NEBObjectiveFunction Class Reference

#include <NudgedElasticBand.h>

Inheritance diagram for NEBObjectiveFunction:

Public Member Functions
	NEBObjectiveFunction (NudgedElasticBand *nebPassed, const Parameters &parametersPassed)
	~NEBObjectiveFunction (void)
VectorXd	getGradient (bool fdstep=false)
double	getEnergy ()
void	setPositions (const VectorXd &x)
VectorXd	getPositions ()
int	degreesOfFreedom ()
bool	isConverged ()
bool	isUncertain ()
double	getConvergence ()
VectorXd	difference (const VectorXd &a, const VectorXd &b)
Public Member Functions inherited from eonc::ObjectiveFunction
	ObjectiveFunction (const Parameters &paramsPassed)
virtual	~ObjectiveFunction ()

Public Attributes
NudgedElasticBand::NEBStatus	status

Private Attributes
NudgedElasticBand *	neb

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

Detailed Description

Definition at line 106 of file NudgedElasticBand.h.

Constructor & Destructor Documentation

NEBObjectiveFunction()

eonc::NEBObjectiveFunction::NEBObjectiveFunction ( NudgedElasticBand * nebPassed, const Parameters & parametersPassed )

inline

Definition at line 108 of file NudgedElasticBand.h.

      : ObjectiveFunction(parametersPassed),
        neb{nebPassed} {}

~NEBObjectiveFunction()

eonc::NEBObjectiveFunction::~NEBObjectiveFunction ( void )

inline

Definition at line 114 of file NudgedElasticBand.h.

{};

Member Function Documentation

degreesOfFreedom()

int eonc::NEBObjectiveFunction::degreesOfFreedom ( )

virtual

Implements eonc::ObjectiveFunction.

Definition at line 56 of file NEBObjectiveFunction.cpp.

                                           {
  return 3 * neb->numImages * neb->atoms;
}

difference()

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

virtual

Implements eonc::ObjectiveFunction.

Definition at line 85 of file NEBObjectiveFunction.cpp.

                                                             {
  VectorXd pbcDiff(3 * neb->numImages * neb->atoms);
  for (int i = 1; i <= neb->numImages; i++) {
    int n = (i - 1) * 3 * neb->atoms;
    int m = 3 * neb->atoms;
    pbcDiff.segment(n, m) =
        neb->path[i]->pbcV(a.segment(n, m) - b.segment(n, m));
  }
  return pbcDiff;
}

getConvergence()

double eonc::NEBObjectiveFunction::getConvergence ( )

virtual

Implements eonc::ObjectiveFunction.

Definition at line 81 of file NEBObjectiveFunction.cpp.

                                            {
  return neb->convergenceForce();
}

getEnergy()

double eonc::NEBObjectiveFunction::getEnergy ( )

virtual

Implements eonc::ObjectiveFunction.

Definition at line 29 of file NEBObjectiveFunction.cpp.

                                       {
  double Energy{0};
  for (long i = 1; i <= neb->numImages; i++) {
    Energy += neb->path[i]->getPotentialEnergy();
  }
  return Energy;
}

getGradient()

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

virtual

Implements eonc::ObjectiveFunction.

Definition at line 16 of file NEBObjectiveFunction.cpp.

                                                      {
  if (neb->movedAfterForceCall)
    neb->updateForces();
  const long seg = 3 * neb->atoms;
  VectorXd gradV(seg * neb->numImages);
  for (long i = 1; i <= neb->numImages; i++) {
    // Negate in-place during copy to avoid a second pass over 40KB
    gradV.segment(seg * (i - 1), seg) =
        -VectorXd::Map(neb->projectedForce[i]->data(), seg);
  }
  return gradV;
}

getPositions()

VectorXd eonc::NEBObjectiveFunction::getPositions ( )

virtual

Implements eonc::ObjectiveFunction.

Definition at line 46 of file NEBObjectiveFunction.cpp.

                                            {
  VectorXd posV;
  posV.resize(3 * neb->atoms * neb->numImages);
  for (long i = 1; i <= neb->numImages; i++) {
    posV.segment(3 * neb->atoms * (i - 1), 3 * neb->atoms) =
        VectorXd::Map(neb->path[i]->getPositions().data(), 3 * neb->atoms);
  }
  return posV;
}

isConverged()

bool eonc::NEBObjectiveFunction::isConverged ( )

virtual

Implements eonc::ObjectiveFunction.

Definition at line 76 of file NEBObjectiveFunction.cpp.

                                       {
  bool force_conv = getConvergence() < params.neb_options.force_tolerance;
  return force_conv;
}

isUncertain()

bool eonc::NEBObjectiveFunction::isUncertain

(

)

Definition at line 60 of file NEBObjectiveFunction.cpp.

                                       {
  double maxMaxUnc = std::numeric_limits<double>::lowest();
  double currentMaxUnc{0};
  for (long idx = 0; idx <= neb->numImages; idx++) {
    currentMaxUnc = neb->path[idx]->getEnergyVariance();
    if (currentMaxUnc > maxMaxUnc) {
      maxMaxUnc = currentMaxUnc;
    }
  }
  bool unc_conv{maxMaxUnc > params.gp_surrogate_options.uncertainty};
  if (unc_conv) {
    this->status = NudgedElasticBand::NEBStatus::MAX_UNCERTAINTY;
  }
  return unc_conv;
}

setPositions()

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

virtual

Implements eonc::ObjectiveFunction.

Definition at line 37 of file NEBObjectiveFunction.cpp.

                                                         {
  neb->movedAfterForceCall = true;
  for (long i = 1; i <= neb->numImages; i++) {
    neb->path[i]->setPositions(AtomMatrix::Map(
        x.segment(3 * neb->atoms * (i - 1), 3 * neb->atoms).data(), neb->atoms,
        3));
  }
}

Member Data Documentation

neb

NudgedElasticBand* eonc::NEBObjectiveFunction::neb

private

Definition at line 128 of file NudgedElasticBand.h.

status

NudgedElasticBand::NEBStatus eonc::NEBObjectiveFunction::status

Definition at line 125 of file NudgedElasticBand.h.

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

• /home/runner/work/eOn/eOn/include/eon/NudgedElasticBand.h
• /home/runner/work/eOn/eOn/client/NEBObjectiveFunction.cpp