Merge branch 'devel' into 'master'

Fixed docs and added Bibtex entries.

See merge request !8

CITATION

@@ -8,3 +8,14 @@ Jacquey, Antoine B., & Cacace, Mauro. (2019, July 30). LYNX: Lithosphere dYnamic
 
 And also a reference to the publication describing the theory and implementation of the LYNX simulator:
 The articles presenting the LYNX simulator are currently under review.
+
+Here are the BibTex entries for LaTeX users:
+
+@misc{LYNXApp,
+  author = {Jacquey, Antoine B. and Cacace, Mauro},
+  title = {{LYNX: Lithosphere dYnamic Numerical toolboX, a MOOSE-based application}},
+  month = {jul},
+  year = {2019},
+  doi = {10.5281/zenodo.3355376},
+  url = {https://doi.org/10.5281/zenodo.3355376}
+}
\ No newline at end of file

doc/content/application_development/damage_rheology.md

@@ -4,7 +4,7 @@ Here we describe the base for the damage rheology implementation in LYNX.
 
 ## Stress update
 
-We rely of the elastic energy and stress formulation of [cite:lyakhovsky1997]:
+We rely of the elastic energy and stress formulation of [!cite](lyakhovsky1997):
 
 \begin{equation}
   \sigma_{ij} = \left(\lambda - \frac{\alpha \gamma}{\xi}\right) \varepsilon_{kk} \delta_{ij} + \left(2G - \alpha \gamma \left(\xi - 2\xi_{0}\right)\right) \varepsilon_{ij}.
@@ -47,7 +47,7 @@ The parameter $\xi_{0}$ represents the modified internal friction of the materia
 
 ## Inelastic model
 
-In LYNX, we rely on a different formulation as the one presented in [cite:lyakhovsky1997,lyakhovsky2015] for the inelastic update. The yield function presented in [cite:lyakhovsky2015] reads:
+In LYNX, we rely on a different formulation as the one presented in [!cite](lyakhovsky1997,lyakhovsky2015) for the inelastic update. The yield function presented in [!cite](lyakhovsky2015) reads:
 
 \begin{equation}
   f = D\varepsilon_{v}^{3} + {\lVert \varepsilon_{ij} \rVert}^{2} \left(\xi - \xi_{0}\right)

doc/content/application_development/identities.md

 ## Some identities
 
-In the following description, we make use of the following identities extended from [cite:dunne2005].
+In the following description, we make use of the following identities extended from [!cite](dunne2005).
 
 Stress invariants:
 

doc/content/application_development/plasticity.md

@@ -51,7 +51,7 @@ Using Eq. 3, the plastic increment can be written:
 
 ## Tangent operator modulus
 
-Here we extend the tangent operator modulus given in [cite:dunne2005] to account for volumetric deformation and non-associative models.
+Here we extend the tangent operator modulus given in [!cite](dunne2005) to account for volumetric deformation and non-associative models.
 The tangent operator modulus is defined as:
 
 \begin{equation}

doc/content/documentation.menu.md

@@ -7,6 +7,10 @@
 
 !col! class=s12 m6 l4
 ## [Application Development](application_development/index.md)
+
+- [Plasticity](application_development/plasticity.md)
+- [Viscoplasticity](application_development/viscoplasticity.md)
+- [Damage rheology](application_development/damage_rheology.md)
 !col-end!
 
 !col! class=s12 m6 l4

doc/content/examples/index.md

 # Examples
 
-- [Frequently Asked Questions](help/faq.md)
-- [Troubleshooting](help/troubleshooting.md)
-- [Developer Tools](help/development/index.md)
-- [GFZ Linux cluster usage](help/glicconnectivity.md)
-- [Contact Us](help/contact_us.md)
+Here we will put some examples