- Oct 28, 2016
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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.
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- Sep 06, 2016
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Benjamin Cumming authored
* move from index_view to const_index_view for mechaninism inintialization. This allows us to pass more generic container types to the constructor while avoiding redundant copies * NOTE: required update of * external/vector * external/modparser * fixed signed-vs-unsigned comparison warning in algorithims.hpp
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- Sep 03, 2016
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Sam Yates authored
* Include new option -g in miniapp to specify cell group size. * Miniapp -r option generates a ring network. * Modify EXPECTS() so that when assertions are disabled we avoid unused variable warnings.
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- Aug 18, 2016
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Benjamin Cumming authored
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- Aug 03, 2016
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Benjamin Cumming authored
- update modparser external repo to a version that fixes some compiler warnings with clang - fix a handful of compiler warnings for signed-unsigned comparison in tests and when ASSERTIONS are on - comment out EXPECTS(has_contiguous_segments) where they fail in the tests so that we can run all the tests with full debug flags
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Sam Yates authored
Plus: coding guidelines compliance.
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- Jul 28, 2016
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Sam Yates authored
* Consistent use of globally defined integer types for indices etc. (catypes.hpp) or template type parameters across simulator. * Support unsigned types in tree, cell_tree and friends. * Use cell_member_type for probe ids (WIP) * Rejig mechanism lookup structure (simplifies, plays nicely with templated index types.) * Move spike, connection, events out of communcation namespace and directory.
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- Jul 05, 2016
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Vasileios Karakasis authored
The previous implementation was failing when nodes were numbered in breadth-first order. Also gave a more descriptive name to the algorithm.
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- Jun 28, 2016
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Sam Yates authored
Sidesteps NDEBUG versus assert() issue; EXPECTS macros are now enabled via a CMake configuration option -DWITH_ASSERTIONS=ON, corresponding to the preprocessor define -DWITH_ASSERTIONS in the code itself. (Note, with assertions enabled, one of the existing tests in test_algorithms.cpp aborts.)
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- Jun 24, 2016
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Sam Yates authored
* Add WITH_MPI CMake option to enable MPI code in application * Use find_package(MPI) and set up flags, etc. for MPI * Extra defines to disable the inclusion of C++ MPI headers for MPICH and OpenMPI. * Fix signed/unsigned compare warning in algorithms.hpp
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- Jun 17, 2016
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Vasileios Karakasis authored
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- Jun 15, 2016
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Vasileios Karakasis authored
At this low level a cell tree is just a sequence of parent indices, where each parent index is the parent of the current index in the sequence. There four basic algorithms: 1. child_count(parent_index): Computes the number of children for each node in parent_index Time: O(N), Space: O(1) 2. branches(parent_index): Returns a set of the branching nodes in parent_index, last branch index equals the parent_index's size. Time: O(N), Space: O(N) 3. expand_branches(branch_index): Takes a branch_index (result from branches()) and expands it at the size of the original tree with all the nodes inside a branch having the same number. Time: O(parent_index), Space: O(1) 4. make_parent_index(parent_index, branch_index): Return a compacted tree (single node per branch) from parent_index and its corresponding branch_index. Time: O(N), Space: O(N) There is another utility function as well: find_branch(branch_index, nid): Returns the id of the branch where nid belongs to. Time: O(N), Space: O(1)
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- Jun 09, 2016
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Wouter Klijn authored
(yes, I'm one of 'those' programmers)
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- Apr 28, 2016
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Benjamin Cumming authored
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- Apr 22, 2016
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Vasileios Karakasis authored
+ some other minor improvements.
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- Apr 20, 2016
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Vasileios Karakasis authored
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- Apr 19, 2016
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Benjamin Cumming authored
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- Apr 18, 2016
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Vasileios Karakasis authored
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Vasileios Karakasis authored
+ converted swc_record::kind to an ``enum class``
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- Apr 14, 2016
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Benjamin Cumming authored
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Benjamin Cumming authored
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- Apr 12, 2016
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Benjamin Cumming authored
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- Apr 08, 2016
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Benjamin Cumming authored
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