diff --git a/source/.case_0.rst.swp b/source/.case_0.rst.swp new file mode 100644 index 0000000..7037b1a Binary files /dev/null and b/source/.case_0.rst.swp differ diff --git a/source/.case_0.rst.un~ b/source/.case_0.rst.un~ new file mode 100644 index 0000000..8447def Binary files /dev/null and b/source/.case_0.rst.un~ differ diff --git a/source/case_0.rst b/source/case_0.rst index b01e445..b20242a 100644 --- a/source/case_0.rst +++ b/source/case_0.rst @@ -1,18 +1,22 @@ .. _case_0: -.. figure:: ./images/case0.png +.. figure:: ./images/case0-1.png :scale: 50 % + :height: 200 px :align: center :figclass: align-center -CESG599 - NHERI - An introduction to NHERI Simcenter tools and DesignSafe Resources -==================================================================================== +Course Introduction +=================== -Author: Pedro arduino ---------------------- +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 ------------------ @@ -47,23 +51,35 @@ Learning Objectives #. Provide a working knowledge for selecting, using, and interpreting tools for Structural and geotechnical design and analysis. - - - Introduction ------------ - -A transfer function is ... This is just a trial to see if GitHub pages works. +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 ------------------- - -A transfer function is somewhat like a filter that is applied to an incoming wave to produce an output signal. It determines how each frequency in the input motion is amplified or suppressed, by the medium of wave travel. Considering a spring-mass system with an excitation motion at input from the foundation connected to the spring and the corresponding response motion of the connected mass in the inertial system. The response motion of the mass will be a composite factor of the elastic and the viscous damping forces which are inherently embedded in the transfer function that determines the output motion we will obtain. In our wave propagation study we also employ transfer functions as a tool to explain the factors that make our input wave motion different from our output wave obtained. Evaluating the transfer function mathematically involves converting our known input motion to a Fourier series. Each term of the Fourier series is multiplied by the transfer function to obtain the Fourier series of the output response. Resonance is a physical phenomenon that occurs when the natural frequency of vibration of particles in a body (in our case the layers) matches the frequency of the forcing function (our input motion). It is experienced as an infinite amplification of the model. +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. @@ -184,4 +200,4 @@ Remarks Plotting FFT's will slow down the animation speed significantly, especially as the length of the time histories increase. -.. bibliography:: references.bib \ No newline at end of file +.. bibliography:: references.bib diff --git a/source/case_0.rst~ b/source/case_0.rst~ new file mode 100644 index 0000000..02ed6b2 --- /dev/null +++ b/source/case_0.rst~ @@ -0,0 +1,191 @@ + +.. _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. + + + + + +Introduction +------------ + +A transfer function is ... This is just a trial to see if GitHub pages works. + + +Problem Description +------------------- + +A transfer function is somewhat like a filter that is applied to an incoming wave to produce an output signal. It determines how each frequency in the input motion is amplified or suppressed, by the medium of wave travel. Considering a spring-mass system with an excitation motion at input from the foundation connected to the spring and the corresponding response motion of the connected mass in the inertial system. The response motion of the mass will be a composite factor of the elastic and the viscous damping forces which are inherently embedded in the transfer function that determines the output motion we will obtain. In our wave propagation study we also employ transfer functions as a tool to explain the factors that make our input wave motion different from our output wave obtained. Evaluating the transfer function mathematically involves converting our known input motion to a Fourier series. Each term of the Fourier series is multiplied by the transfer function to obtain the Fourier series of the output response. Resonance is a physical phenomenon that occurs when the natural frequency of vibration of particles in a body (in our case the layers) matches the frequency of the forcing function (our input motion). It is experienced as an infinite amplification of the model. + + +Solution Strategy +----------------- + +#. 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. + + + +#. 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: . + +* To reset time to **zero**: Type the '0' key or click on the time reset button: . + +* 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): + + + +* 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 diff --git a/source/images/case0-1.png b/source/images/case0-1.png new file mode 100644 index 0000000..314105d Binary files /dev/null and b/source/images/case0-1.png differ diff --git a/test/.buildinfo b/test/.buildinfo index a117f53..18cece2 100644 --- a/test/.buildinfo +++ b/test/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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For more details, the user is encounged to read :cite:`Kramer1996`. +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. -Author: Pedro arduino ---------------------- Introduction ------------ - -A transfer function is ... This is just a trial to see if GitHub pages works. +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 ------------------- - -A transfer function is somewhat like a filter that is applied to an incoming wave to produce an output signal. It determines how each frequency in the input motion is amplified or suppressed, by the medium of wave travel. Considering a spring-mass system with an excitation motion at input from the foundation connected to the spring and the corresponding response motion of the connected mass in the inertial system. The response motion of the mass will be a composite factor of the elastic and the viscous damping forces which are inherently embedded in the transfer function that determines the output motion we will obtain. In our wave propagation study we also employ transfer functions as a tool to explain the factors that make our input wave motion different from our output wave obtained. Evaluating the transfer function mathematically involves converting our known input motion to a Fourier series. Each term of the Fourier series is multiplied by the transfer function to obtain the Fourier series of the output response. Resonance is a physical phenomenon that occurs when the natural frequency of vibration of particles in a body (in our case the layers) matches the frequency of the forcing function (our input motion). It is experienced as an infinite amplification of the model. +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. @@ -144,4 +200,4 @@ Remarks Plotting FFT's will slow down the animation speed significantly, especially as the length of the time histories increase. -.. bibliography:: references.bib \ No newline at end of file +.. bibliography:: references.bib diff --git a/test/_sources/case_1.rst.txt b/test/_sources/case_1.rst.txt index ded7796..0522d85 100644 --- a/test/_sources/case_1.rst.txt +++ b/test/_sources/case_1.rst.txt @@ -9,134 +9,138 @@ Author: Kendra Mutch Introduction ------------ -This page describes basic concepts of one-dimensional ground response analysis and the usage of transfer functions. For more details, the user is encounged to read :cite:`Kramer1996`. +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' - -Problem Description +Project Description ------------------- -A transfer function is somewhat like a filter that is applied to an incoming wave to produce an output signal. It determines how each frequency in the input motion is amplified or suppressed, by the medium of wave travel. Considering a spring-mass system with an excitation motion at input from the foundation connected to the spring and the corresponding response motion of the connected mass in the inertial system. The response motion of the mass will be a composite factor of the elastic and the viscous damping forces which are inherently embedded in the transfer function that determines the output motion we will obtain. In our wave propagation study we also employ transfer functions as a tool to explain the factors that make our input wave motion different from our output wave obtained. Evaluating the transfer function mathematically involves converting our known input motion to a Fourier series. Each term of the Fourier series is multiplied by the transfer function to obtain the Fourier series of the output response. Resonance is a physical phenomenon that occurs when the natural frequency of vibration of particles in a body (in our case the layers) matches the frequency of the forcing function (our input motion). It is experienced as an infinite amplification of the model. +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. -Solution Strategy ------------------ +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. -#. 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. +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. -#. Select all the layers to all have very slow values using the select all option. +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. -#. 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. +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 -#. Push the time increment button for about 1 minute. +.. list-table:: Soil Profile Parameters + :widths: 25 25 50 + :header-rows: 1 -#. Obtain the angular frequency :math:`(2p/T)`, where :math:`T` is the period i.e. time it takes to complete one revolution. + * - 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 + -#. Obtain the maximum displacements from the plots by clicking on the crest of the curves with your cursor. +Example One Solution Strategy - Forward Propagation +--------------------------------------------------- -.. math:: - TF = \frac{1}{\cos(\frac{wH}{v_s})} +#. 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. - AF = \frac{1}{|\cos(\frac{wH}{v_s})|} +#. 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**. -Where +#. 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. -:math:`w` = Angular frequency (2pf) -:math:`H` = distance between any two points in the layers under consideration. +Example Two Solution Strategy - Bayesian and Deterministic Calibration +---------------------------------------------------------------------- -:math:`V` = Velocity of wave travel within the soil layer. +#. Open QuoFEM. Change the UQ method to Bayesain Callibration and keep the default UQ Engine as Dakota. -:math:`TF` = Transfer function -:math:`AF` = Amplification function +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. -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. +#. In the RDV tab, enter the same random variables as the Forward Propagation example. -.. figure:: ./images/case1.png - :scale: 30 % - :align: center - :figclass: align-center +#. 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: -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 + * **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. -Time can be controlled using either the keyboard or the time control buttons: + * **FEM tab** - The FEM is where a python script is input, and a finite element method (such as Openseas) may + be selected. -* To run time **forward**: Press and hold the 'g' key or click and hold the time forward button: . + * **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. -* To reset time to **zero**: Type the '0' key or click on the time reset button: . +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 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. +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 ------------------- - -Dr. Layer's tool palette is illustrated below (Windows version: the Mac version is similar but grouped a bit differently): - - - -* 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. +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 ------- -* 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 \ No newline at end of file diff --git a/test/_sources/case_2.rst.txt b/test/_sources/case_2.rst.txt index 617107a..588ea25 100644 --- a/test/_sources/case_2.rst.txt +++ b/test/_sources/case_2.rst.txt @@ -1,6 +1,6 @@ .. _case_2: -EEUQ - Transfer Function +EEUQ - Transfer Function and Uncertainty ================================ Author: Erick Martinez @@ -9,132 +9,63 @@ Author: Erick Martinez Introduction ------------ -This page describes basic concepts of one-dimensional ground response analysis and the usage of transfer functions. For more details, the user is encounged to read :cite:`Kramer1996`. +This page describes the basic concept of transfer functions and their use in a site response analysis. Along with this, the uncertainty in this process will be explained. For more details, the user is encouraged to read :cite:`Kramer1996`. Problem Description ------------------- -A transfer function is somewhat like a filter that is applied to an incoming wave to produce an output signal. It determines how each frequency in the input motion is amplified or suppressed, by the medium of wave travel. Considering a spring-mass system with an excitation motion at input from the foundation connected to the spring and the corresponding response motion of the connected mass in the inertial system. The response motion of the mass will be a composite factor of the elastic and the viscous damping forces which are inherently embedded in the transfer function that determines the output motion we will obtain. In our wave propagation study we also employ transfer functions as a tool to explain the factors that make our input wave motion different from our output wave obtained. Evaluating the transfer function mathematically involves converting our known input motion to a Fourier series. Each term of the Fourier series is multiplied by the transfer function to obtain the Fourier series of the output response. Resonance is a physical phenomenon that occurs when the natural frequency of vibration of particles in a body (in our case the layers) matches the frequency of the forcing function (our input motion). It is experienced as an infinite amplification of the model. +A transfer function acts as a filter that can amplify or de-amplify an incoming wave from a medium to produce the output signal in another medium. To simplify the idea of a transfer function, a spring-mass system can be used. As a motion is applied on the mass connected to a spring; a responsive outgoing wave will then be propagated through the mass and the spring. This outgoing motion will be a composite factor of the stiffness and elastic damping forces found within the spring-mass system. + +This can be applied to earth systems in the form of ground motions. An example of this is an earthquake motion acting on a rock layer at a certain depth. This motion is then transferred through the soil profile and is reflected as a different motion at the surface. In order to determine the influence of a soil profile on the motion, three major components are required: thickness of layer (H), shear wave velocity (Vs), and damping ratio. As with any engineering properties, there will always be the presence of uncertainty. A layer might have differential thicknesses in certain regions, causing the height to be non-uniform. Shear wave velocity can change very quickly depending on depth and composition of the materials within the layer. Damping can also be affected by changes in stratigraphy and composition. To account for this, uncertainty must be incorporated into a transfer function analysis. This inclusion will aid in the accuracy and reliability of site response analyses. Solution Strategy ----------------- -#. 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. - - - -#. 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})|} - +In earth systems, this relationship between incoming and outgoing wave can be evaluated through mathematically converting an input motion, typically an acceleration-time history, to a Fourier series. In the Fourier space, the motion is then multiplied by the transfer function, resulting in the outgoing Fourier motion. This can then be converted back into various plots, such as acceleration-time history and spectral acceleration vs. period, that allow for analysis of the outgoing motion. An analysis of this ground motion can provide frequencies of interest where ground accelerations would be highest/lowest, which can aid in site response analysis and planning. -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 + +.. figure:: ./images/TF_Rock_to_Soil1.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: +NEEDS FINISHING -* To run time **forward**: Press and hold the 'g' key or click and hold the time forward button: . -* To reset time to **zero**: Type the '0' key or click on the time reset button: . +SimCenter Tool Used +------------------- -* 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). +To understand transfer functions, there are many tools available. One of these tools is the SimCenter Transfer Function Tool (TFT). This tool introduces users to transfer functions by providing the output motion at a site given the motion, thickness of layers, shear wave velocities, and damping ratio. TFT allows for easy analysis of amplification/de-amplification of ground motions based on specific sites. -* 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. +The Earthquake Engineering with Uncertainty Quantification Application (EE-UQ) is a SimCenter research application that also allows for site response predictions due to earthquake loading. In addition to basic transfer function quantification, it allows for the analysis of uncertainty in the predictions based on the uncertainty found within the input model, motion, etc. This workflow application allows the user to run analyses in the background and provides a simple user interface that facilitates its use. Example Application ------------------- -Dr. Layer's tool palette is illustrated below (Windows version: the Mac version is similar but grouped a bit differently): - - - -* 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. +For our purposes, an earthquake motion will be applied to a rock, located at the bottom of a one-dimensional soil profile. In this example, we will analyze the amplification/deamplification effects of the ground motion caused by its propagation through the soil layer. The 10 meter soil layer has a shear wave velocity (Vs) of 500 m/s and a damping ratio of 3%. -* 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. + +.. figure:: ./images/CESG599_TF_image1.png + :scale: 50 % + :align: center + :figclass: align-center - These controls are self-explanatory in regards to their functions. Note the following, however: +Because of the presence of uncertainty in the soil properties, the transfer function will include uncertainty in its effects. Normal distribution values for each variable (H, Vs, damping) will be provided.This uncertainty will be quantified through multiple runs in EE-UQ and expressed as ratios of mean velocity and acceleration, along with standard deviation and skewness. -.. 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. +NEEDS FINISHING 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. +NEEDS FINISHING .. warning:: diff --git a/test/_sources/case_4.rst.txt b/test/_sources/case_4.rst.txt index 4000076..c6bb240 100644 --- a/test/_sources/case_4.rst.txt +++ b/test/_sources/case_4.rst.txt @@ -4,18 +4,24 @@ S3hark - Site Response 2 ======================= Author: Chungen Tai +(Updated : 05/24/24) ------------------- Introduction ------------ -This page describes basic concepts of one-dimensional ground response analysis and the usage of transfer functions. For more details, the user is encounged to read :cite:`Kramer1996`. +This page shows basic concepts of one-dimensional nonlinear site response analysis by using various soil material models (ex: ElasticIsotropic, PM4Sand.).Site response analysis is commonly performed to analyze the propagation of seismic waves through soil. As shown in the below figure, one-dimensional response analyses, as a simplified method, assume that all boundaries are horizontal and that the response of a soil deposit is predominately caused by SH-waves propagating vertically from the underlying bedrock. Ground surface response is usually the major output from these analyses, together with profile plots such as peak horizontal acceleration along the soil profile. When liquefiable soils are presenting, maximum shear strain and excess pore pressure ratio plots are also important. +.. figure:: ./images/siteResponse2.png + :scale: 60 % + :align: center + :figclass: align-center Problem Description ------------------- -A transfer function is somewhat like a filter that is applied to an incoming wave to produce an output signal. It determines how each frequency in the input motion is amplified or suppressed, by the medium of wave travel. Considering a spring-mass system with an excitation motion at input from the foundation connected to the spring and the corresponding response motion of the connected mass in the inertial system. The response motion of the mass will be a composite factor of the elastic and the viscous damping forces which are inherently embedded in the transfer function that determines the output motion we will obtain. In our wave propagation study we also employ transfer functions as a tool to explain the factors that make our input wave motion different from our output wave obtained. Evaluating the transfer function mathematically involves converting our known input motion to a Fourier series. Each term of the Fourier series is multiplied by the transfer function to obtain the Fourier series of the output response. Resonance is a physical phenomenon that occurs when the natural frequency of vibration of particles in a body (in our case the layers) matches the frequency of the forcing function (our input motion). It is experienced as an infinite amplification of the model. +Treasure Island, situated atop sand fill strata overlaying Bay Mud within the San Francisco Bay, was subjected to seismic activity during the 1989 Loma Prieta Earthquake. Adjacent to Treasure Island lies Yerba Buena Island, characterized by its natural rock outcrop. Utilizing the site's soil profile and seismic data recorded on Yerba Buena Island, we endeavor to analyze the site response of Treasure Island. This entails computing parameters such as peak horizontal acceleration and shear strain distribution along the soil profile. Furthermore, we aim to investigate the influence of varying slope configurations on the site's response characteristics. + Solution Strategy diff --git a/test/_sources/case_5.rst.txt b/test/_sources/case_5.rst.txt index e3acaf2..958b1b4 100644 --- a/test/_sources/case_5.rst.txt +++ b/test/_sources/case_5.rst.txt @@ -15,116 +15,92 @@ This page describes basic concepts of geospatial liquefaction hazard modeling. Problem Description ------------------- -Coseismic soil liquefaction is a phenomenon in which the strength and stiffness of a soil is reduced by earthquake shaking. Resilient communities and infrastructure networks, like lifelines or transportation systems, must be built to withstand and respond to hazards posed by coseismic soil liquefaction. Ideally, these predictions could be made quickly, in near-real-time after an event; at high resolution, consistent with the scale of individual assets; and at map-scale, across the regional extent affected by large earthquakes. Common liquefaction models in practice require in-situ testing which cannot be continuously performed across large areas, thus presenting the need for “geospatial” liquefaction models. Prior tests of such models (e.g., [Zhu2017]) have shown both promising potential and severe shortcomings in predicting subsurface conditions with few geospatial predictors[5]. There is a need to advance geospatial liquefaction modeling, integrating geotechnical data, liquefaction mechanics, artificial intelligence (AI), and many geospatial predictor variables to provide reliable, scalable liquefaction predictions for any earthquake event. +Coseismic soil liquefaction is a phenomenon in which the strength and stiffness of a soil is reduced by earthquake shaking. Resilient communities and infrastructure networks, like lifelines or transportation systems, must be built to withstand and respond to hazards posed by coseismic soil liquefaction. Ideally, these predictions could be made: +* quickly, in near-real-time after an event; -Solution Strategy ------------------ +* at high resolution, consistent with the scale of individual assets; and -#. 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. +* at map-scale, across the regional extent affected by large earthquakes. -#. 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. +Common liquefaction models in practice require in-situ testing which cannot be continuously performed across large areas, thus presenting the need for “geospatial” liquefaction models. Prior tests of such models (e.g., :cite:`Zhu2017`) have shown both promising potential and severe shortcomings in predicting subsurface conditions with few geospatial predictors. There is a need to advance geospatial liquefaction modeling by integrating geotechnical data, liquefaction mechanics, artificial intelligence (AI), and many geospatial predictor variables to provide reliable regional liquefaction predictions for any earthquake event. When integrated with regional hazard assessment capabilities, geospatial liquefcation models will provide value throughout the life of infrastructure projects - from initial desk studies to refined project-specific hazard analyses - and will unlock insights beyond conventional practice, with opportunity to: - +* prescribe event-specific emergency response and evacuation routes immediately after an earthquake, -#. Push the time increment button for about 1 minute. +* evaluate network reliability and infrastructure network resiliency using structural databases or other asset inventories, and -#. Obtain the angular frequency :math:`(2p/T)`, where :math:`T` is the period i.e. time it takes to complete one revolution. +* understand the impacts of earthquake events of vulnerable communities using population demographic data. -#. 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})|} +Solution Strategy +----------------- +The state-of-practice geospatial liquefaction model is the :cite:`RB2020` model (updated version of the :cite:`Zhu2017` model), which uses logistic regression to predict probability of liquefaction based on five (5) geospatial variables and trained on a database of liquefaction case histories. -Where +In this problem, another modeling solution strategy is proposed, according to :cite:`Sanger2024`. The :cite:`Sanger2024` approach parses the problem into that which is empirical and best predicted by AI (the relationship between geospatial variables and subsurface traits) and that which is best predicted by mechanics (liquefaction response, conditioned on those traits). In this approach, the subsurface traits are characterized at point locations using available cone penetration testing (CPT) data. The liquefaction response at each CPT location is computed across a range of magnitude-scale peak ground accelerations (PGAM7.5) using state-of-practice liquefaction manifestation models (e.g., liquefaction potential index, LPI), thereby retaining the knowledge of liquefaction mechanics developed over the last 50+ years. The relationship between manifestation index and PGAM7.5 is represented as a functional form (Eqn 1) with two curve-fitting parameters: A and B (Fig 1). Therefore, the liquefaction response (i.e., A and B) at each CPT location becomes target variables of supervised learning AI models. -:math:`w` = Angular frequency (2pf) +.. math:: + MI = \left\{ \begin{array}{ll} + 0, & \text{PGA}_{M7.5} < 0.1g \\ + \arctan(B \cdot (\text{PGA}_{M7.5} - \frac{A}{B})^2) \cdot 100, & \text{PGA}_{M7.5} \geq 0.1g + \end{array} \right. -:math:`H` = distance between any two points in the layers under consideration. +**Eqn 1.** Manifestation index as a function of A, B, and PGAM7.5. -:math:`V` = Velocity of wave travel within the soil layer. -:math:`TF` = Transfer function +.. figure:: ./images/manifestationcurve.png + :scale: 100 % + :align: center + :figclass: align-center + + **Fig 1.** Example manifestation curve of LPI vs. PGAM7.5 for a single CPT. -:math:`AF` = Amplification function +The AI model is trained to predict liquefaction response from a suite of geospatial predictor variables identified as proxies of liquefaction (37 variables). Example predictor variables include mapped or remotely sensed metrics of surface topography and roughness; distance to and elevation above water bodies; geology, geomorphology, hydrology, and more. By applying the final trained AI model to the full predictor datasets, the A and B parameters are predicted geospatially at a defined resolution. A final, key step of the approach is that AI predictions are geostatistically updated via regression kriging in the vicinity of field measurements, such that nearby predictions are based mostly on known subsurface conditions and have lower model uncertainty, whereas distal predictions are based mostly on AI and have greater model uncertainty. In summary, this approach effectively pre-computes liquefaction response across all possible ground motion intensities and durations based on AI-predicted subsurface conditions. These predictions are stored as mapped parameters, awaiting information about a specific earthquake of interest, real or scenario, such as a PGAM7.5 raster from R2D. +Model predictions were then tested against the leading geospatial model :cite:`RB2020` in three case-history events using receiver operating characteristic and area under the curve analyses (Fig 2). The :cite:`Sanger2024` AI model (before kriging) performed significantly better than :cite:`RB2020` and was further improved by kriging (Fig 3). -.. figure:: ./images/manifestationcurve.png - :scale: 30 % +.. figure:: ./images/sanger2024-roc.png + :scale: 100 % :align: center :figclass: align-center + **Fig 2.** Receiver operator characteristic curves and area under the curve (AUC) analyses comparing :cite:`RB2020` (“R&B”), and the :cite:`Sanger2024` *before* regression kriging (“LPI”). + .. figure:: ./images/zhu2017.png - :scale: 30 % + :scale: 100 % :align: center :figclass: align-center -.. figure:: ./images/sanger2024.png - :scale: 30 % + **(a)** + +.. figure:: ./images/sanger2024-ai.png + :scale: 100 % :align: center :figclass: align-center + **(b)** -SimCenter Tool Used -------------------- - -REGIONAL RESILIENCE DETERMINATION `R2D `_ TOOL - -Example Application -------------------- - -.. 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: . - -* To reset time to **zero**: Type the '0' key or click on the time reset button: . - -* 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. - -Dr. Layer's tool palette is illustrated below (Windows version: the Mac version is similar but grouped a bit differently): - - - -* The **Arrow Tool** is used to select and manipulate objects. +.. figure:: ./images/sanger2024-krig.png + :scale: 100 % + :align: center + :figclass: align-center -* The **Panner** and **Camera Orbit Tools** are used to change the viewing point and camera orientation via clicking and dragging. + **(c)** -* The **Plot Box Tool** is used to create one of the various types of plot boxes: + **Fig 3.** Comparison between **(a)** Rashidian & Baise (2020), and this model **(b)** before and **(c)** after regression kriging for the Feb. 2011 M6.1 Christchurch event. - * **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. +SimCenter Tool Used +------------------- - * **Stress-strain plots** can be created by control-clicking (i.e., holding down the control key while clicking) on the desired layer. +The presented problem can be solved using SimCenter's Regional Resilience Determination `R2D `_ Tool. A substantially complete description of the tool is provided in the `R2D Documentation `_. +The :cite:`Zhu2017` model is implemented in the R2D tool (version 4.2.0), whereas the :cite:`Sanger2024` model is not yet implemented in the R2D tool. In this project, the :cite:`Sanger2024` model was implemented in the R2D tool using Python applications file. - 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. +Example Application +------------------- Remarks @@ -142,7 +118,6 @@ Remarks * 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. diff --git a/test/_sources/case_6.rst.txt b/test/_sources/case_6.rst.txt index 6222ba1..19ae9b3 100644 --- a/test/_sources/case_6.rst.txt +++ b/test/_sources/case_6.rst.txt @@ -3,57 +3,67 @@ R2D - Landslides ================ -Author: Luis Guerrero +Author: Luis Angel Guerrero Hoyos --------------------- Introduction ------------ -This page describes basic concepts of one-dimensional ground response analysis and the usage of transfer functions. For more details, the user is encounged to read :cite:`Kramer1996`. +This page describes a preliminarly approach for landslide risk assesment using SimCenter tools (R2D). Problem Description ------------------- -A transfer function is somewhat like a filter that is applied to an incoming wave to produce an output signal. It determines how each frequency in the input motion is amplified or suppressed, by the medium of wave travel. Considering a spring-mass system with an excitation motion at input from the foundation connected to the spring and the corresponding response motion of the connected mass in the inertial system. The response motion of the mass will be a composite factor of the elastic and the viscous damping forces which are inherently embedded in the transfer function that determines the output motion we will obtain. In our wave propagation study we also employ transfer functions as a tool to explain the factors that make our input wave motion different from our output wave obtained. Evaluating the transfer function mathematically involves converting our known input motion to a Fourier series. Each term of the Fourier series is multiplied by the transfer function to obtain the Fourier series of the output response. Resonance is a physical phenomenon that occurs when the natural frequency of vibration of particles in a body (in our case the layers) matches the frequency of the forcing function (our input motion). It is experienced as an infinite amplification of the model. +Studying landslide assessment using Newmark analysis and ground motions is a multidisciplinary effort that integrates engineering, geology, and environmental science. It provides a comprehensive approach to understanding and mitigating the risks associated with landslides, ultimately leading to safer communities and more resilient infrastructure. Here we would like to analyze in a regional scale, what would be the response across a study area located in Seattle, WA, US. The idea is to estimate the predicted displacement in the study area if an earthquake with certain intensity measure (Arias Intensity :math:`I_a`) were to occur. This study integrates the infinite slope approach to estimate the static factor of safety so then the Critical Acceleration :math:`a_c` can be estimated. Finally with these parameters a Newmark displacement could be estimated using Randall W. Jibson correlation :cite:`Jibson1993`. Solution Strategy ----------------- -#. 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. +Jibson proposed model is used to calculate the Newmark displacement as follows: -#. Select all the layers to all have very slow values using the select all option. +.. math:: + log(Dn) = 1.460\:log(I_a)-6.642\:a_c+1.546\:\:\:\:\:\:\:\:\:\:\:\:\:(1) -#. 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. +Where: - +:math:`Dn` = Newmark Displacement [cm]. -#. Push the time increment button for about 1 minute. +:math:`I_a` = Areas Intensity [m/s]. -#. Obtain the angular frequency :math:`(2p/T)`, where :math:`T` is the period i.e. time it takes to complete one revolution. +:math:`a_c` = Critical Acceleration [g]. -#. Obtain the maximum displacements from the plots by clicking on the crest of the curves with your cursor. +Also, .. math:: - TF = \frac{1}{\cos(\frac{wH}{v_s})} + a_c = (FS_{static}-1)\:sin(\beta)\:\:\:\:\:\:\:\:\:\:\:\:\:(2) + +Where: - AF = \frac{1}{|\cos(\frac{wH}{v_s})|} +.. math:: + FS_{static} = \frac{2c}{\gamma\:z\:sin(\beta)} + cot(\beta)\:tan(\phi)\:\:\:\:\:\:\:\:\:\:\:\:\:(3) +:math:`\beta` = Slope Angle [°]. -Where +:math:`FS_{static}` = Static Factor of Safety [-]. -:math:`w` = Angular frequency (2pf) +:math:`c` = Cohesion [kPa]. -:math:`H` = distance between any two points in the layers under consideration. +:math:`\gamma` = Unit Weight [kN/m³]. -:math:`V` = Velocity of wave travel within the soil layer. +:math:`\phi` = Friction Angle [°]. -:math:`TF` = Transfer function +:math:`I_a` = Intensity measure time-history motion specific. -:math:`AF` = Amplification function +In order to estimate the imput parameters of equation 1 the following steps could be done: +#. Create a slope raster for a selected area: this can be created using a DTM model for the area of interest which can be downloaded from the `USGS portal. `_ +#. Use QGIS built-in functions to perform the slope calculations. See QGIS `slope documentation. `_ + +To be continued... +------------------- 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 @@ -139,4 +149,4 @@ Remarks .. warning:: Plotting FFT's will slow down the animation speed significantly, especially as the length of the time histories increase. -.. bibliography:: references.bib +.. bibliography:: references.bib \ No newline at end of file diff --git a/test/_static/basic.css b/test/_static/basic.css index f316efc..7577acb 100644 --- a/test/_static/basic.css +++ b/test/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -237,10 +237,6 @@ a.headerlink { visibility: hidden; } -a:visited { - color: #551A8B; -} - h1:hover > a.headerlink, h2:hover > a.headerlink, h3:hover > a.headerlink, @@ -674,16 +670,6 @@ dd { margin-left: 30px; } -.sig dd { - margin-top: 0px; - margin-bottom: 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AUTHORS. + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/test/_static/documentation_options.js b/test/_static/documentation_options.js index 89435bb..995f333 100644 --- a/test/_static/documentation_options.js +++ b/test/_static/documentation_options.js @@ -1,4 +1,5 @@ -const DOCUMENTATION_OPTIONS = { +var DOCUMENTATION_OPTIONS = { + URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), VERSION: '1.0.0', LANGUAGE: 'en', COLLAPSE_INDEX: false, diff --git a/test/_static/language_data.js b/test/_static/language_data.js index 367b8ed..250f566 100644 --- a/test/_static/language_data.js +++ b/test/_static/language_data.js @@ -5,7 +5,7 @@ * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -13,7 +13,7 @@ var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; -/* Non-minified version is copied as a separate JS file, if available */ +/* Non-minified version is copied as a separate JS file, is available */ /** * Porter Stemmer diff --git a/test/_static/searchtools.js b/test/_static/searchtools.js index 92da3f8..97d56a7 100644 --- a/test/_static/searchtools.js +++ b/test/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -57,12 +57,12 @@ const _removeChildren = (element) => { const _escapeRegExp = (string) => string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string -const _displayItem = (item, searchTerms, highlightTerms) => { +const _displayItem = (item, searchTerms) => { const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT; const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; const [docName, title, anchor, descr, score, _filename] = item; @@ -75,35 +75,28 @@ const _displayItem = (item, searchTerms, highlightTerms) => { if (dirname.match(/\/index\/$/)) dirname = dirname.substring(0, dirname.length - 6); else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; + requestUrl = docUrlRoot + dirname; linkUrl = requestUrl; } else { // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; + requestUrl = docUrlRoot + docName + docFileSuffix; linkUrl = docName + docLinkSuffix; } let linkEl = listItem.appendChild(document.createElement("a")); linkEl.href = linkUrl + anchor; linkEl.dataset.score = score; linkEl.innerHTML = title; - if (descr) { + if (descr) listItem.appendChild(document.createElement("span")).innerHTML = " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } else if (showSearchSummary) fetch(requestUrl) .then((responseData) => responseData.text()) .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) + Search.makeSearchSummary(data, searchTerms) ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); }); Search.output.appendChild(listItem); }; @@ -116,43 +109,26 @@ const _finishSearch = (resultCount) => { ); else Search.status.innerText = _( - "Search finished, found ${resultCount} page(s) matching the search query." - ).replace('${resultCount}', resultCount); + `Search finished, found ${resultCount} page(s) matching the search query.` + ); }; const _displayNextItem = ( results, resultCount, - searchTerms, - highlightTerms, + searchTerms ) => { // results left, load the summary and display it // this is intended to be dynamic (don't sub resultsCount) if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); + _displayItem(results.pop(), searchTerms); setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + () => _displayNextItem(results, resultCount, searchTerms), 5 ); } // search finished, update title and status message else _finishSearch(resultCount); }; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; /** * Default splitQuery function. Can be overridden in ``sphinx.search`` with a @@ -176,26 +152,13 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString, anchor) => { + htmlToText: (htmlString) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlinks", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - + if (docContent !== undefined) return docContent.textContent; console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." ); return ""; }, @@ -268,7 +231,16 @@ const Search = { else Search.deferQuery(query); }, - _parseQuery: (query) => { + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -304,32 +276,16 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename]. - const normalResults = []; - const nonMainIndexResults = []; - + // array of [docname, title, anchor, descr, score, filename] + let results = []; _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase().trim(); + const queryLower = query.toLowerCase(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { let score = Math.round(100 * queryLower.length / title.length) - normalResults.push([ + results.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", @@ -344,47 +300,46 @@ const Search = { // search for explicit entries in index directives for (const [entry, foundEntries] of Object.entries(indexEntries)) { if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ docNames[file], titles[file], id ? "#" + id : "", null, score, filenames[file], - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } + ]); } } } // lookup as object objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) + results.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); // remove duplicate search results // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept @@ -398,19 +353,14 @@ const Search = { return acc; }, []); - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + results = results.reverse(); // for debugging //Search.lastresults = results.slice(); // a copy // console.info("search results:", Search.lastresults); // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); + _displayNextItem(results, results.length, searchTerms); }, /** @@ -508,18 +458,14 @@ const Search = { // add support for partial matches if (word.length > 2) { const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); } // no match but word was a required one @@ -542,8 +488,9 @@ const Search = { // create the mapping files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); }); }); @@ -594,8 +541,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/test/_static/sphinx_highlight.js b/test/_static/sphinx_highlight.js index 8a96c69..aae669d 100644 --- a/test/_static/sphinx_highlight.js +++ b/test/_static/sphinx_highlight.js @@ -29,19 +29,14 @@ const _highlight = (node, addItems, text, className) => { } span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); parent.insertBefore( span, parent.insertBefore( - rest, + document.createTextNode(val.substr(pos + text.length)), node.nextSibling ) ); node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); if (isInSVG) { const rect = document.createElementNS( @@ -145,10 +140,5 @@ const SphinxHighlight = { }, }; -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); +_ready(SphinxHighlight.highlightSearchWords); +_ready(SphinxHighlight.initEscapeListener); diff --git a/test/case_0.html b/test/case_0.html index 0ea656d..56524e7 100644 --- a/test/case_0.html +++ b/test/case_0.html @@ -1,24 +1,20 @@ - + - + - Introduction — CESG-599 1.0.0 documentation - - - - - + Course Introduction — CESG-599 1.0.0 documentation + + + - - - - - + + + @@ -49,18 +45,25 @@