LHCb Research

Research measuring mass difference between D+ and Ds+ mesons. This repository includes all analysis files, including RDataFrames and the more standard MakeSelectors. Also included is the LHCb subdirectory, containing the Ganga scripts and DaVinci ntuple options used to collect the raw data.

Some relevant links:

• Precision measurement of D meson mass differences
• D+ → K−K+π+
• LHCb StarterKit Lessons

Data Collection

All of the necessary files for this step are stored in the /LHCb/ subdirectory. This part of the tutorial assumes that you have a functioning grid certificate through CERN and are able to run Ganga jobs on DIRAC. This is covered in the LHCb StarterKit Lessons linked above. List of files in /LHCb/ and their purpose:

• dp_job.py: Ganga job to get D+ -> KKpi data.
  • dp_options.py: Options file for D+ -> KKpi data. Tells what variables to collect.
• dsp_job.py: Ganga job to get Ds+ -> KKpi data.
  • dsp_options.py: Options file for Ds+ -> KKpi data. Tells what variables to collect.
• symbols.py: Prints out particle symbols as interpreted by Ganga with some additional info.
• jobstatus.py: Prints out status of subjobs of a running job.
• ListLFNs.py: Saves the LFNs (output file locations) of a Ganga job to a .txt file.
• lfn_parse.py: File that is fairly unique to this decay and will almost certainly need to be revised if used again. It looks at the file produced by ListLFNs.py and extracts the important information and "chunks" it for data transfer purposes.
• getEvents.py: Not used in this analysis, but can collect some dms files.
• TeslaTuplesDec15.py: File from Mike in 2015. I borrowed some code from here, specifically regarding the T stations. Great example of what a good ntuple options file looks like.

Run the Ganga scripts:

This is the first step of the analysis- collecting the data. The ntuple options / Ganga scripts used will save the data to EOS, a large area of disk space provided by CERN for users.

1. Start by ssh-ing into CERN computers, proxying into lhcb, and navigating to the directory in which you have saved your job and options files.

$ ssh username@lxplus.cern.ch
$ lhcb-proxy-init
$ cd ddecay/

2. Enter Ganga and run the jobs. For the files I have created this will need to be done four times. Twice for each decay (D+ and Ds+) and again for each magnet polarity. As they are, the job and options files are set up to already discriminate between D+ and Ds+ (As indicated by their names). To change between MagUp and MagDown data, lines 1, 11, 15, and 22 in the job scripts needs to be adjusted. Line 46 (TupleFile) in the options scripts should also be changed to match the output file name (line 22) in the job scripts.

$ ganga
$ ganga dp_job.py

after that is done setting up:

$ ganga
$ ganga dsp_job.py

After both of these are done, make the polarity changes and repeat.

Monitor your jobs

Monitoring running jobs can be done on DIRAC. You will need your certificates functioning in your browser to properly access this site. The process to get this up and running is well documented on CERN wikis and forums. Using the "Job Monitor" tool on DIRAC you can change some parameters to monitor recently scheduled jobs. You can also reschedule jobs that happen to fail. More information about DIRAC including some useful guides can be found here.

Get the data:

1. In lxplus open a dirac sub-shell and proxy to lhcb.

$ lb-dirac bash --norc 
$ lhcb-proxy-init

2. Get a list of all lfns older than d days (probably fine to set d=0), this will output the file "lhcb-user-u-username.lfns" into current directory ("u-username" in my case is j-jbodensc)

$ dirac-dms-user-lfns --Days=d

3. (optional) if you need to get rid of older files, run the above command isolating all data older than d' days (d' > d, such that you only select files older than what you are interested in), then run the following command to remove these lfns. WARNING: they are not going to come back! (Note: There is probably a cleaner way of doing this without [risking] removing older data. Just something to consdier.)

$ dirac-dms-remove-files --File=lhcb-user-u-username.lfns

4. Get the access URLs to the lfns by running the below command with your file containing the LFNs:

$dirac-dms-lfn-accessURL --File=lhcb-user-u-username.lfns > somefilename.txt 

5. Now run the "somefilename.txt" through a parser, selesting the accessURLs. Then these can hadd'd on lxplus, then rsync'd to UC from CERN. I have created an lfn_parse.py script that does this for my lfns and can be modified to parse through your lfns also. I collect and move the data in chunks from CERN computers to UC computers so as to not exceed storage limits. This is also safer in the event that something "breaks"- only a small chunkneeds to be redone.

$ hadd chunk1.root smallfile1.root smallfile2.root ... smallfilen.root

The following line can be done on either lxplus or UC computers, but I prefer to do it on UC computers so I can have only one session of lxplus up where I am hadding chunks together. Done on lxplus:

$ rsync -ap chunk1.root username@sleepy.geop.uc.edu:/share/lazy/yourfolder

Alternatively on UC computers (dot at end can be replaced with destination path, it's probably a good idea to put data in /share/lazy):

$ rsync -ap username@lxplus.cern.ch:/path/to/chunk1.root .

For reference, I store all of the data for this analisys in /share/lazy/D2KKpi/.

Data Analysis

This is the crux of the research. Here we study the many variables of the decays, generating a great number of plots from which we can extract useful information regarding the signals and background. The /image/ and /finalImages/ subdirectories are where I store any plots I create, more important (final) plots going into the /finalImages/ folder. The subdirectories /old_C/ and /old_dsp/ are, as labeled, old. They contain my first attempts at analysis from Summer 2020. The methods used are sometimes similar to more recent code, but in general these are just saved for a rare reference to past work and will certainly not work on existing datasets. The /scripts/ subdirectory contains all fitting functions used. The most improtant file in this folder is new_fit_spectrum.C. It was created to make various fitting techniques "easier" in the Analysis stage, this will be seen later on. The "loose" files in the main ddecay/ directory are what I used for analysis.

Cut the data

Due to the size of the data for this analysis some more "modern" ROOT techniques are applied, namely, RDataFrames. RDataFrames (RDFs) are fairly new to ROOT, as such they aren't documented incredibly well and are not yet as powerful as their predecessor MakeSelector. The official documentation provides a helpful cheat sheet on the functions that can be used with RDFs. The most impactful function call is EnableImplicitMT(). Briefly, this enables multi-threading on the computer so ROOT can run in parallel- immensely speeding up the "cut" process. I encourage you to read more about it as there are a few cases where you can't use it.

In my case, I use RDFs to make my first analysis cuts on the larger data set. I make special use of the Snapshot() function to create smaller, more efficient data sets that include only necessary variables (for fitting, momentum scaling, etc.). I was not able to figure out if it was possible to do fitting in RDFs, so I do all fitting in a MakeSelector. You can make regular plots and histograms in RDFs, but I found the process to have some tedious additional steps- so I generally stuck to the aforementioned method of snapshots. Here is a list of my RDF files and analysis files as well as their purpose:

RDataFrame Files:

• Useful
  • dp_dalitz_rdf.C: Dalitz plots of the D+ decay. Example plot
  • dp_dsp_cut_rdf.C: The big one! This file contains the final cuts and "standardizes" the data so that I can make ONE ntuple containing both D+ and Ds data.
  • dp_ms_reduced_rdf.C: Used in conjunction with quick.py, makes reduced ntuples that are cut and include only variables necessary for momentum scaling steps.
  • extra_info_rdf.C: Commented below the preamble are some helpful functions for getting properties of the ntuple/data (column names, number of entries, ...). Also used to investigate OdinTCKs and the overlap region (see notes.txt).
• Old
  • dp_cuts_rdf.C: Old D+ cuts with some attempts at fitting.
  • dsp_cuts_rdf.C: Old Ds cuts with some attempts at fitting.
  • dp_dsp_rdf.C: Simple plots of the two decays with some cuts. Example plot
  • dp_fit_rdf.C: Failed attempts at fitting.
  • dp_mstest_rdf.C: Old file used to make plots of the T-Stations for momentum scaling. Example plot
  • dp_probtests_rdf.C: Looking at ProbNNx in different regions. Example plot
  • dp_tests_rdf.C: Looking at endvertex cuts. Example plot
  • lifetime_rdf.C: Trying to manually calculate lifetime before eventually remaking ntuples to include the _TAU variable. Example plot

MakeSelectors

Once you have made cuts that you are happy with, you can then fit the data and do other sorts of analyses, such as momentum binning (see /finalImages/deltam/ and differences.xlsx). I was unfortunately unable to determine if RDFs could be used for fitting. I made some minor progress, but overall was unsuccessful. As such, I use the slightly older MakeSelector for [most of] my analysis files. Here is how to make a MakeSelector on sleepy.geop.uc.edu:

1. Load your data file into root.

$ root -l /path/to/data.root

This will attach your root file as _file0.

2. (OPTIONAL) If your ntuple has more than one tree, you will need to cd() to the tree you want to analyze.

root [1] myTree -> cd()

3. Assuming the tree you are interested in is called "DecayTree", make the MakeSelector. (note the intentional lack of ".C" here)

root [1] DecayTree -> MakeSelector("AnalysisFileName")

This will make two new files in your working directory: AnalysisFileName.C and AnalysisFileName.h. You shouldn't need to touch the header file. The .C file is where the analysis work will be done. Pages 48-50 of the ROOT Workshop 2019 explain more about creating Makeselectors and running them.

Here is a rough outline of the four* parts of a MakeSelector (page 49 of the above):

1. Definition Section Define all plots and fits that are going to be used in the analysis.
2. Initialization Section Set features of the plots and fits, such as: ranges, parameter names, aesthetics, etc.
3. Loop Section Loop through the data in the ntuple and fill histograms. This is where cuts should be made.
4. Wrap-up Section Perform any fitting, get and print results, make canvases/pads for plots to live on. Don't forget to save plots!

Analyze the data

After having prepared your MakeSelector, you are ready to analyze the data. This is done similarly to making the MakeSelector:

1. Load your data file into root.

$ root -l /path/to/data.root

This will attach your root file as _file0.

2. (OPTIONAL) If your ntuple has more than one tree, you will need to cd() to the tree you want to analyze.

root [1] myTree -> cd()

3. Assuming the tree name you are interested in is called "DecayTree", process using your analysis file. (note the use of ".C" here)

root [1] DecayTree -> Process("AnalysisFileName.C")

Shortly after, your analysis will either make a nice plot or fail! "Nothing ever works on the first try". Here is a list of some analysis files I used:

Analysis files:

• Useful
  • FinalCutsNew.C/h: Update to FinalCuts. This is the most important analysis file - it makes plots with full spectrum fitting. This MakeSelector is different in that it is tuned for a slightly different data set (combined_cut-may-2021.root) than the original FinalCuts.C. Has many options at start of file to customize fit on the fly. Example plot
  • massDiffComp.C: makes a comparison plot of this new measurement and older measurements (LHCb, BABAR, CLEO, PDG). Example plot
• Old
  • FinalCuts.C/h: First iteration of final analysis. Made plots with full spectrum fitting. Works with older data set (combined_cut.root). Plots from this file are similar in appearance to those made by FinalCutsNew.C.
  • combined_cut_fit.C/h: First attempt at fitting final data where both masses are fit.
  • mass_diff_fit.C/h: First attempt at fitting final data where D+ mass and Δm(Ds-D+) are fit.
  • dp_cuts.C/h: Fitting just the D+ peak. Example plot
• dp_sample.C/h: Fitting just a sample of the D+ peak. Example plot

I also have a few spare files in the directory for quick and dirty work. These are by far not the "best" way of achieving their tasks, but sometimes a quick python script or excel sheet can save a lot of time for something simple.

Here are brief descriptions of other files used:

• differences.xlsx: Quick excel sheet to find Δm(Ds-D+) for momentum regions.
• quick.py: Quickly made python parser used to find what variables are used in Momentum Scaling code.
• notes.txt: Notes file used when searching for missing(ended up none missing) TCKs. Also used to look at the "overlap region".
• README.md: Documentation.