NAMD
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#include <NamdTypes.h>
Public Attributes | |
Position | position |
Charge | charge |
short | vdwType |
unsigned char | partition |
unsigned int | nonbondedGroupSize: 3 |
unsigned int | hydrogenGroupSize: 4 |
unsigned int | isWater: 1 |
Definition at line 52 of file NamdTypes.h.
Charge CompAtom::charge |
Definition at line 54 of file NamdTypes.h.
Referenced by ComputeNonbondedUtil::calcGBIS(), ExclElem::computeForce(), WorkDistrib::createAtomLists(), ComputeEField::doForce(), ComputeMsmSerial::doWork(), ComputeFmmSerial::doWork(), ComputeFullDirect::doWork(), ComputeExt::doWork(), ComputeMsm::doWork(), ComputeGBISser::doWork(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), dumpbench(), HomePatch::positionsReady(), ComputeQM::processFullQM(), HomePatch::qmSwapAtoms(), Sequencer::reloadCharges(), and Sequencer::rescaleSoluteCharges().
unsigned int CompAtom::hydrogenGroupSize |
Definition at line 58 of file NamdTypes.h.
Referenced by Sequencer::berendsenPressure(), WorkDistrib::createAtomLists(), ComputeLCPO::doForce(), dumpbench(), ParallelIOMgr::integrateMigratedAtoms(), Sequencer::langevinPiston(), Sequencer::minimizeMoveDownhill(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Sequencer::newMinimizeDirection(), Sequencer::scalePositionsVelocities(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().
unsigned int CompAtom::isWater |
Definition at line 59 of file NamdTypes.h.
unsigned int CompAtom::nonbondedGroupSize |
Definition at line 57 of file NamdTypes.h.
Referenced by ComputeNonbondedUtil::calcGBIS(), WorkDistrib::createAtomLists(), dumpbench(), and pairlistFromAll().
unsigned char CompAtom::partition |
Definition at line 56 of file NamdTypes.h.
Referenced by AngleElem::computeForce(), CrosstermElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), GromacsPairElem::computeForce(), WorkDistrib::createAtomLists(), ComputePme::doWork(), ComputeEwald::doWork(), dumpbench(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().
Position CompAtom::position |
Definition at line 53 of file NamdTypes.h.
Referenced by Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), average(), Sequencer::berendsenPressure(), ParallelIOMgr::calcAtomsInEachPatch(), ComputeNonbondedUtil::calcGBIS(), AngleElem::computeForce(), CrosstermElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), WorkDistrib::createAtomLists(), ComputeGridForce::do_calc(), ComputeConsTorque::doForce(), ComputeSphericalBC::doForce(), ComputeCylindricalBC::doForce(), ComputeLCPO::doForce(), HomePatch::doPairlistCheck(), ComputeExt::doWork(), ComputeFmmSerial::doWork(), ComputeMsmSerial::doWork(), ComputeFullDirect::doWork(), ComputeMsm::doWork(), ComputeGBISser::doWork(), ComputePme::doWork(), ComputeNonbondedCUDA::doWork(), ComputeEwald::doWork(), dumpbench(), ComputeNonbondedCUDA::finishWork(), Sequencer::langevinPiston(), Sequencer::minimizeMoveDownhill(), mollify(), PatchMgr::moveAllBy(), PatchMgr::moveAtom(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Sequencer::newMinimizePosition(), sortop_x::operator()(), sortop_y::operator()(), sortop_z::operator()(), pairlist_from_pairlist(), pairlistFromAll(), partition(), Patch::positionsReady(), HomePatch::positionsReady(), Sequencer::rattle1(), ComputeGlobal::recvResults(), Sequencer::scalePositionsVelocities(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().
short CompAtom::vdwType |
Definition at line 55 of file NamdTypes.h.
Referenced by ExclElem::computeForce(), WorkDistrib::createAtomLists(), ComputeGBISser::doWork(), ComputeNonbondedCUDA::doWork(), ComputeQM::doWork(), Patch::positionsReady(), ComputeQM::processFullQM(), and HomePatch::qmSwapAtoms().