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  1. Oct 30, 2016
    • Sam Yates's avatar
      Complex compartments · e7a8fb6f
      Sam Yates authored
      * Use divided compartments to determine FVM coefficients.
      * Pick correct control volume in FVM from sgement position (avoids
        off-by-half error.)
      * Add colour override functionality to tsplot: `--colour` option.
      * Add const accessor for cell soma.
      * Source formatting, comments in `math.hpp`
      * Fix `range_view`: was using incorrectly named type trait.
      * Add unit test for `range_view`.
      * Allow points of discontinuity to be omitted from L-infinity norm
        calculations.
      * Add `-d, --min-dt` option to `validate.exe` to control time
        step in validation convergence tests.
      * Add validation test: confirm divided compartment policy does
        not effect results on simple frustrum dendrites.
      * Change default max compartments on validation tests to 100
        (ad hoc observed convergence limit at dt circa 0.001 ms;
        finder spatial division would required much finer dt.)
      * Make NEURON validation data generation scripts use CVODE by
        default, and with `secondorder=2` when non-zero `dt` is given.
      e7a8fb6f
  2. Oct 28, 2016
  3. Oct 27, 2016
  4. Oct 26, 2016
  5. Oct 25, 2016
  6. Oct 24, 2016
    • Sam Yates's avatar
      Bugfix: hh_soma.jl · 7845818c
      Sam Yates authored
      * Use consistent scaling for y[1] scalar voltage in hh_soma.jl
      * Also: add more reserved target names to CMakeLists.txt
        helper function.
      7845818c
    • Sam Yates's avatar
      Reorganize validation data generation · b263eb24
      Sam Yates authored
      * Move generation and data to top-level validation directory.
      * Make BUILD_VALIDATION_DATA and VALIDATION_DATA_DIR cache vars.
      * Add helper CMake functions for data generation.
      
      Note `validation/ref/numeric/foo.sh` is just a placeholder.
      b263eb24
    • Sam Yates's avatar
      Change bulk resistivity default. · d2ce7a68
      Sam Yates authored
      * Align defaults with values used in most of the NEURON
        validation scripts.
      * Use consistent 100 Ω·m bulk resistivity across both
        NEURON test models and basic validation cells.
      d2ce7a68
    • Sam Yates's avatar
      Add soma-less cable cell to test cells. · e751fcd3
      Sam Yates authored
      Also:
      * Ensure intrinsic and passive properties properly set on test cells.
      e751fcd3
  7. Oct 22, 2016
    • Vasileios Karakasis's avatar
      Reverted semantics of assign_by. · bc566ecb
      Vasileios Karakasis authored
      The problem described in previous commit was caused only inside the
      cell's copy constructor, where an assignemt for `std::unique_ptr` was
      attempted. Since `std::unique_ptr`'s cannot be copy-assigned, I have
      made that assignment manually moving the just cloned other's segment to
      the cell being constructed. The original `assign_by` method, relying on
      STL's `assign()` cannot accommodate this without changing its
      semantics (as pointed out by @halfflat), which would then also conflict
      with STL's semantics.
      bc566ecb