eonc::IDPPObjectiveFunction Class Reference

#include <IDPPObjectiveFunction.hpp>

Inheritance diagram for eonc::IDPPObjectiveFunction:

Public Member Functions
	IDPPObjectiveFunction (std::shared_ptr< Matter > matterPassed, const Parameters &paramsPassed, const MatrixXd &targetDistances)
double	getEnergy () override
VectorXd	getGradient (bool fdstep=false) override
void	setPositions (const VectorXd &x) override
VectorXd	getPositions () override
int	degreesOfFreedom () override
bool	isConverged () override
double	getConvergence () override
VectorXd	difference (const VectorXd &a, const VectorXd &b) override
Public Member Functions inherited from eonc::ObjectiveFunction
	ObjectiveFunction (const Parameters &paramsPassed)
virtual	~ObjectiveFunction ()
virtual bool	supportsFiniteDifferenceCurvature () const
virtual std::optional< double >	knownCurvature () const
virtual void	minimumImage (Eigen::Ref< Eigen::Vector3d >) const
virtual VectorXd	getMasses () const
virtual bool	getPeriodic () const

Private Attributes
std::shared_ptr< Matter >	matter
MatrixXd	d_target

Additional Inherited Members
Protected Attributes inherited from eonc::ObjectiveFunction
const Parameters &	params

Detailed Description

Definition at line 24 of file IDPPObjectiveFunction.hpp.

Constructor & Destructor Documentation

IDPPObjectiveFunction()

eonc::IDPPObjectiveFunction::IDPPObjectiveFunction ( std::shared_ptr< Matter > matterPassed, const Parameters & paramsPassed, const MatrixXd & targetDistances )

inline

Definition at line 28 of file IDPPObjectiveFunction.hpp.

      : ObjectiveFunction(paramsPassed), matter{std::move(matterPassed)},
        d_target(targetDistances) {}

Member Function Documentation

degreesOfFreedom()

int eonc::IDPPObjectiveFunction::degreesOfFreedom ( )

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 49 of file IDPPObjectiveFunction.hpp.

                                  {
    return 3 * static_cast<int>(matter->numberOfFreeAtoms());
  }

difference()

VectorXd eonc::IDPPObjectiveFunction::difference ( const VectorXd & a, const VectorXd & b )

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 65 of file IDPPObjectiveFunction.hpp.

                                                                     {
    return matter->pbcV(a - b);
  }

getConvergence()

double eonc::IDPPObjectiveFunction::getConvergence ( )

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 58 of file IDPPObjectiveFunction.hpp.

                                   {
    // Return max force component or norm depending on preference
    // Using norm here for simplicity in path generation
    return getGradient().norm();
  }

getEnergy()

double eonc::IDPPObjectiveFunction::getEnergy ( )

overridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 34 of file IDPPObjectiveFunction.cpp.

                                        {
  double energy = 0.0;
  int natoms = matter->numberOfAtoms();
  AtomMatrix pos = matter->getPositions();
 
  // Loop over unique pairs
  for (int i = 0; i < natoms; ++i) {
    for (int j = i + 1; j < natoms; ++j) {
      // Respect PBC
      double r = matter->pbc(pos.row(i) - pos.row(j)).norm();
 
      // Weight function w = 1 / r^4
      // Avoid division by zero if atoms overlap perfectly (unlikely in IDPP but
      // possible)
      if (r < 1e-4)
        r = 1e-4;
 
      double diff = r - d_target(i, j);
      double r2 = r * r;
      double weight = 1.0 / (r2 * r2); // 1/r^4
 
      energy += 0.5 * weight * diff * diff;
    }
  }
  return energy;
}

getGradient()

VectorXd eonc::IDPPObjectiveFunction::getGradient ( bool fdstep = false )

overridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 61 of file IDPPObjectiveFunction.cpp.

                                                  {
  int natoms = matter->numberOfAtoms();
  AtomMatrix pos = matter->getPositions();
  AtomMatrix forces = AtomMatrix::Zero(natoms, 3);
 
  for (int i = 0; i < natoms; ++i) {
    for (int j = i + 1; j < natoms; ++j) {
      // Vector pointing from j to i
      Eigen::RowVector3d dr_vec = matter->pbc(pos.row(i) - pos.row(j));
      double r = dr_vec.norm();
 
      if (r < 1e-4)
        r = 1e-4;
 
      double diff = r - d_target(i, j);
      double r2 = r * r;
 
      // Derivative of E_pair = 0.5 * (1/r^4) * (r - d_target)^2
      // dE/dr = (r - d_target)/r^4 - 2(r - d_target)^2 / r^5
      // Simplified: (r - d_target) * (1 - 2(r - d_target)/r) / r^4
 
      double r4 = r2 * r2;
      double dEdr = (diff * (1.0 - 2.0 * diff / r)) / r4;
 
      // Force contribution: F = -dE/dr * (dr_vec / r)
      Eigen::RowVector3d f_contribution = -dEdr * (dr_vec / r);
 
      forces.row(i) += f_contribution;
      forces.row(j) -= f_contribution; // Newton's 3rd law
    }
  }
 
  // dV/dx on free atoms only. Frozen rows stay in `forces` for Newton's
  // third law during the pair loop, then are dropped.
  return packFree(*matter, forces) * -1.0;
}

getPositions()

VectorXd eonc::IDPPObjectiveFunction::getPositions ( )

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 47 of file IDPPObjectiveFunction.hpp.

{ return matter->getPositionsFreeV(); }

isConverged()

bool eonc::IDPPObjectiveFunction::isConverged ( )

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 53 of file IDPPObjectiveFunction.hpp.

                              {
    return getConvergence() <
           params.neb_options().initialization.force_tolerance;
  }

setPositions()

void eonc::IDPPObjectiveFunction::setPositions ( const VectorXd & x )

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 43 of file IDPPObjectiveFunction.hpp.

                                                {
    matter->setPositionsFreeV(x);
  }

Member Data Documentation

d_target

MatrixXd eonc::IDPPObjectiveFunction::d_target

private

Definition at line 70 of file IDPPObjectiveFunction.hpp.

matter

std::shared_ptr<Matter> eonc::IDPPObjectiveFunction::matter

private

Definition at line 25 of file IDPPObjectiveFunction.hpp.

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The documentation for this class was generated from the following files:

• /home/runner/work/eOn/eOn/include/eon/IDPPObjectiveFunction.hpp
• /home/runner/work/eOn/eOn/client/IDPPObjectiveFunction.cpp