Complex compartments
* 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.
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- scripts/tsplot 25 additions, 6 deletionsscripts/tsplot
- src/cell.cpp 6 additions, 6 deletionssrc/cell.cpp
- src/cell.hpp 4 additions, 3 deletionssrc/cell.hpp
- src/fvm_multicell.hpp 93 additions, 37 deletionssrc/fvm_multicell.hpp
- src/math.hpp 19 additions, 36 deletionssrc/math.hpp
- src/util/rangeutil.hpp 2 additions, 2 deletionssrc/util/rangeutil.hpp
- tests/unit/test_range.cpp 9 additions, 0 deletionstests/unit/test_range.cpp
- tests/validation/CMakeLists.txt 1 addition, 0 deletionstests/validation/CMakeLists.txt
- tests/validation/convergence_test.hpp 20 additions, 2 deletionstests/validation/convergence_test.hpp
- tests/validation/trace_analysis.cpp 39 additions, 0 deletionstests/validation/trace_analysis.cpp
- tests/validation/trace_analysis.hpp 5 additions, 0 deletionstests/validation/trace_analysis.hpp
- tests/validation/validate.cpp 5 additions, 0 deletionstests/validation/validate.cpp
- tests/validation/validate_ball_and_stick.cpp 23 additions, 13 deletionstests/validation/validate_ball_and_stick.cpp
- tests/validation/validate_compartment_policy.cpp 95 additions, 0 deletionstests/validation/validate_compartment_policy.cpp
- tests/validation/validate_soma.cpp 14 additions, 3 deletionstests/validation/validate_soma.cpp
- tests/validation/validate_synapses.cpp 4 additions, 1 deletiontests/validation/validate_synapses.cpp
- tests/validation/validation_data.hpp 5 additions, 1 deletiontests/validation/validation_data.hpp
- validation/ref/neuron/ball_and_3stick.py 0 additions, 1 deletionvalidation/ref/neuron/ball_and_3stick.py
- validation/ref/neuron/ball_and_squiggle.py 0 additions, 1 deletionvalidation/ref/neuron/ball_and_squiggle.py
- validation/ref/neuron/generate_validation.sh 1 addition, 1 deletionvalidation/ref/neuron/generate_validation.sh
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