Linelist

Linelist#

linelist is one of the core inputs for spectral synthesis. It stores the physical parameters of each transition (element/species, wavelength, log gf, damping parameters, etc.).

Getting a Linelist from VALD#

PySME is designed to work well with all types of line lists in VALD database. A common workflow is:

  1. Download a line list from VALD (typically from extract stellar).

  2. Load it in PySME with ValdFile.

from pysme.linelist.vald import ValdFile

vald = ValdFile("my_linelist.lin")
sme.linelist = vald

Linelist is essentially a DataFrame#

Internally, PySME stores LineList data in a pandas.DataFrame (sme.linelist._lines). So you can use DataFrame-style operations directly: filtering, sorting, editing columns, adding flags, and so on.


# Filter by wavelength range
sub = sme.linelist[(sme.linelist["wlcent"] > 6436.0) & (sme.linelist["wlcent"] < 6444.0)]

# Select one species (for example, Fe I)
fe1 = sme.linelist[sme.linelist["species"] == "Fe 1"]

Short vs Long Format#

VALD provides two line list formats:

  • short: fewer fields, suitable for LTE.

  • long: includes additional upper/lower level and quantum-number information.

If you plan to run NLTE, you should use VALD long format. In PySME, NLTE relies on the extra level information available in long format; short format does not provide enough information for that workflow.

Line parameters#

The short format fields are

species:

A string identifier including the element and ionization state or the molecule

wlcent:

The central wavelength of the line in Angstrom

gflog:

The log of the product of the statistical weight of the lower level and the oscillator strength for the transition.

excit:

The excitation energy in the lower level

ionization:

The ionization state of the species, where 1 is neutral

gamrad:

The radiation broadening parameter

gamqst:

Stark broadening parameter

gamvw:

van der Waals broadening parameter

lande:

The lande factor

depth:

An arbitrary depth estimation of the line

reference:

A citation where this data came from

atom_number:

Identifies the species by the atomic number (i.e. the number of protons)

In addition the long format has the following fields

lande_lower:

The lower Lande factor

lande_upper:

The upper Lande factor

j_lo:

The spin of the lower level

j_up:

The spin of the upper level

e_upp:

The energy of the upper level

term_lower:

The electron configuration of the lower level

term_upper:

The electron configuration of the upper level

error:

An uncertainty estimate for this linedata

Runtime columns#

nlte_flag:

Per-line NLTE usage flag written after synthesis. See NLTE flags in line list.

central_depth:

Estimated central line depth used for line selection/filtering. See Line Filtering.

line_range_s:

Start wavelength of the estimated line-contribution range. See Line Filtering.

line_range_e:

End wavelength of the estimated line-contribution range. See Line Filtering.

Important Note#

As far as the radiative transfer code is concerned the ionization is defined as part of the species term. I.e. a line with species = “Fe 2” will be calculated as ionization = 2. If no number is set within the species field, SME will use an ionization of 1.

Also atom_number is ignored in the radiative transfer calculations and therefore does not need to be set.

Example Linelist#

Below is a typical sme.linelist excerpt (middle rows omitted):

   species     wlcent  gflog     excit  j_lo     e_upp  j_up  lande_lower  \
0     Fe 1  6436.4055 -2.460  4.186364   2.0  6.112128   1.0         0.68
1     Eu 2  6437.6106 -1.242  1.319612   5.0  3.245008   5.0         1.73
2     Eu 2  6437.6121 -1.280  1.319636   5.0  3.245027   5.0         1.73
3     Eu 2  6437.6135 -2.473  1.319612   5.0  3.245008   5.0         1.73
4     Eu 2  6437.6194 -2.511  1.319636   5.0  3.245027   5.0         1.73
..     ...        ...    ...       ...   ...       ...   ...          ...
62    Mn 1  6443.4689 -2.818  3.772307   1.5  5.695960   2.5         1.21
63    Mn 1  6443.4726 -3.538  3.772307   1.5  5.695960   2.5         1.21
64    Mn 1  6443.4821 -2.275  3.772307   1.5  5.695960   2.5         1.21
65    Mn 1  6443.4887 -2.964  3.772307   1.5  5.695960   2.5         1.21
66    Mn 1  6443.4938 -3.918  3.772307   1.5  5.695960   2.5         1.21

    lande_upper  lande  ...        term_lower  couple_upper  \
0          0.56   0.73  ...           3d8 c3F            LS
1          1.79   1.76  ...  4f7.(8S).5d a9D*            JJ
2          1.79   1.76  ...  4f7.(8S).5d a9D*            JJ
3          1.79   1.76  ...  4f7.(8S).5d a9D*            JJ
4          1.79   1.76  ...  4f7.(8S).5d a9D*            JJ
..          ...    ...  ...               ...           ...
62         1.37   1.49  ...       3d5.4s2 b4D            LS
63         1.37   1.49  ...       3d5.4s2 b4D            LS
64         1.37   1.49  ...       3d5.4s2 b4D            LS
65         1.37   1.49  ...       3d5.4s2 b4D            LS
66         1.37   1.49  ...       3d5.4s2 b4D            LS

                         term_upper  error nlte_flag atom_number ionization  \
0        3d6.(3F2).4s.4p.(3P*) v3D*   0.50         0         1.0        1.0
1   4f7.(8S<7/2>).6p<3/2> (7/2,3/2)   1.00         0         1.0        2.0
2   4f7.(8S<7/2>).6p<3/2> (7/2,3/2)   1.00         0         1.0        2.0
3   4f7.(8S<7/2>).6p<3/2> (7/2,3/2)   1.00         0         1.0        2.0
4   4f7.(8S<7/2>).6p<3/2> (7/2,3/2)   1.00         0         1.0        2.0
..                              ...    ...       ...         ...        ...
62                 3d6.(5D).4p z4D*   0.25         0         1.0        1.0
63                 3d6.(5D).4p z4D*   0.25         0         1.0        1.0
64                 3d6.(5D).4p z4D*   0.25         0         1.0        1.0
65                 3d6.(5D).4p z4D*   0.25         0         1.0        1.0
66                 3d6.(5D).4p z4D*   0.25         0         1.0        1.0
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