NamdTypes.h File Reference

#include "common.h"
#include "Vector.h"
#include "ResizeArray.h"

Go to the source code of this file.

Classes
struct	Transform
struct	CompAtom
struct	CompAtomExt
struct	FullAtom
struct	InputAtom
struct	CudaAtom
struct	LocalID
struct	ExtForce
struct	__sort_entry
struct	proxyTreeNode
Typedefs
typedef Vector	Position
typedef Vector	Velocity
typedef Vector	Force
typedef int	AtomID
typedef int	AtomType
typedef float	Mass
typedef float	Charge
typedef double	Coordinate
typedef int	SigIndex
typedef int	AtomSigID
typedef int	ExclSigID
typedef ResizeArray< CudaAtom >	CudaAtomList
typedef ResizeArray< CompAtom >	CompAtomList
typedef ResizeArray< CompAtomExt >	CompAtomExtList
typedef ResizeArray< FullAtom >	FullAtomList
typedef ResizeArray< InputAtom >	InputAtomList
typedef ResizeArray< Position >	PositionList
typedef ResizeArray< Velocity >	VelocityList
typedef ResizeArray< Force >	ForceList
typedef ResizeArray< Transform >	TransformList
typedef ResizeArray< AtomID >	AtomIDList
typedef ResizeArray< BigReal >	BigRealList
typedef ResizeArray< Real >	RealList
typedef float	GBReal
typedef ResizeArray< GBReal >	GBRealList
typedef ResizeArray< int >	IntList
typedef int	PatchID
typedef int	ComputeID
typedef int	NodeID
typedef ResizeArray< PatchID >	PatchIDList
typedef ResizeArray< Patch * >	PatchList
typedef ResizeArray< Compute * >	ComputeList
typedef ResizeArray< NodeID >	NodeIDList
typedef __sort_entry	SortEntry
typedef ResizeArray< proxyTreeNode >	proxyTreeNodeList

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Typedef Documentation

typedef int AtomID

Definition at line 27 of file NamdTypes.h. Referenced by AddAtom(), AddResidues(), AngleElem::AngleElem(), CollectionMaster::CollectVectorInstance::append(), colvarmodule::atom::atom(), BondElem::BondElem(), GlobalMasterTest::calculate(), DihedralElem::DihedralElem(), ARestraint::DistributeForce(), ARestraint::EarlyExit(), ExclElem::ExclElem(), ImproperElem::ImproperElem(), AtomMapper::registerIDsCompAtomExt(), AtomMapper::registerIDsFullAtom(), TholeElem::TholeElem(), AtomMapper::unregisterIDsCompAtomExt(), AtomMapper::unregisterIDsFullAtom(), and ARestraint::UpdateCOMs().

typedef ResizeArray<AtomID> AtomIDList

Definition at line 151 of file NamdTypes.h. Referenced by CollectionMgr::CollectVectorInstance::append(), GlobalMaster::forcedAtoms(), ParallelIOMgr::migrateAtomsMGrp(), GlobalMaster::modifyForcedAtoms(), GlobalMaster::modifyRequestedAtoms(), GlobalMaster::processData(), GlobalMaster::requestedAtoms(), CollectionMgr::CollectVectorSequence::submitData(), CollectionMgr::submitForces(), CollectionMgr::submitPositions(), and CollectionMgr::submitVelocities().

typedef int AtomSigID

Definition at line 73 of file NamdTypes.h.

typedef int AtomType

Definition at line 28 of file NamdTypes.h.

typedef ResizeArray<BigReal> BigRealList

Definition at line 152 of file NamdTypes.h.

typedef float Charge

Definition at line 30 of file NamdTypes.h. Referenced by ComputeGridForce::do_calc().

typedef ResizeArray<CompAtomExt> CompAtomExtList

Definition at line 143 of file NamdTypes.h.

typedef ResizeArray<CompAtom> CompAtomList

Definition at line 142 of file NamdTypes.h.

typedef int ComputeID

Definition at line 159 of file NamdTypes.h. Referenced by ComputeMap::cloneCompute(), PatchMap::newCid(), PatchMap::pack(), ComputeMap::storeCompute(), and PatchMap::unpack().

typedef ResizeArray<Compute *> ComputeList

Definition at line 165 of file NamdTypes.h.

typedef double Coordinate

Definition at line 32 of file NamdTypes.h.

typedef ResizeArray<CudaAtom> CudaAtomList

Definition at line 141 of file NamdTypes.h.

typedef int ExclSigID

Definition at line 74 of file NamdTypes.h.

typedef Vector Force

Definition at line 24 of file NamdTypes.h. Referenced by GlobalMasterFreeEnergy::addForce(), GlobalMasterEasy::addForce(), ARestraintManager::AddForces(), HomePatch::addForceToMomentum(), ExclElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), CrosstermElem::computeForce(), BondElem::computeForce(), AngleElem::computeForce(), ProxyPatch::depositCombinedResultRawMsg(), ARestraint::DistributeForce(), ComputeGridForce::do_calc(), ComputeStir::doForce(), ComputeSphericalBC::doForce(), ComputeRestraints::doForce(), ComputeGridForce::doForce(), ComputeEField::doForce(), ComputeCylindricalBC::doForce(), ComputeConsTorque::doForce(), ComputeConsForce::doForce(), ComputeFullDirect::doWork(), ComputeNonbondedCUDA::finishWork(), ProxyCombinedResultMsg::fromRaw(), ProxyResultVarsizeMsg::getANewMsg(), HomePatch::hardWallDrude(), Sequencer::minimizeMoveDownhill(), Sequencer::newMinimizeDirection(), PACK_MSG(), Patch::positionsReady(), proc_anglegrad(), proc_dihedralgrad(), HomePatch::rattle1(), HomePatch::receiveResults(), ComputeGlobal::recvResults(), ComputeMsmSerial::saveResults(), ComputeMsm::saveResults(), ComputeGBISser::saveResults(), ComputeExt::saveResults(), ComputeGlobal::saveTotalForces(), SELF(), CollectionMgr::submitForces(), Sequencer::submitMinimizeReductions(), ProxyCombinedResultMsg::toRaw(), ComputePme::ungridForces(), OptPmeCompute::ungridForces_finalize(), and ProxyResultMsg::unpack().

typedef ResizeArray<Force> ForceList

Definition at line 148 of file NamdTypes.h. Referenced by HomePatch::addForceToMomentum(), GlobalMaster::appliedForces(), ProxyResultVarsizeMsg::getANewMsg(), GlobalMaster::groupForces(), GlobalMaster::modifyAppliedForces(), GlobalMaster::modifyGroupForces(), ComputeGlobal::saveTotalForces(), and CollectionMgr::submitForces().

typedef ResizeArray<FullAtom> FullAtomList

Definition at line 144 of file NamdTypes.h. Referenced by WorkDistrib::createAtomLists(), PatchMgr::createHomePatch(), WorkDistrib::createHomePatches(), ParallelIOMgr::createHomePatches(), ComputeGBISser::doWork(), dumpbench(), HomePatch::getAtomList(), MovePatchesMsg::MovePatchesMsg(), WorkDistrib::reinitAtoms(), ComputeGlobal::saveTotalForces(), PatchMgr::sendAtoms(), CollectionMgr::submitForces(), CollectionMgr::submitPositions(), and CollectionMgr::submitVelocities().

typedef float GBReal

Definition at line 154 of file NamdTypes.h.

typedef ResizeArray<GBReal> GBRealList

Definition at line 155 of file NamdTypes.h.

typedef ResizeArray<InputAtom> InputAtomList

Definition at line 145 of file NamdTypes.h. Referenced by ParallelIOMgr::migrateAtomsMGrp().

typedef ResizeArray<int> IntList

Definition at line 156 of file NamdTypes.h.

typedef float Mass

Definition at line 29 of file NamdTypes.h.

typedef int NodeID

Definition at line 160 of file NamdTypes.h. Referenced by PatchMap::assignBaseNode(), ComputeMap::newNode(), ProxyMgr::registerProxy(), ProxyMgr::sendResult(), ProxyMgr::sendResults(), ProxyMgr::unregisterProxy(), and HomePatch::unregisterProxy().

typedef ResizeArray<NodeID> NodeIDList

Definition at line 174 of file NamdTypes.h. Referenced by HomePatch::buildSpanningTree(), ProxyMgr::buildSpanningTree0(), Rebalancer::createSpanningTree(), ProxyMgr::recvPatchProxyInfo(), ProxyMgr::recvProxies(), and ProxyMgr::recvSpanningTree().

typedef int PatchID

Definition at line 158 of file NamdTypes.h. Referenced by PatchMap::assignToPatch(), ProxyMgr::createProxies(), Patch::getPatchID(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::initialize(), ProxyMgr::removeUnusedProxies(), and LdbCoordinator::requiredProxies().

typedef ResizeArray<PatchID> PatchIDList

Definition at line 162 of file NamdTypes.h. Referenced by PatchMap::basePatchIDList(), ProxyMgr::buildProxySpanningTree(), ProxyMgr::buildProxySpanningTree2(), ComputeAngles::ComputeAngles(), ComputeAniso::ComputeAniso(), ComputeBonds::ComputeBonds(), ComputeCrossterms::ComputeCrossterms(), ComputeDihedrals::ComputeDihedrals(), ComputeExcls::ComputeExcls(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputeImpropers::ComputeImpropers(), ComputeThole::ComputeThole(), ProxyMgr::createProxies(), and PatchMap::homePatchIDList().

typedef ResizeArray<Patch *> PatchList

Definition at line 163 of file NamdTypes.h.

typedef Vector Position

Definition at line 18 of file NamdTypes.h. Referenced by Lattice::apply_transform(), PatchMap::assignToPatch(), Sequencer::berendsenPressure(), ComputeNonbondedUtil::calcGBIS(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), GridforceFullSubGrid::compute_b(), GridforceLiteGrid::compute_VdV(), GridforceFullBaseGrid::compute_VdV(), GridforceFullMainGrid::compute_VdV(), GridforceGrid::compute_VdV(), TholeElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), CrosstermElem::computeForce(), AnisoElem::computeForce(), AngleElem::computeForce(), WorkDistrib::createAtomLists(), Lattice::delta(), HomePatch::depositMigration(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeLCPO::doForce(), ComputeGridForce::doForce(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeConsForce::doForce(), HomePatch::doPairlistCheck(), GridforceGrid::fits_lattice(), GridforceLiteGrid::get_center(), GridforceFullMainGrid::get_center(), GridforceFullBaseGrid::get_center(), GridforceGrid::get_corner(), GridforceLiteGrid::get_inds(), GridforceFullBaseGrid::get_inds(), GridforceLiteGrid::get_origin(), GridforceFullMainGrid::get_origin(), GridforceFullBaseGrid::get_origin(), GlobalMasterFreeEnergy::getPosition(), GlobalMasterEasy::getPosition(), GridforceFullSubGrid::initialize(), GridforceFullMainGrid::initialize(), Sequencer::langevinPiston(), Lattice::nearest(), pairlistFromAll(), partition(), colvarproxy_namd::position_distance(), GridforceFullBaseGrid::readHeader(), ComputeGlobal::recvResults(), Lattice::rescale(), Lattice::reverse_transform(), Lattice::scale(), colvarproxy_namd::select_closest_image(), Lattice::set(), Sequencer::submitMinimizeReductions(), Sequencer::submitReductions(), Lattice::unscale(), wrap_coor_int(), Lattice::wrap_delta(), Lattice::wrap_nearest_delta(), and GridforceGrid::wrap_position().

typedef ResizeArray<Position> PositionList

Definition at line 146 of file NamdTypes.h. Referenced by CollectionMgr::submitPositions(), and CollectionMgr::submitVelocities().

typedef ResizeArray<proxyTreeNode> proxyTreeNodeList

Definition at line 241 of file NamdTypes.h.

typedef ResizeArray<Real> RealList

Definition at line 153 of file NamdTypes.h.

typedef int SigIndex

Definition at line 72 of file NamdTypes.h. Referenced by buildBondData(), and outputCompressedFile().

typedef struct __sort_entry SortEntry

Referenced by SELF(), sortEntries_bubbleSort(), sortEntries_mergeSort_v1(), sortEntries_mergeSort_v2(), and sortEntries_selectionSort().

typedef ResizeArray<Transform> TransformList

Definition at line 149 of file NamdTypes.h.

typedef Vector Velocity

Definition at line 19 of file NamdTypes.h. Referenced by WorkDistrib::createAtomLists(), Sequencer::langevinPiston(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().

typedef ResizeArray<Velocity> VelocityList

Definition at line 147 of file NamdTypes.h.

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