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	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 unsigned short	AtomSigID
typedef unsigned short	ExclSigID
typedef ResizeArray< CompAtom >	CompAtomList
typedef ResizeArray< CompAtomExt >	CompAtomExtList
typedef ResizeArray< FullAtom >	FullAtomList
typedef ResizeArray< Position >	PositionList
typedef ResizeArray< Velocity >	VelocityList
typedef ResizeArray< Force >	ForceList
typedef ResizeArray< Transform >	TransformList
typedef ResizeArray< AtomID >	AtomIDList
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

---

Typedef Documentation

typedef int AtomID

Definition at line 27 of file NamdTypes.h. Referenced by AddAtom(), AddResidues(), AngleElem::AngleElem(), colvarmodule::atom::atom(), BondElem::BondElem(), GlobalMasterTest::calculate(), DihedralElem::DihedralElem(), ARestraint::DistributeForce(), ARestraint::EarlyExit(), ExclElem::ExclElem(), ImproperElem::ImproperElem(), and ARestraint::UpdateCOMs().

typedef ResizeArray<AtomID> AtomIDList

Definition at line 100 of file NamdTypes.h. Referenced by CollectionMgr::CollectVectorInstance::append(), CollectionMaster::CollectVectorInstance::append(), ComputeGlobal::ComputeGlobal(), GlobalMaster::forcedAtoms(), GlobalMaster::modifyForcedAtoms(), GlobalMaster::modifyRequestedAtoms(), GlobalMaster::processData(), GlobalMaster::requestedAtoms(), CollectionMgr::CollectVectorSequence::submitData(), CollectionMaster::CollectVectorSequence::submitData(), CollectionMgr::submitPositions(), and CollectionMgr::submitVelocities().

typedef unsigned short AtomSigID

Definition at line 71 of file NamdTypes.h.

typedef int AtomType

Definition at line 28 of file NamdTypes.h.

typedef float Charge

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

typedef ResizeArray<CompAtomExt> CompAtomExtList

Definition at line 93 of file NamdTypes.h.

typedef ResizeArray<CompAtom> CompAtomList

Definition at line 91 of file NamdTypes.h.

typedef int ComputeID

Definition at line 103 of file NamdTypes.h. Referenced by PatchMap::newCid(), PatchMap::pack(), ComputeMap::storeCompute(), and PatchMap::unpack().

typedef ResizeArray<Compute *> ComputeList

Definition at line 109 of file NamdTypes.h.

typedef double Coordinate

Definition at line 32 of file NamdTypes.h.

typedef unsigned short ExclSigID

Definition at line 72 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(), ARestraint::DistributeForce(), ComputeStir::doForce(), ComputeSphericalBC::doForce(), ComputeRestraints::doForce(), ComputeEField::doForce(), ComputeCylindricalBC::doForce(), ComputeConsTorque::doForce(), ComputeConsForce::doForce(), ComputeFullDirect::doWork(), ComputeGridForce::finishForce(), ComputeNonbondedCUDA::finishWork(), ProxyResultVarsizeMsg::getANewMsg(), Sequencer::minimizeMoveDownhill(), Sequencer::newMinimizeDirection(), ProxyCombinedResultMsg::pack(), PACK_MSG(), Patch::positionsReady(), proc_anglegrad(), proc_dihedralgrad(), HomePatch::rattle1(), HomePatch::receiveResults(), ComputeGlobal::recvResults(), ComputeExt::saveResults(), ComputeGlobal::saveTotalForces(), SELF(), Sequencer::submitMinimizeReductions(), OptPmeCompute::ungridForces(), ComputePme::ungridForces(), ProxyCombinedResultMsg::unpack(), and ProxyResultMsg::unpack().

typedef ResizeArray<Force> ForceList

Definition at line 97 of file NamdTypes.h. Referenced by HomePatch::addForceToMomentum(), GlobalMaster::appliedForces(), ComputeGlobal::ComputeGlobal(), ProxyResultVarsizeMsg::getANewMsg(), GlobalMaster::groupForces(), GlobalMaster::modifyAppliedForces(), GlobalMaster::modifyGroupForces(), and ComputeGlobal::saveTotalForces().

typedef ResizeArray<FullAtom> FullAtomList

Definition at line 94 of file NamdTypes.h. Referenced by HomePatch::checkpoint(), WorkDistrib::createAtomLists(), PatchMgr::createHomePatch(), WorkDistrib::createHomePatches(), dumpbench(), PatchMgr::fillHomePatchAtomList(), WorkDistrib::fillOnePatchAtoms(), HomePatch::getAtomList(), WorkDistrib::initAndSendHomePatch(), MovePatchesMsg::MovePatchesMsg(), WorkDistrib::reinitAtoms(), HomePatch::revert(), ComputeGlobal::saveTotalForces(), PatchMgr::sendAtoms(), HomePatch::setAtomList(), CollectionMgr::submitPositions(), and CollectionMgr::submitVelocities().

typedef float Mass

Definition at line 29 of file NamdTypes.h. Referenced by ARestraint::DistributeForce(), and ARestraint::UpdateCOMs().

typedef int NodeID

Definition at line 104 of file NamdTypes.h. Referenced by PatchMap::assignBaseNode(), ComputeMap::newNode(), ProxyCombinedResultMsg::pack(), ProxyMgr::registerProxy(), ProxyMgr::sendResults(), and ProxyMgr::unregisterProxy().

typedef ResizeArray<NodeID> NodeIDList

Definition at line 118 of file NamdTypes.h. Referenced by HomePatch::buildSpanningTree(), ProxyMgr::buildSpanningTree0(), Rebalancer::createSpanningTree(), ProxyMgr::recvProxies(), ProxyMgr::recvSpanningTree(), and HomePatch::sendProxies().

typedef int PatchID

Definition at line 102 of file NamdTypes.h. Referenced by PatchMap::assignToPatch(), ProxyMgr::createProxies(), Patch::getPatchID(), ComputeHomeTuples< ExclElem, Exclusion, int >::initialize(), ProxyMgr::removeUnusedProxies(), and LdbCoordinator::requiredProxies().

typedef ResizeArray<PatchID> PatchIDList

Definition at line 106 of file NamdTypes.h. Referenced by PatchMap::basePatchIDList(), ProxyMgr::buildProxySpanningTree(), ProxyMgr::buildProxySpanningTree2(), ComputeAngles::ComputeAngles(), ComputeBonds::ComputeBonds(), ComputeCrossterms::ComputeCrossterms(), ComputeDihedrals::ComputeDihedrals(), ComputeExcls::ComputeExcls(), ComputeHomeTuples< ExclElem, Exclusion, int >::ComputeHomeTuples(), ComputeImpropers::ComputeImpropers(), ProxyMgr::createProxies(), and PatchMap::homePatchIDList().

typedef ResizeArray<Patch *> PatchList

Definition at line 107 of file NamdTypes.h.

typedef Vector Position

Definition at line 18 of file NamdTypes.h. Referenced by Lattice::apply_transform(), PatchMap::assignToPatch(), Sequencer::berendsenPressure(), WorkDistrib::caclNumAtomsInEachPatch(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ImproperElem::computeForce(), DihedralElem::computeForce(), CrosstermElem::computeForce(), AngleElem::computeForce(), WorkDistrib::createAtomLists(), Lattice::delta(), ComputeGridForce::doForce(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeConsForce::doForce(), HomePatch::doPairlistCheck(), WorkDistrib::fillOnePatchAtoms(), ComputeGridForce::finishForce(), GridforceGrid::get_center(), GridforceGrid::get_origin(), GlobalMasterFreeEnergy::getPosition(), GlobalMasterEasy::getPosition(), GridforceGrid::init1(), GridforceGrid::init4(), Sequencer::langevinPiston(), Lattice::nearest(), colvarproxy_namd::position_distance(), 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(), and Lattice::wrap_nearest_delta().

typedef ResizeArray<Position> PositionList

Definition at line 95 of file NamdTypes.h. Referenced by CollectionMgr::submitPositions(), and CollectionMgr::submitVelocities().

typedef ResizeArray<proxyTreeNode> proxyTreeNodeList

Definition at line 185 of file NamdTypes.h.

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 98 of file NamdTypes.h.

typedef Vector Velocity

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

typedef ResizeArray<Velocity> VelocityList

Definition at line 96 of file NamdTypes.h.

---