scatt/nmie-wrapper.cc

///
/// @file   nmie-wrapper.cc
/// @author Ladutenko Konstantin <kostyfisik at gmail (.) com>
/// @date   Tue Sep  3 00:38:27 2013
/// @copyright 2013 Ladutenko Konstantin
///
/// nmie-wrapper is free software: you can redistribute it and/or modify
/// it under the terms of the GNU General Public License as published by
/// the Free Software Foundation, either version 3 of the License, or
/// (at your option) any later version.
///
/// nmie-wrapper is distributed in the hope that it will be useful,
/// but WITHOUT ANY WARRANTY; without even the implied warranty of
/// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
/// GNU General Public License for more details.
///
/// You should have received a copy of the GNU General Public License
/// along with nmie-wrapper.  If not, see <http://www.gnu.org/licenses/>.
///
/// nmie-wrapper uses nmie.c from scattnlay by Ovidio Pena
/// <ovidio@bytesfall.com> as a linked library. He has an additional condition to 
/// his library:
//    The only additional condition is that we expect that all publications         //
//    describing  work using this software , or all commercial products             //
//    using it, cite the following reference:                                       //
//    [1] O. Pena and U. Pal, "Scattering of electromagnetic radiation by           //
//        a multilayered sphere," Computer Physics Communications,                  //
//        vol. 180, Nov. 2009, pp. 2348-2354.                                       //
///
/// @brief  Wrapper class around nMie function for ease of use
///
#include "nmie-wrapper.h"
//#include "nmie.h"
#include <array>
#include <algorithm>
#include <cstdio>
#include <cstdlib>
#include <stdexcept>
#include <vector>

namespace nmie {  
  //helpers
  template<class T> inline T pow2(const T value) {return value*value;}
#define round(x) ((x) >= 0 ? (int)((x) + 0.5):(int)((x) - 0.5))
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  //emulate C call.
  int nMie_wrapper(int L, std::vector<double> x, std::vector<std::complex<double> > m,
         int nTheta, std::vector<double> Theta,
         double *Qext, double *Qsca, double *Qabs, double *Qbk, double *Qpr, double *g, double *Albedo,
		   std::vector<std::complex<double> >& S1, std::vector<std::complex<double> >& S2) {
    
    if (x.size() != L || m.size() != L)
        throw std::invalid_argument("Declared number of layers do not fit x and m!");
    if (Theta.size() != nTheta)
        throw std::invalid_argument("Declared number of sample for Theta is not correct!");
    try {
      MultiLayerMie multi_layer_mie;  
      multi_layer_mie.SetWidthSP(x);
      multi_layer_mie.SetIndexSP(m);
      multi_layer_mie.SetAngles(Theta);
    
      multi_layer_mie.RunMieCalculations();

      *Qext = multi_layer_mie.GetQext();
      *Qsca = multi_layer_mie.GetQsca();
      *Qabs = multi_layer_mie.GetQabs();
      *Qbk = multi_layer_mie.GetQbk();
      *Qpr = multi_layer_mie.GetQpr();
      *g = multi_layer_mie.GetAsymmetryFactor();
      *Albedo = multi_layer_mie.GetAlbedo();
      S1 = multi_layer_mie.GetS1();
      S2 = multi_layer_mie.GetS2();
    } catch( const std::invalid_argument& ia ) {
      // Will catch if  multi_layer_mie fails or other errors.
      std::cerr << "Invalid argument: " << ia.what() << std::endl;
      return -1;
    }  

    return 0;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  double MultiLayerMie::GetQext() {
    if (!isMieCalculated_)
      throw std::invalid_argument("You should run calculations before result reques!");
    return Qext_;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  double MultiLayerMie::GetQabs() {
    if (!isMieCalculated_)
      throw std::invalid_argument("You should run calculations before result reques!");
    return Qabs_;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  double MultiLayerMie::GetQsca() {
    if (!isMieCalculated_)
      throw std::invalid_argument("You should run calculations before result reques!");
    return Qsca_;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  double MultiLayerMie::GetQbk() {
    if (!isMieCalculated_)
      throw std::invalid_argument("You should run calculations before result reques!");
    return Qbk_;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  double MultiLayerMie::GetQpr() {
    if (!isMieCalculated_)
      throw std::invalid_argument("You should run calculations before result reques!");
    return Qpr_;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  double MultiLayerMie::GetAsymmetryFactor() {
    if (!isMieCalculated_)
      throw std::invalid_argument("You should run calculations before result reques!");
    return asymmetry_factor_;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  double MultiLayerMie::GetAlbedo() {
    if (!isMieCalculated_)
      throw std::invalid_argument("You should run calculations before result reques!");
    return albedo_;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  std::vector<std::complex<double> > MultiLayerMie::GetS1() {
    return S1_;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  std::vector<std::complex<double> > MultiLayerMie::GetS2() {
    return S2_;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  void MultiLayerMie::SetAngles(std::vector<double> angles) {
    isMieCalculated_ = false;
    theta_.clear();
    for (auto value : angles) theta_.push_back(value);
  }  // end of SetAngles()
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  void MultiLayerMie::SetWidthSP(std::vector<double> size_parameter) {
    isMieCalculated_ = false;
    size_parameter_.clear();
    double prev_size_parameter = 0.0;
    for (auto layer_size_parameter : size_parameter) {
      if (layer_size_parameter <= 0.0)
        throw std::invalid_argument("Size parameter should be positive!");
      if (prev_size_parameter > layer_size_parameter) 
        throw std::invalid_argument
	  ("Size parameter for next layer should be larger than the previous one!");
      prev_size_parameter = layer_size_parameter;
      size_parameter_.push_back(layer_size_parameter);
    }
  }
  // end of void MultiLayerMie::SetWidthSP(...);
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  void MultiLayerMie::SetIndexSP(std::vector< std::complex<double> > index) {
    isMieCalculated_ = false;
    index_.clear();
    for (auto value : index) index_.push_back(value);
  }  // end of void MultiLayerMie::SetIndexSP(...);  
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  void MultiLayerMie::SetPEC(int layer_position) {
    if (layer_position < 0)
      throw std::invalid_argument("Error! Layers are numbered from 0!");
    PEC_layer_position_ = layer_position;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  void MultiLayerMie::SetMaxTermsNumber(int nmax) {
    nmax_ = nmax;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  void MultiLayerMie::GenerateSizeParameter() {
    size_parameter_.clear();
    double radius = 0.0;
    for (auto width : target_width_) {
      radius += width;
      size_parameter_.push_back(2*PI*radius / wavelength_);
    }
    for (auto width : coating_width_) {
      radius += width;
      size_parameter_.push_back(2*PI*radius / wavelength_);
    }
    total_radius_ = radius;
  }  // end of void MultiLayerMie::GenerateSizeParameter();
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  double MultiLayerMie::GetTotalRadius() {
    if (total_radius_ == 0) GenerateSizeParameter();
    return total_radius_;      
  }  // end of double MultiLayerMie::GetTotalRadius();
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  std::vector< std::array<double,5> >
  MultiLayerMie::GetSpectra(double from_WL, double to_WL, int samples) {
    std::vector< std::array<double,5> > spectra;
    double step_WL = (to_WL - from_WL)/ static_cast<double>(samples);
    double wavelength_backup = wavelength_;
    long fails = 0;
    for (double WL = from_WL; WL < to_WL; WL += step_WL) {
      double Qext, Qsca, Qabs, Qbk;
      wavelength_ = WL;
      try {
        RunMieCalculations();
      } catch( const std::invalid_argument& ia ) {
        fails++;
        continue;
      }
      //printf("%3.1f ",WL);
      spectra.push_back({wavelength_, Qext, Qsca, Qabs, Qbk});
    }  // end of for each WL in spectra
    printf("fails %li\n",fails);
    wavelength_ = wavelength_backup;
    return spectra;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  // Calculate Nstop - equation (17)
  //
  void MultiLayerMie::Nstop() {
    const double& xL = size_parameter_.back();
    if (xL <= 8) {
      nmax_ = round(xL + 4*pow(xL, 1/3) + 1);
    } else if (xL <= 4200) {
      nmax_ = round(xL + 4.05*pow(xL, 1/3) + 2);
    } else {
      nmax_ = round(xL + 4*pow(xL, 1/3) + 2);
    }    
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  void MultiLayerMie::Nmax(int first_layer) {
    int ri, riM1;
    const std::vector<double>& x = size_parameter_;
    const std::vector<std::complex<double> >& m = index_;
    const int& pl = PEC_layer_position_;
    Nstop();  // Set initial nmax_ value
    for (int i = first_layer; i < x.size(); i++) {
      if (i > PEC_layer_position_) 
	ri = round(std::abs(x[i]*m[i]));
      else 
	ri = 0;      
      nmax_ = std::max(nmax_, ri);
      // first layer is pec, if pec is present
      if ((i > first_layer) && ((i - 1) > PEC_layer_position_)) 
	riM1 = round(std::abs(x[i - 1]* m[i]));
      else 
	riM1 = 0;      
      nmax_ = std::max(nmax_, riM1);
    }
    nmax_ += 15;  // Final nmax_ value
  }
  //**********************************************************************************//
  // This function calculates the spherical Bessel (jn) and Hankel (h1n) functions    //
  // and their derivatives for a given complex value z. See pag. 87 B&H.              //
  //                                                                                  //
  // Input parameters:                                                                //
  //   z: Real argument to evaluate jn and h1n                                        //
  //   nmax_: Maximum number of terms to calculate jn and h1n                          //
  //                                                                                  //
  // Output parameters:                                                               //
  //   jn, h1n: Spherical Bessel and Hankel functions                                 //
  //   jnp, h1np: Derivatives of the spherical Bessel and Hankel functions            //
  //                                                                                  //
  // The implementation follows the algorithm by I.J. Thompson and A.R. Barnett,      //
  // Comp. Phys. Comm. 47 (1987) 245-257.                                             //
  //                                                                                  //
  // Complex spherical Bessel functions from n=0..nmax_-1 for z in the upper half      //
  // plane (Im(z) > -3).                                                              //
  //                                                                                  //
  //     j[n]   = j/n(z)                Regular solution: j[0]=sin(z)/z               //
  //     j'[n]  = d[j/n(z)]/dz                                                        //
  //     h1[n]  = h[0]/n(z)             Irregular Hankel function:                    //
  //     h1'[n] = d[h[0]/n(z)]/dz                h1[0] = j0(z) + i*y0(z)              //
  //                                                   = (sin(z)-i*cos(z))/z          //
  //                                                   = -i*exp(i*z)/z                //
  // Using complex CF1, and trigonometric forms for n=0 solutions.                    //
  //**********************************************************************************//
  void MultiLayerMie::sbesjh(std::complex<double> z,
			     std::vector<std::complex<double> >& jn,
			     std::vector<std::complex<double> >& jnp,
			     std::vector<std::complex<double> >& h1n,
			     std::vector<std::complex<double> >& h1np) {
    const int limit = 20000;
    const double accur = 1.0e-12;
    const double tm30 = 1e-30;

    double absc;
    std::complex<double> zi, w;
    std::complex<double> pl, f, b, d, c, del, jn0, jndb, h1nldb, h1nbdb;

    absc = std::abs(std::real(z)) + std::abs(std::imag(z));
    if ((absc < accur) || (std::imag(z) < -3.0)) {
      throw std::invalid_argument("TODO add error description for condition if ((absc < accur) || (std::imag(z) < -3.0))");
    }

    zi = 1.0/z;
    w = zi + zi;

    pl = double(nmax_)*zi;

    f = pl + zi;
    b = f + f + zi;
    d = 0.0;
    c = f;
    for (int n = 0; n < limit; n++) {
      d = b - d;
      c = b - 1.0/c;

      absc = std::abs(std::real(d)) + std::abs(std::imag(d));
      if (absc < tm30) {
	d = tm30;
      }

      absc = std::abs(std::real(c)) + std::abs(std::imag(c));
      if (absc < tm30) {
	c = tm30;
      }

      d = 1.0/d;
      del = d*c;
      f = f*del;
      b += w;

      absc = std::abs(std::real(del - 1.0)) + std::abs(std::imag(del - 1.0));

      if (absc < accur) {
	// We have obtained the desired accuracy
	break;
      }
    }

    if (absc > accur) {
      throw std::invalid_argument("We were not able to obtain the desired accuracy");
    }

    jn[nmax_ - 1] = tm30;
    jnp[nmax_ - 1] = f*jn[nmax_ - 1];

    // Downward recursion to n=0 (N.B.  Coulomb Functions)
    for (int n = nmax_ - 2; n >= 0; n--) {
      jn[n] = pl*jn[n + 1] + jnp[n + 1];
      jnp[n] = pl*jn[n] - jn[n + 1];
      pl = pl - zi;
    }

    // Calculate the n=0 Bessel Functions
    jn0 = zi*std::sin(z);
    h1n[0] = std::exp(std::complex<double>(0.0, 1.0)*z)*zi*(-std::complex<double>(0.0, 1.0));
    h1np[0] = h1n[0]*(std::complex<double>(0.0, 1.0) - zi);

    // Rescale j[n], j'[n], converting to spherical Bessel functions.
    // Recur   h1[n], h1'[n] as spherical Bessel functions.
    w = 1.0/jn[0];
    pl = zi;
    for (int n = 0; n < nmax_; n++) {
      jn[n] = jn0*(w*jn[n]);
      jnp[n] = jn0*(w*jnp[n]) - zi*jn[n];
      if (n != 0) {
	h1n[n] = (pl - zi)*h1n[n - 1] - h1np[n - 1];

	// check if hankel is increasing (upward stable)
	if (std::abs(h1n[n]) < std::abs(h1n[n - 1])) {
	  jndb = z;
	  h1nldb = h1n[n];
	  h1nbdb = h1n[n - 1];
	}

	pl += zi;

	h1np[n] = -(pl*h1n[n]) + h1n[n - 1];
      }
    }
  }

  //**********************************************************************************//
  // This function calculates the spherical Bessel functions (bj and by) and the      //
  // logarithmic derivative (bd) for a given complex value z. See pag. 87 B&H.        //
  //                                                                                  //
  // Input parameters:                                                                //
  //   z: Complex argument to evaluate bj, by and bd                                  //
  //   nmax_: Maximum number of terms to calculate bj, by and bd                       //
  //                                                                                  //
  // Output parameters:                                                               //
  //   bj, by: Spherical Bessel functions                                             //
  //   bd: Logarithmic derivative                                                     //
  //**********************************************************************************//
  void MultiLayerMie::sphericalBessel(std::complex<double> z,
				      std::vector<std::complex<double> >& bj,
				      std::vector<std::complex<double> >& by,
				      std::vector<std::complex<double> >& bd) {
    std::vector<std::complex<double> > jn(nmax_), jnp(nmax_), h1n(nmax_), h1np(nmax_);
    sbesjh(z, jn, jnp, h1n, h1np);

    for (int n = 0; n < nmax_; n++) {
      bj[n] = jn[n];
      by[n] = (h1n[n] - jn[n])/std::complex<double>(0.0, 1.0);
      bd[n] = jnp[n]/jn[n] + 1.0/z;
    }
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  // Calculate an - equation (5)
  std::complex<double> MultiLayerMie::calc_an(int n, double XL, std::complex<double> Ha, std::complex<double> mL,
					      std::complex<double> PsiXL, std::complex<double> ZetaXL,
					      std::complex<double> PsiXLM1, std::complex<double> ZetaXLM1) {

    std::complex<double> Num = (Ha/mL + n/XL)*PsiXL - PsiXLM1;
    std::complex<double> Denom = (Ha/mL + n/XL)*ZetaXL - ZetaXLM1;

    return Num/Denom;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  // Calculate bn - equation (6)
  std::complex<double> MultiLayerMie::calc_bn(int n, double XL, std::complex<double> Hb, std::complex<double> mL,
					      std::complex<double> PsiXL, std::complex<double> ZetaXL,
					      std::complex<double> PsiXLM1, std::complex<double> ZetaXLM1) {

    std::complex<double> Num = (mL*Hb + n/XL)*PsiXL - PsiXLM1;
    std::complex<double> Denom = (mL*Hb + n/XL)*ZetaXL - ZetaXLM1;

    return Num/Denom;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  // Calculates S1 - equation (25a)
  std::complex<double> MultiLayerMie::calc_S1(int n, std::complex<double> an, std::complex<double> bn,
					      double Pi, double Tau) {
    return double(n + n + 1)*(Pi*an + Tau*bn)/double(n*n + n);
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  // Calculates S2 - equation (25b) (it's the same as (25a), just switches Pi and Tau)
  std::complex<double> MultiLayerMie::calc_S2(int n, std::complex<double> an, std::complex<double> bn,
					      double Pi, double Tau) {
    return calc_S1(n, an, bn, Tau, Pi);
  }
  //**********************************************************************************//
  // This function calculates the Riccati-Bessel functions (Psi and Zeta) for a       //
  // real argument (x).                                                               //
  // Equations (20a) - (21b)                                                          //
  //                                                                                  //
  // Input parameters:                                                                //
  //   x: Real argument to evaluate Psi and Zeta                                      //
  //   nmax: Maximum number of terms to calculate Psi and Zeta                        //
  //                                                                                  //
  // Output parameters:                                                               //
  //   Psi, Zeta: Riccati-Bessel functions                                            //
  //**********************************************************************************//
  void MultiLayerMie::calcPsiZeta(double x,
				  std::vector<std::complex<double> > D1,
				  std::vector<std::complex<double> > D3,
				  std::vector<std::complex<double> >& Psi,
				  std::vector<std::complex<double> >& Zeta) {
    //Upward recurrence for Psi and Zeta - equations (20a) - (21b)
    Psi[0] = std::complex<double>(sin(x), 0);
    Zeta[0] = std::complex<double>(sin(x), -cos(x));
    for (int n = 1; n <= nmax_; n++) {
      Psi[n] = Psi[n - 1]*(n/x - D1[n - 1]);
      Zeta[n] = Zeta[n - 1]*(n/x - D3[n - 1]);
    }
  }
  //**********************************************************************************//
  // This function calculates the logarithmic derivatives of the Riccati-Bessel       //
  // functions (D1 and D3) for a complex argument (z).                                //
  // Equations (16a), (16b) and (18a) - (18d)                                         //
  //                                                                                  //
  // Input parameters:                                                                //
  //   z: Complex argument to evaluate D1 and D3                                      //
  //   nmax_: Maximum number of terms to calculate D1 and D3                           //
  //                                                                                  //
  // Output parameters:                                                               //
  //   D1, D3: Logarithmic derivatives of the Riccati-Bessel functions                //
  //**********************************************************************************//
  void MultiLayerMie::calcD1D3(std::complex<double> z,
			       std::vector<std::complex<double> >& D1,
			       std::vector<std::complex<double> >& D3) {


    // Downward recurrence for D1 - equations (16a) and (16b)
    D1[nmax_] = std::complex<double>(0.0, 0.0);
    for (int n = nmax_; n > 0; n--) {
      D1[n - 1] = double(n)/z - 1.0/(D1[n] + double(n)/z);
    }

    // Upward recurrence for PsiZeta and D3 - equations (18a) - (18d)
    PsiZeta_[0] = 0.5*(1.0 - std::complex<double>(cos(2.0*z.real()), sin(2.0*z.real()))*exp(-2.0*z.imag()));
    D3[0] = std::complex<double>(0.0, 1.0);
    for (int n = 1; n <= nmax_; n++) {
      PsiZeta_[n] = PsiZeta_[n - 1]*(static_cast<double>(n)/z - D1[n - 1])*(static_cast<double>(n)/z- D3[n - 1]);
      D3[n] = D1[n] + std::complex<double>(0.0, 1.0)/PsiZeta_[n];
    }
  }
  //**********************************************************************************//
  // This function calculates Pi and Tau for all values of Theta.                     //
  // Equations (26a) - (26c)                                                          //
  //                                                                                  //
  // Input parameters:                                                                //
  //   nmax_: Maximum number of terms to calculate Pi and Tau                          //
  //   nTheta: Number of scattering angles                                            //
  //   Theta: Array containing all the scattering angles where the scattering         //
  //          amplitudes will be calculated                                           //
  //                                                                                  //
  // Output parameters:                                                               //
  //   Pi, Tau: Angular functions Pi and Tau, as defined in equations (26a) - (26c)   //
  //**********************************************************************************//
  void MultiLayerMie::calcPiTau(std::vector< std::vector<double> >& Pi,
				std::vector< std::vector<double> >& Tau) {
    //****************************************************//
    // Equations (26a) - (26c)                            //
    //****************************************************//
    std::vector<double> costheta(theta_.size(), 0.0);
    for (int t = 0; t < theta_.size(); t++) {	
      costheta[t] = cos(theta_[t]);
    }
    for (int n = 0; n < nmax_; n++) {
      for (int t = 0; t < theta_.size(); t++) {	
	if (n == 0) {
	  // Initialize Pi and Tau
	  Pi[n][t] = 1.0;
	  Tau[n][t] = (n + 1)*costheta[t]; 
	} else {
	  // Calculate the actual values
	  Pi[n][t] = ((n == 1) ? ((n + n + 1)*costheta[t]*Pi[n - 1][t]/n)
		   : (((n + n + 1)*costheta[t]*Pi[n - 1][t]
		       - (n + 1)*Pi[n - 2][t])/n));
	  Tau[n][t] = (n + 1)*costheta[t]*Pi[n][t] - (n + 2)*Pi[n - 1][t];
	}
      }
    }
  }
  //**********************************************************************************//
  // This function calculates the scattering coefficients required to calculate       //
  // both the near- and far-field parameters.                                         //
  //                                                                                  //
  // Input parameters:                                                                //
  //   L: Number of layers                                                            //
  //   pl: Index of PEC layer. If there is none just send -1                          //
  //   x: Array containing the size parameters of the layers [0..L-1]                 //
  //   m: Array containing the relative refractive indexes of the layers [0..L-1]     //
  //   nmax: Maximum number of multipolar expansion terms to be used for the          //
  //         calculations. Only use it if you know what you are doing, otherwise      //
  //         set this parameter to -1 and the function will calculate it.             //
  //                                                                                  //
  // Output parameters:                                                               //
  //   an, bn: Complex scattering amplitudes                                          //
  //                                                                                  //
  // Return value:                                                                    //
  //   Number of multipolar expansion terms used for the calculations                 //
  //**********************************************************************************//
  void MultiLayerMie::ScattCoeffs(std::vector<std::complex<double> >& an,
				  std::vector<std::complex<double> >& bn) {
    //************************************************************************//
    // Calculate the index of the first layer. It can be either 0 (default)   //
    // or the index of the outermost PEC layer. In the latter case all layers //
    // below the PEC are discarded.                                           //
    //************************************************************************//
    const std::vector<double>& x = size_parameter_;
    const std::vector<std::complex<double> >& m = index_;
    const int& pl = PEC_layer_position_;
    const int L = index_.size();
    // TODO, is it possible for PEC to have a zero index? If yes than is should be:
    // int fl = (pl > -1) ? pl : 0;
    int fl = (pl > 0) ? pl : 0;
    if (nmax_ <= 0) Nmax(fl);

    std::complex<double> z1, z2;
    //**************************************************************************//
    // Note that since Fri, Nov 14, 2014 all arrays start from 0 (zero), which  //
    // means that index = layer number - 1 or index = n - 1. The only exception //
    // are the arrays for representing D1, D3 and Q because they need a value   //
    // for the index 0 (zero), hence it is important to consider this shift     //
    // between different arrays. The change was done to optimize memory usage.  //
    //**************************************************************************//
    // Allocate memory to the arrays
    std::vector<std::vector<std::complex<double> > > D1_mlxl(L), D1_mlxlM1(L),
      D3_mlxl(L), D3_mlxlM1(L), Q(L), Ha(L), Hb(L);
    for (int l = 0; l < L; l++) {
      D1_mlxl[l].resize(nmax_ + 1);
      D1_mlxlM1[l].resize(nmax_ + 1);
      D3_mlxl[l].resize(nmax_ + 1);
      D3_mlxlM1[l].resize(nmax_ + 1);
      Q[l].resize(nmax_ + 1);
      Ha[l].resize(nmax_);
      Hb[l].resize(nmax_);
    }
    an.resize(nmax_);
    bn.resize(nmax_);
    PsiZeta_.resize(nmax_ + 1);
    std::vector<std::complex<double> > D1XL(nmax_ + 1), D3XL(nmax_ + 1), 
      PsiXL(nmax_ + 1), ZetaXL(nmax_ + 1);
    //*************************************************//
    // Calculate D1 and D3 for z1 in the first layer   //
    //*************************************************//
    if (fl == pl) {  // PEC layer
      for (int n = 0; n <= nmax_; n++) {
	D1_mlxl[fl][n] = std::complex<double>(0.0, -1.0);
	D3_mlxl[fl][n] = std::complex<double>(0.0, 1.0);
      }
    } else { // Regular layer
      z1 = x[fl]* m[fl];
      // Calculate D1 and D3
      calcD1D3(z1, D1_mlxl[fl], D3_mlxl[fl]);
    }
    //******************************************************************//
    // Calculate Ha and Hb in the first layer - equations (7a) and (8a) //
    //******************************************************************//
    for (int n = 0; n < nmax_; n++) {
      Ha[fl][n] = D1_mlxl[fl][n + 1];
      Hb[fl][n] = D1_mlxl[fl][n + 1];
    }
    //*****************************************************//
    // Iteration from the second layer to the last one (L) //
    //*****************************************************//
    for (int l = fl + 1; l < L; l++) {
      //************************************************************//
      //Calculate D1 and D3 for z1 and z2 in the layers fl+1..L     //
      //************************************************************//
      z1 = x[l]*m[l];
      z2 = x[l - 1]*m[l];
      //Calculate D1 and D3 for z1
      calcD1D3(z1, D1_mlxl[l], D3_mlxl[l]);
      //Calculate D1 and D3 for z2
      calcD1D3(z2, D1_mlxlM1[l], D3_mlxlM1[l]);
      //*********************************************//
      //Calculate Q, Ha and Hb in the layers fl+1..L //
      //*********************************************//
      // Upward recurrence for Q - equations (19a) and (19b)
      std::complex<double> Num, Denom;
      Num = exp(-2.0*(z1.imag() - z2.imag()))
	* std::complex<double>(cos(-2.0*z2.real()) - exp(-2.0*z2.imag()), sin(-2.0*z2.real()));
      Denom = std::complex<double>(cos(-2.0*z1.real()) - exp(-2.0*z1.imag()), sin(-2.0*z1.real()));
      Q[l][0] = Num/Denom;

      for (int n = 1; n <= nmax_; n++) {
	std::complex<double> Num, Denom;
	Num = (z1*D1_mlxl[l][n] + double(n))*(double(n) - z1*D3_mlxl[l][n - 1]);
	Denom = (z2*D1_mlxlM1[l][n] + double(n))*(double(n) - z2*D3_mlxlM1[l][n - 1]);
	Q[l][n] = (((x[l - 1]*x[l - 1])/(x[l]*x[l])* Q[l][n - 1])*Num)/Denom;
      }

      // Upward recurrence for Ha and Hb - equations (7b), (8b) and (12) - (15)
      for (int n = 1; n <= nmax_; n++) {
	std::complex<double> G1, G2;
	//Ha
	if ((l - 1) == pl) { // The layer below the current one is a PEC layer
	  G1 = -D1_mlxlM1[l][n];
	  G2 = -D3_mlxlM1[l][n];
	} else {
	  G1 = (m[l]*Ha[l - 1][n - 1]) - (m[l - 1]*D1_mlxlM1[l][n]);
	  G2 = (m[l]*Ha[l - 1][n - 1]) - (m[l - 1]*D3_mlxlM1[l][n]);
	}
	std::complex<double> Temp, Num, Denom;
	Temp = Q[l][n]*G1;
	Num = (G2*D1_mlxl[l][n]) - (Temp*D3_mlxl[l][n]);
	Denom = G2 - Temp;
	Ha[l][n - 1] = Num/Denom;
	//Hb
	if ((l - 1) == pl) { // The layer below the current one is a PEC layer
	  G1 = Hb[l - 1][n - 1];
	  G2 = Hb[l - 1][n - 1];
	} else {
	  G1 = (m[l - 1]*Hb[l - 1][n - 1]) - (m[l]*D1_mlxlM1[l][n]);
	  G2 = (m[l - 1]*Hb[l - 1][n - 1]) - (m[l]*D3_mlxlM1[l][n]);
	}

	Temp = Q[l][n]*G1;
	Num = (G2*D1_mlxl[l][n]) - (Temp* D3_mlxl[l][n]);
	Denom = (G2- Temp);
	Hb[l][n - 1] = (Num/ Denom);
      }
    }
    //**************************************//
    //Calculate D1, D3, Psi and Zeta for XL //
    //**************************************//
    // Calculate D1XL and D3XL
    calcD1D3(x[L - 1],  D1XL, D3XL);
    // Calculate PsiXL and ZetaXL
    calcPsiZeta(x[L - 1], D1XL, D3XL, PsiXL, ZetaXL);
    //*********************************************************************//
    // Finally, we calculate the scattering coefficients (an and bn) and   //
    // the angular functions (Pi and Tau). Note that for these arrays the  //
    // first layer is 0 (zero), in future versions all arrays will follow  //
    // this convention to save memory. (13 Nov, 2014)                      //
    //*********************************************************************//
    for (int n = 0; n < nmax_; n++) {
      //********************************************************************//
      //Expressions for calculating an and bn coefficients are not valid if //
      //there is only one PEC layer (ie, for a simple PEC sphere).          //
      //********************************************************************//
      if (pl < (L - 1)) {
	an[n] = calc_an(n + 1, x[L - 1], Ha[L - 1][n], m[L - 1], PsiXL[n + 1], ZetaXL[n + 1], PsiXL[n], ZetaXL[n]);
	bn[n] = calc_bn(n + 1, x[L - 1], Hb[L - 1][n], m[L - 1], PsiXL[n + 1], ZetaXL[n + 1], PsiXL[n], ZetaXL[n]);
      } else {
	an[n] = calc_an(n + 1, x[L - 1], std::complex<double>(0.0, 0.0), std::complex<double>(1.0, 0.0), PsiXL[n + 1], ZetaXL[n + 1], PsiXL[n], ZetaXL[n]);
	bn[n] = PsiXL[n + 1]/ZetaXL[n + 1];
      }
    }

  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  void MultiLayerMie::InitMieCalculations() {
    // Initialize the scattering parameters
    Qext_ = 0;
    Qsca_ = 0;
    Qabs_ = 0;
    Qbk_ = 0;
    Qpr_ = 0;
    asymmetry_factor_ = 0;
    albedo_ = 0;
    // Initialize the scattering amplitudes
    std::vector<std::complex<double> >	tmp1(theta_.size(),std::complex<double>(0.0, 0.0));
    S1_.swap(tmp1);
    S2_ = S1_;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  //**********************************************************************************//
  // This function calculates the actual scattering parameters and amplitudes         //
  //                                                                                  //
  // Input parameters:                                                                //
  //   L: Number of layers                                                            //
  //   pl: Index of PEC layer. If there is none just send -1                          //
  //   x: Array containing the size parameters of the layers [0..L-1]                 //
  //   m: Array containing the relative refractive indexes of the layers [0..L-1]     //
  //   nTheta: Number of scattering angles                                            //
  //   Theta: Array containing all the scattering angles where the scattering         //
  //          amplitudes will be calculated                                           //
  //   nmax_: Maximum number of multipolar expansion terms to be used for the          //
  //         calculations. Only use it if you know what you are doing, otherwise      //
  //         set this parameter to -1 and the function will calculate it              //
  //                                                                                  //
  // Output parameters:                                                               //
  //   Qext: Efficiency factor for extinction                                         //
  //   Qsca: Efficiency factor for scattering                                         //
  //   Qabs: Efficiency factor for absorption (Qabs = Qext - Qsca)                    //
  //   Qbk: Efficiency factor for backscattering                                      //
  //   Qpr: Efficiency factor for the radiation pressure                              //
  //   g: Asymmetry factor (g = (Qext-Qpr)/Qsca)                                      //
  //   Albedo: Single scattering albedo (Albedo = Qsca/Qext)                          //
  //   S1, S2: Complex scattering amplitudes                                          //
  //                                                                                  //
  // Return value:                                                                    //
  //   Number of multipolar expansion terms used for the calculations                 //
  //**********************************************************************************//
  void MultiLayerMie::RunMieCalculations() {
    if (size_parameter_.size() != index_.size())
      throw std::invalid_argument("Each size parameter should have only one index!");
    std::vector<std::complex<double> > an, bn;
    std::complex<double> Qbktmp(0.0, 0.0);
    const std::vector<double>& x = size_parameter_;
    const std::vector<std::complex<double> >& m = index_;
    // Calculate scattering coefficients
    ScattCoeffs(an, bn);

    // std::vector< std::vector<double> > Pi(nmax_), Tau(nmax_);
    std::vector< std::vector<double> > Pi, Tau;
    Pi.resize(nmax_);
    Tau.resize(nmax_);
    for (int i =0; i< nmax_; ++i) {
      Pi[i].resize(theta_.size());
      Tau[i].resize(theta_.size());
    }
    calcPiTau(Pi, Tau);
    InitMieCalculations();

    // By using downward recurrence we avoid loss of precision due to float rounding errors
    // See: https://docs.oracle.com/cd/E19957-01/806-3568/ncg_goldberg.html
    //      http://en.wikipedia.org/wiki/Loss_of_significance
    for (int i = nmax_ - 2; i >= 0; i--) {
      int n = i + 1;
      // Equation (27)
      Qext_ += (n + n + 1)*(an[i].real() + bn[i].real());
      // Equation (28)
      Qsca_ += (n + n + 1)*(an[i].real()*an[i].real() + an[i].imag()*an[i].imag()
			    + bn[i].real()*bn[i].real() + bn[i].imag()*bn[i].imag());
      // Equation (29) TODO We must check carefully this equation. If we
      // remove the typecast to double then the result changes. Which is
      // the correct one??? Ovidio (2014/12/10) With cast ratio will
      // give double, without cast (n + n + 1)/(n*(n + 1)) will be
      // rounded to integer. Tig (2015/02/24)
      Qpr_ += ((n*(n + 2)/(n + 1))*((an[i]*std::conj(an[n]) + bn[i]*std::conj(bn[n])).real())
	       + ((double)(n + n + 1)/(n*(n + 1)))*(an[i]*std::conj(bn[i])).real());
      // Equation (33)
      Qbktmp = Qbktmp + (double)(n + n + 1)*(1 - 2*(n % 2))*(an[i]- bn[i]);
      // Calculate the scattering amplitudes (S1 and S2)    //
      // Equations (25a) - (25b)                            //
      for (int t = 0; t < theta_.size(); t++) {
	S1_[t] += calc_S1(n, an[i], bn[i], Pi[i][t], Tau[i][t]);
	S2_[t] += calc_S2(n, an[i], bn[i], Pi[i][t], Tau[i][t]);
      }
    }
    double x2 = pow2(x.back());
    Qext_ = 2*(Qext_)/x2;                                 // Equation (27)
    Qsca_ = 2*(Qsca_)/x2;                                 // Equation (28)
    Qpr_ = Qext_ - 4*(Qpr_)/x2;                           // Equation (29)

    Qabs_ = Qext_ - Qsca_;                                // Equation (30)
    albedo_ = Qsca_ / Qext_;                              // Equation (31)
    asymmetry_factor_ = (Qext_ - Qpr_) / Qsca_;                          // Equation (32)

    Qbk_ = (Qbktmp.real()*Qbktmp.real() + Qbktmp.imag()*Qbktmp.imag())/x2;    // Equation (33)

    isMieCalculated_ = true;
    //return nmax;
  }
  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //
  // external scattering field = incident + scattered
  // BH p.92 (4.37), 94 (4.45), 95 (4.50)
  // assume: medium is non-absorbing; refim = 0; Uabs = 0
  void MultiLayerMie::fieldExt(double Rho, double Phi, double Theta, std::vector<double> Pi, std::vector<double> Tau,
			       std::vector<std::complex<double> > an, std::vector<std::complex<double> > bn,
			       std::vector<std::complex<double> >& E, std::vector<std::complex<double> >& H)  {

    double rn = 0.0;
    std::complex<double> zn, xxip, encap;
    std::vector<std::complex<double> > vm3o1n, vm3e1n, vn3o1n, vn3e1n;
    vm3o1n.resize(3);
    vm3e1n.resize(3);
    vn3o1n.resize(3);
    vn3e1n.resize(3);

    std::vector<std::complex<double> > Ei, Hi, Es, Hs;
    Ei.resize(3);
    Hi.resize(3);
    Es.resize(3);
    Hs.resize(3);
    for (int i = 0; i < 3; i++) {
      Ei[i] = std::complex<double>(0.0, 0.0);
      Hi[i] = std::complex<double>(0.0, 0.0);
      Es[i] = std::complex<double>(0.0, 0.0);
      Hs[i] = std::complex<double>(0.0, 0.0);
    }

    std::vector<std::complex<double> > bj, by, bd;
    bj.resize(nmax_);
    by.resize(nmax_);
    bd.resize(nmax_);

    // Calculate spherical Bessel and Hankel functions
    sphericalBessel(Rho, bj, by, bd);

    for (int n = 0; n < nmax_; n++) {
      rn = double(n + 1);

      zn = bj[n] + std::complex<double>(0.0, 1.0)*by[n];
      xxip = Rho*(bj[n] + std::complex<double>(0.0, 1.0)*by[n]) - rn*zn;

      vm3o1n[0] = std::complex<double>(0.0, 0.0);
      vm3o1n[1] = std::cos(Phi)*Pi[n]*zn;
      vm3o1n[2] = -(std::sin(Phi)*Tau[n]*zn);
      vm3e1n[0] = std::complex<double>(0.0, 0.0);
      vm3e1n[1] = -(std::sin(Phi)*Pi[n]*zn);
      vm3e1n[2] = -(std::cos(Phi)*Tau[n]*zn);
      vn3o1n[0] = std::sin(Phi)*rn*(rn + 1.0)*std::sin(Theta)*Pi[n]*zn/Rho;
      vn3o1n[1] = std::sin(Phi)*Tau[n]*xxip/Rho;
      vn3o1n[2] = std::cos(Phi)*Pi[n]*xxip/Rho;
      vn3e1n[0] = std::cos(Phi)*rn*(rn + 1.0)*std::sin(Theta)*Pi[n]*zn/Rho;
      vn3e1n[1] = std::cos(Phi)*Tau[n]*xxip/Rho;
      vn3e1n[2] = -(std::sin(Phi)*Pi[n]*xxip/Rho);

      // scattered field: BH p.94 (4.45)
      encap = std::pow(std::complex<double>(0.0, 1.0), rn)*(2.0*rn + 1.0)/(rn*(rn + 1.0));
      for (int i = 0; i < 3; i++) {
	Es[i] = Es[i] + encap*(std::complex<double>(0.0, 1.0)*an[n]*vn3e1n[i] - bn[n]*vm3o1n[i]);
	Hs[i] = Hs[i] + encap*(std::complex<double>(0.0, 1.0)*bn[n]*vn3o1n[i] + an[n]*vm3e1n[i]);
      }
    }

    // incident E field: BH p.89 (4.21); cf. p.92 (4.37), p.93 (4.38)
    // basis unit vectors = er, etheta, ephi
    std::complex<double> eifac = std::exp(std::complex<double>(0.0, 1.0)*Rho*std::cos(Theta));

    Ei[0] = eifac*std::sin(Theta)*std::cos(Phi);
    Ei[1] = eifac*std::cos(Theta)*std::cos(Phi);
    Ei[2] = -(eifac*std::sin(Phi));

    // magnetic field
    double hffact = 1.0/(cc*mu);
    for (int i = 0; i < 3; i++) {
      Hs[i] = hffact*Hs[i];
    }

    // incident H field: BH p.26 (2.43), p.89 (4.21)
    std::complex<double> hffacta = hffact;
    std::complex<double> hifac = eifac*hffacta;

    Hi[0] = hifac*std::sin(Theta)*std::sin(Phi);
    Hi[1] = hifac*std::cos(Theta)*std::sin(Phi);
    Hi[2] = hifac*std::cos(Phi);

    for (int i = 0; i < 3; i++) {
      // electric field E [V m-1] = EF*E0
      E[i] = Ei[i] + Es[i];
      H[i] = Hi[i] + Hs[i];
    }
  }

  // ********************************************************************** //
  // ********************************************************************** //
  // ********************************************************************** //

  //**********************************************************************************//
  // This function calculates complex electric and magnetic field in the surroundings //
  // and inside (TODO) the particle.                                                  //
  //                                                                                  //
  // Input parameters:                                                                //
  //   L: Number of layers                                                            //
  //   pl: Index of PEC layer. If there is none just send 0 (zero)                    //
  //   x: Array containing the size parameters of the layers [0..L-1]                 //
  //   m: Array containing the relative refractive indexes of the layers [0..L-1]     //
  //   nmax: Maximum number of multipolar expansion terms to be used for the          //
  //         calculations. Only use it if you know what you are doing, otherwise      //
  //         set this parameter to 0 (zero) and the function will calculate it.       //
  //   ncoord: Number of coordinate points                                            //
  //   Coords: Array containing all coordinates where the complex electric and        //
  //           magnetic fields will be calculated                                     //
  //                                                                                  //
  // Output parameters:                                                               //
  //   E, H: Complex electric and magnetic field at the provided coordinates          //
  //                                                                                  //
  // Return value:                                                                    //
  //   Number of multipolar expansion terms used for the calculations                 //
  //**********************************************************************************//

  //   int MultiLayerMie::nField(int L, int pl, std::vector<double> x, std::vector<std::complex<double> > m, int nmax,
  //            int ncoord, std::vector<double> Xp, std::vector<double> Yp, std::vector<double> Zp,
  // 		   std::vector<std::vector<std::complex<double> > >& E, std::vector<std::vector<std::complex<double> > >& H) {

  //   double Rho, Phi, Theta;
  //   std::vector<std::complex<double> > an, bn;

  //   // This array contains the fields in spherical coordinates
  //   std::vector<std::complex<double> > Es, Hs;
  //   Es.resize(3);
  //   Hs.resize(3);


  //   // Calculate scattering coefficients
  //   ScattCoeffs(L, pl, an, bn);

  //   std::vector<double> Pi, Tau;
  //   Pi.resize(nmax_);
  //   Tau.resize(nmax_);

  //   for (int c = 0; c < ncoord; c++) {
  //     // Convert to spherical coordinates
  //     Rho = sqrt(Xp[c]*Xp[c] + Yp[c]*Yp[c] + Zp[c]*Zp[c]);
  //     if (Rho < 1e-3) {
  //       // Avoid convergence problems
  //       Rho = 1e-3;
  //     }
  //     Phi = acos(Xp[c]/sqrt(Xp[c]*Xp[c] + Yp[c]*Yp[c]));
  //     Theta = acos(Xp[c]/Rho);

  //     calcPiTau(Theta, Pi, Tau);

  //     //*******************************************************//
  //     // external scattering field = incident + scattered      //
  //     // BH p.92 (4.37), 94 (4.45), 95 (4.50)                  //
  //     // assume: medium is non-absorbing; refim = 0; Uabs = 0  //
  //     //*******************************************************//

  //     // Firstly the easiest case: the field outside the particle
  //     if (Rho >= x[L - 1]) {
  //       fieldExt(Rho, Phi, Theta, Pi, Tau, an, bn, Es, Hs);
  //     } else {
  //       // TODO, for now just set all the fields to zero
  //       for (int i = 0; i < 3; i++) {
  //         Es[i] = std::complex<double>(0.0, 0.0);
  //         Hs[i] = std::complex<double>(0.0, 0.0);
  //       }
  //     }

  //     //Now, convert the fields back to cartesian coordinates
  //     E[c][0] = std::sin(Theta)*std::cos(Phi)*Es[0] + std::cos(Theta)*std::cos(Phi)*Es[1] - std::sin(Phi)*Es[2];
  //     E[c][1] = std::sin(Theta)*std::sin(Phi)*Es[0] + std::cos(Theta)*std::sin(Phi)*Es[1] + std::cos(Phi)*Es[2];
  //     E[c][2] = std::cos(Theta)*Es[0] - std::sin(Theta)*Es[1];

  //     H[c][0] = std::sin(Theta)*std::cos(Phi)*Hs[0] + std::cos(Theta)*std::cos(Phi)*Hs[1] - std::sin(Phi)*Hs[2];
  //     H[c][1] = std::sin(Theta)*std::sin(Phi)*Hs[0] + std::cos(Theta)*std::sin(Phi)*Hs[1] + std::cos(Phi)*Hs[2];
  //     H[c][2] = std::cos(Theta)*Hs[0] - std::sin(Theta)*Hs[1];
  //   }

  //   return nmax;
  // }  // end of int nField()

}  // end of namespace nmie