def get_atm_variables(mus, muv, phi, height, coeffs):
(ah2o, bh2o, ao3, tau) = coeffs
# From GetAtmVariables
tau_step = np.linspace(TAUSTEP4SPHALB, MAXNUMSPHALBVALUES * TAUSTEP4SPHALB,
MAXNUMSPHALBVALUES)
sphalb0 = csalbr(tau_step)
air_mass = 1.0 / mus + 1 / muv
air_mass = air_mass.where(air_mass <= MAXAIRMASS, -1.0)
taur = tau * xu.exp(-height / SCALEHEIGHT)
rhoray, trdown, trup = chand(phi, muv, mus, taur)
sphalb = sphalb0[np.int32(taur / TAUSTEP4SPHALB + 0.5)]
Ttotrayu = ((2 / 3. + muv) + (2 / 3. - muv) * trup) / (4 / 3. + taur)
Ttotrayd = ((2 / 3. + mus) + (2 / 3. - mus) * trdown) / (4 / 3. + taur)
tO3 = 1.0
tO2 = 1.0
tH2O = 1.0
if ao3 != 0:
tO3 = xu.exp(-air_mass * UO3 * ao3)
if bh2o != 0:
if bUseV171:
tH2O = xu.exp(-xu.exp(ah2o + bh2o * xu.log(air_mass * UH2O)))
else:
tH2O = xu.exp(-(ah2o * ((air_mass * UH2O)**bh2o)))
#t02 = exp(-m * aO2)
TtotraytH2O = Ttotrayu * Ttotrayd * tH2O
tOG = tO3 * tO2
return sphalb, rhoray, TtotraytH2O, tOG
def ds_arithmetics(ds: DatasetLike.TYPE,
op: str,
monitor: Monitor = Monitor.NONE) -> xr.Dataset:
"""
Do arithmetic operations on the given dataset by providing a list of
arithmetic operations and the corresponding constant. The operations will
be applied to the dataset in the order in which they appear in the list.
For example:
'log,+5,-2,/3,*2'
Currently supported arithmetic operations:
log,log10,log2,log1p,exp,+,-,/,*
where:
log - natural logarithm
log10 - base 10 logarithm
log2 - base 2 logarithm
log1p - log(1+x)
exp - the exponential
The operations will be applied element-wise to all arrays of the dataset.
:param ds: The dataset to which to apply arithmetic operations
:param op: A comma separated list of arithmetic operations to apply
:param monitor: a progress monitor.
:return: The dataset with given arithmetic operations applied
"""
ds = DatasetLike.convert(ds)
retset = ds
with monitor.starting('Calculate result', total_work=len(op.split(','))):
for item in op.split(','):
with monitor.child(1).observing("Calculate"):
item = item.strip()
if item[0] == '+':
retset = retset + float(item[1:])
elif item[0] == '-':
retset = retset - float(item[1:])
elif item[0] == '*':
retset = retset * float(item[1:])
elif item[0] == '/':
retset = retset / float(item[1:])
elif item[:] == 'log':
retset = xu.log(retset)
elif item[:] == 'log10':
retset = xu.log10(retset)
elif item[:] == 'log2':
retset = xu.log2(retset)
elif item[:] == 'log1p':
retset = xu.log1p(retset)
elif item[:] == 'exp':
retset = xu.exp(retset)
else:
raise ValueError('Arithmetic operation {} not'
' implemented.'.format(item[0]))
return retset
def ds_arithmetics(ds: xr.Dataset, op: str) -> xr.Dataset:
"""
Do arithmetic operations on the given dataset by providing a list of
arithmetic operations and the corresponding constant. The operations will
be applied to the dataset in the order in which they appear in the list.
For example:
'log,+5,-2,/3,*2'
Currently supported arithmetic operations:
log,log10,log2,log1p,exp,+,-,/,*
where:
log - natural logarithm
log10 - base 10 logarithm
log2 - base 2 logarithm
log1p - log(1+x)
exp - the exponential
The operations will be applied element-wise to all arrays of the dataset.
:param ds: The dataset to which to apply arithmetic operations
:param op: A comma separated list of arithmetic operations to apply
:return: The dataset with given arithmetic operations applied
"""
retset = ds
for item in op.split(','):
item = item.strip()
if item[0] == '+':
retset = retset + float(item[1:])
elif item[0] == '-':
retset = retset - float(item[1:])
elif item[0] == '*':
retset = retset * float(item[1:])
elif item[0] == '/':
retset = retset / float(item[1:])
elif item[:] == 'log':
retset = xu.log(retset)
elif item[:] == 'log10':
retset = xu.log10(retset)
elif item[:] == 'log2':
retset = xu.log2(retset)
elif item[:] == 'log1p':
retset = xu.log1p(retset)
elif item[:] == 'exp':
retset = xu.exp(retset)
else:
raise ValueError('Arithmetic operation {} not'
' implemented.'.format(item[0]))
return retset
swe_mask_align, pr_full = xray.align(swe_mask, pr, join='inner', copy=False)
del pr
gc.collect()
direc = '/raid/gergel'
pdur_file = 'pduration_mod.nc' # this is the one that I regridded to 6 x 6 km using cdo remapcon and /raid9/gergel/agg_snowpack/keepextracopies/grid_info_mine
pdur_full = xray.open_dataset(os.path.join(
direc,
pdur_file)) ## pdur beta parameter for John's transform from Matt Jolly
'''
for j in np.arange(len(pr_full.lat)):
for k in np.arange(len(pr_full.lon)):
if np.isnan(pr_full['precipitation'].values[0,j,k]) == False:
lon_ind = np.argmin(np.abs(pdur_full.lon - pr_full.lon[k]))
lat_ind = np.argmin(np.abs(pdur_full.lat - pr_full.lat[j]))
beta = np.float(pdur_full.isel_points(lon=[lon_ind],lat=[lat_ind])['pdur'])
#u = pr_arr[:,j,k]
# u = np.round(24 * (1 - (np.exp(-beta*pr_full['precipitation'].values[:,j,k]))))
pr_full['precipitation'].values[:,j,k] = np.round(24 * (1 - (np.exp(-beta*pr_full['precipitation'].values[:,j,k]))))
'''
pr_full['precipitation'].values = np.round(24 * (
1 -
(ufuncs.exp(-pdur_full['pdur'].values * pr_full['precipitation'].values))))
direc = '/raid/gergel/pptdur'
filename = '%s_%s.nc' % (model, scenario)
pr_full.to_netcdf(os.path.join(direc, filename))
print('saved dataset to netcdf as %s' % os.path.join(direc, filename))
def global_XCO2(datetime):
execfile('../../rpnenv/bin/activate_this.py',
dict(__file__='../../rpnenv/bin/activate_this.py'))
import fstd2nc
# get the ACOS pressure coefficients and acceleration due to gravity at set pressure levels
acos_plevs = np.load('../earth_data/ACOS_plevs.npy')
grav_plevs, grav = np.load('../earth_data/ACOS_grav.npy')
# get the model files that will be read from
model_fname = datetime.strftime(_rpn_format)
model_fname_prev = (datetime - dt.timedelta(days=1)).strftime(_rpn_format)
model = fstd2nc.Buffer(model_fname,
vars='CO2,HU,P0',
diag_as_model_level=True).to_xarray()
try:
# open files for the day of the observations and the final time step of the previous day
mprev = fstd2nc.Buffer(model_fname_prev,
vars='CO2,HU,P0',
diag_as_model_level=True).to_xarray()
model = xarray.concat([
mprev.sel(time=datetime.strftime('%Y-%m-%dT00:00:00.000000000')),
model
], 'time').transpose('time', 'level', 'lat', 'lon')
except:
# First day - no previous day to get data from, so the first 2 hours will have to be extrapolated
print("Error due to first day of run ignored")
pass
model.load()
model_interp = model.interp(time=datetime, kwargs={'fill_value': None})
print(model_interp)
logp = model_interp.a + model_interp.b * log(model_interp.P0 / 1000.)
p = exp(logp) / 100.
p = p.transpose('level', 'lat', 'lon').values
psurf = model_interp.P0.values
acos_p = psurf[np.newaxis, ...] * acos_plevs[:, np.newaxis, np.newaxis]
CO2 = model_interp.CO2.values
HU = model_interp.CO2.values
print("interpolating to ACOS algorithm pressure levels")
u = np.zeros(acos_p.shape)
q = np.zeros(acos_p.shape)
g = np.zeros(acos_p.shape)
for i in range(p.shape[1]):
for j in range(p.shape[2]):
u[:, i, j] = np.interp(acos_p[:, i, j], p[:, i, j], CO2[:, i, j])
q[:, i, j] = np.interp(acos_p[:, i, j], p[:, i, j], HU[:, i, j])
g[:, i, j] = np.interp(acos_p[:, i, j], grav_plevs, grav)
c = (1. - q) / mdry / g
cavg = 0.5 * (c[:-1, ...] + c[1:, ...])
delp = acos_p[:-1, ...] - acos_p[1:, ...]
hprime = cavg * delp / np.sum(cavg * delp, axis=0)[np.newaxis, ...]
f = 0.5 * np.ones(acos_p.shape)
f[-1,
...] = (psurf - acos_p[-2, ...]) / (acos_p[-1, ...] - acos_p[-2, ...])
h = np.zeros(acos_p.shape)
h[0, ...] = (1. - f[0, ...]) * hprime[0, ...]
h[1:-2, ...] = f[:-3, ...] * hprime[:-2, ...] + (
1. - f[1:-2, ...]) * hprime[1:-1, ...]
h[-2, ...] = f[-3, ...] * hprime[-2, ...] + (
1 - f[-2, ...] * f[-1, ...]) * hprime[-1, ...]
h[-1, ...] = f[-1, ...] * f[-2, ...] * hprime[-1, ...]
profile = 0.0024141666666666665 * u
xco2 = np.sum(h * profile, axis=0)
lats = model_interp.lat.values
lons = model_interp.lon.values
lons[lons > 180.] -= 360.
reorder = np.argsort(lons)
xco2 = xco2[:, reorder]
lons = lons[reorder]
return xco2, lats, lons
def wanninkhof92(T=None,
S=None,
P=None,
u_mean=None,
u_var=None,
xCO2=None,
pCO2_sw=None,
iceFrac=None,
scale_factor=0.27):
'''
Calculate air-sea CO2 flux following Wanninkhof 1992
Inputs
============
T = Temperature [degC]
S = Salinity [parts per thousand]
P = Atmospheric pressure at 10m [atm]
u_mean = mean wind speed [m/s]
u_var = variance of wind speed m/s averaged monthly [m/s]
xcO2 = atmoapheric mixing ratio of CO2 [ppm]
pCO2_sw = CO2 partial pressure of seawter [uatm]
scale_factor = gas transfer scale factor (default=0.27)
Output
============
F_co2 = air-sea co2 flux [molC/m2/yr]
References
============
Weiss (1974) [for solubility of CO2]
Carbon dioxide in water and seawater: the solubility of a non-ideal gas
Weiss and Price (1980) [for saturation vapor pressure, not used here]
Nitrous oxide solubility in water and seawater
Dickson et al (2007) [for saturation vapor pressure]
Guide to best practices for Ocean CO2 measurements, Chapter 5 section 3.2
Wanninkhof (1992) [for gas transfer and Schmidt number]
Relationship between wind speed and gas exchange over the ocean
Sweeney et al. (2007) [for gas transfer scale factor]
Constraining global air‐sea gas exchange for CO2 with recent bomb 14C measurements
Sarmiento and Gruber (2007) [for overview and discussion of CO2 flux]
Ocean biogeochmiecal dynsmics, Ch3 see panel 3.2.1
Notes
============
this code is optimized to work with Xarray
## Notes on partial pressure moist air
P_h20/P = saturation vapor pressure (Weiss and Price 1980)
Water vapor is generally assumed to be at saturation in the vicinity of the air-sea interfae.
p_moist = X_dry (P - P_h20)
= x_dry * P (1-P_h20/P)
= P_dry (1-P_h20/P)
## Notes on U2
Need to add wind speed variance if using Wanninkhof (1992)
If we don't, then we are underestimating the gas-transfer velocity
U2 = (U_mean)^2 + (U_prime)^2, (U_prime)^2 is the standard deviation
See Sarmiento and Gruber (2007) for a discussion of this
## Test values
# T = 298.15
# S = 35
'''
# ==================================================================
# 0. Conversions
# ==================================================================
# Convert from Celsius to kelvin
T_kelvin = T + 273.15
# ==================================================================
# 1. partial pressure of CO2 in moist air
# Units : uatm
# ==================================================================
# Weiss and Price (1980) formula
## P_sat_vapor = xu.exp(24.4543 - 67.4509*(100/T_kelvin) - 4.8489*xu.log(T_kelvin/100) - 0.000544*S)
# Following Dickson et al (2007) Chapter 5 section 3.2
a1 = -7.85951783
a2 = 1.84408259
a3 = -11.7866497
a4 = 22.6807411
a5 = -15.9618719
a6 = 1.80122502
Tc = 647.096
pc = (22.064 * 10**6) / 101325
g = (1 - (T_kelvin / Tc))
# pure water saturation vapor pressure, Wagner and Pruß, 2002
p_h20 = pc * xu.exp(
(Tc / T_kelvin) * (a1 * g + a2 * g**(1.5) + a3 * g**(3) + a4 * g**
(3.5) + a5 * g**(4) + a6 * g**(7.5)))
# total molality
MT = (31.998 * S) / (1000 - 1.005 * S)
# osmotic coefficient at 25C by Millero (1974)
b1 = 0.90799
b2 = -0.08992
b3 = 0.18458
b4 = -0.07395
b5 = -0.00221
phi = b1 + b2 * (0.5 * MT) + b3 * (0.5 * MT)**2 + b4 * (
0.5 * MT)**3 + b5 * (0.5 * MT)**4
# vapor pressure above sea-water, Dickson et al. (2007), Chapter 5, section 3.2
P_sat_vapor = p_h20 * xu.exp(-0.018 * phi * MT)
# Partial pressure of CO2 in moist air, Dickson et al. (2007), SOP 4 section 8.3
P_moist = (P * xCO2) * (1 - P_sat_vapor)
# ==================================================================
# 2. Solubility of CO2
# Notes : T in degC, S in PSU,
# 1.0E-6 converts to correct to muatm
# Units : to mol.kg^{-1}uatm^{-1}
# Reference : Weiss (1974)
# ==================================================================
S_co2 = xu.exp( 9345.17 / T_kelvin - 60.2409 + \
23.3585 * xu.log( T_kelvin / 100 ) + \
S * ( 0.023517 - 0.00023656 * T_kelvin + \
0.0047036 * ( T_kelvin / 100 )**2 )) *1.0E-6
# ==================================================================
# 3. Gas transfer velocity
# Units : cm/hr
# Reference : Wanninkhof (1992)
# Sweeney et al. (2007)
# per.comm with P. Landschutzer Feb. 19 2019
# ==================================================================
# Dimensionless Schmidt number (Sc)
# References Wanninkhof 1992
A = 2073.1
B = 125.62
C = 3.6276
D = 0.043219
# Schmidt number
# units : dimensionless
Sc = A - B * T + C * T**2 - D * T**3
# Gas transfer velocity
# References : Wanninkhof 1992,
# Sweeney et al. 2007 scale factor
k_w = scale_factor * (Sc / 660)**(-0.5) * (u_mean**2 + u_var)
# ================================================
# 4. air-sea CO2 exchange
# Units : mol/m2/yr
# Reference : Wanninkhof (1992)
# ================================================
# Convert from cm*mol/hr/kg to mol/m2/yr
conversion = (1000 / 100) * 365 * 24
# Air-sea CO2 flux
F_co2 = k_w * S_co2 * (1 - iceFrac) * (P_moist - pCO2_sw) * conversion
return F_co2
def exp_precip(data):
data.loc['tp'] = data.loc['tp'].where(data.loc['tp'] > -19, np.nan) # all -20 get nan
data.loc['tp'] = xu.exp(data.loc['tp']) # all nan stay nan
data.loc['tp'] = data.loc['tp'].where(~np.isnan(data.loc['tp']), 0) # all nan get zero precip
return data