fmk - updating to latest

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

@@ -41,6 +41,24 @@ The backend applications are categorized by function into the following workflow
         applications/preprocFEM
         applications/preprocUQ
 
+.. only:: HydroUQ_app
+
+    #. |createEVENT|
+    #. |createSAM|
+    #. |createEDP|
+    #. |performSIMULATION|
+    #. |performUQ|
+
+    .. toctree::
+       :maxdepth: 1
+       :hidden:
+
+       applications/eventApps
+       applications/modelingApps
+       applications/EDPApps
+       applications/simulationApps
+       applications/UQApps
+
 
 .. only:: WEUQ_app
 

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

@@ -2,7 +2,7 @@
 Build the Backend
 *****************
 
-    SimCenterBackendApplications contains a number of applications written in C++, C and Python that are needed by all SimCenter User Interfaces. To build the backend you will need to follow the following steps:
+    SimCenterBackendApplications contains many applications written in C++, C, and Python that are needed by all SimCenter User Interfaces. To build the backend you will need to follow the following steps:
 
     1. Clone the `SimCenterBackendApplications repository <https://github.com/NHERI-SimCenter/SimCenterBackendApplications>`_. 
     2. Build SimCenterBackendApplications using the following steps:
@@ -15,14 +15,14 @@ Build the Backend
 
             This will install all the dependencies and will build dependencies from their source code as needed.
 
-        2.3. Run CMake configuration this can be done using the command ``cmake ..``. Depending on your build environment, especially if you have multiple compiler, you may need to select a specific CMake generator. For instance on Window using Visual Studio 2017, you can configure CMake as follows:
+        2.3. Run CMake configuration this can be done using the command ``cmake ..``. Depending on your build environment, especially if you have multiple compilers, you may need to select a specific CMake generator. For instance, on Windows using Visual Studio 2017, you can configure CMake as follows:
 
             ``cmake .. -G Visual Studio 15 2017 Win64``
 
-        2.4. Build the release version of the backend, this can be done using the generated build system. For instance, on Unix based systems when using make files this can be achieved using the command ``make`` or ``make release``. When using an IDE like Visual Studio on Window or XCode on Mac, the generated project can opened in the IDE and used to build the code. In addition, this can also be done from the terminal using CMake the command:
+        2.4. Build the release version of the backend, this can be done using the generated build system. For instance, on Unix-based systems when using make files this can be achieved using the command ``make`` or ``make release``. When using an IDE like Visual Studio on Windows or XCode on Mac, the generated project can be opened in the IDE and used to build the code. In addition, this can also be done from the terminal using CMake the command:
 
             ``cmake --build . --config Release``
 
-    3. Install the backend applications to a local folder. This can be done by building the ``install target``. When using make on Unix based system. This can also be from IDE (e.g.) by selecting the install target or project and building it. In addition, this can be done from the terminal using the command:
+    3. Install the backend applications to a local folder. This can be done by building the ``install target`` when using make on Unix-based systems. This can also be from IDE (e.g.) by selecting the install target or project and building it. In addition, this can be done from the terminal using the command:
 
-        ``cmake --build . --target install`` or ``cmake --install`` if you have CMake 3.15 or later. If building and installation were successful you should find a folder called ``applications`` in the repository with all the applications inside of it.
+        ``cmake --build . --target install`` or ``cmake --install`` if you have CMake 3.15 or later. If building and installation were successful you should find a folder called ``applications`` in the repository with all the applications inside it.

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

@@ -9,7 +9,7 @@ SimCenter tools all comprise a frontend user interface (UI) and backend applicat
 
 .. note::
 
-   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.
+   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
@@ -45,7 +45,7 @@ First, ensure the following dependencies are installed:
 Build the Backend Applications
 ******************************
 
-Instructions to build the backend workflow applications on your local desktop depend on your operating system, but is a 2 step process involving some initial setup and finally the build.
+Instructions to build the backend workflow applications on your local desktop depend on your operating system. This is a 2-step process involving some initial setup and finally the build.
 
 Setup the development environment with Conan
 ============================================
@@ -130,14 +130,15 @@ Build the applications
 
           
       
-If building and installation were successful, you should find a folder called ``applications`` in the repository with all the applications inside of it.   The name of this folder should not be changed.
+If building and installation were successful, you should find a folder called ``applications`` in the repository with all the applications inside of it. The name of this folder should not be changed.
+
 
 
 ************************
 Build the User Interface
 ************************
 
-To build the interface, you first need to download the repo and a companion repo(SimCenterCommon) from Github using our `github repos <https://github.com/NHERI-SimCenter>`_. In a folder in which you wish to build the application, issue the following two commands.
+To build the interface, you first need to download the repo and a companion repo(SimCenterCommon) from GitHub using our `GitHub repos <https://github.com/NHERI-SimCenter>`_. In a folder in which you wish to build the application, issue the following two commands.
 
 .. only:: quoFEM_app
 
@@ -152,38 +153,45 @@ To build the interface, you first need to download the repo and a companion repo
    .. code::
       
       git clone https://github.com/NHERI-SimCenter/SimCenterCommon.git
-      git clone https://github.com/NHERI-SimCenter/R2DTool.git      
+      git clone https://github.com/NHERI-SimCenter/R2DTool.git
 
 
 .. only:: PBE_app
 
-   .. code::	  
+   .. code::
 
        git clone https://github.com/NHERI-SimCenter/SimCenterCommon.git
-       git clone https://github.com/NHERI-SimCenter/QS3hark.git	  
+       git clone https://github.com/NHERI-SimCenter/QS3hark.git
        git clone https://github.com/NHERI-SimCenter/EE-UQ.git
-       git clone https://github.com/NHERI-SimCenter/PBE.git       
+       git clone https://github.com/NHERI-SimCenter/PBE.git
 
 .. only:: EEUQ_app
 
    .. code::
       
        git clone https://github.com/NHERI-SimCenter/SimCenterCommon.git
-       git clone https://github.com/NHERI-SimCenter/QS3hark.git	  
-       git clone https://github.com/NHERI-SimCenter/EE-UQ.git	  
+       git clone https://github.com/NHERI-SimCenter/QS3hark.git
+       git clone https://github.com/NHERI-SimCenter/EE-UQ.git
+
+.. only:: WEUQ_app
+
+   .. code::
+
+       git clone https://github.com/NHERI-SimCenter/SimCenterCommon.git
+       git clone https://github.com/NHERI-SimCenter/WE-UQ.git
 
-.. only:: WEUQ_app	  
+.. only:: HydroUQ_app	  
 
    .. code::
 
        git clone https://github.com/NHERI-SimCenter/SimCenterCommon.git
-       git clone https://github.com/NHERI-SimCenter/WE-UQ.git	  
+       git clone https://github.com/NHERI-SimCenter/HydroUQ.git	  
 
 
 .. note::
 
 
-   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/>`_
+   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 repos, 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 the terminal application.
 
@@ -244,7 +252,7 @@ Modify the User Interface Preferences
 
 Once built, the tool **Preferences** needs to be modified. To do this, open the |short tool id| tool, then click on File -> Preferences in the main menu if on Windows or |short tool id| -> Preferences if on a Mac. This will bring up a dialog window shown below. You need to modify specific values:
 
-  #. Python: provide the full path to the python interpreter.
+  #. Python: provide the full path to the Python interpreter.
 
   #. OpenSees: provide the full path to the OpenSees executable
 

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

@@ -2,7 +2,7 @@
 Build the Backend
 *****************
 
-    SimCenterBackendApplications contains a number of applications written in C++, C and Python that are needed by all SimCenter User Interfaces. To build the backend you will need to follow the following steps:
+    SimCenterBackendApplications contains many applications written in C++, C, and Python that are needed by all SimCenter User Interfaces. To build the backend you will need to follow the following steps:
 
     1. Clone the `SimCenterBackendApplications repository <https://github.com/NHERI-SimCenter/SimCenterBackendApplications>`_. 
     2. Build SimCenterBackendApplications using the following steps:
@@ -15,16 +15,16 @@ Build the Backend
 
         This will install all the dependencies and build dependencies from their source code as needed.
 
-        2.3. Run CMake configuration this can be done using the command ``cmake ..``. Depending on your build environment, especially if you have multiple compiler, you may need to select a specific CMake generator. For instance on Window using Visual Studio 2017, you can configure CMake as follows:
+        2.3. Run CMake configuration this can be done using the command ``cmake ..``. Depending on your build environment, especially if you have multiple compilers, you may need to select a specific CMake generator. For instance, on Windows using Visual Studio 2017, you can configure CMake as follows:
 
             ``cmake .. -G Visual Studio 15 2017 Win64``
 
-        2.4. Build the release version of the backend, this can be done using the generated build system. For instance, on Unix based systems when using make files this can be achieved using the command ``make`` or ``make release``. When using an IDE like Visual Studio on Window or XCode on Mac, the generated project can opened in the IDE and used to build the code. In addition, this can also be done from the terminal using CMake with the command:
+        2.4. Build the release version of the backend, this can be done using the generated build system. For instance, on Unix-based systems when using make files this can be achieved using the command ``make`` or ``make release``. When using an IDE like Visual Studio on Windows or XCode on Mac, the generated project can be opened in the IDE and used to build the code. In addition, this can also be done from the terminal using CMake with the command:
 
             ``cmake --build . --config Release``
 
     3. Install the backend applications to a local folder. This can be done by building the ``install target`` when using ``make`` on Unix-like systems. This can also be done from an IDE by selecting the install target or project and building it. Finally, this can also be done from the terminal using the following command with CMake 3.15 or later:
 
         ``cmake --build . --target install`` or ``cmake --install`` 
 
-    If building and installation was successful you should find a folder called ``applications`` in the repository with all the applications inside of it.
+    If building and installation were successful you should find a folder called ``applications`` in the repository with all the applications inside it.

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

@@ -10,9 +10,7 @@ How To Cite
 
 .. only:: PBE_app
 
-   1. Adam Zsarnoczay, Frank McKenna, Charles Wang, Stevan Gavrilovic, Kuanshi Zhong, Michael Gardner, Sang-ri Yi, Aakash B. Satish & Wael Elhaddad. (2024).
-      NHERI-SimCenter/PBE: Version 3.3.0 (v3.3.0).
-      Zenodo. `DOI: 10.5281/zenodo.10448044 <https://doi.org/10.5281/zenodo.10448044>`_
+   1. Adam Zsarnoczay, Frank McKenna, Charles Wang, Stevan Gavrilovic, Michael Gardner, Sang-ri Yi, Aakash Bangalore Satish, & Wael Elhaddad. (2024). NHERI-SimCenter/PBE: Version 3.4.0 (V3.4.0). Zenodo. `DOI: 10.5281/zenodo.10902085 <https://doi.org/10.5281/zenodo.10902085>`_
 
 .. only:: EEUQ_app
 
@@ -24,14 +22,14 @@ How To Cite
       Michael Gardner, & Sang-ri Yi. (2024). NHERI-SimCenter/WE-UQ: Version 3.2.0 (v3.2.0). 
       Zenodo. `DOI: 10.5281/zenodo.10806694 <https://doi.org/10.5281/zenodo.10806694>`_
 
-.. only:: quoFEM_app	     
+.. only:: quoFEM_app
 
 
    1. Frank McKenna, Sang-ri Yi, Aakash Bangalore Satish, Adam Zsarnoczay, Kuanshi Zhong, Michael Gardner, & Wael Elhaddad. (2023). 
       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    
+.. only:: HydroUQ_app
 
    1. Frank McKenna, Justin Bonus, Ajay B Harish, & Nicolette Lewis. (2024). 
       NHERI-SimCenter/HydroUQ: Version 3.1.0 (v3.1.0). 

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

@@ -4,4 +4,4 @@
 Acknowledgments
 ***************
 
-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.
+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 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.
+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

@@ -12,13 +12,13 @@ The following terms may be found throughout this document:
       "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.
+      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 it can be a part of a group of programs.
 
    Scientific Workflow
       A sequence of steps that propagate input data through a series of applications to produce output files. It is a loosely coupled application performing workflows in which each of the coordinated tasks is performed using an individual application. Each of the individual applications takes some data inputs and produces data outputs, which are then consumed by subsequent tasks according to the workflow definition. They are termed scientific because they are typically used by scientists to process, manage, and visualize ever-increasing amounts of data applied to "scientific" problems.
 
    Scientific Workflow System
-      An application or application to aid a user in setting up, scheduling, running and monitoring a user-defined scientific workflow.
+      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 components that meet the component interface.