eonc::pbc Namespace Reference

Functions
void	wrapMinimumImage (double *data, size_t n)
void	wrapLegacyUnit (double *data, size_t n)
AtomMatrix	apply (const AtomMatrix &diff, const Matrix3d &cell, const Matrix3d &cellInverse)
AtomMatrix	applyLegacy (const AtomMatrix &coords, const Matrix3d &cell, const Matrix3d &cellInverse)
AtomMatrix	applyPositions (const AtomMatrix &coords, const Matrix3d &cell, const Matrix3d &cellInverse, PbcConvention convention)
VectorXd	applyV (const VectorXd &diffVector, const Matrix3d &cell, const Matrix3d &cellInverse)

Function Documentation

apply()

AtomMatrix eonc::pbc::apply ( const AtomMatrix & diff, const Matrix3d & cell, const Matrix3d & cellInverse )

inline

Definition at line 44 of file Matter.h.

                                                     {
  // Fractional coordinates, minimum-image wrap to [-0.5, 0.5), back to
  // Cartesian. x - floor(x + 0.5), Highway when the build has it.
  AtomMatrix frac = diff * cellInverse;
  wrapMinimumImage(frac.data(), static_cast<size_t>(frac.size()));
  return frac * cell;
}

applyLegacy()

AtomMatrix eonc::pbc::applyLegacy ( const AtomMatrix & coords, const Matrix3d & cell, const Matrix3d & cellInverse )

inline

Definition at line 55 of file Matter.h.

                                                           {
  AtomMatrix frac = coords * cellInverse;
  // Same values as fmod(x + 1, 1): (x + 1) - trunc(x + 1).
  wrapLegacyUnit(frac.data(), static_cast<size_t>(frac.size()));
  return frac * cell;
}

applyPositions()

AtomMatrix eonc::pbc::applyPositions ( const AtomMatrix & coords, const Matrix3d & cell, const Matrix3d & cellInverse, PbcConvention convention )

inline

Definition at line 64 of file Matter.h.

                                                           {
  if (convention == PbcConvention::MinimumImage) {
    return apply(coords, cell, cellInverse);
  }
  return applyLegacy(coords, cell, cellInverse);
}

applyV()

VectorXd eonc::pbc::applyV ( const VectorXd & diffVector, const Matrix3d & cell, const Matrix3d & cellInverse )

inline

Definition at line 73 of file Matter.h.

                                                    {
  AtomMatrix pbcMatrix =
      apply(AtomMatrix::Map(diffVector.data(), diffVector.size() / 3, 3), cell,
            cellInverse);
  return VectorXd(VectorXd::Map(pbcMatrix.data(), diffVector.size()));
}

wrapLegacyUnit()

void eonc::pbc::wrapLegacyUnit	(	double *	data,
		size_t	n )

Definition at line 113 of file PbcSimd.cpp.

                                            {
  wrapLegacyUnitScalar(data, 0, n);
}

wrapMinimumImage()

void eonc::pbc::wrapMinimumImage	(	double *	data,
		size_t	n )

Definition at line 109 of file PbcSimd.cpp.

                                              {
  wrapMinimumImageScalar(data, 0, n);
}