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GENETIS

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Entry time:	Thu Dec 5 16:58:55 2019
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<p style="text-align:center"><u><strong><span style="font-size:18px">Updated To-Do List:</span></strong></u></p> <ol> <li><span style="font-size:16px"><strong>Add ARA constants in plotting code:</strong></span><span style="font-size:12px"><strong> </strong>ie add Veff, theta, R for ARA. This will sit as a constant line for us to compare each evolving parameter to. For example, in the plot Veff vs Generation, we will see a constant line for ARA's Veff to see how it is evolving in time. </span></li> </ol> <p><span style="font-size:14px"><strong>TASK 1: MAKE Veff PLOT.</strong> <em>Note: One of our variables in this run is Energy. Unfortunately, we care about how Veff changes with Energy for ARA<sub>actualBicone</sub></em><em>. This means that before plotting "Veff versus Generation" we need to generate Veff for ARA</em><sub><em>actualBicone</em> </sub><em>at the energy we are assigning the run. </em></span></p> <p style="margin-left:40px"><strong>STEP 1: </strong>Make plotting code to plot "Veff vs Generation". </p> <ul style="margin-left:80px"> <li>You can follow the way we make LRPlot.py. <ul> <li>However, in this case, we will need to take the files /fs/project/PAS0654/BiconeEvolutionOSC/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Run_Ouputs/$RunName/AraOut${gen}_${i}.txt -- ie the AraSim outputs for each individual in <u>ALL generations. ie Gen 0 - ${gen} </u> -- INCLUDING the one we created in Gen 1 for ARA<sub>actualBicone </sub>-- and plot Veff from those. </li> <li>We also want to plot error bars with Veff. The error bars for each are labeled "and Veff (water eq)" at the bottom of these AraSim output files we are already reading in for Veff.  <ul> <li>Note, to know how to read in Veff, you can look at how we are reading that exact line from the AraSim output files in on the fitnessFunction_ARA.cpp code in the Antenna_Performance_Metric directory, since we are doing it there. </li> <li>Note that since we are plotting "Veff vs Generation", we will either have to read in all the files AraOut${gen}_${i}.txt (up to how may ${gen} we are in) every time -- including the ARA<sub>actualBicone </sub>one-- or we can append them all to one .txt file. It's your choice. </li> </ul> </li> <li>Make sure you label the units for each axis every time, and that you have a key! If not, Amy will hate the plot!</li> </ul> </li> </ul> <p style="margin-left:40px"><strong>STEP2:</strong> Add V<sub>eff</sub> for ARA<sub>actualBicone </sub>as a constat in the newly made "Veff vs Gen" plotting code. Remember, as I mentioned above, we must first put the ARA<sub>actualBicone </sub>through AraSim to see Veff at the same energy as the rest of the individuals. Here's what to do:</p> <ul style="margin-left:80px"> <li> Edit the Bash script to submit a job that runs the gain patterns of ARA<sub>actualBicone </sub>through AraSim in the initial gen (gen 0)!  <ul> <li>There's a current file that exits for ARA<sub>actualBicone </sub>that has the gain patterns of the current antenna, in the correct format for AraSim to run. In the bash script (XF_Loop.sh) we need to create ONE more AraSim job submission for this antenna (as a comparison to what we see with our genetically evolved ones) just in gen 0 (the first generation). <ul> <li>This current AraSim input file for ARA<sub>actualBicone </sub>exists in BiconeEvolutionOSC/AraSim/Ara_Bicone6in_output.txt <ul> <li>This needs to be the input for our .job script. </li> </ul> </li> </ul> </li> </ul> </li> <li>Add lines to your newly made "Veff vs Gen" plotting code that reads in the Veff output for this ARA<sub>actualBicone </sub>AraSim output file (whatever you've chosen to name it when you wrote it into the job script. </li> </ul> <p style="margin-left:40px"><strong> STEP 3:</strong> Move the ARA<sub>actualBicone </sub>output file into the $Run_Name directory so it is not overwritten ever. </p> <ul style="margin-left:80px"> <li>We will want to make sure this is not overwritten after the run ends, and we start a new one. </li> <li>We will also be using it for plotting "Veff vs Generation". </li> </ul> <p style="margin-left:40px"><strong>STEP 4: </strong>Correct the "wait" command for the AraSim job submissions. </p> <ul style="margin-left:80px"> <li>The "wait" command, on the first iteration, will have to wait for $NPOP+1 now-- not $NPOP.</li> </ul> <p style="margin-left:40px"> </p> <p><span style="font-size:14px"><strong>TASK 2: MAKE "Theta vs Gen" Plot. </strong> </span></p> <p style="margin-left:40px"><strong>STEP 1: </strong>Make plotting code to plot "Theta vs Generation". </p> <ul style="margin-left:80px"> <li>You can follow the way we make LRPlot.py; however, MAKE SURE YOU LABEL AXIS WITH UNITS, AND HAVE A KEY.</li> <li>This will be exactly the same as this other code, except you will need to: <ol> <li>Read in theta from your generation DNA files</li> <li>Add the ARA<sub>actualBicone </sub>constant to the code as a reference point</li> </ol> </li> </ul> <p><span style="font-size:14px"><strong>TASK 3: Fix "L vs Gen" and "R vs Gen" plot. </strong> </span></p> <p style="margin-left:40px"><strong>STEP 1: </strong>Correct both plots to have labeled the units for each axis every time, and a key. This is plotted in the "LRPlot.py" code. </p> <p style="margin-left:40px"><strong>STEP 2</strong>: Fix our 'R' values. I do believe we are plotting the incorrect "R". Here is what I think is happening:</p> <p style="text-align:center"><img alt="" height="204" src="191206_224336/Screen_Shot_2019-12-06_at_9.43.22_PM.png.png" width="254" /></p> <p style="text-align:center"><img alt="" height="224" src="191206_224420/Screen_Shot_2019-12-06_at_9.42.59_PM.png.png" width="208" /></p> <p> </p> <p style="margin-left:40px"> </p> <ul style="margin-left:80px"> <li>We need to double-check and see what ARA defines "R" as on their current antennas.  <ul> <li>Check with Amy?</li> <li>What does Brian Clark's thesis say?</li> <li>Can you find a paper that shows a picture of how they define it?</li> </ul> </li> <li>If we are wrong, this means we need to change the "R vs Gen" part in the "LRPlot.py" code so that we: <ol> <li>Read in R, L, and Theta for each generation. <ul> <li>See how this is already done for reading in R, and repeat it for L and theta. </li> </ul> </li> <li>Do trig to calculate the same "R" as ARA<sub>actualBicone </sub>defines. See picture below!</li> <li>Store that newly calculated "R" as an array, and plot THAT.</li> <li>Don't forget to add the ARA<sub>actualBicone </sub>Radius as a constant line. </li> </ol> </li> </ul> <p style="text-align:center"><img alt="" height="357" src="191206_230459/Screen_Shot_2019-12-06_at_10.04.21_PM.png.png" width="329" /></p> <p> </p> <p><strong>TASK 4: See PDF for other items!</strong></p> Encoding: HTML ELCode plain Suppress Email notification Resubmit as new entry

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