The SME Structure

The SME Structure#

The SME structure contains all the information necessary to run PySME.
It is by design similar to the IDL structure of SME, but with a lot of changes for ease of use. Note that some parameters depend on the number of segments in the observation. When creating a new structure it is therefore recommended to define the wavelengths first.

Stellar Parameters#

Stellar parameters describe the star in general and are usually what we want to fit.

  • teff: The effective temperature of the star in Kelvin.

  • logg: The surface gravity of the star in log (cgs).

  • monh: The overall metallicity of the star in log₁₀ relative to the individual abundances (see abund).

  • vsini: The (projected) rotation velocity in km s⁻¹. Describes the rotational broadening.

    • If vsini is non-zero, you should set several values for mu.

  • vmic: The micro-turbulence velocity in km s⁻¹. Describes turbulence on scales smaller than the photon mean free path, adding additional line broadening.

  • vmac: The macro-turbulence velocity in km s⁻¹. Describes turbulence on scales larger than the photon mean free path, also contributing to broadening.

  • mu: Limb-angle values (\(\mu = \cos\theta\)) at which the radiative-transfer calculation is performed. \(\mu = 1\) corresponds to disk center, \(0\) to the limb.

Radial velocity and Continuum#

The radial velocity and continuum shift the continuum in wavelength and intensity direction respectively. How to best handle them often depends on the situation and the quality of the observation data. Therefore PySME has many options to determine them.

  • cscale: The polynomial parameters for each segment, that are applied to the synthetic spectrum to match the observation.

    • The polynomial is calculated using the wavelength grid of the observation, shifted so that the first point is 0. I.e. the polynomial is f(wave - wave[0]).

  • vrad: The radial velocity in km/s that was applied to each segment of the synthethized spectrum to match the observation.

  • cscale_flag: Determines how the continuum is fitted, or if it is fitted at all.

    • none: No continuum correction

    • fix: Use whatever continuum scale has been set, but don’t change it.

    • constant: scale everything by a factor

    • linear: First order polynomial, i.e. a straight line

    • quadratic: Second order polynomial

  • vrad_flag: Determines how the radial velocity is fitted, or if it is fitted at all.

    • none: No radial velocity fitting

    • fix: Use the set value for the radial velocity, but don’t change it

    • each: Fit each wavelength segment individally

    • whole: Fit the whole spectrum at once

Spectra#

Spectra are given as a list of arrays[1], where each array represents one wavelength segment of the spectrum. If there is only one segment, the list will only have one element. For legacy reasons there is also an interface to the ‘old’ system and names (e.g. smod instead of synth) from IDL SME. It is recommend however to use the new variables.

wave:

The wavelength grid of the observation and/or the synthetic spectrum

spec:

The observed spectrum

uncs:

The uncertainties of the observed spectrum. If None will use uncertainty 1 for all points.

mask:

The pixel mask for the observation, with defination of 0 as bad pixel, 1 as line pixel, 2 as continuum pixel, and 4 as vrad pixel. The masks are additive, i.e., you can set mask value to 5 for line and vrad pixel. Only the good pixels will contribute to the fit, but the synthetic spectrum will still be calculated. Note that dtype of sme.mask must be int.

synth:

The synthetic spectrum

wran:

The first and last wavelength of each segment. You only need this if you dont have an observation and dont want to specify the exact wavelength grid of the synthetic observation. Note that this is not an Illiffe vector.

wint:

Optional wavelength grid passed to SMElib Transf as adaptive grid for each segment. Accepts the same segment-aware input styles as wave: numpy.ndarray (single segment), list of arrays (multi-segment), or Iliffe_vector. If provided, sme.wint[segment] is used directly for synthesis. If not provided, PySME can reuse an internal cached adaptive grid when reuse_wavelength_grid=True; otherwise SMElib computes a new adaptive grid.

Abundance#

The individal abundances are stored in a seperate Abundance object, which shares the same metallicity as the overall structure. For more detailed information see Abundance.

abund:

The abundance object

Linelist#

The sme structure does contain the whole linelist in the linelist property. For legacy reasons, it also provides direct access to the ‘species’ and ‘atomic’ arrays. They refer directly to the linelist however. For more detailed information see Linelist.

linelist:

The linelist object

species:

Names of the species of each spectral line

atomic:

Atomic linelist data with columns “atom_number”, “ionization”, “wlcent”, “excit”, “gflog”, “gamrad”, “gamqst”, “gamvw”

Atmosphere#

Unlike the linelist the atmosphere is stored in an external file, that is only referenced by name in the structure. For more detailed information see Atmosphere.

atmo:

The atmosphere object

NLTE#

Unlike the linelist, but similar to the atmosphere, the NLTE parameters are stored in external tables, which are only referenced by name. For more detailed information see NLTE grids.

nlte:

The NLTE object

Instrument Parameters#

PySME can also model instrumental broadening as part of the spectral synthesis. For this you need to specify the resolution and the broadening method to use.

ipres:

The resolution of the instrument to simulate

iptype:

The broadening profile of the instrument. One of “gauss”, “sinc”, “table”

ip_x:

The x points of the instrument profile. Only relevant if iptype is ‘table’.

ip_y:

The y points of the instrument profile. Only relevant if iptype is ‘table’.

Fitresults#

fitparameters:

The fitparameters used for the fitting. See fitparameters.

fitresults:

The fitresults object. See fitresults.

System Information#

The sme structure does contain information about the host system. E.g. which operating system was used. This is mostly for legacy reasons, and potential debugging information. For more information see system_info.

system_info:

The system information object. It replaces the idlver object.

Other Parameters#

gam6:

van der Waals scaling factor (usually 1)

h2broad:

flag determing whether to use H2 broadening or not (usually True)

accrt:

Minimum accuracy for synthethized spectrum at wavelength grid points in sme.wint (or SMElib adaptive grid if sme.wint is not set). Values below 1e-4 are not meaningful.

accwi:

Minimum accuracy for linear spectrum interpolation vs. wavelength. Values below 1e-4 are not meaningful.

version:

The version of sme used to create this structure and spectrum

id:

The date and time when this structure or the last synthetic spectrum was created

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