Lattice Class Reference

#include <Lattice.h>

Public Member Functions
	Lattice (void)
NAMD_HOST_DEVICE void	set (Vector A, Vector B, Vector C)
NAMD_HOST_DEVICE void	set (Vector A, Vector B, Vector C, Position Origin)
NAMD_HOST_DEVICE void	rescale (Tensor factor)
NAMD_HOST_DEVICE void	rescale (Position &p, Tensor factor) const
NAMD_HOST_DEVICE Position	unscale (ScaledPosition s) const
NAMD_HOST_DEVICE ScaledPosition	scale (Position p) const
NAMD_HOST_DEVICE Vector	scale_force (Vector f) const
NAMD_HOST_DEVICE Position	nearest (Position data, ScaledPosition ref) const
NAMD_HOST_DEVICE Position	nearest (Position data, ScaledPosition ref, Transform *t) const
NAMD_HOST_DEVICE Position	apply_transform (Position data, const Transform &t) const
NAMD_HOST_DEVICE Position	reverse_transform (Position data, const Transform &t) const
NAMD_HOST_DEVICE Vector	delta (const Position &pos1, const Position &pos2) const
NAMD_HOST_DEVICE Vector	delta_from_diff (const Position &diff_in) const
NAMD_HOST_DEVICE Vector	wrap_delta_scaled (const Position &pos1, const Position &pos2) const
NAMD_HOST_DEVICE Vector	wrap_delta_scaled_fast (const Position &pos1, const Position &pos2) const
NAMD_HOST_DEVICE Vector	delta (const Position &pos1) const
NAMD_HOST_DEVICE Vector	wrap_delta (const Position &pos1) const
NAMD_HOST_DEVICE Vector	wrap_nearest_delta (Position pos1) const
NAMD_HOST_DEVICE Vector	offset (int i) const
NAMD_HOST_DEVICE Vector	a () const
NAMD_HOST_DEVICE Vector	b () const
NAMD_HOST_DEVICE Vector	c () const
NAMD_HOST_DEVICE int	orthogonal () const
NAMD_HOST_DEVICE Vector	origin () const
NAMD_HOST_DEVICE Vector	a_r () const
NAMD_HOST_DEVICE Vector	b_r () const
NAMD_HOST_DEVICE Vector	c_r () const
NAMD_HOST_DEVICE int	a_p () const
NAMD_HOST_DEVICE int	b_p () const
NAMD_HOST_DEVICE int	c_p () const
NAMD_HOST_DEVICE BigReal	volume (void) const
bool	isEqual (const Lattice &other) const

Static Public Member Functions
static NAMD_HOST_DEVICE int	index (int i=0, int j=0, int k=0)
static NAMD_HOST_DEVICE int	offset_a (int i)
static NAMD_HOST_DEVICE int	offset_b (int i)
static NAMD_HOST_DEVICE int	offset_c (int i)

Detailed Description

Definition at line 17 of file Lattice.h.

Constructor & Destructor Documentation

Lattice()

Lattice::Lattice ( void  )

inline

Definition at line 20 of file Lattice.h.

                : a1(0,0,0), a2(0,0,0), a3(0,0,0),
                  b1(0,0,0), b2(0,0,0), b3(0,0,0),
                  o(0,0,0), p1(0), p2(0), p3(0) {};

Member Function Documentation

a()

NAMD_HOST_DEVICE Vector Lattice::a ( ) const

inline

Definition at line 268 of file Lattice.h.

Referenced by Controller::calcPressure(), colvarproxy_namd::calculate(), CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), PmeKSpace::compute_energy(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize(), ComputePmeMgr::initialize_pencils(), lattice_to_unitcell(), cr_sortop_distance::operator()(), Controller::printEnergies(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), and Controller::writeExtendedSystemData().

{ return a1; }

a_p()

NAMD_HOST_DEVICE int Lattice::a_p ( ) const

inline

Definition at line 289 of file Lattice.h.

Referenced by calc_fulldirect(), colvarproxy_namd::calculate(), ComputeMsmMgr::initialize(), lattice_to_unitcell(), WorkDistrib::patchMapInit(), Controller::printEnergies(), SimParameters::readExtendedSystem(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), PatchMap::sizeGrid(), Node::startup(), Controller::writeExtendedSystemData(), and Controller::writeExtendedSystemLabels().

{ return p1; }

a_r()

NAMD_HOST_DEVICE Vector Lattice::a_r ( ) const

inline

Definition at line 284 of file Lattice.h.

Referenced by CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), CudaPmeOneDevice::compute(), LjPmeKSpace::compute_energy(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), ComputeEField::doForce(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize(), ComputePmeMgr::initialize_pencils(), WorkDistrib::patchMapInit(), ComputeMsmSerialMgr::recvCoord(), scale_coordinates(), scale_forces(), LjPmeMgr::setScaledCoordinates(), PatchMap::sizeGrid(), and CudaPmeKSpaceCompute::solve().

{ return b1; }

apply_transform()

NAMD_HOST_DEVICE Position Lattice::apply_transform ( Position  data, const Transform &  t  ) const

inline

Definition at line 137 of file Lattice.h.

References Transform::i, Transform::j, and Transform::k.

Referenced by Sequencer::berendsenPressure(), WorkDistrib::createAtomLists(), HomePatch::depositMigration(), Sequencer::langevinPiston(), PatchMgr::moveAllBy(), and PatchMgr::moveAtom().

  {
    return ( data + t.i*a1 + t.j*a2 + t.k*a3 );
  }

b()

NAMD_HOST_DEVICE Vector Lattice::b ( ) const

inline

Definition at line 269 of file Lattice.h.

Referenced by Controller::calcPressure(), colvarproxy_namd::calculate(), CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), PmeKSpace::compute_energy(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), lattice_to_unitcell(), cr_sortop_distance::operator()(), Controller::printEnergies(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), and Controller::writeExtendedSystemData().

{ return a2; }

b_p()

NAMD_HOST_DEVICE int Lattice::b_p ( ) const

inline

Definition at line 290 of file Lattice.h.

Referenced by calc_fulldirect(), colvarproxy_namd::calculate(), ComputeMsmMgr::initialize(), lattice_to_unitcell(), WorkDistrib::patchMapInit(), Controller::printEnergies(), SimParameters::readExtendedSystem(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), PatchMap::sizeGrid(), Node::startup(), Controller::writeExtendedSystemData(), and Controller::writeExtendedSystemLabels().

{ return p2; }

b_r()

NAMD_HOST_DEVICE Vector Lattice::b_r ( ) const

inline

Definition at line 285 of file Lattice.h.

Referenced by CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), CudaPmeOneDevice::compute(), LjPmeKSpace::compute_energy(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), ComputeEField::doForce(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), WorkDistrib::patchMapInit(), ComputeMsmSerialMgr::recvCoord(), scale_coordinates(), scale_forces(), LjPmeMgr::setScaledCoordinates(), PatchMap::sizeGrid(), and CudaPmeKSpaceCompute::solve().

{ return b2; }

c()

NAMD_HOST_DEVICE Vector Lattice::c ( ) const

inline

Definition at line 270 of file Lattice.h.

Referenced by Controller::calcPressure(), colvarproxy_namd::calculate(), CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), PmeKSpace::compute_energy(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), ComputeEwald::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), HomePatch::hardWallDrude(), ComputeMsmMgr::initialize(), Controller::langevinPiston1(), Controller::langevinPiston2(), lattice_to_unitcell(), Controller::monteCarloPressure_accept(), cr_sortop_distance::operator()(), Controller::printEnergies(), HomePatch::rattle1old(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), and Controller::writeExtendedSystemData().

{ return a3; }

c_p()

NAMD_HOST_DEVICE int Lattice::c_p ( ) const

inline

Definition at line 291 of file Lattice.h.

Referenced by calc_fulldirect(), colvarproxy_namd::calculate(), ComputeMsmMgr::initialize(), lattice_to_unitcell(), WorkDistrib::patchMapInit(), Controller::printEnergies(), SimParameters::readExtendedSystem(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), PatchMap::sizeGrid(), Node::startup(), Controller::writeExtendedSystemData(), and Controller::writeExtendedSystemLabels().

{ return p3; }

c_r()

NAMD_HOST_DEVICE Vector Lattice::c_r ( ) const

inline

Definition at line 286 of file Lattice.h.

Referenced by CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), CudaPmeOneDevice::compute(), LjPmeKSpace::compute_energy(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), ComputeEField::doForce(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeMsmMgr::initialize(), WorkDistrib::patchMapInit(), ComputeMsmSerialMgr::recvCoord(), scale_coordinates(), scale_forces(), LjPmeMgr::setScaledCoordinates(), PatchMap::sizeGrid(), and CudaPmeKSpaceCompute::solve().

{ return b3; }

delta() [1/2]

NAMD_HOST_DEVICE Vector Lattice::delta ( const Position &  pos1, const Position &  pos2  ) const

inline

Definition at line 149 of file Lattice.h.

References delta_from_diff().

Referenced by AngleElem::computeForce(), CrosstermElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), TholeElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), LjPmeCompute::computeNonbonded(), ComputeRestraints::doForce(), colvarproxy_namd::position_distance(), and ComputeQM::processFullQM().

  {
    Vector diff = pos1 - pos2;
    return delta_from_diff(diff);
  }

delta() [2/2]

NAMD_HOST_DEVICE Vector Lattice::delta ( const Position &  pos1 ) const

inline

Definition at line 211 of file Lattice.h.

References namdnearbyint.

  {
    Vector diff = pos1 - o;
    Vector result = diff;
    if ( p1 ) result -= a1*namdnearbyint(b1*diff);
    if ( p2 ) result -= a2*namdnearbyint(b2*diff);
    if ( p3 ) result -= a3*namdnearbyint(b3*diff);
    return result;
  }

delta_from_diff()

NAMD_HOST_DEVICE Vector Lattice::delta_from_diff ( const Position &  diff_in ) const

inline

Definition at line 156 of file Lattice.h.

References namdnearbyint, Vector::x, Vector::y, and Vector::z.

Referenced by delta().

  {
    Vector diff = diff_in;
#ifdef ARCH_POWERPC   //Prevents stack temporaries
    Vector result = diff;
    if ( p1 ) {
      BigReal fval = namdnearbyint(b1*diff); 
      result.x -= a1.x *fval;    
      result.y -= a1.y *fval;    
      result.z -= a1.z *fval;    
    }
    if ( p2 ) {
      BigReal fval = namdnearbyint(b2*diff);
      result.x -= a2.x * fval;
      result.y -= a2.y * fval;
      result.z -= a2.z * fval;
    }
    if ( p3 ) {
      BigReal fval = namdnearbyint(b3*diff);
      result.x -= a3.x * fval;
      result.y -= a3.y * fval;
      result.z -= a3.z * fval;
    }
    return result;
#else
    BigReal f1 = p1 ? namdnearbyint(b1*diff) : 0.;
    BigReal f2 = p2 ? namdnearbyint(b2*diff) : 0.;
    BigReal f3 = p3 ? namdnearbyint(b3*diff) : 0.;
    diff.x -= f1*a1.x + f2*a2.x + f3*a3.x;
    diff.y -= f1*a1.y + f2*a2.y + f3*a3.y;
    diff.z -= f1*a1.z + f2*a2.z + f3*a3.z;
    return diff;
#endif
  }

index()

static NAMD_HOST_DEVICE int Lattice::index ( int  i = 0, int  j = 0, int  k = 0  )

inlinestatic

Definition at line 25 of file Lattice.h.

Referenced by PatchMap::downstreamNeighbors(), PatchMap::getPatchesInOctet(), PatchMap::oneAwayNeighbors(), PatchMap::oneOrTwoAwayNeighbors(), and PatchMap::upstreamNeighbors().

  {
    return 9 * (k+1) + 3 * (j+1) + (i+1);
  }

isEqual()

bool Lattice::isEqual ( const Lattice &  other ) const

inline

Definition at line 298 of file Lattice.h.

Referenced by CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets().

                                           {
    return (a1 == other.a1) && 
           (a2 == other.a2) && 
           (a3 == other.a3) &&
           (o == other.o);
  }

nearest() [1/2]

NAMD_HOST_DEVICE Position Lattice::nearest ( Position  data, ScaledPosition  ref  ) const

inline

Definition at line 95 of file Lattice.h.

References namdnearbyint, scale(), unscale(), Vector::x, Vector::y, and Vector::z.

Referenced by WorkDistrib::createAtomLists(), and HomePatch::depositMigration().

  {
    ScaledPosition sn = scale(data);
    if ( p1 ) {
      sn.x -= namdnearbyint(sn.x - ref.x);
    }
    if ( p2 ) {
      sn.y -= namdnearbyint(sn.y - ref.y);
    }
    if ( p3 ) {
      sn.z -= namdnearbyint(sn.z - ref.z);
    }
    return unscale(sn);
  }

nearest() [2/2]

NAMD_HOST_DEVICE Position Lattice::nearest ( Position  data, ScaledPosition  ref, Transform *  t  ) const

inline

Definition at line 112 of file Lattice.h.

References Transform::i, Transform::j, Transform::k, namdnearbyint, scale(), unscale(), Vector::x, Vector::y, and Vector::z.

  {
    ScaledPosition sn = scale(data);
    if ( p1 ) {
      BigReal tmp = sn.x - ref.x;
      BigReal rit = namdnearbyint(tmp);
      sn.x -= rit;
      t->i -= (int) rit;
    }
    if ( p2 ) {
      BigReal tmp = sn.y - ref.y;
      BigReal rit = namdnearbyint(tmp);
      sn.y -= rit;
      t->j -= (int) rit;
    }
    if ( p3 ) {
      BigReal tmp = sn.z - ref.z;
      BigReal rit = namdnearbyint(tmp);
      sn.z -= rit;
      t->k -= (int) rit;
    }
    return unscale(sn);
  }

offset()

NAMD_HOST_DEVICE Vector Lattice::offset ( int  i ) const

inline

Definition at line 258 of file Lattice.h.

Referenced by ComputeNonbondedPair::doForce().

  {
    return ( (i%3-1) * a1 + ((i/3)%3-1) * a2 + (i/9-1) * a3 );
  }

offset_a()

static NAMD_HOST_DEVICE int Lattice::offset_a ( int  i )

inlinestatic

Definition at line 263 of file Lattice.h.

Referenced by registerUserEventsForAllComputeObjs().

{ return (i%3-1); }

offset_b()

static NAMD_HOST_DEVICE int Lattice::offset_b ( int  i )

inlinestatic

Definition at line 264 of file Lattice.h.

Referenced by registerUserEventsForAllComputeObjs().

{ return ((i/3)%3-1); }

offset_c()

static NAMD_HOST_DEVICE int Lattice::offset_c ( int  i )

inlinestatic

Definition at line 265 of file Lattice.h.

Referenced by registerUserEventsForAllComputeObjs().

{ return (i/9-1); }

origin()

NAMD_HOST_DEVICE Vector Lattice::origin ( ) const

inline

Definition at line 278 of file Lattice.h.

Referenced by Sequencer::berendsenPressure_SOA(), Controller::calcPressure(), ComputeEField::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeEwald::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), PDB::find_extremes(), HomePatch::hardWallDrude(), Sequencer::langevinPiston_SOA(), WorkDistrib::patchMapInit(), Controller::printEnergies(), HomePatch::rattle1old(), ComputeMsmSerialMgr::recvCoord(), scale_coordinates(), Sequencer::scalePositionsVelocities(), LjPmeMgr::setScaledCoordinates(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), Sequencer::submitReductions_SOA(), GridforceGrid::wrap_position(), and Controller::writeExtendedSystemData().

  {
    return o;
  }

orthogonal()

NAMD_HOST_DEVICE int Lattice::orthogonal ( ) const

inline

Definition at line 273 of file Lattice.h.

References Vector::x, Vector::y, and Vector::z.

Referenced by colvarproxy_namd::calculate(), LjPmeKSpace::compute_energy(), and PmeKSpace::compute_energy().

                                          {
    return ( ! ( a1.y || a1.z || a2.x || a2.z || a3.x || a3.y ) );
  }

rescale() [1/2]

NAMD_HOST_DEVICE void Lattice::rescale ( Tensor  factor )

inline

Definition at line 60 of file Lattice.h.

Referenced by Controller::berendsenPressure(), Sequencer::berendsenPressure(), Sequencer::berendsenPressure_SOA(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Sequencer::langevinPiston_SOA(), Controller::monteCarloPressure_prepare(), Sequencer::multigratorPressure(), and Controller::multigratorPressure().

  {
    a1 = factor * a1;
    a2 = factor * a2;
    a3 = factor * a3;
    recalculate();
  }

rescale() [2/2]

NAMD_HOST_DEVICE void Lattice::rescale ( Position &  p, Tensor  factor  ) const

inline

Definition at line 69 of file Lattice.h.

  {
    p -= o;
    p = factor * p;
    p += o;
  }

reverse_transform()

NAMD_HOST_DEVICE Position Lattice::reverse_transform ( Position  data, const Transform &  t  ) const

inline

Definition at line 143 of file Lattice.h.

References Transform::i, Transform::j, and Transform::k.

Referenced by HomePatch::depositMigration(), ComputeGridForce::do_calc(), ComputeConsForce::doForce(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeStir::doForce(), PatchMgr::moveAllBy(), PatchMgr::moveAtom(), ComputeGlobal::recvResults(), and CollectionMgr::submitPositions().

  {
    return ( data - t.i*a1 - t.j*a2 - t.k*a3 );
  }

scale()

NAMD_HOST_DEVICE ScaledPosition Lattice::scale ( Position  p ) const

inline

Definition at line 83 of file Lattice.h.

Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), HomePatch::doAtomMigration(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), ComputeMsmMgr::initialize(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), and nearest().

  {
    p -= o;
    return Vector(b1*p,b2*p,b3*p);
  }

scale_force()

NAMD_HOST_DEVICE Vector Lattice::scale_force ( Vector  f ) const

inline

Definition at line 89 of file Lattice.h.

References Vector::x, Vector::y, and Vector::z.

  {
    return (f.x*b1 + f.y*b2 + f.z*b3);  // calculating A^(-1)f for PME force contributions
  }

set() [1/2]

NAMD_HOST_DEVICE void Lattice::set ( Vector  A, Vector  B, Vector  C  )

inline

Definition at line 31 of file Lattice.h.

Referenced by get_lattice_from_ts(), and SimParameters::readExtendedSystem().

  {
    set(A,B,C,o);
  }

set() [2/2]

NAMD_HOST_DEVICE void Lattice::set ( Vector  A, Vector  B, Vector  C, Position  Origin  )

inline

Definition at line 37 of file Lattice.h.

References Vector::length(), Vector::length2(), and volume().

  {
    a1 = A; a2 = B; a3 = C; o = Origin;
    p1 = ( a1.length2() ? 1 : 0 );
    p2 = ( a2.length2() ? 1 : 0 );
    p3 = ( a3.length2() ? 1 : 0 );
    if ( ! p1 ) a1 = Vector(1.0,0.0,0.0);
    if ( ! p2 ) {
      Vector u1 = a1 / a1.length();
      Vector e_z(0.0,0.0,1.0);
      if ( fabs(e_z * u1) < 0.9 ) { a2 = cross(e_z,a1); }
      else { a2 = cross(Vector(1.0,0.0,0.0),a1); }
      a2 /= a2.length();
    }
    if ( ! p3 ) {
      a3 = cross(a1,a2);
      a3 /= a3.length();
    }
    if ( volume() < 0.0 ) a3 *= -1.0;
    recalculate();
  }

unscale()

NAMD_HOST_DEVICE Position Lattice::unscale ( ScaledPosition  s ) const

inline

Definition at line 77 of file Lattice.h.

References Vector::x, Vector::y, and Vector::z.

Referenced by CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), ComputeNonbondedPair::doForce(), HomePatch::doPairlistCheck(), Patch::forceBoxClosed(), nearest(), Patch::positionsReady(), HomePatch::positionsReady(), and HomePatch::positionsReady_SOA().

  {
    return (o + a1*s.x + a2*s.y + a3*s.z);
  }

volume()

NAMD_HOST_DEVICE BigReal Lattice::volume ( void  ) const

inline

Definition at line 293 of file Lattice.h.

Referenced by Controller::calcPressure(), CudaPmeOneDevice::compute(), LjPmeKSpace::compute_energy(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PressureProfileReduction::getData(), Controller::getTotalPotentialEnergy(), Controller::langevinPiston1(), Controller::langevinPiston2(), NamdState::loadStructure(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), Controller::multigatorCalcEnthalpy(), Controller::multigratorPressure(), Controller::printEnergies(), ComputeEwald::recvResults(), Controller::rescaleaccelMD(), set(), and CudaPmeKSpaceCompute::solve().

  {
    return ( p1 && p2 && p3 ? cross(a1,a2) * a3 : 0.0 );
  }

wrap_delta()

NAMD_HOST_DEVICE Vector Lattice::wrap_delta ( const Position &  pos1 ) const

inline

Definition at line 222 of file Lattice.h.

References namdnearbyint.

Referenced by ComputeEwald::doWork(), ParallelIOMgr::recvFinalClusterCoor(), wrap_coor_int(), wrap_coor_int_dcd_selection(), and GridforceGrid::wrap_position().

  {
    Vector diff = pos1 - o;
    Vector result(0.,0.,0.);
    if ( p1 ) result -= a1*namdnearbyint(b1*diff);
    if ( p2 ) result -= a2*namdnearbyint(b2*diff);
    if ( p3 ) result -= a3*namdnearbyint(b3*diff);
    return result;
  }

wrap_delta_scaled()

NAMD_HOST_DEVICE Vector Lattice::wrap_delta_scaled ( const Position &  pos1, const Position &  pos2  ) const

inline

Definition at line 192 of file Lattice.h.

References namdnearbyint, Vector::x, Vector::y, and Vector::z.

  {
    Vector diff = pos1 - pos2;
    Vector result(0.,0.,0.);
   
    if ( p1 ) result.x = -namdnearbyint(b1*diff);
    if ( p2 ) result.y = -namdnearbyint(b2*diff);
    if ( p3 ) result.z = -namdnearbyint(b3*diff);
    return result;
  }

wrap_delta_scaled_fast()

NAMD_HOST_DEVICE Vector Lattice::wrap_delta_scaled_fast ( const Position &  pos1, const Position &  pos2  ) const

inline

Definition at line 203 of file Lattice.h.

References namdnearbyint.

  {
    Vector diff = pos1 - pos2;
    Vector result(-namdnearbyint(b1*diff), -namdnearbyint(b2*diff), -namdnearbyint(b3*diff));
    return result;
  }

wrap_nearest_delta()

NAMD_HOST_DEVICE Vector Lattice::wrap_nearest_delta ( Position  pos1 ) const

inline

Definition at line 233 of file Lattice.h.

References Vector::length2(), and namdnearbyint.

Referenced by ParallelIOMgr::recvFinalClusterCoor(), wrap_coor_int(), and wrap_coor_int_dcd_selection().

  {
    Vector diff = pos1 - o;
    Vector result0(0.,0.,0.);
    if ( p1 ) result0 -= a1*namdnearbyint(b1*diff);
    if ( p2 ) result0 -= a2*namdnearbyint(b2*diff);
    if ( p3 ) result0 -= a3*namdnearbyint(b3*diff);
    diff += result0;
    BigReal dist = diff.length2();
    Vector result(0.,0.,0.);
    for ( int i1=-p1; i1<=p1; ++i1 ) {
      for ( int i2 =-p2; i2<=p2; ++i2 ) {
        for ( int i3 =-p3; i3<=p3; ++i3 ) {
          Vector newresult = i1*a1+i2*a2+i3*a3;
          BigReal newdist = (diff+newresult).length2();
          if ( newdist < dist ) {
            dist = newdist;
            result = newresult;
          }
        }
      }
    }
    return result0 + result;
  }

---

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

• Lattice.h