Fix failing tests on dev

.github/workflows/run-tests-reusable.yml

@@ -54,15 +54,15 @@ jobs:
           ref: ${{ inputs.base_ref }}
           path: './WEC-Sim'
       - name: Check out MoorDyn
-        if: matrix.folder == 'Mooring' 
+        if: matrix.folder == 'Mooring' || matrix.folder == 'OWC' || matrix.folder == 'Paraview_Visualization'
         uses: actions/checkout@v4
         with:
           repository: WEC-Sim/MoorDyn
           path: './MoorDyn'
       - name: Copy MoorDyn Files
-        if: matrix.folder == 'Mooring' 
+        if: matrix.folder == 'Mooring' || matrix.folder == 'OWC' || matrix.folder == 'Paraview_Visualization'
         run: |
-            cp * ../WEC-Sim/source/functions/moorDyn
+            cp -r * ../WEC-Sim/source/functions/moorDyn
             ls ../WEC-Sim/source/functions/moorDyn
         shell: bash
         working-directory: './MoorDyn'

.github/workflows/wec-sim-dev-tests.yml

@@ -1,5 +1,6 @@
 name: Test WEC-Sim dev branch
 on:
+  workflow_dispatch: {}
   repository_dispatch:
     types:
       - wecsim-dev

.github/workflows/wec-sim-main-tests.yml

@@ -1,5 +1,6 @@
 name: Test WEC-Sim main branch
 on:
+  workflow_dispatch: {}
   repository_dispatch:
     types:
       - wecsim-main

Body-to-Body_Interactions/TestB2B.m

@@ -53,26 +53,32 @@ function checkVisibilityRestored(testCase)
         function testB2B_Case1(testCase)
             cd('B2B_Case1')
             wecSim
+            close_system('RM3',0)
         end
         function testB2B_Case2(testCase)
             cd('B2B_Case2')
             wecSim
+            close_system('RM3',0)
         end
         function testB2B_Case3(testCase)
             cd('B2B_Case3')
             wecSim
+            close_system('RM3',0)
         end        
         function testB2B_Case4(testCase)
             cd('B2B_Case4')
             wecSim
+            close_system('RM3',0)
         end        
         function testB2B_Case5(testCase)
             cd('B2B_Case5')
             wecSim
+            close_system('RM3',0)
         end        
         function testB2B_Case6(testCase)
             cd('B2B_Case6')
             wecSim
+            close_system('RM3',0)
         end        
     end    
 end

Free_Decay/TestFreeDecay.m

@@ -53,26 +53,31 @@ function checkVisibilityRestored(testCase)
         function testFree_Decay_0m(testCase)
             cd('0m')
             wecSim
+            close_system('sphere',0)
             cd(testCase.testDir)
         end        
         function testFree_Decay_1m(testCase)
             cd('1m')
             wecSim
+            close_system('sphere',0)
             cd(testCase.testDir)
         end        
         function testFree_Decay_1m_ME(testCase)
             cd('1m-ME')
             wecSim
+            close_system('sphere',0)
             cd(testCase.testDir)
         end        
         function testFree_Decay_3m(testCase)
             cd('3m')
             wecSim
+            close_system('sphere',0)
             cd(testCase.testDir)
         end        
         function testFree_Decay_5m(testCase)
             cd('5m')
             wecSim
+            close_system('sphere',0)
             cd(testCase.testDir)
         end        
     end    

Mooring/MoorDyn/wecSimInputFile.m

@@ -1,11 +1,11 @@
 %% Simulation Data
 simu = simulationClass();             
 simu.simMechanicsFile = 'RM3MoorDyn.slx';       % WEC-Sim Model File
-simu.mode = 'accelerator';                
+simu.mode = 'accelerator';
 simu.explorer = 'off';
-simu.rampTime = 40;                        
+simu.rampTime = 40;
 simu.endTime = 400;                       
-simu.dt = 0.01;                          
+simu.dt = 0.01;
 simu.cicDt = 0.05;
 
 %% Wave Information

Mooring/TestMooring.m

@@ -56,11 +56,13 @@ function testMoorDyn(testCase)
                         "MoorDyn is not installed");
             cd MoorDyn
             wecSim
+            close_system('RM3MoorDyn',0)
             cd(testCase.testDir)
         end        
         function testMooringMatrix(testCase)
             cd MooringMatrix
             wecSim
+            close_system('RM3MooringMatrix',0)
             cd(testCase.testDir)
         end        
     end    

Morison_Element/TestMorisonElement.m

@@ -53,11 +53,13 @@ function checkVisibilityRestored(testCase)
         function testMorisonElement(testCase)
             cd('morisonElement')
             wecSim
+            close_system('monopile',0)
             cd(testCase.testDir)
         end        
         function testMonopile(testCase)
             cd('monopile')
             wecSim
+            close_system('monopile',0)
             cd(testCase.testDir)
         end        
     end    

Multiple_Condition_Runs/TestMultipleConditionRuns.m

@@ -53,18 +53,22 @@ function checkVisibilityRestored(testCase)
         function testRM3_MCROPT1(testCase)
             cd RM3_MCROPT1
             wecSimMCR
+            close_system('RM3',0)
         end        
         function testRM3_MCROPT2(testCase)
             cd RM3_MCROPT2
             wecSimMCR
+            close_system('RM3',0)
         end        
         function testRM3_MCROPT3(testCase)
             cd RM3_MCROPT3
             wecSimMCR
+            close_system('RM3',0)
         end        
         function testRM3_MCROPT3_SeaState(testCase)
             cd RM3_MCROPT3_SeaState
             wecSimMCR
+            close_system('RM3',0)
         end        
     end    
 end

Nonlinear_Hydro/TestNonlinearHydro.m

@@ -53,18 +53,22 @@ function checkVisibilityRestored(testCase)
         function testNonlinear_Hydro_ode4_Regular(testCase)
             cd(fullfile('ode4', 'Regular'))
             wecSim
+            close_system('ellipsoid',0)
         end        
         function testNonlinear_Hydro_ode4_RegularCIC(testCase)
             cd(fullfile('ode4', 'RegularCIC'))
             wecSim
+            close_system('ellipsoid',0)
         end        
         function testNonlinear_Hydro_ode45_Regular(testCase)
             cd(fullfile('ode45', 'Regular'))
             wecSim
+            close_system('ellipsoid',0)
         end        
         function testNonlinear_Hydro_ode45_RegularCIC(testCase)
             cd(fullfile('ode45', 'RegularCIC'))
             wecSim
+            close_system('ellipsoid',0)
         end        
     end    
 end

OWC/OrificeModel/hydroData/bemio.m

@@ -1,22 +1,43 @@
 %% OWC - WAMIT GBM simulation
+%% Define the despiking structure
+despike = struct();
+despike.negThresh = 1e-3; % the threshold below which negative damping will be removed
+despike.N = 5; % will loop the despiking procedure N time before filtering
+despike.appFilt = 1; % boolean, 1 to apply low pass filter after despiking
 
-%% Run BEMIO for WAMIT Run and despike the hydro data
-% 1) load deSpike.mat, to create structure depSpike in workspace.
-% 2) call >> outHydro=badBemioFix_fcn({'test17a.out'},'WAMIT',deSpike,[1,1;3,3;5,5;7,7])
-% This will despike the resonance associated with the OWC moonpool and generate an h5
-% file with the _clean suffix.
-
-load deSpike.mat
-outHydro = badBemioFix_fcn({'test17a.out'},'WAMIT',deSpike,[1,1;3,3;5,5;7,7]);
-writeBEMIOH5(outHydro);
-
-%% Run BEMIO for WAMIT Run
-
-% hydro = struct();
-% hydro = readWAMIT(hydro,'test17a.out',[]);
-% hydro = radiationIRF(hydro,20,[],[],[],11);
-% hydro = radiationIRFSS(hydro,20,[]);
-% hydro = excitationIRF(hydro,20,[],[],[],11);
-% hydro.plotDofs = [1,1;3,3;5,5;7,7];
-% writeBEMIOH5(hydro);
-% plotBEMIO(hydro);
+% thresholds: applied to 'Threshold' argument of findpeaks
+despike.B.Threshold = 2e-4; % damping
+despike.A.Threshold = 1e-3; % added mass
+despike.ExRe.Threshold = 1e-3; % real part excitation
+despike.ExIm.Threshold = 1e-3; % imag part excitation
+
+% minimum peak prominence, applied to 'MinPeakProminence' argument of findpeaks
+despike.B.Prominence = 2e-4;
+despike.A.Prominence = 1e-3;
+despike.ExRe.Prominence = 1e-3;
+despike.ExIm.Prominence = 1e-3;
+
+% minimum peak distance, applied to 'MinPeakDistance' argument of findpeaks
+despike.A.MinPeakDistance = 3;
+despike.B.MinPeakDistance = 3;
+despike.ExRe.MinPeakDistance = 3;
+despike.ExIm.MinPeakDistance = 3;
+
+% the b and a inputs to MATLAB's filtfilt(b,a,x) function
+despike.Filter.b = 0.02008336556421123561544384017452102853 .* [1 2 1];
+despike.Filter.a = [1 -1.561018075800718163392843962355982512236 0.641351538057563175243558362126350402832];
+
+%% Read and clean WAMIT results
+hydro = struct();
+hydro = readWAMIT(hydro,'test17a.out',[]);
+hydro = cleanBEM(hydro,despike);
+hydro.file = 'test17a_clean';
+
+hydro = radiationIRF(hydro,20,[],[],[],11);
+hydro = radiationIRFSS(hydro,20,[]);
+hydro = excitationIRF(hydro,20,[],[],[],11);
+
+hydro.plotDofs = [1,1;3,3;5,5;7,7];
+% plotBEMIO(hydro);
+
+writeBEMIOH5(hydro);

OWC/TestOWC.m

@@ -58,13 +58,15 @@ function checkVisibilityRestored(testCase)
         function testOWCOrifice(testCase)
             cd('OrificeModel')
             wecSim
+            close_system('OWC_rigid',0)
         end
 
         function testOWCFloating(testCase)
             assumeEqual(testCase, exist("MoorDyn_caller", "file"), 2, ...
                 "MoorDyn is not installed");
             cd('FloatingOWC')
             wecSim
+            close_system('OWC_GBM',0)
         end
     end
 end

Passive_Yaw/PassiveYawRegression/runLoadPassiveYawIrr.m

@@ -34,20 +34,20 @@
 save('IrrYaw','IrrYaw')
 
 %% Plot Old vs. New Comparison
-figure(1); % plots of yaw position
+figure(); % plots of yaw position
 subplot(1,2,1)
 plot(IrrYaw.time_new,IrrYaw.Pos_new,':k','LineWidth',1.4)
 hold on; grid on;
 plot(IrrYaw.time_org,IrrYaw.Pos_org,'-k')
 title('Passive Yaw, irregular wave')
 xlabel('Time(s)'); ylabel('Yaw position (rad)')
 subplot(1,2,2) % plots of yaw position
-plot(IrrYaw.time_new,IrrYaw.Pos_new,':k','LineWidth',1.4)
+plot(IrrYaw.time_new,IrrYaw.Force_new,':k','LineWidth',1.4)
 hold on; grid on;
-plot(IrrYaw.time_org,IrrYaw.Pos_org,'-k')
+plot(IrrYaw.time_org,IrrYaw.Force_org,'-k')
 xlabel('Time(s)'); ylabel('Total Yaw Force (N)')
 legend('New','Original')
-savefig('figYawIrr');                
+savefig('figYawIrr');
 
 %% Clear output and .slx directory
 try

Passive_Yaw/TestPassiveYaw.m

@@ -53,10 +53,12 @@ function checkVisibilityRestored(testCase)
         function testPassiveYawOFF(testCase)
             cd('PassiveYawOFF')
             wecSim
+            close_system('OSWEC',0)
         end        
         function testPassiveYawON(testCase)
             cd('PassiveYawON')
             wecSim
+            close_system('OSWEC',0)
         end        
     end    
 end

Passive_Yaw/TestPassiveYawRegression.m

@@ -32,7 +32,9 @@ function runYawIrrTest(testCase)
             cd(fullfile(testCase.testDir,   ...
                         'PassiveYawRegression'))                     
             runLoadPassiveYawIrr;
+            close_system('OSWEC',0)
             testCase.IrrYaw = load('IrrYaw.mat').("IrrYaw");
+            cd(fullfile(testCase.testDir));
         end        
     end
 

RM3_PTO_Extension/TestRM3PTOExtension.m

@@ -53,11 +53,13 @@ function checkVisibilityRestored(testCase)
         function testRM3_PTO_Extension_float(testCase)
             cd('float')
             wecSim
+            close_system('RM3',0)
             cd(testCase.testDir)
         end        
         function testRM3_PTO_Extension_spar(testCase)
             cd('spar')
             wecSim
+            close_system('RM3',0)
             cd(testCase.testDir)
         end              
     end    

Variable_Hydro/TestVariableHydro.m

@@ -69,10 +69,12 @@ function checkVisibilityRestored(testCase)
         function testPY(testCase)
             cd('Passive_Yaw')
             runCases
+            close_system('OSWEC',0)
         end
         function testVM(testCase)
             cd('Variable_Mass')
             wecSim
+            close_system('OSWEC',0)
         end
     end
 

WECCCOMP/TestWECCCOMP.m

@@ -58,10 +58,12 @@ function checkVisibilityRestored(testCase)
         function testWECCCOMP_Fault(testCase)
             cd('WECCCOMP_Fault_Implementation')
             wecSim
+            close_system('WaveStar',0)
         end
         function testWECCCOMP_MPC(testCase)
             cd('WECCCOMP_Nonlinear_Model_Predictive')
             wecSim
+            close_system('WaveStar',0)
         end    
     end
 end