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Here is a daily log for Jakob Grzesik from 2017.6.5 to 2017.8.5 in Saito Lab in Tohoku Univ.

#contents

*Daily schedule (tentative) [#w23992ea]
*Daily schedule (tentative) [#schedule]

- 10:00-12:00 Finishing/continuing any work from previous day
- 09:00-09:30 Begin climbing to campus
- 09:30-09:35 Succumb to burning feeling in calves and take a break
- 09:35-10:00 Resume climb to lab
- 10:00-11:00 Finishing/continuing any work from previous day
- 11:00-12:00 Discussion with Shoufie-san
- 12:00-13:00 Lunch
- 13:00-14:30 Discussion with Shoufie-san
- 14:30-15:00 Prepare daily report presentation
- 15:00-15:30 Meeting with Saito-sensei
- 15:30-18:00 Continuing work/updating Pukiwiki
- 13:00-13:30 Prepare for daily report presentation
- 13:30-14:30 Meeting with Saito-sensei
- 14:30-18:30 Start working on work for tomorrow's presentation and updating Pukiwiki

*Goal of the project [#v6c2b76f]
*Goal of the project [#goal]

- (Old) To enhance electric field at graphene surface by changing the possible patterns of dielectric thin layers through deep learning algorithms.
- Keywords: graphene, transfer matrix, deep learning
- Synchronization of particle motion

- (New) To understand how the photonic crystal sequence affects the transmission probability T at the central frequency
- Keywords: photonic crystal, transfer matrix, symmetry
*Questions and Answers [#QA]

*Questions and Answers [#cf2dce22]
This section is for posting questions from Jakob-san and answers from other group members.

This section is for posting questions from Haihao-san and answers from other group members.

- Please list here with some simple reasons or details.
- For every problem, give a tag double asterisks (**) in the code so that it will appear in the table of contents.
- For the answer, give a tag triple asterisks (***) in the code below the problem in order to make a proper alignment.
- List from new to old.

**Q: (Placeholder) [#p895f04e]
***A: (Placeholder) [#q305cf42]

*Report [#l307fb28]
*Report [#report]

This part is basically written by Haihao-san. Any other people can add this. Here the information should be from new to old so that we do not need to scroll.
This part is basically written by Jakob-san. Any other people can add this. 
Here the information should be from new to old so that we do not need to scroll.
**July 14 [#a7b2b2af]
- Analytically showed how to express synchronized particles as one larger particles with the parameters of the single, larger particle just being the sum of the parameters of the smaller particles in the group.
- Finished coding and began running the synchronized group counter program.

**August 5 [#h9a635cd]
To do:
- Run tests on random initial conditions to see if there is significant difference between the time it takes for a system to synchronize for various initial conditions.
- Come up with 3 hypotheses pertaining to parameters of the system and the time it takes for the system to syncrhonize.
- Find good threshold values for determining when a system is fully synchronized; may depend on number of oscillators.

- Updated intro to give more context/motivation
- Found recursion formula of Fibonacci lattice charge, only -1, 0, 1
- Qualitatively seems to be relationship between cumulative charge and E field
- Last day in lab!
**July 13 [#a7b2b2af]
- Looked into the idea of condensing a group of synchronized oscillators into a single oscillator. Allows for easy desrciption of the fully syncrhonized system.
- Also started running tests to better observe synchronization times based on phase differences to show that two particles with closer phase with synchronize quicker.
- Working on code to count how many synchronized groups are in the system at as a function of time.

To do:
- Find relationship between cumulative charge and peak E field, power law?
- Write and publish paper
- Finish the code for counting synchronized groups

**August 4 [#d370623d]
**July 12 [#a7b2b2af]
- Presented to Kono-sensei and Sarah-San along with Ogawa-san about my research project for their lab visit.
- Found that the error in the matrix algorithm had to do with the implementation of coupled Runge-Kutta. The implementation to fix this error will probably make this version of the alogrithm take much longer than it's worth, so will be adjusting older, non-matrix form of the algorithm.

- Received feedback from Dr. Kono and Dr. Krupa, will incorporate suggestions
- Saito-sensei had idea, joining to sequences with lowest T (highest and lowest charge, e.g. '10101010' + '01010101'), total charge 0 (T = 1), should have high E field in middle, this is correct! Now have way to design sequence with high E field enhancement
- Continued work on paper, Shoufie-san created figures
- Last day with Shoufie-san! (leaving for Vienna conference)

To do:
- Charge of Fibonacci lattices, find recursion formula?
- Plot cumulative charge, related to E field?
- Develop an algorithm based off the old one that allows for more varied parameters and situations.
- Investigate Kono-sensei's questions from his visit and look at the paper on superradiance he sent, since it's about dipole synchronization.

**August 1-3 [#s77b287e]

- Worked on poster, got feedback from Saito-sensei, Shoufie-san, and lab mates
- Added questions, changed/added colors for better contrast and creating connections, adjusted layout around graph (more info), added contact and acknowledgements

**July 31 [#k90f3d81]
**July 11 [#a7b2b2af]
- Begin retracing steps through both versions of my oscillator program, rederiving carefully the equations and steps used in the first alogrithm.
- Found that the matrix method of the algorithm produced results that seemed strange.

- Visited Yamadera

**July 29 [#y8811abb]

- Continued working on poster
- Leaving party for me and Guo-san
- Guo-san's parents made Chinese dumplings and noodles

**July 28 [#c922bf6b]

- Continued working on poster, neatening layout, almost ready as a first draft
- Saito-sensei gave tips and suggestions on how to present math-heavy, serious topic in way that will attract people
- Suggested cartoons, speech bubbles

**July 27 [#w6ee8469]

- Continued working on poster, making some the graphics
- Tohoku University Open Campus, many high school students visiting, got cool folder and posters
- Saito-sensei came up with formulaic expression for charge of double layer, can now write total charge as a summation on the sequence

**July 26 [#d1b2261b]

- Interviewed Dr. Teng Yang from China Institute of Metals Research for this week's report
- Submitted SCI poster abstract
- Started making poster
- Discussed poster layout with Saito-sensei, moving T spectrum plot showing degeneracy to intro, reducing space for method
- Gave me helpful tips on making presentation more fun and interesting for general audience
- Took another look at group theory, with new perspective of charge
- Number of IR/classes match number of possible charge?
- Tried to define operator on sequence that will give charge, based on similar spin operators

**July 25 [#uda7e806]

- Finished writing mirror symmetry proof in LaTeX, sent to Shoufie-san and Saito-sensei for feedback
- Listened to Pourya-san's defense
- Proved formula for T for even N using induction
- Further developed/clarified/formalized concept of "charge": AB = +1, BA = -1, AA = BB = 0, T is function of total charge of sequence
- Made some significant revisions to abstract to highlights results rather than explain basics
- Planned out poster layout

To do:
- Make draft of poster
- Write outline for paper, in particular order of sections
- Find what is the error in the matrix algorithm and how to fix it.
- Prepare for visit from Kono-sensei and Sarah-san.

**July 24 [#l2d6ba8a]
**July 10 [#a7b2b2af]
- Successfully transfered data from HDD to SSD and began using new SSD.
- Advertised Nakatani program to students visiting from the University of Washington.
- Noticed that my matrix version of the program gave answers not consistent with the previous version of the algorithm. Began immediately looking through code to find potential errors.

- Visited Morioka, had jajamen and chitantan
- Went to Aomori, visited Sannai Maruyama Jomon site, art museum
- Walked around pier, saw huge, amazing nebuta floats in preparation for Nebuta Matsuri next week
- Visited Hirosaki, walked around Hirosaki Park and saw (sort of mini) castle

**July 22 [#pbc05874]

- Finished writing abstract with Saito-sensei and Shoufie-san, both gave final approval
- Started discussing/designing poster
- Discussed suitable journal for publication: Optics Express, Optics Letters, Physical Review X?

To do:
- Finish planning/designing poster layout
- Re-derive the formulae used in both algorithms to see if they are logically correct.
- Look through code again to see if there are any coding errors.
- Begin working on graphing function that'll let me look at previously collected data and "zoom in" on points of interest.

**July 21 [#gbb2670e]
**July 7 [#a7b2b2af]
- Worked on starting tests on the lab computers.
- Met with Saito-sensei and attempted to transfer data from old HDD to new SSD. Transfer was unsuccessful and will be attempted again on Monday.

- Learned basics of LaTeX, started writing mirror symmetry proof
- Worked on writing/discussed abstract with Saito-sensei, Shoufie-san

To do:
- Finish writing abstract, send to Dr. Stanton for approval
- Enjoy Matsushima Bay with mother. 

**July 19-20 [#j9ab6ad8]

- Zao 16 NanoCarbon meeting
- Presented Tuesday night, last speaker
- Took Zao ropeway halfway up mountain, hiked down to lake

**July 15-18 [#ue289e64]

- Met up with family in Tokyo
- Friday Nikko, but was raining so just went to an onsen
- Saturday Tsukiji Market, Miraikan, Odaiba, Ferris wheel, return to HK
- Sunday Chiba, Makuhari Messe, Kaihin Koen, Costco (!), Aeon Mall, Chiba Castle
- Monday met up with Ben, Rony, Youssef in Nagano, Togakushi

**July 14 [#oae71d85]

- Zao presentation practice
- Worked on presentation
- Seem to be "done", have explained pretty much everything
- Seems that group theory is not needed/sort of a dead end
- Discussed possible 2nd quantization view and charge, creation/annihilation operations (adding/removing a '01') to go between T values

**July 6 [#a7b2b2af]
- Returned to lab and worked with Shoufie-san, Shirakura-san and Nugraha-sensei on getting access to the lab computers and running tests.
- Reported to Saito-sensei about the Mid Program meeting and about condition of my computer. Agreed to move data to an SSD.
To do:
- Learn LaTeX, start writing up proofs
- Organize/summarize all findings
- Clear up enough space on HDD to transfer data to new SSD.
- Go over time dependent force in a system and solve equations of motion using Fourier transform.
**July 1-5 [#a7b2b2af]
- Mid Program Meeting in Kyoto.
**June 30 [#a7b2b2af]
- Prepared for departure to Mid Program Meeting.
- Successfully setup Ubuntu on a Virtual Box and began following directions from Shirakura-san on getting access to lab computers.
To do:
- Head to Mid Program Meeting
- Work on Stanton problem.

**July 13 [#kd97c6c6]
**June 29 [#a7b2b2af]
- Linux install was not successful, may be related to my HDD issues. 
- Shift towards using Virtual Box installation of Ubuntu.
- Added finishing touches to Mid Program presentation.

- Picked up Zao travel stipend
- Met JP Nakatani fellow from Tohoku, Miyoshi
- Found formulas for T value for both odd and even N
- Wrote Matlab program to calculate T at central frequency for any arbitrary sequence WITHOUT using transfer matrices (simply counting number of '01' and '10')
- Worked on proof, basic idea adding pair doesn't change TM except for sign (P^2 = -Id)

To do:
- Formalize proofs
- Explore ordering of odd T values wrt. n1:n2
- Submit Mid Prog Presentation.
- Come up with interesting tests to look at.
- Solve the base case presented by Professor Stanton.
 

**July 12 [#y50629bc]
**June 28 [#a7b2b2af]
- Met with Tokyo Nakatani friends
- Continued working on Ubuntu installation, so didn't do more tests on computer.
-Left install running before I left to see if it would finish by my return.

- Meeting Dr. Kono, Sarah, Ogawa-san, and Horikawa-san
- Found atomic site characters
- Wrote proof for double layer permutation
- Looked for pattern in T values, might explain both inversion symmetries (last remaining to prove)

**July 11 [#n6035f32]

- Found 10 conjugacy classes
- Determined isomorphic to D8 x Z2
- Installed GAP, software for computational discrete algebra
- Generated character table for D8 x Z2

To do:
- Find atomic site dot products
- Explain degeneracy?
- See if Linux installed successfully.

**July 10 [#m4606a45]

- Visited Matsushima, took boat cruise from Hon-Shiogama

**July 8 [#z4842272]

- Constructed multiplication table for 4 layers

**June 27 [#a7b2b2af]
- Traveled to Tokyo
- Tried to do more testing on my laptop using the new matrix algorithm.
- Began attempting the base case of the induction approach Professor Stanton suggesting attempting.
- Began trying to setup a Ubuntu dual boot
To do:
- Construct character table for 4 layers
- Come up with interesting cases to look at
- Get Ubuntu installed to begin communicating with lab computers.
**June 26 [#a7b2b2af]
-Tried to keep running experiments on laptop, which was slightly fixed after this weekend. I can run python and access the internet through Google Chrome, but cannot access Skype or Microsoft Office programs on my laptop
- Collected data on 64 oscillator case.
- Began talking to Kazu-san and Shirakura-san about acessing flex and tube computers for later, more intensive tests. Couldn't set up much due to the state of my laptop.
- Made the matrix version of the N oscillator algorithm.

**July 7 [#k5bd683e]

- Found formula for number of patterns in each T value for both even and odd # of layers
- Tried making group of symmetry operations on 2-layer lattices, can't include all operations
- Created multiplication table on restricted operations
- Created character table, does not match degeneracy

To do:
- Find basis for each irreducible representation using projection operator
- Construct multiplication table for 4-layer symmetry operations, adding elements as necessary
- Prepare for departure to Tokyo and mid program meeting.
- Work on fully fixing computer.
- Debug and test matrix algorithm and start using it to do more interesting and variable tests.

**July 3-6 [#o2ba5fb8]

- Mid-program meeting in Kyoto

**July 1 [#le5bcf24]
**June 23[#a7b2b2af]
- Ran experiments with varying numbers of oscillators, with force being applied on a fraction of the oscillators.
- Found that increase in oscillators in general leads to a larger synchronization oscillation amplitude.
- Also saw that if half the oscillators had an applied force, the time it takes for full synchronization approximately doubles.
- Computer suddenly slowed down and can't open some applications now.

- Unable to connect to new drive once again...
- Booted successful by connecting drive via USB, temporary solution, need new HD cable
- Finally able to work on mid-program meeting presentation
- Looked for pattern in number of sequences at each T value

**June 30 [#e7852171]

- Could not install OS, Mac wouldn't even recognize presence of new hard drive
- After ~15 times opening up Mac, adjusting connection, trying with old HDD, following guides and advice online like using tape, FINALLY some combination of the various fixes worked
- Finally installed OS, restored all my files from Time Machine backup
- Slowly reinstalling apps as needed, less space now

- Meanwhile finally found last two hidden symmetries, to explain all operations to get to different patterns with same T!!
- Arbitrary permutation of double layers, pair inversion
- Can explain N/2 + 1 possible T for even layers using generalized concept of pairs: two of the same separated by even number of layers

To do:
- Make presentation and practice
- Prove total inverse, double permutation, and pair inversion symmetries (probably using fact that P^2 = -Id)
- Find all products of operations, adding elements to make closed group
- Find mathematical pattern for number of sequences in each T for arbitrary N-layer
- Proofread Shoufie-san's paper
- Fix computer!!
- Write pseudocode for the matrix implementation.
- Take a look at system on paper to explain the results found today?

**June 29 [#z0c582d9]

- OS install failed, continued trying multitude of things to repair disk, but no matter what unable to repair
- Concluded must be hard drive failure
- BUT saito-sensei gave me a new one! Almost exact same, same brand/year, 320 vs old 500 gb, helped me install
- Discussed mid-program presentation
**June 22 [#a7b2b2af]
- Touched up on presentation
- Presented presentation to Saito-sensei, who gave some more useful suggestions on how to touch it up.
- Continued reading through Pine's paper, specifically on the description of collective electron movement and the screening effect.

To do:
- Install OS on new drive and restore files
- Figure out effect of number of oscillators on the amplitude of position oscillation
- Apply force for a limited time and for a fraction of the total oscillators; this requires that I finish up the matrix version of my Python code so...
- Finish the matrix version of N Oscillators
- Also learn more about screening effect in electrons and its consequences.

**June 28 [#g9cdd8df]
**June 21 [#a7b2b2af]
- Finished working on draft for powerpoint presentation and showed to Saito-sensei
- Using feedback from Saito-sensei, began reworking the presentation.
- Started reeding David Pines 1952 paper on plasmons to get better idea of plasmons.

- Computer crashed! Working on repairing computer
- Main partition seems corrupted, reinstalling OS
- Proved cyclic symmetry, as well as several smaller lemmas and corollaries

To do:
- FIX MAC ASAP
- Fix up the presentation
- Gain better understanding of Pine's paper
- Work on the matrix version of N oscilaltors Runge-Kutta appproximation

**June 27 [#kbbb7e86]

- Worked on proving cyclic symmetry, found several useful lemmas e.g. regarding product of "chain" matching matrices
- Looking for last hidden symmetry/ies
**June 20 [#a7b2b2af]
- Finished code that animated the position vs. velocity graphs for small oscillators.
- Started making presentation for Mid Program Meeting
- Began looking at Kuramoto Model

**June 26 [#z40e08bc]

- Visited Sendai Mediatheque (public library/exhibition space)

**June 24 [#sc1d1c33]

- Found cyclic symmetry
- Found pattern in number of T values: N + 1 for odd, N/2 + 1 for even
- Calculated eigenfunctions and eigenvectors of TMs, will require further investigation

To do:
- Read first 3 chapters of graph theory textbook
- Prove cyclic symmetry
- Finish a draft of presentation for Mid Program Meeting
- Try to learn more about plasmons and phonons and the Kuramoto model.
- Begin thinking about questions to ask self and explore consequences of these questions.

**June 23 [#v7050c05]
**June 19 [#a7b2b2af]
- Coded an animation of two waves, one cosine, the other sine, using matplotlib animation on Python.
-Made code that plots position vs. velocity of a small oscillator.

- Proved mirror symmetry
- Searched for patterns
- Even and odd have different behavior
- Even has inversion (A<->B) symmetry

**June 22 [#t9d0a840]

- Created frequency vs discrete T plot, and T vs Gray code plot for 4 layers
- Identified sequences with identical transmission spectra, found symmetry (e.g. 1101 = 1011)
- Investigated effect of flipping one bit on E field for 4 layer system, still looking at and trying to interpret results (but does not seem to be chaotic at least)

To do:
- Prove using induction that mirrored sequences give identical transmission
- Start making presentation for Mid Program Meeting
- Figure out how to animate the position vs velocity graphs over time.
- Think about how to implement Python matrices into program in order to make it easier to come up with and implement more variations and parameter changes.

**June 21 [#a66d9fdc]

- Talked to CS major friend about problem, suggested hill climbing and genetic algorithms
- Doesn't think there is a need to use machine learning to predict transmission, because we already have a program to do it exactly! ML is only for when you don't know how to program an algorithm to solve the problem
- Agreed that truly chaotic behavior would make any algorithm, including neural networks, not work (imagine predicting a RNG)
- Tried to see what effect of changing one bit really is
- Found that transmission probability is discrete!
- Changing one bit can only move to one level above or below
- Investigated effect of number of layer and changing dielectric constants, levels only depend on ratio between dielectric constants
**June 16 [#a7b2b2af]
- Went over phase and its relation to the position and velocity of a particle. 
- Discussed fully how to use Fourier Transform in solving differential equations.
- Finished coding and running Runge-Kutta program for 2,3,4,and 5 oscillators, with varying initial conditions and parameters.

To do:
- Create frequency vs discrete T plot, and T vs Gray code plot for small number of layers
- Plot phases of particles in phase space.
- Look into how to animate in python or some other software if necessary.
- Figure out how to implement matrix math in python to make future customization of N oscillators problem easier to implement.
- Take a look at WXMaxima computer algebra system 
- Weekend: Report on the quality of Ramen Jiro, and check out Sendai Castle, while exploring other parts of the city.

**June 20 [#t023b203]
**June 15 [#a7b2b2af]
- Learned about different ways to derive and interpret Q value, in particular, Saito-sensei showed me a method using the Fourier Transform, which worked well in deriving values for overdamped and underdamped oscillators. 
- Formalized and derived motions of equations for a system of N small oscillators on top of one larger oscillator
- Wrote up algorithm for doing a Runge-Kutta approximation for N oscillators.

- Found hole/security flaw in SquirrelMail webmail
- Wrote abstract for Zao meeting
- Researched GPUs for deep learning
- Deployed catnet on Matlab, initial tests were big success
- Figured out MNIST wasn't working because of simple division/rescaling of input, not sure if working
- Learned how to use Matlab read/write to file, played with different formatting for saving data

To do:
- Create database of transmission spectra and E field plots
- Compile training data using random 100-layer sequences?
- Try to train with catnet (imagenet)
- Talk to CS friend about how to implement, what type of neural network
- Use Fourier Transform to solve differential equations of 2nd order involving constant and nonlinear forces.
- Code the algorithm that I've written up for Runge-Kutta for N osciallations.

**June 18 [#y0774c6e]

- Sendai castle adventure
- Performance group

**June 17 [#xc697d1e]
**June 14 [#a7b2b2af]
- Finished getting Fast Fourier Transform to work on data points for the system described by two oscillators and plotted the dominant frequencies of the system. Also played around with parameters to see how that would affect the steady state frequency and synchronization.

- Finally got MatCaffe working, MNIST does not seem to be working
- Installed Caffe (/liu/caffe) on tube61 (Ubuntu 15.04) with ATLAS, CPU-only, ran catnet, still slow, maybe even slower than Mac! (~6 min/20 iterations)
- Moved cat images to flex, continued training
- Installed OpenBLAS on tube61 to try to rebuild Caffe with OpenBLAS
- Installed Intel MKL (commercial, got free student license) on tube60, installed caffe (/liu/research/caffe) on tube 60 (Ubuntu 12.04) with MKL, CPU-only, not yet tested catnet

To do:
- Rebuild with OpenBLAS
- Finish training catnet
- Look into OpenMP for parallel processing support, OpenMP+MKL gives performance comparable to GPU
- Derive Q value for a critically damped system, overdamped system, underdamped system.
- Extend Python function to evaluate system for an arbitrary N oscillators. 
- Think about how to measure synchronization of a system and find the phase difference between two objects in a system.

**June 16 [#n78ac706]

- Downloaded 7000+ cat and dog images
- Training catnet is slow! 5 min/20 iter (1000 in total)
- Downloaded MNIST dataset, trained in about ~10 mins
- Python wrapper installed properly, MATLAB not working, so can't yet deploy
**June 13 [#a7b2b2af]
- Got Fast Fourier Transform to work in Python, plotting a line graph that shows the dominant frequencies of the system, whose position is approximated by the previously written Runge-Kutta Approximation program. 
- Attended group meeting and watched Tatsumi-san's presentation of his Doctorate Thesis

To do:
- Test MNIST by deploying on either Matlab or Python
- Look into GPUs, Saito-sensei might buy one to install on lab server
- Find the engineering applications of synchronization.
- Learn about Q value 

**June 15 [#r9bce1de]

- Talked with Shoufie-san about basics of neural networks, showed him the power of genetic algorithms, discussed ideas on how to use networks to find/generate good sequences
- Continued troubleshooting constant errors, build Caffe, but make runtest failing
- Found that laptop's GPU is too old, not powerful enough, built in CPU-only, finally passed all tests

To do:
- Learn how to use Caffe, run example programs MNIST and catnet
- Install MATLAB and Python wrappers/interface

**June 14 [#a7b2b2af]

- Installed Homebrew, Miniconda (lightweight Anaconda Python distro)
- Installed CUDA, other libraries Caffe has as dependencies
- Saito-sensei invited me to join Zao NanoCarbon Meeting, gladly accepted!
**June 12 [#x5e79f4d]
- Finished writing a Python program to approximate and graph solutions for coupled linear differential equations using the Runge Kutta method.
- Met with Saito-sensei and Shoufie-san and discussed Fourier transform
- Found an implementation in Python of Fast Fourier Transform with Shoufie-san and used it to plot already known functions in the frequency domain.

To do:
- Install Caffe

**June 13 [#x5e79f4d]

- Found that integral based error function never gave good score, max ~30 on linear conversion scale for 10 layer system
- Experimented with designing evaluation function based on Q factor for transmission, enhancement and position for E field
- Watching some videos online to learn the basics of how deep learning is implemented, as well as see more examples.

To do:
- File read/write to avoid recalculating every time
- Install Caffe
- Implement Python program on example from Thursday
- Figure out how to implement Fast Fourier Transform on discrete data set in Python. 

**June 10 [#cde372e6]

- Adapted MATLAB programs calculate transfer matrix and plot transmission and enhancement for any arbitrary sequence
- Wrote error function
- Lab party!
**June 9 [#cde372e6]
- Discussed with Shoufie how to extend the Runge-Kutta algorithm I made for a system of a single differential equation to a system of many coupled differential equations. Learning how to better implement matrices in python looks like it'll be helpful.
- Found out that my derivation for Euler-Lagrange equation involving non-conservative forces had a mistake that led to different results than expected. Will be looking over and correcting it this weekend.

To do:
- Evaluate scaling functions (0-100)
- Enjoy the weekend and check out the Kizuna Matsuri, which will be in town.
- Fix derivation of Euler Lagrange equation and apply it a simple situation to verify it works, and then apply it to the more complicated example I discussed with Saito-sensei on Thursday.
- Find damping of a system as a function of frequency. 

**June 9 [#i5309127]
**June 8 [#i5309127]

- Wrote MATLAB program to plot intensity of E field in Fibonacci lattice as function of position (z), looked at positions of enhancement
- Solved problem for HW and did some more exercises with Lagrangian mechanics and ODEs. 
- Learned about an example of synchronization phenomenon with Saito-sensei. Involved first getting equations of motion using Lagrangian mechanics, then applying Linear Algebra and differential equations. Ended up with system that was not analytically solvable and needed to be numerically approximated. 
- Worked on deriving Euler-Lagrange equation in systems with non-conservative forces.

To do:
- Adapt code to calculate transfer matrix and plot transmission and enhancement for any arbitrary sequence
- Design error function (0-100 scale) to measure how close a given transmission or enhancement spectrum is to a target spectrum
- Look into Caffe machine learning
- Begin learning how to plot equations effectively. JSXGraph looks very promising, but difficult to learn.
- Design programs to numerically solve differential equation systems. Start off with Euler's method, than build upon that to do the Runge Kutta method.
- Solidify understanding of EL in non-conservative situation to the extent that I can follow and present the derivation.
**June 7 [#p0ecbca1]

**June 8 [#p0ecbca1]
- Walked to campus, took the right path, so it only took about 25 mins to make it to the lab.
- Plotted results for last night's HW with varying parameters.
- Practiced getting equations of motion for more complicated systems using Lagrangian Mechanics.
- Considered systems with damping forces and modelled motion using differential equations.

- Wrote MATLAB program to construct transfer matrix for n-th Fibonacci lattice
- Plotted transmission probability as a function of frequency, 10th gen made a nice looking fractal

To do:
- Clean up MATLAB code
- Plot E field in Fibonacci lattice as function of distance (z), see points of most enhancement
- Apply linear algebra and ODEs to solve a general second order differential equations problem.
- Learn how to solve ODEs and linear algebra questions using python(Start with Euler's approximation method).

**June 7 [#u2633c67]
**June 6 [#u2633c67]

- Walked to campus, took around 30 mins
- Found explicit formula for n-th Fibonacci number, and wrote Python program to generate n-th iteration of the Fibonacci fractal
- Had lunch with Hasdeo-san, bought lunch by weight from cafeteria (entrees 1.4 yen/g, rice .43 yen/g)
- Derived matching (boundary) and propagation matrices in transfer matrix method, used to calculate R and T probabilities for comparison
- Derived E and H relations from Maxwell's equations (Ampere's)
- Introduced myself at group meeting, shared some omiyage from China
- Set up printer over LAN, had to install driver manually
- Walked to campus, got lost at campus. Took about 45 mins.
- Finished working on HW about action and the Euler Lagrange equation
- Worked on learning about differential equations.
- Worked on applying Lagrangian mechanics to double pendulum. 
- Had lunch with Nulli-san at Espace Ouvert
- First "experiment": synchronization of vegetable can movement within a box due to forces exerted while carrying it and walking at a certain pace.

To do:
- Check that theory agrees with Snell's Law
- Construct transfer matrix for n-th Fibonacci lattice
- Solve equations of motion for a box on a spring with some initial external force over a fixed period of time, both before and after external force is removed.
- Numerically solve ODEs in Python(perhaps using numpy and scipy packages).

**June 5 [#x0e34f61]
- Shoufie-san picked me up from Urban Castle Kawauchi, took me to campus by subway (International Center -> Aobayama, 250 yen ~20 mins total)
- Nugraha-sensei helped me set up lab server access, mail client, etc.
- Got a quick bento lunch on campus and ate with Saito-sensei who played his ukulele
- Learned about Lagrangian mechanics, specifically in the context of a simple pendulum.
- Learned a bit about the general solutions to second-order differential equations.


To do:

- Learn what "action" in physics is
- Derive the Euler-Lagrange Equation