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)
VectorXd	getMasses () const override
bool	supportsFiniteDifferenceCurvature () const override
bool	gradientMatchesEnergy () const override
bool	reuseDisplacementCurvature () const override
Public Member Functions inherited from eonc::ObjectiveFunction
	ObjectiveFunction (const Parameters &paramsPassed)
virtual	~ObjectiveFunction ()
virtual bool	pastClimbCeiling ()
virtual std::optional< double >	knownCurvature () const
virtual void	minimumImage (Eigen::Ref< Eigen::Vector3d >) const
virtual bool	getPeriodic () const

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 146 of file NudgedElasticBand.h.

Constructor & Destructor Documentation

NEBObjectiveFunction()

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

inline

Definition at line 148 of file NudgedElasticBand.h.

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

~NEBObjectiveFunction()

eonc::NEBObjectiveFunction::~NEBObjectiveFunction ( void )

inline

Definition at line 153 of file NudgedElasticBand.h.

{};

Member Function Documentation

degreesOfFreedom()

int eonc::NEBObjectiveFunction::degreesOfFreedom ( )

virtual

Implements eonc::ObjectiveFunction.

Definition at line 93 of file NEBObjectiveFunction.cpp.

                                           {
  return static_cast<int>(nebSegment(*neb) * neb->numImages);
}

difference()

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

virtual

Implements eonc::ObjectiveFunction.

Definition at line 148 of file NEBObjectiveFunction.cpp.

                                                             {
  const long seg = nebSegment(*neb);
  const long atomDof = 3L * neb->atoms;
  VectorXd pbcDiff(seg * neb->numImages);
  for (int i = 1; i <= neb->numImages; i++) {
    const int n = (i - 1) * static_cast<int>(seg);
    pbcDiff.segment(n, atomDof) =
        neb->path[i]->pbcV(a.segment(n, atomDof) - b.segment(n, atomDof));
    if (neb->solidState()) {
      pbcDiff.segment(n + atomDof, 9) =
          a.segment(n + atomDof, 9) - b.segment(n + atomDof, 9);
    }
  }
  return pbcDiff;
}

getConvergence()

double eonc::NEBObjectiveFunction::getConvergence ( )

virtual

Implements eonc::ObjectiveFunction.

Definition at line 118 of file NEBObjectiveFunction.cpp.

                                            {
  return neb->convergenceForce();
}

getEnergy()

double eonc::NEBObjectiveFunction::getEnergy ( )

virtual

Implements eonc::ObjectiveFunction.

Definition at line 47 of file NEBObjectiveFunction.cpp.

                                       {
  // The band update evaluates dirty images as one batch; summing image
  // energies on a moved band would otherwise evaluate them one at a time.
  if (neb->movedAfterForceCall)
    neb->updateForces();
  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 24 of file NEBObjectiveFunction.cpp.

                                                      {
  if (neb->movedAfterForceCall)
    neb->updateForces();
  const long seg = nebSegment(*neb);
  const long atomDof = 3L * 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), atomDof) =
        -VectorXd::Map(neb->projectedForce[i]->data(), atomDof);
    if (neb->solidState()) {
      const eonc::neb::CartesianStep step = eonc::neb::solidStateCartesianStep(
          *neb->path[i], *neb->projectedForce[i], neb->cellForce(i),
          neb->solidJacobian());
      gradV.segment(seg * (i - 1), atomDof) =
          -VectorXd::Map(step.positions.data(), atomDof);
      gradV.segment(seg * (i - 1) + atomDof, 9) =
          -VectorXd::Map(step.cell.data(), 9);
    }
  }
  return gradV;
}

getMasses()

VectorXd eonc::NEBObjectiveFunction::getMasses ( ) const

overridevirtual

Reimplemented from eonc::ObjectiveFunction.

Definition at line 122 of file NEBObjectiveFunction.cpp.

                                               {
  long count = 0;
  for (long i = 1; i <= neb->numImages; ++i) {
    const Matter &image = *neb->path[static_cast<size_t>(i)];
    const AtomMatrix mask = image.getFree();
    for (long atom = 0; atom < image.numberOfAtoms(); ++atom) {
      if (mask.row(atom).sum() > 0.5) {
        ++count;
      }
    }
  }
  VectorXd masses(count);
  long written = 0;
  for (long i = 1; i <= neb->numImages; ++i) {
    const Matter &image = *neb->path[static_cast<size_t>(i)];
    const auto all = image.getMasses();
    const AtomMatrix mask = image.getFree();
    for (long atom = 0; atom < image.numberOfAtoms(); ++atom) {
      if (mask.row(atom).sum() > 0.5) {
        masses(written++) = all(atom);
      }
    }
  }
  return masses;
}

getPositions()

VectorXd eonc::NEBObjectiveFunction::getPositions ( )

virtual

Implements eonc::ObjectiveFunction.

Definition at line 77 of file NEBObjectiveFunction.cpp.

                                            {
  const long seg = nebSegment(*neb);
  const long atomDof = 3L * neb->atoms;
  VectorXd posV(seg * neb->numImages);
  for (long i = 1; i <= neb->numImages; i++) {
    const long offset = seg * (i - 1);
    posV.segment(offset, atomDof) =
        VectorXd::Map(neb->path[i]->getPositions().data(), atomDof);
    if (neb->solidState()) {
      posV.segment(offset + atomDof, 9) =
          VectorXd::Map(neb->path[i]->getCell().data(), 9);
    }
  }
  return posV;
}

gradientMatchesEnergy()

bool eonc::NEBObjectiveFunction::gradientMatchesEnergy ( ) const

inlineoverridevirtual

Reimplemented from eonc::ObjectiveFunction.

Definition at line 170 of file NudgedElasticBand.h.

{ return false; }

isConverged()

bool eonc::NEBObjectiveFunction::isConverged ( )

virtual

Implements eonc::ObjectiveFunction.

Definition at line 113 of file NEBObjectiveFunction.cpp.

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

isUncertain()

bool eonc::NEBObjectiveFunction::isUncertain

(

)

Definition at line 97 of file NEBObjectiveFunction.cpp.

                                       {
  double maxMaxUnc = std::numeric_limits<double>::lowest();
  double currentMaxUnc{0};
  for (long idx = 0; idx <= neb->numImages + 1; 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;
}

reuseDisplacementCurvature()

bool eonc::NEBObjectiveFunction::reuseDisplacementCurvature ( ) const

inlineoverridevirtual

Reimplemented from eonc::ObjectiveFunction.

Definition at line 171 of file NudgedElasticBand.h.

{ return true; }

setPositions()

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

virtual

Implements eonc::ObjectiveFunction.

Definition at line 59 of file NEBObjectiveFunction.cpp.

                                                         {
  neb->movedAfterForceCall = true;
  const long seg = nebSegment(*neb);
  const long atomDof = 3L * neb->atoms;
  for (long i = 1; i <= neb->numImages; i++) {
    const long offset = seg * (i - 1);
    if (neb->solidState()) {
      Matrix3d cell = Matrix3d::Map(x.segment(offset + atomDof, 9).data());
      cell(0, 1) = 0.0;
      cell(0, 2) = 0.0;
      cell(1, 2) = 0.0;
      neb->path[i]->setCell(cell);
    }
    neb->path[i]->setPositions(
        AtomMatrix::Map(x.segment(offset, atomDof).data(), neb->atoms, 3));
  }
}

supportsFiniteDifferenceCurvature()

bool eonc::NEBObjectiveFunction::supportsFiniteDifferenceCurvature ( ) const

inlineoverridevirtual

Reimplemented from eonc::ObjectiveFunction.

Definition at line 167 of file NudgedElasticBand.h.

{ return false; }

Member Data Documentation

neb

NudgedElasticBand* eonc::NEBObjectiveFunction::neb

private

Definition at line 175 of file NudgedElasticBand.h.

status

NudgedElasticBand::NEBStatus eonc::NEBObjectiveFunction::status

Definition at line 172 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