************** Parameter File ************** ``brains`` reads a parameter file to configure its running. A typical parameter file looks like:: % parameter file % lines beginning with '%' are regarded as comments and are neglected % FileDir /home/liyropt/Projects/GIT/BRAINS % directory for where all the output files are stored FlagDim 2 % -2, generate fully random lc; -1, mock lc based on input data; % 0, only continuum modeling; 1, 1d line RM; 2, 2d line RM Redshift 0.0449 % redshift of the object FlagBLRModel 6 % 1, 2, 3, 4, 5, 6, 7, 8; BLR model type % 5 is double power-law model; 6 is Pancoast's model; 7 is two-zone model % 0 is user defined % -1 is user defined, analytical transfer function LineCenter 4861.0 % rest frame, A FlagLineCenter 0 % -1, epoch-dependent offset; 0, not included; 1, uniform offset LineCenterErr 50.0 % km/s %======================================================================== % data file ContinuumFile data/mrk142_con.txt % file for continuum data LineFile data/mrk142_hb.txt % file for line data Line2DFile data/mrk142_hb2d.txt % file for line 2d data %======================================================================== % reconstruction NConRecon 200 % number of points for continuum reconstruction FlagTrend 0 % 0, mean; 1, first-order trend FlagTrendDiff 0 % 0, no difference; 1 or larger, add difference in the long-term trends between continuum and line % the different trend is modelled by a polynomical with the order set by the value of FlagTrendDiff. ConConstructFileOut data/pcon.txt % output filename for continuum reconstruction FlagFixVar 0 % 0, not fixed; 1, fix the parameters of variation from continuum data. NLineRecon 100 % number of points for line reconstruction along time axis LineConstructFileOut data/pline.txt % output filename for 1d line reconstruction TranFileOut data/tran.txt % output filename for 1d transfer function NVelRecon 42 % number of points for line reconstruction along velocity axis Line2DConstructFileOut data/pline2d.txt % output filename for 2d line reconstrction Line2DDataConstructFileOut data/pline2d_data.txt % output filename for 2d transfer function at points same with data Tran2DFileOut data/tran2d.txt % output filename for 2d transfer function Tran2DDataFileOut data/tran2d_data.txt % output filename for 2d transfer function at velocity points same with data NCloudPerCore 5000 % number of clouds per task NVPerCloud 5 % number of velocities per cloud NTau 200 % number of time-lag points calculated in transfer function RCloudMax -1 % outer edge of broad-line region in a unit of light-day; -1, set automatically TimeBack -1 % time prior to the start of continuum in reconstruction; -1, set automatically FlagCloudsOut 1 % 1, save clouds at the last run; 0, do not save CloudsFileOut data/clouds.txt % output filename for clouds %======================================================================== % FlagCloudsForceUpdate 0 % default 0; % 0, only update when BLR parameters are updated % 1, update every MCMC perturb (continuum + BLR) FlagConSysErr 0 % 0, not include systematic error of contininuum; 1, include FlagLineSysErr 0 % 0, not include systematic error of line; 1, include FlagNonlinear 1 % 0, linear response; 1, non-linear response %======================================================================== % spectral broadening FlagInstRes 1 % 0, uniform prior, epoch-independent % 1, uniform prior, but epoch-dependent parameterization % 2, epoch-dependent parameterization, prior stored in "InstResFile" InstRes 220 % instrument broadening (modeled by a Gaussian), in km/s, for FlagInstRes=0, or 1 % Gaussian standard deviation InstResErr 50.0 % instrument broadening error, in km/s, for FlagInstRes=0, or 1 InstResFile data/sim_broaden.txt % file for storing epoch-dependent instrument broadening % two columns: broadening width and error (km/s), in the order of time as the 2d line data %======================================================================== % narrow-line component % use a gaussian to model the narrow-line component FlagNarrowLine 0 % 0, no narrow line; % 1, add fixed narrow line; % 2, add Gaussian priors of the flux for narrow line; % 3, add logarithmic prior of the flux for narrow line FluxNarrowLine 1.5 % flux of narrow line FluxNarrowLineErr 0.50 % flux error of narrow line WidthNarrowLine 93.0 % width km/s WidthNarrowLineErr 10.0 % width error ShiftNarrowLine 0.0 % shift, km/s, with respect to broad line center. ShiftNarrowLineErr 0.0 % shift error %======================================================================== % set fixed BLR parameters and their fixed values % do not put sapce in the strings % 1: fixed; 0: not fixed; % values are separated by ":" BLRParFix 0000000000 BLRParFixVal 2.0:1.0 .. note:: In the subdirectory ``example/``, some examples of parameter file are provided. Users can choose appropriate parameter files with their purposes. The meaning of most parameters are self-explanatory from their names and comments. Some parameters are explained as follows: - ``FlagLineCenter``: whether to include the line center as a free parameter. If included, the line center is allowed to have an offset with respect to the input value (``FlagLineCenter`` =1) or an epoch-dependent offset (``FlagLineCenter`` =-1). If not included (``FlagLineCenter`` =0), the line center is fixed to the input value. - For ``FlagLineCenter`` =1, the line center offset for all epochs is the same. Its prior is Gaussian with a standard deviation of ``LineCenterErr`` in unit of km/s. - For ``FlagLineCenter`` =-1, the line center offset is epoch-dependent. For each epoch, an independent Gaussian prior is used to model it. The standard deviation of the Gaussian distribution is also set by ``LineCenterErr`` in unit of km/s. - The line center parameter in the posterior sample is defined as .. math:: x_v = {\rm LineCenterOffset / LineCenterErr} A positive :math:`x_v` means an increase of the line velocity, namely, a redshift of the line center. A negative :math:`x_v` means the opposite, namely, a blueshift of the line center. The line center offset in unit of km/s can be calculated by multiplying :math:`x_v` with ``LineCenterErr``.