Introduce the trapping configuration class

src/include/tfrfme.h

+/*! \file tfrfme.h
+ *
+ * \brief Representation of the trapping configuration objects.
+ */
+
+#ifndef INCLUDE_TFRFME_H_
+#define INCLUDE_TFRFME_H_
+
+/*! \brief Class to represent the trapping configuration.
+ */
+class TFRFME {
+ private:
+  //! NLMMT = 2 * LM * (LM + 2)
+  int nlmmt;
+  //! NRVC = NXV * NYV * NZV
+  int nrvc;
+  
+ protected:
+  //! Field expansion mode identifier.
+  int lmode;
+  //! Maximim field expansion order;
+  int lm;
+  //! QUESTION: definition?
+  int nkv;
+  //! Number of computed X coordinates.
+  int nxv;
+  //! Number of computed Y coordinates.
+  int nyv;
+  //! Number of computed Z coordinates.
+  int nzv;
+  //! Wave number in scale units
+  double vk;
+  //! External medium refractive index
+  double exri;
+  //! QUESTION: definition?
+  double an;
+  //! QUESTION: definition?
+  double ff;
+  //! QUESTION: definition?
+  double tra;
+  //! QUESTION: definition?
+  double spd;
+  //! QUESTION: definition?
+  double frsh;
+  //! QUESTION: definition?
+  double exril;
+  //! Vector of computed x positions
+  double *xv;
+  //! Vector of computed y positions
+  double *yv;
+  //! Vector of computed z positions
+  double *zv;
+  //! QUESTION: definition?
+  complex<double> **wsum;
+
+ public:
+  /*! \briesf Trapping configuration instance constructor.
+   */
+  TFRFME(
+	 int _lmode, int _lm, int _nkv, int _nxv, int _nyv, int _nzv
+);
+  
+  /*! \briesf Trapping configuration instance destroyer.
+   */
+  ~TFRFME();
+
+  /*! \briesf Load a trapping configuration instance from binary file.
+   *
+   * \param file_name: `string` Name of the file.
+   * \param format: `string` Format of the file (can be either "HDF5"
+   * or "LGEACY". Default is "LEGACY").
+   * \return instance: `TFRFME *` Pointer to anewly created configuration
+   * instance.
+   */
+  TFRFME* from_binary(std::string file_name, std::string format="LEGACY");
+
+  /*! \brief Get an element from the WSUM matrix.
+   *
+   * \param row: `int` Row index of the element to be read.
+   * \param col: `int` Column index of the element to be read.
+   * \return value: `complex<double>` The value of the requested element.
+   */
+  std::complex<double> get_matrix_element(int row, int col);
+
+  /*! \brief Get a configuration parameter.
+   *
+   * \param param_name: `string` Name of the parameter.
+   * \return value: `double` The value of the requested parameter.
+   */
+  double get_param(std::string param_name);
+
+  /*! \brief Set an element in the WSUM matrix.
+   *
+   * \param row: `int` Row index of the element to be read.
+   * \param col: `int` Column index of the element to be read.
+   * \param value: `complex<double>` The value to be placed in the matrix.
+   */
+  void set_matrix_element(int row, int col, std::complex<double> value);
+  
+  /*! \brief Set a configuration parameter.
+   *
+   * \param param_name: `string` Name of the parameter.
+   * \param value: `double` Value to be stored as parameter.
+   */
+  void set_param(std::string param_name, double value);
+
+  /*! \briesf Write a trapping configuration instance to binary file.
+   *
+   * \param file_name: `string` Name of the file.
+   * \param format: `string` Format of the file (can be either "HDF5"
+   * or "LGEACY". Default is "LEGACY").
+   */
+  void write_binary(std::string file_name, std::string format="LEGACY");
+};
+#endif

src/libnptm/tfrfme.cpp

+/*! \file tfrfme.cpp
+ *
+ * \brief Implementation of the trapping configuration objects.
+ */
+
+#include<complex>
+#include<string>
+
+#ifndef INCLUDE_TFRFME_H_
+#include "../include/tfrfme.cpp"
+#endif
+
+using namespace std;
+
+TFRFME::TFRFME(int _lmode, int _lm, int _nkv, int _nxv, int _nyv, int _nzv) {
+  lmode = _lmode;
+  lm = _lm;
+  nkv = _nkv;
+  nxv = _nxv;
+  nyv = _nyv;
+  nzv = _nzv;
+  vk = 0.0;
+  exri = 0.0;
+  an = 0.0;
+  ff = 0.0;
+  tra = 0.0;
+  spd = 0.0;
+  frsh = 0.0;
+  exril = 0.0;
+
+  // Array initialization
+  xv = new double[nxv]();
+  yv = new double[nyv]();
+  zv = new double[nzv]();
+  nlmmt = lm * (lm + 2) * 2;
+  nrvc = nxv * nyv * nzv;
+  wsum = new complex<double>*[nlmmt];
+  for (int wi = 0; wi < nlmmt; wi++) wsum[wi] = new complex<double>[nrvc]();
+}
+
+TFRFME::~TFRFME() {
+  delete[] xv;
+  delete[] yv;
+  delete[] zv;
+  for (int wi = nlmmt - 1; wi > -1; wi--) delete[] wsum[wi];
+  delete[] wsum;
+}
+
+TFRFME::TFRFME* from_binary(string file_name, string format) {
+  TFRFME *instance = NULL;
+  return instance;
+}
+
+TFRFME::double get_param(string param_name) {
+  double value;
+  if (param_name.compare("exri") == 0) value = exri;
+  else if (param_name.compare("an") == 0) value = an;
+  else if (param_name.compare("ff") == 0) value = ff;
+  else if (param_name.compare("tra") == 0) value = tra;
+  else if (param_name.compare("spd") == 0) value = spd;
+  else if (param_name.compare("frsh") == 0) value = frsh;
+  else if (param_name.compare("exril") == 0) value = exril;
+  //TODO: add else clause with exception.
+  return value;
+}
+
+TFRFME::void write_binary(string file_name, string format) {
+  return;
+}

src/trapping/cfrfme.cpp

@@ -412,7 +412,7 @@ void frfme(string data_file, string output_path) {
 	  }
 	  // label 88
 	  for (int ixyz = 0; ixyz < nrvc; ixyz++) {
-	    for (int j = 0; j< jlml; j++) {
+	    for (int j = 0; j < jlml; j++) {
 	      double vreal = wsum[j][ixyz].real();
 	      double vimag = wsum[j][ixyz].imag();
 	      tfrfme.write(reinterpret_cast<char *>(&vreal), sizeof(double));