(Generated on Fri Feb 19 2016 13:25:10 by 1.8.9.1)
Usage

The HEPfit installer generates the library "libHEPfit.a" along with header files including a combined header file, HEPfit.h. To perform a Bayesian statistical analysis with the Markov Chain Monte Carlo [Library mode with MCMC] one can use the given example implementation. Alternatively, one can use the library to obtain predictions of observables for a given point in the parameter space of the model, allowing our computational tool to be called from the user's own program [Library mode without MCMC].

## Monte Carlo mode

The Monte Carlo analysis is performed with the BAT library. First, a text configuration file containing a list of model parameters, model flags and observables to be analyzed has to be prepared. Another configuration file for the Monte Carlo run has to be prepared, too.

### Step 1: Model configuration file:

A configuration file for model parameters, model flags and observables are written as follows:

1 StandardModel
2 # Model parameters:
3 ModelParameter mtop 173.2 0.9 0.
4 ModelParameter mHl 125.6 0.3 0.
5 ...
6 CorrelatedGaussianParameters V1_lattice 2
7 ModelParameter a_0V 0.496 0.067 0.
8 ModelParameter a_1V -2.03 0.92 0.
9 1.00 0.86
10 0.86 1.00
11
12 <All the model parameters have to be listed here>
13
14 # Observables:
15 Observable Mw Mw M_{W} 80.3290 80.4064 MCMC weight 80.385 0.015 0.
16 Observable GammaW GammaW #Gamma_{W} 2.08569 2.09249 MCMC weight 2.085 0.042 0.
17 #
18 # Correlated observables:
19 CorrelatedGaussianObservables Zpole2 7
20 Observable Alepton Alepton A_{l} 0.143568 0.151850 MCMC weight 0.1513 0.0021 0.
21 Observable Rbottom Rbottom R_{b} 0.215602 0.215958 MCMC weight 0.21629 0.00066 0.
22 Observable Rcharm Rcharm R_{c} 0.172143 0.172334 MCMC weight 0.1721 0.0030 0.
23 Observable AFBbottom AFBbottom A_{FB}^{b} 0.100604 0.106484 MCMC weight 0.0992 0.0016 0.
24 Observable AFBcharm AFBcharm A_{FB}^{c} 0.071750 0.076305 MCMC weight 0.0707 0.0035 0.
25 Observable Abottom Abottom A_{b} 0.934320 0.935007 MCMC weight 0.923 0.020 0.
26 Observable Acharm Acharm A_{c} 0.666374 0.670015 MCMC weight 0.670 0.027 0.
27 1.00 0.00 0.00 0.00 0.00 0.09 0.05
28 0.00 1.00 -0.18 -0.10 0.07 -0.08 0.04
29 0.00 -0.18 1.00 0.04 -0.06 0.04 -0.06
30 0.00 -0.10 0.04 1.00 0.15 0.06 0.01
31 0.00 0.07 -0.06 0.15 1.00 -0.02 0.04
32 0.09 -0.08 0.04 0.06 -0.02 1.00 0.11
33 0.05 0.04 -0.06 0.01 0.04 0.11 1.00
34 #
35 # Output correlations:
36 Observable2D MwvsGammaW Mw M_{W} 80.3290 80.4064 noMCMC noweight GammaW #Gamma_{W} 2.08569 2.09249
37 ...
38 Observable2D Bd_Bsbar_mumu noMCMC noweight
39 Observable BR_Bdmumu BR(B_{d}#rightarrow#mu#mu) 1. -1. 1.05e-10 0. 0.
40 Observable BRbar_Bsmumu BR(B_{s}#rightarrow#mu#mu) 1. -1. 3.65e-9 0. 0.
41 ...
42 Observable2D S5_P5 noMCMC noweight
43 BinnedObservable S_5 S_5 1. -1. 0. 0. 0. 4. 6.
44 BinnedObservable P_5 P_5 1. -1. 0. 0. 0. 4. 6.
45 #
46 # Including other configuration files
47 IncludeFile Flavour.conf

where the lines beginning with '#' are commented out.

Each line has to be written as follows:

1. The first line must be the name of the model to be analyzed, where the available models are listed in the page Models.

2. A model parameter is given in the format:

ModelParameter <name> <central value> <Gaussian error> <flat error>

where all the parameters in a given model (see Models) have to be listed in the configuration file.

3. A set of correlated model parameter is specified with "CorrelatedGaussianParameters name Npar" which initializes a set of Npars correlated parameters. It must be followed by exactly Npar Parameter lines and then by Npar lines of Npar numbers for the correlation matrix. See the above example.
4. Optionally, one can set a model flag in the format:

ModelFlag <name> <value>

where the available flags for a given model can be found in the page Models.

5. An observable to be computed is specified in one of the following formats:

Observable <name> <obs label> <histolabel> <min> <max> (no)MCMC (no)weight <central value> <Gaussian error> <flat error>
Observable <name> <obs label> <histolabel> <min> <max> (no)MCMC file <filename> <histoname>
Observable <name> <obs label> <histolabel> <min> <max> noMCMC noweight

• <name> is user given name for different observables which must be unique for each observable
• <obs label> is the theory label of the observable (see Models).
• <histolabel> is used for the label of the output ROOT histogram, while <min> and <max> represent the range of the histogram.
• (no)MCMC is the flag specifying whether the observable should be included in the Monte Carlo prerun or not
• (no)weight specifies if the observable weight will be computed or not. If weigh is specified with noMCMC then the weight of the observable will be stored in the MCout*.root file
• Experimental data is specified as central value Gaussian error flat error. If weight is specified both the errors cannot be 0.
• A histogram in a ROOT file is specifed by the name of the root file (filename) and then the name of the histogram (histoname).

6. Correlations among the data of observables can be taken into account with the line "CorrelatedGaussianObservables name Nobs", which initializes a set of Nobs correlated observables. It must be followed by exactly Nobs Observable lines and then by Nobs lines of Nobs numbers for the correlation matrix. See the above example. One can use the keyword noMCMC and noweight, instead of MCMC and weight.

7. A correlation between two observables can be obtained with:

Observable2D <name> <obs1 label> <histolabel1> <min1> <max1> noMCMC noweight <obs2 label> <histolabel2> <min2> <max2>
Observable2D <name> <obs1 label> <histolabel1> <min1> <max1> MCMC file <filename> <histoname> <obs2 label> <histolabel2> <min2> <max2>
or
Observable2D <name> (no)MCMC (no)weight
(Binned)Observable <obs label 1> <histolabel 1> <min> <max> <central value> <Gaussian error> <flat error> (<bin_min> <bin_max>)
(Binned)Observable <obs label 2> <histolabel 2> <min> <max> <central value> <Gaussian error> <flat error> (<bin_min> <bin_max>)
Observable2D <name> MCMC file filename histoname
(Binned)Observable <obs label 1> <histolabel 1> <min> <max> (<bin_min> <bin_max>)
(Binned)Observable <obs label 2> <histolabel 2> <min> <max> (<bin_min> <bin_max>)

8. Include configuration files with the IncludeFile directive. This is useful if one wants to separate the input configurations for better organization and flexibility.

### Step 2: Monte Carlo configuration file:

The parameters and options of the Monte Carlo run are specified in a configuration file, separate from the one for model parameters, etc. Each line in the file has a pair of a label and its value, separated by space(s) or tab(s). The available parameters and options are:

• NChains : The number of chains in the Monte Carlo run. A minimum of 5 is suggested (default). If the theory space is complicated and/or the number of parameters are large then more is necessary. The amount of statistics collected in the main run is proportional to the numbe rof chains.
• PrerunMaxIter : The maximum number of iterations that the prerun will go through (default: 1000000). The prerun ends automatically when the chains converge (R < 1.1) and all efficiencies are adjusted. While it is not necessary for the prerun to converge for a run to be successful, one should exercise caution in this case.
• Iterations : The number of iterations in the main run. This run is for the purpose of collecting statistics and is at the users discretion. (default: 100000)
• Seed : The seed can be fixed for deterministic runs.
• PrintAllMarginalized : All marginalized distributions will be printed in a pdf file (MonteCarlo_plots_*.pdf).
• PrintCorrelationMatrix : The parametric corellation will be printer in ParamCorrelations*.pdf and ParamCorrelations*.tex.
• PrintKnowledgeUpdatePlots : A comparison between prior and posterior knowledge will be printed in a plot stored in ParamUpdate*.pdf.
• PrintParameterPlot : As summary of the paramters will be printed in ParamSummary*.pdf.
• OrderParameters : This determines whether the parameters will be randomized one at a time or as a whole set in the entire run. While for quick estimates it is not necessary to order the prameters (false), it is suggested to do so for more accurate estimates.
• FindModeWithMinuit : To find global mode with MINUIT starting from the best fit parameters in the MCMC run.
• MinimumEfficiency : This allows the setting of the minimum eifficiency of all the prameters. The default is 0.15.
• WriteChain : The chains will be written in the root file MCout*.root. This can be used for analyzing the performance of the chains.
• CalculateNormalization : The normalization of the theory space will be calculated at the end of the Monte Carlo run. This is useful for model comparison.
• WritePreRunData : The prerun data is written to a file for rerun.
• ReadPreRunData : The prerun data will be read from a previously stored prerun file.

For example, a Monte Carlo configuration file is written as:

1 NChains 10 (Default: 5)
2 PrerunMaxIter 50000 (Default: 1000000)
3 Iterations 10000 (Default: 100000)
4 #Seed 1
5 PrintAllMarginalized true (Default: false)
6 PrintCorrelationMatrix true (Default: false)
7 PrintKnowledgeUpdatePlots false (Default: false)
8 PrintParameterPlot false (Default: false)
9 OrderParameters true (Default: true)

where a '#' can be placed at the beginning of each line to comment it out. These are the most commonly used settings. Some less commonly used settings:

1 FindModeWithMinuit (Default: false)
2 MinimumEfficiency (Default: 0.15, set to 0. - 1.)
3 WriteChain (Default: false)
4 CalculateNormalization (Default: false)
5 WritePreRunData (Mandatory: name of file)

## Library mode with MCMC

An example can be found in examples/MonteCarloMode

1 $cd examples/MonteCarloMode 2$ make

After making the configuration files, run with the command:

1 $analysis <model conf> <Monte Carlo conf> ### Alternative: Run with MPI. HEPfit allows for parallel processing of the MCMC run and the observable computations. To allow for this HEPfit and BAT has to be compiled with MPI support as explained in the Installation page. The command 1$ mpiexec -n N analysis <model conf> <Monte Carlo conf>

will launch analysis on N thread/cores/processors depending on the smallest processing unit of the hardware used. Our MPI implementation allows for runs on multi-threaded single processors as well as clusters with MPI support.

NOTE: Our MPI implementation of HEPfit cannot be used with BAT compiled with the --enable-parallelization option. It is mandatory to use the MPI patched version of BAT as explained in the Installation page.

### Output Files:

• log.txt: This is the log file.
• MCout.root: This is the root file containing all the information of the run and the histogram objects.
• MonteCarlo_results.txt: This file contains the fits to the parameters.
• MonteCarlo_plots.pdf: This File contains the histograms for the parameters.
• Observables: This directory will contain the histograms of all the observables specified in the config file.
• Observables/HistoLog.txt: This file contains the information on over-run and under-run of the histogram filling.
• Observables/Statistics.txt: This file contains the compilation of the statistics extracted from the histograms.

Other files might be generated depending on the options specified in the Monte Carlo configuration file.

## Single event mode

Using the model configuration file used in the Monte Carlo mode, one can obtain predictions of observabes for the central values of the model parameters with the command:

1 \$ analysis <model conf> --noMC

where the results are printed on the standard output.

## Library mode without MCMC

The library mode allows for access to all the observables implemented in HEPfit without a Monte Carlo run. The users can use one of our defined Models and vary ModelParameters according to their own algorithm and get the corresponding predictions for the observables.

• a combined library: libHEPfit.a (installed in HEPFIT_INSTALL_DIR/lib/
• a combined header file: HEPfit.h (installed in HEPFIT_INSTALL_DIR/include/HEPfit/)

The HEPfit library allows for two different implementations of the access algorithm.

### Non-Minimal Mode:

In the non-minimal mode the user can use the SomeModel.conf file to pass the default value of the model parameters. The following elements must be present in the user code to define the parameters and access the observable. (For details of model parameters, observables etc. please lookup Models.)

// Include the necessary header file.
#include <HEPfit.h>
// Define the model configuration file.
std::string ModelConf = "SomeModel.conf";
// Define a map for the observables.
std::map<std::string, double> DObs;
// Define a map for the parameters to be varied.
std::map<std::string, double> DPars;
// Initialize the observables to be returned.
DObs["Mw"] = 0;
DObs["GammaZ"] = 0.;
DObs["AFBbottom"] = 0.;
// Create and object of the class ComputeObservables.
ComputeObservables CO(ModelConf, DObs);
// Vary the parameters that need to be varied in the analysis.
DPars["Mz"] = 91.1875;
DPars["AlsMz"] = 0.1184;
// Get the map of observables with the parameter values defined above.
DObs = CO.compute(DPars);

### Minimal Mode:

In the minimal mode the user can use the default values in InputParameters header file to define the default values of the model parameters therefore not requiring any additional input files to be parsed. (For details of model name, flags, parameters, observables etc. please lookup Models.)

// Include the necessary header file.
#include <HEPfit.h>
// Define a map for the observables.
std::map<std::string, double> DObs;
// Define a map for the mandatory model parameters used during initializing a model.
std::map<std::string, double> DPars_IN;
// Define a map for the parameters to be varied.
std::map<std::string, double> DPars;
// Define a map for the model flags.
std::map<std::string, std::string> DFlags;
// Define the name of the model to be used.
std::string ModelName = "NPZbbbar";
// Create and object of the class InputParameters.
// Read a map for the mandatory model parameters. (Default values in InputParameters.h)
DPars_IN = IP.getInputParameters(ModelName);
// Change the default values of the mandatory model parameters if necessary.
// This can also be done with Dpars after creating an object of ComputeObservables
DPars_IN["mcharm"] = 1.3;
DPars_IN["mub"] = 4.2;
// Initialize the observables to be returned.
DObs["Mw"] = 0;
DObs["GammaZ"] = 0.;
DObs["AFBbottom"] = 0.;
// Initialize the model flags to be set.
DFlags["NPZbbbarLR"] = "TRUE";
// Create and object of the class ComputeObservables.
ComputeObservables CO(ModelName, DPars_IN, DObs);
// Set the flags for the model being used, if necessary.
CO.setFlags(DFlags);
// Vary the parameters that need to be varied in the analysis.
DPars["mtop"] = 170.0;
DPars["mHl"] = 126.0;
// Get the map of observables with the parameter values defined above.
DObs = CO.compute(DPars);

### Use of hepfit-config:

If 'make install' has been done, a hepfit-config script can be found in the HEPFIT_INSTALL_DIR/bin/ directory, which can be invoked with the following options:

1 Library and Library Path: hepfit-config --libs
2
3 Include Path: hepfit-config --cflags
4
5 Parameters List: hepfit-config --variable=parameters | sh

The last command lists all the mandatory parameters in all the models sorted alphabetically and their default values as set in the class InputParameters.