Replace cable cell discretization. (#941)
Replace branch/cable-based cell representation and discretization with free specification of control volumes over the cell morphology. Implements functionality required for issues #859 and #732, and the reworking of inter-CV conductance computation addresses issue #635, although there is possible room for improvement by treating CV voltages as averages rather than point estimates. * Remove arbor/segment.hpp and segment-based representation in `cable_cell`. * Add a new discretization policy `cv_policy_every_sample` that replaces the `compartments_from_discretization` flag in the `cable_cell` constructor. * Remove use of `cable_cell::num_compartments()` in example code (see issue #940). * Add command line argument to `single_cell` example to specify number of CVs per branch. * Replace fvm layout `fvm_discretization` with new representation `fvm_cv_discretization`, which in turn wraps a `cv_geometry` object representing CVs as cables w...
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- arbor/cable_cell.cpp 7 additions, 237 deletionsarbor/cable_cell.cpp
- arbor/cable_cell_param.cpp 31 additions, 0 deletionsarbor/cable_cell_param.cpp
- arbor/fvm_compartment.hpp 0 additions, 261 deletionsarbor/fvm_compartment.hpp
- arbor/fvm_layout.cpp 699 additions, 818 deletionsarbor/fvm_layout.cpp
- arbor/fvm_layout.hpp 78 additions, 62 deletionsarbor/fvm_layout.hpp
- arbor/fvm_lowered_cell_impl.hpp 18 additions, 18 deletionsarbor/fvm_lowered_cell_impl.hpp
- arbor/include/arbor/cable_cell.hpp 2 additions, 62 deletionsarbor/include/arbor/cable_cell.hpp
- arbor/include/arbor/cable_cell_param.hpp 15 additions, 1 deletionarbor/include/arbor/cable_cell_param.hpp
- arbor/include/arbor/morph/locset.hpp 3 additions, 0 deletionsarbor/include/arbor/morph/locset.hpp
- arbor/include/arbor/segment.hpp 0 additions, 345 deletionsarbor/include/arbor/segment.hpp
- arbor/morph/locset.cpp 23 additions, 0 deletionsarbor/morph/locset.cpp
- arbor/util/piecewise.hpp 18 additions, 5 deletionsarbor/util/piecewise.hpp
- arbor/util/rangeutil.hpp 25 additions, 0 deletionsarbor/util/rangeutil.hpp
- example/dryrun/branch_cell.hpp 4 additions, 1 deletionexample/dryrun/branch_cell.hpp
- example/dryrun/dryrun.cpp 4 additions, 12 deletionsexample/dryrun/dryrun.cpp
- example/gap_junctions/gap_junctions.cpp 2 additions, 8 deletionsexample/gap_junctions/gap_junctions.cpp
- example/ring/branch_cell.hpp 4 additions, 1 deletionexample/ring/branch_cell.hpp
- example/ring/ring.cpp 2 additions, 8 deletionsexample/ring/ring.cpp
- example/single/single.cpp 10 additions, 16 deletionsexample/single/single.cpp
- python/cells.cpp 1 addition, 1 deletionpython/cells.cpp
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