Small layout.py & project fix, add layout official example

-- small layout.py fix to work with previous mooringAdjust update that allows multiple line sections to be adjusted for depth
-- small project fix to allow read-in and write-out of exclusion zones to & from ontology files
	- also removed fake exclusion zones from examples & test ontologies to prevent confusion
-- added layout example to examples/06_Design folder
	- includes adjusting mooring and 3D cable design for bathymetry and adjusting cable routing

Author: lsirkis

examples/01_Visualization/project.yaml

@@ -0,0 +1,260 @@
+# -*- coding: utf-8 -*-
+"""
+This example shows a layout optimization with varied bathymetry and soil
+and then application of 3D cable designs, FOWT and substation design details,
+cable rerouting to avoid obstacles, and more.
+
+Layout objects inherit from Project, so they have access to all the
+project methods (including unload etc)
+
+An alternative method to including layout inputs is shown in the example at the bottom of 
+famodel/design/layout.py
+
+This example will take a long time to run if not used on an HPC with the 
+layout setting parallel=True. To simply see what the initial layout looks like 
+instead of optimizing, comment out the sections labeled **COMMENT OUT TO SKIP OPTIMIZATION PROCESS**
+"""
+
+from copy import deepcopy
+import numpy as np
+import moorpy as mp
+import famodel
+from famodel.design.layout import Layout
+from floris import (
+    TimeSeries,
+    WindRose,
+    )
+from moorpy.helpers import lines2ss
+import pandas as pd
+from famodel.mooring.mooring import Mooring
+from famodel.anchors.anchor import Anchor
+from famodel.helpers import adjustMooring
+import ruamel.yaml
+yaml = ruamel.yaml.YAML()
+from pyswarm import pso # change to whatever optimizer you're using
+from famodel.helpers import createRAFTDict
+from famodel.helpers import route_around_anchors
+import os
+
+# - - - - - Input Files
+dir = os.path.dirname(os.path.realpath(__file__))
+mdFile = os.path.join(dir,'Layout_Inputs','FCD_MoorDyn_ST.dat')
+cableFile =  os.path.join(dir,'Layout_Inputs','cableConfigMaine.yaml')
+bathFile =  os.path.join(dir,'Layout_Inputs','GulfofMaine_bathy.txt')
+soilFile =  os.path.join(dir,'Layout_Inputs','GulfofMaine_soil.txt')
+florisFile =  os.path.join(dir,'Layout_Inputs','gch_floating.yaml')
+turbineFile =  os.path.join(dir,'Layout_Inputs','IEA-15-240-RWT.yaml')
+fowtFile =  os.path.join(dir,'Layout_Inputs','VolturnUS.yaml')
+subFile =  os.path.join(dir,'Layout_Inputs','substation.yaml')
+wfile = os.path.join(dir,'Layout_Inputs','GulfOfMaine_metocean_1hr.txt')
+
+# ----- Layout input information
+nt = 20 # number of turbines
+noss = 1 # number of substations
+# conductor sizes for cables
+iac_typical_conductor = np.array([300, 630, 1000])
+# this examle uses a rectangular lease area, but can have any shape you want
+lease_width = 10000 # length/width of the lease area
+lease_length = 10000
+oss_coords = np.array([[0, 0]]) # approx location of oss, will be updated by optimizer to fit in uniform grid
+lease_coords = np.array([
+                        (-lease_width/2, -lease_length/2),
+                        (-lease_width/2, lease_length/2),
+                        (lease_width/2, lease_length/2),
+                        (lease_width/2, -lease_length/2)
+                        ])
+exclusion_coords = np.array([[(2800, 500), # coordinates for an exclusion zone within the lease
+                    (4000, 500),
+                    (3600, 3400),
+                    (2800, 3400),
+                    (2800, 500)]])
+
+# ----- Optimization inputs -----
+opt_mode = 'CAPEX'  # what do you want to optimize? (LCOE = 'LCOE2', AEP='AEP', CapEx='CAPEX')
+opt_method = 'PSO' # optimizer type
+use_FLORIS = False # Change to true if you're running AEP or LCOE optimization
+# Uniform grid design variables initial values (Xu): [x-spacing [km], y-spacing [km], x-translation [km], y-translation [km], grid rotation [deg], grid skew [deg], platform rotation [deg]]
+Xu = [1.65,   1.85, 0, 0 , 20, 10,  0] # this is the initial values for the uniform grid design variables, these will be changed by the optimizer
+# lower and upper boundaries for each design variable in Xu
+boundaries_UG = np.array(([1.111,2.7],[1.111,2.7],[-2.0,2.0],[-2.0,2.0],[0,180],[-30,30],[0,120]))
+swarmsize = 2 # this is a small number for this example, generally would use swarmsize of well over 100+
+niterations = 2 # this is a small number for this example, generally would use well over 100+ iterations
+
+
+
+# ---- LOAD MOORPY SYSTEM -----
+ms = mp.System(file=mdFile)
+ms.initialize()
+ms.solveEquilibrium()
+
+# add in needed info from getLineProps (MBL,cost,d_nom)
+for typ in ms.lineTypes.values():
+    if 'chain' in typ['material']:
+        d_nom = typ['d_vol']/1.8
+        ms.setLineType(d_nom*1000,'chain',name=typ['name'])
+    elif 'poly' in typ['material']:
+        d_nom = typ['d_vol']/.86
+        ms.setLineType(d_nom*1000,'polyester',name=typ['name'])
+        
+msNew = lines2ss(ms)
+
+ss = deepcopy(msNew.lineList[0])
+ss.rad_fair = 58
+ss.z_fair = -14
+rotation_mode = True
+rot_rad = np.zeros((nt))
+
+
+# ----- LOAD WIND DATA -----
+colnames = ['YY','MM','DD','hh','WDIR10m','WSPD10m','WDIR150m','WSPD150m','MWD','WVHT','DPD','CDIR','CSPD','ATMP10m','WTMP']
+
+df = pd.read_csv(wfile,sep='\t',engine='python',header=5,names=colnames)
+
+ws = np.array(df['WSPD150m'].tolist())
+wd = np.array(df['WDIR150m'].tolist())
+
+time_series = TimeSeries(
+    wind_directions=wd, wind_speeds=ws, turbulence_intensities=0.06
+)
+# The TimeSeries class has a method to generate a wind rose from a time series based on binning
+wind_rose = time_series.to_WindRose(wd_step=5, ws_step=1)
+
+
+# ----- SETUP LAYOUT SETTINGS -----
+anchor_settings = {'anchor_design':{'A':15,'zlug':20},
+                   'anchor_type':'DEA',
+                   'anchor_resize':False,
+                   'fix_zlug':True,
+                   'FSdiff_max':{'Ha':.1,'Va':.2},
+                   'FS_min':{'Ha':2,'Va':0},
+                   'mass':9159}
+
+# mooring line adjustment settings
+adjuster_settings = {'method': 'horizontal', # adjust horizontal pretension when bathymetry changes
+                     'i_line': [1], # index of line section to be altered to fit bathymetry
+                     'span': 700-58, # horizontal distance from anchor to fairlead
+                     }
+
+layout_settings = {
+                   'n_turbines': nt,
+                   'n_cluster': 3, # number of cable strings entering each substation
+                   'turb_rot': np.zeros((nt)),
+                   'rotation_mode': True,
+                   'cable_mode': True, # include cable routing
+                   'oss_coords': oss_coords,
+                   'boundary_coords': lease_coords,
+                   'ss': ss,
+                   'mooringAdjuster': adjustMooring, # use fad toolset adjuster function, or replace with your own
+                   'adjuster_settings': adjuster_settings,
+                   'bathymetry_file': bathFile,
+                   'soil_file': soilFile,
+                   'floris_file': florisFile,
+                   'exclusion_coords': exclusion_coords,
+                   'use_FLORIS': use_FLORIS, 
+                   'wind_rose': wind_rose,
+                   'mode': opt_mode,
+                   'optimizer': opt_method,
+                   'parallel': False, # parallelize floris AEP calculations
+                   'anchor_settings': anchor_settings,
+                   'noss': noss,
+                   'iac_typical_conductor': iac_typical_conductor
+                   }
+
+# ----- INITIALIZE LAYOUT ------
+layout1 = Layout(X=[], Xu=Xu, **layout_settings)
+
+# plot the layout 2 ways
+layout1.plotLayout()
+layout1.plot2d()
+
+# --- RUN LAYOUT OPTIMIZATION - **COMMENT OUT TO SKIP OPTIMIZATION PROCESS**---
+# Note: if you're using a different optimizer, you'll need to change this section
+res, fopt = pso(layout1.objectiveFunUG, 
+                lb=boundaries_UG[:,0], 
+                ub=boundaries_UG[:,1], 
+                f_ieqcons=layout1.constraintFunsUG,  
+                swarmsize=swarmsize, 
+                omega=0.72984, 
+                phip=0.6, 
+                phig=0.8, 
+                maxiter=niterations,
+                minstep=1e-8, 
+                minfunc=1e-8, 
+                debug=True)
+layout1.updateLayoutUG(Xu=res, level=2, refresh=True)  # do a higher-fidelity update
+
+# Save best result design variables
+print(res)
+with open('Optimization_results.txt','w') as ofile:
+    ofile.write(str(res))
+ofile.close()
+
+# ----- ADD FULL TURBINE, PLATFORM, & SUBSTATION DESIGN -----
+# ensure fairlead radius and depth are right for FOWT platforms
+for pf in layout1.platformList.values():
+    if pf.entity == 'FOWT':
+        pf.rFair = 58
+        pf.zFair = -14
+        
+with open(turbineFile) as ft:
+    turb = dict(yaml.load(ft))
+layout1.turbineTypes = [turb]
+with open(fowtFile) as ff:
+    fowt = dict(yaml.load(ff))
+layout1.platformTypes = []
+layout1.platformTypes.append(fowt)
+
+# We don't have a substation design, so just make a minimal platform type
+# and combine it with the FOWT platform design for now...
+sub = {'type': 'Substation',
+       'rFair': 38,
+       'zFair': -14}
+sub = sub | fowt
+# Note: this does not include mooring for the substation as
+# it's assumed this will be different. 
+# We only minimally consider substations as a 
+# point(s) towards which we direct the cables 
+# If you want a full substation design with moorings
+# You'll have to add that in here!
+layout1.platformTypes.append(sub)
+
+for pf in layout1.platformList.values():
+    if not pf.entity == 'Substation':
+        layout1.addTurbine(typeID=1,platform=pf,turbine_dd=turb)
+        pf.dd['type'] = 0
+    else:
+        pf.dd['type'] = 1
+    
+
+rd = createRAFTDict(layout1)
+layout1.getRAFT(rd)
+        
+# ----- ADD 3D CABLE DESIGN -----
+# load in cable configs
+with open(cableFile) as fc:
+    cC = yaml.load(fc)
+cableConfig = dict(cC) # different cable designs for max and min depths defined in the file allow us to interpolate the designs and adjust the cable length and buoyancy for dpeth
+
+# apply 3D cable design from cableFile to the layout, adjust dynamic cable headings, and rout static cables around anchors
+layout1.addCablesConnections(layout1.iac_dic, # list of dictionaries describing 2D cable layout
+                             cableConfig=cableConfig, # 3D cable design configurations
+                             heading_buffer=30, # buffer angle between mooring lines and dynamic cabled
+                             )
+layout1.plot2d()
+# let's try adjusting the dynamic cable heading the other way 
+layout1.addCablesConnections(layout1.iac_dic,
+                            cableConfig=cableConfig,
+                            heading_buffer=30,
+                            adj_dir=-1)
+layout1.plot2d()
+# re-route static cables to avoid anchor crossings
+route_around_anchors(layout1,padding=100)
+# re-create moorpy array with 3D cables
+layout1.getMoorPyArray() 
+
+# plot
+layout1.plot3d(plot_fowt=True)
+layout1.plot2d()
+
+# unload to a yaml 
+layout1.unload('optimized_array.yaml')