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- Deleted obsolete ODE control header and implementation files. - Removed ODE interface and related utility functions to streamline the ODE solver. - Eliminated ODE runner and step classes to simplify the integration process. - Updated references in patch, resource_spline, scm, species, and stochastic_species headers to use new ODE interface. - Removed tests related to ODE control and Lorenz system integration.
…e Rcpp bindings - switch ODE-facing C++ types and interfaces from legacy plant::ode symbols to odelia::ode equivalents across core model classes - add solver compatibility wrappers in: - inst/include/plant/ode_solver_compat.h - inst/include/plant/ode_solver_r6.h - introduce/standardize SolverR6 usage for RcppR6-generated OdeRunner bindings to keep generated code compatible with current solver API - update YAML generator config (inst/RcppR6_classes.yml) to use concrete std::vector<double> state types and odelia::ode control/state helpers - regenerate Rcpp outputs (R/RcppExports.R, R/RcppR6.R, src/RcppExports.cpp, src/RcppR6.cpp, RcppR6 pre/post headers) - update individual/stochastic runner helpers and scaffold templates to match new solver types and accessors - adjust docs/vignette references to reflect odelia::ode::Solver naming - verify clean regeneration and build with `make clean RcppR6 all`
- switch SCM and StochasticPatchRunner to `solver.set_state_from_system()` after mutating system state, avoiding unnecessary solver resets - make stochastic patch test deterministic by replacing probabilistic `introduce_new_node(1)` with `introduce_new_node_and_update(1)` This removes flaky failures in `test-stochastic-patch.R` and keeps solver state synchronization consistent after node introduction/death updates.
- replace plant::ode::SolverR6 usages with odelia::ode::Solver in Rcpp bindings and generated headers
- adapt wrapper calls to odelia API (advance_adaptive({t0,t1}), advance_fixed({t0,t1}), get_system())
- update inst/RcppR6_classes.yml OdeRunner mapping to native odelia solver
- remove unused shim headers:
- inst/include/plant/ode_solver_r6.h
- inst/include/plant/ode_solver_compat.h
- disable solver history collection in performance-critical paths:
- SCM constructor
- StochasticPatchRunner constructor
- OdeRunner constructors in src/RcppR6.cpp
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Mutants running and tests passing, but 1.5x original time. Have been investigating why but no answers yet |
- turn off save_RK45_cache when using build_schedule
- Refactor `SCM::run_next()` into `run_next_impl(sync_patch)` to avoid unnecessary patch copies during internal run loops - Keep solver-owned system (`solver.get_system_ref()`) as the hot-path state and only sync back to `patch` when needed - Update `SCM::run()` history collection to use solver state and sync `patch` once at the end - Return SCM time from `solver.time()` for consistent source-of-truth timing - Tighten `SCM::reset()` synchronization to keep `patch` and solver state aligned - Apply the same solver-ref pattern in `StochasticPatchRunner` to reduce copy churn around node introduction and adaptive advancement These changes preserve public behavior while reducing state copy overhead in frequently executed integration paths.
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Speeds now resolved! |
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The core ode stepping machinery from plant has been spun out into a standalone package. This PR tests ability to support plant.
Some issues to resolve