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/technical_manual/desktop/damping.rst.txt

@@ -1,5 +1,6 @@
 .. _lblDamping:
 
+===============
 Damping Options
 ===============
 
@@ -12,8 +13,13 @@ where :math:`U(t), \dot{U}(t), \ddot{U}(t)` are the vectors of displacements, ve
 
 Energy is dissipated by the structure as it deforms, which is why it comes to rest when the force is removed. The :math:`Fs(U(t))` term captures the **hysteretic** energy dissipated through the nonlinear behavior of the structural members. The :math:`C \dot{U}(t)` term, the **viscous** damping term, attempts to capture energy dissipated through other mechanisms present in the structure, e.g. thermal effects from repeated elastic straining of structural materials, repeated straining of nonstructural elements—partition walls, mechanical equipment, fireproofing, and so on—friction at steel connections, opening and closing of microcracks in concrete, friction between the structure itself and nonstructural elements, and other mechanisms, some of which are even difficult to identify. Damping for such is often quantified in terms of **modal** damping ratios, and are typically of the order of 1% (steel buildings) to 5% (concrete buildings). These values have been obtained from field testing and system identification, albeit they have mostly been obtained from buildings undergoing low levels of vibration.
 
-It is the formulation of the :math:`C` matrix that is of interest here. There are two damping options presented to the user as inputs to the :ref:`FEM <lblFEM>` panel: 1) Rayleigh Damping Options and 2) Modal Damping options. This is a brief overview of the theory behind both.
+It is the formulation of the :math:`C` matrix that is of interest here. There are two damping options presented to the user as inputs to the :ref:`FEM <lblFEM>` panel, this section is a brief overview of the theory behind both.
+
+.. contents:: Table of Contents
+   :local:
+   :backlinks: none
 
+.. _lblRayleighDamping:
 
 Rayleigh Damping
 ----------------
@@ -91,9 +97,10 @@ The coefficients :math:`a_0` and :math:`a_1` are typically determined by specify
    Different approaches are of course possible, e.g. where the user explicitly models damping. These must be specified by the user in the optional analysis script they provide.
 
 
+.. _lblModalDamping:
 
 Modal Damping
----------------
+-------------
 
 In modal damping the eigenvectors :math:`\Phi` of the :math:`N` degree-of-freedom system are used to create the :math:`C` matrix.
 

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

@@ -1,16 +1,13 @@
-****************
-Technical Manual
-****************
-
 
 .. toctree-filt::
-   :maxdepth: 1
+   :maxdepth: 3
 
    uqTechnical
    :EEUQ:SimCenterUQTechnical
    :quoFEM:SimCenterUQTechnical
    :quoFEM:UCSDUQTechnical
-
+
+   :Hydro:damping
    :EEUQ:damping
    :WEUQ:damping
    :PBE:damping
@@ -23,7 +20,10 @@ Technical Manual
    :R2D:HazardSimulationTool_useCase
    :R2D:spatial_correlation
    :R2D:hazard_occurrence
-
-..   :WEUQ:WEUQ/computationalWindLoadEvaluation
 
-   
+   :Hydro:hydro/hazards/water
+   :Hydro:hydro/swsolver/swsolver
+   :Hydro:hydro/cfdsolver/cfdsolver
+   :Hydro:hydro/fvm/fvm
+   :Hydro:hydro/mpm/mpm
+   :Hydro:hydro/verification/verification

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

@@ -1,5 +1,6 @@
 .. _lbluqTechnical:
 
+==============
 Dakota Methods
 ==============
 

docs/_sources/common/user_manual/bugs.rst.txt

@@ -8,13 +8,35 @@ Bugs & Feature Requests
 If you find bugs, have feature requests, or have questions about how to install or use the application, please post on the |messageBoard|. 
 To avoid duplication, try the `Search` feature before creating a `New Topic`. When creating a `New Topic` to report a bug or new feature request it would be helpful if you could place in the `Subject` area, as shown in :numref:`figBugReport`, an indication of what the post is about:
 
-   #. **BUG**, for bugs, i.e., BUG: Program crashes when starting
-   #. **FEATURE**, for new feature requests, i.e., FEATURE: Incorporate OpenSeesPy
+.. contents:: Table of Contents
+	:local:
+	:depth: 2
+	:backlinks: none
+
+.. _features:
+
+================
+Feature Requests
+================
+
+For new feature requests, give a high-level description in the `Subject`, i.e., FEATURE: Incorporate OpenSeesPy, with added detail in the body.
+
+If you can relate the feature request to a unimplemented requirement in the `Requirements` section of the documentation, that will increase the importance of the feature for our team.
+
+
+.. _lblbugs:
+
+===========
+Bug Reports
+===========
+
+For bug reports, give a high-level description in the `Subject`,  i.e., BUG: Program crashes when starting, with added detail in the body.
 
 .. _figBugReport:
 
 .. figure:: figures/bugReport.png
 	:align: center
 	:figclass: align-center
 
-	Example of submitting a bug report to the message board.
+	Example of submitting a bug report to the message board.
+

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

@@ -19,7 +19,8 @@ The Mac comes with Python pre-installed, which is currently the somewhat
 dated version 2.7. We recommend installing Python 3.7 from `Python.org <https://www.python.org/downloads/mac-osx>`_ . We recommend installing using the 
 **macOS 64-bit installer**. The installer used to place a python3 executable in your /usr/local/bin directory, whose location should be on your system PATH, Version 3.8 does not appear to do so anymore, see the note below. 
 
-.. note:: 
+.. note::
+
    #. We use the python.org installation over others, due to its simplicity of installation.
    #. In the current installation of **Python** it leaves two script files in a folder when the installation ends. You need to execute both script files to get Python set up correctly so that it can be invoked from the terminal. To execute the files, double click on them. The two files, shown in the image below, are **Update Shell Profile.command.sh** and **Install CertificateCommand.sh**.
 
@@ -40,13 +41,14 @@ Once Python is installed, you need to extend it by installing the following pack
       pip3 install hdf5
 
 .. note:: 
+
    #. To start a terminal window you can use the spotlight app (magnifying glass at the top right corner of the desktop). Start the spotlight app and type in the terminal. The terminal application should appear as the top hit. Click on it to start it.
 
    #. When the |app| is running, open the File/Preferences and make sure that python3 appears under **External Applications:Python**. If you used older versions of SimCenter tools this was not the default.
 
    #. If you forget to invoke the **UpdateShellProfile.command.sh" script at the end of the installation, you can always edit the correct shell file later to add the **PATH** variable. 
 
-  #. As an alternative, you can install the SimCenter's pelicun module, which will include all three of the above
+   #. As an alternative, you can install the SimCenter's pelicun module, which will include all three of the above
 
    .. code-block:: python
 
@@ -65,8 +67,9 @@ OpenSees
 |OpenSeesLink| is the default FEM engine used by the |app| that is publicly available from the |OpenSeesDownload| page. To download the **OpenSees** you have to enter your email address, which may also require you to register (that requirement is going away and may be gone by the time you read this). At the bottom of the page under the section **Mac Version** is a table with two links: one for the **OpenSees** and also a link to |Tcl|, whose libraries OpenSees needs on your computer to run. You will need to follow both links to download both applications.
 
 Steps to Install OpenSees on a Mac:
-      1. Follow the OpenSees link and download the OpenSees.zip file. Uncompress the file and you will have an **OpenSees-3.2.2** folder. Move that folder to the **bin/OpenSees** folder. 
-      2. Download and run the Tcl installer.
+
+   1. Follow the OpenSees link and download the OpenSees.zip file. Uncompress the file and you will have an **OpenSees-3.2.2** folder. Move that folder to the **bin/OpenSees** folder. 
+   2. Download and run the Tcl installer.
 
 
 .. note::
@@ -109,6 +112,7 @@ Test the Install of Python, OpenSees & Dakota
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Steps to Test the Installation of the Applications:
+
    1. Open a terminal window (type ``terminal`` in spotlight search)
    2. Type ``python3`` (this should bring up the Python interpreter)
    3. Enter the following to test the installation of the modules and quit the application:

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

@@ -27,7 +27,6 @@ If you have not yet installed Python 3.7, we recommend installing Python 3.7 fro
 **Windowsx86 64-bit executable installer**.  
 
 .. note::
-
    Allow the installer to change your system environment variables so that the directory containing the executable is on your path. This requires checking the small box asking for this when the installer starts. The box is located at the bottom of the installer application window.
 
 .. warning::
@@ -95,6 +94,7 @@ Test the Install of Python, OpenSees & Dakota
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Steps to Test:
+
    1. Open a command window window(type `cmd` in search)
    2. Type `python3` in the application that starts (this should bring up python interpreter)
    3. Enter the following to test the installation of the modules and quit the application:

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

@@ -101,7 +101,7 @@ Navigate to the |appLink| page, which should resemble |figDownload|, for a list
       quoFEM download page.
 
 
-.. only:: Hydro
+.. only:: HydroUQ_app
 
    .. _figDownloadWin-HydroUQ:
 
@@ -179,15 +179,15 @@ Launch the application to view the user interface as shown in |figWinUI|. It's r
 
     quoFEM application on startup.
 
-.. only:: Hydro
+.. only:: HydroUQ_app
 
-    .. _figWinUI-HydroUQ:
+   .. _figWinUI-HydroUQ:
 
    .. figure:: figures/HydroWIN.png
-    :align: center
-    :figclass: align-center
+      :align: center
+      :figclass: align-center
 
-    HydroUQ tool on startup in Windows 10
+      HydroUQ tool on startup in Windows 10
 
 
 
@@ -200,4 +200,4 @@ If the test example fails, refer to :ref:`troubleshooting<lblTroubleshooting>`.
 
    - Avoid setting the local working directory under cloud-synced folders like OneDrive or Box, which may cause file-not-found errors.
    - Avoid including non-alphabetic characters or spaces in the path, which may potentially lead to encoding or file-not-found errors.
-   - Avoid setting the local working directory on a different drive than the app executable (.exe), which may result in permission errors , e.g. the executable is under the C drive, and the working directory is under the E drive.
+   - Avoid setting the local working directory on a different drive than the app executable (.exe), which may result in permission errors , e.g. the executable is under the C drive, and the working directory is under the E drive.

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

@@ -152,7 +152,7 @@ To download the |app|, navigate to the |appLink| page which should resemble |fig
       quoFEM download page.
 
 
-.. only:: Hydro
+.. only:: HydroUQ_app
 
    .. _figDownload:
 
@@ -242,29 +242,28 @@ Once the application starts, verify the setup by running an example problem |tes
            :figclass: align-center
            :width: 75%
 
-
     quoFEM application on startup.
 
 
-.. only:: Hydro
+.. only:: HydroUQ_app
 
    .. _figUI-HydroUQ:
 
    .. figure:: figures/HydroMac.png
-        :align: center
-        :figclass: align-center
-        :width: 75%
-
-    HydroUQ application on startup.
+      :align: center
+      :figclass: align-center
+      :width: 75%
+      
+      HydroUQ application on startup.
 
 .. note::
 
    When the |app| is running, open the app/preferences or File/Preferences and make sure that python3 appears under **External Applications:Python**, as shown in the figure below. If you used older versions of SimCenter tools this was not the default. The exact location of Python3 that you installed can be found by opening the terminal application and executing the **which python3** command. Enter the path shown as a response in the Preferences panel under Python and then press the **Save** button.
 
-      .. figure:: figures/pythonPreferences.png
-           :align: center
-           :figclass: align-center
-           :width: 75%
+   .. figure:: figures/pythonPreferences.png
+      :align: center
+      :figclass: align-center
+      :width: 75%
 
-    Set Python Preferences.
+      Set Python Preferences.