eonc::AtomicGPDimer Class Reference

#include <AtomicGPDimer.h>

Inheritance diagram for eonc::AtomicGPDimer:

Public Member Functions
	AtomicGPDimer (std::shared_ptr< Matter > matter, const Parameters &params, std::shared_ptr< Potential > pot)
	~AtomicGPDimer ()=default
void	compute (std::shared_ptr< Matter > matter, AtomMatrix initialDirection) override
double	getEigenvalue () override
AtomMatrix	getEigenvector () override
Matrix3d	forceBox () const
Public Member Functions inherited from eonc::LowestEigenmode
	LowestEigenmode (std::shared_ptr< Potential > potPassed, const Parameters &parameters)
virtual	~LowestEigenmode ()=default

Static Public Attributes
static const char	OPT_SCG [] = "scg"
static const char	OPT_LBFGS [] = "lbfgs"
Static Public Attributes inherited from eonc::LowestEigenmode
static const char	MINMODE_DIMER [] = "dimer"
static const char	MINMODE_GPRDIMER [] = "gprdimer"
static const char	MINMODE_LANCZOS [] = "lanczos"
static const char	MINMODE_DAVIDSON [] = "davidson"

Private Attributes
std::shared_ptr< Matter >	matterCenter
AtomMatrix	direction
AtomMatrix	rotationalPlane
gpr::InputParameters	p
atmd::AtomicDimer	atomic_dimer
aux::ProblemSetUp	problem_setup
gpr::AtomsConfiguration	atoms_config
gpr::Observation	init_observations
gpr::Observation	init_middle_point
gpr::Coord	orient_init
gpr::Coord	R_init

Additional Inherited Members
Public Attributes inherited from eonc::LowestEigenmode
long	totalForceCalls {0}
double	statsTorque {0.0}
double	statsCurvature {0.0}
double	statsAngle {0.0}
long	statsRotations {0}
long	totalIterations {0}
Protected Attributes inherited from eonc::LowestEigenmode
std::shared_ptr< Potential >	pot
const Parameters &	params

Detailed Description

Definition at line 26 of file AtomicGPDimer.h.

Constructor & Destructor Documentation

AtomicGPDimer()

eonc::AtomicGPDimer::AtomicGPDimer	(	std::shared_ptr< Matter >	matter,
		const Parameters &	params,
		std::shared_ptr< Potential >	pot )

Definition at line 46 of file AtomicGPDimer.cpp.

    : LowestEigenmode(pot, params) {
  if (!matter) {
    throw std::invalid_argument("AtomicGPDimer: null Matter");
  }
  matterCenter = std::make_shared<Matter>(pot, params);
  *matterCenter = *matter;
  p = eonc::helpers::eon_parameters_to_gpr(params);
  // XTBPot treats a non-zero box as periodic. Matter::computePotential sends
  // a zero box when periodic boundaries are off; the GP force box must match.
  const Matrix3d cell =
      matter->getPeriodic() ? matter->getCell() : Matrix3d::Zero();
  for (int i = 0; i < 9; i++) {
    p.cell_dimensions.value[i] = cell.data()[i];
  }
}

~AtomicGPDimer()

eonc::AtomicGPDimer::~AtomicGPDimer ( )

default

Member Function Documentation

compute()

void eonc::AtomicGPDimer::compute ( std::shared_ptr< Matter > matter, AtomMatrix initialDirection )

overridevirtual

Implements eonc::LowestEigenmode.

Definition at line 73 of file AtomicGPDimer.cpp.

                                                                   {
  // Saddle search moves this Matter after the solver is constructed.
  *matterCenter = *matter;
  atoms_config = eonc::helpers::eon_matter_to_atmconf(matter.get());
  copyAtomMatrixToCoord(matter->getPositionsFree(), R_init);
  init_middle_point.clear();
  init_middle_point.R = R_init;
  init_observations.clear();
  problem_setup.activateFrozenAtoms(
      R_init, params.gpr_dimer_options().active_radius, atoms_config);
  AtomMatrix freeOrient(matterCenter->numberOfFreeAtoms(), 3);
  int j = 0;
  for (int i = 0; i < matterCenter->numberOfAtoms(); i++) {
    if (!matterCenter->getFixed(i)) {
      freeOrient.row(j) = initialDirectionAtomMatrix.row(i);
      j++;
      if (j == matterCenter->numberOfFreeAtoms()) {
        break;
      }
    }
  }
  copyAtomMatrixToCoord(freeOrient, orient_init);
  atomic_dimer.initialize(p, init_observations, init_middle_point, orient_init,
                          atoms_config);
 
  auto potential = eonc::helpers::makePotential(params);
  pot::PotentialWrapper wrapper(
      [&potential](long N, const double *R, const int *atomicNrs, double *F,
                   double *U, double *variance, const double *box) {
        potential->force(N, R, atomicNrs, F, U, variance, box);
      });
  // Restore traps if execute throws. The saddle-search catch must not
  // leave later force calls running with traps still masked.
  {
    eonc::FPEGuard fpe;
    atomic_dimer.execute(wrapper);
  }
  // Forcefully set the right positions
  matter->setPositionsFreeV(atomic_dimer.getFinalCoordOfMidPoint());
  this->totalIterations = atomic_dimer.getIterations();
  this->totalForceCalls = atomic_dimer.getTotalForceCalls();
  pot->forceCallCounter = atomic_dimer.getTotalForceCalls();
  return;
}

forceBox()

Matrix3d eonc::AtomicGPDimer::forceBox ( ) const

nodiscard

Definition at line 65 of file AtomicGPDimer.cpp.

                                       {
  Matrix3d box = Matrix3d::Zero();
  for (int i = 0; i < 9; ++i) {
    box.data()[i] = p.cell_dimensions.value[i];
  }
  return box;
}

getEigenvalue()

double eonc::AtomicGPDimer::getEigenvalue ( )

overridevirtual

Implements eonc::LowestEigenmode.

Definition at line 119 of file AtomicGPDimer.cpp.

                                    {
  return atomic_dimer.getFinalCurvature();
}

getEigenvector()

AtomMatrix eonc::AtomicGPDimer::getEigenvector ( )

overridevirtual

Implements eonc::LowestEigenmode.

Definition at line 123 of file AtomicGPDimer.cpp.

                                         {
  const gpr::Coord &orient = atomic_dimer.getFinalOrientation();
  const long nFree = matterCenter->numberOfFreeAtoms();
  const long nAtoms = matterCenter->numberOfAtoms();
  if (nFree <= 0 || orient.size() != 3 * nFree) {
    return AtomMatrix::Zero(nAtoms, 3);
  }
  AtomMatrix freeMode = Eigen::Map<const AtomMatrix>(orient.data(), nFree, 3);
  if (nFree == nAtoms) {
    return freeMode;
  }
  AtomMatrix full = AtomMatrix::Zero(nAtoms, 3);
  long k = 0;
  for (long i = 0; i < nAtoms; ++i) {
    if (!matterCenter->getFixed(i)) {
      full.row(i) = freeMode.row(k++);
    }
  }
  return full;
}

Member Data Documentation

atomic_dimer

atmd::AtomicDimer eonc::AtomicGPDimer::atomic_dimer

private

Definition at line 51 of file AtomicGPDimer.h.

atoms_config

gpr::AtomsConfiguration eonc::AtomicGPDimer::atoms_config

private

Definition at line 53 of file AtomicGPDimer.h.

direction

AtomMatrix eonc::AtomicGPDimer::direction

private

Definition at line 47 of file AtomicGPDimer.h.

init_middle_point

gpr::Observation eonc::AtomicGPDimer::init_middle_point

private

Definition at line 54 of file AtomicGPDimer.h.

init_observations

gpr::Observation eonc::AtomicGPDimer::init_observations

private

Definition at line 54 of file AtomicGPDimer.h.

matterCenter

std::shared_ptr<Matter> eonc::AtomicGPDimer::matterCenter

private

Definition at line 46 of file AtomicGPDimer.h.

OPT_LBFGS

const char eonc::AtomicGPDimer::OPT_LBFGS = "lbfgs"

static

Definition at line 31 of file AtomicGPDimer.h.

OPT_SCG

const char eonc::AtomicGPDimer::OPT_SCG = "scg"

static

Definition at line 30 of file AtomicGPDimer.h.

orient_init

gpr::Coord eonc::AtomicGPDimer::orient_init

private

Definition at line 55 of file AtomicGPDimer.h.

p

gpr::InputParameters eonc::AtomicGPDimer::p

private

Definition at line 50 of file AtomicGPDimer.h.

problem_setup

aux::ProblemSetUp eonc::AtomicGPDimer::problem_setup

private

Definition at line 52 of file AtomicGPDimer.h.

R_init

gpr::Coord eonc::AtomicGPDimer::R_init

private

Definition at line 55 of file AtomicGPDimer.h.

rotationalPlane

AtomMatrix eonc::AtomicGPDimer::rotationalPlane

private

Definition at line 48 of file AtomicGPDimer.h.

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

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