#include <NamdTypes.h>
Public Attributes | |
| Velocity | velocity |
| Position | fixedPosition |
| double | recipMass |
| Mass | mass |
| union { | |
| Real langevinParam | |
| }; | |
| int32 | status |
| Transform | transform |
| int | migrationGroupSize |
| Real | rigidBondLength |
 Public Attributes inherited from CompAtom | |
| Position | position |
| Charge | charge |
| short | vdwType |
| unsigned char | partition |
| unsigned int | nonbondedGroupSize: 3 |
| unsigned int | hydrogenGroupSize: 4 |
| unsigned int | isWater: 1 |
| Public Attributes inherited from CompAtomExt | |
| int | sortOrder |
| int | id: 30 |
| unsigned int | atomFixed: 1 |
| unsigned int | groupFixed: 1 |
Detailed Description
Definition at line 100 of file NamdTypes.h.
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(), 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 103 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(), 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().
The documentation for this struct was generated from the following file:
