Contains the SpectrumFactory class, which is
the core of the RADIS Line-by-Line module.
Examples
Calculate a CO Spectrum, fetching the lines from HITRAN
# This is how you get a spectrum (see spectrum.py for front-end functions# that do just that)sf=SpectrumFactory(2125,2249.9,molecule='CO',isotope=1,cutoff=1e-30,# for faster calculations. See# `plot_linestrength_hist` for more details**kwargs)sf.fetch_databank()# auto download from HITRANs=sf.eq_spectrum(Tgas=300)s.plot('abscoeff')# opacity# Here we get some extra informations:s.plot('radiance',wunit='nm',Iunit='µW/cm2/sr/nm',# Iunit is arbitrary. Use whatever makes senseshow_points=True)# show_points to have an idea of the resolution
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Notes
Debugging:
Remember one can access all locals variable in a function either by running
%debug after a crash in IPython. Or by adding the line globals().update(locals())
at any point
Performance:
Fast version: iterate over chunks of dataframe
Note that we can’t use the full dataframe because it’s too big and takes too much memory
See Performance for more details.
for Developers:
To implement new database formats, see the databases parsers in cdsd.py / hitran.py,
and the partition function interpolators / calculators methods of SpectrumFactory:
_build_partition_function_calculator() and
_build_partition_function_interpolator()
A class to put together all functions related to loading CDSD / HITRAN
databases, calculating the broadenings, and summing over all the lines.
Parameters:
wmin, wmax (float or Quantity) – a hybrid parameter which can stand for minimum (maximum) wavenumber or minimum
(maximum) wavelength depending upon the unit accompanying it. If dimensionless,
wunit is considered as the accompanying unit.
wunit ('nm', 'cm-1') – the unit accompanying wmin and wmax. Can only be passed with wmin
and wmax. Default is "cm-1".
wavenum_min, wavenum_max (float(cm^-1) or Quantity) – minimum (maximum) wavenumber to be processed in \(cm^{-1}\).
use astropy.units to specify arbitrary inverse-length units.
wavelength_min, wavelength_max (float(nm) or Quantity) – minimum (maximum) wavelength to be processed in \(nm\). This wavelength
can be in 'air' or 'vacuum' depending on the value of the parameter
medium=.
use astropy.units to specify arbitrary length units.
pressure (float(bar) or Quantity) – partial pressure of gas in bar. Default 1.01325 (1 atm).
use astropy.units to specify arbitrary pressure units.
For example, 1013.25*u.mbar.
mole_fraction (float [ 0 - 1]) – species mole fraction. Default 1. Note that the rest of the gas
is considered to be air for collisional broadening.
path_length (float(cm) or Quantity) – path length in cm. Default 1.
use astropy.units to specify arbitrary length units.
molecule (int, str, or None) – molecule id (HITRAN format) or name. If None, the molecule can be inferred
from the database files being loaded. See the list of supported molecules
in MOLECULES_LIST_EQUILIBRIUM
and MOLECULES_LIST_NONEQUILIBRIUM.
Default None.
isotope (int, list, str of the form '1,2', or 'all') – isotope id (sorted by relative density: (eg: 1: CO2-626, 2: CO2-636 for CO2).
See HITRAN documentation for isotope list for all species. If ‘all’,
all isotopes in database are used (this may result in larger computation
times!). Default 'all'
medium ('air', 'vacuum') – propagating medium when giving inputs with 'wavenum_min', 'wavenum_max'.
Does not change anything when giving inputs in wavenumber. Default 'air'
diluent (str or dictionary) – can be a string of a single diluent or a dictionary containing diluent
name as key and its mole_fraction as value. Default air.
Other Parameters:
Tref (K) – Reference temperature for calculations (linestrength temperature
correction). HITRAN database uses 296 Kelvin. Default 296 K
self_absorption (boolean) – Compute self absorption. If False, spectra are optically thin. Default True.
truncation (float (\(cm^{-1}\))) – Half-width over which to compute the lineshape, i.e. lines are truncated
on each side after truncation (\(cm^{-1}\)) from the line center.
If None, use no truncation (lineshapes spread on the full spectral range).
Default is 300\(cm^{-1}\)
Note
Large values (> 50) can induce a performance drop (computation of lineshape
typically scale as \(~truncation ^2\) ). The default 300 was
chosen to maintain a good accuracy, and still exhibit the sub-Lorentzian
behavior of most lines far (few hundreds \(cm^{-1}\)) from the line center.
neighbour_lines (float (\(cm^{-1}\))) – The calculated spectral range is increased (by neighbour_lines cm-1
on each side) to take into account overlaps from out-of-range lines.
Default is 0\(cm^{-1}\).
wstep (float (cm-1) or 'auto') – Resolution of wavenumber grid. Default 0.01 cm-1.
If 'auto', it is ensured that there
are slightly more points for each linewidth than the value of "GRIDPOINTS_PER_LINEWIDTH_WARN_THRESHOLD"
in radis.config (~/radis.json)
Note
wstep = ‘auto’ is optimized for performances while ensuring accuracy,
but is still experimental in 0.9.30. Feedback welcome!
cutoff (float (~ unit of Linestrength: cm-1/(#.cm-2))) – discard linestrengths that are lower that this, to reduce calculation
times. 1e-27 is what is generally used to generate databases such as
CDSD. If 0, no cutoff. Default 1e-27.
parsum_mode (‘full summation’, ‘tabulation’) – how to compute partition functions, at nonequilibrium or when partition
function are not already tabulated. 'fullsummation' : sums over all
(potentially millions) of rovibrational levels. 'tabulation' :
builds an on-the-fly tabulation of rovibrational levels (500 - 4000x faster
and usually accurate within 0.1%). Default fullsummation'
Note
parsum_mode= ‘tabulation’ is new in 0.9.30, and makes nonequilibrium
calculations of small spectra extremely fast. Will become the default
after 0.9.31.
pseudo_continuum_threshold (float) – if not 0, first calculate a rough approximation of the spectrum, then
moves all lines whose linestrength intensity is less than this threshold
of the maximum in a semi-continuum. Values above 0.01 can yield significant
errors, mostly in highly populated areas. 80% of the lines can typically
be moved in a continuum, resulting in 5 times faster spectra. If 0,
no semi-continuum is used. Default 0.
save_memory (boolean) – if True, removes databases calculated by intermediate functions (for
instance, delete the full database once the linestrength cutoff criteria
was applied). This saves some memory but requires to reload the database
& recalculate the linestrength for each new parameter. Default False.
export_populations ('vib', 'rovib', None) – if not None, store populations in Spectrum. Either store vibrational
populations (‘vib’) or rovibrational populations (‘rovib’). Default None
export_lines (boolean) – if True, saves details of all calculated lines in Spectrum. This is
necessary to later use line_survey(),
but can take some space. Default False.
chunksize (int, or None) – Splits the lines database in several chunks during calculation, else
the multiplication of lines over all spectral range takes too much memory
and slows the system down. Chunksize let you change the default chunk
size. If None, all lines are processed directly. Usually faster but
can create memory problems. Default None
optimization ("simple", "min-RMS", None) – If either "simple" or "min-RMS" LDM optimization for lineshape calculation is used:
- "min-RMS" : weights optimized by analytical minimization of the RMS-error (See: [Spectral-Synthesis-Algorithm])
- "simple" : weights equal to their relative position in the grid
If using the LDM optimization, broadening method is automatically set to 'fft'.
If None, no lineshape interpolation is performed and the lineshape of all lines is calculated.
folding_thresh (float) – Folding is a correction procedure that is applied when the lineshape is calculated with
the fft broadening method and the linewidth is comparable to wstep, that prevents
sinc(v) modulation of the lineshape. Folding continues until the lineshape intensity
is below folding_threshold. Setting to 1 or higher effectively disables folding correction.
Range: 0.0 < folding_thresh <= 1.0
Default: 1e-6
zero_padding (int) – Zero padding is used in conjunction with the fft broadening method to prevent circular
convolution at the cost of performance. When set to -1, padding is set equal to the spectrum length,
which guarantees a linear convolution.
broadening_method ("voigt", "convolve", "fft") – Calculates broadening with a direct voigt approximation (‘voigt’) or
by convoluting independently calculated Doppler and collisional
broadening (‘convolve’). First is much faster, 2nd can be used to
compare results. This SpectrumFactory parameter can be manually
adjusted a posteriori with:
Fast fourier transform 'fft' is only available if using the LDM lineshape
calculation optimization. Because the LDM convolves all lines at the same time,
and thus operates on large arrays, 'fft' becomes more appropriate than
convolutions in real space ('voigt', 'convolve' )
By default, use "fft" for any optimization, and "voigt" if
optimization is None .
warnings (bool, or one of ['warn','error','ignore'], dict) – If one of ['warn','error','ignore'], set the default behaviour
for all warnings. Can also be a dictionary to set specific warnings only.
Example:
verbose (boolean, or int) – If False, stays quiet. If True, tells what is going on.
If >=2, gives more detailed messages (for instance, details of
calculation times). Default True.
fromradisimportSpectrumFactoryfromastropyimportunitsasusf=SpectrumFactory(wavelength_min=4165*u.nm,wavelength_max=4200*u.nm,isotope='1,2',truncation=10,# cm-1optimization=None,medium='vacuum',verbose=1,# more for more details)sf.load_databank('HITRAN-CO2-TEST')# predefined in ~/radis.jsons=sf.eq_spectrum(Tgas=300*u.K,path_length=1*u.cm)s.rescale_path_length(0.01)# cms.plot('radiance_noslit',Iunit='µW/cm2/sr/nm')
initial line database after loading.
If for any reason, you want to manipulate the line database manually (for instance, keeping only lines emitting
by a particular level), you need to access the df0 attribute of
SpectrumFactory.
Warning
never overwrite the df0 attribute, else some metadata may be lost in the process.
Only use inplace operations. If reducing the number of lines, add
a df0.reset_index()
For instance:
fromradisimportSpectrumFactorysf=SpectrumFactory(wavenum_min=2150.4,wavenum_max=2151.4,pressure=1,isotope=1)sf.load_databank('HITRAN-CO-TEST')sf.df0.drop(sf.df0[sf.df0.vu!=1].index,inplace=True)# keep lines emitted by v'=1 onlysf.eq_spectrum(Tgas=3000,name='vu=1').plot()
df0 contains the lines as they are loaded from the database.
df1 is generated during the spectrum calculation, after the
line database reduction steps, population calculation, and scaling of intensity and broadening parameters
with the calculated conditions.
Generate a spectrum at equilibrium with calculation of lineshapes
and broadening done on the GPU.
Note
This method requires CUDA compatible hardware to execute.
For more information on how to setup your system to run GPU-accelerated methods
using CUDA and Cython, check GPU Spectrum Calculation on RADIS
Fit an experimental spectrum with an arbitrary model and an arbitrary
number of fit parameters. This method calls fit_legacy()
which is still functional. However, we recommend using fit_spectrum().
Parameters:
s_exp (Spectrum) – experimental spectrum. Should have only spectral array only. Use
take(), e.g:
sf.fit_legacy(s_exp.take('transmittance'))
model (func -> Spectrum) – a line-of-sight model returning a Spectrum. Example :
Tvib12Tvib3Trot_NonLTEModel()
Calculate emission spectrum in non-equilibrium case. Calculates
absorption with broadened linestrength and emission with broadened
Einstein coefficient.
Parameters:
Tvib (float) – vibrational temperature [K]
can be a tuple of float for the special case of more-than-diatomic
molecules (e.g: CO2)
Trot (float) – rotational temperature [K]
Ttrans (float) – translational temperature [K]. If None, translational temperature is
taken as rotational temperature (valid at 1 atm for times above ~ 2ns
which is the RT characteristic time)
mole_fraction (float) – database species mole fraction. If None, Factory mole fraction is used.
diluent (str or dictionary) – can be a string of a single diluent or a dictionary containing diluent
name as key and its mole_fraction as value
path_length (float or Quantity) – slab size (cm). If None, the default Factory
path_length is used.
pressure (float or Quantity) – pressure (bar). If None, the default Factory
pressure is used.
Other Parameters:
vib_distribution ('boltzmann', 'treanor') – vibrational distribution
rot_distribution ('boltzmann') – rotational distribution
overpopulation (dict, or None) –
add overpopulation factors for given levels:
{level:overpopulation_factor}
name (str) – output Spectrum name (useful in batch)
Multi-vibrational temperature. Below we compare non-LTE spectra of CO2 where all
vibrational temperatures are equal, or where the bending & symmetric modes are in
equilibrium with rotation
fromradisimportSpectrumFactorysf=SpectrumFactory(wavenum_min=2000,wavenum_max=3000,molecule="CO2",isotope="1,2,3",)sf.fetch_databank("hitemp",load_columns='noneq')# nonequilibrium between bending+symmetric and asymmetric modes :s1=sf.non_eq_spectrum(Tvib=(600,600,2000),Trot=600,path_length=1,pressure=1)# all vibrational temperatures are equal :s2=sf.non_eq_spectrum(Tvib=(2000,2000,2000),Trot=600,path_length=1,pressure=1)
Calculate total power emitted in equilibrium or non-equilibrium case
in the optically thin approximation: it sums all emission integral over
the total spectral range.
Warning
this is a fast implementation that doesnt take into account
the contribution of lines outside the given spectral range. It is valid for spectral ranges
surrounded by no lines, and spectral ranges much broadened than the typical
line broadening (~ 1-10 cm-1 in the infrared)
If what you’re looking for is an accurate simulation on a narrow spectral range
you better calculate the spectrum (that does take all of that into account)
and integrate it with get_power()
Parameters:
Tgas (float) – equilibrium temperature [K]
If doing a non equilibrium case it should be None. Use Ttrans for
translational temperature
Tvib (float) – vibrational temperature [K]
Trot (float) – rotational temperature [K]
Ttrans (float) – translational temperature [K]. If None, translational temperature is
taken as rotational temperature (valid at 1 atm for times above ~ 2ns
which is the RT characteristic time)
mole_fraction (float) – database species mole fraction. If None, Factory mole fraction is used.
path_length (float) – slab size (cm). If None, Factory mole fraction is used.
unit (str) – output unit. Default 'mW/cm2/sr'
Returns:
float – see unit=.
Return type:
Returns total power density in mW/cm2/sr (unless different unit is chosen),
predict_time(self) uses the input parameters like Spectral Range, Number of lines, wstep,
truncation to predict the estimated calculation time for the Spectrum
broadening step(bottleneck step) for the current optimization and broadening_method. The formula
for predicting time is based on benchmarks performed on various parameters for different optimization,
broadening_method and deriving its time complexity.