OpenMD  2.5
Molecular Dynamics in the Open
OpenMD::FrameData Struct Reference

#include <Snapshot.hpp>

Public Attributes

int id
 
RealType currentTime
 
Mat3x3d hmat
 
Mat3x3d invHmat
 
Mat3x3d bBox
 
Mat3x3d invBbox
 
bool usePBC
 
bool orthoRhombic
 
RealType totalEnergy
 
RealType translationalKinetic
 
RealType rotationalKinetic
 
RealType electronicKinetic
 
RealType kineticEnergy
 
RealType potentialEnergy
 
RealType shortRangePotential
 
RealType longRangePotential
 
RealType reciprocalPotential
 
RealType surfacePotential
 
RealType bondPotential
 
RealType bendPotential
 
RealType torsionPotential
 
RealType inversionPotential
 
potVec lrPotentials
 
RealType selfPotential
 
potVec excludedPotentials
 
RealType restraintPotential
 
RealType rawPotential
 
potVec selectionPotentials
 
RealType xyArea
 
RealType volume
 
RealType pressure
 
RealType temperature
 
pair< RealType, RealType > thermostat
 
RealType electronicTemperature
 
RealType netCharge
 
RealType chargeMomentum
 
pair< RealType, RealType > electronicThermostat
 
Mat3x3d barostat
 
Vector3d COM
 
Vector3d COMvel
 
Vector3d COMw
 
Mat3x3d inertiaTensor
 
RealType gyrationalVolume
 
RealType hullVolume
 
Mat3x3d stressTensor
 
Mat3x3d pressureTensor
 
Vector3d systemDipole
 
Mat3x3d systemQuadrupole
 
Vector3d conductiveHeatFlux
 
Vector3d convectiveHeatFlux
 
RealType conservedQuantity
 

Detailed Description

FrameData is a structure for holding system-wide dynamic data about the simulation.

Definition at line 60 of file Snapshot.hpp.

Member Data Documentation

◆ barostat

Mat3x3d OpenMD::FrameData::barostat

barostat matrix

Definition at line 98 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getBarostat(), OpenMD::Snapshot::setBarostat(), and OpenMD::Snapshot::Snapshot().

◆ bBox

Mat3x3d OpenMD::FrameData::bBox

axes of a bounding box in matrix form

Definition at line 65 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getBoundingBox(), OpenMD::Snapshot::setBoundingBox(), and OpenMD::Snapshot::Snapshot().

◆ bendPotential

RealType OpenMD::FrameData::bendPotential

◆ bondPotential

RealType OpenMD::FrameData::bondPotential

◆ chargeMomentum

RealType OpenMD::FrameData::chargeMomentum

total charge momentum in the system

Definition at line 96 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::clearDerivedProperties(), OpenMD::Snapshot::getChargeMomentum(), and OpenMD::Snapshot::setChargeMomentum().

◆ COM

Vector3d OpenMD::FrameData::COM

location of system center of mass

Definition at line 99 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::clearDerivedProperties(), OpenMD::Snapshot::getCOM(), and OpenMD::Snapshot::setCOM().

◆ COMvel

Vector3d OpenMD::FrameData::COMvel

system center of mass velocity

Definition at line 100 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::clearDerivedProperties(), OpenMD::Snapshot::getCOMvel(), and OpenMD::Snapshot::setCOMvel().

◆ COMw

Vector3d OpenMD::FrameData::COMw

system center of mass angular velocity

Definition at line 101 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::clearDerivedProperties(), OpenMD::Snapshot::getCOMw(), and OpenMD::Snapshot::setCOMw().

◆ conductiveHeatFlux

Vector3d OpenMD::FrameData::conductiveHeatFlux

◆ conservedQuantity

RealType OpenMD::FrameData::conservedQuantity

anything conserved by the integrator

Definition at line 111 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getConservedQuantity(), and OpenMD::Snapshot::setConservedQuantity().

◆ convectiveHeatFlux

Vector3d OpenMD::FrameData::convectiveHeatFlux

◆ currentTime

RealType OpenMD::FrameData::currentTime

current time

Definition at line 62 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getTime(), OpenMD::Snapshot::setTime(), and OpenMD::Snapshot::Snapshot().

◆ electronicKinetic

RealType OpenMD::FrameData::electronicKinetic

◆ electronicTemperature

RealType OpenMD::FrameData::electronicTemperature

temperature of the electronic degrees of freedom

Definition at line 94 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::clearDerivedProperties(), OpenMD::Snapshot::getElectronicTemperature(), and OpenMD::Snapshot::setElectronicTemperature().

◆ electronicThermostat

pair<RealType, RealType> OpenMD::FrameData::electronicThermostat

thermostat variables for electronic degrees of freedom

Definition at line 97 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getElectronicThermostat(), OpenMD::Snapshot::setElectronicThermostat(), and OpenMD::Snapshot::Snapshot().

◆ excludedPotentials

potVec OpenMD::FrameData::excludedPotentials

breakdown of excluded potentials by family

Definition at line 85 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getExcludedPotentials(), OpenMD::Snapshot::setExcludedPotentials(), and OpenMD::Snapshot::Snapshot().

◆ gyrationalVolume

RealType OpenMD::FrameData::gyrationalVolume

gyrational volume for entire system

Definition at line 103 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getGyrationalVolume(), and OpenMD::Snapshot::setGyrationalVolume().

◆ hmat

◆ hullVolume

RealType OpenMD::FrameData::hullVolume

hull volume for entire system

Definition at line 104 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getHullVolume(), and OpenMD::Snapshot::setHullVolume().

◆ id

int OpenMD::FrameData::id

identification number of the snapshot

Definition at line 61 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getID(), OpenMD::Snapshot::setID(), and OpenMD::Snapshot::Snapshot().

◆ inertiaTensor

Mat3x3d OpenMD::FrameData::inertiaTensor

inertia tensor for entire system

Definition at line 102 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getInertiaTensor(), and OpenMD::Snapshot::setInertiaTensor().

◆ invBbox

Mat3x3d OpenMD::FrameData::invBbox

the inverse of the bounding box

Definition at line 66 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getInvBoundingBox(), OpenMD::Snapshot::setBoundingBox(), and OpenMD::Snapshot::Snapshot().

◆ inversionPotential

RealType OpenMD::FrameData::inversionPotential

◆ invHmat

Mat3x3d OpenMD::FrameData::invHmat

◆ kineticEnergy

RealType OpenMD::FrameData::kineticEnergy

◆ longRangePotential

RealType OpenMD::FrameData::longRangePotential

long-range contributions to the potential

Definition at line 76 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::clearDerivedProperties(), and OpenMD::Snapshot::getLongRangePotential().

◆ lrPotentials

potVec OpenMD::FrameData::lrPotentials

◆ netCharge

RealType OpenMD::FrameData::netCharge

total net charge in the system

Definition at line 95 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::clearDerivedProperties(), OpenMD::Snapshot::getNetCharge(), and OpenMD::Snapshot::setNetCharge().

◆ orthoRhombic

bool OpenMD::FrameData::orthoRhombic

is this an orthorhombic periodic box?

Definition at line 68 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::scaleVector(), OpenMD::Snapshot::setHmat(), OpenMD::Snapshot::Snapshot(), and OpenMD::Snapshot::wrapVector().

◆ potentialEnergy

RealType OpenMD::FrameData::potentialEnergy

potential energy of this frame

Definition at line 74 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::clearDerivedProperties(), and OpenMD::Snapshot::getPotentialEnergy().

◆ pressure

RealType OpenMD::FrameData::pressure

◆ pressureTensor

Mat3x3d OpenMD::FrameData::pressureTensor

◆ rawPotential

RealType OpenMD::FrameData::rawPotential

unrestrained potential energy (when restraints are applied)

Definition at line 87 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getRawPotential(), OpenMD::Snapshot::setRawPotential(), and OpenMD::Snapshot::Snapshot().

◆ reciprocalPotential

RealType OpenMD::FrameData::reciprocalPotential

◆ restraintPotential

RealType OpenMD::FrameData::restraintPotential

potential energy of restraints

Definition at line 86 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getRestraintPotential(), OpenMD::Snapshot::setRestraintPotential(), and OpenMD::Snapshot::Snapshot().

◆ rotationalKinetic

RealType OpenMD::FrameData::rotationalKinetic

◆ selectionPotentials

potVec OpenMD::FrameData::selectionPotentials

potential of selected stuntDoubles

Definition at line 88 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getSelectionPotentials(), and OpenMD::Snapshot::setSelectionPotentials().

◆ selfPotential

RealType OpenMD::FrameData::selfPotential

potential energy of self interactions

Definition at line 84 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getSelfPotential(), OpenMD::Snapshot::setSelfPotential(), and OpenMD::Snapshot::Snapshot().

◆ shortRangePotential

RealType OpenMD::FrameData::shortRangePotential

short-range contributions to the potential

Definition at line 75 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::clearDerivedProperties(), and OpenMD::Snapshot::getShortRangePotential().

◆ stressTensor

Mat3x3d OpenMD::FrameData::stressTensor

◆ surfacePotential

RealType OpenMD::FrameData::surfacePotential

◆ systemDipole

Vector3d OpenMD::FrameData::systemDipole

◆ systemQuadrupole

Mat3x3d OpenMD::FrameData::systemQuadrupole

◆ temperature

RealType OpenMD::FrameData::temperature

◆ thermostat

pair<RealType, RealType> OpenMD::FrameData::thermostat

thermostat variables

Definition at line 93 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getThermostat(), OpenMD::Snapshot::setThermostat(), and OpenMD::Snapshot::Snapshot().

◆ torsionPotential

RealType OpenMD::FrameData::torsionPotential

dihedral (torsion angle) contribution to the potential

Definition at line 81 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getShortRangePotential(), OpenMD::Snapshot::getTorsionPotential(), OpenMD::Snapshot::setTorsionPotential(), and OpenMD::Snapshot::Snapshot().

◆ totalEnergy

RealType OpenMD::FrameData::totalEnergy

◆ translationalKinetic

RealType OpenMD::FrameData::translationalKinetic

◆ usePBC

bool OpenMD::FrameData::usePBC

are we using a periodic box?

Definition at line 67 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::Snapshot(), and OpenMD::Snapshot::wrapVector().

◆ volume

RealType OpenMD::FrameData::volume

total volume of this frame

Definition at line 90 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getVolume(), OpenMD::Snapshot::setVolume(), and OpenMD::Snapshot::Snapshot().

◆ xyArea

RealType OpenMD::FrameData::xyArea

XY area of this frame

Definition at line 89 of file Snapshot.hpp.

Referenced by OpenMD::Snapshot::getXYarea(), and OpenMD::Snapshot::Snapshot().


The documentation for this struct was generated from the following file: