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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< CudaAtomCudaAtomList
typedef ResizeArray< CompAtomCompAtomList
typedef ResizeArray< CompAtomExtCompAtomExtList
typedef ResizeArray< FullAtomFullAtomList
typedef ResizeArray< InputAtomInputAtomList
typedef ResizeArray< PositionPositionList
typedef ResizeArray< VelocityVelocityList
typedef ResizeArray< ForceForceList
typedef ResizeArray< TransformTransformList
typedef ResizeArray< AtomIDAtomIDList
typedef ResizeArray< BigRealBigRealList
typedef ResizeArray< RealRealList
typedef float GBReal
typedef ResizeArray< GBRealGBRealList
typedef ResizeArray< int > IntList
typedef int PatchID
typedef int ComputeID
typedef int NodeID
typedef ResizeArray< PatchIDPatchIDList
typedef ResizeArray< Patch * > PatchList
typedef ResizeArray< Compute * > ComputeList
typedef ResizeArray< NodeIDNodeIDList
typedef __sort_entry SortEntry
typedef ResizeArray< proxyTreeNodeproxyTreeNodeList


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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