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‎models/model_dirac_py/.gitignore‎

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**

‎models/model_dirac_py/CMakeLists.txt‎

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# Build AMICI model
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cmake_minimum_required(VERSION 3.22)
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cmake_policy(VERSION 3.22...3.31)
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project(model_dirac_py)
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set(CMAKE_CXX_STANDARD 17)
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set(CMAKE_CXX_STANDARD_REQUIRED ON)
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set(CMAKE_POSITION_INDEPENDENT_CODE ON)
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include(CheckCXXCompilerFlag)
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set(MY_CXX_FLAGS -Wall -Wno-unused-function -Wno-unused-variable)
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if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
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list(APPEND MY_CXX_FLAGS -Wno-unused-but-set-variable)
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endif()
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foreach(flag ${MY_CXX_FLAGS})
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unset(CUR_FLAG_SUPPORTED CACHE)
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check_cxx_compiler_flag(${flag} CUR_FLAG_SUPPORTED)
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if(${CUR_FLAG_SUPPORTED})
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string(APPEND CMAKE_CXX_FLAGS " ${flag}")
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endif()
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endforeach()
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if(DEFINED ENV{AMICI_CXXFLAGS})
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message(STATUS "Appending flags from AMICI_CXXFLAGS: $ENV{AMICI_CXXFLAGS}")
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add_compile_options("$ENV{AMICI_CXXFLAGS}")
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endif()
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if(DEFINED ENV{AMICI_LDFLAGS})
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message(STATUS "Appending flags from AMICI_LDFLAGS: $ENV{AMICI_LDFLAGS}")
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link_libraries("$ENV{AMICI_LDFLAGS}")
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endif()
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find_package(Amici 0.33.0 REQUIRED HINTS
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${CMAKE_CURRENT_LIST_DIR}/../../build)
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message(STATUS "Found AMICI ${Amici_DIR}")
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set_target_properties(Upstream::amici PROPERTIES
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MAP_IMPORTED_CONFIG_RELWITHDEBINFO RelWithDebInfo;Release;
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MAP_IMPORTED_CONFIG_RELEASE Release
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MAP_IMPORTED_CONFIG_DEBUG Debug;RelWithDebInfo;)
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# Debug build?
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if("$ENV{ENABLE_AMICI_DEBUGGING}" OR "$ENV{ENABLE_GCOV_COVERAGE}")
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add_compile_options(-UNDEBUG)
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if(MSVC)
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add_compile_options(-DEBUG)
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else()
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add_compile_options(-O0 -g)
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endif()
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endif()
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# coverage options
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if($ENV{ENABLE_GCOV_COVERAGE})
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string(APPEND CMAKE_CXX_FLAGS_DEBUG " --coverage")
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string(APPEND CMAKE_EXE_LINKER_FLAGS_DEBUG " --coverage")
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endif()
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set(MODEL_DIR ${CMAKE_CURRENT_LIST_DIR})
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set(SRC_LIST_LIB Jy.cpp
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Jy.h
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create_splines.cpp
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dJydsigma.cpp
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dJydy.cpp
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dJydy.h
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deltaqB.cpp
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deltasx.cpp
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deltax.cpp
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dxdotdp_explicit.cpp
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dxdotdp_explicit.h
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dxdotdx_explicit.cpp
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dxdotdx_explicit.h
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dydx.cpp
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h.h
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model_dirac_py.cpp
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model_dirac_py.h
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my.h
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p.h
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root.cpp
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sigmay.cpp
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sigmay.h
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stau.cpp
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stau.h
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sx.h
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w.h
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wrapfunctions.cpp
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wrapfunctions.h
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x.h
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xB.h
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x_old.h
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x_rdata.cpp
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x_rdata.h
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x_solver.cpp
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x_solver.h
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xdot.cpp
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xdot.h
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xdot_old.h
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y.cpp
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y.h ${MODEL_DIR}/wrapfunctions.cpp)
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add_library(${PROJECT_NAME} ${SRC_LIST_LIB})
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# ${PROJECT_NAME} might already be "model"
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if(NOT TARGET model)
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add_library(model ALIAS ${PROJECT_NAME})
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endif()
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# Some special functions require boost
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#
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# TODO: set some flag during code generation whether the given model requires
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# boost. for now, try to find it, add include directories and link against it.
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# let the compiler/linker error if it is required but not found
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find_package(Boost)
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target_include_directories(${PROJECT_NAME} PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}")
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target_link_libraries(
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${PROJECT_NAME}
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PUBLIC Upstream::amici
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PRIVATE $<$<BOOL:${Boost_FOUND}>:Boost::boost>)
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if(NOT "${AMICI_PYTHON_BUILD_EXT_ONLY}")
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set(SRC_LIST_EXE main.cpp)
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add_executable(simulate_${PROJECT_NAME} ${SRC_LIST_EXE})
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target_link_libraries(simulate_${PROJECT_NAME} ${PROJECT_NAME})
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endif()
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# SWIG
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option(ENABLE_SWIG "Build swig/python library?" ON)
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if(ENABLE_SWIG)
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add_subdirectory(swig)
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endif()
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# <Export cmake configuration>
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include(GNUInstallDirs)
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install(
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TARGETS ${PROJECT_NAME}
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EXPORT ${PROJECT_NAME}Targets
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ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
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INCLUDES
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DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
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PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
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export(
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EXPORT ${PROJECT_NAME}Targets
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FILE ${PROJECT_NAME}Config.cmake
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NAMESPACE Upstream::)
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# </Export cmake configuration>

‎models/model_dirac_py/Jy.cpp‎

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#include "amici/symbolic_functions.h"
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#include "amici/defines.h"
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#include "sundials/sundials_types.h"
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#include <gsl/gsl-lite.hpp>
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#include <algorithm>
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#include "p.h"
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#include "y.h"
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#include "sigmay.h"
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#include "my.h"
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namespace amici {
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namespace model_model_dirac_py {
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void Jy_model_dirac_py(realtype *Jy, const int iy, const realtype *p, const realtype *k, const realtype *y, const realtype *sigmay, const realtype *my){
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switch(iy) {
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case 0:
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Jy[0] = 0.5*std::log(2*amici::pi*std::pow(sigma_obs_x2, 2)) + 0.5*std::pow(-mobs_x2 + obs_x2, 2)/std::pow(sigma_obs_x2, 2);
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break;
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}
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}
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} // namespace model_model_dirac_py
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} // namespace amici

‎models/model_dirac_py/Jy.h‎

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#define Jy0 Jy[0]

‎models/model_dirac_py/create_splines.cpp‎

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#include "amici/symbolic_functions.h"
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#include "amici/defines.h"
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#include "sundials/sundials_types.h"
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#include <gsl/gsl-lite.hpp>
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#include <algorithm>
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#include "amici/splinefunctions.h"
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#include <vector>
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#include "p.h"
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namespace amici {
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namespace model_model_dirac_py {
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std::vector<HermiteSpline> create_splines_model_dirac_py(const realtype *p, const realtype *k){
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return {};
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}
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} // namespace model_model_dirac_py
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} // namespace amici

‎models/model_dirac_py/dJydsigma.cpp‎

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#include "amici/symbolic_functions.h"
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#include "amici/defines.h"
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#include "sundials/sundials_types.h"
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#include <gsl/gsl-lite.hpp>
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#include <algorithm>
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#include "p.h"
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#include "y.h"
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#include "sigmay.h"
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#include "my.h"
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namespace amici {
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namespace model_model_dirac_py {
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void dJydsigma_model_dirac_py(realtype *dJydsigma, const int iy, const realtype *p, const realtype *k, const realtype *y, const realtype *sigmay, const realtype *my){
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switch(iy) {
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case 0:
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dJydsigma[0] = 1.0/sigma_obs_x2 - 1.0*std::pow(-mobs_x2 + obs_x2, 2)/std::pow(sigma_obs_x2, 3);
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break;
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}
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}
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} // namespace model_model_dirac_py
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} // namespace amici

‎models/model_dirac_py/dJydy.cpp‎

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#include "amici/sundials_matrix_wrapper.h"
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#include "sundials/sundials_types.h"
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#include <array>
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#include <algorithm>
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namespace amici {
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namespace model_model_dirac_py {
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static constexpr std::array<std::array<sunindextype, 2>, 1> dJydy_colptrs_model_dirac_py_ = {{
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{0, 1},
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}};
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void dJydy_colptrs_model_dirac_py(SUNMatrixWrapper &dJydy, int index){
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dJydy.set_indexptrs(gsl::make_span(dJydy_colptrs_model_dirac_py_[index]));
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}
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} // namespace model_model_dirac_py
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} // namespace amici
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#include "amici/sundials_matrix_wrapper.h"
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#include "sundials/sundials_types.h"
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#include <array>
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#include <algorithm>
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namespace amici {
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namespace model_model_dirac_py {
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static constexpr std::array<std::array<sunindextype, 1>, 1> dJydy_rowvals_model_dirac_py_ = {{
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{0},
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}};
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void dJydy_rowvals_model_dirac_py(SUNMatrixWrapper &dJydy, int index){
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dJydy.set_indexvals(gsl::make_span(dJydy_rowvals_model_dirac_py_[index]));
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}
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} // namespace model_model_dirac_py
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} // namespace amici
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#include "amici/symbolic_functions.h"
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#include "amici/defines.h"
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#include "sundials/sundials_types.h"
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#include <gsl/gsl-lite.hpp>
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#include <algorithm>
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#include "p.h"
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#include "y.h"
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#include "sigmay.h"
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#include "my.h"
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#include "dJydy.h"
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namespace amici {
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namespace model_model_dirac_py {
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void dJydy_model_dirac_py(realtype *dJydy, const int iy, const realtype *p, const realtype *k, const realtype *y, const realtype *sigmay, const realtype *my){
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switch(iy) {
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case 0:
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dJydy[0] = (-1.0*mobs_x2 + 1.0*obs_x2)/std::pow(sigma_obs_x2, 2);
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break;
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}
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}
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} // namespace model_model_dirac_py
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} // namespace amici

‎models/model_dirac_py/dJydy.h‎

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#define dJy0_dobs_x2 dJydy[0]

‎models/model_dirac_py/deltaqB.cpp‎

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#include "amici/symbolic_functions.h"
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#include "amici/defines.h"
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#include "sundials/sundials_types.h"
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#include <gsl/gsl-lite.hpp>
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#include <algorithm>
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#include "x.h"
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#include "p.h"
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#include "h.h"
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#include "xdot.h"
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#include "xdot_old.h"
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#include "x_old.h"
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#include "xB.h"
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namespace amici {
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namespace model_model_dirac_py {
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void deltaqB_model_dirac_py(realtype *deltaqB, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *dx, const int ip, const int ie, const realtype *xdot, const realtype *xdot_old, const realtype *x_old, const realtype *xB){
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switch(ie) {
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case 0:
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switch(ip) {
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case 1:
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deltaqB[0] = xB0*(-dx1dt + xdot_old0) + xB1*(-dx2dt + xdot_old1);
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break;
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}
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break;
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}
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}
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} // namespace model_model_dirac_py
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} // namespace amici

‎models/model_dirac_py/deltasx.cpp‎

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#include "amici/symbolic_functions.h"
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#include "amici/defines.h"
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#include "sundials/sundials_types.h"
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#include <gsl/gsl-lite.hpp>
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#include <algorithm>
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#include "x.h"
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#include "p.h"
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#include "h.h"
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#include "xdot.h"
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#include "xdot_old.h"
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#include "sx.h"
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#include "stau.h"
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#include "x_old.h"
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namespace amici {
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namespace model_model_dirac_py {
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void deltasx_model_dirac_py(realtype *deltasx, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const int ip, const int ie, const realtype *xdot, const realtype *xdot_old, const realtype *sx, const realtype *stau, const realtype *tcl, const realtype *x_old){
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switch(ie) {
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case 0:
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switch(ip) {
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case 0:
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case 1:
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case 2:
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case 3:
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deltasx[0] = stau0*(dx1dt - xdot_old0);
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deltasx[1] = stau0*(dx2dt - xdot_old1);
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break;
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}
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break;
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}
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}
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} // namespace model_model_dirac_py
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} // namespace amici

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