def main():
# Get options
args = options()
# construct a dict with essential info
case_config = {
'Avg': {
'start_date': args.start_date,
'end_date': args.end_date
}
}
case_config['Case'] = {
'CASEROOT': args.caseroot,
'CIMEROOT': args.cimeroot
}
# Create the case instance
dcase = DiagsCase(case_config['Case'])
RUNDIR = dcase.get_value('RUNDIR')
if args.debug:
print('Run directory is:', RUNDIR)
print('Casename is:', dcase.casename)
# Update dict
case_config['Case'].update({'RUNDIR': RUNDIR})
if not os.path.isdir(dcase.casename):
print('Creating {}... \n'.format(dcase.casename))
os.system('mkdir -p {}'.format(dcase.casename))
make_yaml(dcase.casename, case_config)
make_run_script(dcase.casename)
else:
print('Directory {} already exists. \n'.format(dcase.casename))
return
def main(stream=False):
# Get options
args = options()
# Read in the yaml file
diag_config_yml = yaml.load(open(args.diag_config_yml_path, 'r'),
Loader=yaml.Loader)
# Create the case instance
dcase = DiagsCase(diag_config_yml['Case'], xrformat=True)
print('Casename is:', dcase.casename)
RUNDIR = dcase.get_value('RUNDIR')
# read grid
grd = MOM6grid(RUNDIR + '/' + dcase.casename + '.mom6.static.nc',
xrformat=True)
area = grd.area_t.where(grd.wet > 0)
# Get masking for different regions
depth = grd.depth_ocean.values
# remove Nan's, otherwise genBasinMasks won't work
depth[np.isnan(depth)] = 0.0
basin_code = genBasinMasks(grd.geolon.values,
grd.geolat.values,
depth,
xda=True)
#select a few basins, namely, Global, PersianGulf, Arctic, Pacific, Atlantic, Indian, Southern, LabSea and BaffinBay
basins = basin_code.isel(region=[0, 1, 7, 8, 9, 10, 11, 12, 13])
if not args.diff_rms and not args.surface and not args.forcing:
raise ValueError("Please select -diff_rms, -surface and/or -forcing.")
if args.diff_rms:
horizontal_mean_diff_rms(grd, dcase, basins, args)
if args.surface:
variables = ['SSH', 'tos', 'sos', 'mlotst', 'oml']
fname = '.mom6.sfc_*.nc'
xystats(grd, dcase, basins, args)
if args.forcing:
variables = [
'friver', 'ficeberg', 'fsitherm', 'hfsnthermds', 'sfdsi', 'hflso',
'seaice_melt_heat', 'wfo', 'hfds', 'Heat_PmE'
]
fname = '.mom6.hm_*.nc'
xystats(grd, dcase, basins, args)
return
def main(stream=False):
# Get options
args = options()
nw = args.number_of_workers
if not os.path.isdir('PNG/HT'):
print('Creating a directory to place figures (PNG/HT)... \n')
os.system('mkdir -p PNG/HT')
if not os.path.isdir('ncfiles'):
print('Creating a directory to place figures (ncfiles)... \n')
os.system('mkdir ncfiles')
# Read in the yaml file
diag_config_yml = yaml.load(open(args.diag_config_yml_path,'r'), Loader=yaml.Loader)
# Create the case instance
dcase = DiagsCase(diag_config_yml['Case'])
args.case_name = dcase.casename
args.savefigs = True; args.outdir = 'PNG/HT'
RUNDIR = dcase.get_value('RUNDIR')
print('Run directory is:', RUNDIR)
print('Casename is:', dcase.casename)
print('Variables to be processed:', args.variables)
print('Number of workers to be used:', nw)
# set avg dates
avg = diag_config_yml['Avg']
if not args.start_date : args.start_date = avg['start_date']
if not args.end_date : args.end_date = avg['end_date']
# read grid info
grd = MOM6grid(RUNDIR+'/'+dcase.casename+'.mom6.static.nc')
depth = grd.depth_ocean
# remote Nan's, otherwise genBasinMasks won't work
depth[np.isnan(depth)] = 0.0
basin_code = m6toolbox.genBasinMasks(grd.geolon, grd.geolat, depth)
parallel, cluster, client = m6toolbox.request_workers(nw)
print('Reading dataset...')
startTime = datetime.now()
variables = args.variables
def preprocess(ds):
''' Compute montly averages and return the dataset with variables'''
for var in variables:
print('Processing {}'.format(var))
if var not in ds.variables:
print('WARNING: ds does not have variable {}. Creating dataarray with zeros'.format(var))
jm, im = grd.geolat.shape
tm = len(ds.time)
da = xr.DataArray(np.zeros((tm, jm, im)), dims=['time','yq','xh'], \
coords={'yq' : grd.yq, 'xh' : grd.xh, 'time' : ds.time}).rename(var)
ds = xr.merge([ds, da])
#return ds[variables].resample(time="1Y", closed='left', \
# keep_attrs=True).mean(dim='time', keep_attrs=True)
return ds[variables]
if parallel:
ds = xr.open_mfdataset(RUNDIR+'/'+dcase.casename+'.mom6.hm_*.nc', \
parallel=True, data_vars='minimal', chunks={'time': 12},\
coords='minimal', compat='override', preprocess=preprocess)
else:
ds = xr.open_mfdataset(RUNDIR+'/'+dcase.casename+'.mom6.hm_*.nc', \
data_vars='minimal', coords='minimal', compat='override', \
preprocess=preprocess)
print('Time elasped: ', datetime.now() - startTime)
print('Selecting data between {} and {}...'.format(args.start_date, args.end_date))
startTime = datetime.now()
ds_sel = ds.sel(time=slice(args.start_date, args.end_date))
print('Time elasped: ', datetime.now() - startTime)
print('Computing yearly means...')
startTime = datetime.now()
ds_sel = ds_sel.resample(time="1Y", closed='left',keep_attrs=True).mean('time',keep_attrs=True)
print('Time elasped: ', datetime.now() - startTime)
print('Computing time mean...')
startTime = datetime.now()
ds_sel = ds_sel.mean('time').load()
print('Time elasped: ', datetime.now() - startTime)
if parallel:
print('Releasing workers...')
client.close(); cluster.close()
varName = 'T_ady_2d'
print('Saving netCDF files...')
attrs = {'description': 'Time-mean poleward heat transport by components ', 'units': ds[varName].units,
'start_date': args.start_date, 'end_date': args.end_date, 'casename': dcase.casename}
m6toolbox.add_global_attrs(ds_sel,attrs)
ds_sel.to_netcdf('ncfiles/'+dcase.casename+'_heat_transport.nc')
# create a ndarray subclass
class C(np.ndarray): pass
if varName in ds.variables:
tmp = np.ma.masked_invalid(ds_sel[varName].values)
tmp = tmp[:].filled(0.)
advective = tmp.view(C)
advective.units = ds[varName].units
else:
raise Exception('Could not find "T_ady_2d" in file "%s"'%(args.infile+args.monthly))
varName = 'T_diffy_2d'
if varName in ds.variables:
tmp = np.ma.masked_invalid(ds_sel[varName].values)
tmp = tmp[:].filled(0.)
diffusive = tmp.view(C)
diffusive.units = ds[varName].units
else:
diffusive = None
warnings.warn('Diffusive temperature term not found. This will result in an underestimation of the heat transport.')
varName = 'T_lbd_diffy_2d'
if varName in ds.variables:
tmp = np.ma.masked_invalid(ds_sel[varName].values)
tmp = tmp[:].filled(0.)
lbd = tmp.view(C)
#lbd.units = ds[varName].units
else:
lbd = None
warnings.warn('Lateral boundary mixing term not found. This will result in an underestimation of the heat transport.')
plt_heat_transport_model_vs_obs(advective, diffusive, lbd, basin_code, grd, args)
return
def main(stream=False):
# Get options
cmdLineArgs = options()
if cmdLineArgs.save_ncfile:
if not os.path.isdir('ncfiles'):
print('Creating a directory to place figures (ncfiles)... \n')
os.system('mkdir ncfiles')
# Read in the yaml file
diag_config_yml = yaml.load(open(cmdLineArgs.diag_config_yml_path, 'r'),
Loader=yaml.Loader)
# Create the case instance
dcase = DiagsCase(diag_config_yml['Case'])
cmdLineArgs.case_name = dcase.casename
cmdLineArgs.infile = dcase.get_value('RUNDIR')
if cmdLineArgs.infile[-1] != '/':
cmdLineArgs.infile = cmdLineArgs.infile + '/'
if cmdLineArgs.debug:
print('Run directory is:', cmdLineArgs.infile)
print('Casename is:', cmdLineArgs.case_name)
reference = 'Griffies et al., 2016: OMIP contribution to CMIP6: experimental and diagnostic protocol for the physical component of the Ocean Model Intercomparison Project. Geosci. Model. Dev., 9, 3231-3296. doi:10.5194/gmd-9-3231-2016'
title = 'Griffies et al., 2016, Geosci. Model. Dev., 9, 3231-3296. doi:10.5194/gmd-9-3231-2016'
observedFlows = {
'reference': reference,
'title': title,
'Agulhas': (164.4, 182.2),
'Barents Opening': 2.0,
'Bering Strait': (0.7, 1.1),
'Davis Strait': (-2.1, -1.1),
'Denmark Strait': (-4.8, -2.0),
'Drake Passage': (164.4, 182.2),
'English Channel': (0.01, 0.1),
'Faroe-Scotland': (0.8, 1.0),
'Florida-Bahamas': (28.9, 34.3),
'Fram Strait': (-4.7, 0.7),
'Gibraltar Strait': 0.11,
'Gibraltar Strait': (-1.0, 1.0),
'Iceland-Faroe': (4.35, 4.85),
'Indonesian Throughflow': (-15., -13.),
'Mozambique Channel': (-25.6, -7.8),
'Pacific Equatorial Undercurrent': (24.5, 28.3),
'Taiwan-Luzon Strait': (-3.0, -1.8),
'Windward Passage': (-15., 5.)
}
# GMM, we need some estimated transport for the following:
# Bab_al_mandeb_Strait
# Iceland-Norway
# Hormuz Strait
plotSections = []
# leaving this here to catch if start/end years outside the range of the dataset
res = Transport(cmdLineArgs,
'agulhas_section',
'umo',
label='Agulhas',
ylim=(100, 200))
try:
res = Transport(cmdLineArgs,
'agulhas_section',
'umo',
label='Agulhas',
ylim=(100, 250))
plotSections.append(res)
except:
print('WARNING: unable to process Agulhas_section')
try:
res = Transport(cmdLineArgs,
'Bab_al_mandeb_Strait',
'umo',
label='Bab al mandeb Strait',
ylim=(-0.5, 0.5))
plotSections.append(res)
except:
print('WARNING: unable to process Bab Al Mandeb Strait')
try:
res = Transport(cmdLineArgs,
'Bering_Strait',
'vmo',
label='Bering Strait',
ylim=(-2, 3))
plotSections.append(res)
except:
print('WARNING: unable to process Bering_Strait')
try:
res = Transport(cmdLineArgs,
'Barents_opening',
'vmo',
label='Barents Opening',
ylim=(-1, 9))
plotSections.append(res)
except:
print('WARNING: unable to process Barents_opening')
try:
res = Transport(cmdLineArgs,
'Davis_Strait',
'vmo',
label='Davis Strait',
ylim=(-5.0, 0.5))
plotSections.append(res)
except:
print('WARNING: unable to process Davis_Strait')
try:
res = Transport(cmdLineArgs,
'Denmark_Strait',
'vmo',
label='Denmark Strait',
ylim=(-12, 2))
plotSections.append(res)
except:
print('WARNING: unable to process Denmark_Strait')
try:
res = Transport(cmdLineArgs,
'Drake_Passage',
'umo',
label='Drake Passage',
ylim=(100, 250))
plotSections.append(res)
except:
print('WARNING: unable to process Drake_Passage')
try:
res = Transport(cmdLineArgs,
'English_Channel',
'umo',
label='English Channel',
ylim=(-0.4, 0.4))
plotSections.append(res)
except:
print('WARNING: unable to process English_Channel')
#try: res = Transport(cmdLineArgs,'Faroe_Scotland','umo',label='Faroe-Scotland',ylim=(-5,12)); plotSections.append(res)
#except: print('WARNING: unable to process Faroe_Scotland')
try:
res = Transport(cmdLineArgs,
'Florida_Bahamas',
'vmo',
label='Florida-Bahamas',
ylim=(5, 35))
plotSections.append(res)
except:
print('WARNING: unable to process Florida_Bahamas')
try:
res = Transport(cmdLineArgs,
'Fram_Strait',
'vmo',
label='Fram Strait',
ylim=(-8, 4))
plotSections.append(res)
except:
print('WARNING: unable to process Fram_Strait')
try:
res = Transport(cmdLineArgs,
'Gibraltar_Strait',
'umo',
label='Gibraltar Strait',
ylim=(-1.0, 1.0))
plotSections.append(res)
except:
print('WARNING: unable to process Gibraltar_Strait')
try:
res = Transport(cmdLineArgs,
'Hormuz_Strait',
'umo',
label='Hormuz Strait',
ylim=(-0.5, 0.5))
plotSections.append(res)
except:
print('WARNING: unable to process Hormuz_Strait')
#try: res = Transport(cmdLineArgs,['Iceland_Faroe_U','Iceland_Faroe_V'],['umo','vmo'],label='Iceland-Faroe'); plotSections.append(res)
#except: print('WARNING: unable to process Iceland_Faroe_U and Iceland_Faroe_V')
try:
res = Transport(cmdLineArgs,
'Iceland_Norway',
'vmo',
label='Iceland-Norway',
ylim=(-5, 15))
plotSections.append(res)
except:
print('WARNING: unable to process Iceland_Norway')
try:
res = Transport(cmdLineArgs,
'Indonesian_Throughflow',
'vmo',
label='Indonesian Throughflow',
ylim=(-40, 10))
plotSections.append(res)
except:
print('WARNING: unable to process Indonesian_Throughflow')
try:
res = Transport(cmdLineArgs,
'Mozambique_Channel',
'vmo',
label='Mozambique Channel',
ylim=(-50, 10))
plotSections.append(res)
except:
print('WARNING: unable to process Mozambique_Channel')
try:
res = Transport(cmdLineArgs,
'Pacific_undercurrent',
'umo',
label='Pacific Equatorial Undercurrent',
ylim=None,
zlim=(0, 350))
plotSections.append(res)
except:
print('WARNING: unable to process Pacific_undercurrent')
try:
res = Transport(cmdLineArgs,
'Taiwan_Luzon',
'umo',
label='Taiwan-Luzon Strait',
ylim=(-15, 10))
plotSections.append(res)
except:
print('WARNING: unable to process Taiwan_Luzon')
try:
res = Transport(cmdLineArgs,
'Windward_Passage',
'vmo',
label='Windward Passage',
ylim=(-10, 10))
plotSections.append(res)
except:
print('WARNING: unable to process Windward_Passage')
if cmdLineArgs.save_ncfile:
print('Saving netCDF file with transports...\n')
# create a dataaray
labels = []
for n in range(len(plotSections)):
labels.append(plotSections[n].label)
var = numpy.zeros((len(plotSections), len(plotSections[0].time)))
ds = xr.Dataset(data_vars={'transport': (('sections', 'time'), var)},
coords={
'sections': labels,
'time': plotSections[0].time
})
for n in range(len(plotSections)):
ds.transport.values[n, :] = plotSections[n].data
ds.to_netcdf('ncfiles/' + cmdLineArgs.case_name +
'_section_transports.nc')
print('Plotting {} sections...\n'.format(len(plotSections)))
imgbufs = []
fig = plt.figure(figsize=(13, 17))
for n in range(0, len(plotSections)):
plotPanel(plotSections[n], n, observedFlows=observedFlows)
fig.text(0.5,
0.955,
str(plotSections[n - 1].case_name),
horizontalalignment='center',
fontsize=14)
fig.text(0.5,
0.925,
'Observations summarized in ' + observedFlows['title'],
horizontalalignment='center',
fontsize=11)
plt.subplots_adjust(hspace=0.3)
if stream != None:
fig.text(0.5,
0.05,
str('Generated by mom6-tools'),
horizontalalignment='center',
fontsize=12)
#plt.show(block=False)
if stream is True: objOut = io.BytesIO()
else:
if not os.path.isdir(cmdLineArgs.outdir):
os.system('mkdir -p ' + cmdLineArgs.outdir)
objOut = cmdLineArgs.outdir + '/' + cmdLineArgs.case_name + '_section_transports.png'
plt.savefig(objOut)
if stream is True: imgbufs.append(objOut)
if stream is True:
return imgbufs
def main():
# Get options
args = options()
nw = args.number_of_workers
if not os.path.isdir('PNG/MOC'):
print('Creating a directory to place figures (PNG/MOC)... \n')
os.system('mkdir -p PNG/MOC')
if not os.path.isdir('ncfiles'):
print('Creating a directory to place figures (ncfiles)... \n')
os.system('mkdir ncfiles')
# Read in the yaml file
diag_config_yml = yaml.load(open(args.diag_config_yml_path, 'r'),
Loader=yaml.Loader)
# Create the case instance
dcase = DiagsCase(diag_config_yml['Case'])
args.case_name = dcase.casename
args.savefigs = True
args.outdir = 'PNG/MOC/'
RUNDIR = dcase.get_value('RUNDIR')
print('Run directory is:', RUNDIR)
print('Casename is:', dcase.casename)
print('Number of workers to be used:', nw)
# set avg dates
avg = diag_config_yml['Avg']
if not args.start_date: args.start_date = avg['start_date']
if not args.end_date: args.end_date = avg['end_date']
# read grid info
grd = MOM6grid(RUNDIR + '/' + dcase.casename + '.mom6.static.nc')
depth = grd.depth_ocean
# remote Nan's, otherwise genBasinMasks won't work
depth[np.isnan(depth)] = 0.0
basin_code = m6toolbox.genBasinMasks(grd.geolon, grd.geolat, depth)
parallel, cluster, client = m6toolbox.request_workers(nw)
print('Reading {} dataset...'.format(args.file_name))
startTime = datetime.now()
# load data
def preprocess(ds):
variables = ['vmo', 'vhml', 'vhGM']
for v in variables:
if v not in ds.variables:
ds[v] = xr.zeros_like(ds.vo)
return ds[variables]
if parallel:
ds = xr.open_mfdataset(
RUNDIR + '/' + dcase.casename + args.file_name,
parallel=True,
combine="nested", # concatenate in order of files
concat_dim="time", # concatenate along time
preprocess=preprocess,
).chunk({"time": 12})
else:
ds = xr.open_mfdataset(RUNDIR+'/'+dcase.casename+args.file_name, data_vars='minimal', \
coords='minimal', compat='override', preprocess=preprocess)
print('Time elasped: ', datetime.now() - startTime)
# compute yearly means first since this will be used in the time series
print('Computing yearly means...')
startTime = datetime.now()
ds_yr = ds.resample(time="1Y", closed='left').mean('time')
print('Time elasped: ', datetime.now() - startTime)
print('Selecting data between {} and {}...'.format(args.start_date,
args.end_date))
startTime = datetime.now()
ds_sel = ds_yr.sel(time=slice(args.start_date, args.end_date))
print('Time elasped: ', datetime.now() - startTime)
print('Computing time mean...')
startTime = datetime.now()
ds_mean = ds_sel.mean('time').compute()
print('Time elasped: ', datetime.now() - startTime)
# create a ndarray subclass
class C(np.ndarray):
pass
varName = 'vmo'
conversion_factor = 1.e-9
tmp = np.ma.masked_invalid(ds_mean[varName].values)
tmp = tmp[:].filled(0.)
VHmod = tmp.view(C)
VHmod.units = ds[varName].units
Zmod = m6toolbox.get_z(ds, depth, varName) # same here
if args.case_name != '': case_name = args.case_name
else: case_name = ''
# Global MOC
m6plot.setFigureSize([16, 9], 576, debug=False)
axis = plt.gca()
cmap = plt.get_cmap('dunnePM')
zg = Zmod.min(axis=-1)
psiPlot = MOCpsi(VHmod) * conversion_factor
psiPlot = 0.5 * (psiPlot[0:-1, :] + psiPlot[1::, :])
yyg = grd.geolat_c[:, :].max(axis=-1) + 0 * zg
ci = m6plot.pmCI(0., 40., 5.)
plotPsi(
yyg, zg, psiPlot, ci, 'Global MOC [Sv],' + 'averaged between ' +
args.start_date + ' and ' + args.end_date)
plt.xlabel(r'Latitude [$\degree$N]')
plt.suptitle(case_name)
plt.gca().invert_yaxis()
findExtrema(yyg, zg, psiPlot, max_lat=-30.)
findExtrema(yyg, zg, psiPlot, min_lat=25., min_depth=250.)
findExtrema(yyg, zg, psiPlot, min_depth=2000., mult=-1.)
objOut = args.outdir + str(case_name) + '_MOC_global.png'
plt.savefig(objOut)
if 'zl' in ds:
zl = ds.zl.values
elif 'z_l' in ds:
zl = ds.z_l.values
else:
raise ValueError("Dataset does not have vertical coordinate zl or z_l")
# create dataset to store results
moc = xr.Dataset(data_vars={
'moc': (('zl', 'yq'), psiPlot),
'amoc': (('zl', 'yq'), np.zeros((psiPlot.shape))),
'moc_FFM': (('zl', 'yq'), np.zeros((psiPlot.shape))),
'moc_GM': (('zl', 'yq'), np.zeros((psiPlot.shape))),
'amoc_45': (('time'), np.zeros((ds_yr.time.shape))),
'moc_GM_ACC': (('time'), np.zeros((ds_yr.time.shape))),
'amoc_26': (('time'), np.zeros((ds_yr.time.shape)))
},
coords={
'zl': zl,
'yq': ds.yq,
'time': ds_yr.time
})
attrs = {
'description': 'MOC time-mean sections and time-series',
'units': 'Sv',
'start_date': avg['start_date'],
'end_date': avg['end_date'],
'casename': dcase.casename
}
m6toolbox.add_global_attrs(moc, attrs)
# Atlantic MOC
m6plot.setFigureSize([16, 9], 576, debug=False)
cmap = plt.get_cmap('dunnePM')
m = 0 * basin_code
m[(basin_code == 2) | (basin_code == 4) | (basin_code == 6) |
(basin_code == 7) | (basin_code == 8)] = 1
ci = m6plot.pmCI(0., 22., 2.)
z = (m * Zmod).min(axis=-1)
psiPlot = MOCpsi(VHmod,
vmsk=m * np.roll(m, -1, axis=-2)) * conversion_factor
psiPlot = 0.5 * (psiPlot[0:-1, :] + psiPlot[1::, :])
yy = grd.geolat_c[:, :].max(axis=-1) + 0 * z
plotPsi(
yy, z, psiPlot, ci, 'Atlantic MOC [Sv],' + 'averaged between ' +
args.start_date + ' and ' + args.end_date)
plt.xlabel(r'Latitude [$\degree$N]')
plt.suptitle(case_name)
plt.gca().invert_yaxis()
findExtrema(yy, z, psiPlot, min_lat=26.5, max_lat=27.,
min_depth=250.) # RAPID
findExtrema(yy, z, psiPlot, max_lat=-33.)
findExtrema(yy, z, psiPlot)
findExtrema(yy, z, psiPlot, min_lat=5.)
objOut = args.outdir + str(case_name) + '_MOC_Atlantic.png'
plt.savefig(objOut, format='png')
moc['amoc'].data = psiPlot
print('Plotting AMOC profile at 26N...')
rapid_vertical = xr.open_dataset(
'/glade/work/gmarques/cesm/datasets/RAPID/moc_vertical.nc')
fig, ax = plt.subplots(nrows=1, ncols=1)
ax.plot(rapid_vertical.stream_function_mar.mean('time'),
rapid_vertical.depth,
'k',
label='RAPID')
ax.plot(moc['amoc'].sel(yq=26, method='nearest'), zl, label=case_name)
ax.legend()
plt.gca().invert_yaxis()
plt.grid()
ax.set_xlabel('AMOC @ 26N [Sv]')
ax.set_ylabel('Depth [m]')
objOut = args.outdir + str(case_name) + '_MOC_profile_26N.png'
plt.savefig(objOut, format='png')
print('Computing time series...')
startTime = datetime.now()
# time-series
dtime = ds_yr.time
amoc_26 = np.zeros(len(dtime))
amoc_45 = np.zeros(len(dtime))
moc_GM_ACC = np.zeros(len(dtime))
if args.debug: startTime = datetime.now()
# loop in time
for t in range(len(dtime)):
tmp = np.ma.masked_invalid(ds_yr[varName][t, :].values)
tmp = tmp[:].filled(0.)
# m is still Atlantic ocean
psi = MOCpsi(tmp, vmsk=m * np.roll(m, -1, axis=-2)) * conversion_factor
psi = 0.5 * (psi[0:-1, :] + psi[1::, :])
amoc_26[t] = findExtrema(yy,
z,
psi,
min_lat=26.,
max_lat=27.,
plot=False,
min_depth=250.)
amoc_45[t] = findExtrema(yy,
z,
psi,
min_lat=44.,
max_lat=46.,
plot=False,
min_depth=250.)
tmp_GM = np.ma.masked_invalid(ds_yr['vhGM'][t, :].values)
tmp_GM = tmp_GM[:].filled(0.)
psiGM = MOCpsi(tmp_GM) * conversion_factor
psiGM = 0.5 * (psiGM[0:-1, :] + psiGM[1::, :])
moc_GM_ACC[t] = findExtrema(yyg,
zg,
psiGM,
min_lat=-65.,
max_lat=-30,
mult=-1.,
plot=False)
print('Time elasped: ', datetime.now() - startTime)
# add dataarays to the moc dataset
moc['amoc_26'].data = amoc_26
moc['amoc_45'].data = amoc_45
moc['moc_GM_ACC'].data = moc_GM_ACC
if parallel:
print('Releasing workers ...')
client.close()
cluster.close()
print('Plotting...')
# load AMOC time series data (5th) cycle used in Danabasoglu et al., doi:10.1016/j.ocemod.2015.11.007
path = '/glade/p/cesm/omwg/amoc/COREII_AMOC_papers/papers/COREII.variability/data.original/'
amoc_core_26 = xr.open_dataset(path + 'AMOCts.cyc5.26p5.nc')
# load AMOC from POP JRA-55
amoc_pop_26 = xr.open_dataset(
'/glade/u/home/bryan/MOM6-modeloutputanalysis/'
'AMOC_series_26n.g210.GIAF_JRA.v13.gx1v7.01.nc')
# load RAPID time series
rapid = xr.open_dataset(
'/glade/work/gmarques/cesm/datasets/RAPID/moc_transports.nc').resample(
time="1Y", closed='left', keep_attrs=True).mean('time',
keep_attrs=True)
# plot
fig = plt.figure(figsize=(12, 6))
plt.plot(np.arange(len(moc.time)) + 1958.5,
moc['amoc_26'].values,
color='k',
label=case_name,
lw=2)
# core data
core_mean = amoc_core_26['MOC'].mean(axis=0).data
core_std = amoc_core_26['MOC'].std(axis=0).data
plt.plot(amoc_core_26.time,
core_mean,
'k',
label='CORE II (group mean)',
color='#1B2ACC',
lw=1)
plt.fill_between(amoc_core_26.time,
core_mean - core_std,
core_mean + core_std,
alpha=0.25,
edgecolor='#1B2ACC',
facecolor='#089FFF')
# pop data
plt.plot(np.arange(len(amoc_pop_26.time)) + 1958.5,
amoc_pop_26.AMOC_26n.values,
color='r',
label='POP',
lw=1)
# rapid
plt.plot(np.arange(len(rapid.time)) + 2004.5,
rapid.moc_mar_hc10.values,
color='green',
label='RAPID',
lw=1)
plt.title('AMOC @ 26 $^o$ N', fontsize=16)
plt.ylim(5, 20)
plt.xlim(1948, 1958.5 + len(moc.time))
plt.xlabel('Time [years]', fontsize=16)
plt.ylabel('Sv', fontsize=16)
plt.legend(fontsize=13, ncol=2)
objOut = args.outdir + str(case_name) + '_MOC_26N_time_series.png'
plt.savefig(objOut, format='png')
amoc_core_45 = xr.open_dataset(path + 'AMOCts.cyc5.45.nc')
amoc_pop_45 = xr.open_dataset(
'/glade/u/home/bryan/MOM6-modeloutputanalysis/'
'AMOC_series_45n.g210.GIAF_JRA.v13.gx1v7.01.nc')
# plot
fig = plt.figure(figsize=(12, 6))
plt.plot(np.arange(len(moc.time)) + 1958.5,
moc['amoc_45'],
color='k',
label=case_name,
lw=2)
# core data
core_mean = amoc_core_45['MOC'].mean(axis=0).data
core_std = amoc_core_45['MOC'].std(axis=0).data
plt.plot(amoc_core_45.time,
core_mean,
'k',
label='CORE II (group mean)',
color='#1B2ACC',
lw=2)
plt.fill_between(amoc_core_45.time,
core_mean - core_std,
core_mean + core_std,
alpha=0.25,
edgecolor='#1B2ACC',
facecolor='#089FFF')
# pop data
plt.plot(np.arange(len(amoc_pop_45.time)) + 1958.5,
amoc_pop_45.AMOC_45n.values,
color='r',
label='POP',
lw=1)
plt.title('AMOC @ 45 $^o$ N', fontsize=16)
plt.ylim(5, 20)
plt.xlim(1948, 1958 + len(moc.time))
plt.xlabel('Time [years]', fontsize=16)
plt.ylabel('Sv', fontsize=16)
plt.legend(fontsize=14)
objOut = args.outdir + str(case_name) + '_MOC_45N_time_series.png'
plt.savefig(objOut, format='png')
# Submesoscale-induced Global MOC
class C(np.ndarray):
pass
varName = 'vhml'
conversion_factor = 1.e-9
tmp = np.ma.masked_invalid(ds_mean[varName].values)
tmp = tmp[:].filled(0.)
VHml = tmp.view(C)
VHml.units = ds[varName].units
Zmod = m6toolbox.get_z(ds, depth, varName) # same here
m6plot.setFigureSize([16, 9], 576, debug=False)
axis = plt.gca()
cmap = plt.get_cmap('dunnePM')
z = Zmod.min(axis=-1)
psiPlot = MOCpsi(VHml) * conversion_factor
psiPlot = 0.5 * (psiPlot[0:-1, :] + psiPlot[1::, :])
yy = grd.geolat_c[:, :].max(axis=-1) + 0 * z
ci = m6plot.pmCI(0., 20., 2.)
plotPsi(yy,
z,
psiPlot,
ci,
'Global FFH MOC [Sv],' + 'averaged between ' + args.start_date +
' and ' + args.end_date,
zval=[0., -400., -1000.])
plt.xlabel(r'Latitude [$\degree$N]')
plt.suptitle(case_name)
plt.gca().invert_yaxis()
objOut = args.outdir + str(case_name) + '_FFH_MOC_global.png'
plt.savefig(objOut)
moc['moc_FFM'].data = psiPlot
# GM-induced Global MOC
class C(np.ndarray):
pass
varName = 'vhGM'
conversion_factor = 1.e-9
tmp = np.ma.masked_invalid(ds_mean[varName].values)
tmp = tmp[:].filled(0.)
VHGM = tmp.view(C)
VHGM.units = ds[varName].units
Zmod = m6toolbox.get_z(ds, depth, varName) # same here
m6plot.setFigureSize([16, 9], 576, debug=False)
axis = plt.gca()
cmap = plt.get_cmap('dunnePM')
z = Zmod.min(axis=-1)
psiPlot = MOCpsi(VHGM) * conversion_factor
psiPlot = 0.5 * (psiPlot[0:-1, :] + psiPlot[1::, :])
yy = grd.geolat_c[:, :].max(axis=-1) + 0 * z
ci = m6plot.pmCI(0., 20., 2.)
plotPsi(
yy, z, psiPlot, ci, 'Global GM MOC [Sv],' + 'averaged between ' +
args.start_date + ' and ' + args.end_date)
plt.xlabel(r'Latitude [$\degree$N]')
plt.suptitle(case_name)
plt.gca().invert_yaxis()
findExtrema(yy, z, psiPlot, min_lat=-65., max_lat=-30, mult=-1.)
objOut = args.outdir + str(case_name) + '_GM_MOC_global.png'
plt.savefig(objOut)
moc['moc_GM'].data = psiPlot
print('Saving netCDF files...')
moc.to_netcdf('ncfiles/' + str(case_name) + '_MOC.nc')
return
def driver(args):
nw = args.number_of_workers
if not os.path.isdir('PNG/TS_levels'):
print('Creating a directory to place figures (PNG)... \n')
os.system('mkdir -p PNG/TS_levels')
if not os.path.isdir('ncfiles'):
print('Creating a directory to place netCDF files (ncfiles)... \n')
os.system('mkdir ncfiles')
# Read in the yaml file
diag_config_yml = yaml.load(open(args.diag_config_yml_path, 'r'),
Loader=yaml.Loader)
# Create the case instance
dcase = DiagsCase(diag_config_yml['Case'])
RUNDIR = dcase.get_value('RUNDIR')
args.casename = dcase.casename
print('Run directory is:', RUNDIR)
print('Casename is:', args.casename)
print('Number of workers: ', nw)
# set avg dates
avg = diag_config_yml['Avg']
if not args.start_date: args.start_date = avg['start_date']
if not args.end_date: args.end_date = avg['end_date']
# read grid info
grd = MOM6grid(RUNDIR + '/' + args.casename + '.mom6.static.nc')
grd_xr = MOM6grid(RUNDIR + '/' + args.casename + '.mom6.static.nc',
xrformat=True)
# create masks
depth = grd.depth_ocean
# remote Nan's, otherwise genBasinMasks won't work
depth[np.isnan(depth)] = 0.0
basin_code = genBasinMasks(grd.geolon, grd.geolat, depth, xda=True)
# TODO: improve how obs are selected
if args.obs == 'PHC2':
# load PHC2 data
obs_path = '/glade/p/cesm/omwg/obs_data/phc/'
obs_temp = xr.open_mfdataset(obs_path +
'PHC2_TEMP_tx0.66v1_34lev_ann_avg.nc',
decode_coords=False,
decode_times=False)
obs_salt = xr.open_mfdataset(obs_path +
'PHC2_SALT_tx0.66v1_34lev_ann_avg.nc',
decode_coords=False,
decode_times=False)
elif args.obs == 'WOA18':
# load WOA18 data
obs_path = '/glade/u/home/gmarques/Notebooks/CESM_MOM6/WOA18_remapping/'
obs_temp = xr.open_dataset(
obs_path + 'WOA18_TEMP_tx0.66v1_34lev_ann_avg.nc',
decode_times=False).rename({'theta0': 'TEMP'})
obs_salt = xr.open_dataset(obs_path +
'WOA18_SALT_tx0.66v1_34lev_ann_avg.nc',
decode_times=False).rename({'s_an': 'SALT'})
else:
raise ValueError("The obs selected is not available.")
parallel, cluster, client = request_workers(nw)
print('Reading surface dataset...')
startTime = datetime.now()
variables = ['thetao', 'so', 'time', 'time_bnds']
def preprocess(ds):
''' Compute montly averages and return the dataset with variables'''
return ds[variables] #.resample(time="1Y", closed='left', \
#keep_attrs=True).mean(dim='time', keep_attrs=True)
if parallel:
ds = xr.open_mfdataset(RUNDIR+'/'+dcase.casename+'.mom6.h_*.nc', \
parallel=True, data_vars='minimal', \
coords='minimal', compat='override', preprocess=preprocess)
else:
ds = xr.open_mfdataset(RUNDIR+'/'+dcase.casename+'.mom6.h_*.nc', \
data_vars='minimal', coords='minimal', compat='override', preprocess=preprocess)
print('Time elasped: ', datetime.now() - startTime)
print('Selecting data between {} and {}...'.format(args.start_date,
args.end_date))
startTime = datetime.now()
ds = ds.sel(time=slice(args.start_date, args.end_date))
print('Time elasped: ', datetime.now() - startTime)
print('\n Computing yearly means...')
startTime = datetime.now()
ds = ds.resample(time="1Y", closed='left',
keep_attrs=True).mean('time', keep_attrs=True)
print('Time elasped: ', datetime.now() - startTime)
print('Time averaging...')
startTime = datetime.now()
temp = np.ma.masked_invalid(ds.thetao.mean('time').values)
salt = np.ma.masked_invalid(ds.so.mean('time').values)
print('Time elasped: ', datetime.now() - startTime)
print('Computing stats for different basins...')
startTime = datetime.now()
# construct a 3D area with land values masked
area = np.ma.masked_where(grd.wet == 0, grd.area_t)
tmp = np.repeat(area[np.newaxis, :, :], len(obs_temp.depth), axis=0)
area_mom3D = xr.DataArray(tmp,
dims=('depth', 'yh', 'xh'),
coords={
'depth': obs_temp.depth.values,
'yh': grd.yh,
'xh': grd.xh
})
for k in range(len(area_mom3D.depth)):
area_mom3D[k, :] = grd_xr.area_t.where(
grd_xr.depth_ocean >= area_mom3D.depth[k])
# temp
thetao_mean = ds.thetao.mean('time')
temp_diff = thetao_mean.rename({
'z_l': 'depth'
}).rename('TEMP') - obs_temp['TEMP']
temp_stats = myStats_da(temp_diff, area_mom3D,
basins=basin_code).rename('thetao_bias_stats')
# salt
so_mean = ds.so.mean('time')
salt_diff = so_mean.rename({
'z_l': 'depth'
}).rename('SALT') - obs_salt['SALT']
salt_stats = myStats_da(salt_diff, area_mom3D,
basins=basin_code).rename('so_bias_stats')
# plots
depth = temp_stats.depth.values
basin = temp_stats.basin.values
interfaces = np.zeros(len(depth) + 1)
for k in range(1, len(depth) + 1):
interfaces[k] = interfaces[k -
1] + (2 *
(depth[k - 1] - interfaces[k - 1]))
reg = np.arange(len(temp_stats.basin.values) + 1)
figname = 'PNG/TS_levels/' + str(dcase.casename) + '_'
temp_label = r'Potential temperature [$^o$C]'
salt_label = 'Salinity [psu]'
# minimum
score_plot2(basin,
interfaces,
temp_stats[:, 0, :],
nbins=30,
cmap=plt.cm.viridis,
cmin=temp_stats[:, 0, :].min().values,
units=temp_label,
fname=figname + 'thetao_bias_min.png',
title='Minimun temperature difference (model-{})'.format(
args.obs))
score_plot2(basin,
interfaces,
salt_stats[:, 0, :],
nbins=30,
cmap=plt.cm.viridis,
cmin=salt_stats[:, 0, :].min().values,
units=salt_label,
fname=figname + 'so_bias_min.png',
title='Minimun salinity difference (model-{})'.format(
args.obs))
# maximum
score_plot2(basin,
interfaces,
temp_stats[:, 1, :],
nbins=30,
cmap=plt.cm.viridis,
cmin=temp_stats[:, 1, :].min().values,
units=temp_label,
fname=figname + 'thetao_bias_max.png',
title='Maximum temperature difference (model-{})'.format(
args.obs))
score_plot2(basin,
interfaces,
salt_stats[:, 1, :],
nbins=30,
cmap=plt.cm.viridis,
cmin=salt_stats[:, 1, :].min().values,
units=salt_label,
fname=figname + 'so_bias_max.png',
title='Maximum salinity difference (model-{})'.format(
args.obs))
# mean
score_plot2(basin,
interfaces,
temp_stats[:, 2, :],
nbins=30,
cmap=plt.cm.seismic,
units=temp_label,
fname=figname + 'thetao_bias_mean.png',
title='Mean temperature difference (model-{})'.format(
args.obs))
score_plot2(basin,
interfaces,
salt_stats[:, 2, :],
nbins=30,
cmap=plt.cm.seismic,
units=salt_label,
fname=figname + 'so_bias_mean.png',
title='Mean salinity difference (model-{})'.format(args.obs))
# std
score_plot2(basin,
interfaces,
temp_stats[:, 3, :],
nbins=30,
cmap=plt.cm.viridis,
cmin=1.0E-15,
units=temp_label,
fname=figname + 'thetao_bias_std.png',
title='Std temperature difference (model-{})'.format(args.obs))
score_plot2(basin,
interfaces,
salt_stats[:, 3, :],
nbins=30,
cmap=plt.cm.viridis,
cmin=1.0E-15,
units=salt_label,
fname=figname + 'so_bias_std.png',
title='Std salinity difference (model-{})'.format(args.obs))
# rms
score_plot2(basin,
interfaces,
temp_stats[:, 4, :],
nbins=30,
cmap=plt.cm.viridis,
cmin=1.0E-15,
units=temp_label,
fname=figname + 'thetao_bias_rms.png',
title='Rms temperature difference (model-{})'.format(args.obs))
score_plot2(basin,
interfaces,
salt_stats[:, 4, :],
nbins=30,
cmap=plt.cm.viridis,
cmin=1.0E-15,
units=salt_label,
fname=figname + 'so_bias_rms.png',
title='Rms salinity difference (model-{})'.format(args.obs))
print('Time elasped: ', datetime.now() - startTime)
print('Saving netCDF files...')
startTime = datetime.now()
attrs = {
'description': 'model - obs at depth levels',
'start_date': args.start_date,
'end_date': args.end_date,
'casename': dcase.casename,
'obs': args.obs,
'module': os.path.basename(__file__)
}
# create dataset to store results
add_global_attrs(temp_stats, attrs)
temp_stats.to_netcdf('ncfiles/' + str(args.casename) +
'_thetao_bias_ann_mean_stats.nc')
add_global_attrs(salt_stats, attrs)
salt_stats.to_netcdf('ncfiles/' + str(args.casename) +
'_so_bias_ann_mean_stats.nc')
thetao = xr.DataArray(thetao_mean,
dims=['z_l', 'yh', 'xh'],
coords={
'z_l': ds.z_l,
'yh': grd.yh,
'xh': grd.xh
}).rename('thetao')
temp_bias = np.ma.masked_invalid(thetao.values - obs_temp['TEMP'].values)
ds_thetao = xr.Dataset(data_vars={
'thetao': (('z_l', 'yh', 'xh'), thetao),
'thetao_bias': (('z_l', 'yh', 'xh'), temp_bias)
},
coords={
'z_l': ds.z_l,
'yh': grd.yh,
'xh': grd.xh
})
add_global_attrs(ds_thetao, attrs)
ds_thetao.to_netcdf('ncfiles/' + str(args.casename) +
'_thetao_time_mean.nc')
so = xr.DataArray(ds.so.mean('time'),
dims=['z_l', 'yh', 'xh'],
coords={
'z_l': ds.z_l,
'yh': grd.yh,
'xh': grd.xh
}).rename('so')
salt_bias = np.ma.masked_invalid(so.values - obs_salt['SALT'].values)
ds_so = xr.Dataset(data_vars={
'so': (('z_l', 'yh', 'xh'), so),
'so_bias': (('z_l', 'yh', 'xh'), salt_bias)
},
coords={
'z_l': ds.z_l,
'yh': grd.yh,
'xh': grd.xh
})
add_global_attrs(ds_so, attrs)
ds_so.to_netcdf('ncfiles/' + str(args.casename) + '_so_time_mean.nc')
print('Time elasped: ', datetime.now() - startTime)
if parallel:
print('\n Releasing workers...')
client.close()
cluster.close()
print('Global plots...')
km = len(obs_temp['depth'])
for k in range(km):
if ds['z_l'][k].values < 1200.0:
figname = 'PNG/TS_levels/' + str(dcase.casename) + '_' + str(
ds['z_l'][k].values) + '_'
temp_obs = np.ma.masked_invalid(obs_temp['TEMP'][k, :].values)
xycompare(temp[k, :],
temp_obs,
grd.geolon,
grd.geolat,
area=grd.area_t,
title1='model temperature, depth =' +
str(ds['z_l'][k].values) + 'm',
title2='observed temperature, depth =' +
str(obs_temp['depth'][k].values) + 'm',
suptitle=dcase.casename + ', averaged ' +
str(args.start_date) + ' to ' + str(args.end_date),
extend='both',
dextend='neither',
clim=(-1.9, 30.),
dlim=(-2, 2),
dcolormap=plt.cm.bwr,
save=figname + 'global_temp.png')
salt_obs = np.ma.masked_invalid(obs_salt['SALT'][k, :].values)
xycompare(salt[k, :],
salt_obs,
grd.geolon,
grd.geolat,
area=grd.area_t,
title1='model salinity, depth =' +
str(ds['z_l'][k].values) + 'm',
title2='observed salinity, depth =' +
str(obs_temp['depth'][k].values) + 'm',
suptitle=dcase.casename + ', averaged ' +
str(args.start_date) + ' to ' + str(args.end_date),
extend='both',
dextend='neither',
clim=(30., 39.),
dlim=(-2, 2),
dcolormap=plt.cm.bwr,
save=figname + 'global_salt.png')
print('Antarctic plots...')
for k in range(km):
if (ds['z_l'][k].values < 1200.):
temp_obs = np.ma.masked_invalid(obs_temp['TEMP'][k, :].values)
polarcomparison(temp[k, :],
temp_obs,
grd,
title1='model temperature, depth =' +
str(ds['z_l'][k].values) + 'm',
title2='observed temperature, depth =' +
str(obs_temp['depth'][k].values) + 'm',
extend='both',
dextend='neither',
clim=(-1.9, 10.5),
dlim=(-2, 2),
dcolormap=plt.cm.bwr,
suptitle=dcase.casename + ', averaged ' +
str(args.start_date) + ' to ' + str(args.end_date),
proj='SP',
save=figname + 'antarctic_temp.png')
salt_obs = np.ma.masked_invalid(obs_salt['SALT'][k, :].values)
polarcomparison(salt[k, :],
salt_obs,
grd,
title1='model salinity, depth =' +
str(ds['z_l'][k].values) + 'm',
title2='observed salinity, depth =' +
str(obs_temp['depth'][k].values) + 'm',
extend='both',
dextend='neither',
clim=(33., 35.),
dlim=(-2, 2),
dcolormap=plt.cm.bwr,
suptitle=dcase.casename + ', averaged ' +
str(args.start_date) + ' to ' + str(args.end_date),
proj='SP',
save=figname + 'antarctic_salt.png')
print('Arctic plots...')
for k in range(km):
if (ds['z_l'][k].values < 100.):
temp_obs = np.ma.masked_invalid(obs_temp['TEMP'][k, :].values)
polarcomparison(temp[k, :],
temp_obs,
grd,
title1='model temperature, depth =' +
str(ds['z_l'][k].values) + 'm',
title2='observed temperature, depth =' +
str(obs_temp['depth'][k].values) + 'm',
extend='both',
dextend='neither',
clim=(-1.9, 11.5),
dlim=(-2, 2),
dcolormap=plt.cm.bwr,
suptitle=dcase.casename + ', averaged ' +
str(args.start_date) + ' to ' + str(args.end_date),
proj='NP',
save=figname + 'arctic_temp.png')
salt_obs = np.ma.masked_invalid(obs_salt['SALT'][k, :].values)
polarcomparison(salt[k, :],
salt_obs,
grd,
title1='model salinity, depth =' +
str(ds['z_l'][k].values) + 'm',
title2='observed salinity, depth =' +
str(obs_temp['depth'][k].values) + 'm',
extend='both',
dextend='neither',
clim=(31.5, 35.),
dlim=(-2, 2),
dcolormap=plt.cm.bwr,
suptitle=dcase.casename + ', averaged ' +
str(args.start_date) + ' to ' + str(args.end_date),
proj='NP',
save=figname + 'arctic_salt.png')
return
def main(stream=False):
# Get options
args = options()
if not args.diff_rms and not args.surface and not args.forcing and not args.time_series:
raise ValueError(
"Please select -diff_rms, -time_series, -surface and/or -forcing.")
# Read in the yaml file
diag_config_yml = yaml.load(open(args.diag_config_yml_path, 'r'),
Loader=yaml.Loader)
# set avg dates
avg = diag_config_yml['Avg']
if not args.start_date: args.start_date = avg['start_date']
if not args.end_date: args.end_date = avg['end_date']
# Create the case instance
dcase = DiagsCase(diag_config_yml['Case'], xrformat=True)
print('Casename is:', dcase.casename)
RUNDIR = dcase.get_value('RUNDIR')
if not os.path.isdir('PNG/Horizontal_mean_biases'):
print('Creating a directory to place figures (PNG)... \n')
os.system('mkdir -p PNG/Horizontal_mean_biases')
if not os.path.isdir('ncfiles'):
print('Creating a directory to place netCDF files (ncfiles)... \n')
os.system('mkdir ncfiles')
# read grid
grd = MOM6grid(RUNDIR + '/' + dcase.casename + '.mom6.static.nc',
xrformat=True)
area = grd.area_t.where(grd.wet > 0)
# Get masking for different regions
depth = grd.depth_ocean.values
# remove Nan's, otherwise genBasinMasks won't work
depth[np.isnan(depth)] = 0.0
basin_code = genBasinMasks(grd.geolon.values,
grd.geolat.values,
depth,
xda=True)
#select a few basins, namely, Global, MedSea,BalticSea,HudsonBay Arctic,
# Pacific, Atlantic, Indian, Southern, LabSea and BaffinBay
basins = basin_code.isel(region=[0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13])
if args.diff_rms:
horizontal_mean_diff_rms(grd, dcase, basins, args)
if args.surface:
#variables = ['SSH','tos','sos','mlotst','oml','speed', 'SSU', 'SSV']
variables = ['SSH', 'tos', 'sos', 'mlotst', 'oml', 'speed']
fname = '.mom6.hm_*.nc'
xystats(fname, variables, grd, dcase, basins, args)
if args.forcing:
variables = [
'friver', 'ficeberg', 'fsitherm', 'hfsnthermds', 'sfdsi', 'hflso',
'seaice_melt_heat', 'wfo', 'hfds', 'Heat_PmE'
]
fname = '.mom6.hm_*.nc'
xystats(fname, variables, grd, dcase, basins, args)
if args.time_series:
variables = ['thetaoga', 'soga']
fname = '.mom6.hm_*.nc'
extract_time_series(fname, variables, grd, dcase, args)
return
def __init__(self, climo_config: OrderedDict, diags_case: DiagsCase):
"""
Parameters
----------
climo_config : OrderedDict
A dictionary containing the configuration for average or climatology data to generate
This is usually read from a yaml file but may also be generated manually. An example
yaml file to generate this dictionary:
Climo:
type: "avg" # "climo" or "avg"
date0: "0001-01-01"
date1: "0005-12-31"
fields: ["thetao","so"] # fields to average
freqs: ["1Y", "5Y"] # 1- and 5-yearly averages
diags_case : mom6_tools.DiagsCase.
Case instance
"""
self._climo_config = climo_config
self.diags_case = diags_case
# check if all the required entries are provided in climo_config:
if len(self.required_entries - set(self._climo_config)) > 0:
raise RuntimeError("Must provide all reqired fields:" +
str(self.required_entries))
self._fields = self._climo_config['fields']
date_regex = "^\d{4}-\d{2}-\d{2}$"
self._date0 = None
self._date1 = None
cft_datetime_constr = None
calendar = diags_case.get_value("CALENDAR")
if calendar == "NO_LEAP":
cft_datetime_constr = cft.DatetimeNoLeap
elif calendar == "GREGORIAN":
cft_datetime_constr = cft.DatetimeGregorian
else:
raise RuntimeError(f"Unknown calendar type: {calendar}")
allowable_types = ['avg', 'climo']
if self._climo_config['type'] not in allowable_types:
raise RuntimeError("The type must be set to one of: " +
str(allowable_types))
if 'date0' in self._climo_config:
date0_str = self._climo_config['date0']
assert re.search(date_regex,
date0_str), f"Invalid date0 entry: {date0_str}"
calendar = diags_case.get_value("CALENDAR")
self._date0 = cft_datetime_constr(int(date0_str[:4]),
int(date0_str[5:7]),
int(date0_str[8:10]))
log.info(f"Climo date0: {self._date0}")
if 'date1' in self._climo_config:
date1_str = self._climo_config['date1']
assert re.search(date_regex,
date1_str), f"Invalid date1 entry: {date1_str}"
calendar = diags_case.get_value("CALENDAR")
self._date1 = cft_datetime_constr(int(date1_str[:4]),
int(date1_str[5:7]),
int(date1_str[8:10]))
log.info(f"Climo date1: {self._date1}")
def main():
# Get options
args = options()
nw = args.number_of_workers
if not os.path.isdir('ncfiles'):
print('Creating a directory to place figures (ncfiles)... \n')
os.system('mkdir ncfiles')
# Read in the yaml file
diag_config_yml = yaml.load(open(args.diag_config_yml_path,'r'), Loader=yaml.Loader)
# Create the case instance
dcase = DiagsCase(diag_config_yml['Case'])
args.case_name = dcase.casename
RUNDIR = dcase.get_value('RUNDIR')
print('Run directory is:', RUNDIR)
print('Casename is:', dcase.casename)
print('Number of workers to be used:', nw)
# set avg dates
avg = diag_config_yml['Avg']
if not args.start_date : args.start_date = avg['start_date']
if not args.end_date : args.end_date = avg['end_date']
# read grid info
grd = MOM6grid(RUNDIR+'/'+dcase.casename+'.mom6.static.nc')
depth = grd.depth_ocean
# remote Nan's, otherwise genBasinMasks won't work
depth[np.isnan(depth)] = 0.0
basin_code = m6toolbox.genBasinMasks(grd.geolon, grd.geolat, depth)
parallel, cluster, client = m6toolbox.request_workers(nw)
print('Reading {} dataset...'.format(args.file_name))
startTime = datetime.now()
# load data
def preprocess(ds):
variables = ['diftrblo', 'difmxylo' ,'difmxybo', 'diftrelo']
for v in variables:
if v not in ds.variables:
ds[v] = xr.zeros_like(ds.vo)
return ds[variables]
ds = xr.open_mfdataset(RUNDIR+'/'+dcase.casename+args.file_name,
parallel=True,
combine="nested", # concatenate in order of files
concat_dim="time", # concatenate along time
preprocess=preprocess,
).chunk({"time": 12})
print('Time elasped: ', datetime.now() - startTime)
# compute yearly means first
print('Computing yearly means...')
startTime = datetime.now()
ds_yr = ds.resample(time="1Y", closed='left').mean('time')
print('Time elasped: ', datetime.now() - startTime)
print('Selecting data between {} and {}...'.format(args.start_date, args.end_date))
startTime = datetime.now()
ds_sel = ds_yr.sel(time=slice(args.start_date, args.end_date))
print('Time elasped: ', datetime.now() - startTime)
print('Computing time mean...')
startTime = datetime.now()
ds_mean = ds_sel.mean('time').compute()
print('Time elasped: ', datetime.now() - startTime)
attrs = {'description': 'Time-mean mixing coefficients', 'units': 'm^2/s', 'start_date': avg['start_date'],
'end_date': avg['end_date'], 'casename': dcase.casename}
m6toolbox.add_global_attrs(ds_mean,attrs)
print('Saving netCDF files...')
ds_mean.to_netcdf('ncfiles/'+str(args.case_name)+'_avg_mixing_coeffs.nc')
print('Releasing workers ...')
client.close(); cluster.close()
return
def driver(args):
nw = args.number_of_workers
if not os.path.isdir('PNG/Equatorial'):
print('Creating a directory to place figures (PNG/Equatorial)... \n')
os.system('mkdir -p PNG/Equatorial')
if not os.path.isdir('ncfiles'):
print('Creating a directory to place netCDF files (ncfiles)... \n')
os.system('mkdir ncfiles')
# Read in the yaml file
diag_config_yml = yaml.load(open(args.diag_config_yml_path,'r'), Loader=yaml.Loader)
# Create the case instance
dcase = DiagsCase(diag_config_yml['Case'])
RUNDIR = dcase.get_value('RUNDIR')
args.casename = dcase.casename
print('Run directory is:', RUNDIR)
print('Casename is:', args.casename)
print('Number of workers: ', nw)
# set avg dates
avg = diag_config_yml['Avg']
if not args.start_date : args.start_date = avg['start_date']
if not args.end_date : args.end_date = avg['end_date']
# read grid info
grd = MOM6grid(RUNDIR+'/'+args.casename+'.mom6.static.nc', xrformat=True)
# select Equatorial region
grd_eq = grd.sel(yh=slice(-10,10))
# load obs
phc_path = '/glade/p/cesm/omwg/obs_data/phc/'
phc_temp = xr.open_mfdataset(phc_path+'PHC2_TEMP_tx0.66v1_34lev_ann_avg.nc', decode_coords=False, decode_times=False)
phc_salt = xr.open_mfdataset(phc_path+'PHC2_SALT_tx0.66v1_34lev_ann_avg.nc', decode_coords=False, decode_times=False)
johnson = xr.open_dataset('/glade/p/cesm/omwg/obs_data/johnson_pmel/meanfit_m.nc')
# get T and S and rename variables
thetao_obs = phc_temp.TEMP.rename({'X': 'xh','Y': 'yh', 'depth': 'z_l'});
salt_obs = phc_salt.SALT.rename({'X': 'xh','Y': 'yh', 'depth': 'z_l'});
parallel, cluster, client = request_workers(nw)
print('Reading surface dataset...')
startTime = datetime.now()
#variables = ['thetao', 'so', 'uo', 'time', 'time_bnds', 'e']
#def preprocess(ds):
# ''' Compute yearly averages and return the dataset with variables'''
# return ds[variables].resample(time="1Y", closed='left', \
# keep_attrs=True).mean(dim='time', keep_attrs=True)
# load data
def preprocess(ds):
variables = ['thetao', 'so', 'uo', 'time', 'time_bnds', 'e']
return ds[variables]
if parallel:
ds = xr.open_mfdataset(RUNDIR+'/'+dcase.casename+'.mom6.h_*.nc', \
parallel=True, data_vars='minimal', \
coords='minimal', compat='override', preprocess=preprocess)
else:
ds = xr.open_mfdataset(RUNDIR+'/'+dcase.casename+'.mom6.monthly_*.nc', concat_dim=['time'],\
data_vars='minimal', coords='minimal', compat='override', preprocess=preprocess)
print('Time elasped: ', datetime.now() - startTime)
# set obs coords to be same as model
thetao_obs['xh'] = ds.xh; thetao_obs['yh'] = ds.yh;
salt_obs['xh'] = ds.xh; salt_obs['yh'] = ds.yh;
print('Selecting data between {} and {} (time) and -10 to 10 (yh)...'.format(args.start_date, \
args.end_date))
startTime = datetime.now()
ds = ds.sel(time=slice(args.start_date, args.end_date)).sel(yh=slice(-10,10)).isel(z_i=slice(0,15)).isel(z_l=slice(0,14))
print('Time elasped: ', datetime.now() - startTime)
print('Yearly mean...')
startTime = datetime.now()
ds = ds.resample(time="1Y", closed='left',keep_attrs=True).mean('time',keep_attrs=True).compute()
print('Time elasped: ', datetime.now() - startTime)
print('Time averaging...')
startTime = datetime.now()
thetao = ds.thetao.mean('time')
so = ds.so.mean('time')
uo = ds.uo.mean('time')
eta = ds.e.mean('time')
# find point closest to eq. and select data
j = np.abs( grd_eq.geolat[:,0].values - 0. ).argmin()
temp_eq = np.ma.masked_invalid(thetao.isel(yh=j).values)
salt_eq = np.ma.masked_invalid(so.isel(yh=j).values)
u_eq = np.ma.masked_invalid(uo.isel(yh=j).values)
e_eq = np.ma.masked_invalid(eta.isel(yh=j).values)
thetao_obs_eq = np.ma.masked_invalid(thetao_obs.sel(yh=slice(-10,10)).isel(yh=j).isel(z_l=slice(0,14)).values)
salt_obs_eq = np.ma.masked_invalid(salt_obs.sel(yh=slice(-10,10)).isel(yh=j).isel(z_l=slice(0,14)).values)
print('Time elasped: ', datetime.now() - startTime)
if parallel:
print('\n Releasing workers...')
client.close(); cluster.close()
print('Equatorial Upper Ocean plots...')
y = ds.yh.values
zz = ds.z_i.values
x = ds.xh.values
[X, Z] = np.meshgrid(x, zz)
z = 0.5 * ( Z[:-1] + Z[1:])
figname = 'PNG/Equatorial/'+str(dcase.casename)+'_'
yzcompare(temp_eq , thetao_obs_eq, x, -Z,
title1 = 'model temperature', ylabel='Longitude', yunits='',
title2 = 'observed temperature (PHC/Levitus)', #contour=True,
suptitle=dcase.casename + ', averaged '+str(args.start_date)+ ' to ' +str(args.end_date),
extend='neither', dextend='neither', clim=(6,31.), dlim=(-5,5), dcolormap=plt.cm.bwr,
save=figname+'Equatorial_Global_temperature.png')
yzcompare(salt_eq , salt_obs_eq, x, -Z,
title1 = 'model salinity', ylabel='Longitude', yunits='',
title2 = 'observed salinity (PHC/Levitus)', #contour=True,
suptitle=dcase.casename + ', averaged '+str(args.start_date)+ ' to ' +str(args.end_date),
extend='neither', dextend='neither', clim=(33.5,37.), dlim=(-1,1), dcolormap=plt.cm.bwr,
save=figname+'Equatorial_Global_salinity.png')
# create dataarays and saving data
temp_eq_da = xr.DataArray(temp_eq, dims=['zl','xh'],
coords={'zl' : z[:,0], 'xh' : x[:]}).rename('temp_eq')
temp_eq_da.to_netcdf('ncfiles/'+str(args.casename)+'_temp_eq.nc')
salt_eq_da = xr.DataArray(salt_eq, dims=['zl','xh'],
coords={'zl' : z[:,0], 'xh' : x[:]}).rename('salt_eq')
salt_eq_da.to_netcdf('ncfiles/'+str(args.casename)+'_salt_eq.nc')
# Shift model data to compare against obs
tmp, lonh = shiftgrid(thetao.xh[-1].values, thetao[0,0,:].values, ds.thetao.xh.values)
tmp, lonq = shiftgrid(uo.xq[-1].values, uo[0,0,:].values, uo.xq.values)
thetao['xh'].values[:] = lonh
so['xh'].values[:] = lonh
uo['xq'].values[:] = lonq
# y and z from obs
y_obs = johnson.YLAT11_101.values
zz = np.arange(0,510,10)
[Y, Z_obs] = np.meshgrid(y_obs, zz)
z_obs = 0.5 * ( Z_obs[0:-1,:] + Z_obs[1:,] )
# y and z from model
y_model = thetao.yh.values
z = eta.z_i.values
[Y, Z_model] = np.meshgrid(y_model, z)
z_model = 0.5 * ( Z_model[0:-1,:] + Z_model[1:,:] )
# longitutes to be compared
longitudes = [143., 156., 165., 180., 190., 205., 220., 235., 250., 265.]
for l in longitudes:
# Temperature
fig, (ax1, ax2) = plt.subplots(nrows=1, ncols=2, figsize=(16,8))
dummy_model = np.ma.masked_invalid(thetao.sel(xh=l, method='nearest').values)
dummy_obs = np.ma.masked_invalid(johnson.POTEMPM.sel(XLON=l, method='nearest').values)
yzplot(dummy_model, y_model, -Z_model, clim=(7,30), axis=ax1, zlabel='Depth', ylabel='Latitude', title=str(dcase.casename))
cs1 = ax1.contour( y_model + 0*z_model, -z_model, dummy_model, levels=np.arange(0,30,2), colors='k',); plt.clabel(cs1,fmt='%3.1f', fontsize=14)
ax1.set_ylim(-400,0)
yzplot(dummy_obs, y_obs, -Z_obs, clim=(7,30), axis=ax2, zlabel='Depth', ylabel='Latitude', title='Johnson et al (2002)')
cs2 = ax2.contour( y_obs + 0*z_obs, -z_obs, dummy_obs, levels=np.arange(0,30,2), colors='k',); plt.clabel(cs2,fmt='%3.1f', fontsize=14)
ax2.set_ylim(-400,0)
plt.suptitle('Temperature [C] @ '+str(l)+ ', averaged between '+str(args.start_date)+' and '+str(args.end_date))
plt.savefig(figname+'temperature_'+str(l)+'.png')
# Salt
fig, (ax1, ax2) = plt.subplots(nrows=1, ncols=2, figsize=(16,8))
dummy_model = np.ma.masked_invalid(so.sel(xh=l, method='nearest').values)
dummy_obs = np.ma.masked_invalid(johnson.SALINITYM.sel(XLON=l, method='nearest').values)
yzplot(dummy_model, y_model, -Z_model, clim=(32,36), axis=ax1, zlabel='Depth', ylabel='Latitude', title=str(dcase.casename))
cs1 = ax1.contour( y_model + 0*z_model, -z_model, dummy_model, levels=np.arange(32,36,0.5), colors='k',); plt.clabel(cs1,fmt='%3.1f', fontsize=14)
ax1.set_ylim(-400,0)
yzplot(dummy_obs, y_obs, -Z_obs, clim=(32,36), axis=ax2, zlabel='Depth', ylabel='Latitude', title='Johnson et al (2002)')
cs2 = ax2.contour( y_obs + 0*z_obs, -z_obs, dummy_obs, levels=np.arange(32,36,0.5), colors='k',); plt.clabel(cs2,fmt='%3.1f', fontsize=14)
ax2.set_ylim(-400,0)
plt.suptitle('Salinity [psu] @ '+str(l)+ ', averaged between '+str(args.start_date)+' and '+str(args.end_date))
plt.savefig(figname+'salinity_'+str(l)+'.png')
# uo
fig, (ax1, ax2) = plt.subplots(nrows=1, ncols=2, figsize=(16,8))
dummy_model = np.ma.masked_invalid(uo.sel(xq=l, method='nearest').values)
dummy_obs = np.ma.masked_invalid(johnson.UM.sel(XLON=l, method='nearest').values)
yzplot(dummy_model, y_model, -Z_model, clim=(-0.6,1.2), axis=ax1, zlabel='Depth', ylabel='Latitude', title=str(dcase.casename))
cs1 = ax1.contour( y_model + 0*z_model, -z_model, dummy_model, levels=np.arange(-1.2,1.2,0.1), colors='k',); plt.clabel(cs1,fmt='%3.1f', fontsize=14)
ax1.set_ylim(-400,0)
yzplot(dummy_obs, y_obs, -Z_obs, clim=(-0.6,1.2), axis=ax2, zlabel='Depth', ylabel='Latitude', title='Johnson et al (2002)')
cs2 = ax2.contour( y_obs + 0*z_obs, -z_obs, dummy_obs, levels=np.arange(-1.2,1.2,0.1), colors='k',); plt.clabel(cs2,fmt='%3.1f', fontsize=14)
ax2.set_ylim(-400,0)
plt.suptitle('Eastward velocity [m/s] @ '+str(l)+ ', averaged between '+str(args.start_date)+' and '+str(args.end_date))
plt.savefig(figname+'uo_'+str(l)+'.png')
# Eastward velocity [m/s] along the Equatorial Pacific
x_obs = johnson.XLON.values
[X_obs, Z_obs] = np.meshgrid(x_obs, zz)
z_obs = 0.5 * ( Z_obs[:-1,:] + Z_obs[1:,:] )
x_model = so.xh.values
z = eta.z_i.values
[X, Z_model] = np.meshgrid(x_model, z)
z_model = 0.5 * ( Z_model[:-1,:] + Z_model[1:,:] )
#from mom6_tools.m6plot import
fig, (ax1, ax2) = plt.subplots(nrows=1, ncols=2, figsize=(16,8))
dummy_obs = np.ma.masked_invalid(johnson.UM.sel(YLAT11_101=0).values)
dummy_model = np.ma.masked_invalid(uo.sel(yh=0, method='nearest').values)
yzplot(dummy_model, x_model, -Z_model, clim=(-0.6,1.2), axis=ax1, landcolor=[0., 0., 0.], title=str(dcase.casename), ylabel='Longitude')
cs1 = ax1.contour( x_model + 0*z_model, -z_model, dummy_model, levels=np.arange(-1.2,1.2,0.1), colors='k'); plt.clabel(cs1,fmt='%2.1f', fontsize=14)
ax1.set_xlim(143,265); ax1.set_ylim(-400,0)
yzplot(dummy_obs, x_obs, -Z_obs, clim=(-0.4,1.2), ylabel='Longitude', yunits='', axis=ax2, title='Johnson et al (2002)')
cs1 = ax2.contour( x_obs + 0*z_obs, -z_obs, dummy_obs, levels=np.arange(-1.2,1.2,0.1), colors='k'); plt.clabel(cs1,fmt='%2.1f', fontsize=14)
ax2.set_xlim(143,265); ax2.set_ylim(-400,0)
plt.suptitle('Eastward velocity [m/s] along the Equatorial Pacific, averaged between '+str(args.start_date)+' and '+str(args.end_date))
plt.savefig(figname+'Equatorial_Pacific_uo.png')
plt.close('all')
return