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_sources/case_0.rst.txt

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+
+.. _case_0:
+
+.. figure:: ./images/case0-1.png
+    :scale: 50 %
+    :height: 200 px
+    :align: center
+    :figclass: align-center
+
+
+Course Introduction
+===================
+
+CESG599 - NHERI - An introduction to NHERI Simcenter tools and DesignSafe Resources
+-----------------------------------------------------------------------------------
+
+Authors:
+--------
+**Kendra Mutch, Erick Martinez, Jose Barreto, Chungen Tai, Morgan Sanger, Luis Guerrero, Daniel Acosta, and Pedro Arduino**
+
+Course Description
+------------------
+In this course, we explore the fundamentals of SimCenter tools and the DesignSafe infrastructure.
+The course adopts a self-directed approach, where students follow a well-established framework tailored 
+for this format. Over the course of 10 weeks, we investigate the core concepts of SimCenter and DesignSafe, 
+and examine four to five SimCenter tools, covering one every two weeks. Students are tasked with mastering 
+the essentials of each tool and delivering presentations to the class. Additionally, they work through one 
+or more practical examples for each tool, presenting their findings to their peers. Constructive feedback for 
+each tool presentation is an integral part of the learning experience. DesignSafe and SimCenter personnel are 
+invited to give Zoom presentations based on availability. At the end of the course, a small final project, 
+with a topic of choice for each student or group of students, is required, providing an opportunity for 
+deeper exploration and application of the learned concepts.
+
+
+SimCenter provides next-generation computational modeling and simulation software tools, user support, 
+and educational materials to the natural hazards engineering research community with the goal of advancing 
+the user’s capability to simulate the impact of natural hazards on structures, lifelines, and communities.
+
+DesignSafe is a comprehensive cyberinfrastructure that provides cloud-based tools to manage, analyze, understand, 
+and publish critical data for research to understand the impacts of natural hazards. The capabilities within 
+the DesignSafe infrastructure are available at no-cost to all researchers working in natural hazards.
+
+
+Learning Objectives
+-------------------
+
+#. Develop a familiarity with Simcenter tools and DesignSafe cyberinfrastructure
+#. Develop a familiarity with the breath of SimCenter tools.
+#. Develop a suitable background for using HPC resources.
+#. Introduce/revise concepts related to structural and geotechnical engineering including UQ concepts, FEM, PB, etc.
+#. Provide a working knowledge for selecting, using, and interpreting tools for Structural and geotechnical design and analysis.
+#. Introduce markup language to develop easy-to-read, easy-to-write documents in the sphinx python package.
+
+
+Introduction
+------------
+This section should provide a brief executive summary, giving an overview of the project. It should be written last to ensure it accurately reflects the content of the entire report. Aim for a short paragraph that highlights the key points, objectives, and outcomes of the project.
+
+
+Problem Description
+-------------------
+Clearly describe the problem being addressed. Use text and images to illustrate the issue, ensuring that even readers unfamiliar with the topic can understand the context and significance. This section should detail the background, relevance, and any previous attempts to solve the problem.
+
+
+Solution Strategy
+-----------------
+Outline the strategy used to solve the problem. This should include a detailed explanation of the methods, processes, and any equations or theoretical frameworks involved. Be sure to make this section as comprehensive as necessary to fully explain the approach taken.
+
+SimCenter Tool Used
+-------------------
+Provide a brief description of the SimCenter tool(s) used in the project. Explain its relevance and how it was applied. This section should be informative yet concise, offering enough detail to understand the tool's role and capabilities without overwhelming the reader.
+
+Example of Application
+----------------------
+Give a concrete example of how the solution strategy was applied, using text and images. This helps to illustrate the practical application of the theoretical concepts and methods discussed earlier. Ensure the example is detailed enough to show the effectiveness of the solution.
+
+Remarks
+-------
+Use this section for any additional comments or observations that do not fit into the other sections. This could include limitations, unexpected findings, future directions, or any acknowledgments.
+
+
+EXAMPLELS of LISTS, FIGURES, TABLE, REFERENCE, etc
+--------------------------------------------------
+
+#. Open the Dr. Layer program. By default we get twelve layers. The top six layers are hardwired into the system with a velocity of specified as very fast. The bottom six layers are hardwired with a velocity of very slow.
+
+#. Select all the layers to all have very slow values using the select all option.
+
+#. On the top left hand corner of the menu box choose the plot box tool and apply a plot box at the top of the layers. Do the same at four arbitrary points along the soil layers. Note the height (:math:`H`) you place the plots.
+
+    <insert image>
+
+#. Push the time increment button for about 1 minute.
+
+#. Obtain the angular frequency :math:`(2p/T)`, where :math:`T` is the period i.e. time it takes to complete one revolution.
+
+#. Obtain the maximum displacements from the plots by clicking on the crest of the curves with your cursor.
+
+.. math::
+    TF = \frac{1}{\cos(\frac{wH}{v_s})}
+
+    AF = \frac{1}{|\cos(\frac{wH}{v_s})|}
+
+
+Where
+
+:math:`w` = Angular frequency (2pf)
+
+:math:`H` = distance between any two points in the layers under consideration.
+
+:math:`V` = Velocity of wave travel within the soil layer.
+
+:math:`TF` = Transfer function
+
+:math:`AF` = Amplification function
+
+
+Dr. Layer's operation is controlled via menu commands (with associated keyboard accelerators), manipulation tools, scaling buttons, the load tool bar, and time control buttons. The program displays the results of its calculations visually in the form of animated displacements, and also in the form of dynamically generated time history plots. There are also mechanisms for getting numerical values.
+
+.. figure:: ./images/case1.png
+    :scale: 30 %
+    :align: center
+    :figclass: align-center
+
+
+SimCenter Tool Used
+-------------------
+
+blablabla
+
+.. list-table:: Title
+   :widths: 25 25 50
+   :header-rows: 1
+
+   * - Heading row 1, column 1
+     - Heading row 1, column 2
+     - Heading row 1, column 3
+   * - Row 1, column 1
+     -
+     - Row 1, column 3
+   * - Row 2, column 1
+     - Row 2, column 2
+     - Row 2, column 3
+
+Time can be controlled using either the keyboard or the time control buttons:
+
+* To run time **forward**: Press and hold the 'g' key or click and hold the time forward button: <insert icon>.
+
+* To reset time to **zero**: Type the '0' key or click on the time reset button: <insert icon>.
+
+* The current analysis time is **displayed** in the feedback pane at the bottom of the screen.
+
+* The analysis time step size can be controlled via the Time Step menu (there are combinations of material properties and time steps that intentionally lead to unstable results, so beware).
+
+* The display time step can be controlled via the Animation Speed menu. Internally, this command controls how many analysis time steps are computed between screen updates.
+
+
+Example Application
+-------------------
+
+Dr. Layer's tool palette is illustrated below (Windows version: the Mac version is similar but grouped a bit differently):
+
+<insert tool palette image>
+
+* The **Arrow Tool** is used to select and manipulate objects.
+
+* The **Panner** and **Camera Orbit Tools** are used to change the viewing point and camera orientation via clicking and dragging.
+
+* The **Plot Box Tool** is used to create one of the various types of plot boxes: 
+
+    * **Displacement Time History plots** are created by clicking on the relevant layer. The top node in the layer is used as the plotting target.
+
+    * **Fast Fourier Transform (FFT) plots** of a displacement history can be created by clicking on the time history plot.
+
+    * **Stress-strain plots** can be created by control-clicking (i.e., holding down the control key while clicking) on the desired layer.
+
+
+ These controls are self-explanatory in regards to their functions. Note the following, however:
+
+.. note::
+    The scaling buttons will continue to scale as long as they are held down. It is not necessary to click multiple times to get this effect.
+
+
+Remarks
+-------
+
+* To adjust the **plotting scales**, use the small expansion/contraction triangular buttons on the plot for the horizontal scale, and the plot scale buttons on the `Scale Button Toolbar <#scaling-buttons>`_ for the vertical scale. 
+
+.. note::
+    You will notice that all plots scale together. This is so that plots of a given type can be compared visually without any misleading differences in scale factors.
+
+* To adjust the **horizontal offset** of a plot, click in the plot and drag horizontally to scroll back and forth.
+
+.. note::
+    In general, plots will automatically scroll as necessary as time is running. Once you have manually scrolled a plot, though, the automatic scrolling will cease until time is reset to zero.
+
+* Plot boxes can be added or removed at any time, but they only accumulate data beginning from the time they are installed, with the exception of FFT plots, which always plot the according to the data accumulated in the target time history. FFT plots can use up to the first 1024 points in a time history.
+
+
+.. warning:: 
+    Plotting FFT's will slow down the animation speed significantly, especially as the length of the time histories increase.
+
+
+.. bibliography:: references.bib

_sources/case_1.rst.txt

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+.. _case_1:
+
+quoFEM - Settlements
+================================
+
+Author: Kendra Mutch
+---------------------
+
+Introduction
+------------
+
+This page describes basic concepts of computing settlement computations in QuoFEM. The calculation methods discussed include forward propagation, deterministic and Bayesian calibration, and sensitivity analysis. For more details, the user is encounged to read :cite:`Holtz and Kovacs 2011'
+
+Project Description
+-------------------
+
+The goal of this project is to quantify settlement, parameters impacting settlement, and observe how uncertainty in various input parameters impact the ultimate settlement of a cohesive soil. These copmutations make use of the program QuoFEM. The following report discusses the features of the program, theory regarding the settlement and uncertainty concepts discussed above, as well as three example problems applying different features of QuoFEM.
+
+The first example makes use of the Forward Propagation feature of QuoFEM, which allows one to apply uncertainty to input parameters (such as preconsolidation pressure, compression and recommpression index, void ratio, unit weight, etc.) to determine which paramter(s) impact the ultimate settlement most. In-situ testing, lab testing, and various models used to determine soil paramters may all contain uncertainty. Thus, it is important to consider uncertainty in geotechnical calculations, such as settlement, and not accept a single predicted value without accounting for uncertainty as completely true to reality. The forward propagation analysis will help us translate uncertainty in soil parameters to uncertainty in ultimate settlement, reducing chances of highly underpredicting or overpredicting settlement.
+
+In the second example, Bayesian and Deterministic Calibration are used to optimize the value of an input parameter to yield a desired settlement. In other words, given a specific value of ultimate settlement, we can calculate the value of an unknown input paramter.
+
+The final example applies the Sensitivity Analysis feature of QuoFEM to determine which input parameters impact the resulting ultimate settlement most. As the discussion of results will reveal, settlement shows a strong correlation with some soil parameters, and a weaker correlation with other paramters. By knowing which parameters settlement is most dependent on, one can allocate funds in site investigation or lab testing to use the most accurate methods for predicting such parameters. Or, one may simply be cautious that potential uncertainty in such parameters, especially compounded uncertainty of multiple parameters, could lead to high uncertainty in the predicted settlement, and perhaps a more conservative design should be implemented. 
+
+All examples will use a python input script, paired with the Dakota uncertainty quantification tool in QuoFEM. These aspects of the project are discussed in further detail throughout the report.
+
+The soil profile and problem scenario are the same for all three examples and are depicted in the image and table below.
+
+.. figure:: ./images/ProblemScenarioP1.png
+
+.. list-table:: Soil Profile Parameters
+   :widths: 25 25 50
+   :header-rows: 1
+
+   * - Parameter
+     - Mean Value
+     - Coefficient of Variation (%)
+   * - h1
+     - 3 ft
+     - 5
+   * - h2
+     - 25 ft
+     - 5
+   * - Cc
+     - 0.75
+     - 20
+   * - eo
+     - 1.54
+     - 7
+   * - Cr
+     - 0.05
+     - 20
+   * - change in pressure
+     - 200 psf
+     - 50
+   * - k
+     - 10E-6 (cm/sec)
+     - 200
+   * - unit weight of fill
+     - 130 pcf
+     - 7
+   * - height of fill
+     - 5 ft
+     - 2
+     
+
+Example One Solution Strategy - Forward Propagation
+---------------------------------------------------
+
+#. Open the QuoFEM. By default, the UQ method is Forward Propagation and the UQ Engine is Dakota. In this example, we will use these defaults. Specify a sample number of 200 and a seed number of 949. Ensure the **Parellel Execution** and the **Save Working dirs** boxes are checked.
+
+#. Select the FEM tab. From the drop down menu, select Python. Navigate to the location of the **Input Script** and the **Parameters Script**.
+
+#. Select the RV tab. Enter the random variables (listed in the table in the problem description). Selelct a normal distribution for each random variable, and enter the mean and standard deviation. Remember, the standard deviation must be calculated for each variable from the given coefficient of variation. The below formula may be used to convert coefficient of variation to the standard deviation.
+   
+#. In the EDP tab, specify the variable of interest as **Settlement** and assign it a **Length** of **1**.
+
+#. Run the example either on your machine or in the cloud. For running in the cloud, see the **SimCenter Tool Used** section for additional details.
+
+
+Example Two Solution Strategy - Bayesian and Deterministic Calibration
+----------------------------------------------------------------------
+
+#. Open QuoFEM. Change the UQ method to Bayesain Callibration and keep the default UQ Engine as Dakota.
+
+
+Example Three Solution Strategy - Sensitivity Analysis
+------------------------------------------------------
+#. In the UQ tab, select **Sensitivity Analysis** as the UQ Method. From the UQ Engine drop down, select **SimCenterUQ**. In the Method drop down, select **Monte Carlo**. For the # of samples, enter 500, and for the seed number, enter 106.
+
+#. Select the FEM tab. From the FEM drop down, select **Python**. Locate the file path for the Input Script and the Paramters Script.
+
+#. In the RDV tab, enter the same random variables as the Forward Propagation example.
+
+#. In the EDP tab, use the same inputs as the Forward Propagation example.
+
+#. Choose to run the example either on your machine in the cloud. For running in the cloud, see the **SimCenter Tool Used** section for additional details.
+
+SimCenter Tool Used
+-------------------
+QouFEM allows the integration of finite element and hazard compuatations with uncertainty quantification tools. There are five different tabs in QuoFEM; four input tabs and one results tab. The four input tabs are outlined below:
+
+    * **UQ tab** - The UQ tab allows one to select the analysis method (Forward Propagation, Bayesian 
+      Callibration, Sensitivity Analysis, etc.). Additionally, one can specify a statistics model and the number 
+      of samples to run.
+
+    * **FEM tab** - The FEM is where a python script is input, and a finite element method (such as Openseas) may 
+      be selected. 
+
+    * **RV tab** - The RV tab allows you define random variables and apply desired uncertainty and statistical 
+      models (normal distribution, uniform distribution etc.) to each variable.
+      
+    * **EDP tab** - The EDP tab allows one to define quantities of interest. For example, the ultimate settlement.
+
+After entering the inputs for your project, you may choose run the project on your machine by simply clicking **Run** or you may run the project in the cloud by selecting **Run at Design Safe**. If you choose to run your project in the cloud, you must login to you Design Safe account and specify a maximum run time. To ensure that your project does not expire while waiting in the que,, select a run time of at least 10 hours.
+
+The results tab contains both a "Summary" page and a "Data Values" page. The "Summary" page contains a brief 
+outline of the values computed. The "Data Values" page contains a more comprehensive set of results and figures.
+
+
+Example Application
+-------------------
+There are various features within the "Data Values" page of the Results tab which may aid in analysis. Below is information about navigating the "Data Values" page to extract desired information:
+    
+    * **To View a Scatterplot of a Parameter vs. Run Number** - left click once on any column.
+    
+   * **To View a Cumulative Frequency Distribution for a Variable** - First left click once on the column for the 
+     variable that you want to view a cumulative frequency distribution for. Then right click once on the same 
+     column.
+     
+   * **To View a Histogram for a Variable** - After following the steps to display a cumulative frequency 
+     distribution, left click on the same column once more to display the histogram.
+     
+   * **To View a Scatterplot of One Variable vs. another Variable** - Right click once on one of the variables. 
+     This defines which variable will be on the x-axis. Then, left click once on the variable which you want 
+     plotted on the y-axis.
+   
+   * **To Export the Data Table** - Select the Save Table icon above the data, and choose a location for saving 
+     the table as a .csv file.
+
+
+Remarks
+-------
+
+
+.. bibliography:: references.bib