|
NAMD
|
#include <iostream>#include <sstream>Go to the source code of this file.
Classes | |
| class | infostream |
Macros | |
| #define | iFILE __FILE__<<'('<<__LINE__<<"): " |
| #define | iINFOF iINFO << iFILE |
| #define | iWARNF iWARN << iFILE |
| #define | iERRORF iERROR << iFILE |
| #define | iDEBUGF iDEBUG << iFILE |
| #define | iout infostream::access_iout_obj() |
Functions | |
| std::ostream & | operator<< (std::ostream &strm, const Vector &v1) |
| std::ostream & | operator<< (std::ostream &strm, const Tensor &t1) |
| std::ostream & | endi (std::ostream &s) |
| std::ostream & | iINFO (std::ostream &s) |
| std::ostream & | iWARN (std::ostream &s) |
| std::ostream & | iERROR (std::ostream &s) |
| std::ostream & | iDEBUG (std::ostream &s) |
| std::ostream & | iPE (std::ostream &s) |
Definition at line 49 of file InfoStream.h.
Definition at line 48 of file InfoStream.h.
| #define iFILE __FILE__<<'('<<__LINE__<<"): " |
Definition at line 45 of file InfoStream.h.
Definition at line 46 of file InfoStream.h.
| #define iout infostream::access_iout_obj() |
Definition at line 51 of file InfoStream.h.
Referenced by Controller::adaptTempInit(), Controller::adaptTempUpdate(), Controller::adaptTempWriteRestart(), after_backend_init(), Controller::algorithm(), ResidueLookupElem::append(), Rebalancer::assign(), Parameters::assign_angle_index(), Parameters::assign_dihedral_index(), Parameters::assign_vdw_index(), WorkDistrib::assignNodeToPatch(), average(), ParallelIOMgr::bcastHydroBasedCounter(), ParallelIOMgr::bcastMolInfo(), Controller::berendsenPressure(), Molecule::build_go_arrays(), Molecule::build_go_params(), Molecule::build_go_sigmas(), Molecule::build_go_sigmas2(), Molecule::build_gridforce_params(), buildExclusions(), WorkDistrib::buildNodeAwarePeOrdering(), ProxyMgr::buildProxySpanningTree(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), GlobalMasterIMD::calculate(), ComputeQMMgr::calcUSR(), ParseOptions::check_consistency(), LdbCoordinator::collectLoads(), colvarproxy_namd::colvarproxy_namd(), Controller::compareChecksums(), ConfigList::ConfigList(), Output::coordinate(), Controller::correctMomentum(), WorkDistrib::createAtomLists(), ComputeCUDAMgr::createCudaGlobalMaster(), WorkDistrib::createHomePatches(), Rebalancer::deAssign(), Molecule::delete_qm_bonded(), ComputeGridForce::do_calc(), ARestraint::EarlyExit(), GlobalMasterMisc::easy_calc(), GlobalMasterMisc::easy_init(), Fopen(), Output::force(), ParseOptions::get(), GlobalMasterIMD::get_vmd_forces(), PressureProfileReduction::getData(), ParseOptions::getfromptr(), GlobalMasterIMD::GlobalMasterIMD(), GlobalMasterSMD::GlobalMasterSMD(), GlobalMasterTMD::GlobalMasterTMD(), GromacsTopFile::GromacsTopFile(), Sequencer::hardWallDrude(), HomePatch::hardWallDrude(), GridforceFullMainGrid::initialize(), GridforceFullSubGrid::initialize(), ParallelIOMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize(), ComputePmeCUDAMgr::initialize(), ComputeMsmMgr::initialize_create(), Controller::langevinPiston1(), Controller::langevinPiston2(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), colvarproxy_namd::log(), main::main(), PatchMap::makePatches(), Sequencer::maximumMove(), Sequencer::maximumMove_SOA(), Controller::minimize(), HomePatch::minimize_rattle2(), HomePatch::mollyAverage(), Controller::monteCarloPressure_accept(), Ambertoppar::moveto(), Rebalancer::multirefine(), my_assert(), my_imd_connect(), NAMD_backup_file(), NAMD_file_exists(), NAMD_write(), RefineTorusLB::newRefine(), LdbCoordinator::nodeDone(), Sync::openSync(), LjPmeMgr::optimizeFFT(), AVector::Out(), AVector::Output(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), AmberParm7Reader::parse_section(), WorkDistrib::patchMapInit(), Patch::positionsReady(), Molecule::prepare_qm(), IRSet::print(), Parameters::print_crossterm_params(), ARestraintManager::Print_dU_dLambda_Info(), ALambdaManager::Print_dU_dLambda_Summary(), ALambdaManager::Print_MCTI_Integration(), Parameters::print_param_summary(), Controller::printEnergies(), ARestraintManager::PrintEnergyInfo(), Controller::printFepMessage(), ALambdaControl::PrintHeader(), APosRestraint::PrintInfo(), ADistRestraint::PrintInfo(), AnAngleRestraint::PrintInfo(), ADiheRestraint::PrintInfo(), ALambdaControl::PrintLambdaHeader(), Rebalancer::printLoads(), ARestraintManager::PrintPreInfo(), ARestraintManager::PrintRestraintInfo(), Rebalancer::printResults(), ALambdaManager::PrintSomeSpaces(), GroupRestraintParam::PrintSummary(), Rebalancer::printSummary(), Controller::printTiMessage(), Controller::printTiming(), ProblemParsing(), ComputeQMMgr::procQMRes(), ParseOptions::range(), Sequencer::rattle1(), HomePatch::rattle1(), Sequencer::rattle1_SOA(), HomePatch::rattle1_SOA(), HomePatch::rattle1old(), HomePatch::rattle2(), AmberParm7Reader::read_amber_parm_stage2(), read_binary_file(), Parameters::read_charmm_parameter_file(), Parameters::read_ener_table(), Molecule::read_go_file(), Parameters::read_parm(), SimParameters::readExtendedSystem(), Ambertoppar::readparm(), AmberParm7Reader::readparm(), Controller::reassignVelocities(), LdbCoordinator::rebalance(), Controller::receivePressure(), ParallelIOMgr::recvAtomsCntPerPatch(), ComputeFmmSerialMgr::recvCoord(), ComputeMgr::recvCudaGlobalMasterCreateMsg(), ComputeMgr::recvCudaGlobalMasterRemoveMsg(), ComputeMgr::recvCudaGlobalMasterUpdateMsg(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), Output::recvReplicaDcdData(), Output::recvReplicaDcdInit(), Rebalancer::refine(), PatchMap::registerPatch(), Controller::rescaleaccelMD(), LdbCoordinator::resumeReady(), Node::run(), ComputeNonbondedUtil::select(), ComputePmeMgr::sendDataPart(), ComputePmeMgr::sendPencils(), ParseOptions::set(), GroupRestraintParam::SetForce(), GroupRestraintParam::SetGroup1AtomFileIndices(), GroupRestraintParam::SetGroup1AtomListIndices(), GroupRestraintParam::SetGroup1RefPosition(), GroupRestraintParam::SetGroup2AtomFileIndices(), GroupRestraintParam::SetGroup2AtomListIndices(), GroupRestraintParam::SetResCenter(), SimParameters::setupIDWS(), ComputePmeCUDAMgr::setupPencils(), Node::startup(), ComputeQMMgr::storeQMRes(), NamdCentLB::Strategy(), Rebalancer::strategy(), tbsoft_sendusage(), TopoManagerWrapper::TopoManagerWrapper(), ComputePme::ungridForces(), ParseOptions::units(), Output::velocity(), Controller::write_accelMDG_rest_file(), ComputeMgr::~ComputeMgr(), and Rebalancer::~Rebalancer().
Definition at line 47 of file InfoStream.h.
| std::ostream& endi | ( | std::ostream & | s | ) |
modifiers
Definition at line 54 of file InfoStream.C.
Referenced by Controller::adaptTempInit(), Controller::adaptTempUpdate(), Controller::adaptTempWriteRestart(), GridforceFullSubGrid::addToSubgridsFlat(), after_backend_init(), Controller::algorithm(), ResidueLookupElem::append(), Rebalancer::assign(), Parameters::assign_angle_index(), Parameters::assign_dihedral_index(), Parameters::assign_vdw_index(), WorkDistrib::assignNodeToPatch(), average(), ParallelIOMgr::bcastHydroBasedCounter(), ParallelIOMgr::bcastMolInfo(), Controller::berendsenPressure(), Molecule::build_go_arrays(), Molecule::build_go_params(), Molecule::build_go_sigmas(), Molecule::build_go_sigmas2(), Molecule::build_gridforce_params(), buildExclusions(), WorkDistrib::buildNodeAwarePeOrdering(), ProxyMgr::buildProxySpanningTree(), GridforceFullMainGrid::buildSubgridsFlat(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), GlobalMasterIMD::calculate(), ComputeQMMgr::calcUSR(), ParseOptions::check_consistency(), LdbCoordinator::collectLoads(), colvarproxy_namd::colvarproxy_namd(), Controller::compareChecksums(), GridforceFullMainGrid::compute_b(), GridforceFullSubGrid::compute_b(), GridforceLiteGrid::compute_derivative_grids(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), ComputePmeCUDADevice::ComputePmeCUDADevice(), ConfigList::ConfigList(), Output::coordinate(), Controller::correctMomentum(), WorkDistrib::createAtomLists(), ComputeCUDAMgr::createCudaGlobalMaster(), WorkDistrib::createHomePatches(), Rebalancer::deAssign(), Molecule::delete_qm_bonded(), ComputeGridForce::do_calc(), ComputeConsForce::doForce(), ComputeGridForce::doForce(), ComputeGlobal::doWork(), ARestraint::EarlyExit(), GlobalMasterMisc::easy_calc(), GlobalMasterMisc::easy_init(), PmeAtomFiler::fileAtoms(), GridforceGrid::fits_lattice(), Fopen(), Output::force(), ParseOptions::get(), GridforceFullMainGrid::get_all_gridvals(), GridforceLiteGrid::get_all_gridvals(), GridforceGrid::get_corner(), GlobalMasterIMD::get_vmd_forces(), PressureProfileReduction::getData(), ParseOptions::getfromptr(), GlobalMasterIMD::GlobalMasterIMD(), GlobalMasterSMD::GlobalMasterSMD(), GlobalMasterTMD::GlobalMasterTMD(), GridforceFullSubGrid::GridforceFullSubGrid(), Sequencer::hardWallDrude(), HomePatch::hardWallDrude(), GridforceFullMainGrid::initialize(), GridforceFullSubGrid::initialize(), GridforceLiteGrid::initialize(), ParallelIOMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize(), ComputePmeCUDADevice::initialize(), ComputePmeCUDAMgr::initialize(), ComputeMsmMgr::initialize_create(), ComputePmeCUDAMgr::initialize_pencils(), Sequencer::integrate(), Sequencer::integrate_SOA(), GridforceLiteGrid::linear_interpolate(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), colvarproxy_namd::log(), main::main(), PatchMap::makePatches(), Sequencer::maximumMove(), Sequencer::maximumMove_SOA(), Controller::minimize(), HomePatch::minimize_rattle2(), GlobalMaster::modifyRequestedAtoms(), GlobalMaster::modifyRequestedGridObjects(), HomePatch::mollyAverage(), Controller::monteCarloPressure_accept(), Ambertoppar::moveto(), Rebalancer::multirefine(), my_assert(), my_imd_connect(), NAMD_backup_file(), NAMD_file_exists(), NAMD_write(), RefineTorusLB::newRefine(), LdbCoordinator::nodeDone(), Sync::openSync(), LjPmeMgr::optimizeFFT(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), GridforceFullBaseGrid::pack(), GridforceFullMainGrid::pack(), GridforceFullSubGrid::pack(), AmberParm7Reader::parse_section(), WorkDistrib::patchMapInit(), Patch::positionsReady(), Molecule::prepare_qm(), Molecule::print_atoms(), Molecule::print_bonds(), ARestraintManager::Print_dU_dLambda_Info(), ALambdaManager::Print_dU_dLambda_Summary(), Molecule::print_exclusions(), ALambdaManager::Print_MCTI_Integration(), Parameters::print_param_summary(), Controller::printEnergies(), ARestraintManager::PrintEnergyInfo(), Controller::printFepMessage(), ALambdaControl::PrintHeader(), APosRestraint::PrintInfo(), ADistRestraint::PrintInfo(), AnAngleRestraint::PrintInfo(), ADiheRestraint::PrintInfo(), ALambdaControl::PrintLambdaHeader(), Rebalancer::printLoads(), ARestraintManager::PrintRestraintInfo(), GroupRestraintParam::PrintSummary(), Rebalancer::printSummary(), Controller::printTiMessage(), Controller::printTiming(), ProblemParsing(), ComputeQMMgr::procQMRes(), ParseOptions::range(), Sequencer::rattle1(), HomePatch::rattle1(), Sequencer::rattle1_SOA(), HomePatch::rattle1_SOA(), HomePatch::rattle1old(), HomePatch::rattle2(), AmberParm7Reader::read_amber_parm_stage2(), read_binary_file(), Parameters::read_charmm_parameter_file(), Parameters::read_ener_table(), Molecule::read_go_file(), SimParameters::readExtendedSystem(), GridforceFullBaseGrid::readHeader(), Ambertoppar::readparm(), AmberParm7Reader::readparm(), GridforceFullBaseGrid::readSubgridHierarchy(), Controller::reassignVelocities(), LdbCoordinator::rebalance(), Controller::receivePressure(), ComputePmeCUDAMgr::recvAtoms(), ParallelIOMgr::recvAtomsCntPerPatch(), ComputeFmmSerialMgr::recvCoord(), ComputeMgr::recvCudaGlobalMasterCreateMsg(), ComputeMgr::recvCudaGlobalMasterRemoveMsg(), ComputeMgr::recvCudaGlobalMasterUpdateMsg(), GlobalMasterServer::recvData(), ComputePmeCUDAMgr::recvDevices(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), Output::recvReplicaDcdData(), Output::recvReplicaDcdInit(), Rebalancer::refine(), PatchMap::registerPatch(), GridforceFullMainGrid::reinitialize(), Node::reloadGridforceGrid(), Controller::rescaleaccelMD(), LdbCoordinator::resumeReady(), Node::run(), ComputeNonbondedUtil::select(), Molecule::send_Molecule(), ComputePmeMgr::sendDataPart(), ComputePmeMgr::sendPencils(), ParseOptions::set(), GridforceFullMainGrid::set_all_gridvals(), GridforceLiteGrid::set_all_gridvals(), GroupRestraintParam::SetForce(), GroupRestraintParam::SetGroup1AtomFileIndices(), GroupRestraintParam::SetGroup1AtomListIndices(), GroupRestraintParam::SetGroup1RefPosition(), GroupRestraintParam::SetGroup2AtomFileIndices(), GroupRestraintParam::SetGroup2AtomListIndices(), GroupRestraintParam::SetResCenter(), SimParameters::setupIDWS(), ComputePmeCUDAMgr::setupPencils(), ComputePmeCUDAMgr::skip(), Node::startup(), ComputeQMMgr::storeQMRes(), NamdCentLB::Strategy(), tbsoft_sendusage(), TopoManagerWrapper::TopoManagerWrapper(), ComputePme::ungridForces(), ParseOptions::units(), GridforceFullBaseGrid::unpack(), GridforceFullMainGrid::unpack(), GridforceFullSubGrid::unpack(), Node::updateGridScale(), Output::velocity(), Controller::write_accelMDG_rest_file(), ComputeMgr::~ComputeMgr(), and Rebalancer::~Rebalancer().
| std::ostream& iDEBUG | ( | std::ostream & | s | ) |
Definition at line 84 of file InfoStream.C.
| std::ostream& iERROR | ( | std::ostream & | s | ) |
Definition at line 83 of file InfoStream.C.
Referenced by Controller::berendsenPressure(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), ParseOptions::check_consistency(), Controller::compareChecksums(), Controller::correctMomentum(), Molecule::delete_qm_bonded(), ParseOptions::get(), ParseOptions::getfromptr(), Sequencer::hardWallDrude(), HomePatch::hardWallDrude(), Sequencer::maximumMove(), Sequencer::maximumMove_SOA(), NAMD_backup_file(), NAMD_file_exists(), AmberParm7Reader::parse_section(), Molecule::prepare_qm(), Controller::printEnergies(), ParseOptions::range(), Sequencer::rattle1(), HomePatch::rattle1(), Sequencer::rattle1_SOA(), HomePatch::rattle1_SOA(), HomePatch::rattle1old(), AmberParm7Reader::read_amber_parm_stage2(), AmberParm7Reader::readparm(), ComputeMgr::recvCudaGlobalMasterCreateMsg(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), ComputeNonbondedUtil::select(), ComputePmeMgr::sendDataPart(), ComputePmeMgr::sendPencils(), ParseOptions::set(), ComputePme::ungridForces(), and ParseOptions::units().
| std::ostream& iINFO | ( | std::ostream & | s | ) |
common messages iINFO, iWARN, iERROR, iDEBUG provide initial headings. iINFOF, iWARNF, iERRORF, iDEBUGF provide initial headings with file name and line numbers.
Definition at line 81 of file InfoStream.C.
Referenced by Controller::adaptTempInit(), after_backend_init(), WorkDistrib::assignNodeToPatch(), average(), ParallelIOMgr::bcastHydroBasedCounter(), ParallelIOMgr::bcastMolInfo(), Molecule::build_go_arrays(), Molecule::build_go_params(), Molecule::build_go_sigmas(), Molecule::build_go_sigmas2(), buildExclusions(), ProxyMgr::buildProxySpanningTree(), GlobalMasterIMD::calculate(), Controller::compareChecksums(), ConfigList::ConfigList(), ComputeCUDAMgr::createCudaGlobalMaster(), WorkDistrib::createHomePatches(), Rebalancer::deAssign(), Molecule::delete_qm_bonded(), GlobalMasterMisc::easy_calc(), GlobalMasterMisc::easy_init(), GlobalMasterIMD::get_vmd_forces(), GlobalMasterIMD::GlobalMasterIMD(), GlobalMasterSMD::GlobalMasterSMD(), GlobalMasterTMD::GlobalMasterTMD(), ParallelIOMgr::initialize(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize(), ComputePmeCUDAMgr::initialize(), ComputeMsmMgr::initialize_create(), Controller::langevinPiston1(), Controller::langevinPiston2(), NamdState::loadStructure(), main::main(), PatchMap::makePatches(), Rebalancer::multirefine(), Sync::openSync(), LjPmeMgr::optimizeFFT(), AmberParm7Reader::parse_section(), WorkDistrib::patchMapInit(), Patch::positionsReady(), Molecule::prepare_qm(), Parameters::print_param_summary(), Controller::printEnergies(), Rebalancer::printResults(), GroupRestraintParam::PrintSummary(), Rebalancer::printSummary(), ComputeQMMgr::procQMRes(), read_binary_file(), SimParameters::readExtendedSystem(), AmberParm7Reader::readparm(), Controller::receivePressure(), ParallelIOMgr::recvAtomsCntPerPatch(), ComputeFmmSerialMgr::recvCoord(), ComputeMgr::recvCudaGlobalMasterCreateMsg(), ComputeMgr::recvCudaGlobalMasterRemoveMsg(), ComputeMgr::recvCudaGlobalMasterUpdateMsg(), ComputeQMMgr::recvPartQM(), Rebalancer::refine(), Node::run(), ComputeNonbondedUtil::select(), GroupRestraintParam::SetGroup1AtomFileIndices(), GroupRestraintParam::SetGroup2AtomFileIndices(), ComputePmeCUDAMgr::setupPencils(), Node::startup(), NamdCentLB::Strategy(), Rebalancer::strategy(), tbsoft_sendusage(), TopoManagerWrapper::TopoManagerWrapper(), and ComputeMgr::~ComputeMgr().
| std::ostream& iPE | ( | std::ostream & | s | ) |
Definition at line 61 of file InfoStream.C.
Referenced by PatchMap::registerPatch().
| std::ostream& iWARN | ( | std::ostream & | s | ) |
Definition at line 82 of file InfoStream.C.
Referenced by Controller::adaptTempUpdate(), ResidueLookupElem::append(), Parameters::assign_angle_index(), Parameters::assign_dihedral_index(), Parameters::assign_vdw_index(), Molecule::build_gridforce_params(), WorkDistrib::buildNodeAwarePeOrdering(), GlobalMasterIMD::calculate(), Controller::compareChecksums(), ConfigList::ConfigList(), ComputeGridForce::do_calc(), ParseOptions::get(), GlobalMasterIMD::get_vmd_forces(), GlobalMasterIMD::GlobalMasterIMD(), GromacsTopFile::GromacsTopFile(), GridforceFullMainGrid::initialize(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), main::main(), HomePatch::minimize_rattle2(), HomePatch::mollyAverage(), Controller::monteCarloPressure_accept(), Ambertoppar::moveto(), Rebalancer::multirefine(), my_imd_connect(), NAMD_write(), WorkDistrib::patchMapInit(), Molecule::prepare_qm(), Controller::printEnergies(), Controller::printTiming(), HomePatch::rattle1(), HomePatch::rattle1_SOA(), HomePatch::rattle1old(), HomePatch::rattle2(), AmberParm7Reader::read_amber_parm_stage2(), read_binary_file(), Parameters::read_charmm_parameter_file(), Molecule::read_go_file(), Parameters::read_parm(), ComputeQMMgr::recvPartQM(), Controller::rescaleaccelMD(), ParseOptions::set(), GroupRestraintParam::SetForce(), GroupRestraintParam::SetGroup1AtomFileIndices(), GroupRestraintParam::SetGroup1AtomListIndices(), GroupRestraintParam::SetGroup1RefPosition(), GroupRestraintParam::SetGroup2AtomFileIndices(), GroupRestraintParam::SetGroup2AtomListIndices(), GroupRestraintParam::SetResCenter(), SimParameters::setupIDWS(), and Controller::write_accelMDG_rest_file().
| std::ostream& operator<< | ( | std::ostream & | strm, |
| const Vector & | v1 | ||
| ) |
| std::ostream& operator<< | ( | std::ostream & | strm, |
| const Tensor & | t1 | ||
| ) |
Definition at line 70 of file InfoStream.C.
References Tensor::xx, Tensor::xy, Tensor::xz, Tensor::yx, Tensor::yy, Tensor::yz, Tensor::zx, Tensor::zy, and Tensor::zz.
1.8.14