A user's guide to CossamDoppler

CossamDoppler :

The free Zeeman Doppler mapping code

A user's guide to CossamDoppler (version 02-02-2017)

Step 1 : Downloading the code

CossamDoppler (binary executable file)

Note: In order to be able to execute CossamDoppler make sure that your system provides unlimited stacksize.
With the tcsh shell for example set "limit stacksize unlimited"

Step 2 : Getting the data files

You need a complete set of files from the CossamMulti run, e.g.

cospot_eps.01.7012470949
cospot_eps.02.7012470949
cospot_eps.03.7012470949
cospot_eps.04.7012470949
cospot_eps.05.7012470949
cospot_eps.06.7012470949
cospot_eps.07.7012470949
cospot_eps.08.7012470949
cospot_eps.09.7012470949
cospot_eps.10.7012470949
cospot_pprof_r01.7012470949
cospot_pprof_r02.7012470949
cospot_pprof_r03.7012470949
cospot_pprof_r04.7012470949
cospot_pprof_r05.7012470949
cospot_pprof_r06.7012470949
cospot_pprof_r07.7012470949
cospot_pprof_r08.7012470949
cospot_pprof_r09.7012470949
cospot_pprof_r10.7012470949
cossam_eps.7012470949
cossam_multi_run.7012470949 lines_run.7012365600sysom_ess.7012365600sysom_line.7012365600sysom_stream.7012365600 t8300_410_i.filgrev_sau.abund.Fe_0800grev_sau.abund.Fe_0825grev_sau.abund.Fe_0845grev_sau.abund.Fe_0865grev_sau.abund.Fe_0885grev_sau.abund.Fe_0905grev_sau.abund.Fe_0925grev_sau.abund.Fe_0945Fe_koch.list

Step 3 : Starting the inversion

The code is invoked by

./cossam_doppler input_file sysom_ess_extension profile_set_extension

input_file	sysom_ess_extension	profile_set_extension
Any arbitrary name, e.g. cossam_doppler.inp	the 10-digit ext. of the line data files created with Lines	the 10-digit ext. of the profile files created with CossamMulti

One can also start the iterations with a given abundance map. This is done by

./cossam_doppler input_file sysom_ess_extension profile_set_extension ham-file

./cossam_doppler cossam_doppler.inp 7012365600 7012470949 701247038_dir/dopimag_ham.701247038E

What you have to specify in the input file

Number of processors (cores)
Atmospheric model file

Polarised formal solver option

'Z'	Zeeman Feautrier solver (default)
'z'	Zeeman Feautrier solver without magneto-optical terms

Hydrogen option (must agree with the values given in 'sysom_ess_extension')
Cossam checks for contradictions. You may only exchange 'h' for 'H' and vice versa

'h' or 'H'	Hydrogen line profiles according to the analytical formula of Hubeny
'-'	No hydrogen lines considered

Element file name

Finally there is the keyword MODELS (models), followed by the Oblique Rotator Model data -
for their definition see Stift, MNRAS 172, 133 (1975) - and the grid data

The inclination i    (in degrees)
The 3 Eulerian angles alpha, beta, gamma    (in degrees)
The decentring parameters y_2 and y_3   [-1 < y_2 < 1, -1 < y_3 < 1]

The dipole moment - half the polar field strength for a centred dipole (in Gauss)
The projected rotational velocity v sin i (in km/s)
The number of rings (permitted values are : 15, 18, 20, 24, 25, 30, 36, 40, 45, 50, 60, 72, 75, 90)

No. of rings	No. of surface elements
15	284
24	732
40	2034
90	10310

element        e.g. 26 (to map iron)
eps               the starting abundance
delta_eps     leave unchanged at 0.20
f_QU            weight of Stokes Q and U in the overall profile fit (zero when not used)
f_V               weight of Stokes V in the overall profile fit (zero when not used)
sigma          leave unchanged at 0.0005
weight         e.g. 0.9999 at the beginning to bring the rms scatter down
                    e.g. 0.95 when refining an almost converged run
step             up to some 0.80 at the beginning
                    maybe just 0.04 for final refinements
S/N              a S/N ratio of 20000 means virtually noise-free spectra

Step 4 : Understanding the output

CossamDoppler creates a sub-directory for the entire output. The results of the calculations are written

into 5 sets of files, e.g.

701247038_dir/cossam_doppler_run.7012470381        log file

701247038_dir/dopimag_res.7012470381               quality of the inversion

701247038_dir/dopimag_eps.701247038[*]             not really needed

701247038_dir/dopimag_ham.701247038[*]             needed for subsequent Hammer projection plots

701247038_dir/dopimag_pro.701247038[*]             "observed" and "theoretical" Stokes profiles

The final character [*] reflects the iteration number which goes from (A-Z)(a-z)(0-9) as specified below

Char : ARRAY (0..61) OF Character := "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789";

rainbow

Contents of the file sysom_ess.7012365600

ZS A KCIB
t8300_410_i.fil
Fe_koch.list
7012365600
8300.0 4.10 0.07834 0.00
7 54 54 103 526 72 4990.000 5410.000
12.000 12.000 12.000 12.000 12.000 12.000 12.000 12.000 12.000 12.000 12.000 ....
....

Contents of the file cossam_doppler.inp

                                :
Always start here               : !
                                :
No. of processors               : 32
Atmospheric model               : t8300_410_i.fil
Formal solver option            : Z
Hydrogen option                 : -
Element file                    : grev_sau.abund.Fe_0800
                                : MODELS
Incl Alp Bet Gam y_2 y_3   : 60.0   -90.0   90.0   90.0   0.00   0.00
Dipole_moment Vrot No_rings   : 1250.0 40.0   60
Element Eps Delta_eps f_QU f_V : 26   8.00 0.20 0.0 0.0
Sigma     weight   step   S/N   : 0.0005   0.995 0.08   20000.0

Contents of the file 701247038_dir/dopimag_res.7012470381

the iteration where the rms scatter reaches its minimum is marked in red

Number of grid points     :   4584
Sum(epsilon)              :    8.821E+11
Entropy                   :    7.999E+00
Minimum field strength    :     1250.0
Maximum field strength    :     2498.7
Maximum absolute velocity :     39.97
Epsilon_total Entropy_total Chi_square_total :        8.8209E+11      7.999018E+00      1.316981E-03      3.999509E-02
Epsilon_total Entropy_total Chi_square_total :        8.9807E+11      7.973456E+00      1.188258E-03      7.923539E-01
Epsilon_total Entropy_total Chi_square_total :        8.9564E+11      7.963609E+00      1.109270E-03      1.259860E+00
Epsilon_total Entropy_total Chi_square_total :        9.1902E+11      7.941794E+00      1.053339E-03      1.576061E+00
Epsilon_total Entropy_total Chi_square_total :        8.9199E+11      7.948511E+00      1.110205E-03      1.239113E+00
Epsilon_total Entropy_total Chi_square_total :        9.1925E+11      7.936118E+00      9.965521E-04      1.913569E+00
Epsilon_total Entropy_total Chi_square_total :        9.0637E+11      7.944691E+00      1.006758E-03      1.860462E+00
Epsilon_total Entropy_total Chi_square_total :        9.0463E+11      7.951343E+00      1.048330E-03      1.615880E+00
Epsilon_total Entropy_total Chi_square_total :        8.9973E+11      7.961156E+00      1.109933E-03      1.253400E+00
Epsilon_total Entropy_total Chi_square_total :        8.9428E+11      7.971601E+00      1.179125E-03      8.456958E-01
Epsilon_total Entropy_total Chi_square_total :        8.8187E+11      7.991031E+00      1.307180E-03      9.123661E-02

Contents of the file 701247038_dir/dopimag_pro.701247038K

For every phase wavelength, "observed" normalised Stokes IQUV and synthesised Stokes IQUV are listed

    1
    5005.000 0.9967 0.0007 0.0001 0.0010 0.9963 0.0007 0.0001 0.0011
    5005.050 0.9897 0.0007 0.0002 0.0030 0.9893 0.0007 0.0002 0.0030
    5005.100 0.9783 0.0003 0.0003 0.0049 0.9779 0.0003 0.0003 0.0048
    5005.150 0.9662 0.0007 0.0003 0.0051 0.9658 0.0007 0.0003 0.0050
    ....
    5243.050 0.9789 0.0003 -0.0003 0.0022 0.9791 0.0003 -0.0003 0.0021
    5243.100 0.9843 0.0006 -0.0005 0.0026 0.9843 0.0006 -0.0005 0.0026
    5243.150 0.9913 0.0003 -0.0003 0.0023 0.9913 0.0003 -0.0003 0.0023
    5243.200 0.9974 0.0006 -0.0001 0.0009 0.9973 0.0006 -0.0001 0.0009
    2
    5005.000 0.9972 0.0009 -0.0002 0.0003 0.9970 0.0009 -0.0002 0.0004
    5005.050 0.9900 0.0014 -0.0001 0.0019 0.9898 0.0014 -0.0001 0.0020
    5005.100 0.9782 0.0011 0.0001 0.0038 0.9780 0.0011 0.0001 0.0038
    5005.150 0.9654 0.0016 0.0000 0.0049 0.9653 0.0016 0.0000 0.0049
    ....
    5243.050 0.9783 0.0001 0.0003 0.0019 0.9797 0.0001 0.0003 0.0014
    5243.100 0.9851 0.0000 -0.0000 0.0022 0.9852 0.0000 -0.0001 0.0021
    5243.150 0.9918 -0.0001 -0.0001 0.0024 0.9918 -0.0001 -0.0001 0.0025
    5243.200 0.9976 0.0001 -0.0002 0.0011 0.9975 0.0001 -0.0002 0.0012
    3
    5005.000 0.9977 0.0002 -0.0003 -0.0005 0.9976 0.0002 -0.0003 -0.0005
    5005.050 0.9909 0.0012 -0.0007 -0.0006 0.9907 0.0012 -0.0007 -0.0006
    5005.100 0.9788 0.0016 -0.0005 0.0010 0.9787 0.0016 -0.0005 0.0009
    5005.150 0.9660 0.0020 -0.0007 0.0030 0.9660 0.0020 -0.0007 0.0030
    ....

The element file

The abundances in the element file are logarithmic with the abundance of hydrogen = 12.00). A complex example:

1 H   12.00    1.008 2   : -
2 He 10.93    4.00 3   : -
,,,,
11 Na   6.33   23.00 6   : -
12 Mg   7.58   24.32 6   : - Mg.koch
13 Al   6.47   26.97 6   : -
14 Si   7.55   28.06 6   : - 8.05
15 P    5.45   30.98 6   : -
....
19 K    5.12   39.10 5   : -
20 Ca   6.36   40.08 5   : - 6.00
21 Sc   3.17   45.10 5   : -
22 Ti   5.02   47.90 5   : -
23 V    4.00   50.95 5   : -
24 Cr   5.67   52.01 5   : - Cr.koch
25 Mn   5.39   54.93 5   : -
26 Fe   7.50   55.85 5   : - Fe.koch
27 Co   4.92   58.94 5   : -
....

All elements are listed with:
atomic number, element symbol, solar abundance, atomic weight,
number of ionisation stages considered.

To specify a different constant abundance over optical depth,
enter the new value after the '-' (preceded by a blank).

To specify a different non-constant abundance over optical depth,
enter the name of a file after the '-' (preceded by a blank).
The file must contain an abundance value for each optical depth.

There must be no blanks following the '-' or the new abundances

The atmospheric model file

The input file for a Kurucz model with T_eff = 8300 K, log_g = 4.10 and 72 depth points look as follows

72
8300.0 4.10 0.07834
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
1.7194E-03 5.0123E-06 0.9299 -1.2300 1.3353 26.2146 ....
2.1170E-03 6.2391E-06 0.9231 -1.1351 1.4257 26.1666 ....
2.5564E-03 7.7462E-06 0.9174 -1.0522 1.5076 26.1224 ....
3.0430E-03 9.6017E-06 0.9113 -0.9697 1.5832 26.0747 ....
3.5796E-03 1.1888E-05 0.9052 -0.8896 1.6538 26.0257 ....
4.1702E-03 1.4710E-05 0.8990 -0.8113 1.7201 25.9756 ....
4.8196E-03 1.8195E-05 0.8929 -0.7348 1.7829 25.9247 ....
5.5333E-03 2.2504E-05 0.8867 -0.6598 1.8429 25.8733 ....
6.3176E-03 2.7836E-05 0.8806 -0.5862 1.9005 25.8216 ....
......

M_dep
T_eff, log_g, He

rho_x, tau, theta,
log_pe, log_pg,
log_k ....

M_dep

T_eff
log_g
He
rho_x
tau
theta
log_pe
log_pg
log_k

Number of depth points
M_dep must be negative if there are no columns with H and He number densities
M_dep must be positive if there are these columns
effective temperature
logarithm of gravity
He abundance (by number)
column mass
optical depth at 5000 A
reciprocal temperature 5040 / T
logarithm of electron pressure
logarithm of gas pressure
scaled logarithm of continuous opacity at 5000 A

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