eonc::pbc Namespace Reference

Functions
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 42 of file Matter.h.

                                                     {
  // Transform to fractional coordinates, wrap to [-0.5, 0.5), transform back.
  // Uses floor(x + 0.5) instead of double-fmod: single x86 vroundsd instruction
  // vs expensive fmod library call. Vectorized via Eigen .array() operations.
  AtomMatrix frac = diff * cellInverse;
  frac.array() -= (frac.array() + 0.5).floor();
  return frac * cell;
}

applyLegacy()

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

inline

Definition at line 54 of file Matter.h.

                                                           {
  AtomMatrix frac = coords * cellInverse;
  for (int i = 0; i < frac.rows(); i++) {
    for (int j = 0; j < 3; j++) {
      frac(i, j) = std::fmod(frac(i, j) + 1.0, 1.0);
    }
  }
  return frac * cell;
}

applyPositions()

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

inline

Definition at line 66 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 75 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()));
}