SME tutorial January 31 – February 2, 2011

Uppsala

Schedule

Monday

Short intro to SME

Installation and testing of the installation

Tuesday

3 exercises (creating SME input structure,

solving of global parameters, tuning line

parameters)

Starting to work on your data

SME physics

SME (= Spectroscopy Made Easy)

computes spectral synthesis and adjusts

free parameters based on comparison

with observations

SME spectral synthesis consists of

molecular and ionization equilibrium

solver EOS, continuous opacity package

CONTOP, line opacity package LINEOP

and RT solver RTINT

EOS

Abundances Zatom is the ratio natom / ntotal

is the number of particular

atoms in a particular species

(e.g. )

is the total number of atoms in a

particular species (e.g. )

charge of a given species:

Species

AtomX

2 2H O H O

H C2, 0X X

SpeciesX

2H O 3X

speciesqTiO+

H

1

1

q

q

Abundance and conservation

equations

Abundances (X is the number of atoms in a

given species):

Total number of particles:

Charge conservation (q is the electric charge):

Species

species Atom

species

Atom Species

species

species

n X

Zn X

species total

species

en n n P kT

species

species

species

en q n

Chemistry

Chemical reaction in which species A and B

form AB can be described by the chemical

equilibrium equation:

Ionization can be described in exact same way:

Saha equation!

3322

2

2( )

ABA B A B A B

AB AB AB

D

kTn n m m U UkTK T e

n h m U

32

2

22( )

Ae eA A

A A

I

kTn n Um kT

K T en h U

Using EOS

EOS has partition functions for 6 ionization stages of the first 99 atoms in the periodic table

EOS has partition functions for 257 molecules (up to four atoms) fitted over the range from 10K to 8000K

Input consists of T, P and abundances. Pe can be also imposed

EOS is using rather unique solving strategy making it robust

CONTOP

Continuous opacities are from ATLAS12

Modifications: partial pressures of

absorbers and their partition functions

are taken from EOS

List of absorbers: H, H2+, H-, He, He+, He-,

Si, Si+, Mg, Mg+, Al, C, Fe, Ca+, N, O, Ne, S,

List of scatterers: H, H2, He, e-

LINEOP

Given partial number densities of the line absorbers and their partition functions computes line opacities

Voigt profiles except for hydrogen lines

Natural, Stark and van der Waals broadening

Two-parameter van der Waals broadening (Anstee, Barklem & O'Mara, http://www.astro.uu.se/~barklem/howto.html)

Hydrogen lines are computed using Barklem and Piskunov code HLINOP (http://www.astro.uu.se/~barklem/hlinop.html) taking into account self broadening and other effects.

Stark broadening and Stark shift are explicitly computed for the lines of neutral helium.

RTINT

Single pass short-characteristics algorithm

developed for 3D radiative transfer code:

fast and robust even on a sparse grid.

Attenuation operator with quadratic

Bezier spline approximation to the source

function

Bezier spline prevents overshooting

RTINT: equations

RT equation:

Formal solution:

Approximation to the source function:

𝑆𝜈 𝑡 ≈ 𝑎𝑡2 + 𝑏𝑡 + 𝑐 for 𝜏𝑖 ≤ 𝑡 ≤ 𝜏𝑖+1

Attenuation operator:

𝐼𝑖+1 = 𝑒−∆𝜏𝑖𝐼𝑖 + 𝛼 𝑆𝜈 𝜏𝑖−1 + 𝛽𝑆𝜈 𝜏𝑖 + 𝛾𝑆𝜈 𝜏𝑖+1

1

1

1

( )

1

( )

( ) ( )

( )

i i

i

i

i

i i

t

I e I

S t e dt

𝑑𝐼𝜈

𝑑𝜏= 𝐼𝜈 − 𝑆𝜈

RTINT: Bezier spline

SME implementation

SME consists of two independent parts: GUI and solver

Solver consists of the IDL routines for preparing spectral synthesis and performing optimization and an external library for computing synthetic spectra

GUI let you prepare data for the solver and interpret the results but there at least two other packages to do it non-interactively

Solver

Spectral synthesis requires various data: line list, wavelength range, atmospheric model(s), initial parameters. All of this (except when model interpolation is required) are collected in one structure – the so-called input structure

Solver takes the input structure and performs its tasks and saves the results into an output structure.

Both input and output structures have name sme

Once the input structure is prepared you can run solver manually: restore,’input_sme.sav’

sme_main,sme

save,sme,file=‘output_sme.sav’

Solver

You can also examine the sme structure in your idl session: help,sme,/str

The external library is written in C++ and Fortran and it has about ten entry points.

Conventionally the library should be located in the same place where sme_main.pro is and must be called sme_synth.so. Normally one would create a link with this name to the correct library.

This are used in particular sequence: setting wavelength range, passing atmospheric model, passing line list, solving for molecular-ionization equilibrium, performing spectral synthesis etc.

Things computed within the library with each call are stored in separate memory and can be prompted from IDL using the corresponding calls.

GUI

GUI is interactive tool for creating input structures and examining the output structures

GUI includes tools for importing line lists in VALD format, for importing observations, setting abundances, selecting atmospheric model(s), free parameters etc.

When you save the results of GUI setup, it will automatically create an input structure!

GUI can also read both input and output structures.

GUI also has a graphics tool to show the results.