amici 0.26.2__tar.gz → 0.26.3__tar.gz

{amici-0.26.2 → amici-0.26.3}/MANIFEST.in

@@ -11,6 +11,7 @@ include LICENSE.md
 exclude amici/*.so
 exclude amici/*.dll
 prune **/build
+prune **/install
 prune amici/share
 prune amici/lib
 prune amici/ThirdParty/SuiteSparse/lib

{amici-0.26.2/amici.egg-info → amici-0.26.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: amici
-Version: 0.26.2
+Version: 0.26.3
 Summary: Advanced multi-language Interface to CVODES and IDAS
 Author: Jan Hasenauer, AMICI contributors
 Author-email: Fabian Froehlich <froehlichfab@gmail.com>, Daniel Weindl <sci@danielweindl.de>

{amici-0.26.2 → amici-0.26.3}/amici/CMakeLists.txt

@@ -1,10 +1,10 @@
 #
 # Build AMICI library
 #
-cmake_minimum_required(VERSION 3.15)
+cmake_minimum_required(VERSION 3.22)
 # When updating the policy version, please also update it in
 # src/CMakeLists.template.cmake
-cmake_policy(VERSION 3.15...3.30)
+cmake_policy(VERSION 3.22...3.30)
 
 project(amici)
 
@@ -130,7 +130,8 @@ elseif(AMICI_TRY_ENABLE_HDF5)
 endif()
 
 set(VENDORED_SUNDIALS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/ThirdParty/sundials)
-set(SUNDIALS_PRIVATE_INCLUDE_DIRS "${VENDORED_SUNDIALS_DIR}/src")
+set(SUNDIALS_PRIVATE_INCLUDE_DIRS
+    "${VENDORED_SUNDIALS_DIR}/src;${VENDORED_SUNDIALS_DIR}/src/sundials")
 # Handle different sundials build/install dirs, depending on whether we are
 # building the Python extension only or the full C++ interface
 if(AMICI_PYTHON_BUILD_EXT_ONLY)
@@ -224,7 +225,14 @@ set(AMICI_CXX_OPTIONS
     ""
     CACHE STRING "C++ options for libamici (semicolon-separated)")
 target_compile_options(${PROJECT_NAME} PRIVATE "${AMICI_CXX_OPTIONS}")
-
+set_property(
+  SOURCE src/solver_cvodes.cpp
+  APPEND
+  PROPERTY INCLUDE_DIRECTORIES "${SUNDIALS_PRIVATE_INCLUDE_DIRS}")
+set_property(
+  SOURCE src/solver_idas.cpp
+  APPEND
+  PROPERTY INCLUDE_DIRECTORIES "${SUNDIALS_PRIVATE_INCLUDE_DIRS}")
 add_dependencies(${PROJECT_NAME} version)
 
 file(GLOB PUBLIC_HEADERS include/amici/*.h)
@@ -237,8 +245,7 @@ target_include_directories(
          $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
          $<BUILD_INTERFACE:${GSL_LITE_INCLUDE_DIR}>
          $<INSTALL_INTERFACE:${CMAKE_INSTALL_DATADIR}/amici/swig>
-         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/swig>
-  PRIVATE ${SUNDIALS_PRIVATE_INCLUDE_DIRS})
+         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/swig>)
 
 if("$ENV{ENABLE_AMICI_DEBUGGING}"
    OR "$ENV{ENABLE_GCOV_COVERAGE}"

{amici-0.26.2 → amici-0.26.3}/amici/cmake/AmiciConfig.cmake.in

@@ -7,23 +7,8 @@ find_package(OpenMP)
 # Current SUNDIALSConfig.cmake doesn't use KLU's FindKLU, but hardcodes paths,
 # and is not relocatable. This does not work with Python package installation in
 # tmpdirs.
-list(APPEND CMAKE_MODULE_PATH
-     @CMAKE_SOURCE_DIR@/ThirdParty/SuiteSparse/lib/cmake/SuiteSparse/)
-if(NOT DEFINED SUITESPARSE_CONFIG_ROOT)
-  set(SUITESPARSE_CONFIG_ROOT @CMAKE_SOURCE_DIR@/ThirdParty/SuiteSparse/)
-endif()
-if(NOT DEFINED AMD_ROOT)
-  set(AMD_ROOT @CMAKE_SOURCE_DIR@/ThirdParty/SuiteSparse/)
-endif()
-if(NOT DEFINED BTF_ROOT)
-  set(BTF_ROOT @CMAKE_SOURCE_DIR@/ThirdParty/SuiteSparse/)
-endif()
-if(NOT DEFINED COLAMD_ROOT)
-  set(COLAMD_ROOT @CMAKE_SOURCE_DIR@/ThirdParty/SuiteSparse/)
-endif()
-if(NOT DEFINED KLU_ROOT)
-  set(KLU_ROOT @CMAKE_SOURCE_DIR@/ThirdParty/SuiteSparse/)
-endif()
+list(APPEND CMAKE_PREFIX_PATH
+     @CMAKE_SOURCE_DIR@/ThirdParty/SuiteSparse/install/)
 find_dependency(SuiteSparse_config REQUIRED)
 find_dependency(AMD REQUIRED)
 find_dependency(BTF REQUIRED)

amici-0.26.3/amici/git_version.txt

@@ -0,0 +1 @@
+v0.26.3

{amici-0.26.2 → amici-0.26.3}/amici/include/amici/model.h

@@ -112,10 +112,6 @@ class Model : public AbstractModel, public ModelDimensions {
      * @param o2mode Second order sensitivity mode
      * @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 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.
      */
@@ -123,9 +119,7 @@ class Model : public AbstractModel, public ModelDimensions {
         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,
+        std::vector<int> z2event,
         std::map<realtype, std::vector<int>> state_independent_events = {}
     );
 
@@ -1427,19 +1421,20 @@ class Model : public AbstractModel, public ModelDimensions {
      * @param x_solver State variables with conservation laws applied
      * (solver returns this)
      */
-    void fx_rdata(AmiVector& x_rdata, AmiVector const& x_solver);
+    void fx_rdata(gsl::span<realtype> x_rdata, AmiVector const& x_solver);
 
     /**
      * @brief Expand conservation law for state sensitivities.
      * @param sx_rdata Output buffer for state variables sensitivities with
-     * conservation laws expanded (stored in `amici::ReturnData`).
+     * conservation laws expanded
+     * (stored in `amici::ReturnData` shape `nplist` x `nx`, row-major).
      * @param sx_solver State variables sensitivities with conservation laws
      * applied (solver returns this)
      * @param x_solver State variables with conservation laws
      * applied (solver returns this)
      */
     void fsx_rdata(
-        AmiVectorArray& sx_rdata, AmiVectorArray const& sx_solver,
+        gsl::span<realtype> sx_rdata, AmiVectorArray const& sx_solver,
         AmiVector const& x_solver
     );
 
@@ -1457,9 +1452,6 @@ class Model : public AbstractModel, public ModelDimensions {
      */
     std::vector<int> const& getReinitializationStateIdxs() const;
 
-    /** Flag indicating Matlab- or Python-based model generation */
-    bool pythonGenerated = false;
-
     /**
      * @brief getter for dxdotdp (matlab generated)
      * @return dxdotdp
@@ -1488,17 +1480,7 @@ class Model : public AbstractModel, public ModelDimensions {
      *
      * @return Steady-state mask
      */
-    std::vector<double> get_steadystate_mask() const {
-        return steadystate_mask_.getVector();
-    };
-
-    /**
-     * @brief Get steady-state mask as AmiVector.
-     *
-     * See `set_steadystate_mask` for details.
-     * @return Steady-state mask
-     */
-    AmiVector const& get_steadystate_mask_av() const {
+    std::vector<realtype> get_steadystate_mask() const {
         return steadystate_mask_;
     };
 
@@ -1513,7 +1495,7 @@ class Model : public AbstractModel, public ModelDimensions {
      *
      * @param mask Mask of length `nx_solver`.
      */
-    void set_steadystate_mask(std::vector<double> const& mask);
+    void set_steadystate_mask(std::vector<realtype> const& mask);
 
     /**
      * Flag indicating whether for
@@ -2107,18 +2089,6 @@ class Model : public AbstractModel, public ModelDimensions {
     realtype min_sigma_{50.0};
 
   private:
-    /** Sparse dwdp implicit temporary storage (shape `ndwdp`) */
-    mutable std::vector<SUNMatrixWrapper> dwdp_hierarchical_;
-
-    /** Sparse dwdw temporary storage (shape `ndwdw`) */
-    mutable SUNMatrixWrapper dwdw_;
-
-    /** Sparse dwdx implicit temporary storage (shape `ndwdx`) */
-    mutable std::vector<SUNMatrixWrapper> dwdx_hierarchical_;
-
-    /** Recursion */
-    int w_recursion_depth_{0};
-
     /** Simulation parameters, initial state, etc. */
     SimulationParameters simulation_parameters_;
 
@@ -2129,7 +2099,7 @@ class Model : public AbstractModel, public ModelDimensions {
      * Negative values indicate that the corresponding state variable should
      * be ignored.
      */
-    AmiVector steadystate_mask_;
+    std::vector<realtype> steadystate_mask_;
 };
 
 bool operator==(Model const& a, Model const& b);

{amici-0.26.2 → amici-0.26.3}/amici/include/amici/model_dae.h

@@ -36,10 +36,6 @@ class Model_DAE : public Model {
      * @param o2mode second order sensitivity mode
      * @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
-     * @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.
      */
@@ -47,15 +43,12 @@ class Model_DAE : public Model {
         ModelDimensions const& model_dimensions,
         SimulationParameters simulation_parameters,
         SecondOrderMode const 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,
+        std::vector<int> const& z2event,
         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, state_independent_events
+              state_independent_events
           ) {
         derived_state_.M_ = SUNMatrixWrapper(nx_solver, nx_solver);
         auto M_nnz = static_cast<sunindextype>(

{amici-0.26.2 → amici-0.26.3}/amici/include/amici/model_dimensions.h

@@ -9,7 +9,7 @@ namespace amici {
 /**
  * @brief Container for model dimensions.
  *
- * Holds number of states, observables, etc.
+ * Holds number of state variables, observables, etc.
  */
 struct ModelDimensions {
     /** Default ctor */
@@ -54,6 +54,11 @@ struct ModelDimensions {
      * @param nnz Number of nonzero elements in Jacobian
      * @param ubw Upper matrix bandwidth in the Jacobian
      * @param lbw Lower matrix bandwidth in the Jacobian
+     * @param pythonGenerated Flag indicating model creation from Matlab or
+     * Python
+     * @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
      */
     ModelDimensions(
         int const nx_rdata, int const nxtrue_rdata, int const nx_solver,
@@ -64,7 +69,8 @@ struct ModelDimensions {
         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 lbw, bool pythonGenerated = false, int ndxdotdp_explicit = 0,
+        int ndxdotdx_explicit = 0, int w_recursion_depth = 0
     )
         : nx_rdata(nx_rdata)
         , nxtrue_rdata(nxtrue_rdata)
@@ -92,7 +98,11 @@ struct ModelDimensions {
         , nnz(nnz)
         , nJ(nJ)
         , ubw(ubw)
-        , lbw(lbw) {
+        , lbw(lbw)
+        , pythonGenerated(pythonGenerated)
+        , ndxdotdp_explicit(ndxdotdp_explicit)
+        , ndxdotdx_explicit(ndxdotdx_explicit)
+        , w_recursion_depth(w_recursion_depth) {
         Expects(nxtrue_rdata >= 0);
         Expects(nxtrue_rdata <= nx_rdata);
         Expects(nxtrue_solver >= 0);
@@ -128,6 +138,9 @@ struct ModelDimensions {
         Expects(nJ >= 0);
         Expects(ubw >= 0);
         Expects(lbw >= 0);
+        Expects(ndxdotdp_explicit >= 0);
+        Expects(ndxdotdx_explicit >= 0);
+        Expects(w_recursion_depth >= 0);
     }
 
     /** Number of states */
@@ -229,6 +242,18 @@ struct ModelDimensions {
 
     /** Lower bandwidth of the Jacobian */
     int lbw{0};
+
+    /** Flag indicating model creation from Matlab or Python */
+    bool pythonGenerated = false;
+
+    /** Number of nonzero elements in `dxdotdx_explicit` */
+    int ndxdotdp_explicit = 0;
+
+    /** Number of nonzero elements in `dxdotdp_explicit` */
+    int ndxdotdx_explicit = 0;
+
+    /** Recursion depth of fw */
+    int w_recursion_depth = 0;
 };
 
 } // namespace amici

{amici-0.26.2 → amici-0.26.3}/amici/include/amici/model_ode.h

@@ -35,10 +35,6 @@ class Model_ODE : public Model {
      * @param o2mode second order sensitivity mode
      * @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
-     * @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.
      */
@@ -46,15 +42,12 @@ class Model_ODE : public Model {
         ModelDimensions const& model_dimensions,
         SimulationParameters simulation_parameters,
         SecondOrderMode const 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,
+        std::vector<int> const& z2event,
         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, state_independent_events
+              state_independent_events
           ) {}
 
     void

{amici-0.26.2 → amici-0.26.3}/amici/include/amici/model_state.h

@@ -43,9 +43,6 @@ struct ModelState {
      * (dimension: nplist)
      */
     std::vector<int> plist;
-
-    /** temporary storage for spline values */
-    std::vector<realtype> spl_;
 };
 
 inline bool operator==(ModelState const& a, ModelState const& b) {
@@ -323,6 +320,21 @@ struct ModelStateDerived {
     /** temporary storage of positified state variables according to
      * stateIsNonNegative (dimension: `nx_solver`) */
     AmiVector x_pos_tmp_{0};
+
+    /** temporary storage for spline values */
+    std::vector<realtype> spl_;
+
+    /** Sparse dwdp implicit temporary storage (shape `ndwdp`) */
+    std::vector<SUNMatrixWrapper> dwdp_hierarchical_;
+
+    /** Sparse dwdw temporary storage (shape `ndwdw`) */
+    SUNMatrixWrapper dwdw_;
+
+    /** Sparse dwdx implicit temporary storage (shape `ndwdx`) */
+    std::vector<SUNMatrixWrapper> dwdx_hierarchical_;
+
+    /** Temporary storage for dense dJydy (dimension: `nJ` x `ny`) */
+    SUNMatrixWrapper dJydy_dense_;
 };
 
 /**
@@ -332,11 +344,19 @@ struct ModelStateDerived {
 struct SimulationState {
     /** timepoint */
     realtype t;
-    /** state variables */
+    /**
+     * partial state vector, excluding states eliminated from conservation laws
+     */
     AmiVector x;
-    /** state variables */
+    /**
+     * partial time derivative of state vector, excluding states eliminated
+     * from conservation laws
+     */
     AmiVector dx;
-    /** state variable sensitivity */
+    /**
+     * partial sensitivity state vector array, excluding states eliminated from
+     * conservation laws
+     */
     AmiVectorArray sx;
     /** state of the model that was used for simulation */
     ModelState state;

amici-0.26.3/amici/include/amici/newton_solver.h

@@ -0,0 +1,115 @@
+#ifndef amici_newton_solver_h
+#define amici_newton_solver_h
+
+#include "amici/solver.h"
+#include "amici/vector.h"
+
+namespace amici {
+
+class Model;
+class Solver;
+class AmiVector;
+struct SimulationState;
+
+/**
+ * @brief The NewtonSolver class sets up the linear solver for the Newton
+ * method.
+ */
+
+class NewtonSolver {
+
+  public:
+    /**
+     * @brief Initializes solver according to the dimensions in the provided
+     * model
+     *
+     * @param model the model object
+     * @param linsol_type type of linear solver to use
+     */
+    explicit NewtonSolver(Model const& model, LinearSolver linsol_type);
+
+    NewtonSolver(NewtonSolver const&) = delete;
+
+    NewtonSolver& operator=(NewtonSolver const& other) = delete;
+
+    /**
+     * @brief Computes the solution of one Newton iteration
+     *
+     * @param delta containing the RHS of the linear system, will be
+     * overwritten by solution to the linear system
+     * @param model the model instance
+     * @param state current simulation state
+     */
+    void getStep(AmiVector& delta, Model& model, SimulationState const& state);
+
+    /**
+     * @brief Computes steady state sensitivities
+     *
+     * @param sx state variable sensitivities
+     * @param model the model instance
+     * @param state current simulation state
+     */
+    void computeNewtonSensis(
+        AmiVectorArray& sx, Model& model, SimulationState const& state
+    );
+
+    /**
+     * @brief Writes the Jacobian for the Newton iteration and passes it to the
+     * linear solver
+     *
+     * @param model the model instance
+     * @param state current simulation state
+     */
+    void prepareLinearSystem(Model& model, SimulationState const& state);
+
+    /**
+     * Writes the Jacobian (JB) for the Newton iteration and passes it to the
+     * linear solver
+     *
+     * @param model the model instance
+     * @param state current simulation state
+     */
+    void prepareLinearSystemB(Model& model, SimulationState const& state);
+
+    /**
+     * @brief Solves the linear system for the Newton step
+     *
+     * @param rhs containing the RHS of the linear system, will be
+     * overwritten by solution to the linear system
+     */
+    void solveLinearSystem(AmiVector& rhs);
+
+    /**
+     * @brief Reinitialize the linear solver
+     *
+     */
+    void reinitialize();
+
+    /**
+     * @brief Checks whether the linear system is singular
+     *
+     * @param model the model instance
+     * @param state current simulation state
+     * @return boolean indicating whether the linear system is singular
+     * (condition number < 1/machine precision)
+     */
+    bool is_singular(Model& model, SimulationState const& state) const;
+
+  private:
+    /** dummy rhs, used as dummy argument when computing J and JB */
+    AmiVector xdot_;
+    /** dummy state, attached to linear solver */
+    AmiVector x_;
+    /** dummy adjoint state, used as dummy argument when computing JB */
+    AmiVector xB_;
+    /** dummy differential adjoint state, used as dummy argument when computing
+     * JB */
+    AmiVector dxB_;
+
+    /** linear solver */
+    std::unique_ptr<SUNLinSolWrapper> linsol_;
+};
+
+} // namespace amici
+
+#endif // NEWTON_SOLVER