Implement static output for single sphere TM (281e5c6c) · Commits · Giacomo Mulas / NP_TMcode

src/include/TransitionMatrix.h

+73 −4

Original line number	Diff line number	Diff line
		@@ -60,8 +60,8 @@ class TransitionMatrix {
		*
		* 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.
		* to the HDF5 standard without a pre-existing instance. It is designed to
		* work for the case of a cluster 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)).
		@@ -75,13 +75,33 @@ class TransitionMatrix {
		double _exri, dcomplex **_am0m
		);

		/*! \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 without a pre-existing instance. It is designed to
		* work for the case of a single sphere.
		*
		* \param file_name: `string` Name of the binary configuration data file.
		* \param _lm: `int` Maximum field expansion order.
		* \param _vk: `double` Wave number in scale units.
		* \param _exri: `double` External medium refractive index.
		* \param _rmi: `complex double **`
		* \param _rei: `complex double **`
		* \param _sphere_radius: `double` Radius of the sphere.
		*/
		static void write_hdf5(
		std::string file_name, int _lm, double _vk, double _exri,
		dcomplex _rmi, dcomplex _rei, double _sphere_radius
		);

		/*! \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.
		/*! \brief Write transition matrix data to binary output using legacy format.
		*
		* This function takes care of the specific task of writing the transition
		* matrix memory data structure to a binary output file formatted according
		@@ -100,6 +120,26 @@ class TransitionMatrix {
		double _exri, dcomplex **_am0m
		);

		/*! \brief Write transition matrix data to binary output using legacy format.
		*
		* 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 original code structure without a pre-existing instance. It is designed
		* to work for the case of a single sphere.
		*
		* \param file_name: `string` Name of the binary configuration data file.
		* \param _lm: `int` Maximum field expansion order.
		* \param _vk: `double` Wave number in scale units.
		* \param _exri: `double` External medium refractive index.
		* \param _rmi: `complex double **`
		* \param _rei: `complex double **`
		* \param _sphere_radius: `double` Radius of the sphere.
		*/
		static void write_legacy(
		std::string file_name, int _lm, double _vk, double _exri,
		dcomplex _rmi, dcomplex _rei, double _sphere_radius
		);

		public:
		/*! \brief Default Transition Matrix instance constructor.
		*
		@@ -181,7 +221,7 @@ 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.
		/*! \brief Write a cluster 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
		@@ -208,6 +248,35 @@ class TransitionMatrix {
		double _exri, dcomplex **_am0m, std::string mode="LEGACY"
		);

		/*! \brief Write a single sphere 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 single sphere 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 _lm: `int` Maximum field expansion order.
		* \param _vk: `double` Wave number in scale units.
		* \param _exri: `double` External medium refractive index.
		* \param _rmi: `complex double **`
		* \param _rei: `complex double **`
		* \param _sphere_radius: `double` Radius of the sphere.
		* \param mode: `string` Binary encoding. Can be one of ["LEGACY", "HDF5"] . Optional
		* (default is "LEGACY").
		*/
		static void write_binary(
		std::string file_name, int _lm, double _vk, double _exri,
		dcomplex _rmi, dcomplex _rei, double _sphere_radius,
		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,

src/libnptm/TransitionMatrix.cpp

+105 −6

Original line number	Diff line number	Diff line
		@@ -94,7 +94,7 @@ TransitionMatrix::TransitionMatrix(
		}
		}

		TransitionMatrix* TransitionMatrix::from_binary(string file_name, string mode) {
		TransitionMatrix* TransitionMatrix::from_binary(std::string file_name, std::string mode) {
		TransitionMatrix *tm = NULL;
		if (mode.compare("LEGACY") == 0) {
		tm = TransitionMatrix::from_legacy(file_name);
		@@ -107,7 +107,7 @@ TransitionMatrix* TransitionMatrix::from_binary(string file_name, string mode) {
		return tm;
		}

		TransitionMatrix* TransitionMatrix::from_hdf5(string file_name) {
		TransitionMatrix* TransitionMatrix::from_hdf5(std::string file_name) {
		TransitionMatrix *tm = NULL;
		unsigned int flags = H5F_ACC_RDONLY;
		HDFFile *hdf_file = new HDFFile(file_name, flags);
		@@ -160,7 +160,7 @@ TransitionMatrix* TransitionMatrix::from_hdf5(string file_name) {
		return tm;
		}

		TransitionMatrix* TransitionMatrix::from_legacy(string file_name) {
		TransitionMatrix* TransitionMatrix::from_legacy(std::string file_name) {
		fstream ttms;
		TransitionMatrix *tm = NULL;
		ttms.open(file_name, ios::binary \| ios::in);
		@@ -207,7 +207,7 @@ TransitionMatrix* TransitionMatrix::from_legacy(string file_name) {
		return tm;
		}

		void TransitionMatrix::write_binary(string file_name, string mode) {
		void TransitionMatrix::write_binary(std::string file_name, std::string mode) {
		if (mode.compare("LEGACY") == 0) {
		write_legacy(file_name);
		} else if (mode.compare("HDF5") == 0) {
		@@ -232,7 +232,22 @@ void TransitionMatrix::write_binary(
		}
		}

		void TransitionMatrix::write_hdf5(string file_name) {
		void TransitionMatrix::write_binary(
		std::string file_name, int _lm, double _vk, double _exri,
		dcomplex _rmi, dcomplex _rei, double _sphere_radius,
		std::string mode
		) {
		if (mode.compare("LEGACY") == 0) {
		write_legacy(file_name, _lm, _vk, _exri, _rmi, _rei, _sphere_radius);
		} else if (mode.compare("HDF5") == 0) {
		write_hdf5(file_name, _lm, _vk, _exri, _rmi, _rei, _sphere_radius);
		} else {
		string message = "Unknown format mode: \"" + mode + "\"";
		throw UnrecognizedFormatException(message);
		}
		}

		void TransitionMatrix::write_hdf5(std::string file_name) {
		if (is == 1 \|\| is == 1111) {
		List<string> rec_name_list(1);
		List<string> rec_type_list(1);
		@@ -328,7 +343,58 @@ void TransitionMatrix::write_hdf5(
		delete hdf_file;
		}

		void TransitionMatrix::write_legacy(string file_name) {
		void TransitionMatrix::write_hdf5(
		std::string file_name, int _lm, double _vk, double _exri,
		dcomplex _rmi, dcomplex _rei, double _sphere_radius
		) {
		int is = 1111;
		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);
		dcomplex _elements = new dcomplex[2 _lm]();
		for (int ei = 0; ei < _lm; ei++) {
		_elements[2 * ei] = -1.0 / _rmi[ei][0];
		_elements[2 * ei + 1] = -1.0 / _rei[ei][0];
		}
		rec_name_list.append("ELEMENTS");
		str_type = "COMPLEX128_(" + to_string(_lm) + "," + to_string(2) + ")";
		rec_type_list.append(str_type);
		rec_ptr_list.append(_elements);
		rec_name_list.append("RADIUS");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&_sphere_radius);

		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();

		delete[] _elements;
		delete[] rec_names;
		delete[] rec_types;
		delete[] rec_pointers;
		delete hdf_file;
		}

		void TransitionMatrix::write_legacy(std::string file_name) {
		fstream ttms;
		if (is == 1111 \|\| is == 1) {
		ttms.open(file_name, ios::binary \| ios::out);
		@@ -388,6 +454,39 @@ void TransitionMatrix::write_legacy(
		}
		}

		void TransitionMatrix::write_legacy(
		std::string file_name, int _lm, double _vk, double _exri,
		dcomplex _rmi, dcomplex _rei, double _sphere_radius
		) {
		fstream ttms;
		int is = 1111;
		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;
		dcomplex element;
		for (int ei = 0; ei < _lm; ei++) {
		element = -1.0 / _rmi[ei][0];
		rval = real(element);
		ival = imag(element);
		ttms.write(reinterpret_cast<char *>(&rval), sizeof(double));
		ttms.write(reinterpret_cast<char *>(&ival), sizeof(double));
		element = -1.0 / _rei[ei][0];
		rval = real(element);
		ival = imag(element);
		ttms.write(reinterpret_cast<char *>(&rval), sizeof(double));
		ttms.write(reinterpret_cast<char *>(&ival), sizeof(double));
		}
		ttms.write(reinterpret_cast<char *>(&_sphere_radius), 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;