def merge_bedmap2_changes (orig_file, updated_files, out_file):
# Read all the files
data_orig = np.fromfile(orig_file, dtype='<f4')
num_files = len(updated_files)
data_new = np.empty([num_files, data_orig.size])
for i in range(num_files):
data_new[i,:] = np.fromfile(updated_files[i], dtype='<f4')
# Make sure none of the changes overlap
changes = (data_new!=data_orig).astype(float)
if np.amax(np.sum(changes, axis=0)) > 1:
# Some changes overlap, but maybe they are the same changes.
stop = False
for i in range(num_files):
for j in range(i+1, num_files):
index = (changes[i,:]==1)*(changes[j,:]==1)
if (data_new[i,:][index] != data_new[j,:][index]).any():
stop = True
print updated_files[i] + ' contradicts ' + updated_files[j]
if stop:
print 'Error (merge_bedmap2_changes): some changes are contradictory'
sys.exit()
# Apply the changes
data_final = np.copy(data_orig)
for i in range(num_files):
data_tmp = data_new[i,:]
index = data_tmp != data_orig
data_final[index] = data_tmp[index]
# Write to file
write_binary(data_final, out_file, prec=32, endian='little')
def fix_eraint_humidity (in_dir, out_dir, prec=32):
in_dir = real_dir(in_dir)
out_dir = real_dir(out_dir)
# File paths
in_head = in_dir + 'era_a_'
in_tail = '_075.nc'
out_head = out_dir + 'ERAinterim_spfh2m_'
start_year = 1979
end_year = 2017
for year in range(start_year, end_year+1):
in_file = in_head + str(year) + in_tail
print 'Reading ' + in_file
# Need temperature, pressure, and dew point
temp = read_netcdf(in_file, 't2m')
press = read_netcdf(in_file, 'msl')
dewpoint = read_netcdf(in_file, 'd2m')
# Calculate vapour pressure
e = es0*np.exp(Lv/Rv*(1/temp - 1/dewpoint))
# Calculate specific humidity
spf = sh_coeff*e/(press - (1-sh_coeff)*e)
# Now flip in latitude to match Matlab-generated files
spf = spf[:,::-1,:]
out_file = out_head + str(year)
write_binary(spf, out_file, prec=prec)
if year == end_year:
# Copy the last timestep as in era_dummy_year
spf_last = spf[-1,:]
out_file = out_head + str(year+1)
write_binary(spf_last, out_file, prec=prec)
def mit_ics (grid_path, source_file, output_dir, nc_out=None, prec=64):
from file_io import NCfile, read_netcdf
from interpolation import interp_reg
output_dir = real_dir(output_dir)
# Fields to interpolate
fields = ['THETA', 'SALT', 'SIarea', 'SIheff', 'SIhsnow']
# Flag for 2D or 3D
dim = [3, 3, 2, 2, 2]
# End of filenames for output
outfile_tail = '_MIT.ini'
print 'Building grids'
source_grid = Grid(source_file)
model_grid = Grid(grid_path)
# Extract land mask of source grid
source_mask = source_grid.hfac==0
print 'Building mask for points to fill'
# Select open cells according to the model, interpolated to the source grid
fill = np.ceil(interp_reg(model_grid, source_grid, np.ceil(model_grid.hfac), fill_value=0)).astype(bool)
# Extend into mask a few times to make sure there are no artifacts near the coast
fill = extend_into_mask(fill, missing_val=0, use_3d=True, num_iters=3)
# Set up a NetCDF file so the user can check the results
if nc_out is not None:
ncfile = NCfile(nc_out, model_grid, 'xyz')
# Process fields
for n in range(len(fields)):
print 'Processing ' + fields[n]
out_file = output_dir + fields[n] + outfile_tail
# Read the January climatology
source_data = read_netcdf(source_file, fields[n], time_index=0)
# Discard the land mask, and extrapolate slightly into missing regions so the interpolation doesn't get messed up.
print '...extrapolating into missing regions'
if dim[n] == 3:
source_data = discard_and_fill(source_data, source_mask, fill)
else:
# Just care about the surface layer
source_data = discard_and_fill(source_data, source_mask[0,:], fill[0,:], use_3d=False)
print '...interpolating to model grid'
data_interp = interp_reg(source_grid, model_grid, source_data, dim=dim[n])
# Fill the land mask with zeros
if dim[n] == 3:
data_interp[model_grid.hfac==0] = 0
else:
data_interp[model_grid.hfac[0,:]==0] = 0
write_binary(data_interp, out_file, prec=prec)
if nc_out is not None:
print '...adding to ' + nc_out
if dim[n] == 3:
ncfile.add_variable(fields[n], data_interp, 'xyz')
else:
ncfile.add_variable(fields[n], data_interp, 'xy')
if nc_out is not None:
ncfile.close()
def seaice_drag_scaling(grid_path,
output_file,
rd_scale=1,
bb_scale=1,
ft_scale=1,
prec=64):
# Longitude bounds on each region
rd_bounds = [-80, -58] # Western bound is well into land
bb_bounds = [-49, -45]
ft_bounds = [-42, -38]
# Max distance from the ice front (km)
max_dist = 100
print 'Building grid'
grid = Grid(grid_path)
lon, lat = grid.get_lon_lat()
print 'Selecting regions'
# First find ice shelf front points
front_points = ice_shelf_front_points(grid, ice_mask=grid.fris_mask)
# Also coastal points for Berkner Island
bi_front_points = ice_shelf_front_points(grid, ice_mask=grid.get_bi_mask())
# Combine the two arrays
front_points = np.maximum(front_points, bi_front_points)
# Now get i and j indices of these points
i_vals, j_vals = np.meshgrid(range(grid.nx), range(grid.ny))
i_front = i_vals[front_points]
j_front = j_vals[front_points]
num_points = len(i_front)
# Find the distance from each point in the domain to the closest ice shelf front point, by looping over all the ice shelf front points.
# Start with an array of infinity, and update it with any smaller values each iteration. So the first iteration will fully overwrite it.
dist_to_front = np.zeros([grid.ny, grid.nx]) + np.inf
for posn in range(num_points):
# Calculate the distance of each point to this point, and convert to km
dist_to_point = dist_btw_points(
(grid.lon_1d[i_front[posn]], grid.lat_1d[j_front[posn]]),
(lon, lat)) * 1e-3
dist_to_front = np.minimum(dist_to_front, dist_to_point)
# Now select the three regions
# Must be between the given longitude bounds and not more than max_dist km away from the ice shelf front
rd_mask = (lon >= rd_bounds[0]) * (lon <= rd_bounds[1]) * (
dist_to_front <= max_dist)
bb_mask = (lon >= bb_bounds[0]) * (lon <= bb_bounds[1]) * (
dist_to_front <= max_dist)
ft_mask = (lon >= ft_bounds[0]) * (lon <= ft_bounds[1]) * (
dist_to_front <= max_dist)
print 'Setting scaling factors'
scale = np.ones([grid.ny, grid.nx])
scale[rd_mask] = rd_scale
scale[bb_mask] = bb_scale
scale[ft_mask] = ft_scale
# Smooth
scale = smooth_xy(scale, sigma=2)
# Reset ice shelf points
scale[grid.ice_mask] = 1
# Write to file
write_binary(scale, output_file, prec=prec)
def era_dummy_year (bin_dir, last_year, option='era5', nlon=None, nlat=None, out_dir=None, prec=32):
bin_dir = real_dir(bin_dir)
if out_dir is None:
out_dir = bin_dir
if nlon is None:
if option == 'era5':
nlon = 1440
elif option == 'eraint':
nlon = 480
else:
print 'Error (era_dummy_year): invalid option ' + option
sys.exit()
if nlat is None:
# The same for both cases, assuming ERA5 was cut off at 30S
nlat = 241
# Figure out the file paths
if option == 'era5':
var_names = ['apressure', 'atemp', 'aqh', 'uwind', 'vwind', 'precip', 'swdown', 'lwdown', 'evap']
file_head = 'ERA5_'
elif option == 'eraint':
var_names = ['msl', 'tmp2m_degC', 'spfh2m', 'u10m', 'v10m', 'rain', 'dsw', 'dlw']
file_head = 'ERAinterim_'
for var in var_names:
file_in = bin_dir + file_head + var + '_' + str(last_year)
# Select the last time index
data = read_binary(file_in, [nlon, nlat], 'xyt', prec=prec)[-1,:]
file_out = out_dir + file_head + var + '_' + str(last_year+1)
write_binary(data, file_out, prec=prec)
def write_topo_files (nc_grid, bathy_file, draft_file, prec=64):
bathy = read_netcdf(nc_grid, 'bathy')
draft = read_netcdf(nc_grid, 'draft')
write_binary(bathy, bathy_file, prec=prec)
write_binary(draft, draft_file, prec=prec)
print 'Files written successfully. Now go try them out! Make sure you update all the necessary variables in data, data.shelfice, SIZE.h, job scripts, etc.'
def iceberg_meltwater(grid_path, input_dir, output_file, nc_out=None, prec=32):
from plot_latlon import latlon_plot
input_dir = real_dir(input_dir)
file_head = 'icebergs_'
file_tail = '.nc'
print 'Building grids'
# Read the NEMO grid from the first file
# It has longitude in the range -180 to 180
file_path = input_dir + file_head + '01' + file_tail
nemo_lon = read_netcdf(file_path, 'nav_lon')
nemo_lat = read_netcdf(file_path, 'nav_lat')
# Build the model grid
model_grid = Grid(grid_path, max_lon=180)
print 'Interpolating'
icebergs_interp = np.zeros([12, model_grid.ny, model_grid.nx])
for month in range(12):
print '...month ' + str(month + 1)
# Read the data
file_path = input_dir + file_head + '{0:02d}'.format(month +
1) + file_tail
icebergs = read_netcdf(file_path, 'berg_total_melt', time_index=0)
# Interpolate
icebergs_interp_tmp = interp_nonreg_xy(nemo_lon,
nemo_lat,
icebergs,
model_grid.lon_1d,
model_grid.lat_1d,
fill_value=0)
# Make sure the land and ice shelf cavities don't get any iceberg melt
icebergs_interp_tmp[model_grid.land_mask + model_grid.ice_mask] = 0
# Save to the master array
icebergs_interp[month, :] = icebergs_interp_tmp
write_binary(icebergs_interp, output_file, prec=prec)
print 'Plotting'
# Make a nice plot of the annual mean
latlon_plot(mask_land_ice(np.mean(icebergs_interp, axis=0), model_grid),
model_grid,
include_shelf=False,
vmin=0,
title=r'Annual mean iceberg melt (kg/m$^2$/s)')
if nc_out is not None:
# Also write to NetCDF file
print 'Writing ' + nc_out
ncfile = NCfile(nc_out, model_grid, 'xyt')
ncfile.add_time(np.arange(12) + 1, units='months')
ncfile.add_variable('iceberg_melt',
icebergs_interp,
'xyt',
units='kg/m^2/s')
ncfile.close()
def make_sose_climatology (in_file, out_file):
from MITgcmutils import rdmds
# Strip .data from filename before reading
data = rdmds(in_file.replace('.data', ''))
climatology = np.zeros(tuple([12]) + data.shape[1:])
for month in range(12):
climatology[month,:] = np.mean(data[month::12,:], axis=0)
write_binary(climatology, out_file)
def thermo_correction(grid_dir,
var_name,
cmip_file,
era5_file,
out_file,
prec=64):
grid = Grid(grid_dir)
data = []
for fname in [cmip_file, era5_file]:
data.append(read_netcdf(fname, var_name))
data_diff = data[1] - data[0]
latlon_plot(data_diff, grid, ctype='plusminus', figsize=(10, 6))
write_binary(data_diff, out_file, prec=prec)
def polynya_mask(grid_path, polynya, mask_file, prec=64):
from plot_latlon import latlon_plot
# Define the centre and radii of the ellipse bounding the polynya
if polynya == 'maud_rise': # Area 2.6 x 10^5 km^2
lon0 = 0.
lat0 = -65.
rlon = 8.
rlat = 2.
elif polynya == 'near_shelf': # Area 2.6 x 10^5 km^2
lon0 = -30.
lat0 = -70.
rlon = 9.
rlat = 2.2
elif polynya == 'maud_rise_big': # Area 6.2 x 10^5 km^2
lon0 = 0.
lat0 = -65.
rlon = 15.
rlat = 2.5
elif polynya == 'maud_rise_small': # Area 0.34 x 10^5 km^2
lon0 = 0
lat0 = -65.
rlon = 2.8
rlat = 0.75
else:
print 'Error (polynya_mask): invalid polynya option ' + polynya
sys.exit()
# Build the grid
grid = Grid(grid_path)
# Set up the mask
mask = np.zeros([grid.ny, grid.nx])
# Select the polynya region
index = (grid.lon_2d - lon0)**2 / rlon**2 + (grid.lat_2d -
lat0)**2 / rlat**2 <= 1
mask[index] = 1
# Print the area of the polynya
print 'Polynya area is ' + str(area_integral(mask, grid) * 1e-6) + ' km^2'
# Plot the mask
latlon_plot(mask_land_ice(mask, grid),
grid,
include_shelf=False,
title='Polynya mask',
figsize=(10, 6))
# Write to file
write_binary(mask, mask_file, prec=prec)
def monthly_era5_files (file_head_in, start_year, end_year, file_head_out):
grid = ERA5Grid()
per_day = 24/6
for year in range(start_year, end_year+1):
print 'Processing year ' + str(year)
data = read_binary(file_head_in+'_'+str(year), [grid.nx, grid.ny], 'xyt')
data_monthly = np.empty([12, grid.ny, grid.nx])
t = 0
for month in range(12):
nt = days_per_month(month+1, year)*per_day
print 'Indices ' + str(t) + ' to ' + str(t+nt-1)
data_monthly[month,:] = np.mean(data[t:t+nt,:], axis=0)
t += nt
write_binary(data_monthly, file_head_out+'_'+str(year))
def calc_load_anomaly (grid, out_file, option='constant', ini_temp_file=None, ini_salt_file=None, ini_temp=None, ini_salt=None, constant_t=-1.9, constant_s=34.4, eosType='MDJWF', rhoConst=1035, tAlpha=None, sBeta=None, Tref=None, Sref=None, hfac=None, prec=64, check_grid=True):
errorTol = 1e-13 # convergence criteria
# Build the grid if needed
if check_grid:
grid = choose_grid(grid, None)
# Decide which hfac to use
if hfac is None:
hfac = grid.hfac
# Set temperature and salinity
if ini_temp is not None and ini_salt is not None:
# Deep copy of the arrays
temp = np.copy(ini_temp)
salt = np.copy(ini_salt)
elif ini_temp_file is not None and ini_salt_file is not None:
# Read from file
temp = read_binary(ini_temp_file, [grid.nx, grid.ny, grid.nz], 'xyz', prec=prec)
salt = read_binary(ini_salt_file, [grid.nx, grid.ny, grid.nz], 'xyz', prec=prec)
else:
print 'Error (calc_load_anomaly): Must either specify ini_temp and ini_salt OR ini_temp_file and ini_salt_file'
sys.exit()
# Fill in the ice shelves
# The bathymetry will get filled too, but that doesn't matter because pressure is integrated from the top down
closed = hfac==0
if option == 'constant':
# Fill with constant values
temp[closed] = constant_t
salt[closed] = constant_s
elif option == 'nearest':
# Select the layer immediately below the ice shelves and tile to make it 3D
temp_top = xy_to_xyz(select_top(np.ma.masked_where(closed, temp), return_masked=False), grid)
salt_top = xy_to_xyz(select_top(np.ma.masked_where(closed, salt), return_masked=False), grid)
# Fill the mask with these values
temp[closed] = temp_top[closed]
salt[closed] = salt_top[closed]
elif option == 'precomputed':
for data in [temp, salt]:
# Make sure there are no missing values
if (data[~closed]==0).any():
print 'Error (calc_load_anomaly): you selected the precomputed option, but there are appear to be missing values in the land mask.'
sys.exit()
# Make sure it's not a masked array as this will break the rms
if isinstance(data, np.ma.MaskedArray):
# Fill the mask with zeros
data[data.mask] = 0
data = data.data
else:
print 'Error (calc_load_anomaly): invalid option ' + option
sys.exit()
# Get vertical integrands considering z at both centres and edges of layers
dz_merged = np.zeros(2*grid.nz)
dz_merged[::2] = abs(grid.z - grid.z_edges[:-1]) # dz of top half of each cell
dz_merged[1::2] = abs(grid.z_edges[1:] - grid.z) # dz of bottom half of each cell
# Tile to make 3D
z = z_to_xyz(grid.z, grid)
dz_merged = z_to_xyz(dz_merged, grid)
# Initial guess for pressure (dbar) at centres of cells
press = abs(z)*gravity*rhoConst*1e-4
# Iteratively calculate pressure load anomaly until it converges
press_old = np.zeros(press.shape) # Dummy initial value for pressure from last iteration
rms_error = 0
while True:
rms_old = rms_error
rms_error = rms(press, press_old)
print 'RMS error = ' + str(rms_error)
if rms_error < errorTol or np.abs(rms_error-rms_old) < 0.1*errorTol:
print 'Converged'
break
# Save old pressure
press_old = np.copy(press)
# Calculate density anomaly at centres of cells
drho_c = density(eosType, salt, temp, press, rhoConst=rhoConst, Tref=Tref, Sref=Sref, tAlpha=tAlpha, sBeta=sBeta) - rhoConst
# Use this for both centres and edges of cells
drho = np.zeros(dz_merged.shape)
drho[::2,...] = drho_c
drho[1::2,...] = drho_c
# Integrate pressure load anomaly (Pa)
pload_full = np.cumsum(drho*gravity*dz_merged, axis=0)
# Update estimate of pressure
press = (abs(z)*gravity*rhoConst + pload_full[1::2,...])*1e-4
# Extract pload at each level edge (don't care about centres anymore)
pload_edges = pload_full[::2,...]
# Now find pload at the ice shelf base
# For each xy point, calculate three variables:
# (1) pload at the base of the last fully dry ice shelf cell
# (2) pload at the base of the cell beneath that
# (3) hFacC for that cell
# To calculate (1) we have to shift pload_3d_edges upward by 1 cell
pload_edges_above = neighbours_z(pload_edges)[0]
pload_above = select_top(np.ma.masked_where(closed, pload_edges_above), return_masked=False)
pload_below = select_top(np.ma.masked_where(closed, pload_edges), return_masked=False)
hfac_below = select_top(np.ma.masked_where(closed, hfac), return_masked=False)
# Now we can interpolate to the ice base
pload = pload_above + (1-hfac_below)*(pload_below - pload_above)
# Write to file
write_binary(pload, out_file, prec=prec)
def make_obcs (location, grid_path, input_path, output_dir, source='SOSE', use_seaice=True, nc_out=None, prec=32, split=180):
from grid import SOSEGrid
from file_io import NCfile, read_netcdf
from interpolation import interp_bdry
if source == 'SOSE':
input_path = real_dir(input_path)
output_dir = real_dir(output_dir)
# Fields to interpolate
# Important: SIarea has to be before SIuice and SIvice so it can be used for masking
fields = ['THETA', 'SALT', 'UVEL', 'VVEL', 'SIarea', 'SIheff', 'SIuice', 'SIvice', 'ETAN']
# Flag for 2D or 3D
dim = [3, 3, 3, 3, 2, 2, 2, 2, 2]
# Flag for grid type
gtype = ['t', 't', 'u', 'v', 't', 't', 'u', 'v', 't']
if source == 'MIT':
# Also consider snow thickness
fields += ['SIhsnow']
dim += [2]
gtype += ['t']
# End of filenames for input
infile_tail = '_climatology.data'
# End of filenames for output
outfile_tail = '_'+source+'.OBCS_'+location
print 'Building MITgcm grid'
if source == 'SOSE':
model_grid = grid_check_split(grid_path, split)
elif source == 'MIT':
model_grid = Grid(grid_path)
# Figure out what the latitude or longitude is on the boundary, both on the centres and outside edges of those cells
if location == 'S':
lat0 = model_grid.lat_1d[0]
lat0_e = model_grid.lat_corners_1d[0]
print 'Southern boundary at ' + str(lat0) + ' (cell centre), ' + str(lat0_e) + ' (cell edge)'
elif location == 'N':
lat0 = model_grid.lat_1d[-1]
lat0_e = 2*model_grid.lat_corners_1d[-1] - model_grid.lat_corners_1d[-2]
print 'Northern boundary at ' + str(lat0) + ' (cell centre), ' + str(lat0_e) + ' (cell edge)'
elif location == 'W':
lon0 = model_grid.lon_1d[0]
lon0_e = model_grid.lon_corners_1d[0]
print 'Western boundary at ' + str(lon0) + ' (cell centre), ' + str(lon0_e) + ' (cell edge)'
elif location == 'E':
lon0 = model_grid.lon_1d[-1]
lon0_e = 2*model_grid.lon_corners_1d[-1] - model_grid.lon_corners_1d[-2]
print 'Eastern boundary at ' + str(lon0) + ' (cell centre), ' + str(lon0_e) + ' (cell edge)'
else:
print 'Error (make_obcs): invalid location ' + str(location)
sys.exit()
if source == 'SOSE':
print 'Building SOSE grid'
source_grid = SOSEGrid(input_path+'grid/', model_grid=model_grid, split=split)
elif source == 'MIT':
print 'Building grid from source model'
source_grid = Grid(input_path)
else:
print 'Error (make_obcs): invalid source ' + source
sys.exit()
# Calculate interpolation indices and coefficients to the boundary latitude or longitude
if location in ['N', 'S']:
# Cell centre
j1, j2, c1, c2 = interp_slice_helper(source_grid.lat_1d, lat0)
# Cell edge
j1_e, j2_e, c1_e, c2_e = interp_slice_helper(source_grid.lat_corners_1d, lat0_e)
else:
# Pass lon=True to consider the possibility of boundary near 0E
i1, i2, c1, c2 = interp_slice_helper(source_grid.lon_1d, lon0, lon=True)
i1_e, i2_e, c1_e, c2_e = interp_slice_helper(source_grid.lon_corners_1d, lon0_e, lon=True)
# Set up a NetCDF file so the user can check the results
if nc_out is not None:
ncfile = NCfile(nc_out, model_grid, 'xyzt')
ncfile.add_time(np.arange(12)+1, units='months')
# Process fields
for n in range(len(fields)):
if fields[n].startswith('SI') and not use_seaice:
continue
print 'Processing ' + fields[n]
if source == 'SOSE':
in_file = input_path + fields[n] + infile_tail
out_file = output_dir + fields[n] + outfile_tail
# Read the monthly climatology at all points
if source == 'SOSE':
if dim[n] == 3:
source_data = source_grid.read_field(in_file, 'xyzt')
else:
source_data = source_grid.read_field(in_file, 'xyt')
else:
source_data = read_netcdf(input_path, fields[n])
if fields[n] == 'SIarea' and source == 'SOSE':
# We'll need this field later for SIuice and SIvice, as SOSE didn't mask those variables properly
print 'Interpolating sea ice area to u and v grids for masking of sea ice velocity'
source_aice_u = interp_grid(source_data, source_grid, 't', 'u', time_dependent=True, mask_with_zeros=True, periodic=True)
source_aice_v = interp_grid(source_data, source_grid, 't', 'v', time_dependent=True, mask_with_zeros=True, periodic=True)
# Set sea ice velocity to zero wherever sea ice area is zero
if fields[n] in ['SIuice', 'SIvice'] and source == 'SOSE':
print 'Masking sea ice velocity with sea ice area'
if fields[n] == 'SIuice':
index = source_aice_u==0
else:
index = source_aice_v==0
source_data[index] = 0
# Choose the correct grid for lat, lon, hfac
source_lon, source_lat = source_grid.get_lon_lat(gtype=gtype[n], dim=1)
source_hfac = source_grid.get_hfac(gtype=gtype[n])
model_lon, model_lat = model_grid.get_lon_lat(gtype=gtype[n], dim=1)
model_hfac = model_grid.get_hfac(gtype=gtype[n])
# Interpolate to the correct grid and choose the correct horizontal axis
if location in ['N', 'S']:
if gtype[n] == 'v':
source_data = c1_e*source_data[...,j1_e,:] + c2_e*source_data[...,j2_e,:]
# Multiply hfac by the ceiling of hfac on each side, to make sure we're not averaging over land
source_hfac = (c1_e*source_hfac[...,j1_e,:] + c2_e*source_hfac[...,j2_e,:])*np.ceil(source_hfac[...,j1_e,:])*np.ceil(source_hfac[...,j2_e,:])
else:
source_data = c1*source_data[...,j1,:] + c2*source_data[...,j2,:]
source_hfac = (c1*source_hfac[...,j1,:] + c2*source_hfac[...,j2,:])*np.ceil(source_hfac[...,j1,:])*np.ceil(source_hfac[...,j2,:])
source_haxis = source_lon
model_haxis = model_lon
if location == 'S':
model_hfac = model_hfac[:,0,:]
else:
model_hfac = model_hfac[:,-1,:]
else:
if gtype[n] == 'u':
source_data = c1_e*source_data[...,i1_e] + c2_e*source_data[...,i2_e]
source_hfac = (c1_e*source_hfac[...,i1_e] + c2_e*source_hfac[...,i2_e])*np.ceil(source_hfac[...,i1_e])*np.ceil(source_hfac[...,i2_e])
else:
source_data = c1*source_data[...,i1] + c2*source_data[...,i2]
source_hfac = (c1*source_hfac[...,i1] + c2*source_hfac[...,i2])*np.ceil(source_hfac[...,i1])*np.ceil(source_hfac[...,i2])
source_haxis = source_lat
model_haxis = model_lat
if location == 'W':
model_hfac = model_hfac[...,0]
else:
model_hfac = model_hfac[...,-1]
if source == 'MIT' and model_haxis[0] < source_haxis[0]:
# Need to extend source data to the west or south. Just add one row.
source_haxis = np.concatenate(([model_haxis[0]-0.1], source_haxis))
source_data = np.concatenate((np.expand_dims(source_data[:,...,0], -1), source_data), axis=-1)
source_hfac = np.concatenate((np.expand_dims(source_hfac[:,0], 1), source_hfac), axis=1)
# For 2D variables, just need surface hfac
if dim[n] == 2:
source_hfac = source_hfac[0,:]
model_hfac = model_hfac[0,:]
# Now interpolate each month to the model grid
if dim[n] == 3:
data_interp = np.zeros([12, model_grid.nz, model_haxis.size])
else:
data_interp = np.zeros([12, model_haxis.size])
for month in range(12):
print '...interpolating month ' + str(month+1)
data_interp_tmp = interp_bdry(source_haxis, source_grid.z, source_data[month,:], source_hfac, model_haxis, model_grid.z, model_hfac, depth_dependent=(dim[n]==3))
if fields[n] not in ['THETA', 'SALT']:
# Zero in land mask is more physical than extrapolated data
index = model_hfac==0
data_interp_tmp[index] = 0
data_interp[month,:] = data_interp_tmp
write_binary(data_interp, out_file, prec=prec)
if nc_out is not None:
print '...adding to ' + nc_out
# Construct the dimension code
if location in ['S', 'N']:
dimension = 'x'
else:
dimension = 'y'
if dim[n] == 3:
dimension += 'z'
dimension += 't'
ncfile.add_variable(fields[n] + '_' + location, data_interp, dimension)
if nc_out is not None:
ncfile.close()
def seaice_drag_scaling (grid_path, output_file, rd_scale=1, bb_scale=1, ft_scale=1, prec=64):
from plot_latlon import latlon_plot
# Cutoff latitude
max_lat = -74
# Longitude bounds on each region
rd_bounds = [-62, -58]
bb_bounds = [-57, -49]
ft_bounds = [-48, -35]
bounds = [rd_bounds, bb_bounds, ft_bounds]
scale_factors = [rd_scale, bb_scale, ft_scale]
# Max distance from the coast (km)
scale_dist = 150
# Sigma for smoothing
sigma = 2
print 'Building grid'
grid = Grid(grid_path)
print 'Selecting coastal points'
coast_mask = grid.get_coast_mask(ignore_iceberg=True)
lon_coast = grid.lon_2d[coast_mask].ravel()
lat_coast = grid.lat_2d[coast_mask].ravel()
print 'Selecting regions'
scale_coast = np.ones(lon_coast.shape)
for n in range(3):
index = (lon_coast >= bounds[n][0])*(lon_coast <= bounds[n][1])*(lat_coast <= max_lat)
scale_coast[index] = scale_factors[n]
print 'Calculating distance from the coast'
min_dist = None
nearest_scale = None
# Loop over all the coastal points
for i in range(lon_coast.size):
# Calculate distance of every point in the model grid to this specific coastal point, in km
dist_to_pt = dist_btw_points([lon_coast[i], lat_coast[i]], [grid.lon_2d, grid.lat_2d])*1e-3
if min_dist is None:
# Initialise the arrays
min_dist = dist_to_pt
nearest_scale = np.zeros(min_dist.shape) + scale_coast[i]
else:
# Figure out which cells have this coastal point as the closest one yet, and update the arrays
index = dist_to_pt < min_dist
min_dist[index] = dist_to_pt[index]
nearest_scale[index] = scale_coast[i]
# Smooth the result, and mask out the land and ice shelves
min_dist = mask_land_ice(min_dist, grid)
nearest_scale = mask_land_ice(smooth_xy(nearest_scale, sigma=sigma), grid)
print 'Extending scale factors offshore'
# Cosine function moving from scaling factor to 1 over distance of 300 km offshore
scale_extend = (min_dist < scale_dist)*(nearest_scale - 1)*np.cos(np.pi/2*min_dist/scale_dist) + 1
print 'Plotting'
latlon_plot(scale_extend, grid, ctype='ratio', include_shelf=False, title='Scaling factor', figsize=(10,6))
latlon_plot(scale_extend, grid, ctype='ratio', include_shelf=False, title='Scaling factor', zoom_fris=True)
print 'Writing to file'
# Replace mask with zeros
mask = scale_extend.mask
scale_extend = scale_extend.data
scale_extend[mask] = 0
write_binary(scale_extend, output_file, prec=prec)
def process_era5 (in_dir, out_dir, year, six_hourly=True, first_year=False, last_year=False, prec=32):
in_dir = real_dir(in_dir)
out_dir = real_dir(out_dir)
if year == 1979 and not first_year:
print 'Warning (process_era): last we checked, 1979 was the first year of ERA5. Unless this has changed, you need to set first_year=True.'
if year == 2018 and not last_year:
print 'Warning (process_era): last we checked, 2018 was the last year of ERA5. Unless this has changed, you need to set last_year=True.'
# Construct file paths for input and output files
in_head = in_dir + 'era5_'
var_in = ['msl', 't2m', 'd2m', 'u10', 'v10', 'tp', 'ssrd', 'strd', 'e']
if six_hourly:
accum_flag = '_2'
in_tail = '_' + str(year) + '.nc'
out_head = out_dir + 'ERA5_'
var_out = ['apressure', 'atemp', 'aqh', 'uwind', 'vwind', 'precip', 'swdown', 'lwdown', 'evap']
out_tail = '_' + str(year)
# Northermost latitude to keep
lat0 = -30
# Length of ERA5 time interval in seconds
dt = 3600.
# Read the grid from the first file
first_file = in_head + var_in[0] + in_tail
lon = read_netcdf(first_file, 'longitude')
lat = read_netcdf(first_file, 'latitude')
# Find the index of the last latitude we don't care about (remember that latitude goes from north to south in ERA files!)
j_bound = np.nonzero(lat < lat0)[0][0] - 2
# Trim and flip latitude
lat = lat[:j_bound:-1]
# Also read the first time index for the starting date
start_date = netcdf_time(first_file, monthly=False)[0]
if first_year:
# Print grid information to the reader
print '\n'
print 'For var in ' + str(var_out) + ', make these changes in input/data.exf:\n'
print 'varstartdate1 = ' + start_date.strftime('%Y%m%d')
if six_hourly:
print 'varperiod = ' + str(6*dt)
else:
print 'varperiod = ' + str(dt)
print 'varfile = ' + 'ERA5_var'
print 'var_lon0 = ' + str(lon[0])
print 'var_lon_inc = ' + str(lon[1]-lon[0])
print 'var_lat0 = ' + str(lat[0])
print 'var_lat_inc = ' + str(lat.size-1) + '*' + str(lat[1]-lat[0])
print 'var_nlon = ' + str(lon.size)
print 'var_nlat = ' + str(lat.size)
print '\n'
# Loop over variables
for i in range(len(var_in)):
in_file = in_head + var_in[i] + in_tail
print 'Reading ' + in_file
data = read_netcdf(in_file, var_in[i])
print 'Processing'
# Trim and flip over latitude
data = data[:,:j_bound:-1,:]
if var_in[i] == 'msl':
# Save pressure for later conversions
press = np.copy(data)
elif var_in[i] == 't2m':
# Convert from Kelvin to Celsius
data -= temp_C2K
elif var_in[i] == 'd2m':
# Calculate specific humidity from dew point temperature and pressure
# Start with vapour pressure
e = es0*np.exp(Lv/Rv*(1/temp_C2K - 1/data))
data = sh_coeff*e/(press - (1-sh_coeff)*e)
elif var_in[i] in ['tp', 'ssrd', 'strd', 'e']:
# Accumulated variables
# This is more complicated
if six_hourly:
# Need to read data from the following hour to interpolate to this hour. This was downloaded into separate files.
in_file_2 = in_head + var_in[i] + accum_flag + in_tail
print 'Reading ' + in_file_2
data_2 = read_netcdf(in_file_2, var_in[i])
data_2 = data_2[:,:j_bound:-1,:]
# not six_hourly will be dealt with after the first_year check
if first_year:
# The first 7 hours of the accumulated variables are missing during the first year of ERA5. Fill this missing period with data from the next available time indices.
if six_hourly:
# The first file is missing two indices (hours 0 and 6)
data = np.concatenate((data[:2,:], data), axis=0)
# The second file is missing one index (hour 1)
data_2 = np.concatenate((data_2[:1,:], data_2), axis=0)
else:
# The first file is missing 7 indices (hours 0 to 6)
data = np.concatenate((data[:7,:], data), axis=0)
if not six_hourly:
# Now get data from the following hour. Just shift one timestep ahead.
# First need data from the first hour of next year
if last_year:
# There is no such data; just copy the last hour of this year
data_next = data[-1,:]
else:
in_file_2 = in_head + var_in[i] + '_' + str(year+1) + '.nc'
data_next = read_netcdf(in_file_2, var_in[i], time_index=0)
data_next = data_next[:j_bound:-1,:]
data_2 = np.concatenate((data[1:,:], np.expand_dims(data_next,0)), axis=0)
# Now we can interpolate to the given hour: just the mean of either side
data = 0.5*(data + data_2)
# Convert from integrals to time-averages
data /= dt
if var_in[i] in ['ssrd', 'strd', 'e']:
# Swap sign on fluxes
data *= -1
out_file = out_head + var_out[i] + out_tail
write_binary(data, out_file, prec=prec)
def cmip6_atm_forcing (var, expt, mit_start_year=None, mit_end_year=None, model_path='/badc/cmip6/data/CMIP6/CMIP/MOHC/UKESM1-0-LL/', ensemble_member='r1i1p1f2', out_dir='./', out_file_head=None):
import netCDF4 as nc
# Days per year (assumes 30-day months)
days_per_year = 12*30
# Make sure it's a real variable
if var not in ['tas', 'huss', 'uas', 'vas', 'psl', 'pr', 'rsds', 'rlds']:
print 'Error (cmip6_atm_forcing): unknown variable ' + var
sys.exit()
# Construct out_file_head if needed
if out_file_head is None:
out_file_head = expt+'_'+var+'_'
elif out_file_head[-1] != '_':
# Add an underscore if it's not already there
out_file_head += '_'
out_dir = real_dir(out_dir)
# Figure out where all the files are, and which years they cover
in_files, start_years, end_years = find_cmip6_files(model_path, expt, ensemble_member, var, 'day')
if mit_start_year is None:
mit_start_year = start_years[0]
if mit_end_year is None:
mit_end_year = end_years[-1]
# Tell the user what to write about the grid
lat = read_netcdf(in_files[0], 'lat')
lon = read_netcdf(in_files[0], 'lon')
print '\nChanges to make in data.exf:'
print '*_lon0='+str(lon[0])
print '*_lon_inc='+str(lon[1]-lon[0])
print '*_lat0='+str(lat[0])
print '*_lat_inc='+str(lat[1]-lat[0])
print '*_nlon='+str(lon.size)
print '*_nlat='+str(lat.size)
# Loop over each file
for t in range(len(in_files)):
file_path = in_files[t]
print 'Processing ' + file_path
print 'Covers years '+str(start_years[t])+' to '+str(end_years[t])
# Loop over years
t_start = 0 # Time index in file
t_end = t_start+days_per_year
for year in range(start_years[t], end_years[t]+1):
if year >= mit_start_year and year <= mit_end_year:
print 'Processing ' + str(year)
# Read data
print 'Reading ' + str(year) + ' from indicies ' + str(t_start) + '-' + str(t_end)
data = read_netcdf(file_path, var, t_start=t_start, t_end=t_end)
# Conversions if necessary
if var == 'tas':
# Kelvin to Celsius
data -= temp_C2K
elif var == 'pr':
# kg/m^2/s to m/s
data /= rho_fw
elif var in ['rsds', 'rlds']:
# Swap sign on radiation fluxes
data *= -1
# Write data
write_binary(data, out_dir+out_file_head+str(year))
# Update time range for next time
t_start = t_end
t_end = t_start + days_per_year
def sose_ics (grid_path, sose_dir, output_dir, nc_out=None, constant_t=-1.9, constant_s=34.4, split=180, prec=64):
from grid import SOSEGrid
from file_io import NCfile
from interpolation import interp_reg
sose_dir = real_dir(sose_dir)
output_dir = real_dir(output_dir)
# Fields to interpolate
fields = ['THETA', 'SALT', 'SIarea', 'SIheff']
# Flag for 2D or 3D
dim = [3, 3, 2, 2]
# Constant values for ice shelf cavities
constant_value = [constant_t, constant_s, 0, 0]
# End of filenames for input
infile_tail = '_climatology.data'
# End of filenames for output
outfile_tail = '_SOSE.ini'
print 'Building grids'
# First build the model grid and check that we have the right value for split
model_grid = grid_check_split(grid_path, split)
# Now build the SOSE grid
sose_grid = SOSEGrid(sose_dir+'grid/', model_grid=model_grid, split=split)
# Extract land mask
sose_mask = sose_grid.hfac == 0
print 'Building mask for SOSE points to fill'
# Figure out which points we need for interpolation
# Find open cells according to the model, interpolated to SOSE grid
model_open = np.ceil(interp_reg(model_grid, sose_grid, np.ceil(model_grid.hfac), fill_value=1))
# Find ice shelf cavity points according to model, interpolated to SOSE grid
model_cavity = np.ceil(interp_reg(model_grid, sose_grid, xy_to_xyz(model_grid.ice_mask, model_grid), fill_value=0)).astype(bool)
# Select open, non-cavity cells
fill = model_open*np.invert(model_cavity)
# Extend into the mask a few times to make sure there are no artifacts near the coast
fill = extend_into_mask(fill, missing_val=0, use_3d=True, num_iters=3)
# Set up a NetCDF file so the user can check the results
if nc_out is not None:
ncfile = NCfile(nc_out, model_grid, 'xyz')
# Process fields
for n in range(len(fields)):
print 'Processing ' + fields[n]
in_file = sose_dir + fields[n] + infile_tail
out_file = output_dir + fields[n] + outfile_tail
print '...reading ' + in_file
# Just keep the January climatology
if dim[n] == 3:
sose_data = sose_grid.read_field(in_file, 'xyzt')[0,:]
else:
# Fill any missing regions with zero sea ice, as we won't be extrapolating them later
sose_data = sose_grid.read_field(in_file, 'xyt', fill_value=0)[0,:]
# Discard the land mask, and extrapolate slightly into missing regions so the interpolation doesn't get messed up.
print '...extrapolating into missing regions'
if dim[n] == 3:
sose_data = discard_and_fill(sose_data, sose_mask, fill)
# Fill cavity points with constant values
sose_data[model_cavity] = constant_value[n]
else:
# Just care about surface layer
sose_data = discard_and_fill(sose_data, sose_mask[0,:], fill[0,:], use_3d=False)
print '...interpolating to model grid'
data_interp = interp_reg(sose_grid, model_grid, sose_data, dim=dim[n])
# Fill the land mask with zeros
if dim[n] == 3:
data_interp[model_grid.hfac==0] = 0
else:
data_interp[model_grid.hfac[0,:]==0] = 0
write_binary(data_interp, out_file, prec=prec)
if nc_out is not None:
print '...adding to ' + nc_out
if dim[n] == 3:
ncfile.add_variable(fields[n], data_interp, 'xyz')
else:
ncfile.add_variable(fields[n], data_interp, 'xy')
if nc_out is not None:
ncfile.close()
def latlon_points (xmin, xmax, ymin, ymax, res, dlat_file, prec=64):
# Number of iterations for latitude convergence
num_lat_iter = 10
if xmin > xmax:
print "Error (latlon_points): looks like your domain crosses 180E. Try again with your longitude in the range (0, 360) instead of (-180, 180)."
sys.exit()
# Build longitude values
lon = np.arange(xmin, xmax+res, res)
# Update xmax if the range doesn't evenly divide by res
if xmax != lon[-1]:
xmax = lon[-1]
print 'Eastern boundary moved to ' + str(xmax)
# Put xmin in the range (0, 360) for namelist
if xmin < 0:
xmin += 360
# First guess for latitude: resolution scaled by latitude of southern edge
lat = [ymin]
while lat[-1] < ymax:
lat.append(lat[-1] + res*np.cos(lat[-1]*deg2rad))
lat = np.array(lat)
# Now iterate to converge on resolution scaled by latitude of centres
for iter in range(num_lat_iter):
lat_old = np.copy(lat)
# Latitude at centres
lat_c = 0.5*(lat[:-1] + lat[1:])
j = 0
lat = [ymin]
while lat[-1] < ymax and j < lat_c.size:
lat.append(lat[-1] + res*np.cos(lat_c[j]*deg2rad))
j += 1
lat = np.array(lat)
# Update ymax
ymax = lat[-1]
print 'Northern boundary moved to ' + str(ymax)
# Write latitude resolutions to file
dlat = lat[1:] - lat[:-1]
write_binary(dlat, dlat_file, prec=prec)
# Remind the user what to do in their namelist
print '\nChanges to make to input/data:'
print 'xgOrigin=' + str(xmin)
print 'ygOrigin=' + str(ymin)
print 'dxSpacing=' + str(res)
print "delYfile='" + dlat_file + "' (and copy this file into input/)"
# Find dimensions of tracer grid
Nx = lon.size-1
Ny = lat.size-1
# Find all the factors
factors_x = factors(Nx)
factors_y = factors(Ny)
print '\nNx = ' + str(Nx) + ' which has the factors ' + str(factors_x)
print 'Ny = ' + str(Ny) + ' which has the factors ' + str(factors_y)
print 'If you are happy with this, proceed with interp_bedmap2. At some point, choose your tile size based on the factors and update code/SIZE.h.'
print 'Otherwise, tweak the boundaries and try again.'
return lon, lat
def sose_sss_restoring (grid_path, sose_dir, output_salt_file, output_mask_file, nc_out=None, h0=-1250, obcs_sponge=0, split=180, prec=64):
sose_dir = real_dir(sose_dir)
print 'Building grids'
# First build the model grid and check that we have the right value for split
model_grid = grid_check_split(grid_path, split)
# Now build the SOSE grid
sose_grid = SOSEGrid(sose_dir+'grid/', model_grid=model_grid, split=split)
# Extract surface land mask
sose_mask = sose_grid.hfac[0,:] == 0
print 'Building mask'
mask_surface = np.ones([model_grid.ny, model_grid.nx])
# Mask out land and ice shelves
mask_surface[model_grid.hfac[0,:]==0] = 0
# Save this for later
mask_land_ice = np.copy(mask_surface)
# Mask out continental shelf
mask_surface[model_grid.bathy > h0] = 0
# Smooth, and remask the land and ice shelves
mask_surface = smooth_xy(mask_surface, sigma=2)*mask_land_ice
if obcs_sponge > 0:
# Also mask the cells affected by OBCS and/or its sponge
mask_surface[:obcs_sponge,:] = 0
mask_surface[-obcs_sponge:,:] = 0
mask_surface[:,:obcs_sponge] = 0
mask_surface[:,-obcs_sponge:] = 0
# Make a 3D version with zeros in deeper layers
mask_3d = np.zeros([model_grid.nz, model_grid.ny, model_grid.nx])
mask_3d[0,:] = mask_surface
print 'Reading SOSE salinity'
# Just keep the surface layer
sose_sss = sose_grid.read_field(sose_dir+'SALT_climatology.data', 'xyzt')[:,0,:,:]
# Figure out which SOSE points we need for interpolation
# Restoring mask interpolated to the SOSE grid
fill = np.ceil(interp_reg(model_grid, sose_grid, mask_3d[0,:], dim=2, fill_value=1))
# Extend into the mask a few times to make sure there are no artifacts near the coast
fill = extend_into_mask(fill, missing_val=0, num_iters=3)
# Process one month at a time
sss_interp = np.zeros([12, model_grid.nz, model_grid.ny, model_grid.nx])
for month in range(12):
print 'Month ' + str(month+1)
print '...filling missing values'
sose_sss_filled = discard_and_fill(sose_sss[month,:], sose_mask, fill, use_3d=False)
print '...interpolating'
# Mask out land and ice shelves
sss_interp[month,0,:] = interp_reg(sose_grid, model_grid, sose_sss_filled, dim=2)*mask_land_ice
write_binary(sss_interp, output_salt_file, prec=prec)
write_binary(mask_3d, output_mask_file, prec=prec)
if nc_out is not None:
print 'Writing ' + nc_out
ncfile = NCfile(nc_out, model_grid, 'xyzt')
ncfile.add_time(np.arange(12)+1, units='months')
ncfile.add_variable('salinity', sss_interp, 'xyzt', units='psu')
ncfile.add_variable('restoring_mask', mask_3d, 'xyz')
ncfile.close()
def katabatic_correction(grid_dir,
cmip_file,
era5_file,
out_file_scale,
out_file_rotate,
scale_cap=3,
xmin=None,
xmax=None,
ymin=None,
ymax=None,
prec=64):
var_names = ['uwind', 'vwind']
scale_dist = 150.
# Radius for smoothing
sigma = 2
print 'Building grid'
grid = Grid(grid_dir)
print 'Selecting coastal points'
coast_mask = grid.get_coast_mask(ignore_iceberg=True)
lon_coast = grid.lon_2d[coast_mask].ravel()
lat_coast = grid.lat_2d[coast_mask].ravel()
if xmin is None:
xmin = np.amin(grid.lon_2d)
if xmax is None:
xmax = np.amax(grid.lon_2d)
if ymin is None:
ymin = np.amin(grid.lat_2d)
if ymax is None:
ymax = np.amax(grid.lat_2d)
print 'Calculating winds in polar coordinates'
magnitudes = []
angles = []
for fname in [cmip_file, era5_file]:
u = read_netcdf(fname, var_names[0])
v = read_netcdf(fname, var_names[1])
magnitudes.append(np.sqrt(u**2 + v**2))
angle = np.arctan2(v, u)
angles.append(angle)
print 'Calculating corrections'
# Take minimum of the ratio of ERA5 to CMIP wind magnitude, and the scale cap
scale = np.minimum(magnitudes[1] / magnitudes[0], scale_cap)
# Smooth and mask the land and ice shelf
scale = mask_land_ice(smooth_xy(scale, sigma=sigma), grid)
# Take difference in angles
rotate = angles[1] - angles[0]
# Take mod 2pi when necessary
index = rotate < -np.pi
rotate[index] += 2 * np.pi
index = rotate > np.pi
rotate[index] -= 2 * np.pi
# Smoothing would be weird with the periodic angle, so just mask
rotate = mask_land_ice(rotate, grid)
print 'Calculating distance from the coast'
min_dist = None
# Loop over all the coastal points
for i in range(lon_coast.size):
# Skip over any points that are out of bounds
if lon_coast[i] < xmin or lon_coast[i] > xmax or lat_coast[
i] < ymin or lat_coast[i] > ymax:
continue
# Calculate distance of every point in the model grid to this specific coastal point, in km
dist_to_pt = dist_btw_points([lon_coast[i], lat_coast[i]],
[grid.lon_2d, grid.lat_2d]) * 1e-3
if min_dist is None:
# Initialise the array
min_dist = dist_to_pt
else:
# Figure out which cells have this coastal point as the closest one yet, and update the array
index = dist_to_pt < min_dist
min_dist[index] = dist_to_pt[index]
print 'Tapering function offshore'
# Cosine function moving from scaling factor to 1 over distance of scale_dist km offshore
scale_tapered = (min_dist < scale_dist) * (scale - 1) * np.cos(
np.pi / 2 * min_dist / scale_dist) + 1
# For the rotation, move from scaling factor to 0
rotate_tapered = (min_dist < scale_dist) * rotate * np.cos(
np.pi / 2 * min_dist / scale_dist)
print 'Plotting'
data_to_plot = [min_dist, scale_tapered, rotate_tapered]
titles = ['Distance to coast (km)', 'Scaling factor', 'Rotation factor']
ctype = ['basic', 'ratio', 'plusminus']
fig_names = ['min_dist.png', 'scale.png', 'rotate.png']
for i in range(len(data_to_plot)):
for fig_name in [None, fig_names[i]]:
latlon_plot(data_to_plot[i],
grid,
ctype=ctype[i],
include_shelf=False,
title=titles[i],
figsize=(10, 6),
fig_name=fig_name)
print 'Writing to file'
fields = [scale_tapered, rotate_tapered]
out_files = [out_file_scale, out_file_rotate]
for n in range(len(fields)):
# Replace mask with zeros
mask = fields[n].mask
data = fields[n].data
data[mask] = 0
write_binary(data, out_files[n], prec=prec)
def balance_obcs (grid_path, option='balance', obcs_file_w_u=None, obcs_file_e_u=None, obcs_file_s_v=None, obcs_file_n_v=None, d_eta=None, d_t=None, max_deta_dt=0.5, prec=32):
if option == 'correct' and (d_eta is None or d_t is None):
print 'Error (balance_obcs): must set d_eta and d_t for option="correct"'
sys.exit()
print 'Building grid'
grid = Grid(grid_path)
# Calculate integrands of area, scaled by hFacC
# Note that dx and dy are only available on western and southern edges of cells respectively; for the eastern and northern boundary, will just have to use 1 cell in. Not perfect, but this correction wouldn't perfectly conserve anyway.
# Area of western face = dy*dz*hfac
dA_w = xy_to_xyz(grid.dy_w, grid)*z_to_xyz(grid.dz, grid)*grid.hfac
# Area of southern face = dx*dz*hfac
dA_s = xy_to_xyz(grid.dx_s, grid)*z_to_xyz(grid.dz, grid)*grid.hfac
# Now extract the area array at each boundary, and wrap up into a list for easy iteration later
dA_bdry = [dA_w[:,:,0], dA_w[:,:,-1], dA_s[:,0,:], dA_s[:,-1,:]]
# Some more lists:
bdry_key = ['W', 'E', 'S', 'N']
files = [obcs_file_w_u, obcs_file_e_u, obcs_file_s_v, obcs_file_n_v]
dimensions = ['yzt', 'yzt', 'xzt', 'xzt']
sign = [1, -1, 1, -1] # Multiply velocity variable by this to get incoming transport
# Initialise number of timesteps
num_time = None
# Integrate the total area of ocean cells on boundaries
total_area = 0
for i in range(len(files)):
if files[i] is not None:
print 'Calculating area of ' + bdry_key[i] + ' boundary'
total_area += np.sum(dA_bdry[i])
# Calculate the net transport into the domain
if option in ['balance', 'dampen']:
# Transport based on OBCS normal velocities
if option == 'balance':
net_transport = 0
elif option == 'dampen':
net_transport = None
for i in range(len(files)):
if files[i] is not None:
print 'Processing ' + bdry_key[i] + ' boundary from ' + files[i]
# Read data
vel = read_binary(files[i], [grid.nx, grid.ny, grid.nz], dimensions[i], prec=prec)
if num_time is None:
# Find number of time indices
num_time = vel.shape[0]
elif num_time != vel.shape[0]:
print 'Error (balance_obcs): inconsistent number of time indices between OBCS files'
sys.exit()
if option == 'dampen' and net_transport is None:
# Initialise transport per month
net_transport = np.zeros(num_time)
if option == 'balance':
# Time-average velocity (this is equivalent to calculating the transport at each month and then time-averaging at the end - it's all just sums)
vel = np.mean(vel, axis=0)
# Integrate net transport through this boundary into the domain, and add to global sum
net_transport += np.sum(sign[i]*vel*dA_bdry[i])
elif option == 'dampen':
# Integrate net transport at each month
for t in range(num_time):
net_transport[t] += np.sum(sign[i]*vel[t,:]*dA_bdry[i])
elif option == 'correct':
# Transport based on simulated changes in sea surface height
# Need area of sea surface
dA_sfc = np.sum(grid.dA*np.invert(grid.land_mask).astype(float))
# Calculate transport in m^3/s
net_transport = d_eta*dA_sfc/(d_t*sec_per_year)
# Inner function to nicely print the net transport to the user
def print_net_transport (transport):
if transport < 0:
direction = 'out of the domain'
else:
direction = 'into the domain'
print 'Net transport is ' + str(abs(transport*1e-6)) + ' Sv ' + direction
if option == 'dampen':
for t in range(num_time):
print 'Month ' + str(t+1)
print_net_transport(net_transport[t])
else:
print_net_transport(net_transport)
if option == 'dampen':
# Calculate the acceptable maximum absolute transport
# First need total area of sea surface (including cavities) in domain
surface_area = np.sum(mask_land(grid.dA, grid))
max_transport = max_deta_dt*surface_area/(sec_per_day*30)
print 'Maximum allowable transport is ' + str(max_transport*1e-6) + ' Sv'
if np.max(np.abs(net_transport)) <= max_transport:
print 'OBCS satisfy this; nothing to do'
return
# Work out by what factor to dampen the transports
scale_factor = max_transport/np.max(np.abs(net_transport))
print 'Will scale transports by ' + str(scale_factor)
# Calculate corresponding velocity correction at each month
correction = np.zeros(num_time)
for t in range(num_time):
correction[t] = (scale_factor-1)*net_transport[t]/total_area
print 'Month ' + str(t+1) + ': will apply correction of ' + str(correction[t]) + ' m/s to normal velocity at each boundary'
else:
# Calculate single correction in m/s
correction = -1*net_transport/total_area
print 'Will apply correction of ' + str(correction) + ' m/s to normal velocity at each boundary'
# Now apply the correction
for i in range(len(files)):
if files[i] is not None:
print 'Correcting ' + files[i]
# Read all the data again
vel = read_binary(files[i], [grid.nx, grid.ny, grid.nz], dimensions[i], prec=prec)
# Apply the correction
if option == 'dampen':
for t in range(num_time):
vel[t,:] += sign[i]*correction[t]
else:
vel += sign[i]*correction
# Overwrite the file
write_binary(vel, files[i], prec=prec)
if option in ['balance', 'dampen']:
# Recalculate the transport to make sure it worked
if option == 'balance':
net_transport_new = 0
elif option == 'dampen':
net_transport_new = np.zeros(num_time)
for i in range(len(files)):
if files[i] is not None:
vel = read_binary(files[i], [grid.nx, grid.ny, grid.nz], dimensions[i], prec=prec)
if option == 'balance':
vel = np.mean(vel, axis=0)
net_transport_new += np.sum(sign[i]*vel*dA_bdry[i])
elif option == 'dampen':
for t in range(num_time):
net_transport_new[t] += np.sum(sign[i]*vel[t,:]*dA_bdry[i])
if option == 'balance':
print_net_transport(net_transport_new)
elif option == 'dampen':
for t in range(num_time):
print 'Month ' + str(t+1)
print_net_transport(net_transport_new[t])
def pace_atm_forcing (var, ens, in_dir, out_dir):
import netCDF4 as nc
start_year = 1920
end_year = 2013
days_per_year = 365
months_per_year = 12
ens_str = str(ens).zfill(2)
if var not in ['TREFHT', 'QBOT', 'PSL', 'UBOT', 'VBOT', 'PRECT', 'FLDS', 'FSDS']:
print 'Error (pace_atm_forcing): Invalid variable ' + var
sys.exit()
path = real_dir(in_dir)
# Decide if monthly or daily data
monthly = var in ['FLDS', 'FSDS']
if monthly:
path += 'monthly/'
else:
path += 'daily/'
path += var + '/'
for year in range(start_year, end_year+1):
print 'Processing ' + str(year)
# Construct the file based on the year (after 2006 use RCP 8.5) and whether it's monthly or daily
if year < 2006:
file_head = 'b.e11.B20TRLENS.f09_g16.SST.restoring.ens'
if monthly:
file_tail = '.192001-200512.nc'
else:
file_tail = '.19200101-20051231.nc'
else:
file_head = 'b.e11.BRCP85LENS.f09_g16.SST.restoring.ens'
if monthly:
file_tail = '.200601-201312.nc'
else:
file_tail = '.20060101-20131231.nc'
if monthly:
file_mid = '.cam.h0.'
else:
file_mid = '.cam.h1.'
file_path = path + file_head + ens_str + file_mid + var + file_tail
# Choose time indicies
if monthly:
per_year = months_per_year
else:
per_year = days_per_year
t_start = (year-start_year)*per_year
t_end = t_start + per_year
print 'Reading indices ' + str(t_start) + '-' + str(t_end-1)
# Read data
data = read_netcdf(file_path, var, t_start=t_start, t_end=t_end)
# Unit conversions
if var in ['FLDS', 'FSDS']:
# Swap sign
data *= -1
elif var == 'TREFHT':
# Convert from K to C
data -= temp_C2K
elif var == 'QBOT':
# Convert from mixing ratio to specific humidity
data = data/(1.0 + data)
# Write data
out_file = real_dir(out_dir) + 'PACE_ens' + ens_str + '_' + var + '_' + str(year)
write_binary(data, out_file)