NAMD
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#include <SimParameters.h>
Static Public Member Functions | |
static void | nonbonded_select () |
static void | pme_select () |
Definition at line 139 of file SimParameters.h.
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inline |
Definition at line 1197 of file SimParameters.h.
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inline |
Definition at line 1198 of file SimParameters.h.
References initialize_config_data().
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inline |
Definition at line 1201 of file SimParameters.h.
size_t SimParameters::alchGetNumOfPMEGrids | ( | ) | const |
Definition at line 8564 of file SimParameters.C.
Referenced by CudaPmeOneDevice::CudaPmeOneDevice().
void SimParameters::close_dcdfile | ( | ) |
Definition at line 858 of file Output.C.
References Molecule::dcdSelectionParams, END_OF_RUN, dcd_params::frequency, Node::molecule, Node::Object(), Node::output, and dcd_params::tag.
void SimParameters::close_veldcdfile | ( | ) |
Definition at line 874 of file Output.C.
References END_OF_RUN, Node::Object(), and Node::output.
Definition at line 8559 of file SimParameters.C.
Referenced by Controller::computeAlchWork(), and Controller::outputTiEnergy().
BigReal SimParameters::getCurrentLambda | ( | const int | step | ) | const |
Definition at line 8480 of file SimParameters.C.
Referenced by Controller::calcPressure(), Controller::computeAlchWork(), colvarproxy_namd::get_alch_lambda(), Controller::getTotalPotentialEnergy(), and Controller::printEnergies().
BigReal SimParameters::getCurrentLambda2 | ( | const int | step | ) | const |
Definition at line 8430 of file SimParameters.C.
Referenced by Controller::outputTiEnergy(), and Controller::printEnergies().
Definition at line 8522 of file SimParameters.C.
Referenced by Controller::computeAlchWork(), and Controller::outputTiEnergy().
char * SimParameters::getfromparseopts | ( | const char * | name, |
char * | outbuf | ||
) |
Definition at line 107 of file SimParameters.C.
BigReal SimParameters::getLambdaDelta | ( | void | ) | const |
Definition at line 8554 of file SimParameters.C.
Definition at line 8536 of file SimParameters.C.
Referenced by Controller::computeAlchWork(), and Controller::outputTiEnergy().
void SimParameters::initialize_config_data | ( | ConfigList * | config, |
char *& | cwd | ||
) |
Definition at line 135 of file SimParameters.C.
References ParseOptions::check_consistency(), NAMD_die(), and ParseOptions::set().
Referenced by SimParameters().
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inline |
Definition at line 1226 of file SimParameters.h.
References fullElectFrequency, and nonbondedFrequency.
Referenced by Controller::calcPressure().
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inline |
Definition at line 1223 of file SimParameters.h.
References proxyRecvSpanningTree.
Referenced by Node::startup().
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inline |
Definition at line 1224 of file SimParameters.h.
References proxyRecvSpanningTree.
Referenced by WorkDistrib::savePatchMap(), and WorkDistrib::sendPatchMap().
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inline |
Definition at line 1221 of file SimParameters.h.
References proxySendSpanningTree.
Referenced by Node::startup().
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inline |
Definition at line 1222 of file SimParameters.h.
References proxySendSpanningTree.
Referenced by WorkDistrib::savePatchMap(), and WorkDistrib::sendPatchMap().
int SimParameters::issetinparseopts | ( | const char * | name | ) |
Definition at line 117 of file SimParameters.C.
int SimParameters::istrueinparseopts | ( | const char * | name | ) |
Definition at line 112 of file SimParameters.C.
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static |
Definition at line 473 of file SimParameters.C.
References ComputeNonbondedUtil::select().
Referenced by Node::resendMolecule(), and Node::startup().
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static |
Definition at line 477 of file SimParameters.C.
References ComputePmeUtil::select().
Referenced by Node::resendMolecule(), and Node::startup().
void SimParameters::readExtendedSystem | ( | const char * | filename, |
Lattice * | latptr = 0 |
||
) |
Definition at line 2616 of file SimParameters.C.
References Lattice::a_p(), Lattice::b_p(), Lattice::c_p(), endi(), iINFO(), iout, NAMD_die(), and Lattice::set().
void SimParameters::receive_SimParameters | ( | MIStream * | msg | ) |
Definition at line 8371 of file SimParameters.C.
References MIStream::get().
void SimParameters::scriptSet | ( | const char * | param, |
const char * | value | ||
) |
Definition at line 177 of file SimParameters.C.
References atobool(), ComputeCUDAMgr::getComputeCUDAMgr(), MAX_SCRIPT_PARAM_SIZE, NAMD_die(), PRESSUREFACTOR, SCRIPT_PARSE_BOOL, SCRIPT_PARSE_FLOAT, SCRIPT_PARSE_INT, SCRIPT_PARSE_MOD_FLOAT, SCRIPT_PARSE_STRING, SCRIPT_PARSE_VECTOR, ComputePmeUtil::select(), ComputeNonbondedUtil::select(), and ComputeCUDAMgr::update().
Referenced by Node::scriptParam().
void SimParameters::send_SimParameters | ( | MOStream * | msg | ) |
Definition at line 8313 of file SimParameters.C.
References MOStream::end(), and MOStream::put().
int SimParameters::setupIDWS | ( | ) |
Definition at line 8440 of file SimParameters.C.
References endi(), iout, iWARN(), and NAMD_die().
int SimParameters::aaAngleExp |
Definition at line 1102 of file SimParameters.h.
BigReal SimParameters::accelMDalpha |
Definition at line 721 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Bool SimParameters::accelMDDebugOn |
Definition at line 716 of file SimParameters.h.
Referenced by Controller::receivePressure(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces().
Bool SimParameters::accelMDdihe |
Definition at line 714 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), and ComputeGlobal::saveTotalForces().
Bool SimParameters::accelMDdual |
Definition at line 715 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Sequencer::integrate(), Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().
BigReal SimParameters::accelMDE |
Definition at line 720 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
BigReal SimParameters::accelMDFirstStep |
Definition at line 717 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Bool SimParameters::accelMDG |
Definition at line 725 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
int SimParameters::accelMDGcMDPrepSteps |
Definition at line 729 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
int SimParameters::accelMDGcMDSteps |
Definition at line 727 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
int SimParameters::accelMDGEquiPrepSteps |
Definition at line 730 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
int SimParameters::accelMDGEquiSteps |
Definition at line 728 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
int SimParameters::accelMDGiE |
Definition at line 726 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Bool SimParameters::accelMDGresetVaftercmd |
Definition at line 736 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
Bool SimParameters::accelMDGRestart |
Definition at line 734 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
char SimParameters::accelMDGRestartFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 735 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
BigReal SimParameters::accelMDGSigma0D |
Definition at line 733 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
BigReal SimParameters::accelMDGSigma0P |
Definition at line 732 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
int SimParameters::accelMDGStatWindow |
Definition at line 731 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
BigReal SimParameters::accelMDLastStep |
Definition at line 718 of file SimParameters.h.
Referenced by Sequencer::rescaleaccelMD(), and Controller::rescaleaccelMD().
Bool SimParameters::accelMDOn |
Definition at line 713 of file SimParameters.h.
Referenced by Controller::calcPressure(), colvarproxy_namd::colvarproxy_namd(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), Sequencer::integrate(), Controller::receivePressure(), Sequencer::rescaleaccelMD(), Controller::rescaleaccelMD(), ComputeGlobal::saveTotalForces(), and Sequencer::Sequencer().
int SimParameters::accelMDOutFreq |
Definition at line 719 of file SimParameters.h.
Referenced by Controller::receivePressure(), and Controller::rescaleaccelMD().
BigReal SimParameters::accelMDTalpha |
Definition at line 723 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
BigReal SimParameters::accelMDTE |
Definition at line 722 of file SimParameters.h.
Referenced by Controller::rescaleaccelMD().
BigReal SimParameters::adaptTempAutoDt |
Definition at line 747 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
int SimParameters::adaptTempBins |
Definition at line 748 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
BigReal SimParameters::adaptTempCgamma |
Definition at line 750 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Bool SimParameters::adaptTempDebug |
Definition at line 740 of file SimParameters.h.
Referenced by Controller::adaptTempUpdate().
BigReal SimParameters::adaptTempDt |
Definition at line 749 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
int SimParameters::adaptTempFirstStep |
Definition at line 741 of file SimParameters.h.
Referenced by Controller::rescaleVelocities().
int SimParameters::adaptTempFreq |
Definition at line 744 of file SimParameters.h.
Referenced by Sequencer::adaptTempUpdate(), and Controller::adaptTempUpdate().
char SimParameters::adaptTempInFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 753 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Bool SimParameters::adaptTempLangevin |
Definition at line 751 of file SimParameters.h.
Referenced by Sequencer::langevinVelocities(), and Sequencer::langevinVelocitiesBBK2().
int SimParameters::adaptTempLastStep |
Definition at line 742 of file SimParameters.h.
Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), and Controller::rescaleVelocities().
Bool SimParameters::adaptTempOn |
Definition at line 739 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), Controller::adaptTempWriteRestart(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), and Controller::rescaleVelocities().
int SimParameters::adaptTempOutFreq |
Definition at line 743 of file SimParameters.h.
Referenced by Controller::adaptTempUpdate().
Bool SimParameters::adaptTempRandom |
Definition at line 756 of file SimParameters.h.
Referenced by Controller::adaptTempUpdate().
Bool SimParameters::adaptTempRescale |
Definition at line 752 of file SimParameters.h.
Referenced by Controller::rescaleVelocities().
char SimParameters::adaptTempRestartFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 754 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
int SimParameters::adaptTempRestartFreq |
Definition at line 755 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), and Controller::adaptTempWriteRestart().
BigReal SimParameters::adaptTempTmax |
Definition at line 746 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
BigReal SimParameters::adaptTempTmin |
Definition at line 745 of file SimParameters.h.
Referenced by Controller::adaptTempInit().
Bool SimParameters::alchBondDecouple |
Definition at line 518 of file SimParameters.h.
BigReal SimParameters::alchBondLambdaEnd |
Definition at line 512 of file SimParameters.h.
Bool SimParameters::alchDecouple |
Definition at line 517 of file SimParameters.h.
BigReal SimParameters::alchElecLambdaStart |
Definition at line 495 of file SimParameters.h.
Bool SimParameters::alchEnsembleAvg |
Definition at line 490 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), and Controller::writeFepEnergyData().
int SimParameters::alchEquilSteps |
Definition at line 492 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), and Controller::printTiMessage().
Bool SimParameters::alchFepOn |
Definition at line 472 of file SimParameters.h.
Referenced by CudaPmeOneDevice::CudaPmeOneDevice(), CudaPmeOneDevice::finishReduction(), Controller::outputFepEnergy(), Controller::printEnergies(), and Controller::printFepMessage().
Bool SimParameters::alchFepOnAtStartup |
Definition at line 469 of file SimParameters.h.
int SimParameters::alchIDWSFreq |
Definition at line 481 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), and Controller::writeFepEnergyData().
BigReal SimParameters::alchLambda |
Definition at line 478 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), Controller::printTiMessage(), colvarproxy_namd::send_alch_lambda(), and Controller::writeFepEnergyData().
BigReal SimParameters::alchLambda2 |
Definition at line 479 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), and Controller::printFepMessage().
int SimParameters::alchLambdaFreq |
Definition at line 482 of file SimParameters.h.
Referenced by Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), Controller::printTiMessage(), colvarproxy_namd::send_alch_lambda(), and Controller::writeTiEnergyData().
BigReal SimParameters::alchLambdaIDWS |
Definition at line 480 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), Controller::printFepMessage(), and Controller::writeFepEnergyData().
int SimParameters::alchMethod |
Definition at line 477 of file SimParameters.h.
Bool SimParameters::alchOn |
Definition at line 471 of file SimParameters.h.
Referenced by CudaPmeOneDevice::compute(), WorkDistrib::createAtomLists(), CudaPmeOneDevice::CudaPmeOneDevice(), CudaPmeOneDevice::finishReduction(), Sequencer::integrate(), Sequencer::integrate_SOA(), NamdState::loadStructure(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printFepMessage(), Controller::printTiMessage(), and colvarproxy_namd::request_alch_energy_freq().
Bool SimParameters::alchOnAtStartup |
Definition at line 468 of file SimParameters.h.
char SimParameters::alchOutFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 491 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), and Controller::outputTiEnergy().
int SimParameters::alchOutFreq |
Definition at line 489 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::integrate_SOA(), Controller::outputFepEnergy(), and Controller::outputTiEnergy().
BigReal SimParameters::alchRepLambdaEnd |
Definition at line 506 of file SimParameters.h.
BigReal SimParameters::alchTemp |
Definition at line 488 of file SimParameters.h.
Referenced by Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printFepMessage(), and Controller::writeFepEnergyData().
Bool SimParameters::alchThermIntOn |
Definition at line 475 of file SimParameters.h.
Referenced by CudaPmeOneDevice::CudaPmeOneDevice(), CudaPmeOneDevice::finishReduction(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printTiMessage(), and colvarproxy_namd::request_alch_energy_freq().
Bool SimParameters::alchThermIntOnAtStartup |
Definition at line 470 of file SimParameters.h.
BigReal SimParameters::alchVdwLambdaEnd |
Definition at line 501 of file SimParameters.h.
BigReal SimParameters::alchVdwShiftCoeff |
Definition at line 493 of file SimParameters.h.
Bool SimParameters::alchWCAOn |
Definition at line 476 of file SimParameters.h.
BigReal SimParameters::alpha_cutoff |
Definition at line 615 of file SimParameters.h.
BigReal SimParameters::alpha_max |
Definition at line 616 of file SimParameters.h.
Bool SimParameters::amberOn |
Definition at line 1126 of file SimParameters.h.
Referenced by buildExclusions(), and NamdState::loadStructure().
char SimParameters::auxFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 284 of file SimParameters.h.
Referenced by CollectionMaster::receiveDataStream().
int SimParameters::benchmarkTime |
Definition at line 1020 of file SimParameters.h.
Referenced by Controller::printTiming().
Bool SimParameters::benchTimestep |
Definition at line 233 of file SimParameters.h.
BigReal SimParameters::berendsenPressureCompressibility |
Definition at line 780 of file SimParameters.h.
Referenced by Controller::berendsenPressure().
int SimParameters::berendsenPressureFreq |
Definition at line 782 of file SimParameters.h.
Referenced by Controller::berendsenPressure(), Sequencer::berendsenPressure(), and Sequencer::berendsenPressure_SOA().
Bool SimParameters::berendsenPressureOn |
Definition at line 778 of file SimParameters.h.
Referenced by Controller::berendsenPressure(), Sequencer::berendsenPressure(), and Sequencer::integrate_SOA().
BigReal SimParameters::berendsenPressureRelaxationTime |
Definition at line 781 of file SimParameters.h.
Referenced by Controller::berendsenPressure().
BigReal SimParameters::berendsenPressureTarget |
Definition at line 779 of file SimParameters.h.
Referenced by Controller::berendsenPressure().
Bool SimParameters::binaryOutput |
Definition at line 304 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists().
Bool SimParameters::binaryRestart |
Definition at line 302 of file SimParameters.h.
char* SimParameters::binAtomFile |
Definition at line 1165 of file SimParameters.h.
char* SimParameters::binCoorFile |
Definition at line 1166 of file SimParameters.h.
char* SimParameters::binRefFile |
Definition at line 1168 of file SimParameters.h.
char* SimParameters::binVelFile |
Definition at line 1167 of file SimParameters.h.
uint32 SimParameters::bondedCUDA |
Definition at line 919 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
uint32 SimParameters::bondedGPU |
replacement keyword for bondedCUDA
Definition at line 920 of file SimParameters.h.
zVector SimParameters::cellBasisVector1 |
Definition at line 191 of file SimParameters.h.
zVector SimParameters::cellBasisVector2 |
Definition at line 192 of file SimParameters.h.
zVector SimParameters::cellBasisVector3 |
Definition at line 193 of file SimParameters.h.
zVector SimParameters::cellOrigin |
Definition at line 194 of file SimParameters.h.
Bool SimParameters::COLDOn |
Definition at line 680 of file SimParameters.h.
BigReal SimParameters::COLDRate |
Definition at line 682 of file SimParameters.h.
BigReal SimParameters::COLDTemp |
Definition at line 683 of file SimParameters.h.
Bool SimParameters::colvarsOn |
Definition at line 653 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), Sequencer::integrate(), Sequencer::integrate_SOA(), and Sequencer::minimize().
Bool SimParameters::commOnly |
Definition at line 1060 of file SimParameters.h.
Referenced by Sequencer::integrate().
Bool SimParameters::comMove |
Definition at line 255 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists(), NamdState::loadStructure(), and Controller::receivePressure().
int SimParameters::computeEnergies |
Definition at line 1004 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::integrate_SOA(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printTiming(), and colvarproxy_namd::request_alch_energy_freq().
char SimParameters::computeMapFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 1174 of file SimParameters.h.
char SimParameters::consForceFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 1001 of file SimParameters.h.
Bool SimParameters::consForceOn |
Definition at line 1000 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and WorkDistrib::mapComputes().
BigReal SimParameters::consForceScaling |
Definition at line 1002 of file SimParameters.h.
Referenced by ComputeConsForce::doForce().
char SimParameters::consTorqueAxisFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 424 of file SimParameters.h.
char SimParameters::consTorqueFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 422 of file SimParameters.h.
BigReal SimParameters::consTorqueGlobVal |
Definition at line 426 of file SimParameters.h.
Bool SimParameters::consTorqueOn |
Definition at line 421 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and WorkDistrib::mapComputes().
char SimParameters::consTorquePivotFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 425 of file SimParameters.h.
char SimParameters::consTorqueValFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 427 of file SimParameters.h.
int SimParameters::constraintExp |
Definition at line 339 of file SimParameters.h.
BigReal SimParameters::constraintScaling |
Definition at line 373 of file SimParameters.h.
Bool SimParameters::constraintsOn |
Definition at line 337 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and WorkDistrib::mapComputes().
Bool SimParameters::constrXOn |
Definition at line 364 of file SimParameters.h.
Bool SimParameters::constrYOn |
Definition at line 364 of file SimParameters.h.
Bool SimParameters::constrZOn |
Definition at line 364 of file SimParameters.h.
Bool SimParameters::cosAngles |
Definition at line 635 of file SimParameters.h.
BigReal SimParameters::coulomb_radius_offset |
Definition at line 609 of file SimParameters.h.
char SimParameters::crashFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 295 of file SimParameters.h.
int SimParameters::crashOutputFlag |
Definition at line 296 of file SimParameters.h.
int SimParameters::cudaGlobalProfilingFreq |
Definition at line 1191 of file SimParameters.h.
Bool SimParameters::CUDASOAintegrate |
Definition at line 173 of file SimParameters.h.
Referenced by colvarproxy_namd::add_energy(), Sequencer::algorithm(), Controller::calcPressure(), colvarproxy_namd::calculate(), Controller::compareChecksums(), ComputeCUDAMgr::createCudaComputeNonbonded(), ComputeGlobal::doWork(), CudaComputeNonbonded::doWork(), CudaComputeNonbonded::finishPatches(), GlobalMaster::getCurrentReduction(), Controller::getTotalPotentialEnergy(), Controller::integrate(), CudaComputeNonbonded::openBoxesOnPe(), CudaComputeNonbonded::patchReady(), Controller::printEnergies(), Controller::receivePressure(), ComputeGlobal::recvResults(), Sequencer::runComputeObjects_SOA(), ComputeGlobal::saveTotalForces(), ComputeMgr::sendComputeGlobalData(), ComputeMgr::sendComputeGlobalResults(), and Node::startup().
Bool SimParameters::CUDASOAintegrateMode |
mode flag set by "CUDASOAintegrate on" in config file this remains set the same, no matter whether our activity is dynamics or minimization
Definition at line 163 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), Controller::Controller(), CudaPmeOneDevice::CudaPmeOneDevice(), GlobalMaster::GlobalMaster(), CudaComputeNonbonded::initialize(), Sequencer::minimize(), WorkDistrib::patchMapInit(), Sequencer::Sequencer(), and Sequencer::~Sequencer().
BigReal SimParameters::cutoff |
Definition at line 306 of file SimParameters.h.
Referenced by ComputeQM::initialize(), Sequencer::integrate_SOA(), Sequencer::maximumMove(), and ComputeQMMgr::recvPntChrg().
char SimParameters::cylindricalBCAxis |
Definition at line 971 of file SimParameters.h.
int SimParameters::cylindricalBCexp1 |
Definition at line 976 of file SimParameters.h.
int SimParameters::cylindricalBCexp2 |
Definition at line 977 of file SimParameters.h.
BigReal SimParameters::cylindricalBCk1 |
Definition at line 978 of file SimParameters.h.
BigReal SimParameters::cylindricalBCk2 |
Definition at line 979 of file SimParameters.h.
BigReal SimParameters::cylindricalBCl1 |
Definition at line 974 of file SimParameters.h.
BigReal SimParameters::cylindricalBCl2 |
Definition at line 975 of file SimParameters.h.
Bool SimParameters::cylindricalBCOn |
Definition at line 968 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
BigReal SimParameters::cylindricalBCr1 |
Definition at line 972 of file SimParameters.h.
BigReal SimParameters::cylindricalBCr2 |
Definition at line 973 of file SimParameters.h.
zVector SimParameters::cylindricalCenter |
Definition at line 970 of file SimParameters.h.
BigReal SimParameters::daCutoffDist |
Definition at line 1109 of file SimParameters.h.
BigReal SimParameters::daOffDist |
Definition at line 1109 of file SimParameters.h.
BigReal SimParameters::daOnDist |
Definition at line 1109 of file SimParameters.h.
char SimParameters::dcdFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 285 of file SimParameters.h.
int SimParameters::dcdFrequency |
Definition at line 274 of file SimParameters.h.
Referenced by Sequencer::integrate_SOA().
int SimParameters::dcdSelectionOn |
Definition at line 283 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and Node::startup().
int SimParameters::dcdUnitCell |
Definition at line 276 of file SimParameters.h.
BigReal SimParameters::dhaCutoffAngle |
Definition at line 1105 of file SimParameters.h.
BigReal SimParameters::dhaOffAngle |
Definition at line 1105 of file SimParameters.h.
BigReal SimParameters::dhaOnAngle |
Definition at line 1105 of file SimParameters.h.
BigReal SimParameters::dielectric |
Definition at line 262 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Bool SimParameters::dihedralOn |
Definition at line 679 of file SimParameters.h.
Bool SimParameters::disableTopology |
Definition at line 230 of file SimParameters.h.
int SimParameters::distAttExp |
Definition at line 1102 of file SimParameters.h.
int SimParameters::distRepExp |
Definition at line 1102 of file SimParameters.h.
BigReal SimParameters::drudeBondConst |
Definition at line 627 of file SimParameters.h.
BigReal SimParameters::drudeBondLen |
Definition at line 625 of file SimParameters.h.
Referenced by Sequencer::submitMinimizeReductions().
BigReal SimParameters::drudeDamping |
Definition at line 623 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Bool SimParameters::drudeHardWallOn |
Definition at line 621 of file SimParameters.h.
Referenced by Sequencer::hardWallDrude(), Sequencer::newMinimizeDirection(), Sequencer::newMinimizePosition(), and Sequencer::submitMinimizeReductions().
BigReal SimParameters::drudeNbtholeCut |
Definition at line 628 of file SimParameters.h.
Referenced by CudaComputeNonbonded::initialize().
Bool SimParameters::drudeOn |
Definition at line 620 of file SimParameters.h.
Referenced by CudaComputeNonbonded::initialize(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Controller::printEnergies(), Controller::receivePressure(), Sequencer::reinitVelocities(), and Sequencer::submitReductions().
BigReal SimParameters::drudeTemp |
Definition at line 622 of file SimParameters.h.
Referenced by Sequencer::langevinVelocitiesBBK2().
BigReal SimParameters::dt |
Definition at line 187 of file SimParameters.h.
Referenced by Controller::berendsenPressure(), colvarproxy_namd::colvarproxy_namd(), Controller::Controller(), Sequencer::integrate(), Sequencer::integrate_SOA(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::multigratorPressure(), Controller::multigratorTemperature(), Controller::printEnergies(), Controller::printTiming(), ComputeQMMgr::recvPartQM(), and colvarproxy_namd::setup().
zVector SimParameters::eField |
Definition at line 983 of file SimParameters.h.
BigReal SimParameters::eFieldFreq |
Definition at line 984 of file SimParameters.h.
Bool SimParameters::eFieldNormalized |
Definition at line 982 of file SimParameters.h.
Bool SimParameters::eFieldOn |
Definition at line 981 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
BigReal SimParameters::eFieldPhase |
Definition at line 985 of file SimParameters.h.
int SimParameters::emptyPatchLoad |
Definition at line 1078 of file SimParameters.h.
ExclusionSettings SimParameters::exclude |
Definition at line 263 of file SimParameters.h.
Referenced by buildExclusions().
Bool SimParameters::excludeFromPressure |
Definition at line 767 of file SimParameters.h.
Referenced by NamdState::loadStructure().
char SimParameters::extCoordFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 544 of file SimParameters.h.
char SimParameters::extForceFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 545 of file SimParameters.h.
char SimParameters::extForcesCommand[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 543 of file SimParameters.h.
Bool SimParameters::extForcesOn |
Definition at line 542 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Bool SimParameters::extraBondsCosAngles |
Definition at line 997 of file SimParameters.h.
Bool SimParameters::extraBondsCosAnglesSetByUser |
Definition at line 998 of file SimParameters.h.
Bool SimParameters::extraBondsOn |
Definition at line 996 of file SimParameters.h.
Referenced by Molecule::delete_qm_bonded(), NamdState::loadStructure(), and Molecule::prepare_qm().
Bool SimParameters::FFTWEstimate |
Definition at line 937 of file SimParameters.h.
Bool SimParameters::FFTWPatient |
Definition at line 938 of file SimParameters.h.
Bool SimParameters::FFTWUseWisdom |
Definition at line 939 of file SimParameters.h.
char SimParameters::FFTWWisdomFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 940 of file SimParameters.h.
char* SimParameters::FFTWWisdomString |
Definition at line 941 of file SimParameters.h.
int SimParameters::firstLdbStep |
Definition at line 207 of file SimParameters.h.
Referenced by Controller::printEnergies().
int SimParameters::firstTimestep |
Definition at line 1032 of file SimParameters.h.
Referenced by Sequencer::adaptTempUpdate(), Controller::adaptTempUpdate(), Controller::algorithm(), colvarproxy_namd::colvarproxy_namd(), CudaPmeOneDevice::compute(), GlobalMasterSymmetry::GlobalMasterSymmetry(), GlobalMasterTMD::GlobalMasterTMD(), Controller::integrate(), Sequencer::integrate(), Sequencer::integrate_SOA(), Controller::minimize(), Sequencer::minimize(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::outputTiEnergy(), Controller::printEnergies(), Controller::printTiming(), ComputeQMMgr::recvPartQM(), ComputeQMMgr::recvPntChrg(), Controller::rescaleaccelMD(), Sequencer::submitCollections(), and Controller::writeFepEnergyData().
Bool SimParameters::fixCellDims |
Definition at line 773 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::monteCarloPressure_prepare(), and Controller::receivePressure().
Bool SimParameters::fixCellDimX |
Definition at line 774 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::monteCarloPressure_prepare(), and Controller::receivePressure().
Bool SimParameters::fixCellDimY |
Definition at line 775 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::monteCarloPressure_prepare(), and Controller::receivePressure().
Bool SimParameters::fixCellDimZ |
Definition at line 776 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::monteCarloPressure_prepare(), and Controller::receivePressure().
Bool SimParameters::fixedAtomsForceOutput |
Definition at line 657 of file SimParameters.h.
Referenced by CollectionMgr::submitForces().
Bool SimParameters::fixedAtomsForces |
Definition at line 656 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
Bool SimParameters::fixedAtomsOn |
Definition at line 655 of file SimParameters.h.
Referenced by Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), Sequencer::berendsenPressure(), Sequencer::calcFixVirial(), Sequencer::correctMomentum(), WorkDistrib::createAtomLists(), Sequencer::langevinPiston(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::minimizeMoveDownhill(), Sequencer::multigratorPressure(), Sequencer::newMinimizeDirection(), Molecule::prepare_qm(), Sequencer::reassignVelocities(), Controller::receivePressure(), Sequencer::reinitVelocities(), ComputeGlobal::saveTotalForces(), Sequencer::scalePositionsVelocities(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().
int SimParameters::FMAFFTBlock |
Definition at line 829 of file SimParameters.h.
Bool SimParameters::FMAFFTOn |
Definition at line 828 of file SimParameters.h.
int SimParameters::FMALevels |
Definition at line 826 of file SimParameters.h.
int SimParameters::FMAMp |
Definition at line 827 of file SimParameters.h.
Bool SimParameters::FMAOn |
Definition at line 825 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), and WorkDistrib::patchMapInit().
BigReal SimParameters::fmaTheta |
Definition at line 203 of file SimParameters.h.
int SimParameters::FMMLevels |
Definition at line 873 of file SimParameters.h.
Bool SimParameters::FMMOn |
Definition at line 872 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), and WorkDistrib::patchMapInit().
BigReal SimParameters::FMMPadding |
Definition at line 874 of file SimParameters.h.
char SimParameters::forceDcdFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 287 of file SimParameters.h.
int SimParameters::forceDcdFrequency |
Definition at line 279 of file SimParameters.h.
Referenced by Sequencer::integrate_SOA().
Bool SimParameters::freeEnergyOn |
Definition at line 651 of file SimParameters.h.
BigReal SimParameters::fsMax |
Definition at line 606 of file SimParameters.h.
Bool SimParameters::fullDirectOn |
Definition at line 831 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), and WorkDistrib::mapComputes().
int SimParameters::fullDispersionFrequency |
Definition at line 201 of file SimParameters.h.
int SimParameters::fullElectFrequency |
Definition at line 199 of file SimParameters.h.
Referenced by Controller::compareChecksums(), Controller::integrate(), Sequencer::integrate(), Sequencer::integrate_SOA(), isMultiTimeStepping(), Sequencer::minimize(), Sequencer::runComputeObjects(), and Sequencer::runComputeObjects_SOA().
BigReal SimParameters::gbis_beta |
Definition at line 613 of file SimParameters.h.
BigReal SimParameters::gbis_delta |
Definition at line 612 of file SimParameters.h.
BigReal SimParameters::gbis_gamma |
Definition at line 614 of file SimParameters.h.
Bool SimParameters::GBISOn |
Definition at line 605 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), ComputeCUDAMgr::createCudaComputeNonbonded(), CudaComputeNonbonded::finishReductions(), Sequencer::integrate(), and Sequencer::minimize().
Bool SimParameters::GBISserOn |
Definition at line 607 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), and WorkDistrib::mapComputes().
Bool SimParameters::genCompressedPsf |
Definition at line 1149 of file SimParameters.h.
Referenced by NamdState::configListInit(), and NamdState::loadStructure().
Bool SimParameters::globalForcesOn |
Definition at line 636 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
int SimParameters::globalMasterFrequency |
How frequently (time steps) global master (i.e., colvars, tclForces, etc. is called. Default value 1.
Definition at line 638 of file SimParameters.h.
Referenced by ComputeGlobal::doWork(), GlobalMasterServer::GlobalMasterServer(), and ComputeGlobal::recvResults().
Bool SimParameters::globalMasterScaleByFrequency |
Scale globalMaster forces by a factor of frequency? Default value off.
Definition at line 640 of file SimParameters.h.
Referenced by ComputeGlobal::recvResults().
Bool SimParameters::globalMasterStaleForces |
Do MTS by the stale forces method instead of scaling by frequency. Default off.
Definition at line 642 of file SimParameters.h.
Bool SimParameters::globalOn |
Definition at line 678 of file SimParameters.h.
char SimParameters::goCoordinates[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 384 of file SimParameters.h.
Bool SimParameters::goForcesOn |
Definition at line 382 of file SimParameters.h.
Referenced by NamdState::loadStructure(), Controller::printEnergies(), Molecule::receive_GoMolecule(), and Molecule::send_GoMolecule().
Bool SimParameters::goGroPair |
Definition at line 381 of file SimParameters.h.
Referenced by Controller::compareChecksums(), WorkDistrib::mapComputes(), and Controller::printEnergies().
GoChoices SimParameters::goMethod |
Definition at line 386 of file SimParameters.h.
Referenced by NamdState::loadStructure(), Molecule::receive_GoMolecule(), and Molecule::send_GoMolecule().
char SimParameters::goParameters[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 383 of file SimParameters.h.
Bool SimParameters::GPUresidentMode |
"GPUresident on" will be replacing "CUDASOAintegrate on"
Definition at line 167 of file SimParameters.h.
Bool SimParameters::GPUresidentSingleProcessMode |
Use shared memory communication instead of Charm++ when possible
Definition at line 170 of file SimParameters.h.
Referenced by Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), and SimpleBroadcastObject< Tensor >::SimpleBroadcastObject().
Bool SimParameters::gridforcechecksize |
Definition at line 350 of file SimParameters.h.
Bool SimParameters::gridforceContA1 |
Definition at line 345 of file SimParameters.h.
Bool SimParameters::gridforceContA2 |
Definition at line 346 of file SimParameters.h.
Bool SimParameters::gridforceContA3 |
Definition at line 347 of file SimParameters.h.
Bool SimParameters::gridforceLite |
Definition at line 349 of file SimParameters.h.
Bool SimParameters::gridforceOn |
Definition at line 342 of file SimParameters.h.
zVector SimParameters::gridforceScale |
Definition at line 344 of file SimParameters.h.
zVector SimParameters::gridforceVOffset |
Definition at line 348 of file SimParameters.h.
Bool SimParameters::gridforceVolts |
Definition at line 343 of file SimParameters.h.
Bool SimParameters::gromacsOn |
Definition at line 1132 of file SimParameters.h.
Referenced by NamdState::loadStructure().
GroupRestraintList SimParameters::groupRestraints |
Definition at line 357 of file SimParameters.h.
int SimParameters::groupRestraintsCount |
Definition at line 358 of file SimParameters.h.
Bool SimParameters::groupRestraintsOn |
Definition at line 356 of file SimParameters.h.
int SimParameters::haAngleExp |
Definition at line 1102 of file SimParameters.h.
BigReal SimParameters::hgroupCutoff |
Definition at line 1044 of file SimParameters.h.
int SimParameters::hybridGroupSize |
Definition at line 211 of file SimParameters.h.
Bool SimParameters::HydrogenBonds |
Definition at line 1092 of file SimParameters.h.
Bool SimParameters::ignoreMass |
Definition at line 1041 of file SimParameters.h.
int SimParameters::IMDfreq |
Definition at line 1115 of file SimParameters.h.
Referenced by Sequencer::integrate_SOA(), Controller::printEnergies(), and Sequencer::submitCollections().
int SimParameters::IMDignore |
Definition at line 1118 of file SimParameters.h.
Referenced by GlobalMasterIMD::GlobalMasterIMD().
int SimParameters::IMDignoreForces |
Definition at line 1120 of file SimParameters.h.
Referenced by GlobalMasterIMD::GlobalMasterIMD().
int SimParameters::IMDon |
Definition at line 1112 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), Controller::printEnergies(), and Sequencer::submitCollections().
int SimParameters::IMDport |
Definition at line 1114 of file SimParameters.h.
Referenced by GlobalMasterIMD::GlobalMasterIMD().
IMDSessionInfo SimParameters::IMDsendsettings = {0,0,1,1,0,0,1} |
Definition at line 1121 of file SimParameters.h.
Referenced by GlobalMasterIMD::GlobalMasterIMD(), Controller::printEnergies(), and Sequencer::submitCollections().
int SimParameters::IMDversion |
Definition at line 1113 of file SimParameters.h.
Referenced by GlobalMasterIMD::GlobalMasterIMD(), Controller::printEnergies(), GlobalMasterIMD::send_energies(), GlobalMasterIMD::send_fcoords(), and Sequencer::submitCollections().
int SimParameters::IMDwait |
Definition at line 1116 of file SimParameters.h.
Referenced by GlobalMasterIMD::get_vmd_forces(), and GlobalMasterIMD::GlobalMasterIMD().
BigReal SimParameters::initialTemp |
Definition at line 253 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), Controller::algorithm(), WorkDistrib::createAtomLists(), Sequencer::integrate(), and Sequencer::reinitVelocities().
BigReal SimParameters::ion_concentration |
Definition at line 611 of file SimParameters.h.
BigReal SimParameters::kappa |
Definition at line 610 of file SimParameters.h.
Bool SimParameters::langevin_useBAOAB |
Definition at line 668 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), and Sequencer::langevinVelocitiesBBK2().
BigReal SimParameters::langevinDamping |
Definition at line 662 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Bool SimParameters::langevinGammasDiffer |
Flag set internally - when all gammas are identical we can avoid extra call to satisfy rigid bond constraints.
Definition at line 664 of file SimParameters.h.
Referenced by Sequencer::langevinVelocitiesBBK2_SOA().
Bool SimParameters::langevinHydrogen |
Definition at line 663 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Bool SimParameters::langevinOn |
Definition at line 660 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK1_SOA(), Sequencer::langevinVelocitiesBBK2(), Sequencer::langevinVelocitiesBBK2_SOA(), NamdState::loadStructure(), Controller::receivePressure(), and colvarproxy_namd::update_target_temperature().
Bool SimParameters::langevinOnAtStartup |
Definition at line 659 of file SimParameters.h.
Bool SimParameters::langevinPistonBarrier |
Definition at line 785 of file SimParameters.h.
Referenced by Controller::langevinPiston1().
BigReal SimParameters::langevinPistonDecay |
Definition at line 788 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), and Controller::langevinPiston2().
Bool SimParameters::langevinPistonOn |
Definition at line 784 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::integrate_SOA(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::writeExtendedSystemData(), and Controller::writeExtendedSystemLabels().
BigReal SimParameters::langevinPistonPeriod |
Definition at line 787 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), and Controller::langevinPiston2().
BigReal SimParameters::langevinPistonTarget |
Definition at line 786 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), and Controller::langevinPiston2().
BigReal SimParameters::langevinPistonTemp |
Definition at line 789 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), and Controller::langevinPiston2().
BigReal SimParameters::langevinTemp |
Definition at line 661 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), Sequencer::adaptTempUpdate(), Sequencer::integrate(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), and colvarproxy_namd::update_target_temperature().
int SimParameters::lastLdbStep |
Definition at line 209 of file SimParameters.h.
Lattice SimParameters::lattice |
Definition at line 195 of file SimParameters.h.
Referenced by NamdState::configListInit(), WorkDistrib::createAtomLists(), GlobalMasterServer::GlobalMasterServer(), Patch::Patch(), WorkDistrib::patchMapInit(), PatchMgr::setLattice(), and Node::startup().
Bool SimParameters::LCPOOn |
Definition at line 617 of file SimParameters.h.
Referenced by Sequencer::integrate(), WorkDistrib::mapComputes(), Sequencer::minimize(), and WorkDistrib::patchMapInit().
int SimParameters::ldBalancer |
Definition at line 204 of file SimParameters.h.
BigReal SimParameters::ldbBackgroundScaling |
Definition at line 212 of file SimParameters.h.
BigReal SimParameters::ldbHomeBackgroundScaling |
Definition at line 214 of file SimParameters.h.
int SimParameters::ldbPeriod |
Definition at line 206 of file SimParameters.h.
BigReal SimParameters::ldbPMEBackgroundScaling |
Definition at line 213 of file SimParameters.h.
BigReal SimParameters::ldbRelativeGrainsize |
Definition at line 215 of file SimParameters.h.
int SimParameters::ldbStrategy |
Definition at line 205 of file SimParameters.h.
Bool SimParameters::ldbUnloadOne |
Definition at line 247 of file SimParameters.h.
Bool SimParameters::ldbUnloadOutputPEs |
Definition at line 248 of file SimParameters.h.
Bool SimParameters::ldbUnloadPME |
Definition at line 245 of file SimParameters.h.
Bool SimParameters::ldbUnloadZero |
Definition at line 246 of file SimParameters.h.
int SimParameters::lesFactor |
Definition at line 524 of file SimParameters.h.
Referenced by Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::reassignVelocities(), and Sequencer::reinitVelocities().
Bool SimParameters::lesOn |
Definition at line 523 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::reassignVelocities(), and Sequencer::reinitVelocities().
Bool SimParameters::lesReduceMass |
Definition at line 526 of file SimParameters.h.
Bool SimParameters::lesReduceTemp |
Definition at line 525 of file SimParameters.h.
Referenced by Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK2(), Sequencer::reassignVelocities(), and Sequencer::reinitVelocities().
BigReal SimParameters::limitDist |
Definition at line 313 of file SimParameters.h.
int SimParameters::lincsOn |
Definition at line 148 of file SimParameters.h.
Bool SimParameters::LJcorrection |
Definition at line 185 of file SimParameters.h.
Referenced by Controller::calcPressure(), Controller::getTotalPotentialEnergy(), NamdState::loadStructure(), Controller::printEnergies(), and Controller::rescaleaccelMD().
Bool SimParameters::LJcorrectionAlt |
Definition at line 186 of file SimParameters.h.
Referenced by Controller::calcPressure(), NamdState::loadStructure(), Controller::printEnergies(), and Controller::rescaleaccelMD().
BigReal SimParameters::LJPMEEwaldCoefficient |
Definition at line 879 of file SimParameters.h.
int SimParameters::LJPMEGridSizeX |
Definition at line 881 of file SimParameters.h.
int SimParameters::LJPMEGridSizeY |
Definition at line 882 of file SimParameters.h.
int SimParameters::LJPMEGridSizeZ |
Definition at line 883 of file SimParameters.h.
BigReal SimParameters::LJPMEGridSpacing |
Definition at line 884 of file SimParameters.h.
int SimParameters::LJPMEInterpOrder |
Definition at line 880 of file SimParameters.h.
Bool SimParameters::LJPMEOn |
Definition at line 877 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists(), Sequencer::integrate(), and WorkDistrib::mapComputes().
Bool SimParameters::LJPMESerial |
Definition at line 888 of file SimParameters.h.
Referenced by LjPmeCompute::computeLJpotential(), Sequencer::integrate(), and LJTable::LJTable().
BigReal SimParameters::LJPMETolerance |
Definition at line 878 of file SimParameters.h.
Bool SimParameters::loadComputeMap |
Definition at line 1176 of file SimParameters.h.
Bool SimParameters::lonepairs |
Definition at line 182 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::minimize(), and Sequencer::runComputeObjects().
int SimParameters::longSplitting |
Definition at line 1038 of file SimParameters.h.
BigReal SimParameters::loweAndersenCutoff |
Definition at line 675 of file SimParameters.h.
Bool SimParameters::loweAndersenOn |
Definition at line 672 of file SimParameters.h.
Referenced by Sequencer::integrate(), and colvarproxy_namd::update_target_temperature().
BigReal SimParameters::loweAndersenRate |
Definition at line 674 of file SimParameters.h.
BigReal SimParameters::loweAndersenTemp |
Definition at line 673 of file SimParameters.h.
Referenced by colvarproxy_namd::update_target_temperature().
Bool SimParameters::mallocTest |
Definition at line 1153 of file SimParameters.h.
Referenced by Node::startup().
BigReal SimParameters::margin |
Definition at line 307 of file SimParameters.h.
Bool SimParameters::martiniDielAllow |
Definition at line 323 of file SimParameters.h.
Bool SimParameters::martiniSwitching |
Definition at line 321 of file SimParameters.h.
int SimParameters::maxExclusionFlags |
Definition at line 1080 of file SimParameters.h.
BigReal SimParameters::maximumMove |
Definition at line 953 of file SimParameters.h.
Referenced by Sequencer::maximumMove().
int SimParameters::maxPairPart |
Definition at line 1066 of file SimParameters.h.
int SimParameters::maxPatches |
Definition at line 244 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
int SimParameters::maxSelfPart |
Definition at line 1064 of file SimParameters.h.
Bool SimParameters::mergeCrossterms |
Definition at line 1030 of file SimParameters.h.
Referenced by Controller::printEnergies().
MGridforceParamsList SimParameters::mgridforcelist |
Definition at line 353 of file SimParameters.h.
Referenced by colvarproxy_namd::check_volmap_by_name(), colvarproxy_namd::get_volmap_id_from_name(), colvarproxy_namd::init_volmap_by_name(), Node::reloadGridforceGrid(), and Node::updateGridScale().
Bool SimParameters::mgridforceOn |
Definition at line 352 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and WorkDistrib::mapComputes().
int SimParameters::mic_deviceThreshold |
Definition at line 1184 of file SimParameters.h.
int SimParameters::mic_hostSplit |
Definition at line 1179 of file SimParameters.h.
int SimParameters::mic_numParts_pair_p1 |
Definition at line 1181 of file SimParameters.h.
int SimParameters::mic_numParts_pair_p2 |
Definition at line 1182 of file SimParameters.h.
int SimParameters::mic_numParts_self_p1 |
Definition at line 1180 of file SimParameters.h.
int SimParameters::mic_singleKernel |
Definition at line 1185 of file SimParameters.h.
int SimParameters::mic_unloadMICPEs |
Definition at line 1183 of file SimParameters.h.
int SimParameters::minAtomsPerPatch |
Definition at line 1076 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
BigReal SimParameters::minBabyStep |
Definition at line 950 of file SimParameters.h.
Bool SimParameters::minimizeCGOn |
Definition at line 947 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Bool SimParameters::minimizeOn |
Definition at line 952 of file SimParameters.h.
Referenced by Sequencer::minimizationQuenchVelocity().
BigReal SimParameters::minLineGoal |
Definition at line 951 of file SimParameters.h.
Referenced by Controller::minimize().
BigReal SimParameters::minTinyStep |
Definition at line 949 of file SimParameters.h.
Bool SimParameters::minVerbose |
Definition at line 948 of file SimParameters.h.
Referenced by Controller::minimize().
Bool SimParameters::miscForcesOn |
Definition at line 652 of file SimParameters.h.
int SimParameters::mollyIter |
Definition at line 1048 of file SimParameters.h.
int SimParameters::mollyOn |
Definition at line 1046 of file SimParameters.h.
Referenced by Controller::compareChecksums(), Sequencer::integrate(), and Sequencer::minimize().
BigReal SimParameters::mollyTol |
Definition at line 1047 of file SimParameters.h.
BigReal SimParameters::monteCarloAcceptanceRate |
Definition at line 795 of file SimParameters.h.
Referenced by Controller::monteCarloPressure_accept().
int SimParameters::monteCarloAdjustmentFreq |
Definition at line 797 of file SimParameters.h.
Referenced by Controller::monteCarloPressure_accept().
zVector SimParameters::monteCarloMaxVolume |
Definition at line 796 of file SimParameters.h.
Referenced by Controller::Controller().
int SimParameters::monteCarloPressureFreq |
Definition at line 798 of file SimParameters.h.
Referenced by Controller::monteCarloPressure_accept(), and Controller::monteCarloPressure_prepare().
Bool SimParameters::monteCarloPressureOn |
Definition at line 792 of file SimParameters.h.
Referenced by Controller::Controller(), NamdState::loadStructure(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), Controller::writeExtendedSystemData(), and Controller::writeExtendedSystemLabels().
Bool SimParameters::monteCarloPressureOnAtStartup |
Definition at line 791 of file SimParameters.h.
BigReal SimParameters::monteCarloPressureTarget |
Definition at line 793 of file SimParameters.h.
Referenced by Controller::monteCarloPressure_accept().
BigReal SimParameters::monteCarloTemp |
Definition at line 794 of file SimParameters.h.
Referenced by Controller::monteCarloPressure_accept().
char SimParameters::movDragFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 404 of file SimParameters.h.
BigReal SimParameters::movDragGlobVel |
Definition at line 406 of file SimParameters.h.
Referenced by Sequencer::addMovDragToPosition().
Bool SimParameters::movDragOn |
Definition at line 403 of file SimParameters.h.
Referenced by Sequencer::integrate(), and NamdState::loadStructure().
char SimParameters::movDragVelFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 407 of file SimParameters.h.
int SimParameters::movingAverageWindowSize |
Definition at line 176 of file SimParameters.h.
Referenced by Controller::resetMovingAverage().
Bool SimParameters::movingConstraintsOn |
Definition at line 390 of file SimParameters.h.
zVector SimParameters::movingConsVel |
Definition at line 392 of file SimParameters.h.
int SimParameters::mshakeOn |
Definition at line 147 of file SimParameters.h.
int SimParameters::MSMApprox |
Definition at line 841 of file SimParameters.h.
int SimParameters::MSMBlockSizeX |
Definition at line 851 of file SimParameters.h.
int SimParameters::MSMBlockSizeY |
Definition at line 852 of file SimParameters.h.
int SimParameters::MSMBlockSizeZ |
Definition at line 853 of file SimParameters.h.
BigReal SimParameters::MSMGridSpacing |
Definition at line 855 of file SimParameters.h.
int SimParameters::MSMLevels |
Definition at line 847 of file SimParameters.h.
Bool SimParameters::MSMOn |
Definition at line 834 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), WorkDistrib::patchMapInit(), and Node::startup().
BigReal SimParameters::MSMPadding |
Definition at line 857 of file SimParameters.h.
int SimParameters::MSMQuality |
Definition at line 837 of file SimParameters.h.
Bool SimParameters::MsmSerialOn |
Definition at line 870 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), and Node::startup().
int SimParameters::MSMSplit |
Definition at line 844 of file SimParameters.h.
BigReal SimParameters::MSMxmax |
Definition at line 864 of file SimParameters.h.
BigReal SimParameters::MSMxmin |
Definition at line 863 of file SimParameters.h.
BigReal SimParameters::MSMymax |
Definition at line 866 of file SimParameters.h.
BigReal SimParameters::MSMymin |
Definition at line 865 of file SimParameters.h.
BigReal SimParameters::MSMzmax |
Definition at line 868 of file SimParameters.h.
BigReal SimParameters::MSMzmin |
Definition at line 867 of file SimParameters.h.
MTSChoices SimParameters::MTSAlgorithm |
Definition at line 1035 of file SimParameters.h.
Referenced by Sequencer::integrate().
int SimParameters::multigratorNoseHooverChainLength |
Definition at line 807 of file SimParameters.h.
Referenced by Controller::Controller(), Controller::multigatorCalcEnthalpy(), and Controller::multigratorTemperature().
Bool SimParameters::multigratorOn |
Definition at line 800 of file SimParameters.h.
Referenced by Controller::Controller(), Sequencer::integrate(), Sequencer::multigratorPressure(), Controller::multigratorPressure(), Sequencer::multigratorTemperature(), Controller::multigratorTemperature(), Controller::printEnergies(), Sequencer::Sequencer(), and Sequencer::submitHalfstep().
int SimParameters::multigratorPressureFreq |
Definition at line 803 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::multigratorPressure(), Controller::multigratorPressure(), Sequencer::multigratorTemperature(), and Controller::multigratorTemperature().
BigReal SimParameters::multigratorPressureRelaxationTime |
Definition at line 802 of file SimParameters.h.
Referenced by Controller::multigatorCalcEnthalpy(), and Controller::multigratorPressure().
BigReal SimParameters::multigratorPressureTarget |
Definition at line 801 of file SimParameters.h.
Referenced by Controller::multigatorCalcEnthalpy(), and Controller::multigratorPressure().
int SimParameters::multigratorTemperatureFreq |
Definition at line 806 of file SimParameters.h.
Referenced by Sequencer::integrate(), Sequencer::multigratorTemperature(), and Controller::multigratorTemperature().
BigReal SimParameters::multigratorTemperatureRelaxationTime |
Definition at line 805 of file SimParameters.h.
Referenced by Controller::Controller(), and Controller::multigratorTemperature().
BigReal SimParameters::multigratorTemperatureTarget |
Definition at line 804 of file SimParameters.h.
Referenced by Controller::Controller(), Controller::multigatorCalcEnthalpy(), Controller::multigratorPressure(), and Controller::multigratorTemperature().
int SimParameters::N |
Definition at line 188 of file SimParameters.h.
Referenced by colvarproxy_namd::calculate(), Controller::integrate(), Sequencer::integrate(), Sequencer::integrate_SOA(), Controller::minimize(), Sequencer::minimize(), Sequencer::multigratorPressure(), Controller::outputExtendedSystem(), Controller::outputFepEnergy(), Controller::printEnergies(), Controller::printTiming(), and Controller::rescaleaccelMD().
int SimParameters::nonbondedFrequency |
Definition at line 197 of file SimParameters.h.
Referenced by Controller::integrate(), Sequencer::integrate(), Sequencer::integrate_SOA(), and isMultiTimeStepping().
BigReal SimParameters::nonbondedScaling |
Definition at line 273 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists(), and ComputeQMMgr::recvPntChrg().
Bool SimParameters::noPatchesOnOne |
Definition at line 251 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Bool SimParameters::noPatchesOnOutputPEs |
Definition at line 250 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Bool SimParameters::noPatchesOnZero |
Definition at line 249 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Bool SimParameters::nsPerDayOn |
Definition at line 179 of file SimParameters.h.
Referenced by Controller::printEnergies(), and Controller::printTiming().
int SimParameters::numAtomsPair |
Definition at line 1072 of file SimParameters.h.
int SimParameters::numAtomsPair2 |
Definition at line 1074 of file SimParameters.h.
int SimParameters::numAtomsSelf |
Definition at line 1068 of file SimParameters.h.
int SimParameters::numAtomsSelf2 |
Definition at line 1070 of file SimParameters.h.
int SimParameters::numinputprocs |
Definition at line 1164 of file SimParameters.h.
Referenced by NamdState::loadStructure().
int SimParameters::numoutputprocs |
Definition at line 1171 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and WorkDistrib::patchMapInit().
int SimParameters::numoutputwrts |
Definition at line 1172 of file SimParameters.h.
Referenced by NamdState::loadStructure().
int SimParameters::numTraceSteps |
Definition at line 218 of file SimParameters.h.
Referenced by Controller::integrate(), and Sequencer::integrate().
Bool SimParameters::oldParmReader |
Definition at line 1127 of file SimParameters.h.
Referenced by NamdState::loadStructure().
int SimParameters::outputCudaTiming |
Definition at line 1024 of file SimParameters.h.
int SimParameters::outputEnergies |
Definition at line 1005 of file SimParameters.h.
Referenced by Controller::monteCarloPressure_accept(), and Controller::printEnergies().
int SimParameters::outputEnergiesPrecision |
Definition at line 1008 of file SimParameters.h.
Referenced by Controller::printEnergies().
char SimParameters::outputFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 289 of file SimParameters.h.
Referenced by colvarproxy_namd::calculate(), colvarproxy_namd::colvarproxy_namd(), Controller::outputExtendedSystem(), and ComputeQMMgr::recvPartQM().
Bool SimParameters::outputMaps |
Definition at line 226 of file SimParameters.h.
Referenced by Node::outputPatchComputeMaps().
int SimParameters::outputMomenta |
Definition at line 1010 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Controller::printEnergies().
int SimParameters::outputPairlists |
Definition at line 335 of file SimParameters.h.
Referenced by Controller::compareChecksums(), and Controller::printEnergies().
Bool SimParameters::outputPatchDetails |
Definition at line 1082 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists().
Bool SimParameters::outputPerformance |
Definition at line 1016 of file SimParameters.h.
Referenced by Controller::printTiming().
int SimParameters::outputPressure |
Definition at line 1027 of file SimParameters.h.
Referenced by Sequencer::integrate(), and Controller::printEnergies().
int SimParameters::outputTiming |
Definition at line 1013 of file SimParameters.h.
Referenced by Controller::printTiming().
int SimParameters::pairInteractionGroup1 |
Definition at line 631 of file SimParameters.h.
int SimParameters::pairInteractionGroup2 |
Definition at line 632 of file SimParameters.h.
Bool SimParameters::pairInteractionOn |
Definition at line 630 of file SimParameters.h.
Referenced by Sequencer::calcKineticEnergy(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Sequencer::multigratorPressure(), Controller::printEnergies(), Controller::receivePressure(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().
Bool SimParameters::pairInteractionSelf |
Definition at line 633 of file SimParameters.h.
Referenced by Sequencer::calcKineticEnergy(), NamdState::loadStructure(), WorkDistrib::mapComputes(), Sequencer::multigratorPressure(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().
BigReal SimParameters::pairlistDist |
Definition at line 325 of file SimParameters.h.
BigReal SimParameters::pairlistGrow |
Definition at line 333 of file SimParameters.h.
int SimParameters::pairlistMinProcs |
Definition at line 327 of file SimParameters.h.
BigReal SimParameters::pairlistShrink |
Definition at line 332 of file SimParameters.h.
int SimParameters::pairlistsPerCycle |
Definition at line 331 of file SimParameters.h.
Referenced by Sequencer::Sequencer().
BigReal SimParameters::pairlistTrigger |
Definition at line 334 of file SimParameters.h.
Bool SimParameters::paraTypeCharmmOn |
Definition at line 377 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Bool SimParameters::paraTypeXplorOn |
Definition at line 376 of file SimParameters.h.
Referenced by NamdState::loadStructure().
BigReal SimParameters::patchDimension |
Definition at line 308 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Bool SimParameters::PMEBarrier |
Definition at line 902 of file SimParameters.h.
BigReal SimParameters::PMEEwaldCoefficient |
Definition at line 893 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
int SimParameters::PMEGridSizeX |
Definition at line 895 of file SimParameters.h.
int SimParameters::PMEGridSizeY |
Definition at line 896 of file SimParameters.h.
int SimParameters::PMEGridSizeZ |
Definition at line 897 of file SimParameters.h.
BigReal SimParameters::PMEGridSpacing |
Definition at line 898 of file SimParameters.h.
int SimParameters::PMEInterpOrder |
Definition at line 894 of file SimParameters.h.
int SimParameters::PMEMinPoints |
Definition at line 901 of file SimParameters.h.
int SimParameters::PMEMinSlices |
Definition at line 900 of file SimParameters.h.
Bool SimParameters::PMEOffload |
Definition at line 910 of file SimParameters.h.
Referenced by PmePencil< CBase_PmeZPencil >::order_init().
Bool SimParameters::PMEOn |
Definition at line 891 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), WorkDistrib::mapComputes(), Molecule::prepare_qm(), Controller::printEnergies(), ComputeQMMgr::procQMRes(), ComputeQMMgr::recvPntChrg(), Node::resendMolecule(), and Node::startup().
int SimParameters::PMEPencils |
Definition at line 903 of file SimParameters.h.
int SimParameters::PMEPencilsX |
Definition at line 904 of file SimParameters.h.
int SimParameters::PMEPencilsXLayout |
Definition at line 908 of file SimParameters.h.
int SimParameters::PMEPencilsY |
Definition at line 905 of file SimParameters.h.
int SimParameters::PMEPencilsYLayout |
Definition at line 907 of file SimParameters.h.
int SimParameters::PMEPencilsZ |
Definition at line 906 of file SimParameters.h.
int SimParameters::PMEProcessors |
Definition at line 899 of file SimParameters.h.
int SimParameters::PMESendOrder |
Definition at line 909 of file SimParameters.h.
BigReal SimParameters::PMETolerance |
Definition at line 892 of file SimParameters.h.
int SimParameters::pressureProfileAtomTypes |
Definition at line 814 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), and Sequencer::Sequencer().
Bool SimParameters::pressureProfileEwaldOn |
Definition at line 815 of file SimParameters.h.
Referenced by Controller::Controller(), and WorkDistrib::mapComputes().
int SimParameters::pressureProfileEwaldX |
Definition at line 816 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald().
int SimParameters::pressureProfileEwaldY |
Definition at line 817 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald().
int SimParameters::pressureProfileEwaldZ |
Definition at line 818 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald().
int SimParameters::pressureProfileFreq |
Definition at line 813 of file SimParameters.h.
Referenced by Controller::Controller(), and Controller::printEnergies().
Bool SimParameters::pressureProfileOn |
Definition at line 811 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), and Sequencer::Sequencer().
int SimParameters::pressureProfileSlabs |
Definition at line 812 of file SimParameters.h.
Referenced by ComputeEwald::ComputeEwald(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::ComputeHomeTuples(), Controller::Controller(), Sequencer::Sequencer(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().
Bool SimParameters::printBadContacts |
Definition at line 602 of file SimParameters.h.
Referenced by Sequencer::submitMinimizeReductions().
Bool SimParameters::printExclusions |
Definition at line 1154 of file SimParameters.h.
int SimParameters::proxyRecvSpanningTree |
Definition at line 1158 of file SimParameters.h.
Referenced by isRecvSpanningTreeOn(), and isRecvSpanningTreeUnset().
int SimParameters::proxySendSpanningTree |
Definition at line 1157 of file SimParameters.h.
Referenced by isSendSpanningTreeOn(), and isSendSpanningTreeUnset().
int SimParameters::proxyTreeBranchFactor |
Definition at line 1160 of file SimParameters.h.
Referenced by Node::startup().
char SimParameters::qmBaseDir[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 558 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
char SimParameters::qmBondColumn[16] |
Definition at line 568 of file SimParameters.h.
Bool SimParameters::qmBondColumnDefined |
Definition at line 569 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Bool SimParameters::qmBondDist |
Definition at line 570 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Bool SimParameters::qmBondGuess |
Definition at line 571 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Bool SimParameters::qmBondOn |
Definition at line 567 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
int SimParameters::qmBondScheme |
Definition at line 575 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
char SimParameters::qmBondSchemeS[16] |
Definition at line 574 of file SimParameters.h.
int SimParameters::qmBondValType |
Definition at line 572 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPartQM().
char SimParameters::qmBondValueTypeS[16] |
Definition at line 573 of file SimParameters.h.
Bool SimParameters::qmChrgFromPSF |
Definition at line 552 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
int SimParameters::qmChrgMode |
Definition at line 556 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
char SimParameters::qmChrgModeS[16] |
Definition at line 555 of file SimParameters.h.
char SimParameters::qmColumn[16] |
Definition at line 557 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Bool SimParameters::qmCSMD |
Definition at line 595 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
char SimParameters::qmCSMDFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 596 of file SimParameters.h.
Bool SimParameters::qmCustomPCSel |
Definition at line 587 of file SimParameters.h.
Referenced by ComputeQM::initialize(), Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().
Bool SimParameters::qmElecEmbed |
Definition at line 585 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
int SimParameters::qmEnergyOutFreq |
Definition at line 598 of file SimParameters.h.
Referenced by ComputeQMMgr::storeQMRes().
char SimParameters::qmExecPath[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 553 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Bool SimParameters::qmForcesOn |
Definition at line 549 of file SimParameters.h.
Referenced by Controller::compareChecksums(), NamdState::loadStructure(), WorkDistrib::mapComputes(), and Controller::printEnergies().
int SimParameters::qmFormat |
Definition at line 563 of file SimParameters.h.
Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPntChrg().
int SimParameters::qmLSSFreq |
Definition at line 590 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
int SimParameters::qmLSSMode |
Definition at line 593 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
char SimParameters::qmLSSModeS[16] |
Definition at line 592 of file SimParameters.h.
Bool SimParameters::qmLSSOn |
Definition at line 589 of file SimParameters.h.
Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().
char SimParameters::qmLSSResname[5] |
Definition at line 591 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Bool SimParameters::qmMOPACAddConfigChrg |
Definition at line 565 of file SimParameters.h.
Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPntChrg().
Bool SimParameters::qmNoPC |
Definition at line 584 of file SimParameters.h.
Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPartQM().
int SimParameters::qmOutFreq |
Definition at line 599 of file SimParameters.h.
Referenced by ComputeQMMgr::procQMRes(), and ComputeQMMgr::recvPartQM().
char SimParameters::qmParamPDB[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 550 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Bool SimParameters::qmParamPDBDefined |
Definition at line 551 of file SimParameters.h.
Referenced by NamdState::loadStructure().
int SimParameters::qmPCScheme |
Definition at line 580 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
char SimParameters::qmPCSchemeS[16] |
Definition at line 579 of file SimParameters.h.
int SimParameters::qmPCSelFreq |
Definition at line 586 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
Bool SimParameters::qmPCSwitchOn |
Definition at line 576 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
int SimParameters::qmPCSwitchType |
Definition at line 578 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
char SimParameters::qmPCSwitchTypeS[16] |
Definition at line 577 of file SimParameters.h.
int SimParameters::qmPosOutFreq |
Definition at line 600 of file SimParameters.h.
Referenced by ComputeQMMgr::procQMRes(), and ComputeQMMgr::recvPartQM().
char SimParameters::qmPrepProc[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 561 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Bool SimParameters::qmPrepProcOn |
Definition at line 562 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Bool SimParameters::qmReplaceAll |
Definition at line 564 of file SimParameters.h.
Referenced by NamdState::loadStructure().
char SimParameters::qmSecProc[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 559 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
Bool SimParameters::qmSecProcOn |
Definition at line 560 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
int SimParameters::qmSimsPerNode |
Definition at line 581 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPartQM().
char SimParameters::qmSoftware[128] |
Definition at line 554 of file SimParameters.h.
Bool SimParameters::qmVDW |
Definition at line 583 of file SimParameters.h.
Referenced by Molecule::prepare_qm().
unsigned int SimParameters::randomSeed |
Definition at line 823 of file SimParameters.h.
Referenced by colvarproxy_namd::colvarproxy_namd(), Controller::Controller(), Sequencer::Sequencer(), and Node::startup().
Bool SimParameters::readExclusions |
Definition at line 1128 of file SimParameters.h.
Referenced by buildExclusions().
int SimParameters::reassignFreq |
Definition at line 759 of file SimParameters.h.
Referenced by Sequencer::integrate(), Controller::reassignVelocities(), Sequencer::reassignVelocities(), and colvarproxy_namd::update_target_temperature().
BigReal SimParameters::reassignHold |
Definition at line 762 of file SimParameters.h.
Referenced by Controller::reassignVelocities(), and Sequencer::reassignVelocities().
BigReal SimParameters::reassignIncr |
Definition at line 761 of file SimParameters.h.
Referenced by Controller::reassignVelocities(), and Sequencer::reassignVelocities().
BigReal SimParameters::reassignTemp |
Definition at line 760 of file SimParameters.h.
Referenced by Controller::reassignVelocities(), Sequencer::reassignVelocities(), and colvarproxy_namd::update_target_temperature().
Bool SimParameters::replicaUniformPatchGrids |
Definition at line 1084 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
int SimParameters::rescaleFreq |
Definition at line 710 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), Sequencer::integrate(), Controller::rescaleVelocities(), Sequencer::rescaleVelocities(), and colvarproxy_namd::update_target_temperature().
BigReal SimParameters::rescaleTemp |
Definition at line 711 of file SimParameters.h.
Referenced by Controller::adaptTempInit(), Sequencer::integrate(), Controller::rescaleVelocities(), and colvarproxy_namd::update_target_temperature().
char SimParameters::restartFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 294 of file SimParameters.h.
Referenced by colvarproxy_namd::calculate(), colvarproxy_namd::colvarproxy_namd(), and Controller::outputExtendedSystem().
int SimParameters::restartFrequency |
Definition at line 298 of file SimParameters.h.
Referenced by colvarproxy_namd::calculate(), colvarproxy_namd::colvarproxy_namd(), Sequencer::integrate_SOA(), Controller::outputExtendedSystem(), and Controller::rescaleaccelMD().
Bool SimParameters::restartSave |
Definition at line 300 of file SimParameters.h.
Referenced by Controller::outputExtendedSystem().
Bool SimParameters::restartSaveDcd |
Definition at line 301 of file SimParameters.h.
int SimParameters::rigidBonds |
Definition at line 1050 of file SimParameters.h.
Referenced by NamdState::configListInit(), WorkDistrib::createAtomLists(), NamdState::loadStructure(), outputCompressedFile(), Sequencer::rattle1(), and Sequencer::rattle1_SOA().
int SimParameters::rigidDie |
Definition at line 1055 of file SimParameters.h.
int SimParameters::rigidIter |
Definition at line 1054 of file SimParameters.h.
BigReal SimParameters::rigidTol |
Definition at line 1053 of file SimParameters.h.
zVector SimParameters::rotConsAxis |
Definition at line 397 of file SimParameters.h.
zVector SimParameters::rotConsPivot |
Definition at line 398 of file SimParameters.h.
Bool SimParameters::rotConstraintsOn |
Definition at line 395 of file SimParameters.h.
BigReal SimParameters::rotConsVel |
Definition at line 399 of file SimParameters.h.
char SimParameters::rotDragAxisFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 414 of file SimParameters.h.
char SimParameters::rotDragFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 412 of file SimParameters.h.
BigReal SimParameters::rotDragGlobVel |
Definition at line 416 of file SimParameters.h.
Referenced by Sequencer::addRotDragToPosition().
Bool SimParameters::rotDragOn |
Definition at line 411 of file SimParameters.h.
Referenced by Sequencer::integrate(), and NamdState::loadStructure().
char SimParameters::rotDragPivotFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 415 of file SimParameters.h.
char SimParameters::rotDragVelFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 417 of file SimParameters.h.
BigReal SimParameters::scale14 |
Definition at line 267 of file SimParameters.h.
BigReal SimParameters::scale14alt |
Definition at line 269 of file SimParameters.h.
BigReal SimParameters::scriptArg1 |
Definition at line 1138 of file SimParameters.h.
Referenced by Sequencer::algorithm(), and Controller::algorithm().
BigReal SimParameters::scriptArg2 |
Definition at line 1139 of file SimParameters.h.
BigReal SimParameters::scriptArg3 |
Definition at line 1140 of file SimParameters.h.
BigReal SimParameters::scriptArg4 |
Definition at line 1141 of file SimParameters.h.
BigReal SimParameters::scriptArg5 |
Definition at line 1142 of file SimParameters.h.
int SimParameters::scriptIntArg1 |
Definition at line 1143 of file SimParameters.h.
Referenced by Controller::algorithm().
int SimParameters::scriptIntArg2 |
Definition at line 1144 of file SimParameters.h.
char SimParameters::scriptStringArg1[128] |
Definition at line 1145 of file SimParameters.h.
Referenced by Controller::algorithm().
char SimParameters::scriptStringArg2[128] |
Definition at line 1146 of file SimParameters.h.
Bool SimParameters::sdScaling |
Definition at line 474 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
Bool SimParameters::selectConstraintsOn |
Definition at line 362 of file SimParameters.h.
int SimParameters::simulatedNodeSize |
Definition at line 229 of file SimParameters.h.
Referenced by Node::outputPatchComputeMaps(), and Node::startup().
int SimParameters::simulatedPEs |
Definition at line 228 of file SimParameters.h.
Referenced by WorkDistrib::assignNodeToPatch(), Node::outputPatchComputeMaps(), WorkDistrib::patchMapInit(), and Node::startup().
Bool SimParameters::simulateInitialMapping |
Definition at line 227 of file SimParameters.h.
Referenced by WorkDistrib::assignNodeToPatch(), Node::outputPatchComputeMaps(), WorkDistrib::patchMapInit(), and Node::startup().
Bool SimParameters::singleTopology |
Definition at line 473 of file SimParameters.h.
Referenced by Sequencer::integrate(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), Sequencer::minimize(), and Sequencer::runComputeObjects().
zVector SimParameters::SMDDir |
Definition at line 434 of file SimParameters.h.
char SimParameters::SMDFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 437 of file SimParameters.h.
BigReal SimParameters::SMDk |
Definition at line 435 of file SimParameters.h.
BigReal SimParameters::SMDk2 |
Definition at line 436 of file SimParameters.h.
Bool SimParameters::SMDOn |
Definition at line 432 of file SimParameters.h.
int SimParameters::SMDOutputFreq |
Definition at line 438 of file SimParameters.h.
BigReal SimParameters::SMDVel |
Definition at line 433 of file SimParameters.h.
Bool SimParameters::SOAintegrateOn |
Definition at line 161 of file SimParameters.h.
Referenced by Sequencer::algorithm(), and Sequencer::rescaleSoluteCharges().
Bool SimParameters::soluteScalingAll |
enables scaling for bond and angle terms (default is off)
Definition at line 539 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
BigReal SimParameters::soluteScalingFactor |
scaling factor for solute interactions
Definition at line 531 of file SimParameters.h.
Referenced by ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples().
BigReal SimParameters::soluteScalingFactorCharge |
optional independent control over scaling factor for electrostatic interactions of solute
Definition at line 533 of file SimParameters.h.
Referenced by Sequencer::algorithm(), and Sequencer::Sequencer().
BigReal SimParameters::soluteScalingFactorVdw |
optional independent control over scaling factor for van der Waals interactions of solute
Definition at line 536 of file SimParameters.h.
Bool SimParameters::soluteScalingOn |
REST2 (replica exchange solute tempering) on?
Definition at line 529 of file SimParameters.h.
Referenced by LJTable::LJTable(), NamdState::loadStructure(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::loadTuples(), and Sequencer::Sequencer().
BigReal SimParameters::solvent_dielectric |
Definition at line 608 of file SimParameters.h.
int SimParameters::sphericalBCexp1 |
Definition at line 965 of file SimParameters.h.
int SimParameters::sphericalBCexp2 |
Definition at line 966 of file SimParameters.h.
BigReal SimParameters::sphericalBCk1 |
Definition at line 959 of file SimParameters.h.
BigReal SimParameters::sphericalBCk2 |
Definition at line 961 of file SimParameters.h.
Bool SimParameters::sphericalBCOn |
Definition at line 956 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
BigReal SimParameters::sphericalBCr1 |
Definition at line 963 of file SimParameters.h.
BigReal SimParameters::sphericalBCr2 |
Definition at line 964 of file SimParameters.h.
zVector SimParameters::sphericalCenter |
Definition at line 958 of file SimParameters.h.
Bool SimParameters::sphericalConstraintsOn |
Definition at line 370 of file SimParameters.h.
zVector SimParameters::sphericalConstrCenter |
Definition at line 371 of file SimParameters.h.
int SimParameters::splitPatch |
Definition at line 1043 of file SimParameters.h.
Bool SimParameters::staticAtomAssignment |
Definition at line 1083 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists(), and WorkDistrib::patchMapInit().
Bool SimParameters::statsOn |
Definition at line 1061 of file SimParameters.h.
Referenced by Controller::integrate(), and Sequencer::integrate().
int SimParameters::stepsPerCycle |
Definition at line 189 of file SimParameters.h.
Referenced by Controller::integrate(), Sequencer::integrate(), Sequencer::integrate_SOA(), Sequencer::minimize(), Sequencer::multigratorPressure(), Molecule::prepare_qm(), and Sequencer::Sequencer().
zVector SimParameters::stirAxis |
Definition at line 993 of file SimParameters.h.
char SimParameters::stirFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 988 of file SimParameters.h.
BigReal SimParameters::stirK |
Definition at line 992 of file SimParameters.h.
Bool SimParameters::stirOn |
Definition at line 987 of file SimParameters.h.
Referenced by NamdState::loadStructure(), and WorkDistrib::mapComputes().
zVector SimParameters::stirPivot |
Definition at line 994 of file SimParameters.h.
BigReal SimParameters::stirStartingTheta |
Definition at line 990 of file SimParameters.h.
BigReal SimParameters::stirVel |
Definition at line 991 of file SimParameters.h.
int SimParameters::stochRescaleFreq |
How frequently (time steps) stochastic velocity rescaling occurs.
Definition at line 702 of file SimParameters.h.
Referenced by Controller::Controller(), Controller::stochRescaleVelocities(), Sequencer::stochRescaleVelocities(), and Sequencer::stochRescaleVelocities_SOA().
Bool SimParameters::stochRescaleHeat |
Flag TRUE enables calculation and reporting of heat transfer and work. The computation is cumulative from step = firstTimestep.
Definition at line 705 of file SimParameters.h.
Referenced by Controller::printEnergies().
Bool SimParameters::stochRescaleOn |
Flag TRUE enables the stochastic velocity rescaling method of Bussi, Donadio, and Parrinello. The method is an extension to the Berendsen thermostat, where a stochastic update to the velocity rescaling produces correct sampling of the NVT ensemble.
Definition at line 689 of file SimParameters.h.
Referenced by Controller::Controller(), Sequencer::integrate(), Sequencer::integrate_SOA(), Controller::printEnergies(), Controller::stochRescaleVelocities(), and colvarproxy_namd::update_target_temperature().
BigReal SimParameters::stochRescalePeriod |
Timescale (ps) for stochastic velocity rescaling.
Definition at line 699 of file SimParameters.h.
Referenced by Controller::Controller().
BigReal SimParameters::stochRescaleTemp |
Temperature for stochastic velocity rescaling.
Definition at line 696 of file SimParameters.h.
Referenced by Controller::stochRescaleCoefficient(), and colvarproxy_namd::update_target_temperature().
Bool SimParameters::storeComputeMap |
Definition at line 1175 of file SimParameters.h.
zVector SimParameters::strainRate |
Definition at line 820 of file SimParameters.h.
Referenced by Controller::Controller().
zVector SimParameters::strainRate2 |
Definition at line 821 of file SimParameters.h.
Referenced by Controller::Controller().
BigReal SimParameters::surface_tension |
Definition at line 618 of file SimParameters.h.
BigReal SimParameters::surfaceTensionTarget |
Definition at line 809 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::langevinPiston2(), and Controller::monteCarloPressure_accept().
Bool SimParameters::switchingActive |
Definition at line 315 of file SimParameters.h.
BigReal SimParameters::switchingDist |
Definition at line 319 of file SimParameters.h.
Referenced by ComputeQMMgr::recvPntChrg().
char SimParameters::symmetryFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 462 of file SimParameters.h.
int SimParameters::symmetryFirstFullStep |
Definition at line 464 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
int SimParameters::symmetryFirstStep |
Definition at line 464 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
BigReal SimParameters::symmetryk |
Definition at line 460 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
char SimParameters::symmetrykfile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 461 of file SimParameters.h.
int SimParameters::symmetryLastFullStep |
Definition at line 464 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
int SimParameters::symmetryLastStep |
Definition at line 464 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
char SimParameters::symmetryMatrixFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 463 of file SimParameters.h.
Bool SimParameters::symmetryOn |
Definition at line 459 of file SimParameters.h.
Bool SimParameters::symmetryScaleForces |
Definition at line 459 of file SimParameters.h.
Referenced by GlobalMasterSymmetry::GlobalMasterSymmetry().
char SimParameters::tableInterpType[128] |
Definition at line 445 of file SimParameters.h.
BigReal SimParameters::tableMaxDist |
Definition at line 447 of file SimParameters.h.
int SimParameters::tableNumTypes |
Definition at line 443 of file SimParameters.h.
Real SimParameters::tableSpacing |
Definition at line 446 of file SimParameters.h.
Bool SimParameters::tabulatedEnergies |
Definition at line 442 of file SimParameters.h.
char SimParameters::tabulatedEnergiesFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 444 of file SimParameters.h.
char SimParameters::tclBCArgs[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 650 of file SimParameters.h.
Bool SimParameters::tclBCOn |
Definition at line 648 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
char* SimParameters::tclBCScript |
Definition at line 649 of file SimParameters.h.
Bool SimParameters::tclForcesOn |
Definition at line 637 of file SimParameters.h.
Referenced by ComputeGlobal::ComputeGlobal(), Sequencer::integrate(), Sequencer::integrate_SOA(), and Sequencer::minimize().
Bool SimParameters::tclIsThreaded |
Definition at line 646 of file SimParameters.h.
Bool SimParameters::tCoupleOn |
Definition at line 685 of file SimParameters.h.
Referenced by NamdState::loadStructure(), Controller::tcoupleVelocities(), Sequencer::tcoupleVelocities(), and colvarproxy_namd::update_target_temperature().
BigReal SimParameters::tCoupleTemp |
Definition at line 687 of file SimParameters.h.
Referenced by Controller::tcoupleVelocities(), and colvarproxy_namd::update_target_temperature().
Bool SimParameters::testOn |
Definition at line 1059 of file SimParameters.h.
Bool SimParameters::TMDDiffRMSD |
Definition at line 451 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
char SimParameters::TMDFile[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 453 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
char SimParameters::TMDFile2[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 453 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
BigReal SimParameters::TMDFinalRMSD |
Definition at line 456 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
int SimParameters::TMDFirstStep |
Definition at line 455 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
BigReal SimParameters::TMDInitialRMSD |
Definition at line 456 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
BigReal SimParameters::TMDk |
Definition at line 452 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
int SimParameters::TMDLastStep |
Definition at line 455 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
Bool SimParameters::TMDOn |
Definition at line 451 of file SimParameters.h.
int SimParameters::TMDOutputFreq |
Definition at line 454 of file SimParameters.h.
Referenced by GlobalMasterTMD::GlobalMasterTMD().
int SimParameters::totalAtoms |
Definition at line 1063 of file SimParameters.h.
int SimParameters::traceStartStep |
Definition at line 217 of file SimParameters.h.
Referenced by Controller::integrate(), and Sequencer::integrate().
int SimParameters::twoAwayX |
Definition at line 241 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
int SimParameters::twoAwayY |
Definition at line 242 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
int SimParameters::twoAwayZ |
Definition at line 243 of file SimParameters.h.
Referenced by WorkDistrib::patchMapInit().
Bool SimParameters::updateAtomMap |
Used for experimenting with atom maps
Definition at line 935 of file SimParameters.h.
Bool SimParameters::useAntecedent |
Definition at line 1095 of file SimParameters.h.
Bool SimParameters::useAVXTiles |
Definition at line 1188 of file SimParameters.h.
Referenced by Patch::positionsReady(), ProxyPatch::receiveAll(), and ProxyPatch::receiveData().
int SimParameters::useCkLoop |
Definition at line 239 of file SimParameters.h.
Referenced by PmeZPencil::backward_fft(), PmeYPencil::backward_fft(), PmeXPencil::backward_fft(), PmeZPencil::forward_fft(), PmeYPencil::forward_fft(), PmeXPencil::forward_fft(), ComputePmeCUDADevice::gatherForceDone(), PmeZPencil::send_all_ungrid(), PmeZPencil::send_trans(), PmeYPencil::send_trans(), PmeYPencil::send_untrans(), PmeXPencil::send_untrans(), ComputePmeMgr::sendTrans(), ComputePmeMgr::sendUngrid(), ComputePmeMgr::sendUntrans(), and Node::startup().
Bool SimParameters::useCompressedPsf |
Definition at line 1148 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Bool SimParameters::useConstantArea |
Definition at line 770 of file SimParameters.h.
Referenced by Controller::langevinPiston1(), Controller::monteCarloPressure_accept(), and Controller::monteCarloPressure_prepare().
Bool SimParameters::useConstantRatio |
Definition at line 771 of file SimParameters.h.
Referenced by Controller::calcPressure(), Controller::Controller(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), and Controller::writeExtendedSystemData().
Bool SimParameters::useCUDAdisable |
Flag TRUE to automatically disable individual CUDA kernels that are incompatible with simulation options. Default is TRUE. Specifically, disable CUDA bonds for Drude oscillator simulation and disable CUDA dihedral and CUDA crossterms kernels for accelMDdihe and accelMDdual simulation. Set FALSE to manually control kernel use for development.
Definition at line 922 of file SimParameters.h.
Bool SimParameters::useCudaGlobal |
Definition at line 1190 of file SimParameters.h.
Bool SimParameters::useCUDANonbondedForceTable |
direct nonbonded kernel math for non-PME steps (experimental)
Definition at line 930 of file SimParameters.h.
Bool SimParameters::useDeviceMigration |
atom migration on GPU (experimental)
Definition at line 933 of file SimParameters.h.
Referenced by Sequencer::minimize(), CudaComputeNonbonded::patchReady(), and Sequencer::submitCollections_SOA().
Bool SimParameters::useDPME |
Definition at line 912 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes().
Bool SimParameters::useFlexibleCell |
Definition at line 769 of file SimParameters.h.
Referenced by Controller::calcPressure(), Controller::Controller(), Controller::langevinPiston1(), Controller::langevinPiston2(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), and Controller::writeExtendedSystemData().
Bool SimParameters::useGPUAtomMigration |
replacement for useDeviceMigration
Definition at line 934 of file SimParameters.h.
Bool SimParameters::useGPUNonbondedForceTable |
replacement for useCUDANonbondedForceTable
Definition at line 931 of file SimParameters.h.
Bool SimParameters::useGroupPressure |
Definition at line 764 of file SimParameters.h.
Referenced by Sequencer::berendsenPressure(), Sequencer::berendsenPressure_SOA(), Controller::calcPressure(), Sequencer::langevinPiston(), Sequencer::langevinPiston_SOA(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Controller::receivePressure(), Sequencer::scalePositionsVelocities(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().
int SimParameters::usePairlists |
Definition at line 329 of file SimParameters.h.
Referenced by Sequencer::runComputeObjects(), and Sequencer::runComputeObjects_SOA().
Bool SimParameters::usePluginIO |
Definition at line 1151 of file SimParameters.h.
Referenced by NamdState::loadStructure().
Bool SimParameters::usePMECUDA |
Flag TRUE to use the PME CUDA version. Default is TRUE if running on 4 nodes or less.
Definition at line 914 of file SimParameters.h.
Referenced by WorkDistrib::mapComputes(), and Node::startup().
Bool SimParameters::usePMEGPU |
replacement keyword for usePMECUDA
Definition at line 917 of file SimParameters.h.
Bool SimParameters::usePytorchForces |
Definition at line 1192 of file SimParameters.h.
Bool SimParameters::useSettle |
Definition at line 1057 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists().
Bool SimParameters::vdwForceSwitching |
Definition at line 317 of file SimParameters.h.
Bool SimParameters::vdwGeometricSigma |
Definition at line 1135 of file SimParameters.h.
BigReal SimParameters::vdwscale14 |
Definition at line 1129 of file SimParameters.h.
Referenced by NamdState::loadStructure().
char SimParameters::velDcdFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 286 of file SimParameters.h.
int SimParameters::velDcdFrequency |
Definition at line 277 of file SimParameters.h.
Referenced by Sequencer::integrate_SOA().
Bool SimParameters::verboseTopology |
Definition at line 231 of file SimParameters.h.
WaterModel SimParameters::watmodel |
Definition at line 183 of file SimParameters.h.
Referenced by WorkDistrib::createAtomLists(), and Sequencer::runComputeObjects().
Bool SimParameters::wrapAll |
Definition at line 260 of file SimParameters.h.
Referenced by colvarproxy_namd::setup().
Bool SimParameters::wrapNearest |
Definition at line 261 of file SimParameters.h.
Bool SimParameters::wrapWater |
Definition at line 259 of file SimParameters.h.
char SimParameters::xstFilename[NAMD_FILENAME_BUFFER_SIZE] |
Definition at line 288 of file SimParameters.h.
Referenced by Controller::outputExtendedSystem().
int SimParameters::xstFrequency |
Definition at line 281 of file SimParameters.h.
Referenced by Controller::outputExtendedSystem().
Bool SimParameters::zeroMomentum |
Definition at line 257 of file SimParameters.h.
Referenced by Controller::integrate(), and Sequencer::integrate().
Bool SimParameters::zeroMomentumAlt |
Definition at line 258 of file SimParameters.h.
Referenced by Sequencer::correctMomentum(), and Sequencer::submitMomentum().