#include <AtomicGPDimer.h>

Inheritance diagram for 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)
double	getEigenvalue ()
AtomMatrix	getEigenvector ()
Public Member Functions inherited from eonc::LowestEigenmode
	LowestEigenmode (std::shared_ptr< Potential > potPassed, const Parameters &parameters)
	~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()

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

Definition at line 43 of file AtomicGPDimer.cpp.

    : LowestEigenmode(pot, params) {
  matterCenter = std::make_shared<Matter>(pot, params);
  *matterCenter = *matter;
  p = eonc::helpers::eon_parameters_to_gpr(params);
  const Matrix3d cell = matter->getCell();
  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 AtomicGPDimer::compute	(	std::shared_ptr< Matter >	matter,
		AtomMatrix	initialDirection )

Definition at line 56 of file AtomicGPDimer.cpp.

                                                                   {
  atoms_config = eonc::helpers::eon_matter_to_atmconf(matter.get());
  copyAtomMatrixToCoord(matterCenter->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);
      });
  eonc::FPEHandler fpeh;
  fpeh.eat_fpe();
  atomic_dimer.execute(wrapper);
  fpeh.restore_fpe();
  // 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;
}

◆ getEigenvalue()

double AtomicGPDimer::getEigenvalue ( )

Definition at line 98 of file AtomicGPDimer.cpp.

                                    {
  return atomic_dimer.getFinalCurvature();
}

◆ getEigenvector()

AtomMatrix AtomicGPDimer::getEigenvector ( )

Definition at line 102 of file AtomicGPDimer.cpp.

                                         {
  const gpr::Coord &orient = atomic_dimer.getFinalOrientation();
  long nFree = matterCenter->numberOfFreeAtoms();
  return Eigen::Map<const AtomMatrix>(orient.data(), nFree, 3);
}