FullAtom Struct Reference

#include <NamdTypes.h>

Inheritance diagram for FullAtom:

Public Attributes
Velocity	velocity
Position	fixedPosition
double	recipMass
Mass	mass
union {
Real   langevinParam
};
union {
PerAtomFlags   flags
int32   status
	Atom status bit fields defined in structures.h. More...
};
Transform	transform
int32	migrationGroupSize
Real	rigidBondLength
Public Attributes inherited from CompAtom
Position	position
Charge	charge
int16	vdwType
uint8	partition
uint8	nonbondedGroupSize: 3
uint8	hydrogenGroupSize: 4
uint8	isWater: 1
Public Attributes inherited from CompAtomExt
DispCoef	dispcoef
int32	sortOrder
uint32	id: 30
uint32	atomFixed: 1
uint32	groupFixed: 1

Detailed Description

Definition at line 210 of file NamdTypes.h.

Member Data Documentation

@71

union { ... }

@73

union { ... }

fixedPosition

Position FullAtom::fixedPosition

Definition at line 212 of file NamdTypes.h.

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

flags

PerAtomFlags FullAtom::flags

Definition at line 226 of file NamdTypes.h.

langevinParam

Real FullAtom::langevinParam

Definition at line 220 of file NamdTypes.h.

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

mass

Mass FullAtom::mass

Definition at line 218 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().

migrationGroupSize

int32 FullAtom::migrationGroupSize

Definition at line 230 of file NamdTypes.h.

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

recipMass

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 213 of file NamdTypes.h.

Referenced by WorkDistrib::createAtomLists().

rigidBondLength

Real FullAtom::rigidBondLength

Definition at line 231 of file NamdTypes.h.

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

status

int32 FullAtom::status

Atom status bit fields defined in structures.h.

Definition at line 227 of file NamdTypes.h.

Referenced by WorkDistrib::createAtomLists().

transform

Transform FullAtom::transform

Definition at line 229 of file NamdTypes.h.

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

velocity

Velocity FullAtom::velocity

Definition at line 211 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(), print_vel_AOS(), 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().

---

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

• NamdTypes.h