From de34825f4e6413723b1fcbc07b002e972deac4b5 Mon Sep 17 00:00:00 2001 From: Pedro Arduino Date: Tue, 11 Jun 2024 12:07:07 -0700 Subject: [PATCH] adding reference rst --- source/.case_1.rst.un~ | Bin 0 -> 2579 bytes source/.case_2.rst.swp | Bin 16384 -> 0 bytes source/.case_5.rst.swp | Bin 53248 -> 0 bytes source/.case_5.rst.un~ | Bin 7561 -> 3188 bytes source/.case_r.rst.un~ | Bin 0 -> 3376 bytes source/case_1.rst | 9 +- source/case_1.rst~ | 346 +++++++++++++++++++++++++++++++++++++++++ source/case_2.rst | 2 - source/case_5.rst | 6 - source/case_5.rst~ | 27 +++- source/case_6.rst | 2 - source/case_7.rst | 4 - source/case_r.rst | 9 ++ source/case_r.rst~ | 8 + source/index.rst | 3 +- source/references.bib | 23 ++- 16 files changed, 406 insertions(+), 33 deletions(-) create mode 100644 source/.case_1.rst.un~ delete mode 100644 source/.case_2.rst.swp delete mode 100644 source/.case_5.rst.swp create mode 100644 source/.case_r.rst.un~ create mode 100644 source/case_1.rst~ create mode 100644 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b/source/case_1.rst index ac774fe..a0488fb 100644 --- a/source/case_1.rst +++ b/source/case_1.rst @@ -1,7 +1,7 @@ .. _case_1: QuoFEM - Settlements -================================ +==================== Author: Kendra Mutch --------------------- @@ -9,7 +9,7 @@ Author: Kendra Mutch Introduction ------------ -The goal of this project is to quantify settlement, parameters impacting settlement, and observe how uncertainty in input parameters impacts the ultimate settlement of a cohesive soil. These calculations are performed through use of the SimCenter QuoFEM tool. For more details on settlement calculations, the user is encounged to read *Holtz and Kovacs 2011*. +The goal of this project is to quantify settlement, parameters impacting settlement, and observe how uncertainty in input parameters impacts the ultimate settlement of a cohesive soil. These calculations are performed through use of the SimCenter QuoFEM tool. For more details on settlement calculations, the user is encounged to read :cite:`Holtz2011`. Project Description ------------------- @@ -340,7 +340,4 @@ A more in-depth analysis using prior and posterior distributions reveals that th Remarks ------- -By accounting for uncertainty in settlement, chances of highly underpredicting or overpredicting settlement are reduced. - - - [Hol2011] R. D. Holtz and W. D. Kovacs. *An Introduction to Geotechnical Engineering*. Pearson, 2011. ISBN 978-0137011322. +By accounting for uncertainty in settlement, chances of highly underpredicting or overpredicting settlement are reduced. diff --git a/source/case_1.rst~ b/source/case_1.rst~ new file mode 100644 index 0000000..3e347e2 --- /dev/null +++ b/source/case_1.rst~ @@ -0,0 +1,346 @@ +.. _case_1: + +QuoFEM - Settlements +==================== + +Author: Kendra Mutch +--------------------- + +Introduction +------------ + +The goal of this project is to quantify settlement, parameters impacting settlement, and observe how uncertainty in input parameters impacts the ultimate settlement of a cohesive soil. These calculations are performed through use of the SimCenter QuoFEM tool. For more details on settlement calculations, the user is encounged to read :cite:`Holtz2011`. + +Project Description +------------------- + +Soil settlement is characterized by a change in the effective stress of soil, often driven by either a change in the ground water table, placement of fill/surchage load, or dissipation of excess pore water pressure. While a minimal amount of settlement is expected and may not prove hazardous, larger magnitudes of settlment, or differential settlement, can be detrimental to the integretity and functionality of a super-structure. Settlement of cohesive soil is especially hazardous, as the small pore space in fine grained soil restricts water from draining quickly through the voids. As a result, cohesive soil may continue to settle for a long period of time following the placement of a structure. Granular soil exhibits a significantly lower settlement hazard, as water tends to drain rapidly through the large pore space in the soil, meaning, much of the settlement of coarse grained soil is complete before construction ends. This project focuses on the hazard pertaining to the settlement of cohesive soil. + +When computing settlement, it is important to consider uncertainty and not accept a single predicted value as completely true to reality, as in-situ testing, lab testing, and various models used to determine soil paramters all contain uncertainty. Additionally, soil may differ vastly throughout a project site, with only a few samples taken to represent the whole site. This project uses the program QuoFEM to integrate standard settlement equations with uncertainty quantifiction tools. + +The example problems in this project will utilize the scenario, soil profile, and paramters depicted below (modified from S. Kramer CESG-562 class notes): + +**Scenario:** +*A site adjacent to San Francisco Bay is underlain by San Francisco Bay Mud. The site is to be readied for development by placement of 5ft of fill material, and the ultimamte settlement of the fill is of interest. The site conditions, shown below, indicate the presence of a crust of desiccated Bay Mud with thickness, h1, which is not expected to consolidate noticeably. The clay is underlain by a dense gravel, which will also not consolidate.* + +.. figure:: ./images/case1_settlementProblem.png + :scale: 45 % + :align: center + + Fig. 1. Problem statement. + + + + +.. 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 pre-consol pres. + - 200 psf + - 50 + * - k + - 10E-6 (cm/sec) + - 200 + * - unit weight of fill + - 130 pcf + - 7 + * - height of fill + - 5 ft + - 2 + + +Solution Strategy +----------------- +The magnitude of settlement can be predicted using conventional consolidation theory, as outlined in the equations below: + +#. If soil is normally consolidated, σp' = σo': + + .. math:: + H_{ult} = \frac{C_c}{1+e_o}log(\frac{σ_f'}{σ_o'})H_o + + +#. If soil is over consolidated, σp' > σo' and σo' + Δσ' < or = σp': + + .. math:: + H_{ult} = \frac{C_r}{1+e_o}log(\frac{σ_f'}{σ_o'})H_o + + +#. If soil is over consolidated, σp' > σo' and σo' + Δσ' > σp': + + .. math:: + H_{ult} = \frac{C_r}{1+e_o}log(\frac{σ_p'}{σ_o'})H_o + \frac{C_c}{1+e_o}log(\frac{σ_f'}{σ_p'})H_o + +Where: + + - :math:`H_{ult}` = Ultimate Settlement + - :math:`C_c` = Commpression Index + - :math:`e_o` = Void Ratio + - :math:`C_r` = Recompression Index + - :math:`σ_f'` = Final Vertical Effective Stress + - :math:`σ_o'` = Initial Vertical Effective Stress + - :math:`σ_p'` = Preconsolidation Pressure + - :math:`Δσ'` = Change in Vertical Effective Stress + - :math:`H_o` = Thickness of Compressible Layer + +For an accurate evaluation of ultimate settlement, it is recommended to subdivide the compressible layer into sublayers. These equations should be applied to each sublayer using corresponding estimations of initial and final effective stress, as well as material properties, particularly preconsolidation pressure. + +Though these equations provide a starting point for predicting settlement, they don't capture uncertainty. To account for uncertainty, methods such as Forward Propagation, Sensitivity Analysis, and Parameter Calibration integrate standard equations with uncertainty quantification. + +Forward Propagation allows us to determine how uncertainty in soil parameters translates to uncertainty in ultimate settlement. This analysis method enables us to understand the effect of compounding uncertainty. + +Sensitivity Analysis allows us to determine which input parameters impact the resulting ultimate settlement most. Sensitivity Analysis may be performed in both Python and QuoFEM. A Python script performing Sensitivity Analysis may be found here. This script produces a **tornado diagram** (as depicted below), a visual representation of the change in magnitude of settlement resulting from the application of uncertainty to a single variable at a time. These results indicate that, for the given example and material properties, the compression index (Cc), unit weight of the fill (gamma_fill), and preconsolidation pressure are the most relevant parameters. + +Finally, Parameter Calibration, allows one to determine an unknown soil paramter, given a value (or set of values) of ultimate settlement. Two examples of parameter calibartion are discussed in the **Example Applications** section. One example utilizes Bayesian Calibration, while another example utilizes Deterministic Calibration. + +.. figure:: ./images/case1_TornadoDiagram.png + :scale: 50 % + :align: center + + Fig. 2. Tornado diagram. + + +SimCenter Tool Used +------------------- +In this project we use the SimCenter tool QuoFEM. QouFEM allows the integration of the finite element method and hazard compuatations with uncertainty quantification tools. Although the tool was originally developed for finite element applications, it can also be utilized with other solution methods. In this project, the settlement calculations are implemented in a simple Python script that propagates settlement evaluations through sublayers to determine the ultimate surface settlement. This python script can be easily uploaded in QuoFEM instead of specifying a FEM application. + +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 statistic distributions + (normal distribution, uniform distribution etc.) to each variable. + + * **EDP tab** - The EDP tab allows one to define quantities of interest to compute (i.e., ultimate settlement). + + .. figure:: ./images/case1_InputResultsTabs.png + :align: center + + Fig. 3. QuoFEM interface. + + + +After entering parameters in the input tabs, one may choose run the project on their machine by simply clicking **Run** or to run the project in the cloud by selecting **Run at Design Safe**. When choosing to run a project in the cloud, one must login to Design Safe and specify a maximum run time. To ensure that the project does not expire while waiting in the queue, 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. 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. + + +Example Applications +-------------------- + +The following sections utilize the settlement scenario to demonstrate the various capabilities of QuoFEM in incorporating uncertainty quantification into the analysis. These capabilities include the propagation of uncertainty, deterministic and Bayesian calibration, as well as sensitivity analysis. + +Example One - Forward Propagation +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +#. Open 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**. Both Python scripts are available at the below links: + + * *settlement.py* + * *params.py* + +#. Select the **RV** tab. Enter the random variables (listed in the table in the problem description). Select **Normal Distribution** for each random variable, and enter the mean and standard deviation. The standard deviation must be calculated for each variable from the given coefficient of variation. The below table shows values which should be input for each random variable. + + .. list-table:: Random Variables + :widths: 25 25 50 50 + :header-rows: 1 + + * - Variable Name + - Distribution + - Mean Value + - Standard Deviation + * - h1 + - Normal Distribution + - 3 + - 0.15 + * - h2 + - Normal Distribution + - 25 + - 1.25 + * - Cc + - Normal Distribution + - 0.75 + - 0.15 + * - Cr + - Normal Distribution + - 0.05 + - 0.01 + * - eo + - Normal Distribution + - 1.54 + - 0.1078 + * - Δσ' + - Normal Distribution + - 200 + - 100 + * - k + - Normal Distribution + - 0.000001 + - 0.000002 + * - unit weight of fill + - Normal Distribution + - 130 + - 9.1 + * - height of fill + - Normal Distribution + - 5 + - 0.1 +#. 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. + +The results for Forward Propagation are outlined below: + +.. figure:: ./images/case1_ForwardPropagationResults.png + :align: center + + Fig. 4. Forward propagation results. + + +The results indicate that, given the mean parameters and standard deviation, a total settlement of 1.31 inches is expected with a standard deviation of 0.88 inches (CoV = 0.66). The corresponding histogram, based on Latin Hypercube Sampling (LHS), along with the associated normal distribution curve, is shown in the figure below: + +.. figure:: ./images/case1_propagation_Normalized_Settl_histogram.png + :scale: 40% + :align: center + + Fig. 5. QuoFEM propagation histogram. + + +Example Two - 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 **Number 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**. Both Python scripts are available at the below links. + + * *Input Script.py* + * *Parameters Script.py* + +#. In the **RV** 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. + +The results for the Sensitivity Analysis in QuoFEM are outlined below. Uncertainty in preconsolidation pressure and compression index translate to the greatest uncertainty in the predicted settlement. These findings are consistent with the results shown in the tornado diagram. + +.. figure:: ./images/case1_Sensitivity2.png + :scale: 60 % + :align: center + + Fig. 6. QuoFEM sensitivity results. + +.. figure:: ./images/case1_Sensitivity.png + :scale: 100 % + :align: center + + Fig. 7. QuoFEM sensitivity results - most relevant parameters. + + +Example Three - Parameter Calibration +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Two parameter calibration strategies available in QuoFEM are explored: i) Deterministic calibration and ii) Bayesian calibration. In both cases, parameters are identified to match assumed field settlement data at several locations, with an average total settlement of 0.88 inches. + + +Deterministic Calibration +^^^^^^^^^^^^^^^^^^^^^^^^^ + +Two deterministic calibration methods are used: i)NL2SOL and ii)OPT++GaussNewton). + +When testing the two different deterministic calibration algorithms supported in QuoFEM, we found that they provided vastly different results. This indicates that there are multiple combinations of the compression index (Cc) and preconsolidation pressure that can be considered optimal. To further explore this issue, the figure below shows a settlement field for varying values of Cc and preconsolidation pressure. It is evident that the settlement field is nonlinear due to the logarithmic nature of the solution equation. Additionally, when examining points with constant settlement (e.g., 0.88 or 1.316 inches), the red lines indicate that multiple combinations of compression index (Cc) and preconsolidation pressure yield the same settlement with the black dots representing two solutions obtained using the two deterministic calibration methoods in QuoFEM. Clearly, for this scenario, deterministic calibration cannot identify a single optimal value, making Bayesian calibration necessary. + +.. figure:: ./images/case1_SettlementField.png + :scale: 80% + :align: center + + Fig. 8. Settlement field as a function of Cc and Precon pressure. + +Bayesian Calibration +^^^^^^^^^^^^^^^^^^^^ + +This is a classic scenario where Bayesian methods can be preferred instead of deterministic methods - Bayesian methods show that there is not just one best parameter value but several values are almost equally good. This issue frequently arises when we have many parameters to be calibrated with not much data. A single best parameter value is usually “unidentifiable” in such cases + + + +#. Open QuoFEM. In the **UQ** tab, change the **UQ method** to **Bayesain Callibration** and change the **UQ Engine** to **UCSD-UQ**. For the model, select **Non-hierarchical**. Enter a **Sample** number of 500 and **Seed** number of 85. For the **Calibration Data File**, navigate to **data_2.txt**. This text file may be downloaded at the below link: + + * *data_2.txt* + +#. In the **FEM** tab, navigate to the location of the **Input Script** and **Parameter Script**. The Bayesian Calibration Python scripts may be downloaded at the below links: + + * *Settlement_2.py* + * *params.py* + +#. In the **RV** tab, enter the same random variables as the Forward Propagation example. + +#. In the EDP tab, add two variables of interset. The first variable is **settlement** with a **Length** of **1**, and the second variable is a **dummy** variable with a **Length** of 1. + +#. 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. + +The results for Bayesian Calibration are outlined below: + +.. figure:: ./images/case1_BayesianResults1.png + +.. figure:: ./images/case1_BayesianResults2.png + :align: center + + Fig. 9. QuoFEM Bayesian calibration results. + +The figure shows Cc and Precon pressure are the most relevant parameters. + +A more in-depth analysis using prior and posterior distributions reveals that the posterior distributions from the Bayesian calibration process result in more accurate and less uncertain settlement estimations. The figure below illustrates these distributions. + +.. figure:: ./images/case1_calibration_PriorPost.png + :scale: 70% + :align: center + + Fig. 10. Prior and posterior distributions from Bayesian calibration. + + +Remarks +------- +By accounting for uncertainty in settlement, chances of highly underpredicting or overpredicting settlement are reduced. + +.. bibliography:: + :filter: cited diff --git a/source/case_2.rst b/source/case_2.rst index 941e470..f9070b0 100644 --- a/source/case_2.rst +++ b/source/case_2.rst @@ -721,5 +721,3 @@ I'd like to thank everyone at SimCenter, specifically Sang-ri Yi, Frank McKenna, Transfer function is one of my favorite topics in geotechnical engineering. I'd really like to continue working with site response and performance based design so being able to create this example along with my class was great. Finally, I'd like to thank Prof. Arduino who made all of this possible. His determination and motivation was contagious throughout the academic quarter. There are many great professors but there is only one Pedro Arduino. - -.. bibliography:: references.bib diff --git a/source/case_5.rst b/source/case_5.rst index 9a3eb2c..c79761b 100644 --- a/source/case_5.rst +++ b/source/case_5.rst @@ -606,9 +606,3 @@ Remarks :width: 600px :align: center :figclass: align-center - - - -References ----------- -.. bibliography:: references.bib diff --git a/source/case_5.rst~ b/source/case_5.rst~ index b60343b..33d9910 100644 --- a/source/case_5.rst~ +++ b/source/case_5.rst~ @@ -410,6 +410,17 @@ The following code snippet shows the implementation of the :cite:`Zhu2017` model return {"liq_prob":prob_liq, "liq_susc":liq_susc} +.. raw:: html + + + + + +.. raw:: html + +

+ + **RESULTS** @@ -549,6 +560,15 @@ In this example, the :cite:`Sanger2024` model is implemented in the R2D tool usi return {"liq_prob":prob_liq, "liq_susc":LPI} +.. raw:: html + + + + + +.. raw:: html + +

**RESULTS** @@ -587,8 +607,5 @@ Remarks :align: center :figclass: align-center - - -References ----------- -.. bibliography:: references.bib +.. bibliography:: + :filter: cited diff --git a/source/case_6.rst b/source/case_6.rst index dc0713d..94a5965 100644 --- a/source/case_6.rst +++ b/source/case_6.rst @@ -146,5 +146,3 @@ Remarks * A `Jupyter Notebook `_ ('hazardNewmark.ipynb') was coded to simulate the process that could be implemented to R2D for earthquake-induced landslides hazard so the user could then estimate damage and losses. Please if refering to this notebook, careful read the instructions in the readme first. Find this work in the CESG599 repository. When trying to run this notebook, you must have access to the M9 project in DesignSafe machines. * Earthquake induced landslides prediction may be a difficult task to adress, but there are models out there that can be implemented to predict the hazard and subsequently, this hazard can be used to predict damage amd losses. The idea is in this section is to provide a procedure that could ve developed within the SiimCenter R2D tool to predict the hazard and subsequently, to predict damage amd losses. - -.. bibliography:: references.bib \ No newline at end of file diff --git a/source/case_7.rst b/source/case_7.rst index a900ee8..4ed0219 100644 --- a/source/case_7.rst +++ b/source/case_7.rst @@ -267,7 +267,3 @@ Remarks * In locations such as Vieques, Puerto Rico, a comprehensive building inventory to assess huricane impact to infrastructure assets is limited. Assessing hazard exposure and consequences are key to increase resilience. * R2D possess vast capabilities to adress this challenge, allowing researches to input hazard data and construct building inventories with BRAILS tools. * This example provides strategies for creating building inventories in locations where data is scarce and implementing them in a format that could be used in R2D for regional analysis. - -References ----------- -.. bibliography:: references.bib diff --git a/source/case_r.rst b/source/case_r.rst new file mode 100644 index 0000000..31523b1 --- /dev/null +++ b/source/case_r.rst @@ -0,0 +1,9 @@ + +.. _case_r: + + +References +========== + +.. bibliography:: + :filter: cited diff --git a/source/case_r.rst~ b/source/case_r.rst~ new file mode 100644 index 0000000..640be98 --- /dev/null +++ b/source/case_r.rst~ @@ -0,0 +1,8 @@ + +.. _case_r: + + +References +========== + +.. bibliography:: references.bib diff --git a/source/index.rst b/source/index.rst index 36b1686..98d650d 100644 --- a/source/index.rst +++ b/source/index.rst @@ -19,7 +19,8 @@ The course is intended for graduate students and researchers in the field of civ case_4 case_5 case_6 - case_7 + case_7 + case_r .. Acknowledgements Acknowledgements diff --git a/source/references.bib b/source/references.bib index 1b85c9f..dfe694c 100644 --- a/source/references.bib +++ b/source/references.bib @@ -55,14 +55,23 @@ @article{Gey2020 publisher={American Society of Civil Engineers} } +@book{Holtz2011, + author = {Holtz, R.D. and Kovacs, W.D. and Sheahan, T.C.}, + publisher = {Prentice Hall}, + isbn = {978-0137011322}, + pages = {853}, + title = {An Introduction to Geotechnical Engineering}, + year = {2011} +} + @book{Kramer1996, -author = {Kramer, S. L.}, -publisher = {Pearson}, -isbn = {9783642196294}, -issn = {1532-2793}, -pages = {653}, -title = {Geotechnical Earthquake Engineering}, -year = {1996} + author = {Kramer, S. L.}, + publisher = {Pearson}, + isbn = {9783642196294}, + issn = {1532-2793}, + pages = {653}, + title = {Geotechnical Earthquake Engineering}, + year = {1996} } @article{Jibson1993,