OpenMD  2.5
Molecular Dynamics in the Open
OpenMD::Snapshot Class Reference

The Snapshot class is a repository storing dynamic data during a Simulation. Every Snapshot contains FrameData (for global information) as well as DataStorage (one for Atoms, one for RigidBodies, and one for CutoffGroups). More...

#include <Snapshot.hpp>

Public Member Functions

 Snapshot (int nAtoms, int nRigidbodies, int nCutoffGroups, bool usePBC)
 
 Snapshot (int nAtoms, int nRigidbodies, int nCutoffGroups, int storageLayout, bool usePBC)
 
int getID ()
 
void setID (int id)
 
void clearDerivedProperties ()
 
int getSize ()
 
int getNumberOfAtoms ()
 
int getNumberOfRigidBodies ()
 
int getNumberOfCutoffGroups ()
 
Mat3x3d getHmat ()
 
void setHmat (const Mat3x3d &m)
 
Mat3x3d getInvHmat ()
 
Mat3x3d getBoundingBox ()
 
void setBoundingBox (const Mat3x3d &m)
 
Mat3x3d getInvBoundingBox ()
 
RealType getVolume ()
 
RealType getXYarea ()
 
void setVolume (const RealType vol)
 
void wrapVector (Vector3d &v)
 
Vector3d scaleVector (Vector3d &v)
 
void setCOM (const Vector3d &com)
 
void setCOMvel (const Vector3d &comVel)
 
void setCOMw (const Vector3d &comw)
 
Vector3d getCOM ()
 
Vector3d getCOMvel ()
 
Vector3d getCOMw ()
 
RealType getTime ()
 
void increaseTime (const RealType dt)
 
void setTime (const RealType time)
 
void setBondPotential (const RealType bp)
 
void setBendPotential (const RealType bp)
 
void setTorsionPotential (const RealType tp)
 
void setInversionPotential (const RealType ip)
 
RealType getBondPotential ()
 
RealType getBendPotential ()
 
RealType getTorsionPotential ()
 
RealType getInversionPotential ()
 
RealType getShortRangePotential ()
 
void setLongRangePotential (const potVec lrPot)
 
RealType getLongRangePotential ()
 
potVec getLongRangePotentials ()
 
void setReciprocalPotential (const RealType rp)
 
RealType getReciprocalPotential ()
 
void setSurfacePotential (const RealType sp)
 
RealType getSurfacePotential ()
 
void setSelfPotential (const RealType sp)
 
RealType getSelfPotential ()
 
void setExcludedPotentials (const potVec exPot)
 
potVec getExcludedPotentials ()
 
void setRestraintPotential (const RealType rp)
 
RealType getRestraintPotential ()
 
void setRawPotential (const RealType rp)
 
RealType getRawPotential ()
 
void setSelectionPotentials (const potVec selPot)
 
potVec getSelectionPotentials ()
 
RealType getPotentialEnergy ()
 
RealType getKineticEnergy ()
 
RealType getTranslationalKineticEnergy ()
 
RealType getRotationalKineticEnergy ()
 
RealType getElectronicKineticEnergy ()
 
void setKineticEnergy (const RealType ke)
 
void setTranslationalKineticEnergy (const RealType tke)
 
void setRotationalKineticEnergy (const RealType rke)
 
void setElectronicKineticEnergy (const RealType eke)
 
RealType getTotalEnergy ()
 
void setTotalEnergy (const RealType te)
 
RealType getConservedQuantity ()
 
void setConservedQuantity (const RealType cq)
 
RealType getTemperature ()
 
void setTemperature (const RealType temp)
 
RealType getElectronicTemperature ()
 
void setElectronicTemperature (const RealType eTemp)
 
RealType getNetCharge ()
 
void setNetCharge (const RealType nChg)
 
RealType getChargeMomentum ()
 
void setChargeMomentum (const RealType cMom)
 
RealType getPressure ()
 
void setPressure (const RealType pressure)
 
Mat3x3d getPressureTensor ()
 
void setPressureTensor (const Mat3x3d &pressureTensor)
 
Mat3x3d getStressTensor ()
 
void setStressTensor (const Mat3x3d &stressTensor)
 
Vector3d getConductiveHeatFlux ()
 
void setConductiveHeatFlux (const Vector3d &chf)
 
Vector3d getConvectiveHeatFlux ()
 
void setConvectiveHeatFlux (const Vector3d &chf)
 
Vector3d getHeatFlux ()
 
Vector3d getSystemDipole ()
 
void setSystemDipole (const Vector3d &bd)
 
Mat3x3d getSystemQuadrupole ()
 
void setSystemQuadrupole (const Mat3x3d &bq)
 
pair< RealType, RealType > getThermostat ()
 
void setThermostat (const pair< RealType, RealType > &thermostat)
 
pair< RealType, RealType > getElectronicThermostat ()
 
void setElectronicThermostat (const pair< RealType, RealType > &eThermostat)
 
Mat3x3d getBarostat ()
 
void setBarostat (const Mat3x3d &barostat)
 
Mat3x3d getInertiaTensor ()
 
void setInertiaTensor (const Mat3x3d &inertiaTensor)
 
RealType getGyrationalVolume ()
 
void setGyrationalVolume (const RealType gv)
 
RealType getHullVolume ()
 
void setHullVolume (const RealType hv)
 
void setOrthoTolerance (RealType orthoTolerance)
 

Static Public Member Functions

static int getFrameDataSize ()
 

Public Attributes

DataStorage atomData
 
DataStorage rigidbodyData
 
DataStorage cgData
 
FrameData frameData
 
bool hasTotalEnergy
 
bool hasTranslationalKineticEnergy
 
bool hasRotationalKineticEnergy
 
bool hasElectronicKineticEnergy
 
bool hasKineticEnergy
 
bool hasShortRangePotential
 
bool hasLongRangePotential
 
bool hasPotentialEnergy
 
bool hasXYarea
 
bool hasVolume
 
bool hasPressure
 
bool hasTemperature
 
bool hasElectronicTemperature
 
bool hasNetCharge
 
bool hasChargeMomentum
 
bool hasCOM
 
bool hasCOMvel
 
bool hasCOMw
 
bool hasPressureTensor
 
bool hasSystemDipole
 
bool hasSystemQuadrupole
 
bool hasConvectiveHeatFlux
 
bool hasInertiaTensor
 
bool hasGyrationalVolume
 
bool hasHullVolume
 
bool hasConservedQuantity
 
bool hasBoundingBox
 

Private Attributes

RealType orthoTolerance_
 

Detailed Description

The Snapshot class is a repository storing dynamic data during a Simulation. Every Snapshot contains FrameData (for global information) as well as DataStorage (one for Atoms, one for RigidBodies, and one for CutoffGroups).

Definition at line 122 of file Snapshot.hpp.

Constructor & Destructor Documentation

◆ Snapshot() [1/2]

◆ Snapshot() [2/2]

Member Function Documentation

◆ clearDerivedProperties()

void OpenMD::Snapshot::clearDerivedProperties ( )

◆ getBarostat()

◆ getBendPotential()

RealType OpenMD::Snapshot::getBendPotential ( )

Definition at line 421 of file Snapshot.cpp.

References OpenMD::FrameData::bendPotential, and frameData.

Referenced by OpenMD::Stats::collectStats().

◆ getBondPotential()

RealType OpenMD::Snapshot::getBondPotential ( )

Definition at line 418 of file Snapshot.cpp.

References OpenMD::FrameData::bondPotential, and frameData.

Referenced by OpenMD::Stats::collectStats().

◆ getBoundingBox()

Mat3x3d OpenMD::Snapshot::getBoundingBox ( )

Returns the Bounding Box

Definition at line 284 of file Snapshot.cpp.

References OpenMD::FrameData::bBox, and frameData.

Referenced by OpenMD::ForceMatrixDecomposition::buildNeighborList(), and OpenMD::Thermo::getBoundingBox().

◆ getChargeMomentum()

RealType OpenMD::Snapshot::getChargeMomentum ( )

Definition at line 609 of file Snapshot.cpp.

References OpenMD::FrameData::chargeMomentum, and frameData.

Referenced by OpenMD::Thermo::getChargeMomentum().

◆ getCOM()

Vector3d OpenMD::Snapshot::getCOM ( )

Definition at line 377 of file Snapshot.cpp.

References OpenMD::FrameData::COM, and frameData.

Referenced by OpenMD::Thermo::getCom(), and OpenMD::Thermo::getComAll().

◆ getCOMvel()

Vector3d OpenMD::Snapshot::getCOMvel ( )

Definition at line 381 of file Snapshot.cpp.

References OpenMD::FrameData::COMvel, and frameData.

Referenced by OpenMD::Thermo::getComAll(), and OpenMD::Thermo::getComVel().

◆ getCOMw()

Vector3d OpenMD::Snapshot::getCOMw ( )

◆ getConductiveHeatFlux()

Vector3d OpenMD::Snapshot::getConductiveHeatFlux ( )

◆ getConservedQuantity()

RealType OpenMD::Snapshot::getConservedQuantity ( )

Definition at line 573 of file Snapshot.cpp.

References OpenMD::FrameData::conservedQuantity, and frameData.

Referenced by OpenMD::Stats::collectStats().

◆ getConvectiveHeatFlux()

Vector3d OpenMD::Snapshot::getConvectiveHeatFlux ( )

Definition at line 653 of file Snapshot.cpp.

References OpenMD::FrameData::convectiveHeatFlux, and frameData.

Referenced by getHeatFlux().

◆ getElectronicKineticEnergy()

RealType OpenMD::Snapshot::getElectronicKineticEnergy ( )

Definition at line 536 of file Snapshot.cpp.

References OpenMD::FrameData::electronicKinetic, and frameData.

Referenced by OpenMD::Thermo::getElectronicKinetic().

◆ getElectronicTemperature()

RealType OpenMD::Snapshot::getElectronicTemperature ( )

◆ getElectronicThermostat()

pair< RealType, RealType > OpenMD::Snapshot::getElectronicThermostat ( )

◆ getExcludedPotentials()

◆ getFrameDataSize()

int OpenMD::Snapshot::getFrameDataSize ( )
static

Returns the number of bytes in a FrameData structure

Definition at line 209 of file Snapshot.cpp.

Referenced by OpenMD::BlockSnapshotManager::BlockSnapshotManager().

◆ getGyrationalVolume()

RealType OpenMD::Snapshot::getGyrationalVolume ( )

Definition at line 724 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::gyrationalVolume.

Referenced by OpenMD::Thermo::getGyrationalVolume().

◆ getHeatFlux()

Vector3d OpenMD::Snapshot::getHeatFlux ( )

Definition at line 662 of file Snapshot.cpp.

References getConductiveHeatFlux(), and getConvectiveHeatFlux().

◆ getHmat()

Mat3x3d OpenMD::Snapshot::getHmat ( )

Returns the H-Matrix

Definition at line 214 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::hmat.

Referenced by OpenMD::ForceMatrixDecomposition::buildNeighborList(), OpenMD::NgammaT::calcConservedQuantity(), OpenMD::NPrT::calcConservedQuantity(), OpenMD::Electrostatic::calcSurfaceTerm(), OpenMD::RNEMD::collectData(), OpenMD::RCorrFuncZ::computeFrame(), OpenMD::LegendreCorrFuncZ::correlateFrames(), OpenMD::COHZ::correlateFrames(), OpenMD::ContactAngle2::doFrame(), OpenMD::RNEMD::doNIVS(), OpenMD::RNEMD::doSwap(), OpenMD::RNEMD::doVSS(), OpenMD::NgammaT::evolveEtaA(), OpenMD::NPrT::evolveEtaA(), OpenMD::NgammaT::evolveEtaB(), OpenMD::NPrT::evolveEtaB(), OpenMD::ReplicateVisitor::internalVisit(), main(), OpenMD::DensityPlot::process(), OpenMD::RhoZ::process(), OpenMD::Hxy::process(), OpenMD::TetrahedralityParamXYZ::process(), OpenMD::TetrahedralityParamZ::process(), OpenMD::RNEMDZ::processFrame(), OpenMD::SlabStatistics::processFrame(), OpenMD::TwoDGofR::processHistogram(), OpenMD::Electrostatic::ReciprocalSpaceSum(), OpenMD::RNEMD::RNEMD(), OpenMD::NPTsz::scaleSimBox(), OpenMD::NPTxyz::scaleSimBox(), OpenMD::NPTi::scaleSimBox(), OpenMD::NPTf::scaleSimBox(), OpenMD::NPrT::scaleSimBox(), OpenMD::NPAT::scaleSimBox(), OpenMD::NgammaT::scaleSimBox(), OpenMD::NPA::scaleSimBox(), OpenMD::TetrahedralityParamXYZ::TetrahedralityParamXYZ(), OpenMD::XYZVisitor::writeFrame(), OpenMD::DumpWriter::writeFrameProperties(), OpenMD::TetrahedralityParamXYZ::writeQxyz(), and OpenMD::ZconstraintForceManager::ZconstraintForceManager().

◆ getHullVolume()

RealType OpenMD::Snapshot::getHullVolume ( )

Definition at line 733 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::hullVolume.

Referenced by OpenMD::Thermo::getHullVolume().

◆ getID()

◆ getInertiaTensor()

Mat3x3d OpenMD::Snapshot::getInertiaTensor ( )

◆ getInvBoundingBox()

Mat3x3d OpenMD::Snapshot::getInvBoundingBox ( )

Returns the inverse Bounding Box

Definition at line 296 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::invBbox.

Referenced by OpenMD::ForceMatrixDecomposition::buildNeighborList().

◆ getInversionPotential()

RealType OpenMD::Snapshot::getInversionPotential ( )

Definition at line 427 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::inversionPotential.

Referenced by OpenMD::Stats::collectStats().

◆ getInvHmat()

Mat3x3d OpenMD::Snapshot::getInvHmat ( )

Returns the inverse H-Matrix

Definition at line 279 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::invHmat.

Referenced by OpenMD::ForceMatrixDecomposition::buildNeighborList(), and OpenMD::Hxy::process().

◆ getKineticEnergy()

RealType OpenMD::Snapshot::getKineticEnergy ( )

Definition at line 540 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::kineticEnergy.

Referenced by OpenMD::Thermo::getKinetic().

◆ getLongRangePotential()

◆ getLongRangePotentials()

potVec OpenMD::Snapshot::getLongRangePotentials ( )

◆ getNetCharge()

RealType OpenMD::Snapshot::getNetCharge ( )

Definition at line 600 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::netCharge.

Referenced by OpenMD::Thermo::getNetCharge().

◆ getNumberOfAtoms()

int OpenMD::Snapshot::getNumberOfAtoms ( )

◆ getNumberOfCutoffGroups()

int OpenMD::Snapshot::getNumberOfCutoffGroups ( )

Returns the number of rigid bodies

Definition at line 204 of file Snapshot.cpp.

References cgData, and OpenMD::DataStorage::getSize().

◆ getNumberOfRigidBodies()

int OpenMD::Snapshot::getNumberOfRigidBodies ( )

Returns the number of rigid bodies

Definition at line 199 of file Snapshot.cpp.

References OpenMD::DataStorage::getSize(), and rigidbodyData.

◆ getPotentialEnergy()

RealType OpenMD::Snapshot::getPotentialEnergy ( )

◆ getPressure()

RealType OpenMD::Snapshot::getPressure ( )

Definition at line 618 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::pressure.

Referenced by OpenMD::Thermo::getPressure().

◆ getPressureTensor()

Mat3x3d OpenMD::Snapshot::getPressureTensor ( )

Definition at line 627 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::pressureTensor.

Referenced by OpenMD::Thermo::getPressureTensor().

◆ getRawPotential()

RealType OpenMD::Snapshot::getRawPotential ( )

Definition at line 516 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::rawPotential.

Referenced by OpenMD::Stats::collectStats().

◆ getReciprocalPotential()

RealType OpenMD::Snapshot::getReciprocalPotential ( )

Definition at line 454 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::reciprocalPotential.

Referenced by OpenMD::Stats::collectStats().

◆ getRestraintPotential()

RealType OpenMD::Snapshot::getRestraintPotential ( )

◆ getRotationalKineticEnergy()

RealType OpenMD::Snapshot::getRotationalKineticEnergy ( )

Definition at line 532 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::rotationalKinetic.

Referenced by OpenMD::Thermo::getRotationalKinetic().

◆ getSelectionPotentials()

potVec OpenMD::Snapshot::getSelectionPotentials ( )

◆ getSelfPotential()

RealType OpenMD::Snapshot::getSelfPotential ( )

Definition at line 462 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::selfPotential.

◆ getShortRangePotential()

◆ getSize()

int OpenMD::Snapshot::getSize ( )

Definition at line 189 of file Snapshot.cpp.

References atomData, OpenMD::DataStorage::getSize(), and rigidbodyData.

◆ getStressTensor()

Mat3x3d OpenMD::Snapshot::getStressTensor ( )

◆ getSurfacePotential()

RealType OpenMD::Snapshot::getSurfacePotential ( )

Definition at line 446 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::surfacePotential.

Referenced by OpenMD::Stats::collectStats().

◆ getSystemDipole()

Vector3d OpenMD::Snapshot::getSystemDipole ( )

Definition at line 667 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::systemDipole.

Referenced by OpenMD::Thermo::getSystemDipole().

◆ getSystemQuadrupole()

Mat3x3d OpenMD::Snapshot::getSystemQuadrupole ( )

Definition at line 676 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::systemQuadrupole.

Referenced by OpenMD::Thermo::getSystemQuadrupole().

◆ getTemperature()

RealType OpenMD::Snapshot::getTemperature ( )

Definition at line 582 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::temperature.

Referenced by OpenMD::Thermo::getTemperature().

◆ getThermostat()

◆ getTime()

RealType OpenMD::Snapshot::getTime ( )

Definition at line 389 of file Snapshot.cpp.

References OpenMD::FrameData::currentTime, and frameData.

Referenced by OpenMD::ZconstraintForceManager::calcForces(), OpenMD::RestraintForceManager::calcForces(), OpenMD::ZconstraintForceManager::checkZConsState(), OpenMD::Stats::collectStats(), OpenMD::Rattle::constraintB(), OpenMD::Shake::constraintF(), OpenMD::TimeCorrFunc::correlateBlocks(), OpenMD::BondCorrFunc::correlateFrames(), OpenMD::DirectionalRCorrFunc::correlateFrames(), OpenMD::ActionCorrFunc::correlateFrames(), OpenMD::StressCorrFunc::correlateFrames(), OpenMD::FrameTimeCorrFunc::correlateFrames(), OpenMD::SystemDipoleCorrFunc::correlateFrames(), OpenMD::LegendreCorrFunc::correlateFrames(), OpenMD::ParticleTimeCorrFunc::correlateFrames(), OpenMD::SelectionCorrFunc::correlateFrames(), OpenMD::LegendreCorrFuncZ::correlateFrames(), OpenMD::COHZ::correlateFrames(), OpenMD::MomentumCorrFunc::correlateFrames(), OpenMD::EnergyCorrFunc::correlateFrames(), OpenMD::VelocityVerletIntegrator::doIntegrate(), OpenMD::SequentialAnalyzer::doSequence(), increaseTime(), OpenMD::RestraintForceManager::init(), OpenMD::ZconstraintForceManager::init(), OpenMD::VelocityVerletIntegrator::initialize(), main(), OpenMD::VelocityVerletIntegrator::postStep(), OpenMD::VelocityVerletIntegrator::preStep(), OpenMD::NanoLength::process(), OpenMD::PotDiff::process(), OpenMD::NanoVolume::process(), OpenMD::ZConsVisitor::update(), OpenMD::ConstraintWriter::writeConstraintForces(), OpenMD::XYZVisitor::writeFrame(), OpenMD::DumpWriter::writeFrameProperties(), OpenMD::ZConsWriter::writeFZ(), OpenMD::RNEMD::writeOutputFile(), and OpenMD::RestWriter::writeRest().

◆ getTorsionPotential()

RealType OpenMD::Snapshot::getTorsionPotential ( )

Definition at line 424 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::torsionPotential.

Referenced by OpenMD::Stats::collectStats().

◆ getTotalEnergy()

RealType OpenMD::Snapshot::getTotalEnergy ( )

Definition at line 564 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::totalEnergy.

Referenced by OpenMD::Thermo::getTotalEnergy().

◆ getTranslationalKineticEnergy()

RealType OpenMD::Snapshot::getTranslationalKineticEnergy ( )

◆ getVolume()

◆ getXYarea()

◆ increaseTime()

void OpenMD::Snapshot::increaseTime ( const RealType  dt)

Definition at line 393 of file Snapshot.cpp.

References getTime(), and setTime().

Referenced by OpenMD::VelocityVerletIntegrator::postStep().

◆ scaleVector()

Vector3d OpenMD::Snapshot::scaleVector ( Vector3d pos)
inline

Scaling a vector to multiples of the periodic box

Definition at line 347 of file Snapshot.cpp.

References frameData, OpenMD::FrameData::invHmat, and OpenMD::FrameData::orthoRhombic.

◆ setBarostat()

◆ setBendPotential()

void OpenMD::Snapshot::setBendPotential ( const RealType  bp)

◆ setBondPotential()

void OpenMD::Snapshot::setBondPotential ( const RealType  bp)

◆ setBoundingBox()

void OpenMD::Snapshot::setBoundingBox ( const Mat3x3d m)

◆ setChargeMomentum()

void OpenMD::Snapshot::setChargeMomentum ( const RealType  cMom)

◆ setCOM()

void OpenMD::Snapshot::setCOM ( const Vector3d com)

Definition at line 362 of file Snapshot.cpp.

References OpenMD::FrameData::COM, frameData, and hasCOM.

Referenced by OpenMD::Thermo::getCom(), and OpenMD::Thermo::getComAll().

◆ setCOMvel()

void OpenMD::Snapshot::setCOMvel ( const Vector3d comVel)

◆ setCOMw()

void OpenMD::Snapshot::setCOMw ( const Vector3d comw)

◆ setConductiveHeatFlux()

void OpenMD::Snapshot::setConductiveHeatFlux ( const Vector3d chf)

◆ setConservedQuantity()

void OpenMD::Snapshot::setConservedQuantity ( const RealType  cq)

◆ setConvectiveHeatFlux()

void OpenMD::Snapshot::setConvectiveHeatFlux ( const Vector3d chf)

◆ setElectronicKineticEnergy()

void OpenMD::Snapshot::setElectronicKineticEnergy ( const RealType  eke)

◆ setElectronicTemperature()

void OpenMD::Snapshot::setElectronicTemperature ( const RealType  eTemp)

◆ setElectronicThermostat()

◆ setExcludedPotentials()

void OpenMD::Snapshot::setExcludedPotentials ( const potVec  exPot)

◆ setGyrationalVolume()

void OpenMD::Snapshot::setGyrationalVolume ( const RealType  gv)

◆ setHmat()

◆ setHullVolume()

void OpenMD::Snapshot::setHullVolume ( const RealType  hv)

◆ setID()

void OpenMD::Snapshot::setID ( int  id)

Sets the id of this Snapshot

Definition at line 185 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::id.

Referenced by OpenMD::SimSnapshotManager::advance(), OpenMD::BlockSnapshotManager::loadFrame(), and main().

◆ setInertiaTensor()

void OpenMD::Snapshot::setInertiaTensor ( const Mat3x3d inertiaTensor)

◆ setInversionPotential()

void OpenMD::Snapshot::setInversionPotential ( const RealType  ip)

◆ setKineticEnergy()

void OpenMD::Snapshot::setKineticEnergy ( const RealType  ke)

Definition at line 559 of file Snapshot.cpp.

References frameData, hasKineticEnergy, and OpenMD::FrameData::kineticEnergy.

Referenced by OpenMD::Thermo::getKinetic().

◆ setLongRangePotential()

◆ setNetCharge()

void OpenMD::Snapshot::setNetCharge ( const RealType  nChg)

Definition at line 604 of file Snapshot.cpp.

References frameData, hasNetCharge, and OpenMD::FrameData::netCharge.

Referenced by OpenMD::Thermo::getNetCharge().

◆ setOrthoTolerance()

void OpenMD::Snapshot::setOrthoTolerance ( RealType  orthoTolerance)

Definition at line 737 of file Snapshot.cpp.

References orthoTolerance_.

◆ setPressure()

void OpenMD::Snapshot::setPressure ( const RealType  pressure)

Definition at line 622 of file Snapshot.cpp.

References frameData, hasPressure, and OpenMD::FrameData::pressure.

Referenced by OpenMD::Thermo::getPressure().

◆ setPressureTensor()

void OpenMD::Snapshot::setPressureTensor ( const Mat3x3d pressureTensor)

◆ setRawPotential()

void OpenMD::Snapshot::setRawPotential ( const RealType  rp)

◆ setReciprocalPotential()

void OpenMD::Snapshot::setReciprocalPotential ( const RealType  rp)

◆ setRestraintPotential()

void OpenMD::Snapshot::setRestraintPotential ( const RealType  rp)

◆ setRotationalKineticEnergy()

void OpenMD::Snapshot::setRotationalKineticEnergy ( const RealType  rke)

◆ setSelectionPotentials()

void OpenMD::Snapshot::setSelectionPotentials ( const potVec  selPot)

◆ setSelfPotential()

void OpenMD::Snapshot::setSelfPotential ( const RealType  sp)

Definition at line 458 of file Snapshot.cpp.

References frameData, and OpenMD::FrameData::selfPotential.

◆ setStressTensor()

void OpenMD::Snapshot::setStressTensor ( const Mat3x3d stressTensor)

◆ setSurfacePotential()

void OpenMD::Snapshot::setSurfacePotential ( const RealType  sp)

◆ setSystemDipole()

void OpenMD::Snapshot::setSystemDipole ( const Vector3d bd)

◆ setSystemQuadrupole()

void OpenMD::Snapshot::setSystemQuadrupole ( const Mat3x3d bq)

◆ setTemperature()

void OpenMD::Snapshot::setTemperature ( const RealType  temp)

Definition at line 586 of file Snapshot.cpp.

References frameData, hasTemperature, and OpenMD::FrameData::temperature.

Referenced by OpenMD::Thermo::getTemperature().

◆ setThermostat()

◆ setTime()

void OpenMD::Snapshot::setTime ( const RealType  time)

◆ setTorsionPotential()

void OpenMD::Snapshot::setTorsionPotential ( const RealType  tp)

◆ setTotalEnergy()

void OpenMD::Snapshot::setTotalEnergy ( const RealType  te)

Definition at line 568 of file Snapshot.cpp.

References frameData, hasTotalEnergy, and OpenMD::FrameData::totalEnergy.

Referenced by OpenMD::Thermo::getTotalEnergy().

◆ setTranslationalKineticEnergy()

void OpenMD::Snapshot::setTranslationalKineticEnergy ( const RealType  tke)

◆ setVolume()

void OpenMD::Snapshot::setVolume ( const RealType  vol)

◆ wrapVector()

void OpenMD::Snapshot::wrapVector ( Vector3d pos)

Wrapping the vector according to periodic boundary condition

Wrap a vector according to periodic boundary conditions

Definition at line 325 of file Snapshot.cpp.

References frameData, OpenMD::FrameData::hmat, OpenMD::FrameData::invHmat, OpenMD::FrameData::orthoRhombic, OpenMD::roundMe(), and OpenMD::FrameData::usePBC.

Referenced by OpenMD::ForceMatrixDecomposition::buildNeighborList(), OpenMD::GhostBend::calcForce(), OpenMD::GhostTorsion::calcForce(), OpenMD::Bond::calcForce(), OpenMD::Inversion::calcForce(), OpenMD::Torsion::calcForce(), OpenMD::Bend::calcForce(), OpenMD::SCDElem::calcSCD(), OpenMD::Electrostatic::calcSurfaceTerm(), OpenMD::ZconstraintForceManager::checkZConsState(), OpenMD::RNEMD::collectData(), OpenMD::GofRAngle2::collectHistogram(), OpenMD::GofR::collectHistogram(), OpenMD::TwoDGofR::collectHistogram(), OpenMD::GofXyz::collectHistogram(), OpenMD::GofZ::collectHistogram(), OpenMD::Kirkwood::collectHistogram(), OpenMD::GofAngle2::collectHistogram(), OpenMD::GofRZ::collectHistogram(), OpenMD::GofRAngle::collectHistogram(), OpenMD::KirkwoodQuadrupoles::collectHistogram(), OpenMD::SelectionEvaluator::compareProperty(), OpenMD::HBondJump::computeFrame(), OpenMD::RCorrFuncZ::computeProperty1(), OpenMD::Rattle::constraintPairA(), OpenMD::Rattle::constraintPairB(), OpenMD::Shake::constraintPairF(), OpenMD::Shake::constraintPairR(), OpenMD::LegendreCorrFuncZ::correlateFrames(), OpenMD::COHZ::correlateFrames(), OpenMD::GCNSeq::doFrame(), OpenMD::ZconstraintForceManager::doHarmonic(), OpenMD::RNEMD::doNIVS(), OpenMD::RNEMD::doSwap(), OpenMD::RNEMD::doVSS(), OpenMD::GofRTheta::evaluateAngle(), OpenMD::GofROmega::evaluateAngle(), OpenMD::DistanceFinder::find(), OpenMD::ForceMatrixDecomposition::getAtomToGroupVectorColumn(), OpenMD::ForceMatrixDecomposition::getAtomToGroupVectorRow(), OpenMD::SlabStatistics::getBin(), OpenMD::ForceMatrixDecomposition::getInteratomicVector(), OpenMD::ForceMatrixDecomposition::getIntergroupVector(), OpenMD::Electrostatic::getSitePotentials(), OpenMD::Thermo::getSystemDipole(), OpenMD::Thermo::getSystemQuadrupole(), OpenMD::Thermo::getTaggedAtomPairDistance(), OpenMD::Bond::getValue(), OpenMD::GofXyz::initializeHistogram(), OpenMD::LipidTransVisitor::internalVisit(), OpenMD::WrappingVisitor::internalVisit(), OpenMD::ForceManager::longRangeInteractions(), main(), OpenMD::DensityPlot::process(), OpenMD::RippleOP::process(), OpenMD::MultipoleSum::process(), OpenMD::P2OrderParameter::process(), OpenMD::SurfaceDiffusion::process(), OpenMD::BOPofR::process(), OpenMD::RhoZ::process(), OpenMD::BondAngleDistribution::process(), OpenMD::pAngle::process(), OpenMD::HBondGeometric::process(), OpenMD::CoordinationNumber::process(), OpenMD::TetrahedralityHBMatrix::process(), OpenMD::TetrahedralityParamXYZ::process(), OpenMD::TetrahedralityParam::process(), OpenMD::TetrahedralityParamZ::process(), OpenMD::TetrahedralityParamDens::process(), OpenMD::BondOrderParameter::process(), OpenMD::Electrostatic::ReciprocalSpaceSum(), OpenMD::ZconstraintForceManager::update(), and OpenMD::LipidTransVisitor::update().

Member Data Documentation

◆ atomData

◆ cgData

◆ frameData

FrameData OpenMD::Snapshot::frameData

Definition at line 284 of file Snapshot.hpp.

Referenced by clearDerivedProperties(), OpenMD::ForceMatrixDecomposition::collectData(), getBarostat(), getBendPotential(), getBondPotential(), getBoundingBox(), getChargeMomentum(), getCOM(), getCOMvel(), getCOMw(), getConductiveHeatFlux(), getConservedQuantity(), getConvectiveHeatFlux(), getElectronicKineticEnergy(), getElectronicTemperature(), getElectronicThermostat(), getExcludedPotentials(), getGyrationalVolume(), getHmat(), getHullVolume(), getID(), getInertiaTensor(), getInvBoundingBox(), getInversionPotential(), getInvHmat(), getKineticEnergy(), getLongRangePotential(), getLongRangePotentials(), getNetCharge(), getPotentialEnergy(), getPressure(), getPressureTensor(), getRawPotential(), getReciprocalPotential(), getRestraintPotential(), getRotationalKineticEnergy(), getSelectionPotentials(), getSelfPotential(), getShortRangePotential(), getStressTensor(), getSurfacePotential(), getSystemDipole(), getSystemQuadrupole(), getTemperature(), getThermostat(), getTime(), getTorsionPotential(), getTotalEnergy(), getTranslationalKineticEnergy(), getVolume(), getXYarea(), scaleVector(), setBarostat(), setBendPotential(), setBondPotential(), setBoundingBox(), setChargeMomentum(), setCOM(), setCOMvel(), setCOMw(), setConductiveHeatFlux(), setConservedQuantity(), setConvectiveHeatFlux(), setElectronicKineticEnergy(), setElectronicTemperature(), setElectronicThermostat(), setExcludedPotentials(), setGyrationalVolume(), setHmat(), setHullVolume(), setID(), setInertiaTensor(), setInversionPotential(), setKineticEnergy(), setLongRangePotential(), setNetCharge(), setPressure(), setPressureTensor(), setRawPotential(), setReciprocalPotential(), setRestraintPotential(), setRotationalKineticEnergy(), setSelectionPotentials(), setSelfPotential(), setStressTensor(), setSurfacePotential(), setSystemDipole(), setSystemQuadrupole(), setTemperature(), setThermostat(), setTime(), setTorsionPotential(), setTotalEnergy(), setTranslationalKineticEnergy(), setVolume(), Snapshot(), and wrapVector().

◆ hasBoundingBox

bool OpenMD::Snapshot::hasBoundingBox

◆ hasChargeMomentum

bool OpenMD::Snapshot::hasChargeMomentum

◆ hasCOM

bool OpenMD::Snapshot::hasCOM

◆ hasCOMvel

bool OpenMD::Snapshot::hasCOMvel

◆ hasCOMw

bool OpenMD::Snapshot::hasCOMw

◆ hasConservedQuantity

bool OpenMD::Snapshot::hasConservedQuantity

Definition at line 311 of file Snapshot.hpp.

Referenced by clearDerivedProperties(), and setConservedQuantity().

◆ hasConvectiveHeatFlux

bool OpenMD::Snapshot::hasConvectiveHeatFlux

Definition at line 307 of file Snapshot.hpp.

Referenced by clearDerivedProperties(), and setConvectiveHeatFlux().

◆ hasElectronicKineticEnergy

bool OpenMD::Snapshot::hasElectronicKineticEnergy

◆ hasElectronicTemperature

bool OpenMD::Snapshot::hasElectronicTemperature

◆ hasGyrationalVolume

bool OpenMD::Snapshot::hasGyrationalVolume

◆ hasHullVolume

bool OpenMD::Snapshot::hasHullVolume

◆ hasInertiaTensor

bool OpenMD::Snapshot::hasInertiaTensor

◆ hasKineticEnergy

bool OpenMD::Snapshot::hasKineticEnergy

◆ hasLongRangePotential

bool OpenMD::Snapshot::hasLongRangePotential

Definition at line 292 of file Snapshot.hpp.

Referenced by clearDerivedProperties(), and getLongRangePotential().

◆ hasNetCharge

bool OpenMD::Snapshot::hasNetCharge

◆ hasPotentialEnergy

bool OpenMD::Snapshot::hasPotentialEnergy

Definition at line 293 of file Snapshot.hpp.

Referenced by clearDerivedProperties(), and getPotentialEnergy().

◆ hasPressure

bool OpenMD::Snapshot::hasPressure

Definition at line 296 of file Snapshot.hpp.

Referenced by clearDerivedProperties(), OpenMD::Thermo::getPressure(), and setPressure().

◆ hasPressureTensor

bool OpenMD::Snapshot::hasPressureTensor

◆ hasRotationalKineticEnergy

bool OpenMD::Snapshot::hasRotationalKineticEnergy

◆ hasShortRangePotential

bool OpenMD::Snapshot::hasShortRangePotential

Definition at line 291 of file Snapshot.hpp.

Referenced by clearDerivedProperties(), and getShortRangePotential().

◆ hasSystemDipole

bool OpenMD::Snapshot::hasSystemDipole

◆ hasSystemQuadrupole

bool OpenMD::Snapshot::hasSystemQuadrupole

◆ hasTemperature

bool OpenMD::Snapshot::hasTemperature

◆ hasTotalEnergy

bool OpenMD::Snapshot::hasTotalEnergy

◆ hasTranslationalKineticEnergy

bool OpenMD::Snapshot::hasTranslationalKineticEnergy

◆ hasVolume

bool OpenMD::Snapshot::hasVolume

Definition at line 295 of file Snapshot.hpp.

Referenced by clearDerivedProperties(), getVolume(), setHmat(), and setVolume().

◆ hasXYarea

bool OpenMD::Snapshot::hasXYarea

Definition at line 294 of file Snapshot.hpp.

Referenced by clearDerivedProperties(), and getXYarea().

◆ orthoTolerance_

RealType OpenMD::Snapshot::orthoTolerance_
private

Definition at line 315 of file Snapshot.hpp.

Referenced by setHmat(), and setOrthoTolerance().

◆ rigidbodyData

DataStorage OpenMD::Snapshot::rigidbodyData

Definition at line 282 of file Snapshot.hpp.

Referenced by getNumberOfRigidBodies(), and getSize().


The documentation for this class was generated from the following files: