These instructions assume you've already worked through the downloading, compiling and testing steps documented on the Getting Started page. If that's the case, then read on to learn how to run GYRE!
Making a Place to Work
When starting a new project, it's a good idea to create a dedicated directory to contain the various input and output files GYRE operates on. These commands will make a new subdirectory with the name
cd $GYRE_DIR mkdir work
Grabbing a Stellar Model
The next step is to grab a stellar model which will form the basis for GYRE's calculation. There are a number of models provided beneath the
$GYRE_DIR/models subdirectory; the following commands will copy a model for a 5M☉ slowly pulsating B (SPB) star into the newly-created work area:
cp $GYRE_DIR/models/mesa/spb/spb.mesa $GYRE_DIR/work/
Creating a Namelist File
Now comes the fun part: creating an input file containing the various parameters which control a GYRE run. Using a text editor, create the file
$GYRE_DIR/work/gyre.in with the following contents:
&constants / &model model_type = 'EVOL' ! Obtain stellar structure from an evolutionary model file = 'spb.mesa' ! File name of the evolutionary model file_format = 'MESA' ! File format of the evolutionary model / &mode l = 2 ! Harmonic degree / &osc outer_bound = 'VACUUM' ! Use a zero-pressure outer mechanical boundary condition / &num diff_scheme = 'COLLOC_GL4' ! 4th-order collocation scheme for difference equations / &scan grid_type = 'INVERSE' ! Scan for modes using a uniform-in-period grid; best for g modes freq_min = 0.5 ! Minimum frequency to scan from freq_max = 1.0 ! Maximum frequency to scan to n_freq = 250 ! Number of frequency points in scan / &grid alpha_osc = 10 ! Ensure at least 10 points per wavelength in propagation regions alpha_exp = 2 ! Ensure at least 2 points per scale length in evanescent regions n_inner = 5 ! Ensure at least 5 points between center and inner turning point / &ad_output summary_file = 'summary.txt' ! File name for summary file summary_file_format = 'TXT' ! Format of summary file summary_item_list = 'M_star,R_star,l,n_pg,omega,E_norm' ! Items to appear in summary file mode_template = 'mode.%J.txt' ! File-name template for mode files mode_file_format = 'TXT' ! Format of mode files mode_item_list = 'l,n_pg,omega,x,xi_r,xi_h' ! Items to appear in mode files / &nad_output /
(The file doesn't have to be called
gyre.in, but that's the convention followed in this documentation.)
This file is an example of a Fortran ''namelist'' file, containing multiple namelist groups. Each group begins with the line
name is the name of the group); a list of name-value pairs follows, and the group ends with a slash
/. Detailed information on the namelist groups expected in GYRE's input files can be found here; for now, let's just focus on some of the more-important aspects of the file above:
constantsnamelist group is used to override constants such as the gravitational constant; here it's empty, indicating that default values should be used
modelnamelist group instructs GYRE to read an evolutionary model, in MESA format, from the file
modenamelist group instructs GYRE to consider quadrupole (ℓ=2) modes
oscnamelist group instructs GYRE to apply a zero-pressure outer mechanical boundary condition in the oscillation equations
scannamelist group instructs GYRE to scan a region of dimensionless angular frequency space typically occupied by gravity modes
gridnamelist group instructs GYRE to perform calculations on a refinement of the model grid (see Understanding Grids for details on how this works)
ad_outputnamelist group instructs GYRE to write out summary data to the file
summary.txt, and individual mode data to files having the prefix
nad_outputnamelist group is empty, telling GYRE not to write out any non-adiabatic data (see Non-adiabatic Calculations for more info)
Running the Code
With the hard work done, it's now trivial to run the code:
cd $GYRE_DIR/work ../bin/gyre gyre.in
As it runs (on multiple cores, if you have a multi-core machine; see here for more details), the code will print lots of data to the screen. Let's break down this output, chunk by chunk. First, GYRE prints out its version number, tells us (in OpenMP threads) how many cores it is running on, and indicates which file it is reading parameters from (here,
gyre [5.0] ---------- OpenMP Threads : 12 Input filename : gyre.in
Next, GYRE loads the stellar model from the file
spb.mesa. This model comprises 1814 points, and extends from the surface all the way to the center (which is why GYRE decides not to add a central point).
Model Init ---------- Reading from MESA file File name spb.mesa File version 1.00 Read 1814 points No need to add central point
Next, GYRE prepares to searching for modes with harmonic degree l=2 and azimuthal order m=0 (not specified in
gyre.in, but assumed by default), by setting up a frequency scan and a spatial (x) grid. The frequency scan specifies the frequencies at which GYRE samples the discriminant function D(omega), whose roots are the stellar eigenfrequencies (see Townsend & Teitler 2013); while the x grid specifies the spatial distribution of points used to discretize the oscillation equations.
Mode Search ----------- Mode parameters l : 2 m : 0 Building frequency scan added scan interval : 0.5000E+00 -> 0.1000E+01 (250 points, INVERSE) Building x grid Found inner turning points, x range 0.1041 -> 0.1048 Adding 0 inner point(s) Adding 21 global point(s) in iteration 1 Adding 0 global point(s) in iteration 2 Final grid has 1 segment(s) and 1835 point(s): Segment 1 : x range 0.0000 -> 1.0000 (1 -> 1835)
Next, GYRE attempts to bracket roots of the discriminant function by looking for changes in its sign:
Starting search (adiabatic) Root bracketing Time elapsed : 3.314 s
Finally, for each sign change found GYRE uses a root solver to converge to the eigenfrequency. Each row of output here corresponds to an eigenfrequency:
Root Solving l m n_pg n_p n_g Re(omega) Im(omega) chi n_iter 2 0 -16 0 16 0.51863442E+00 0.00000000E+00 0.2679E-13 6 2 0 -15 0 15 0.55636128E+00 0.00000000E+00 0.8611E-13 5 2 0 -14 0 14 0.59457157E+00 0.00000000E+00 0.6864E-14 7 2 0 -13 0 13 0.62301181E+00 0.00000000E+00 0.1796E-13 8 2 0 -12 0 12 0.67563541E+00 0.00000000E+00 0.8523E-13 6 2 0 -11 0 11 0.74334524E+00 0.00000000E+00 0.4626E-13 5 2 0 -10 0 10 0.79690725E+00 0.00000000E+00 0.3680E-12 6 2 0 -9 0 9 0.87153108E+00 0.00000000E+00 0.8141E-13 7 2 0 -8 0 8 0.99747127E+00 0.00000000E+00 0.2521E-13 7 Time elapsed : 0.580 s
The columns appearng are as follows:
l: harmonic degree
m: azimuthal order
n_pg: radial order (in the Eckart-Osaki-Scuflaire-Takata scheme)
n_p: acoustic-wave winding number
n_g: gravity-wave winding number
Re(omega): dimensionless eigenfrequency (real part)
Im(omega): dimensionless eigenfrequency (imaginary part; zero here because we've performed adiabatic calculations)
chi: convergence parameter
n_iter: number of iterations required for convergence
These values are printed to screen primarily to give an idea of GYRE's progress; more-detailed information about the modes found is given in the output files discussed below. Some things to watch out for:
- The convergence parameter
chi, defined as the ratio of discriminant values before and after the root finding, should small (on the order of 1E-9 to 1E-13). If it is significantly larger than this, the mode may not be properly converged; and if it is significantly smaller than this, there may be numerical issues with the discretization scheme.
- The number of iterations
n_itershould be moderate; values above 20 or so indicate that GYRE is having problems converging.
- The mode index
n_pgshould be monotonic-increasing. Departures from this behavior can happen for a number of reasons:
- Missing values can indicate that GYRE has skipped a mode in frequency space; the fix is to use a finer omega grid.
- Missing values together with duplicate and/or non-monotonic values can indicate that GYRE isn't resolving the spatial structure of eigenfunctions; the fix is to use a finer x grid.
- Missing values together with duplicate and/or non-monotonic values can also incdicate problems with the input stellar model --- for instance, incorrect values for the Brunt-Vaisala frequency across density discontinuities; the fix is to stop expecting GYRE to give sensible output when fed crap stellar models.
Interpreting Output Files
Overall properties of all modes found (eigenfrequencies, inertias, etc.) are collected together in the file
summary.txt. For each mode GYRE also writes a file with the name
mode.NNNNN.txt, containing data (eigenfrequency, eigenfunctions, etc.) specific to the mode. Here,
NNNNN denotes a 5-digit index which increments (starting at
00001) for each mode found. Note that this index bears no relation to the radial order
n_pg; it merely serves as a unique label for the modes.
Both the sumamry file and the mode files are text-based (it's possible to write HDF5-format files instead; see the Output Files page for details). Running
will print out the first 10 lines of the summary file, which should look something like this:
1 2 M_star R_star 0.9945999999999999E+034 0.3016908790335515E+012 1 2 3 4 5 l n_pg Re(omega) Im(omega) E_norm 2 -16 0.5186344189658061E+000 0.0000000000000000E+000 0.1083833699332999E-002 2 -15 0.5563612831705177E+000 0.0000000000000000E+000 0.1378396850031880E-002 2 -14 0.5945715662438735E+000 0.0000000000000000E+000 0.3226917642759320E-002 2 -13 0.6230118072964337E+000 0.0000000000000000E+000 0.3598212959967747E-002
The first three lines give column numbers, labels, and values for the scalar data — here, the stellar mass
M_star and radius
R_star, expressed in cgs units. The next two lines give column numbers and labels for the per-mode data (
E_norm is the normalized mode inertia, and the other columns are the same as described above for the screen output); the subsequent lines then give the corresponding values (one line per mode). The mode files have a similar layout, with scalar data followed by array data representing the eigenfunctions (one line per radial grid point).
The choice of which data appear in output files isn't hardwired, but rather determined by the
mode_item_list parameters of the
&nad_output namelist groups. Changing these parameters allows you to tailor the files to contain exactly the data you need. For a full list of possible items, consult the Output Files page.