def test_plot_compare_with_nan(plot=True,
verbose=True,
close_plots=True,
*args,
**kwargs):
if plot and close_plots:
import matplotlib.pyplot as plt
plt.close("all")
s = calc_spectrum(
1900,
2300, # cm-1
molecule="CO",
isotope="1,2,3",
pressure=1.01325, # bar
Tgas=700, # K
mole_fraction=0.1,
path_length=1, # cm
)
s = Radiance_noslit(s)
s._q["radiance_noslit"][0] = np.nan
# Test get_residual methods when there are nans in the spectra
diff1 = get_residual(
s,
s * 1.2,
var="radiance_noslit",
ignore_nan=True,
normalize=True,
normalize_how="mean",
)
diff2 = get_residual(
s,
s * 1.2,
var="radiance_noslit",
ignore_nan=True,
normalize=True,
normalize_how="area",
)
# TODO Write similar testcase for normalize_how="mean"
# Test Plot function when there are Nans in the spectrum:
if plot:
s.plot(normalize=True)
s.plot(normalize=(2200, 2250))
# Test plot_diff function when there are Nans in the spectra:
if plot:
plot_diff(s, s * 1.2, normalize=True)
plot_diff(s, s * 1.2, "radiance_noslit", normalize=(2000, 2100))
def test_broadening_DLM_noneq(verbose=True, plot=False, *args, **kwargs):
'''
Test Noneq version of DLM and makes sure it gives the same results as the eq
one when used with Tvib=Trot
'''
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
setup_test_line_databases() # add HITRAN-CO2-TEST in ~/.radis if not there
# Conditions
p = 1
wstep = 0.002
wmin = 2380 # cm-1
wmax = 2400 # cm-1
broadening_max_width = 10 # cm-1
# %% Calculate with RADIS
# ----------
sf = SpectrumFactory(
wavenum_min=wmin,
wavenum_max=wmax,
mole_fraction=1,
path_length=1, # doesnt change anything
wstep=wstep,
pressure=p,
broadening_max_width=broadening_max_width,
isotope='1',
verbose=3,
warnings={'MissingSelfBroadeningWarning':'ignore',
'NegativeEnergiesWarning':'ignore',
'HighTemperatureWarning':'ignore',
'GaussianBroadeningWarning':'ignore'}
) # 0.2)
sf.load_databank('HITRAN-CO2-TEST')
# DLM:
sf.misc['chunksize'] = 'DLM'
s_dlm_eq = sf.eq_spectrum(Tgas=3000)
s_dlm_eq.name = 'DLM eq ({0:.2f}s)'.format(s_dlm_eq.conditions['calculation_time'])
s_dlm_noneq = sf.non_eq_spectrum(Tvib=3000, Trot=3000)
s_dlm_noneq.name = 'DLM noneq ({0:.2f}s)'.format(s_dlm_noneq.conditions['calculation_time'])
# Compare
res = get_residual(s_dlm_eq, s_dlm_noneq, 'radiance_noslit')
if verbose:
print('Residual:', res)
# plot
if plot:
plot_diff(s_dlm_eq, s_dlm_noneq)
assert res <= 4e-5
def test_broadening_methods_different_wstep(verbose=True, plot=False, *args, **kwargs):
'''
Test direct Voigt broadening vs convolution of Gaussian x Lorentzian
for different spectral grid resolution
'''
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
setup_test_line_databases() # add HITRAN-CO-TEST in ~/.radis if not there
# Conditions
T = 3000
p = 1
wmin = 2150 # cm-1
wmax = 2152 # cm-1
broadening_max_width = 10 # cm-1
for i, wstep in enumerate([0.01, 0.1, 0.5]):
# %% Calculate with RADIS
# ----------
sf = SpectrumFactory(
wavenum_min=wmin,
wavenum_max=wmax,
mole_fraction=1,
path_length=1, # doesnt change anything
wstep=wstep,
pressure=p,
broadening_max_width=broadening_max_width,
isotope='1',
verbose=False,
warnings={'MissingSelfBroadeningWarning':'ignore',
'NegativeEnergiesWarning':'ignore',
'HighTemperatureWarning':'ignore',
'GaussianBroadeningWarning':'ignore'}
) # 0.2)
sf.load_databank('HITRAN-CO-TEST')
# s = pl.non_eq_spectrum(Tvib=T, Trot=T, Ttrans=T)
sf._broadening_method = 'voigt'
s_voigt = sf.eq_spectrum(Tgas=T, name='direct')
sf._broadening_method = 'convolve'
s_convolve = sf.eq_spectrum(Tgas=T, name='convolve')
res = get_residual(s_voigt, s_convolve, 'abscoeff')
if verbose:
print('Residual:', res)
# plot the last one
if plot:
plot_diff(s_voigt, s_convolve, 'abscoeff', nfig='test_voigt_broadening_methods'+str(i),
title='P {0} bar, T {1} K, wstep {2} cm-1'.format(p, T, wstep))
assert res < 2e-4
def test_noneq_continuum(plot=False,
verbose=2,
warnings=True,
*args,
**kwargs):
"""
Test calculation with pseudo-continuum under nonequilibrium
Assert results on emisscoeff dont change
Notes
-----
Uses HITRAN so it can deployed and tested on `Travis CI <https://travis-ci.com/radis/radis>`_, but we should switch
to HITEMP if some HITEMP files can be downloaded automatically at the
execution time.
"""
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
if verbose:
printm(">>> test_noneq_continuum")
sf = SpectrumFactory(
wavelength_min=4200,
wavelength_max=4500,
cutoff=1e-23,
molecule="CO2",
isotope="1,2",
broadening_max_width=10,
path_length=0.1,
mole_fraction=1e-3,
medium="vacuum",
optimization=None,
verbose=verbose,
)
sf.warnings.update({
"MissingSelfBroadeningWarning": "ignore",
"NegativeEnergiesWarning": "ignore",
"LinestrengthCutoffWarning": "ignore",
"HighTemperatureWarning": "ignore",
})
sf.fetch_databank(
"hitran"
) # uses HITRAN: not really valid at this temperature, but runs on all machines without install
# sf.load_databank('HITEMP-CO2-DUNHAM') # to take a real advantage of abscoeff continuum, should calculate with HITEMP
sf._export_continuum = True # activate it
# Calculate one without pseudo-continuum
sf.params.pseudo_continuum_threshold = 0
s1 = sf.non_eq_spectrum(Tvib=2000, Trot=1000)
s1.name = "All lines resolved ({0}) ({1:.1f}s)".format(
s1.conditions["lines_calculated"], s1.conditions["calculation_time"])
assert s1.conditions["pseudo_continuum_threshold"] == 0
# Calculate one with pseudo-continuum
sf.params.pseudo_continuum_threshold = 0.05
s2 = sf.non_eq_spectrum(Tvib=2000, Trot=1000)
s2.name = "Semi-continuum + {0} lines ({1:.1f}s)".format(
s2.conditions["lines_calculated"], s2.conditions["calculation_time"])
assert s2.conditions["pseudo_continuum_threshold"] == 0.05
assert "abscoeff_continuum" in s2.get_vars()
assert "emisscoeff_continuum" in s2.get_vars()
# Plot
if plot:
plot_diff(
s1,
s2,
"radiance_noslit",
Iunit="µW/cm2/sr/nm",
nfig="test_noneq_continuum: diff",
)
plt.figure("test_noneq_continuum: show continuum").clear()
s2.plot("emisscoeff",
label=s2.name,
nfig="test_noneq_continuum: show continuum")
s2.plot(
"emisscoeff_continuum",
nfig="same",
label="Pseudo-continuum (aggreg. {0:g} lines)".format(
s2.conditions["lines_in_continuum"]),
force=True,
)
# Compare
res = get_residual(s1, s2, "abscoeff") + get_residual(s1, s2, "emisscoeff")
if verbose:
printm("residual:", res)
assert res < 5.2e-6
def test_broadening_DLM_FT(verbose=True, plot=False, *args, **kwargs):
"""
Test use of DLM with and without Fourier Transform
Ensures that results are the same, and compare calculation times.
"""
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
setup_test_line_databases() # add HITRAN-CO-TEST in ~/.radis if not there
# Conditions
T = 3000
p = 1
wstep = 0.002
wmin = 2000 # cm-1
wmax = 2300 # cm-1
broadening_max_width = 10 # cm-1
# %% Calculate with RADIS
# ----------
sf = SpectrumFactory(
wavenum_min=wmin,
wavenum_max=wmax,
mole_fraction=1,
path_length=1, # doesnt change anything
wstep=wstep,
pressure=p,
broadening_max_width=broadening_max_width,
isotope="1",
verbose=verbose,
chunksize="DLM",
warnings={
"MissingSelfBroadeningWarning": "ignore",
"NegativeEnergiesWarning": "ignore",
"HighTemperatureWarning": "ignore",
"GaussianBroadeningWarning": "ignore",
},
) # 0.2)
sf.load_databank("HITRAN-CO-TEST")
# DLM, real space
if verbose:
print("\nConvolve version \n")
sf._broadening_method = "convolve"
s_dlm = sf.eq_spectrum(Tgas=T)
s_dlm.name = "DLM ({0:.2f}s)".format(s_dlm.conditions["calculation_time"])
# DLM , with Fourier
if verbose:
print("\nFFT version \n")
sf.params.broadening_method = "fft"
s_dlm_fft = sf.eq_spectrum(Tgas=T)
s_dlm_fft.name = "DLM FFT ({0:.2f}s)".format(
s_dlm_fft.conditions["calculation_time"])
# Compare
res = get_residual(s_dlm, s_dlm_fft, "abscoeff")
if verbose:
print("Residual:", res)
# plot
if plot:
plot_diff(s_dlm, s_dlm_fft, "abscoeff")
plt.legend()
assert res < 5e-6
def test_broadening_DLM(verbose=True, plot=False, *args, **kwargs):
"""
Test use of lineshape template for broadening calculation.
Ensures that results are the same with and without DLM.
"""
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
setup_test_line_databases() # add HITRAN-CO-TEST in ~/.radis if not there
# Conditions
T = 3000
p = 1
wstep = 0.002
wmin = 2150 # cm-1
wmax = 2152 # cm-1
broadening_max_width = 10 # cm-1
# %% Calculate with RADIS
# ----------
sf = SpectrumFactory(
wavenum_min=wmin,
wavenum_max=wmax,
mole_fraction=1,
path_length=1, # doesnt change anything
wstep=wstep,
pressure=p,
broadening_max_width=broadening_max_width,
isotope="1",
verbose=False,
warnings={
"MissingSelfBroadeningWarning": "ignore",
"NegativeEnergiesWarning": "ignore",
"HighTemperatureWarning": "ignore",
"GaussianBroadeningWarning": "ignore",
},
) # 0.2)
sf.load_databank("HITRAN-CO-TEST")
# Reference: calculate without DLM
assert sf.misc["chunksize"] is None
s_ref = sf.eq_spectrum(Tgas=T)
s_ref.name = "Reference ({0:.2f}s)".format(
s_ref.conditions["calculation_time"])
# DLM:
sf.misc["chunksize"] = "DLM"
sf.params.broadening_method = "convolve"
s_dlm = sf.eq_spectrum(Tgas=T)
s_dlm.name = "DLM ({0:.2f}s)".format(s_dlm.conditions["calculation_time"])
# DLM Voigt with Whiting approximation:
sf.params.broadening_method = "voigt"
s_dlm_voigt = sf.eq_spectrum(Tgas=T)
s_dlm_voigt.name = "DLM Whiting ({0:.2f}s)".format(
s_dlm_voigt.conditions["calculation_time"])
# Compare
res = get_residual(s_ref, s_dlm, "abscoeff")
res_voigt = get_residual(s_dlm, s_dlm_voigt, "abscoeff")
if verbose:
print("Residual:", res)
# plot the last one
if plot:
plot_diff(s_ref, s_dlm, "abscoeff")
plt.legend()
plot_diff(s_dlm, s_dlm_voigt, "abscoeff")
assert res < 1.2e-5
assert res_voigt < 1e-5
def test_broadening_methods_different_wstep(verbose=True,
plot=False,
*args,
**kwargs):
"""
Test direct Voigt broadening vs convolution of Gaussian x Lorentzian
for different spectral grid resolution
"""
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
setup_test_line_databases() # add HITRAN-CO-TEST in ~/.radis if not there
# Conditions
T = 3000
p = 1
wmin = 2150 # cm-1
wmax = 2152 # cm-1
broadening_max_width = 10 # cm-1
for i, wstep in enumerate([0.01, 0.1, 0.5]):
# %% Calculate with RADIS
# ----------
sf = SpectrumFactory(
wavenum_min=wmin,
wavenum_max=wmax,
mole_fraction=1,
path_length=1, # doesnt change anything
wstep=wstep,
pressure=p,
broadening_max_width=broadening_max_width,
isotope="1",
optimization=None,
verbose=False,
warnings={
"MissingSelfBroadeningWarning": "ignore",
"NegativeEnergiesWarning": "ignore",
"HighTemperatureWarning": "ignore",
"GaussianBroadeningWarning": "ignore",
"AccuracyError": "ignore",
"AccuracyWarning": "ignore",
},
) # 0.2)
sf.load_databank("HITRAN-CO-TEST")
# s = pl.non_eq_spectrum(Tvib=T, Trot=T, Ttrans=T)
sf.params.broadening_method = "voigt"
s_voigt = sf.eq_spectrum(Tgas=T, name="direct")
sf.params.broadening_method = "convolve"
s_convolve = sf.eq_spectrum(Tgas=T, name="convolve")
res = get_residual(s_voigt, s_convolve, "abscoeff")
if verbose:
print("Residual:", res)
# plot the last one
if plot:
plot_diff(
s_voigt,
s_convolve,
"abscoeff",
nfig="test_voigt_broadening_methods" + str(i),
title="P {0} bar, T {1} K, wstep {2} cm-1".format(p, T, wstep),
)
assert res < 2e-4
def test_broadening_methods_different_conditions(verbose=True,
plot=False,
*args,
**kwargs):
"""
Test direct Voigt broadening vs convolution of Gaussian x Lorentzian
for different spectral grid resolution
Notes
-----
Reference broadening calculated manually with the HWHM formula of
`HITRAN.org <https://hitran.org/docs/definitions-and-units/>`_
"""
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
setup_test_line_databases() # add HITRAN-CO-TEST in ~/.radis if not there
# Conditions
wstep = 0.005
wmin = 2150.4 # cm-1
wmax = 2151.4 # cm-1
broadening_max_width = 2 # cm-1
for (T, p, fwhm_lorentz, fwhm_gauss) in [
# K, bar, expected FWHM for Lotentz, gauss (cm-1)
(3000, 1, 0.02849411, 0.01594728),
(300, 1, 0.16023415, 0.00504297),
(3000, 0.01, 0.00028494, 0.01594728),
]:
# %% Calculate with RADIS
# ----------
sf = SpectrumFactory(
wavenum_min=wmin,
wavenum_max=wmax,
mole_fraction=1,
path_length=1, # doesnt change anything
wstep=wstep,
pressure=p,
broadening_max_width=broadening_max_width,
isotope="1",
verbose=False,
warnings={
"MissingSelfBroadeningWarning": "ignore",
"NegativeEnergiesWarning": "ignore",
"HighTemperatureWarning": "ignore",
"OutOfRangeLinesWarning": "ignore",
"GaussianBroadeningWarning": "ignore",
"CollisionalBroadeningWarning": "ignore",
},
)
sf.load_databank("HITRAN-CO-TEST")
# Manually filter line database, keep one line only:
sf.df0.drop(sf.df0[sf.df0.vu != 1].index, inplace=True)
assert isclose(sf.df0.wav, 2150.856008)
# Calculate spectra (different broadening methods)
sf.params.broadening_method = "voigt"
s_voigt = sf.eq_spectrum(Tgas=T, name="direct")
# assert broadening FWHM are correct
assert isclose(2 * float(sf.df1.hwhm_gauss), fwhm_gauss)
assert isclose(2 * float(sf.df1.hwhm_lorentz), fwhm_lorentz)
sf.params.broadening_method = "convolve"
s_convolve = sf.eq_spectrum(Tgas=T, name="convolve")
# assert broadening FWHM are correct
assert isclose(2 * float(sf.df1.hwhm_gauss), fwhm_gauss)
assert isclose(2 * float(sf.df1.hwhm_lorentz), fwhm_lorentz)
res = get_residual(s_voigt, s_convolve, "abscoeff")
if verbose:
print(
"{0} K, {1} bar: FWHM lorentz = {2:.3f} cm-1, FWHM gauss = {3:.3f} cm-1"
.format(T, p, 2 * float(sf.df1.hwhm_lorentz),
2 * float(sf.df1.hwhm_gauss)))
if plot:
plot_diff(
s_voigt,
s_convolve,
"abscoeff",
title=
r"T {0} K, p {1} bar: w$_\mathrm{{L}}$ {2:.3f}, w$_\mathrm{{G}}$ {3:.3f} cm$^{{-1}}$"
.format(T, p, 2 * float(sf.df1.hwhm_lorentz),
float(sf.df1.hwhm_gauss)),
)
# assert all broadening methods match
assert res < 2e-4
def test_noneq_continuum(plot=False,
verbose=2,
warnings=True,
*args,
**kwargs):
'''
Test calculation with pseudo-continuum under nonequilibrium
Assert results on emisscoeff dont change
Notes
-----
Uses HITRAN so it can deployed and tested on [Travis]_, but we should switch
to HITEMP if some HITEMP files can be downloaded automatically at the
execution time.
'''
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
try:
if verbose:
printm('>>> test_noneq_continuum')
sf = SpectrumFactory(wavelength_min=4200,
wavelength_max=4500,
parallel=False,
bplot=False,
cutoff=1e-23,
molecule='CO2',
isotope='1,2',
db_use_cached=True,
broadening_max_width=10,
path_length=0.1,
mole_fraction=1e-3,
medium='vacuum',
verbose=verbose)
sf.warnings.update({
'MissingSelfBroadeningWarning': 'ignore',
'NegativeEnergiesWarning': 'ignore',
'LinestrengthCutoffWarning': 'ignore',
'HighTemperatureWarning': 'ignore'
})
sf.fetch_databank(
) # uses HITRAN: not really valid at this temperature, but runs on all machines without install
# sf.load_databank('HITEMP-CO2-DUNHAM') # to take a real advantage of abscoeff continuum, should calculate with HITEMP
sf._export_continuum = True # activate it
# Calculate one without pseudo-continuum
sf.params.pseudo_continuum_threshold = 0
s1 = sf.non_eq_spectrum(Tvib=2000, Trot=1000)
s1.name = 'All lines resolved ({0}) ({1:.1f}s)'.format(
s1.conditions['lines_calculated'],
s1.conditions['calculation_time'])
assert s1.conditions['pseudo_continuum_threshold'] == 0
# Calculate one with pseudo-continuum
sf.params.pseudo_continuum_threshold = 0.05
s2 = sf.non_eq_spectrum(Tvib=2000, Trot=1000)
s2.name = 'Semi-continuum + {0} lines ({1:.1f}s)'.format(
s2.conditions['lines_calculated'],
s2.conditions['calculation_time'])
assert s2.conditions['pseudo_continuum_threshold'] == 0.05
assert 'abscoeff_continuum' in s2.get_vars()
assert 'emisscoeff_continuum' in s2.get_vars()
# Plot
if plot:
plot_diff(s1,
s2,
'radiance_noslit',
Iunit='µW/cm2/sr/nm',
nfig='test_noneq_continuum: diff')
s2.plot('emisscoeff',
label=s2.name,
nfig='test_noneq_continuum: show continuum')
s2.plot('emisscoeff_continuum',
nfig='same',
label='Pseudo-continuum (aggreg. {0:g} lines)'.format(
s2.conditions['lines_in_continuum']),
force=True)
# Compare
res = get_residual(s1, s2, 'abscoeff') + get_residual(
s1, s2, 'emisscoeff')
if verbose:
printm('residual:', res)
assert res < 5e-6
except DatabankNotFound as err:
assert IgnoreMissingDatabase(err, __file__, warnings)
def test_plot_all_CO2_bandheads(verbose=True, plot=False, *args, **kwargs):
"""In this test we use the :meth:`~radis.lbl.bands.BandFactory.non_eq_bands`
method to calculate separately all vibrational bands of CO2, and compare
them with the final Spectrum.
"""
# Note: only with iso1 at the moment
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
Tgas = 1000
sf = SpectrumFactory(
wavelength_min=4160,
wavelength_max=4220,
mole_fraction=1,
path_length=0.3,
cutoff=1e-23,
molecule="CO2",
isotope=1,
optimization=None,
verbose=verbose,
)
sf.warnings["MissingSelfBroadeningWarning"] = "ignore"
sf.warnings["NegativeEnergiesWarning"] = "ignore"
sf.warnings["HighTemperatureWarning"] = "ignore"
sf.fetch_databank("hitran")
s_tot = sf.non_eq_spectrum(Tvib=Tgas, Trot=Tgas)
s_bands = sf.non_eq_bands(Tvib=Tgas, Trot=Tgas)
if verbose:
printm("{0} bands in spectrum".format(len(s_bands)))
assert len(s_bands) == 6
# Ensure that recombining gives the same
s_merged = MergeSlabs(*list(s_bands.values()))
assert s_tot.compare_with(s_merged, "radiance_noslit", plot=False)
if verbose:
printm("Recombining bands give the same Spectrum")
# %%
if plot:
s_tot.apply_slit(1, "nm")
s_tot.name = "Full spectrum"
s_tot.plot(wunit="nm", lw=3)
for band, s in s_bands.items():
s.plot(wunit="nm", nfig="same")
plt.legend(loc="upper left")
plt.ylim(ymax=0.25)
# %% Compare with equilibrium bands now
s_bands_eq = sf.eq_bands(Tgas)
s_merged_eq = MergeSlabs(*list(s_bands_eq.values()))
assert get_residual(s_tot, s_merged_eq, "radiance_noslit") < 1.5e-5
return True
def test_get_residual():
from radis import calc_spectrum, experimental_spectrum
s1 = calc_spectrum(
1900,
2300,
molecule="CO",
isotope="1,2,3",
pressure=1.01325,
Tgas=1000,
mole_fraction=0.1,
)
s1.apply_slit(1, "nm")
w1, I1 = s1.get("radiance", copy=False, wunit=s1.get_waveunit())
# Fake experimental spectrum (identical)
s_expe_1 = experimental_spectrum(w1, I1, Iunit="mW/cm2/sr/nm", wunit="cm-1")
residual1 = get_residual(
s1,
s_expe_1,
"radiance",
# ignore_nan=False,
normalize=True,
)
assert residual1 == 0
# Fake experimental spectrum with a new unit (but identical)
I2 = I1 * 1e-3
s_expe_2 = experimental_spectrum(w1, I2, Iunit="W/cm2/sr/nm", wunit="cm-1")
residual2 = get_residual(
s1,
s_expe_2,
"radiance",
normalize=False,
)
assert residual2 < 1e-10
for bool_how in ["max", "area", "mean"]:
residual2_bis = get_residual(
s1,
s_expe_2,
"radiance",
ignore_nan=False,
normalize=True,
normalize_how=bool_how,
)
# print('residu2 ={}'.format(residual2))
assert residual2_bis < 1e-13
# Fake experimental spectrum with a nan
I3 = I1.copy()
I3[0] = np.nan
s_expe_3 = experimental_spectrum(w1, I3, Iunit="W/cm2/sr/nm", wunit="cm-1")
# Intrestingly, the "mean" method seams to be not adapted for spectra with nans
criterion = [1e-10, 2e-6, 2e-2]
for index, bool_how in enumerate(["max", "area", "mean"]):
residual3 = get_residual(
s1,
s_expe_3,
"radiance",
ignore_nan=True,
normalize=True,
normalize_how=bool_how,
)
# print('residu3 ={}'.format(residual3))
assert residual3 < criterion[index]
def test_optically_thick_limit_1iso(verbose=True, plot=True, *args, **kwargs):
""" Test that we find Planck in the optically thick limit
In particular, this test will fail if :
- linestrength are not properly calculated
- at noneq, linestrength and emission integrals are mixed up
The test should be run for 1 and several isotopes, because different
calculations paths are used internally, and this can lead to different
errors.
Also, this test is used to run with DEBUG_MODE = True, which will
check that isotopes and molecule ids are what we expect in all the
groupby() loops that make the production code very fast.
Notes
-----
switched from large band calculation with [HITRAN-2016]_ to a calculation with
the embedded [HITEMP-2010]_ fragment (shorter range, but no need to download files)
"""
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
# Force DEBUG_MODE
DEBUG_MODE = radis.DEBUG_MODE
radis.DEBUG_MODE = True
try:
wavenum_min = 2284.2
wavenum_max = 2284.6
P = 0.017 # bar
wstep = 0.001 # cm-1
Tgas = 1200
# %% Generate some CO2 emission spectra
# --------------
sf = SpectrumFactory(
wavenum_min=wavenum_min,
wavenum_max=wavenum_max,
molecule="CO2",
mole_fraction=1,
path_length=0.05,
cutoff=1e-25,
broadening_max_width=1,
export_populations=False, #'vib',
export_lines=False,
isotope=1,
use_cached=True,
wstep=wstep,
pseudo_continuum_threshold=0,
pressure=P,
verbose=False,
)
# sf.fetch_databank('astroquery')
sf.warnings["NegativeEnergiesWarning"] = "ignore"
sf.load_databank("HITEMP-CO2-TEST")
pb = ProgressBar(3, active=verbose)
s_eq = sf.eq_spectrum(Tgas=Tgas, mole_fraction=1, name="Equilibrium")
pb.update(1)
s_2T = sf.non_eq_spectrum(Tvib=Tgas,
Trot=Tgas,
mole_fraction=1,
name="Noneq (2T)")
pb.update(2)
s_4T = sf.non_eq_spectrum(Tvib=(Tgas, Tgas, Tgas),
Trot=Tgas,
mole_fraction=1,
name="Noneq (4T)")
pb.update(3)
s_plck = sPlanck(
wavelength_min=2000, # =wavelength_min,
wavelength_max=
5000, # =wavelength_max - wstep, # there is a border effect on last point
T=Tgas,
)
pb.done()
# %% Post process:
# MAke optically thick, and compare with Planck
for s in [s_eq, s_2T, s_4T]:
s.rescale_path_length(1e6)
if plot:
nfig = "test_opt_thick_limit_1iso {0}".format(s.name)
plt.figure(nfig).clear()
s.plot(wunit="nm", nfig=nfig, lw=4)
s_plck.plot(wunit="nm", nfig=nfig, Iunit="mW/cm2/sr/nm", lw=2)
plt.legend()
if verbose:
printm(
"Residual between opt. thick CO2 spectrum ({0}) and Planck: {1:.2g}"
.format(
s.name,
get_residual(s,
s_plck,
"radiance_noslit",
ignore_nan=True),
))
# assert get_residual(s, s_plck, 'radiance_noslit', ignore_nan=True) < 1e-3
assert get_residual(s, s_plck, "radiance_noslit",
ignore_nan=True) < 0.9e-4
if verbose:
printm("Tested optically thick limit is Planck (1 isotope): OK")
finally:
# Reset DEBUG_MODE
radis.DEBUG_MODE = DEBUG_MODE
def test_plot_all_CO2_bandheads(verbose=True, plot=False, *args, **kwargs):
''' In this test we use the :meth:`~radis.lbl.bands.BandFactory.non_eq_bands`
method to calculate separately all vibrational bands of CO2, and compare
them with the final Spectrum.
'''
# Note: only with iso1 at the moment
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
verbose = True
Tgas = 1000
sf = SpectrumFactory(wavelength_min=4160,
wavelength_max=4220,
mole_fraction=1,
path_length=0.3,
cutoff=1e-23,
molecule='CO2',
isotope=1,
db_use_cached=True,
lvl_use_cached=True,
verbose=verbose)
sf.warnings['MissingSelfBroadeningWarning'] = 'ignore'
sf.warnings['NegativeEnergiesWarning'] = 'ignore'
sf.warnings['HighTemperatureWarning'] = 'ignore'
sf.fetch_databank()
s_tot = sf.non_eq_spectrum(Tvib=Tgas, Trot=Tgas)
s_bands = sf.non_eq_bands(Tvib=Tgas, Trot=Tgas)
if verbose:
printm('{0} bands in spectrum'.format(len(s_bands)))
assert len(s_bands) == 6
# Ensure that recombining gives the same
s_merged = MergeSlabs(*list(s_bands.values()))
assert s_tot.compare_with(s_merged, 'radiance_noslit', plot=False)
if verbose:
printm('Recombining bands give the same Spectrum')
# %%
if plot:
s_tot.apply_slit(1, 'nm')
s_tot.name = 'Full spectrum'
s_tot.plot(wunit='nm', lw=3)
for band, s in s_bands.items():
s.plot(wunit='nm', nfig='same')
plt.legend(loc='upper left')
plt.ylim(ymax=0.25)
# %% Compare with equilibrium bands now
s_bands_eq = sf.eq_bands(Tgas)
s_merged_eq = MergeSlabs(*list(s_bands_eq.values()))
assert get_residual(s_tot, s_merged_eq, 'radiance_noslit') < 1e-5
return True
def test_abscoeff_continuum(plot=False,
verbose=2,
warnings=True,
threshold=0.1,
*args,
**kwargs):
"""
Test calculation with pseudo-continuum
Assert results on abscoeff dont change
Notes
-----
Uses HITRAN so it can deployed and tested on [Travis]_, but we should switch
to HITEMP if some HITEMP files can be downloaded automatically at the
execution time.
"""
if plot: # Make sure matplotlib is interactive so that test are not stuck in pytest
plt.ion()
try:
if verbose:
printm(">>> test_abscoeff_continuum")
sf = SpectrumFactory(
wavelength_min=4200,
wavelength_max=4500,
parallel=False,
bplot=False,
cutoff=1e-23,
molecule="CO2",
isotope="1,2",
db_use_cached=True,
broadening_max_width=10,
path_length=0.1,
mole_fraction=1e-3,
medium="vacuum",
verbose=verbose,
)
sf.warnings.update({
"MissingSelfBroadeningWarning": "ignore",
"NegativeEnergiesWarning": "ignore",
"LinestrengthCutoffWarning": "ignore",
"HighTemperatureWarning": "ignore",
})
sf.fetch_databank(
) # uses HITRAN: not really valid at this temperature, but runs on all machines without install
# sf.load_databank('HITEMP-CO2-DUNHAM') # to take a real advantage of abscoeff continuum, should calculate with HITEMP
sf._export_continuum = True # activate it
# Calculate one without pseudo-continuum
sf.params.pseudo_continuum_threshold = 0
s1 = sf.eq_spectrum(Tgas=2000)
s1.name = "All lines resolved ({0}) ({1:.1f}s)".format(
s1.conditions["lines_calculated"],
s1.conditions["calculation_time"])
assert s1.conditions["pseudo_continuum_threshold"] == 0
# Calculate one with pseudo-continuum
sf.params.pseudo_continuum_threshold = threshold
s2 = sf.eq_spectrum(Tgas=2000)
s2.name = "Semi-continuum + {0} lines ({1:.1f}s)".format(
s2.conditions["lines_calculated"],
s2.conditions["calculation_time"])
assert s2.conditions["pseudo_continuum_threshold"] == threshold
assert "abscoeff_continuum" in s2.get_vars()
# Plot
if plot:
plot_diff(
s1,
s2,
"radiance_noslit",
Iunit="µW/cm2/sr/nm",
nfig="test_abscoeff_continuum: diff",
)
s2.plot(
"abscoeff",
label="Full spectrum",
nfig="test_abscoeff_continuum: show continuum",
force=True,
)
s2.plot(
"abscoeff_continuum",
nfig="same",
label="Pseudo-continuum".format(
s2.conditions["lines_in_continuum"]),
force=True,
)
plt.legend()
# Compare
res = get_residual(s1, s2, "abscoeff")
if verbose:
printm("residual:", res)
globals().update(locals())
assert res < 1.32e-6
except DatabankNotFound as err:
assert IgnoreMissingDatabase(err, __file__, warnings)
