NAMD
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#include <HomePatch.h>
Classes | |
struct | checkpoint_t |
struct | RattleList |
Public Attributes | |
int | marginViolations |
std::vector< int > | settleList |
std::vector< RattleList > | rattleList |
std::vector< RattleParam > | rattleParam |
std::vector< int > | noconstList |
bool | rattleListValid |
std::vector< Vector > | velNew |
std::vector< Vector > | posNew |
int | checkpoint_task |
std::map< std::string, checkpoint_t * > | checkpoints |
int | exchange_dst |
int | exchange_src |
int | exchange_req |
ExchangeAtomsMsg * | exchange_msg |
LDObjHandle | ldObjHandle |
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Lattice & | lattice |
Flags | flags |
Protected Member Functions | |
virtual void | boxClosed (int) |
void | doPairlistCheck () |
void | doGroupSizeCheck () |
void | doMarginCheck () |
void | doAtomMigration () |
Friends | |
class | PatchMgr |
class | Sequencer |
class | ComputeGlobal |
Definition at line 273 of file HomePatch.h.
HomePatch::~HomePatch | ( | ) |
Definition at line 321 of file HomePatch.C.
References Patch::atomMapper, ResizeArray< T >::begin(), ResizeArray< T >::end(), and AtomMapper::unregisterIDsFullAtom().
void HomePatch::addForceToMomentum | ( | FullAtom *__restrict | atom_arr, |
const Force *__restrict | force_arr, | ||
const BigReal | dt, | ||
int | num_atoms | ||
) |
Definition at line 1933 of file HomePatch.C.
References SimParameters::fixedAtomsOn, num_atoms, Node::Object(), and Node::simParameters.
Referenced by Sequencer::addForceToMomentum().
void HomePatch::addForceToMomentum3 | ( | FullAtom *__restrict | atom_arr, |
const Force *__restrict | force_arr1, | ||
const Force *__restrict | force_arr2, | ||
const Force *__restrict | force_arr3, | ||
const BigReal | dt1, | ||
const BigReal | dt2, | ||
const BigReal | dt3, | ||
int | num_atoms | ||
) |
Definition at line 1962 of file HomePatch.C.
References SimParameters::fixedAtomsOn, num_atoms, Node::Object(), and Node::simParameters.
Referenced by Sequencer::addForceToMomentum3().
Definition at line 2372 of file HomePatch.C.
References Patch::f, Results::normal, Patch::numAtoms, outer(), and velNew.
Referenced by rattle1().
void HomePatch::addVelocityToPosition | ( | FullAtom *__restrict | atom_arr, |
const BigReal | dt, | ||
int | num_atoms | ||
) |
Definition at line 2001 of file HomePatch.C.
References SimParameters::fixedAtomsOn, num_atoms, Node::Object(), and Node::simParameters.
Referenced by Sequencer::addVelocityToPosition().
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protectedvirtual |
Implements Patch.
Definition at line 334 of file HomePatch.C.
References Sequencer::awaken(), Patch::boxesOpen, DebugM, Patch::dEdaSumBox, Flags::doGBIS, Flags::doNonbonded, Patch::f, Patch::flags, ExtForce::force, OwnerBox< Owner, Data >::isOpen(), Results::maxNumForces, Results::normal, Patch::numAtoms, Patch::patchID, Patch::psiSumBox, and ResizeArray< T >::size().
void HomePatch::buildRattleList | ( | ) |
Definition at line 2230 of file HomePatch.C.
References RattleParam::dsq, SimParameters::fixedAtomsOn, RattleParam::ia, RattleParam::ib, HomePatch::RattleList::icnt, HomePatch::RattleList::ig, NAMD_die(), noconstList, Patch::numAtoms, Node::Object(), posNew, rattleList, rattleParam, RattleParam::rma, RattleParam::rmb, settle1init(), settleList, Node::simParameters, SimParameters::useSettle, velNew, WAT_SWM4, WAT_TIP4, and SimParameters::watmodel.
Referenced by rattle1().
Definition at line 674 of file HomePatch.C.
References ResizeArray< T >::begin(), compDistance(), ResizeArray< T >::end(), ResizeArray< T >::find(), NAMD_bug(), PatchMap::numNodesWithPatches(), PatchMap::numPatchesOnNode(), PatchMap::Object(), Patch::patchID, proxySpanDim, ResizeArray< T >::resize(), sendSpanningTree(), ResizeArray< T >::setall(), ResizeArray< T >::size(), and ResizeArray< T >::swap().
Referenced by ProxyMgr::buildProxySpanningTree().
Definition at line 3450 of file HomePatch.C.
References ResizeArray< T >::copy(), and Patch::lattice.
Referenced by Sequencer::algorithm().
void HomePatch::depositMigration | ( | MigrateAtomsMsg * | msg | ) |
Definition at line 3999 of file HomePatch.C.
References ResizeArray< T >::add(), Lattice::apply_transform(), Sequencer::awaken(), ResizeArray< T >::begin(), DebugM, ResizeArray< T >::end(), inMigration, Patch::lattice, MigrateAtomsMsg::migrationList, msgbuf, Lattice::nearest(), numMlBuf, Patch::patchID, Lattice::reverse_transform(), and ResizeArray< T >::size().
Referenced by MigrateAtomsCombinedMsg::distribute(), and doAtomMigration().
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Definition at line 3839 of file HomePatch.C.
References ResizeArray< T >::add(), atomIndex, Patch::atomMapper, ResizeArray< T >::begin(), DebugM, ResizeArray< T >::del(), depositMigration(), ResizeArray< T >::end(), inMigration, Patch::lattice, marginViolations, MigrationInfo::mList, msgbuf, NAMD_EVENT_START, NAMD_EVENT_STOP, numMlBuf, PatchMgr::Object(), Patch::patchID, ResizeArray< T >::resize(), Lattice::scale(), PatchMgr::sendMigrationMsgs(), ResizeArray< T >::size(), Sequencer::suspend(), AtomMapper::unregisterIDsFullAtom(), Vector::x, Vector::y, and Vector::z.
Referenced by positionsReady().
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protected |
Definition at line 3718 of file HomePatch.C.
References ResizeArray< T >::begin(), Flags::doNonbonded, ResizeArray< T >::end(), Patch::flags, SimParameters::hgroupCutoff, Flags::maxGroupRadius, NAMD_bug(), Node::Object(), Node::simParameters, x, y, and z.
Referenced by positionsReady().
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Definition at line 3762 of file HomePatch.C.
References Lattice::a(), Lattice::a_r(), Lattice::b(), Lattice::b_r(), ResizeArray< T >::begin(), Lattice::c(), Lattice::c_r(), SimParameters::cutoff, ResizeArray< T >::end(), Patch::lattice, SimParameters::margin, marginViolations, NAMD_die(), Node::Object(), SimParameters::patchDimension, Lattice::scale(), Node::simParameters, Vector::unit(), Vector::x, Vector::y, and Vector::z.
Referenced by positionsReady().
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Definition at line 3629 of file HomePatch.C.
References ResizeArray< T >::begin(), Patch::flags, Patch::getPatchID(), Patch::lattice, Vector::length2(), Flags::maxAtomMovement, NAMD_EVENT_START_EX, NAMD_EVENT_STOP, NamdProfileEventStr, Patch::numAtoms, Node::Object(), SimParameters::pairlistGrow, SimParameters::pairlistShrink, Flags::pairlistTolerance, SimParameters::pairlistTrigger, CompAtom::position, ResizeArray< T >::resize(), Flags::savePairlists, Node::simParameters, Lattice::unscale(), Flags::usePairlists, Vector::x, Vector::y, and Vector::z.
Referenced by positionsReady().
void HomePatch::exchangeAtoms | ( | int | scriptTask | ) |
Definition at line 3574 of file HomePatch.C.
References ExchangeAtomsMsg::atoms, ResizeArray< T >::begin(), exchange_dst, exchange_msg, exchange_req, exchange_src, ExchangeAtomsMsg::lattice, Patch::lattice, ExchangeAtomsMsg::numAtoms, Patch::numAtoms, Node::Object(), PatchMgr::Object(), Patch::patchID, ExchangeAtomsMsg::pid, recvExchangeReq(), SCRIPT_ATOMRECV, SCRIPT_ATOMSEND, SCRIPT_ATOMSENDRECV, SimParameters::scriptArg1, SimParameters::scriptArg2, PatchMgr::sendExchangeReq(), and Node::simParameters.
Referenced by Sequencer::algorithm().
void HomePatch::exchangeCheckpoint | ( | int | scriptTask, |
int & | bpc | ||
) |
Definition at line 3478 of file HomePatch.C.
References checkpoint_task, Node::Object(), PatchMgr::Object(), Patch::patchID, SimParameters::scriptIntArg1, SimParameters::scriptStringArg1, PatchMgr::sendCheckpointReq(), and Node::simParameters.
Referenced by Sequencer::algorithm().
void HomePatch::gbisComputeAfterP1 | ( | ) |
Definition at line 3147 of file HomePatch.C.
References SimParameters::alpha_max, Patch::bornRad, SimParameters::coulomb_radius_offset, Patch::flags, SimParameters::gbis_beta, SimParameters::gbis_delta, SimParameters::gbis_gamma, gbisP2Ready(), Patch::intRad, Patch::numAtoms, Node::Object(), Patch::pExt, Patch::psiFin, Patch::psiSum, Flags::sequence, and Node::simParameters.
void HomePatch::gbisComputeAfterP2 | ( | ) |
Definition at line 3175 of file HomePatch.C.
References Patch::bornRad, COULOMB, SimParameters::coulomb_radius_offset, Patch::dEdaSum, Patch::dHdrPrefix, SimParameters::dielectric, Patch::flags, SimParameters::gbis_beta, SimParameters::gbis_delta, SimParameters::gbis_gamma, gbisP3Ready(), Patch::intRad, SimParameters::kappa, Patch::numAtoms, Node::Object(), Patch::pExt, Patch::psiFin, Flags::sequence, Node::simParameters, and SimParameters::solvent_dielectric.
void HomePatch::gbisP2Ready | ( | ) |
Definition at line 3219 of file HomePatch.C.
References ResizeArray< T >::begin(), ProxyGBISP2DataMsg::bornRad, Patch::bornRad, ProxyGBISP2DataMsg::destPe, Patch::flags, GB2_PROXY_DATA_PRIORITY, Patch::gbisP2Ready(), Patch::numAtoms, ProxyGBISP2DataMsg::origPe, ProxyGBISP2DataMsg::patch, PATCH_PRIORITY, Patch::patchID, PRIORITY_SIZE, Flags::sequence, SET_PRIORITY, and ResizeArray< T >::size().
Referenced by gbisComputeAfterP1().
void HomePatch::gbisP3Ready | ( | ) |
Definition at line 3239 of file HomePatch.C.
References ResizeArray< T >::begin(), ProxyGBISP3DataMsg::destPe, ProxyGBISP3DataMsg::dHdrPrefix, Patch::dHdrPrefix, ProxyGBISP3DataMsg::dHdrPrefixLen, Flags::doFullElectrostatics, Patch::flags, GB3_PROXY_DATA_PRIORITY, Patch::gbisP3Ready(), ProxyGBISP3DataMsg::origPe, ProxyGBISP3DataMsg::patch, PATCH_PRIORITY, Patch::patchID, PRIORITY_SIZE, Flags::sequence, SET_PRIORITY, and ResizeArray< T >::size().
Referenced by gbisComputeAfterP2().
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inline |
Definition at line 455 of file HomePatch.h.
Referenced by ComputeHomePatch::doWork(), and dumpbench().
int HomePatch::hardWallDrude | ( | const BigReal | timestep, |
Tensor * | virial, | ||
SubmitReduction * | ppreduction | ||
) |
Definition at line 2024 of file HomePatch.C.
References BOLTZMANN, Lattice::c(), SimParameters::drudeBondLen, SimParameters::drudeHardWallOn, SimParameters::drudeTemp, endi(), SimParameters::fixedAtomsOn, iERROR(), iout, SubmitReduction::item(), Patch::lattice, Node::molecule, Patch::numAtoms, Node::Object(), Lattice::origin(), outer(), partition(), SimParameters::pressureProfileSlabs, SimParameters::rigidDie, Node::simParameters, TIMEFACTOR, Vector::x, Tensor::xx, Vector::y, Tensor::yy, Vector::z, z, and Tensor::zz.
Referenced by Sequencer::hardWallDrude().
void HomePatch::loweAndersenFinish | ( | ) |
void HomePatch::loweAndersenVelocities | ( | ) |
Definition at line 3098 of file HomePatch.C.
References DebugM, Node::molecule, Patch::numAtoms, Node::Object(), and Node::simParameters.
Referenced by positionsReady().
Definition at line 2963 of file HomePatch.C.
References ResizeArray< T >::begin(), endi(), Patch::f, SimParameters::fixedAtomsOn, iout, iWARN(), Node::molecule, NAMD_bug(), NAMD_die(), Results::normal, Patch::numAtoms, Node::Object(), outer(), SimParameters::rigidDie, SimParameters::rigidIter, SimParameters::rigidTol, settle2(), Node::simParameters, TIMEFACTOR, SimParameters::useSettle, WAT_SWM4, WAT_TIP4, SimParameters::watmodel, Vector::x, Vector::y, and Vector::z.
Referenced by Sequencer::newMinimizeDirection(), and Sequencer::submitMinimizeReductions().
void HomePatch::mollyAverage | ( | ) |
Definition at line 3313 of file HomePatch.C.
References average(), endi(), SimParameters::fixedAtomsOn, iout, iWARN(), Node::molecule, SimParameters::mollyIter, SimParameters::mollyTol, NAMD_die(), Patch::numAtoms, Node::Object(), Patch::p_avg, ResizeArray< T >::resize(), and Node::simParameters.
Referenced by positionsReady().
Definition at line 3387 of file HomePatch.C.
References Patch::f, SimParameters::fixedAtomsOn, Node::molecule, mollify(), NAMD_die(), Patch::numAtoms, Node::Object(), outer(), Patch::p_avg, ResizeArray< T >::resize(), Node::simParameters, and Results::slow.
void HomePatch::positionsReady | ( | int | doMigration = 0 | ) |
Definition at line 925 of file HomePatch.C.
References ProxyDataMsg::avgPlLen, ProxyDataMsg::avgPositionList, Patch::avgPositionPtrBegin, Patch::avgPositionPtrEnd, ResizeArray< T >::begin(), CompAtom::charge, COULOMB, ProxyDataMsg::cudaAtomList, Patch::cudaAtomPtr, DebugM, ComputeNonbondedUtil::dielectric_1, doAtomMigration(), Flags::doGBIS, doGroupSizeCheck(), Flags::doLCPO, Flags::doLoweAndersen, doMarginCheck(), Flags::doMolly, doPairlistCheck(), ResizeArray< T >::end(), SimParameters::fixedAtomsForces, SimParameters::fixedAtomsOn, ProxyDataMsg::flags, Patch::flags, Patch::getPatchID(), Patch::intRad, ProxyDataMsg::intRadList, Patch::lattice, Patch::lcpoType, ProxyDataMsg::lcpoTypeList, loweAndersenVelocities(), mollyAverage(), NAMD_EVENT_START_EX, NAMD_EVENT_STOP, NamdProfileEventStr, Patch::numAtoms, PatchMap::numNodesWithPatches(), PatchMap::numPatchesOnNode(), PatchMap::Object(), Sync::Object(), Node::Object(), ProxyMgr::Object(), Patch::p_avg, ProxyDataMsg::patch, PATCH_PRIORITY, Patch::patchID, Sync::PatchReady(), Patch::pExt, ProxyDataMsg::plExtLen, ProxyDataMsg::plLen, CompAtom::position, ProxyDataMsg::positionExtList, ProxyDataMsg::positionList, Patch::positionsReady(), PRIORITY_SIZE, PROXY_DATA_PRIORITY, proxySendSpanning, proxySpanDim, CudaAtom::q, SimParameters::qmLSSOn, qmSwapAtoms(), rattleListValid, ResizeArray< T >::resize(), ComputeNonbondedUtil::scaling, ProxyMgr::sendProxyAll(), ProxyMgr::sendProxyData(), Flags::sequence, SET_PRIORITY, setGBISIntrinsicRadii(), setLcpoType(), Node::simParameters, ResizeArray< T >::size(), sortAtomsForCUDA(), CompAtomExt::sortOrder, SimParameters::staticAtomAssignment, Lattice::unscale(), SimParameters::useAVXTiles, Patch::v, ProxyDataMsg::velocityList, Patch::velocityPtrBegin, Patch::velocityPtrEnd, ProxyDataMsg::vlLen, Vector::x, CudaAtom::x, Vector::y, CudaAtom::y, Vector::z, and CudaAtom::z.
void HomePatch::qmSwapAtoms | ( | ) |
Definition at line 866 of file HomePatch.C.
References ResizeArray< T >::begin(), CompAtom::charge, SortedArray< Type >::find(), Molecule::get_numQMAtoms(), Molecule::get_qmAtmChrg(), Molecule::get_qmAtmIndx(), Molecule::get_qmAtomGroup(), CompAtomExt::id, lssSubs(), Node::molecule, LSSSubsDat::newCharge, LSSSubsDat::newID, LSSSubsDat::newVdWType, Patch::numAtoms, Node::Object(), SimParameters::PMEOn, Node::simParameters, and CompAtom::vdwType.
Referenced by positionsReady().
int HomePatch::rattle1 | ( | const BigReal | timestep, |
Tensor * | virial, | ||
SubmitReduction * | ppreduction | ||
) |
Definition at line 2382 of file HomePatch.C.
References addRattleForce(), buildRattleList(), endi(), SimParameters::fixedAtomsOn, iERROR(), iout, iWARN(), noconstList, Patch::numAtoms, Node::Object(), posNew, rattle1old(), rattleList, rattleListValid, rattleN(), rattlePair< 1 >(), rattleParam, SimParameters::rigidDie, SimParameters::rigidIter, SimParameters::rigidTol, settle1_SIMD< 1 >(), settle1_SIMD< 2 >(), settleList, Node::simParameters, TIMEFACTOR, SimParameters::useSettle, velNew, WAT_TIP3, SimParameters::watmodel, Vector::x, Vector::y, and Vector::z.
Referenced by Sequencer::minimize(), Sequencer::minimizeMoveDownhill(), Sequencer::newMinimizePosition(), and Sequencer::rattle1().
int HomePatch::rattle1old | ( | const BigReal | timestep, |
Tensor * | virial, | ||
SubmitReduction * | ppreduction | ||
) |
Definition at line 2559 of file HomePatch.C.
References Lattice::c(), endi(), Patch::f, SimParameters::fixedAtomsOn, iERROR(), iout, SubmitReduction::item(), iWARN(), Patch::lattice, Node::molecule, NAMD_die(), Results::normal, Patch::numAtoms, Node::Object(), Lattice::origin(), outer(), partition(), SimParameters::pressureProfileSlabs, SimParameters::rigidDie, SimParameters::rigidIter, SimParameters::rigidTol, settle1(), settle1init(), Node::simParameters, TIMEFACTOR, SimParameters::useSettle, WAT_SWM4, WAT_TIP4, SimParameters::watmodel, Vector::x, Tensor::xx, Vector::y, Tensor::yy, Vector::z, z, and Tensor::zz.
Referenced by rattle1().
Definition at line 2829 of file HomePatch.C.
References endi(), SimParameters::fixedAtomsOn, iout, iWARN(), Node::molecule, NAMD_bug(), NAMD_die(), Patch::numAtoms, Node::Object(), outer(), SimParameters::rigidDie, SimParameters::rigidIter, SimParameters::rigidTol, settle2(), Node::simParameters, TIMEFACTOR, SimParameters::useSettle, WAT_SWM4, WAT_TIP4, SimParameters::watmodel, Vector::x, Vector::y, and Vector::z.
void HomePatch::receiveResult | ( | ProxyGBISP1ResultMsg * | msg | ) |
Definition at line 3262 of file HomePatch.C.
References Sequencer::awaken(), Patch::boxesOpen, Flags::doNonbonded, Patch::flags, Patch::psiFin, ProxyGBISP1ResultMsg::psiSum, ProxyGBISP1ResultMsg::psiSumLen, and ResizeArray< T >::size().
Referenced by ProxyMgr::recvResult().
void HomePatch::receiveResult | ( | ProxyGBISP2ResultMsg * | msg | ) |
Definition at line 3287 of file HomePatch.C.
References Sequencer::awaken(), Patch::boxesOpen, ProxyGBISP2ResultMsg::dEdaSum, ProxyGBISP2ResultMsg::dEdaSumLen, Patch::dHdrPrefix, Flags::doNonbonded, Patch::flags, and ResizeArray< T >::size().
void HomePatch::receiveResults | ( | ProxyResultVarsizeMsg * | msg | ) |
Definition at line 796 of file HomePatch.C.
References OwnerBox< Owner, Data >::clientClose(), OwnerBox< Owner, Data >::clientOpen(), DebugM, Results::f, ProxyResultVarsizeMsg::flLen, ProxyResultVarsizeMsg::forceArr, Patch::forceBox, ProxyResultVarsizeMsg::isZero, Results::maxNumForces, ProxyResultVarsizeMsg::node, and Patch::patchID.
Referenced by ProxyMgr::recvResults().
void HomePatch::receiveResults | ( | ProxyResultMsg * | msg | ) |
Definition at line 820 of file HomePatch.C.
References ResizeArray< T >::begin(), OwnerBox< Owner, Data >::clientClose(), OwnerBox< Owner, Data >::clientOpen(), DebugM, ResizeArray< T >::end(), Results::f, Patch::f, Patch::forceBox, ProxyResultMsg::forceList, Results::maxNumForces, ProxyResultMsg::node, and Patch::patchID.
void HomePatch::receiveResults | ( | ProxyCombinedResultRawMsg * | msg | ) |
Definition at line 837 of file HomePatch.C.
References OwnerBox< Owner, Data >::clientClose(), OwnerBox< Owner, Data >::clientOpen(), DebugM, Results::f, Patch::f, ProxyCombinedResultRawMsg::flLen, ProxyCombinedResultRawMsg::forceArr, Patch::forceBox, ProxyCombinedResultRawMsg::isForceNonZero, Results::maxNumForces, ProxyCombinedResultRawMsg::nodeSize, Patch::patchID, Vector::x, Vector::y, and Vector::z.
void HomePatch::recvCheckpointAck | ( | ) |
Definition at line 3569 of file HomePatch.C.
Referenced by PatchMgr::recvCheckpointAck(), and recvCheckpointLoad().
void HomePatch::recvCheckpointLoad | ( | CheckpointAtomsMsg * | msg | ) |
Definition at line 3516 of file HomePatch.C.
References Patch::atomMapper, CheckpointAtomsMsg::atoms, ResizeArray< T >::begin(), CheckpointAtomsMsg::berendsenPressure_count, Sequencer::berendsenPressure_count, checkpoint_task, ResizeArray< T >::end(), CheckpointAtomsMsg::key, CheckpointAtomsMsg::lattice, Patch::lattice, NAMD_bug(), CheckpointAtomsMsg::numAtoms, Patch::numAtoms, Node::Object(), PatchMgr::Object(), Patch::patchID, CheckpointAtomsMsg::pe, CheckpointAtomsMsg::pid, rattleListValid, recvCheckpointAck(), AtomMapper::registerIDsFullAtom(), CheckpointAtomsMsg::replica, ResizeArray< T >::resize(), SCRIPT_CHECKPOINT_FREE, SCRIPT_CHECKPOINT_LOAD, SCRIPT_CHECKPOINT_STORE, SCRIPT_CHECKPOINT_SWAP, SimParameters::scriptIntArg1, SimParameters::scriptStringArg1, PatchMgr::sendCheckpointStore(), Node::simParameters, and AtomMapper::unregisterIDsFullAtom().
Referenced by PatchMgr::recvCheckpointLoad().
void HomePatch::recvCheckpointReq | ( | int | task, |
const char * | key, | ||
int | replica, | ||
int | pe | ||
) |
Definition at line 3486 of file HomePatch.C.
References CheckpointAtomsMsg::atoms, HomePatch::checkpoint_t::atoms, ResizeArray< T >::begin(), CheckpointAtomsMsg::berendsenPressure_count, HomePatch::checkpoint_t::berendsenPressure_count, checkpoints, CheckpointAtomsMsg::lattice, HomePatch::checkpoint_t::lattice, NAMD_die(), CheckpointAtomsMsg::numAtoms, HomePatch::checkpoint_t::numAtoms, PatchMgr::Object(), Patch::patchID, CheckpointAtomsMsg::pe, CheckpointAtomsMsg::pid, CheckpointAtomsMsg::replica, SCRIPT_CHECKPOINT_FREE, SCRIPT_CHECKPOINT_LOAD, SCRIPT_CHECKPOINT_SWAP, PatchMgr::sendCheckpointAck(), and PatchMgr::sendCheckpointLoad().
Referenced by PatchMgr::recvCheckpointReq().
void HomePatch::recvCheckpointStore | ( | CheckpointAtomsMsg * | msg | ) |
Definition at line 3555 of file HomePatch.C.
References CheckpointAtomsMsg::atoms, HomePatch::checkpoint_t::atoms, ResizeArray< T >::begin(), CheckpointAtomsMsg::berendsenPressure_count, HomePatch::checkpoint_t::berendsenPressure_count, checkpoints, CheckpointAtomsMsg::key, CheckpointAtomsMsg::lattice, HomePatch::checkpoint_t::lattice, CheckpointAtomsMsg::numAtoms, HomePatch::checkpoint_t::numAtoms, PatchMgr::Object(), Patch::patchID, CheckpointAtomsMsg::pe, CheckpointAtomsMsg::replica, ResizeArray< T >::resize(), and PatchMgr::sendCheckpointAck().
Referenced by PatchMgr::recvCheckpointStore().
void HomePatch::recvExchangeMsg | ( | ExchangeAtomsMsg * | msg | ) |
Definition at line 3606 of file HomePatch.C.
References Patch::atomMapper, ExchangeAtomsMsg::atoms, ResizeArray< T >::begin(), ResizeArray< T >::end(), ExchangeAtomsMsg::lattice, Patch::lattice, ExchangeAtomsMsg::numAtoms, rattleListValid, AtomMapper::registerIDsFullAtom(), ResizeArray< T >::resize(), and AtomMapper::unregisterIDsFullAtom().
Referenced by PatchMgr::recvExchangeMsg().
void HomePatch::recvExchangeReq | ( | int | req | ) |
Definition at line 3595 of file HomePatch.C.
References exchange_dst, exchange_msg, exchange_req, PatchMgr::Object(), and PatchMgr::sendExchangeMsg().
Referenced by exchangeAtoms(), and PatchMgr::recvExchangeReq().
void HomePatch::recvNodeAwareSpanningTree | ( | ProxyNodeAwareSpanningTreeMsg * | msg | ) |
Definition at line 630 of file HomePatch.C.
Referenced by ProxyMgr::recvNodeAwareSpanningTreeOnHomePatch().
void HomePatch::recvSpanningTree | ( | int * | t, |
int | n | ||
) |
Definition at line 636 of file HomePatch.C.
References proxySpanDim, ResizeArray< T >::resize(), sendSpanningTree(), and ResizeArray< T >::size().
Referenced by ProxyMgr::recvSpanningTreeOnHomePatch().
void HomePatch::registerProxy | ( | RegisterProxyMsg * | msg | ) |
Definition at line 402 of file HomePatch.C.
References ResizeArray< T >::add(), ResizeArray< T >::begin(), OwnerBox< Owner, Data >::clientAdd(), DebugM, Patch::forceBox, RegisterProxyMsg::node, Patch::patchID, Random::reorder(), and ResizeArray< T >::size().
Referenced by ProxyMgr::recvRegisterProxy().
Definition at line 3460 of file HomePatch.C.
References Patch::atomMapper, ResizeArray< T >::begin(), ResizeArray< T >::copy(), ResizeArray< T >::end(), Patch::lattice, rattleListValid, AtomMapper::registerIDsFullAtom(), ResizeArray< T >::size(), and AtomMapper::unregisterIDsFullAtom().
Referenced by Sequencer::algorithm().
void HomePatch::saveForce | ( | const int | ftag = Results::normal | ) |
Definition at line 1336 of file HomePatch.C.
References Patch::f, Patch::numAtoms, and ResizeArray< T >::resize().
Referenced by Sequencer::saveForce().
void HomePatch::sendNodeAwareSpanningTree | ( | ) |
Definition at line 631 of file HomePatch.C.
void HomePatch::sendProxies | ( | ) |
Definition at line 468 of file HomePatch.C.
References ResizeArray< T >::begin(), ProxyMgr::Object(), Patch::patchID, ProxyMgr::sendProxies(), NodeProxyMgr::sendProxyList(), and ResizeArray< T >::size().
Referenced by ProxyMgr::buildProxySpanningTree2().
void HomePatch::sendSpanningTree | ( | ) |
Definition at line 659 of file HomePatch.C.
References ResizeArray< T >::copy(), ProxySpanningTreeMsg::node, ProxyMgr::Object(), ProxySpanningTreeMsg::patch, Patch::patchID, ProxyMgr::sendSpanningTree(), ResizeArray< T >::size(), and ProxySpanningTreeMsg::tree.
Referenced by buildSpanningTree(), and recvSpanningTree().
void HomePatch::setGBISIntrinsicRadii | ( | ) |
Definition at line 3132 of file HomePatch.C.
References SimParameters::coulomb_radius_offset, Patch::intRad, MassToRadius(), MassToScreen(), Node::molecule, Patch::numAtoms, Node::Object(), ResizeArray< T >::resize(), ResizeArray< T >::setall(), and Node::simParameters.
Referenced by positionsReady().
void HomePatch::setLcpoType | ( | ) |
Definition at line 3121 of file HomePatch.C.
References Molecule::getLcpoParamType(), Patch::lcpoType, Node::molecule, Patch::numAtoms, Node::Object(), Patch::pExt, and ResizeArray< T >::resize().
Referenced by positionsReady().
void HomePatch::submitLoadStats | ( | int | timestep | ) |
Definition at line 3620 of file HomePatch.C.
References LdbCoordinator::Object(), Patch::patchID, and LdbCoordinator::patchLoad().
Referenced by Sequencer::rebalanceLoad().
void HomePatch::unregisterProxy | ( | UnregisterProxyMsg * | msg | ) |
Definition at line 416 of file HomePatch.C.
References ResizeArray< T >::begin(), OwnerBox< Owner, Data >::clientRemove(), ResizeArray< T >::del(), Patch::forceBox, and UnregisterProxyMsg::node.
Referenced by ProxyMgr::recvUnregisterProxy().
Definition at line 265 of file HomePatch.C.
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Definition at line 276 of file HomePatch.h.
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friend |
Definition at line 274 of file HomePatch.h.
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friend |
Definition at line 275 of file HomePatch.h.
int HomePatch::checkpoint_task |
Definition at line 428 of file HomePatch.h.
Referenced by exchangeCheckpoint(), and recvCheckpointLoad().