NAMD
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#include <Node.h>
Static Public Member Functions | |
static Node * | Object () |
static void | messageRun () |
static void | messageStartUp () |
static void | messageBOCCheckIn () |
Public Attributes | |
int | mallocTest_size |
float | initVM |
float | initRSS |
int | curTimeStep |
int | curMFlopStep |
bool | specialTracing |
WorkDistrib * | workDistrib |
ComputeMgr * | computeMgr |
Random * | rand |
Molecule * | molecule |
Parameters * | parameters |
SimParameters * | simParameters |
ConfigList * | configList |
PDB * | pdb |
NamdState * | state |
Output * | output |
IMDOutput * | imd |
colvarmodule * | colvars |
Vector * | coords |
Protected Attributes | |
AtomMap * | atomMap |
PatchMap * | patchMap |
ComputeMap * | computeMap |
LdbCoordinator * | ldbCoordinator |
Node::Node | ( | GroupInitMsg * | msg | ) |
Definition at line 291 of file Node.C.
References atomMap, colvars, configList, DebugM, GroupInitMsg::group, imd, PatchMap::Instance(), AtomMap::Instance(), ComputeMap::Instance(), molecule, NAMD_bug(), output, parameters, patchMap, pdb, recvCheckpointCAck_handler(), recvCheckpointCReq_handler(), simParameters, specialTracing, state, x, y, and z.
Node::~Node | ( | void | ) |
void Node::awaitBOCCheckIn | ( | ) |
void Node::BOCCheckIn | ( | ) |
Definition at line 1365 of file Node.C.
References sendEnableEarlyExit().
Referenced by Sequencer::hardWallDrude(), Sequencer::maximumMove(), Sequencer::rattle1(), and recvEnableEarlyExit().
Definition at line 1343 of file Node.C.
References sendEnableExitScheduler().
Referenced by BackEnd::awaken(), and recvEnableExitScheduler().
void Node::enableScriptBarrier | ( | ) |
Definition at line 192 of file Node.h.
Referenced by Output::coordinate(), colvarproxy_namd::init_tcl_pointers(), and Controller::printEnergies().
void Node::mallocTest | ( | int | step | ) |
float Node::measureMemory | ( | ) |
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inline |
Definition at line 188 of file Node.h.
Referenced by ComputeMgr::createComputes(), WorkDistrib::distributeHomePatches(), and LdbCoordinator::initialize().
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inline |
Definition at line 189 of file Node.h.
Referenced by WorkDistrib::assignNodeToPatch(), and LdbCoordinator::initialize().
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inlinestatic |
Definition at line 86 of file Node.h.
Referenced by HomePatch::addForceToMomentum(), HomePatch::addForceToMomentum3(), Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), HomePatch::addVelocityToPosition(), after_backend_init(), Controller::algorithm(), WorkDistrib::assignNodeToPatch(), BackEnd::awaken(), PmeZPencil::backward_fft(), PmeYPencil::backward_fft(), PmeXPencil::backward_fft(), ComputeNonbondedCUDA::build_exclusions(), HomePatch::buildRattleList(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), Controller::calcPressure(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), ComputePmeMgr::chargeGridSubmitted(), colvarproxy_namd::check_atom_id(), SimParameters::close_dcdfile(), SimParameters::close_veldcdfile(), colvarproxy_namd::colvarproxy_namd(), Controller::compareChecksums(), ComputeCylindricalBC::ComputeCylindricalBC(), ComputeEwald::ComputeEwald(), AngleElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), GromacsPairElem::computeForce(), ComputeFullDirect::ComputeFullDirect(), ComputeGlobal::ComputeGlobal(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputeLCPO::ComputeLCPO(), ComputeMsm::ComputeMsm(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), ComputePme::ComputePme(), ComputeRestraints::ComputeRestraints(), ComputeSphericalBC::ComputeSphericalBC(), ComputeStir::ComputeStir(), ComputeTclBC::ComputeTclBC(), Controller::Controller(), Output::coordinate(), Output::coordinateNeeded(), ComputeMgr::createComputes(), ComputeCUDAMgr::createCudaComputeNonbonded(), ParallelIOMgr::createHomePatches(), LdbCoordinator::createLoadBalancer(), CudaComputeNonbonded::CudaComputeNonbonded(), CollectionMaster::disposeForces(), CollectionMaster::disposePositions(), CollectionMaster::disposeVelocities(), ComputeConsForce::doForce(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeStir::doForce(), ComputeGridForce::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeRestraints::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), HomePatch::doPairlistCheck(), ComputePme::doQMWork(), ComputeTclBC::doWork(), ComputeGBISser::doWork(), ComputeNonbondedCUDA::doWork(), CudaComputeNonbonded::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), dumpbench(), HomePatch::exchangeAtoms(), HomePatch::exchangeCheckpoint(), ComputeNonbondedCUDA::finishReductions(), CudaComputeNonbonded::finishReductions(), ComputeNonbondedCUDA::finishWork(), Output::force(), Patch::forceBoxClosed(), Output::forceNeeded(), PmeZPencil::forward_fft(), PmeYPencil::forward_fft(), PmeXPencil::forward_fft(), ComputePmeCUDADevice::gatherForceDone(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), GlobalMasterIMD::get_vmd_forces(), GlobalMasterEasy::GlobalMasterEasy(), GlobalMasterFreeEnergy::GlobalMasterFreeEnergy(), GlobalMasterIMD::GlobalMasterIMD(), GlobalMasterServer::GlobalMasterServer(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), ComputePmeMgr::gridCalc2R(), Sequencer::hardWallDrude(), HomePatch::hardWallDrude(), colvarproxy_namd::init_atom_group(), colvarproxy_namd::init_tcl_pointers(), colvarproxy_namd::init_volmap(), ComputePmeCUDA::initialize(), LdbCoordinator::initialize(), ComputeQM::initialize(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_computes(), ComputePmeMgr::initialize_pencils(), Sequencer::integrate(), Controller::integrate(), isPmeProcessor(), Sequencer::langevinPiston(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), CudaComputeNonbonded::launchWork(), LJTable::LJTable(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::loweAndersenVelocities(), WorkDistrib::mapComputes(), Sequencer::maximumMove(), ScriptTcl::measure(), Sequencer::minimize(), HomePatch::minimize_rattle2(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), Controller::multigatorCalcEnthalpy(), NamdHybridLB::NamdHybridLB(), ComputeNonbondedCUDA::noWork(), PmePencil< CBase_PmeZPencil >::order_init(), Patch::Patch(), WorkDistrib::patchMapInit(), PmeXPencil::pme_kspace(), Patch::positionsReady(), HomePatch::positionsReady(), Controller::printDynamicsEnergies(), Controller::printEnergies(), Controller::printMinimizeEnergies(), HomePatch::qmSwapAtoms(), Sequencer::rattle1(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), LdbCoordinator::rebalance(), Controller::rebalanceLoad(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), CollectionMaster::receiveDataStream(), CollectionMaster::receiveForces(), CollectionMaster::receivePositions(), Controller::receivePressure(), CollectionMaster::receiveVelocities(), recursive_bisect_with_curve(), ParallelIOMgr::recvAtomsCntPerPatch(), recvCheckpointCAck_handler(), recvCheckpointCReq_handler(), HomePatch::recvCheckpointLoad(), ComputeMgr::recvComputeConsForceMsg(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGBISserMgr::recvCoord(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), recvReplicaDcdData(), recvReplicaDcdInit(), ComputeNonbondedCUDA::recvYieldDevice(), ComputeNonbondedCUDA::registerPatches(), Sequencer::reloadCharges(), Controller::rescaleaccelMD(), Sequencer::rescaleSoluteCharges(), ScriptTcl::run(), ComputeQM::saveResults(), ComputeGlobal::saveTotalForces(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), PmeZPencil::send_all_ungrid(), PmeZPencil::send_trans(), PmeYPencil::send_trans(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), ComputePmeMgr::sendTrans(), ComputePmeMgr::sendUngrid(), ComputePmeMgr::sendUntrans(), HomePatch::setGBISIntrinsicRadii(), PatchMgr::setLattice(), HomePatch::setLcpoType(), ComputePmeCUDAMgr::setupPencils(), ComputeNonbondedCUDA::skip(), NamdHybridLB::splitComputes(), CollectionMaster::startNextRoundOutputForce(), CollectionMaster::startNextRoundOutputPos(), CollectionMaster::startNextRoundOutputVel(), NamdCentLB::Strategy(), CollectionMgr::submitForces(), ComputePmeMgr::submitReductions(), Tcl_centerOfMass(), Tcl_centerOfNumber(), Tcl_loadCoords(), Tcl_radiusOfGyration(), Sequencer::tcoupleVelocities(), ComputePme::ungridForces(), colvarproxy_namd::update_atom_properties(), colvarproxy_namd::update_group_properties(), ComputeMgr::updateLocalComputes4(), Output::velocity(), Output::velocityNeeded(), wrap_coor_int(), and CollectionMaster::wrapCoorFinished().
void Node::outputPatchComputeMaps | ( | const char * | filename, |
int | tag | ||
) |
Definition at line 1521 of file Node.C.
References Patch::getNumAtoms(), PatchMap::gridsize_a(), PatchMap::gridsize_b(), PatchMap::gridsize_c(), NAMD_die(), ComputeMap::node(), PatchMap::node(), ComputeMap::numComputes(), PatchMap::numPatches(), numPatches, PatchMap::Object(), ComputeMap::Object(), SimParameters::outputMaps, PatchMap::patch(), ComputeMap::pid(), simParameters, SimParameters::simulatedNodeSize, SimParameters::simulatedPEs, SimParameters::simulateInitialMapping, and ComputeMap::type().
Referenced by Controller::rebalanceLoad(), and startup().
void Node::papiMeasureBarrier | ( | int | turnOnMeasure, |
int | step | ||
) |
Definition at line 1426 of file Node.C.
References curMFlopStep.
void Node::recvCheckpointAck | ( | CheckpointMsg * | msg | ) |
Definition at line 1326 of file Node.C.
References CheckpointMsg::checkpoint, Controller::recvCheckpointAck(), and state.
Referenced by recvCheckpointCAck_handler().
void Node::recvCheckpointReq | ( | CheckpointMsg * | msg | ) |
Definition at line 1304 of file Node.C.
References CheckpointMsg::checkpoint, CheckpointMsg::key, Controller::recvCheckpointReq(), CheckpointMsg::replica, state, and CheckpointMsg::task.
Referenced by recvCheckpointCReq_handler().
void Node::reloadCharges | ( | const char * | filename | ) |
Definition at line 1153 of file Node.C.
References charge, molecule, NAMD_die(), and Molecule::numAtoms.
void Node::reloadCharges | ( | float | charge[], |
int | n | ||
) |
Definition at line 1170 of file Node.C.
References molecule, and Molecule::reloadCharges().
void Node::reloadGridforceGrid | ( | const char * | key | ) |
Definition at line 1176 of file Node.C.
References DebugM, MGridforceParamsList::find_key(), Molecule::get_gridfrc_grid(), MGridforceParamsList::index_for_key(), SimParameters::mgridforcelist, MGRIDFORCEPARAMS_DEFAULTKEY, molecule, NAMD_bug(), NAMD_die(), GridforceGrid::reinitialize(), and simParameters.
void Node::reloadGridforceGrid | ( | int | gridnum | ) |
Definition at line 1245 of file Node.C.
References ALLBUTME, BUFSIZE, DebugM, MOStream::end(), Molecule::get_gridfrc_grid(), GRIDFORCEGRIDTAG, molecule, NAMD_bug(), GridforceGrid::pack_grid(), Molecule::set_gridfrc_grid(), and GridforceGrid::unpack_grid().
void Node::reloadStructure | ( | const char * | fname, |
const char * | pdbname | ||
) |
Definition at line 1007 of file Node.C.
References NamdState::loadStructure(), molecule, pdb, and state.
void Node::resendMolecule | ( | ) |
Definition at line 1020 of file Node.C.
References ALLBUTME, BUFSIZE, computeMgr, molecule, MOLECULETAG, SimParameters::nonbonded_select(), Molecule::numAtoms, parameters, SimParameters::pme_select(), SimParameters::PMEOn, Molecule::receive_Molecule(), Parameters::receive_Parameters(), Molecule::send_Molecule(), Parameters::send_Parameters(), ComputeMgr::sendBuildCudaExclusions(), simParameters, and STATICPARAMSTAG.
void Node::resendMolecule2 | ( | ) |
Definition at line 1054 of file Node.C.
References AtomMap::allocateMap(), molecule, node_molecule, node_parameters, Molecule::numAtoms, AtomMap::Object(), and parameters.
void Node::resumeAfterPapiMeasureBarrier | ( | CkReductionMsg * | msg | ) |
Definition at line 1478 of file Node.C.
References curMFlopStep, simParameters, and state.
void Node::resumeAfterTraceBarrier | ( | CkReductionMsg * | msg | ) |
Definition at line 1420 of file Node.C.
References curTimeStep, Controller::resumeAfterTraceBarrier(), and state.
Definition at line 1105 of file Node.C.
References ResizeArrayIter< Type >::begin(), DebugM, ResizeArrayIter< Type >::end(), endi(), PatchMap::homePatchList(), iINFO(), iout, memusage_MB(), PatchMap::Object(), NamdState::runController(), HomePatch::runSequencer(), and state.
Referenced by messageRun().
Definition at line 1381 of file Node.C.
References configList, molecule, parameters, pdb, simParameters, and state.
void Node::scriptParam | ( | ScriptParamMsg * | msg | ) |
Definition at line 1148 of file Node.C.
References ScriptParamMsg::param, SimParameters::scriptSet(), simParameters, and ScriptParamMsg::value.
void Node::sendCheckpointReq | ( | int | remote, |
const char * | key, | ||
int | task, | ||
Lattice & | lat, | ||
ControllerState & | cs | ||
) |
Definition at line 1280 of file Node.C.
References CheckpointMsg::checkpoint, CheckpointMsg::key, Controller::checkpoint::lattice, CheckpointMsg::replica, Controller::checkpoint::state, and CheckpointMsg::task.
Referenced by Controller::algorithm().
Definition at line 1356 of file Node.C.
Referenced by enableEarlyExit().
Definition at line 1332 of file Node.C.
Referenced by enableExitScheduler().
void Node::startHPM | ( | ) |
void Node::startup | ( | ) |
Definition at line 429 of file Node.C.
References Lattice::a_p(), AtomMap::allocateMap(), WorkDistrib::assignNodeToPatch(), Lattice::b_p(), SimParameters::bondedCUDA, ProxyMgr::buildProxySpanningTree(), Lattice::c_p(), computeMap, computeMgr, ComputeMgr::createComputes(), WorkDistrib::createHomePatches(), LdbCoordinator::createLoadBalancer(), ProxyMgr::createProxies(), DebugM, WorkDistrib::distributeHomePatches(), endi(), BackEnd::exit(), PDB::get_extremes(), ProxyMgr::getRecvSpanning(), ProxyMgr::getSendSpanning(), iINFO(), LdbCoordinator::initialize(), iout, SimParameters::isRecvSpanningTreeOn(), SimParameters::isSendSpanningTreeOn(), SimParameters::lattice, SimParameters::mallocTest, mallocTest_size, WorkDistrib::mapComputes(), memusage_MB(), messageRun(), molecule, SimParameters::MSMOn, SimParameters::MsmSerialOn, NAMD_bug(), NAMD_EVENT_START_EX, NAMD_EVENT_STOP, NamdProfileEventStr, node_molecule, node_parameters, node_simParameters, SimParameters::nonbonded_select(), Molecule::numAtoms, ComputeMap::numComputes(), numPatches, PatchMap::Object(), AtomMap::Object(), Sync::Object(), ComputeMap::Object(), LdbCoordinator::Object(), ProxyMgr::Object(), Sync::openSync(), output, outputPatchComputeMaps(), parameters, WorkDistrib::patchMapInit(), pdb, SimParameters::pme_select(), SimParameters::PMEOn, proxyRecvSpanning, proxySendSpanning, SimParameters::proxyTreeBranchFactor, rand, SimParameters::randomSeed, registerUserEventsForAllComputeObjs(), WorkDistrib::sendComputeMap(), WorkDistrib::sendPatchMap(), WorkDistrib::setPatchMapArrived(), ProxyMgr::setProxyTreeBranchFactor(), ProxyMgr::setRecvSpanning(), ProxyMgr::setSendSpanning(), simParameters, SimParameters::simulatedNodeSize, SimParameters::simulatedPEs, SimParameters::simulateInitialMapping, MsmInitMsg::smax, MsmInitMsg::smin, Random::split(), SimParameters::useCkLoop, SimParameters::useCUDA2, SimParameters::usePMECUDA, and workDistrib.
Referenced by messageStartUp().
void Node::stopHPM | ( | ) |
void Node::traceBarrier | ( | int | turnOnTrace, |
int | step | ||
) |
Definition at line 1204 of file Node.C.
References DebugM, MGridforceParamsList::find_key(), Molecule::get_gridfrc_grid(), MGridforceParamsList::index_for_key(), SimParameters::mgridforcelist, MGRIDFORCEPARAMS_DEFAULTKEY, molecule, NAMD_bug(), NAMD_die(), simParameters, Vector::x, Vector::y, and Vector::z.
void Node::updateGridScale | ( | int | gridnum, |
float | sx, | ||
float | sy, | ||
float | sz | ||
) |
Definition at line 1229 of file Node.C.
References MGridforceParamsList::at_index(), DebugM, Molecule::get_gridfrc_grid(), MGridforceParams::gridforceScale, SimParameters::mgridforcelist, molecule, NAMD_bug(), GridforceGrid::set_scale(), and simParameters.
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colvarmodule* Node::colvars |
Definition at line 184 of file Node.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), and Node().
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ComputeMgr* Node::computeMgr |
Definition at line 169 of file Node.h.
Referenced by Sequencer::integrate(), Sequencer::minimize(), resendMolecule(), and startup().
ConfigList* Node::configList |
Definition at line 179 of file Node.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), WorkDistrib::createAtomLists(), GlobalMasterSymmetry::GlobalMasterSymmetry(), Node(), ComputeQMMgr::recvPntChrg(), and saveMolDataPointers().
Vector* Node::coords |
Definition at line 185 of file Node.h.
Referenced by ScriptTcl::measure(), Tcl_centerOfMass(), Tcl_centerOfNumber(), Tcl_loadCoords(), and Tcl_radiusOfGyration().
int Node::curMFlopStep |
Definition at line 156 of file Node.h.
Referenced by papiMeasureBarrier(), and resumeAfterPapiMeasureBarrier().
int Node::curTimeStep |
Definition at line 151 of file Node.h.
Referenced by resumeAfterTraceBarrier(), and traceBarrier().
IMDOutput* Node::imd |
Definition at line 183 of file Node.h.
Referenced by Output::coordinate(), GlobalMasterIMD::get_vmd_forces(), GlobalMasterIMD::GlobalMasterIMD(), Node(), and Controller::printEnergies().
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int Node::mallocTest_size |
Definition at line 129 of file Node.h.
Referenced by mallocTestQd(), and startup().
Molecule* Node::molecule |
Definition at line 176 of file Node.h.
Referenced by Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), WorkDistrib::assignNodeToPatch(), ComputeNonbondedCUDA::build_exclusions(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), Controller::calcPressure(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), colvarproxy_namd::check_atom_id(), Controller::compareChecksums(), AngleElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), TholeElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), Controller::Controller(), WorkDistrib::createAtomLists(), ComputeMgr::createComputes(), ComputeConsForce::doForce(), ComputeConsTorque::doForce(), ComputeStir::doForce(), ComputeGridForce::doForce(), ComputeRestraints::doForce(), ComputePme::doQMWork(), ComputeNonbondedCUDA::doWork(), dumpbench(), ComputeNonbondedCUDA::finishWork(), GlobalMasterEasy::GlobalMasterEasy(), GlobalMasterFreeEnergy::GlobalMasterFreeEnergy(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), HomePatch::hardWallDrude(), colvarproxy_namd::init_atom_group(), colvarproxy_namd::init_volmap(), ComputeQM::initialize(), ParallelIOMgr::initialize(), Sequencer::langevinPiston(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), LJTable::LJTable(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::loweAndersenVelocities(), HomePatch::minimize_rattle2(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), Controller::multigatorCalcEnthalpy(), Node(), WorkDistrib::patchMapInit(), Controller::printDynamicsEnergies(), Controller::printEnergies(), Controller::printMinimizeEnergies(), HomePatch::qmSwapAtoms(), HomePatch::rattle1old(), HomePatch::rattle2(), Controller::receivePressure(), ComputeMgr::recvComputeConsForceMsg(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGBISserMgr::recvCoord(), ComputeQMMgr::recvPartQM(), Sequencer::reloadCharges(), reloadCharges(), reloadGridforceGrid(), reloadStructure(), Controller::rescaleaccelMD(), Sequencer::rescaleSoluteCharges(), resendMolecule(), resendMolecule2(), saveMolDataPointers(), ComputeQM::saveResults(), ComputeNonbondedUtil::select(), HomePatch::setGBISIntrinsicRadii(), HomePatch::setLcpoType(), startup(), Tcl_centerOfMass(), Tcl_centerOfNumber(), Tcl_loadCoords(), Tcl_radiusOfGyration(), Sequencer::tcoupleVelocities(), colvarproxy_namd::update_atom_properties(), colvarproxy_namd::update_group_properties(), updateGridScale(), and wrap_coor_int().
Output* Node::output |
Definition at line 182 of file Node.h.
Referenced by SimParameters::close_dcdfile(), SimParameters::close_veldcdfile(), CollectionMaster::disposeForces(), CollectionMaster::disposePositions(), CollectionMaster::disposeVelocities(), Node(), recvReplicaDcdData(), recvReplicaDcdInit(), startup(), and ~Node().
Parameters* Node::parameters |
Definition at line 177 of file Node.h.
Referenced by ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), ComputeNonbondedCUDA::doWork(), LJTable::LJTable(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Node(), resendMolecule(), resendMolecule2(), saveMolDataPointers(), ComputeNonbondedUtil::select(), and startup().
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PDB* Node::pdb |
Definition at line 180 of file Node.h.
Referenced by WorkDistrib::createAtomLists(), Node(), WorkDistrib::patchMapInit(), reloadStructure(), saveMolDataPointers(), and startup().
Random* Node::rand |
Definition at line 172 of file Node.h.
Referenced by ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), startup(), and ~Node().
SimParameters* Node::simParameters |
Definition at line 178 of file Node.h.
Referenced by HomePatch::addForceToMomentum(), HomePatch::addForceToMomentum3(), HomePatch::addVelocityToPosition(), WorkDistrib::assignNodeToPatch(), PmeZPencil::backward_fft(), PmeYPencil::backward_fft(), PmeXPencil::backward_fft(), HomePatch::buildRattleList(), Controller::calcPressure(), ComputePmeMgr::chargeGridSubmitted(), colvarproxy_namd::colvarproxy_namd(), ComputeCylindricalBC::ComputeCylindricalBC(), ComputeEwald::ComputeEwald(), AngleElem::computeForce(), CrosstermElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), TholeElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), GromacsPairElem::computeForce(), ComputeFullDirect::ComputeFullDirect(), ComputeGlobal::ComputeGlobal(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), ComputeLCPO::ComputeLCPO(), ComputeMsm::ComputeMsm(), ComputeNonbondedCUDA::ComputeNonbondedCUDA(), ComputeNonbondedPair::ComputeNonbondedPair(), ComputeNonbondedSelf::ComputeNonbondedSelf(), ComputePme::ComputePme(), ComputeRestraints::ComputeRestraints(), ComputeSphericalBC::ComputeSphericalBC(), ComputeStir::ComputeStir(), ComputeTclBC::ComputeTclBC(), Output::coordinate(), Output::coordinateNeeded(), WorkDistrib::createAtomLists(), ComputeMgr::createComputes(), ComputeCUDAMgr::createCudaComputeNonbonded(), LdbCoordinator::createLoadBalancer(), CudaComputeNonbonded::CudaComputeNonbonded(), ComputeConsForce::doForce(), ComputeEField::doForce(), ComputeConsTorque::doForce(), ComputeStir::doForce(), ComputeGridForce::doForce(), ComputeNonbondedPair::doForce(), ComputeNonbondedSelf::doForce(), ComputeRestraints::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), HomePatch::doPairlistCheck(), ComputeTclBC::doWork(), ComputeGBISser::doWork(), ComputeNonbondedCUDA::doWork(), CudaComputeNonbonded::doWork(), dumpbench(), HomePatch::exchangeAtoms(), HomePatch::exchangeCheckpoint(), PmeZPencil::fft_init(), PmeYPencil::fft_init(), PmeXPencil::fft_init(), ComputeNonbondedCUDA::finishReductions(), CudaComputeNonbonded::finishReductions(), ComputeNonbondedCUDA::finishWork(), Output::force(), Output::forceNeeded(), PmeZPencil::forward_fft(), PmeYPencil::forward_fft(), PmeXPencil::forward_fft(), ComputePmeCUDADevice::gatherForceDone(), HomePatch::gbisComputeAfterP1(), HomePatch::gbisComputeAfterP2(), GlobalMasterIMD::get_vmd_forces(), GlobalMasterFreeEnergy::GlobalMasterFreeEnergy(), GlobalMasterIMD::GlobalMasterIMD(), GlobalMasterServer::GlobalMasterServer(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), HomePatch::hardWallDrude(), ComputePmeCUDA::initialize(), LdbCoordinator::initialize(), ComputeQM::initialize(), ParallelIOMgr::initialize(), ComputePmeMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize_computes(), ComputePmeMgr::initialize_pencils(), isPmeProcessor(), CudaComputeNonbonded::launchWork(), LJTable::LJTable(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), HomePatch::loweAndersenVelocities(), WorkDistrib::mapComputes(), HomePatch::minimize_rattle2(), HomePatch::mollyAverage(), HomePatch::mollyMollify(), Controller::multigatorCalcEnthalpy(), NamdHybridLB::NamdHybridLB(), Node(), ComputeNonbondedCUDA::noWork(), PmePencil< CBase_PmeZPencil >::order_init(), outputPatchComputeMaps(), Patch::Patch(), WorkDistrib::patchMapInit(), Patch::positionsReady(), HomePatch::positionsReady(), Controller::printDynamicsEnergies(), Controller::printEnergies(), HomePatch::qmSwapAtoms(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), ProxyPatch::receiveAll(), ProxyPatch::receiveData(), CollectionMaster::receiveDataStream(), Controller::receivePressure(), recursive_bisect_with_curve(), HomePatch::recvCheckpointLoad(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeQMMgr::recvPartQM(), ComputeNonbondedCUDA::recvYieldDevice(), ComputeNonbondedCUDA::registerPatches(), reloadGridforceGrid(), resendMolecule(), resumeAfterPapiMeasureBarrier(), ScriptTcl::run(), saveMolDataPointers(), WorkDistrib::savePatchMap(), ComputeGlobal::saveTotalForces(), scriptParam(), ComputePmeUtil::select(), ComputeNonbondedUtil::select(), PmeZPencil::send_all_ungrid(), PmeZPencil::send_trans(), PmeYPencil::send_trans(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), WorkDistrib::sendPatchMap(), ComputePmeMgr::sendTrans(), ComputePmeMgr::sendUngrid(), ComputePmeMgr::sendUntrans(), HomePatch::setGBISIntrinsicRadii(), PatchMgr::setLattice(), ComputePmeCUDAMgr::setupPencils(), ComputeNonbondedCUDA::skip(), NamdHybridLB::splitComputes(), startup(), NamdCentLB::Strategy(), CollectionMgr::submitForces(), ComputePmeMgr::submitReductions(), ComputePme::ungridForces(), updateGridScale(), ComputeMgr::updateLocalComputes4(), Output::velocity(), Output::velocityNeeded(), and wrap_coor_int().
NamdState* Node::state |
Definition at line 181 of file Node.h.
Referenced by Node(), recvCheckpointAck(), recvCheckpointReq(), reloadStructure(), resumeAfterPapiMeasureBarrier(), resumeAfterTraceBarrier(), run(), and saveMolDataPointers().
WorkDistrib* Node::workDistrib |
Definition at line 166 of file Node.h.
Referenced by ParallelIOMgr::createHomePatches(), and startup().