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AMICI-dev · Jul 10, 2024 · 37ba89d · 37ba89d
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Showing 10 changed files with 65 additions and 53 deletions.
diff --git a/include/amici/model_dae.h b/include/amici/model_dae.h
@@ -53,10 +53,10 @@ class Model_DAE : public Model {
         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
-        ) {
+              model_dimensions, simulation_parameters, o2mode, idlist, z2event,
+              pythonGenerated, ndxdotdp_explicit, ndxdotdx_explicit,
+              w_recursion_depth, state_independent_events
+          ) {
         derived_state_.M_ = SUNMatrixWrapper(nx_solver, nx_solver);
         auto M_nnz = static_cast<sunindextype>(
             std::reduce(idlist.begin(), idlist.end())

diff --git a/include/amici/model_ode.h b/include/amici/model_ode.h
@@ -52,10 +52,10 @@ class Model_ODE : public Model {
         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
-        ) {}
+              model_dimensions, simulation_parameters, o2mode, idlist, z2event,
+              pythonGenerated, ndxdotdp_explicit, ndxdotdx_explicit,
+              w_recursion_depth, state_independent_events
+          ) {}
 
     void
     fJ(realtype t, realtype cj, AmiVector const& x, AmiVector const& dx,

diff --git a/src/edata.cpp b/src/edata.cpp
@@ -59,9 +59,9 @@ ExpData::ExpData(
 
 ExpData::ExpData(Model const& model)
     : ExpData(
-        model.nytrue, model.nztrue, model.nMaxEvent(), model.getTimepoints(),
-        model.getFixedParameters()
-    ) {
+          model.nytrue, model.nztrue, model.nMaxEvent(), model.getTimepoints(),
+          model.getFixedParameters()
+      ) {
     reinitializeFixedParameterInitialStates
         = model.getReinitializeFixedParameterInitialStates()
           && model.getReinitializationStateIdxs().empty();
@@ -70,9 +70,9 @@ ExpData::ExpData(Model const& model)
 
 ExpData::ExpData(ReturnData const& rdata, realtype sigma_y, realtype sigma_z)
     : ExpData(
-        rdata, std::vector<realtype>(rdata.nytrue * rdata.nt, sigma_y),
-        std::vector<realtype>(rdata.nztrue * rdata.nmaxevent, sigma_z)
-    ) {}
+          rdata, std::vector<realtype>(rdata.nytrue * rdata.nt, sigma_y),
+          std::vector<realtype>(rdata.nztrue * rdata.nmaxevent, sigma_z)
+      ) {}
 
 ExpData::ExpData(
     ReturnData const& rdata, std::vector<realtype> sigma_y,

diff --git a/src/exception.cpp b/src/exception.cpp
@@ -37,17 +37,17 @@ CvodeException::CvodeException(
     int const error_code, char const* function, char const* extra
 )
     : AmiException(
-        "CVODE routine %s failed with error code %i. %s", function, error_code,
-        extra ? extra : ""
-    ) {}
+          "CVODE routine %s failed with error code %i. %s", function,
+          error_code, extra ? extra : ""
+      ) {}
 
 IDAException::IDAException(
     int const error_code, char const* function, char const* extra
 )
     : AmiException(
-        "IDA routine %s failed with error code %i. %s", function, error_code,
-        extra ? extra : ""
-    ) {}
+          "IDA routine %s failed with error code %i. %s", function, error_code,
+          extra ? extra : ""
+      ) {}
 
 IntegrationFailure::IntegrationFailure(int code, realtype t)
     : AmiException("AMICI failed to integrate the forward problem")
@@ -61,8 +61,8 @@ IntegrationFailureB::IntegrationFailureB(int code, realtype t)
 
 NewtonFailure::NewtonFailure(int code, char const* function)
     : AmiException(
-        "NewtonSolver routine %s failed with error code %i", function, code
-    ) {
+          "NewtonSolver routine %s failed with error code %i", function, code
+      ) {
     error_code = code;
 }
 

diff --git a/src/interface_matlab.cpp b/src/interface_matlab.cpp
@@ -423,8 +423,10 @@ void setModelData(mxArray const* prhs[], int nrhs, Model& model) {
                 model.setParameterScale(
                     static_cast<ParameterScaling>(dbl2int(mxGetScalar(a)))
                 );
-            } else if((mxGetM(a) == 1 && gsl::narrow<int>(mxGetN(a)) == model.np())
-                       || (mxGetN(a) == 1 && gsl::narrow<int>(mxGetM(a)) == model.np())) {
+            } else if ((mxGetM(a) == 1
+                        && gsl::narrow<int>(mxGetN(a)) == model.np())
+                       || (mxGetN(a) == 1
+                           && gsl::narrow<int>(mxGetM(a)) == model.np())) {
                 auto pscaleArray = static_cast<double*>(mxGetData(a));
                 std::vector<ParameterScaling> pscale(model.np());
                 for (int ip = 0; ip < model.np(); ++ip) {
@@ -597,7 +599,9 @@ void mexFunction(int nlhs, mxArray* plhs[], int nrhs, mxArray const* prhs[]) {
                 ex.what()
             );
         }
-    } else if (solver->getSensitivityOrder() >= amici::SensitivityOrder::first && solver->getSensitivityMethod() == amici::SensitivityMethod::adjoint) {
+    } else if (solver->getSensitivityOrder() >= amici::SensitivityOrder::first
+               && solver->getSensitivityMethod()
+                      == amici::SensitivityMethod::adjoint) {
         mexErrMsgIdAndTxt("AMICI:mex:setup", "No data provided!");
     }
 

diff --git a/src/newton_solver.cpp b/src/newton_solver.cpp
@@ -145,7 +145,7 @@ void NewtonSolverDense::solveLinearSystem(AmiVector& rhs) {
         throw NewtonFailure(status, "SUNLinSolSolve_Dense");
 }
 
-void NewtonSolverDense::reinitialize(){
+void NewtonSolverDense::reinitialize() {
     /* dense solver does not need reinitialization */
 };
 

diff --git a/src/rdata.cpp b/src/rdata.cpp
@@ -15,14 +15,14 @@ namespace amici {
 
 ReturnData::ReturnData(Solver const& solver, Model const& model)
     : ReturnData(
-        model.getTimepoints(),
-        ModelDimensions(static_cast<ModelDimensions const&>(model)),
-        model.nplist(), model.nMaxEvent(), model.nt(),
-        solver.getNewtonMaxSteps(), model.getParameterScale(), model.o2mode,
-        solver.getSensitivityOrder(), solver.getSensitivityMethod(),
-        solver.getReturnDataReportingMode(), model.hasQuadraticLLH(),
-        model.getAddSigmaResiduals(), model.getMinimumSigmaResiduals()
-    ) {}
+          model.getTimepoints(),
+          ModelDimensions(static_cast<ModelDimensions const&>(model)),
+          model.nplist(), model.nMaxEvent(), model.nt(),
+          solver.getNewtonMaxSteps(), model.getParameterScale(), model.o2mode,
+          solver.getSensitivityOrder(), solver.getSensitivityMethod(),
+          solver.getReturnDataReportingMode(), model.hasQuadraticLLH(),
+          model.getAddSigmaResiduals(), model.getMinimumSigmaResiduals()
+      ) {}
 
 ReturnData::ReturnData(
     std::vector<realtype> ts, ModelDimensions const& model_dimensions,

diff --git a/src/spline.cpp b/src/spline.cpp
@@ -217,7 +217,7 @@ double seval(
                     j = k; /* move the upper bound */
                 if (u >= x[k])
                     i = k; /* move the lower bound */
-            }              /* there are no more segments to search */
+            } /* there are no more segments to search */
             while (j > i + 1);
         }
     }
@@ -273,7 +273,7 @@ double sinteg(
                 j = k; /* move the upper bound */
             if (u >= x[k])
                 i = k; /* move the lower bound */
-        }              /* there are no more segments to search */
+        } /* there are no more segments to search */
         while (j > i + 1);
     }
 

diff --git a/src/splinefunctions.cpp b/src/splinefunctions.cpp
@@ -145,9 +145,9 @@ HermiteSpline::HermiteSpline(
     bool logarithmic_parametrization
 )
     : AbstractSpline(
-        std::move(nodes), std::move(node_values), equidistant_spacing,
-        logarithmic_parametrization
-    )
+          std::move(nodes), std::move(node_values), equidistant_spacing,
+          logarithmic_parametrization
+      )
     , node_values_derivative_(std::move(node_values_derivative))
     , first_node_bc_(firstNodeBC)
     , last_node_bc_(lastNodeBC)
@@ -602,21 +602,25 @@ void HermiteSpline::compute_coefficients_extrapolation_sensi(
         case SplineExtrapolation::linear:
             if (first_node_bc_ == SplineBoundaryCondition::zeroDerivative) {
                 sm0 = 0;
-            } else if (get_node_derivative_by_fd() && first_node_bc_ == SplineBoundaryCondition::given) {
+            } else if (get_node_derivative_by_fd()
+                       && first_node_bc_ == SplineBoundaryCondition::given) {
                 sm0 = (dvaluesdp[spline_offset + ip + nplist] - sp0)
                       / (nodes_[1] - nodes_[0]);
 
-            } else if (get_node_derivative_by_fd() && first_node_bc_ == SplineBoundaryCondition::natural) {
+            } else if (get_node_derivative_by_fd()
+                       && first_node_bc_ == SplineBoundaryCondition::natural) {
                 throw AmiException(
                     "Natural boundary condition for "
                     "Hermite splines with linear extrapolation is "
                     "not yet implemented."
                 );
 
-            } else if (!get_node_derivative_by_fd() && first_node_bc_ == SplineBoundaryCondition::given) {
+            } else if (!get_node_derivative_by_fd()
+                       && first_node_bc_ == SplineBoundaryCondition::given) {
                 sm0 = dslopesdp[spline_offset + ip];
 
-            } else if (!get_node_derivative_by_fd() && first_node_bc_ == SplineBoundaryCondition::natural) {
+            } else if (!get_node_derivative_by_fd()
+                       && first_node_bc_ == SplineBoundaryCondition::natural) {
                 throw AmiException(
                     "Natural boundary condition for "
                     "Hermite splines with linear extrapolation is "
@@ -662,24 +666,28 @@ void HermiteSpline::compute_coefficients_extrapolation_sensi(
         case SplineExtrapolation::linear:
             if (last_node_bc_ == SplineBoundaryCondition::zeroDerivative) {
                 sm_end = 0;
-            } else if (get_node_derivative_by_fd() && last_node_bc_ == SplineBoundaryCondition::given) {
+            } else if (get_node_derivative_by_fd()
+                       && last_node_bc_ == SplineBoundaryCondition::given) {
                 sm_end = (sp_end
                           - dvaluesdp
                               [spline_offset + ip + (n_nodes() - 2) * nplist])
                          / (nodes_[n_nodes() - 1] - nodes_[n_nodes() - 2]);
 
-            } else if (get_node_derivative_by_fd() && last_node_bc_ == SplineBoundaryCondition::natural) {
+            } else if (get_node_derivative_by_fd()
+                       && last_node_bc_ == SplineBoundaryCondition::natural) {
                 throw AmiException(
                     "Natural boundary condition for "
                     "Hermite splines with linear extrapolation is "
                     "not yet implemented."
                 );
 
-            } else if (!get_node_derivative_by_fd() && last_node_bc_ == SplineBoundaryCondition::given) {
+            } else if (!get_node_derivative_by_fd()
+                       && last_node_bc_ == SplineBoundaryCondition::given) {
                 sm_end
                     = dslopesdp[spline_offset + ip + (n_nodes() - 1) * nplist];
 
-            } else if (!get_node_derivative_by_fd() && last_node_bc_ == SplineBoundaryCondition::natural) {
+            } else if (!get_node_derivative_by_fd()
+                       && last_node_bc_ == SplineBoundaryCondition::natural) {
                 throw AmiException(
                     "Natural boundary condition for "
                     "Hermite splines with linear extrapolation is "

diff --git a/src/sundials_linsol_wrapper.cpp b/src/sundials_linsol_wrapper.cpp
@@ -277,8 +277,8 @@ N_Vector SUNLinSolSPBCGS::getResid() const {
 
 SUNLinSolSPFGMR::SUNLinSolSPFGMR(AmiVector const& x, int pretype, int maxl)
     : SUNLinSolWrapper(
-        SUNLinSol_SPFGMR(const_cast<N_Vector>(x.getNVector()), pretype, maxl)
-    ) {
+          SUNLinSol_SPFGMR(const_cast<N_Vector>(x.getNVector()), pretype, maxl)
+      ) {
     if (!solver_)
         throw AmiException("Failed to create solver.");
 }
@@ -311,8 +311,8 @@ N_Vector SUNLinSolSPFGMR::getResid() const {
 
 SUNLinSolSPGMR::SUNLinSolSPGMR(AmiVector const& x, int pretype, int maxl)
     : SUNLinSolWrapper(
-        SUNLinSol_SPGMR(const_cast<N_Vector>(x.getNVector()), pretype, maxl)
-    ) {
+          SUNLinSol_SPGMR(const_cast<N_Vector>(x.getNVector()), pretype, maxl)
+      ) {
     if (!solver_)
         throw AmiException("Failed to create solver.");
 }
@@ -404,8 +404,8 @@ SUNNonLinSolFixedPoint::SUNNonLinSolFixedPoint(
     int count, const_N_Vector x, int m
 )
     : SUNNonLinSolWrapper(
-        SUNNonlinSol_FixedPointSens(count, const_cast<N_Vector>(x), m)
-    ) {}
+          SUNNonlinSol_FixedPointSens(count, const_cast<N_Vector>(x), m)
+      ) {}
 
 int SUNNonLinSolFixedPoint::getSysFn(SUNNonlinSolSysFn* SysFn) const {
     return SUNNonlinSolGetSysFn_FixedPoint(solver, SysFn);