Note, Marmoset1/bin should be added to your $PATH. For the most part, all executables should be run from a runDir directory. See the help files on workflow to learn how to perform an OSET analysis and use the exec in practice. Usage is displayed for all scripts by typing the executable name and pressing enter.

The list here is probably outdated.

None of the files in the Marmoset directory should be modified by the user (unless you know what you are doing).

• Marmoset/Marmoset : contains c++ .h header files included in .cpp files
• Marmoset/src : contains .cpp files, modified pythia .f files. Executables do not belong here.
• Marmoset/utilities : contains .cpp executables and modified HPGS running exec generate_mc.f
• Marmoset/scripts : contains all exec scripts used in the Marmoset workflow
• Marmoset/runDir : contains the template working directory used for OSET construction. This should not be modified by the user; use makeRunDir instead.
• Marmoset/lib : libraries
• Marmoset/bin : contains exec copied by Makefile after compilation

• generate_mc : Fortran based MC generation exec. This operates with the same syntax that olympicsH in HPGS uses. This exec takes pythia inputs, generates mc using pythia, passes the stdhep through HPGS (with triggers), and then return a .lhco file (default format for HPGS). generate_mc is the basic exec used for mc generation!

• generate_interactive_tree : C++ exec that generates mc for a specific process specified in an interactive mode. The input is a model.dat file that defines the OSET. NOT FUNCTIONAL NOW
• generate_meta_files : C++ exec that creates a list of tree strings and a coefficient lookup table for a given OSET model. The input is a model.dat file defining the OSET and it places files in meta/
• parse_meta_files : C++ exec that converts meta/* files into pythia input files. This exec is designed to be run after generate_meta_files and used its output for input. Requires stem names as input.

• match_rates : C++ exec for fitting. Currently, the default is to use a chi-square. Takes as input a meta/metaFileStem, a sigs/sigFileStem, sigs/targetSigFile and analysis/analysisFileStem. See fitOSET_C documentation.

• doAll : tcsh exec used to enter interactive mode, specify a process using a .dat file, generate MC, and then make analysis plots using procPlot. This script calls generate_interactive_tree, generate_mc, and procPlot
• compareProc : tcsh exec used to compare a Marmoset process to a pythia process. This is usefule for matrix element analysis. The Marmoset process is specified in interactive mode. The pythis process is specified in a .par file. MC is generated and comparison plots are made. This script calls generate_interactive_tree, generate_mc, and procPlot

• convertPar2Card : sh exec that looks for .par files in input/ and makes the required pythia input needed by generate_mc.
• buildMC : sniffs for .card and .proc files in input/ and generates some number of events specified in the input. This exec needs to be integrated out of Marmoset but is currently useful for .par based mc generation.

• genProcFiles : tcsh exec used to generate the pythia input files for an OSET. First step of MC generation workflow. This script calls generate_meta_files, parse_meta_files

• prepMCJobs : perl exec used to prepare pythia input files for an MC run. This should be called before every MC run.
• generateMCBatch : perl exec for generating MC. This script calls generate_mc and controls file I/O.
• cafGenerateMC : perl exec for generating MC on the caf. Uses the input/*.mcindex file creted by prepMCJobs. This script calls generateMCBatch

• buildSigFile : sh exec that makes a single .raw file placed in the sigs directory. Takes as input a single .lhco.gz file. This exec calls runSigs in MPotato
• buildFitSigs : sh exec that makes .raw files placed in the sigs directory for every .lhco.gz in mc/ This script call buildSigFile on all .lhco files in mc/
• buildBkgSubSigFile : tcsh exec that makes a .raw file consisting of pseudodata-bkg with appropriate errors. This exec calls runBkgSubSigs in MPotato.

• fitOSET : tcsh exec that controls the C++ fitting. See documentation on fitOSET. This script calls match_br, and weightProcesses

• cutMCFile : sh exec that takes in a .lhco.gz file, applies cuts specified in a mycuts.dat file and writes out a .lhco.gz file with events that pass the cuts. This exec uses cutEvents in MPotato.
• sleuthToTrigger : perl exec that takes a scriptPs.txt file from sleuth and sets up a mycuts.dat file picking out the channels that sleuth finds interesting above some threshold. This exec is based on MPotato functionality…

• procPlot : Basic script for plotting taking as input two .lhco.gz files. This calls runSigs and plotCompare in MPotato.

• makePlot : Basic script for plotting taking as inptu -one- .lhco.gz file This calls runSigs and makePlot in MPotato.
• bkgComparePlot : sh exec that takes a bkg.lhco.gz and pseudodata.lhco.gz file and makes plots that overlay bkg with pseudodata and show the subtraction plots with errors (in an inset). This calls runSigs and bkgCompare in MPotato.
• hypComparePlot : sh exec that takes a bkg.lhco.gz, pseudodata.lhco.gz, and hypothesis.lhco.gz and makes plots that overlay the hyp.lhcp.gz with pseudodata-bkg. This calls runSigs and hypCompare in MPotato.
• weightProcesses : Basic script for plotting using a .wt file to create a .lhco.gz for comparison against a target. This script calls procPlot

• makeRunDir : Copies the template runDir to a dir with name and location of your choice.
• buildMaskFile : Makes a .mask file
• checkForRunDir : Checks that current dir has runDir structure.
• epsselect : makes .eps file from .ps output of procPlot
• initwt : makes an initial .wt file.

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