fmk - updating to latest

docs/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: dfe7311502e66a5e1a89ccacdc216591
+config: 7cdd6d3258f1dad27bb3b8e9c861e266
 tags: b812aa65388374b20f6c919e0a750ea9

docs/_sources/common/developer_manual/architecture/desktop/architecture.rst.txt

@@ -4,7 +4,7 @@
 Software Architecture
 *********************
 
-The |app| is one of the SimCenter's computational applications, which are `scientific workflow systems <https://en.wikipedia.org/wiki/Scientific_workflow_system>`_ that execute a sequence of computational tasks specialized for natural hazard engineering (NHE) problems. In contrast to more general-purpose scientific workflow systems (such as `Taverna <https://taverna.incubator.apache.org/>`_, `Kepler <https://kepler-project.org/>`_, and `Pegasus <https://pegasus.isi.edu/>`_), SimCenter workflow systems include the following features:
+The |app| is one of the SimCenter's computational applications, which are `scientific workflow systems <https://en.wikipedia.org/wiki/Scientific_workflow_system>`_ that executes a sequence of computational tasks specialized for natural hazard engineering (NHE) problems. In contrast to more general-purpose scientific workflow systems (such as `Taverna <https://taverna.incubator.apache.org/>`_, `Kepler <https://kepler-project.org/>`_, and `Pegasus <https://pegasus.isi.edu/>`_), SimCenter workflow systems include the following features:
 
    - access to high-performance computing resources, available on the cloud through |DesignSafe|, to enable parallel workflows for non-trivial large-scale NHE problems;
    - uncertainty quantification capabilities using `Dakota <https://dakota.sandia.gov/>`_, which allows users to introduce input uncertainties that are propagated through the workflow with random variables;

docs/_sources/common/developer_manual/how_to_build/desktop/how_to_build.rst.txt

@@ -4,20 +4,20 @@
 How to Build
 ============
 
-SimCenter tools all comprise a frontend UI and some backend applications. They are kept in separate GitHub repositories and are also built separately. The following3 sections outline (1) the applications needed to build and run, (2) instructions for building the backend applications, (3) instructions for building the frontend UI, and (4) operations to perform in the running UI to link the UI and the backend.
+SimCenter tools all comprise a frontend user interface (UI) and backend applications. They are kept in separate GitHub repositories and are also built separately. The following sections outline (1) the applications needed to build and run, (2) instructions for building the backend applications, (3) instructions for building the frontend UI, and (4) operations to perform in the running UI to link the UI and the backend.
 
 
 .. note::
 
-   As part of our continuous integration process, |app| is built evrey time we check code into the NHERI-SimCenter repositories. To do this we make use of a CI service. That current service is `appveyor <https://www.appveyor.com/>`_. As a consequence in the |app| repo that you will clone as part of this build process there is a file **appveyor.yml**. This file contains shell commands that are issued to set-up the operating system, download the software and build it. If the following commands fail for you, look at the appveyor.yml file to see what commands are currently beeing called as these may be more up to date than what is presented below.
+   As part of our continuous integration process, |app| is built every time we check code into the NHERI-SimCenter repositories. To do this we make use of a CI service. That current service is `appveyor <https://www.appveyor.com/>`_. As a consequence in the |app| repo that you will clone as part of this build process there is a file **appveyor.yml**. This file contains shell commands that are issued to set up the operating system, download the software and build it. If the following commands fail for you, look at the appveyor.yml file to see what commands are currently being called as these may be more up-to-date than what is presented below.
 
 ********************
 Install Dependencies
 ********************
 
 First, ensure the following dependencies are installed:
 
-* **C++17 compliant compiler**: many of the workflow applications included use C++17 features; consequently, they may need a newer C++17 compliant compiler. For Windows users, MSVC in `Visual Studio 2019 (Community Edition) <https://visualstudio.microsoft.com/vs/older-downloads/Install Dependencies>`_ can be used. Some extensions of Visual Studio are also needed: Open Visual Studio Installer, go to Installed / More / Modify, under the Workloads tab, check Desktop development with C++ and Visual Studio extension development; under the Individual components tab, check C++ CMake tools for windows. Then click Modify.
+* **C++17 compliant compiler**: many of the workflow applications included use C++17 features; consequently, they may need a newer C++17 compliant compiler. For Windows users, MSVC in `Visual Studio 2019 (Community Edition) <https://visualstudio.microsoft.com/vs/older-downloads>`_ can be used. Some extensions of Visual Studio are also needed: Open Visual Studio Installer, go to Installed / More / Modify, under the Workloads tab, check Desktop development with C++ and Visual Studio extension development; under the Individual components tab, check C++ CMake tools for Windows. Then click Modify.
 
 * **OpenSees**: The workflow applications require an installation of `OpenSees <http://opensees.berkeley.edu/>`_ to carry out a structural analysis using the finite element method.
 
@@ -85,10 +85,10 @@ Build the applications
 
         git clone https://github.com/NHERI-SimCenter/SimCenterBackendApplications	 
 
-#. To build the applications you need to now navigate to the **SimCenterBackendApplications** folder that was created with the **git clone** command. Once there you will issue the following set of commands to create a **build** folder, change director to that folder, install needed software using conan, and finally use **cmake** to build and install thge applications. The following are the set of commands to type in the terminal (see notes below the code block if the commands fail).
+#. To build the applications you need to now navigate to the **SimCenterBackendApplications** folder that was created with the **git clone** command. Once there you will issue the following set of commands to create a **build** folder, change directory to that folder, install needed software using conan, and finally use **cmake** to build and install the applications. The following are the set of commands to type in the terminal (see notes below the code block if the commands fail).
 
 
-    For those developers using the Windows operating system, in a terminal or powershell window you need to type the following:
+    For those developers using the Windows operating system, in a terminal or power-shell window you need to type the following:
 
             .. code:: console
 
@@ -185,14 +185,14 @@ To build the interface, you first need to download the repo and a companion repo
 
    Use the above links if you just want to download and build the applications. If you intend to make changes to any of the code in the repo's, you should fork that repo and then clone your forked repo. Forking a repo at **github** is done through your browser as shown on the following `github guides page <https://guides.github.com/activities/forking/>`_
 
-You now have two ways to build the application: (1) using the **Qt Creator** desktop application provided by **Qt** and (2) from terminal application.
+You now have two ways to build the application: (1) using the **Qt Creator** desktop application provided by **Qt** and (2) from the terminal application.
 
 
 Build using Qt Creator
 ========================
 
 1. Start Qt Creator, then open the |short tool id|.pro file located in the |short tool id| directory that was downloaded in the previous step.
-2. Setup the development kit in Qt Creator. This is usually done by selecting the Qt version, compiler, and configuration and following the onscreen dialog.
+2. Set up the development kit in Qt Creator. This is usually done by selecting the Qt version, compiler, and configuration and following the onscreen dialog.
 3. Build the application and run it in Qt Creator IDE using the **Run** button. This can be done using the keyboard shortcut ``F5`` to build and start the tool.
 
 
@@ -201,7 +201,7 @@ Build from the Terminal
 
 The operations are similar to what was done when building the backend applications. In the terminal application, starting inside the directory of the cloned application again, you will create a build directory, cd into that build directory, run **qmake**, and finally make (or on Windows nmake) to create the application.
 
-Windows developers will type the following in a terminal or a powershell window:
+Windows developers will type the following in a terminal or a power-shell window:
 
     .. parsed-literal::
 

docs/_sources/common/front-matter/cite.rst.txt

@@ -6,8 +6,7 @@ How To Cite
 
 .. only:: R2D_app
 
-   1. Frank McKenna, Stevan Gavrilovic, Zsarnoczay, A., Zhao, J., Zhong, K., Barbaros Cetiner, Yi, S.-. ri ., Elhaddad, W., & Arduino, P. (2024).
-   NHERI-SimCenter/R2DTool: Version 4.0.0 (v4.0.0). Zenodo. `DOI 10.5281/zenodo.4483614 <https://doi.org/10.5281/zenodo.4483614>`_
+   1. Frank McKenna, Stevan Gavrilovic, Jinyan Zhao, Kuanshi Zhong, Adam Zsarnoczay, Barbaros Cetiner, Sang-ri Yi, Pedro Arduino, & Wael Elhaddad. (2024). NHERI-SimCenter/R2DTool: Version 4.1.0 (v4.1.0). Zenodo. `<https://doi.org/10.5281/zenodo.10902064>`_
 
 .. only:: PBE_app
 
@@ -17,10 +16,7 @@ How To Cite
 
 .. only:: EEUQ_app
 
-   1.  Frank McKenna, Kuanshi Zhong, Michael Gardner, Adam Zsarnoczay, Sang-ri Yi, Aakash Bangalore Satish,
-       Charles Wang, & Wael Elhaddad. (2023).
-       NHERI-SimCenter/EE-UQ: Version 3.3.0 (v3.3.0).
-       Zenodo. "https://doi.org/10.5281/zenodo.7790405
+   1.  Frank McKenna, Kuanshi Zhong, Michael Gardner, Adam Zsarnoczay, Sang-ri Yi, Aakash Bangalore Satish, Charles Wang, & Wael Elhaddad. (2024). NHERI-SimCenter/EE-UQ: Version 3.5.0 (v3.5.0). Zenodo. `<https://doi.org/10.5281/zenodo.10902075>`_
 
 .. only:: WEUQ_app
 
@@ -35,6 +31,11 @@ How To Cite
       NHERI-SimCenter/quoFEM: Version 3.5.0 (v3.5.0). 
       Zenodo. `DOI: 10.5281/zenodo.10443180 <https://doi.org/10.5281/zenodo.10443180>`_
 
+.. only:: HydroUQ_app    
+
+   1. Frank McKenna, Justin Bonus, Ajay B Harish, & Nicolette Lewis. (2024). 
+      NHERI-SimCenter/HydroUQ: Version 3.1.0 (v3.1.0). 
+      Zenodo. `DOI: 0.5281/zenodo.10902090 <https://doi.org/10.5281/zenodo.10902090>`_
 
 2. Gregory G. Deierlein, Frank McKenna, Adam Zsarnóczay, Tracy Kijewski-Correa, Ahsan Kareem,
    Wael Elhaddad, Laura Lowes, Matt J. Schoettler, and Sanjay Govindjee (2020)

docs/_sources/common/front-matter/desktop/ack.rst.txt

@@ -4,4 +4,4 @@
 Acknowledgments
 ***************
 
-This material is based upon work supported by the National Science Foundation under Grants No. 1621843 and No. 2131111. Any opinions, findings, conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
+This material is based upon work supported by the U.S. National Science Foundation under Grants No. 1612843 and No. 2131111. Any opinions, findings, conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the U.S. National Science Foundation.

docs/_sources/common/front-matter/desktop/ack_pbe.rst.txt

@@ -8,7 +8,7 @@ Acknowledgments
 National Science Foundation
 ---------------------------
 
-This material is based upon work supported by the National Science Foundation under Grants No. 1621843 and No. 2131111. Any opinions, findings, conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
+This material is based upon work supported by the U.S. National Science Foundation under Grants No. 1612843 and No. 2131111. Any opinions, findings, conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the U.S. National Science Foundation.
 
 ------------
 Contributors

docs/_sources/common/front-matter/glossary.rst.txt

@@ -9,7 +9,7 @@ The following terms may be found throughout this document:
 .. glossary::
 
    Workflow
-      The automation of a business process, in whole or part, during which documents, information or tasks are passed from one participant to another for action, according to a set of procedural rules.” [Workflow Management Coalition].
+      "The automation of a business process, in whole or part, during which documents, information or tasks are passed from one participant to another for action, according to a set of procedural rules." [`Workflow Management Coalition <https://wfmc.org/>`_].
 
    Application
       A software application performs operations on data residing in a computer for a user or another program; it can be self-contained, typically termed a program or part of a group of programs.
@@ -21,4 +21,4 @@ The following terms may be found throughout this document:
       An application or application to aid a user in setting up, scheduling, running and monitoring a user-defined scientific workflow.
 
    Software Framework
-      A software framework defines a set of component interfaces. It provides a set of implementations in the code of these interfaces, which allows developers to build applications for the domain for which the framework has been designed. For example, a C++ framework will provide a set of abstract classes that define interfaces and a set of concrete classes that implement the interfaces, which will allow developers to quickly build and release applications using the concrete classes.  Frameworks allow developers to extend the functionality of the applications by introducing their components that meet the component interface.
+      A software framework defines a set of component interfaces. It provides a set of implementations in the code of these interfaces, which allows developers to build applications for the domain for which the framework has been designed. For example, a C++ framework will provide a set of abstract classes that define interfaces and a set of concrete classes that implement the interfaces, which will allow developers to quickly build and release applications using the concrete classes.  Frameworks allow developers to extend the functionality of the applications by introducing components that meet the component interface.