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Updates from Pat, including addition of IChR2 (optogenetics) plugin

Patrick Boyle requested to merge PMB_add_IChR2 into master

What does this MR do?

  • Added myself as a contributor (yay). For the record I also wrote a lot of other (likely bug-filled) code that is already committed, like the Rosenbrock solver and some of the models like ARPF :)
  • Added IChR2.model -- plugin for light-induced current mediated by the optogenetic non-selective cation channel ChR2
  • Added a few potentially helpful debugging messages to sim_utils.cc (warnings for bad .so files and conflicting t_sentinel parameters)

Related issues

#83 (closed)

Author's checklist

Note: Not sure I did the labels thing thing correctly

Reviewer's checklist

All reviewers can help ensure accuracy, clarity, completeness, and adherence to the Contribution Guidelines.

Example for how to use this (in bench): for EE in 0.00{1,2,5} 0.0{1,2,5}0 0.{1,2,5}00; do /Software/cme/openCARP/bin/bench.opt --imp=TT2 --plug-in=IChR2 --numstim=1 --stim-start=0 --stim-curr=0 --light-numstim=1 --light-start=50 --light-dur=10 --duration=500 --light-irrad=$EE --fout=TT2+LightStim-Ee${EE}; done;

I can provide more examples (tissue scale) if need be.

Reviewer

  • Review by a code reviewer or other selected colleague to confirm accuracy, clarity, and completeness. This can be skipped for minor fixes without substantive content changes.

Maintainer

  • Review by assigned maintainer, who can always request/require the above reviews.
  • Ensure a release milestone is set.
Edited by Patrick Boyle

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