reader_moana_0 = reader_ROMS_native_MOANA.Reader(paths[start_month]) # load data for that year
reader_moana_1 = reader_ROMS_native_MOANA.Reader(paths[start_month+1]) # load data for that year
reader_moana_2 = reader_ROMS_native_MOANA.Reader(paths[start_month+2]) # load data for that year
reader_moana_0.multiprocessing_fail = True # bypass the use of multi core for coordinates conversion and seems to make the model run much faster.
reader_moana_1.multiprocessing_fail = True # bypass the use of multi core for coordinates conversion and seems to make the model run much faster.
reader_moana_2.multiprocessing_fail = True # bypass the use of multi core for coordinates conversion and seems to make the model run much faster.
# # Making customised landmask - not required here, we are using the ROMS landmask i.e. included in netcdf files
# reader_landmask = reader_global_landmask.Reader(
# llcrnrlon=171.0, llcrnrlat=184.5,
# urcrnrlon=-42.0, urcrnrlat=-34.0)
# use native landmask of ROMS files
o.add_reader([reader_moana_0, reader_moana_1, reader_moana_2]) #
o.set_config('general:use_auto_landmask', False) # prevent opendrift from making a new dynamical landmask
###############################
# PARTICLE SEEDING
###############################
#Reinga
lons = [172.75, 172.8, 172.8, 172.75]
lats = [-34.3, -34.3, -34.35, -34.35]
def create_seed_times(start, end, delta):
"""
crate times at given interval to seed particles
"""
out = []
start_t = start
end_t = datetime.strptime(str(end), "%Y-%m-%d %H:%M:%S")
import time
import numpy as np
import matplotlib
from datetime import datetime, timedelta
from opendrift.readers import reader_ROMS_native_MOANA
from opendrift.models.bivalvelarvae import BivalveLarvae
r = reader_ROMS_native_MOANA.Reader('input/nz5km_avg_200601.nc')
o = BivalveLarvae(loglevel=30)
o.add_reader([r])
###############################
#Set Configs
###############################
o.set_config('general:use_auto_landmask', True)
o.set_config('environment:fallback:x_wind', 0.0)
o.set_config('environment:fallback:y_wind', 0.0)
o.set_config('environment:fallback:x_sea_water_velocity', 0.0)
o.set_config('environment:fallback:y_sea_water_velocity', 0.0)
o.set_config('environment:fallback:sea_floor_depth_below_sea_level', 100000.0)
Kxy = 0.1176 #m2/s-1
Kz = 0.01 #m2/s-1
o.set_config('drift:horizontal_diffusivity',Kxy)
o.set_config('environment:fallback:ocean_vertical_diffusivity', Kz)
o.set_config('seed:ocean_only',True)
o.set_config('drift:advection_scheme','runge-kutta4')
o.set_config('drift:current_uncertainty', 0.0)
o.set_config('drift:max_age_seconds', 3600*24*35)
###############################
# READERS
###############################
thredds_path_1 = 'http://thredds.moanaproject.org:8080/thredds/dodsC/moana/ocean/NZB/v1.9/monthly_avg/nz5km_avg_201603.nc'
reader_moana_v19 = reader_ROMS_native_MOANA.Reader(thredds_path_1) # load data for that year
reader_moana_v19.multiprocessing_fail = True # bypass the use of multi core for coordinates conversion and seems to make the model run much faster.
# # Making customised landmask - not required here, using ROMS landmask
# reader_landmask = reader_global_landmask.Reader(
# llcrnrlon=171.0, llcrnrlat=184.5,
# urcrnrlon=-42.0, urcrnrlat=-34.0)
# max is 185deg
# use native landmask of ROMS files
o.add_reader([reader_moana_v19]) # [reader_landmask,reader_moana_v19]
o.set_config('general:use_auto_landmask', False) # prevent opendrift from making a new dynamical landmask
###############################
# PARTICLE SEEDING
###############################
# generic point release location for test
# Define the starting position of the particles within the buffer of intertidal rocky shore on the West Coast of the North Island (NZ)
nb_parts = 100
points = np.loadtxt('./Release_centroid_nat_dist_paua.xyz', delimiter='\t', dtype=str)
plon = points[:,0].astype(np.float)
plat = points[:,1].astype(np.float)
tot_parts = nb_parts * len(plon) # total number of particles released
plon = np.tile(plon, nb_parts)
plat = np.tile(plat, nb_parts)
o = BivalveLarvae(loglevel=100) # Set loglevel to 0 for debug information
o.max_speed = 5.0 #
###############################
# READERS
###############################
reader_moana_v19_1 = reader_ROMS_native_MOANA.Reader(
'/nesi/nobackup/mocean02574/NZB_N50/nz5km_his_201706.nc')
reader_moana_v19_2 = reader_ROMS_native_MOANA.Reader(
'/nesi/nobackup/mocean02574/NZB_N50/nz5km_his_201707.nc')
reader_moana_v19_3 = reader_ROMS_native_MOANA.Reader(
'/nesi/nobackup/mocean02574/NZB_N50/nz5km_his_201708.nc')
o.add_reader([reader_moana_v19_1, reader_moana_v19_2, reader_moana_v19_3])
o.set_config('general:use_auto_landmask', False) # dynamical landmask if true
###############################
# PARTICLE SEEDING
###############################
# Define the starting position of the particles within the buffer of intertidal rocky shore on the West Coast of the North Island (NZ)
nb_parts = 250 # number of particles released per point during the release interval
points = np.loadtxt(
'/nesi/project/vuw03295/Regional_projects/Ninety_miles_beach/First_foreward_input_files/Release_points_rocky_shore_005deg_Moana_all_poly.xyz',
delimiter='\t',
dtype=str)
plon = points[:, 0].astype(np.float)
plat = points[:, 1].astype(np.float)
tot_parts = nb_parts * len(plon) # total number of particles released
plon = np.tile(plon, nb_parts)
#
# Atmospheric model for wind
# reader_arome = reader_netCDF_CF_generic.Reader(o.test_data_folder() +
# '16Nov2015_NorKyst_z_surface/arome_subset_16Nov2015.nc')
# Ocean model for current
# reader_norkyst = reader_netCDF_pytCF_generic.Reader(o.test_data_folder() +
# '16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
# # Creating and adding reader for Nordic 4km current dataset
nordic_native = reader_ROMS_native.Reader(
o.test_data_folder() +
'2Feb2016_Nordic_sigma_3d/Nordic-4km_SLEVELS_avg_00_subset2Feb2016.nc')
o.add_reader(nordic_native)
# default values for forcing variables
o.set_config('environment:fallback:ocean_vertical_diffusivity', 0.001) # m2/s
####################################################################################################################
####################################################################################################################
# SEEDING
# time = datetime.utcnow()
o.seed_elements(lon=12.0,
lat=68.3,
z=-3.0,
radius=100,
number=100,
time=nordic_native.start_time,
neutral_buoyancy_salinity=31.25)
####################################################################################################################
# CONFIG
###############################
# READERS
###############################
thredds_path_1 = 'http://thredds.moanaproject.org:8080/thredds/dodsC/moana/ocean/NZB/v1.9/monthly_avg/nz5km_avg_201706.nc'
reader_moana_v19 = reader_ROMS_native_MOANA.Reader(thredds_path_1) # load data for that year
reader_moana_v19.multiprocessing_fail = True # bypass the use of multi core for coordinates conversion and seems to make the model run much faster.
# # Making customised landmask - not required here, using ROMS landmask
# reader_landmask = reader_global_landmask.Reader(
# llcrnrlon=171.0, llcrnrlat=184.5,
# urcrnrlon=-42.0, urcrnrlat=-34.0)
# max is 185deg
# use native landmask of ROMS files
o.add_reader([reader_moana_v19]) # [reader_landmask,reader_moana_v19]
o.set_config('general:use_auto_landmask', True) # prevent opendrift from making a new dynamical landmask
###############################
# Define habitat
###############################
shp, bins = o.habitat('./habitat/Test_habitat.shp') # Location of the shapefile with the habitat
###############################
# PARTICLE SEEDING
###############################
# generic point release location for test
# Define the starting position of the particles within the buffer of intertidal rocky shore on the West Coast of the North Island (NZ)
nb_parts = 1
points = np.loadtxt('./Release_test.xyz', delimiter='\t', dtype=str)
plon = points[:,0].astype(np.float)
# python example_bivalvelarvae_moana.py 0, for example with no habitat
# python example_bivalvelarvae_moana.py 1 for example with habitat
use_habitat = int(sys.argv[1])
o = BivalveLarvae(loglevel=0) # Set loglevel to 0 for debug information
###############################
# READERS
###############################
thredds_path_1 = 'http://thredds.moanaproject.org:8080/thredds/dodsC/moana/ocean/NZB/v1.9/monthly_avg/nz5km_avg_201603.nc'
reader_moana_v19 = reader_ROMS_native_MOANA.Reader(thredds_path_1) # load data for that year
reader_moana_v19.multiprocessing_fail = True # bypass the use of multi core for coordinates conversion and seems to make the model run much faster.
# use native landmask of ROMS files
o.add_reader([reader_moana_v19]) # [reader_landmask,reader_moana_v19]
o.set_config('general:use_auto_landmask', False) # prevent opendrift from making a new dynamical landmask
###############################
# PARTICLE SEEDING
###############################
# 174.949513895 -40.029317969 28045 Taranaki Bight
o.seed_elements( lon = 174.949513895-.1, lat = -40.029317969-.1,
number=100, z = - np.linspace(2,50,100) ,
radius = 1000,
terminal_velocity = -1.0, # setting a large settling velocity on purpose to make seafloor contacts
time = reader_moana_v19.start_time)
###############################
# PHYSICS & CONFIG
###############################
# horizontal and vertical diffusion
Kxy = 0.1 # m2/s-1
Kz = 0.001 # m2/s-1 - setting a large
reader1 = reader_ROMS_native_MOANA.Reader(data_path1)
reader0.multiprocessing_fail = True #No idea what these lines do, but Simon told me that they make the model ruun faster so I've always included them
reader1.multiprocessing_fail = True
#add readers to the simulation
o.add_reader([reader0, reader1])
##############################
#SET CONFIGURATIONS
##############################
#There are a bunch of configs you can set, I'll just explain the ones I've used
o.set_config(
'general:use_auto_landmask', False
) #If you use True, opendrift will automatically create a higher-res landmask and project data to try and fill in the gaps. False runs using the backbone's block, 5km landmask.
# setting fallback values
o.set_config('environment:fallback:x_wind', 0.0)
o.set_config('environment:fallback:y_wind', 0.0)
o.set_config('environment:fallback:x_sea_water_velocity', 0.0)
o.set_config('environment:fallback:y_sea_water_velocity', 0.0)
o.set_config('environment:fallback:sea_floor_depth_below_sea_level', 100000.0)
#setting diffusion— some horizontal and vertical randomization
Kxy = 0.1176 #m2/s-1. These numbers come from some calculation based on the resolution of the model, some one calculated this a while ago for the backbone
Kz = 0.01 #m2/s-1
o.set_config('drift:horizontal_diffusivity', Kxy)
o.set_config('environment:fallback:ocean_vertical_diffusivity', Kz)
o.set_config(
