formalize calibration parameters

Author: mrp089

src/interface/interface.cpp

@@ -5,7 +5,7 @@
 
 #include <cmath>
 
-#include "SimulationParameters.h"
+#include "Parameters.h"
 
 // Static member data.
 int SolverInterface::problem_id_count_ = 0;

src/optimize/LevenbergMarquardtOptimizer.cpp

@@ -5,18 +5,17 @@
 #include <iomanip>
 
 LevenbergMarquardtOptimizer::LevenbergMarquardtOptimizer(
-    Model* model, int num_obs, int num_params, double lambda0, double tol_grad,
-    double tol_inc, int max_iter) {
+    Model* model, int num_obs, int num_params, CalibrationParameters cali_params) {
   this->model = model;
   this->num_obs = num_obs;
   this->num_params = num_params;
   this->num_eqns = model->dofhandler.get_num_equations();
   this->num_vars = model->dofhandler.get_num_variables();
   this->num_dpoints = this->num_obs * this->num_eqns;
-  this->lambda = lambda0;
-  this->tol_grad = tol_grad;
-  this->tol_inc = tol_inc;
-  this->max_iter = max_iter;
+  this->lambda = cali_params.lambda0;
+  this->tol_grad = cali_params.tolerance_gradient;
+  this->tol_inc = cali_params.tolerance_increment;
+  this->max_iter = cali_params.maximum_iterations;
 
   jacobian = Eigen::SparseMatrix<double>(num_dpoints, num_params);
   residual = Eigen::Matrix<double, Eigen::Dynamic, 1>::Zero(num_dpoints);

src/optimize/LevenbergMarquardtOptimizer.h

@@ -11,6 +11,7 @@
 #include <Eigen/Sparse>
 
 #include "Model.h"
+#include "Parameters.h"
 
 /**
  * @brief Levenberg-Marquardt optimization class
@@ -81,14 +82,10 @@ class LevenbergMarquardtOptimizer {
    * @param model The 0D model
    * @param num_obs Number of observations in optimization
    * @param num_params Number of parameters in optimization
-   * @param lambda0 Initial damping factor
-   * @param tol_grad Gradient tolerance
-   * @param tol_inc Parameter increment tolerance
-   * @param max_iter Maximum iterations
+   * @param cali_params Calibration parameters
    */
   LevenbergMarquardtOptimizer(Model* model, int num_obs, int num_params,
-                              double lambda0, double tol_grad, double tol_inc,
-                              int max_iter);
+                              CalibrationParameters cali_params);
 
   /**
    * @brief Run the optimization algorithm

src/optimize/calibrate.cpp

@@ -3,22 +3,13 @@
 #include "calibrate.h"
 
 #include "LevenbergMarquardtOptimizer.h"
-#include "SimulationParameters.h"
+#include "Parameters.h"
 
 nlohmann::json calibrate(const nlohmann::json& config) {
   auto output_config = nlohmann::json(config);
 
   // Read calibration parameters
-  DEBUG_MSG("Parse calibration parameters");
-  auto const& calibration_parameters = config["calibration_parameters"];
-  double gradient_tol =
-      calibration_parameters.value("tolerance_gradient", 1e-5);
-  double increment_tol =
-      calibration_parameters.value("tolerance_increment", 1e-10);
-  int max_iter = calibration_parameters.value("maximum_iterations", 100);
-  bool zero_capacitance =
-      calibration_parameters.value("set_capacitance_to_zero", false);
-  double lambda0 = calibration_parameters.value("initial_damping_factor", 1.0);
+  CalibrationParameters cali_params = load_calibration_params(config);
 
   // Setup model
   auto model = Model();
@@ -138,8 +129,7 @@ nlohmann::json calibrate(const nlohmann::json& config) {
   // Run optimization
   DEBUG_MSG("Start optimization");
   auto lm_alg =
-      LevenbergMarquardtOptimizer(&model, num_obs, param_counter, lambda0,
-                                  gradient_tol, increment_tol, max_iter);
+      LevenbergMarquardtOptimizer(&model, num_obs, param_counter, cali_params);
 
   alpha = lm_alg.run(alpha, y_all, dy_all);
 
@@ -153,12 +143,9 @@ nlohmann::json calibrate(const nlohmann::json& config) {
   for (auto& vessel_config : output_config["vessels"]) {
     std::string vessel_name = vessel_config["vessel_name"];
     auto block = model.get_block(vessel_name);
-    double stenosis_coeff = 0.0;
-    stenosis_coeff = alpha[block->global_param_ids[3]];
-    double c_value = 0.0;
-    if (!zero_capacitance) {
-      c_value = alpha[block->global_param_ids[1]];
-    }
+    double stenosis_coeff = alpha[block->global_param_ids[3]];
+    double c_value = alpha[block->global_param_ids[1]];
+
     vessel_config["zero_d_element_values"] = {
         {"R_poiseuille", alpha[block->global_param_ids[0]]},
         {"C", std::max(c_value, 0.0)},

src/solve/CMakeLists.txt

@@ -7,14 +7,14 @@ set(lib svzero_solve_library)
 
 set(CXXSRCS 
   csv_writer.cpp 
-  SimulationParameters.cpp 
+  Parameters.cpp 
   Solver.cpp
 )
 
 set(HDRS 
   csv_writer.h 
   debug.h 
-  SimulationParameters.h 
+  Parameters.h 
   Solver.h 
 )
 

src/solve/SimulationParameters.cpp src/solve/Parameters.cppsrc/solve/SimulationParameters.cpp renamed to src/solve/Parameters.cpp

@@ -1,6 +1,6 @@
 // SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the
 // University of California, and others. SPDX-License-Identifier: BSD-3-Clause
-#include "SimulationParameters.h"
+#include "Parameters.h"
 
 bool get_param_scalar(const nlohmann::json& data, const std::string& name,
                       const InputParameter& param, double& val) {
@@ -260,6 +260,16 @@ void load_simulation_model(const nlohmann::json& config, Model& model) {
   model.finalize();
 }
 
+CalibrationParameters load_calibration_params(const nlohmann::json& config) {
+  DEBUG_MSG("Loading calibration parameters");
+  CalibrationParameters calib_params;
+  calib_params.tolerance_gradient = config.value("tolerance_gradient", 1e-5);
+  calib_params.tolerance_increment = config.value("tolerance_increment", 1e-10);
+  calib_params.maximum_iterations = config.value("maximum_iterations", 100);
+  calib_params.lambda0 = config.value("lambda0", 1.0);
+  return calib_params;
+}
+
 void load_calibration_model(const nlohmann::json& config, Model& model) {
   std::vector<std::tuple<std::string, std::string>> connections;
 

src/solve/SimulationParameters.h src/solve/Parameters.hsrc/solve/SimulationParameters.h renamed to src/solve/Parameters.h

@@ -1,7 +1,7 @@
 // SPDX-FileCopyrightText: Copyright (c) Stanford University, The Regents of the
 // University of California, and others. SPDX-License-Identifier: BSD-3-Clause
 /**
- * @file SimulationParameters.h
+ * @file Parameters.h
  * @brief Source file to read simulation configuration
  */
 #ifndef SVZERODSOLVER_SIMULATIONPARAMETERS_HPP_
@@ -54,6 +54,13 @@ struct SimulationParameters {
                                        ///< running coupled
 };
 
+struct CalibrationParameters {
+  double tolerance_gradient{0.0};    ///< Tolerance for gradient
+  double tolerance_increment{0.0};  ///< Tolerance for increment
+  int maximum_iterations{0};        ///< Maximum number of iterations
+  double lambda0{0.0};                ///< Initial damping factor
+};
+
 /// @brief Wrapper class for nlohmann:json with error checking
 class JsonWrapper : public nlohmann::json {
  public:
@@ -152,9 +159,17 @@ SimulationParameters load_simulation_params(const nlohmann::json& config);
  */
 void load_simulation_model(const nlohmann::json& config, Model& model);
 
+/**
+ * @brief Load the calibration parameters from a JSON configuration
+ *
+ * @param config The JSON configuration
+ * @return SimulationParameters Simulation parameters read from configuration
+ */
+CalibrationParameters load_calibration_params(const nlohmann::json& config);
+
 /**
  * @brief Load the 0D block in the model from a configuration for an inverse
- * problen
+ * problem
  *
  * @param config The json configuration
  * @param model The 0D model
@@ -238,7 +253,7 @@ void create_junctions(
  *
  * @param model The model the block is associated with
  * @param connections Vector storing the connections between blocks
- */    
+ */
 void create_connections(
     Model& model,
     std::vector<std::tuple<std::string, std::string>>& connections);

src/solve/Solver.h

@@ -7,7 +7,7 @@
 
 #include "Integrator.h"
 #include "Model.h"
-#include "SimulationParameters.h"
+#include "Parameters.h"
 #include "State.h"
 #include "debug.h"
 

tests/cases/steadyFlow_calibration.json

@@ -873,7 +873,6 @@
         "tolerance_gradient": 1e-5,
         "tolerance_increment": 1e-10,
         "maximum_iterations": 100,
-        "set_capacitance_to_zero": false,
         "initial_damping_factor": 1.0
     }
 }

tests/cases/vmr/input/0080_0001_calibrate_from_0d.json

@@ -5146,8 +5146,7 @@
     "calibration_parameters": {
         "tolerance_gradient": 1e-05,
         "tolerance_increment": 1e-09,
-        "maximum_iterations": 20,
-        "set_capacitance_to_zero": false
+        "maximum_iterations": 20
     },
     "y": {
         "flow:branch0_seg0:J0": [