[Bug fix] Mac path fixes and make outputDir public (#874)

* Moved simulationClass.outputDir to public. * Replaced paths with fullfile paths in CompareBEMIO.m. The paths didd not work on Mac due to file separator. * Update line 38 in reaadAQWA.m so it works on a Mac. * change filesep in BEMIO examples, update readAQWA fileparts * Update stopWecSim.m Replaced hardcoded 'output' string with simu.outputDir. * Removed clc and close all from initializeWecSim. It should be up to the user to clear the command windows and close the figures. Co-authored-by: Lermart96 <anders.brandt@oceanharvesting.com> Co-authored-by: akeeste <akeeste@sandia.gov>
WEC-Sim · akeeste · Jul 1, 2022 · May 20, 2022 · May 20, 2022 · Jun 29, 2022
commit 466c1ce4abecb7d829fa30c137a5b03d31ae3ca4
diff --git a/examples/BEMIO/CAPYTAINE/coer_comp/bemio.m b/examples/BEMIO/CAPYTAINE/coer_comp/bemio.m
@@ -1,6 +1,6 @@
 hydro = struct();
 
-hydro = readCAPYTAINE(hydro,'.\coer_comp_full.nc');
+hydro = readCAPYTAINE(hydro,'coer_comp_full.nc');
 hydro = radiationIRF(hydro,10,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);
 hydro = excitationIRF(hydro,20,[],[],[],[]);

diff --git a/examples/BEMIO/CAPYTAINE/cubes/bemio.m b/examples/BEMIO/CAPYTAINE/cubes/bemio.m
@@ -1,6 +1,6 @@
 hydro = struct();
 
-hydro = readCAPYTAINE(hydro,'.\cubes_full.nc');
+hydro = readCAPYTAINE(hydro,'cubes_full.nc');
 hydro = radiationIRF(hydro,30,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);
 hydro = excitationIRF(hydro,200,[],[],[],[]);

diff --git a/examples/BEMIO/CAPYTAINE/cylinder/bemio.m b/examples/BEMIO/CAPYTAINE/cylinder/bemio.m
@@ -1,6 +1,6 @@
 hydro = struct();
 
-hydro = readCAPYTAINE(hydro,'.\cylinder_full.nc');
+hydro = readCAPYTAINE(hydro,'cylinder_full.nc');
 hydro = radiationIRF(hydro,15,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);
 hydro = excitationIRF(hydro,15,[],[],[],[]);

diff --git a/examples/BEMIO/CAPYTAINE/ellipsoid/bemio.m b/examples/BEMIO/CAPYTAINE/ellipsoid/bemio.m
@@ -1,6 +1,6 @@
 hydro = struct();
 
-hydro = readCAPYTAINE(hydro,'.\ellipsoid_full.nc');
+hydro = readCAPYTAINE(hydro,'ellipsoid_full.nc');
 hydro = radiationIRF(hydro,15,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);
 hydro = excitationIRF(hydro,15,[],[],[],[]);

diff --git a/examples/BEMIO/CAPYTAINE/oswec/bemio.m b/examples/BEMIO/CAPYTAINE/oswec/bemio.m
@@ -1,6 +1,6 @@
 hydro = struct();
 
-hydro = readCAPYTAINE(hydro,'.\oswec_full.nc');
+hydro = readCAPYTAINE(hydro,'oswec_full.nc');
 hydro = radiationIRF(hydro,40,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);
 hydro = excitationIRF(hydro,75,[],[],[],[]);

diff --git a/examples/BEMIO/CAPYTAINE/rm3/bemio.m b/examples/BEMIO/CAPYTAINE/rm3/bemio.m
@@ -1,6 +1,6 @@
 hydro = struct();
 
-hydro = readCAPYTAINE(hydro,'.\rm3_full.nc');
+hydro = readCAPYTAINE(hydro,'rm3_full.nc');
 hydro = radiationIRF(hydro,60,[],[],[],1.9);
 hydro = radiationIRFSS(hydro,[],[]);
 hydro = excitationIRF(hydro,157,[],[],[],1.9);

diff --git a/examples/BEMIO/CAPYTAINE/sphere/bemio.m b/examples/BEMIO/CAPYTAINE/sphere/bemio.m
@@ -1,6 +1,6 @@
 hydro = struct();
 
-hydro = readCAPYTAINE(hydro,'.\sphere_full.nc');
+hydro = readCAPYTAINE(hydro,'sphere_full.nc');
 hydro = radiationIRF(hydro,15,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);
 hydro = excitationIRF(hydro,15,[],[],[],[]);

diff --git a/examples/BEMIO/NEMOH/Coer_Comp/bemio.m b/examples/BEMIO/NEMOH/Coer_Comp/bemio.m
@@ -1,7 +1,7 @@
 hydro = struct();
 
-hydro = readNEMOH(hydro,'..\Coer_Comp\');
-% hydro = readWAMIT(hydro,'..\..\WAMIT\Coer_Comp\coer_comp.out',[]);
+hydro = readNEMOH(hydro,'../Coer_Comp/');
+% hydro = readWAMIT(hydro,'../../WAMIT/Coer_Comp/coer_comp.out',[]);
 % hydro = combineBEM(hydro); % Compare to WAMIT
 hydro = radiationIRF(hydro,10,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);

diff --git a/examples/BEMIO/NEMOH/Cubes/bemio.m b/examples/BEMIO/NEMOH/Cubes/bemio.m
@@ -1,7 +1,7 @@
 hydro = struct();
 
-hydro = readNEMOH(hydro,'..\Cubes\');
-% hydro = readWAMIT(hydro,'..\..\WAMIT\Cubes\cubes.out',[]);
+hydro = readNEMOH(hydro,'../Cubes/');
+% hydro = readWAMIT(hydro,'../../WAMIT/Cubes/cubes.out',[]);
 % hydro = combineBEM(hydro); % Compare WAMIT
 hydro = radiationIRF(hydro,20,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);

diff --git a/examples/BEMIO/NEMOH/Cylinder/bemio.m b/examples/BEMIO/NEMOH/Cylinder/bemio.m
@@ -1,7 +1,7 @@
 hydro = struct();
 
-hydro = readNEMOH(hydro,'..\Cylinder\');
-% hydro = readWAMIT(hydro,'..\..\WAMIT\Cylinder\cyl.out',[]);
+hydro = readNEMOH(hydro,'../Cylinder/');
+% hydro = readWAMIT(hydro,'../../WAMIT/Cylinder/cyl.out',[]);
 % hydro = combineBEM(hydro);   % Compare to WAMIT
 hydro = radiationIRF(hydro,5,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);

diff --git a/examples/BEMIO/NEMOH/Ellipsoid/bemio.m b/examples/BEMIO/NEMOH/Ellipsoid/bemio.m
@@ -1,7 +1,7 @@
 hydro = struct();
 
-hydro = readNEMOH(hydro,'..\Ellipsoid\');
-% hydro = readWAMIT(hydro,'..\..\WAMIT\Ellipsoid\ellipsoid.out',[]);
+hydro = readNEMOH(hydro,'../Ellipsoid/');
+% hydro = readWAMIT(hydro,'../../WAMIT/Ellipsoid/ellipsoid.out',[]);
 % hydro = combineBEM(hydro); % Compare to WAMIT
 hydro = radiationIRF(hydro,10,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);

diff --git a/examples/BEMIO/NEMOH/OSWEC/bemio.m b/examples/BEMIO/NEMOH/OSWEC/bemio.m
@@ -1,7 +1,7 @@
 hydro = struct();
 
-hydro = readNEMOH(hydro,'..\OSWEC\');
-% hydro = readWAMIT(hydro,'..\..\WAMIT\OSWEC\oswec.out',[]);
+hydro = readNEMOH(hydro,'../OSWEC/');
+% hydro = readWAMIT(hydro,'../../WAMIT/OSWEC/oswec.out',[]);
 % hydro = combineBEM(hydro); % Compare WAMIT
 hydro = radiationIRF(hydro,20,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);

diff --git a/examples/BEMIO/NEMOH/RM3/bemio.m b/examples/BEMIO/NEMOH/RM3/bemio.m
@@ -1,7 +1,7 @@
 hydro = struct();
 
-hydro = readNEMOH(hydro,'..\RM3\');
-% hydro = readWAMIT(hydro,'..\..\WAMIT\RM3\rm3.out',[]);
+hydro = readNEMOH(hydro,'../RM3/');
+% hydro = readWAMIT(hydro,'../../WAMIT/RM3/rm3.out',[]);
 % hydro = combineBEM(hydro); % Compare WAMIT
 hydro = radiationIRF(hydro,60,[],[],[],1.9);
 hydro = radiationIRFSS(hydro,[],[]);

diff --git a/examples/BEMIO/NEMOH/Sphere/bemio.m b/examples/BEMIO/NEMOH/Sphere/bemio.m
@@ -1,7 +1,7 @@
 hydro = struct();
 
-hydro = readNEMOH(hydro,'..\Sphere\');
-% hydro = readWAMIT(hydro,'..\..\WAMIT\Sphere\sphere.out',[]);
+hydro = readNEMOH(hydro,'../Sphere/');
+% hydro = readWAMIT(hydro,'../../WAMIT/Sphere/sphere.out',[]);
 % hydro = combineBEM(hydro); % Compare to WAMIT
 hydro = radiationIRF(hydro,15,[],[],[],[]);
 hydro = radiationIRFSS(hydro,[],[]);

diff --git a/examples/BEMIO/compareBEMIO.m b/examples/BEMIO/compareBEMIO.m
@@ -5,7 +5,7 @@
 
 % Load WAMIT hydro data 
 WAMIT_hydro = struct();
-WAMIT_out = '.\WAMIT\Sphere\sphere.out';
+WAMIT_out = fullfile('.', 'WAMIT', 'Sphere', 'sphere.out');
 WAMIT_hydro = readWAMIT(WAMIT_hydro,WAMIT_out,[]);
 WAMIT_hydro = radiationIRF(WAMIT_hydro,15,[],[],[],[]);
 WAMIT_hydro = excitationIRF(WAMIT_hydro,15,[],[],[],[]);
@@ -14,15 +14,15 @@
 
 % Load AQWA hydro data 
 AQWA_hydro = struct();
-AQWA_AH1 = '.\AQWA\Sphere\sphere.AH1';
-AQWA_LIS = '.\AQWA\Sphere\sphere.LIS';
+AQWA_AH1 = fullfile('.','AQWA', 'Sphere', 'sphere.AH1');
+AQWA_LIS = fullfile('.','AQWA', 'Sphere', 'sphere.LIS');
 AQWA_hydro = readAQWA(AQWA_hydro, AQWA_AH1, AQWA_LIS);
 AQWA_hydro = radiationIRF(AQWA_hydro,15,[],[],[],[]);
 AQWA_hydro = excitationIRF(AQWA_hydro,15,[],[],[],[]);
 
 % Load Capytaine hydro data 
 CAP_hydro = struct();
-CAP_nc = '.\Capytaine\Sphere\sphere_full.nc';
+CAP_nc = fullfile('.', 'Capytaine', 'Sphere', 'sphere_full.nc');
 CAP_hydro = readCAPYTAINE(CAP_hydro,CAP_nc);
 CAP_hydro = radiationIRF(CAP_hydro,15,[],[],[],[]);
 CAP_hydro = excitationIRF(CAP_hydro,15,[],[],[],[]);
@@ -43,29 +43,29 @@
 
 % Load WAMIT hydro data 
 WAMIT_hydro = struct();
-WAMIT_out = '.\WAMIT\RM3\rm3.out';
+WAMIT_out = fullfile('.', 'WAMIT', 'RM3', 'rm3.out');
 WAMIT_hydro = readWAMIT(WAMIT_hydro,WAMIT_out,[]);
 WAMIT_hydro = radiationIRF(WAMIT_hydro,60,[],[],[],[]);
 WAMIT_hydro = excitationIRF(WAMIT_hydro,20,[],[],[],[]);
 
 % Load AQWA hydro data 
 AQWA_hydro = struct();
-AQWA_AH1 = '.\AQWA\RM3\RM3.AH1';
-AQWA_LIS = '.\AQWA\RM3\RM3.LIS';
+AQWA_AH1 = fullfile('.', 'AQWA', 'RM3', 'RM3.AH1');
+AQWA_LIS = fullfile('.', 'AQWA', 'RM3', 'RM3.LIS');
 AQWA_hydro = readAQWA(AQWA_hydro, AQWA_AH1, AQWA_LIS);
 AQWA_hydro = radiationIRF(AQWA_hydro,60,[],[],[],[]);
 AQWA_hydro = excitationIRF(AQWA_hydro,20,[],[],[],[]);
 
 % Load Capytaine hydro data 
 CAP_hydro = struct();
-CAP_nc = '.\Capytaine\RM3\rm3_full.nc';
+CAP_nc = fullfile('.', 'Capytaine', 'RM3', 'rm3_full.nc');
 CAP_hydro = readCAPYTAINE(CAP_hydro,CAP_nc);
 CAP_hydro = radiationIRF(CAP_hydro,60,[],[],[],1.9);
 CAP_hydro = excitationIRF(CAP_hydro,20,[],[],[],1.9);
 
 % Load NEMOH hydro data 
 NEMOH_hydro = struct();
-NEMOH_dir = '.\NEMOH\RM3';
+NEMOH_dir = fullfile('.', 'NEMOH', 'RM3');
 NEMOH_hydro = readNEMOH(NEMOH_hydro,NEMOH_dir);
 NEMOH_hydro = radiationIRF(NEMOH_hydro,60,[],[],[],1.9);
 NEMOH_hydro = excitationIRF(NEMOH_hydro,20,[],[],[],1.9);
@@ -86,15 +86,15 @@
 
 % Load WAMIT hydro data 
 WAMIT_hydro = struct();
-WAMIT_out = '.\WAMIT\WEC3\wec3.out';
+WAMIT_out = fullfile('.', 'WAMIT', 'WEC3', 'wec3.out');
 WAMIT_hydro = readWAMIT(WAMIT_hydro,WAMIT_out,[]);
 WAMIT_hydro = radiationIRF(WAMIT_hydro,160,[],[],[],[]);
 WAMIT_hydro = excitationIRF(WAMIT_hydro,160,[],[],[],[]);
 
 % Load AQWA hydro data 
 AQWA_hydro = struct();
-AQWA_AH1 = '.\AQWA\WEC3\wec3.AH1';
-AQWA_LIS = '.\AQWA\WEC3\wec3.LIS';
+AQWA_AH1 = fullfile('.', 'AQWA', 'WEC3', 'wec3.AH1');
+AQWA_LIS = fullfile('.', 'AQWA', 'WEC3', 'wec3.LIS');
 AQWA_hydro = readAQWA(AQWA_hydro, AQWA_AH1, AQWA_LIS);
 AQWA_hydro = radiationIRF(AQWA_hydro,160,[],[],[],[]);
 AQWA_hydro = excitationIRF(AQWA_hydro,160,[],[],[],[]);

diff --git a/source/functions/BEMIO/readAQWA.m b/source/functions/BEMIO/readAQWA.m
@@ -35,8 +35,8 @@
 
 hydro(F).code   = 'AQWA';
 V182            = 0; % Set AqwaVersion flag "Version 18.2 or larger" to 0
-tmp             = strsplit(ah1Filename,{' ','\','.'});
-hydro(F).file   = tmp{length(tmp)-1};  % Base filename
+[~,tmp,~]       = fileparts(ah1Filename);
+hydro(F).file   = tmp;  % Base filename
 
 fileID          = fopen(ah1Filename);
 raw1            = textscan(fileID,'%[^\n\r]'); %Read/copy raw output, ah1

diff --git a/source/functions/initializeWecSim.m b/source/functions/initializeWecSim.m
@@ -19,7 +19,7 @@
 
 %% Start WEC-Sim log
 % Clear old input, plots, log file and start new log file.
-clc; diary off; close all;
+diary off
 clear body waves simu output pto constraint ptoSim mooring values names InParam
 try delete('*.log'); end
 diary('simulation.log')

diff --git a/source/functions/stopWecSim.m b/source/functions/stopWecSim.m
@@ -47,7 +47,7 @@
        cd(pctDir);
        simu.caseDir = [simu.caseDir filesep pctDir];
     end
-    outputFile = [simu.caseDir filesep 'output' filesep simu.caseFile];
+    outputFile = [simu.caseDir filesep simu.outputDir filesep simu.caseFile];
     save(outputFile,'-v7.3')
     if exist('pctDir') 
         filename = sprintf('savedData%03d.mat', imcr);

diff --git a/source/objects/simulationClass.m b/source/objects/simulationClass.m
@@ -62,6 +62,7 @@
         stateSpace          = 0                                            % (`integer`) Flag for convolution integral or state-space calculation, Options: 0 (convolution integral), 1 (state-space). Default = ``0``
         startTime           = 0                                            % (`float`) Simulation start time. Default = ``0`` s        
         zeroCross           = 'DisableAll'                                 % (`string`) Disable zero cross control. Default = ``'DisableAll'``
+        outputDir           = 'output'                                     % (`string`) Data output directory name. Default = ``'output'``
     end
 
     properties (SetAccess = 'public', GetAccess = 'public') % internal WEC-Sim
@@ -83,7 +84,6 @@
         date                = datetime                                     % (`string`) Simulation date and time
         gitCommit           = []                                           % (`string`) GitHub commit
         maxIt               = []                                           % (`integer`) Total number of simulation time steps. Approximate for variable step solvers. Default = dependent
-        outputDir           = 'output'                                     % (`string`) Data output directory name. Default = ``'output'``
         wsVersion           = '5.0'                                        % (`string`) WEC-Sim version
     end