FullAtom Struct Reference

#include <NamdTypes.h>

Inheritance diagram for FullAtom:

List of all members.

Public Attributes
Velocity	velocity
Position	fixedPosition
double	recipMass
Mass	mass
union {
Real   langevinParam
};
int32	status
Transform	transform
int	migrationGroupSize
Real	rigidBondLength

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Detailed Description

Definition at line 100 of file NamdTypes.h.

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Member Data Documentation

union { ... }

Position FullAtom::fixedPosition

Definition at line 102 of file NamdTypes.h.

Referenced by Sequencer::calcFixVirial(), WorkDistrib::createAtomLists(), ComputeRestraints::doForce(), PatchMgr::moveAllBy(), and PatchMgr::moveAtom().

Real FullAtom::langevinParam

Definition at line 110 of file NamdTypes.h.

Referenced by WorkDistrib::createAtomLists(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), and Sequencer::langevinVelocitiesBBK2().

Mass FullAtom::mass

Definition at line 108 of file NamdTypes.h.

Referenced by Sequencer::berendsenPressure(), Sequencer::calcKineticEnergy(), WorkDistrib::createAtomLists(), Sequencer::langevinPiston(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), ComputeQM::processFullQM(), Sequencer::reassignVelocities(), ComputeGlobal::recvResults(), Sequencer::reinitVelocities(), Sequencer::scalePositionsVelocities(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), Sequencer::submitMomentum(), and Sequencer::submitReductions().

int FullAtom::migrationGroupSize

Definition at line 117 of file NamdTypes.h.

Referenced by WorkDistrib::createAtomLists(), HomePatch::depositMigration(), HomePatch::doAtomMigration(), and sortAtomsForPatches().

double FullAtom::recipMass

The reciprocal mass is set to 1/mass or to 0 for massless particles. Calculating this apriori allows us to remove the divide instruction from the integration loops and the Langevin velocity updates.

Definition at line 104 of file NamdTypes.h.

Referenced by WorkDistrib::createAtomLists().

Real FullAtom::rigidBondLength

Definition at line 118 of file NamdTypes.h.

Referenced by WorkDistrib::createAtomLists(), and ParallelIOMgr::integrateMigratedAtoms().

int32 FullAtom::status

Definition at line 115 of file NamdTypes.h.

Referenced by WorkDistrib::createAtomLists().

Transform FullAtom::transform

Definition at line 116 of file NamdTypes.h.

Referenced by WorkDistrib::createAtomLists(), HomePatch::depositMigration(), ComputeGridForce::do_calc(), PatchMgr::moveAllBy(), PatchMgr::moveAtom(), and ComputeGlobal::recvResults().

Velocity FullAtom::velocity

Definition at line 101 of file NamdTypes.h.

Referenced by Sequencer::calcKineticEnergy(), WorkDistrib::createAtomLists(), Sequencer::langevinPiston(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), Sequencer::langevinVelocitiesBBK2(), Sequencer::maximumMove(), Sequencer::minimizationQuenchVelocity(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Sequencer::newMinimizeDirection(), Sequencer::newMinimizePosition(), Sequencer::quenchVelocities(), Sequencer::rattle1(), Sequencer::reassignVelocities(), Sequencer::reinitVelocities(), Sequencer::rescaleVelocities(), Sequencer::rescaleVelocitiesByFactor(), Sequencer::scalePositionsVelocities(), Sequencer::scaleVelocities(), Sequencer::stochRescaleVelocities(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), Sequencer::submitMomentum(), Sequencer::submitReductions(), and Sequencer::tcoupleVelocities().

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

• NamdTypes.h