink), [Balthasar Reute
 ## Version 
 * Version 0.1 as published in the paper *Frank, Reuter, Aizinger, Knabner:* "FESTUNG: A MATLAB / GNU Octave toolbox for the discontinuous Galerkin method. Part I: Diffusion operator". *In: Computers & Mathematics with Applications 70 (2015) 11-46, Available online 15 May 2015, ISSN 0898-1221, http://dx.doi.org/10.1016/j.camwa.2015.04.013.*
 * Version 0.2 as published in the paper *Reuter, Aizinger, Wieland, Frank, Knabner:* "FESTUNG: A MATLAB / GNU Octave toolbox for the discontinuous Galerkin method. Part II: Advection operator and slope limiting". *In: Computers & Mathematics with Applications 72 (2016) 1896-1925, Available online 25 August 2016, ISSN 0898-1221, http://dx.doi.org/doi:10.1016/j.camwa.2016.08.006.*
-* Version 0.3 as published in the paper *Jaust, Reuter, Aizinger, Schuetz, Knabner:* "FESTUNG: A MATLAB / GNU Octave toolbox for the discontinuous Galerkin method. Part III: Hybridized discontinuous Galerkin (HDG) formulation". *Submitted to: Computers & Mathematics with Applications (2017).  Preprint on arXiv: https://arxiv.org/abs/1709.04390.*
+* Version 0.3 as published in the paper *Jaust, Reuter, Aizinger, Schuetz, Knabner:* "FESTUNG: A MATLAB / GNU Octave toolbox for the discontinuous Galerkin method. Part III: Hybridized discontinuous Galerkin (HDG) formulation". *In: Computers & Mathematics with Applications (2018) in press, Available online 2 May 2018, ISSN 0898-1221, https://doi.org/10.1016/j.camwa.2018.03.045.*
+* Version 0.4 as published in the paper *Reuter, Rupp, Aizinger, Frank, Knabner:* "FESTUNG: A MATLAB / GNU Octave toolbox for the discontinuous Galerkin method. Part IV: Generic problem framework and model-coupling interface". *Submitted to Computers & Mathematics with Applications (2018).*
 
 ## Contact
 * Homepage: [https://math.fau.de/FESTUNG](https://math.fau.de/FESTUNG)
diff --git a/doxyfileFESTUNG → doxyfile b/doxyfileFESTUNG → doxyfile
diff --git a/doxygen/gallery.md b/doxygen/gallery.md
@@ -10,7 +10,7 @@ The routine [visualizeDataLagr.m](visualizeDataLagr_8m.html) writes simulation d
 
 Author: [Hennes Hajduk](http://www.mathematik.tu-dortmund.de/de/personen/person/Hennes+Hajduk.html)
 
-References: \ref HHAR2018
+References: [[HHAR2018]](@ref HHAR2018)
 
 ![Galveston Bay model domain with computational mesh, velocity magnitude, and surface elevation after a 10 days simulation.](doxygen/images/sweBVE.png "Galveston Bay model domain with computational mesh.")
 

diff --git a/doxygen/references.dox b/doxygen/references.dox
@@ -3,12 +3,19 @@
 //! 
 //! @section TAG_REF_1 FESTUNG articles
 //!
+//! @subsection RRAFP2018 [RRAFP2018]
+//! B. Reuter, A. Rupp, V. Aizinger, F. Frank, P.Knabner,<br>
+//! <b>&ldquo;FESTUNG: A MATLAB/GNU Octave toolbox for the discontinuous Galerkin 
+//! method, Part IV: Generic problem framework and model-coupling 
+//! interface&rdquo;</b>,<br>
+//! Submitted to Computers & Mathematics with Applications (2018).
+//!
 //! @subsection JRASK2017 [JRASK2017]
 //! A. Jaust, B. Reuter, V. Aizinger, J. Schütz, P. Knabner,<br>
 //! <b>&ldquo;FESTUNG: A MATLAB/GNU Octave toolbox for the discontinuous 
-//! Galerkin method, Part III: Hybridized discontinuous (HDG) formulation&rdquo;</b>.<br>
-//! Submitted to: Computers & Mathematics with Applications.<br>
-//! Preprint on arXiv: https://arxiv.org/abs/1709.04390.
+//! Galerkin method, Part III: Hybridized discontinuous (HDG) formulation&rdquo;</b>,<br>
+//! Computers & Mathematics with Applications (2018) <i>in press</i>.<br>
+//! [<code>doi:10.1016/j.camwa.2018.03.045</code>](https://doi.org/10.1016/j.camwa.2018.03.045).
 //!
 //! @subsection RAWFK2016 [RAWFK2016]
 //! B. Reuter, V. Aizinger, M. Wieland, F. Frank, P. Knabner,<br>
@@ -28,7 +35,7 @@
 //!
 //! @subsection HHAR2018 [HHAR2018]
 //! H. Hajduk, B.R. Hodges, V. Aizinger, B. Reuter,<br>
-//! <b>&ldquo;Locally Filtered Transport for computational efficiency in multi-component advection-reaction models&rdquo;</b>,<br>
+//! <b>&ldquo;Locally Filtered Transport for computational efficiency in multi-component advection-reaction models&rdquo;</b>,\.<br>
 //! Environmental Modeling & Software 102 (2018), 185-198.<br>
 //! [<code>doi:20.1016/j.envsoft.2018.01.003</code>](https://doi.org/10.1016/j.envsoft.2018.01.003).
 //!

diff --git a/doxygen/solverStructure.md b/doxygen/solverStructure.md
@@ -1,6 +1,4 @@
-Solver structure
-================
-
+# Solver structure
 
 The solver structure of FESTUNG is built around the perception that almost
 every solver for a PDE problem can be subdivided into three major steps:
@@ -29,6 +27,8 @@ working problem definition with do-nothing steps.
 The implemented solver is then executed from the FESTUNG main directory
 using the command 
 
-    $ main('template')
+```matlab
+main('template')
+```
 
 where `'template'` is to be replaced by the name of the folder.
diff --git a/namingConvention.md b/namingConvention.md
@@ -26,18 +26,22 @@ For **variable names and function names** we use the *lower camel case* notation
 
 Some examples:
 
-    phi(...)
-    integrateRefElemPhiPhi(...)
-    dataDisc
-    tEnd
-    eta
+```matlab
+phi(...)
+integrateRefElemPhiPhi(...)
+dataDisc
+tEnd
+eta
+```
 
 For **class names** we use the *upper camel case* notation, i. e., the first letter of the name is always upper case. Since no classes are implemented, yet, this is for future code versions. 
 
 Some examples:
 
-    TimeStepper
-    Quadrature
+```matlab
+TimeStepper
+Quadrature
+```
 
 ## Variable Names
 Use the *lower camel case* notation and use meaningful names. One letter variables can be sufficient (e. g., when abbreviating the number of basis functions as ```N``` all the way through the code) but should be the exception.