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LauraGomezNavarroLauraGomezNavarro
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GKDE calcs
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Lines changed: 268 additions & 29 deletions

‎Code/Calculations/kde_func.py‎

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# conda activate venv_kde_xarray
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## Written on 18/01/2021 by Laura Gomez Navarro
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# Modules:
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from glob import glob
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import xarray as xr
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import numpy as np
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from scipy.stats import gaussian_kde
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def rem_nans(ds):
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"""
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This renders lon and lat variables without nans for the last timestep.
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"""
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bad_indices = np.isnan(ds['lon'][:,-1]) | np.isnan(ds['lat'][:,-1])
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good_indices = ~bad_indices
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lon_end_nonans = ds['lon'][:,-1][good_indices]
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lat_end_nonans = ds['lat'][:,-1][good_indices]
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return lon_end_nonans, lat_end_nonans
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def kde_vals(lon_end_nonans, lat_end_nonans):
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"""
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TO DO
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"""
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x = lon_end_nonans.copy()
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y = lat_end_nonans.copy()
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xy = np.vstack([x, y])
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z = gaussian_kde(xy)(xy)
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idx = z.argsort()
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x, y, z = x[idx], y[idx], z[idx]
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return x, y, z
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def kde_parcels(nfile):
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"""
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Inputs
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nfile : filedir + filename
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Outputs
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KDE for end fields of lon and lat
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"""
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ds = xr.open_dataset(nfile)
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# Remove nans:
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lon_end_nonans, lat_end_nonans = rem_nans(ds)
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kde_x, kde_y, kde_z = kde_vals(lon_end_nonans, lat_end_nonans)
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savedir = '/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/kde_calcs/'
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savename = savedir + 'KDE_' + nfile.split('/')[-1].split('.nc')[0] + '.npz'
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np.savez(savename, kde_x=kde_x, kde_y=kde_y, kde_z=kde_z)
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return kde_x, kde_y, kde_z
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def kde_parcels_bws(nfile, bw_set):
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"""
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bw_set = np.arange(0.01, 0.26, 0.01)
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"""
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ds = xr.open_dataset(nfile)
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# Remove nans:
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lon_end_nonans, lat_end_nonans = rem_nans(ds)
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x = lon_end_nonans.copy()
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y = lat_end_nonans.copy()
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xy = np.vstack([x, y])
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KDE_dict = {}
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for ii in range(0, len(bw_set)):
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KDE_dict["z%02d" %ii] = gaussian_kde(xy, bw_method=bw_set[ii])(xy)
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# Saving:
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savedir = '/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/kde_calcs/'
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savename = savedir + 'KDE_' + nfile.split('/')[-1].split('.nc')[0] + '_bws.npz'
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np.savez(savename, bw_set=bw_set, KDE_dict=KDE_dict)
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‎Code/Calculations/kde_parcels_azores_eNATL60_monthly.sh‎

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#/bin/sh
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# SGE: the job name
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#$ -N Azores_eNATL60_KDE_weekly_Dec_Jun
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#
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# The requested run-time, expressed as (xxxx sec or hh:mm:ss)
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#$ -l h_rt=02:00:00
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#
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# SGE: your Email here, for job notification
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#$ -M l.gomeznavarro@uu.nl
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#
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# SGE: when do you want to be notified (b : begin, e : end, s : error)?
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#$ -m es
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#
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# SGE: output in the current working dir
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#$ -cwd
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#
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cd /nethome/gomez023/parcels_Azores/kde_calcs/
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#python3 -c 'from kde_func import *; _,_,_=kde_parcels("/scratch/gomez023/outputs_parcels/Particle_AZO_grid100000p_no_tides_1201_hourly_MONTH.nc")'
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#python3 -c 'from kde_func import *; _,_,_=kde_parcels("/scratch/gomez023/outputs_parcels/Particle_AZO_grid100000p_tides_1201_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/scratch/gomez023/outputs_parcels/Particle_AZO_grid100000p_no_tides_0601_hourly_MONTH.nc")'
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#python3 -c 'from kde_func import *; _,_,_=kde_parcels("/scratch/gomez023/outputs_parcels/Particle_AZO_grid100000p_tides_0601_hourly_MONTH.nc")'

‎Code/Calculations/kde_parcels_azores_eNATL60_monthly_Apr_May.sh‎

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#/bin/sh
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# SGE: the job name
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#$ -N Azores_eNATL60_KDE_MONTH_nT_wT_Apr_May
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#
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# The requested run-time, expressed as (xxxx sec or hh:mm:ss)
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#$ -l h_rt=02:00:00
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#
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# SGE: your Email here, for job notification
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#$ -M l.gomeznavarro@uu.nl
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#
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# SGE: when do you want to be notified (b : begin, e : end, s : error)?
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#$ -m es
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#
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# SGE: output in the current working dir
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#$ -cwd
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#
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cd /nethome/gomez023/parcels_Azores/kde_calcs/
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/Azores/eNATL60/ntides/monthly/Particle_AZO_grid100000p_ntides_0401_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/Azores/eNATL60/wtides/monthly/Particle_AZO_grid100000p_wtides_0401_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/Azores/eNATL60/ntides/monthly/Particle_AZO_grid100000p_ntides_0501_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/Azores/eNATL60/wtides/monthly/Particle_AZO_grid100000p_wtides_0501_hourly_MONTH.nc")'
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‎Code/Calculations/kde_parcels_azores_eNATL60_monthly_Jan_Feb.sh‎

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#/bin/sh
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# SGE: the job name
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#$ -N Azores_eNATL60_KDE_MONTH_nT_wT_Jan_Feb
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#
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# The requested run-time, expressed as (xxxx sec or hh:mm:ss)
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#$ -l h_rt=02:00:00
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#
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# SGE: your Email here, for job notification
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#$ -M l.gomeznavarro@uu.nl
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#
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# SGE: when do you want to be notified (b : begin, e : end, s : error)?
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#$ -m es
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#
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# SGE: output in the current working dir
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#$ -cwd
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#
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cd /nethome/gomez023/parcels_Azores/kde_calcs/
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#python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/input_data/eNATL60/Azores/outputs_parcels/Particle_AZO_grid100000p_no_tides_0101_hourly_MONTH.nc")'
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#python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/input_data/eNATL60/Azores/outputs_parcels/Particle_AZO_grid100000p_tides_0101_hourly_MONTH.nc")'
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#python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/input_data/eNATL60/Azores/outputs_parcels/Particle_AZO_grid100000p_no_tides_0201_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/input_data/eNATL60/Azores/outputs_parcels/Particle_AZO_grid100000p_tides_0201_hourly_MONTH.nc")'
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‎Code/Calculations/kde_parcels_azores_eNATL60_monthly_Jul_Aug.sh‎

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#/bin/sh
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# SGE: the job name
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#$ -N Azores_eNATL60_KDE_weekly_nT_wT_Jul_Aug
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#
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# The requested run-time, expressed as (xxxx sec or hh:mm:ss)
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#$ -l h_rt=02:00:00
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#
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# SGE: your Email here, for job notification
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#$ -M l.gomeznavarro@uu.nl
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#
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# SGE: when do you want to be notified (b : begin, e : end, s : error)?
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#$ -m es
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#
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# SGE: output in the current working dir
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#$ -cwd
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#
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cd /nethome/gomez023/parcels_Azores/kde_calcs/
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/scratch/gomez023/outputs_parcels/Particle_AZO_grid100000p_no_tides_0701_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/scratch/gomez023/outputs_parcels/Particle_AZO_grid100000p_tides_0701_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/scratch/gomez023/outputs_parcels/Particle_AZO_grid100000p_no_tides_0801_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/scratch/gomez023/outputs_parcels/Particle_AZO_grid100000p_tides_0801_hourly_MONTH.nc")'

‎Code/Calculations/kde_parcels_azores_eNATL60_monthly_Oct_Nov.sh‎

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#/bin/sh
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# SGE: the job name
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#$ -N Azores_eNATL60_KDE_MONTH_nT_wT_Oct_Nov
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#
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# The requested run-time, expressed as (xxxx sec or hh:mm:ss)
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#$ -l h_rt=02:00:00
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#
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# SGE: your Email here, for job notification
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#$ -M l.gomeznavarro@uu.nl
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#
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# SGE: when do you want to be notified (b : begin, e : end, s : error)?
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#$ -m es
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#
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# SGE: output in the current working dir
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#$ -cwd
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#
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cd /nethome/gomez023/parcels_Azores/kde_calcs/
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/Azores/eNATL60/ntides/monthly/Particle_AZO_grid100000p_ntides_1001_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/Azores/eNATL60/wtides/monthly/Particle_AZO_grid100000p_wtides_1001_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/Azores/eNATL60/ntides/monthly/Particle_AZO_grid100000p_ntides_1101_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/Azores/eNATL60/wtides/monthly/Particle_AZO_grid100000p_wtides_1101_hourly_MONTH.nc")'
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‎Code/Calculations/kde_parcels_azores_eNATL60_monthly_Sep_Mar.sh‎

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#/bin/sh
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# SGE: the job name
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#$ -N Azores_eNATL60_KDE_MONTH_nT_wT_Sep_Mar
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#
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# The requested run-time, expressed as (xxxx sec or hh:mm:ss)
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#$ -l h_rt=02:00:00
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#
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# SGE: your Email here, for job notification
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#$ -M l.gomeznavarro@uu.nl
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#
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# SGE: when do you want to be notified (b : begin, e : end, s : error)?
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#$ -m es
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#
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# SGE: output in the current working dir
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#$ -cwd
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#
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cd /nethome/gomez023/parcels_Azores/kde_calcs/
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/ntides/monthly/Particle_AZO_grid100000p_ntides_0901_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/wtides/monthly/Particle_AZO_grid100000p_wtides_0901_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/ntides/monthly/Particle_AZO_grid100000p_ntides_0301_hourly_MONTH.nc")'
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python3 -c 'from kde_func import *; _,_,_=kde_parcels("/data/oceanparcels/output_data/data_LauraGN/outputs_parcels/wtides/monthly/Particle_AZO_grid100000p_wtides_0301_hourly_MONTH.nc")'
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