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Ay219 Stellar Abundance Measurements
Evan Kirby
In this exercise, you will measure the abundances of the metal-poor abundance standard HD122563. This star is a red giant in the Milky Way stellar
halo. The procedure described below is to measure the equivalent widths (EWs)
in IRAF, generate an ATLAS9 model atmosphere, compile an atomic line list,
and measure the abundances of a few elements in HD122563 using MOOG.
You do not need to follow this procedure to the letter. Variations on this
procedure include
• Use the spectrum of a different star (see last section).
• Use VALD or the Kurucz database for your line list, rather than NIST.
• Measure EWs with a program other than IRAF.
• Use MARCS instead of ATLAS9 model atmospheres.
• Compute abundances with SME or Turbospectrum, rather than MOOG.
• Measure abundances with spectral synthesis instead of EWs.
All files can be found at
Pick an element to measure
Pick one or more elements you would like to measure. The elements available to
measure in HD122563 are C, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Co, Ni, Y,
Zr, Ba, Nd, Dy, and Ho. Ideally, the class as a whole will measure most of these
elements. Note that C comes with extra special complications! Some elements,
like Fe and Ti, have many lines to choose from. Other elements, like Na, have
very few.
If you need inspiration or an idea of how many lines of each element you can
measure, take a peek at my own line list for this star: HD122563.ew.
Make a line list
Look at the NIST database:
Find all the lines for your element in the spectral range 3190–5990 Å, which is
the range of the HIRES spectrum. Be sure to
• Pick a species, like “Ti I-II,” which will search for Ti I and Ti II lines.
• Set the lower wavelength limit to 3190 Å.
• Set the upper wavelength limit to 5990 Å.
• Set the units of wavelength to Å.
• Set energy level units to eV.
• Set “Transition strength bounds will apply to” log(gf ).
• Set the minimum log(gf ) to be −5.
• Select lines “only with transition probabilities.”
• Check the box for log(gf ).
If the list is a manageable size, then make a line list. If the list is very long
(more than 20 lines), then consult me on how to trim it down. For each entry
in the line list, record the wavelength of the line in Å, the species (e.g., Mg I),
the energy of the lower energy level in eV (a.k.a. excitation potential, or EP),
and the oscillator strength (log(gf )).
The format of the line list is a text file with one title line. The first line of
the file can be any text you like. Then, there is one line of text per absorption
line. Each line will have four numbers in the order listed above: λ, a code for the
species, EP, and log(gf ). The species code is the atomic number, followed by
a decimal point, and then a number indicating the number of ionized electrons.
For example, Fe I is 26.0. Ti II is 22.1. Each number should take up 10 character
spaces. Here is an example of one entry in a line list:
Measure equivalent widths
Download the Keck/HIRES spectrum of the abundance standard HD122563:
HD122563.fits. Make a directory, and save the file there.
1. Open IRAF: xgterm, cl -e
2. cd to the directory containing HD122563.fits
3. noao, onedspec, splot HD122563
4. Zoom in to the spectrum by placing your cursor at the left edge of your
desired zoom window and type a. Move your cursor to the right edge of
your desired zoom window and type a again.
5. If you want to start over, press c to redraw the full spectrum, zoomed out.
6. In order to identify lines, you need to know their wavelengths. Your line
list tells you the wavelengths at rest, but stars have radial velocities. The
radial velocity of HD122563 is vr = −24.67 km/s. When you look for the
wavelengths of lines, you’re actually looking for λobs = λrest (1 + vr /c),
where c = 3 × 105 km/s is the speed of light.
7. To measure the EW of a line, move your cursor to the continuum above
the line. Your cursor should be in the approximate center of the line
horizontally and near the continuum vertically. Press h and then c. The
text at the bottom of the screen displays eqw = some number. That is the
EW in Å. Record the value for later reference. It may help to know that
the file splot.log in your working directory has saved a log of your work.
8. If you are unhappy with the EW you measured, you can try again by
specifying the exact bounds of the continuum and the line profile. Move
your cursor to the continuum on the left side of the line and press k. Move
your cursor to the right side of the line and press g for a Gaussian fit, l
for a Lorentzian fit, or v for a Voigt fit.
9. Record the EW in your line list. The units are mÅ. The EW should
occupy character spaces 61-70. For example:
Get a model atmosphere
Usually, you would compute the effective temperature (Teff ), the surface gravity (log g), and the microturbulent velocity (ξ) through excitation equilibrium,
ionization balance, and removing any trend of abundance vs. EW. For the purposes of this exercise, I will just tell you that the parameters for HD122563 are
Teff = 4666 K, log g = 1.36, and ξ = 2.48 km/s. In computing a model atmosphere, you will also need a best guess at metallicity ([Fe/H]). A good guess for
this star is [Fe/H] = −2.88.
I have already generated an ATLAS9 model atmosphere by interpolated
between the grid points computed by Castelli & Kurucz (2004, arXiv:astroph/0405087). You can download it from the course website: HD122563.atm.
If you’re ambitious, you can try browsing through the grids of model atmospheres at Be warned that the file
formats aren’t exactly user friendly. Alternatively, you can play with MARCS
model atmospheres:
Compute abundances with MOOG
First, you need to install MOOG:
1. Download the 2014 version of MOOG:
2. Make a new directory, and un-tar the file there.
3. Look through the first dozen or so lines of Moog.f and change the path
names to match your computer.
4. Edit the variables X11LIB, SMLIB, and (for Mac users) AQLIB in the
Makefile for your system (e.g., Makefile.maclap).
• You’re looking for the libraries libX11.a, libplotsub.a, libdevices.a,
libutils.a, and (for Mac users) libaquaterm.a.
• If you don’t have libplotsub.a, libdevices.a, and libutils.a, you can
find them at /usr/local/lib/ on the Caltech astro network.
5. make -f Makefile.XXX where XXX is your machine’s architecture.
6. If you can’t get this to work, then the 2010 version of MOOG is installed
on the astro network: /usr/local/optical/moog/MOOG
In order to run MOOG, you need a parameter file. You can download an
example here: HD122563.par.
Note that the first line of the parameter file is abfind. MOOG uses “drivers,”
of which abfind is one. This driver tells MOOG to “find abundances.” MOOG
can be run with other drivers. For example, blends tells MOOG to find the
abundance of a line that is blended with other lines. In the next section, I will
introduce the synth driver.
Check the parameter file to make sure that its file naming conventions agree
with yours. In particular, make sure that model in is the name of your model
atmosphere and lines in is the name of your line list.
Keep all of your HD122563 files (parameter file, model atmosphere, and
line list) in one directory. Run MOOG in that directory by typing MOOG. If
it’s not in your path, then you will need to enter the full path name, e.g.,
/usr/local/optical/moog/MOOG. MOOG will ask you for your parameter file.
Tell it: HD122563.par.
After showing you a bunch of information, including the abundances, MOOG
will return you to the command line. You will have two new files in your
directory. The standard out file, called HD122563.out1 in my parameter file,
contains a whole bunch of information. We can go over that in class. The
summary out file, called HD122563.out2 in my parameter file, summarizes the
Calculate the [X/Fe] ratio
For the element X that you chose, compute the ratio [X/Fe]. If you did not calculate [Fe/H] yourself, then you can use [Fe/H] = −2.88. E-mail me ([email protected])
the abundance ratio that you found by Sunday, March 1. I will compile everyone’s measurements so that we can compare the abundances in HD122563 to
other stars in the Milky Way’s stellar halo.
Spectral synthesis
If you run MOOG with the synth driver, then you will make a synthetic spectrum. This is useful for modeling lines with unusual shapes, such as lines with
large isotopic splitting. It is also useful for modeling crowded spectral regions,
such as the G band of absorption caused by the CH molecule.
Download CH.par and CH.list. Have a look at CH.par. Notice that the first
line tells MOOG to use the synth driver. Also notice the synlimits parameters.
The first two numbers (4100.000 and 4500.000) are the minimum and maximum
wavelengths to synthesize. The next number (0.02) is the wavelength step size
in Å. The last number (1.00) tells MOOG to consider lines within 1.00 Å of the
current wavelength in the flux computation.
Run MOOG using this parameter file. The summary out file, called CH.out2
in my parameter file, is a list of all of the flux decrements at every wavelength
step. The flux decrement is 1 − f , where f is the flux normalized such that
the continuum is f = 1. You may notice a lot of very small negative numbers.
These are just rounding errors in MOOG.
You can write your own code to read this file, or you can download my IDL
code: read moog You can use it as follows: data = read moog spec(’CH.out2’,
/newmoog), where the newmoog flag distinguishes the 2010-and-later versions of
MOOG from earlier versions. The variable data is a structure, which you can
view by typing help, data, /str. The relevant tags are LAMBDA and SPEC.
You can view the spectrum by typing, e.g., splot, data.lambda, data.spec.
See how good of a match the synthetic spectrum is to the observed spectrum
by overplotting them. Remember to correct the observed spectrum for the
Doppler shift.
Explore the bottom of the HD122563.atm file to get a sense of how to change
the abundances of elements in the spectral synthesis. Here’s a hint: the numbers listed under NATOMS are atomic number and abundance expressed as 12 +
log(n(X)/n(H)). The atomic number of C is 6, and its abundance in the sun is
8.43. Remember that this is a metal-poor star, so its C abundance will be about
3 orders of magnitude less than in the sun. Re-synthesize the spectrum with a
different C abundance to see how it changes. Documentation on the MOOG parameter file is available here:
Explore another star
If you’re interested, play with a different metal-poor abundance standard, HD115444.
You can find all of the necessary files at the course website:
The radial velocity of HD115444 is vr = −25.80 km/s.