C++ Hybrid Solver: Events #594
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- Added `Event` class - Added basic macros for event parameters and their associated static methods
In order to accommodate for SBML features, parameters must be vectorized instead of global variables. - Added `get_parameters` and `get_constants` template functions - Heap-allocates data for each type of variable - Replaced all references in C++ solver to parameters with vectorized equivalents - Replaced call to `sanitized_parameter_names` with manual sanitization in Python model - Instead of `P0, P1, etc` parameters are `P[0], P[1], etc` for variables and `C[0], C[1], etc` for constants - Modified rate rules to accept vectorized parameters - Removed `IPropensityFunction` and replaced with static `propensity` method - Static member of the `Reaction` class
- Added `execute` member methods to assign variables to state vecs - Added `use_state` member method to save the current state for later execution - Implemented rule of 5 for `Event` class - Implemented template injection functions - Added new implementation of `use_events`, no longer uses lambdas - Added new `assign` static method to dispatch event assignments
- Added `species_id` and `param_id` dicts to `SanitizedModel` class - Maps un-sanitized species/parameter names to their IDs - Modified `TauHybridCSolver` options to provide definitions - Defs for: events, # of events, assignments, # of event assignments
- Modified `TauHybridCSolver` template option generation to use a globally unique assignment ID - Added a (currently useless) call to `use_events` just to test
- Updated template to determine `use_trigger_state` and `persistent` flags - Updated event eval functions (`trigger`, `delay`, `priority`) to support expressions - Added `EventExecution` object to represent execution state of event - Call `Even#get_execution` to use, saves state automatically - Added `execution_time` property to execution state - Moved persistent state from `Event` to `EventExecution` - Removed `Event` as "unsupported SBML feature" in Python solver
Still missing trigger state memory (currently executes constantly) - Added events vector to solver function signature - Added priority queues to Hybrid solver iteration - Added comparison operators to `EventExecution` object - Moved `priority` method from `Event` to `EventExecution` - Added copy of assignments list on copy/move constructors - Fixed sizing issue for event template - Fixed off-by-1 error when generating assignment IDs in Python
- Added `is_persistent()` method to `Event` class - Added `volatile_queue` list for events that need to be re-checked continuously
- Added methods to `Integrator` class to enable root-finding - Modified trigger pipeline to fire detected events without using trigger calls directly
All triggers are evaluated at the end of every iteration. No root-finding is performed. - Removed calls to `use_events()` in integrator.cpp - Added `trigger_state` to track transition state of each trigger
Goal is to use new layout where root-finder can search for both events and reactions. - Added `Integrator#use_events` and `Integrator#use_reactions` - Updated `Integrator#integrate` to use new layout
- Added "trigger pool" data set to track event trigger state - Added "roots found" return parameters to `integrate()` method
Parameter bug was caused by parameters never been templated as variable (always constants). - Fixed bug where parameter assignments are ignored - Added `variable` member to `SanitizedModel` - Removed `variable` param from `SanitizedModel#get_template`, instead pulls from `self` - Updated docstrings in new integrator methods - Updated root-finder return to apply direct reactions - Fixed parameter overrides not applying - Added array to track which parameters have overrides
- Added comprehensive test cases for event features - Fixed non-persistent triggers by reordering volatile trigger checks - Fixed delay time checks - Fixed calls to `memcpy` in `EventExecution`'s copy constructor
- Added `initial_value` handling to template gen - Added initial value as macro parameter for `EVENT`
Comp - Moved event execution code to separate `EventList` class - Contains exact same code, just abstracted away - Added check to trigger state at beginning of trajectory - Moved first trajectory value to be after events have been processed
- Bug occurred when stochastic event fired - Root-finder list was never cleared - Errant `continue` skipped over state update code - Bug occurred when array is not zero-initialized - Caused compiler-specific bug where stochastic events were impossible to find
seanebum
approved these changes
Jan 6, 2022
BryanRumsey
approved these changes
Jan 7, 2022
…ts, and Function Definitions.
…ature/cpp-hybrid-events
briandrawert
approved these changes
Jan 7, 2022
Merged
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Adds features of SBML
Eventobjects (and their related objects, includingEventTriggers andEventAssignments) to the C++ hybrid solver, as referenced in SBML Language Specification v3.2.Major Changes
Event,EventList,EventExecutionclasses to C++ back endIPropensityFunctioninterface with static call tomap_propensitytest_hybrid_c_events.pyfor unit testing the hybrid solver's event triggersEventtriggers and direct reactions (only when Events are found)Closes #628