ELOG GENETIS

A useful reference on bicone antennas

Daily Update

Name	Update for Today	Plans for Tomorrow
Alex M	Fixed up a few more errors in the new roulette algorithm with the length cut. Started a run to test the loop. Edited and added a few things to the paper.	My goal is to get a few generations done over night to look at in the morning. If it looks like things are working out, we're going to go ahead and start the process of merging (by adding our edits in to the database version fitst, then Eliot and Leo's asymmetric version, then merging on Wednesday hopefully).
Alex P	Worked with Alex M to have our length test run and also helped ben with an issue with his code when submitted as a job	Look at run in the morning and if it is good start merging and continuing to test the database feature on a variable amount of genes
Eliot
Leo
Evelyn
Ryan	Continued refining the Roulette function in Paperclips. Now negative or zero fitness scores cannot be passed along and the roulette can be isolated from algorithm 1 in the code.	For now, I am continuing to have the last two algorithms mutate for the rest of the individuals but am planning to write in the roulette to create new individuals that are mutated from the chosen. Once I complete this, I plan of coding in a way for user input to decide how many individuals are sent to each algorithm for selection and mutation.
Ben
Ethan

Thu Jul 2 23:13:05 2020

Amy

I found this datasheet on bicone antennas, that is a useful reference for seeing the relationship between bicone dimensions and bandwidth. From these it looks like the lower end of the band is at about f_low=c/(4*L_E), where L_E is the entire length of the antenna (twice the length of one cone), although we'd expect the peak gain to be where a quarter wavelength is just one of the cones (and the figure may roughly support that).

The attached file comes from this website:

https://www.ramayes.com/Biconical_Antennas.htm

Thu Jul 2 15:03:39 2020

Daily Update 7/2/20

Name	Today's Update	Plans for Tomorrow
Alex M	Worked with Alex to change the roulette algorithm to implement a cut on the minimum length for the Antennas. Amy showed that we don't want to generate antennas which are shorter than 37.5 cm in length (for each cone, so a total of 75 cm all together) because anything shorter than that won't be reliably simulated in XF for our frequency range. To do this, we made the roulette algorithm reselect individuals in the 0th generation if they were below this length. When it's making new individuals for the next generation, we made it so that the algorithm doesn't apply mutations that would make the antenna smaller than the minimum length (but we may revisit this with other methods, like letting the individual die if its below that length). Spoke to Ben about AREA. He can run it, but there are some errors, and it looks like the job was killed when we tried submitting it to the queue. We'll have to see if we can track down some of the errors.	Alex and I will try to run the loop using our changes to the roulette algorithm and see what the new individuals look like and if the effective volumes are reasonable.
Alex P	Worked on converting the c++ programs I made for database to work with a variable amount of genes rather than just LRT. After that Amy met with Alex and me and discussed the proper length to limit the antennas to and then worked with Alex to put a clamp within the roulette algorithm on both the initial generation and the generation of lengths through mutation. Then deciding to just cut the individuals that have too low lengths and discussing how that would be implemented.	Will continue to implement and test the changes to clamping the length by eliminating low length individuals and once that is sorted start working on being able to make our changes work on other branches too so we can start to merge.
Eliot
Leo
Evelyn
Ryan
Ben
Ethan

Wed Jul 1 16:18:35 2020

Daily Update 7/1/20

Name	Today's Update	Plans for Tomorrow
Alex M	Worked to make the frequency plots up to ~2.5 GHz. Amy said we should put a cut off for the length of the antennas based on the minimum frequency, but right now I'm not sure how to find what that minimum length should be based on the frequency (we should be using the lowest frequency for this calculation though, since it corresponds to the highest minimum length).	I'll keep looking at how to figure out the minimum length and implement it into the loop.
Alex P
Eliot	Implemented the asymmetric radius and separation parameter throughout the rest of the loop. Began a first test.	Will check on and fix any errors and either tonight or tomorrow do a run for Alex to see about length convergence.
Leo
Evelyn	Continued working on code academy, got about 3/4 of the way done	Try to finish the code academy class before my free trial runs out!
Ryan	Fixed the issues in the roulette function from Monday and integrated it into the rest of the code. seems to be running fine so far.	Next step is to code in a user input for how many of ten individuals get selected by tournament vs roulette. Once this is complete I will try to run some tests and probably try to have the results output to a file to save results for comparisons.
Ben
Ethan

Tue Jun 30 17:12:32 2020

Daily Update 6/30/20

Name	Update for Today	Plans for Tomorrow
Alex M	Continued looking in XF for why the frequency where two antennas separated by a small amount give the same gain. I made a script which plots the gain at each frequency for a chosen number of individuals at a specific polar angle and used it on two antennas, one with a separation of 0.01 cm and one with a separation of 0.005 cm. The plots look similar, but there is some difference--see the genstudents slack.	I'll continue to work on figuring out the frequency where these antennas start to give the same gain. Our ultimate goal is to find a minimum length for the antennas to cut off at so that we don't evolve antennas that are too small.
Alex P
Eliot	Made little progress on the separation gene throughout the loop, however we know where all we need to make changes(I think).	Should be able to make significant strides in regard to separation throughout the loop(ie plotting, fitness function, etc). Hopefully can also begin testing and debugging.
Leo
Evelyn
Ryan
Ben
Ethan

Mon Jun 29 15:57:41 2020

Daily Update 6/29/20

Name	Today's Update	Plans for Tomorrow
Alex M	Worked with Alex P to look at the different gain patterns for antennas with different separation distances. We found that there wasn't a clear frequency where they started to agree--looking at the average frequency gain plots we sent on slack, they look very different. We're trying to resimulate them with some higher frequencies to see the pattern more clearly and find where they start to agree.	I should be able to finish making those frequency plots in the morning. I think I'm going to try spending some time with Karoo tomorrow and see what Julie's been able to figure out.
Alex P	Looking at differences between small antennas and how the spacing affected their gains to see where differences occurred and saw at 350 MHz is last one where bigger spacing is better and after that it seems like the smaller spacing is better at 366.7 MHz and above. We checked and it actually flips back and forth between which is better and couldn't find a real pattern there. Switched to make an average gain plot for each frequency to see a pattern in the average gain since the 3D graphs use color and sometimes it can be hard to tell by how much the differences are.	Continue to work with the spacing to find which frequencies cause problems for antennas according to their sizes.
Eliot	Implemented the option of an asymmetric radius within the GA. Now, our new gene (separation) is the only gene without the possible asymmetry. This is because an asymmetric separation wouldn't do anything as the separation in XF(ie its offset from the origin) does not constitue a physical significance in AraSim.	Leo and I will begin to implement the separation gene throughout the remainder of the loop.
Leo
Ryan	Continued working on the roulette function for paperclips1.0.1.cpp. Ran into some issues with returning an array.	Debug the roulette function, maybe test if I get everything working and sent to the correct places.
Evelyn
Ben
Ethan

Fri Jun 26 16:13:18 2020

Daily Update

Name	Today's Update	Plans for Monday
Alex M	Worked to run the loop with Alex P to test a smaller initial mean and standard deviation of the opening angle. Worked some more on the paper too--I fixed some citations issues (and found some good ones to add) but the references are still spilling into the margins and off the page.	I'm going to look for where the 3D gain plots in XF for small antennas with different cone separations start to converge so that we can figure out what length we want to set as a cut off minimum to stop them from evolving to be so small.
Alex P
Eliot
Leo
Ryan
Evelyn	(Finally) got Code Academy to work on my browser, started on the git tutotial	Get as far into the git tutorial as I can
Ben
Ethan

Thu Jun 25 15:22:50 2020

Daily Update 6/25/20

Name	Today's Update	Plans for Tomorrow
Alex M	Worked with Alex P on figuring out why we keep evolving towards small antennas. We think it's because the initial angle is so large, and the standard deviation of makes it more difficult to bring the antenna within the confines of the hole by mutating the angle than by mutating the the length. So we started a run with a much lower angle (pi/24 instead of pi/12) to see if that yields antennas which are longer with better effective volumes. I also edited some more of the paper and added in a few citations, but I'd like to make sure that those citations are written correctly (for example, I couldn't find the eprint for all of them).	I'll keep this run going tomorrow and monitor it while I write some more in the paper. Now that we have a better understanding of the xmacros and can have debugged a lot, we can probably start a real run soon and I can write some more details in the PAEA section of the paper. Also, since I'm better acquainted with XF, I think I'll be able to get images of the bicones from there to put in the paper.
Alex P	Running and ran into some errors with XF solver. Found a fix to it but came into a possible oversight. So I think one reason why we keep getting this trend towards lower antennas is that the initial thetas from the 0th generation in the GA are too large and that makes it so all the longer lengths end up making too wide antennas which get penalized and hence why it tends toward small because while we do have mutation to make different thetas it only varies by so much and I think the opening angles are just too large to start in the distribution. This doesn't fully solve why the small antenna tend to give higher results than expected but it still is a problem because it's causing all the larger gen 0 antenna to get a zero fitness score because they are almost always too large. Currently if all the mean values in the distribution were used to make gen 0, the outer radius would be way bigger than the hole by a factor of 2.	Started run with change to the GA to have a lower theta as the mean in the distribution. Will see if this starts to favor the larger antennas. Possibly look more into why that XF solver error was being caused and effects of changing the spacing between cones on the bicone.
Eliot
Leo	Today we started work on adding seperation as a 4th gene. We updated the GA and tested it in a mini bash successfully. We then moved onto editing the Xmacros scripts and tested using a GUI.	Tomorrow we plan to move onto the fitness funciton and plotting scripts.
Evelyn
Ryan

Tue Jun 23 14:37:07 2020

Daily Update 6/23/20

Name	Today's Update	Plans for Tomorrow
Alex M	Worked with Aelx P on running the loop with decreasing grid spacing. I also worked in the XF GUI some more and figured out how to make 3D gain plots (per Cade's suggestion) and tried comparing different grid sizes for a single antenna with proGrid on.	Alex P and I are gonna meet with Cade tomorrow to talk about XF some more so we can figure out where progrid is having an impact and decide on what the best idea is for making sure we get the correct effective volumes out of AraSim.
Alex P	Continued today running the loop and while we had the next level of smaller grid spacing running, tested how to get the PrOGrid working and managed to get a script that would work with it. We got rid of the grid size variable but kept cell size as a constant. Although there should also be an option to make cell size automatically set via PrOGrid and there are other options that you can enable PrOGrid to handle as well so we may need to mess with more to find which are valuable.	Figure out how PrOGrid affects vEff compared to the variety of Grid sizes we've tested and also look at this for larger antennas too. Possibly tweek more settings too
Eliot
Leo	After testing the GA outside the loop with a initial generation, it was still giving the same "stoped" error. We thought it might be getting stuck in an infinite loop somewhere and decided to add a few flags to get a better idea of where. We found in was during a section that checks that Tourney_pop+Roulette_pop=NPOP but this was never achieved so it was getting stuck. This is because we had 5 individuals and had tournement proportion set to .5 with an NPOP of 5, so we think the GA didn't know what to do with 2.5 individuals in each. To fix this we changed tournement proportion to .4 so we would get 2 and 3 individuals in each. We then did a run and noticed that tournement was having some issues. So, we ran with tournement proportion at 0 and are going to fix tournement later. We ran, but our second generation was interupted in XF by someone else's run. We waited a few hours for people to finish and ran again at night.	Check on results of last run to see what other errors need fixing. Also, check on tournement and try to fix those errors.
Evelyn
Ryan

Mon Jun 22 13:52:32 2020

Daily Update 6/22/20

Name	Today's Update	Plans for Tomorrow
Alex M	Worked with Alex to run XF with smaller grid spacing. We're down to 0.001 cm, but below that we were getting long times on the XF GUI that made it seem like it was hanging. I also investigated XF from a Pitzer desktop to see how to use the progrid setting. I can get the scripts to load--I checked that the original one is indeed making a bicone and that Eliot and Leo's makes an asymmetric bicone. Helped Ryan some more with the paper clip. We're taking it step by step, so the next thing he'll want to do is make sure he can get the function for the roulette algorithm to be called correctly in the paperclip script and have the correct information passed to it (like the fitness scores).	I'm gonna continue investigating XF from the pitzer desktop to see how the progrid works. When Alex and I finish this generation of the loop, we'll try putting the progrid in an see what the results from XF are to compare it to the results frmo previous generations when we explicitly set the grid size.
Alex P	Along with continuing runs of XF to find optimal grid spacing also looked through the HTML files in the XF directory to find the scripting documentation. Found where the PrOGrid options were along with the other features PrOGrid enables. Currently we have other variables that use our Grid Size as an input so we would have to find a way to replace those to work with what PrOGrid generates.	Continue to check on status of grid size for our current runs and its affects, we might have found a cut off point so we can go back and find the optimal spacing for small sizes before swtiching to tests with large sizes. And possibly start experimenting with PrOGrid since we can compare the output it gives to an array of different grid spacings to see if it would need any tweeks.
Eliot	Continued debugging the Loop to work with 2 chromosomes ie 5 parameters. Ran inside and outside the loop trying to find the error. Finally, we placed a number of flags throughout and determined the error to be within the GA. It is inside the roulette function. We will edit this tomorrow.	Edited the roulette selection as needed. There is also an error in tournament, but for now we turned it off and are focused on testing the updated roulette.
Leo
Evelyn
Ryan	Debugged the Roulette algorithm and have it running. But, I need to check the Gaussians against the paperclips tournament to refine it and make sure I can get a fitness score for the paperclips.	Get fitness scores for the paperclips and begin to compare to tournament.

Fri Jun 19 16:27:53 2020

Daily Update 6/19/20

Name	Today's Update	Plans for Monday
Alex M	Ran the loop with the same individuals in each "generation" to test how decreasing the grid size would affect the effective volume. Using individuals with lengths of 5cm, I startde with a grid spacing of 0.01 cm and kept cutting down by a factor of 2. I'm down to 0.00125 cm right now. Once I find where the effective volumes stop decreasing, I'll do a binary search for what the optimal grid spacing is for that size.	I'll try doing the same thing that I'm doing for small antennas for large ones to see what the optimal grid size is there, but I think ultimately we're going to want to compare to the progrid to see if XF optimizes better. Amy came up with an idea for finding a function for what the grid spacing should be at a given length, so we'll try to compare that to the progrid. Meaning I'll spend Monday looking through more XF scripting while the large antennas run.
Alex P
Eliot
Leo
Evelyn
Ryan

Thu Jun 18 14:33:32 2020

Daily Update 6/18/20

Name	Update for Today	Plans for tomorrow
Alex M	Alex P and I implemented the changes we discussed with Amy to Detector.cc. We're currently running a test to see how the grid spacing affects the gains from XF. We started with small antennas using a grid spacing of 0.01 and we're cutting down by factors of 2 each generation (until we see that the gains stop changing, then we'll do something of a binary search between the last two grid sizes to search for the largest reasonable size). I also played around with the XF scripting more. My goal is to try to be able to edit the scripts we use to do help us check our results, like save images and load models for the antennas. I can currently run our macro script in XF by loading it in with 1 individual (using a generationDNA.csv file I moved to my user space). I can view and play with the model and it saves an image of it when I run the script (though the image doesn't give much detail). Hopefully this will lead to better understanding XF and being able to check our work and use the progrid option.	I'll continue with the grid space test tomorrow morning and try to play with XF a bit, but I haven't gotten to address many of Amy's comments on the paper from last week so I'll probably prioritize that while the loop is running the AraSim jobs.
Alex P	After asking about the change to replacing negative gains with 0 in the lower frequencies, we implemented that and ran a few individuals through that. We started a normal large antenna run with that change but stopped in order to test the affect of grid spacing on small antennas. We ran a .01 grid spacing and then .005 grid spacing on the same individuals and will continue so on until we see no change in the results. Specifically checking the affects at the 300 MHz frequency but also overall results.	If this works we will find the proper grid spacing for an antenna's size and the next step will be to implement a feature to properly scale that with the antennas. If we still encounter the smaller antennas giving an abnormally high vEffective we will probably have to continue looking into what could be causing that. I won't be online most of tomorrow, I might check in at a few points but Alex M will handle running the tests instead.
Eliot
Leo	Did a run with 5 individ and 5 generations. It successful ran through the loop 5 times, but didn't seem to evolve. In particular, "GenerationDNA" wasn't changing throughout the 5 generations.	Tomorrow, we plan to investigate where this error is coming from within the loop. As of now, we aren't sure whether this is part of the loop or GA. Also we are getting an error message about the file "AraOut_ActualBicone" but doesn't seem to stop the loop, so we want to check in about this as well.
Evelyn
Ryan

Wed Jun 17 17:21:16 2020

Daily Update 6/17/20

Name	Update for Today	Plans for tomorrow
Alex M	Worked more with Alex P on AraSim. We've found the cause of the low effective volumes. The function GainToHeight in Report.cc uses another function called GetGain_1D_OutZero in Detector.cc. The problem is that for some small individuals, we get that the output from GetGain_1D_OutZero is negative, which leads to -nan values from GainToHeight because it takes the square root of the negative values from GetGain_1D_OutZero. We aren't quite sure why we're getting those negative values (we know which variables and operations are giving them, but not why they're so different for some small individuals), but we think a solution is to set any negative output from GetGain_1D_OutZero to just be 0, since they're all lower than the lowest frequency in the band of interest anyway.	We can implement the change to fix these effective volumes. I'm still concerned that we're getting high effective volumes from this, when I would have expected the resolution to have decreased effective volumes for all of the small antennas. We should also be testing this with the actual Bicone to see how it changes that effective volume.
Alex P
Eliot
Leo
Evelyn
Ryan	Possibly made progress with the roulette algorithm for paperclips. However I will not know for sure until I fix the syntax errors in the code ( which seems to be largely just me mistyping something up to this point).	fix the errors in roulette.cpp and make sure the output is desired. Fingers crossed.

Tue Jun 16 16:10:52 2020

Daily Update 6/16/20

Name	Update for today	Plans for Tomorrow
Alex M	Continued working to find the AraSim error. We think we're very close to finding where the difference between the two individuals (one with nonzero effective volume, one with 0) is arising. We've pinned it down to a series of if statements around line 952 of Report.cc. We should be able to piece it apart tomorrow.	Continue working on AraSim to find the error we think it in that if statement.
Alex P
Eliot	Tried to run a couple tests of asymmetric bicone. Finished up on the git codecademy. Getting close to being ready for merge.	Test runs, meeting, hopefully develop new plans.
Leo
Evelyn
Ryan

Mon Jun 15 15:52:45 2020

Daily Update 6/15/20

Name	Today's Update	Plans for Tomorrow
Alex M	Worked with Alex P on looking for the problem in AraSim. We looked in Report.cc where Amy suggested there was an inequality involving a variable called "Full_window" being compared to the trigger threshold. We followed this down to another function in Report.cc where Full_window is used and compared fdiode_real between individuals, which was identical. We then tried printing V_Total_forconvlv, which was different between indviduals, yielding either all 0s or -nans in the individual with 0 effective volume. Helped Ryan some more with working on the roulette algorithm in paperclip. We're going to take it step by step and start with getting a hang of the code with print statements and modifications to see how things work and adding in a function for the roulette algorithm that will simply select the individuals. Once we have that working, we can move onto the next step of properly implementing the roulette algorithm in the code in a manner similar to what we have in the bicone algorithm. I made some small edits in the paper, mostly just pulling some citations from the proceeding but I also think I fixed the format of the references so that the numbers look nicer.	Alex P and I will continue looking in AraSim for the cause of the error. I'll also take some more time to contnue making edits to the paper.
Alex P	Made a generation with an indiviudal we know got a zero fitness score and reduced the grid spacing to see if it would have any affect, it might stay zero as we've done this on a generation before and it lowered all the results so the outliers might not be the zeroes but instead the normal scores with the small antenna. Talked with Amy about looking for errors and started testing what gets passed into the myconvlv function and found that the fdiodes are equal between individuals but the V_Total_forconvlv array was different, and the indiviudal that had zero had a lot more "nans" than the one the had a real score.	Continue investigating the source of where the changes in AraSim that allow for the zero fitness scores come from, marking off one variable at a time to find what makes the difference at each step
Eliot
Leo
Evelyn
Ryan	Ran into more issues attempting to write in the genes for the roulette algorithm for paperclips. So, I'm taking a new approach to attempt to write a roulette function into the existing paperclips evolution to see If I can get it to work before I try to implement the paperclips genes into the roulette algorithm.	Continue writing and attempting to run the roulette function inside of paperclips.

Thu Jun 11 15:14:33 2020

Daily Update 6/11/20

Name	Today's Update	Plans for Tomorrow
Alex M	Helped Alex P look through AraSim some more. We wanted to keep trying to nail down whether or not the threshold was passed (the files said no before, but we wanted to try confirming by looking at the actual values). The files were big but from the values we saw none exceeded the threshold for the individuals with 0 effective volume.	Amy has some more notes for the paper that I'll try to work on. I think we can try semi-running the loop to repeatedly pass in the same individuals and check the results with decreasing grid spacings from XF.
Alex P	Worked with Alex M today to continue to comb through AraSim. Did in fact find the proper place where it checks the trigger and started by printing out the values it compares. When we printed all values instead of just the values that passed we got files that were 5-7 GB and didn't even finish, and weren't told much useful information since the failures were just 0 or -nan. Started by trying to work backwards and see where the value in the trigger comes from, but after looking through multiple files trying to trace back there ended up being a lot of possibilities of where it could have come from so we started looking from the top down and to look where the gainfile's values are used since we now know where the ending is it might be easier to find the path to the end from the start now.	Continue to look through AraSim and trace the gainfile's path to affecting the trigger conditions to see what values would make it pass. Also continuing to investigate the grid spacing's affect on the gain file's values might be worthwhile after we know more about how those values matter. I do have a doctor's appointment tomorrow so will have to leave early and won't make it for group meeting.
Eliot	Finished the plotting software to work and plot everything we want. Entire loop now ~should~ run in its entirety with asymmetry. Looking to do a couple of test runs over the next few days. Worked on CodeCademy git lesson.	Continue work on git lesson and try to get a OSC interactive job. Make a few small edits that might be helpful from a user perspective.
Leo
Evelyn
Ryan

Wed Jun 10 15:47:43 2020

Daily Update 6/10/20

Name	Today's Update	Plans for Tomorrow
Alex M	I wasn't available for most of the day, but I jumped onto the meeting to help Alex P continue looking for the problem with the effective volumes. Amy asked us to investigate the phase responses coming out of XF. I posted the plots in the drop box--see the text below this table for more details.	I think we need to try a run of XF with variable grid spacings so that we can put in the same individuals with increasingly small grid spacings and get a clear view of how that affects the gain/phase vs frequency.
Alex P
Eliot
Leo
Evelyn
Ryan	Continued working on the Roulette algorithm all the function definitions, constants and most of the main function are complete aside from parts that pertain to the genes of the paperclip antennas.	If all goes well, I hope to find the gene parameters used in the paperclip tournament algorithm and then implement those into the work I did today and finish the roulette algorithm completely. If I complete that I plan on testing to make sure everything is working properly before merging onto the main development branch.

For the phase vs frequency plots, see this link: https://www.dropbox.com/home/GP_Antennas/Updates/Phase%20vs%20Frequency%20plots .The plots show the average phase vs frequency for all 10 individuals in one generation of a run. The names of the plot files correspond to which run they come from.The runs which were examined were: XF_Data_Test, Grid_Space_Test, and Ryan_test_run3. They were chosen because they provide use with different antenna, grid spacing, and effective volume data.

The plot for XF_Data_Test is named p_vs_f_XFDT.png. The plot for Grid_Space_Test is named p_vs_f_GST.png. The plot for Ryan_test_run3 is named p_vs_f_Rtr3.png.

XF_Data_Test a grid spacing of 0.1 cm. The antennas in generation 0 were large, but it evolved to make small antennas in generation 5, which is what the phase plot comes from. Individuals 7 and 10 had effective volumes of 0, while the remaining effective volumes were large.
Grid_Space_Test used a grid spacing of 0.01 cm. The antennas in generation 0 were small, which is where the phase plot comes from. None of the individuals had 0 effective volume, but overall the effective volumes were lower than in the similarly sized antennas in generation 5 of XF_Data_Test.
Ryan_test_run3 used a grid spacing of 0.1 cm. The antennas in generation 0, which is where the plot is from, were large and all had similar effective volumes to the actual bicone.

There are two things we noticed about these plots. First, they seem very noisy at low frequencies--they don't have much of a nice pattern here (actually, XF_Data_Test shows generally high phases at low frequencies that decrease with frequency up until around 200 MHz). The other detail we noticed is the periodic behavior of the average phase once it settles down beyond low frequencies. We don't know why this would occur. It's also worth noting that the phase diverge seemingly randomly at the last frequency--we assumed this was similar to how the phase is always wild at theta = 0 and theta = 360 in the .uan files.

Tue Jun 9 15:00:09 2020

Daily Update 6/9/20

Name	Today's Update	Plams for Tomorrow
Alex M	Alex P and I kept working on finding differences in AraSim between antennas. We still haven't found any and we've checked: electric field, maximum peak voltage, effective height, threshold (factor and offset), and the fft (and maybe more I'm forgetting). I'm not sure where to go from here in investigating AraSim. I tried running the loop with a smaller grid size to see if we could get some more comparisons, but I ran into errors that I need to resolve. Julie and I resolved some comments on the paper.
Alex P	Went through more of AraSim after more of Amy's comments. Found V_forfft and they were the same between individuals and then looked for other information to compare but what is interesting is that with the smaller grid spacing on the smaller antennas we have two generations with the exact same dimensions and the smaller grid spacing had lower vEff across the board, such as the larger grid spacing on small antennas had 4 individuals with a vEffective above 5 but the small grid spacing didn't have any that got above 5. So it is possible that the zero vEffective for the small antennas wasn't an error but that the larger fitness scores were the error.	Plan is to continue to look into how grid spacing affects the vEffectives especially of smaller antennas and also make sure the grid spacing we were using for the larger antenna is appropriate and then look into the automatic grid spacing whether we can do it within XF or by having it automatically update the Xmacro based off the lengths
Eliot
Leo
Evelyn
Ryan

Mon Jun 8 15:16:16 2020

Daily GENETIS Update 6/8/20

Name	Today's Update	Plans for Tomorrow
Alex M.	Worked with Alex on finding the variables Amy suggested to us in AraSim. We found the Efield and max peak voltage variables and printed them, comparing three antennas: a small one with normal veffective (nonzero), a small on with 0 veffective, and the actual bicone. The electic field was the same for all antennas, but the peak voltages were all very low for the antenna with 0 veffective. Actually, after reinvestigating, it looks like the maximum peak voltages were the same between all the antennas. I've been looking into using the automatic grid spacing in XF. I think I need to get a better understanding of XF, so I started playing with it to design things in the GUI. I want to be able to make a model using the xmacros that I can look at in the GUI so I can understand all of the functions being used. Since we've checked AraSim pretty extensively, we think that the issue is with XF. I think the grid spacing might be allowing small antennas to appear better than they are.	I think to investigate if the problem is in XF we should do a run of the same antenna with different grid spacing and look at the average gain plots. A preliminary test could be to try modeling a small antenna with a very large grid size--if that gives a very high gain, then it would suggest that the issue is with grid spacing being too large for small antennas. I think I'll also keep playing with Karoo. I've been reviewing some ML material to refamiliarize myself and see if I can write a few simple programs. I got Karoo running on OSC last week but I don't really understand the outputs (using the practice dataset).
Alex P.	Worked through more with AraSim looking at Amy's suggestions she sent over the weekend. Was able to print the PeakV and the Electric Fields, the Electric Fields matched and were the same which is what should have happened and the PeakV varied depending on how well it detected the event. Also the trigger threshold is already printed so we looked at that too.	We believe that AraSim is functioning properly so next we will look more into XF, and the grid spacing. ProGrid we think is the option from what we talked with Cade but we will continue to look further into it.
Eliot & Leo
Evelyn
Ryan	Was added as a collaborator to the paperclip repository on git hub and created a new dev branch and directory. Afterward, I started writing the new roulette algorithm. All changes have been pushed to the githhub repository.	Continue writing the roulette algorithm and start work on the github classes on Codecademy.

Fri Jun 5 14:29:56 2020