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 ofLineCenterErrin 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 byLineCenterErrin unit of km/s.The line center parameter in the posterior sample is defined as
\[x_v = {\rm LineCenterOffset / LineCenterErr}\]A positive \(x_v\) means an increase of the line velocity, namely, a redshift of the line center. A negative \(x_v\) means the opposite, namely, a blueshift of the line center. The line center offset in unit of km/s can be calculated by multiplying \(x_v\) with
LineCenterErr.