NAMD
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#include <ComputeNonbondedPair.h>
Public Member Functions | |
ComputeNonbondedPair (ComputeID c, PatchID pid[], int trans[], ComputeNonbondedWorkArrays *_workArrays, int minPartition=0, int maxPartition=1, int numPartitions=1) | |
~ComputeNonbondedPair () | |
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ComputePatchPair (ComputeID c, PatchID pid[], int t[]) | |
virtual | ~ComputePatchPair () |
virtual void | atomUpdate () |
virtual void | doWork () |
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Compute (ComputeID) | |
int | type () |
virtual | ~Compute () |
void | setNumPatches (int n) |
int | getNumPatches () |
virtual void | patchReady (PatchID, int doneMigration, int seq) |
virtual void | finishPatch (int) |
int | sequence (void) |
int | priority (void) |
int | getGBISPhase (void) |
virtual void | gbisP2PatchReady (PatchID, int seq) |
virtual void | gbisP3PatchReady (PatchID, int seq) |
Public Attributes | |
nonbonded | params |
GBISParamStruct | gbisParams |
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const ComputeID | cid |
LDObjHandle | ldObjHandle |
LocalWorkMsg *const | localWorkMsg |
Protected Member Functions | |
virtual void | initialize () |
virtual int | noWork () |
virtual void | doForce (CompAtom *p[2], CompAtomExt *pExt[2], Results *r[2]) |
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void | enqueueWork () |
Static Protected Attributes | |
static const int | numGBISPairlists = 4 |
Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.
Definition at line 14 of file ComputeNonbondedPair.h.
ComputeNonbondedPair::ComputeNonbondedPair | ( | ComputeID | c, |
PatchID | pid[], | ||
int | trans[], | ||
ComputeNonbondedWorkArrays * | _workArrays, | ||
int | minPartition = 0 , |
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int | maxPartition = 1 , |
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int | numPartitions = 1 |
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Definition at line 25 of file ComputeNonbondedPair.C.
References Node::Object(), ReductionMgr::Object(), pairlistsValid, pairlistTolerance, Node::parameters, nonbonded::parameters, params, ComputeNonbondedUtil::pressureProfileAtomTypes, pressureProfileData, ComputeNonbondedUtil::pressureProfileOn, pressureProfileReduction, ComputeNonbondedUtil::pressureProfileSlabs, Node::rand, nonbonded::random, reduction, REDUCTIONS_BASIC, REDUCTIONS_PPROF_NONBONDED, Node::simParameters, nonbonded::simParameters, and ReductionMgr::willSubmit().
ComputeNonbondedPair::~ComputeNonbondedPair | ( | ) |
Definition at line 82 of file ComputeNonbondedPair.C.
References avgPositionBox, bornRadBox, dEdaSumBox, dHdrPrefixBox, intRadBox, ComputePatchPair::patch, pressureProfileData, pressureProfileReduction, psiSumBox, reduction, Patch::unregisterAvgPositionPickup(), Patch::unregisterBornRadPickup(), Patch::unregisterDEdaSumDeposit(), Patch::unregisterDHdrPrefixPickup(), Patch::unregisterIntRadPickup(), Patch::unregisterPsiSumDeposit(), Patch::unregisterVelocityPickup(), and velocityBox.
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protectedvirtual |
Reimplemented from ComputePatchPair.
Definition at line 177 of file ComputeNonbondedPair.C.
References GBISParamStruct::a_cut, GBISParamStruct::alpha_max, avgPositionBox, GBISParamStruct::beta, GBISParamStruct::bornRad, bornRadBox, Lattice::c(), ComputeNonbondedUtil::calcFullPair, ComputeNonbondedUtil::calcFullPairEnergy, ComputeNonbondedUtil::calcGBIS(), ComputeNonbondedUtil::calcMergePair, ComputeNonbondedUtil::calcMergePairEnergy, ComputeNonbondedUtil::calcPair, ComputeNonbondedUtil::calcPairEnergy, ComputeNonbondedUtil::calcSlowPair, ComputeNonbondedUtil::calcSlowPairEnergy, PatchMap::center(), Compute::cid, GBISParamStruct::cid, Box< Owner, Data >::close(), ComputeNonbondedUtil::commOnly, GBISParamStruct::cutoff, ComputeNonbondedUtil::cutoff, DebugM, GBISParamStruct::dEdaSum, dEdaSumBox, GBISParamStruct::delta, GBISParamStruct::dHdrPrefix, dHdrPrefixBox, Flags::doEnergy, GBISParamStruct::doEnergy, Flags::doFullElectrostatics, GBISParamStruct::doFullElectrostatics, Flags::doGBIS, GBISParamStruct::doGBIS, Flags::doLoweAndersen, nonbonded::doLoweAndersen, GBISParamStruct::doSmoothing, GBISParamStruct::epsilon_p, GBISParamStruct::epsilon_s, Results::f, nonbonded::ff, Patch::flags, GBISParamStruct::fsMax, nonbonded::fullf, GBISParamStruct::gamma, GBISParamStruct::gbInterEnergy, gbisParams, Compute::gbisPhase, GBISParamStruct::gbisPhase, gbisStepPairlists, GBISParamStruct::gbisStepPairlists, GBISParamStruct::gbSelfEnergy, Patch::getPatchID(), nonbonded::groupplcutoff, GBISParamStruct::intRad, intRadBox, SubmitReduction::item(), GBISParamStruct::kappa, Patch::lattice, Vector::length(), Flags::maxAtomMovement, Flags::maxGroupRadius, GBISParamStruct::maxGroupRadius, maxPart, nonbonded::maxPart, minPart, nonbonded::minPart, ComputePatchPair::numAtoms, nonbonded::numAtoms, numGBISPairlists, numParts, nonbonded::numParts, GBISParamStruct::numPatches, PatchMap::Object(), Node::Object(), nonbonded::offset, Lattice::offset(), nonbonded::offset_f, Box< Owner, Data >::open(), Lattice::origin(), ComputePatchPair::p, nonbonded::p, pairlists, nonbonded::pairlists, pairlistsValid, Flags::pairlistTolerance, pairlistTolerance, ComputeNonbondedUtil::pairlistWarningIndex, params, ComputePatchPair::patch, ComputePatchPair::patchID, GBISParamStruct::patchID, ComputePatchPair::pExt, nonbonded::pExt, nonbonded::plcutoff, ComputeNonbondedUtil::pressureProfileAtomTypes, pressureProfileData, ComputeNonbondedUtil::pressureProfileMin, ComputeNonbondedUtil::pressureProfileOn, pressureProfileReduction, nonbonded::pressureProfileReduction, ComputeNonbondedUtil::pressureProfileSlabs, ComputeNonbondedUtil::pressureProfileThickness, nonbonded::projLineVec, GBISParamStruct::psiSum, psiSumBox, ComputePatchPair::r, reduction, nonbonded::reduction, REDUCTION_ELECT_ENERGY, reductionData, ComputeNonbondedUtil::reductionDataSize, GBISParamStruct::rho_0, nonbonded::savePairlists, Compute::sequence(), GBISParamStruct::sequence, Node::simParameters, simParams, Results::slow, Flags::step, nonbonded::step, SubmitReduction::submit(), ComputeNonbondedUtil::submitPressureProfileData(), ComputeNonbondedUtil::submitReductionData(), TRACE_COMPOBJ_IDOFFSET, ComputePatchPair::trans, Lattice::unscale(), Flags::usePairlists, nonbonded::usePairlists, nonbonded::v, velocityBox, workArrays, nonbonded::workArrays, and Vector::z.
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protectedvirtual |
Reimplemented from ComputePatchPair.
Definition at line 66 of file ComputeNonbondedPair.C.
References avgPositionBox, bornRadBox, dEdaSumBox, dHdrPrefixBox, ComputePatchPair::initialize(), intRadBox, ComputePatchPair::patch, psiSumBox, Patch::registerAvgPositionPickup(), Patch::registerBornRadPickup(), Patch::registerDEdaSumDeposit(), Patch::registerDHdrPrefixPickup(), Patch::registerIntRadPickup(), Patch::registerPsiSumDeposit(), Patch::registerVelocityPickup(), and velocityBox.
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protectedvirtual |
Reimplemented from Compute.
Definition at line 115 of file ComputeNonbondedPair.C.
References avgPositionBox, bornRadBox, dEdaSumBox, dHdrPrefixBox, ComputePatchPair::forceBox, Compute::gbisPhase, intRadBox, SubmitReduction::item(), Compute::ldObjHandle, ComputePatchPair::numAtoms, LdbCoordinator::Object(), ComputePatchPair::patch, ComputePatchPair::positionBox, ComputeNonbondedUtil::pressureProfileOn, pressureProfileReduction, psiSumBox, reduction, REDUCTION_COMPUTE_CHECKSUM, Box< Owner, Data >::skip(), LdbCoordinator::skipWork(), SubmitReduction::submit(), and velocityBox.
Definition at line 35 of file ComputeNonbondedPair.h.
Referenced by doForce(), initialize(), noWork(), and ~ComputeNonbondedPair().
Definition at line 43 of file ComputeNonbondedPair.h.
Referenced by doForce(), initialize(), noWork(), and ~ComputeNonbondedPair().
Definition at line 44 of file ComputeNonbondedPair.h.
Referenced by doForce(), initialize(), noWork(), and ~ComputeNonbondedPair().
Definition at line 45 of file ComputeNonbondedPair.h.
Referenced by doForce(), initialize(), noWork(), and ~ComputeNonbondedPair().
GBISParamStruct ComputeNonbondedPair::gbisParams |
Definition at line 22 of file ComputeNonbondedPair.h.
Referenced by doForce().
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Definition at line 47 of file ComputeNonbondedPair.h.
Referenced by doForce().
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Definition at line 40 of file ComputeNonbondedPair.h.
Definition at line 41 of file ComputeNonbondedPair.h.
Referenced by doForce(), initialize(), noWork(), and ~ComputeNonbondedPair().
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Definition at line 60 of file ComputeNonbondedPair.h.
Referenced by doForce().
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Definition at line 60 of file ComputeNonbondedPair.h.
Referenced by doForce().
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staticprotected |
Definition at line 46 of file ComputeNonbondedPair.h.
Referenced by doForce().
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Definition at line 60 of file ComputeNonbondedPair.h.
Referenced by doForce().
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Definition at line 56 of file ComputeNonbondedPair.h.
Referenced by doForce().
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Definition at line 57 of file ComputeNonbondedPair.h.
Referenced by ComputeNonbondedPair(), and doForce().
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Definition at line 58 of file ComputeNonbondedPair.h.
Referenced by ComputeNonbondedPair(), and doForce().
nonbonded ComputeNonbondedPair::params |
Definition at line 21 of file ComputeNonbondedPair.h.
Referenced by ComputeNonbondedPair(), and doForce().
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Definition at line 52 of file ComputeNonbondedPair.h.
Referenced by ComputeNonbondedPair(), doForce(), and ~ComputeNonbondedPair().
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Definition at line 51 of file ComputeNonbondedPair.h.
Referenced by ComputeNonbondedPair(), doForce(), noWork(), and ~ComputeNonbondedPair().
Definition at line 42 of file ComputeNonbondedPair.h.
Referenced by doForce(), initialize(), noWork(), and ~ComputeNonbondedPair().
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Definition at line 50 of file ComputeNonbondedPair.h.
Referenced by ComputeNonbondedPair(), doForce(), noWork(), and ~ComputeNonbondedPair().
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Definition at line 49 of file ComputeNonbondedPair.h.
Referenced by doForce().
Definition at line 37 of file ComputeNonbondedPair.h.
Referenced by doForce(), initialize(), noWork(), and ~ComputeNonbondedPair().
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Definition at line 54 of file ComputeNonbondedPair.h.
Referenced by doForce().