NAMD
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#include <NamdTypes.h>
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 |
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Position | position |
Charge | charge |
int16 | vdwType |
uint8 | partition |
uint8 | nonbondedGroupSize: 3 |
uint8 | hydrogenGroupSize: 4 |
uint8 | isWater: 1 |
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int32 | sortOrder |
uint32 | id: 30 |
uint32 | atomFixed: 1 |
uint32 | groupFixed: 1 |
Definition at line 200 of file NamdTypes.h.
union { ... } |
union { ... } |
Position FullAtom::fixedPosition |
Definition at line 202 of file NamdTypes.h.
Referenced by Sequencer::calcFixVirial(), WorkDistrib::createAtomLists(), ComputeRestraints::doForce(), PatchMgr::moveAllBy(), and PatchMgr::moveAtom().
PerAtomFlags FullAtom::flags |
Definition at line 216 of file NamdTypes.h.
Real FullAtom::langevinParam |
Definition at line 210 of file NamdTypes.h.
Referenced by WorkDistrib::createAtomLists(), Sequencer::langevinVelocities(), Sequencer::langevinVelocitiesBBK1(), and Sequencer::langevinVelocitiesBBK2().
Mass FullAtom::mass |
Definition at line 208 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().
int32 FullAtom::migrationGroupSize |
Definition at line 220 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 203 of file NamdTypes.h.
Referenced by WorkDistrib::createAtomLists().
Real FullAtom::rigidBondLength |
Definition at line 221 of file NamdTypes.h.
Referenced by WorkDistrib::createAtomLists(), and ParallelIOMgr::integrateMigratedAtoms().
int32 FullAtom::status |
Atom status bit fields defined in structures.h.
Definition at line 217 of file NamdTypes.h.
Referenced by WorkDistrib::createAtomLists().
Transform FullAtom::transform |
Definition at line 219 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 201 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().