Updating Application Readmes to include citations

.gitignore

@@ -56,42 +56,45 @@ $ cat .gitignore
 *.vtp
 *.zip
 
+# Other
+.DS_Store
+view_html.sh
+*vis-temp*
+folder.json
+include.json
+
 # MATLAB
 **/output/
 **/output_previous/
 **/slprj/
 *build_exception*
 
+# WAMIT
+*.1
+*.3
+*.3fk
+*.3sc
+*.4
+*.h5
+*.p2f
+*.pot
+
 # Applications
 **/mooring/*.out
 !**/mooring/lines.txt
 **/vtk/*
 savedData*.mat
+!/Generalized_Body_Modes/hydroData/WAMIT/*
+!/Mean_Drift/WAMIT/inputFiles/*
+!/Mean_Drift/WAMIT/outputFiles/*
+MOST/**/**/*.mat
+MOST/**/**/**/*.mat
 WECCCOMP/**/SS*.mat
 WECCCOMP/**/SS*.fig
 !WECCCOMP/WECCCOMP_Nonlinear_Model_Predictive/waveData/*.mat
 Passive_Yaw/**/IrrYaw.mat
 Passive_Yaw/**/figYawIrr.fig
 yaw*.mat
 
-# BEM
-*.1
-*.3
-*.3fk
-*.3sc
-*.4
-*.h5
-*.hst
-*.p2f
-*.pot
-!/Generalized_Body_Modes/hydroData/WAMIT/*
-!/Mean_Drift/WAMIT/inputFiles/*
-!/Mean_Drift/WAMIT/outputFiles/*
-!/OWC/OrificeModel/hydroData/*.h5
 
-# Other
-.DS_Store
-view_html.sh
-*vis-temp*
-folder.json
-include.json
+

Body-to-Body_Interactions/README.md

@@ -2,9 +2,14 @@
 
 **Author:**  	Kelley Ruehl
 
-**Version:** 	WEC-Sim v2.2
-
 **Geometry:**	RM3
 
-Example using [Body-to-Body (B2B)](http://wec-sim.github.io/WEC-Sim/advanced_features.html#body-to-body-interactions) to run WEC-Sim for the [RM3](http://wec-sim.github.io/WEC-Sim/tutorials.html#two-body-point-absorber-rm3) geometry. The scripts run and plot the RM3 model with B2B on/off and with Regular/RegularCIC. Execute the `runB2B.m` script to run this case. 
+**Original Version:** 	WEC-Sim v2.2
+
+**Description**	
+
+Example using [Body-to-Body (B2B)](https://wec-sim.github.io/WEC-Sim/main/user/advanced_features.html#body-to-body-interactions) to run WEC-Sim for the RM3 geometry. The scripts run and plot the RM3 model with B2B on/off and with Regular/RegularCIC. Execute the `runB2B.m` script to run this case. 
+
+**Relevant Citation(s)**
 
+Ruehl, K.; Michelen, C.; Yu, Y.; Lawson, M. (2016). Update on WEC-Sim Validation Testing and Code Development. Paper presented at 4th Annual Marine Energy Technology Symposium (METS), Washington D.C., USA.

Cable/README.md

@@ -2,12 +2,14 @@
 
 **Author:**	Dominic Forbush
 
-**Version:** 	WEC-Sim v4.4
-
 **Geometry:**	MBARI-WEC, and open-source WEC from Monterey Bay Aquarium Research Institute.
 
-**Dependency:**	N/A
+**Original Version:** 	WEC-Sim v4.4
 
-**Note:**	More WEC information can be found: https://link.springer.com/article/10.1007/s40722-021-00197-9
+**Description**
 
 Example using WEC-Sim to simulate a [Cable](http://wec-sim.github.io/WEC-Sim/advanced_features.html) connecting two rigid bodies for the MBARI geometry. 
+
+**Relevant Citation(s)**
+
+Hamilton, A., Cazenave, F., Forbush, D. et al. The MBARI-WEC: a power source for ocean sensing. J. Ocean Eng. Mar. Energy 7, 189�200 (2021). https://doi.org/10.1007/s40722-021-00197-9

Controls/Declutching/README.md

@@ -1,16 +1,15 @@
-# WEC-Sim Controls Examples
+# Declutching Controller
 
-**Author:**          Jeff Grasberger (Sandia)
+**Author:**          Jeff Grasberger 
 
-**WEC-Sim Version:** v5.0 (or newer)
+**Geometry:**	Sphere
 
-**Matlab Version:** 2020b (or newer)
+**Original Version:** v5.0 
 
-**WEC-Sim Model**
-Numerical model for a semi-submerged sphere (diameter = 10 m)  with a declutching controller. "wecSim" can be typed into 
-the command window to run the example with the default setup. "optimalTimeCalc.m" is used to calculate the 
-optimal declutching time. The "mcrBuildTimes.m" script can be run to set up multiple conditions runs, then 
-"wecSimMCR" can be typed into the command window to run the different cases with varying declutching times.
+**Description**
 
-**Questions?**
-* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
+Numerical model for a semi-submerged sphere (diameter = 10 m)  with a declutching controller. `wecSim` can be typed into the command window to run the example with the default setup. `optimalTimeCalc.m` is used to calculate the optimal declutching time. The `mcrBuildTimes.m` script can be run to set up multiple conditions runs, then `wecSimMCR` can be typed into the command window to run the different cases with varying declutching times.
+
+**Relevant Citation(s)**
+
+Leon, J.; Grasberger, J.; Forbush, D.; Sirigu, M.; Ancellin, M.; Tom, N.; Keester, A.; Ruehl, K.; Ogden, D.; Husain, S. (2024). Advanced Features and Recent Developments in the WEC-Sim Open-Source Design Tool . Paper presented at Pan American Marine Energy Conference (PAMEC 2024), Barranquilla, Colombia.

Controls/Latching/README.md

@@ -1,16 +1,15 @@
-# WEC-Sim Controls Examples
+# Latching Controller
 
-**Author:**          Jeff Grasberger (Sandia)
+**Author:**          Jeff Grasberger 
 
-**WEC-Sim Version:** v5.0 (or newer)
+**Geometry:**	Sphere
 
-**Matlab Version:** 2020b (or newer)
+**Original Version:** v5.0 
 
-**WEC-Sim Model**
-Numerical model for a semi-submerged sphere (diameter = 10 m) with a latching controller. "wecSim" can be typed into 
-the command window to run the example with the default setup. "optimalTimeCalc.m" is used to calculate the 
-optimal latching time. The "mcrBuildTimes.m" script can be run to set up multiple conditions runs, then 
-"wecSimMCR" can be typed into the command window to run the different cases with varying latching times.
+**Description**
 
-**Questions?**
-* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
+Numerical model for a semi-submerged sphere (diameter = 10 m) with a latching controller. `wecSim` can be typed into the command window to run the example with the default setup. `optimalTimeCalc.m` is used to calculate the optimal latching time. The `mcrBuildTimes.m` script can be run to set up multiple conditions runs, then `wecSimMCR` can be typed into the command window to run the different cases with varying latching times.
+
+**Relevant Citation(s)**
+
+Leon, J.; Grasberger, J.; Forbush, D.; Sirigu, M.; Ancellin, M.; Tom, N.; Keester, A.; Ruehl, K.; Ogden, D.; Husain, S. (2024). Advanced Features and Recent Developments in the WEC-Sim Open-Source Design Tool . Paper presented at Pan American Marine Energy Conference (PAMEC 2024), Barranquilla, Colombia.

Controls/MPC/README.md

@@ -1,28 +1,24 @@
-# WEC-Sim Controls Examples
+# Model Predictive Controller (MPC)
 
-**Author:**          Jeff Grasberger (Sandia)
+**Author:**          Ratanak So and Jeff Grasberger 
 
-**WEC-Sim Version:** v5.0 (or newer)
+**Geometry:**	Sphere
 
-**Matlab Version:** 2020b (or newer)
+**Original Version:** v5.0 
 
 **Dependencies:**
 
-   Optimization Toolbox 		            -->	for quadprog command
-   System Identification Toolbox	        -->	for ssdata, tfest, tfdata commands
-   Statistics and Machine Learning Toolbox  -->	for regress command
-   Control System Toolbox		            -->	for frd command
-   Symbolic Math Toolbox		            -->	for subs command
-
-**Description:**
-Numerical model for a semi-submerged sphere (diameter = 10 m) with a model predictive controller (MPC).
-"wecSim" can be typed into the command window to run the example with the default setup. 
-"plotFreqDep.m" solves for and plots the frequency dependent coefficients, 
-which are stored in "coeff.mat". "setupMPC.m" sets the controller up using "makePlantModel.m" 
-and "makePredictiveModel.m" and is called by the input file when "wecSim" 
-is run from the command window. "fexcPrediction.m" and "mpcFcn.m" predict the excitation forces 
-and solve the quadratic programming problem, respectively, and are both called by "sphereMPC.slx" 
-during the simulation. The model predictive controller parameters can be changed in the input file. 
-
-**Questions?**
-* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
+* Control System Toolbox
+* Optimization Toolbox
+* Statistics and Machine Learning Toolbox
+
+**Description**
+
+Numerical model for a semi-submerged sphere (diameter = 10 m) with a model predictive controller (MPC). `wecSim` can be typed into the command window to run the example with the default setup. `plotFreqDep.m` solves for and plots the frequency dependent coefficients, which are stored in `coeff.mat`. `setupMPC.m` sets the controller up using `makePlantModel.m` and `makePredictiveModel.m` and is called by the input file when `wecSim` is run from the command window. `fexcPrediction.m` and `mpcFcn.m` predict the excitation forces and solve the quadratic programming problem, respectively, and are both called by `sphereMPC.slx` during the simulation. The model predictive controller parameters can be changed in the input file. 	
+
+**Relevant Citation(s)**
+
+Leon, J.; Grasberger, J.; Forbush, D.; Sirigu, M.; Ancellin, M.; Tom, N.; Keester, A.; Ruehl, K.; Ogden, D.; Husain, S. (2024). Advanced Features and Recent Developments in the WEC-Sim Open-Source Design Tool . Paper presented at Pan American Marine Energy Conference (PAMEC 2024), Barranquilla, Colombia.
+
+R. So, M. Starrett, K. Ruehl and T. K. A. Brekken, "Development of control-Sim: Control strategies for power take-off integrated wave energy converter," 2017 IEEE Power & Energy Society General Meeting, Chicago, IL, USA, 2017, pp. 1-5, doi: 10.1109/PESGM.2017.8274314. keywords: {Force;Damping;Cost function;Springs;Sea state;Laboratories;wave energy;optimization;power take off;model predictive control},
+

Controls/Passive (P)/README.md

@@ -1,17 +1,15 @@
-# WEC-Sim Controls Examples
+# Passive Controller
 
-**Author:**          Jeff Grasberger (Sandia)
+**Author:**          Jeff Grasberger 
 
-**WEC-Sim Version:** v5.0 (or newer)
+**Geometry:**	Sphere
 
-**Matlab Version:** 2020b (or newer)
+**Original Version:** v5.0 
 
-**WEC-Sim Model**
-Numerical model for a semi-submerged sphere (diameter = 10 m) with a passive controller. 
-"wecSim" can be typed into the command window to run the example with the default setup. "optimalGainCalc.m" 
-is used to calculate the optimal proportional gain. The "mcrBuildGains.m" script can be run to set up 
-multiple conditions runs, then "wecSimMCR" can be typed into the command window to run the different 
-cases with varying proportional gain values.
+**Description**
 
-**Questions?**
-* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
+Numerical model for a semi-submerged sphere (diameter = 10 m) with a passive controller. `wecSim` can be typed into the command window to run the example with the default setup. `optimalGainCalc.m` is used to calculate the optimal proportional gain. The `mcrBuildGains.m` script can be run to set up multiple conditions runs, then `wecSimMCR` can be typed into the command window to run the different cases with varying proportional gain values.
+
+**Relevant Citation(s)**
+
+Leon, J.; Grasberger, J.; Forbush, D.; Sirigu, M.; Ancellin, M.; Tom, N.; Keester, A.; Ruehl, K.; Ogden, D.; Husain, S. (2024). Advanced Features and Recent Developments in the WEC-Sim Open-Source Design Tool . Paper presented at Pan American Marine Energy Conference (PAMEC 2024), Barranquilla, Colombia.

Controls/Reactive (PI)/README.md

@@ -1,17 +1,15 @@
-# WEC-Sim Controls Examples
+# Reactive Controller
 
-**Author:**          Jeff Grasberger (Sandia)
+**Author:**          Jeff Grasberger 
 
-**WEC-Sim Version:** v5.0 (or newer)
+**Geometry:**	Sphere
 
-**Matlab Version:** 2020b (or newer)
+**Original Version:** v5.0 
 
-**WEC-Sim Model**
-Numerical model for a semi-submerged sphere (diameter = 10 m) with a reactive controller. 
-"wecSim" can be typed into the command window to run the example with the default setup. "optimalGainCalc.m" 
-is used to calculate the optimal proportional and integral gains. The "mcrBuildGains.m" script can be run to set up 
-multiple conditions runs, then "wecSimMCR" can be typed into the command window to run the different 
-cases with varying proportional and integral gain values.
+**Description**
 
-**Questions?**
-* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
+Numerical model for a semi-submerged sphere (diameter = 10 m) with a reactive controller. `wecSim` can be typed into the command window to run the example with the default setup. `optimalGainCalc.m` is used to calculate the optimal proportional and integral gains. The `mcrBuildGains.m` script can be run to set up multiple conditions runs, then `wecSimMCR` can be typed into the command window to run the different cases with varying proportional and integral gain values.
+
+**Relevant Citation(s)**
+
+Leon, J.; Grasberger, J.; Forbush, D.; Sirigu, M.; Ancellin, M.; Tom, N.; Keester, A.; Ruehl, K.; Ogden, D.; Husain, S. (2024). Advanced Features and Recent Developments in the WEC-Sim Open-Source Design Tool . Paper presented at Pan American Marine Energy Conference (PAMEC 2024), Barranquilla, Colombia.

Controls/ReactiveWithPTO/README.md

@@ -1,19 +1,15 @@
-# WEC-Sim Controls Examples
+# Reactive Controller with Direct Drive Power Take-Off
 
-**Author:**          Jeff Grasberger (Sandia)
+**Author:**	Jeff Grasberger 
 
-**WEC-Sim Version:** v5.0 (or newer)
+**Geometry:**	Sphere
 
-**Matlab Version:** 2020b (or newer)
+**Original Version:** v5.0 
 
-**WEC-Sim Model**
-Numerical model for a semi-submerged sphere (diameter = 10 m) with a reactive controller and 
-simple direct drive power take-off. This example demonstrates the different controller gains required
-for electrical power maximization when compared to mechanical power maximization. "wecSim" can be 
-typed into the command window to run the example with the default setup. The 
-"mcrBuildGains.m" script can be run to set up multiple conditions runs, then "wecSimMCR" can be 
-typed into the command window to run the different cases with varying proportional and integral 
-gain values.
+**Description**
 
-**Questions?**
-* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
+Numerical model for a semi-submerged sphere (diameter = 10 m) with a reactive controller and simple direct drive power take-off. This example demonstrates the different controller gains required for electrical power maximization when compared to mechanical power maximization. `wecSim` can be typed into the command window to run the example with the default setup. The `mcrBuildGains.m` script can be run to set up multiple conditions runs, then `wecSimMCR` can be typed into the command window to run the different cases with varying proportional and integral gain values.
+
+**Relevant Citation(s)**
+
+Leon, J.; Grasberger, J.; Forbush, D.; Sirigu, M.; Ancellin, M.; Tom, N.; Keester, A.; Ruehl, K.; Ogden, D.; Husain, S. (2024). Advanced Features and Recent Developments in the WEC-Sim Open-Source Design Tool . Paper presented at Pan American Marine Energy Conference (PAMEC 2024), Barranquilla, Colombia.

Desalination/README.md

@@ -1,12 +1,21 @@
-# Desalination 
+# Wave-Powered Desalination 
 
-**Author:** 	Yi-Hsiang Yu
-
-**Version:**	WEC-Sim v4.0
+**Author:** 	Yi-Hsiang Yu, Scott Jenne, and Kelley Ruehl
 
 **Geometry:**	OSWEC
 
-**Dependency:**	SimScape Fluids
+**Original Version:**	WEC-Sim v4.0
+
+**Dependencies:**	SimScape Fluids
+
+**Description**	
+
+Example using WEC-Sim for wave-powered desalination using the OSWEC. 
+
+**Relevant Citation(s)**
+
+Ruehl, K.; Klise, K.; Hinks, M.; Grasberger, J. (2025). Framework for Assessing Impact of Wave-Powered Desalination on Resilience of Coastal Communities. Journal of Marine Science and Engineering, 13(2), 219. https://doi.org/10.3390/jmse13020219
 
+Yu, Y.; Jenne, D. (2018). Numerical Modeling and Dynamic Analysis of a Wave-Powered Reverse-Osmosis System. Journal of Marine Science and Engineering, 6(4), 17. https://doi.org/10.3390/jmse6040132
 
-Example using WEC-Sim for desalination based on the [OSWEC](http://wec-sim.github.io/WEC-Sim/tutorials.html#oscillating-surge-wec-oswec) geometry. Note the dependency on SimScape Fluids to run this desalination case. 
+Yu, Y.; Jenne, D. (2017). Analysis of a Wave-Powered, Reverse-Osmosis System and Its Economic Availability in the United States. Paper presented at 36th International Conference on Ocean, Offshore & Arctic Engineering (OMAE 2017), Trondheim, Norway.

End_Stops/README.md

@@ -2,13 +2,13 @@
 
 **Author:**  	Dominic Forbush
 
-**Version:** 	WEC-Sim v4.1
+**Geometry**	RM3
 
-**Dependency:**	MATLAB 2019a or newer
+**Original Version:** 	WEC-Sim v4.1
 
-**Geometry**	RM3
+**Description**
 
-Example on using [End-Stops] (http://wec-sim.github.io/WEC-Sim/man/advanced_features.html#constraint-and-pto-features) to run WEC-Sim for the RM3 geometry. 
+Example on using [End-Stops](https://wec-sim.github.io/WEC-Sim/main/user/advanced_features.html#modifying-constraints-and-ptos) to run WEC-Sim for the RM3 geometry. 
 
 
 

Free_Decay/README.md

@@ -2,13 +2,20 @@
 
 **Author:**	Fabian Wendt
 
-**Version:**	WEC-Sim v2.2
-
 **Geometry:**	Sphere
 
-**Note:**	This case was developed for IEA OES Task 10 international comparison of numerical simulations to experimental data.
+**Original Version:**	WEC-Sim v2.2
+
+**Description**
+
+Example using WEC-Sim to simulate [free decay](https://wec-sim.github.io/WEC-Sim/main/user/advanced_features.html#decay-tests) of a sphere in heave, using [Multiple Condition Runs](https://wec-sim.github.io/WEC-Sim/main/user/advanced_features.html#multiple-condition-runs-mcr).  Execute the `runFreeDecay.m` script to run this case. This case was developed for IEA OES Task 10 international comparison of numerical simulations to experimental data.
+
+**Relevant Citation(s)**
+
+Wendt, F.; Nielsen, K.; Yu, Y.; Bingham, H.; Eskilsson, C.; Kramer, M.; Babarit, A.; Bunnik, T.; Costello, R.; Crowley, S.; Gendron, B.; Giorgi, G.; Giorgi, S.; Girardin, S.; Greaves, D.; Heras, P.; Hoffman, J.; Islam, H.; Jakobsen, K.; Janson, C.; Jansson, J.; Kim, H.; Kim, J.; Kim, K.; Kurniawan, A.; Leoni, M.; Mathai, T.; Nam, B.; Park, S.; Rajagopalan, K.; Ransley, E.; Read, R.; Ringwood, J.; Rodrigues, J.; Rosenthal, B.; Roy, A.; Ruehl, K.; Schofield, P.; Sheng, W.; Shiri, A.; Thomas, S.; Touzon, I.; Yasutaka, I. (2019). Ocean Energy Systems Wave Energy Modelling Task: Modelling, Verification and Validation of Wave Energy Converters. Journal of Marine Science and Engineering, 7(11), 379. https://doi.org/10.3390/jmse7110379 
 
-Example using WEC-Sim to simulate [free decay](http://wec-sim.github.io/WEC-Sim/advanced_features.html#decay-tests) of a sphere in heave, using [Multiple Condition Runs](http://wec-sim.github.io/WEC-Sim/advanced_features.html#multiple-condition-runs-mcr).  Execute the `runFreeDecay.m` script to run this case. 
+Nielsen, K.; Wendt, F.; Yu, Y.; Ruehl, K.; Touzon, I.; Nam, B.; Kim, J.; Kim, K.; Crowley, S.; Sheng, W.; Kurniawan, A.; Kramer, M.; Ogden, D.; Girardin, S.; Babarit, A.; Costello, R.; Giorgi, S.; Roy, A.; Bingham, H.; Read, R. (2018). OES Task 10 WEC heaving sphere performance modelling verification. Paper presented at 3rd International Conference on Renewable Energies Offshore, Lisbon, Portugal.
 
+Wendt, F.; Yu, Y.; Nielsen, K.; Ruehl, K.; Bunnik, T.; Touzon, I.; Nam, B.; Kim, J.; Kim, K.; Janson, C.; Jakobsen, K.; Crowley, S.; Vega, L.; Rajagopolan, K.; Mathai, T.; Greaves, D.; Ransley, E.; Lamont-Kane, P.; Sheng, W.; Costello, R.; Kennedy, B.; Thomas, S.; Heras, P.; Bingham, H.; Wuillaume, P.; Steinke, D.; Roy, A.; Beatty, S.; Shofield, P.; Jansson, J.; Hoffman, J. (2017). International Energy Agency Ocean Energy Systems Task 10 Wave Energy Converter Modeling Verification and Validation. Paper presented at 12th European Wave and Tidal Energy Conference (EWTEC 2017), Cork, Ireland.
 
 

Generalized_Body_Modes/README.md

@@ -1,9 +1,15 @@
-# Generalized Body Modes 
+# Generalized Body Modes (GBM)
 
 **Author:** 	Yi-Hsiang Yu
 
-**Version:**	WEC-Sim v4.0
-
 **Geometry:**	Barge
 
-Example using [Generalized Body Modes](http://wec-sim.github.io/WEC-Sim/advanced_features.html#generalized-body-modes) in WEC-Sim. 
+**Original Version:**	WEC-Sim v4.0
+
+**Description**
+
+Example using [Generalized Body Modes](https://wec-sim.github.io/WEC-Sim/main/user/advanced_features.html#generalized-body-modes) in WEC-Sim. 
+
+**Relevant Citation(s)**
+
+Ogden, David, et al. "Review of WEC-Sim development and applications." International Marine Energy Journal, vol. 5, no. 3, Dec. 2022. https://doi.org/10.36688/imej.5.293-303