adding reference rst

source/case_1.rst

@@ -1,15 +1,15 @@
 .. _case_1:
 
 QuoFEM - Settlements
-================================
+====================
 
 Author: Kendra Mutch
 ---------------------
 
 Introduction
 ------------
 
-The goal of this project is to quantify settlement, parameters impacting settlement, and observe how uncertainty in input parameters impacts the ultimate settlement of a cohesive soil. These calculations are performed through use of the SimCenter QuoFEM tool. For more details on settlement calculations, the user is encounged to read *Holtz and Kovacs 2011*.
+The goal of this project is to quantify settlement, parameters impacting settlement, and observe how uncertainty in input parameters impacts the ultimate settlement of a cohesive soil. These calculations are performed through use of the SimCenter QuoFEM tool. For more details on settlement calculations, the user is encounged to read :cite:`Holtz2011`.
 
 Project Description
 -------------------
@@ -340,7 +340,4 @@ A more in-depth analysis using prior and posterior distributions reveals that th
 
 Remarks
 -------
-By accounting for uncertainty in settlement, chances of highly underpredicting or overpredicting settlement are reduced. 
-
-
-    [Hol2011] R. D. Holtz and W. D. Kovacs. *An Introduction to Geotechnical Engineering*. Pearson, 2011. ISBN 978-0137011322.
+By accounting for uncertainty in settlement, chances of highly underpredicting or overpredicting settlement are reduced.

source/case_2.rst

@@ -721,5 +721,3 @@ I'd like to thank everyone at SimCenter, specifically Sang-ri Yi, Frank McKenna,
 Transfer function is one of my favorite topics in geotechnical engineering. I'd really like to continue working with site response and performance based design so being able to create this example along with my class was great.
 
 Finally, I'd like to thank Prof. Arduino who made all of this possible. His determination and motivation was contagious throughout the academic quarter. There are many great professors but there is only one Pedro Arduino. 
-
-.. bibliography:: references.bib

source/case_5.rst

@@ -606,9 +606,3 @@ Remarks
         :width: 600px
         :align: center
         :figclass: align-center
-
-
-
-References
-----------
-.. bibliography:: references.bib

source/case_5.rst~

@@ -410,6 +410,17 @@ The following code snippet shows the implementation of the :cite:`Zhu2017` model
             return {"liq_prob":prob_liq, "liq_susc":liq_susc}
 
 
+.. raw:: html
+
+    </code></pre>
+    </details>
+
+
+.. raw:: html
+
+    <br><br>
+
+
 
 **RESULTS**
 
@@ -549,6 +560,15 @@ In this example, the :cite:`Sanger2024` model is implemented in the R2D tool usi
 
         return {"liq_prob":prob_liq, "liq_susc":LPI}
 
+.. raw:: html
+
+    </code></pre>
+    </details>
+
+
+.. raw:: html
+
+    <br><br>
 
 
 **RESULTS**
@@ -587,8 +607,5 @@ Remarks
         :align: center
         :figclass: align-center
 
-
-
-References
-----------
-.. bibliography:: references.bib
+.. bibliography::
+   :filter: cited

source/case_6.rst

@@ -146,5 +146,3 @@ Remarks
 
 * A `Jupyter Notebook <https://github.com/parduino/CESG599_NHERI.documentation/tree/main/source/landslides-M9motions/>`_ ('hazardNewmark.ipynb') was coded to simulate the process that could be implemented to R2D for earthquake-induced landslides hazard so the user could then estimate damage and losses. Please if refering to this notebook, careful read the instructions in the readme first. Find this work in the CESG599 repository. When trying to run this notebook, you must have access to the M9 project in DesignSafe machines. 
 * Earthquake induced landslides prediction may be a difficult task to adress, but there are models out there that can be implemented to predict the hazard and subsequently, this hazard can be used to predict damage amd losses. The idea is in this section is to provide a procedure that could ve developed within the SiimCenter R2D tool to predict the hazard and subsequently, to predict damage amd losses. 
-
-.. bibliography:: references.bib

source/case_7.rst

@@ -267,7 +267,3 @@ Remarks
 * In locations such as Vieques, Puerto Rico, a comprehensive building inventory to assess huricane impact to infrastructure assets is limited. Assessing hazard exposure and consequences are key to increase resilience.
 * R2D possess vast capabilities to adress this challenge, allowing researches to input hazard data and construct building inventories with BRAILS tools.
 * This example provides strategies for creating building inventories in locations where data is scarce and implementing them in a format that could be used in R2D for regional analysis.
-
-References
-----------
-.. bibliography:: references.bib

source/case_r.rst

@@ -0,0 +1,9 @@
+
+.. _case_r:
+
+
+References
+==========
+
+.. bibliography::
+   :filter: cited

source/case_r.rst~

@@ -0,0 +1,8 @@
+
+.. _case_r:
+
+
+References
+==========
+
+.. bibliography:: references.bib

source/index.rst

@@ -19,7 +19,8 @@ The course is intended for graduate students and researchers in the field of civ
    case_4
    case_5
    case_6
-   case_7 
+   case_7
+   case_r 
 .. Acknowledgements
 
 Acknowledgements

source/references.bib

@@ -55,14 +55,23 @@ @article{Gey2020
   publisher={American Society of Civil Engineers}
 }
 
+@book{Holtz2011,
+  author = {Holtz, R.D. and Kovacs, W.D. and Sheahan, T.C.},
+  publisher = {Prentice Hall},
+  isbn = {978-0137011322},
+  pages = {853},
+  title = {An Introduction to Geotechnical Engineering},
+  year = {2011}
+}
+
 @book{Kramer1996,
-author = {Kramer, S. L.},
-publisher = {Pearson},
-isbn = {9783642196294},
-issn = {1532-2793},
-pages = {653},
-title = {Geotechnical Earthquake Engineering},
-year = {1996}
+  author = {Kramer, S. L.},
+  publisher = {Pearson},
+  isbn = {9783642196294},
+  issn = {1532-2793},
+  pages = {653},
+  title = {Geotechnical Earthquake Engineering},
+  year = {1996}
 }
 
 @article{Jibson1993,