Fall 2020 Semester

9/15/2020 - Alternative Connection Method

I used MobaXterm, which was the recommended x-server terminal for use in CMSC216, to connect to the LHC Cluster. Outlined steps below:

1. Opened MobaXterm

2. Clicked Session in the top left corner

9/16/2020 - Class Notes: Linux Introduction and Fundamental Particles

• • Starting with linux

    • Basic command structure

      • [Command_name] <Options> <Options> <Options>

      • Options usually -(some letter)

      • usually --help will allow you to access manual for the command

    • Directory structure

      • use "pwd" to show current directory

      • use "ls" to list contents of directory

      • use "mkdir" to create a new directory

    • Files

      • use "touch" to make a new file

      • use "cat" to print contents of a file in shell

      • use "find" to search for specific files

        • check --help for details about use

      • use "rm" to permenetly remove file

  • HW: Go through HW1-HW3 for Linux stuff

    • Emacs

      • "-nw" option means no windows, opening emacs in terminal mode

    • Maybe install VScode? 

      • https://code.visualstudio.com/docs/setup/linux

    • Shell Scripts

      • make a ".tcsh" file which contains the script

        • $1, $2, $3, etc as input arguments when running the script

      • to run the script, use "tcsh" command with the filename and arguments after

      • cntl + x to write buffer, basically saving your changes to the file, and cntl + c to close

      • Make sure to have a newline at the end of the file to make sure all lines are read for scripting and coding purposes

  • Physics stuff

    • Fundamental particles

      • Spin

        • For fundamental particles, based on symmetry...?

          • either up or down for electrons

        • One of the first properties identified about fundamental particles

        • Measure is = to how many "spins" to takes to return to "original state"...?

        • Fermions

          • Half spins

          • Leptons and Quarks

        • Bosons

          • 0 or integer spins

9/20/2020 - HW1-2: Shell Commands and Emacs

HW1

• Goals:

  • Connecting to Cluster

    • • refer to 9/15/2020 entry

  • Similarities and differences of the electron, muon, and tau leptons

    • • Similarities

        • All negatively charged

      • Differences

        • Only the electron is stable, muon and tau both decay very quickly

        • All three have different mass, in increasing order: electron, muon, and tau

  • What do the commands 'mkdir' and 'cd ../ ..' do?

    • • mkdir is a command which makes a directory:

• • • • the option '..' is the parent of the current directory

HW2

• Goals:

  • What are the fundamental particles and forces? How many particles does the standard model of particle physics have?

    • • There are the leptons: electrons, muons, and tau with their respective neutrino pairs, and the quarks: up, down, charm, strange, top, and bottom

      • There are four fundamental forces: gravity, electromagnetism, strong nuclear, and weak nuclear

      • The standard model has 17 particles

  • What is spin of a fundamental particle?

    • •  This is a good question... I'm not really sure how to explain it, but here's a video:

      • https://www.youtube.com/watch?v=cd2Ua9dKEl8

  • What is the difference between bosons and fermions?

    • • Fermions have 1/2 spin

      • Bosons have integer value spins

  • What is Linux?

    • • A class of operating systems which are based on the Linux kernal

  • What is a Linux Shell?

• • • A command-line interpreter

• • How do you find which shell you are working in?

• • • 'echo $0' or 'echo $SHELL'

• • What is the basic linux command structure?

• • • [command name] -[options] [targets]

• • What do the following commands do?

• • • 'pwd'

      • • prints current directory

    • 'ls', 'ls -l', 'ls -lr', 'ls ..', 'ls -CFx'

• • • • lists directory contents

      • '-l' option lists contents in long format

      • '-lr' compound option lists contents in long format and reverse order 

      • 'ls ..' lists contents of parent directory

      • '-CFx' compound option lists entries in columns, with indicators appended to classify files vs directories, and listed in lines instead of by columns

• • • 'cd', 'cd ..'

• • • • refer to HW1

• • • 'mkdir'

      • • refer to HW1

    • 'find'

• • • • finds files that match the given regex given a target directory and a regex

• • • 'rmdir'

      • • removes the target directory

    • 'which'

      • • searches for command in path

    • 'whoami'

• • • • prints username

• • • 'echo'

      • • console repeats target

    • 'cat'

• • • • prints file contents in console

• • • 'more'

      • • prints file contents in console, but one screen at a time

• • What is the difference between 'ls', 'ls .', and 'ls ..', 'ls /', 'ls ./'?

• • • 'ls' and 'ls .' both list the current directory

    • 'ls ..' lists contents of the parent of current directory

      • 'ls /' lists contents of root directory

      • 'ls ./' lists contents of current directory

• • How can I get help to learn more about Linux commands on the command line?

• • • use --help option after the command

• • What is the symbol '~' used for in the directory structure?

• • • home directory

• • What do uparrow and enter keys do?

• • • go through command history and run command

• • What kind of programs/apps can you use to open the following file types: 

• • • '.txt'

    • '.c'

    • '.cpp'

    • '.root'

    • '.sh'

    • '.csh'

      • you can open all of these files with text editors. Emacs is an example 

• • What do operators, '>' and '>>' do?

    • • both redirect std out to a file or create that file if it doesn't already exist, '>' will overwrite anything in the file whereas '>>' will append it to the end

  • What is emacs?

• • • a text editor

• • What is the difference between the commands

• • • emacs -nw mycode.c

      • opens the mycode.c file in emacs in the terminal (no window)

    • emacs mycode.c

      • opens the mycode.c file in emacs in a separate window

    • emacs mycode.c &

      • opens the mycode.c file in emacs in a separate window from a different process

      • main process can still process shell commands

• • What do you expect to happen if you run the command 'emacs myfile.txt &' where the file 'myfile.txt' does not exist already?

• • • emacs creates the file

• • How to you save a file in emacs?

• • • ctrl + x, or with the button at the top if in windowed mode

• • How do you search some string in emacs?

• • • ctrl + s, then the string, then enter

• TODO:

  • What did it seem like the 'touch' command does?

    • • Creates new file if it doesn't exist, and updates the timestamp for the file if it does

  • Why do you think we include '.' after the 'find' commands?

    • • To specify that we want it to search in the current directory

  • Based on the outputs from the four 'find' commands, what purpose do you think the '*' character serves? (Hint: it's called the "wildcard" character in Linux jargon)

    • • In classic regular expressions, * is often used to specify 0 or more of the preceding character

      • in unix though, it just means 0 or more of any character

  • What did the 'rm' command do, and how do you think 'rm' differs from the 'rmdir' command we saw earlier? Warning: There is no way to undo the 'rm' command

    • • 'rm' is specifically for removing files, whereas 'rmdir' is for removing directories

  • Finally, to test your understanding, why do you think that you should never run the command 'rm *'? True story: a thoughtless 'rm *' almost deleted all of Toy Story 2! (https://www.youtube.com/watch?v=8dhp_20j0Ys)

    • • 'rm *' will remove all files in the current directory since all files match with '*'

  • What do the '>' and '>>' operators do? How are they similar? How are they different?

    • • both redirect std out to a file or create that file if it doesn't already exist, '>' will overwrite anything in the file whereas '>>' will append it to the end

  • What is one potential danger of using the '>' operator?

    • • overwriting the contents of a file which you might not have wanted to overwrite

  • What do you expect to see if you run: 'ls -l > log.txt' then 'cat log.txt'

    • • I would expect to see the output of 'ls -l'

  • Use google and collect 10 Linux commands that you think could be useful for you. For example, one such command would be to find and replace a word of phrase in a large text file. Show that your commands actually work.

• • • cp - copy file to a directory

• • • sudo

      • I better not for this one...

9/21/2020 - Class Notes: Quantum Mechanics and more computing

• Quantum Mechanics

  • probability and uncertainty

    • all calculations have a probability associated with it

    • uncertainty - measurements interfere with the object being observed

    • bar h is the plank constant

    • constants of nature

      • the parameters of nature in our equations which need to be measured

      • we know that two things have some proportional relationship, but we need to measure the world itself to find that particular proportion

      • can they change?

        • yes, our universe may be in a quasi-stable stable, which could change as we fall to a lower energy state, which would change all of the constants of nature

          • vacuum decay video: https://www.youtube.com/watch?v=ijFm6DxNVyI

  • Duality between particles and waves

    • wavefunction

      • a good way of visualizing particle interactions

      • the act of looking at something... changes its existence?

• Computing

  • 'ssh -xy siab-1' to connect to a terminal with vs code

    • x-terminal set-up doesn't work, maybe because it's an indirect connection...?

  • issue with not allowing to logout because a task is suspended:

    • 'ps ux' to display tasks and their information

    • then 'kill [PID]' for the task you need to kill

    • then, 'logout' should work

  • Do HW 3 by the end of the week

• Link to my webnovel (as requested): https://www.webnovel.com/book/three-trees_10664707705095205

  • • Don't expect too much, I don't upload regularly and the story hasn't even gotten going yet.

9/23/2020 - Class Notes: More Quantum Mechanics and HW3

• • Quantum Mechanics (Continued)

    • Fermions and Bosons

      • half integer and integer spins

    • Quantum number

      • are conserved in quantum interactions

      • Examples:

        • charge

        • spin

          • not actually spin, just algebraically similar

          • spin is 1/ how many times a particle needs to be rotated before it looks identical

            • rotation?

              • mathematical transformation

            • identical?

              • same "position" in the multidimensional grid

        • isospin

          • again, not actually spin

          • related to the strong force

        • hypercharge

        • weak spin

        • weak hypercharge

        • lepton number

        • baryon number

        • strange-ness

        • top-ness

        • bottom-ness

    • Symmetries

      • continuous space-time transformations

      • discrete transformations

      • transformations of internal symmetries

    • Weak force bosons must have mass to limit the range of the force

      • other force particles don't have mass?

      • led to prediction of the higgs boson

HW3

• Goals:

  • What is a shell script?

    • A series of shell commands that are put in a file for the shell to run

  • What does the line #!/bin/tcsh on top of a shell script mean?

    • It specifies that the program that should run this file is the tcsh program in bin

  • What is command 'chmod +x' used for?

    • 'chmod' modifies the file permissions of a file. The +x makes the file an executable one.

  • What do 'touch' command do?

    • • touch creates a file, or updates the timestamp on a file that already exists

  • How do you execute shell scripts?

    • • use 'tcsh' command on it or make it an executable and just execute it

  • What is the difference between 'sometext' and '$sometext' in a shell script?

    • a string vs a variable

  • What is piping (|) in Linux and how do you use it?

    • piping is transferring data from now process to another

    • it is used between commands to transfer information from left command to right command

  • How can you search and replace something in a file from command line or from within a shell script?

    • 'sed'

• TODO:

  • Can you figure out what this script does?

    • • Yes

  • What do you think chmod command does?

    • • Change the file permissions for a file

  • Now, as an exercise, try using emacs to write a simple a simple script based on testscript.tcsh called homesearch.tcsh which takes one input, <input>. homesearch.tcsh should search your home directory and its subdirectories for any files which contain <input> somewhere in their name. Finally, homesearch.tcsh should log the results of the search to a file called homesearch_<input>.txt. (Don't forget to 'chmod+x' your new script!) 

• • Try: 

    • • touch testfile

      • ./homesearch.tcsh testfile

• • • cat homesearch_testfile.txt

• • What is the output of this script?

• • In Linux, what is piping (done with the symbol | )? Write a short description.

    • • <left> | <right>; the pipe pipes command output from the left to right

  • The command

• • • sed -i -e 's/one/two/g' test.txt

• • searches the word "one" everywhere in the file test.txt and replaces it with the word "two"

• • • Copy paste the following text to create test.txt file in your directory. Write a script that uses this and/or other commands to replace every "was" with "is"

      • sed -i -e 's/was/is/g' test.txt

9/28/2020 - Class Notes: LHC Details

• • Accelerator process

    • Hydrogen gas has its electrons stripped and accelerated by electromagnets

      • first stage is straight

      • second stage is circular with pulsing magnetic fields

        • 95% speed of light

      • stage 3 

        • larger circular accelerator

        • 99% speed of light

        • increase mass/energy not momentum

      • stage 4

        • like stage 3, but larger circle and higher energies

      • stage 5 (actual collider)

        • like stage 4, but even higher energy

        • electromagnets kept super cold to maintain superconductivity

        • 7000 times heavier than original proton mass

    • Energy and Mass measured in same units

    • Linear vs circular accelerators

      • circular provides infinite distance as the loop is reused

      • circle diameter needs to be increased as particles gain mass as it becomes more difficult to make them change direction

        • the amount of force superconductors can push on them with is limited

    • Special terms

      • energy = energy of the collision

      • cross section = probability a particular particle is produced from a particular collision

      • luminosity = number of collisions that can be produced per cm^2

  • Read chapters 1-2 of discovery of the god particle and chapter 6 of elementary particle physics by next Monday

  • Do HW4 by this Friday

9/30/2020 - Class Notes: Particle Detection

• • Particle detection

    • Common "stable" particles

      • photons

      • electrons

      • muons

      • charged hadron

      • neutral hadron

      • "neutrino"

    • Multiple materials which interact differently with different particles

      • Tracking chamber

        • layers of semiconductors

        • only detects charged particles

      • Electromagnetic calorimeter

        • material that interacts with electromagnetic particles

          • "catches" photons and electrons

      • Hadron calorimeter

        • material that interacts with hadrons

          • "catches" hadrons

      • Muon chamber

        • iron return yoke?

        • no calorimeter?

    • Particles that are indirectly detected

      • neutrinos through conservation of energy

      • the signitures of unstable particles can be observed due to a shift in trajectory

    • There are lots of collisions, problem of filtering and identifying trajectories

    • Damage to detector

      • Tracking chamber and calorimeter need to be replaced, and damage to the detector needs to be accounted for in observations

        • Radiation hardness is a significant consideration for determining detector material

      • parts are replaced every few years.

10/2/2020 - HW4: Muons and C++

• Physics

  • • Why do muons travel farthest in the detector? You can find the answer using google. Give the reference of your source with the answer.

      • Muons travel the farthest in the detector because it does not interact much with the two types of calorimeters. The calorimeters, both electromagnetic and hadronic, work because their material interacts with the incoming particle in ways that cause the particle to lose its energy, which is absorbed and measured by the calorimeter. The hadronic calorimeter is designed to interact via the strong nuclear force, so it catches the charged and neutral hardons. The electromagnetic calorimeter interacts via the electromagnetic force, allowing it to catch electrons and photons. The muon interacts electromagnetically and weakly, not strongly, so the hadronic calorimeter does not catch them. And, although they interact electromagnetically, it is also classified as a minimum ionizing particle, meaning its energy loss rate through matter is close to the minimum (and something to do with its high mass relative to electrons). So, while the other particles are all captured and measured, muons continue travelling.

      • Sources:

      • https://www.lhc-closer.es/taking_a_closer_look_at_lhc/1.detectors

      • https://en.wikipedia.org/wiki/Calorimeter_(particle_physics)#:~:text=Often%20it%20is%20the%20most,the%20detector%2C%20such%20as%20neutrinos.

      • https://en.wikipedia.org/wiki/Stopping_power_(particle_radiation)#Minimum_ionizing_particle

      • https://physics.stackexchange.com/questions/340673/why-are-needed-seperate-detectors-for-muons#:~:text=Hadrons%2C%20protons%20and%20neutrons%2C%20will,track%20footprint%20in%20the%20calorimeters.

      • https://www.quora.com/Why-do-muons-penetrate-the-calorimeters-in-a-particle-accelerator

• For the code below, comment on each line to show what it does and paste the commented code in the logbook for grading. This includes any questions embedded in the discussion of the code.

• • Getting Started

• • Variables

• • Some operations with numbers

• • Non-numeric variable

• • Loops

    • 1:

• • Debugging

10/5/2020 - Class Notes: More on Particle Detection

• • Calorimeters

    • Electromagnetic

      • doesn't really interact much with hadronic particles because they're too massive to have significant interactions

      • "Showering" of hadronic particles can still happen here, but it's less common than in the hadronic calorimeter

    • Hadronic

      • Material designed to interact with hadronic particles and produce "showers"

    • "Shower" means to produce more particles from an interaction

  • Using Tools

    • Online 3D Event Display

    • https://ispy-webgl.web.cern.ch/#

      • Demo video: https://www.screencast.com/t/SLQyyXy8

  • Jets from gluons and quarks

    • Chromodynamics

      • Group theory

      • Look up SU3 group

      • So, must have 3 particles

        • but, can't see them

        • so, they must not be able to exist independently...?

    • Since they can't live alone, when they break off, they produce lots of pairs, resulting in a jet which is composed of the products of the quark decay

  • Do Homework 5 by Friday

10/7/2020 - Class Notes: Particle Detection and Identification

• • Channels of data

    • Tracker has ~70M different channels

    • Entire structure has ~100M different channels

    • Each channel is a separate stream of data

  • Detectors only detect certain "stable" particles

    • Original particle can be predicted from its feynman diagram

    • "stable" particles have certain signitures in terms of charge, energy, etc. that are measured by the various layers of the detector

  • Quarks and gluons can be identified as jets due to chromodynamics

    • Jets can be seen as clusters of measurements on phi eta space

    • High energy clusters

  • phi eta space

    • the surface of the cylindrical detector spread flat into a sheet

    • positions on the cylinder are defined with r, theta, and phi

      • r = radius of the cylinder

      • theta = from 0 to pi along the edge of the cylinder

        • eta, related to theta, but different

      • phi = from 0 to 2pi to transverse the circle at the end of the cylinder

    • Why two angles and one length instead of two lengths and one angle?

      • more useful for our current application

        • we care about the direction of showers and jets, which is best described with 2 angles

      • angles are easier to work with, I think, computing-wise

        • value can be capped, with a given resolution

  • Resolution

    • tracker:

      • 10^-6 meters

• Read Chapters 5 and 7 by Monday

10/9/2020 - HW5: More C++

• Goals

  • Logic statements in C++, if-else.

    • See exercises

  • How do you define pointers in C++? How can you get the address and the value of a pointer?

    • • Use the '*' operator in the declaration of the variable to define the pointer.

      • Use the '&' operator to get the address of a variable; Use the '*' operator in front of the pointer to get the value at that address

  • How can you define a pointer with a new memory address?

    • • the 'new' keyword

  • Use 'date' and 'awk' commands in a script.

    • • See exercises

• Exercises

  • logic statements

• • Pointers

• Computing

  • Write a small C++ code that shows examples of if and while logic statements. (START in class). Explain what the code does by using cout statements.

• • • Alter the script given below so that it outputs the list of files that were updated within the current month. Note that the marks which surround date | awk `{print $2}` are not apostrophes, but rather backticks. The backtick can be found on the same key as '~' (to the left of the '1/!' key). (Hint: the resulting script will be shorter and simpler :-))

      • will be done with bash due to connection issues with the cluster (bash and tcsh are very similar anyways):

10/12/2020 - Class Notes: Review and Relativity

• LHC Cluster Down

  • HW5 due date delayed to this Friday

  • Reminder for self: lookup more SU3 group info

  • Building blocks

    • 3 quark families

      • up and down

      • charm and strange

      • top and bottom

    • 3 leptons

      • electron and its neutrino

      • muon and its neutrino

      • tau and its neutrino

    • force carriers particles

  • Theory composition

    • QM + fields + relativity + symmetry

  • Accelerators and detector

    • collides protons and high-resolution camera

  • Particle Detection

    • stable particles

      • elections

      • muons

      • photons

      • kaons

      • pions

      • protons

      • neutrons

      • quarks

      • gluons

      • neutrinos

    • Neutrinos detected indirectly through conservation of energy and momentum

      • possibly some other particles which interact minimally

  • Relativity

    • E=mc^2

    • "Matter tells spacetime how to curve, and spacetime tells matter how to move."

    • Reference frame

      • Newtonian transformation:

        • x = x' +vt

        • t = t'

          • where v = velocity of the frame x

          • The same applies to y and z axises

      • Lorentz transformation:

        • x = `gamma`(x'+vt)

        • t = `gamma`(t' + v x' / c^2)

        • `gamma`=1/sqrt(1 - v^2/c^2)

          • when v is far less than c, approaches Newtonian transformation

          • as v approaches c, `gamma` goes to infinity, creating a limit on v

        • m = `gamma` m_0

      • inertial reference frame

        • physics stay the same within the frame

        • speed of light is a constant

        • Google HW Exercise: Speed of light as a constant vs. speed of light changes depending on its medium

          • Phase velocity and group velocity in relation to the speed of light

          • In a vacuum and in medium

          • Cherenkov radiation

          • Brian Greene's world science

          • what is the value of C?

    • Binomial expansion

      • decreasing series, so later terms can be ignored depending on how specific you want your answer to be

    • 4 vectors

      • distance: (x, y, z, ct)

        • because we need the t to be the same units as the other distance measurements

      • momentum: (P_x, P_y, P_z, E)

        • P is momentum

        • E is energy

      • Eta, a variable that stays constant despite a change in frame of reference

      • Natural Units

        • set c as 1

        • set h as 1

        • everything becomes units of energy

    • Read Chapter 3 from Experimental Higgs Physics

10/14/2020 - Class Notes: More on Relativity

• • Relativity

    • Fundamental assumptions

      • Laws of physics stay the same

      • speed of light, c, is a constant

    • as v << c

      • Einsteinian Physics --> Newtonian Physics

    • Time dilation

      • relative to an observer at rest, a frame in motion experiences time slower than the observer at rest

      • Twins paradox

        • there are two twins, one is sent away on a spaceship traveling at the speed of light and then returns

        • Both twins see the other moving away at light speed, so according to the other, each undergoes time dilation, so when they meet again, who is younger?

          • The twin on the spaceship, because one is accelerating, so not in an inertial frame of reference...? (look this up)

    • Google: Limit on graviton mass from gravitational wave experiments

  • Why is velocity relative but acceleration not? -ish

    • More like why does acceleration put you out of an inertial frame of reference.

10/16/2020 - HW5 Addendum: Google exercise

• • Speed of light as a constant vs. speed of light changes depending on the medium

    • So... its speed is different in a medium because of wave interference

    • https://www.youtube.com/watch?v=CiHN0ZWE5bk

    • https://medium.com/starts-with-a-bang/ask-ethan-does-light-always-move-at-the-same-speed-a05b76e54dd5

  • phase velocity and group velocity

    • Phase velocity is the velocity of a basic sin wave

    • https://en.wikipedia.org/wiki/Phase_velocity

    • group velocity is the velocity of a combination of basic waves into a single wave structure

    • https://en.wikipedia.org/wiki/Group_velocity

  • Cherenkov radiation

    • charged particles moving faster than light because in a medium

    • https://www.youtube.com/watch?v=Yjx0BSXa0Ks

    • https://en.wikipedia.org/wiki/Cherenkov_radiation

  • What is the value of c?

  • 299792458 meters per second

  • the speed of light in a vacuum

    • https://en.wikipedia.org/wiki/Speed_of_light

  • Limit on graviton mass from gravitational wave experiments

  • 7.7×10−23

    • https://en.wikipedia.org/wiki/Graviton#:~:text=Alternatively%2C%20if%20gravitons%20are%20massive,%E2%88%9223%20eV%2Fc2.

    • https://en.wikipedia.org/wiki/Compton_wavelength

10/19/2020 - Class Notes: Proper time and Proper length

• • Lorentz transformation

  • Postulates of relativity

  • c = constant

  • x, t are no longer absolute

    • x(x', t')

    • t(x', t')

    • dependent on the frame of reference

    • factor or gamma

      • gamma = sqrt(1-v^2/c^2)

  • Contraction of length and dilation of time

    • beta = v/c (percentage of lightspeed)

    • gamma = sqrt(1-(beta)^2)

    • natural units

      • h = 1

      • c = 1

    • Proper time (tau)

      • the measure of time from the frame where the position is stationary

        • from the reference frame of the object itself

      • The frame of reference with the smallest time 

        • t = 1/gamma * tau

        • where t is the time observed from the frame of reference

        • v is the velocity of the frame of reference

      • When doing experiments at LHC, it is down from the center of mass frame

    • Proper length

      • length as measured from a stationary frame of reference as opposed to relative to the object being measured

      • L = gamma * l

• Do HW6 by the end of the week

• Google Monte Carlo Distribution / Simulation

10/21/2020 - Class Notes: Quantum Entanglement

• Cluster is back, do not use hn server anymore!

  • Core-vectors?

    • x, t (position and time)

      • results in time dilation and length contraction

    • E, P (Energy and Momentum)

      • E= KE + mc^2

      • KE = ('gamma'-1)mc^2

      • E ~ P when KE is tiny

    • Relativity creates a non-linear relationship between energy and velocity

      • as v approaches c, 'gamma' approaches v

    • Action at a distance (entanglement)

      • seems to violate the speed limit

  • Breakout exercise

    • A page on quantum entanglement, action at a distance, relativity (speed limit of light) 

    • Muon lifetime and relativity

• Accessing ROOT on the cluster

  • Updated directions in HW6

10/23/2020 - HW6 (P1): More C++

• Goals

  • What is ROOT? (answer in the context of LHC data analysis. We are not concerned with any other uses of the word ‘root’)

    • • ROOT is a c++ data analysis and visualization library.

  • What does command ‘cmsenv’ do?

• • • It sets up an environment for ROOT.

• • What happens when you run command ‘root'?

• • • The program root is run, which switches terminal input to the root shell interpreter.

• • What is the difference between commands ‘root' and 'root -l’

• • • Run the root program with or without the splash screen.

• • How do you quit a root session?

    • • .q

  • How can you add single and multiline comments in C++?

    • • Use "//" before single line comments and "/* */" around multiline comments.

  • How to read data from a file in C++ code?

    • • Open a file with an ifstream from the fstream library, then extract contents with ">>"

  • How to create, write into, and close a txt file in C++?

    • • Use either an ofstream or an ifstream for writing or reading, respectively.

      • Opening a file with ofstream which doesn't currently exist will create a new file.

      • Using the .close() function on the file stream closes the file and flushes the read/write buffers

  • What is the difference between a vector and a scalar in C++?

• • • Vectors hold multiple values whereas scalars hold only one.

• • How to use vectors in C++?

• • • Declare using type and then follow the variable name with a [n] where n is the desired length of the vector.

• • How to use a random number generator in C++? Which #include file is needed to use this function in your C++ code?

• • • TODO in P2

• • What do we mean by the ’seed’ of a random number generator?

    • • TODO in P2

  • What changes in the distribution of random numbers as you increase statistics?

    • • TODO in P2

  • What is ‘class' in C++?

    • • TODO in P2

  • Name two classes you have used in C++ code in this class?

    • • TODO in P2

  • How do you run C++ code with root?

    • • TODO in P2

  • How do you book, fill, draw, and save a histogram in C++ code to be used in root?

    • • TODO in P2

• Arrays and vectors in C++

• • How are these elements distributed in rows and columns?

    • • The elements fill the rows first before starting to fill the next column.

      • {{1, 2, 3}, {4, 5, 6}}

  • Note: you can, and in some cases should, use braces to specify rows and columns. Find a simple example on google.

    • • use more {} to specify division between rows

• • • https://www.geeksforgeeks.org/multidimensional-arrays-c-cpp/

• Reading data from a file

10/26/2020 - Class Notes: Computing

• • Computing

  • Modify main.cpp and dotprod.cpp from HW6 to actually use std::vector

  • Quantum entanglement and relativity write-up

10/28/2020 - Class Notes: ROOT

• • Computing

    • ROOT setup 

      • Top of HW6

    • Make sure X-11 forwarding is enabled!

    • Using root

      • .L to load code file

      • after loading ana.C, ana can be used as a command to create an ana object with a given name

        • "ana t" creates ana object called t

      • TBrowser

        • opens a windowed interface for viewing data

11/2/2020 - Class Notes: Reading research

• FINISH HW6 BY THIS WEEK

  • Reading research papers

    • Try to understand the general process

    • Don't go down too many rabbits holes

      • don't stray too far from the topic

  • Computing tips

    • wsl doesn't seem to support recursive X-11 forwarding

      • use something like PuTTY or MobaXTerm instead 

  • Research paper interpretation

    • source: https://arxiv.org/pdf/1207.7235.pdf

    • Interpretation:

    • Introduction (paragraph generalizations):

      • • The standard model of elementary particles describes interactions through the exchange of force carriers. Its predictions have been extensively confirmed, but we don't know how the W and Z bosons have mass, while the photon doesn't.

        • Spontaneous symmetry breaking could explain why W and Z bosons have mass while the photon doesn't and also predicts the Higgs field/ Higgs boson. Over the course of many experiments, the range of possible masses for the Higgs boson has been further and further limited.

        • There were more experiments at higher energies that further narrowed down the range of possible masses to search through. In particular, 125 Gev seemed to have an excess of events.

        • There are five decay modes for the Higgs in the mass range from 110 to 160 GeV. The cross-section of the decay is predicted to have values between 23 or 29 on the higher end and 10 or 14 on the lower end in pb. Of the decay states, one or more ZZ and WW will be off the mass shell, meaning they don't obey classic motion equations.

        • The methods of analysis used for the current study were reoptimized for the higher energy equipment, and more formalized than previous studies.

        • Given all of the above, the experiment is consistent with the production of a new particle with a mass near 125 GeV, of which the decay modes which most strongly support this are H --> \gamma\gamma and H --> ZZ. The decay into to photons (\gamma) indicates that the new particle is a boson with a spin different from one (somehow).

11/4/2020 - Class Notes: Standard model (group theory) and ROOT

• • Standard model

    • SU(1) *SU(2) * SU(3)

      • group theory

        • involves QM, relativity, fields, and symmetries

      • particles predicted by symmetry groups

    • SU(1) associated with the electromagnetic force

    • SU(2) associated with weak nuclear force

    • SU(3) associated with strong nuclear force

    • Electroweak force

      • combination of EM and the weak nuclear force

      • "strength" of forces varies with energy

  • Computing:

    • reference ROOT docs for details on functions

    • Google tip:

      • use site: "foo.net" ("query")

        • searches for "query" specifically on "foo.net"

11/6/2020 - HW6 (P2): Random, Classes, and ROOT

• Goals (cont.)

  • How to use a random number generator in C++? Which #include file is needed to use this function in your C++ code?

    • • Use the stand function provided by the stdlib library. Include <stdlib.h> and <time.h> to be able to use it.

  • What do we mean by the ’seed’ of a random number generator?

    • • The seed of the random number generator is the input for the complicated math function which produces the "random" number.

  • What changes in the distribution of random numbers as you increase statistics?

    • • TODO in P2

  • What is ‘class' in C++?

    • • A blueprint for the creation of a complex variable (combinations of fields and methods)

  • Name two classes you have used in C++ code in this class?

    • • String

      • ana

  • How do you run C++ code with root?

    • • TODO in P2

  • How do you book, fill, draw, and save a histogram in C++ code to be used in root?

    • • TODO in P2

• Vectors and combine code from different files

• • • main

• • • dotprod

• Random numbers

• • • Try removing the & and see how the result changes. What does the & do?

    • The & makes the function parameter refer to the address of the argument, since usually for primitive types, values are passed in by copy, which means that the value of inew can now be changed from inside the function.

    • Without the &, the value of inew stays the same and the function returns the same number every time as a consequence.

    • Show why unsigned n-byte data with a value up to 2^{8n}-1 can be stored.

      • technically, this is only true for unsigned integers (not for floats). If you have m bits, then the maximum value that can be stored will be m ones. A 1 in the (m+1)th position = 2^m, and a number of m ones is just 1 less than that (adding one to it will produce a 1 in the m+1 position and zero in all previous positions), so the value of m ones must be 2^m-1. And since there are 8 bits in a byte, a number with n bytes can hold up to the value 2^{8n}-1.

• • What happens when you run the executable multiple times?

    • • The number numbers come out in the same order (the first 10 numbers were always the same).

  • What happens when you change the seed?

    • • The numbers change when you change the seed.

  • What happens to the contents of the histogram as you iterate more and more?

    • • They even out. The probability of being in any bin becomes equal.

• Classes

  • • They exist...

• Physics

• • Set N=1 and run it. From this "data", what would you guess the mass of the mother particle is? And, how far would you guess the true mother mass could be from this measured value?

    • It looks like it has a mass of about 56. I would guess that it's about 35 off (since after reading through the code, it looks like the actual mass was set to be 91).

  • Now change N to 10. What do you find?

    • • The range of values for the mass is now spread from about 85 to 135. there was one repeat value at about 105.

  • Change N to 100. What do you find?

    • • The spread of the values is now between about 5 and 140. There are multiple repeat values, with a peak of 3 at about 70.

  • Change N to 1000. What do you find?

    • • It's looking more and more like a binomial distribution centered around 90.

  • Now open secretparameters.txt and change the first number in it to 1. Repeat with N=1, 10, 100, and 1000. What have you learned?

    • It looks like the first number in secret parameters is the actual mass, as indicated by its name in the code.

      • It was demonstrated that having more data is better because it better shows the whole distribution of possible values the actual mass could be.

11/9/2020 - Class Notes: Higgs Boson Paper

• • Higgs paper

    • Modes of detection

      • the decay routes that are being examined

    • Importance of photon mode (vs. bb)

      • detection of photons is much more precise

      • bb are quarks (can't live alone), results in a jet which 

  • Book Recommendation

    • The God Particle

    • Higgs field

      • photons don't have mass (don't interact with the Higgs field), but Higgs has photon-photon decay mode?

        • indirectly producing photons, usually through top quarks

      • top quarks decay before hadronizing (quantum properties aren't disturbed by paired quark)

      • Higgs boson is just the Higgs field interacting with itself

      • How does it fit in with relativity?

        • It works with special relativity

        • For general relativity though... more work is needed

    • Statistics

      • sigma is traditionally 68%

      • more sigma means more deviation from simulated values, which means a smaller p-value

11/11/2020 - Class Notes: MadGraph

• • Computing

    • use scp to transfer files between servers

    • MadGraph, explore details here:

    • http://madgraph.physics.illinois.edu/

11/16/2020 - Class Notes: Higgs Research Paper

• • Research Paper (Class discussions)

  • Read the CMS section on your own

    • Event reconstruction

      • converting direct input into human understandable data

        • some hardware

        • mostly software

    • decay modes for high mass resolution

      • BDT

        • boosted decision trees

      • Despite the high number of collisions, there ware very few decay events from Higgs

        • More background events that Higgs decay events

      • Big dip in observed vs expected values at 125 GeV

        • very small p-value

      • H -> ZZ

        • ZZ decays into 4 leptons

      • Importance of local deviations

        • maybe not significant overall, but if deviations consistently tend towards a certain direction, then it may still be a significant result.

  • Look into BDT

  • Research Paper (Breakout room discussions)

    • The chart on page 9

      • ggH: gluon gluon Higgs

      • VBF: Vector Boson Fusion?

      • VH: ZZ or WW Higgs?

      • ttH: top top Higgs

      • FWHM: Full width at half mass

        • Used as a lower bound for standard deviation (according to Zach)

    • The graph on page 10

      • the dotted line represents how far the observed data dip should be if the Higgs boson had that mass

11/18/2020 - Class Notes: ROOT and iSpy

• • Computing

    • a little on Monte Carlo

      • events are generated completely at random and events that don't conform with the constraints (the theory) are filtered out

    • Don't forget to use TBrowser command to view result graphics

    • PID

      • particles are assigned ID numbers

  • Finish HW 7 by the end of the week

    • can ignore the questions on filtering and graphing top quark events (not purple)

    • use the Higgs discovery paper and iSpy for the purple questions

    • disregard errors about lines being skipped

      • they don't affect the root interpretability of the produced root file

11/21/2020 - HW7: Madgraph and online 3D event display

• Goals

  • A brief intro to the major parts of detectors in the CMS detector.

    • Refer to first magenta question

  • What is missing energy?

    • leftover energy not accounted for by the observed particles and their energies

  • What are jets?

    • • the resulting shower from hadronic interaction events

  • How to distinguish between physics objects in the detector?

    • electrons

      • tracked by tracker, caught by EM calorimeter 

    • muons

      • Tracked by all detector layers

    • photons

      • not tracked by tracker, caught by EM calorimeter

    • jets

      • Caught by hadronic calorimeter

    • missing energy

      • • calculated based off of observed tracks

    • vertices

      • calculated based off of observed tracks

  • What is the MadGrapgh package used for?

    • • Generating simulated data for particular collisions

  • How is tar command used? what is the difference between xvzf and cvzf options for tar?

    • • tar is used to zip and unzip files;  -xvzf for unzip and -cvzf for zipping

  • What kind of information can you find in the madgraph output .lhe file?

    • data specifying the collision events in a given run

  • What is Montecarlo (MC) ID?

    • The id for a particular particle in the simulation

• Write a brief description of the major parts of the CMS detector. Beam pipe, tracker, calorimeter, solenoid, muon tracker. What are the physical dimensions of each part? 

  • Beam pipe

  • tracker

  • calorimeter

  • solenoid

  • muon tracker

• Find how to change the display to show you a view along the beam pipe?

  • Drag mouse while holding down left mouse to change view orientation, or slick a button on the top tab to perfectly orient with the x-y plane

• Which color tracks are electrons

  • green

• Which color tracks are muon?

  • red

• Which color track missing energy is represented with? 

  • magenta

• How are jets depicted in this visualization?

  • Orange cones

• Can you figure out if a track has clockwise curvature, it is  +vely charged or negatively charged? (when looking at the x-y view, with x along the horizontal axis)

  • Looking at the muon tracks, it looks like a clockwise curvature is associated with a positive charge while a counter-clockwise curvature is associated with a negative charge

• Study at least 2 events from each category in the files available with the display and specify how many objects of each kind are seen in every event?

  • electrons

  • muons

  • photons

  • jets

  • missing energy

  • vertices

  • Hto4l_120-130GeV.ig:Events/Run_201191/Event_1357605031

    • electrons: 4

    • muons: 2

    • photons: 4

    • jets: 49

    • missing energy: 1

    • vertices: 15

  • Hto4l_120-130GeV.ig:Events/Run_199319/Event_1203594102

    • • electrons: 2

      • muons: 4

      • photons: 0

      • jets: 44

      • missing energy: 1

      • vertices: 11

11/23/2020 - Class Notes: HW8

• Goals

  • How to use TLorentz vector class to get the invariant mass of a particle that decays into two particles?

    • Use the parameters of the two particles to create TLorentz vectors and then add them to get the TLorentz vector for the original particle. Then, the invariant mass of that particle can be fetched with a method.

  • How to get C++ class code automatically from a root file?

    • From inside of root, run the 'HZZ4LeptonsAnalysisReduced->MakeClass("HiggsAnalysis")' Command

• What does this command do? HZZ4LeptonsAnalysisReduced->MakeClass("HiggsAnalysis")

  • • This command creates the c++ code files (.c and .h) for HZZ4LeptonsAnalysis and calls them HiggsAnalysis.c and HiggsAnalysis.c, respectively.

• HiggsAnalysis.C

• in the above code add new TLorentzVector el3, el4 for the 3rd and 4th lepton and set their pt, eta phi, mass.  

• Add these two vectors to get a new vector TLorentzVector zCandidate2.

• Add the two vectors zCandidate and zCandidate2 to get a new TLorentzVector Higgs.

• DEfine a new histogram H_zz 

  • TH1F* H_zz = new TH1F("H_zz", "ZZ candidate invariant mass", 200, 0, 300);

• Fill the H_zz histogram with HIggs mass.  (using Higgs.M() )

• Write the H_zz histogram. 

• open the output file and paste the Z_ee and H_zz histograms in your HW file.

  • Z_ee

• • H_zz

11/30/2020 - Class Notes: HW8 and Machine Learning

• • Everyone else finishing HW8...

  • Machine Learning

    • Cuts

      • Setting a threshold for a certain measurement metric to filter between signal and background

      • for example, for finding the Higgs boson, any electron with energy lower than ~40 GeV could not have decayed from a Higgs, so we cut them out

        • not necessarily accurate, but that's the general idea

12/2/2020 - Class Notes: Python

• • The presentation should generally have the same sections as the paper

    • maybe goes off on certain tangents to explain sub-topics

    • Use graphics and videos for clarity (fewer words)

  • Python

    • and operator

      • returns the first value if it is false and the second value if it is true

        • 0 is false

          • really small floats round to zero

    • & operator

      • bitwise and

  • Finish HW9 by the end of the week

12/11/2020 - HW9

https://colab.research.google.com/drive/14IVMHbp3JhXmAAIrGg9J0Ip2I5QM7su8?usp=sharing

EOF Stub