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<!DOCTYPE html>
<html>
<head>
<title>
SoCIS 2016 DevLog
</title>
<!--Import custom stylesheet -->
<link type="text/css" rel="stylesheet" href="css/index.css">
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<header>
<div class="brown darken-2 white-text z-depth-2">
<div class="container">
<div class="row">
<div class="col s12">
<h3>
<b>SoCIS 2016 DevLog</b>
</h3>
<h6 style="margin-bottom: 15px">
Tracking project progress and contributions for TARDIS.
</h6>
</div>
</div>
</div>
</div>
</header>
<main>
<div class="container">
<a class="gh-icon red lighten-1 btn-floating right btn-large z-depth-2"
href="https://trello.com/b/o66aebcJ/tardis-socis-2016" >
<i class="mega-octicon octicon-repo-clone"></i>
</a>
<!-- AND THE DEV LOG STARTS FROM HERE -->
<ul class="collapsible popout" data-collapsible="expandable">
<li>
<div class="collapsible-header active waves-effect waves-light grey darken-2 white-text">
<i class="mega-octicon octicon-calendar"></i>
<b>Week 29</b>
</div>
<div class="collapsible-body grey lighten-5">
<ul class="details">
<li>
<b>July 18</b><p>Worked on documentation, mainly making a diagram to show the integration geometry.</p>
</li>
<li>
<b>July 19</b><p>Kept on documenting, reached a sort of <a href="https://github.com/tardis-sn/tardis/pull/621">end point</a>. Also ran test with just black body, one shell and no actual source function in the integral, this gave good enough agreement that its important to do all the details properly. That is put the integral into physical units and make sure the MC and integral methods are compared on the same frequency grid.</p>
</li>
<li>
<b>July 20</b><p>Made comparisons between integrator and MC for one shell model of pure silicon. Shape agreement reasonable but normalization way off, factor of 10^18. <img src="http://i.imgur.com/OsM5Q29.png" alt="Spectra">. After poking around a bit I got out a pure black body spectrum, off by magnitudes.</p>
</li>
<li>
<b>July 21</b><p>After fixing regresson from the 20:th, kept on trying to find the source of the missing magnitudes.</p>
</li>
<li>
<b>July 22</b><p>Found the missing magnitudes, it was a missing dp. Still some magnitude missing, but turned out to be due to too few binns in impact parameter space</p>
</li>
</ul>
</div>
</li>
<li>
<div class="collapsible-header waves-effect waves-light grey darken-2 white-text">
<i class="mega-octicon octicon-calendar"></i>
<b>Week 28</b>
</div>
<div class="collapsible-body grey lighten-5">
<ul class="details">
<li>
<b>July 11</b><p>Fixed bugs in the part of the integrator I had until it actually ran the example. It gave wildly unrealistic results.</p>
</li>
<li>
<b>July 12</b><p>Found the source of the wildly unrealistic results. Now it gives sketchy results, but it still does not have the bit that is directly driven by a black body.</p>
</li>
<li>
<b>July 13</b><p>Working on getting in code to integrate on the inner half of the impact parameter space.</p>
</li>
<li>
<b>July 14</b><p>Finished up the integrator, in now does the complete impact parameter range. The results are still bad.</p> <img src="http://i.imgur.com/YYrMHjv.png" alt="Spectra" rel="nofollow"> Image shows spectra of the example produced by the integrator. Horisontal axis is frequency in Hertz.
</li>
<li>
<b>July 17</b><p>Wrote documentation and made a diagram. Also fixed bug found by @yeganer, which significantly improved the end result. </p>
<img src="http://i.imgur.com/fZaWUG4.png" alt="Spectra" rel="nofollow">
</li>
</ul>
</div>
</li>
<li>
<div class="collapsible-header waves-effect waves-light grey darken-2 white-text">
<i class="mega-octicon octicon-calendar"></i>
<b>Week 27</b>
</div>
<div class="collapsible-body grey lighten-5">
<ul class="details">
<li>
<b>July 4</b><p>Finished up the documentation. Though about how the integral could be derived from a general volume integral. Had a meeting about the integral and started on the exercise about the integral. <i>The integral.</i></p>
</li>
<li>
<b>July 5</b><p>Concluded the integral exercise. Though about how it all fit together, understood and felt enlightened. Scribbled notes about how it all should work.</p>
</li>
<li>
<b>July 6</b><p>Though more about the integral and wrote a rought outline of how the <a href="https://docs.google.com/document/d/1eLgg_f-09xJwZgxwz1ri_NdJcpmn9De2bAkyjUPaYV0/edit">integral</a> would work</p>
</li>
<li>
<b>July 7</b><p>Reached limit of what I could plan in vacuuo, started on a skeleton on which to hack to get a complete implementation.</p>
</li>
<li>
<b>July 8</b><p>Got sick.</p>
</li>
<li>
<b>July 10</b><p>Not as sick. Wrote out an integrator that manages impact parameters greater than the inner radius of the shell. That is the case with no blackbody providing initial intensity.</p>
</li>
</ul>
</div>
</li>
<li>
<div class="collapsible-header waves-effect waves-light grey darken-2 white-text">
<i class="mega-octicon octicon-calendar"></i>
<b>Week 26</b>
</div>
<div class="collapsible-body grey lighten-5">
<ul class="details">
<li>
<b>June 27</b><p>Tried to fix problem with varaiables for the unit test not working. Read code to figure out how to do the level absorption sums.</p>
</li>
<li>
<b>June 28</b><p>Implemented fix to the unit test after @yeganer found the cause. Discussed with @wkerzendorf how to do the level absorption sum, and how atomic data is stored. The conclusion was that doing the sum in pandas can be done at the cost of a few hundred miliseconds.</p>
</li>
<li>
<b>June 29</b><p>Implemented code to calculate the attenuated source function using pandas.</p>
</li>
<li>
<b>June 30</b><p>Wrote a unit test for the attenuated source function. Considered the details of the final impact parameter integral. The simplest interpretation is that the way the intensities are derived "flattens" the problem so that the integration simply amounts to summing up the intensities according to whitin which shell a given impact parameter lies. This of course does not have any interpretation in the case of p less than R, so it's probably not correct. </p>
</li>
<li>
<b>July 1</b><p>Read the existing documentation and started working on documenting my additions to TARDIS.</p>
</li>
</ul>
</div>
</li>
<li>
<div class="collapsible-header waves-effect waves-light grey darken-2 white-text">
<i class="mega-octicon octicon-calendar"></i>
<b>Week 25</b>
</div>
<div class="collapsible-body grey lighten-5">
<ul class="details">
<li>
<b>June 20</b><p>Trying to run tardis example on a new computer using my changes. Eventually stopped by #593.</p>
</li>
<li>
<b>June 21</b><p>Created PR for my changes so far, and update it after comments. Tried to exclude some unintended changes but failed.</p>
</li>
<li>
<b>June 22</b><p>Finished up the line emission estimator and looked at what it produced.</p>
</li>
<li>
<b>June 23</b><p>Moved the line emission estimator into the cyton code. Wrote a unit test and tried to run it, encountered unrelated problem.</p>
</li>
<li>
<b>June 24</b><p>Fixed problem with unit tests not running at all. My addition did however not work, seems to be a problem with initializing the storage: the code never takes the branch that would actually increment the sum.</p>
</li>
</ul>
</div>
</li>
<li>
<div class="collapsible-header waves-effect waves-light grey darken-2 white-text">
<i class="mega-octicon octicon-calendar"></i>
<b>Week 24</b>
</div>
<div class="collapsible-body grey lighten-5">
<ul class="details">
<li>
<b>June 14</b><p>Rereading Lucy 345. We will need to add a second line list, but how to structure it? </p>
</li>
<li>
<b>June 15</b><p>Had a meeting with Uill, spent the rest of the day following code around in cmontecarlo.</p>
</li>
<li>
<b>June 16</b><p>More studying of the verious papers and the TARDIS code. In the end we arrived at a firm understanding of what needs to be added in principle regarding the line absorption estimation. There is only very limited changes to be done to the monte carlo loops.</p>
</li>
<li>
<b>June 17</b><p>Implemented the changes in a local branch, renamed things as apropriate and ran test of the C code. It passed.</p>
</li>
</ul>
</div>
</li>
<li>
<div class="collapsible-header waves-effect waves-light grey darken-2 white-text">
<i class="mega-octicon octicon-calendar"></i>
<b>Week 23</b>
</div>
<div class="collapsible-body grey lighten-5">
<ul class="details">
<li>
<b>June 6</b><p>Using jekyll to simplify managing the weblog continued to be a bad idea. Gave up and accepted writing html by hand. Looked for branching ratio treatment in cmontecarlo.</p>
</li>
<li>
<b>June 7</b><p>Mostly worked on presentation.</p>
</li>
<li>
<b>June 8</b><p>Looked a bit more at how cmontecarlo does its thing.</p>
</li>
</ul>
</div>
</li>
<li>
<div class="collapsible-header waves-effect waves-light grey darken-2 white-text">
<i class="mega-octicon octicon-calendar"></i>
<b>Week 22</b>
</div>
<div class="collapsible-body grey lighten-5">
<ul class="details">
<li>
<b>June 1</b><p>Started reading Mazzali, agreed on skype meeting with Ulli. Tried installing TARDIS on local machine and realized I had to repartition.</p>
</li><br/>
<li>
<b>June 2</b><p>Reading Mazzali. Had a skype meeting with Ulli, Wolfie and Markus about the start of the project. Then attended TARDIS meeting. Read Lucy 345.</p>
</li><br/>
<li>
<b>June 3</b><p>Worked on setting up a devlog for the project. Got a starting point from Karan, tried to use jekyll to simplify it a bit. </p>
</li><br/>
<b>June 4</b><p>Worked on setting up a devlog for the project. Tried to use jekyll to simplify it a bit. Failed.</p>
</li><br/>
<b>June 5</b><p>Using jekyll to simplify managing the weblog continued to be a bad idea.</p>
</li><br/>
</ul>
</div>
</li>
</ul>
</div>
</main>
<!--
./setup.py test --test-path=tardis/montecarlo/tests
-->
</body>
</html>