Add newton parameters to the time stepper

* This change requires the parameter tree to contain new parameters
* Updates the tests to always include a default set of newton parameters

dune/copasi/common/stepper.hh

@@ -183,10 +183,13 @@ public:
    * @brief Construct a new object
    *
    * @param rk_method   PDELab time stepping Runge-Kutta paramameters
+   * @param solver_parameters parameter options for the newton solver
    */
   RKStepper(
-    std::unique_ptr<PDELab::TimeSteppingParameterInterface<Time>> rk_method)
+    std::unique_ptr<PDELab::TimeSteppingParameterInterface<Time>> rk_method,
+    const ParameterTree& solver_parameters)
     : _rk_method{ std::move(rk_method) }
+    , _solver_parameters{ solver_parameters }
     , _logger{ Logging::Logging::componentLogger({}, "stepper") }
   {
     _logger.detail("Setting up time stepper"_fmt);
@@ -197,9 +200,10 @@ public:
    * @brief Construct a new object
    *
    * @param rk_method   Keyword with the RK method type
+   * @param solver_parameters parameter options for the newton solver
    */
-  RKStepper( std::string rk_method)
-    : RKStepper(make_rk_method(rk_method))
+  RKStepper(std::string rk_method, const ParameterTree& solver_parameters)
+    : RKStepper(make_rk_method(rk_method), solver_parameters)
   {}
 
   /**
@@ -294,7 +298,7 @@ public:
   const Logging::Logger& logger() const { return _logger; }
 
 private:
-  //! Setup and cache solver for a system
+  //! Setup and cache solver for a given system
   template<class System>
   auto& get_solver(const System& system) const
   {
@@ -329,6 +333,51 @@ private:
     auto non_linear_operator =
       std::make_unique<NonLinearOperator>(grid_operator, *linear_solver);
 
+    // Add settings to the newton solver
+    auto reduction = _solver_parameters.template get<double>("reduction");
+    non_linear_operator->setReduction(reduction);
+
+    auto min_reduction =
+      _solver_parameters.template get<double>("min_linear_reduction");
+    non_linear_operator->setMinLinearReduction(min_reduction);
+
+    auto fixed_reduction =
+      _solver_parameters.template get<bool>("fixed_linear_reduction");
+    non_linear_operator->setFixedLinearReduction(fixed_reduction);
+
+    auto max_it = _solver_parameters.template get<uint>("max_iterations");
+    non_linear_operator->setMaxIterations(max_it);
+
+    auto abs_limit = _solver_parameters.template get<double>("absolute_limit");
+    non_linear_operator->setAbsoluteLimit(abs_limit);
+
+    auto reassemble =
+      _solver_parameters.template get<double>("reassemble_threshold");
+    non_linear_operator->setReassembleThreshold(reassemble);
+
+    auto keep_matrix = _solver_parameters.template get<bool>("keep_matrix");
+    non_linear_operator->setKeepMatrix(keep_matrix);
+
+    auto force_iteration =
+      _solver_parameters.template get<bool>("force_iteration");
+    non_linear_operator->setForceIteration(force_iteration);
+
+    const auto& ls = _solver_parameters.sub("linear_search", true);
+
+    auto ls_strategy = ls.template get<std::string>("strategy");
+    try {
+      non_linear_operator->setLineSearchStrategy(ls_strategy);
+    } catch (const Dune::Exception& e) {
+      _logger.error("Not valid linear search strategy: {}"_fmt, ls_strategy);
+      DUNE_THROW(IOError, "Not valid linear search strategy: " << ls_strategy);
+    }
+
+    auto ls_max_it = ls.template get<uint>("max_iterations");
+    non_linear_operator->setLineSearchMaxIterations(ls_max_it);
+
+    auto ls_damping = ls.template get<double>("damping_factor");
+    non_linear_operator->setLineSearchDampingFactor(ls_damping);
+
     _logger.trace("Get one step operator"_fmt);
     auto one_step_operator = std::make_unique<OneStepOperator>(
       *_rk_method, grid_operator, *non_linear_operator);
@@ -346,6 +395,7 @@ private:
 private:
   std::unique_ptr<const PDELab::TimeSteppingParameterInterface<Time>>
     _rk_method;
+  const ParameterTree _solver_parameters;
   const Logging::Logger _logger;
   mutable std::any _internal_state;
 };
@@ -459,8 +509,10 @@ make_default_stepper(const ParameterTree& config)
   log.trace("Decrease factor: {}"_fmt,decrease_factor);
   log.trace("Runge-Kutta method: {}"_fmt,rk_type);
 
+
+  const auto& newton_parameters = config.sub("newton", true);
   using RKStepper = Dune::Copasi::RKStepper<double>;
-  auto rk_stepper = RKStepper{ rk_type };
+  auto rk_stepper = RKStepper{ rk_type, newton_parameters };
   using Stepper = Dune::Copasi::SimpleAdaptiveStepper<RKStepper>;
   return Stepper{
     std::move(rk_stepper), min_step, max_step, decrease_factor, increase_factor

test/default_time_stepping.ini

+######################## Time stepping settings #############################
+# Common options for the time stepping section including its newton solver
+
+[model.time_stepping]
+rk_method = alexander_2
+decrease_factor = 0.5
+increase_factor = 1.5
+
+[model.time_stepping.newton]
+reduction = 1e-8
+min_linear_reduction = 1e-3
+fixed_linear_reduction = false
+max_iterations = 40
+absolute_limit = 1e-12
+reassemble_threshold = 0.0
+keep_matrix = true
+force_iteration = false
+
+[model.time_stepping.newton.linear_search]
+strategy = hackbuschReusken
+max_iterations = 10
+damping_factor = 0.5

test/test_NFkappaB.mini

 # Test: Check that complicated problems have an approximately same analytic and
 #   numeric jacobian
 
-import logging.ini
+import default_logging.ini
+import default_time_stepping.ini
 
 __name = test_NFkappaB
 
@@ -14,14 +15,11 @@ initial_level = 0
 order = 1
 
 [model.time_stepping]
-rk_method = alexander_2
 begin = 0.
 end = 365
 initial_step = 1e-0
 min_step = 1e-3
 max_step = 1e-0
-decrease_factor = 0.9
-increase_factor = 1.1
 
 [model.compartments]
 cytoplasm = 0

test/test_cell.mini

 # Test: Compare a simple multidomain diffusion-reaction problem with respect
 #   to a reference solution produced by stable versions of the program
 
-import logging.ini
+import default_logging.ini
+import default_time_stepping.ini
 
 __name = test_cell
 
@@ -14,7 +15,6 @@ initial_level = 0
 order = 1
 
 [model.time_stepping]
-rk_method = alexander_2
 begin = 0.
 end = 0.01
 step = 2e-3

test/test_exp.mini

-import logging.ini
+# Test: Compare a simple exponential ODE with its analytic result
+
+import default_logging.ini
+import default_time_stepping.ini
 
 _grow_rate = 0.2
 _initial = 1
@@ -14,14 +17,11 @@ initial_level = 0
 order = 1
 
 [model.time_stepping]
-rk_method = alexander_2
 begin = 0
 end = 10
 initial_step = 1e-2
 min_step = 1e-3
 max_step = 1e-1
-decrease_factor = 0.5
-increase_factor = 1.5
 
 [model.writer]
 file_path = {__name}

test/test_gauss.mini

 # Test: Check that the first steps of a pure diffusive problem evolve as a
 #   gaussian process
 
-import logging.ini
+import default_logging.ini
+import default_time_stepping.ini
 
 _diffusion = 0.005
 _t0 = 1.
@@ -19,14 +20,11 @@ initial_level = 4
 order = 0, 1 | expand geometry_type
 
 [model.time_stepping]
-rk_method = alexander_2
 begin = {_t0}
 end = 2
 initial_step = 1e-2
 min_step = 1e-3
 max_step = 1e-1
-decrease_factor = 0.5
-increase_factor = 1.5
 
 [model.writer]
 file_path = {__name}

test/test_gauss_mixed_geometry.mini

 # Test: Check that the first steps of a pure diffusive problem evolve as a
 #   gaussian process (mixed geometry version)
 
+import default_logging.ini
+import default_time_stepping.ini
+
 __name = test_gauss_mixed_geometry
 
 _diffusion = 0.005
@@ -16,14 +19,11 @@ initial_level = 4
 order = 1
 
 [model.time_stepping]
-rk_method = alexander_2
 begin = {_t0}
 end = 2
 initial_step = 1e-2
 min_step = 1e-3
 max_step = 1e-1
-decrease_factor = 0.5
-increase_factor = 1.5
 
 [model.writer]
 file_path = {__name}

test/test_in_out.mini

 # Test that checks fluxes on membranes with a reference vtk file produced with
 #   previous versions of dune_copasi_md
 
-import logging.ini
+import default_logging.ini
+import default_time_stepping.ini
 
 __name = test_in_out
 
@@ -14,15 +15,11 @@ initial_level = 1
 order = 1
 
 [model.time_stepping]
-rk_method = alexander_2
 begin = 0
 end = 1
 initial_step = 0.3
 min_step = 1e-3
 max_step = 0.35
-decrease_factor = 0.5
-increase_factor = 1.5
-
 [model.writer]
 file_path = {__name}
 

test/test_initial.mini

 # Test: Check the interpolation output for math expression initialization
 
-import logging.ini
+import default_logging.ini
+import default_time_stepping.ini
 
 _diffusion = 0.01
 _t0 = 1.
@@ -18,15 +19,11 @@ initial_level = 6
 order = 0, 1 | expand geometry_type
 
 [model.time_stepping]
-rk_method = alexander_2
 begin = {_t0}
 end = {_t0}
-step = 0.1
 initial_step = 0.1
 min_step = 1e-3
 max_step = 1e-0
-decrease_factor = 0.9
-increase_factor = 1.1
 
 [model.compartments]
 domain = 0

test/test_no_writer.mini

 # Test: An inifile without `writer` section must be valid
 
-import logging.ini
+import default_logging.ini
+import default_time_stepping.ini
 
 __name = test_no_writer
 
@@ -13,14 +14,11 @@ initial_level = 0
 order = 1
 
 [model.time_stepping]
-rk_method = alexander_2
 begin = 0
 end = 1
 initial_step = 0.1
 min_step = 1e-3
 max_step = 1e-0
-decrease_factor = 0.9
-increase_factor = 1.1
 
 [model.compartments]
 domain     = 0

test/test_tiff.mini

 # Test: Checks interpolation of TIFF files with a reference vtk file
 #   produced with previous versions of dune_copasi_sd/md
 
-import logging.ini
+import default_logging.ini
+import default_time_stepping.ini
 
 __name = test_tiff
 
@@ -14,15 +15,11 @@ initial_level = 3
 order = 1
 
 [model.time_stepping]
-rk_method = alexander_2
 begin = 0.
 end = 0.
-step = 0.1
 initial_step = 0.1
 min_step = 1e-3
 max_step = 1e-0
-decrease_factor = 0.9
-increase_factor = 1.1
 
 [model.writer]
 file_path = {__name}