Resolve conflicts between variable hydro and GBM (WEC-Sim#1317)

* fix linearDamping expansion in GBM

* fix linearDamping expansion in GBM v2

* prevent GBM and variable hydro together

* update MoorDyn README based on one in WEC-Sim/MoorDyn repo

* prevent user defined Fexc and VH together

* fixed user defined functions

* fix GBM and VH compatibility

source/functions/initializeWecSim.m

@@ -161,7 +161,7 @@
 dragBodLogic = zeros(length(body(1,:)),1);
 for ii = 1:length(body(1,:))
     body(ii).setNumber(ii);
-    body(ii).checkInputs(simu.explorer, simu.stateSpace, simu.FIR);
+    body(ii).checkInputs(simu.explorer, simu.stateSpace, simu.FIR, waves.typeNum);
     if body(ii).nonHydro==0
         if numNonHydroBodies > 0 || numDragBodies > 0
             error('All hydro bodies must be specified before any drag or non-hydro bodies.')

source/functions/moorDyn/README.md

@@ -29,7 +29,7 @@ along with MoorDyn.  If not, see <http://www.gnu.org/licenses/>.
 
 ---------------------- More Information -------------------------
 
-More information about MoorDyn is now available at <moordyn.readthedocs.io> -- including the User's Guide, source code, and examples.  
+More information about MoorDyn is now available at [moordyn.readthedocs.io](https://moordyn.readthedocs.io/en/latest/) -- including the User's Guide, source code, and examples.  
 
 For information about MoorDyn's formulation and some validation 
 results, see M. Hall and A. Goupee, ìValidation of a lumped-mass 

source/objects/bodyClass.m

@@ -46,7 +46,7 @@
             'angle',                                0)                      % (`structure`) Defines the initial displacement of the body. ``displacement`` (`1x3 float vector`) is defined as the initial displacement of the body center of gravity (COG) [m] in the following format [x y z], Default = [``0 0 0``]. ``axis`` (`1x3 float vector`) is defined as the axis of rotation in the following format [x y z], Default = [``0 1 0``]. ``angle`` (`float`) is defined as the initial angular displacement of the body COG [rad], Default = ``0``.
         largeXYDisplacement (1,1) struct            = struct(...            %
             'option',                               0)                      %
-        linearDamping (6,6,:) {mustBeNumeric}       = zeros(6)              % (`6x6 float matrix`) Defines linear damping coefficient matrix. Create a 3D matrix (6x6xn) for variable hydrodynamics. Default = ``zeros(6)``.
+        linearDamping {mustBeNumeric}               = zeros(6)              % (`6x6 float matrix`) Defines linear damping coefficient matrix. Create a 3D matrix (6x6xn) for variable hydrodynamics. Default = ``zeros(6)``.
         mass (1,:)                                  = []                    % (`float`) Translational inertia or mass [kg]. Defined by the user or specify 'equilibrium' to set the mass equal to the fluid density times displaced volume. Default = ``[]``.
         meanDrift (1,1) {mustBeInteger}             = 0                     % (`integer`) Flag for mean drift force, Options:  0 (no), 1 (yes, from control surface) or 2 (yes, from momentum conservation). Default = ``0``.
         morisonElement (1,1) struct                 = struct(...            % (`structure`) Defines the Morison Element properties connected to the body.
@@ -132,7 +132,7 @@
 
         end
 
-        function checkInputs(obj, explorer, stateSpace, FIR)
+        function checkInputs(obj, explorer, stateSpace, FIR, typeNum)
             % This method checks WEC-Sim user inputs for each body and generates error messages if parameters are not properly defined for the bodyClass
 
             % Check struct inputs:
@@ -302,6 +302,9 @@ function checkInputs(obj, explorer, stateSpace, FIR)
                     if FIR == 1
                         error('The FIR filter radiation force method is not compatible with variable hydrodynamics.');
                     end
+                    if typeNum >= 30
+                        error('The user defined wave excitation force is not compatible with variable hydrodynamics.');
+                    end
                 end
             elseif obj.nonHydro>0
                 % This method checks WEC-Sim user inputs for each drag or non-hydro
@@ -354,6 +357,9 @@ function loadHydroData(obj, hydroData, iH)
                 obj.dofEnd          = hydroData.properties.dofEnd;
                 obj.gbmDOF          = obj.dof-6;
             end
+            if obj.dof > 6 && obj.variableHydro.option == 1
+                error('Variable hydro is not compatible with Generalized body modes.');
+            end
         end
 
         function nonHydroForcePre(obj,rho)
@@ -403,13 +409,18 @@ function hydroForcePre(obj, waves, simu, iH)
                 % obj.linearDamping = [obj.linearDamping zeros(1,obj.dof-length(obj.linearDamping))];
                 tmp0 = obj.linearDamping;
                 tmp1 = size(obj.linearDamping);
-                obj.linearDamping = zeros(obj.dof, obj.dof, tmp1(3));
-                obj.linearDamping(1:tmp1(1),1:tmp1(2),:) = tmp0;
+                if ndims(tmp0) > 2
+                    obj.linearDamping = zeros(obj.dof, obj.dof, tmp1(3));
+                    obj.linearDamping(1:tmp1(1),1:tmp1(2),:) = tmp0;
+                else
+                    obj.linearDamping = zeros(obj.dof);
+                    obj.linearDamping(1:tmp1(1),1:tmp1(2)) = tmp0;
+                end
 
                 for i = 1:length(obj.quadDrag)
                     tmp0 = obj.quadDrag(i).drag;
                     tmp1 = size(obj.quadDrag(i).drag);
-                    obj.quadDrag(i).drag = zeros (obj.dof);
+                    obj.quadDrag(i).drag = zeros(obj.dof);
                     obj.quadDrag(i).drag(1:tmp1(1),1:tmp1(2)) = tmp0;
 
                     obj.quadDrag(i).cd   = [obj.quadDrag(i).cd   zeros(1,obj.dof-length(obj.quadDrag(i).cd))];