Refactor(C++): Extract SimulationParameters from Model and ExpData

CMakeLists.txt

@@ -127,7 +127,7 @@ set(AMICI_SRC_LIST
     ${CMAKE_SOURCE_DIR}/src/rdata.cpp
     ${CMAKE_SOURCE_DIR}/src/edata.cpp
     ${CMAKE_SOURCE_DIR}/src/exception.cpp
-
+    ${CMAKE_SOURCE_DIR}/src/simulation_parameters.cpp
     ${CMAKE_SOURCE_DIR}/src/spline.cpp
     ${CMAKE_SOURCE_DIR}/src/solver.cpp
     ${CMAKE_SOURCE_DIR}/src/solver_cvodes.cpp

include/amici/edata.h

@@ -4,6 +4,7 @@
 #include "amici/defines.h"
 #include "amici/vector.h"
 #include "amici/misc.h"
+#include "amici/simulation_parameters.h"
 
 #include <vector>
 
@@ -16,7 +17,7 @@ class ReturnData;
  * @brief ExpData carries all information about experimental or
  * condition-specific data
  */
-class ExpData {
+class ExpData : public SimulationParameters {
 
   public:
     /**
@@ -381,58 +382,6 @@ class ExpData {
      */
     const realtype *getObservedEventsStdDevPtr(int ie) const;
 
-    /**
-     * @brief condition-specific fixed parameters of size Model::nk() or empty
-     */
-    std::vector<realtype> fixedParameters;
-    /**
-     * @brief condition-specific fixed parameters for pre-equilibration of size
-     * Model::nk() or empty. Overrides Solver::newton_preeq
-     */
-    std::vector<realtype> fixedParametersPreequilibration;
-    /**
-     * @brief condition-specific fixed parameters for pre-simulation of
-     * size Model::nk() or empty.
-     */
-    std::vector<realtype> fixedParametersPresimulation;
-
-    /**
-     * @brief condition-specific parameters of size Model::np() or empty
-     */
-    std::vector<realtype> parameters;
-    /**
-     * @brief condition-specific initial conditions of size Model::nx() or
-     * empty
-     */
-    std::vector<realtype> x0;
-    /**
-     * @brief condition-specific initial condition sensitivities of size
-     * Model::nx() * Model::nplist(), Model::nx() * ExpData::plist.size(), if
-     * ExpData::plist is not empty, or empty
-     */
-    std::vector<realtype> sx0;
-    /**
-     * @brief condition-specific parameter scales of size Model::np()
-     */
-    std::vector<ParameterScaling> pscale;
-    /**
-     * @brief condition-specific parameter list
-     */
-    std::vector<int> plist;
-
-    /**
-     * @brief duration of pre-simulation
-     * if this is > 0, presimulation will be performed from
-     * (model->t0 - t_presim) to model->t0 using the fixedParameters in
-     * fixedParametersPresimulation
-     */
-    realtype t_presim = 0;
-
-    /** flag indicating whether reinitialization of states depending on
-     *  fixed parameters is activated
-     */
-    bool reinitializeFixedParameterInitialStates = false;
-
   protected:
     /**
      * @brief resizes observedData, observedDataStdDev, observedEvents and
@@ -478,9 +427,6 @@ class ExpData {
     /** @brief maximal number of event occurrences */
     int nmaxevent_{0};
 
-    /** @brief observation timepoints (dimension: nt) */
-    std::vector<realtype> ts_;
-
     /** @brief observed data (dimension: nt x nytrue, row-major) */
     std::vector<realtype> observed_data_;
     /**

include/amici/model.h

@@ -5,6 +5,7 @@
 #include "amici/defines.h"
 #include "amici/sundials_matrix_wrapper.h"
 #include "amici/vector.h"
+#include "amici/simulation_parameters.h"
 
 #include <map>
 #include <memory>
@@ -476,10 +477,8 @@ class Model : public AbstractModel, public ModelDimensions {
     /**
      * @brief Constructor with model dimensions.
      * @param model_dimensions Model dimensions
+     * @param simulation_parameters Simulation parameters
      * @param o2mode Second order sensitivity mode
-     * @param p Parameters
-     * @param k Constants
-     * @param plist Indexes wrt to which sensitivities are to be computed
      * @param idlist Indexes indicating algebraic components (DAE only)
      * @param z2event Mapping of event outputs to events
      * @param pythonGenerated Flag indicating matlab or python wrapping
@@ -488,9 +487,9 @@ class Model : public AbstractModel, public ModelDimensions {
      * @param w_recursion_depth Recursion depth of fw
      */
     Model(ModelDimensions const& model_dimensions,
+          SimulationParameters simulation_parameters,
           amici::SecondOrderMode o2mode,
-          const std::vector<amici::realtype> &p, std::vector<amici::realtype> k,
-          const std::vector<int> &plist, std::vector<amici::realtype> idlist,
+          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);
@@ -2092,10 +2091,6 @@ class Model : public AbstractModel, public ModelDimensions {
      */
     ModelStateDerived derived_state_;
 
-    /** original user-provided, possibly scaled parameter array (dimension: np)
-     */
-    std::vector<realtype> original_parameters_;
-
     /** index indicating to which event an event output belongs */
     std::vector<int> z2event_;
 
@@ -2105,9 +2100,6 @@ class Model : public AbstractModel, public ModelDimensions {
     /** sensitivity initialization (size nx_rdata x nplist, row-major) */
     std::vector<realtype> sx0data_;
 
-    /** timepoints (size nt) */
-    std::vector<realtype> ts_;
-
     /** vector of bools indicating whether state variables are to be assumed to
      * be positive */
     std::vector<bool> state_is_non_negative_;
@@ -2118,22 +2110,11 @@ class Model : public AbstractModel, public ModelDimensions {
     /** maximal number of events to track */
     int nmaxevent_ {10};
 
-    /** parameter transformation of `originalParameters` (dimension np) */
-    std::vector<ParameterScaling> pscale_;
-
-    /** starting time */
-    realtype tstart_ {0.0};
-
     /** flag indicating whether steadystate sensitivities are to be computed
      *  via FSA when steadyStateSimulation is used
      */
     SteadyStateSensitivityMode steadystate_sensitivity_mode_ {SteadyStateSensitivityMode::newtonOnly};
 
-    /** flag indicating whether reinitialization of states depending on
-     *  fixed parameters is activated
-     */
-    bool reinitialize_fixed_parameter_initial_states_ {false};
-
     /** Indicates whether the result of every call to `Model::f*` should be
      * checked for finiteness */
     bool always_check_finite_ {false};
@@ -2150,6 +2131,9 @@ class Model : public AbstractModel, public ModelDimensions {
 
     /** Recursion */
     int w_recursion_depth_ {0};
+
+    /** Simulation parameters, initial state, etc. */
+    SimulationParameters simulation_parameters_;
 };
 
 bool operator==(const Model &a, const Model &b);

include/amici/model_dae.h

@@ -32,23 +32,21 @@ class Model_DAE : public Model {
     /**
      * @brief Constructor with model dimensions
      * @param model_dimensions Model dimensions
+     * @param simulation_parameters Simulation parameters
      * @param o2mode second order sensitivity mode
-     * @param p parameters
-     * @param k constants
-     * @param plist indexes wrt to which sensitivities are to be computed
      * @param idlist indexes indicating algebraic components (DAE only)
      * @param z2event mapping of event outputs to events
      * @param pythonGenerated flag indicating matlab or python wrapping
      * @param ndxdotdp_explicit number of nonzero elements dxdotdp_explicit
      */
-    Model_DAE(const ModelDimensions &model_dimensions, const SecondOrderMode o2mode,
-              std::vector<realtype> const &p, std::vector<realtype> const &k,
-              std::vector<int> const &plist,
+    Model_DAE(const ModelDimensions &model_dimensions,
+              SimulationParameters simulation_parameters,
+              const SecondOrderMode o2mode,
               std::vector<realtype> const &idlist,
               std::vector<int> const &z2event, const bool pythonGenerated=false,
               const int ndxdotdp_explicit=0)
-        : Model(model_dimensions,
-                o2mode, p, k, plist, idlist, z2event, pythonGenerated,
+        : Model(model_dimensions, simulation_parameters,
+                o2mode, idlist, z2event, pythonGenerated,
                 ndxdotdp_explicit) {
         derived_state_.M_ = SUNMatrixWrapper(nx_solver, nx_solver);
     }

include/amici/model_ode.h

@@ -32,10 +32,8 @@ class Model_ODE : public Model {
     /**
      * @brief Constructor with model dimensions
      * @param model_dimensions Model dimensions
+     * @param simulation_parameters Simulation parameters
      * @param o2mode second order sensitivity mode
-     * @param p parameters
-     * @param k constants
-     * @param plist indexes wrt to which sensitivities are to be computed
      * @param idlist indexes indicating algebraic components (DAE only)
      * @param z2event mapping of event outputs to events
      * @param pythonGenerated flag indicating matlab or python wrapping
@@ -44,15 +42,14 @@ class Model_ODE : public Model {
      * @param w_recursion_depth Recursion depth of fw
      */
     Model_ODE(ModelDimensions const& model_dimensions,
+              SimulationParameters simulation_parameters,
               const SecondOrderMode o2mode,
-              std::vector<realtype> const &p, std::vector<realtype> const &k,
-              std::vector<int> const &plist,
               std::vector<realtype> const &idlist,
               std::vector<int> const &z2event, const bool pythonGenerated=false,
               const int ndxdotdp_explicit=0, const int ndxdotdx_explicit=0,
               const int w_recursion_depth=0)
-        : Model(model_dimensions,
-                o2mode, p, k, plist, idlist, z2event, pythonGenerated,
+        : Model(model_dimensions, simulation_parameters,
+                o2mode, idlist, z2event, pythonGenerated,
                 ndxdotdp_explicit, ndxdotdx_explicit, w_recursion_depth) {}
 
     void fJ(realtype t, realtype cj, const AmiVector &x, const AmiVector &dx,

include/amici/serialization.h

@@ -103,25 +103,43 @@ void serialize(Archive &ar, amici::CVodeSolver &s, const unsigned int /*version*
 template <class Archive>
 void serialize(Archive &ar, amici::Model &m, const unsigned int /*version*/) {
     ar &dynamic_cast<amici::ModelDimensions&>(m);
+    ar &m.simulation_parameters_;
     ar &m.o2mode;
     ar &m.z2event_;
     ar &m.idlist;
     ar &m.state_.h;
     ar &m.state_.unscaledParameters;
-    ar &m.original_parameters_;
     ar &m.state_.fixedParameters;
-    ar &m.reinitialize_fixed_parameter_initial_states_;
     ar &m.state_.plist;
     ar &m.x0data_;
     ar &m.sx0data_;
-    ar &m.ts_;
     ar &m.nmaxevent_;
-    ar &m.pscale_;
-    ar &m.tstart_;
     ar &m.state_is_non_negative_;
     ar &m.pythonGenerated;
 }
 
+
+/**
+ * @brief Serialize amici::SimulationParameters to boost archive
+ * @param ar Archive
+ * @param s amici::SimulationParameters instance to serialize
+ */
+template <class Archive>
+void serialize(Archive &ar, amici::SimulationParameters &s, const unsigned int /*version*/) {
+    ar &s.fixedParameters;
+    ar &s.fixedParametersPreequilibration;
+    ar &s.fixedParametersPresimulation;
+    ar &s.parameters;
+    ar &s.x0;
+    ar &s.sx0;
+    ar &s.pscale;
+    ar &s.plist;
+    ar &s.ts_;
+    ar &s.tstart_;
+    ar &s.t_presim;
+    ar &s.reinitializeFixedParameterInitialStates;
+}
+
 /**
  * @brief Serialize amici::ReturnData to boost archive
  * @param ar Archive