Split expressions into static and dynamic

.github/actions/setup-amici-cpp/action.yml

@@ -18,6 +18,9 @@ runs:
     - run: echo "ENABLE_GCOV_COVERAGE=TRUE" >> $GITHUB_ENV
       shell: bash
 
+    - run: echo "PYTHONFAULTHANDLER=1" >> $GITHUB_ENV
+      shell: bash
+
     - name: Set up Sonar tools
       uses: ./.github/actions/setup-sonar-tools
 

include/amici/abstract_model.h

@@ -820,11 +820,15 @@ class AbstractModel {
      * @param h Heaviside vector
      * @param tcl total abundances for conservation laws
      * @param spl spline value vector
+     * @param include_static Whether to (re-)evaluate only dynamic expressions
+     * (false) or also static expressions (true).
+     * Dynamic expressions are those that depend directly or indirectly on time,
+     * static expressions are those that don't.
      */
     virtual void
     fw(realtype* w, realtype const t, realtype const* x, realtype const* p,
        realtype const* k, realtype const* h, realtype const* tcl,
-       realtype const* spl);
+       realtype const* spl, bool include_static = true);
 
     /**
      * @brief Model-specific sparse implementation of dwdp
@@ -840,12 +844,16 @@ class AbstractModel {
      * @param spl spline value vector
      * @param sspl sensitivities of spline values vector w.r.t. parameters \f$ p
      * \f$
+     * @param include_static Whether to (re-)evaluate only dynamic expressions
+     * (false) or also static expressions (true).
+     * Dynamic expressions are those that depend directly or indirectly on time,
+     * static expressions are those that don't.
      */
     virtual void fdwdp(
         realtype* dwdp, realtype const t, realtype const* x, realtype const* p,
         realtype const* k, realtype const* h, realtype const* w,
         realtype const* tcl, realtype const* stcl, realtype const* spl,
-        realtype const* sspl
+        realtype const* sspl, bool include_static = true
     );
 
     /**
@@ -860,28 +868,6 @@ class AbstractModel {
      */
     virtual void fdwdp_rowvals(SUNMatrixWrapper& dwdp);
 
-    /**
-     * @brief Model-specific sensitivity implementation of dwdp
-     * @param dwdp Recurring terms in xdot, parameter derivative
-     * @param t timepoint
-     * @param x vector with the states
-     * @param p parameter vector
-     * @param k constants vector
-     * @param h Heaviside vector
-     * @param w vector with helper variables
-     * @param tcl total abundances for conservation laws
-     * @param stcl sensitivities of total abundances for conservation laws
-     * @param spl spline value vector
-     * @param sspl sensitivities of spline values vector
-     * @param ip sensitivity parameter index
-     */
-    virtual void fdwdp(
-        realtype* dwdp, realtype const t, realtype const* x, realtype const* p,
-        realtype const* k, realtype const* h, realtype const* w,
-        realtype const* tcl, realtype const* stcl, realtype const* spl,
-        realtype const* sspl, int ip
-    );
-
     /**
      * @brief Model-specific implementation of dwdx, data part
      * @param dwdx Recurring terms in xdot, state derivative
@@ -893,11 +879,15 @@ class AbstractModel {
      * @param w vector with helper variables
      * @param tcl total abundances for conservation laws
      * @param spl spline value vector
+     * @param include_static Whether to (re-)evaluate only dynamic expressions
+     * (false) or also static expressions (true).
+     * Dynamic expressions are those that depend directly or indirectly on time,
+     * static expressions are those that don't.
      */
     virtual void fdwdx(
         realtype* dwdx, realtype const t, realtype const* x, realtype const* p,
         realtype const* k, realtype const* h, realtype const* w,
-        realtype const* tcl, realtype const* spl
+        realtype const* tcl, realtype const* spl, bool include_static = true
     );
 
     /**
@@ -922,11 +912,15 @@ class AbstractModel {
      * @param h Heaviside vector
      * @param w vector with helper variables
      * @param tcl Total abundances for conservation laws
+     * @param include_static Whether to (re-)evaluate only dynamic expressions
+     * (false) or also static expressions (true).
+     * Dynamic expressions are those that depend directly or indirectly on time,
+     * static expressions are those that don't.
      */
     virtual void fdwdw(
         realtype* dwdw, realtype t, realtype const* x, realtype const* p,
         realtype const* k, realtype const* h, realtype const* w,
-        realtype const* tcl
+        realtype const* tcl, bool include_static = true
     );
 
     /**

include/amici/model.h

@@ -239,6 +239,18 @@ class Model : public AbstractModel, public ModelDimensions {
         bool computeSensitivities, std::vector<int>& roots_found
     );
 
+    /**
+     * @brief Re-initialize model properties after changing simulation context.
+     * @param t Timepoint
+     * @param x Reference to state variables
+     * @param sx Reference to state variable sensitivities
+     * @param computeSensitivities Flag indicating whether sensitivities are to
+     * be computed
+     */
+    void reinitialize(
+        realtype t, AmiVector& x, AmiVectorArray& sx, bool computeSensitivities
+    );
+
     /**
      * @brief Initialize model properties.
      * @param xB Adjoint state variables
@@ -1828,29 +1840,45 @@ class Model : public AbstractModel, public ModelDimensions {
      * @brief Compute recurring terms in xdot.
      * @param t Timepoint
      * @param x Array with the states
+     * @param include_static Whether to (re-)evaluate only dynamic expressions
+     * (false) or also static expressions (true).
+     * Dynamic expressions are those that depend directly or indirectly on time,
+     * static expressions are those that don't.
      */
-    void fw(realtype t, realtype const* x);
+    void fw(realtype t, realtype const* x, bool include_static = true);
 
     /**
      * @brief Compute parameter derivative for recurring terms in xdot.
      * @param t Timepoint
      * @param x Array with the states
+     * @param include_static Whether to (re-)evaluate only dynamic expressions
+     * (false) or also static expressions (true).
+     * Dynamic expressions are those that depend directly or indirectly on time,
+     * static expressions are those that don't.
      */
-    void fdwdp(realtype t, realtype const* x);
+    void fdwdp(realtype t, realtype const* x, bool include_static = true);
 
     /**
      * @brief Compute state derivative for recurring terms in xdot.
      * @param t Timepoint
      * @param x Array with the states
+     * @param include_static Whether to (re-)evaluate only dynamic expressions
+     * (false) or also static expressions (true).
+     * Dynamic expressions are those that depend directly or indirectly on time,
+     * static expressions are those that don't.
      */
-    void fdwdx(realtype t, realtype const* x);
+    void fdwdx(realtype t, realtype const* x, bool include_static = true);
 
     /**
      * @brief Compute self derivative for recurring terms in xdot.
      * @param t Timepoint
      * @param x Array with the states
+     * @param include_static Whether to (re-)evaluate only dynamic expressions
+     * (false) or also static expressions (true).
+     * Dynamic expressions are those that depend directly or indirectly on time,
+     * static expressions are those that don't.
      */
-    void fdwdw(realtype t, realtype const* x);
+    void fdwdw(realtype t, realtype const* x, bool include_static = true);
 
     /**
      * @brief Compute fx_rdata.

matlab/@amifun/getArgs.m

@@ -108,11 +108,11 @@
         case 'dJrzdsigma'
             this.argstr = '(double *dJrzdsigma, const int iz, const realtype *p, const realtype *k, const double *rz, const double *sigmaz)';
         case 'w'
-            this.argstr = '(realtype *w, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *tcl, const realtype *spl)';
+            this.argstr = '(realtype *w, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *tcl, const realtype *spl, bool include_static)';
         case 'dwdp'
-            this.argstr = '(realtype *dwdp, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *tcl, const realtype *stcl, const realtype *spl, const realtype *sspl)';
+            this.argstr = '(realtype *dwdp, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *tcl, const realtype *stcl, const realtype *spl, const realtype *sspl, bool include_static)';
         case 'dwdx'
-            this.argstr = '(realtype *dwdx, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *tcl, const realtype *spl)';
+            this.argstr = '(realtype *dwdx, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *tcl, const realtype *spl, bool include_static)';
         case 'M'
             this.argstr = '(realtype *M, const realtype t, const realtype *x, const realtype *p, const realtype *k)';
         otherwise

matlab/@amimodel/generateC.m

@@ -209,7 +209,7 @@ function generateC(this)
 end
 fprintf(fid,'};\n\n');
 fprintf(fid,['} // namespace model_' this.modelname '\n\n']);
-fprintf(fid,'} // namespace amici \n\n');
+fprintf(fid,'} // namespace amici\n\n');
 fprintf(fid,['#endif /* _amici_' this.modelname '_h */\n']);
 fclose(fid);
 
@@ -253,6 +253,7 @@ function generateC(this)
 
 argstr = strrep(argstr,'realtype','');
 argstr = strrep(argstr,'int','');
+argstr = strrep(argstr,'bool','');
 argstr = strrep(argstr,'const','');
 argstr = strrep(argstr,'double','');
 argstr = strrep(argstr,'SUNMatrixContent_Sparse','');

models/model_calvetti/CMakeLists.txt

@@ -1,5 +1,11 @@
 # Build AMICI model
 cmake_minimum_required(VERSION 3.15)
+cmake_policy(VERSION 3.15...3.27)
+
+# cmake >=3.27
+if(POLICY CMP0144)
+  cmake_policy(SET CMP0144 NEW)
+endif(POLICY CMP0144)
 
 project(model_calvetti)
 
@@ -14,7 +20,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
 endif()
 foreach(flag ${MY_CXX_FLAGS})
   unset(CUR_FLAG_SUPPORTED CACHE)
-  check_cxx_compiler_flag(-Werror ${flag} CUR_FLAG_SUPPORTED)
+  check_cxx_compiler_flag(${flag} CUR_FLAG_SUPPORTED)
   if(${CUR_FLAG_SUPPORTED})
     string(APPEND CMAKE_CXX_FLAGS " ${flag}")
   endif()
@@ -33,6 +39,23 @@ find_package(Amici  REQUIRED HINTS
              ${CMAKE_CURRENT_LIST_DIR}/../../build)
 message(STATUS "Found AMICI ${Amici_DIR}")
 
+# Debug build?
+if("$ENV{ENABLE_AMICI_DEBUGGING}" OR "$ENV{ENABLE_GCOV_COVERAGE}")
+  add_compile_options(-UNDEBUG)
+  if(MSVC)
+    add_compile_options(-DEBUG)
+  else()
+    add_compile_options(-O0 -g)
+  endif()
+  set(CMAKE_BUILD_TYPE "Debug")
+endif()
+
+# coverage options
+if($ENV{ENABLE_GCOV_COVERAGE})
+  string(APPEND CMAKE_CXX_FLAGS_DEBUG " --coverage")
+  string(APPEND CMAKE_EXE_LINKER_FLAGS_DEBUG " --coverage")
+endif()
+
 set(MODEL_DIR ${CMAKE_CURRENT_LIST_DIR})
 
 set(SRC_LIST_LIB ${MODEL_DIR}/JSparse.cpp
@@ -73,18 +96,6 @@ if(NOT "${AMICI_PYTHON_BUILD_EXT_ONLY}")
   target_link_libraries(simulate_${PROJECT_NAME} ${PROJECT_NAME})
 endif()
 
-# Debug build?
-if("$ENV{ENABLE_AMICI_DEBUGGING}" OR "$ENV{ENABLE_GCOV_COVERAGE}")
-  add_compile_options(-UNDEBUG -O0 -g)
-  set(CMAKE_BUILD_TYPE "Debug")
-endif()
-
-# coverage options
-if($ENV{ENABLE_GCOV_COVERAGE})
-  string(APPEND CMAKE_CXX_FLAGS_DEBUG " --coverage")
-  string(APPEND CMAKE_EXE_LINKER_FLAGS_DEBUG " --coverage")
-endif()
-
 # SWIG
 option(ENABLE_SWIG "Build swig/python library?" ON)
 if(ENABLE_SWIG)

models/model_calvetti/dwdx.cpp

@@ -10,7 +10,7 @@ namespace amici {
 
 namespace model_model_calvetti{
 
-void dwdx_model_calvetti(realtype *dwdx, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *tcl, const realtype *spl) {
+void dwdx_model_calvetti(realtype *dwdx, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *tcl, const realtype *spl, bool include_static) {
   dwdx[0] = 1.0/(x[0]*x[0]*x[0])*-2.0;
   dwdx[1] = k[1]*w[15]*dwdx[0];
   dwdx[2] = dwdx[1];

models/model_calvetti/main.cpp

@@ -1,14 +1,13 @@
 #include <iostream>
 
-#include <amici/amici.h>    /* AMICI base functions */
-#include "wrapfunctions.h"  /* model-provided functions */
+#include "wrapfunctions.h" /* model-provided functions */
+#include <amici/amici.h>   /* AMICI base functions */
 
-template < class T >
-std::ostream& operator << (std::ostream& os, const std::vector<T>& v)
-{
+template <class T>
+std::ostream& operator<<(std::ostream& os, std::vector<T> const& v) {
     os << "[";
-    for (typename std::vector<T>::const_iterator ii = v.begin(); ii != v.end(); ++ii)
-    {
+    for (typename std::vector<T>::const_iterator ii = v.begin(); ii != v.end();
+         ++ii) {
         os << " " << *ii;
     }
     os << "]";
@@ -21,9 +20,9 @@
  */
 
 int main() {
-    std::cout<<"********************************"<<std::endl;
-    std::cout<<"** Running forward simulation **"<<std::endl;
-    std::cout<<"********************************"<<std::endl<<std::endl;
+    std::cout << "********************************" << std::endl;
+    std::cout << "** Running forward simulation **" << std::endl;
+    std::cout << "********************************" << std::endl << std::endl;
 
     // Create a model instance
     auto model = amici::generic_model::getModel();
@@ -44,21 +43,20 @@
 
     // Print observable time course
     auto observable_ids = model->getObservableIds();
-    std::cout<<"Simulated observables for timepoints "<<rdata->ts<<"\n\n";
-    for(int i_observable = 0; i_observable < rdata->ny; ++i_observable) {
-        std::cout<<observable_ids[i_observable]<<":\n\t";
-        for(int i_time = 0; i_time < rdata->nt; ++i_time) {
+    std::cout << "Simulated observables for timepoints " << rdata->ts << "\n\n";
+    for (int i_observable = 0; i_observable < rdata->ny; ++i_observable) {
+        std::cout << observable_ids[i_observable] << ":\n\t";
+        for (int i_time = 0; i_time < rdata->nt; ++i_time) {
             // rdata->y is a flat 2D array in row-major ordering
-            std::cout<<rdata->y[i_time * rdata->ny + i_observable]<<" ";
+            std::cout << rdata->y[i_time * rdata->ny + i_observable] << " ";
         }
-        std::cout<<std::endl<<std::endl;
+        std::cout << std::endl << std::endl;
     }
 
-
-    std::cout<<std::endl;
-    std::cout<<"**********************************"<<std::endl;
-    std::cout<<"** Forward sensitivity analysis **"<<std::endl;
-    std::cout<<"**********************************"<<std::endl<<std::endl;
+    std::cout << std::endl;
+    std::cout << "**********************************" << std::endl;
+    std::cout << "** Forward sensitivity analysis **" << std::endl;
+    std::cout << "**********************************" << std::endl << std::endl;
 
     // Enable first-order sensitivity analysis
     solver->setSensitivityOrder(amici::SensitivityOrder::first);
@@ -78,18 +76,17 @@
     auto state_ids = model->getStateIds();
     auto parameter_ids = model->getParameterIds();
 
-    std::cout<<"State sensitivities for timepoint "
-              <<rdata->ts[i_time]
-              <<std::endl;//nt x nplist x nx
-    for(int i_state= 0; i_state < rdata->nx; ++i_state) {
-        std::cout<<"\td("<<state_ids[i_state]<<")/d("
-                  <<parameter_ids[model->plist(i_nplist)]<<") = ";
+    std::cout << "State sensitivities for timepoint " << rdata->ts[i_time]
+              << std::endl; // nt x nplist x nx
+    for (int i_state = 0; i_state < rdata->nx; ++i_state) {
+        std::cout << "\td(" << state_ids[i_state] << ")/d("
+                  << parameter_ids[model->plist(i_nplist)] << ") = ";
 
         // rdata->sx is a flat 3D array in row-major ordering
-        std::cout<<rdata->sx[i_time * rdata->nplist * rdata->nx
-                              + i_nplist * rdata->nx
-                              + i_state];
-        std::cout<<std::endl;
+        std::cout << rdata->sx
+                         [i_time * rdata->nplist * rdata->nx
+                          + i_nplist * rdata->nx + i_state];
+        std::cout << std::endl;
     }
 
     return 0;