univariate_functions.h

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/**
 *  \file IMP/isd/univariate_functions.h
 *  \brief Classes for general functions
 *
 *  Copyright 2007-2014 IMP Inventors. All rights reserved.
 */

#ifndef IMPISD_UNIVARIATE_FUNCTIONS_H
#define IMPISD_UNIVARIATE_FUNCTIONS_H

#include <IMP/isd/isd_config.h>
#include <IMP/kernel/Particle.h>
#include <IMP/isd/Nuisance.h>
#include <IMP/isd/Scale.h>
#include <IMP/isd/Switching.h>
#include <IMP/base/Object.h>
#include <IMP/algebra/eigen3/Eigen/Dense>

#define IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM 1e-7

IMPISD_BEGIN_NAMESPACE

//! Base class for functions of one variable
class IMPISDEXPORT UnivariateFunction : public base::Object {
 public:
  UnivariateFunction(std::string str) : Object(str) {}

  //! evaluate the function at a certain point
  virtual Floats operator()(const Floats& x) const = 0;

  //! evaluate the function at a list of points
  virtual IMP_Eigen::VectorXd operator()(const IMP::FloatsList& xlist)
      const = 0;

  //! used for testing only
  virtual FloatsList operator()(const IMP::FloatsList& xlist,
                                bool stupid) const = 0;

  //! return true if internal parameters have changed.
  virtual bool has_changed() const = 0;

  //! update internal parameters
  virtual void update() = 0;

  //! update derivatives of particles
  /* add to each particle the derivative of the function
   * times the weight of the DA.
   */
  virtual void add_to_derivatives(const Floats& x,
                                  DerivativeAccumulator& accum) const = 0;

  //! update derivatives of particles
  /* add to the given particle the specified derivative
   * guarantees that the particle_no (starting at 0) matches with
   * the columns of get_derivative_matrix.
   */
  virtual void add_to_particle_derivative(unsigned particle_no, double value,
                                          DerivativeAccumulator& accum)
      const = 0;

  //! return derivative vector
  /* m_ij = d(func(xlist[i]))/dparticle_j
   * the matrix has N rows and M columns
   * where N = xlist.size() and M is the number of particles
   * associated to this function.
   */
  virtual IMP_Eigen::VectorXd get_derivative_vector(
      unsigned particle_no, const FloatsList& xlist) const = 0;

  //! for testing purposes
  virtual FloatsList get_derivative_matrix(const FloatsList& xlist,
                                           bool stupid) const = 0;

  //! return second derivative vector
  virtual IMP_Eigen::VectorXd get_second_derivative_vector(
      unsigned particle_a, unsigned particle_b,
      const FloatsList& xlist) const = 0;

  //! for testing purposes
  virtual FloatsList get_second_derivative_vector(unsigned particle_a,
                                                  unsigned particle_b,
                                                  const FloatsList& xlist,
                                                  bool stupid) const = 0;

  //! returns the number of input dimensions
  virtual unsigned get_ndims_x() const = 0;

  //! returns the number of output dimensions
  virtual unsigned get_ndims_y() const = 0;

  //! returns the number of particles that this function uses
  virtual unsigned get_number_of_particles() const = 0;

  //! returns true if the particle whose index is provided is optimized
  virtual bool get_particle_is_optimized(unsigned particle_no) const = 0;

  //! returns the number of particles that are optimized
  virtual unsigned get_number_of_optimized_particles() const = 0;

  //! particle manipulation
  virtual kernel::ParticlesTemp get_input_particles() const = 0;
  virtual ContainersTemp get_input_containers() const = 0;

  IMP_REF_COUNTED_DESTRUCTOR(UnivariateFunction);
};
//
//! Linear one-dimensional function
/* f(x) = a*x + b, where a,b are ISD nuisances, and f(x) and x are doubles.
 */
class IMPISDEXPORT Linear1DFunction : public UnivariateFunction {
 public:
  Linear1DFunction(kernel::Particle* a, kernel::Particle* b)
      : UnivariateFunction("Linear1DFunction %1%"), a_(a), b_(b) {
    IMP_LOG_TERSE("Linear1DFunction: constructor" << std::endl);
    IMP_IF_CHECK(USAGE_AND_INTERNAL) { Nuisance::decorate_particle(a); }
    IMP_IF_CHECK(USAGE_AND_INTERNAL) { Nuisance::decorate_particle(b); }
    a_val_ = Nuisance(a).get_nuisance();
    b_val_ = Nuisance(b).get_nuisance();
    update();
  }

  bool has_changed() const {
    double tmpa = Nuisance(a_).get_nuisance();
    double tmpb = Nuisance(b_).get_nuisance();
    if ((std::abs(tmpa - a_val_) > IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM) ||
        (std::abs(tmpb - b_val_) > IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM)) {
      IMP_LOG_TERSE("Linear1DFunction: has_changed():");
      IMP_LOG_TERSE("true" << std::endl);
      return true;
    } else {
      return false;
    }
  }

  void update() {
    a_val_ = Nuisance(a_).get_nuisance();
    b_val_ = Nuisance(b_).get_nuisance();
    IMP_LOG_TERSE("Linear1DFunction: update()  a:= " << a_val_ << " b:="
                                                     << b_val_ << std::endl);
  }

  Floats operator()(const Floats& x) const {
    IMP_USAGE_CHECK(x.size() == 1, "expecting a 1-D vector");
    Floats ret(1, a_val_ * x[0] + b_val_);
    return ret;
  }

  IMP_Eigen::VectorXd operator()(const FloatsList& xlist) const {
    unsigned M = xlist.size();
    IMP_Eigen::VectorXd retlist(M);
    for (unsigned i = 0; i < M; i++) {
      IMP_USAGE_CHECK(xlist[i].size() == 1, "expecting a 1-D vector");
      retlist(i) = a_val_ * xlist[i][0] + b_val_;
    }
    return retlist;
  }

  FloatsList operator()(const FloatsList& xlist, bool) const {
    IMP_Eigen::VectorXd vec((*this)(xlist));
    FloatsList ret;
    for (unsigned i = 0; i < xlist.size(); i++)
      ret.push_back(Floats(1, vec(i)));
    return ret;
  }

  void add_to_derivatives(const Floats& x, DerivativeAccumulator& accum) const {
    // d[f(x)]/da = x
    Nuisance(a_).add_to_nuisance_derivative(x[0], accum);
    // d[f(x)]/db = 1
    Nuisance(b_).add_to_nuisance_derivative(1, accum);
  }

  void add_to_particle_derivative(unsigned particle_no, double value,
                                  DerivativeAccumulator& accum) const {
    switch (particle_no) {
      case 0:
        Nuisance(a_).add_to_nuisance_derivative(value, accum);
        break;
      case 1:
        Nuisance(b_).add_to_nuisance_derivative(value, accum);
        break;
      default:
        IMP_THROW("Invalid particle number", ModelException);
    }
  }

  IMP_Eigen::VectorXd get_derivative_vector(unsigned particle_no,
                                            const FloatsList& xlist) const {
    unsigned N = xlist.size();
    IMP_Eigen::VectorXd ret(N);
    switch (particle_no) {
      case 0:  // a
        for (unsigned i = 0; i < N; i++) ret(i) = xlist[i][0];
        break;
      case 1:  // b
        ret.setOnes();
        break;
      default:
        IMP_THROW("Invalid particle number", ModelException);
    }
    return ret;
  }

  FloatsList get_derivative_matrix(const FloatsList& xlist, bool) const {
    IMP_Eigen::MatrixXd mat(xlist.size(), 2);
    mat.col(0) = get_derivative_vector(0, xlist);
    mat.col(1) = get_derivative_vector(1, xlist);
    FloatsList ret;
    for (int i = 0; i < mat.rows(); i++) {
      Floats line;
      for (int j = 0; j < mat.cols(); j++) line.push_back(mat(i, j));
      ret.push_back(line);
    }
    return ret;
  }

  IMP_Eigen::VectorXd get_second_derivative_vector(
      unsigned, unsigned, const FloatsList& xlist) const {
    // The Hessian is zero for all particles.
    unsigned N = xlist.size();
    IMP_Eigen::VectorXd H(IMP_Eigen::VectorXd::Zero(N));
    return H;
  }

  FloatsList get_second_derivative_vector(unsigned particle_a,
                                          unsigned particle_b,
                                          const FloatsList& xlist, bool) const {
    IMP_Eigen::VectorXd mat(
        get_second_derivative_vector(particle_a, particle_b, xlist));
    FloatsList ret;
    for (int i = 0; i < mat.rows(); i++) {
      Floats line;
      for (int j = 0; j < mat.cols(); j++) line.push_back(mat(i, j));
      ret.push_back(line);
    }
    return ret;
  }

  unsigned get_ndims_x() const { return 1; }
  unsigned get_ndims_y() const { return 1; }

  unsigned get_number_of_particles() const { return 2; }

  bool get_particle_is_optimized(unsigned particle_no) const {
    switch (particle_no) {
      case 0:  // a
        return Nuisance(a_).get_nuisance_is_optimized();
      case 1:  // b
        return Nuisance(b_).get_nuisance_is_optimized();
      default:
        IMP_THROW("Invalid particle number", ModelException);
    }
  }

  unsigned get_number_of_optimized_particles() const {
    unsigned count = 0;
    if (Nuisance(a_).get_nuisance_is_optimized()) count++;
    if (Nuisance(b_).get_nuisance_is_optimized()) count++;
    return count;
  }

  kernel::ParticlesTemp get_input_particles() const {
    kernel::ParticlesTemp ret;
    ret.push_back(a_);
    ret.push_back(b_);
    return ret;
  }

  ContainersTemp get_input_containers() const {
    ContainersTemp ret;
    return ret;
  }

  /*IMP_OBJECT_INLINE(Linear1DFunction, out << "y = " << a_val_
    << " * x + " << b_val_ << std::endl, {});*/
  IMP_OBJECT_METHODS(Linear1DFunction);

 private:
  base::Pointer<kernel::Particle> a_, b_;
  double a_val_, b_val_;
};

//! 1D mean function for SAS data
/*  Generalized Guinier-Porod model (Hammouda, J. Appl. Cryst., 2010, eq 3 & 4
 *  to which a constant offset is added)
 *  I(q) = A + G/q^s exp(-(q.Rg)^2/(3-s)) for q <= q1
 *  I(q) = A + D/q^d for q > q1
 *  q1 = 1/Rg * ((d-s)(3-s)/2)^(1/2)
 *  D = G exp(-(q1.Rg)^2/(3-s)) q1^(d-s)
 *  only valid for q>0 Rg>0  0<s<d s<3 G>0
 *  s=0 in the globular case.
 *  G, Rg, d, s and A are particles (ISD Scales).
 */
class IMPISDEXPORT GeneralizedGuinierPorodFunction : public UnivariateFunction {
 public:
  GeneralizedGuinierPorodFunction(kernel::Particle* G, kernel::Particle* Rg,
                                  kernel::Particle* d, kernel::Particle* s,
                                  kernel::Particle* A)
      : UnivariateFunction("GeneralizedGuinierPorodFunction %1%"),
        G_(G),
        Rg_(Rg),
        d_(d),
        s_(s),
        A_(A) {
    IMP_LOG_TERSE("GeneralizedGuinierPorodFunction: constructor" << std::endl);
    IMP_IF_CHECK(USAGE_AND_INTERNAL) { Scale::decorate_particle(G); }
    IMP_IF_CHECK(USAGE_AND_INTERNAL) { Scale::decorate_particle(Rg); }
    IMP_IF_CHECK(USAGE_AND_INTERNAL) { Scale::decorate_particle(d); }
    IMP_IF_CHECK(USAGE_AND_INTERNAL) { Scale::decorate_particle(s); }
    IMP_IF_CHECK(USAGE_AND_INTERNAL) { Nuisance::decorate_particle(A); }
    update();
  }

  bool has_changed() const {
    double tmpG = Scale(G_).get_scale();
    double tmpRg = Scale(Rg_).get_scale();
    double tmpd = Scale(d_).get_scale();
    double tmps = Scale(s_).get_scale();
    double tmpA = Nuisance(A_).get_nuisance();
    if ((std::abs(tmpG - G_val_) > IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM) ||
        (std::abs(tmpRg - Rg_val_) > IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM) ||
        (std::abs(tmpd - d_val_) > IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM) ||
        (std::abs(tmps - s_val_) > IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM) ||
        (std::abs(tmpA - A_val_) > IMP_ISD_UNIVARIATE_FUNCTIONS_MINIMUM)) {
      IMP_LOG_TERSE("GeneralizedGuinierPorodFunction: has_changed():");
      IMP_LOG_TERSE("true" << std::endl);
      return true;
    } else {
      return false;
    }
  }

  void update() {
    G_val_ = Scale(G_).get_scale();
    Rg_val_ = Scale(Rg_).get_scale();
    d_val_ = Scale(d_).get_scale();
    s_val_ = Scale(s_).get_scale();
    if (d_val_ == s_val_) {
      IMP_LOG_TERSE("Warning: d==s !" << std::endl);
      if (s_val_ > 0.001) {
        s_val_ -= 0.001;
      } else {
        d_val_ += 0.001;
      }
      // IMP_THROW("d == s ! ", ModelException);
    }
    A_val_ = Nuisance(A_).get_nuisance();
    q1_param_ = std::sqrt((d_val_ - s_val_) * (3 - s_val_) / 2.);
    D_param_ = G_val_ * std::exp(-IMP::square(q1_param_) / (3 - s_val_));
    q1_param_ = q1_param_ / Rg_val_;
    D_param_ *= std::pow(q1_param_, d_val_ - s_val_);
    IMP_LOG_TERSE("GeneralizedGuinierPorodFunction: update()  G:= "
                  << G_val_ << " Rg:=" << Rg_val_ << " d:=" << d_val_
                  << " s:=" << s_val_ << " A:=" << A_val_ << " Q1.Rg ="
                  << q1_param_ * Rg_val_ << " D =" << D_param_ << std::endl);
    /*std::cout << "cpp"
        << " 3:Q1 " << q1_param_
        << " 5:D " << D_param_
        << " 7:G " << G_val_
        << " 9:Rg " << Rg_val_
        << " 11:d " << d_val_
        << " 13:s " << s_val_
        << " 15:val " << get_value(0.1)
        <<std::endl;*/
  }

  Floats operator()(const Floats& x) const {
    IMP_USAGE_CHECK(x.size() == 1, "expecting a 1-D vector");
    Floats ret(1, get_value(x[0]));
    return ret;
  }

  IMP_Eigen::VectorXd operator()(const FloatsList& xlist) const {
    unsigned M = xlist.size();
    IMP_Eigen::VectorXd retlist(M);
    for (unsigned i = 0; i < M; i++) {
      IMP_USAGE_CHECK(xlist[i].size() == 1, "expecting a 1-D vector");
      retlist(i) = get_value(xlist[i][0]);
    }
    return retlist;
  }

  FloatsList operator()(const FloatsList& xlist, bool) const {
    IMP_Eigen::VectorXd vec((*this)(xlist));
    FloatsList ret;
    for (unsigned i = 0; i < xlist.size(); i++)
      ret.push_back(Floats(1, vec(i)));
    return ret;
  }

  void add_to_derivatives(const Floats& x, DerivativeAccumulator& accum) const {
    double qval = x[0];
    double value = get_value(qval) - A_val_;
    double deriv;
    // d[f(x)+A]/dG = f(x)/G
    deriv = value / G_val_;
    IMP_INTERNAL_CHECK(!base::isnan(deriv), "derivative for G is nan.");
    Scale(G_).add_to_nuisance_derivative(deriv, accum);
    if (qval <= q1_param_) {
      // d[f(x)]/dRg = - f(x) * 2 q^2 Rg / (3-s)
      deriv = -value * 2 * IMP::square(qval) * Rg_val_ / (3 - s_val_);
      IMP_INTERNAL_CHECK(!base::isnan(deriv), "derivative for Rg is nan.");
      Scale(Rg_).add_to_nuisance_derivative(deriv, accum);
      // d[f(x)]/dd = 0
      //
      // d[f(x)]/ds = - f(x) * ( (q Rg / (3-s))^2 + log(q) )
      deriv = -value *
              (IMP::square((qval * Rg_val_) / (3 - s_val_)) + std::log(qval));
      IMP_INTERNAL_CHECK(!base::isnan(deriv), "derivative for s is nan.");
      Scale(s_).add_to_nuisance_derivative(deriv, accum);
    } else {
      // d[f(x)]/dRg = f(x) * (s-d)/Rg
      deriv = value * (s_val_ - d_val_) / Rg_val_;
      IMP_INTERNAL_CHECK(!base::isnan(deriv), "derivative for Rg is nan.");
      Scale(Rg_).add_to_nuisance_derivative(deriv, accum);
      // d[f(x)]/dd = f(x) * log(q1/q)
      deriv = value * std::log(q1_param_ / qval);
      IMP_INTERNAL_CHECK(!base::isnan(deriv), "derivative for d is nan.");
      Scale(d_).add_to_nuisance_derivative(deriv, accum);
      // d[f(x)]/ds = - f(x) * ( (d-s)/(2(3-s)) + log(q1) )
      deriv = -value *
              ((d_val_ - s_val_) / (2 * (3 - s_val_)) + std::log(q1_param_));
      IMP_INTERNAL_CHECK(!base::isnan(deriv), "derivative for d is nan.");
      Scale(s_).add_to_nuisance_derivative(deriv, accum);
    }
    // d[f(x)+A]/dA = 1
    deriv = 1;
    Nuisance(A_).add_to_nuisance_derivative(deriv, accum);
  }

  void add_to_particle_derivative(unsigned particle_no, double value,
                                  DerivativeAccumulator& accum) const {
    switch (particle_no) {
      case 0:
        IMP_INTERNAL_CHECK(!base::isnan(value), "derivative for G is nan.");
        Scale(G_).add_to_scale_derivative(value, accum);
        break;
      case 1:
        IMP_INTERNAL_CHECK(!base::isnan(value), "derivative for Rg is nan.");
        Scale(Rg_).add_to_scale_derivative(value, accum);
        break;
      case 2:
        IMP_INTERNAL_CHECK(!base::isnan(value), "derivative for d is nan.");
        Scale(d_).add_to_scale_derivative(value, accum);
        break;
      case 3:
        IMP_INTERNAL_CHECK(!base::isnan(value), "derivative for s is nan.");
        Scale(s_).add_to_scale_derivative(value, accum);
        break;
      case 4:
        IMP_INTERNAL_CHECK(!base::isnan(value), "derivative for A is nan.");
        Nuisance(A_).add_to_nuisance_derivative(value, accum);
        break;
      default:
        IMP_THROW("Invalid particle number", ModelException);
    }
  }

  IMP_Eigen::VectorXd get_derivative_vector(unsigned particle_no,
                                            const FloatsList& xlist) const {
    unsigned N = xlist.size();
    IMP_Eigen::VectorXd ret(N);
    switch (particle_no) {
      case 0:  // G
        // d[f(x)]/dG = f(x)/G
        ret = ((*this)(xlist) - IMP_Eigen::VectorXd::Constant(N, A_val_)) /
              G_val_;
        break;
      case 1:  // Rg
        for (unsigned i = 0; i < N; i++) {
          double qval = xlist[i][0];
          if (qval <= q1_param_) {
            // d[f(x)]/dRg = - f(x) * 2 q^2 Rg / (3-s)
            ret(i) = -(get_value(qval) - A_val_) * 2 * IMP::square(qval) *
                     Rg_val_ / (3 - s_val_);
          } else {
            // d[f(x)]/dRg = f(x) * (s-d)/Rg
            ret(i) = (get_value(qval) - A_val_) * (s_val_ - d_val_) / Rg_val_;
          }
        }
        break;
      case 2:  // d
        for (unsigned i = 0; i < N; i++) {
          double qval = xlist[i][0];
          if (qval <= q1_param_) {
            // d[f(x)]/dd = 0
            ret(i) = 0;
          } else {
            // d[f(x)]/dd = f(x) * log(q1/q)
            ret(i) = (get_value(qval) - A_val_) * std::log(q1_param_ / qval);
          }
        }
        break;
      case 3:  // s
        for (unsigned i = 0; i < N; i++) {
          double qval = xlist[i][0];
          if (qval <= q1_param_) {
            // d[f(x)]/ds = - f(x)
            //    * (q^2 Rg^2 + (3-s)^2 log(q)) / (3-s)^2
            ret(i) =
                -(get_value(qval) - A_val_) *
                (IMP::square((qval * Rg_val_) / (3 - s_val_)) + std::log(qval));
          } else {
            // d[f(x)]/ds = - f(x) * ( (d-s)/(2(3-s)) + log(q1) )
            ret(i) =
                -(get_value(qval) - A_val_) *
                ((d_val_ - s_val_) / (2 * (3 - s_val_)) + std::log(q1_param_));
          }
        }
        break;
      case 4:  // A
        ret = IMP_Eigen::VectorXd::Constant(N, 1);
        break;
      default:
        IMP_THROW("Invalid particle number", ModelException);
    }
    return ret;
  }

  FloatsList get_derivative_matrix(const FloatsList& xlist, bool) const {
    IMP_Eigen::MatrixXd mat(xlist.size(), 5);
    mat.col(0) = get_derivative_vector(0, xlist);
    mat.col(1) = get_derivative_vector(1, xlist);
    mat.col(2) = get_derivative_vector(2, xlist);
    mat.col(3) = get_derivative_vector(3, xlist);
    mat.col(4) = get_derivative_vector(4, xlist);
    FloatsList ret;
    for (int i = 0; i < mat.rows(); i++) {
      Floats line;
      for (int j = 0; j < mat.cols(); j++) line.push_back(mat(i, j));
      ret.push_back(line);
    }
    return ret;
  }

  IMP_Eigen::VectorXd get_second_derivative_vector(
      unsigned particle_a, unsigned particle_b, const FloatsList& xlist) const {
    if (particle_a >= 5) IMP_THROW("Invalid particle 1 number", ModelException);
    if (particle_b >= 5) IMP_THROW("Invalid particle 2 number", ModelException);
    unsigned N = xlist.size();
    // hessian involving A is always 0
    if (particle_a == 4 || particle_b == 4) return IMP_Eigen::VectorXd::Zero(N);
    unsigned pa = std::min(particle_a, particle_b);
    unsigned pb = std::max(particle_a, particle_b);
    IMP_Eigen::VectorXd ret(N);
    switch (pa) {
      case 0:  // G
        switch (pb) {
          case 0:  // G
            // d2f/dG2 = 0
            ret.noalias() = IMP_Eigen::VectorXd::Zero(N);
            break;

          case 1:  // Rg
            // d2f/dGdRg = df/dRg * 1/G
            ret.noalias() = get_derivative_vector(1, xlist) / G_val_;
            break;

          case 2:  // d
            // d2f/dGdd = df/dd * 1/G
            ret.noalias() = get_derivative_vector(2, xlist) / G_val_;
            break;

          case 3:  // s
            // d2f/dGds = df/ds * 1/G
            ret.noalias() = get_derivative_vector(3, xlist) / G_val_;
            break;

          default:
            IMP_THROW("Invalid particle 2 number", ModelException);
            break;
        }
        break;

      case 1:  // Rg
        switch (pb) {
          case 1:  // Rg
            for (unsigned i = 0; i < N; i++) {
              double qval = xlist[i][0];
              if (qval <= q1_param_) {
                // d2[f(x)]/dRg2 =
                // f(x) * (2 q^2 / (3-s))
                //  * (2 q^2 Rg^2 / (3-s) - 1)
                ret(i) = (get_value(qval) - A_val_) * 2 * IMP::square(qval) /
                         (3 - s_val_) *
                         (2 * IMP::square(qval * Rg_val_) / (3 - s_val_) - 1);
              } else {
                // d2[f(x)]/dRg2=f(x) * (d-s)/Rg^2 * (d-s+1)
                ret(i) = (get_value(qval) - A_val_) * (d_val_ - s_val_) /
                         IMP::square(Rg_val_) * (d_val_ - s_val_ + 1);
              }
            }
            break;

          case 2:  // d
            for (unsigned i = 0; i < N; i++) {
              double qval = xlist[i][0];
              if (qval <= q1_param_) {
                // d2[f(x)]/dddRg = 0
                ret(i) = 0;
              } else {
                // d2[f(x)]/dddRg = -f(x)/Rg
                //           - (d-s)/Rg *df(x)/dd
                double val = (get_value(qval) - A_val_);
                ret(i) = -val / Rg_val_ - (val * std::log(q1_param_ / qval) *
                                           (d_val_ - s_val_) / Rg_val_);
              }
            }
            break;

          case 3:  // s
            for (unsigned i = 0; i < N; i++) {
              double qval = xlist[i][0];
              double val = (get_value(qval) - A_val_);
              if (qval <= q1_param_) {
                // d2[f(x)]/dsdRg = -2q^2Rg/(3-s)
                //     * (df(x)/ds + f(x)/(3-s))
                double deriv =
                    -val * (IMP::square((qval * Rg_val_) / (3 - s_val_)) +
                            std::log(qval));
                ret(i) = -2 * IMP::square(qval) * Rg_val_ / (3 - s_val_) *
                         (deriv + val / (3 - s_val_));
              } else {
                // d2[f(x)]/dsdRg =
                //          1/Rg * (f(x)- (d-s)*df(x)/ds)
                double deriv = -val * ((d_val_ - s_val_) / (2 * (3 - s_val_)) +
                                       std::log(q1_param_));
                ret(i) = (val - (d_val_ - s_val_) * deriv) / Rg_val_;
              }
            }
            break;

          default:
            IMP_THROW("Invalid particle 2 number", ModelException);
            break;
        }
        break;

      case 2:  // d
        switch (pb) {
          case 2:  // d
            for (unsigned i = 0; i < N; i++) {
              double qval = xlist[i][0];
              if (qval <= q1_param_) {
                // d2[f(x)]/dddd = 0
                ret(i) = 0;
              } else {
                // d2[f(x)]/dddd =
                //         f(x)*(log(q1/q)^2 + 1/(2*(d-s)))
                double val = (get_value(qval) - A_val_);
                ret(i) = val * (IMP::square(std::log(q1_param_ / qval)) +
                                1 / (2 * (d_val_ - s_val_)));
              }
            }
            break;

          case 3:  // s
          {
            double lterm =
                (d_val_ - s_val_) / (2 * (3 - s_val_)) + std::log(q1_param_);
            double rterm = 0.5 * (1 / (3 - s_val_) + 1 / (d_val_ - s_val_));
            for (unsigned i = 0; i < N; i++) {
              double qval = xlist[i][0];
              if (qval <= q1_param_) {
                // d2[f(x)]/ddds = 0
                ret(i) = 0;
              } else {
                // d2[f(x)]/ddds = log(q1/q)*df(x)/ds
                //      - (1/(3-s) + 1/(d-s))*f(x)/2
                //
                double val = (get_value(qval) - A_val_);
                ret(i) = -val * (std::log(q1_param_ / qval) * lterm + rterm);
              }
            }
          } break;

          default:
            IMP_THROW("Invalid particle 2 number", ModelException);
            break;
        }
        break;

      case 3:  // s
        switch (pb) {
          case 3:  // s
          {
            double cterm =
                IMP::square(0.5 * (d_val_ - s_val_) / (3 - s_val_) +
                            std::log(q1_param_)) +
                0.5 * ((6 - s_val_ - d_val_) / IMP::square(3 - s_val_) +
                       1. / (d_val_ - s_val_));
            for (unsigned i = 0; i < N; i++) {
              double qval = xlist[i][0];
              double val = (get_value(qval) - A_val_);
              if (qval <= q1_param_) {
                // d2[f(x)]/dsds = f(x) *
                //  ( [(qRg)^2/(3-s)^2 + log q ]^2
                //    - 2(qRg)^2/(3-s)^3 )
                double factor = IMP::square((qval * Rg_val_) / (3 - s_val_));
                ret(i) = val * (IMP::square(factor + std::log(qval)) -
                                2 * factor / (3 - s_val_));
              } else {
                // d2[f(x)]/dsds = f(x)
                // * ( [ (d-s)/(2*(3-s)) + log(q1) ]^2
                //     + 1/2 * [ (6-s-d)/(3-s)^2
                //               + 1/(d-s) ] )
                ret(i) = val * cterm;
              }
            }
          } break;

          default:
            IMP_THROW("Invalid particle 2 number", ModelException);
            break;
        }
        break;

      default:
        IMP_THROW("Invalid particle 1 number", ModelException);
        break;
    }
    return ret;
  }

  FloatsList get_second_derivative_vector(unsigned particle_a,
                                          unsigned particle_b,
                                          const FloatsList& xlist, bool) const {
    IMP_Eigen::VectorXd mat(
        get_second_derivative_vector(particle_a, particle_b, xlist));
    FloatsList ret;
    for (int i = 0; i < mat.rows(); i++) {
      Floats line;
      for (int j = 0; j < mat.cols(); j++) line.push_back(mat(i, j));
      ret.push_back(line);
    }
    return ret;
  }

  unsigned get_ndims_x() const { return 1; }
  unsigned get_ndims_y() const { return 1; }

  unsigned get_number_of_particles() const { return 5; }

  bool get_particle_is_optimized(unsigned particle_no) const {
    switch (particle_no) {
      case 0:  // G
        return Scale(G_).get_scale_is_optimized();
      case 1:  // Rg
        return Scale(Rg_).get_scale_is_optimized();
      case 2:  // d
        return Scale(d_).get_scale_is_optimized();
      case 3:  // s
        return Scale(s_).get_scale_is_optimized();
      case 4:  // A
        return Nuisance(A_).get_nuisance_is_optimized();
      default:
        IMP_THROW("Invalid particle number", ModelException);
    }
  }

  unsigned get_number_of_optimized_particles() const {
    unsigned count = 0;
    if (Scale(G_).get_scale_is_optimized()) count++;
    if (Scale(Rg_).get_scale_is_optimized()) count++;
    if (Scale(d_).get_scale_is_optimized()) count++;
    if (Scale(s_).get_scale_is_optimized()) count++;
    if (Nuisance(A_).get_nuisance_is_optimized()) count++;
    return count;
  }

  kernel::ParticlesTemp get_input_particles() const {
    kernel::ParticlesTemp ret;
    ret.push_back(G_);
    ret.push_back(Rg_);
    ret.push_back(d_);
    ret.push_back(s_);
    ret.push_back(A_);
    return ret;
  }

  ContainersTemp get_input_containers() const {
    ContainersTemp ret;
    return ret;
  }

  /*IMP_OBJECT_INLINE(GeneralizedGuinierPorodFunction, out
          << " G = " << G_val_
          << " Rg = " << Rg_val_
          << " d = " << d_val_
          << " s = " << s_val_
          << " A = " << A_val_
          << " Q1.Rg = " << q1_param_*Rg_val_
          << std::endl, {});*/
  IMP_OBJECT_METHODS(GeneralizedGuinierPorodFunction);

 private:
  inline double get_value(double q) const {
    double value;
    if (q <= q1_param_) {
      value = A_val_ + G_val_ / std::pow(q, s_val_) *
                           std::exp(-IMP::square(q * Rg_val_) / (3 - s_val_));
    } else {
      value = A_val_ + D_param_ / std::pow(q, d_val_);
    }
    return value;
  }

  base::Pointer<kernel::Particle> G_, Rg_, d_, s_, A_;
  double G_val_, Rg_val_, d_val_, s_val_, A_val_, q1_param_, D_param_;
};

IMPISD_END_NAMESPACE

#endif /* IMPISD_UNIVARIATE_FUNCTIONS_H */