Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

If ion concentrations are read and written in the INITIAL blocks of mechanisms, this ensures that the reading mechanisms will receive the correct values.
Fixes #896

* Group common linear system solver code across `SparseSolverVisitor`, `SparseNonlinearSolverVisitor`, and `LinearSolverVisitor`.
* Normalize intermediate values in Gaussian elimination when the matrix has more than 5 rows.

Fixes #890

Fix linear scaling of model initialization w.r.t. number of MPI ranks.

Fixes #909.

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

Also change the way we handle unitson/unitsoff.
UNITSON, UNITSOFF, COMMENT, ENDCOMMENT are now all handled in Lexer::parse

Fixes #14 
Fixes #885

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

Also renumber operator precedence.

Fixes #25

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

Also emit "abs" in cexpr_emit.cpp because the simd backend implements abs

Fixes #887

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

Calling vector::reserve to increase the size of the synapse vector by 1 causes significant performance degradation.

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

Fixes #892

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

Completely remove managed memory from the gpu backend.
`managed_vector<level>` is split into:
- A device vector of structs containing meta data about each level 
- A device vector containing concatenated lengths of each branch in a level for all levels
- A device vector containing concatenated parents of each branch in a level for all levels

All other instances of managed memory in `matrix_fine` are easily replaced by device vectors  
Managed memory is also removed from the unit tests. 

Fixes #841

* Make access to `segment`s in a `cable_cell` read only
* Change cell constructor to require morphology and label dictionary; `make_cable_cell` no longer required.
* Consolidate paint/place functionality on `cable_cell`.
* Add simple cell builder wrapping new API for use in unit tests.
* Remove validation test code: appropriate validation tests will need to be implemented in nsuite.

Fixes #871 

* Remove improper std::move of mechanism description with for loop in cell::paint().

* Fix modcc segmentation fault caused by improper check for the presence of a symbol, triggered when a symbol defined in a RANGE is absent from the ASSIGNED and PARAMETER blocks.

* Accept `tok::ne` for conditional expressions in modcc, and emit correctly as '!=' in `cexpr_emit`.

* Add support for non-linear kinetic schemes in modcc, using a non-linear backwards Euler method with a fixed number of iterations of Newton's method.

* Provide correct assignment operator.

akuesters authored 5 years ago and Benjamin Cumming committed 5 years ago

Ensure that errors in Python callbacks that are called from multithreaded C++ code propogate the correct Python error back to the parent Python callback site, and that no callbacks are called from other threads if an error has already ocurred.
- protects each recipe callback with a mutex, stores python exception, catches and throws python exception if occured
- methods calling recipe (in simulation and partition_load_balance) are protected as well by try catch, resets and rethrows python exception (if occured) or else throws C++ exception

fixes #792

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

Sets the diameter of a CV as the diameter at the middle of a CV
Exposes the diameter in `shared_state` and `mechanism`
Adds support in modcc to treat `diam` as a special parameter 
Implements unit tests

Fixes #850 

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

* Add new `cv_policy` class that wraps classes derived from `cv_policy_base`, which in turn provide a facility for producing CV boundaries on morphology trees from a `cable_cell`.
* Implement fixed-CVs-per-branch and maximum-CV-length policies, with flags that allow for single-CV oots and for CVs that terminate at fork points or which are centred on fork points.
* Expose locset `join` expressions.
* Add `empty()` test method on `morphology`.
* Expose branch length on `em_morphology` via member function.
* Account for the length of a spherical root branch in `em_morphology`.
* Test for validity but do not canonicalize locations when thingifying.
* Rename `root_sample_has_same_tag_as_child` to `root_sample_tag_differs_from_children` to better reflect sense of test.
* Add unit tests for CV policies, branch_length method.

* Modify `SparseSolverVisitor` to allow solving kinetic equations at steady state. 

Addresses #837 

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

- Implement inlining functions with multiple statements
- Implement inlining nested function calls
- Implement inlining if/else statements. Compilation fails if a function fails to set the return value.

Fixes #741, #742, #862 

Adds

* to `recipe.cpp`: 
`num_probes` and `get_probe` with helper function `cable_probe(kind, id, location)`
* `sample.cpp`: 
`sample` type with attributes `time` and `value`; a `sampler` with `samples()` and `clear()` and helper functions `attach_sampler(sim, dt)` for adding all probes as well as `attach_sampler(sim, dt, probe_id)` for adding one probe
* `morphology.cpp`: 
`location` as `arb::mlocation` with `branch` and `position` 
* corresponding docs and example
* update to new cable cell semantics in c++ validation test

fixes #762

WIP on implementation of new cable cell API.

* Hide implementation and state using PIMPL
* Add consistent `place` methods for adding synapse, stimuls, gap junction site and spike detectors to `cable_cell`.
* Add default constructor for `region` and `locset` that create empty `nil` instances.

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

* Remove or implement move ctor/assign operations for ostream-derived classes.
* Add explicit test for a zero row in modcc's sparse and linear solver finalize routines.
* Forward declare `morphology_impl` as a struct.
* Remove redundant capture in a lambda expression in fvm_layout.cpp.
* Add extra parens in an assign-and-test condition in mechcat.cpp.

* Add `minset` method for location lists that computes the minimal set by the partial order imposed by the morphology tree.

* Add new "embedded morphology" `em_morphology`, constructed from a `morphology`, that: caches derived information such as terminal points, locations of sample points, branch lengths; provides services for canonicalizing locations and interpolation; and is used for the realisation of regions and locsets (see below).
* Add simple DSL for describing locsets and regions, which are abstract descriptions of sets of locations and regions on morphologies, together with a set of operations.
* Add a new class `label_dict` that associates names with regions and locsets.
* Extend `cable_cell` to hold a `label_dict` argument, which is used by a new method `paint` for associating mechanisms with regions.

Fixes #845.

* Adds modcc support for COMPARTMENT statements of the form: `COMPARTMENT v {state_0, state_1, ..., state_n}`.
* Use `COMPARTMENT` values `v` to multiply the derivative of state variables `state_0, state_1, ..., state_n` in associated kinetic scheme blocks.

Fixes #838.

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

* Change VERSION to 0.2.3-dev.

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

New version to capture fix to Arbor's installed
CMake config module and optional libunwind dependance.

* libunwind is optional, and off by default.

* fix description of CMake option

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

* Replace derivation of cylindrical cable equation formula with S–L approach.
* Relate analysis of cylindrical form to Rallpack 1 in a separate section.
* Add analysis of tapered cable case.
* Unify discussion of cable with constant electrical properties but varying geometry.
* Add section describing how one can well-estimate the inter-cell flux given point samples or CV means for the membrane voltage.

Refactor the example code so that all examples have a single C++ source file, and the source file, source path and executable all have the same name.

Fixes  #847.

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

* Set VERSION to 0.2.1.
* Add .zenodo.json metadata file which will hopefully ease our auto-DOI-publishing woes.
* Remove .json from .gitignore.

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

Add support for parsing and processing `LINEAR` blocks: 

Changes: 
* `SOLVE` expressions can be called from inside an `INITIAL` block, but only if they are solving a linear system
* Tilde expressions can now be either linear expressions or reaction expressions
* Linear expressions need to be rewritten before being sent to the solver, this is done using `LinearRewriter`
* The linear system is setup in `LinearSolverVisitor` fills the lhs and rhs of the symbolic matrix   
* The matrix is recued using `gj_reduce`, which now works on non-diagonal matrices. 

Fixes #839 

Nora Abi Akar authored 5 years ago and Benjamin Cumming committed 5 years ago

Fix `mc_cell_group.gpu_test`: use the nerst equations for the reversal potential calculation for `na`, `ca` and `k`

* Replace old `arb::morphology` class with new `arb::sample_tree` and `arb::morphology` types, where `arb::sample_tree` manages a set of morphology sample points and their topology, and `arb::morphology` presents a branch-based view over samples described by an `arb::sample_tree`. The new classes support morphologies with cable-like or spherical somata.
* Supply a new conversion routine for forming a `arb::cable_cell` from a morphology, with support for both classes of soma.

Fixes #835