Add benchmark

CMakeLists.txt

@@ -42,3 +42,9 @@ if(TUG_ENABLE_TESTING)
 endif()
 
 add_subdirectory(examples)
+
+option(TUG_NAAICE_EXAMPLE "Enables NAAICE examples with export of CSV files" OFF)
+
+if (TUG_NAAICE_EXAMPLE)
+  add_subdirectory(naaice)
+endif()

naaice/BTCS_2D_NAAICE.cpp

@@ -0,0 +1,150 @@
+#include <Eigen/Eigen>
+#include <cstdint>
+#include <fstream>
+#include <iostream>
+#include <ostream>
+#include <stdexcept>
+#include <string>
+#include <string_view>
+#include <tug/Simulation.hpp>
+#include <vector>
+
+#include "files.hpp"
+
+template <typename T> inline T parseString(const std::string &str) {
+  T result;
+  std::istringstream iss(str);
+
+  if (!(iss >> result)) {
+    throw std::invalid_argument("Invalid input for parsing.");
+  }
+
+  return result;
+}
+
+template <typename T>
+std::vector<T> tokenize(const std::string &input, char delimiter) {
+  std::vector<T> tokens;
+  std::istringstream tokenStream(input);
+  std::string token;
+
+  while (std::getline(tokenStream, token, delimiter)) {
+    tokens.push_back(parseString<T>(token));
+  }
+
+  return tokens;
+}
+
+template <typename T>
+std::vector<std::vector<T>> CSVToVector(const char *filename) {
+  std::ifstream in_file(filename);
+  if (!in_file.is_open()) {
+    throw std::runtime_error("Error opening file \'" + std::string(filename) +
+                             "\'.");
+  }
+
+  std::vector<std::vector<T>> csv_data;
+
+  std::string line;
+  while (std::getline(in_file, line)) {
+    csv_data.push_back(tokenize<T>(line, ','));
+  }
+
+  in_file.close();
+
+  return csv_data;
+}
+
+template <typename T>
+Eigen::MatrixXd CMVecToRMMatrix(const std::vector<std::vector<T>> &vec,
+                                std::uint32_t exp_rows,
+                                std::uint32_t exp_cols) {
+  if (exp_rows != vec.size()) {
+    throw std::runtime_error(
+        "Mismatch in y dimension while converting to Eigen::Matrix.");
+  }
+
+  Eigen::MatrixXd out_mat(exp_rows, exp_cols);
+
+  for (std::uint32_t ri = 0; ri < exp_rows; ri++) {
+    const auto &vec_row = vec[ri];
+    if (vec[ri].size() != exp_cols) {
+      throw std::runtime_error(
+          "Mismatch in x dimension while converting to Eigen::Matrix.");
+    }
+    for (std::uint32_t cj = 0; cj < exp_cols; cj++) {
+      out_mat(ri, cj) = vec_row[cj];
+    }
+  }
+
+  return out_mat;
+}
+
+int main(int argc, char *argv[]) {
+  // EASY_PROFILER_ENABLE;
+  // profiler::startListen();
+  // **************
+  // **** GRID ****
+  // **************
+  // profiler::startListen();
+  // create a grid with a 5 x 10 field
+  constexpr int row = 5;
+  constexpr int col = 10;
+  Grid grid = Grid(row, col);
+
+  // (optional) set the domain, e.g.:
+  grid.setDomain(0.005, 0.01);
+
+  const auto init_values_vec = CSVToVector<double>(INPUT_CONC_FILE);
+  MatrixXd concentrations = CMVecToRMMatrix(init_values_vec, row, col);
+  grid.setConcentrations(concentrations);
+
+  // // (optional) set alphas of the grid, e.g.:
+  const auto alphax_vec = CSVToVector<double>(INPUT_ALPHAX_FILE);
+  MatrixXd alphax = CMVecToRMMatrix(alphax_vec, row, col);
+
+  constexpr double alphay_val = 5e-10;
+  MatrixXd alphay = MatrixXd::Constant(row, col, alphay_val); // row,col,value
+  grid.setAlpha(alphax, alphay);
+
+  // // ******************
+  // // **** BOUNDARY ****
+  // // ******************
+
+  // create a boundary with constant values
+  Boundary bc = Boundary(grid);
+  bc.setBoundarySideClosed(BC_SIDE_LEFT);
+  bc.setBoundarySideClosed(BC_SIDE_RIGHT);
+  bc.setBoundarySideClosed(BC_SIDE_TOP);
+  bc.setBoundarySideClosed(BC_SIDE_BOTTOM);
+
+  // // ************************
+  // // **** SIMULATION ENV ****
+  // // ************************
+
+  // set up a simulation environment
+  Simulation simulation = Simulation(
+      grid, bc, BTCS_APPROACH); // grid,boundary,simulation-approach
+
+  // set the timestep of the simulation
+  simulation.setTimestep(360); // timestep
+
+  // set the number of iterations
+  simulation.setIterations(1);
+
+  // set kind of output [CSV_OUTPUT_OFF (default), CSV_OUTPUT_ON,
+  // CSV_OUTPUT_VERBOSE]
+  simulation.setOutputCSV(CSV_OUTPUT_ON);
+
+  simulation.setOutputConsole(CONSOLE_OUTPUT_ON);
+
+  // // **** RUN SIMULATION ****
+
+  // // run the simulation
+
+  // // EASY_BLOCK("SIMULATION")
+  simulation.run();
+  // // EASY_END_BLOCK;
+  // // profiler::dumpBlocksToFile("test_profile.prof");
+  // // profiler::stopListen();
+}

naaice/CMakeLists.txt

@@ -0,0 +1,9 @@
+add_executable(naaice BTCS_2D_NAAICE.cpp)
+
+get_filename_component(IN_CONC_FILE "init_conc.csv" REALPATH)
+get_filename_component(IN_ALPHAX_FILE "alphax.csv" REALPATH)
+
+configure_file(files.hpp.in files.hpp)
+target_include_directories(naaice PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
+
+target_link_libraries(naaice PUBLIC tug)

naaice/alphax.csv

@@ -0,0 +1,5 @@
+9.35863547772169e-10,4.1475358910393e-10,7.40997499064542e-10,4.63898729439825e-10,5.50232032872736e-10,1.83670640387572e-10,5.84096802584827e-10,4.72976535512134e-10,2.92526249657385e-10,5.8247926668264e-10
+8.08492869278416e-10,3.5943602763582e-10,6.87254608655348e-10,1.52116895909421e-10,5.95404988038354e-10,8.90064929216169e-10,6.13143724552356e-10,1.23507722397335e-10,2.898759260308e-10,9.90528965741396e-10
+3.12359050870873e-10,6.34084914484993e-10,8.28234328492545e-10,1.60584925650619e-10,1.31777092232369e-10,7.34155903453939e-10,9.86383097898215e-10,5.42474469379522e-10,1.23030534153804e-10,2.33146838657558e-10
+7.76231796317734e-10,1.69479642040096e-10,6.74477553134784e-10,2.4903867142275e-10,2.70820381003432e-10,1.67315319390036e-10,7.1631961625535e-10,4.51548034301959e-10,2.41610987577587e-10,4.98075650655665e-10
+7.33895266707987e-10,5.82150935800746e-10,1.49088777275756e-10,5.00345975253731e-10,8.26257051993161e-10,5.28838745504618e-10,9.94136832957156e-10,7.44971914449707e-10,7.53557282453403e-10,7.54089470859617e-10

naaice/files.hpp.in

@@ -0,0 +1,7 @@
+#ifndef FILES_H_
+#define FILES_H_
+
+const char *INPUT_CONC_FILE = "@IN_CONC_FILE@";
+const char *INPUT_ALPHAX_FILE = "@IN_ALPHAX_FILE@";
+
+#endif // FILES_H_

naaice/init_conc.csv

@@ -0,0 +1,5 @@
+6.92023e-07,6.92023e-07,6.92023e-07,6.92023e-07,6.92023e-07,2.02396e-08,2.02396e-08,2.02396e-08,2.02396e-08,2.02396e-08
+6.92023e-07,6.92023e-07,6.92023e-07,6.92023e-07,6.92023e-07,2.02396e-08,2.02396e-08,2.02396e-08,2.02396e-08,2.02396e-08
+6.92023e-07,6.92023e-07,6.92023e-07,6.92023e-07,6.92023e-07,2.02396e-08,2.02396e-08,2.02396e-08,2.02396e-08,2.02396e-08
+6.92023e-07,6.92023e-07,6.92023e-07,6.92023e-07,6.92023e-07,2.02396e-08,2.02396e-08,2.02396e-08,2.02396e-08,2.02396e-08
+6.92023e-07,6.92023e-07,6.92023e-07,6.92023e-07,6.92023e-07,2.02396e-08,2.02396e-08,2.02396e-08,2.02396e-08,2.02396e-08

src/CMakeLists.txt

@@ -1,8 +1,6 @@
 add_library(tug Boundary.cpp Grid.cpp Simulation.cpp FTCS.cpp BTCSv2.cpp)
 
-option(TUG_WRITE_CSV "Write CSV during Thomas algorithm with consecutive numbers for each call" OFF)
-
-IF(TUG_WRITE_CSV)
+IF(TUG_NAAICE_EXAMPLE)
   target_compile_definitions(tug PRIVATE WRITE_THOMAS_CSV)
 endif()