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 log_10 relative to the indvidual abundances. See Abundance

vsini:

The (projected) rotation velocity in km/s. Describes the rotational broadening. If vsini is none zero, you need to set several values for mu.

vmic:

The microturbulence velocity in km/s. Describes the turbuluence on scales smaller than the mean free path of the light. Adds broadening to the spectrum.

vmac:

The macroturbulence velocity in km/s. Describes the turbuluence on scales larger than the mean free path of the light. Adds broadening to the spectrum.

mu:

Mu values to calculate radiative transfer at. They describe the distance from the center of the stellar disk to the edge with mu = cos(theta), where theta is the angle of the observation, i.e. mu = 1 at the center of the disk and 0 at the edge.

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

normalize_by_continuum:

A flag that determines, whether the synthetic flux should be normalized by the continous intensities or not. As long as you have a normalized observation this should be True, but if you have a flux calibrated spectrum this should be set to False. Note that even if this is False, you can still fit a continuum normally using cscale_flag.

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.

[1]

They are called Illiffe vectors in the code, and they were that in IDL. But they are technically not Illiffe vectors anymore, but just lists of individal numpy arrays.

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 bad pixel mask for the observation. Only the good pixels will contribute to the fit, but the synthetic spectrum will still be calculated

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.

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.

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.wave. Values below 1e-4 are not meaningful

accwt:

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

md5:

The md5 hash of the structure