NAMD
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#include <Vector.h>
Public Member Functions | |
NAMD_HOST_DEVICE | Vector (void) |
NAMD_HOST_DEVICE | Vector (BigReal newx, BigReal newy, BigReal newz) |
NAMD_HOST_DEVICE | Vector (BigReal newv) |
NAMD_HOST_DEVICE | Vector (const FloatVector &v) |
NAMD_HOST_DEVICE | Vector (double3 vec) |
NAMD_HOST_DEVICE | operator double3 () const |
NAMD_HOST_DEVICE BigReal & | operator[] (int i) |
NAMD_HOST_DEVICE Vector & | operator= (const BigReal &v2) |
NAMD_HOST_DEVICE void | operator+= (const Vector &v2) |
NAMD_HOST_DEVICE void | operator-= (const Vector &v2) |
NAMD_HOST_DEVICE void | operator*= (const BigReal &v2) |
NAMD_HOST_DEVICE void | operator/= (const BigReal &v2) |
NAMD_HOST_DEVICE BigReal | length (void) const |
NAMD_HOST_DEVICE BigReal | length2 (void) const |
NAMD_HOST_DEVICE BigReal | rlength (void) const |
NAMD_HOST_DEVICE Vector | unit (void) const |
NAMD_HOST_DEVICE void | cross (const Vector &v2) |
NAMD_HOST_DEVICE BigReal | dot (const Vector &v2) const |
Bool | set (const char *s) |
Public Attributes | |
BigReal | x |
BigReal | y |
BigReal | z |
Friends | |
NAMD_HOST_DEVICE friend int | operator== (const Vector &v1, const Vector &v2) |
NAMD_HOST_DEVICE friend int | operator!= (const Vector &v1, const Vector &v2) |
NAMD_HOST_DEVICE friend Vector | operator+ (const Vector &v1, const Vector &v2) |
NAMD_HOST_DEVICE friend Vector | operator- (const Vector &v1) |
NAMD_HOST_DEVICE friend Vector | operator- (const Vector &v1, const Vector &v2) |
NAMD_HOST_DEVICE friend BigReal | operator* (const Vector &v1, const Vector &v2) |
NAMD_HOST_DEVICE friend Vector | operator* (const BigReal &f, const Vector &v1) |
NAMD_HOST_DEVICE friend Vector | operator* (const Vector &v1, const BigReal &f) |
NAMD_HOST_DEVICE friend Vector | operator/ (const Vector &v1, const BigReal &f) |
NAMD_HOST_DEVICE friend Vector | cross (const Vector &v1, const Vector &v2) |
NAMD_HOST_DEVICE friend Vector | cross (const Real &k, const Vector &v1, const Vector &v2) |
NAMD_HOST_DEVICE friend Vector | cross (const BigReal &k, const Vector &v1, const Vector &v2) |
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Definition at line 202 of file Vector.h.
Referenced by Sequencer::addRotDragToPosition(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), ComputeQMMgr::calcUSR(), PmeKSpace::compute_energy(), AngleElem::computeForce(), CrosstermElem::computeForce(), ImproperElem::computeForce(), BondElem::computeForce(), ComputeConsTorque::doForce(), ComputeStir::doForce(), ComputeNonbondedPair::doForce(), ComputeRestraints::doForce(), ComputeMsmMgr::initialize(), lattice_to_unitcell(), Sequencer::maximumMove(), GroupRestraintParam::PrintSummary(), proc_anglegrad(), proc_dihedralgrad(), proc_getangle(), proc_getdihedral(), ComputeQM::processFullQM(), Lattice::set(), unit(), and vec_rotation_matrix().
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Definition at line 206 of file Vector.h.
Referenced by Sequencer::calcKineticEnergy(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcUSR(), GroupRestraintParam::CheckParam(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), LjPmeCompute::computeNonbonded(), Controller::correctMomentum(), HomePatch::doPairlistCheck(), Sequencer::maximumMove(), Sequencer::minimizeMoveDownhill(), Sequencer::multigratorPressure(), Sequencer::newMinimizeDirection(), Lattice::set(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), Sequencer::submitReductions(), and Lattice::wrap_nearest_delta().
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Definition at line 210 of file Vector.h.
References namd_rsqrt, x, y, and z.
Referenced by AngleElem::computeForce(), DihedralElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), and rescale_nonperiodic_cell().
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Definition at line 261 of file Vector.h.
References FALSE, TRUE, x, y, and z.
Referenced by colvarproxy_namd::calculate(), ParseOptions::get(), GroupRestraintParam::SetGroup1RefPosition(), and GroupRestraintParam::SetResCenter().
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Definition at line 215 of file Vector.h.
References length(), Vector(), x, y, and z.
Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcUSR(), CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), PmeKSpace::compute_energy(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), ComputeMsmMgr::initialize(), ComputePmeMgr::initialize(), ComputePmeMgr::initialize_pencils(), Sequencer::minimizeMoveDownhill(), ComputeQMMgr::recvPntChrg(), settle1(), settlev(), PatchMap::sizeGrid(), and Sequencer::submitMinimizeReductions().
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BigReal Vector::x |
Definition at line 74 of file Vector.h.
Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), Sequencer::berendsenPressure_SOA(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), Controller::calcPressure(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), CudaPmeOneDevice::checkPatchLevelLatticeCompatibilityAndComputeOffsets(), CudaPmeOneDevice::compute(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), LjPmeKSpace::compute_energy(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), LjPmeCompute::computeNonbonded(), Controller::Controller(), Controller::correctMomentum(), cross(), Lattice::delta_from_diff(), ProxyPatch::depositCombinedResultMsg(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeSphericalBC::doForce(), ComputeGridForce::doForce(), ComputeCylindricalBC::doForce(), ComputeRestraints::doForce(), ComputeLCPO::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeEwald::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), Patch::forceBoxClosed(), ProxyCombinedResultMsg::fromRaw(), ComputeMsmMgr::gc_c1hermite_elem_accum(), get_3D_vector(), PDB::get_all_positions(), get_lattice_from_ts(), PDB::get_position_for_atom(), GlobalMasterIMD::get_vmd_forces(), ProxyResultVarsizeMsg::getANewMsg(), colvarproxy_namd::GridForceGridLoop(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap_by_name(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), Sequencer::integrate_SOA(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), Lattice::nearest(), obj_3D_vector(), operator double3(), sortop_x::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlistFromAll(), partition(), partition_SOA(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), PRINT_VECTOR(), Controller::printEnergies(), GroupRestraintParam::PrintSummary(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGlobal::recvResults(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeMsmSerial::saveResults(), ComputeLjPmeSerial::saveResults(), ComputeFmmSerial::saveResults(), ComputeGlobal::saveTotalForces(), scale_coordinates(), Lattice::scale_force(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), GroupRestraintParam::SetResDirection(), LjPmeMgr::setScaledCoordinates(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitReductions(), Sequencer::submitReductions_SOA(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), Lattice::wrap_delta_scaled(), and Controller::writeExtendedSystemData().
BigReal Vector::y |
Definition at line 74 of file Vector.h.
Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), Sequencer::berendsenPressure_SOA(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), Controller::calcPressure(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), CudaPmeOneDevice::compute(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), LjPmeKSpace::compute_energy(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), LjPmeCompute::computeNonbonded(), Controller::Controller(), Controller::correctMomentum(), cross(), Lattice::delta_from_diff(), ProxyPatch::depositCombinedResultMsg(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeSphericalBC::doForce(), ComputeGridForce::doForce(), ComputeCylindricalBC::doForce(), ComputeLCPO::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeEwald::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), Patch::forceBoxClosed(), ProxyCombinedResultMsg::fromRaw(), ComputeMsmMgr::gc_c1hermite_elem_accum(), get_3D_vector(), PDB::get_all_positions(), get_lattice_from_ts(), PDB::get_position_for_atom(), GlobalMasterIMD::get_vmd_forces(), ProxyResultVarsizeMsg::getANewMsg(), colvarproxy_namd::GridForceGridLoop(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap_by_name(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), Sequencer::integrate_SOA(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), Lattice::nearest(), obj_3D_vector(), operator double3(), sortop_y::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlistFromAll(), partition(), partition_SOA(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), PRINT_VECTOR(), print_vel_AOS(), Controller::printEnergies(), GroupRestraintParam::PrintSummary(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), Sequencer::rattle1(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeMsmSerialMgr::recvCoord(), ComputeExtMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGlobal::recvResults(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeFmmSerial::saveResults(), ComputeMsmSerial::saveResults(), ComputeLjPmeSerial::saveResults(), ComputeGlobal::saveTotalForces(), scale_coordinates(), Lattice::scale_force(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), GroupRestraintParam::SetResDirection(), LjPmeMgr::setScaledCoordinates(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), Sequencer::submitReductions(), Sequencer::submitReductions_SOA(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), Lattice::wrap_delta_scaled(), and Controller::writeExtendedSystemData().
BigReal Vector::z |
Definition at line 74 of file Vector.h.
Referenced by msm::PatchData::anterpolation(), msm::PatchData::anterpolationC1Hermite(), PatchMap::assignToPatch(), Sequencer::berendsenPressure_SOA(), ComputeNonbondedUtil::calcGBIS(), ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), Controller::calcPressure(), GlobalMasterTest::calculate(), colvarproxy_namd::calculate(), ComputeQMMgr::calcUSR(), CudaPmeOneDevice::compute(), GridforceFullSubGrid::compute_b(), GridforceFullBaseGrid::compute_d2V(), GridforceFullBaseGrid::compute_dV(), LjPmeKSpace::compute_energy(), PmeKSpace::compute_energy(), PmeKSpace::compute_energy_orthogonal_helper(), PmeRealSpace::compute_forces_order4_partial(), GridforceFullBaseGrid::compute_VdV(), GridforceLiteGrid::compute_VdV(), GridforceLiteGrid::compute_wts(), AngleElem::computeForce(), CrosstermElem::computeForce(), DihedralElem::computeForce(), ImproperElem::computeForce(), AnisoElem::computeForce(), TholeElem::computeForce(), BondElem::computeForce(), ExclElem::computeForce(), GromacsPairElem::computeForce(), LjPmeCompute::computeNonbonded(), Controller::Controller(), Controller::correctMomentum(), cross(), Lattice::delta_from_diff(), ProxyPatch::depositCombinedResultMsg(), ProxyPatch::depositCombinedResultRawMsg(), Tensor::diagonal(), ComputeGridForce::do_calc(), HomePatch::doAtomMigration(), ComputeStir::doForce(), ComputeNonbondedPair::doForce(), ComputeSphericalBC::doForce(), ComputeNonbondedSelf::doForce(), ComputeGridForce::doForce(), ComputeCylindricalBC::doForce(), ComputeLCPO::doForce(), HomePatch::doGroupSizeCheck(), HomePatch::doMarginCheck(), HomePatch::doMarginCheck_SOA(), HomePatch::doPairlistCheck(), dot(), ComputeFullDirect::doWork(), ComputePme::doWork(), ComputeEwald::doWork(), ComputeHomeTuples< TholeElem, Thole, TholeValue >::doWork(), dump_param(), dumpbench(), PmeAtomFiler::fileAtoms(), PDB::find_extremes(), Patch::forceBoxClosed(), ProxyCombinedResultMsg::fromRaw(), ComputeMsmMgr::gc_c1hermite_elem_accum(), get_3D_vector(), PDB::get_all_positions(), get_lattice_from_ts(), PDB::get_position_for_atom(), GlobalMasterIMD::get_vmd_forces(), ProxyResultVarsizeMsg::getANewMsg(), colvarproxy_namd::GridForceGridLoop(), HomePatch::hardWallDrude(), colvarproxy_namd::init_volmap_by_name(), GridforceFullSubGrid::initialize(), ComputeMsmMgr::initialize(), Sequencer::integrate_SOA(), msm::PatchData::interpolation(), msm::PatchData::interpolationC1Hermite(), Sequencer::langevinPiston(), Controller::langevinPiston1(), Controller::langevinPiston2(), Sequencer::langevinPiston_SOA(), Sequencer::langevinVelocitiesBBK2_SOA(), length(), length2(), PatchMap::makePatches(), mat_multiply_vec(), HomePatch::minimize_rattle2(), Controller::monteCarloPressure_accept(), Controller::monteCarloPressure_prepare(), Lattice::nearest(), obj_3D_vector(), operator double3(), sortop_z::operator()(), cr_sortop_distance::operator()(), operator*=(), operator+=(), operator-=(), operator/=(), operator<<(), operator=(), operator[](), Lattice::orthogonal(), outer(), Tensor::outerAdd(), pairlistFromAll(), partition(), partition_SOA(), WorkDistrib::patchMapInit(), colvarproxy_namd::position_distance(), Patch::positionsReady(), HomePatch::positionsReady(), HomePatch::positionsReady_SOA(), PRINT_VECTOR(), print_vel_AOS(), Controller::printEnergies(), GroupRestraintParam::PrintSummary(), proc_dihedralgrad(), ComputeQMMgr::procQMRes(), Sequencer::rattle1(), HomePatch::rattle1(), HomePatch::rattle1old(), HomePatch::rattle2(), GridforceFullBaseGrid::readHeader(), HomePatch::receiveResults(), ComputeExtMgr::recvCoord(), ComputeMsmSerialMgr::recvCoord(), ComputeLjPmeSerialMgr::recvCoord(), ComputeFmmSerialMgr::recvCoord(), ComputeGlobal::recvResults(), CudaComputeNonbonded::registerComputePair(), rescale_nonperiodic_cell(), rlength(), ComputeMsmSerial::saveResults(), ComputeLjPmeSerial::saveResults(), ComputeFmmSerial::saveResults(), ComputeGlobal::saveTotalForces(), scale_coordinates(), Lattice::scale_force(), scale_forces(), set(), PDB::set_all_positions(), SetEqual(), GroupRestraintParam::SetResDirection(), LjPmeMgr::setScaledCoordinates(), settle1(), settle1_SIMD(), PatchMap::sizeGrid(), CudaPmeKSpaceCompute::solve(), Sequencer::submitHalfstep(), Sequencer::submitMinimizeReductions(), Sequencer::submitReductions(), Sequencer::submitReductions_SOA(), Tensor::symmetric(), Tcl_centerOfMass(), Tcl_centerOfNumber(), ProxyCombinedResultMsg::toRaw(), Tensor::triangular(), ComputePme::ungridForces(), unit(), ProxyResultMsg::unpack(), Lattice::unscale(), Node::updateGridScale(), vec_rotation_matrix(), Lattice::wrap_delta_scaled(), and Controller::writeExtendedSystemData().