- Oct 30, 2016
-
-
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.
-
- Oct 28, 2016
-
-
Ben Cumming authored
Feature/divided compartments
-
Ben Cumming authored
Consolidate validation tests (issue #41)
-
Sam Yates authored
* Make `algorithm::sum`, `algorithm::mean` more generic, allowing use with array types. * Add `div_compartment` compartment representation, that holds geometric information for each half of a compartment that will then be used in calculating control volumes. * Add three compartmentalisation schemes/policies that discretize a segment into `div_compartment` objects: * `div_compartment_by_ends` divides based only on the segment end points and radii. * `div_compartment_sampler` forms frusta by sampling the segment radius at each compartment boundary * `div_compartment_integrator` computes the compartment areas and volumes exactly by summing all frustra in the intersection of the segment and the compartmnet span.
-
Sam Yates authored
* Simplify trace analysis and reporting code in `trace_analysis.hpp` * Consolidate convergence test run procedures into new class `convergence_test_runner`.
-
Ben Cumming authored
Feature/new test model
-
Ben Cumming authored
More range functionality, unit tests.
-
Sam Yates authored
* Add documentation of template parameters for `filter_iterator`. * Document use of `uninitalized<F>` for holding functional objects in `filter_iterator` and `transform_iterator`
-
- Oct 27, 2016
-
-
Sam Yates authored
* Make `test_common_cells.hpp` and `ball_and_taper.py` agree. * Add `ball_and_squiggle` model that has a tapering undulating profile.
-
Sam Yates authored
* New `filter` view: lazily selects based on predicate. * Generic `front` and `back` for sequences. * New rangeutil STL wrappers `stable_sort_by`, `all_of`, `any_of`. * Consolidate common utility unit testing structures into `tests/unit/common.hpp`
-
Sam Yates authored
* Tests for `math::pi`, `math::lerp`, `math::area_frustrum` and `math::volume_frustrum` * Fix `math:pi<long double>()`.
-
Sam Yates authored
-
Ben Cumming authored
modcc: Support for units syntax within a state block.
-
Vasileios Karakasis authored
-
Ben Cumming authored
Add "lib" to search prefixes for libtbb
-
Ben Cumming authored
Address deprecated use of 'symbol' warning.
-
Sam Yates authored
Julia 0.5 deprecates use of `symbol` instead of `Symbol`. This patch just substitutes the correct call.
-
Sam Yates authored
Julia 0.5 deprecates use of `symbol` instead of `Symbol`. This patch just substitutes the correct call.
-
Sam Yates authored
* Fix quoting error in library search. * Add "lib" to prefixes when system is "Linux".
-
- Oct 26, 2016
-
-
Vasileios Karakasis authored
-
Vasileios Karakasis authored
-
Ben Cumming authored
Feature/cable validation
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
-
Sam Yates authored
* Implement Rallpack1 validation test (with a workaround for inability to set membrane conductance). * Fix bug in L≠1 case in PassiveCable.jl (this may still be wrong). * Fix bug in peak delta computation in trace analysis when both traces have no local maxima. * Gentle failure on missing `numeric_soma.json` * Allow multiple `-s` selection operations for `tsplot`, acting disjunctively.
-
- Oct 25, 2016
-
-
Sam Yates authored
* Amend data directory path in validation tests. * Enmodulate `hh_soma.jl` * Add HH channel reference data generations script. * Switch `validate_soma.cpp` to numeric reference data. * Consolidate common code in `validate_ball_and_stick.cpp` * Add (nearly) Rallpack1 validation test (see below). * Gentle failure on absence of reference data in `validate_ball_and_stick.cpp` Can't yet override mechanism default parameter values, so the cable cell model added to `test_common_cells.hpp` lets the default stand; validation script will have to use the default membrane conductance rather than that given by Rallpack1.
-
Vasileios Karakasis authored
Address bug in fix for cell clone ctor.
-
Sam Yates authored
* Add test for cell clone semantics. * Fix `1cell::cell(clone_cell_t, const cell&)` for correct copy semantics.
-
Sam Yates authored
Fixes Clang 3.7 failure to compile.
-
Ben Cumming authored
Add analytic simple cable solver.
-
- Oct 24, 2016
-
-
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.
-
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.
-
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.
-
Sam Yates authored
Also: * Ensure intrinsic and passive properties properly set on test cells.
-
- Oct 22, 2016
-
-
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.
-