Here is a daily log for Haihao Liu from 2016.6.6 to 2016.8.5 in Saito Lab in Tohoku Univ.

Daily schedule (tentative)

  • 10:00-12:00 Finishing/continuing any work from previous day
  • 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

Goal of the project

  • (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
  • (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

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)

A: (Placeholder)

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.

August 5

  • 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!

To do:

  • Find relationship between cumulative charge and peak E field, power law?
  • Write and publish paper

August 4

  • 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?

August 1-3

  • 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

  • Visited Yamadera

July 29

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

July 28

  • 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

  • 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

  • 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

  • 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

July 24

  • 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

  • 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

July 21

  • 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

July 19-20

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

July 15-18

  • 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

  • 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

To do:

  • Learn LaTeX, start writing up proofs
  • Organize/summarize all findings

July 13

  • 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

July 12

  • 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

  • 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?

July 10

  • Visited Matsushima, took boat cruise from Hon-Shiogama

July 8

  • Constructed multiplication table for 4 layers

To do:

  • Construct character table for 4 layers

July 7

  • 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

July 3-6

  • Mid-program meeting in Kyoto

July 1

  • 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

  • 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

June 29

  • 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

To do:

  • Install OS on new drive and restore files

June 28

  • 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

June 27

  • Worked on proving cyclic symmetry, found several useful lemmas e.g. regarding product of "chain" matching matrices
  • Looking for last hidden symmetry/ies

June 26

  • Visited Sendai Mediatheque (public library/exhibition space)

June 24

  • 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

June 23

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

June 22

  • 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

June 21

  • 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

To do:

  • Create frequency vs discrete T plot, and T vs Gray code plot for small number of layers

June 20

  • 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

June 18

  • Sendai castle adventure
  • Performance group

June 17

  • 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

June 16

  • 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

To do:

  • Test MNIST by deploying on either Matlab or Python
  • Look into GPUs, Saito-sensei might buy one to install on lab server

June 15

  • 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

  • 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!

To do:

  • Install Caffe

June 13

  • 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

June 10

  • Adapted MATLAB programs calculate transfer matrix and plot transmission and enhancement for any arbitrary sequence
  • Wrote error function
  • Lab party!

To do:

  • Evaluate scaling functions (0-100)

June 9

  • Wrote MATLAB program to plot intensity of E field in Fibonacci lattice as function of position (z), looked at positions of enhancement

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

June 8

  • 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

June 7

  • 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

To do:

  • Check that theory agrees with Snell's Law
  • Construct transfer matrix for n-th Fibonacci lattice

June 6

  • Shoufie-san picked me up from Urban Castle Kawauchi, took me to campus by subway (International Center -> Aobayama, 200 yen ~20 mins total)
  • Nugraha-sensei helped me set up lab server access, mail client, etc.
  • Bento lunch from Espace Ouvert restaurant (next to 7-11 on bottom floor of new building), ate with Saito-sensei who played his ukulele
  • Learned how to derive boundary conditions for EM wave passing from one dielectric media to another, using Maxwell's equations (Faraday's and Ampere's)
  • Solved for reflection and transmission probabilities at boundary for normal incident wave

To do:

  • Test SHH from dorm room
  • Read pages on reflection and transmission of EM waves at boundary, and derive probabilities for both TE and TM both of oblique incident waves

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Last-modified: 2016-08-13 (Sat) 10:30:35 (406d)