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 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.

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).

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. 

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).

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.

Found a bug while running the loop, fixed it and starting running again. Added a few things to the paper.

Continued the run from yesterday. Alex P and I applied the changes we made to the bash script for fixing the bugs we found in the simulation number to the database version. Once we get 15 generations of data for this run we'll start testing the database version. Once that works we'll have Eliot and Leo run their version with only 3 genes and if we get the same genes all around we'll be able to merge the asymmetric branch with the database branch and then merge with master. I also fixed up a bug I found in one of the plotting programs that meant it was missing the first individual, it should be good now.

Ryan and I talked a bit about how to apply crossover and mutation to the paperclip. I'm not sure that crossover makes sense, but I think it's possible. He's going to start by doing crossover of the chromosomes and then when that's working he can try crossing over the genes (this is where I'm not sure things make sense, but who knows). Then he can implement mutation in that function.

Julie and I spoke with Ben about AREA and started helping him siftt through all the files. We're going to meet with Ethan tomorrow to catch him up to speed and start reviewing the bash script that runs all of AREA.

Finish this run, test the database. I'll meet with Julie, Ben, and Ethan to talk about AREA. Also, Eliot and Leo found a potential issue in the roulette algorithm that I asked them to look at, so we might try making a fix in there and see if that allows our mutations to be more reasonable. Alex and I are going to have to meet with Eliot and Leo soon so we can all work together on merging our branches and resolving merge conflicts.

The name of this run is Data_Base_Test_7_10.

The name of the previous run we are comparing against is Length_Cutoff_Test_3.

(See below the table for a review of the past couple of days since ELOG has been down.)
We may have found what was causing the error in Eliot and Leo's version. They were getting 0 effective volumes. I edited their output macroskeletons to use pro grid (I figured it was the default setting, but it looks like not). This seems to have fixed the issue with their .uan files having all 0s and 180s for the phase and -300 gain. However, it wasn't writing to the vEffective.csv and fitnessScores.csv files correctly. We realized they may have needed to recompile. We did that and ran a preliminary tset, where we got some promising results. The effective volumes and fitness scores seem to have been read out and plotted correctly, but they didn't appear to match the previous two runs Alex P and I did. That might be because we were messing around with the save state sloppily. Currently, Eliot is rerunning from the beginning with the intention of seeing if it will go all the way through generation 0 smoothly. From there, we'll need to compare the effective volumes and fitness scores with the previous two runs Alex P and I did (although I can confirm that the generation 0 DNA matches). Then we'll need to let it run for a few more generations to make sure it evolves the same individuals those two previous runs evolved.

If it looks like these fixes worked and the effective volumes are being made correctly and the same individuals are evolved as in the previous two runs Alex P and I did, then we'll be ready to start merging. The first step will be to fix a merge conflict on the asymmetric bicone branch. Then, we'll have to carefully merge and resolve merge conflicts. The order should be that the asymmetric bicone branch merges onto the database branch, which will then merge onto the master branch. Once that's done, we'll be able to do a proper run.

Today's Tasks

Mitchell, Evelyn, Eliot, Ryan: Work through the bash project; Mitchell is done, Ryan and Evelyn are close to being finished.

Leo: Worked on next presentation (not sure when he'll present--either Friday or next Tuesday).

Alex M: Continued commenting code and helped Alex P. with changes in Part_B and Roulette_algorithm .

Alex P: Fixed errors in loop, tested with an interactive job (using CPU). Errors look to be fixed up through part B. Arasim should be launching and using the $tmpdir, though we need to get further in the testing to see for sure.

Made a copy of the loop that functions without GPUs so that if GPU is unavailable some progress can be made even if it is slow.

While waiting for a GPU Alex P ran on CPUs, at half scale factor one indiviudal in XF took 32 minutes (although it was predicted to be over 2 hours). 

Alex P.