Source code for opendrift.models.radionuclides

# This file is part of OpenDrift.
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# OpenDrift is free software: you can redistribute it and/or modify
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# the Free Software Foundation, version 2
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# Copyright 2015, Magne Simonsen, MET Norway

import numpy as np
import logging; logger = logging.getLogger(__name__)

from opendrift.models.oceandrift import OceanDrift, Lagrangian3DArray
from opendrift.config import CONFIG_LEVEL_ESSENTIAL, CONFIG_LEVEL_BASIC, CONFIG_LEVEL_ADVANCED
import pyproj

# Defining the radionuclide element properties
[docs] class Radionuclide(Lagrangian3DArray): """Extending Lagrangian3DArray with specific properties for radionuclides """ variables = Lagrangian3DArray.add_variables([ ('diameter', {'dtype': np.float32, 'units': 'm', 'default': 0.}), ('neutral_buoyancy_salinity', {'dtype': np.float32, 'units': '[]', 'default': 31.25}), # for NEA Cod ('density', {'dtype': np.float32, 'units': 'kg/m^3', 'default': 2650.}), # Mineral particles ('specie', {'dtype': np.int32, 'units': '', 'default': 0}), # ('transfer_rates1D', {'dtype':np.array(3, dtype=np.float32), # 'units': '1/s', # 'default': 0.}) # ('LMM_fraction', {'dtype':np.float32, # 'units':'', # 'default':0, # 'seed':False}), # ('particle_fraction', {'dtype':np.float32, # 'units':'', # 'default':0, # 'seed':False}) ])
[docs] class RadionuclideDrift(OceanDrift): """Radionuclide particle trajectory model based on the OpenDrift framework. Developed at MET Norway Generic module for particles that are subject to vertical turbulent mixing with the possibility for positive or negative buoyancy Particles could be e.g. oil droplets, plankton, or sediments Radionuclide functionality include interactions with solid matter (particles and sediments) through transformation processes, implemented with stochastic approach for speciation. Under construction. """ ElementType = Radionuclide required_variables = { 'x_sea_water_velocity': {'fallback': None}, 'y_sea_water_velocity': {'fallback': None}, 'sea_surface_height': {'fallback': 0}, 'x_wind': {'fallback': 0}, 'y_wind': {'fallback': 0}, 'land_binary_mask': {'fallback': None}, 'sea_floor_depth_below_sea_level': {'fallback': None}, 'ocean_vertical_diffusivity': {'fallback': 0.0001, 'profiles': True}, 'ocean_mixed_layer_thickness': {'fallback': 50}, 'sea_water_temperature': {'fallback': 10, 'profiles': True}, 'sea_water_salinity': {'fallback': 34, 'profiles': True}, # 'surface_downward_x_stress': {'fallback': 0}, # 'surface_downward_y_stress': {'fallback': 0}, # 'turbulent_kinetic_energy': {'fallback': 0}, # 'turbulent_generic_length_scale': {'fallback': 0}, 'upward_sea_water_velocity': {'fallback': 0}, 'conc3': {'fallback': 1.e-3}, }
[docs] def specie_num2name(self,num): return self.name_species[num]
[docs] def specie_name2num(self,name): num = self.name_species.index(name) return num
def __init__(self, *args, **kwargs): # Calling general constructor of parent class super(RadionuclideDrift, self).__init__(*args, **kwargs) # TODO: descriptions and units must be added in config setting below self._add_config({ 'radionuclide:dissolved_diameter': {'type': 'float', 'default': 0, 'min': 0, 'max': 100e-6, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:particle_diameter': {'type': 'float', 'default': 5e-6, 'min': .45e-6, 'max': 63.e-6, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': 'Mean particle diameter. Determines the settling velocity.'}, 'radionuclide:particle_diameter_uncertainty': {'type': 'float', 'default': 1e-7, 'min': 0, 'max': 100e-6, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': 'Standard deviation of particle size distribution.'}, 'radionuclide:particle_diameter_minimum': {'type': 'float', 'default': 0.45e-6, 'min': 0, 'max': 100e-6, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': 'Mimimum particle size.'}, 'radionuclide:particle_diameter_maximum': {'type': 'float', 'default': 63.e-6, 'min': 0, 'max': 100e-6, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': 'Maximum particle size.'}, 'radionuclide:particlesize_distribution': {'type':'enum', 'enum': ['normal','lognormal'], 'default':'normal', 'level':CONFIG_LEVEL_ADVANCED, 'description':'Distribution of particle diameter around a mean value at seeding, NB: not at sorption!'}, 'seed:LMM_fraction': {'type': 'float','default': .1, 'min': 0, 'max': 1, 'units': '1', 'level': CONFIG_LEVEL_ESSENTIAL, 'description': 'Fraction of initial discharge released as LMM species'}, 'seed:particle_fraction': {'type': 'float','default': 0.9, 'min': 0, 'max': 1, 'units': '1', 'level': CONFIG_LEVEL_ESSENTIAL, 'description': 'Fraction of initial discharge released as particle species'}, 'seed:slowly_fraction': {'type': 'float','default': 0., 'min': 0, 'max': 1, 'units': '1', 'level': CONFIG_LEVEL_ESSENTIAL, 'description': 'Fraction of PARTICLE discharge released as slowly reversible particle species'}, 'seed:total_release': {'type': 'float','default': 100.e9, 'min': 0, 'max': 1e36, 'units': 'Bq', 'level': CONFIG_LEVEL_ESSENTIAL, 'description': 'Total release (Bq)'}, # ISOTOPES 'radionuclide:isotope': {'type': 'enum', 'default': '137Cs', 'enum': ['Al', '137Cs', '129I', '241Am', 'manual'], 'level':CONFIG_LEVEL_ESSENTIAL, 'description':'Isotope'}, 'radionuclide:specie_setup': {'type': 'enum', 'default': 'LMM + Rev', 'enum': ['LMM + Rev', 'LMM + Rev + Slow rev', 'LMM + Rev + Irrev', 'LMM + Rev + Slow rev + Irrev', 'LMM + Colloid + Rev'], 'level':CONFIG_LEVEL_ESSENTIAL, 'description':'Species enabled'}, # Transformation parameters 'radionuclide:transformations:Kd': {'type': 'float', 'default': 2.0, 'min': 0, 'max': 1e9, 'units': 'm3/kg', 'level': CONFIG_LEVEL_BASIC, 'description': ''}, 'radionuclide:transformations:Dc': {'type': 'float', 'default': 1.16e-5, 'min': 0, 'max': 1e6, 'units': '', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:transformations:slow_coeff': {'type': 'float', 'default': 1.2e-7, 'min': 0, 'max': 1e6, 'units': '', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, # Sediment 'radionuclide:sediment:sedmixdepth': {'type': 'float', 'default': 1, 'min': 0, 'max': 100, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:sediment:sediment_density': {'type': 'float', 'default': 2600, 'min': 0, 'max': 10000, 'units': 'kg/m3', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:sediment:effective_fraction': {'type': 'float', 'default': 0.9, 'min': 0, 'max': 1, 'units': '', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:sediment:corr_factor': {'type': 'float', 'default': 0.1, 'min': 0, 'max': 10, 'units': '', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:sediment:porosity': {'type': 'float', 'default': 0.6, 'min': 0, 'max': 1, 'units': '', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:sediment:layer_thick': {'type': 'float', 'default': 1, 'min': 0, 'max': 100, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:sediment:desorption_depth': {'type': 'float', 'default': 1, 'min': 0, 'max': 100, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:sediment:desorption_depth_uncert': {'type': 'float', 'default': .5, 'min': 0, 'max': 100, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:sediment:resuspension_depth': {'type': 'float', 'default': 1, 'min': 0, 'max': 100, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:sediment:resuspension_depth_uncert': {'type': 'float', 'default': .5, 'min': 0, 'max': 100, 'units': 'm', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, 'radionuclide:sediment:resuspension_critvel': {'type': 'float', 'default': .01, 'min': 0, 'max': 1, 'units': 'm/s', 'level': CONFIG_LEVEL_ADVANCED, 'description': ''}, # OUTPUT config 'radionuclide:output:depthintervals': {'type':'str', 'default': '-25, -10., -5., -1.', 'min_length':0, 'max_length':60, 'level':CONFIG_LEVEL_ESSENTIAL, 'description':'Depth intervals for computation of concentration'}, })
[docs] def prepare_run(self): logger.info( 'Number of species: {}'.format(self.nspecies) ) for i,sp in enumerate(self.name_species): logger.info( '{:>3} {}'.format( i, sp ) ) logger.info( 'Isotope: %s' % self.get_config('radionuclide:isotope')) logger.info( 'specie setup: %s' % self.get_config('radionuclide:specie_setup')) logger.info('nspecies: %s' % self.nspecies) logger.info('Transfer rates:\n %s' % self.transfer_rates) tmp = self.get_config('radionuclide:output:depthintervals') self.depthintervals = [float(item) for item in tmp.split(',')] logger.info('DEPTH_INTERVALS: %s',self.depthintervals) super(RadionuclideDrift, self).prepare_run()
[docs] def init_species(self): # Initialize slowly and irrev fractions to False, set True later if enabled self.species_slowly_fraction = False self.species_irreversible_fraction = False # Initialize species, add enabled species to name_species list self.name_species=[] self.specie_setup = self.get_config('radionuclide:specie_setup') if 'lmm + rev' in self.specie_setup.casefold(): self.name_species.append('LMM') self.name_species.append('Particle reversible') self.name_species.append('Sediment reversible') # else: # if not self.isotope == 'Al': # logger.error('No valid specie setup {}'.format(self.get_config('radionuclide:specie_setup'))) # else: # pass if '+ slow rev' in self.specie_setup.casefold(): self.name_species.append('Particle slowly reversible') self.name_species.append('Sediment slowly reversible') self.species_slowly_fraction = True if '+ irrev' in self.specie_setup.casefold(): self.name_species.append('Particle irreversible') self.name_species.append('Sediment irreversible') self.species_irreversible_fraction = True if self.specie_setup.casefold() == 'lmm + colloid + rev': self.name_species.append('LMMcation') self.name_species.append('LMManion') self.name_species.append('Humic colloid') self.name_species.append('Polymer') self.name_species.append('Particle reversible') self.name_species.append('Sediment reversible') self.nspecies = len(self.name_species) logger.info( 'Number of species: {}'.format(self.nspecies) ) for i,sp in enumerate(self.name_species): logger.info( '{:>3} {}'.format( i, sp ) )
[docs] def set_init_diameter(self, num, idxs,diam): """ Initialize diameter for particles, according to size distribution """ distr = self.get_config('radionuclide:particlesize_distribution') init_diam = np.zeros(num) npart = len(idxs) mu = 0. uncert = self.get_config('radionuclide:particle_diameter_uncertainty') if diam>0: uncert_ln = uncert/diam * 3. else: uncert_ln = 0. rng = np.random.default_rng() if distr=='normal': truncs = rng.normal(mu, uncert, npart) init_diam[idxs] = diam + truncs elif distr=='lognormal': truncs = rng.lognormal(mu, uncert_ln, size=npart ) # * diameter init_diam[idxs] = diam * truncs else: logger.error('Not available distribution: %s',distr) pmin = self.get_config('radionuclide:particle_diameter_minimum') pmax = self.get_config('radionuclide:particle_diameter_maximum') init_diam[idxs][init_diam[idxs]<pmin] = pmin init_diam[idxs][init_diam[idxs]>pmax] = pmax return init_diam
[docs] def check_speciation(self): isotop = self.get_config('radionuclide:isotope') specie_setup = self.get_config('radionuclide:specie_setup') legal_species = { '137Cs' : ['LMM + Rev', 'LMM + Rev + Slow rev', 'LMM + Rev + Irrev', 'LMM + Rev + Slow rev + Irrev'], '129I' : ['LMM + Rev', 'LMM + Rev + Slow rev + Irrev'], '241Am' : ['LMM + Rev', 'LMM + Rev + Slow rev', 'LMM + Rev + Slow rev + Irrev'], 'Al' : ['LMM + Colloid + Rev'], } if specie_setup in legal_species[isotop]: logger.info(f'All good, isotop: {isotop}, species: {specie_setup}') else: logger.info(f'Not a legal combination of isotop: {isotop} and speciation: {specie_setup}') logger.error('Illegal speciation for %s: %s',isotop, specie_setup) exit()
[docs] def seed_elements(self, *args, **kwargs): self.check_speciation() self.init_species() self.init_transfer_rates() if 'number' in kwargs: num_elements = kwargs['number'] else: num_elements = self.get_config('seed:number') # Initialize species if 'specie' in kwargs: print('num_elements', num_elements) try: print('len specie:',len(kwargs['specie'])) except: print('specie:',kwargs['specie']) init_specie = np.ones(num_elements,dtype=int) init_specie[:] = kwargs['specie'] kwargs['specie'] = init_specie[:] else: # Set initial speciation if 'particle_fraction' in kwargs: particle_frac = kwargs['particle_fraction'] else: particle_frac = self.get_config('seed:particle_fraction') if 'LMM_fraction' in kwargs: lmm_frac = kwargs['LMM_fraction'] else: lmm_frac = self.get_config('seed:LMM_fraction') if not lmm_frac + particle_frac == 1.: logger.error('Fraction does not sum up to 1: %s' % str(lmm_frac+particle_frac) ) logger.error('LMM fraction: %s ' % str(lmm_frac)) logger.error( 'Particle fraction %s '% str(particle_frac) ) raise ValueError('Illegal specie fraction combination : ' + str(lmm_frac) + ' '+ str(particle_frac) ) init_specie = np.ones(num_elements, int) dissolved = np.random.rand(num_elements)<lmm_frac ndiss = np.sum(dissolved) if 'LMMcation' in self.name_species: init_specie[dissolved] = self.num_lmmcation elif 'LMM' in self.name_species: init_specie[dissolved] = self.num_lmm else: logger.error('No dissolved species present %s: ',self.name_species) if self.get_config('seed:slowly_fraction')>0 and 'Particle slowly reversible' in self.name_species: ndiss = np.sum(dissolved) prtidx = np.where(~dissolved)[0] slowprt = np.random.rand(num_elements-ndiss)<self.get_config('seed:slowly_fraction') init_specie[prtidx[slowprt]] = self.num_psrev init_specie[prtidx[~slowprt]] = self.num_prev else: init_specie[~dissolved] = self.num_prev kwargs['specie'] = init_specie logger.info('Initial speciation:') for i,sp in enumerate(self.name_species): logger.info( '{:>9} {:>3} {:24} '.format( np.sum(init_specie==i), i, sp ) ) if all(init_specie == self.num_srev): print( 'ALL ELEMENTS ARE SEDIMENTS') kwargs['z'] = 'seafloor' # TODO SET MOVING = 0 elif any(init_specie == self.num_srev): print( 'SOME ELEMENTS ARE SEDIMENTS') exit() # Set initial particle size according to speciation if 'diameter' in kwargs: diameter = kwargs['diameter'] else: diameter = self.get_config('radionuclide:particle_diameter') logger.info('PARTICLE DIAMETER %s',diameter) particles = [] for i,sp in enumerate(self.name_species): if 'particle' in sp.casefold(): prt = np.where(init_specie==i)[0] particles.extend(prt) init_diam = self.set_init_diameter(num_elements, particles, diameter) try: logger.info('Min: {:.2e}, Max: {:.2e}, Numer of particles seeded: {}, at {} distribution'.format( np.min(init_diam[init_diam>0.]), np.max(init_diam[init_diam>0.]), sum(init_diam>0.), self.get_config('radionuclide:particlesize_distribution'))) except Exception: logger.info('All diameters are 0 (min:{}, max: {})'.format( np.min(init_diam), np.max(init_diam)) ) kwargs['diameter'] = init_diam # Set z to seabed for sediments # sediments = [] # for i,sp in enumerate(self.name_species): # if 'sediment' in sp.casefold(): # sed = np.where(init_specie==i)[0] # sediments.extend(sed) # kwargs['z'] = 'seafloor' # logger.debug('Seafloor is selected, neglecting z') # init_z = np.ones(num_elements,dtype=float) # init_z[:] = kwargs['z'] # init_z[sediments] = -10000. #\ # #-1.*self.environment.sea_floor_depth_below_sea_level[sediments] # # self.elements.moving[sediments] = 0 # kwargs['z'] = init_z super(RadionuclideDrift, self).seed_elements(*args, **kwargs)
[docs] def init_kd(self): ''' Initialization of Kd value, dependent on simulated radionuclide ''' # Values from IAEA (2004) kd_values = { '137Cs' : 4.0e0, '129I' : 7.0e-2, '241Am' : 2.0e3, 'Al' : None, } print('ISOTOPE',self.isotope) if self.isotope == 'manual': self.kd = self.get_config('radionuclide:transformations:Kd') return if not self.isotope in kd_values.keys(): logger.error('No Kd value implemented for %s ', self.isotope) else: self.kd = kd_values[self.isotope]
[docs] def init_transfer_rates(self): ''' Initialization of background values in the transfer rates 2D array. ''' # logger.info( 'transfer setup: %s' % transfer_setup) self.isotope = self.get_config('radionuclide:isotope') self.init_kd() logger.info('ISOTOPE %s',self.isotope) logger.info('SPECIE SETUP %s',self.specie_setup) logger.info('Kd: %s',self.kd) self.transfer_rates = np.zeros([self.nspecies,self.nspecies]) self.ntransformations = np.zeros([self.nspecies,self.nspecies]) if 'lmm + rev' in self.specie_setup.casefold(): self.num_lmm = self.specie_name2num('LMM') self.num_prev = self.specie_name2num('Particle reversible') self.num_srev = self.specie_name2num('Sediment reversible') # Simpler version of Values from Simonsen et al (2019a) # Only consider the reversible fraction Kd = self.kd # depends on isotope Dc = self.get_config('radionuclide:transformations:Dc') susp_mat = 1.e-3 # concentration of available suspended particulate matter (kg/m3) sedmixdepth = self.get_config('radionuclide:sediment:sedmixdepth') # sediment mixing depth (m) default_density = self.get_config('radionuclide:sediment:sediment_density') # default particle density (kg/m3) f = self.get_config('radionuclide:sediment:effective_fraction') # fraction of effective sorbents phi = self.get_config('radionuclide:sediment:corr_factor') # sediment correction factor poro = self.get_config('radionuclide:sediment:porosity') # sediment porosity layer_thick = self.get_config('radionuclide:sediment:layer_thick') # thickness of seabed interaction layer (m) self.transfer_rates[self.num_lmm,self.num_prev] = Dc * Kd * susp_mat self.transfer_rates[self.num_prev,self.num_lmm] = Dc self.transfer_rates[self.num_lmm,self.num_srev] = \ Dc * Kd * sedmixdepth * default_density * (1.-poro) * f * phi / layer_thick self.transfer_rates[self.num_srev,self.num_lmm] = Dc * phi else: logger.error('No transfer setup available') if '+ slow rev' in self.specie_setup.casefold(): self.num_psrev = self.specie_name2num('Particle slowly reversible') self.num_ssrev = self.specie_name2num('Sediment slowly reversible') slow_coeff = self.get_config('radionuclide:transformations:slow_coeff') self.transfer_rates[self.num_srev,self.num_ssrev] = slow_coeff self.transfer_rates[self.num_prev,self.num_psrev] = slow_coeff self.transfer_rates[self.num_ssrev,self.num_srev] = slow_coeff*.1 self.transfer_rates[self.num_psrev,self.num_prev] = slow_coeff*.1 if '+ irrev' in self.specie_setup.casefold(): self.num_pirrev = self.specie_name2num('Particle irreversible') self.num_sirrev = self.specie_name2num('Sediment irreversible') slow_coeff = self.get_config('radionuclide:transformations:slow_coeff') self.transfer_rates[self.num_ssrev,self.num_sirrev] = slow_coeff self.transfer_rates[self.num_psrev,self.num_pirrev] = slow_coeff if self.specie_setup.casefold() == 'lmm + colloid + rev' and \ self.isotope.casefold() == 'al': # Use values from Simonsen et al (2019b) self.num_lmmanion = self.specie_name2num('LMManion') self.num_lmmcation = self.specie_name2num('LMMcation') self.num_humcol = self.specie_name2num('Humic colloid') self.num_polymer = self.specie_name2num('Polymer') self.num_prev = self.specie_name2num('Particle reversible') self.num_srev = self.specie_name2num('Sediment reversible') Dc = self.get_config('radionuclide:transformations:Dc') self.salinity_intervals = [0,1,10,20] # Resize transfer rates array self.transfer_rates = np.zeros([len(self.salinity_intervals),self.transfer_rates.shape[0],self.transfer_rates.shape[1]]) # Salinity interval 0-1 psu self.transfer_rates[0,self.num_lmmcation, self.num_humcol] = 1.2e-5 self.transfer_rates[0,self.num_lmmcation, self.num_prev] = 4.e-6 self.transfer_rates[0,self.num_humcol, self.num_lmmcation] = .3*Dc self.transfer_rates[0,self.num_humcol, self.num_prev] = 2.e-6 self.transfer_rates[0,self.num_prev, self.num_lmmcation] = .3*Dc self.transfer_rates[0,self.num_srev, self.num_lmmcation] = .03*Dc # Salinity interval 1-10 psu self.transfer_rates[1,self.num_lmmcation, self.num_humcol] = 1.e-5 self.transfer_rates[1,self.num_lmmcation, self.num_prev] = 3.e-6 self.transfer_rates[1,self.num_lmmcation, self.num_polymer] = 1.2e-4 self.transfer_rates[1,self.num_humcol, self.num_lmmcation] = 7.*Dc self.transfer_rates[1,self.num_humcol, self.num_prev] = 4.e-6 self.transfer_rates[1,self.num_prev, self.num_lmmcation] = .5*Dc self.transfer_rates[1,self.num_srev, self.num_lmmcation] = .05*Dc self.transfer_rates[1,self.num_lmmanion, self.num_polymer] = 5.e-6 self.transfer_rates[1,self.num_polymer, self.num_lmmanion] = 12.*Dc self.transfer_rates[1,self.num_polymer, self.num_prev] = 2.4e-5 # Salinity interval 10-20 psu self.transfer_rates[2,self.num_lmmcation, self.num_humcol] = 8.e-6 self.transfer_rates[2,self.num_lmmcation, self.num_prev] = 2.e-6 self.transfer_rates[2,self.num_lmmcation, self.num_polymer] = 1.4e-4 self.transfer_rates[2,self.num_humcol, self.num_lmmcation] = 7.*Dc self.transfer_rates[2,self.num_humcol, self.num_prev] = 6.e-6 self.transfer_rates[2,self.num_prev, self.num_lmmcation] = .6*Dc self.transfer_rates[2,self.num_srev, self.num_lmmcation] = .06*Dc self.transfer_rates[2,self.num_lmmanion, self.num_polymer] = 5.e-6 self.transfer_rates[2,self.num_polymer, self.num_lmmanion] = 12.*Dc self.transfer_rates[2,self.num_polymer, self.num_prev] = 6.e-5 # Salinity interval >20 psu self.transfer_rates[3,self.num_lmmcation, self.num_humcol] = 6.e-6 self.transfer_rates[3,self.num_lmmcation, self.num_prev] = 1.8e-6 self.transfer_rates[3,self.num_lmmcation, self.num_polymer] = 1.5e-4 self.transfer_rates[3,self.num_humcol, self.num_lmmcation] = 7.*Dc self.transfer_rates[3,self.num_humcol, self.num_prev] = 1.e-5 self.transfer_rates[3,self.num_prev, self.num_lmmcation] = .8*Dc self.transfer_rates[3,self.num_srev, self.num_lmmcation] = .08*Dc self.transfer_rates[3,self.num_lmmanion, self.num_polymer] = 5.e-6 self.transfer_rates[3,self.num_polymer, self.num_lmmanion] = 12.*Dc self.transfer_rates[3,self.num_polymer, self.num_prev] = 8.e-5 # Set diagonal to 0. (not possible to transform to present specie) if len(self.transfer_rates.shape) == 3: for ii in range(self.transfer_rates.shape[0]): np.fill_diagonal(self.transfer_rates[ii,:,:],0.) else: np.fill_diagonal(self.transfer_rates,0.)
[docs] def update_terminal_velocity(self, Tprofiles=None, Sprofiles=None, z_index=None): """Calculate terminal velocity for Pelagic Egg according to S. Sundby (1983): A one-dimensional model for the vertical distribution of pelagic fish eggs in the mixed layer Deep Sea Research (30) pp. 645-661 Method copied from ibm.f90 module of LADIM: Vikebo, F., S. Sundby, B. Aadlandsvik and O. Otteraa (2007), Fish. Oceanogr. (16) pp. 216-228 """ g = 9.81 # ms-2 # Particle properties that determine settling velocity partsize = self.elements.diameter # prepare interpolation of temp, salt if not (Tprofiles is None and Sprofiles is None): if z_index is None: z_i = range(Tprofiles.shape[0]) # evtl. move out of loop # evtl. move out of loop z_index = interp1d(-self.environment_profiles['z'], z_i, bounds_error=False) zi = z_index(-self.elements.z) upper = np.maximum(np.floor(zi).astype(np.uint8), 0) lower = np.minimum(upper+1, Tprofiles.shape[0]-1) weight_upper = 1 - (zi - upper) # do interpolation of temp, salt if profiles were passed into # this function, if not, use reader by calling self.environment if Tprofiles is None: T0 = self.environment.sea_water_temperature else: T0 = Tprofiles[upper, range(Tprofiles.shape[1])] * \ weight_upper + \ Tprofiles[lower, range(Tprofiles.shape[1])] * \ (1-weight_upper) if Sprofiles is None: S0 = self.environment.sea_water_salinity else: S0 = Sprofiles[upper, range(Sprofiles.shape[1])] * \ weight_upper + \ Sprofiles[lower, range(Sprofiles.shape[1])] * \ (1-weight_upper) DENSw = self.sea_water_density(T=T0, S=S0) DENSpart = self.elements.density dr = DENSw-DENSpart # density difference # water viscosity my_w = 0.001*(1.7915 - 0.0538*T0 + 0.007*(T0**(2.0)) - 0.0023*S0) # ~0.0014 kg m-1 s-1 # terminal velocity for low Reynolds numbers W = (1.0/my_w)*(1.0/18.0)*g*partsize**2 * dr self.elements.terminal_velocity = W * self.elements.moving
[docs] def update_transfer_rates(self): '''Pick out the correct row from transfer_rates for each element. Modify the transfer rates according to local environmental conditions ''' if not self.specie_setup.casefold() == 'lmm + colloid + rev': self.elements.transfer_rates1D = self.transfer_rates[self.elements.specie,:] if 'Sediment reversible' in self.name_species: # Only LMM radionuclides close to seabed are allowed to interact with sediments # minimum height/maximum depth for each particle Zmin = -1.*self.environment.sea_floor_depth_below_sea_level interaction_thick = self.get_config('radionuclide:sediment:layer_thick') # thickness of seabed interaction layer (m) dist_to_seabed = self.elements.z - Zmin self.elements.transfer_rates1D[(self.elements.specie == self.num_lmm) & (dist_to_seabed > interaction_thick), self.num_srev] = 0. if 'Particle reversible' in self.name_species: # Modify particle adsorption according to local particle concentration # (LMM -> reversible particles) kktmp = self.elements.specie == self.num_lmm self.elements.transfer_rates1D[kktmp, self.num_prev] = \ self.elements.transfer_rates1D[kktmp, self.num_prev] * \ self.environment.conc3[kktmp] / 1.e-3 # self.environment.particle_conc[kktmp] / 1.e-3 elif self.specie_setup.casefold() == 'lmm + colloid + rev' and self.isotope=='Al': sal = self.environment.sea_water_salinity sali = np.searchsorted(self.salinity_intervals, sal) - 1 self.elements.transfer_rates1D = self.transfer_rates[sali,self.elements.specie,:]
[docs] def update_speciation(self): '''Check if transformation processes shall occur Do transformation (change value of self.elements.specie) Update element properties for the transformed elements ''' specie_in = self.elements.specie.copy() # for storage of the out speciation specie_out = self.elements.specie.copy() # for storage of the out speciation deltat = self.time_step.total_seconds() # length of a time step phaseshift = np.array(self.num_elements_active()*[False]) # Denotes which trajectory that shall be transformed p = 1. - np.exp(-self.elements.transfer_rates1D*deltat) # Probability for transformation psum = np.sum(p,axis=1) ran1=np.random.random(self.num_elements_active()) # Transformation where ran1 < total probability for transformation phaseshift[ ran1 < psum ] = True logger.info('Number of transformations: %s' % sum(phaseshift)) if sum(phaseshift) == 0: return ran4 = np.random.random(sum(phaseshift)) # New random number to decide which specie to end up in ttmp=[] # list for storing the out specie # Loop through each trajectory for ii in range(sum(phaseshift)): # Compare random number to the relative probability for each transfer process ttmp.append(np.searchsorted(np.cumsum(p[phaseshift][ii]/psum[phaseshift][ii]),ran4[ii])) specie_out[phaseshift] = np.array(ttmp) # Set the new speciation self.elements.specie=specie_out logger.debug('old species: %s' % specie_in[phaseshift]) logger.debug('new species: %s' % specie_out[phaseshift]) for iin in range(self.nspecies): for iout in range(self.nspecies): self.ntransformations[iin,iout]+=sum((specie_in[phaseshift]==iin) & (specie_out[phaseshift]==iout)) logger.debug('Number of transformations total:\n %s' % self.ntransformations ) # Update radionuclide properties after transformations self.update_radionuclide_diameter(specie_in, specie_out) self.sorption_to_sediments(specie_in, specie_out) self.desorption_from_sediments(specie_in, specie_out)
[docs] def sorption_to_sediments(self,sp_in=None,sp_out=None): '''Update radionuclide properties when sorption to sediments occurs''' # Set z to local sea depth if 'LMM' in self.name_species: self.elements.z[(sp_out==self.num_srev) & (sp_in==self.num_lmm)] = \ -1.*self.environment.sea_floor_depth_below_sea_level[(sp_out==self.num_srev) & (sp_in==self.num_lmm)] self.elements.moving[(sp_out==self.num_srev) & (sp_in==self.num_lmm)] = 0 if 'LMMcation' in self.name_species: self.elements.z[(sp_out==self.num_srev) & (sp_in==self.num_lmmcation)] = \ -1.*self.environment.sea_floor_depth_below_sea_level[(sp_out==self.num_srev) & (sp_in==self.num_lmmcation)] self.elements.moving[(sp_out==self.num_srev) & (sp_in==self.num_lmmcation)] = 0 # avoid setting positive z values if np.nansum(self.elements.z>0): logger.debug('Number of elements lowered down to sea surface: %s' % np.nansum(self.elements.z>0)) self.elements.z[self.elements.z > 0] = 0
[docs] def desorption_from_sediments(self,sp_in=None,sp_out=None): '''Update radionuclide properties when desorption from sediments occurs''' desorption_depth = self.get_config('radionuclide:sediment:desorption_depth') std = self.get_config('radionuclide:sediment:desorption_depth_uncert') if 'LMM' in self.name_species: self.elements.z[(sp_out==self.num_lmm) & (sp_in==self.num_srev)] = \ -1.*self.environment.sea_floor_depth_below_sea_level[(sp_out==self.num_lmm) & (sp_in==self.num_srev)] + desorption_depth self.elements.moving[(sp_out==self.num_lmm) & (sp_in==self.num_srev)] = 1 if std > 0: logger.debug('Adding uncertainty for desorption from sediments: %s m' % std) self.elements.z[(sp_out==self.num_lmm) & (sp_in==self.num_srev)] += np.random.normal( 0, std, sum((sp_out==self.num_lmm) & (sp_in==self.num_srev))) if 'LMMcation' in self.name_species: self.elements.z[(sp_out==self.num_lmmcation) & (sp_in==self.num_srev)] = \ -1.*self.environment.sea_floor_depth_below_sea_level[(sp_out==self.num_lmmcation) & (sp_in==self.num_srev)] + desorption_depth self.elements.moving[(sp_out==self.num_lmmcation) & (sp_in==self.num_srev)] = 1 if std > 0: logger.debug('Adding uncertainty for desorption from sediments: %s m' % std) self.elements.z[(sp_out==self.num_lmmcation) & (sp_in==self.num_srev)] += np.random.normal( 0, std, sum((sp_out==self.num_lmmcation) & (sp_in==self.num_srev))) # avoid setting positive z values if np.nansum(self.elements.z>0): logger.debug('Number of elements lowered down to sea surface: %s' % np.nansum(self.elements.z>0)) self.elements.z[self.elements.z > 0] = 0
[docs] def update_radionuclide_diameter(self,sp_in=None,sp_out=None): '''Update the diameter of the radionuclides when specie is changed''' dia_part=self.get_config('radionuclide:particle_diameter') dia_diss=self.get_config('radionuclide:dissolved_diameter') # Transform to particle species to_particles = np.where( (sp_out==self.num_prev) & (sp_in!=self.num_prev) ) [0] if self.species_slowly_fraction: to_particles = np.append(to_particles, np.where((sp_out==self.num_psrev) & (sp_in==self.num_ssrev))[0] ) if self.species_irreversible_fraction: to_particles = np.append(to_particles, np.where((sp_out==self.num_pirrev) & (sp_in==self.num_sirrev))[0] ) new_diam = self.set_init_diameter(self.num_elements_total(), to_particles, dia_part) self.elements.diameter[to_particles] = new_diam[to_particles] # Transform to LMM and colloid species if 'LMM' in self.name_species: to_diss = np.where( (sp_out==self.num_lmm) & (sp_in!=self.num_lmm) )[0] elif 'LMMcation' and 'LMManion' in self.name_species: to_diss = np.where( (sp_out==self.num_lmmcation) & (sp_in!=self.num_lmmcation) )[0] to_diss = np.append( to_diss, np.where( (sp_out==self.num_lmmanion) & (sp_in!=self.num_lmmanion) )[0] ) if 'Colloid' in self.name_species: to_diss = np.append(to_diss, np.where( (sp_out==self.num_col) & (sp_in!=self.num_col) )[0] ) if 'Humic_colloid' in self.name_species: to_diss = np.append( to_diss, np.where( (sp_out==self.num_humcol) & (sp_in!=self.num_humcol) )[0] ) if 'Polymer' in self.name_species: to_diss = np.append( to_diss, np.where( (sp_out==self.num_polymer) & (sp_in!=self.num_polymer) )[0] ) new_diam = self.set_init_diameter(self.num_elements_total(), to_diss, dia_diss) self.elements.diameter[to_diss] = new_diam[to_diss]
[docs] def bottom_interaction(self,Zmin=None): ''' Change speciation of radionuclides that reach bottom due to settling. particle specie -> sediment specie ''' if not ( ('Particle reversible' in self.name_species) & ('Sediment reversible' in self.name_species) or self.species_slowly_fraction or self.species_irreversible_fraction): print('RETURN: ', ('Particle reversible' in self.name_species), ('Sediment reversible' in self.name_species), self.species_slowly_fraction, self.species_irreversible_fraction) return bottom = np.array(np.where(self.elements.z <= Zmin)[0]) kktmp = np.array(np.where(self.elements.specie[bottom] == self.num_prev)[0]) self.elements.specie[bottom[kktmp]] = self.num_srev self.ntransformations[self.num_prev,self.num_srev]+=len(kktmp) self.elements.moving[bottom[kktmp]] = 0 # self.elements.moving[bottom] = 0 if self.species_slowly_fraction: kktmp = np.array(np.where(self.elements.specie[bottom] == self.num_psrev)[0]) self.elements.specie[bottom[kktmp]] = self.num_ssrev self.ntransformations[self.num_psrev,self.num_ssrev]+=len(kktmp) self.elements.moving[bottom[kktmp]] = 0 if self.species_irreversible_fraction: kktmp = np.array(np.where(self.elements.specie[bottom] == self.num_pirrev)[0]) self.elements.specie[bottom[kktmp]] = self.num_sirrev self.ntransformations[self.num_pirrev,self.num_sirrev]+=len(kktmp) self.elements.moving[bottom[kktmp]] = 0
[docs] def resuspension(self): """ Simple method to estimate the resuspension of sedimented particles, checking whether the current speed near the bottom is above a critical velocity Sediment species -> Particle specie """ # Exit function if particles and sediments not are present # if not ((self.get_config('radionuclide:species:Particle_reversible')) & # (self.get_config('radionuclide:species:Sediment_reversible'))): # return if not ('Particle reversible' in self.name_species and 'Sediment reversible' in self.name_species): logger.info('No sediments and particles present...') return specie_in = self.elements.specie.copy() critvel = self.get_config('radionuclide:sediment:resuspension_critvel') resusp_depth = self.get_config('radionuclide:sediment:resuspension_depth') std = self.get_config('radionuclide:sediment:resuspension_depth_uncert') Zmin = -1.*self.environment.sea_floor_depth_below_sea_level x_vel = self.environment.x_sea_water_velocity y_vel = self.environment.y_sea_water_velocity speed = np.sqrt(x_vel*x_vel + y_vel*y_vel) bottom = (self.elements.z <= Zmin) resusp = ( (bottom) & (speed >= critvel) ) logger.info('Number of resuspended particles: {}'.format(np.sum(resusp))) self.elements.moving[resusp] = 1 self.elements.z[resusp] = Zmin[resusp] + resusp_depth if std > 0: logger.debug('Adding uncertainty for resuspension from sediments: %s m' % std) self.elements.z[resusp] += np.random.normal( 0, std, sum(resusp)) # avoid setting positive z values if np.nansum(self.elements.z>0): logger.debug('Number of elements lowered down to sea surface: %s' % np.nansum(self.elements.z>0)) self.elements.z[self.elements.z > 0] = 0 self.ntransformations[self.num_srev,self.num_prev]+=sum((resusp) & (self.elements.specie==self.num_srev)) self.elements.specie[(resusp) & (self.elements.specie==self.num_srev)] = self.num_prev # if self.get_config('radionuclide:slowly_fraction'): if self.species_slowly_fraction: self.ntransformations[self.num_ssrev,self.num_psrev]+=sum((resusp) & (self.elements.specie==self.num_ssrev)) self.elements.specie[(resusp) & (self.elements.specie==self.num_ssrev)] = self.num_psrev if self.species_irreversible_fraction: # if self.get_config('radionuclide:irreversible_fraction'): self.ntransformations[self.num_sirrev,self.num_pirrev]+=sum((resusp) & (self.elements.specie==self.num_sirrev)) self.elements.specie[(resusp) & (self.elements.specie==self.num_sirrev)] = self.num_pirrev specie_out = self.elements.specie.copy() self.update_radionuclide_diameter(specie_in, specie_out)
[docs] def update(self): """Update positions and properties of radionuclide particles.""" # Workaround due to conversion of datatype self.elements.specie = self.elements.specie.astype(np.int32) # Radionuclide speciation self.update_transfer_rates() self.update_speciation() # Turbulent Mixing if self.get_config('drift:vertical_mixing') is True: self.update_terminal_velocity() self.vertical_mixing() else: self.update_terminal_velocity() self.vertical_buoyancy() # Resuspension self.resuspension() logger.info('Speciation: {} {}'.format([sum(self.elements.specie==ii) for ii in range(self.nspecies)],self.name_species)) #self.elements.moving[self.elements.z <= -1*self.environment.sea_floor_depth_below_sea_level] = 0. # Horizontal advection self.advect_ocean_current() # Vertical advection if self.get_config('drift:vertical_advection') is True: self.vertical_advection()
# ################ # POSTPROCESSING
[docs] def write_netcdf_radionuclide_density_map(self, filename, pixelsize_m='auto', zlevels=None, deltat=None, density_proj=None, llcrnrlon=None, llcrnrlat=None, urcrnrlon=None, urcrnrlat=None, activity_unit=None, time_avg_conc=False, horizontal_smoothing=False, smoothing_cells=0, reader_sea_depth=None, ): '''Write netCDF file with map of radionuclide species densities and concentrations''' from netCDF4 import Dataset, date2num #, stringtochar logger.info('Postprocessing: Write density and concentration to netcdf file') if pixelsize_m == 'auto': lon, lat = self.get_lonlats() latspan = lat.max()-lat.min() pixelsize_m=30 if latspan > .05: pixelsize_m = 50 if latspan > .1: pixelsize_m = 300 if latspan > .3: pixelsize_m = 500 if latspan > .7: pixelsize_m = 1000 if latspan > 2: pixelsize_m = 2000 if latspan > 5: pixelsize_m = 4000 if reader_sea_depth is not None: from opendrift.readers import reader_netCDF_CF_generic,reader_ROMS_native reader = reader_sea_depth else: for readerName in self.env.readers: reader = self.env.readers[readerName] if 'sea_floor_depth_below_sea_level' in reader.variables: break try: self.conc_lat = reader.get_variables('latitude', x=[reader.xmin,reader.xmax], y=[reader.ymin,reader.ymax])['latitude'][:] except: self.conc_lat = reader.get_variables('grid_latitude_at_cell_center', x=[reader.xmin,reader.xmax], y=[reader.ymin,reader.ymax])['grid_latitude_at_cell_center'][:] try: self.conc_lon = reader.get_variables('longitude', x=[reader.xmin,reader.xmax], y=[reader.ymin,reader.ymax])['longitude'][:] except: self.conc_lon = reader.get_variables('grid_longitude_at_cell_center', x=[reader.xmin,reader.xmax], y=[reader.ymin,reader.ymax])['grid_longitude_at_cell_center'][:] self.conc_topo = reader.get_variables('sea_floor_depth_below_sea_level', x=[reader.xmin,reader.xmax], y=[reader.ymin,reader.ymax])['sea_floor_depth_below_sea_level'][:] if density_proj is None: # add default projection with equal-area property density_proj = pyproj.Proj('+proj=moll +ellps=WGS84 +lon_0=0.0') if activity_unit==None: activity_unit='Bq' # default unit for radionuclides activity_per_element = self.get_config('seed:total_release') / self.num_elements_total() z = self.get_property('z')[0] if not zlevels==None: zlevels = np.sort(zlevels) z_array = np.append(np.append(-10000, zlevels) , max(0,np.nanmax(z))) else: z_array = [min(-10000,np.nanmin(z)), max(0,np.nanmax(z))] logger.info('z_array: {}'.format( [str(item) for item in z_array] ) ) # # H is array containing number of elements within each box defined by lon_array, lat_array and z_array H, lon_array, lat_array = \ self.get_radionuclide_density_array(pixelsize_m, z_array, density_proj=density_proj, llcrnrlon=llcrnrlon, llcrnrlat=llcrnrlat, urcrnrlon=urcrnrlon, urcrnrlat=urcrnrlat ) lon_array = (lon_array[:-1,:-1] + lon_array[1:,1:])/2 lat_array = (lat_array[:-1,:-1] + lat_array[1:,1:])/2 if horizontal_smoothing: # Compute horizontally smoother field logger.info('H.shape: ' + str(H.shape)) Hsm = np.zeros_like(H) for zi in range(len(z_array)-1): for sp in range(self.nspecies): for ti in range(H.shape[0]): Hsm[ti,sp,zi,:,:] = self.horizontal_smooth(H[ti,sp,zi,:,:],n=smoothing_cells) # Convert from density to concentration logger.info('Activity: '+str(activity_per_element)+' '+ activity_unit+ ' per unit') # Compute mean depth and volume in each pixel grid cell pixel_mean_depth = self.get_pixel_mean_depth(lon_array, lat_array) pixel_volume = np.zeros_like(H[0,0,:,:,:]) for zi,zz in enumerate(z_array[:-1]): topotmp = -pixel_mean_depth.copy() topotmp[np.where(topotmp < zz)] = zz topotmp = z_array[zi+1] - topotmp topotmp[np.where(topotmp < .1)] = 0. pixel_volume[zi,:,:] = topotmp * pixelsize_m**2 pixel_volume[np.where(pixel_volume==0.)] = np.nan conc = np.zeros_like(H) if horizontal_smoothing: conc_sm = np.zeros_like(Hsm) for ti in range(H.shape[0]): for sp in range(self.nspecies): conc[ti,sp,:,:,:] = H[ti,sp,:,:,:] / pixel_volume * activity_per_element if horizontal_smoothing: conc_sm[ti,sp,:,:,:] = Hsm[ti,sp,:,:,:] / pixel_volume * activity_per_element times = np.array( self.get_time_array()[0] ) if time_avg_conc: conctmp = conc[:-1,:,:,:,:] cshape = conctmp.shape mdt = np.mean(times[1:] - times[:-1]) # output frequency in opendrift output file if deltat==None: ndt = 1 else: ndt = int( deltat / (mdt.total_seconds()/3600.) ) times2 = times[::ndt] times2 = times2[1:] odt = int(cshape[0]/ndt) logger.info ('ndt '+ str(ndt)) # number of time steps over which to average in conc file logger.info ('odt '+ str(odt)) # number of average slices # This may probably be written more efficiently! mean_conc = np.zeros( [odt,cshape[1],cshape[2],cshape[3],cshape[4]] ) for ii in range(odt): meantmp = np.mean(conctmp[(ii*ndt):(ii+1)*ndt,:,:,:,:],axis=0) mean_conc[ii,:,:,:,:] = meantmp nc = Dataset(filename, 'w') nc.createDimension('x', lon_array.shape[0]) nc.createDimension('y', lon_array.shape[1]) nc.createDimension('depth', len(z_array)-1) nc.createDimension('specie', self.nspecies) nc.createDimension('time', H.shape[0]) # times = self.get_time_array()[0] timestr = 'seconds since 1970-01-01 00:00:00' nc.createVariable('time', 'f8', ('time',)) nc.variables['time'][:] = date2num(times, timestr) nc.variables['time'].units = timestr nc.variables['time'].standard_name = 'time' if time_avg_conc: nc.createDimension('avg_time', odt) nc.createVariable('avg_time', 'f8', ('avg_time',)) nc.variables['avg_time'][:] = date2num(times2, timestr) # np.arange(mean_conc.shape[0]) nc.variables['avg_time'].units = timestr # Projection nc.createVariable('projection', 'i8') nc.variables['projection'].proj4 = density_proj.definition_string() # nc.createVariable('concfactor','f8') nc.variables['concfactor'][:] = activity_per_element nc.variables['concfactor'].long_name = 'Activity per unit element' nc.variables['concfactor'].unit = activity_unit # Cell size nc.createVariable('cell_size','f8') nc.variables['cell_size'][:] = pixelsize_m nc.variables['cell_size'].long_name = 'Length of cell' nc.variables['cell_size'].unit = 'm' nc.createVariable('smoothing_cells','i8') nc.variables['smoothing_cells'][:] = smoothing_cells nc.variables['smoothing_cells'].long_name = 'Number of cells in each direction for horizontal smoothing' nc.variables['smoothing_cells'].units = '1' # Coordinates nc.createVariable('lon', 'f8', ('y','x')) nc.createVariable('lat', 'f8', ('y','x')) nc.createVariable('depth', 'f8', ('depth',)) nc.createVariable('specie', 'i4', ('specie',)) nc.variables['lon'][:] = lon_array.T nc.variables['lon'].long_name = 'longitude' nc.variables['lon'].short_name = 'longitude' nc.variables['lon'].units = 'degrees_east' nc.variables['lat'][:] = lat_array.T nc.variables['lat'].long_name = 'latitude' nc.variables['lat'].short_name = 'latitude' nc.variables['lat'].units = 'degrees_north' nc.variables['depth'][:] = z_array[1:] nc.variables['specie'][:] = np.arange(self.nspecies) outstr = ['{}:{}'.format(isp,sp) for isp,sp in enumerate(self.name_species)] nc.variables['specie'].names = outstr # Density nc.createVariable('density', 'i4', ('time','specie','depth','y', 'x'),fill_value=-999) H = np.swapaxes(H, 3, 4).astype('i4') H = np.ma.masked_where(H==0, H) nc.variables['density'][:] = H nc.variables['density'].long_name = 'Number of elements in grid cell' nc.variables['density'].grid_mapping = 'projection' nc.variables['density'].units = '1' if horizontal_smoothing: nc.createVariable('density_smooth', 'f8', ('time','specie','depth','y', 'x'),fill_value=1.e36) Hsm = np.swapaxes(Hsm, 3, 4).astype('f8') #Hsm = np.ma.masked_where(Hsm==0, Hsm) nc.variables['density_smooth'][:] = Hsm nc.variables['density_smooth'].long_name = 'Horizontally smoothed number of elements in grid cell' nc.variables['density_smooth'].comment = 'Smoothed over '+str(smoothing_cells)+' grid points in all horizontal directions' # Radionuclide concentration, horizontally smoothed nc.createVariable('concentration', 'f8', ('time','specie','depth','y', 'x'),fill_value=1.e36) conc = np.swapaxes(conc, 3, 4) #.astype('i4') #conc = np.ma.masked_where(conc==0, conc) nc.variables['concentration'][:] = conc nc.variables['concentration'].long_name = 'Radionuclide concentration' nc.variables['concentration'].grid_mapping = 'projection_lonlat' nc.variables['concentration'].units = activity_unit+'/m3' if horizontal_smoothing: # Radionuclide concentration, horizontally smoothed nc.createVariable('concentration_smooth', 'f8', ('time','specie','depth','y', 'x'),fill_value=1.e36) conc_sm = np.swapaxes(conc_sm, 3, 4) #.astype('i4') # conc_sm = np.ma.masked_where(conc_sm==0, conc_sm) nc.variables['concentration_smooth'][:] = conc_sm nc.variables['concentration_smooth'].long_name = 'Horizontally smoothed radionuclide concentration' nc.variables['concentration_smooth'].grid_mapping = 'projection_lonlat' nc.variables['concentration_smooth'].units = activity_unit+'/m3' nc.variables['concentration_smooth'].comment = 'Smoothed over '+str(smoothing_cells)+' grid points in all horizontal directions' if time_avg_conc: nc.createVariable('concentration_avg', 'f8', ('avg_time','specie','depth','y', 'x'),fill_value=0) conc2 = np.swapaxes(mean_conc, 3, 4) #.astype('i4') conc2 = np.ma.masked_where(conc2==0, conc2) nc.variables['concentration_avg'][:] = conc2 nc.variables['concentration_avg'].long_name = 'Time averaged radionuclide concentration' nc.variables['concentration_avg'].grid_mapping = 'projection_lonlat' nc.variables['concentration_avg'].units = activity_unit+'/m3' # Volume of boxes nc.createVariable('volume', 'f8', ('depth','y', 'x'),fill_value=0) pixel_volume = np.swapaxes(pixel_volume, 1, 2) #.astype('i4') pixel_volume = np.ma.masked_where(pixel_volume==0, pixel_volume) nc.variables['volume'][:] = pixel_volume nc.variables['volume'].long_name = 'Volume of grid cell' nc.variables['volume'].grid_mapping = 'projection_lonlat' nc.variables['volume'].units = 'm3' # Topography nc.createVariable('topo', 'f8', ('y', 'x'),fill_value=0) pixel_mean_depth = np.ma.masked_where(pixel_mean_depth==0, pixel_mean_depth) nc.variables['topo'][:] = pixel_mean_depth.T nc.variables['topo'].long_name = 'Depth of grid point' nc.variables['topo'].grid_mapping = 'projection_lonlat' nc.variables['topo'].units = 'm' nc.close() logger.info('Wrote to '+filename)
[docs] def get_radionuclide_density_array(self, pixelsize_m, z_array, density_proj=None, llcrnrlon=None,llcrnrlat=None, urcrnrlon=None,urcrnrlat=None, weight=None): ''' compute a particle concentration map from particle positions Use user defined projection (density_proj=<proj4_string>) or create a lon/lat grid (density_proj=None) ''' lon = self.get_property('lon')[0] lat = self.get_property('lat')[0] times = self.get_time_array()[0] # Redundant ?? if density_proj is None: # add default projection with equal-area property density_proj = pyproj.Proj('+proj=moll +ellps=WGS84 +lon_0=0.0') # create a grid in the specified projection x,y = density_proj(lon, lat) if llcrnrlon is not None: llcrnrx,llcrnry = density_proj(llcrnrlon,llcrnrlat) urcrnrx,urcrnry = density_proj(urcrnrlon,urcrnrlat) else: llcrnrx,llcrnry = x.min()-pixelsize_m, y.min()-pixelsize_m urcrnrx,urcrnry = x.max()+pixelsize_m, y.max()+pixelsize_m x_array = np.arange(llcrnrx,urcrnrx, pixelsize_m) y_array = np.arange(llcrnry,urcrnry, pixelsize_m) bins=(x_array, y_array) outsidex, outsidey = max(x_array)*1.5, max(y_array)*1.5 z = self.get_property('z')[0] if weight is not None: weight_array = self.get_property(weight)[0] status = self.get_property('status')[0] specie = self.get_property('specie')[0] Nspecies = self.nspecies H = np.zeros((len(times), Nspecies, len(z_array) - 1, len(x_array) - 1, len(y_array) - 1 )) for sp in range(Nspecies): for i in range(len(times)): if weight is not None: weights = weight_array[i,:] else: weights = None for zi in range(len(z_array)-1): kktmp = ( (specie[i,:]==sp) & (z[i,:]>z_array[zi]) & (z[i,:]<=z_array[zi+1]) ) H[i,sp,zi,:,:], dummy, dummy = \ np.histogram2d(x[i,kktmp], y[i,kktmp], weights=weights, bins=bins) if density_proj is not None: Y,X = np.meshgrid(y_array, x_array) lon_array, lat_array = density_proj(X,Y,inverse=True) return H, lon_array, lat_array
[docs] def get_pixel_mean_depth(self,lons,lats): from scipy import interpolate # Ocean model depth and lat/lon h_grd = self.conc_topo h_grd[np.isnan(h_grd)] = 0. nx = h_grd.shape[0] ny = h_grd.shape[1] lat_grd = self.conc_lat[:nx,:ny] lon_grd = self.conc_lon[:nx,:ny] # Interpolate topography to new grid h = interpolate.griddata((lon_grd[h_grd.mask==False].flatten(),lat_grd[h_grd.mask==False].flatten()), h_grd[h_grd.mask==False].flatten(), (lons, lats), method='linear') return h
[docs] def horizontal_smooth(self, a, n=0): if n==0: num_coarse=a return num_coarse xdm=a.shape[1] ydm=a.shape[0] #msk = self.conc_mask b=np.zeros([ydm+2*n,xdm+2*n],dtype=int) b[n:-n,n:-n]=a num_coarse = np.zeros([ydm,xdm],dtype=float) smo_tmp1=np.zeros([ydm,xdm]) #smo_msk1=np.zeros([ydm-2*n,xdm-2*n],dtype=float) nlayers = 0 for ism in np.arange(-n,n+1): for jsm in np.arange(-n,n+1): smo_tmp = b[n+jsm:ydm+n+jsm, n+ism:xdm+n+ism] smo_tmp1+=smo_tmp # Must preferrably take care of land points # smo_msk = msk[n+jsm:ydm-n+jsm, n+ism:xdm-n+ism] # smo_msk1+=smo_msk nlayers+=1 if n>0: # num_coarse[n:-n,n:-n] = smo_tmp1 / smo_msk1 num_coarse[:,:] = smo_tmp1 / nlayers else: num_coarse = smo_tmp1 # num_coarse = num_coarse*msk return num_coarse
[docs] def gui_postproc(self): from os.path import expanduser logger.info('Postprocessing radionuclides') logger.info('Final speciation:') for isp,sp in enumerate(self.name_species): logger.info ('{:32}: {:>6}'.format(sp,sum(self.elements.specie==isp))) homefolder = expanduser("~") filename = homefolder+'/conc_radio_gui.nc' self.guipp_saveconcfile(filename)
""" zlayer = [-1,-2] self.guipp_plotandsaveconc(filename=filename, outfilename=homefolder+'/radio_plots/RadioConc', zlayers=zlayer, specie= ['Total', 'LMM', 'Particle reversible'], ) """
[docs] def guipp_saveconcfile(self,filename='none', pixelsize_m=200., reader_sea_depth=None): if reader_sea_depth is not None: from opendrift.readers import reader_netCDF_CF_generic reader_sea_depth = reader_netCDF_CF_generic.Reader(reader_sea_depth) else: for readerName in self.env.readers: reader = self.env.readers[readerName] if 'sea_floor_depth_below_sea_level' in reader.variables: break self.conc_lon = reader.get_variables('longitude', x=[reader.xmin,reader.xmax], y=[reader.ymin,reader.ymax])['longitude'][:] self.conc_lat = reader.get_variables('latitude', x=[reader.xmin,reader.xmax], y=[reader.ymin,reader.ymax])['latitude'][:] self.conc_topo = reader.get_variables('sea_floor_depth_below_sea_level', x=[reader.xmin,reader.xmax], y=[reader.ymin,reader.ymax])['sea_floor_depth_below_sea_level'][:] self.write_netcdf_radionuclide_density_map(filename, pixelsize_m=pixelsize_m, zlevels=self.depthintervals, activity_unit='Bq', horizontal_smoothing=True, smoothing_cells=1, )
[docs] def guipp_showanimationprofile(self): self.animation_profile(color='specie', vmin=0,vmax=self.nspecies-1, legend=[self.specie_num2name(i) for i in range(self.nspecies)], legend_loc =3, # markersize=10 )
[docs] def guipp_plotandsaveconc(self, filename=None, outfilename=None, zlayers=None, time=None, specie=None): import netCDF4 from datetime import timedelta, datetime import cartopy.crs as ccrs import matplotlib.pyplot as plt from os.path import expanduser if zlayers==None: zlayers=[-1] logger.info('Plotting concentration for {} at layer {} at time {}'.format(specie, zlayers, time)) homefolder = expanduser("~") outdir = homefolder+'/radio_plots' vcmin = 0 vcmaxt = self.get_config('seed:total_release') * 1.e-8 cblabel= 'Bq/m$^3$' proj_pp=ccrs.PlateCarree() cmap = 'CMRmap_r' if specie==None: specie_arr = ['Total', 'LMM', 'Particle reversible', 'Sediment reversible'] else: specie_arr = specie # for readerName in self.readers: # reader = self.readers[readerName] # if 'sea_floor_depth_below_sea_level' in reader.variables: # break # gtopo = reader.get_variables('sea_floor_depth_below_sea_level', # x=[reader.xmin,reader.xmax], # y=[reader.ymin,reader.ymax])['sea_floor_depth_below_sea_level'][:] logger.info (' READ DATA FILE: {}'.format(filename)) nc=netCDF4.Dataset(filename,'r') time = nc.variables['time'][:] t_units = nc.variables['time'].units #conc = nc.variables['concentration_smooth'][:]; print('concentration_smooth') specie = nc.variables['specie'][:] sp_names = nc.variables['specie'].names lat = nc.variables['lat'][:] lon = nc.variables['lon'][:] depth = nc.variables['depth'][:] topo = nc.variables['topo'][:] #nc.close() Nspecies = len(specie[:]) logger.info ('Nspecies: {}'.format(Nspecies)) if Nspecies>1: specie_names = [i.split(':')[1] for i in sp_names] else: specie_names = [sp_names.split(':')[1]] logger.info(specie_names) # Ndepths = len(depth) # logger.info ('Ndepths: {}'.format(Ndepths) ) # [print(item) for item in depth] # if Ndepths==1: # figsize=[5,6] # elif Ndepths==2: # figsize=[10,8] # elif Ndepths==3: # figsize=[13,8] ntime=len(time) time = netCDF4.num2date(time,units=t_units,only_use_cftime_datetimes=False,only_use_python_datetimes=True) for sp in specie_arr: fig, ax, crs, x, y, index_of_first, index_of_last = \ self.set_up_map() cb=False if not sp=='Total': try: spi = specie_names.index(sp) logger.debug('{} {}'.format(sp, spi)) except Exception: logger.debug(sp) break for date_idx in np.arange(0,len(time)): idx1=date_idx t1 = time[idx1] for zlayer in zlayers: if sp=='Total': tmp = np.sum(nc.variables['concentration_smooth'][idx1,:,zlayer,:,:],axis=0) else: tmp = nc.variables['concentration_smooth'][idx1,spi,zlayer,:,:] pcm=ax.pcolormesh(lon,lat,tmp, vmin=vcmin,vmax=vcmaxt, #norm=colors.LogNorm(vmin=vcmin,vmax=vcmax), cmap=cmap, zorder=-1, transform=proj_pp ) c1 = ax.contour(lon,lat,tmp, [1.e-6,1.e-5,1.e-4,1.e-3,1.e-2,1.e-1,1.e0,1.e1,1.e2,1.e3,1.e4], colors='darkgrey',linewidths=.6,zorder=4, transform=proj_pp) if not cb: plt.colorbar(pcm,extend='both',label=cblabel) cb=True title=sp+' concentration, layer '+str(depth[zlayer])+' '+t1.strftime('%Y%m%d %H:%M') fig.suptitle(title) title = title.replace(' ','').replace('\n','_').replace(':','') if outfilename: ofn = outfilename+'_'+sp.replace(' ','')+'L'+str(depth[zlayer])+'_'+t1.strftime('%Y%m%dT%H%M')+'.png' else: ofn = outdir+'/'+title+'_'+'.png' plt.savefig(ofn, dpi=300,bbox_inches='tight') # remove contour lines and shading for level in c1.collections: level.remove() pcm.remove() logger.info(ofn) plt.close() logger.info('DONE')