improved commentary

examples/FTCS_2D_proto_example.cpp

@@ -78,6 +78,7 @@ int main(int argc, char *argv[]) {
 
     // set kind of output [CSV_OUTPUT_OFF (default), CSV_OUTPUT_ON, CSV_OUTPUT_VERBOSE]
     simulation.setOutputCSV(CSV_OUTPUT_VERBOSE);
+
     
     // **** RUN SIMULATION ****
     

include/tug/Boundary.hpp

@@ -1,7 +1,7 @@
 /**
  * @file Boundary.hpp
- * @brief 
+ * @brief API of Boundary class, that holds all information for each boundary condition 
- * 
+ *        at the edges of the diffusion grid. 
  * 
  */
 #ifndef BOUNDARY_H_
@@ -13,11 +13,19 @@
 using namespace std;
 using namespace Eigen;
 
+/**
+ * @brief Enum defining the two implemented boundary conditions. 
+ * 
+ */
 enum BC_TYPE {
     BC_TYPE_CLOSED,
     BC_TYPE_CONSTANT
 };
 
+/**
+ * @brief Enum defining all 4 possible sides to a 1D and 2D grid. 
+ * 
+ */
 enum BC_SIDE {
     BC_SIDE_LEFT,
     BC_SIDE_RIGHT,
@@ -149,12 +157,18 @@ class Boundary {
        * @brief Returns the boundary condition of a specified side as a vector
        *        of BoundarsElement objects.
        *
-       * @param side Boundary side from which the boundaryconditions are to be returned.
+       * @param side Boundary side from which the boundary conditions are to be returned.
        * @return vector<BoundaryElement> Contains the boundary conditions as BoundaryElement objects.
        */
       vector<BoundaryElement> getBoundarySide(BC_SIDE side);
 
-      // TODO write documentation and tests for this method
+      /**
+       * @brief Get thes Boundary Side Values as a vector. Value is -1 in case some specific 
+                boundary is closed.
+       * 
+       * @param side Boundary side for which the values are to be returned.
+       * @return VectorXd Vector with values as doubles. 
+       */
       VectorXd getBoundarySideValues(BC_SIDE side);
 
       /**
@@ -192,9 +206,9 @@ class Boundary {
       double getBoundaryElementValue(BC_SIDE side, int index);
 
     private:
-        Grid grid;
+        Grid grid; // Boundary is directly dependent on the dimensions of a predefined
         
-        vector<vector<BoundaryElement>> boundaries;
+        vector<vector<BoundaryElement>> boundaries; // Vector with Boundary Element information
 };
 
 #endif

include/tug/Grid.hpp

@@ -163,8 +163,8 @@ class Grid {
         int domainRow; // number of domain rows
         double deltaCol; // delta in x-direction (between columns)
         double deltaRow; // delta in y-direction (between rows)
-        MatrixXd concentrations; 
+        MatrixXd concentrations; // Matrix holding grid concentrations 
-        MatrixXd alphaX;
+        MatrixXd alphaX; // Matrix holding alpha coefficients in x-direction
-        MatrixXd alphaY;
+        MatrixXd alphaY; // Matrix holding alpha coefficients in y-direction
 
 };

include/tug/Simulation.hpp

@@ -1,34 +1,52 @@
 /**
  * @file Simulation.hpp
- * @brief  
+ * @brief API of Simulation class, that holds all information regarding a specific simulation
+ *        run like its timestep, number of iterations and output options. Simulation object
+ *        also holds a predefined Grid and Boundary object. 
+ *
  */
 #include "Boundary.hpp"
 #include <ios>
 
 using namespace std;
 
+/**
+ * @brief Enum defining the two implemented solution approaches. 
+ * 
+ */
 enum APPROACH {
     FTCS_APPROACH, // Forward Time-Centered Space
     BTCS_APPROACH // Backward Time-Centered Space
 };
 
+/**
+ * @brief Enum holding different options for .csv output.
+ * 
+ */
 enum CSV_OUTPUT {
     CSV_OUTPUT_OFF, // do not produce csv output
     CSV_OUTPUT_ON, // produce csv output with last concentration matrix
     CSV_OUTPUT_VERBOSE, // produce csv output with all concentration matrices
-    CSV_OUTPUT_XTREME // produce csv output with all concentration matrices and boundary conditions at beginning
+    CSV_OUTPUT_XTREME // csv output like VERBOSE but additional boundary conditions at beginning
 };
 
+/**
+ * @brief Enum holding different options for console output.
+ * 
+ */
 enum CONSOLE_OUTPUT {
     CONSOLE_OUTPUT_OFF, // do not print any output to console
     CONSOLE_OUTPUT_ON, // print before and after concentrations to console
     CONSOLE_OUTPUT_VERBOSE // print all concentration matrices to console
 };
 
+/**
+ * @brief Enum holding different options for time measurement. 
+ * 
+ */
 enum TIME_MEASURE {
     TIME_MEASURE_OFF, // do not print any time measures
-    TIME_MEASURE_ON, // print time measure after last iteration
+    TIME_MEASURE_ON // print time measure after last iteration
-    TIME_MEASURE_VERBOSE // print time measures after each iteration
 };
 
 /**

src/Grid.cpp

@@ -13,7 +13,6 @@ Grid::Grid(int length) {
     this->deltaCol = double(this->domainCol)/double(this->col); // -> 1
     this->dim = 1;
 
-    // TODO move to the case when Simulation is set to constant and use as default
     this->concentrations = MatrixXd::Constant(1, col, 20);
     this->alphaX = MatrixXd::Constant(1, col, 1);
 }
@@ -31,7 +30,6 @@ Grid::Grid(int row, int col) {
     this->deltaCol = double(this->domainCol)/double(this->col); // -> 1
     this->dim = 2;
 
-    // TODO move to the case when Simulation is set to constant and use as default
     this->concentrations = MatrixXd::Constant(row, col, 20);
     this->alphaX = MatrixXd::Constant(row, col, 1);
     this->alphaY = MatrixXd::Constant(row, col, 1);

src/Simulation.cpp

@@ -19,14 +19,6 @@ Simulation::Simulation(Grid &grid, Boundary &bc, APPROACH approach) : grid(grid)
     this->timestep = -1; // error per default
     this->iterations = -1;
     this->innerIterations = 1;
-
-    // MDL no: we need to distinguish between "required dt" and
-    // "number of (outer) iterations" at which the user needs an
-    // output and the actual CFL-allowed timestep and consequently the
-    // number of "inner" iterations which the explicit FTCS needs to
-    // reach them. The following, at least at the moment, cannot be
-    // computed here since "timestep" is not yet set when this
-    // function is called. I brought everything into "FTCS_2D"!
     
     this->csv_output = CSV_OUTPUT_OFF;
     this->console_output = CONSOLE_OUTPUT_OFF;
@@ -35,7 +27,6 @@ Simulation::Simulation(Grid &grid, Boundary &bc, APPROACH approach) : grid(grid)
 
 void Simulation::setOutputCSV(CSV_OUTPUT csv_output) {
     if (csv_output < CSV_OUTPUT_OFF && csv_output > CSV_OUTPUT_VERBOSE) {
-        // throw invalid_argument("Invalid CSV output option given!");
         throw_invalid_argument("Invalid CSV output option given!");
     }
 
@@ -90,7 +81,7 @@ void Simulation::setTimestep(double timestep) {
     double CFL_Wiki = 1 / (4 * maxAlpha * ((1/deltaRowSquare) + (1/deltaColSquare))); // Formula from Wikipedia
 
     cout << "FTCS_2D :: CFL condition MDL: " << CFL_MDL << endl;
-    cout << "FTCS_2D :: CFL condition Wiki: " << CFL_Wiki << endl;
+    // cout << "FTCS_2D :: CFL condition Wiki: " << CFL_Wiki << endl;
     cout << "FTCS_2D :: required dt=" << timestep <<  endl;
 
     if (timestep > CFL_MDL) {
@@ -139,7 +130,6 @@ string Simulation::createCSVfile() {
     int appendIdent = 0;
     string appendIdentString;
 
-     // APPROACH_ROW_COL_ITERATIONS
     string approachString = (approach == 0) ? "FTCS" : "BTCS";
     string row = to_string(grid.getRow());
     string col = to_string(grid.getCol());
@@ -150,8 +140,7 @@ string Simulation::createCSVfile() {
     while (filesystem::exists(filename)) {
         appendIdent += 1;
         appendIdentString = to_string(appendIdent);
-        // ?? TODO why double filename?
+        filename = approachString + "_" + row + "_" + col + "_" + numIterations + "-" + appendIdentString + ".csv";
-        filename = filename = approachString + "_" + row + "_" + col + "_" + numIterations + "-" + appendIdentString + ".csv";
     }
 
     file.open(filename);
@@ -159,21 +148,14 @@ string Simulation::createCSVfile() {
         exit(1);
     }
 
+    // adds lines at the beginning of verbose output csv that represent the boundary conditions and their values
+    // -1 in case of closed boundary
     if (csv_output == CSV_OUTPUT_XTREME) {
-        //rows
-        //cols
-        //iterations
-        //boundary left
-        //boundary right
-        //boundary top
-        //boundary bottom
         IOFormat one_row(StreamPrecision, DontAlignCols, "", " ");
-        file << bc.getBoundarySideValues(BC_SIDE_LEFT).format(one_row) << endl;
+        file << bc.getBoundarySideValues(BC_SIDE_LEFT).format(one_row) << endl; // boundary left
-        file << bc.getBoundarySideValues(BC_SIDE_RIGHT).format(one_row) << endl;
+        file << bc.getBoundarySideValues(BC_SIDE_RIGHT).format(one_row) << endl; // boundary right
-        file << bc.getBoundarySideValues(BC_SIDE_TOP).format(one_row) << endl;
+        file << bc.getBoundarySideValues(BC_SIDE_TOP).format(one_row) << endl; // boundary top
-        file << bc.getBoundarySideValues(BC_SIDE_BOTTOM).format(one_row) << endl;
+        file << bc.getBoundarySideValues(BC_SIDE_BOTTOM).format(one_row) << endl; // boundary bottom
-        // TODO
-        // file << to_string(bc.printBoundarySide) << endl;
         file << endl << endl;
     }
 
@@ -212,12 +194,10 @@ void Simulation::run() {
         filename = createCSVfile();
     }
 
+    auto begin = std::chrono::high_resolution_clock::now();
+
     if (approach == FTCS_APPROACH) {
-        auto begin = std::chrono::high_resolution_clock::now();
-        progressbar bar(iterations * innerIterations);
         for (int i = 0; i < iterations * innerIterations; i++) {
-	    // MDL: distinguish between "outer" and "inner" iterations
-	    // std::cout << ":: run(): Outer iteration " << i+1 << "/" << iterations << endl;
             if (console_output == CONSOLE_OUTPUT_VERBOSE && i > 0) {
                 printConcentrationsConsole();
             }
@@ -226,13 +206,14 @@ void Simulation::run() {
             }
 
             FTCS(this->grid, this->bc, this->timestep);
-            bar.update();
+    
+            if (i % (iterations * innerIterations / 100) == 0) {
+                double percentage = (double)i / ((double)iterations * (double)innerIterations) * 100;
+                if ((int)percentage % 10 == 0) {
+                    cout << "Progress: " << percentage << "%" << endl;
+                }
+            }
         }
-        auto end = std::chrono::high_resolution_clock::now();
-        auto milliseconds = std::chrono::duration_cast<std::chrono::milliseconds>(end - begin);
-
-	// MDL: meaningful stdout messages
-        std::cout << "\n:: run() finished in " << milliseconds.count() << "ms" << endl;
 
     } else if (approach == BTCS_APPROACH) {
 
@@ -250,12 +231,19 @@ void Simulation::run() {
 
     }
 
+    auto end = std::chrono::high_resolution_clock::now();
+    auto milliseconds = std::chrono::duration_cast<std::chrono::milliseconds>(end - begin);
+
     if (this->console_output > CONSOLE_OUTPUT_OFF) {
         printConcentrationsConsole();
     }
     if (this->csv_output > CSV_OUTPUT_OFF) {
         printConcentrationsCSV(filename);
     }
-
+    if (this->time_measure > TIME_MEASURE_OFF) {
+        string approachString = (approach == 0) ? "FTCS" : "BTCS";
+        string dimString = (grid.getDim() == 1) ? "-1D" : "-2D";
+        cout << approachString << dimString << ":: run() finished in " << milliseconds.count() << "ms" << endl;
+    }
     
 }