Loading src/include/TransitionMatrix.h +69 −3 Original line number Diff line number Diff line Loading @@ -48,19 +48,58 @@ class TransitionMatrix { /*! \brief Write the Transition Matrix to HDF5 binary output. * * This function takes care of the specific task of building a transition * matrix memory data structure from a binary input file formatted according * to the structure used by the original FORTRAN code. * This function takes care of the specific task of writing the transition * matrix memory data structure to a binary output file formatted according * to the HDF5 standard. * * \param file_name: `string` Name of the binary configuration data file. */ void write_hdf5(std::string file_name); /*! \brief Write transition matrix data to HDF5 binary output. * * This function takes care of the specific task of writing the transition * matrix memory data structure to a binary output file formatted according * to the HDF5 standard. It is designed to work for the case of clusters of * spheres. * * \param file_name: `string` Name of the binary configuration data file. * \param _nlemt: `np_int` Size of the matrix (2 * LE * (LE + 2)). * \param _lm: `int` Maximum field expansion order. * \param _vk: `double` Wave number in scale units. * \param _exri: `double` External medium refractive index. * \param _am0m: `complex double **` */ static void write_hdf5( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m ); /*! \brief Write the Transition Matrix to legacy binary output. * * \param file_name: `string` Name of the binary configuration data file. */ void write_legacy(std::string file_name); /*! \brief Write transition matrix data to HDF5 binary output. * * This function takes care of the specific task of writing the transition * matrix memory data structure to a binary output file formatted according * to the format used by the legacy FORTRAN code. It is designed to work for * the case of clusters of spheres. * * \param file_name: `string` Name of the binary configuration data file. * \param _nlemt: `np_int` Size of the matrix (2 * LE * (LE + 2)). * \param _lm: `int` Maximum field expansion order. * \param _vk: `double` Wave number in scale units. * \param _exri: `double` External medium refractive index. * \param _am0m: `complex double **` */ static void write_legacy( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m ); public: /*! \brief Default Transition Matrix instance constructor. * Loading Loading @@ -142,6 +181,33 @@ class TransitionMatrix { */ void write_binary(std::string file_name, std::string mode="LEGACY"); /*! \brief Write a Transition Matrix to a binary file without instanciating it. * * Transition Matrix data can take a large amount of memory. For such reason, attempts * to create TransitionMatrix instances only for writing purposes can create * unnecessary resource consumption and computing time to duplicate the data into * the output buffer. This function offers output to file as a static method. It * takes the arguments of a constructor together with the usual arguments to specify * the output file name and format, to write the required data directly to a file, * without creating a new TransitionMatrix instance. The implementation works for * TransitionMatrix objects built for the CLUSTER case. It belongs to the public class * interface and it calls the proper versions of `write_legacy()` and `write_hdf5()`, * depending on the requested output format. * * \param file_name: `string` Name of the file to be written. * \param _nlemt: `np_int` Size of the matrix (2 * LE * (LE + 2)). * \param _lm: `int` Maximum field expansion order. * \param _vk: `double` Wave number in scale units. * \param _exri: `double` External medium refractive index. * \param _am0m: `complex double **` * \param mode: `string` Binary encoding. Can be one of ["LEGACY", "HDF5"] . Optional * (default is "LEGACY"). */ static void write_binary( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m, std::string mode="LEGACY" ); /*! \brief Test whether two instances of TransitionMatrix are equal. * * Transition matrices can be the result of a calculation or of a file input operation, Loading src/libnptm/TransitionMatrix.cpp +91 −11 Original line number Diff line number Diff line Loading @@ -218,6 +218,20 @@ void TransitionMatrix::write_binary(string file_name, string mode) { } } void TransitionMatrix::write_binary( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m, std::string mode ) { if (mode.compare("LEGACY") == 0) { write_legacy(file_name, _nlemt, _lm, _vk, _exri, _am0m); } else if (mode.compare("HDF5") == 0) { write_hdf5(file_name, _nlemt, _lm, _vk, _exri, _am0m); } else { string message = "Unknown format mode: \"" + mode + "\""; throw UnrecognizedFormatException(message); } } void TransitionMatrix::write_hdf5(string file_name) { if (is == 1 || is == 1111) { List<string> rec_name_list(1); Loading @@ -237,17 +251,10 @@ void TransitionMatrix::write_hdf5(string file_name) { rec_type_list.append("FLOAT64_(1)"); rec_ptr_list.append(&exri); rec_name_list.append("ELEMENTS"); str_type = "FLOAT64_(" + to_string(shape[0]) + "," + to_string(2 * shape[1]) + ")"; str_type = "COMPLEX128_(" + to_string(shape[0]) + "," + to_string(shape[1]) + ")"; rec_type_list.append(str_type); // The (N x M) matrix of complex is converted to a (N x 2M) matrix of double, // where REAL(E_i,j) -> E_i,(2 j) and IMAG(E_i,j) -> E_i,(2 j + 1) int num_elements = 2 * shape[0] * shape[1]; double *ptr_elements = new double[num_elements](); for (int ei = 0; ei < num_elements / 2; ei++) { ptr_elements[2 * ei] = real(elements[ei]); ptr_elements[2 * ei + 1] = imag(elements[ei]); } rec_ptr_list.append(ptr_elements); dcomplex *p_first = elements; rec_ptr_list.append(p_first); if (is == 1111) { rec_name_list.append("RADIUS"); rec_type_list.append("FLOAT64_(1)"); Loading @@ -264,7 +271,7 @@ void TransitionMatrix::write_hdf5(string file_name) { hdf_file->write(rec_names[ri], rec_types[ri], rec_pointers[ri]); hdf_file->close(); delete[] ptr_elements; p_first = NULL; delete[] rec_names; delete[] rec_types; delete[] rec_pointers; Loading @@ -275,6 +282,52 @@ void TransitionMatrix::write_hdf5(string file_name) { } } void TransitionMatrix::write_hdf5( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m ) { int is = 1; List<string> rec_name_list(1); List<string> rec_type_list(1); List<void *> rec_ptr_list(1); string str_type, str_name; rec_name_list.set(0, "IS"); rec_type_list.set(0, "INT32_(1)"); rec_ptr_list.set(0, &is); rec_name_list.append("L_MAX"); rec_type_list.append("INT32_(1)"); rec_ptr_list.append(&_lm); rec_name_list.append("VK"); rec_type_list.append("FLOAT64_(1)"); rec_ptr_list.append(&_vk); rec_name_list.append("EXRI"); rec_type_list.append("FLOAT64_(1)"); rec_ptr_list.append(&_exri); rec_name_list.append("ELEMENTS"); str_type = "COMPLEX128_(" + to_string(_nlemt) + "," + to_string(_nlemt) + ")"; rec_type_list.append(str_type); // The (N x M) matrix of complex is converted to a (N x 2M) matrix of double, // where REAL(E_i,j) -> E_i,(2 j) and IMAG(E_i,j) -> E_i,(2 j + 1) dcomplex *p_first = _am0m[0]; rec_ptr_list.append(p_first); string *rec_names = rec_name_list.to_array(); string *rec_types = rec_type_list.to_array(); void **rec_pointers = rec_ptr_list.to_array(); const int rec_num = rec_name_list.length(); FileSchema schema(rec_num, rec_types, rec_names); HDFFile *hdf_file = HDFFile::from_schema(schema, file_name, H5F_ACC_TRUNC); for (int ri = 0; ri < rec_num; ri++) hdf_file->write(rec_names[ri], rec_types[ri], rec_pointers[ri]); hdf_file->close(); p_first = NULL; delete[] rec_names; delete[] rec_types; delete[] rec_pointers; delete hdf_file; } void TransitionMatrix::write_legacy(string file_name) { fstream ttms; if (is == 1111 || is == 1) { Loading Loading @@ -308,6 +361,33 @@ void TransitionMatrix::write_legacy(string file_name) { } } void TransitionMatrix::write_legacy( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m ) { fstream ttms; int is = 1; ttms.open(file_name, ios::binary | ios::out); if (ttms.is_open()) { ttms.write(reinterpret_cast<char *>(&is), sizeof(int)); ttms.write(reinterpret_cast<char *>(&_lm), sizeof(int)); ttms.write(reinterpret_cast<char *>(&_vk), sizeof(double)); ttms.write(reinterpret_cast<char *>(&_exri), sizeof(double)); double rval, ival; for (np_int ei = 0; ei < _nlemt; ei++) { for (np_int ej = 0; ej < _nlemt; ej++) { rval = real(_am0m[ei][ej]); ival = imag(_am0m[ei][ej]); ttms.write(reinterpret_cast<char *>(&rval), sizeof(double)); ttms.write(reinterpret_cast<char *>(&ival), sizeof(double)); } } ttms.close(); } else { // Failed to open output file. Should never happen. printf("ERROR: could not open Transition Matrix file for writing.\n"); } } bool TransitionMatrix::operator ==(TransitionMatrix &other) { if (is != other.is) { return false; Loading Loading
src/include/TransitionMatrix.h +69 −3 Original line number Diff line number Diff line Loading @@ -48,19 +48,58 @@ class TransitionMatrix { /*! \brief Write the Transition Matrix to HDF5 binary output. * * This function takes care of the specific task of building a transition * matrix memory data structure from a binary input file formatted according * to the structure used by the original FORTRAN code. * This function takes care of the specific task of writing the transition * matrix memory data structure to a binary output file formatted according * to the HDF5 standard. * * \param file_name: `string` Name of the binary configuration data file. */ void write_hdf5(std::string file_name); /*! \brief Write transition matrix data to HDF5 binary output. * * This function takes care of the specific task of writing the transition * matrix memory data structure to a binary output file formatted according * to the HDF5 standard. It is designed to work for the case of clusters of * spheres. * * \param file_name: `string` Name of the binary configuration data file. * \param _nlemt: `np_int` Size of the matrix (2 * LE * (LE + 2)). * \param _lm: `int` Maximum field expansion order. * \param _vk: `double` Wave number in scale units. * \param _exri: `double` External medium refractive index. * \param _am0m: `complex double **` */ static void write_hdf5( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m ); /*! \brief Write the Transition Matrix to legacy binary output. * * \param file_name: `string` Name of the binary configuration data file. */ void write_legacy(std::string file_name); /*! \brief Write transition matrix data to HDF5 binary output. * * This function takes care of the specific task of writing the transition * matrix memory data structure to a binary output file formatted according * to the format used by the legacy FORTRAN code. It is designed to work for * the case of clusters of spheres. * * \param file_name: `string` Name of the binary configuration data file. * \param _nlemt: `np_int` Size of the matrix (2 * LE * (LE + 2)). * \param _lm: `int` Maximum field expansion order. * \param _vk: `double` Wave number in scale units. * \param _exri: `double` External medium refractive index. * \param _am0m: `complex double **` */ static void write_legacy( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m ); public: /*! \brief Default Transition Matrix instance constructor. * Loading Loading @@ -142,6 +181,33 @@ class TransitionMatrix { */ void write_binary(std::string file_name, std::string mode="LEGACY"); /*! \brief Write a Transition Matrix to a binary file without instanciating it. * * Transition Matrix data can take a large amount of memory. For such reason, attempts * to create TransitionMatrix instances only for writing purposes can create * unnecessary resource consumption and computing time to duplicate the data into * the output buffer. This function offers output to file as a static method. It * takes the arguments of a constructor together with the usual arguments to specify * the output file name and format, to write the required data directly to a file, * without creating a new TransitionMatrix instance. The implementation works for * TransitionMatrix objects built for the CLUSTER case. It belongs to the public class * interface and it calls the proper versions of `write_legacy()` and `write_hdf5()`, * depending on the requested output format. * * \param file_name: `string` Name of the file to be written. * \param _nlemt: `np_int` Size of the matrix (2 * LE * (LE + 2)). * \param _lm: `int` Maximum field expansion order. * \param _vk: `double` Wave number in scale units. * \param _exri: `double` External medium refractive index. * \param _am0m: `complex double **` * \param mode: `string` Binary encoding. Can be one of ["LEGACY", "HDF5"] . Optional * (default is "LEGACY"). */ static void write_binary( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m, std::string mode="LEGACY" ); /*! \brief Test whether two instances of TransitionMatrix are equal. * * Transition matrices can be the result of a calculation or of a file input operation, Loading
src/libnptm/TransitionMatrix.cpp +91 −11 Original line number Diff line number Diff line Loading @@ -218,6 +218,20 @@ void TransitionMatrix::write_binary(string file_name, string mode) { } } void TransitionMatrix::write_binary( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m, std::string mode ) { if (mode.compare("LEGACY") == 0) { write_legacy(file_name, _nlemt, _lm, _vk, _exri, _am0m); } else if (mode.compare("HDF5") == 0) { write_hdf5(file_name, _nlemt, _lm, _vk, _exri, _am0m); } else { string message = "Unknown format mode: \"" + mode + "\""; throw UnrecognizedFormatException(message); } } void TransitionMatrix::write_hdf5(string file_name) { if (is == 1 || is == 1111) { List<string> rec_name_list(1); Loading @@ -237,17 +251,10 @@ void TransitionMatrix::write_hdf5(string file_name) { rec_type_list.append("FLOAT64_(1)"); rec_ptr_list.append(&exri); rec_name_list.append("ELEMENTS"); str_type = "FLOAT64_(" + to_string(shape[0]) + "," + to_string(2 * shape[1]) + ")"; str_type = "COMPLEX128_(" + to_string(shape[0]) + "," + to_string(shape[1]) + ")"; rec_type_list.append(str_type); // The (N x M) matrix of complex is converted to a (N x 2M) matrix of double, // where REAL(E_i,j) -> E_i,(2 j) and IMAG(E_i,j) -> E_i,(2 j + 1) int num_elements = 2 * shape[0] * shape[1]; double *ptr_elements = new double[num_elements](); for (int ei = 0; ei < num_elements / 2; ei++) { ptr_elements[2 * ei] = real(elements[ei]); ptr_elements[2 * ei + 1] = imag(elements[ei]); } rec_ptr_list.append(ptr_elements); dcomplex *p_first = elements; rec_ptr_list.append(p_first); if (is == 1111) { rec_name_list.append("RADIUS"); rec_type_list.append("FLOAT64_(1)"); Loading @@ -264,7 +271,7 @@ void TransitionMatrix::write_hdf5(string file_name) { hdf_file->write(rec_names[ri], rec_types[ri], rec_pointers[ri]); hdf_file->close(); delete[] ptr_elements; p_first = NULL; delete[] rec_names; delete[] rec_types; delete[] rec_pointers; Loading @@ -275,6 +282,52 @@ void TransitionMatrix::write_hdf5(string file_name) { } } void TransitionMatrix::write_hdf5( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m ) { int is = 1; List<string> rec_name_list(1); List<string> rec_type_list(1); List<void *> rec_ptr_list(1); string str_type, str_name; rec_name_list.set(0, "IS"); rec_type_list.set(0, "INT32_(1)"); rec_ptr_list.set(0, &is); rec_name_list.append("L_MAX"); rec_type_list.append("INT32_(1)"); rec_ptr_list.append(&_lm); rec_name_list.append("VK"); rec_type_list.append("FLOAT64_(1)"); rec_ptr_list.append(&_vk); rec_name_list.append("EXRI"); rec_type_list.append("FLOAT64_(1)"); rec_ptr_list.append(&_exri); rec_name_list.append("ELEMENTS"); str_type = "COMPLEX128_(" + to_string(_nlemt) + "," + to_string(_nlemt) + ")"; rec_type_list.append(str_type); // The (N x M) matrix of complex is converted to a (N x 2M) matrix of double, // where REAL(E_i,j) -> E_i,(2 j) and IMAG(E_i,j) -> E_i,(2 j + 1) dcomplex *p_first = _am0m[0]; rec_ptr_list.append(p_first); string *rec_names = rec_name_list.to_array(); string *rec_types = rec_type_list.to_array(); void **rec_pointers = rec_ptr_list.to_array(); const int rec_num = rec_name_list.length(); FileSchema schema(rec_num, rec_types, rec_names); HDFFile *hdf_file = HDFFile::from_schema(schema, file_name, H5F_ACC_TRUNC); for (int ri = 0; ri < rec_num; ri++) hdf_file->write(rec_names[ri], rec_types[ri], rec_pointers[ri]); hdf_file->close(); p_first = NULL; delete[] rec_names; delete[] rec_types; delete[] rec_pointers; delete hdf_file; } void TransitionMatrix::write_legacy(string file_name) { fstream ttms; if (is == 1111 || is == 1) { Loading Loading @@ -308,6 +361,33 @@ void TransitionMatrix::write_legacy(string file_name) { } } void TransitionMatrix::write_legacy( std::string file_name, np_int _nlemt, int _lm, double _vk, double _exri, dcomplex **_am0m ) { fstream ttms; int is = 1; ttms.open(file_name, ios::binary | ios::out); if (ttms.is_open()) { ttms.write(reinterpret_cast<char *>(&is), sizeof(int)); ttms.write(reinterpret_cast<char *>(&_lm), sizeof(int)); ttms.write(reinterpret_cast<char *>(&_vk), sizeof(double)); ttms.write(reinterpret_cast<char *>(&_exri), sizeof(double)); double rval, ival; for (np_int ei = 0; ei < _nlemt; ei++) { for (np_int ej = 0; ej < _nlemt; ej++) { rval = real(_am0m[ei][ej]); ival = imag(_am0m[ei][ej]); ttms.write(reinterpret_cast<char *>(&rval), sizeof(double)); ttms.write(reinterpret_cast<char *>(&ival), sizeof(double)); } } ttms.close(); } else { // Failed to open output file. Should never happen. printf("ERROR: could not open Transition Matrix file for writing.\n"); } } bool TransitionMatrix::operator ==(TransitionMatrix &other) { if (is != other.is) { return false; Loading
