NAMD
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#include <Lattice.h>
Static Public Member Functions | |
static int | index (int i=0, int j=0, int k=0) |
static int | offset_a (int i) |
static int | offset_b (int i) |
static int | offset_c (int i) |
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Definition at line 252 of file Lattice.h.
Referenced by colvarproxy_namd::calculate(), PmeKSpace::compute_energy(), HomePatch::doMarginCheck(), ComputeNonbondedCUDA::doWork(), GridforceFullMainGrid::initialize(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), lattice_to_unitcell(), cr_sortop_distance::operator()(), Controller::printEnergies(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), and Controller::writeExtendedSystemData().
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Definition at line 273 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().
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Definition at line 268 of file Lattice.h.
Referenced by PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), ComputeEField::doForce(), HomePatch::doMarginCheck(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), WorkDistrib::patchMapInit(), ComputeMsmSerialMgr::recvCoord(), scale_coordinates(), scale_forces(), PatchMap::sizeGrid(), and CudaPmeKSpaceCompute::solve().
Definition at line 132 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().
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Definition at line 253 of file Lattice.h.
Referenced by colvarproxy_namd::calculate(), PmeKSpace::compute_energy(), HomePatch::doMarginCheck(), ComputeNonbondedCUDA::doWork(), GridforceFullMainGrid::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), lattice_to_unitcell(), cr_sortop_distance::operator()(), Controller::printEnergies(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), and Controller::writeExtendedSystemData().
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Definition at line 274 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().
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Definition at line 269 of file Lattice.h.
Referenced by PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), ComputeEField::doForce(), HomePatch::doMarginCheck(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_pencils(), WorkDistrib::patchMapInit(), ComputeMsmSerialMgr::recvCoord(), scale_coordinates(), scale_forces(), PatchMap::sizeGrid(), and CudaPmeKSpaceCompute::solve().
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Definition at line 254 of file Lattice.h.
Referenced by colvarproxy_namd::calculate(), PmeKSpace::compute_energy(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), HomePatch::doMarginCheck(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), HomePatch::hardWallDrude(), GridforceFullMainGrid::initialize(), ComputeMsmMgr::initialize(), Controller::langevinPiston1(), Controller::langevinPiston2(), lattice_to_unitcell(), cr_sortop_distance::operator()(), Controller::printEnergies(), HomePatch::rattle1old(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeNonbondedCUDA::recvYieldDevice(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), and Controller::writeExtendedSystemData().
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Definition at line 275 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().
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Definition at line 270 of file Lattice.h.
Referenced by PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), ComputeEField::doForce(), HomePatch::doMarginCheck(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), ComputeMsmMgr::initialize(), WorkDistrib::patchMapInit(), ComputeMsmSerialMgr::recvCoord(), scale_coordinates(), scale_forces(), PatchMap::sizeGrid(), and CudaPmeKSpaceCompute::solve().
Definition at line 144 of file Lattice.h.
References namdnearbyint, Vector::x, Vector::y, and Vector::z.
Referenced by AngleElem::computeForce(), CrosstermElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), TholeElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), ComputeRestraints::doForce(), colvarproxy_namd::position_distance(), and ComputeQM::processFullQM().
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Definition at line 25 of file Lattice.h.
Referenced by PatchMap::downstreamNeighbors(), PatchMap::getPatchesInOctet(), PatchMap::oneAwayNeighbors(), PatchMap::oneOrTwoAwayNeighbors(), and PatchMap::upstreamNeighbors().
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Definition at line 90 of file Lattice.h.
References namdnearbyint, scale(), unscale(), Vector::x, Vector::y, and Vector::z.
Referenced by WorkDistrib::createAtomLists(), and HomePatch::depositMigration().
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Definition at line 107 of file Lattice.h.
References Transform::i, Transform::j, Transform::k, namdnearbyint, scale(), unscale(), Vector::x, Vector::y, and Vector::z.
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Definition at line 242 of file Lattice.h.
Referenced by ComputeNonbondedPair::doForce().
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Definition at line 247 of file Lattice.h.
Referenced by registerUserEventsForAllComputeObjs().
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Definition at line 248 of file Lattice.h.
Referenced by registerUserEventsForAllComputeObjs().
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Definition at line 249 of file Lattice.h.
Referenced by registerUserEventsForAllComputeObjs().
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Definition at line 262 of file Lattice.h.
Referenced by Controller::calcPressure(), ComputeEField::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeEwald::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), PDB::find_extremes(), HomePatch::hardWallDrude(), WorkDistrib::patchMapInit(), Controller::printEnergies(), HomePatch::rattle1old(), ComputeMsmSerialMgr::recvCoord(), scale_coordinates(), Sequencer::scalePositionsVelocities(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), GridforceGrid::wrap_position(), and Controller::writeExtendedSystemData().
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Definition at line 257 of file Lattice.h.
References Vector::x, Vector::y, and Vector::z.
Referenced by colvarproxy_namd::calculate(), and PmeKSpace::compute_energy().
Definition at line 60 of file Lattice.h.
Referenced by Sequencer::berendsenPressure(), Controller::berendsenPressure(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Sequencer::multigratorPressure(), and Controller::multigratorPressure().
Definition at line 138 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().
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Definition at line 83 of file Lattice.h.
Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), HomePatch::doAtomMigration(), HomePatch::doMarginCheck(), ComputeMsmMgr::initialize(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), and nearest().
Definition at line 31 of file Lattice.h.
Referenced by get_lattice_from_ts(), and SimParameters::readExtendedSystem().
Definition at line 37 of file Lattice.h.
References A, B, cross(), Vector::length(), Vector::length2(), and volume().
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Definition at line 77 of file Lattice.h.
References Vector::x, Vector::y, and Vector::z.
Referenced by ComputeNonbondedPair::doForce(), HomePatch::doPairlistCheck(), ComputeNonbondedCUDA::doWork(), Patch::forceBoxClosed(), nearest(), Patch::positionsReady(), and HomePatch::positionsReady().
Definition at line 277 of file Lattice.h.
References cross().
Referenced by Controller::calcPressure(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PressureProfileReduction::getData(), Controller::langevinPiston1(), Controller::langevinPiston2(), NamdState::loadStructure(), Controller::multigatorCalcEnthalpy(), Controller::multigratorPressure(), Controller::printEnergies(), ComputeEwald::recvResults(), Controller::rescaleaccelMD(), set(), and CudaPmeKSpaceCompute::solve().
Definition at line 206 of file Lattice.h.
References namdnearbyint.
Referenced by ComputeEwald::doWork(), ParallelIOMgr::recvFinalClusterCoor(), wrap_coor_int(), and GridforceGrid::wrap_position().
Definition at line 217 of file Lattice.h.
References Vector::length2(), and namdnearbyint.
Referenced by ParallelIOMgr::recvFinalClusterCoor(), and wrap_coor_int().