NAMD
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#include <packmsg.h>
Public Types | |
typedef Elem * | iterator |
typedef const Elem * | const_iterator |
Public Member Functions | |
iterator | begin (void) |
iterator | end (void) |
const_iterator | const_begin (void) const |
const_iterator | const_end (void) const |
ResizeArray (void) | |
ResizeArray (int s) | |
void | copy (ResizeArray< Elem > &ra) |
void | swap (ResizeArray< Elem > &ra) |
bool | shared () const |
ResizeArray (Elem **array, int arraySize, int allocSize=0) | |
~ResizeArray (void) | |
void | resize (int i) |
void | reserve (int i) |
void | clear () |
void | setall (const Elem &elem) |
int | add (const Elem &elem) |
void | del (int index, int num=1) |
int | insert (const Elem &elem, int index) |
Elem & | item (int i) |
Elem & | operator[] (int index) |
const Elem & | operator[] (int index) const |
int | size (void) const |
int | find (const Elem &e) const |
Protected Attributes | |
ResizeArrayRaw< Elem > | rep |
Friends | |
class | ResizeArrayIter< Elem > |
typedef const Elem* ResizeArray< Elem >::const_iterator |
Definition at line 38 of file ResizeArray.h.
typedef Elem* ResizeArray< Elem >::iterator |
Definition at line 35 of file ResizeArray.h.
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Definition at line 43 of file ResizeArray.h.
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Definition at line 46 of file ResizeArray.h.
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Definition at line 77 of file ResizeArray.h.
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Definition at line 80 of file ResizeArray.h.
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Definition at line 101 of file ResizeArray.h.
Referenced by MigrateAtomsCombinedMsg::add(), VDWTable::add14Type(), GenericMol::addAngle(), GenericMol::addAtom(), GenericMol::addBond(), GenericMol::addDihedral(), GlobalMasterEasy::addForce(), GlobalMasterFreeEnergy::addForce(), PairTable::addPairGaussType2(), PairTable::addPairLJType2(), AtomTable::addType(), BondTable::addType(), AngleTable::addType(), DihedralTable::addType(), VDWTable::addType(), CollectionMgr::CollectVectorInstance::append(), Parameters::assign_vdw_index(), CudaComputeNonbonded::assignPatchesOnPe(), PatchMap::basePatchIDList(), Molecule::build_go_sigmas2(), GlobalMasterTest::calculate(), GlobalMasterIMD::calculate(), colvarproxy_namd::calculate(), WorkDistrib::createAtomLists(), ProxyPatch::depositCombinedResultMsg(), ProxyPatch::depositCombinedResultRawMsg(), HomePatch::depositMigration(), HomePatch::doAtomMigration(), ComputeGlobal::doWork(), CollectionMaster::CollectVectorSequence::enqueue(), ProxyCombinedResultMsg::fromRaw(), BondTable::getIndex(), AngleTable::getIndex(), ObjectArena< char >::getNewArray(), GromacsTopFile::GromacsTopFile(), PatchMap::homePatchIDList(), colvarproxy_namd::init_atom(), colvarproxy_namd::init_volmap_by_id(), colvarproxy_namd::init_volmap_by_name(), ComputeQM::initialize(), ComputePmeMgr::initialize(), ParallelIOMgr::migrateAtomsMGrp(), ComputePme::noWork(), ComputeQM::processFullQM(), ComputeMgr::recvComputeGlobalResults(), ProxyMgr::recvNodeAwareSpanningTree(), ComputeQMMgr::recvPartQM(), ProxyMgr::recvSpanningTree(), HomePatch::registerProxy(), ProxyMgr::removeUnusedProxies(), GlobalMasterEasy::requestAtom(), GlobalMasterFreeEnergy::requestAtom(), ComputeGlobal::saveTotalForces(), ParallelIOMgr::sendAtomsToHomePatchProcs(), PatchMgr::sendMigrationMsgs(), colvarproxy_namd::update_atoms_map(), ComputeMgr::updateLocalComputes(), and ParallelIOMgr::wrapCoor().
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Definition at line 36 of file ResizeArray.h.
Referenced by Sequencer::addForceToMomentum(), Sequencer::addForceToMomentum3(), Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), Sequencer::addVelocityToPosition(), CollectionMaster::CollectVectorInstance::append(), CollectionMaster::CollectVectorInstanceDcdSelection::append(), Sequencer::berendsenPressure(), Molecule::build_go_sigmas2(), WorkDistrib::buildNodeAwarePeOrdering(), HomePatch::buildSpanningTree(), Sequencer::calcFixVirial(), Sequencer::calcKineticEnergy(), colvarproxy_namd::calculate(), ComputeGridForce::checkGridForceRatio(), Sequencer::correctMomentum(), WorkDistrib::createAtomLists(), ComputeGridForce::createGridForcedIdxList(), ProxyPatch::depositCombinedResultMsg(), ProxyPatch::depositCombinedResultRawMsg(), HomePatch::depositMigration(), CollectionMaster::disposeForces(), CollectionMaster::disposePositions(), CollectionMaster::disposeVelocities(), HomePatch::doAtomMigration(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), HomePatch::doPairlistCheck(), ComputeHomePatch::doWork(), ComputePme::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), HomePatch::exchangeAtoms(), Patch::forceBoxClosed(), ProxyCombinedResultMsg::fromRaw(), HomePatch::gbisP2Ready(), HomePatch::gbisP3Ready(), ProxyResultVarsizeMsg::getANewMsg(), Patch::getCompAtomExtInfo(), Patch::getCompAtomInfo(), PairTable::getPairGaussArrays2(), PairTable::getPairLJArrays2(), ComputePmeMgr::initialize(), Sequencer::integrate(), Sequencer::langevinPiston(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), CudaComputeNonbonded::launchWork(), Sequencer::maximumMove(), Sequencer::maximumMove_SOA(), ParallelIOMgr::migrateAtomsMGrp(), Sequencer::minimizationQuenchVelocity(), Sequencer::minimize(), HomePatch::minimize_rattle2(), Sequencer::minimizeMoveDownhill(), PatchMgr::moveAllBy(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Sequencer::newMinimizeDirection(), Sequencer::newMinimizePosition(), outputCompressedFile(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), Molecule::prepare_qm(), HomePatch::qmSwapAtoms(), Sequencer::quenchVelocities(), Sequencer::reassignVelocities(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), CollectionMaster::receiveDataStream(), HomePatch::receiveResults(), PmeZPencil::recv_grid(), HomePatch::recvCheckpointLoad(), HomePatch::recvCheckpointReq(), HomePatch::recvCheckpointStore(), GlobalMasterServer::recvData(), HomePatch::recvExchangeMsg(), ComputeGlobal::recvResults(), HomePatch::registerProxy(), Sequencer::reinitVelocities(), Sequencer::reloadCharges(), ProxyMgr::removeUnusedProxies(), Sequencer::rescaleSoluteCharges(), Sequencer::rescaleVelocities(), Sequencer::rescaleVelocitiesByFactor(), HomePatch::revert(), Sequencer::runComputeObjects(), ComputeGlobal::saveTotalForces(), Sequencer::scalePositionsVelocities(), Sequencer::scaleVelocities(), ParallelIOMgr::sendAtomsToHomePatchProcs(), CollectionMgr::sendDataStream(), HomePatch::sendProxies(), ProxyMgr::sendSpanningTrees(), PmeRealSpace::set_num_atoms(), ResizeArray< GromacsPairElem >::setall(), PatchMgr::setLattice(), WorkDistrib::sortPmePes(), Sequencer::stochRescaleVelocities(), CollectionMgr::submitForces(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), Sequencer::submitMomentum(), Sequencer::submitReductions(), CollectionMgr::submitVelocities(), Sequencer::tcoupleVelocities(), ProxyCombinedResultMsg::toRaw(), ComputePme::ungridForces(), ProxyResultMsg::unpack(), HomePatch::unregisterProxy(), HomePatch::~HomePatch(), and ProxyPatch::~ProxyPatch().
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Definition at line 91 of file ResizeArray.h.
Referenced by colvarproxy_namd::calculate(), ParallelIOMgr::migrateAtomsMGrp(), ComputeQM::processFullQM(), ComputeQMMgr::recvFullQM(), ComputeQMMgr::recvPntChrg(), colvarproxy_namd::reset(), ParallelIOMgr::sendAtomsToHomePatchProcs(), and ComputeMgr::updateLocalComputes3().
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Definition at line 39 of file ResizeArray.h.
Referenced by Sequencer::addForceToMomentum(), Sequencer::addForceToMomentum3(), and Sequencer::rattle1().
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Definition at line 40 of file ResizeArray.h.
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Definition at line 59 of file ResizeArray.h.
Referenced by HomePatch::checkpoint(), ProxyMgr::recvSpanningTree(), HomePatch::revert(), and HomePatch::sendSpanningTree().
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Definition at line 108 of file ResizeArray.h.
Referenced by SortedArray< PatchElem >::del(), HomePatch::doAtomMigration(), ComputeMgr::enableComputeGlobalResults(), GlobalMasterIMD::get_vmd_forces(), CollectionMaster::CollectVectorSequence::removeReady(), CollectionMaster::CollectVectorSequenceDcdSelection::removeReady(), and HomePatch::unregisterProxy().
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Definition at line 37 of file ResizeArray.h.
Referenced by ResizeArray< GromacsPairElem >::add(), Molecule::build_go_sigmas2(), HomePatch::buildSpanningTree(), colvarproxy_namd::calculate(), ProxyPatch::depositCombinedResultMsg(), HomePatch::depositMigration(), HomePatch::doAtomMigration(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), PairTable::getPairGaussArrays2(), PairTable::getPairLJArrays2(), ComputePmeMgr::initialize(), Sequencer::integrate(), CudaComputeNonbonded::launchWork(), Sequencer::minimize(), PatchMgr::moveAllBy(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), Molecule::prepare_qm(), ProxyPatch::receiveAll(), HomePatch::receiveResults(), HomePatch::recvCheckpointLoad(), GlobalMasterServer::recvData(), HomePatch::recvExchangeMsg(), ComputeGlobal::recvResults(), ProxyMgr::removeUnusedProxies(), HomePatch::revert(), ComputeGlobal::saveTotalForces(), ResizeArray< GromacsPairElem >::setall(), PatchMgr::setLattice(), HomePatch::~HomePatch(), and ProxyPatch::~ProxyPatch().
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Definition at line 141 of file ResizeArray.h.
Referenced by HomePatch::buildSpanningTree(), and ProxyMgr::buildSpanningTree0().
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Definition at line 113 of file ResizeArray.h.
Referenced by UniqueSortedArray< PatchElem >::insert().
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Definition at line 119 of file ResizeArray.h.
Referenced by GlobalMasterTest::calculate(), GlobalMasterIMD::calculate(), and ProxyMgr::recvNodeAwareSpanningTree().
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Definition at line 127 of file ResizeArray.h.
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Definition at line 128 of file ResizeArray.h.
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Definition at line 88 of file ResizeArray.h.
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Definition at line 84 of file ResizeArray.h.
Referenced by CollectionMaster::CollectVectorInstance::append(), CollectionMaster::CollectVectorInstanceDcdSelection::append(), PatchMap::basePatchIDList(), HomePatch::buildSpanningTree(), ProxyMgr::buildSpanningTree0(), GlobalMasterTest::calculate(), GlobalMasterTcl::calculate(), GlobalMasterIMD::calculate(), colvarproxy_namd::calculate(), ComputeGlobal::ComputeGlobal(), ComputeTclBC::ComputeTclBC(), Rebalancer::createSpanningTree(), MigrateAtomsCombinedMsg::distribute(), HomePatch::doAtomMigration(), HomePatch::doPairlistCheck(), ComputePme::doWork(), PDB::find_extremes(), Patch::forceBoxClosed(), ProxyCombinedResultMsg::fromRaw(), PatchMap::homePatchIDList(), colvarproxy_namd::init_atom_group(), ComputeHomePatches::initialize(), ComputeQM::initialize(), ComputePmeMgr::initialize(), ResizeArray< GromacsPairElem >::item(), HomePatch::loweAndersenFinish(), HomePatch::loweAndersenVelocities(), lssDistSort::lssDistSort(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), lssDistSort::operator=(), outputCompressedFile(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), HomePatch::recvCheckpointLoad(), HomePatch::recvCheckpointStore(), HomePatch::recvExchangeMsg(), ProxyMgr::recvPatchProxyInfo(), ProxyMgr::recvProxies(), ComputeGlobal::recvResults(), HomePatch::recvSpanningTree(), CollectionMgr::CollectVectorInstance::reset(), CollectionMaster::CollectVectorInstance::reset(), HomePatch::saveForce(), CollectionMgr::sendDataStream(), PatchMgr::sendMigrationMsgs(), PatchMgr::sendMovePatches(), PmeRealSpace::set_num_atoms(), HomePatch::setGBISIntrinsicRadii(), HomePatch::setLcpoType(), ComputePmeMgr::submitReductions(), ComputePme::ungridForces(), ProxyResultMsg::unpack(), ComputeMgr::updateLocalComputes(), Parameters::~Parameters(), and ProxyPatch::~ProxyPatch().
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Definition at line 94 of file ResizeArray.h.
Referenced by HomePatch::buildSpanningTree(), ProxyMgr::buildSpanningTree0(), GlobalMasterTcl::calculate(), colvarproxy_namd::calculate(), Patch::positionsReady(), and HomePatch::setGBISIntrinsicRadii().
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Definition at line 72 of file ResizeArray.h.
Referenced by PatchMgr::sendAtoms(), PatchMgr::sendMovePatches(), and PatchMgr::sendOneHomePatch().
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Definition at line 131 of file ResizeArray.h.
Referenced by MigrateAtomsCombinedMsg::add(), CollectionMgr::CollectVectorInstance::append(), Parameters::assign_vdw_index(), CudaComputeNonbonded::assignPatchesOnPe(), HomePatch::boxClosed(), SortableResizeArray< PatchElem >::bsearch(), ProxyMgr::buildProxySpanningTree(), ProxyMgr::buildProxySpanningTree2(), HomePatch::buildSpanningTree(), ProxyMgr::buildSpanningTree0(), GlobalMasterTest::calculate(), GlobalMasterIMD::calculate(), ComputePmeMgr::chargeGridReady(), GlobalMaster::check(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputePmeCUDA::ComputePmeCUDA(), WorkDistrib::createAtomLists(), WorkDistrib::createHomePatches(), ProxyMgr::createProxies(), Rebalancer::decrSTLoad(), SortedArray< PatchElem >::del(), HomePatch::depositMigration(), CollectionMaster::disposeForces(), CollectionMaster::disposePositions(), CollectionMaster::disposeVelocities(), MigrateAtomsCombinedMsg::distribute(), HomePatch::doAtomMigration(), ComputeMsm::doWork(), ComputePme::doWork(), ComputeQM::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), ComputeMgr::enableComputeGlobalResults(), ResizeArrayPrimIter< T >::end(), ResizeArrayIter< PatchElem >::end(), HomePatch::gbisP2Ready(), HomePatch::gbisP3Ready(), GlobalMasterIMD::get_vmd_forces(), ProxyResultVarsizeMsg::getANewMsg(), GenericMol::getAngle(), GromacsTopFile::getAngle(), GenericMol::getAtom(), GromacsTopFile::getAtom(), GenericMol::getBond(), GromacsTopFile::getBond(), GenericMol::getDihedral(), GromacsTopFile::getDihedral(), GromacsTopFile::getExclusions(), BondTable::getIndex(), AngleTable::getIndex(), DihedralTable::getIndex(), GenericMol::getNumAngles(), GromacsTopFile::getNumAngles(), GenericMol::getNumAtoms(), GromacsTopFile::getNumAtoms(), GenericMol::getNumBonds(), GromacsTopFile::getNumBonds(), Patch::getNumComputes(), GenericMol::getNumDihedrals(), GromacsTopFile::getNumDihedrals(), GenericMol::getNumRes(), AtomTable::getParams(), BondTable::getParams(), AngleTable::getParams(), DihedralTable::getParams(), AtomTable::getType(), GromacsTopFile::GromacsTopFile(), Rebalancer::incrSTLoad(), colvarproxy_namd::init_atom_group(), ComputeHomePatches::initialize(), ComputePmeMgr::initialize(), ResizeArray< GromacsPairElem >::item(), lssDistSort::lssDistSort(), ParallelIOMgr::migrateAtomsMGrp(), PmeZPencil::node_process_grid(), ComputePme::noWork(), lssDistSort::operator=(), lssDistSort::operator==(), outputProxyTree(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), Molecule::prepare_qm(), ComputeQM::processFullQM(), ComputeQMMgr::procQMRes(), HomePatch::receiveResult(), ComputeMgr::recvComputeConsForceMsg(), GlobalMasterServer::recvData(), ParallelIOMgr::recvFinalClusterCoor(), ComputeQMMgr::recvFullQM(), PatchMgr::recvMigrateAtomsCombined(), ProxyMgr::recvNodeAwareSpanningTree(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), ComputePmeMgr::recvRecipEvir(), ComputeGlobal::recvResults(), ProxyMgr::recvSpanningTree(), HomePatch::recvSpanningTree(), Patch::registerDEdaSumDeposit(), Patch::registerForceDeposit(), HomePatch::registerProxy(), Patch::registerPsiSumDeposit(), CollectionMaster::CollectVectorSequence::removeReady(), CollectionMaster::CollectVectorSequenceDcdSelection::removeReady(), HomePatch::revert(), ComputeQM::saveResults(), PmeZPencil::send_all_ungrid(), GlobalMasterIMD::send_energies(), GlobalMasterIMD::send_fcoords(), ParallelIOMgr::sendAtomsToHomePatchProcs(), ComputePmeMgr::sendChargeGridReady(), PatchMgr::sendMigrationMsgs(), PatchMgr::sendMovePatches(), HomePatch::sendProxies(), HomePatch::sendSpanningTree(), ProxyMgr::sendSpanningTrees(), colvarproxy_namd::setup(), AtomTable::size(), BondTable::size(), AngleTable::size(), DihedralTable::size(), SortableResizeArray< PatchElem >::sort(), CollectionMgr::submitForces(), CollectionMgr::submitPositions(), ComputePmeMgr::submitReductions(), CollectionMgr::submitVelocities(), ProxyCombinedResultMsg::toRaw(), ComputePmeMgr::ungridCalc(), colvarproxy_namd::update_group_properties(), ComputeMgr::updateLocalComputes3(), ParallelIOMgr::wrapCoor(), GlobalMasterIMD::~GlobalMasterIMD(), ObjectArena< char >::~ObjectArena(), and Parameters::~Parameters().
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Definition at line 64 of file ResizeArray.h.
Referenced by HomePatch::buildSpanningTree(), ProxyMgr::buildSpanningTree0(), and MovePatchesMsg::MovePatchesMsg().
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Definition at line 28 of file ResizeArray.h.
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Definition at line 31 of file ResizeArray.h.
Referenced by ResizeArray< GromacsPairElem >::add(), ResizeArray< GromacsPairElem >::begin(), SortableResizeArray< PatchElem >::bsearch(), ResizeArray< GromacsPairElem >::clear(), ResizeArray< GromacsPairElem >::const_begin(), ResizeArray< GromacsPairElem >::const_end(), ResizeArray< GromacsPairElem >::copy(), SortedArray< PatchElem >::del(), ResizeArray< GromacsPairElem >::del(), ResizeArray< GromacsPairElem >::end(), ResizeArray< GromacsPairElem >::find(), ResizeArray< GromacsPairElem >::insert(), ResizeArray< GromacsPairElem >::item(), ResizeArrayIter< PatchElem >::operator*(), ResizeArrayIter< PatchElem >::operator->(), ResizeArray< GromacsPairElem >::operator[](), ResizeArray< GromacsPairElem >::reserve(), ResizeArray< GromacsPairElem >::resize(), ResizeArray< GromacsPairElem >::ResizeArray(), ResizeArray< GromacsPairElem >::size(), SortableResizeArray< PatchElem >::sort(), ResizeArray< GromacsPairElem >::swap(), and ResizeArray< GromacsPairElem >::~ResizeArray().