Created a new reactor type MBSampledReactor for modeling laser lab Mass-Spec experiments

[jimchu10]

Motivation or Problem

To model the sampling delay in mass-spec of Green group laser apparatus, it is important to generate a new reactor type.

Description of Changes

New reactor type added, and can be used in simulate.py

Testing

The MBSampledReactor added works same as what it was before rebase on master. Same time-dependent concentration for species by giving same input files

Reviewer Tips

[codecov]

Codecov Report

Merging #1669 into master will increase coverage by 0.11%.
The diff coverage is 77.94%.

@@            Coverage Diff             @@
##           master    #1669      +/-   ##
==========================================
+ Coverage   41.75%   41.87%   +0.11%     
==========================================
  Files         176      177       +1     
  Lines       29423    29490      +67     
  Branches     6075     6097      +22     
==========================================
+ Hits        12286    12349      +63     
- Misses      16261    16262       +1     
- Partials      876      879       +3

Impacted Files	Coverage Δ
rmgpy/tools/data/sim/mbSampled/input.py	100% <100%> (ø)
rmgpy/rmg/input.py	37.94% <69.76%> (+2.55%)	⬆️
rmgpy/tools/loader.py	43.75% <87.5%> (+6.25%)	⬆️
rmgpy/data/kinetics/family.py	52.9% <0%> (+0.23%)	⬆️
rmgpy/tools/plot.py	46.51% <0%> (+0.58%)	⬆️
rmgpy/tools/simulate.py	77.35% <0%> (+5.66%)	⬆️

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[mliu49]

I think it would make sense for MBSampledReactor to be a subclass of SimpleReactor. I compared the two, and it seemed like only the residual method was changed. Doing it this way would make it much easier to maintain.

I added a commit making this change, but have not tested it yet beyond checking that it compiled correctly. Could you run a simulation to see if this works and gives the same result as before?

[mliu49]

Update regarding my previous commit. Turns out that it won't work because SimpleReactor defines a jacobian method which necessarily cannot be included for MBSampledReactor.

[amarkpayne]

I have looked over the unit test portions as requested. There is just one quick fix, but otherwise this looks good. I am about to test that the tests run properly by running locally, but go ahead and rebase with the fix squashed.

[amarkpayne]

When I run the test locally, this is the plot that I get. Is this what the simulation is supposed to do?

[mliu49]

Yeah, the concentrations are all extremely low, so they don't show up on the plot.

[amarkpayne]

The unit test commits are approved as far as I am concerned. If the reactor commit is fine with you then this PR can be merged

[mliu49]

To document offline discussion, we decided that even though the MBSampledReactor is not up to date with all of the changes to SimpleReactor, it's ok because it does not need to be used in RMG jobs. The workflow currently used is to generate an RMG model using SimpleReactor and then use MBSampledReactor to simulate and compare to the experiments.