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One Dimensional Freely Propagating Flame Physics and Example, as well as b#591

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klbudzin wants to merge 44 commits intogrinsfem:masterfrom
klbudzin:master_merge
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One Dimensional Freely Propagating Flame Physics and Example, as well as b#591
klbudzin wants to merge 44 commits intogrinsfem:masterfrom
klbudzin:master_merge

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This is a pull request for the one dimensional freely propagating flame physics I have been working on for my masters. Here a new od_premixed_flame physics class is added as well as two new qoi's, the flame_speed, and adiabatic_flame_temperature( which currently just calculates the temperature at a set point in the domain). An example was for a one dimensional methane flame using the gri30 mechanism at stoichiometric conditions is also added.

On top of this is a bug fix for the side_time_derivative method in the multi_physics class where the side_time_derivative method of the implemented physics was not being called correctly. Also some clipping methods were added to cantera to clip negative temperatures and densities.

…eed to adjust how i construct the chemistry as it is done in a deprecated manner atm.
… a certain reaction type, still needs more automation to just read everything from the xml, and require less input between checks
…o rethink how Im calculating them, might be best to return all as a vector, since you will usually use them all when needed, and cantera calculates the vector every call anyways
…ere I wasnt pulling in the values from the side of the element
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