Using HELIOS-K

Before HELIOS-K can be used, the molecular or atomic line-lists must be downloaded and pre-processed. HELIOS-K provides some scripts for that, which are described in the previous section.

All necessary parameters for HELIOS-K are set in the file param.dat, which is described next. Some parameters can also be set by console arguments.

HELIOS-K can be started with

./heliosk

followed by optional console arguments, which are listed later.

HELIOS-K Input parameters

The input parameters can be specified in the param.dat file. The used parameters are listed here, the order can not be changed.

  • name: This name will appear in the output filenames.

  • T: Temperature in Kelvin

  • P: Pressure in Atmospheres

  • PFile: A ‘-‘ ignores this option, otherwise this option specifies a filename which contains multiple values for P.

  • Species Name: The name of the molecular or atomic param file. e.g. 01_hit16 or 1H2-16O__BT2.

  • SpeciesFile: A ‘-‘ ignores this option, otherwise this option specifies a filename which contains multiple species for gas mixtures.

  • ciaSystem: A ‘-‘ ignores this option, otherwise a cia system is read here. supported are H2-H2, H2-H2_eq, H2_H2_norm, H2-He, H2-He_eq, H2-He_norm, H2-CH4_eq, H2-CH4_norm and H2-H.

  • pathToData: The location where the HITRAN or HITEMP data files are located, e.g. pathToData = ../HITEMP/ , pathToData = /data/HITEMP/ or empty when the files are in the same directory pathToData =

  • numin: minimum wavenumber in 1/cm

  • numax: maximum wavenumber in 1/cm

  • dnu: spatial resolution in wavenumber in 1/cm

  • Nnu per bin: The number of points in wavenumbers nu per bin.

    • 0; Nnu is ignored and dnu is used

    • otherwise, dnu is overwritten.

  • cutMode: Set the voigt profile cutting mode:

    • 0: cut at absolute wavenumbers

    • 1: cut at multiple values of Lorentz half widths

    • 2: cut at multiple values of Doppler half widths

  • cut: value where to cut the line wings, according to the cutMode, if cut = 0, then no cutting is performed.

  • doResampling:

    • 0: no resampling is done.

    • 1: all the sorted opacity functions per bin are resampled with a Chebyshev polynomial, and the coefficients from all bins are written to the file Out_<name>_cbin.dat.

    • 2: all the sorted opacity functions per bin are resampled with a Chebyshev

polynomial, and the coefficients from each bin are written to a sepparate file Out_<name>_cbin<bin_number>.dat.

  • nC: Number of Chebyshev coefficients use for the resampling.

  • doTransmission: Compute the transmission function tau for a set of column masses m.

    • 0: no transmission function is calculated.

    • 1: the transmission function per bin is calculated, and all bins are written to the file Out_<name>_tr.dat.

    • 2: the transmission function per bin is calculated, and each bin is written to a sepparate file Out_<name>_tr<bin_number>.dat.

  • nTr: nummber of points used for the transmission function.

  • dTr: spacing of the points used for the transmission function in exp space: m_i = exp((i - nTr/2) * dTr)

  • doStoreFullK:

    • 0: the opacity functions is not written to a file.

    • 1: the full unsorted opacity function is written to the text file Out_<name>.dat.

    • 2: the full unsorted opacity function is written to the binary file Out_<name>.bin.

    • -1: the opacity functions is not calculated, but read in from a text file. The name of the file is specified in the next argument.

    • -2: the opacity function is nor calculated, but read in from a binary file. The name of the file is specified in the next argument.

  • pathToK: path and filename to read in an opacity function. When left blank, then no file is read in.

  • doStoreSK:

    • 0: the resampled opacity function is not written to a file.

    • 1: all bins from the resampled opacity function are written to the same file Out_<name>_bin.dat.

    • 2: all bins from the resampled opacity function are written to a sepparate file with names Out_<name>_bin<bin_number>.dat.

  • nbins: number of bins

  • binsfile: A ‘-‘ ignores this option, otherwise this option specifies a filename which contains the edges of the bins, which can be irregular. This option overrides the numin, numax and nbins arguments.

  • OutputEdgesFile: A ‘-‘ ignores this option, otherwise this option specifies a file name which contains the edges of the output locations in y for each bin.

  • kmin: minimal value for the opacity function

  • qalphaL: q value in the Lorentzian half width q = Pself / P

  • gammaF: scaling factor for the Lorentzian half width gamma factor, gamma = gamma * gammaF

  • doMean:

    • 0: nothing is done here.

    • 1: Calculate the Planck and Rosseland opacity means.

  • Units: The units of the opacities.

    • 0: cm^2 / g,

    • 1: cm^2 / molecule

  • ReplaceFile:

    • 1: all existing output files are overwritten.

    • 0: the data is appended to the existing files.

  • profile:

    • 1: Voigt

    • 2: Lorentzian

    • 3: Gaussian

    • 4: Integrated Binned Gaussian

  • subLorentzianfile: A ‘-‘ ignores this option, otherwise this option specifies a file name which contains the chi factor parameters for sub-Lorentzian CO2 profiles.

  • removePlinth:

  • 0: nothing is done here

  • 1: the plinth (base) is removed from cutted line profiles

  • doTuning:

    • 0: nothing is done here

    • 1: use self tuning routines to specify the best kernel parameters.

Console Arguments

Instead of using the parameter file, some arguments can also be set by console arguments. The console arguments have the highest priority and are overwriting the arguments of the param.dat file. The options are:

  • -name <c>: name

  • -T <double> : T

  • -P <double> : P

  • -M <int> : Molecule Name

  • -path <c> : pathToData

  • -pathK <c> : pathToK

  • -numin <double> : numin

  • -numax <double> : numax

  • -dnu <double> : dnu

  • -cutM <int> : cutMode

  • -cut <double> : cut

  • -dR <int> : doResampling

  • -nC <int> : nC

  • -dT <int> : doTRansmission

  • -nTr <int> : nTr

  • -dTr <double> : dTr

  • -dSF <int> : doStoreFullK

  • -dSS <int> : doStoreSK

  • -nbins <int> : nbins

  • -kmin <double> : kmin

  • -dev <int> : Device number (For multiple GPU systems)

  • -q <double> : qalphaL

  • -gammaF <double> : gammaF

  • -Mean <int> : doMean

  • -tuning <int> : doTuning

where <c>is a string, <double> a floating point number, and <int>an integer.

Code parameters

The file define.h contains the physical parameters and some code parameters. After changing some entry here, the code needs to be recompiled. The code parameters are:

  • def_TOL: Tolerance parameter in the Voigt function. See Algorithm 916

  • def_nthmax: Maximum number of threads per kernel launch. In 2.0 GPUs it can not be larger than 32768.

  • def_nlmax: Maximum number of molecular lines per kernel launch. Setting a lower number prevents from a time-out on Desktop machines.

  • def_maxlines: Maximum number of lines stored on the GPU.

  • def_maxfiles: Maximum number of files per molecule.

  • def_NmaxSample: Maximum Number of resample coefficients for K(y)

When using a Desktop GPU running an x session, the runtime of a single kernel launch can be limited to a few seconds. Choosing smaller values for nlmax and nthmax splits the kernel into smaller parts. But it makes the code a bit slower.