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 ()

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) {
 
    // Initialize working variables to avoid re-allocation
    int natoms = matter->numberOfAtoms();
  }

Member Function Documentation

degreesOfFreedom()

int eonc::IDPPObjectiveFunction::degreesOfFreedom ( )

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 58 of file IDPPObjectiveFunction.hpp.

{ return 3 * matter->numberOfAtoms(); }

difference()

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

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 71 of file IDPPObjectiveFunction.hpp.

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

getConvergence()

double eonc::IDPPObjectiveFunction::getConvergence ( )

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 64 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 IDPPObjectiveFunction::getEnergy ( )

overridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 18 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 IDPPObjectiveFunction::getGradient ( bool fdstep = false )

overridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 45 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;
      double r5 = r2 * r2 * 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
    }
  }
 
  // Convert N x 3 matrix to 3N vector and return negative gradient (force)
  // BUT getGradient expects the Gradient (positive derivative), so we return
  // -Forces Actually, typical eOn getGradient returns dV/dx.
  return VectorXd::Map(forces.data(), 3 * natoms) * -1.0;
}

getPositions()

VectorXd eonc::IDPPObjectiveFunction::getPositions ( )

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 52 of file IDPPObjectiveFunction.hpp.

                                   {
    // Map Matter positions to 3N vector
    return VectorXd::Map(matter->getPositions().data(),
                         3 * matter->numberOfAtoms());
  }

isConverged()

bool eonc::IDPPObjectiveFunction::isConverged ( )

inlineoverridevirtual

Implements eonc::ObjectiveFunction.

Definition at line 60 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 47 of file IDPPObjectiveFunction.hpp.

                                                {
    // Map 3N vector back to Matter
    matter->setPositions(AtomMatrix::Map(x.data(), matter->numberOfAtoms(), 3));
  }

Member Data Documentation

d_target

MatrixXd eonc::IDPPObjectiveFunction::d_target

private

Definition at line 76 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