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Contents
Personal Information
My name is Amanda Wert and I am a double major in Math and Computer Science at Benedictine College in Kansas. I am planning on graduating in December of 2012 and hopefully move back to Appleton, Wisconsin and be a software developer.
Time Log
Week 1
Tuesday, May 31
 Was orientated
 Learned expectations
 Toured campus
 Filed paperwork
Time: 6 1/2 hrs
Wednesday, June 1
 Worked with the Wiki
 Created user page and updated recent activities
 Met with Dr. Spiller and Dr. Scott and received readings
 Read the first chapter of a textbook on Chaotic Dynamics
 Read Driscoll, Tobin A. Learning MATLAB. 2009 Chapters 14 and 6
 Played around with MATLAB
 Reread Learning MATLAB chapter 2
 Read Chapter 6 (Diff Eq) section 1 (IVP and Euler's Method) of a textbook on Numerical Analysis
Time: 8 hrs
Thursday, June 2
 Reread Learning MATLAB chapters 3 and 4
 Feel very comfortable with MATLAB and prepared to examine the code I'll be working with
 Researched Linear Shallow Water Equations online
 Found general background information but did not find an understandable technical description of the equations or how to use them
 Met with Dr. Scott and discussed:
 The code for the program that measures how a fluid particle's path covers the sample space among other things
 Goals for the summer
 Pere the super computer
 Logged onto Pere
 Went to the talk by Dr. Factor on good research practices and learned:
 To be careful because internet sources can lie
 To be both thorough and reasonable
 The goal of the summer is to gather information to make a conjecture and then support it
 Listened to a presentation on how to use the library online resources
 Familiarized myself with the Ergodic Defect script
 I am comfortable with what the program is doing though not with all the technical math behind it
 Read about how to submit jobs to Pere and looked up words/concepts I didn't know
 Need to find out how to run the job in Octave
 Skimmed Condor manual: http://www.cs.wisc.edu/condor/manual
 Began skimming Apte, Jones, Stuart. A Bayesian approach to Lagrangian data assimilation. 2007.
Time: 8 hrs
Friday, June 3
 Reviewed the Ergodic Defect script
 I am now very comfortable with everything the program does though still not with all of the technical math behind it
 Reviewed the Runge Kutta 4 script
 Reread the first chapter of a textbook on Chaotic Dynamics
 Played with the Ergodic Defect script
 Researched Condor
 Unsure how to submit MATLAB jobs but does not matter as I will be now using PBS/Torque
 Met with Dr. Scott
 Discussed goals
 Emailed Feng for help with Condor
 Answered my questions on the scripts
 Worked with Feng
 He showed my how to submit jobs using PBS :)
 Worked with PBS on my own
 I now know how to submit jobs and edit things on ssh
 Added goals and project page to wiki
Time: 6 hrs
Saturday, June 4
 Read Chapter 6 (Diff Eq) sections 14 of a textbook on Numerical Analysis
 Skimmed Apte, Jones, Stuart. A Bayesian approach to Lagrangian data assimilation. 2007.
Time: 4 hrs
Week 2
Sunday, June 5
 Read Chapter 6 (Diff Eq) sections 57 of a textbook on Numerical Analysis
 Read Apte, Jones, Stuart. A Bayesian approach to Lagrangian data assimilation. 2007.
 Sections 1 and 2
 Looked at running Ergodic Defect script in Pere
 How to put changing inputs in and get intelligible outputs out
Time: 3 hrs
Monday, June 6
 Reread the first chapter of a textbook on Chaotic Dynamics
 Worked with MATLAB and Pere
 Ran MATLAB functions that took input and output files on both
 Made an edited version of the Ergodic Defect script that takes an input file and writes to an output file
 Ran the edited version on Pere
 Ran an array of jobs using different inputs of the edited version on Pere
 Reviewed the two uses of Runge Kutta 4 Methods for Ergodic Defect Script
 Became more familiar with LSW equations
 Made a generic Runge Kutta 4 method for a system of up to 4 equations
 Put as a subfunction into a modified Erg Def script and used for flow field RK
 Same speed (maybe a bit slower)
 Should be useful when the third dimension will be added
 Put as a subfunction into a modified Erg Def script and used for flow field RK
 Wrote a program that will generate input files for the parameter sweep
 Still needs to be tested
 Reexamined Ergodic Defect code to prepare for adding a third dimension
 Marked places where dimension matters
 Rewent through variables to better understand calculations
 Need to finish this tomorrow morning
Time: 9 hrs
Tuesday, June 7
 Tested the input writing program
 Got everything ready in Pere to run a parameter sweep
 Finished going over variables to better understand calculations
 Edited Ergodic Defect code to easily take a third dimension
 Met with Dr. Spiller, Regis, and Paul to discuss Numerical Analysis theory
 Looked at previous posters and made a rough outline for presentation
 Read for background information
 Shalizi, Cosma Ergodic Theory
 Scott, Sherry E., et al. “Capturing deviation from ergodicity at different scales.” Physica D, 2009.
 Vreugdenhil C.B. "Numerical Methods for ShallowWater Flow" Kluwer Academic Publishers. Dordrecht, The Netherlands. 1994.
 Acheson D.J. "Elementary Fluid Dynamics" Oxford University Press, Oxford. 1990.
Time: 9 hrs
Wednesday, June 8
 Read Learning MATLAB chapter 5 for knowledge of graphics
 Researched MATLAB graphics functions
 Found  MathwWorks' MATLAB Help Section very useful
 Sketched out what would needed for a grayscale picture of the ergodic defects of individual trajectories
 Met with Dr. Scott to discuss making the ergodic defect picture
 Implemented the code and got a picture
 Tried to run on Pere
 Had problems with writing/displaying the picture as output
 Found out I was using functions from the Image Procession Toolkit which the version of MATLAB on Pere does not have
 Feng Xizhou fixed that for me :)
 Now it works perfectly and is the version I am using
 Worked on a method of drawing the picture that does not use those functions
 Continued working after the problem was fixed because this way may be better overall
 Ended up failing
 Changed the script to calculate the average of individual ergodic defects at 5 scales
Time: 9 hrs
Thursday, June 9
 Added additional outputs to average picture script
 Got Pere ready
 Skimmed Rypina, I.I., et al. "Investigating the connection between complexity of isolated trajectories and Lagrangian coherent structures." 2011
 Met with Dr. Scott
 Submited the base case
 Went to the working lunch
 Worked on adding a title to the picturedidn't work
 Worked on creating a scale diagram to go with the pictures
 Tried to remote log onto Pere from home but it didn't work
Time: 7 hrs
Friday, June 10
 Tried to log onto Pere
 Had to go through Pascal and then Pere shut down
 Tried to download Octave
 Didn't work
 Handwrote plan for some cases Dr. Scott requested because text editor on Pascal wasn't working
 Typed up and ran the cases until Pere shut down again
 Pretty sure they are bug free and will quickly run in the morning
Time: 4 hrs
Saturday, June 11
 Ran the cases Dr. Scott had asked for
 The base case with the same gray scale
 The trajectories of the two particles
 Started the parameter sweep
 Ran the first 500
 Found out Monday I had made a mistake and would have to rerun
Time: 3 hrs
Week 3
Monday, June 13
 Discovered I had a problem with the inputs for my parameter sweep
 Fixed it and restarted the sweep
 Made a gray scale diagram for the LSW pictures
 Met with Dr. Scott and discussed:
 Parameter sweep
 MMW flows
 Future applications
 Reread Apte, Jones, Stuart. A Bayesian approach to Lagrangian data assimilation. 2007.
 Read the beginning of Malhotra, Mezic, Wiggins. Patchiness: A New Diagnostic for Lagrangian Trajectory Analysis in TimeDependent Fluid Flows. 1998.
 Compared the equations for the two
 Adjusted the Ergodic Defect code to use the MMW equations
 Edited/cleaned up my project page on the wiki
 Found out I was doing the parameter sweep inefficiently
Time: 8 hrs
Tuesday, June 14
 Printed off pictures of MMW in preparation for meeting with Dr. Scott
 Added titles to the pictures
 Troubleshooted with Pere
 No jobs I submit will run
 Met with Dr. Scott and discussed:
 MMW flows
 Trajectories
 She gave me code that another student had made that made a movie of the flow
 Went to a talk on Good Research Presentations and Good Research Papers by Dr. Brylow
 Worked with the MMW trajectories
 Realized my problemI had forgotten to modify the mod function when I modified the rest of the code
 Fixed that
 Made the ergodic defect picture drawing scripts more efficient
 Combined loops and used a build in function in find(...) instead of max(find(...))
 Thought about where I wanted to go with my research
 Tried different things on Pere to get it to work
 Worked with trajectories to make sure I had the correct code
Time: 9 3/4 hrs
Wednesday, June 15
 My birthday! whoot!
 Worked with the trajectories to try to make Fig. 2 from the MMW paper
 Went to the conference on cloud computing in Appleton
Time: Conference + 3/4 hrs
Thursday, June 16
 Used Gabe's code to make a movie of the MMW trajectories
 Tried to run the parameter sweep
 Pere was working but then it stopped...:/
 Working lunch
 Went to a required NSF talk on Research Ethics
 Met with Dr. Scott
 Made small edits to MMW script
 Started the 10 T's but again, Pere won't run any jobs
 Started reading Bullitt, Elizabeth, et al. "Measuring Tortuosity of the Intracerebral Vasculature from MRA Images." 2003.
Time: 8 1/2 hrs
Friday, June 17
 Read Bullitt paper
 Thought about how to measure ergodic defect of sine graphs
 Edited code to measure the ergodic defect of sine graphs
 Varying frequency and amplitude
 Tried to submit jobs in Condor because Pere still wasn't running the jobs
 Didn't work
 Ran sine graph code to see if there is a correspondence with tortuosity
 I couldn't find one
 Made a code that drew the trajectories for the sine graphs
 Learned how to use Condor from Adam
 Met with Dr. Scott
Time: 7 hrs
Week 4
Monday, June 20
 Organized and prioritized tasks to be completed
 Run MMW sweep for the various T's
 Skimmed RomKedar, V., and Poje, A. C. "Universal Properties of Chaotic Transport in teh Presence of Diffusion." 1999.
 Set up the RomKedar flow script
 Did not find explicit u and v so used my calculator to solve for the complicated partial derivatives
 Fixed the dxdy problem for MMW, tortuosity, and RomKedar
 Hadn't been using the correct area
 Skimmed Scott, Sherry E., et al. “Capturing deviation from ergodicity at different scales.” Physica D, 2009.
 Researched various terms on google to try to understand the underlying math and notation
 Adjusted domain of tortuosity d value calculations
 Made code for the coil tortuosity
Time: 9 1/2 hrs
Tuesday, June 21
 Collected output from LSW parameter sweep
 Tried to print the toruosity trajectories for the new domain
 There was some problem either with the moding or the plot function, the trajectories were unintelligible
 Looked at the problems in the script with calculating the defect
 The normalization factor and maybe another constant had gotten lost from the code
 Fixed RomKedar code for ln instead of log10
 Skimmed Capturing deviation from ergodicity at different scales some more
 Fixed the sine trajectory picture
 Cleaned up various scripts
 Added normalization factors to various scripts
 May not be needed...
 Skimmed some papers on chaotic advectation
 Went through the LSW parameter sweep data to look for patterns
Time: 9 hrs
Wednesday, June 22
 Looked at the temperature data
 Consolidated the LSW parameter sweep data into a single matrix
 Made graphs using data
 Skyped/talked with Dr. Scott
 Found a way to save the trajectories of the particles in the flow
 Started jobs to get more detail on h1=+.5
 Thought about how to make the code faster
Time: 8 hrs
Thursday, June 23
 Made trajectory movies
 Examined data
 Grayscale pictures
 Individual trajectory
 Made combined graphs for Avg d vs u1 and Avg d vs h1 with the varying other parameter (u1 or h1)
 Working lunch
 Made the script much faster
 Wrote outline for presentation
 Worked more with the movies
 Skyped with Dr. Scott
Time: 9 hrs
Friday, June 24
 Made more combined graphs
 Adjusted code for mapping
 Made tortuosity pictures
 Worked with the LSW movie
 Obtained tortuosity sine data
 Worked with coil toruosity
 Varies u0 to see if the step size needs to be increased
Time: 8 1/2 hrs
Week 5
Monday, June 27
 Finished varying u0
 Do not need to change step size
 Made pictures of the coil trajectories
 Wrote setup sheets for tortuosity and MMW
 Obtained tortuosity coil data
 d values, xyindcounts, and pictures
 Tested for number of uncounted boundary cases
 Very few compared to the number of counts so its ok
 Skimmed the chapter on LSW to review for presentation
 Ensured synthetic tortuosity matched the Bullitt et al 2003 paper
 Had trouble with corresponding same start/end voxel
 Reread the tortuosity paper
 Worked on my presentation
 Met with Dr. Scott
 Worked u0
Time: 9 hrs
Tuesday, June 28
 Worked on presentation
 Made the start/end voxels the same for tort
 Ready Rypina paper on Largrangian structures and Scott paper on ergodic defect
 Met with Dr. Scott
 Set up u0 varying parameter sweep
Time: 8 hrs
Wednesday, June 29
 Worked on presentation
 Made the coil 3d
 Worked with u0 data
 Finished collecting and consolidated data
 Reread Scott, et. al on the Ergodic Defect
Time: 7 hrs
Thursday, June 30
 Worked on presentation
 Thought about how to use ergodic defect to measure tortuosity effectively
 Listened to other present and gave my presentation
 Worked with u0 data
 Tried to figure out an informative way to graph
Time: 8 hrs
Friday, July 1
 Read various papers for background info
 Looking for inspiration on how to process LSW data and how to measure tortuosity
 Worked with u0 data
 Researched vessel segmentation
 Read on chaotic advection
Time: 7 hrs
Week 6
Tuesday, July 5
 Worked on making tortuosity sampling evenly spaced
 Read on chaotic advection
 Went to a talk on making a good poster
 Started 3 small parameter sweeps exploring
 LSW for h1=0:0.01:0.1 and u1=0.5:0.1:0.5
 LSW for h1=0.3:0.1:0.5 and u1=5:0.1:1.9
 MMW for Epsilon 0:.05:0.5 and T=0.5:0.5:3
 Found out I made a mistake and so restarted the run on Thursday
Time: 9 hrs
Wednesday, July 6
 Worked with the temperature data
 Consolidated and calculated ergodic defects
 Made grayscale pictures
 Dealt with the NaN values
 Broke the data into 4 sets for more detailed graphing
 Worked with tortuosity
Time: 8 hrs
Thursday, July 7
 Consolidated data from the small parameter sweeps from Tuesday
 Fixed MMW and restarted small sweep
 Worked with the tortuosity data
 Cleaned up folders
 Working lunch
 Listened to a talk by Dr. Struble
Time: 7 hrs
Week 7
Monday, July 11
 Worked with the tortuosity data
 Wrote a program to automatically write the excel file for me
 Consolidated the MMW data
 Edited the sine and coil scripts so that the number of scales can be varied
Time: 8 hrs
Tuesday, July 12
 Worked with the tortuosity averaging scales 3 to 5
 Put comments in code describing purpose and reasoning
 Tortuosity
 LSW
Time: 8 hrs
Wednesday, July 13
 Fixed the Arclength program
 Used it to calculate the ergodic defect of the sine waves
 Made the tortuosity set up sheet more detailed
 Worked with the Rom Kedar flows
 Fixed the equations
 Attempted ways to make it faster
Time: 7 1/2 hrs
Thursday, July 14
 Made sure everything in the tortuosity and Rom Kedar sections were good to go
 Made the LSW set up and observations sheet more detailed
 Added observations to the detailed tortuosity set up sheet
 Went to the working lunch
 Further commented the code
 MMW
 Rome Kedar
 Temperature
 Started editing code to calculate the ergodicity defect of the temperature of the floats
Time: 8 1/2 hrs
Friday, July 15
 Finished editing the code to calculate the ergodicity defect of the temperature of the floats
 Made grayscale pictures
 Made a comparison graph between the two types of defectsposition and temperature
 Proofed comments of various codes and made more detailed
 Went over comments from the presentation to improve for next time
 Read the paper on the Loop Current in the Gulf of Mexico
 Calculated the defect for more detailed synthetic sine wave data
 Met with Dr. Scott and went over:
 MMWhow to get fig 2.
 Rom Kedar  how to get fig 3 and 4
Time: 7 1/2 hrs
Week 8
Monday, July 18
 Tried various ways to make fig 2 pic 1 for MMW
 Tried to make fig 3 for Rom Kedar
 Didn't succeed at all
 Met with Dr. Scott and discussed:
 Other ways to get MMW and Rom Kedar right
Time: 7 1/2 hrs
Tuesday, July 19
 Set up more detailed u0 sweep
 Made movies of various trajectories
 Tried to make fig 2 pic 1 for MMW
 Somewhat succeeded but mine is more continuous
 Tried to make fig 3 for Rom Kedar
 Didn't succeed at first
 Ran for a much longer time interval and it worked
 Met with Dr. Scott to discuss achievements so far
 Played around with LSW trajectory movies
Time: 8 1/2 hrs
Wednesday, July 20
 Examined relationship and effects of parameters
 Why white line is where it is when u0=0
 What happens as you vary u1 and h1 for u0=0
 Examined change as u0 approaches 0
 Made trajectory movies
 Documented observations so far
 Consolidated u0 data and graphed
 Tried to get fig 3 from Rom Kedar
 Succeeded in fig 3c
 Met with Dr. Scott to discuss current progress
 Tried to obtain fig 2 from MMW
Time: 8 hrs
Thursday, July 21
 Ran some trials with u1=u0=0 for a larger endt
 Tried to obtain fig 2 from MMW
 Was able to get a discrete grayscale like theirs
 Worked on my final presentation
 Made some movies of LSW gray scale pictures
 Went to the working lunch
 Met with Dr. Scott and discussed
 Tortuosity data to come tomorrow! :D
 Crazy LSW behavior
 Thought about why certain LSW behavior occurs
 Got a script ready to process the real tortuosity data for tomorrow
Time: 9 1/2 hours
Friday, July 22
 Explored why the the white line appears where it does
 Reread MMW and tortuosity
 Looked at LSW with different endt
 Tried to reproduce fig 2 of MMW
Time: 6 hrs
Week 9
Monday, July 25
 Found the mean Temperature values
 Worked on my poster
 Tried to get the tortuosity software to work
 Met with Dr. Scott
 Extracted vessel XYZ data and tested with script
Time: 9 hrs
Tuesday, July 26
 Played around with Paraview
 Worked on my poster
 Met with Dr. Scott
 Made graphs for the tortuosity
Time: 7 1/2 hrs
Wednesday, July 27
 Worked on my poster
 Fixed the problem with LSW quiver plots
 Played around with tortuosity data
Time: 7 1/2 hrs
Thursday, July 28
 Worked with tortuosity data
 Documented my work with LSW
 Went to the working lunch
 Met with Dr. Scott
Time: 8 hours
Friday, July 29
 Worked on my abstract for my final talk
 Worked with tortuosity data
 Met with Dr. Scott
Time: 10 1/2 hrs
Week 10
Monday, August 1
 Worked with tortuosity data
 Met with Dr. Scott
 Submitted our abstract for the SPIE conference
 Worked on presentation
Time: 7 hrs
Tuesday, August 2
 Presented posters
 Worked on presentation
Time: 5 hrs
Wednesday, August 3
 Worked on presentation
 Gave and listened to presentations
 Worked on final paper
Time: hrs