Define a TransitionMatrix class (dfe9251b) · Commits · Giacomo Mulas / NP_TMcode

src/cluster/cluster.cpp

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		@@ -2,8 +2,8 @@
		*
		* \brief Implementation of the calculation for a cluster of spheres.
		*/
		#include <cstdio>
		#include <complex>
		#include <cstdio>
		#include <exception>
		#include <fstream>
		#include <string>

src/include/TransitionMatrix.h

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		/*! \file TransitionMatrix.h
		*
		* \brief Representation of the Transition Matrix.
		*/

		#ifndef INCLUDE_TRANSITIONMATRIX_H_
		#define INCLUDE_TRANSITIONMATRIX_H_

		/**
		* \brief Exception for unrecognized file formats.
		*/
		class UnrecognizedFormatException: public std::exception {
		protected:
		//! Description of the problem.
		std::string message;
		public:
		/**
		* \brief Exception instance constructor.
		*
		* \param problem: `string` Description of the problem that occurred.
		*/
		UnrecognizedFormatException(std::string problem) { message = problem; }
		/**
		* \brief Exception message.
		*/
		virtual const char* what() const throw() {
		return message.c_str();
		}
		};

		/*! \brief Class to represent the Transition Matrix.
		*/
		class TransitionMatrix {
		protected:
		//! Matrix type identifier.
		int is;
		//! Maximum field expansion order.
		int l_max;
		//! Wave number in scale units.
		double vk;
		//! External medium refractive index.
		double exri;
		//! Vectorized matrix elements.
		std::complex<double> *elements;
		//! Sphere radius.
		double sphere_radius;
		//! Matrix shape
		int *shape;

		/*! \brief Write the Transition Matrix to HDF5 binary output.
		*
		* \param file_name: `string` Name of the binary configuration data file.
		*/
		void write_hdf5(std::string file_name);

		/*! \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);
		public:
		/*! \brief Transition Matrix instance constructor for single sphere.
		*
		* \param _lm: `int` Maximum field expansion order.
		* \param _vk: `double` Wave number in scale units.
		* \param _exri: `double` External medium refractive index.
		* \param _rmi: Matrix of complex.
		* \param _rei: Matrix of complex.
		* \param _sphere_radius: `double` Radius of the sphere.
		*/
		TransitionMatrix(
		int _lm, double _vk, double _exri, std::complex<double> **_rmi,
		std::complex<double> **_rei, double _sphere_radius
		);

		/*! \brief Transition Matrix instance constructor for a cluster of spheres.
		*
		* \param _nlemt: `int` Size of the matrix (2 * LE * (LE + 2)).
		* \param _lm: `int` Maximum field expansion order.
		* \param _vk: `double`
		* \param _exri: `double`
		* \param _am0m: Matrix of complex.
		*/
		TransitionMatrix(int _nlemt, int _lm, double _vk, double _exri, std::complex<double> **am0m);

		/*! \brief Transition Matrix instance destroyer.
		*/
		~TransitionMatrix();

		/*! \brief Write the Transition Matrix to a binary file.
		*
		* \param file_name: `string` Name of the file to be written.
		* \param mode: `string` Binary encoding. Can be one of ["LEGACY", "HDF5"] . Optional
		* (default is "LEGACY").
		*/
		void write_binary(std::string file_name, std::string mode="LEGACY");
		};

		#endif

src/libnptm/TransitionMatrix.cpp

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		/*! \file TransitionMatrix.cpp
		*
		* \brief Implementation of the Transition Matrix structure.
		*/
		#include <complex>
		#include <exception>
		#include <fstream>

		#ifndef INCLUDE_TRANSITIONMATRIX_H_
		#include "../include/TransitionMatrix.h"
		#endif

		using namespace std;

		TransitionMatrix::~TransitionMatrix() {
		if (elements != NULL) delete[] elements;
		if (shape != NULL) delete[] shape;
		}

		TransitionMatrix::TransitionMatrix(
		int _lm, double _vk, double _exri, complex<double> **_rmi,
		complex<double> **_rei, double _sphere_radius
		) {
		is = 1111;
		shape = new int[2];
		shape[0] = _lm;
		shape[1] = 2;
		l_max = _lm;
		vk = _vk;
		exri = _exri;
		sphere_radius = _sphere_radius;
		elements = new complex<double>[2 * l_max]();
		for (int ei = 0; ei < l_max; ei++) {
		elements[2 * ei] = -1.0 / _rmi[ei][0];
		elements[2 * ei + 1] = -1.0 / _rei[ei][0];
		}
		}

		TransitionMatrix::TransitionMatrix(
		int _nlemt, int _lm, double _vk, double _exri,
		std::complex<double> **am0m
		) {
		is = 1;
		shape = new int[2];
		shape[0] = _nlemt;
		shape[1] = _nlemt;
		l_max = _lm;
		vk = _vk;
		exri = _exri;
		sphere_radius = 0.0;
		elements = new complex<double>[_nlemt * _nlemt]();
		for (int ei = 0; ei < _nlemt; ei++) {
		for (int ej = 0; ej < _nlemt; ej++) elements[_nlemt * ei + ej] = am0m[ei][ej];
		}
		}

		void TransitionMatrix::write_binary(string file_name, string mode) {
		if (mode.compare("LEGACY") == 0) {
		write_legacy(file_name);
		} else if (mode.compare("HDF5") == 0) {
		write_hdf5(file_name);
		} else {
		string message = "Unknown format mode: \"" + mode + "\"";
		throw UnrecognizedFormatException(message);
		}
		}

		void TransitionMatrix::write_hdf5(string file_name) {
		// TODO: needs implementation.
		return;
		}

		void TransitionMatrix::write_legacy(string file_name) {
		fstream ttms;
		if (is == 1111 \|\| 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 *>(&l_max), sizeof(int));
		ttms.write(reinterpret_cast<char *>(&vk), sizeof(double));
		ttms.write(reinterpret_cast<char *>(&exri), sizeof(double));
		}
		} else {
		string message = "Unrecognized matrix data.";
		throw UnrecognizedFormatException(message);
		}
		if (ttms.is_open()) {
		int num_elements = shape[0] * shape[1];
		for (int ei = 0; ei < num_elements; ei++) {
		complex<double> element1 = elements[ei];
		double vreal, vimag;
		vreal = element1.real();
		vimag = element1.imag();
		ttms.write(reinterpret_cast<char *>(&vreal), sizeof(double));
		ttms.write(reinterpret_cast<char *>(&vimag), sizeof(double));
		}
		if (is == 1111) {
		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");
		}
		}

src/sphere/Makefile

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		@@ -17,8 +17,8 @@ edfb: edfb.o
		sph: sph.o
		$(FC) $(FCFLAGS) -o $(BUILDDIR)/sph $(BUILDDIR)/sph.o $(LDFLAGS)

		np_sphere: $(BUILDDIR)/np_sphere.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/sphere.o
		$(CXX) $(CXXFLAGS) -o $(BUILDDIR)/np_sphere $(BUILDDIR)/np_sphere.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/sphere.o $(CXXLDFLAGS)
		np_sphere: $(BUILDDIR)/np_sphere.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/sphere.o $(BUILDDIR)/TransitionMatrix.o
		$(CXX) $(CXXFLAGS) -o $(BUILDDIR)/np_sphere $(BUILDDIR)/np_sphere.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/sphere.o $(BUILDDIR)/TransitionMatrix.o $(CXXLDFLAGS)

		#$(BUILDDIR)/np_sphere.o:
		# $(CXX) $(CXXFLAGS) -c np_sphere.cpp -o $(BUILDDIR)/np_sphere.o

src/sphere/sphere.cpp

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		@@ -2,10 +2,11 @@
		*
		* \brief Implementation of the single sphere calculation.
		*/
		#include <complex>
		#include <cstdio>
		#include <exception>
		#include <fstream>
		#include <string>
		#include <complex>

		#ifndef INCLUDE_CONFIGURATION_H_
		#include "../include/Configuration.h"
		@@ -19,6 +20,10 @@
		#include "../include/sph_subs.h"
		#endif

		#ifndef INCLUDE_TRANSITIONMATRIX_H_
		#include "../include/TransitionMatrix.h"
		#endif

		using namespace std;

		/*! \brief C++ implementation of SPH
		@@ -286,34 +291,9 @@ void sphere(string config_file, string data_file, string output_path) {
		} // i132
		if (sconf->idfc >= 0 and nsph == 1 and jxi == gconf->jwtm) {
		// This is the condition that writes the transition matrix to output.
		int is = 1111;
		fstream ttms;
		TransitionMatrix ttms(gconf->l_max, vk, exri, c1->rmi, c1->rei, sconf->radii_of_spheres[0]);
		string ttms_name = output_path + "/c_TTMS";
		ttms.open(ttms_name.c_str(), ios::binary \| ios::out);
		if (ttms.is_open()) {
		ttms.write(reinterpret_cast<char *>(&is), sizeof(int));
		ttms.write(reinterpret_cast<char *>(&(gconf->l_max)), sizeof(int));
		ttms.write(reinterpret_cast<char *>(&vk), sizeof(double));
		ttms.write(reinterpret_cast<char *>(&exri), sizeof(double));
		for (int lmi = 0; lmi < gconf->l_max; lmi++) {
		complex<double> element1 = -1.0 / c1->rmi[lmi][0];
		complex<double> element2 = -1.0 / c1->rei[lmi][0];
		double vreal, vimag;
		vreal = element1.real();
		vimag = element1.imag();
		ttms.write(reinterpret_cast<char *>(&vreal), sizeof(double));
		ttms.write(reinterpret_cast<char *>(&vimag), sizeof(double));
		vreal = element2.real();
		vimag = element2.imag();
		ttms.write(reinterpret_cast<char *>(&vreal), sizeof(double));
		ttms.write(reinterpret_cast<char *>(&vimag), sizeof(double));
		}
		ttms.write(reinterpret_cast<char *>(&(sconf->radii_of_spheres[0])), sizeof(double));
		ttms.close();
		} else { // Failed to open output file. Should never happen.
		printf("ERROR: could not open TTMS file.\n");
		tppoan.close();
		}
		ttms.write_binary(ttms_name, "LEGACY");
		}
		double cs0 = 0.25 * vk * vk * vk / half_pi;
		//printf("DEBUG: cs0 = %lE\n", cs0);