#include <NamdTypes.h>
Public Attributes | |
| Position | position |
| Charge | charge |
| int16 | vdwType |
| uint8 | partition |
| uint8 | nonbondedGroupSize: 3 |
| uint8 | hydrogenGroupSize: 4 |
| uint8 | isWater: 1 |
Detailed Description
Definition at line 76 of file NamdTypes.h.
Member Data Documentation
◆ charge
| Charge CompAtom::charge |
Definition at line 78 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(), ComputeEwald::doWork(), dumpbench(), HomePatch::positionsReady(), ComputeQM::processFullQM(), HomePatch::qmSwapAtoms(), Sequencer::reloadCharges(), and Sequencer::rescaleSoluteCharges().
◆ hydrogenGroupSize
| uint8 CompAtom::hydrogenGroupSize |
Definition at line 88 of file NamdTypes.h.
Referenced by Sequencer::berendsenPressure(), WorkDistrib::createAtomLists(), HomePatch::depositMigration(), HomePatch::doAtomMigration(), ComputeLCPO::doForce(), HomePatch::doGroupSizeCheck(), dumpbench(), ParallelIOMgr::integrateMigratedAtoms(), Sequencer::langevinPiston(), Sequencer::minimizeMoveDownhill(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Sequencer::newMinimizeDirection(), Sequencer::scalePositionsVelocities(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().
◆ isWater
| uint8 CompAtom::isWater |
Definition at line 89 of file NamdTypes.h.
Referenced by WorkDistrib::createAtomLists().
◆ nonbondedGroupSize
| uint8 CompAtom::nonbondedGroupSize |
ngs is number of atoms, starting with parent, that are all within 0.5*hgroupCutoff. Value is reset before each force calculation. XXX Looks like ngs is unused for CUDA and KNL kernels. XXX Limited to 5. Why?
Definition at line 81 of file NamdTypes.h.
Referenced by ComputeNonbondedUtil::calcGBIS(), WorkDistrib::createAtomLists(), HomePatch::doGroupSizeCheck(), dumpbench(), and pairlistFromAll().
◆ partition
| uint8 CompAtom::partition |
Definition at line 80 of file NamdTypes.h.
Referenced by AngleElem::computeForce(), CrosstermElem::computeForce(), ImproperElem::computeForce(), DihedralElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), WorkDistrib::createAtomLists(), ComputePme::doWork(), ComputeEwald::doWork(), dumpbench(), Sequencer::submitHalfstep(), and Sequencer::submitReductions().
◆ position
| Position CompAtom::position |
Definition at line 77 of file NamdTypes.h.
Referenced by Sequencer::addMovDragToPosition(), Sequencer::addRotDragToPosition(), average(), Sequencer::berendsenPressure(), ParallelIOMgr::calcAtomsInEachPatch(), ComputeNonbondedUtil::calcGBIS(), AngleElem::computeForce(), ImproperElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), WorkDistrib::createAtomLists(), HomePatch::depositMigration(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeConsTorque::doForce(), ComputeSphericalBC::doForce(), ComputeCylindricalBC::doForce(), ComputeLCPO::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), HomePatch::doPairlistCheck(), ComputeExt::doWork(), ComputeLjPmeSerial::doWork(), ComputeFmmSerial::doWork(), ComputeMsmSerial::doWork(), ComputeFullDirect::doWork(), ComputeMsm::doWork(), ComputeGBISser::doWork(), ComputePme::doWork(), ComputeEwald::doWork(), dumpbench(), Sequencer::langevinPiston(), Sequencer::minimizeMoveDownhill(), mollify(), PatchMgr::moveAllBy(), PatchMgr::moveAtom(), Sequencer::multigratorPressure(), Sequencer::multigratorTemperature(), Sequencer::newMinimizePosition(), sortop_x::operator()(), sortop_y::operator()(), sortop_z::operator()(), pairlistFromAll(), partition(), Patch::positionsReady(), HomePatch::positionsReady(), Sequencer::rattle1(), ComputeGlobal::recvResults(), Sequencer::scalePositionsVelocities(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), and Sequencer::submitReductions().
◆ vdwType
| int16 CompAtom::vdwType |
Definition at line 79 of file NamdTypes.h.
Referenced by ExclElem::computeForce(), WorkDistrib::createAtomLists(), ComputeLjPmeSerial::doWork(), ComputeGBISser::doWork(), ComputeQM::doWork(), Patch::positionsReady(), ComputeQM::processFullQM(), and HomePatch::qmSwapAtoms().
The documentation for this struct was generated from the following file:
