Small bug fix platform.setPosition, loadDesign update, helpers, documentation updates

-- bug fix in platoform.setPosition to remove reliance on mooring_headings property. That way, if a mooring line is removed then added setPosition still works with new order
	- this required addition of a 'rel_heading' property to the mooring class.
-- new helpers functions
	- removeMooring will remove mooring object's attachments, delete the mooring object from the mooringList, and optionally re-create the MoorPy ms
	- calcMinimumDists will calculate the minimum distance between 2 lists of objects
	- calcMaterialMasses (work in progress) will calculate the total material mass of all subcomponents in an object
-- update loadDesign so that if fairleads are defined in yaml but fairlead indices are not defined in mooring setup, it will use the rFair and zFair if that is provided.
-- various documentation updates

Author: lsirkis

README.md

@@ -99,7 +99,14 @@ information in an ontology yaml file. FAD has been designed
 to work with a specific ontology yaml setup, which is described 
 in detail in the [Ontology ReadMe](./famodel/ontology/README.md).
 
-The [example driver file](./famodel/example_driver.py) creates a FAD Project 
+For examples of ontologies and driver files of common use cases, 
+we recommend starting with the numbered examples in the examples folder.
+The [visualization examples](./examples/01_Visualization/) are a good place
+to start. Run the .py files and inspect the .yaml files with the same name 
+to see what information is required for different uses and how they are conveyed
+in the ontology.
+
+To see an example with all use cases, the [example driver file](./examples/example_driver.py) creates a FAD Project 
 object from a pre-set ontology file and shows the syntax and outputs of 
 various capabilities. For guidance on creating your own ontology yaml file, 
 it is recommended to read through the [Ontology ReadMe](./famodel/ontology/README.md), 

famodel/README.md

@@ -346,12 +346,32 @@ Interpolate soil properties at specified location from the soil
 properties grid and return a dictionary of soil properties that
 can be used in anchor capacity calculations.
 
-### calcAnchorCapacity
+<!--### calcAnchorCapacity
 
 Compute holding capacity of a given anchor based on the soil
 info at its position. The anchor object's anchor properties and
 location will be used to determine the holding capacity, which
-will be saved to the anchor object.
+will be saved to the anchor object.-->
+
+### convertUniformToLayered
+
+Converts self.soilProps (uniform format) into profile_map (layered format)
+using a default thickness and assuming uniform clay profile.
+Matches the structure of layered CPT-based soil profiles.
+
+### convertLayeredToUniform
+
+Converts self.profile_map (layered format) into soilProps (uniform format)
+assuming a single clay layer with linear Su(z) = Su0 + k*z.
+Matches the structure expected by uniform soil models.
+        
+### updateAnchor
+
+update the location and soil types stored in anchor objects
+
+### setSoilAtLocation
+
+set the soil profile at the location
 
 ### getDepthAtLocation
 
@@ -376,6 +396,18 @@ and returns a matrix of these distances for the array.
 
 Calculates the cable's length based on its routing
 
+### loadBoundary
+
+Load a lease area boundary for the project from an input file.
+
+### setBoundary
+
+Set the boundaries of the project based on x-y polygon vertices
+
+### setExclusionZone
+
+Set exclusion zones of the project based on x-y vertices
+
 ### checkCableExclusions
 
 Checks whether a cable crosses over any exclusions or other out of bounds areas
@@ -385,6 +417,43 @@ Checks whether a cable crosses over any exclusions or other out of bounds areas
 Trims bathymetry and soil grid information that is outside the project boundaries, 
 for faster execution and plotting.
 
+### addPlatform
+
+Convenience method to add a platform object. Can specify a variety of information 
+about the platform such as location, entity, heading, ID, design, etc
+
+### addFairlead
+
+Method to create a fairlead object and attach it to a Platform
+
+### addMooring
+
+Function to create a mooring object  and save in mooringList
+Optionally does the following:
+    - create design dictionary if section_types, section_lengths, connectors, and span provided
+    - create id if none provided
+    - reposition mooring object and any associated anchor object, update anchor object depth for new location
+    - attach mooring object to end A and end B object
+
+### addAnchor
+
+Function to create and add an anchor to the project
+
+### addTurbine
+
+Method to create and add a Turbine object to the project
+
+### addSubstation
+
+Method to create and add a Substation object to the project.
+Note that Substation objects sit on top of platforms - the platform 
+portion of the substation is defined in the Platform object and the 
+topside information is defined in the Substation object
+
+### addJtube
+
+method to create and add a Jtube object, and attach it to a platform object
+
 ### addCablesConnections
 
 Creates cable objects from a list and connects them to platforms. If a cable configuration dictionary is provided, full 3d cable designs will be loaded in and cable headings/routing will be adjusted to avoid mooring line clashing. If only list of cable connections is provided, only basic information such as cable cross-sectional properties, conductor size, and connections will be loaded. Designed to work with the output list format from FADesign/CableLayout_functions.getCableLayout(), which will be publicly available in the near future.
@@ -423,9 +492,9 @@ Create a RAFT object and store in the project class
 Calls the addMarineGrowth mooring and/or cable class method for the chosen mooring and/or cable objects, and applies the specified marine growth thicknesses at the specified depth ranges for the specified marine growth densities.
 
 
-### getCorrosion
+<!--### getCorrosion
 
-Function to reduce MBL of specified lines based on corrosion thickness
+Function to reduce MBL of specified lines based on corrosion thickness-->
 
 ### updateUniformArray
 
@@ -464,10 +533,33 @@ Function to unload information to an ontology yaml file
 Function to extract farm-level information required to create FAST.Farm case simulations. 
 Currently under development.
 
-## FFarmCompatibleMDOutput
+### FFarmCompatibleMDOutput
 
 Function to create a FAST.Farm-compatible MoorDyn input file.
 
+### resetArrayCenter
+
+Function to reset array center such that the farm origin is the mid-point 
+between all FOWT platforms in y and the minimum_x turbine location in x:
+
+### reorientArray
+
+Reorients the array based on a given wind heading. The array will be reoriented such that wind faces East (the zero in FFarm). 
+Useful to allign the array with the wind direction.
+
+### repositionArray
+
+Method to reposition all platforms in the array at once with input arrays
+ of positions and headings
+
+### mapRAFTResults
+
+Function to map RAFT results to the project class. This
+maps the results from RAFT to the project class.
+
+### generateSheets
+
+Generates sheets in an Excel workbook with RAFT cases, platform, and mooring line information.
 
 ### getFromDict
 

famodel/helpers.py

@@ -10,6 +10,8 @@
 import moorpy as mp
 from moorpy.helpers import loadPointProps, getPointProps
 import shapely as sh
+#from famodel.mooring.mooring import Mooring
+#from famodel.platform.platform import Platform
 
 
 def cart2pol(x, y):
@@ -1136,6 +1138,44 @@ def attachFairleads(moor, end, platform, fair_ID_start=None, fair_ID=None, fair_
         end_subcons[ii].join(fairs[-1])
 
     return(fairs)
+
+def removeMooring(mooring, project, reset_ms=False):
+    '''
+    Removes mooring object from project
+
+    Parameters
+    ----------
+    mooring : TYPE
+        DESCRIPTION.
+
+    Returns
+    -------
+    None.
+
+    '''
+    if not isinstance(mooring, list):
+        mooring = [mooring]
+    
+    for moor in mooring:
+        # go through platform attachment list and find which index in mooring_headings list
+        # for att in moor.attached_to:
+        #     if hasattr(att,'rFair'):
+        #         inds_to_remove = []
+        #         for ii,attP in enumerate(att.getMoorings.values()):
+        #             if attP == moor:
+        #                 inds_to_remove.append(ii)
+        #         for ind in list(inds_to_remove.reverse()):
+        #             att.mooring_headings.pop(ind)
+        # detach mooring from each end
+        moor.detach_From('A')
+        moor.detach_From('B')
+        
+        # remove from mooringList
+        project.mooringList.pop(moor.id)
+        
+        # redo ms if asked
+        if reset_ms:
+            project.getMoorPyArray()
 
 def calc_heading(pointA, pointB):
     '''calculate a compass heading from points, if pointA or pointB is a list of points,
@@ -1480,6 +1520,67 @@ def compareDicts(d1, d2):
             return(False)
     return(True)
 
+def calcMinimumDists(obj_list_A,obj_list_B=None, coords_list=None):
+    '''
+    Calculates and returns the minimum distance between 2 lists of objects.
+
+    Parameters
+    ----------
+    obj_list_A : list
+        List of component objects to calculate distance from second list
+    obj_list_B : list, optional
+        Second list of component objects to calculate distance from obj_list_A locations
+    coords_list : list, optional
+        List of coordinates, such as a lease boundary, to compare distance from obj_list_A
+
+    Returns
+    -------
+    A2B : float
+        Minimum distance between the compared locations
+
+    '''
+    A2B=np.inf
+    
+    if obj_list_B is not None:
+        for objA in obj_list_A:
+            for objB in obj_list_B:
+                if objA != objB:
+                    dist = np.linalg.norm(np.array(objA.r[:2]) - np.array(objB.r[:2]))
+                    A2B = min(A2B, dist)
+    elif coords_list!=None:
+        for objA in obj_list_A:
+            dist = np.linalg.norm(objA.r[:2] - coords_list, axis=1)
+            A2B = min(A2B, np.min(dist))
+    else:
+        raise Exception('Either obj_list_B or coords_list must not be None')
+        
+    return(A2B)
+
+def calcMaterialMasses(obj_list):
+    '''
+    Calculates and returns the sum of masses for each material used in the list of objects
+    
+    For example, a list of mooring lines composed of chain and polyester would return 
+    the total mass of chain across all lines and the total mass of polyester across all lines
+    '''
+    masses={}
+    
+    for obj in obj_list:
+        if hasattr(obj, 'ss'):
+            # pull out list of subcomponent masses by material
+            for line in obj.ss.lineList:
+                mat = line.type['material']
+                if not mat in masses:
+                    masses[mat] = 0
+                masses[mat] += line.type['mass']*line.L
+        elif hasattr(obj, 'm'):
+            # check if there's a type or entity
+            if hasattr(obj,'entity'):
+                if not obj.entity in masses:
+                    masses[obj.entity] = 0 
+                masses[obj.entity] += obj.m
+
+
 def cleanDataTypes(info, convert_lists=True):
     '''
     cleans data types in a dictionary to be yaml-writeable data types, usually for 

famodel/mooring/mooring.py

@@ -184,6 +184,7 @@ def __init__(self, dd=None, subsystem=None, anchor=None,
         # end point absolute coordinates, to be set later
         self.rA = np.array([-self.rad_anch, 0, self.z_anch])
         self.rB = np.array([-self.rad_fair, 0, self.z_fair])
+        self.rel_heading = 270 # compass heading relative to platform B heading
         self.heading = 270  # compass heading from B to A [deg]
 
         self.adjuster = None  # custom function that can adjust the mooring
@@ -890,6 +891,8 @@ def updateState(self, stateDict, ms=None):
             - 'creep': Boolean indicating whether to apply creep.
             - 'corrosion': Boolean indicating whether to apply corrosion.
             - 'marineGrowth': Dictionary for marine growth configuration (same as addMarineGrowth).
+        ms : MoorPy system, optional
+            Overall moorpy system that is associated with this
         '''
 
         # Extract global number of years

famodel/platform/platform.py

@@ -46,9 +46,9 @@ def __init__(self, id, r=[0,0,0], heading=0, mooring_headings=[60,180,300],rFair
 
         self.body = None # body object in MoorPy associated with the platform
 
-        self.mooring_headings = list(np.radians(mooring_headings)) # headings of mooring lines [rad]
+        # self.mooring_headings = list(np.radians(mooring_headings)) # headings of mooring lines [rad]
 
-        self.n_mooring = len(mooring_headings) # number of mooring lines
+        # self.n_mooring = len(mooring_headings) # number of mooring lines
 
         self.entity = None # describes what type of platform this is/what its topside carries (for floating wind turbine, entity = 'FOWT', for substation, entity = 'OSS')
 
@@ -83,7 +83,8 @@ def setPosition(self, r, heading=None, degrees=False,project=None, update_moorin
             The heading of the platform [deg or rad] depending on
             degrees parameter (True or False) in compass direction
         '''
-        
+        # store old platform heading
+        old_phi = self.phi
 
         # first call the Node method to take care of the platform and what's directly attached
         if heading: # save compass heading in radians
@@ -99,36 +100,26 @@ def setPosition(self, r, heading=None, degrees=False,project=None, update_moorin
         # Update the position of any Moorings
         count = 0 # mooring counter (there are some attachments that aren't moorings)
         if update_moorings:
-            for i, att in enumerate(self.attachments):
-                if isinstance(self.attachments[att]['obj'], Mooring): 
-                    # Heading of the mooring line
-                    heading_i = self.mooring_headings[count] + self.phi
-                    # Reposition the whole Mooring if it is an anchored line
-                    if not self.attachments[att]['obj'].shared:
-                        self.attachments[att]['obj'].reposition(r_center=self.r, heading=heading_i,project=project)
-                    
-                    count += 1
-                    
-                if isinstance(self.attachments[att]['obj'], Cable):
-                    
-                    cab = self.attachments[att]['obj']
-                    
-                    # update heading stored in subcomponent for attached end
-                    # pf_phis = [cab.attached_to[0].phi, cab.attached_to[1].phi]
-                    # headings = [cab.subcomponents[0].headingA + pf_phis[0], cab.subcomponents[-1].headingB + pf_phis[1]]
+            for moor in self.getMoorings().values():
+                # Heading of the mooring line
+                heading_i = np.radians(moor.rel_heading) + self.phi #self.attachments[att]['obj'].heading - old_phi + self.phi
+                # Reposition the whole Mooring if it is an anchored line
+                if not moor.shared:
+                    moor.reposition(r_center=self.r, heading=heading_i,project=project)
+
 
-                    # reposition the cable
-                    cab.reposition(project=project)            
+            for cab in self.getCables().values():
+                
+                # reposition the cable
+                cab.reposition(project=project)            
 
         self.updateMooringPoints()
 
         if not update_moorings:
             # update span in case it changed if pf location changes but anchor does not 
-            for i, att in enumerate(self.attachments):
-                if isinstance(self.attachments[att]['obj'], Mooring):
-                    moor = self.attachments[att]['obj']
-                    moor.dd['span'] = np.linalg.norm(moor.rA[:2]-moor.rB[:2])
-                    moor.span=moor.dd['span']
+            for moor in self.getMoorings().values():
+                moor.dd['span'] = np.linalg.norm(moor.rA[:2]-moor.rB[:2])
+                moor.span=moor.dd['span']
 
     def mooringSystem(self,rotateBool=0,mList=None,bodyInfo=None, project=None):
         '''