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  • Sam Yates's avatar
    New revpot and per-cell/segment parameters. (#823) · fd4f4def
    Sam Yates authored
    * Collect cable cell parameter setting structures into `include/cable_cell_param.hpp`.
    * Restructure electrical specifications (axial resistance, membrane capacitance) and ionic concentrations and reversal potentials on cable cells, so that these can be specified with a global default, per-cell defaults, and per-segment values.
    * Allow reversal potentials to be set by a mechanism of a new kind 'revpot', which are prohibited from maintaining state or writing to any shared state other than ionic reversal potentials.
    * Specify reversal potential mechanisms as global defaults or per-cell. Reversal potential mechanisms may not be specified at the level of a segment in order to avoid non-linearities arising from the discretization.
    * Supply default cable cell parameter data that matches NEURON values (this is _not_ used by default).
    * Replace the d_lambda calculation with one that approximates more faithfully the effect of tapered segments, and which will use the electrical values inherited by cell or global defaults.
    * Supply a bundled mechanism 'nernst' that replaces the previous hard-coded Nernst potential calculation, for use (together with ion rebinding) in the new ion description scheme.
    * All ions used in a cable_cell model must be present in the top level global parameter table, together with their charge.
    * Extend semantics of external variables in modcc, to permit direct assignment (as opposed to just += or -=.)
    * Extend `util::binary_search_index` to allow for a projection functional analagous to other range utilites.
    * Add documentation on the cable cell API, sketching over many of the details, but describing in particular the interface changes for default parameters and reversal potential behaviour.
    * Adjust pyarb for new API
    * Hard code global cable cell properties in the python recipe shim to useneuron default parameters.
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