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Updating Application Readmes to include citations (#82)
* updated MOST readme * updated MOST * adding original wec-sim version and relavant citation fields * added more pto-sim citations * updating readmes * adding desal readme * added passive yaw citation * updated nonlinear hydro * added wecccomp citations * updated cable and controls readmes * updated controls readmes * updated end stop citation * added free decay citations * minor formatting uppates * added GBM citation * adding mean drift citation * added citations for mooring * added ME citations * added mcr citation * updated multiple wave spectra and changed dir name * updated paraview readme * updated paraview and pto extension readmes * added citations * minor formatting changes * minor formatting changes * minor formatting changes * minor formatting changes * readme formatting * remove mpc dependencies no longer used * updating OWC dependencies * updated readmes * refer pto ext to pr * minor formatting changes * Update Paraview_Visualization/README.md --------- Co-authored-by: akeeste <akeeste@sandia.gov> Co-authored-by: Adam Keester <72414466+akeeste@users.noreply.github.com>
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‎.gitignore‎

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

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**Author:** Kelley Ruehl
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**Version:** WEC-Sim v2.2
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**Geometry:** RM3
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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.
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**Original Version:** WEC-Sim v2.2
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**Description**
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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.
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**Relevant Citation(s)**
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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

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**Author:** Dominic Forbush
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**Version:** WEC-Sim v4.4
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**Geometry:** MBARI-WEC, and open-source WEC from Monterey Bay Aquarium Research Institute.
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**Dependency:** N/A
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**Original Version:** WEC-Sim v4.4
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**Note:** More WEC information can be found: https://link.springer.com/article/10.1007/s40722-021-00197-9
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**Description**
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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.
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**Relevant Citation(s)**
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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

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# WEC-Sim Controls Examples
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# Declutching Controller
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**Author:** Jeff Grasberger (Sandia)
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**Author:** Jeff Grasberger
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**WEC-Sim Version:** v5.0 (or newer)
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**Geometry:** Sphere
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**Matlab Version:** 2020b (or newer)
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**Original Version:** v5.0
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**WEC-Sim Model**
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Numerical model for a semi-submerged sphere (diameter = 10 m) with a declutching controller. "wecSim" can be typed into
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the command window to run the example with the default setup. "optimalTimeCalc.m" is used to calculate the
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optimal declutching time. The "mcrBuildTimes.m" script can be run to set up multiple conditions runs, then
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"wecSimMCR" can be typed into the command window to run the different cases with varying declutching times.
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**Description**
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**Questions?**
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* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
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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.
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**Relevant Citation(s)**
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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

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# WEC-Sim Controls Examples
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# Latching Controller
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**Author:** Jeff Grasberger (Sandia)
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**Author:** Jeff Grasberger
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**WEC-Sim Version:** v5.0 (or newer)
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**Geometry:** Sphere
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**Matlab Version:** 2020b (or newer)
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**Original Version:** v5.0
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**WEC-Sim Model**
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Numerical model for a semi-submerged sphere (diameter = 10 m) with a latching controller. "wecSim" can be typed into
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the command window to run the example with the default setup. "optimalTimeCalc.m" is used to calculate the
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optimal latching time. The "mcrBuildTimes.m" script can be run to set up multiple conditions runs, then
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"wecSimMCR" can be typed into the command window to run the different cases with varying latching times.
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**Description**
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**Questions?**
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* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
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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.
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**Relevant Citation(s)**
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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

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# WEC-Sim Controls Examples
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# Model Predictive Controller (MPC)
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**Author:** Jeff Grasberger (Sandia)
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**Author:** Ratanak So and Jeff Grasberger
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**WEC-Sim Version:** v5.0 (or newer)
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**Geometry:** Sphere
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**Matlab Version:** 2020b (or newer)
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**Original Version:** v5.0
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**Dependencies:**
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Optimization Toolbox --> for quadprog command
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System Identification Toolbox --> for ssdata, tfest, tfdata commands
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Statistics and Machine Learning Toolbox --> for regress command
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Control System Toolbox --> for frd command
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Symbolic Math Toolbox --> for subs command
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**Description:**
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Numerical model for a semi-submerged sphere (diameter = 10 m) with a model predictive controller (MPC).
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"wecSim" can be typed into the command window to run the example with the default setup.
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"plotFreqDep.m" solves for and plots the frequency dependent coefficients,
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which are stored in "coeff.mat". "setupMPC.m" sets the controller up using "makePlantModel.m"
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and "makePredictiveModel.m" and is called by the input file when "wecSim"
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is run from the command window. "fexcPrediction.m" and "mpcFcn.m" predict the excitation forces
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and solve the quadratic programming problem, respectively, and are both called by "sphereMPC.slx"
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during the simulation. The model predictive controller parameters can be changed in the input file.
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**Questions?**
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* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
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* Control System Toolbox
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* Optimization Toolbox
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* Statistics and Machine Learning Toolbox
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**Description**
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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.
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**Relevant Citation(s)**
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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.
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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},
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‎Controls/Passive (P)/README.md‎

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# WEC-Sim Controls Examples
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# Passive Controller
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**Author:** Jeff Grasberger (Sandia)
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**Author:** Jeff Grasberger
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**WEC-Sim Version:** v5.0 (or newer)
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**Geometry:** Sphere
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**Matlab Version:** 2020b (or newer)
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**Original Version:** v5.0
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**WEC-Sim Model**
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Numerical model for a semi-submerged sphere (diameter = 10 m) with a passive controller.
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"wecSim" can be typed into the command window to run the example with the default setup. "optimalGainCalc.m"
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is used to calculate the optimal proportional gain. The "mcrBuildGains.m" script can be run to set up
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multiple conditions runs, then "wecSimMCR" can be typed into the command window to run the different
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cases with varying proportional gain values.
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**Description**
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**Questions?**
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* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
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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.
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**Relevant Citation(s)**
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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

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# WEC-Sim Controls Examples
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# Reactive Controller
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**Author:** Jeff Grasberger (Sandia)
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**Author:** Jeff Grasberger
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**WEC-Sim Version:** v5.0 (or newer)
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**Geometry:** Sphere
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**Matlab Version:** 2020b (or newer)
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**Original Version:** v5.0
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**WEC-Sim Model**
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Numerical model for a semi-submerged sphere (diameter = 10 m) with a reactive controller.
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"wecSim" can be typed into the command window to run the example with the default setup. "optimalGainCalc.m"
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is used to calculate the optimal proportional and integral gains. The "mcrBuildGains.m" script can be run to set up
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multiple conditions runs, then "wecSimMCR" can be typed into the command window to run the different
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cases with varying proportional and integral gain values.
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**Description**
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**Questions?**
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* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
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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.
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**Relevant Citation(s)**
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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

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# WEC-Sim Controls Examples
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# Reactive Controller with Direct Drive Power Take-Off
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**Author:** Jeff Grasberger (Sandia)
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**Author:** Jeff Grasberger
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**WEC-Sim Version:** v5.0 (or newer)
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**Geometry:** Sphere
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**Matlab Version:** 2020b (or newer)
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**Original Version:** v5.0
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**WEC-Sim Model**
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Numerical model for a semi-submerged sphere (diameter = 10 m) with a reactive controller and
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simple direct drive power take-off. This example demonstrates the different controller gains required
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for electrical power maximization when compared to mechanical power maximization. "wecSim" can be
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typed into the command window to run the example with the default setup. The
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"mcrBuildGains.m" script can be run to set up multiple conditions runs, then "wecSimMCR" can be
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typed into the command window to run the different cases with varying proportional and integral
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gain values.
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**Description**
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**Questions?**
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* Post all WEC-Sim modeling questions to the [WEC-Sim online forum](https://github.com/WEC-Sim/WEC-Sim/issues).
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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.
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**Relevant Citation(s)**
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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

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# Desalination
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# Wave-Powered Desalination
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**Author:** Yi-Hsiang Yu
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**Author:** Yi-Hsiang Yu, Scott Jenne, and Kelley Ruehl
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**Dependency:** SimScape Fluids
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**Original Version:** WEC-Sim v4.0
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**Dependencies:** SimScape Fluids
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**Description**
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Example using WEC-Sim for wave-powered desalination using the OSWEC.
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**Relevant Citation(s)**
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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
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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
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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.
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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.

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