Handle events occuring at fixed timepoints without root-finding

A first attempt towards AMICI-dev#2185 For events that occur at known timepoints, we don't need sundials' root-finding. We can just stop the solver at the respective timepoints and handle the events. To be extended to parameterized but state-independent trigger functions.
dweindl · Dec 4, 2023 · baa13af · baa13af
1 parent 81872cc
commit baa13af
Showing 26 changed files with 234 additions and 43 deletions.
diff --git a/include/amici/forwardproblem.h b/include/amici/forwardproblem.h
@@ -197,7 +197,9 @@ class ForwardProblem {
     SimulationState const& getSimulationStateTimepoint(int it) const {
         if (model->getTimepoint(it) == initial_state_.t)
             return getInitialSimulationState();
-        return timepoint_states_.find(model->getTimepoint(it))->second;
+        auto map_iter = timepoint_states_.find(model->getTimepoint(it));
+        assert(map_iter != timepoint_states_.end());
+        return map_iter->second;
     };
 
     /**

diff --git a/include/amici/model.h b/include/amici/model.h
@@ -12,7 +12,6 @@
 #include "amici/vector.h"
 
 #include <map>
-#include <memory>
 #include <vector>
 
 namespace amici {
@@ -117,14 +116,17 @@ class Model : public AbstractModel, public ModelDimensions {
      * @param ndxdotdp_explicit Number of nonzero elements in `dxdotdp_explicit`
      * @param ndxdotdx_explicit Number of nonzero elements in `dxdotdx_explicit`
      * @param w_recursion_depth Recursion depth of fw
+     * @param state_independent_events Map of events with state-independent
+     * triggers functions, mapping trigger timepoints to event indices.
      */
     Model(
         ModelDimensions const& model_dimensions,
         SimulationParameters simulation_parameters,
         amici::SecondOrderMode o2mode, std::vector<amici::realtype> idlist,
         std::vector<int> z2event, bool pythonGenerated = false,
         int ndxdotdp_explicit = 0, int ndxdotdx_explicit = 0,
-        int w_recursion_depth = 0
+        int w_recursion_depth = 0,
+        std::map<realtype, std::vector<int>> state_independent_events = {}
     );
 
     /** Destructor. */
@@ -1449,6 +1451,8 @@ class Model : public AbstractModel, public ModelDimensions {
      */
     SUNMatrixWrapper const& get_dxdotdp_full() const;
 
+    virtual std::vector<double> get_trigger_timepoints() const;
+
     /**
      * Flag indicating whether for
      * `amici::Solver::sensi_` == `amici::SensitivityOrder::second`
@@ -1462,6 +1466,8 @@ class Model : public AbstractModel, public ModelDimensions {
     /** Logger */
     Logger* logger = nullptr;
 
+    std::map<realtype, std::vector<int>> state_independent_events_ = {};
+
   protected:
     /**
      * @brief Write part of a slice to a buffer according to indices specified

diff --git a/include/amici/model_dimensions.h b/include/amici/model_dimensions.h
@@ -31,6 +31,7 @@ struct ModelDimensions {
      * @param nz Number of event observables
      * @param nztrue Number of event observables of the non-augmented model
      * @param ne Number of events
+     * @param ne_solver Number of events that require root-finding
      * @param nspl Number of splines
      * @param nJ Number of objective functions
      * @param nw Number of repeating elements
@@ -58,11 +59,12 @@ struct ModelDimensions {
         int const nx_rdata, int const nxtrue_rdata, int const nx_solver,
         int const nxtrue_solver, int const nx_solver_reinit, int const np,
         int const nk, int const ny, int const nytrue, int const nz,
-        int const nztrue, int const ne, int const nspl, int const nJ,
-        int const nw, int const ndwdx, int const ndwdp, int const ndwdw,
-        int const ndxdotdw, std::vector<int> ndJydy, int const ndxrdatadxsolver,
-        int const ndxrdatadtcl, int const ndtotal_cldx_rdata, int const nnz,
-        int const ubw, int const lbw
+        int const nztrue, int const ne, int const ne_solver, int const nspl,
+        int const nJ, int const nw, int const ndwdx, int const ndwdp,
+        int const ndwdw, int const ndxdotdw, std::vector<int> ndJydy,
+        int const ndxrdatadxsolver, int const ndxrdatadtcl,
+        int const ndtotal_cldx_rdata, int const nnz, int const ubw,
+        int const lbw
     )
         : nx_rdata(nx_rdata)
         , nxtrue_rdata(nxtrue_rdata)
@@ -76,6 +78,7 @@ struct ModelDimensions {
         , nz(nz)
         , nztrue(nztrue)
         , ne(ne)
+        , ne_solver(ne_solver)
         , nspl(nspl)
         , nw(nw)
         , ndwdx(ndwdx)
@@ -104,6 +107,8 @@ struct ModelDimensions {
         Expects(nztrue >= 0);
         Expects(nztrue <= nz);
         Expects(ne >= 0);
+        Expects(ne_solver >= 0);
+        Expects(ne >= ne_solver);
         Expects(nspl >= 0);
         Expects(nw >= 0);
         Expects(ndwdx >= 0);
@@ -164,7 +169,10 @@ struct ModelDimensions {
     /** Number of events */
     int ne{0};
 
-    /** numer of spline functions in the model */
+    /** Number of events that require root-finding */
+    int ne_solver{0};
+
+    /** Number of spline functions in the model */
     int nspl{0};
 
     /** Number of common expressions */

diff --git a/include/amici/model_ode.h b/include/amici/model_ode.h
@@ -39,19 +39,23 @@ class Model_ODE : public Model {
      * @param ndxdotdp_explicit number of nonzero elements dxdotdp_explicit
      * @param ndxdotdx_explicit number of nonzero elements dxdotdx_explicit
      * @param w_recursion_depth Recursion depth of fw
+     * @param state_independent_events Map of events with state-independent
+     * triggers functions, mapping trigger timepoints to event indices.
      */
     Model_ODE(
         ModelDimensions const& model_dimensions,
         SimulationParameters simulation_parameters,
         const SecondOrderMode o2mode, std::vector<realtype> const& idlist,
         std::vector<int> const& z2event, bool const pythonGenerated = false,
         int const ndxdotdp_explicit = 0, int const ndxdotdx_explicit = 0,
-        int const w_recursion_depth = 0
+        int const w_recursion_depth = 0,
+        std::map<realtype, std::vector<int>> state_independent_events
+        = {}
     )
         : Model(
             model_dimensions, simulation_parameters, o2mode, idlist, z2event,
             pythonGenerated, ndxdotdp_explicit, ndxdotdx_explicit,
-            w_recursion_depth
+            w_recursion_depth, state_independent_events
         ) {}
 
     void

diff --git a/include/amici/serialization.h b/include/amici/serialization.h
@@ -260,6 +260,7 @@ void serialize(
     ar& m.nz;
     ar& m.nztrue;
     ar& m.ne;
+    ar& m.ne_solver;
     ar& m.nspl;
     ar& m.nw;
     ar& m.ndwdx;

diff --git a/models/model_calvetti/model_calvetti.h b/models/model_calvetti/model_calvetti.h
@@ -46,6 +46,7 @@ class Model_model_calvetti : public amici::Model_DAE {
                   0,
                   4,
                   0,
+                  0,
                   1,
                   38,
                   53,
@@ -207,6 +208,6 @@ class Model_model_calvetti : public amici::Model_DAE {
 
 } // namespace model_model_calvetti
 
-} // namespace amici 
+} // namespace amici
 
 #endif /* _amici_model_calvetti_h */
diff --git a/models/model_dirac/model_dirac.h b/models/model_dirac/model_dirac.h
@@ -46,6 +46,7 @@ class Model_model_dirac : public amici::Model_ODE {
                   0,
                   2,
                   0,
+                  0,
                   1,
                   0,
                   0,
@@ -204,6 +205,6 @@ class Model_model_dirac : public amici::Model_ODE {
 
 } // namespace model_model_dirac
 
-} // namespace amici 
+} // namespace amici
 
 #endif /* _amici_model_dirac_h */
diff --git a/models/model_events/model_events.h b/models/model_events/model_events.h
@@ -60,6 +60,7 @@ class Model_model_events : public amici::Model_ODE {
                   2,
                   6,
                   0,
+                  0,
                   1,
                   0,
                   0,
@@ -232,6 +233,6 @@ class Model_model_events : public amici::Model_ODE {
 
 } // namespace model_model_events
 
-} // namespace amici 
+} // namespace amici
 
 #endif /* _amici_model_events_h */
diff --git a/models/model_jakstat_adjoint/model_jakstat_adjoint.h b/models/model_jakstat_adjoint/model_jakstat_adjoint.h
@@ -49,6 +49,7 @@ class Model_model_jakstat_adjoint : public amici::Model_ODE {
                   0,
                   0,
                   0,
+                  0,
                   1,
                   2,
                   1,
@@ -210,6 +211,6 @@ class Model_model_jakstat_adjoint : public amici::Model_ODE {
 
 } // namespace model_model_jakstat_adjoint
 
-} // namespace amici 
+} // namespace amici
 
 #endif /* _amici_model_jakstat_adjoint_h */
diff --git a/models/model_jakstat_adjoint_o2/model_jakstat_adjoint_o2.h b/models/model_jakstat_adjoint_o2/model_jakstat_adjoint_o2.h
@@ -49,6 +49,7 @@ class Model_model_jakstat_adjoint_o2 : public amici::Model_ODE {
                   0,
                   0,
                   0,
+                  0,
                   18,
                   10,
                   2,
@@ -210,6 +211,6 @@ class Model_model_jakstat_adjoint_o2 : public amici::Model_ODE {
 
 } // namespace model_model_jakstat_adjoint_o2
 
-} // namespace amici 
+} // namespace amici
 
 #endif /* _amici_model_jakstat_adjoint_o2_h */
diff --git a/models/model_nested_events/model_nested_events.h b/models/model_nested_events/model_nested_events.h
@@ -49,6 +49,7 @@ class Model_model_nested_events : public amici::Model_ODE {
                   0,
                   4,
                   0,
+                  0,
                   1,
                   0,
                   0,
@@ -210,6 +211,6 @@ class Model_model_nested_events : public amici::Model_ODE {
 
 } // namespace model_model_nested_events
 
-} // namespace amici 
+} // namespace amici
 
 #endif /* _amici_model_nested_events_h */
diff --git a/models/model_neuron/model_neuron.h b/models/model_neuron/model_neuron.h
@@ -63,6 +63,7 @@ class Model_model_neuron : public amici::Model_ODE {
                   1,
                   1,
                   0,
+                  0,
                   1,
                   0,
                   0,
@@ -238,6 +239,6 @@ class Model_model_neuron : public amici::Model_ODE {
 
 } // namespace model_model_neuron
 
-} // namespace amici 
+} // namespace amici
 
 #endif /* _amici_model_neuron_h */
diff --git a/models/model_neuron_o2/model_neuron_o2.h b/models/model_neuron_o2/model_neuron_o2.h
@@ -65,6 +65,7 @@ class Model_model_neuron_o2 : public amici::Model_ODE {
                   1,
                   1,
                   0,
+                  0,
                   5,
                   2,
                   2,
@@ -242,6 +243,6 @@ class Model_model_neuron_o2 : public amici::Model_ODE {
 
 } // namespace model_model_neuron_o2
 
-} // namespace amici 
+} // namespace amici
 
 #endif /* _amici_model_neuron_o2_h */
diff --git a/models/model_robertson/model_robertson.h b/models/model_robertson/model_robertson.h
@@ -47,6 +47,7 @@ class Model_model_robertson : public amici::Model_DAE {
                   0,
                   0,
                   0,
+                  0,
                   1,
                   1,
                   2,
@@ -209,6 +210,6 @@ class Model_model_robertson : public amici::Model_DAE {
 
 } // namespace model_model_robertson
 
-} // namespace amici 
+} // namespace amici
 
 #endif /* _amici_model_robertson_h */
diff --git a/models/model_steadystate/model_steadystate.h b/models/model_steadystate/model_steadystate.h
@@ -46,6 +46,7 @@ class Model_model_steadystate : public amici::Model_ODE {
                   0,
                   0,
                   0,
+                  0,
                   1,
                   2,
                   2,
@@ -204,6 +205,6 @@ class Model_model_steadystate : public amici::Model_ODE {
 
 } // namespace model_model_steadystate
 
-} // namespace amici 
+} // namespace amici
 
 #endif /* _amici_model_steadystate_h */
diff --git a/python/sdist/amici/de_export.py b/python/sdist/amici/de_export.py
@@ -1425,13 +1425,24 @@ def num_expr(self) -> int:
         return len(self.sym("w"))
 
     def num_events(self) -> int:
+        """
+        Total number of Events (those for which root-functions are added and those without).
+
+        :return:
+            number of events
+        """
+        return len(self.sym("h"))
+
+    def num_events_solver(self) -> int:
         """
         Number of Events.
 
         :return:
             number of event symbols (length of the root vector in AMICI)
         """
-        return len(self.sym("h"))
+        return sum(
+            not event.triggers_at_fixed_timepoint() for event in self.events()
+        )
 
     def sym(self, name: str) -> sp.Matrix:
         """
@@ -1750,6 +1761,16 @@ def parse_events(self) -> None:
             # add roots of heaviside functions
             self.add_component(root)
 
+        # re-order events - first those that require root tracking, then the others
+        self._events = list(
+            chain(
+                itertools.filterfalse(
+                    Event.triggers_at_fixed_timepoint, self._events
+                ),
+                filter(Event.triggers_at_fixed_timepoint, self._events),
+            )
+        )
+
     def get_appearance_counts(self, idxs: List[int]) -> List[int]:
         """
         Counts how often a state appears in the time derivative of
@@ -3642,6 +3663,7 @@ def _write_model_header_cpp(self) -> None:
             "NZ": self.model.num_eventobs(),
             "NZTRUE": self.model.num_eventobs(),
             "NEVENT": self.model.num_events(),
+            "NEVENT_SOLVER": self.model.num_events_solver(),
             "NOBJECTIVE": "1",
             "NSPL": len(self.model.splines),
             "NW": len(self.model.sym("w")),
@@ -3736,6 +3758,7 @@ def _write_model_header_cpp(self) -> None:
                 )
             ),
             "Z2EVENT": ", ".join(map(str, self.model._z2event)),
+            "STATE_INDEPENDENT_EVENTS": self._get_state_independent_event_intializer(),
             "ID": ", ".join(
                 (
                     str(float(isinstance(s, DifferentialState)))
@@ -3871,6 +3894,25 @@ def _get_symbol_id_initializer_list(self, name: str) -> str:
             for idx, symbol in enumerate(self.model.sym(name))
         )
 
+    def _get_state_independent_event_intializer(self) -> str:
+        tmp_map = {}
+        for event_idx, event in enumerate(self.model.events()):
+            if not event.triggers_at_fixed_timepoint():
+                continue
+            trigger_time = float(event.get_trigger_time())
+            try:
+                tmp_map[trigger_time].append(event_idx)
+            except KeyError:
+                tmp_map[trigger_time] = [event_idx]
+
+        def vector_initializer(v):
+            return f"{{{', '.join(map(str, v))}}}"
+
+        return ", ".join(
+            f"{{{trigger_time}, {vector_initializer(event_idxs)}}}"
+            for trigger_time, event_idxs in tmp_map.items()
+        )
+
     def _write_c_make_file(self):
         """Write CMake ``CMakeLists.txt`` file for this model."""
         sources = "\n".join(