fmk - updating to latest

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

@@ -197,31 +197,31 @@ The operations are similar to what was done when building the backend applicatio
 
 Windows developers will type the following in a terminal or a PowerShell window:
 
-    .. code:: console
+    .. parsed-literal::
 
-      mkdir build
-      cd build
-      conan install .. --build missing
-      qmake ../|short tool id|.pro
-      nmake
+       mkdir build
+       cd build
+       conan install .. --build missing
+       qmake ../|short tool id|.pro
+       nmake
 
 Linux or Mac users will type the following in a terminal window from inside the |app| directory:
 
-    .. code:: console
+    .. parsed-literal::
 
-      mkdir build
-      cd build
-      conan install .. --build missing
-      qmake ../|short tool id|.pro
-      make
+       mkdir build
+       cd build
+       conan install .. --build missing
+       qmake ../|short tool id|.pro
+       make
 
 .. note::
 
    #. qmake is an application installed with Qt. To be able to run the command as known, the path to the Qt bin folder needs to be added to your **PATH** environment variable. Alternatively, you need to specify the full path to qmake, i.e., on my desktop (if I had not set my PATH variable), I would replace line 3 with the following:
+
+       .. parsed-literal::
 
-      .. code:: console
-
-        /Users/fmckenna/Qt/5.15.2/clang_64/bin/qmake ../|short tool id|.pro
+           /Users/fmckenna/Qt/5.15.2/clang_64/bin/qmake ../|short tool id|.pro
 
    #. On Windows 10 and later with Visual Studio, the above commands need to be performed using a `Visual Studio x64 command prompt <https://docs.microsoft.com/en-us/cpp/build/how-to-enable-a-64-bit-visual-cpp-toolset-on-the-command-line?view=msvc-160>`_.
 

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

@@ -10,7 +10,7 @@ How To Cite
 
 .. only:: PBE_app
 
-   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>`_
+   1. Adam Zsarnoczay, Frank McKenna, Michael Gardner, Michael Gardner, Charles Wang, Sang-ri Yi, Aakash Bangalore Satish, Amin Pakzad, & Wael Elhaddad. (2024). NHERI-SimCenter/PBE: Version 4.1.0 (v4.1.0). Zenodo. `DOI: https://doi.org/10.5281/zenodo.13865401 <https://doi.org/10.5281/zenodo.13865401>`_
 
 .. only:: EEUQ_app
 

docs/_sources/common/technical_manual/desktop/technical_manual.rst.txt

@@ -16,7 +16,6 @@
    :WEUQ:WEUQ/dataInformedStochasticWind
 
    :EEUQ:spatial_correlation
-   :PBE:spatial_correlation
    :R2D:HazardSimulationTool_useCase
    :R2D:spatial_correlation
    :R2D:hazard_occurrence

docs/_sources/common/user_manual/installation/desktop/install_macOS.rst.txt

@@ -228,11 +228,11 @@ Once the application starts, verify the setup by running an example problem |tes
    .. _figUI-PBE:
 
    .. figure:: figures/PBE_startup.png
-	:align: center
-        :figclass: align-center
-        :width: 75%
+      :align: center
+      :figclass: align-center
+      :width: 75%
 
-    PBE application on startup.
+      PBE application on startup.
 
 .. only:: EEUQ_app
 

docs/_sources/common/user_manual/releases/pbeCapabilities.rst.txt

@@ -5,7 +5,7 @@
 Capabilities
 ************
 
-The following functionality is available in **version 3.4** of the |app| that was released on **March 31, 2024**.
+The following functionality is available in **version 4.1** of the |app| that was released on **September 30, 2024**.
 
 Structural Response
 ===================

docs/_sources/common/user_manual/releases/pbePlans.rst.txt

@@ -7,21 +7,19 @@ Release Plans
 *************
 
 The following features are planned to be developed for upcoming releases of |app|. We are actively working on the features in the next release. Farther development priorities may change depending on feedback from the community. If you have any suggestions, we encourage you to contribute and contact us through the SimCenter Forum.
-
-Sept 2024
----------
-    #. Facilitate wind damage and loss calculations by adding relevant vulnerability and loss components. The building-level components from the Hazus Hurricane Methodology will be complemented by components from recent research that supports higher resolution analyses. (1.3.5.1)
-
-   #. Integrate additional functional recovery simulation engines, including the ATC 138 methodology and TREADS. This will enable benchmarking and further development of these methods
-
-   #. Automatic access to physics-based ground motion simulation results (1.1.1.3)
-
 
 Dec 2024
 --------
 
+   #. Facilitate wind damage and loss calculations by adding relevant vulnerability and loss components. The building-level components from the Hazus Hurricane Methodology will be complemented by components from recent research that supports higher resolution analyses. (1.3.5.1)
+
    #. Facilitate water damage and loss calculation by adding relevant vulnerability and loss components. The building-level components from the Hazus Flood Methodology will be complemented by components from recent research that supports higher resolution analyses (1.3.5.2)
 
+March 2025
+----------
+
+   #. Integrate additional functional recovery simulation engines, including the ATC 138 methodology and TREADS. This will enable benchmarking and further development of these methods.
+
  .. note::
 
     The numbers in parentheses are for internal tracking purposes.

docs/_sources/common/user_manual/releases/pbeReleaseNotes.rst.txt

@@ -5,20 +5,44 @@
 Release Notes
 *************
 
-Version 3
+Version 4
 =========
 
-   .. dropdown::    Version 3.5 (:blue:`Current`)
+   .. dropdown::    Version 4.1 (:blue:`Current`)
       :open:
 
+      **Release date:** September 2024
+
+      **Major updates:**
+
+      - Domain Reduction Method option added in tools to create events for buildings given large physics- based simulations.
+
+      - ShakerMaker option added to tool to perform earthquake rupture simulations.
+
+      - OpenSees@DesignSafe option added in tools to allow users to run OpenSees, OpenSeesMP, OpenSeesSP, and OpenSeesPy simulations utilizing TACC HPC resources from their desktop.      
+
+   .. dropdown::    Version 4.0
+
+      **Release date:** August 2024
+
+      **Major updates:**
+
+      - A needed release for changes required to interact with DesignSafe and new TapisV3 interface.
+
+      - Due to AI generated spam on message board, users now directed to post questions using github discussions.
+
+Version 3
+=========
+
+   .. dropdown::    Version 3.5
+
       **Release date:** June 2024
 
       **Major updates:**
 
       - Ability to include different events in multi-model and multi-fidelity simulations
 
    .. dropdown::    Version 3.4
-      :open:
 
       **Release date:** March 2024
 
@@ -63,7 +87,6 @@ Version 3
               - A lot of minor bugs fixed and robustness of the Pelicun engine ensured by bringing back continuous integration.
 
    .. dropdown::    Version 3.3 
-      :open:
 
       **Release date:** Jan 2024
 

docs/_sources/common/user_manual/usage/desktop/OpenSeesTool.rst.txt

@@ -0,0 +1,61 @@
+.. _OpenSeesTool:
+
+OpenSees@DesignSafe Tool
+------------------------
+
+This tool allows users to submit **OpenSees**, **OpenSeesSP**, **OpenSeesMP**, and **OpenSeesPy** scripts to 
+** `TACC <https://tacc.utexas.edu/>`_ ** to be run on some of the most powerful HPC computers in the
+world. The only requirement for users is that they have a ** `DesignSafe <https://www.designsafe-ci.org/>`_ **
+account and an allocation at TACC, which can be obtained by `submitting a ticket to 
+DesignSafe <https://www.designsafe-ci.org/help/new-ticket/>`_ requesting HPC access
+to ** `Frontera <https://tacc.utexas.edu/systems/frontera/>`_ ** and ** `Stampede3 <https://tacc.utexas.edu/systems/stampede3/>`_ **.
+
+As shown in the figure below, the user provides a memorable job name, the input script to run, the application 
+to use, and its version. When the user selects the **Run at DesignSafe** button, additional inputs are
+requested, such as the number of nodes, the number of processors per node, the maximum runtime in minutes, and the allocation to use.
+
+.. figure:: ../figures/OpenSeesTool.png
+   :align: center
+   :figclass: align-center
+
+   OpenSees@DesignSafe Tool
+
+After pressing the **Submit** button, the tool will zip the folder containing the script and, using Tapis,
+create a folder in your DesignSafe DataDepot account. The zipped file will be sent to this folder, and a
+**simcenter-opensees** job will be submitted to run with this folder and the selected application. Once the
+job is complete, the contents of the folder, now containing output files, will be zipped again and stored in
+DesignSafe for you.
+
+To check the status of the submitted job and download the final folder, click the **Get from DesignSafe**
+button. A table will appear, showing the status of all submitted jobs. By right-clicking on any job in the
+table, a menu will appear with the option to **Retrieve Data**. If this option is selected, the zipped
+folder will be retrieved, unzipped, and the contents will be placed in the currently specified
+**Output Folder**.
+
+.. caution::
+
+   Gotcha's to running OpenSees scripts at DesignSafe
+      Given how this application runs, or any DesignSafe OpenSees offering, the script you run can only reference files in it's current directory or directories below the current. Nor can the script save files outside of these locations. 
+
+.. note::
+
+   ** 1. Which version of OpenSeesPy is run? **
+
+   The version run depends on your setup on the TACC HPC machine. All the tool does is run **python3** in your working environment. What is run as a consequence is the first python3 application found on your path.
+
+   ** 2. Why run OpenSees Jobs utilzing this application at DesignSafe? **
+
+      1. DesignSafe is providing access to some of the fastest HPC computers in the world, you can run for example OpenSeesMP jobs that utilize thousands of processors.
+
+      2. You can be running multiple jobs at the same time, though here is a limit to how many you can have runing at once!
+
+      3. The resulting folder containing your scripts is stored at DesignSafe. You can get that data. assuming you gave them a memorable job name, for jobs that ran today, yesterday, last week, last month, last year, ...
+
+
+   ** 3. Why this tool and not submit through DesignSafe Workspace OpenSees offerings? **
+
+      It's simply the quickest way of getting the files to DesignSafe and submitting the job!
+
+
+
+

docs/_sources/index.rst.txt

@@ -129,6 +129,8 @@
    :WEUQ:common/user_manual/usage/desktop/wind/tools
    :Hydro:common/user_manual/usage/desktop/hydro/tools
    :EEUQ:common/user_manual/usage/desktop/earthquake/tools
+   :PBE:common/user_manual/usage/desktop/PBE/tools
+   :quoFEM:common/user_manual/usage/desktop/quoFEM/tools      
 
    :EEUQ:common/user_manual/examples/desktop/examples
    :WEUQ:common/user_manual/examples/desktop/examples

docs/common/developer_manual/how_to_build/desktop/how_to_build.html

@@ -387,31 +387,27 @@ <h3><span class="section-number">1.3.2. </span>Build from the Terminal<a class="
 <p>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 <strong>qmake</strong>, and finally make (or on Windows, nmake) to create the application.</p>
 <p>Windows developers will type the following in a terminal or a PowerShell window:</p>
 <blockquote>
-<div><div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">mkdir build</span>
-<span class="go">cd build</span>
-<span class="go">conan install .. --build missing</span>
-<span class="go">qmake ../|short tool id|.pro</span>
-<span class="go">nmake</span>
-</pre></div>
-</div>
+<div><pre class="literal-block">mkdir build
+cd build
+conan install .. --build missing
+qmake ../R2D.pro
+nmake</pre>
 </div></blockquote>
 <p>Linux or Mac users will type the following in a terminal window from inside the R2D app directory:</p>
 <blockquote>
-<div><div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">mkdir build</span>
-<span class="go">cd build</span>
-<span class="go">conan install .. --build missing</span>
-<span class="go">qmake ../|short tool id|.pro</span>
-<span class="go">make</span>
-</pre></div>
-</div>
+<div><pre class="literal-block">mkdir build
+cd build
+conan install .. --build missing
+qmake ../R2D.pro
+make</pre>
 </div></blockquote>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
 <ol class="arabic">
 <li><p>qmake is an application installed with Qt. To be able to run the command as known, the path to the Qt bin folder needs to be added to your <strong>PATH</strong> environment variable. Alternatively, you need to specify the full path to qmake, i.e., on my desktop (if I had not set my PATH variable), I would replace line 3 with the following:</p>
-<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="go">/Users/fmckenna/Qt/5.15.2/clang_64/bin/qmake ../|short tool id|.pro</span>
-</pre></div>
-</div>
+<blockquote>
+<div><pre class="literal-block">/Users/fmckenna/Qt/5.15.2/clang_64/bin/qmake ../R2D.pro</pre>
+</div></blockquote>
 </li>
 <li><p>On Windows 10 and later with Visual Studio, the above commands need to be performed using a <a class="reference external" href="https://docs.microsoft.com/en-us/cpp/build/how-to-enable-a-64-bit-visual-cpp-toolset-on-the-command-line?view=msvc-160">Visual Studio x64 command prompt</a>.</p></li>
 <li><p>If installed, jom can also be used to build in parallel.</p></li>

docs/common/user_manual/releases/pbeCapabilities.html

@@ -215,7 +215,7 @@
 
   <div class="section" id="capabilities">
 <span id="lbl-capabilities-pbe"></span><h1>Capabilities<a class="headerlink" href="#capabilities" title="Permalink to this heading">¶</a></h1>
-<p>The following functionality is available in <strong>version 3.4</strong> of the R2D app that was released on <strong>March 31, 2024</strong>.</p>
+<p>The following functionality is available in <strong>version 4.1</strong> of the R2D app that was released on <strong>September 30, 2024</strong>.</p>
 <div class="section" id="structural-response">
 <h2>Structural Response<a class="headerlink" href="#structural-response" title="Permalink to this heading">¶</a></h2>
 <p>Obtain a set of response quantities that can characterize the demands acting on the structure under the natural hazard event.</p>

docs/common/user_manual/releases/pbePlans.html

@@ -216,26 +216,21 @@
   <div class="section" id="release-plans">
 <span id="lbl-future-pbe"></span><h1>Release Plans<a class="headerlink" href="#release-plans" title="Permalink to this heading">¶</a></h1>
 <p>The following features are planned to be developed for upcoming releases of R2D app. We are actively working on the features in the next release. Farther development priorities may change depending on feedback from the community. If you have any suggestions, we encourage you to contribute and contact us through the SimCenter Forum.</p>
-<div class="section" id="sept-2024">
-<h2>Sept 2024<a class="headerlink" href="#sept-2024" title="Permalink to this heading">¶</a></h2>
+<div class="section" id="dec-2024">
+<h2>Dec 2024<a class="headerlink" href="#dec-2024" title="Permalink to this heading">¶</a></h2>
 <blockquote>
-<div><blockquote>
 <div><ol class="arabic simple">
 <li><p>Facilitate wind damage and loss calculations by adding relevant vulnerability and loss components. The building-level components from the Hazus Hurricane Methodology will be complemented by components from recent research that supports higher resolution analyses. (1.3.5.1)</p></li>
-</ol>
-</div></blockquote>
-<ol class="arabic simple">
-<li><p>Integrate additional functional recovery simulation engines, including the ATC 138 methodology and TREADS. This will enable benchmarking and further development of these methods</p></li>
-<li><p>Automatic access to physics-based ground motion simulation results (1.1.1.3)</p></li>
+<li><p>Facilitate water damage and loss calculation by adding relevant vulnerability and loss components. The building-level components from the Hazus Flood Methodology will be complemented by components from recent research that supports higher resolution analyses (1.3.5.2)</p></li>
 </ol>
 </div></blockquote>
 </div>
-<div class="section" id="dec-2024">
-<h2>Dec 2024<a class="headerlink" href="#dec-2024" title="Permalink to this heading">¶</a></h2>
+<div class="section" id="march-2025">
+<h2>March 2025<a class="headerlink" href="#march-2025" title="Permalink to this heading">¶</a></h2>
 <blockquote>
 <div><blockquote>
 <div><ol class="arabic simple">
-<li><p>Facilitate water damage and loss calculation by adding relevant vulnerability and loss components. The building-level components from the Hazus Flood Methodology will be complemented by components from recent research that supports higher resolution analyses (1.3.5.2)</p></li>
+<li><p>Integrate additional functional recovery simulation engines, including the ATC 138 methodology and TREADS. This will enable benchmarking and further development of these methods.</p></li>
 </ol>
 </div></blockquote>
 <div class="admonition note">