Updates for paper. Fix issues #38, #40, #43, #46.

#66 Merged at af0ce0d
  1. Raymond Smith
  • Update MHC with BV-like exchange current density.

  • Replace j_plus with R_Vp.

    • fix equations in mod_cell
    • geometry no longer needs epsbeta vec
    • replace epsbeta -> beta in io_utils
    • fix initial guesses in sim (Also, fix a c0 -> c_ref in io_utils) Seems to work at least for a simple test case.
  • Change conductivity variable names.

    These agree better with the paper now: - mcond -> sigma_s - kappa (in electrolyte) -> sigma

  • Update tests for new conductivity variable names.

  • More cleanup from other changes.

    • eliminate epsbeta referenece in plot_data call to geometry
    • update test_defns for mcond->sigma_s
  • Default to generating all plots for tests.

    Make a note in the readme that test failures aren't necessarily the worst.

  • Change scaling of k0 to match paper.

    Store nondimensional reaction rate, not "volumetric" reaction rate. Tests pass with minor differences. Only notable difference is small deviation on small part of V(t) for test010, CHR2 cylinder.

  • Add some missing temperature factors to elyte flux

  • Make function/class names more PEP8 compliant.

  • More gracefully handle run w/o input param file.

  • Minor revision of simulation repeat instructions.

  • Update way to get daetools config options.

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