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	ID	Date	Author	Subject
	10	Tue Mar 5 16:36:51 2019	Julie Rolla	3/5 Task Updates
Tue Mar 5 17:29:02 2019 The things we worked on this week is in bold. Below the bold items is a description of exactly what we took care of. Paper: Julie added Amy's edits. Julie let Kai know he is welcome to edit, too. Julie will also keep edits updated as they come in! Get loop working-- specifically XF: Cade has now officially gotten reasonable outputs for his XF scripts. See the attached images for the XF outputs and associated CAD drawing. It seems to look like a reasonable gain pattern. The loop now works until AraSim. We are now getting the following AraSim errors: XF_Loop.sh: line 244: ./AraSim: No such file or directory XF_Loop.sh: line 244: ./AraSim: No such file or directory Julie is going to help Cade make sure that this directory is correct and that it has been compiled! More info to come. Test GA (Suren): I've been working on creating a gaussian fitness score with which I can test the performance of our genetic algorithm. The idea is as follows: We run the GA and get a generation of individuals. We provide their fitness score by simply taking the values {radius, length, angle} as the {x, y, z} coordinate in a 3D space. We can then use a 3D gaussian to output a value at that location, and use that number as our fitness score. The beauty of this method is that we can then plot the progress of our genetic algorithm each generation as a dot in this 3D space, and we can see it slowly snake to the center. Additionally, we can use more complex fitness scores, like one with a local maxima and a global maxima to see if it get's stuck in the local maxima. Below, I have an image I generated on python of a 2D section contour plot of a 3D gaussian in length-angle space. The dark purple is a lower value and the yellow is a higher value of the gaussian. The lines and dots hand-drawn on top are an idea of what it would look for like to start the GA at the red dot and see it's progress each generation until it reaches the center, shown by the white dots. Running this for our current roulette algorithm would make a very nice GA proof of concept plot for the paper, I believe! Gain pattern plots -- Make them 3D (Evelyn) & put on GitHub We need to figure out how to make a group Github. We have a lot of Githubs made by people and we need them all accessible from a group account. Right now the old dipole Github and the CalPoly stuff are linked to a group account. We need to find out how to get the Bicone account held by Max, and Evelyn's plotting code all on the group account: https://github.com/gp-antennas. Update: Evelyn and Max have contacted Brian to get their accounts linked. It looks like Amy, Brian, and Stephanie (Cal Poly) are the owners. Insert LR plot & Gain plot to loop (?) Edit bash script Update Github AraSim plots (Julie and Max) -- see #2 and #3 here: http://radiorm.physics.ohio-state.edu/elog/GENETIS/7 for details. Max and Julie have gotten sample data on Owens. located at /users/PCON0003/cond0068/ARA/AraSim/branches/AraSimLite/outputs Max and Julie have gotten sample programs from Jorge. https://github.com/toej93/AraSim_noise_calib/blob/master/readTree.cc https://github.com/toej93/AraSim_noise_calib/blob/master/M.readTree Julie installed root, and had Max source Julie's thisroot.sh files to run root on Owens. Max installed Arasim to his user. Next step: run plotting software given by Jorge. Update manual with things from Suren's last post here: http://radiorm.physics.ohio-state.edu/elog/GENETIS/8
Attachment 4: data.csv
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	9	Wed Feb 27 16:29:35 2019	Julie Rolla	New To-Do List
Here are the following things we need to work on: Paper (Julie and Suren) Get loop working-- specifically XF (Cade) Test GA (Suren) Gain pattern plots -- Make them 3D (Evelyn) & put on GitHub Insert LR plot & Gain plot to loop (?) Edit bash script Update Github AraSim plots (Julie and Max) -- see #2 and #3 here: http://radiorm.physics.ohio-state.edu/elog/GENETIS/7 for details. Update manual with things from Suren's last post (?)
	8	Fri Feb 22 17:09:28 2019	Suren Gourapura	Updates that need to be added to the manual
We are redesigning the way we simulate antennas in our loop. To do this, we changed our simulationPEC macro skeletons and our output skeleton. To make this easier, we changed the way we name the files, from i.uan where i is the simulation number, to i_j.uan where i is the antenna and j is the frequency. We also rewrote XFintoARA.py so it's clean. Note that before there were comments from a previous author claiming it was VERY questionably written. This has now been cleaned up. We also changed the bash script relevant to the above changes. This change needs to be added to the manual, and until we update this update, we have not done it.
	7	Fri Feb 22 15:46:33 2019	Julie Rolla	Updated To-Do List
We are getting to the stage where we would like to verify each step. It has been requested by Amy that we verify them visually. Here are the plots we need to make. Add plotting for L & R parameters (note that we already have similar software to this from the dipole check. You can find this in the GitHub from the dipole test here: https://github.com/hchasan/XF-Scripts). This should be between A, and B in the loop drawing on the manual. (Done) Plot the distribution of theta and phi of incoming signal. This should be after D in the loop drawing on the manual. Plot the distribution in cartesian coordinates of the neutrino interaction position. Maybe we can also plot the distance between the interaction point and the antenna. This should be after D in the loop drawing on the manual. Finally, as a tasks not to do with plotting, we need to make sure we don't lose any data as we go. We want to make sure that we keep tagged or labelled which individuals survive, and save the data flagged for those as we go.
	6	Fri Feb 22 15:43:36 2019	Julie Rolla	Proposal requests for XF (Remcom)
Here are a list of things we wish XF would do. We are keeping this list in hopes to add it to a proposal with them. Save pictures of CAD drawings of simulations. Close/quit XF GUI. App.quit doesn't actually work for us. Suppress the GUI and run solely through terminal.
	5	Thu Feb 21 14:07:14 2019	Julie Rolla	Logging into Nutau via XRDP
As mentioned in the manual, using ssh to login to Nutau causes delays; the XFdtd GUI cannot be surpress and must be forwarded via X11 forwarding, and this is extremely slow. We are currently looking into using a newly suggested option, XRDP. Information will be added as this process continues.
	4	Wed Feb 6 17:36:24 2019	Julie Rolla	GENETIS update 2/6
Atttendance: Julie, Max, Cade, Suren, Evelyn, Sophie Today's tasks: Max works on AraSim section (needs to do more research and reading) Julie, Suren, Sophie, Evelyn work on plotting software to plot gain patterns of indiviudals Cade preps impuse XF code to be implemented To-Do list: I. Divide up sections on paper, and work on them. See http://radiorm.physics.ohio-state.edu/elog/GENETIS/1 for section assignments. II. Implement impuse code. This will require us to change XFintoARA.py so that it takes less output files. Is there anything else different with the output files? III. Finish Evelyn and Sophie's plotting software. This means also puting it onto Nutau, and adding in lines to the bash script (both to move and save the images, and to run the code!) Here are things we can do if we are waiting for Remcom: I. Change sides of bicone to be sinusoid instead of lines. II. Take known bicone parameters and put it through AraSim to check if it's working properly. This also means we should make plots with it to triple check. III. Test GA and make it maximize other paramaters to see how it does.
	3	Wed Feb 6 17:30:51 2019	Julie Rolla	Our Github, Dropbox, & Slack links
Slack: https://gpantennas.slack.com/messages elog:http://radiorm.physics.ohio-state.edu/elog/GENETIS/ Github link: https://github.com/mclowdus/BiconeEvolution DropBox link: https://www.dropbox.com/home/GP_Antennas Old GitHub for the evolution of the dipole: https://github.com/hchasan/XF_Scripts
	2	Wed Feb 6 17:28:29 2019	Julie Rolla	Bicone User Manual (w/ links to Dipole work)
Hi all, The working copy of the user manual can be found here: https://www.overleaf.com/6955763886pjtkckprxsyp It still need to be tested by someone new to see if edits need to be made. I have uploaded the copy that is finalized as of this day. Note if you click on the overleaf version that may be more up-to-date. This copy is added as a PDF so we can keep track of versions.
Attachment 1: GENETIS_Manual_1_25_19.pdf
	1	Wed Feb 6 17:23:18 2019	Julie Rolla	GENETIS Paper working draft
The current working draft of the GENETIS paper can be seen here: https://www.overleaf.com/6783528497tvqbjphsgvzn Additionally, here's our outline for the paper. The section assignments are as follows: I. Intro (Julie) II. Types of Algorithms (Suren) III. XFdtd (Cade) IV. AraSim -- will be called something else... (Max) V. Fitness function (Suren) VI. Results (Julie) VII. Conclusion (We will see..) Note that the order of the sections may change.
Attachment 1: IMG_2881.JPG.jpeg

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