Spruced up ch02.ipynb a bit by adding comments to most of the inputs#6

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lkissin2 wants to merge 6 commits intophysics-codes:masterfrom

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Commits on Mar 17, 2019

added illuminating comments to most of the inputs
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used markdown to add notes to ch03. Also put some code in where it may help
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Commits on Mar 18, 2019

Commits on Apr 1, 2019

updated ch6 with markdown and a little bit of code examples
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Commits on Apr 7, 2019

put commentary in the analysis chapter with markdown
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